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
RBM23	55147	hgsc.bcm.edu	37	14	23371265	23371266	+	In_Frame_Ins	INS	-	-	GCA	rs376457710		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	17	63	.	0.378	.	.	.	weak	.	RBM23	44	.	NM_001077351	exon12	c.1170_1171insTGC	p.A390delinsAA	.	.	PASS	Pindel,Atlas-Indel
CCDC180	0	hgsc.bcm.edu	37	9	100092968	100092969	+	In_Frame_Ins	INS	-	-	GAGGAG	rs113264216	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	17	19	.	0.531	.	-|0.500;GAGGAG|0.500	0.500	strong	.	.	.	.	NM_020893	exon18	c.2325_2326insGAGGAG	p.E775delinsEEE	.	.	PASS	Pindel,Atlas-Indel
RNU6-81	100873780	hgsc.bcm.edu	37	2	132248330	132248331	+	RNA	INS	-	-	GC	rs111311763	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	45	238	.	0.196	.	-|0.500;GC|0.500	0.500	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
NUCB2	4925	hgsc.bcm.edu	37	11	17352478	17352480	+	In_Frame_Del	DEL	ACA	ACA	-	rs3842269	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	45	177	.	0.331	.	ACA|0.718;-|0.282	0.282	strong	.	NUCB2	31	.	NM_005013	exon13	c.1202_1204del	p.401_402del	.	.	PASS	Pindel,Atlas-Indel
ETFB	2109	hgsc.bcm.edu	37	19	51857614	51857615	+	Frame_Shift_Ins	INS	-	-	G	rs141529162	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	13	60	.	0.295	.	-|0.980;G|0.020	0.020	strong	.	ETFB	46	.	NM_001014763	exon1	c.279_280insC	p.P93fs	.	.	PASS	Pindel,Atlas-Indel
HOXB1	3211	hgsc.bcm.edu	37	17	46608184	46608185	+	In_Frame_Ins	INS	-	-	GGGCGCTGT	rs145570960	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	13	62	.	0.481	.	.	.	strong	.	HOXB1	67	.	NM_002144	exon1	c.83_84insACAGCGCCC	p.P28delinsHSAP	.	.	PASS	Pindel,Atlas-Indel
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249503	71249532	+	In_Frame_Del	DEL	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	13	153	0	0.0828025	0	.	.	none	.	KRTAP5-8	28	.	NM_021046	exon1	c.401_430del	p.134_144del	.	.	PASS	Atlas-Indel
BPNT1	10380	hgsc.bcm.edu	37	1	220231181	220231181	+	RNA	DEL	T	T	-	rs34887640	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	77	133	.	0.472	.	T|0.776;-|0.224	0.224	strong	.	BPNT1	29	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
OR8B3	390271	hgsc.bcm.edu	37	11	124266697	124266698	+	Frame_Shift_Ins	INS	-	-	G	rs201661436	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	999	198	588	0	0.198198	0	-|0.977;G|0.023	0.023	strong	.	OR8B3	36	.	NM_001005467	exon1	c.551_552insC	p.L184fs	.	.	PASS	Atlas-Indel
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577707	+	Frame_Shift_Del	DEL	G	G	-	rs202116886	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	32	107	0	0.438356	0	.	.	alt	.	CASP8AP2	108	.	NM_012115	exon8	c.4697delT	p.L1566X	.	.	PASS	Atlas-Indel
ZFHX4	79776	hgsc.bcm.edu	37	8	77765299	77765301	+	In_Frame_Del	DEL	CCT	CCT	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	25	76	0	0.257732	0	.	.	none	.	ZFHX4	878	.	NM_024721	exon10	c.6141_6143del	p.2047_2048del	.	.	PASS	Atlas-Indel
FZD2	2535	hgsc.bcm.edu	37	17	42636477	42636477	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	19	96	.	0.211	.	.	.	none	.	FZD2	81	.	NM_001466	exon1	c.1420delA	p.T474fs	.	.	PASS	Pindel,Atlas-Indel
EPB41L4A	64097	hgsc.bcm.edu	37	5	111500816	111500817	+	Splice_Site	INS	-	-	TAAAA	rs145708081	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	43	104	0	0.367521	0	-|0.025;TAAAA|0.975	0.975	strong	.	EPB41L4A	130	.	NM_022140	exon24	c.1933-1->TTTTA	.	.	.	PASS	Atlas-Indel
MICA	100507436	hgsc.bcm.edu	37	6	31380161	31380161	+	Frame_Shift_Del	DEL	G	G	-	rs67841474	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	12	158	0	0.0794702	0	.	.	strong	.	MICA	21	.	NM_001177519	exon5	c.951delT	p.A317fs	.	.	PASS	Atlas-Indel
AUTS2	26053	hgsc.bcm.edu	37	7	70255576	70255577	+	In_Frame_Ins	INS	-	-	CCA	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	13	55	.	0.183	.	.	.	none	.	AUTS2	173	.	NM_015570	exon19	c.3374_3375insCCA	p.S1125delinsSH	.	.	PASS	Pindel,Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51723598	51723599	+	Frame_Shift_Ins	INS	-	-	G	rs17860363	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	19	83	.	0.345	.	-|0.851;G|0.149	0.149	strong	.	CELA1	39	.	NM_001971	exon7	c.629_630insC	p.L210fs	.	.	PASS	Pindel,Atlas-Indel
SYT14	255928	hgsc.bcm.edu	37	1	210267894	210267896	+	In_Frame_Del	DEL	GAA	GAA	-	rs144713062	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	51	182	.	0.233	.	GAA|0.912;-|0.088	0.088	strong	.	SYT14	89	.	NM_001146264	exon6	c.804_806del	p.268_269del	.	.	PASS	Pindel,Atlas-Indel
PRDM2	7799	hgsc.bcm.edu	37	1	14106394	14106395	+	In_Frame_Ins	INS	-	-	CTC	rs2308040	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	12	107	.	0.179	.	-|0.492;CTC|0.508	0.508	strong	.	PRDM2	147	.	NM_015866	exon8	c.2104_2105insCTC	p.T702delinsTP	.	.	PASS	Pindel,Atlas-Indel
CD33	945	hgsc.bcm.edu	37	19	51729104	51729107	+	Frame_Shift_Del	DEL	CCGG	CCGG	-	rs201074739	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCGG	CCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	28	102	.	0.304	.	CCGG|0.992;-|0.008	0.008	strong	.	CD33	55	.	NM_001772	exon3	c.463_466del	p.155_156del	.	.	PASS	Pindel,Atlas-Indel
MAGI1	9223	hgsc.bcm.edu	37	3	65425560	65425561	+	In_Frame_Ins	INS	-	-	CTG	rs142043619	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	13	73	.	0.220	.	.	.	strong	.	MAGI1	481	.	NM_001033057	exon9	c.1264_1265insCAG	p.T422delinsQT	.	.	PASS	Pindel,Atlas-Indel
OR2C1	4993	hgsc.bcm.edu	37	16	3406757	3406757	+	Frame_Shift_Del	DEL	T	T	-	rs142397376	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	51	154	.	0.315	.	T|0.962;-|0.038	0.038	strong	.	OR2C1	38	.	NM_012368	exon1	c.816delG	p.K272fs	.	.	PASS	Pindel,Atlas-Indel
C19orf33	64073	hgsc.bcm.edu	37	19	38795547	38795549	+	In_Frame_Del	DEL	GAA	GAA	-	rs139805446	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	65	321	.	0.244	.	GAA|0.847;-|0.153	0.153	strong	.	C19orf33	9	.	NM_033520	exon4	c.263_265del	p.88_89del	.	.	PASS	Pindel,Atlas-Indel
C20orf202	400831	hgsc.bcm.edu	37	20	1187535	1187536	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	37	135	.	0.346	.	.	.	none	.	C20orf202	12	.	NM_001009612	exon2	c.157_158del	p.53_53del	.	.	PASS	Pindel,Atlas-Indel
CARD8	22900	hgsc.bcm.edu	37	19	48735017	48735018	+	Frame_Shift_Ins	INS	-	-	TT	rs140826611	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	38	87	.	0.349	.	-|0.962;TT|0.038	0.038	strong	.	CARD8	53	.	NM_001184900	exon5	c.442_443insAA	p.V148fs	.	.	PASS	Pindel,Atlas-Indel
OR51F1	256892	hgsc.bcm.edu	37	11	4790874	4790874	+	Frame_Shift_Del	DEL	G	G	-	rs34672924	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	37	137	.	0.314	.	G|0.772;-|0.228	0.228	strong	OR51F1,NS,carcinoma,-1,1	OR51F1	60	1	NM_001004752	exon1	c.275delG	p.R92fs	.	.	PASS	Pindel,Atlas-Indel
PGGT1B	5229	hgsc.bcm.edu	37	5	114557642	114557643	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	423	73	475	.	0.173	.	.	.	none	.	PGGT1B	26	.	NM_005023	exon7	c.722_723insT	p.S241fs	.	.	PASS	Pindel,Atlas-Indel
CLSPN	63967	hgsc.bcm.edu	37	1	36203660	36203662	+	In_Frame_Del	DEL	TTC	TTC	-	rs200760879	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	14	50	.	0.286	.	TTC|0.962;-|0.038	0.038	strong	.	CLSPN	248	.	NM_022111	exon22	c.3596_3598del	p.1199_1200del	.	.	PASS	Pindel,Atlas-Indel
COL6A3	1293	hgsc.bcm.edu	37	2	238244864	238244866	+	In_Frame_Del	DEL	GCA	GCA	-	rs35879189	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	16	53	.	0.308	.	GCA|0.935;-|0.065	0.065	strong	.	COL6A3	608	.	NM_004369	exon40	c.8878_8880del	p.2960_2960del	.	.	PASS	Pindel,Atlas-Indel
KRTAP9-8	83901	hgsc.bcm.edu	37	17	39394711	39394725	+	In_Frame_Del	DEL	GACCACCTGCTGCAG	GACCACCTGCTGCAG	-	rs373648251		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GACCACCTGCTGCAG	GACCACCTGCTGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	220	26	314	0	0.118182	0	.	.	weak	.	KRTAP9-8	29	.	NM_031963	exon1	c.407_421del	p.136_141del	.	.	PASS	Atlas-Indel
TRAK1	22906	hgsc.bcm.edu	37	3	42251577	42251578	+	In_Frame_Ins	INS	-	-	GGA	rs10634555	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	11	88	.	0.153	.	.	.	strong	TRAK1,caecum,carcinoma,0,1	TRAK1	188	1	NM_001265608	exon14	c.2063_2064insGGA	p.T688delinsTE	.	.	PASS	Pindel,Atlas-Indel
AKAP9	10142	hgsc.bcm.edu	37	7	91652178	91652179	+	In_Frame_Ins	INS	-	-	AAC	rs10644111	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	38	58	.	0.731	.	-|0.604;AAC|0.396	0.396	strong	.	AKAP9	788	.	NM_005751	exon14	c.4003_4004insAAC	p.K1335delinsKQ	.	.	PASS	Pindel,Atlas-Indel
ZNF681	148213	hgsc.bcm.edu	37	19	23927742	23927743	+	Frame_Shift_Del	DEL	CA	CA	-	rs61397759	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	19	73	.	0.352	.	CA|0.870;-|0.130	0.130	strong	LOC148213,extremity,malignant_melanoma,-1,1	ZNF681	76	1	NM_138286	exon4	c.610_611del	p.204_204del	.	.	PASS	Pindel,Atlas-Indel
PRSS48	345062	hgsc.bcm.edu	37	4	152201018	152201019	+	Frame_Shift_Ins	INS	-	-	CAGGT	rs148861921	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	25	194	.	0.177	.	.	.	strong	.	PRSS48	91	.	NM_183375	exon2	c.123_124insCAGGT	p.W41fs	.	.	PASS	Pindel,Atlas-Indel
CRIPAK	285464	hgsc.bcm.edu	37	4	1388375	1388376	+	Frame_Shift_Ins	INS	-	-	CA	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	30	212	0	0.157068	0	.	.	none	.	CRIPAK	185	.	NM_175918	exon1	c.76_77insCA	p.S26fs	.	.	PASS	Atlas-Indel
HACE1	57531	hgsc.bcm.edu	37	6	105192108	105192110	+	Splice_Site	DEL	AAC	AAC	-	rs72218235	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	35	129	.	0.292	.	AAC|0.835;-|0.165	0.165	strong	.	HACE1	96	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
SLC22A1	6580	hgsc.bcm.edu	37	6	160560898	160560905	+	In_Frame_Del	DEL	TGGTAAGT	TGGTAAGT	-	rs113569197	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGGTAAGT	TGGTAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	24	102	.	0.686	.	TGGTAAGT|0.311;-|0.689	0.689	strong	.	SLC22A1	69	.	NM_153187	exon7	c.1274_1276del	p.425_426del	.	.	PASS	Pindel,Atlas-Indel
SHKBP1	92799	hgsc.bcm.edu	37	19	41095087	41095112	+	Splice_Site	DEL	GAGGACAGTCCTGTCCAACAGGGAGG	GAGGACAGTCCTGTCCAACAGGGAGG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGGACAGTCCTGTCCAACAGGGAGG	GAGGACAGTCCTGTCCAACAGGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	29	95	.	0.500	.	.	.	none	.	SHKBP1	68	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
REXO1	57455	hgsc.bcm.edu	37	19	1825928	1825930	+	In_Frame_Del	DEL	CTC	CTC	-	rs149465929	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	56	189	.	0.301	.	CTC|0.704;-|0.296	0.296	strong	.	REXO1	55	.	NM_020695	exon3	c.1925_1927del	p.642_643del	.	.	PASS	Pindel,Atlas-Indel
SIRPA	140885	hgsc.bcm.edu	37	20	1896052	1896054	+	In_Frame_Del	DEL	CGA	CGA	-	rs139878822	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	26	464	0	0.102767	0	.	.	strong	SIRPA,NS,carcinoma,-1,1	SIRPA	83	1	NM_001040022	exon3	c.386_388del	p.129_130del	.	.	PASS	Atlas-Indel
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184747	+	In_Frame_Ins	INS	-	-	TCT	rs34966908	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	14	39	.	0.241	.	-|0.500;TCT|0.500	0.500	strong	.	FERD3L	63	.	NM_152898	exon1	c.240_241insAGA	p.E80delinsEE	.	.	PASS	Pindel,Atlas-Indel
ODF1	4956	hgsc.bcm.edu	37	8	103573011	103573037	+	In_Frame_Del	DEL	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	49	142	.	0.247	.	.	.	none	.	ODF1	55	.	NM_024410	exon2	c.651_677del	p.217_226del	.	.	PASS	Pindel,Atlas-Indel
CPS1	1373	hgsc.bcm.edu	37	2	211421452	211421453	+	In_Frame_Ins	INS	-	-	TCT	rs3835047	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	14	137	0	0.166667	0	-|0.556;TCT|0.444	0.444	strong	.	CPS1	485	.	NM_001122633	exon2	c.13_14insTCT	p.I5delinsIF	.	.	PASS	Atlas-Indel
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs111905975	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	38	89	.	0.396	.	TCC|0.852;-|0.148	0.148	strong	.	KANK3	35	.	NM_198471	exon8	c.2023_2025del	p.675_675del	.	.	PASS	Pindel,Atlas-Indel
PDE4DIP	9659	hgsc.bcm.edu	37	1	144915624	144915624	+	Frame_Shift_Del	DEL	G	G	-	rs66512216	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	30	159	.	0.169	.	G|0.808;-|0.192	0.192	strong	.	PDE4DIP	817	.	NM_001002811	exon10	c.2291delT	p.L764fs	.	.	PASS	Pindel,Atlas-Indel
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305776	+	In_Frame_Ins	INS	-	-	GGCAGCAGCTGGGGC	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	34	64	0	0.653846	0	.	.	none	KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	NM_033188	exon1	c.245_246insGCCCCAGCTGCTGCC	p.Q82delinsRPSCCQ	.	.	PASS	Atlas-Indel
VSIG10	54621	hgsc.bcm.edu	37	12	118506328	118506333	+	In_Frame_Del	DEL	TCCTCC	TCCTCC	-	rs72125532	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCCTCC	TCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	45	330	0	0.193966	0	.	.	strong	.	VSIG10	41	.	NM_019086	exon8	c.1417_1422del	p.473_474del	.	.	PASS	Atlas-Indel
HOMEZ	57594	hgsc.bcm.edu	37	14	23744801	23744803	+	In_Frame_Del	DEL	CAT	CAT	-	rs148005528	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	40	145	.	0.186	.	.	.	strong	.	HOMEZ	80	.	NM_020834	exon2	c.1635_1637del	p.545_546del	.	.	PASS	Pindel,Atlas-Indel
SULT2B1	6820	hgsc.bcm.edu	37	19	49102605	49102610	+	In_Frame_Del	DEL	CCAGCC	CCAGCC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCAGCC	CCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	38	244	.	0.187	.	.	.	none	.	SULT2B1	72	.	NM_177973	exon7	c.1039_1044del	p.347_348del	.	.	PASS	Pindel,Atlas-Indel
TRDN	10345	hgsc.bcm.edu	37	6	123594510	123594511	+	Splice_Site	INS	-	-	A	rs147062785	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	21	45	.	0.339	.	-|0.740;A|0.260	0.260	strong	.	TRDN	88	.	NM_006073	exon29	c.1598-2->T	.	.	.	PASS	Pindel,Atlas-Indel
THAP2	83591	hgsc.bcm.edu	37	12	72070506	72070508	+	In_Frame_Del	DEL	GTT	GTT	-	rs140783391	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	37	117	.	0.343	.	GTT|0.969;-|0.031	0.031	strong	.	THAP2	29	.	NM_031435	exon3	c.304_306del	p.102_102del	.	.	PASS	Pindel,Atlas-Indel
RP1L1	94137	hgsc.bcm.edu	37	8	10467569	10467571	+	In_Frame_Del	DEL	CTC	CTC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	13	184	0	0.0625	0	.	.	none	.	RP1L1	453	.	NM_178857	exon4	c.4038_4040del	p.1346_1347del	.	.	PASS	Atlas-Indel
C1orf86	199990	hgsc.bcm.edu	37	1	2124345	2124346	+	In_Frame_Ins	INS	-	-	TTG	rs142041547	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	11	42	0	0.22	0	.	.	strong	.	C1orf86	20	.	NM_001256946	exon4	c.540_541insCAA	p.K180delinsNK	.	.	PASS	Atlas-Indel
OR1B1	347169	hgsc.bcm.edu	37	9	125391770	125391771	+	Frame_Shift_Ins	INS	-	-	A	rs11421222	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	21	60	.	0.269	.	-|0.589;A|0.411	0.411	strong	.	OR1B1	48	.	NM_001004450	exon1	c.45_46insT	p.L15fs	.	.	PASS	Pindel,Atlas-Indel
DLEC1	9940	hgsc.bcm.edu	37	3	38162039	38162042	+	Frame_Shift_Del	DEL	GAGA	GAGA	-	rs140494598	bycluster;by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGA	GAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	301	66	322	.	0.219	.	.	.	alt	.	DLEC1	278	.	NM_007335	exon34	c.4804_4807del	p.1602_1603del	.	.	PASS	Pindel,Atlas-Indel
MEF2B	100271849	hgsc.bcm.edu	37	19	19257101	19257102	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	11	21	0	0.333333	0	.	.	none	.	MEF2B	41	.	NM_001145785	exon8	c.862_863insC	p.A288fs	.	.	PASS	Atlas-Indel
PDE4DIP	9659	hgsc.bcm.edu	37	1	144923729	144923729	+	Frame_Shift_Del	DEL	T	T	-	rs3215779	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	612	94	468	.	0.154	.	.	.	weak	.	PDE4DIP	817	.	NM_001002811	exon2	c.1219delC	p.L407fs	.	.	PASS	Pindel,Atlas-Indel
GOLGA2P5	55592	hgsc.bcm.edu	37	12	100550838	100550839	+	RNA	INS	-	-	GGAG	rs150871002	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	16	84	.	0.225	.	-|0.969;GGAG|0.031	0.031	strong	.	.	.	.	NR_036632	exon11	c.1670-2->CTCC	.	.	.	PASS	Pindel,Atlas-Indel
WDR87	83889	hgsc.bcm.edu	37	19	38377392	38377409	+	In_Frame_Del	DEL	CCTCCTCCTCCTCCCTTA	CCTCCTCCTCCTCCCTTA	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCTCCTCCTCCTCCCTTA	CCTCCTCCTCCTCCCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	10	42	.	0.200	.	.	.	none	.	WDR87	191	.	NM_031951	exon6	c.6786_6803del	p.2262_2268del	.	.	PASS	Pindel,Atlas-Indel
DOK3	79930	hgsc.bcm.edu	37	5	176930172	176930174	+	In_Frame_Del	DEL	GAG	GAG	-	rs138153794	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	29	85	.	0.296	.	GAG|0.466;-|0.534	0.534	strong	.	DOK3	41	.	NM_001144875	exon6	c.866_868del	p.289_290del	.	.	PASS	Pindel,Atlas-Indel
MICA	100507436	hgsc.bcm.edu	37	6	31380158	31380161	+	Frame_Shift_Del	DEL	GCTG	GCTG	-	rs138201170	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GCTG	GCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	30	167	.	0.194	.	.	.	strong	.	MICA	21	.	NM_001177519	exon5	c.948_951del	p.316_317del	.	.	PASS	Pindel,Atlas-Indel
CD200R1L	344807	hgsc.bcm.edu	37	3	112545911	112545911	+	Frame_Shift_Del	DEL	T	T	-	rs58161637	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	89	162	.	0.533	.	T|0.815;-|0.185	0.185	strong	CD200R1L,NS,carcinoma,-1,1	CD200R1L	47	1	NM_001008784	exon4	c.609delC	p.H203fs	.	.	PASS	Pindel,Atlas-Indel
DHRS4L2	317749	hgsc.bcm.edu	37	14	24470690	24470691	+	Frame_Shift_Ins	INS	-	-	A	rs368539076		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	73	936	.	0.507	.	.	.	weak	.	DHRS4L2	29	.	NM_198083	exon6	c.629_630insA	p.L210fs	.	.	PASS	Pindel,Atlas-Indel
GGA3	23163	hgsc.bcm.edu	37	17	73234805	73234806	+	Frame_Shift_Ins	INS	-	-	TCTG	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	45	203	.	0.220	.	.	.	none	GGA3,NS,carcinoma,0,1	GGA3	54	1	NM_138619	exon16	c.1989_1990insCAGA	p.E663fs	.	.	PASS	Pindel,Atlas-Indel
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577712	90577728	+	Frame_Shift_Del	DEL	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	26	104	0	0.4	0	.	.	none	.	CASP8AP2	108	.	NM_012115	exon8	c.4702_4718del	p.1568_1573del	.	.	PASS	Atlas-Indel
KIAA0040	9674	hgsc.bcm.edu	37	1	175129946	175129946	+	Frame_Shift_Del	DEL	C	C	-	rs60195884	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	25	110	0	0.189394	0	-|1.000	.	weak	.	KIAA0040	2	.	NM_001162893	exon5	c.205delA	p.K69fs	.	.	PASS	Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	In_Frame_Ins	INS	-	-	CTC	rs145742571	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	58	205	.	0.487	.	.	.	strong	.	KIAA1751	92	.	NM_001080484	exon11	c.1213_1214insGAG	p.K405delinsEK	.	.	PASS	Pindel,Atlas-Indel
CACNA1A	773	hgsc.bcm.edu	37	19	13395957	13395959	+	In_Frame_Del	DEL	TCC	TCC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	45	170	.	0.262	.	.	.	none	.	CACNA1A	715	.	NM_001127221	exon21	c.3619_3621del	p.1207_1207del	.	.	PASS	Pindel,Atlas-Indel
CCL27	10850	hgsc.bcm.edu	37	9	34661945	34661945	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	32	122	.	0.299	.	.	.	none	.	CCL27	6	.	NM_006664	exon3	c.336delC	p.G112fs	.	.	PASS	Pindel,Atlas-Indel
BPTF	2186	hgsc.bcm.edu	37	17	65955758	65955759	+	In_Frame_Ins	INS	-	-	CCTCCAGCC	rs139709271	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	46	207	.	0.434	.	-|0.707;CCTCCAGCC|0.293	0.293	strong	BPTF_ENST00000335221,rectum,carcinoma,0,2	BPTF	415	2	NM_182641	exon24	c.8028_8029insCCTCCAGCC	p.A2676delinsAPPA	.	.	PASS	Pindel,Atlas-Indel
ARSD	414	hgsc.bcm.edu	37	X	2835999	2836007	+	In_Frame_Del	DEL	CCACGCCGG	CCACGCCGG	-	rs113556864		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCACGCCGG	CCACGCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	24	148	0	0.282353	0	CCACGCCGG|0.500;-|0.500	0.500	weak	.	ARSD	47	.	NM_001669	exon5	c.702_710del	p.234_237del	.	.	PASS	Atlas-Indel
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524657	10524659	+	In_Frame_Del	DEL	GAC	GAC	-	rs56252625	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAC	GAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	98	278	.	0.485	.	GAC|0.396;-|0.604	0.604	strong	.	ATF7IP2	40	.	NM_001256160	exon4	c.179_181del	p.60_61del	.	.	PASS	Pindel,Atlas-Indel
DLGAP2	9228	hgsc.bcm.edu	37	8	1626460	1626461	+	In_Frame_Ins	INS	-	-	CAC	rs200151488	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	43	108	.	0.274	.	-|0.982;CAC|0.018	0.018	strong	.	DLGAP2	292	.	NM_004745	exon9	c.2129_2130insCAC	p.I710delinsIT	.	.	PASS	Pindel,Atlas-Indel
C1orf141	400757	hgsc.bcm.edu	37	1	67558870	67558874	+	Frame_Shift_Del	DEL	TCATT	TCATT	-	rs200104842	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCATT	TCATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	14	267	0	0.112	0	TCATT|0.994;-|0.006	0.006	strong	.	C1orf141	58	.	NM_001276351	exon8	c.1018_1022del	p.340_341del	.	.	PASS	Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51740415	51740416	+	Frame_Shift_Del	DEL	AC	AC	-	rs370927847		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	14	210	0	0.10687	0	.	.	weak	.	CELA1	39	.	NM_001971	exon1	c.8_9del	p.3_3del	.	.	PASS	Atlas-Indel
ACIN1	22985	hgsc.bcm.edu	37	14	23548783	23548784	+	In_Frame_Ins	INS	-	-	GAACGT	rs148403158	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	294	53	165	0	0.180272	0	.	.	strong	.	ACIN1	147	.	NM_014977	exon6	c.1935_1936insACGTTC	p.S645delinsSRS	.	.	PASS	Atlas-Indel
EIF3A	8661	hgsc.bcm.edu	37	10	120819176	120819187	+	In_Frame_Del	DEL	AAGGAACCAAAG	AAGGAACCAAAG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AAGGAACCAAAG	AAGGAACCAAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	25	215	0	0.142045	0	.	.	none	.	EIF3A	142	.	NM_003750	exon10	c.1371_1382del	p.457_461del	.	.	PASS	Atlas-Indel
CHD8	57680	hgsc.bcm.edu	37	14	21862616	21862616	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	30	121	.	0.192	.	.	.	none	.	CHD8	339	.	NM_001170629	exon30	c.5420delA	p.Y1807fs	.	.	PASS	Pindel,Atlas-Indel
CDKN2AIP	55602	hgsc.bcm.edu	37	4	184367559	184367561	+	In_Frame_Del	DEL	CTG	CTG	-	rs147291711	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	11	64	.	0.204	.	CTG|0.559;-|0.441	0.441	strong	.	CDKN2AIP	31	.	NM_017632	exon3	c.721_723del	p.241_241del	.	.	PASS	Pindel,Atlas-Indel
TDG	6996	hgsc.bcm.edu	37	12	104373728	104373729	+	Frame_Shift_Ins	INS	-	-	A	rs151041931	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	35	131	0	0.257353	0	.	.	strong	.	TDG	43	.	NM_003211	exon3	c.286_287insA	p.E96fs	.	.	PASS	Atlas-Indel
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084471	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	441	69	726	0	0.156463	0	.	.	none	OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	NM_001005522	exon1	c.151_152insG	p.H51fs	.	.	PASS	Atlas-Indel
OR1J2	26740	hgsc.bcm.edu	37	9	125273385	125273386	+	Frame_Shift_Ins	INS	-	-	T	rs145911830	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	36	135	.	0.257	.	-|0.940;T|0.060	0.060	strong	.	OR1J2	64	.	NM_054107	exon1	c.305_306insT	p.Y102fs	.	.	PASS	Pindel,Atlas-Indel
RHBG	57127	hgsc.bcm.edu	37	1	156354348	156354348	+	Frame_Shift_Del	DEL	C	C	-	rs11303415	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	66	170	.	0.353	.	-|1.000;|0.000	1.000	strong	.	RHBG	133	.	NM_020407	exon9	c.1264delT	p.S422fs	.	.	PASS	Pindel,Atlas-Indel
TMPRSS6	164656	hgsc.bcm.edu	37	22	37465386	37465390	+	Splice_Site	DEL	TGGGG	TGGGG	-	rs200434923	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGGGG	TGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	22	116	0	0.226804	0	TGGGG|0.528;-|0.472	0.472	strong	.	TMPRSS6	99	.	.	.	.	.	.	.	PASS	Atlas-Indel
FOXD4L4	349334	hgsc.bcm.edu	37	9	42719280	42719280	+	Frame_Shift_Del	DEL	C	C	-	rs59364037		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	26	308	.	0.188	.	.	.	weak	.	FOXD4L4	5	.	NM_199244	exon1	c.1214delG	p.C405fs	.	.	PASS	Pindel,Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51740413	51740414	+	Frame_Shift_Ins	INS	-	-	C	rs17860279	byfrequency;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	14	215	0	0.104478	0	-|0.426;TGGACCATATCCACTTACCATAAAGGAC|0.574	.	alt	CELA1,NS,carcinoma,+1,1	CELA1	39	1	NM_001971	exon1	c.10_11insG	p.L4fs	.	.	PASS	Atlas-Indel
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547094	+	In_Frame_Ins	INS	-	-	CAG	rs376034029		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	43	89	0	0.309353	0	.	.	weak	EP400,NS,carcinoma,0,15	EP400	370	15	NM_015409	exon47	c.8181_8182insCAG	p.Q2727delinsQQ	.	.	PASS	Atlas-Indel
C2orf71	388939	hgsc.bcm.edu	37	2	29287926	29287927	+	In_Frame_Ins	INS	-	-	GCT	rs139768554	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	15	55	.	0.349	.	.	.	strong	.	C2orf71	146	.	NM_001029883	exon2	c.3676_3677insAGC	p.E1226delinsSE	.	.	PASS	Pindel,Atlas-Indel
SPAG16	79582	hgsc.bcm.edu	37	2	215013915	215013915	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	55	307	.	0.307	.	.	.	none	.	SPAG16	134	.	NM_024532	exon15	c.1644delC	p.D548fs	.	.	PASS	Pindel,Atlas-Indel
KIAA0040	9674	hgsc.bcm.edu	37	1	175129948	175129955	+	Frame_Shift_Del	DEL	TCTTCTTG	TCTTCTTG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCTTCTTG	TCTTCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	25	111	0	0.19084	0	.	.	none	.	KIAA0040	2	.	NM_001162893	exon5	c.196_203del	p.66_68del	.	.	PASS	Atlas-Indel
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586693	79586695	+	In_Frame_Del	DEL	GTG	GTG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	22	57	.	0.564	.	.	.	none	.	ANKRD34C	29	.	NM_001146341	exon2	c.1066_1068del	p.356_356del	.	.	PASS	Pindel,Atlas-Indel
SH3BGR	6450	hgsc.bcm.edu	37	21	40883671	40883672	+	In_Frame_Ins	INS	-	-	AGA	rs3831201	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	41	86	.	0.418	.	.	.	strong	SH3BGR,colon,carcinoma,0,1	SH3BGR	29	1	NM_007341	exon6	c.689_690insAGA	p.G230delinsGE	.	.	PASS	Pindel,Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51740388	51740416	+	In_Frame_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs372974824	byfrequency;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	21	204	.	0.152	.	-|0.574;CACCAGGAAGCG|0.426	0.574	alt	.	CELA1	39	.	NM_001971	exon1	c.8_16del	p.3_6del	.	.	PASS	Pindel
SCNN1G	6340	hgsc.bcm.edu	37	16	23226618	23226619	+	In_Frame_Ins	INS	-	-	TCC	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	36	91	.	0.383	.	.	.	none	.	SCNN1G	82	.	NM_001039	exon13	c.1778_1779insTCC	p.N593delinsNP	.	.	PASS	Pindel
HSP90B1	7184	hgsc.bcm.edu	37	12	104332202	104332204	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	41	185	.	0.268	.	.	.	none	.	HSP90B1	72	.	NM_003299	exon7	c.939_941del	p.313_314del	.	.	PASS	Pindel
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937852	88937854	+	In_Frame_Del	DEL	TTT	TTT	-	rs34431437	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	75	227	.	0.307	.	.	.	weak	.	ZCCHC6	105	.	NM_024617	exon13	c.2812_2814del	p.938_938del	.	.	PASS	Pindel
HSPBAP1	79663	hgsc.bcm.edu	37	3	122459290	122459291	+	In_Frame_Ins	INS	-	-	AGA	rs16338	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	384	93	394	.	0.242	.	-|0.847;AGA|0.153	0.153	strong	HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	NM_024610	exon8	c.1369_1370insTCT	p.Q457delinsSQ	.	.	PASS	Pindel
MIR943	100126332	hgsc.bcm.edu	37	4	1988188	1988189	+	RNA	INS	-	-	CT	rs3034718	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	42	192	.	0.278	.	CT|1.000;|0.000	1.000	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel
LRRC49	54839	hgsc.bcm.edu	37	15	71276481	71276483	+	In_Frame_Del	DEL	CAA	CAA	-	rs3834543	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	55	216	.	0.500	.	CAA|0.500;-|0.500	0.500	strong	.	LRRC49	73	.	NM_001199017	exon11	c.1068_1070del	p.356_357del	.	.	PASS	Pindel
PLD1	5337	hgsc.bcm.edu	37	3	171455452	171455452	+	Splice_Site	DEL	A	A	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	33	63	.	0.412	.	.	.	none	.	PLD1	134	.	NM_001130081	exon4	c.161-2T>-	.	.	.	PASS	Pindel
RIMBP3C	150221	hgsc.bcm.edu	37	22	21739333	21739335	+	In_Frame_Del	DEL	GAG	GAG	-	rs201364657	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	74	211	.	0.409	.	GAG|0.990;-|0.010	0.010	strong	.	RIMBP3C	6	.	NM_001128633	exon1	c.1185_1187del	p.395_396del	.	.	PASS	Pindel
KIAA1841	84542	hgsc.bcm.edu	37	2	61361326	61361326	+	Frame_Shift_Del	DEL	G	G	-	rs142269591	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	57	178	.	0.335	.	G|0.962;-|0.038	0.038	strong	.	KIAA1841	95	.	NM_032506	exon21	c.2082delT	p.S694fs	.	.	PASS	Pindel
KIAA1751	85452	hgsc.bcm.edu	37	1	1887092	1887112	+	In_Frame_Del	DEL	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	-	rs139735565	bycluster;by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	24	110	.	0.393	.	-|0.223;G|0.777	0.223	alt	.	KIAA1751	92	.	NM_001080484	exon18	c.2195_2215del	p.732_739del	.	.	PASS	Pindel
TPSD1	23430	hgsc.bcm.edu	37	16	1306560	1306560	+	Frame_Shift_Del	DEL	G	G	-	rs3830782	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	90	234	.	0.495	.	G|0.731;-|0.269	0.269	strong	.	TPSD1	47	.	NM_012217	exon2	c.125delA	p.Q42fs	.	.	PASS	Pindel
INF2	64423	hgsc.bcm.edu	37	14	105173863	105173868	+	In_Frame_Del	DEL	CCCCAC	CCCCAC	-	rs3840831	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCCCAC	CCCCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	19	83	.	0.207	.	.	.	alt	.	INF2	148	.	NM_001031714	exon8	c.1258_1263del	p.420_421del	.	.	PASS	Pindel
KIAA0040	9674	hgsc.bcm.edu	37	1	175129925	175129933	+	In_Frame_Del	DEL	CTTCTTCTT	CTTCTTCTT	-	rs150137790	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTTCTTCTT	CTTCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	39	116	.	0.298	.	.	.	strong	.	KIAA0040	2	.	NM_001162893	exon5	c.218_226del	p.73_76del	.	.	PASS	Pindel
C16orf96	342346	hgsc.bcm.edu	37	16	4644390	4644392	+	In_Frame_Del	DEL	AGG	AGG	-	rs139232890	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	46	133	.	0.287	.	AGG|0.931;-|0.069	0.069	strong	.	C16orf96	28	.	NM_001145011	exon13	c.2905_2907del	p.969_969del	.	.	PASS	Pindel
ANKRD36	375248	hgsc.bcm.edu	37	2	97779488	97779488	+	Frame_Shift_Del	DEL	C	C	-	rs141447363	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	43	178	.	0.289	.	C|0.967;-|0.033	0.033	strong	ANKRD36_ENST00000420699,right_lower_lobe,carcinoma,0,2	ANKRD36	170	2	NM_001164315	exon1	c.11delG	p.G4fs	.	.	PASS	Pindel
HLA-L	3139	hgsc.bcm.edu	37	6	30229034	30229035	+	RNA	INS	-	-	T	rs111358359	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	54	177	.	0.290	.	-|0.500;T|0.500	0.500	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel
BTBD10	84280	hgsc.bcm.edu	37	11	13410691	13410694	+	Splice_Site	DEL	GAAA	GAAA	-	rs3833472	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAAA	GAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	14	41	.	0.269	.	GAAA|0.908;-|0.092	0.092	strong	.	BTBD10	43	.	.	.	.	.	.	.	PASS	Pindel
DICER1	23405	hgsc.bcm.edu	37	14	95562995	95562997	+	In_Frame_Del	DEL	TCC	TCC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	75	156	.	0.310	.	.	.	none	.	DICER1	181	.	NM_001271282	exon23	c.4261_4263del	p.1421_1421del	.	.	PASS	Pindel
VWDE	221806	hgsc.bcm.edu	37	7	12391268	12391269	+	Frame_Shift_Ins	INS	-	-	A	rs11454536	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	67	170	.	0.337	.	-|0.844;A|0.156	0.156	strong	.	VWDE	123	.	NM_001135924	exon19	c.3817_3818insT	p.K1273_E1274delinsX	.	.	PASS	Pindel
MUC5B	727897	hgsc.bcm.edu	37	11	1271219	1271221	+	In_Frame_Del	DEL	CCA	CCA	-	rs199629887	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	293	64	323	.	0.218	.	CCA|0.926;-|0.074	0.074	strong	.	MUC5B	473	.	NM_002458	exon31	c.13108_13110del	p.4370_4370del	.	.	PASS	Pindel
INPP5F	22876	hgsc.bcm.edu	37	10	121587063	121587065	+	In_Frame_Del	DEL	CTT	CTT	-	rs201053908	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	37	157	.	0.287	.	CTT|0.994;-|0.006	0.006	strong	.	INPP5F	112	.	NM_014937	exon20	c.3169_3171del	p.1057_1057del	.	.	PASS	Pindel
SLC28A1	9154	hgsc.bcm.edu	37	15	85438311	85438312	+	In_Frame_Ins	INS	-	-	TTG	rs151038463	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	29	121	.	0.500	.	-|0.732;TTG|0.268	0.268	strong	.	SLC28A1	118	.	NM_201651	exon6	c.418_419insTTG	p.L140delinsLV	.	.	PASS	Pindel
PI4KAP2	375133	hgsc.bcm.edu	37	22	21829514	21829517	+	RNA	DEL	TGTC	TGTC	-	rs113567369	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	36	123	.	0.305	.	TGTC|0.500;-|0.500	0.500	strong	.	PI4KAP2	11	.	.	.	.	.	.	.	PASS	Pindel
SF3A2	8175	hgsc.bcm.edu	37	19	2248152	2248153	+	In_Frame_Ins	INS	-	-	GGAGTCCACCCTCCAGCCCCC	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	16	10	28	.	0.625	.	.	.	none	SF3A2,colon,carcinoma,0,1	SF3A2	22	1	NM_007165	exon9	c.1002_1003insGGAGTCCACCCTCCAGCCCCC	p.P334delinsPGVHPPAP	.	.	PASS	Pindel
CDCP2	200008	hgsc.bcm.edu	37	1	54605319	54605320	+	Frame_Shift_Ins	INS	-	-	C	rs36013100	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	44	120	.	0.579	.	.	.	strong	.	CDCP2	52	.	NM_201546	exon4	c.1224_1225insG	p.P408fs	.	.	PASS	Pindel
OR2B11	127623	hgsc.bcm.edu	37	1	247615262	247615262	+	Frame_Shift_Del	DEL	A	A	-	rs35305980	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	90	138	.	0.581	.	A|0.570;-|0.430	0.430	strong	.	OR2B11	102	.	NM_001004492	exon1	c.24delC	p.F8fs	.	.	PASS	Pindel
FAM171B	165215	hgsc.bcm.edu	37	2	187559047	187559048	+	In_Frame_Ins	INS	-	-	CAA	rs144403657	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	30	85	.	0.429	.	-|0.371;CAA|0.629	0.629	strong	FAM171B,NS,carcinoma,0,1	FAM171B	146	1	NM_177454	exon1	c.147_148insCAA	p.Q49delinsQQ	.	.	PASS	Pindel
NPL	80896	hgsc.bcm.edu	37	1	182763576	182763576	+	Splice_Site	DEL	T	T	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	61	140	.	0.363	.	.	.	none	.	NPL	55	.	NM_001200051	exon3	c.68+1T>-	.	.	.	PASS	Pindel
TPTE	7179	hgsc.bcm.edu	37	21	10942925	10942927	+	In_Frame_Del	DEL	CTT	CTT	-	rs113444703	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	816	129	536	.	0.158	.	CTT|0.500;-|0.500	0.500	strong	.	TPTE	513	.	NM_199261	exon12	c.661_663del	p.221_221del	.	.	PASS	Pindel
CHD1	1105	hgsc.bcm.edu	37	5	98192165	98192167	+	In_Frame_Del	DEL	AGG	AGG	-	rs138635992	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	255	69	296	.	0.271	.	AGG|0.775;-|0.225	0.225	strong	.	CHD1	137	.	NM_001270	exon35	c.5051_5053del	p.1684_1685del	.	.	PASS	Pindel
ZNF772	400720	hgsc.bcm.edu	37	19	57988666	57988667	+	In_Frame_Ins	INS	-	-	GCC	rs34678661	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	51	286	.	0.260	.	GCC|1.000;|0.000	1.000	strong	ZNF772,colon,carcinoma,0,1	ZNF772	42	1	NM_001144068	exon1	c.12_13insGGC	p.A4delinsAA	.	.	PASS	Pindel
PCDHA4	56144	hgsc.bcm.edu	37	5	140186979	140186990	+	In_Frame_Del	DEL	GGGCCGCGGAGG	GGGCCGCGGAGG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GGGCCGCGGAGG	GGGCCGCGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	13	73	.	0.448	.	.	.	none	.	PCDHA4	419	.	NM_031500	exon1	c.206_217del	p.69_73del	.	.	PASS	Pindel
CRIPAK	285464	hgsc.bcm.edu	37	4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	47	184	.	0.299	.	.	.	none	.	CRIPAK	185	.	NM_175918	exon1	c.294_322del	p.98_108del	.	.	PASS	Pindel
TRIOBP	11078	hgsc.bcm.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs67890459	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	35	128	.	0.297	.	-|0.368;CAA|0.632	0.368	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.1191_1193del	p.397_398del	.	.	PASS	Pindel
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427685	70427685	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	26	310	.	0.198	.	.	.	weak	.	FOXD4L4	5	.	NM_199244	exon1	c.1216delT	p.W406fs	.	.	PASS	Pindel
KIAA0754	643314	hgsc.bcm.edu	37	1	39879397	39879435	+	In_Frame_Del	DEL	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	19	197	.	0.292	.	.	.	none	.	KIAA0754	93	.	NM_015038	exon1	c.3459_3497del	p.1153_1166del	.	.	PASS	Pindel
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176769	70176769	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	24	322	.	0.176	.	.	.	weak	.	FOXD4L5	27	.	NM_001126334	exon1	c.1216delT	p.W406fs	.	.	PASS	Pindel
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577728	+	Frame_Shift_Del	DEL	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	-	rs202116886	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	32	103	.	0.438	.	.	.	alt	.	CASP8AP2	108	.	NM_001137668	exon8	c.4697_4718del	p.1566_1573del	.	.	PASS	Pindel
NEDD8-MDP1	100528064	hgsc.bcm.edu	37	14	24683267	24683267	+	Frame_Shift_Del	DEL	A	A	-	rs3215610	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	83	151	.	0.401	.	A|0.812;-|0.188	0.188	strong	.	.	.	.	NM_001199823	exon7	c.546delG	p.L182fs	.	.	PASS	Pindel
PEBP4	157310	hgsc.bcm.edu	37	8	22570908	22570908	+	Frame_Shift_Del	DEL	T	T	-	rs35121552	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	69	127	.	0.312	.	T|0.680;-|0.320	0.320	strong	.	PEBP4	23	.	NM_144962	exon7	c.660delC	p.N220fs	.	.	PASS	Pindel
TEP1	7011	hgsc.bcm.edu	37	14	20841707	20841707	+	Missense_Mutation	SNP	C	C	T	rs1713449	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	75	130	0	0.378788	0	C|0.712;T|0.288	0.288	strong	TEP1,NS,carcinoma,0,1	TEP1	224	1	NM_007110	exon46	c.G6640A	p.V2214I	GCCCGACGGTTAC	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56457044	56457044	+	Missense_Mutation	SNP	T	T	C	rs186813964	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	64	197	0	0.48855	0	T|0.998;C|0.002	0.002	strong	DST_ENST00000370769,NS,lymphoid_neoplasm,0,2	DST	1427	2	NM_015548	exon30	c.A4970G	p.K1657R	AAGTGTTTGCTCG	.	PASS	Atlas-SNP
LRRC27	80313	hgsc.bcm.edu	37	10	134161517	134161517	+	Missense_Mutation	SNP	C	C	T	rs2474329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	49	136	0	0.404959	0	C|0.864;T|0.136	0.136	strong	.	LRRC27	64	.	NM_001143757	exon6	c.C583T	p.R195C	ACCCTCCGTGACC	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113403684	113403684	+	Silent	SNP	C	C	T	rs2240188	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	54	123	0	0.465517	0	C|0.728;T|0.272	0.272	strong	.	OAS3	63	.	NM_006187	exon12	c.C2539T	p.L847L	GCCCAGCTGGAGG	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112480041	112480041	+	Silent	SNP	A	A	G	rs3752577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	106	226	0	0.527363	0	A|0.915;G|0.085	0.085	strong	.	LAMA4	227	.	NM_001105206	exon14	c.T1710C	p.S570S	TAGTTCACTTTTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513411	195513411	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	659	19	521	7	0.0288316	0.0134357	.	.	none	MUC4_ENST00000463781,trunk,malignant_melanoma,-2,4	MUC4	1505	4	NM_018406	exon2	c.T5040A	p.P1680P	AGGAAGAGGGGTG	.	scavenged	Atlas-SNP
CNNM2	54805	hgsc.bcm.edu	37	10	104836853	104836853	+	Silent	SNP	C	C	T	rs35647154	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	26	50	0	0.702703	0	C|0.952;T|0.048	0.048	strong	.	CNNM2	119	.	NM_017649	exon8	c.C2544T	p.D848D	GCCAGACGAGACA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677586	100677586	+	Silent	SNP	A	A	G	rs189731103	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	527	170	184	0	0.322581	0	A|0.999;G|0.001	0.001	weak	.	MUC17	804	.	NM_001040105	exon3	c.A2889G	p.S963S	CACTTCATCTCCT	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385042	16385042	+	Missense_Mutation	SNP	G	G	A	rs77667563	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	17	91	0	0.395349	0	G|0.646;A|0.354	0.354	strong	FAM131C,NS,other,0,1	FAM131C	21	1	NM_182623	exon7	c.C733T	p.R245W	GCCGCCGCCGATG	.	PASS	Atlas-SNP
MFSD4	148808	hgsc.bcm.edu	37	1	205554085	205554085	+	Missense_Mutation	SNP	G	G	C	rs7526132	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	156	161	1	0.993631	0.00621118	G|0.514;C|0.486	0.486	strong	.	MFSD4	46	.	NM_181644	exon5	c.G941C	p.G314A	TCACGGGCGCCCT	.	PASS	Atlas-SNP
C10orf10	11067	hgsc.bcm.edu	37	10	45473317	45473317	+	Silent	SNP	C	C	T	rs3740094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	28	85	0	0.823529	0	C|0.872;T|0.128	0.128	strong	.	C10orf10	6	.	NM_007021	exon2	c.G162A	p.L54L	CTTGTCCAGCACA	.	PASS	Atlas-SNP
GATA2	2624	hgsc.bcm.edu	37	3	128204951	128204951	+	Missense_Mutation	SNP	C	C	T	rs2335052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	62	145	0	0.413333	0	C|0.800;T|0.200	0.200	strong	GATA2,colon,carcinoma,0,2	GATA2	122	2	NM_001145662	exon3	c.G490A	p.A164T	AGTGGGCTGCTGT	.	PASS	Atlas-SNP
TTC38	55020	hgsc.bcm.edu	37	22	46685380	46685380	+	Silent	SNP	C	C	T	rs11705624	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	58	110	0	0.537037	0	C|0.932;T|0.068	0.068	strong	.	TTC38	40	.	NM_017931	exon12	c.C1164T	p.D388D	TGAGGACGGGAAC	.	PASS	Atlas-SNP
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773812	140773812	+	Missense_Mutation	SNP	G	G	A	rs144796076	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	78	166	0	0.428571	0	G|0.996;A|0.004	0.004	strong	.	PCDHGA8	146	.	NM_014004	exon1	c.G1432A	p.D478N	GCACACGACCCCG	.	PASS	Atlas-SNP
OR5H15	403274	hgsc.bcm.edu	37	3	97888337	97888337	+	Missense_Mutation	SNP	C	C	T	rs13082608	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	113	314	0	0.502222	0	C|0.771;T|0.229	0.229	strong	.	OR5H15	70	.	NM_001005515	exon1	c.C794T	p.P265L	CATCTCCGCAAGC	.	PASS	Atlas-SNP
GBE1	2632	hgsc.bcm.edu	37	3	81720086	81720086	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	35	95	0	0.336538	0	.	.	none	GBE1_ENST00000429644,colon,carcinoma,0,1	GBE1	111	1	NM_000158	exon3	c.C332T	p.S111L	GGGTACGAAAATG	.	PASS	Atlas-SNP
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73932560	73932560	+	Silent	SNP	A	A	G	rs17851629	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	306	71	158	0	0.232026	0	A|0.744;G|0.256	0.256	strong	.	GTF2IRD1	91	.	NM_001199207	exon5	c.A609G	p.E203E	GCCCGAAGGCCTG	.	PASS	Atlas-SNP
SRCAP	10847	hgsc.bcm.edu	37	16	30732558	30732558	+	Missense_Mutation	SNP	C	C	A	rs149248373	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	60	124	0	0.472441	0	C|0.996;A|0.004	0.004	strong	.	SRCAP	298	.	NM_006662	exon21	c.C3302A	p.T1101K	CTCCCACGCCAAC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7023371	7023371	+	Silent	SNP	A	A	G	rs684634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	82	83	1	0.987952	0.0120482	A|0.524;G|0.476	0.476	strong	LAMA1,NS,adenoma,0,1	LAMA1	458	1	NM_005559	exon19	c.T2493C	p.C831C	ATCTGCACATCTG	.	scavenged	Atlas-SNP
WDR46	9277	hgsc.bcm.edu	37	6	33256653	33256653	+	Silent	SNP	G	G	A	rs34931270	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	34	100	0	0.425	0	G|0.977;A|0.023	0.023	strong	.	WDR46	43	.	NM_005452	exon2	c.C207T	p.I69I	CTTAGAGATCCGA	.	PASS	Atlas-SNP
FASTKD2	22868	hgsc.bcm.edu	37	2	207631461	207631461	+	Missense_Mutation	SNP	G	G	A	rs3762568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	34	180	0	0.265625	0	G|0.885;A|0.115	0.115	strong	.	FASTKD2	49	.	NM_001136193	exon2	c.G44A	p.S15N	TGGAGAGCAAAAT	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220353013	220353013	+	Silent	SNP	G	G	A	rs875098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	14	66	0	0.27451	0	G|0.747;A|0.253	0.253	strong	.	SPEG	272	.	NM_005876	exon32	c.G7839A	p.P2613P	TGCACCGCACATC	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33709898	33709898	+	Missense_Mutation	SNP	T	T	A	rs370904237	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	39	125	0	0.419355	0	.	.	alt	.	ELP2	70	.	NM_001242879	exon1	c.T2A	p.M1K	GCGACATGGTGGC	.	PASS	Atlas-SNP
DVL2	1856	hgsc.bcm.edu	37	17	7133609	7133609	+	Silent	SNP	G	G	A	rs2074216	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	48	102	0	0.527473	0	G|0.674;A|0.326	0.326	strong	.	DVL2	49	.	NM_004422	exon3	c.C405T	p.S135S	CTGGAAGGATGGA	.	PASS	Atlas-SNP
ANAPC1	64682	hgsc.bcm.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	T	C	rs12466309	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	672	14	834	6	0.0208333	0.00719424	T|0.500;C|0.500	0.500	strong	ANAPC1,NS,carcinoma,0,9	ANAPC1	116	9	NM_022662	exon14	c.A1609G	p.T537A	TTGGAGTACTAAC	.	scavenged	Atlas-SNP
LOR	4014	hgsc.bcm.edu	37	1	153234295	153234295	+	Silent	SNP	G	G	A	rs12043009	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	25	83	0	0.337838	0	G|0.777;A|0.223	0.223	strong	.	LOR	19	.	NM_000427	exon2	c.G870A	p.G290G	CTCCGGGAGTGGC	.	PASS	Atlas-SNP
C10orf35	219738	hgsc.bcm.edu	37	10	71391538	71391538	+	Silent	SNP	T	T	C	rs1381932	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	47	134	0	0.691176	0	T|0.773;C|0.227	0.227	strong	.	C10orf35	22	.	NM_145306	exon3	c.T39C	p.D13D	GCAGGATGACGAC	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20666195	20666195	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	4	121	0	0.0273973	0	.	.	none	ABCB5_ENST00000404938,NS,carcinoma,0,1	ABCB5	357	1	NM_001163941	exon3	c.G69A	p.Q23Q	AGAACAGCCAAAA	.	scavenged	Atlas-SNP
ZNF641	121274	hgsc.bcm.edu	37	12	48736985	48736985	+	Missense_Mutation	SNP	T	T	G	rs2732481	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	218	215	1	0.995434	0.00465116	T|0.801;G|0.199	0.199	strong	.	ZNF641	28	.	NM_152320	exon7	c.A1088C	p.Q363P	GCACGCTGCCGTT	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3191823	3191823	+	Missense_Mutation	SNP	C	C	T	rs2388556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	49	102	0	0.777778	0	C|0.892;T|0.108	0.108	strong	.	PITRM1	109	.	NM_014889	exon16	c.G1861A	p.V621I	TGAGGACGCTGCA	.	PASS	Atlas-SNP
MYH13	8735	hgsc.bcm.edu	37	17	10219113	10219113	+	Missense_Mutation	SNP	C	C	T	rs17690195	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	87	213	0	0.494318	0	C|0.857;T|0.143	0.143	strong	.	MYH13	533	.	NM_003802	exon29	c.G3881A	p.R1294Q	TCCACTCGGTGGC	.	PASS	Atlas-SNP
DAG1	1605	hgsc.bcm.edu	37	3	49570200	49570200	+	Silent	SNP	C	C	T	rs1801143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	70	117	0	0.48951	0	C|0.722;T|0.278	0.278	strong	.	DAG1	60	.	NM_001177642	exon4	c.C2256T	p.H752H	CCTGCACACAGTC	.	PASS	Atlas-SNP
MAP9	79884	hgsc.bcm.edu	37	4	156276289	156276289	+	Silent	SNP	C	C	T	rs2341894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	47	200	0	0.626667	0	C|0.324;T|0.676	0.676	strong	.	MAP9	79	.	NM_001039580	exon10	c.G1314A	p.V438V	TAAATACACATTT	.	PASS	Atlas-SNP
GLI3	2737	hgsc.bcm.edu	37	7	42005836	42005836	+	Silent	SNP	C	C	G	rs61758978	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	25	80	0	0.403226	0	C|0.986;G|0.014	0.014	strong	.	GLI3	312	.	NM_000168	exon15	c.G2835C	p.L945L	GTTGGGCAGGGGC	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197176	39197176	+	Silent	SNP	G	G	A	rs41535252		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	130	239	0	0.543933	0	G|1.000;|0.000	.	weak	.	KRTAP1-1	23	.	NM_030967	exon1	c.C474T	p.Y158Y	TCCACAGTAGGAT	.	PASS	Atlas-SNP
TAF4B	6875	hgsc.bcm.edu	37	18	23866185	23866185	+	Missense_Mutation	SNP	G	G	C	rs74947492	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	38	63	0	0.520548	0	G|0.926;C|0.074	0.074	strong	.	TAF4B	71	.	NM_005640	exon7	c.G1312C	p.V438L	CCACTTGTGACAT	.	PASS	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792003	8792003	+	Silent	SNP	C	C	T	rs9915880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	66	74	0	1	0	C|0.736;T|0.264	0.264	strong	.	PIK3R5	79	.	NM_001142633	exon10	c.G1101A	p.S367S	CGGCCCCGAGGCC	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144522457	144522457	+	Missense_Mutation	SNP	G	G	A	rs36083358	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	38	94	0	0.336283	0	G|0.973;A|0.027	0.027	strong	.	ZC3H3	75	.	NM_015117	exon11	c.C2569T	p.P857S	GGGGAGGTGCAGC	.	PASS	Atlas-SNP
CBR3	874	hgsc.bcm.edu	37	21	37507501	37507501	+	Missense_Mutation	SNP	G	G	A	rs8133052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	34	26	0	0.586207	0	G|0.602;A|0.398	0.398	strong	CBR3,NS,carcinoma,0,1	CBR3	11	1	NM_001236	exon1	c.G11A	p.C4Y	CGTCCTGCAGCCG	.	PASS	Atlas-SNP
C17orf78	284099	hgsc.bcm.edu	37	17	35743010	35743010	+	Missense_Mutation	SNP	C	C	G	rs1714987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	46	159	0	0.438095	0	C|0.700;G|0.300	0.300	strong	C17orf78,NS,carcinoma,0,1	C17orf78	23	1	NM_173625	exon4	c.C455G	p.T152S	CCACCACTGCCCC	.	PASS	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117078702	117078702	+	Silent	SNP	A	A	C	rs596314	bysubmitter	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1188	984	819	176	0.828283	0.214896	.	.	weak	PCSK7,NS,carcinoma,0,1	PCSK7	59	1	NM_004716	exon14	c.T1770G	p.L590L	GATGACAAGCCTG	.	scavenged	Atlas-SNP
OR52E2	119678	hgsc.bcm.edu	37	11	5080337	5080337	+	Missense_Mutation	SNP	T	T	C	rs61746343	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	29	83	0	0.5	0	T|0.770;C|0.230	0.230	strong	.	OR52E2	63	.	NM_001005164	exon1	c.A521G	p.H174R	ATTACATGATTCC	.	PASS	Atlas-SNP
KLHL31	401265	hgsc.bcm.edu	37	6	53519062	53519062	+	Silent	SNP	A	A	G	rs10948758	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	213	245	2	0.990698	0.00816326	A|0.316;G|0.684	0.684	strong	.	KLHL31	48	.	NM_001003760	exon2	c.T1009C	p.L337L	TATACAAGATGTC	.	PASS	Atlas-SNP
AIFM3	150209	hgsc.bcm.edu	37	22	21330787	21330787	+	Silent	SNP	C	C	T	rs7285694	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	27	70	0	0.473684	0	C|0.743;T|0.257	0.257	strong	.	AIFM3	49	.	NM_001146288	exon11	c.C1008T	p.A336A	GCTGGCCCGAGGC	.	PASS	Atlas-SNP
SURF2	6835	hgsc.bcm.edu	37	9	136228006	136228006	+	Silent	SNP	G	G	A	rs34939258	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	17	71	0	0.320755	0	G|0.940;A|0.060	0.060	strong	.	SURF2	9	.	NM_017503	exon6	c.G762A	p.Q254Q	TAAACAGCCAGGT	.	PASS	Atlas-SNP
PSMB6	5694	hgsc.bcm.edu	37	17	4699552	4699552	+	Silent	SNP	G	G	A	rs3169950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	23	38	0	0.5	0	A|0.322;C|0.010;G|0.668;T|0.000	0.322	strong	.	PSMB6	20	.	NM_002798	exon1	c.G63A	p.A21A	GGAGGCGTTCACT	.	PASS	Atlas-SNP
CD79B	974	hgsc.bcm.edu	37	17	62007498	62007498	+	Silent	SNP	A	A	G	rs2070776	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	66	139	1	0.437086	0.00719424	A|0.371;G|0.629	0.629	strong	CD79B,NS,carcinoma,0,1	CD79B	38	1	NM_001039933	exon3	c.T369C	p.C123C	CTGCTGACAGAAG	.	scavenged	Atlas-SNP
CEP41	95681	hgsc.bcm.edu	37	7	130051013	130051013	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	54	128	0	0.760563	0	.	.	none	TSGA14,NS,carcinoma,+1,1	.	.	1	NM_018718	exon5	c.T227C	p.L76P	TCAGAGAGGGAAG	.	PASS	Atlas-SNP
SCLT1	132320	hgsc.bcm.edu	37	4	129867280	129867280	+	Missense_Mutation	SNP	T	T	A	rs10028124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	111	172	0	0.991071	0	T|0.257;A|0.743	0.743	strong	.	SCLT1	136	.	NM_144643	exon16	c.A1321T	p.S441C	AATCACTCTCATT	.	PASS	Atlas-SNP
CSTA	1475	hgsc.bcm.edu	37	3	122060404	122060404	+	Missense_Mutation	SNP	C	C	T	rs34173813	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	43	85	0	0.438776	0	T|0.104;G|0.000;C|0.895	0.104	strong	.	CSTA	11	.	NM_005213	exon3	c.C287T	p.T96M	AGCTGACGGGCTT	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220354365	220354365	+	Silent	SNP	C	C	T	rs56132883	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	25	148	0	0.235849	0	C|0.748;T|0.252	0.252	strong	.	SPEG	272	.	NM_005876	exon36	c.C8625T	p.F2875F	GCCTTTCGTCCTT	.	PASS	Atlas-SNP
CHD7	55636	hgsc.bcm.edu	37	8	61765419	61765419	+	Silent	SNP	G	G	A	rs6999971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	25	23	54	0	0.92	0	G|0.976;A|0.024	0.024	strong	.	CHD7	534	.	NM_017780	exon31	c.G6135A	p.P2045P	TGAGCCGATCACA	.	PASS	Atlas-SNP
METTL25	84190	hgsc.bcm.edu	37	12	82752543	82752543	+	Missense_Mutation	SNP	T	T	G	rs112592060	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	80	278	0	0.357143	0	T|0.938;G|0.062	0.062	strong	.	.	.	.	NM_032230	exon1	c.T199G	p.S67A	TCAGCGTCGGAGA	.	PASS	Atlas-SNP
PLCD1	5333	hgsc.bcm.edu	37	3	38051941	38051941	+	Silent	SNP	T	T	C	rs9857730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	83	200	1	0.522013	0.005	T|0.725;C|0.275	0.275	strong	PLCD1_ENST00000463876,NS,carcinoma,0,2	PLCD1	87	2	NM_001130964	exon6	c.A966G	p.P322P	GCTAAGTGGCTGG	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169511755	169511755	+	Missense_Mutation	SNP	T	T	C	rs4524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	361	352	294	0	0.975069	0	T|0.760;C|0.240	0.240	strong	.	F5	301	.	NM_000130	exon13	c.A2573G	p.K858R	TGACTTTTGAATT	.	PASS	Atlas-SNP
FAM170A	340069	hgsc.bcm.edu	37	5	118969960	118969960	+	Missense_Mutation	SNP	C	C	T	rs328694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	58	170	0	0.432836	0	C|0.562;T|0.438	0.438	strong	FAM170A,NS,carcinoma,0,1	FAM170A	47	1	NM_182761	exon3	c.C517T	p.P173S	ACTCCCCCCTCTG	.	PASS	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	37	4	3444593	3444593	+	Silent	SNP	G	G	A	rs2073504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	58	117	0	0.453125	0	G|0.806;A|0.194	0.194	strong	HGFAC,NS,carcinoma,0,1	HGFAC	69	1	NM_001528	exon2	c.G252A	p.P84P	GCTCCCGCCCCCG	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88780090	88780090	+	Silent	SNP	G	G	A	rs2290904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	20	120	0	0.15748	0	G|0.834;A|0.166	0.166	strong	CTU2_ENST00000453996,NS,carcinoma,0,4	CTU2	66	4	NM_001012759	exon9	c.G909A	p.V303V	GGTGGTGGTGCGG	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	37	12	133357412	133357412	+	Missense_Mutation	SNP	T	T	C	rs2291260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	19	47	0	0.487179	0	T|0.724;C|0.276	0.276	strong	GOLGA3,NS,carcinoma,0,1	GOLGA3	234	1	NM_005895	exon18	c.A3554G	p.K1185R	TTCTCCTTCTCCT	.	PASS	Atlas-SNP
TTC7A	57217	hgsc.bcm.edu	37	2	47301029	47301029	+	Silent	SNP	A	A	G	rs3739099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	307	136	277	0	0.442997	0	A|0.774;G|0.226	0.226	strong	TTC7A,NS,carcinoma,0,1	TTC7A	80	1	NM_020458	exon20	c.A2544G	p.V848V	CCCTGTACTGCCC	.	PASS	Atlas-SNP
IQCE	23288	hgsc.bcm.edu	37	7	2645526	2645526	+	Missense_Mutation	SNP	G	G	A	rs10950797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	313	89	266	2	0.284345	0.0075188	G|0.768;A|0.232	0.232	strong	IQCE,NS,carcinoma,+1,1	IQCE	66	1	NM_152558	exon20	c.G1760A	p.R587H	TGCCCCGCGTTCC	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179395555	179395555	+	Missense_Mutation	SNP	C	C	A	rs67254537	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	331	130	391	2	0.392749	0.00511509	C|0.993;A|0.007	0.007	strong	TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	NM_001267550	exon358	c.G105787T	p.A35263S	ATACGGCTTTCGG	.	scavenged	Atlas-SNP
LRRC4B	94030	hgsc.bcm.edu	37	19	51051935	51051935	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	19	38	0	0.575758	0	.	.	none	.	LRRC4B	89	.	NM_001080457	exon2	c.C161T	p.A54V	GAGGTGGCCGGCG	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193052769	193052769	+	Nonsense_Mutation	SNP	G	G	A	rs74437357	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	78	213	0	0.52349	0	G|0.979;A|0.021	0.021	strong	.	ATP13A5	171	.	NM_198505	exon10	c.C1063T	p.Q355X	TGACCTGGATAAC	.	PASS	Atlas-SNP
ANKDD1A	348094	hgsc.bcm.edu	37	15	65235776	65235776	+	Missense_Mutation	SNP	A	A	G	rs34988193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	69	183	0	0.676471	0	A|0.742;G|0.258	0.258	strong	ANKDD1A,NS,carcinoma,0,1	ANKDD1A	47	1	NM_182703	exon11	c.A1063G	p.K355E	AGAGATAAGGTAC	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919763	28919763	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	52	166	0	0.376812	0	.	.	none	DSG1,NS,carcinoma,-2,1	DSG1	176	1	NM_001942	exon11	c.A1462C	p.N488H	TTTGGTAATGACG	.	PASS	Atlas-SNP
FAM200A	221786	hgsc.bcm.edu	37	7	99145845	99145845	+	Silent	SNP	C	C	T	rs10238965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	384	135	300	0	0.351562	0	C|0.566;T|0.434	0.434	strong	.	FAM200A	27	.	NM_145111	exon2	c.G186A	p.L62L	CGATGACAATAAG	.	PASS	Atlas-SNP
PRDM5	11107	hgsc.bcm.edu	37	4	121737704	121737704	+	Missense_Mutation	SNP	G	G	A	rs190835070	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	24	99	1	0.307692	0.010101	G|1.000;A|0.000	0.000	strong	PRDM5,NS,carcinoma,+1,1	PRDM5	76	1	NM_018699	exon7	c.C769T	p.R257W	CCCCCCGGCAAGT	.	scavenged	Atlas-SNP
HSD17B13	345275	hgsc.bcm.edu	37	4	88231429	88231429	+	Missense_Mutation	SNP	G	G	A	rs62305723	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	130	365	1	0.490566	0.00273973	G|0.956;A|0.044	0.044	strong	.	HSD17B13	27	.	NM_178135	exon6	c.C778T	p.P260S	ACGATGGAACAAA	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50760716	50760716	+	Silent	SNP	C	C	G	rs378811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	53	113	0	0.546392	0	C|0.617;G|0.383	0.383	strong	MYH14_ENST00000262269,NS,carcinoma,0,4	MYH14	261	4	NM_001145809	exon18	c.C2205G	p.R735R	TGTCCGCTGCATT	.	PASS	Atlas-SNP
CLEC3A	10143	hgsc.bcm.edu	37	16	78064733	78064733	+	Missense_Mutation	SNP	C	C	A	rs2072663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	84	146	1	0.865979	0.00684932	C|0.867;A|0.133	0.133	strong	.	CLEC3A	39	.	NM_005752	exon3	c.C616A	p.Q206K	ATCCCTCAATAGG	.	PASS	Atlas-SNP
CABYR	26256	hgsc.bcm.edu	37	18	21739725	21739725	+	Silent	SNP	T	T	C	rs1049684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	62	119	0	0.48062	0	T|0.561;C|0.439	0.439	strong	.	CABYR	51	.	NM_153769	exon5	c.T831C	p.P277P	TCTTCCTGGACAT	.	PASS	Atlas-SNP
OR51F2	119694	hgsc.bcm.edu	37	11	4843164	4843164	+	Silent	SNP	C	C	T	rs113211514	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	67	154	0	0.458904	0	C|0.971;T|0.029	0.029	strong	.	OR51F2	72	.	NM_001004753	exon1	c.C549T	p.C183C	CTTCTGCAGTTCT	.	PASS	Atlas-SNP
GAS8	2622	hgsc.bcm.edu	37	16	90103659	90103659	+	Missense_Mutation	SNP	G	G	A	rs17178299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	30	277	0	0.128205	0	G|0.958;A|0.042	0.042	strong	.	GAS8	29	.	NM_001481	exon7	c.G776A	p.R259Q	ACATGCGGAAGAA	.	PASS	Atlas-SNP
RNF151	146310	hgsc.bcm.edu	37	16	2018912	2018912	+	Missense_Mutation	SNP	A	A	G	rs62617079	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	33	84	0	0.39759	0	A|0.963;G|0.037	0.037	strong	.	RNF151	12	.	NM_174903	exon4	c.A724G	p.I242V	GCCAACATACCTT	.	PASS	Atlas-SNP
CARNS1	57571	hgsc.bcm.edu	37	11	67191346	67191346	+	Silent	SNP	C	C	T	rs3741180	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	48	103	0	0.484848	0	C|0.981;T|0.019	0.019	strong	.	CARNS1	60	.	NM_001166222	exon10	c.C2127T	p.A709A	CGAGGCCGACCAC	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	rs142972518	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	97	209	0	0.386454	0	G|0.986;C|0.014	0.014	strong	.	PKHD1L1	522	.	NM_177531	exon29	c.G3434C	p.G1145A	ATGTAGGGGGTGA	.	PASS	Atlas-SNP
NLRP10	338322	hgsc.bcm.edu	37	11	7981822	7981822	+	Missense_Mutation	SNP	A	A	G	rs143403695	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	34	63	0	0.641509	0	A|0.999;G|0.001	0.001	strong	.	NLRP10	146	.	NM_176821	exon2	c.T1337C	p.F446S	CTCAGGAAAGCGG	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242157241	242157241	+	Missense_Mutation	SNP	G	G	A	rs76832527	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	48	111	1	0.5	0.00900901	G|0.874;A|0.126	0.126	strong	ANO7,colon,carcinoma,-2,1	ANO7	136	1	NM_001001891	exon20	c.G2275A	p.A759T	GAGCGCGCCCAGG	.	scavenged	Atlas-SNP
BCL9L	283149	hgsc.bcm.edu	37	11	118772413	118772413	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	2	109	0	0.0101523	0	.	.	none	BCL9L_ENST00000392849,colon,carcinoma,-1,3	BCL9L	254	3	NM_182557	exon6	c.G2039A	p.R680Q	TGGTGCCGCAGCA	.	scavenged	Atlas-SNP
ZNF568	374900	hgsc.bcm.edu	37	19	37487975	37487975	+	Missense_Mutation	SNP	G	G	A	rs16971886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	8	8	5	1	1	0.2	G|0.732;A|0.267	0.267	strong	ZNF568_ENST00000455427,NS,carcinoma,0,1	ZNF568	106	1	NM_001204838	exon10	c.G1382A	p.R461H	CTTTTCGTTATGA	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149523277	149523277	+	Missense_Mutation	SNP	A	A	G	rs1004200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	6	72	0	0.1875	0	A|0.586;G|0.414	0.414	strong	.	.	.	.	NM_198455	exon101	c.A14360G	p.H4787R	AGCGACATCGGAC	.	PASS	Atlas-SNP
GSDMD	79792	hgsc.bcm.edu	37	8	144642854	144642854	+	Silent	SNP	G	G	A	rs11551202	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	77	191	0	0.306773	0	G|0.836;A|0.164	0.164	strong	GSDMD,NS,carcinoma,0,1	GSDMD	28	1	NM_001166237	exon7	c.G492A	p.L164L	GGTGCTGCAGACA	.	PASS	Atlas-SNP
BPIFA1	51297	hgsc.bcm.edu	37	20	31825568	31825568	+	Silent	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	3	106	1	0.0280374	0.00943396	.	.	none	PLUNC,NS,carcinoma,+1,1	.	.	1	NM_016583	exon2	c.C51A	p.T17T	CCAGACCATGGCC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276377	152276377	+	Missense_Mutation	SNP	C	C	G	rs75235053	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	272	45	183	0	0.165441	0	C|0.500;G|0.500	0.500	weak	FLG,extremity,malignant_melanoma,0,2	FLG	900	2	NM_002016	exon3	c.G10985C	p.S3662T	GCCTGACTACCAC	.	scavenged	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151171542	151171542	+	Silent	SNP	A	A	G	rs7621591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	76	86	0	1	0	A|0.195;G|0.805	0.805	strong	.	IGSF10	279	.	NM_178822	exon3	c.T345C	p.N115N	GACTTTATTATAG	.	PASS	Atlas-SNP
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777196	18777196	+	Missense_Mutation	SNP	A	A	C	rs41268983	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	35	73	0	0.530303	0	A|0.895;C|0.105	0.105	strong	.	ADAMTSL1	306	.	NM_001040272	exon19	c.A2969C	p.E990A	CGAAGGAGGCCCT	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6585838	6585838	+	Silent	SNP	G	G	A	rs11825255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	29	82	0	0.391892	0	G|0.816;A|0.184	0.184	strong	.	DNHD1	198	.	NM_144666	exon32	c.G10560A	p.Q3520Q	GGAGCAGTACCAG	.	PASS	Atlas-SNP
HTR2A	3356	hgsc.bcm.edu	37	13	47469939	47469939	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	42	84	0	0.518519	0	.	.	none	.	HTR2A	98	.	NM_000621	exon2	c.G103A	p.G35R	CTTCTCCGGAGTT	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41563685	41563685	+	Silent	SNP	G	G	A	rs1137177	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	76	87	0	0.684685	0	G|0.832;N|0.000	.	strong	.	ANK1	497	.	NM_001142446	exon18	c.C2172T	p.G724G	CATGACGCCGTGT	.	PASS	Atlas-SNP
DGCR6L	85359	hgsc.bcm.edu	37	22	20307256	20307256	+	Silent	SNP	G	G	A	rs7235	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	291	129	320	2	0.443299	0.00625	G|0.703;A|0.297	0.297	strong	DGCR6L,NS,carcinoma,0,1	DGCR6L	9	1	NM_033257	exon2	c.C177T	p.T59T	GAACACGGTGCCG	.	scavenged	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	37	8	17817553	17817553	+	Missense_Mutation	SNP	G	G	T	rs17635381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	63	149	0	0.310345	0	G|0.834;N|0.000	.	strong	.	PCM1	120	.	NM_006197	exon14	c.G2071T	p.A691S	ATCTCTGCCAGTG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160697271	160697271	+	Missense_Mutation	SNP	G	G	A	rs147904044	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	61	125	0	0.462121	0	G|0.996;A|0.004	0.004	strong	.	LY75	151	.	NM_002349	exon25	c.C3476T	p.S1159F	AAGGAAGAGTTGT	.	PASS	Atlas-SNP
MPC2	25874	hgsc.bcm.edu	37	1	167893759	167893759	+	Silent	SNP	G	G	A	rs9618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	89	170	2	0.581699	0.0117647	G|0.609;A|0.391	0.391	strong	BRP44,caecum,carcinoma,0,1	.	.	1	NM_001143674	exon3	c.C126T	p.F42F	CCAGAAGAAAACT	.	scavenged	Atlas-SNP
FAM189A1	23359	hgsc.bcm.edu	37	15	29544656	29544656	+	Silent	SNP	T	T	C	rs4583203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	93	241	0	0.699248	0	T|0.529;C|0.471	0.471	strong	FAM189A1,NS,carcinoma,-1,1	FAM189A1	20	1	NM_015307	exon3	c.A303G	p.A101A	ACACACTGCAGAA	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49376582	49376582	+	Missense_Mutation	SNP	G	G	A	rs564196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	11	22	0	0.37931	0	G|0.729;A|0.271	0.271	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G92A	p.R31H	TCAGCCGCGCCTG	.	PASS	Atlas-SNP
AMT	275	hgsc.bcm.edu	37	3	49455330	49455330	+	Silent	SNP	C	C	T	rs11715915	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	43	84	0	0.511905	0	C|0.736;T|0.264	0.264	strong	.	AMT	22	.	NM_001164712	exon8	c.G954A	p.R318R	ACGCCTCCGCTGC	.	PASS	Atlas-SNP
C8orf31	286122	hgsc.bcm.edu	37	8	144124609	144124609	+	Missense_Mutation	SNP	T	T	C	rs11136300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	53	134	0	0.407692	0	T|0.317;C|0.683	0.683	strong	.	C8orf31	18	.	NM_173687	exon3	c.T116C	p.L39P	GGCTGCTGGCTGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506917	195506917	+	Missense_Mutation	SNP	A	A	C	rs150128295	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40	23	95	4	0.575	0.0421053	A|0.832;C|0.168	0.168	strong	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.T11534G	p.I3845S	GAAGGGATGGTGA	.	scavenged	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126237971	126237971	+	Silent	SNP	C	C	T	rs72928772	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	6	78	0	0.133333	0	C|0.831;T|0.169	0.169	strong	.	FAT4	1752	.	NM_024582	exon1	c.C405T	p.F135F	CGTTTTCCCGGAC	.	PASS	Atlas-SNP
ANKRD33	341405	hgsc.bcm.edu	37	12	52285086	52285086	+	Missense_Mutation	SNP	G	G	A	rs3180417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	45	60	0	0.9375	0	G|0.851;A|0.149	0.149	strong	.	ANKRD33	33	.	NM_001130015	exon6	c.G781A	p.V261I	ACAGAAGTAGGGG	.	PASS	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105344823	105344823	+	Silent	SNP	G	G	A	rs41314519	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	47	72	1	0.364341	0.0138889	G|0.969;A|0.031	0.031	strong	KIAA0284_ENST00000414716,NS,carcinoma,0,1	.	.	1	NM_001112726	exon5	c.G318A	p.P106P	AGTCCCGGAGGAG	.	scavenged	Atlas-SNP
TRRAP	8295	hgsc.bcm.edu	37	7	98602800	98602800	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	3	82	0	0.0243902	0	.	.	none	TRRAP_ENST00000359863,NS,carcinoma,0,2	TRRAP	863	2	NM_001244580	exon68	c.C10540T	p.R3514W	GCAGCCCGGCGGC	.	scavenged	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7189437	7189437	+	Missense_Mutation	SNP	G	G	A	rs201588284	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	31	40	0	0.525424	0	G|0.999;A|0.001	0.001	strong	RREB1_ENST00000379938,NS,carcinoma,-2,2	RREB1	242	2	NM_001003700	exon6	c.G307A	p.G103R	ATCTGCGGAAAGT	.	PASS	Atlas-SNP
DHRS4L2	317749	hgsc.bcm.edu	37	14	24459520	24459520	+	Silent	SNP	T	T	C	rs61738427	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	237	299	1	0.971311	0.00334448	T|0.868;C|0.132	0.132	strong	DHRS4L2,colon,carcinoma,0,1	DHRS4L2	29	1	NM_198083	exon2	c.T258C	p.T86T	GGGCACTGTGTGC	.	PASS	Atlas-SNP
C1orf105	92346	hgsc.bcm.edu	37	1	172431386	172431386	+	Splice_Site	SNP	G	G	A	rs41310899	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	255	76	207	0	0.298039	0	G|0.948;A|0.052	0.052	strong	.	C1orf105	24	.	NM_139240	exon5	c.341+1G>A	.	TTATAGGTAAGTC	.	PASS	Atlas-SNP
KCTD17	79734	hgsc.bcm.edu	37	22	37458586	37458586	+	Silent	SNP	C	C	T	rs116956945	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	46	92	0	0.589744	0	C|0.965;T|0.035	0.035	strong	KCTD17,NS,carcinoma,0,1	KCTD17	17	1	NM_024681	exon8	c.C846T	p.P282P	GGCACCCGGATGT	.	PASS	Atlas-SNP
ARMC4	55130	hgsc.bcm.edu	37	10	28257852	28257852	+	Missense_Mutation	SNP	C	C	T	rs7920186	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	697	233	1045	1	0.33429	0.000956938	C|0.500;T|0.500	0.500	weak	ARMC4,rectum,NS,-1,1	ARMC4	177	1	NM_018076	exon9	c.G1238A	p.R413Q	ACATACCGAAGTA	.	scavenged	Atlas-SNP
HEBP2	23593	hgsc.bcm.edu	37	6	138734029	138734029	+	Silent	SNP	A	A	C	rs2076279	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	76	204	0	0.426966	0	A|0.961;C|0.039	0.039	strong	.	HEBP2	12	.	NM_014320	exon4	c.A432C	p.G144G	CGATGGATTTTCT	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47808679	47808679	+	Missense_Mutation	SNP	C	C	T	rs7279204	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	80	129	1	0.592593	0.00775194	C|0.883;T|0.117	0.117	strong	PCNT,face,carcinoma,-1,1	PCNT	283	1	NM_006031	exon18	c.C3487T	p.R1163C	GCCCTGCGCAGGC	.	scavenged	Atlas-SNP
SEMG2	6407	hgsc.bcm.edu	37	20	43850400	43850400	+	Missense_Mutation	SNP	C	C	A	rs2233896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	79	265	0	0.39899	0	C|0.876;A|0.124	0.124	strong	SEMG2,caecum,carcinoma,0,1	SEMG2	92	1	NM_003008	exon2	c.C127A	p.Q43K	CATGGACAAAAGG	.	PASS	Atlas-SNP
AP3D1	8943	hgsc.bcm.edu	37	19	2116649	2116649	+	Silent	SNP	A	A	G	rs2074960	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	29	105	1	0.376623	0.00952381	A|0.834;G|0.166	0.166	strong	AP3D1,NS,carcinoma,-1,1	AP3D1	81	1	NM_001261826	exon17	c.T1956C	p.R652R	CTTGGGACGCCGC	.	scavenged	Atlas-SNP
ZNF622	90441	hgsc.bcm.edu	37	5	16465442	16465442	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	66	147	0	0.461538	0	.	.	none	ZNF622,NS,carcinoma,-2,1	ZNF622	49	1	NM_033414	exon1	c.A333G	p.E111E	GTTCTTTTCATTC	.	PASS	Atlas-SNP
MANEA	79694	hgsc.bcm.edu	37	6	96053922	96053922	+	Missense_Mutation	SNP	T	T	A	rs35772543	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	56	46	0	1	0	T|0.936;A|0.064	0.064	strong	.	MANEA	58	.	NM_024641	exon5	c.T1030A	p.F344I	AAATTATTTTGTG	.	PASS	Atlas-SNP
MLLT4	4301	hgsc.bcm.edu	37	6	168317816	168317816	+	Silent	SNP	A	A	C	rs6906754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	98	226	0	0.547486	0	A|0.869;C|0.131	0.131	strong	.	MLLT4	351	.	NM_001040000	exon19	c.A2592C	p.P864P	CATTCCAAATATA	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152712440	152712440	+	Missense_Mutation	SNP	G	G	T	rs117480635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	55	104	0	0.470085	0	G|0.998;T|0.002	0.002	strong	.	SYNE1	3227	.	NM_033071	exon52	c.C7997A	p.T2666N	TCCAGGGTGTCTT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152286367	152286367	+	Missense_Mutation	SNP	C	C	A	rs41267154	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	538	180	383	1	0.334572	0.00261097	C|0.793;A|0.207	0.207	strong	.	FLG	900	.	NM_002016	exon3	c.G995T	p.G332V	CTGGAGCCATCTC	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103794	53103794	+	Missense_Mutation	SNP	C	C	T	rs73357087	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	29	37	0	0.690476	0	C|0.843;T|0.157	0.157	strong	POM121L12,NS,carcinoma,-1,1	POM121L12	146	1	NM_182595	exon1	c.C430T	p.P144S	GCGCCCCCTGAGC	.	PASS	Atlas-SNP
TRAPPC11	60684	hgsc.bcm.edu	37	4	184600571	184600571	+	Silent	SNP	C	C	A	rs62357990	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	8	53	0	0.140351	0	C|0.939;A|0.061	0.061	strong	.	.	.	.	NM_021942	exon9	c.C897A	p.I299I	ACACATCGACTTG	.	PASS	Atlas-SNP
FTH1P18	441490	hgsc.bcm.edu	37	X	37061389	37061389	+	Missense_Mutation	SNP	C	C	T	rs28675922	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	8	8	13	0	1	0	C|0.736;T|0.264	0.264	strong	.	.	.	.	NM_001271682	exon1	c.G373A	p.G125R	GCTTCCCGACGTC	.	PASS	Atlas-SNP
DDC	1644	hgsc.bcm.edu	37	7	50607649	50607649	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	2	154	0	0.010929	0	.	.	none	DDC_ENST00000380984,NS,carcinoma,-2,2	DDC	100	2	NM_001082971	exon3	c.G279A	p.M93I	GCACAGCATGTCC	.	scavenged	Atlas-SNP
ZNF543	125919	hgsc.bcm.edu	37	19	57839567	57839567	+	Missense_Mutation	SNP	T	T	A	rs1968090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	94	118	0	0.989474	0	T|0.268;A|0.732	0.732	strong	.	ZNF543	61	.	NM_213598	exon4	c.T737A	p.L246H	AGCACCTCATCAT	.	PASS	Atlas-SNP
FFAR4	338557	hgsc.bcm.edu	37	10	95326676	95326676	+	Missense_Mutation	SNP	C	C	T	rs61866610	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	72	113	0	0.878049	0	C|0.920;T|0.080	0.080	strong	.	.	.	.	NM_001195755	exon1	c.C199T	p.R67C	GTGGCGCGCCGAC	.	PASS	Atlas-SNP
TMEM199	147007	hgsc.bcm.edu	37	17	26684707	26684707	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	16	49	0	0.390244	0	.	.	none	.	TMEM199	15	.	NM_152464	exon1	c.T14A	p.L5X	CCTCTTTGCTTGC	.	PASS	Atlas-SNP
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462926	37462926	+	Silent	SNP	G	G	A	rs2235321	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	99	194	0	0.492537	0	G|0.622;A|0.377	0.377	strong	TMPRSS6,NS,carcinoma,0,1	TMPRSS6	99	1	NM_153609	exon17	c.C2217T	p.Y739Y	CACCTGGTAGCGA	.	PASS	Atlas-SNP
GAA	2548	hgsc.bcm.edu	37	17	78084769	78084769	+	Silent	SNP	G	G	A	rs1042396	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	62	154	0	0.473282	0	G|0.800;A|0.200	0.200	strong	GAA,NS,carcinoma,0,1	GAA	66	1	NM_001079803	exon12	c.G1581A	p.R527R	CATCAGGGGCTCT	.	PASS	Atlas-SNP
PLEKHH2	130271	hgsc.bcm.edu	37	2	43926943	43926943	+	Silent	SNP	T	T	A	rs7606783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	101	287	0	0.463303	0	T|0.440;A|0.560	0.560	strong	.	PLEKHH2	156	.	NM_172069	exon8	c.T846A	p.P282P	GGCTCCTGTGAGT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179400718	179400718	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	2	86	0	0.019802	0	.	.	none	TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	NM_001267550	exon357	c.G100756A	p.E33586K	CCACTTCCAAGGA	.	scavenged	Atlas-SNP
CASP8	841	hgsc.bcm.edu	37	2	202137432	202137432	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	71	139	0	0.663551	0	.	.	none	.	CASP8	272	.	NM_001080125	exon4	c.A660G	p.K220K	CCTGAAAAGAGTC	.	PASS	Atlas-SNP
ZNF534	147658	hgsc.bcm.edu	37	19	52937339	52937339	+	Silent	SNP	G	G	A	rs17780173	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	96	254	0	0.395062	0	G|0.765;A|0.235	0.235	strong	.	ZNF534	105	.	NM_001143939	exon2	c.G147A	p.E49E	AGGTGAGGATAAT	.	PASS	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	37	9	35712003	35712003	+	Missense_Mutation	SNP	G	G	A	rs2295795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	17	42	0	0.548387	0	G|0.785;A|0.215	0.215	strong	.	TLN1	185	.	NM_006289	exon28	c.C3680T	p.S1227L	CCTACCGAGTCAC	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592606	167592606	+	Silent	SNP	T	T	A	rs201866116	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	44	75	0	0.335878	0	T|0.927;A|0.073	0.073	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.T765A	p.V255V	CGGAGTTGCTGGT	.	PASS	Atlas-SNP
CLK2	1196	hgsc.bcm.edu	37	1	155235736	155235736	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	2	163	0	0.0108108	0	.	.	none	CLK2,NS,carcinoma,-1,1	CLK2	55	1	NM_003993	exon8	c.A845G	p.D282G	TTGTTATCATGGA	.	scavenged	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115769	168115769	+	Missense_Mutation	SNP	G	G	C	rs16853344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	52	138	0	0.477064	0	G|0.841;C|0.159	0.159	strong	.	XIRP2	914	.	NM_001199143	exon11	c.G2812C	p.E938Q	AGCCATGAATGTA	.	PASS	Atlas-SNP
LURAP1L	286343	hgsc.bcm.edu	37	9	12775855	12775855	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17	7	15	0	0.411765	0	.	.	none	.	.	.	.	NM_203403	exon1	c.T141C	p.G47G	GAGCGGTGGTGGT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511354	4511354	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	336	12	302	3	0.0357143	0.00993378	.	.	none	PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	NM_001080400	exon3	c.C2576T	p.A859V	ACTTTCGCAGCAC	.	scavenged	Atlas-SNP
SYT2	127833	hgsc.bcm.edu	37	1	202574784	202574784	+	Silent	SNP	G	G	A	rs1968583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	338	331	286	0	0.97929	0	G|0.596;A|0.404	0.404	strong	.	SYT2	51	.	NM_177402	exon2	c.C117T	p.S39S	CTCCTGGCTCTCC	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318821	21318821	+	Missense_Mutation	SNP	A	A	C	rs1714865	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	32	306	2	0.143498	0.00653595	A|0.988;C|0.012	0.012	strong	KCNJ12,NS,carcinoma,0,3	.	.	3	NM_001194958	exon3	c.A167C	p.E56A	ACATTGAGTTCGC	.	scavenged	Atlas-SNP
CDC6	990	hgsc.bcm.edu	37	17	38457151	38457151	+	Missense_Mutation	SNP	G	G	A	rs13706	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	119	236	0	0.506383	0	G|0.734;A|0.266	0.266	strong	.	CDC6	53	.	NM_001254	exon10	c.G1321A	p.V441I	TCAGAAGTTGATG	.	PASS	Atlas-SNP
QRICH1	54870	hgsc.bcm.edu	37	3	49067904	49067904	+	Missense_Mutation	SNP	T	T	C	rs61729488	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	49	88	0	0.49	0	T|0.927;C|0.073	0.073	strong	.	QRICH1	48	.	NM_198880	exon10	c.A2312G	p.N771S	CTTGCATTGGCCA	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11757556	11757556	+	Silent	SNP	C	C	G	rs12449553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	153	139	0	1	0	C|0.605;G|0.395	0.395	strong	DNAH9,NS,carcinoma,0,1	DNAH9	695	1	NM_001372	exon50	c.C9744G	p.P3248P	AGACCCCGAGTTC	.	PASS	Atlas-SNP
NACA2	342538	hgsc.bcm.edu	37	17	59668517	59668517	+	Missense_Mutation	SNP	C	C	A	rs61748812	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	28	56	0	0.430769	0	C|0.980;A|0.020	0.020	strong	.	NACA2	33	.	NM_199290	exon1	c.G25T	p.V9F	CAGGGACGGTTTC	.	PASS	Atlas-SNP
GRAMD1B	57476	hgsc.bcm.edu	37	11	123480981	123480981	+	Silent	SNP	T	T	C	rs10893053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	168	132	1	0.994083	0.00757576	T|0.767;C|0.233	0.233	strong	.	GRAMD1B	122	.	NM_020716	exon13	c.T1425C	p.H475H	CTACCATGACTAC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7080048	7080048	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	116	315	0	0.471545	0	.	.	none	.	LAMA1	458	.	NM_005559	exon3	c.A271G	p.N91D	ACCAGTTATTGGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678421	100678421	+	Missense_Mutation	SNP	T	T	A	rs10265276	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	244	137	2	0.97992	0.0145985	T|0.819;A|0.181	0.181	strong	MUC17,NS,carcinoma,-1,1	MUC17	804	1	NM_001040105	exon3	c.T3724A	p.S1242T	TCAACATCTCCCG	.	scavenged	Atlas-SNP
GPR146	115330	hgsc.bcm.edu	37	7	1097895	1097895	+	Silent	SNP	A	A	G	rs61910751	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	26	37	0	0.634146	0	A|0.893;G|0.106;T|0.000	0.106	strong	.	GPR146	20	.	NM_138445	exon1	c.A744G	p.P248P	GACGCCACACTAT	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17017878	17017878	+	Missense_Mutation	SNP	G	G	A	rs56408444	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	89	212	0	0.45641	0	G|0.803;A|0.197	0.197	strong	CPAMD8,NS,carcinoma,0,1	CPAMD8	192	1	NM_015692	exon30	c.C4052T	p.A1351V	AGGGGCGCAGCAG	.	PASS	Atlas-SNP
NIPAL3	57185	hgsc.bcm.edu	37	1	24785393	24785393	+	Silent	SNP	C	C	T	rs2272935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	95	188	2	0.766129	0.0106383	C|0.732;T|0.268	0.268	strong	NIPAL3,NS,carcinoma,+1,1	NIPAL3	36	1	NM_020448	exon9	c.C789T	p.A263A	TCAAGCCTCACAG	.	scavenged	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117079654	117079654	+	Missense_Mutation	SNP	A	A	T	rs471009	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	424	23	422	3	0.0542453	0.007109	A|0.994;T|0.006	0.006	strong	PCSK7,NS,carcinoma,0,2	PCSK7	59	2	NM_004716	exon13	c.T1650A	p.S550R	CATGCCACTGGGG	.	scavenged	Atlas-SNP
SSUH2	51066	hgsc.bcm.edu	37	3	8675539	8675539	+	Missense_Mutation	SNP	G	G	A	rs2276800	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	61	137	0	0.480315	0	G|0.689;A|0.311	0.311	strong	C3orf32,NS,carcinoma,0,2	.	.	2	NM_015931	exon4	c.C86T	p.P29L	TCACGCGGGCCAG	.	PASS	Atlas-SNP
ZFP106	64397	hgsc.bcm.edu	37	15	42744094	42744094	+	Missense_Mutation	SNP	A	A	G	rs12440118	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	83	123	0	0.988095	0	A|0.907;G|0.093	0.093	strong	.	ZFP106	117	.	NM_022473	exon2	c.T307C	p.W103R	GTCTCCATTGGGG	.	PASS	Atlas-SNP
ALOX12B	242	hgsc.bcm.edu	37	17	7989492	7989492	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	130	275	0	0.488722	0	.	.	none	.	ALOX12B	61	.	NM_001139	exon2	c.T194C	p.I65T	ATGATGATGAGCT	.	PASS	Atlas-SNP
TOX4	9878	hgsc.bcm.edu	37	14	21960816	21960816	+	Silent	SNP	T	T	C	rs1060722	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	144	117	1	0.986301	0.00854701	T|0.514;C|0.486	0.486	strong	.	TOX4	50	.	NM_014828	exon7	c.T1041C	p.L347L	CACCCTTTCATCC	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207741312	207741312	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	514	5	368	2	0.00972763	0.00543478	.	.	none	CR1_ENST00000367049,NS,carcinoma,-2,2	CR1	354	2	NM_000651	exon25	c.A4096G	p.S1366G	GGAGAGAGCACCA	.	scavenged	Atlas-SNP
CLCF1	23529	hgsc.bcm.edu	37	11	67135006	67135006	+	Silent	SNP	A	A	T	rs867193	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	91	155	0	0.522988	0	A|0.928;T|0.072	0.072	strong	.	CLCF1	15	.	NM_013246	exon2	c.T108A	p.P36P	GGGGCCAGGCCCT	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50726570	50726570	+	Silent	SNP	G	G	A	rs4801822	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	62	138	1	0.392405	0.00724638	G|0.507;A|0.494	0.494	strong	MYH14_ENST00000262269,NS,carcinoma,0,2	MYH14	261	2	NM_001077186	exon5	c.G657A	p.A219A	CGTGGCGTCGTCT	.	scavenged	Atlas-SNP
CPT1A	1374	hgsc.bcm.edu	37	11	68560787	68560787	+	Silent	SNP	C	C	T	rs2229737	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	45	158	0	0.387931	0	C|0.914;T|0.086	0.086	strong	.	CPT1A	89	.	NM_001876	exon9	c.G963A	p.E321E	ACCTGTCTCCTCT	.	PASS	Atlas-SNP
LRTM1	57408	hgsc.bcm.edu	37	3	54958968	54958968	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	3	124	0	0.0265487	0	.	.	none	LRTM1,NS,carcinoma,-1,1	LRTM1	52	1	NM_020678	exon2	c.C282T	p.F94F	CCCATGGAAAGCT	.	scavenged	Atlas-SNP
PF4V1	5197	hgsc.bcm.edu	37	4	74719624	74719624	+	Silent	SNP	C	C	G	rs34446485	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	25	180	0	0.203252	0	C|0.981;G|0.019	0.019	strong	PF4V1,NS,carcinoma,0,1	PF4V1	8	1	NM_002620	exon2	c.C225G	p.L75L	CCAACTCATGTGA	.	scavenged	Atlas-SNP
SERPINB8	5271	hgsc.bcm.edu	37	18	61654463	61654463	+	Missense_Mutation	SNP	A	A	G	rs3826616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	73	135	0	0.532847	0	A|0.466;G|0.534	0.534	strong	.	SERPINB8	42	.	NM_198833	exon7	c.A1076G	p.H359R	TCAGGCACCACAA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179621184	179621184	+	Silent	SNP	G	G	A	rs72955212	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	73	129	1	0.548872	0.00775194	G|0.990;A|0.010	0.010	strong	TTN_ENST00000342175,NS,carcinoma,-2,1	TTN	18412	1	NM_001267550	exon46	c.C11019T	p.C3673C	GTCACCGCACTTT	.	scavenged	Atlas-SNP
PEX11G	92960	hgsc.bcm.edu	37	19	7550844	7550844	+	Silent	SNP	G	G	A	rs34970001	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	40	116	0	0.5	0	G|0.725;A|0.275	0.275	strong	.	PEX11G	16	.	NM_001270539	exon2	c.C129T	p.S43S	CACTTCGGACCTG	.	PASS	Atlas-SNP
OCM2	4951	hgsc.bcm.edu	37	7	97617822	97617822	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	2	202	0	0.0103093	0	.	.	none	OCM2,NS,malignant_melanoma,+1,1	OCM2	19	1	NM_006188	exon2	c.T100C	p.S34P	GGCCTGACGTCTG	.	scavenged	Atlas-SNP
GTF2A1	2957	hgsc.bcm.edu	37	14	81686832	81686832	+	Splice_Site	SNP	C	C	G	rs201410281	by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	21	32	0	0.283784	0	C|1.000;T|0.000	.	alt	.	GTF2A1	34	.	NM_015859	exon2	c.30+1G>C	.	TCCTTACCACGGT	.	PASS	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100961704	100961704	+	Missense_Mutation	SNP	C	C	T	rs34769888	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	64	144	0	0.474074	0	C|0.994;T|0.006	0.006	strong	.	TBC1D2	70	.	NM_001267571	exon13	c.G2746A	p.E916K	AGCCCTCGGACAC	.	PASS	Atlas-SNP
SLC2A14	144195	hgsc.bcm.edu	37	12	7967076	7967076	+	Silent	SNP	A	A	G	rs10845983	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	65	131	0	0.524194	0	A|0.760;G|0.240	0.240	strong	SLC2A14,NS,carcinoma,+2,1	SLC2A14	78	1	NM_153449	exon12	c.T1399C	p.L467L	AGGCCAAGAAGGT	.	PASS	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102265183	102265183	+	Missense_Mutation	SNP	G	G	A	rs2295772	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	68	217	0	0.641509	0	G|0.808;A|0.192	0.192	strong	.	SEC31B	84	.	NM_015490	exon10	c.C1114T	p.P372S	TCAGTGGTGCTTG	.	PASS	Atlas-SNP
ABCA5	23461	hgsc.bcm.edu	37	17	67290840	67290840	+	Missense_Mutation	SNP	T	T	C	rs17686569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	54	60	0	1	0	T|0.839;C|0.161	0.161	strong	.	ABCA5	162	.	NM_018672	exon10	c.A1451G	p.Q484R	GTCTTCTGAATAC	.	PASS	Atlas-SNP
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625517	74625517	+	Silent	SNP	T	T	C	rs139045542	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	395	204	386	0	0.516456	0	T|0.996;C|0.004	0.004	strong	.	ST6GALNAC1	42	.	NM_018414	exon2	c.A408G	p.T136T	TGACAGTGTGTTC	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41583294	41583294	+	Silent	SNP	C	C	T	rs2304873	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	9	94	0	0.333333	0	C|0.900;T|0.100	0.100	strong	.	ANK1	497	.	NM_001142446	exon6	c.G696A	p.P232P	CACGTCCGGGTTG	.	PASS	Atlas-SNP
SMAD3	4088	hgsc.bcm.edu	37	15	67473790	67473790	+	Silent	SNP	C	C	T	rs2230745	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	25	48	0	0.714286	0	.	.	weak	.	SMAD3	119	.	NM_005902	exon6	c.C870T	p.I290I	ACACATCGGTATG	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134062764	134062764	+	Missense_Mutation	SNP	C	C	T	rs12292394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	29	111	0	0.204225	0	C|0.962;T|0.038	0.038	strong	.	NCAPD3	141	.	NM_015261	exon16	c.G1865A	p.R622Q	ACCCCCCGCAACC	.	PASS	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	37	1	20650001	20650001	+	Silent	SNP	C	C	T	rs146423282	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	8	37	0	0.170213	0	C|0.995;T|0.005	0.005	strong	.	VWA5B1	44	.	NM_001039500	exon8	c.C1119T	p.S373S	CATGAGCGGGATC	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113573237	113573237	+	Missense_Mutation	SNP	C	C	G	rs7960087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	96	240	2	0.482412	0.00833333	C|0.974;G|0.026	0.026	strong	RASAL1,NS,carcinoma,0,2	RASAL1	89	2	NM_004658	exon2	c.G31C	p.V11L	CCACCACGCGAAC	.	scavenged	Atlas-SNP
EEF1A2	1917	hgsc.bcm.edu	37	20	62126185	62126185	+	Silent	SNP	A	A	G	rs310617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	29	42	0	0.483333	0	A|0.419;G|0.581	0.581	strong	EEF1A2,NS,carcinoma,0,3	EEF1A2	60	3	NM_001958	exon4	c.T594C	p.G198G	GTTGTCACCGTGC	.	PASS	Atlas-SNP
AAK1	22848	hgsc.bcm.edu	37	2	69709919	69709919	+	Silent	SNP	A	A	G	rs6721259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	55	106	0	0.45082	0	A|0.862;G|0.138	0.138	strong	.	AAK1	121	.	NM_014911	exon18	c.T2391C	p.S797S	GTCAGGAGATTTG	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2835985	2835985	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	40	176	0	0.373832	0	.	.	none	.	ARSD	47	.	NM_001669	exon5	c.C723T	p.F241F	AGAGATGAAAAAC	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43575982	43575982	+	Silent	SNP	C	C	T	rs150568950	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	108	249	1	0.461538	0.00401606	C|0.998;T|0.002	0.002	strong	PSG2,NS,carcinoma,-1,1	PSG2	84	1	NM_031246	exon4	c.G834A	p.K278K	CTGAAACTTCCCA	.	PASS	Atlas-SNP
CCDC40	55036	hgsc.bcm.edu	37	17	78071052	78071052	+	Silent	SNP	T	T	C	rs12952612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	28	48	0	0.518519	0	T|0.282;C|0.718	0.718	strong	CCDC40,NS,carcinoma,0,1	CCDC40	198	1	NM_017950	exon19	c.T3030C	p.D1010D	CACCGATGAGTGC	.	PASS	Atlas-SNP
PLRG1	5356	hgsc.bcm.edu	37	4	155459194	155459194	+	Silent	SNP	A	A	T	rs7668818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	120	258	2	0.779221	0.00775194	A|0.748;T|0.252	0.252	strong	.	PLRG1	43	.	NM_002669	exon13	c.T1218A	p.I406I	ATTTTGAATGAAA	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129046371	129046371	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	85	193	0	0.456989	0	.	.	none	.	DOCK1	188	.	NM_001380	exon28	c.G2884A	p.V962I	GATGTGGTAGTAA	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103124135	103124135	+	Silent	SNP	T	T	G	rs11225634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	432	294	289	1	0.680556	0.00346021	T|0.824;G|0.176	0.176	strong	.	DYNC2H1	246	.	NM_001080463	exon67	c.T10185G	p.T3395T	TGTTACTGAGGTT	.	PASS	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	37	3	126741041	126741041	+	Silent	SNP	C	C	T	rs150052583	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	67	206	0	0.446667	0	C|0.992;T|0.008	0.008	strong	PLXNA1,colon,carcinoma,+2,1	PLXNA1	185	1	NM_032242	exon21	c.C4152T	p.R1384R	CATGCGCGACCGC	.	PASS	Atlas-SNP
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441478	39441478	+	Missense_Mutation	SNP	C	C	A	rs138934952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	425	197	455	0	0.463529	0	C|0.998;A|0.002	0.002	strong	.	APOBEC3F	37	.	NM_145298	exon4	c.C497A	p.P166Q	GTCAGCCATTCAT	.	PASS	Atlas-SNP
RNF151	146310	hgsc.bcm.edu	37	16	2018578	2018578	+	Missense_Mutation	SNP	C	C	G	rs45488492	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	50	89	0	0.537634	0	C|0.963;G|0.037	0.037	strong	.	RNF151	12	.	NM_174903	exon4	c.C390G	p.H130Q	AGAGCACCGGCAG	.	PASS	Atlas-SNP
PPM1F	9647	hgsc.bcm.edu	37	22	22287862	22287862	+	Silent	SNP	G	G	A	rs2027789	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	29	63	0	0.3625	0	G|0.665;A|0.335	0.335	strong	.	PPM1F	34	.	NM_014634	exon5	c.C648T	p.N216N	GGCAGCGTTGGTG	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159667961	159667961	+	Silent	SNP	T	T	G	rs294911	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	63	146	0	0.61165	0	T|0.835;G|0.165	0.165	strong	.	FNDC1	250	.	NM_032532	exon15	c.T4650G	p.T1550T	TGACACTGCAGTA	.	PASS	Atlas-SNP
PHPT1	29085	hgsc.bcm.edu	37	9	139744524	139744524	+	Silent	SNP	C	C	T	rs8666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	82	167	0	0.465909	0	C|0.972;T|0.028	0.028	strong	.	PHPT1	14	.	NM_001135861	exon2	c.C220T	p.L74L	GAGTGTCTGGGCG	.	PASS	Atlas-SNP
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461074	141461074	+	Silent	SNP	A	A	G	rs61739560	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	50	75	0	0.390625	0	A|0.913;G|0.087	0.087	strong	.	TRAPPC9	114	.	NM_031466	exon2	c.T693C	p.A231A	GTAGAAAGCCACG	.	PASS	Atlas-SNP
CLEC11A	6320	hgsc.bcm.edu	37	19	51228634	51228634	+	Silent	SNP	G	G	A	rs11084024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	25	59	0	0.390625	0	G|0.808;A|0.192	0.192	strong	.	CLEC11A	23	.	NM_002975	exon4	c.G882A	p.E294E	GCTCGAGAACTGC	.	PASS	Atlas-SNP
TONSL	4796	hgsc.bcm.edu	37	8	145661320	145661320	+	Silent	SNP	G	G	A	rs2721140	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	12	10	13	0	0.833333	0	G|0.603;A|0.397	0.397	strong	TONSL_ENST00000409379,rectum,carcinoma,0,2	TONSL	128	2	NM_013432	exon17	c.C2496T	p.A832A	GTCCCCGGCCAGG	.	PASS	Atlas-SNP
IPO9	55705	hgsc.bcm.edu	37	1	201798367	201798367	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	19	44	0	0.316667	0	.	.	none	.	IPO9	98	.	NM_018085	exon1	c.C30T	p.A10A	TGCGGCCTCCGGG	.	PASS	Atlas-SNP
OTX1	5013	hgsc.bcm.edu	37	2	63283178	63283178	+	Silent	SNP	C	C	G	rs17850223	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	275	136	268	0	0.494545	0	C|0.884;G|0.116	0.116	strong	OTX1,NS,carcinoma,0,1	OTX1	49	1	NM_014562	exon5	c.C792G	p.L264L	CCAGCTCAGCCCC	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117395707	117395707	+	Silent	SNP	C	C	T	rs142205484	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	2	89	0	0.0206186	0	C|0.999;T|0.001	0.001	strong	DSCAML1,colon,carcinoma,0,1	DSCAML1	286	1	NM_020693	exon5	c.G930A	p.S310S	GTAGCCCGAGGCG	.	scavenged	Atlas-SNP
FGF3	2248	hgsc.bcm.edu	37	11	69625385	69625385	+	Silent	SNP	C	C	T	rs35420992	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	75	200	0	0.407609	0	C|0.931;T|0.069	0.069	strong	.	FGF3	27	.	NM_005247	exon3	c.G408A	p.T136T	AGACACCGTCCGG	.	PASS	Atlas-SNP
ACPT	93650	hgsc.bcm.edu	37	19	51297826	51297826	+	Missense_Mutation	SNP	C	C	A	rs55735528	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	41	84	0	0.476744	0	C|0.752;A|0.248	0.248	strong	.	ACPT	43	.	NM_033068	exon9	c.C974A	p.A325D	ATCCCGCCAAAGA	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102508056	102508056	+	Missense_Mutation	SNP	C	C	A	rs10129889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	48	131	0	0.335664	0	C|0.882;A|0.118	0.118	strong	.	DYNC1H1	395	.	NM_001376	exon65	c.C12087A	p.H4029Q	GACCCACATTGTG	.	PASS	Atlas-SNP
SH3TC2	79628	hgsc.bcm.edu	37	5	148407893	148407893	+	Missense_Mutation	SNP	C	C	A	rs6875902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	30	55	0	0.566038	0	C|0.784;A|0.216	0.216	strong	.	SH3TC2	178	.	NM_024577	exon11	c.G1402T	p.A468S	TGGGGGCGAAGTT	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7435194	7435194	+	Silent	SNP	G	G	A	rs12498567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	28	76	0	0.583333	0	G|0.868;A|0.132	0.132	strong	PSAPL1_ENST00000319098,NS,carcinoma,-1,2	PSAPL1	51	2	NM_001085382	exon1	c.C1413T	p.G471G	CCTGGGGCCGTGG	.	PASS	Atlas-SNP
FAM108A1	81926	hgsc.bcm.edu	37	19	1880950	1880950	+	Missense_Mutation	SNP	T	T	C	rs4807160	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	55	116	0	0.462185	0	T|0.372;C|0.628	0.628	strong	FAM108A1,NS,carcinoma,0,1	FAM108A1	29	1	NM_031213	exon3	c.A430G	p.K144E	AGCTCTTGCCCAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105413649	105413649	+	Silent	SNP	A	A	G	rs201545349	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281	13	239	2	0.0462633	0.0083682	A|0.998;G|0.002	0.002	weak	AHNAK2_ENST00000333244,NS,carcinoma,-2,1	AHNAK2	719	1	NM_138420	exon7	c.T8139C	p.D2713D	TTTCACATCCACC	.	scavenged	Atlas-SNP
DOK7	285489	hgsc.bcm.edu	37	4	3494847	3494847	+	Silent	SNP	G	G	A	rs6831659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	38	92	0	0.584615	0	G|0.740;A|0.260	0.260	strong	.	DOK7	44	.	NM_173660	exon7	c.G1134A	p.A378A	AGCAGCGGGGGCC	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427452	427452	+	Missense_Mutation	SNP	C	C	T	rs146645376	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	76	124	0	0.457831	0	C|0.998;T|0.002	0.002	strong	.	TMEM8A	49	.	NM_021259	exon3	c.G433A	p.V145I	GGGAAACGTTGAC	.	PASS	Atlas-SNP
TSSC1	7260	hgsc.bcm.edu	37	2	3261173	3261173	+	Silent	SNP	A	A	G	rs10188932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	92	209	0	0.479167	0	A|0.960;G|0.040	0.040	strong	.	TSSC1	39	.	NM_003310	exon4	c.T313C	p.L105L	ATTCCAATTCCTT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678405	100678405	+	Silent	SNP	T	T	C	rs4729648	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	72	140	1	0.284585	0.00714286	T|0.936;C|0.064	0.064	strong	MUC17,caecum,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.T3708C	p.A1236A	TGAGGCTAGCACC	.	scavenged	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552090	178552090	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	3	223	3	0.0170455	0.0134529	.	.	none	ADAMTS2,caecum,carcinoma,0,2	ADAMTS2	190	2	NM_014244	exon19	c.G2842A	p.D948N	TGTTGTCGTGTAG	.	scavenged	Atlas-SNP
PLEKHM2	23207	hgsc.bcm.edu	37	1	16044401	16044401	+	Silent	SNP	G	G	A	rs16851970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	17	103	0	0.265625	0	G|0.797;A|0.203	0.203	strong	.	PLEKHM2	94	.	NM_015164	exon4	c.G291A	p.L97L	CTGGCTGTACCTG	.	PASS	Atlas-SNP
HEXB	3074	hgsc.bcm.edu	37	5	73985215	73985215	+	Missense_Mutation	SNP	A	A	G	rs11556045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	95	202	0	0.452381	0	A|0.792;G|0.208	0.208	strong	HEXB,NS,carcinoma,0,1	HEXB	34	1	NM_000521	exon2	c.A362G	p.K121R	AGGCTAAAACCCA	.	PASS	Atlas-SNP
TICRR	90381	hgsc.bcm.edu	37	15	90168693	90168693	+	Missense_Mutation	SNP	T	T	A	rs1866928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	52	90	0	0.753623	0	T|0.635;A|0.365	0.365	strong	.	.	.	.	NM_152259	exon20	c.T5152A	p.S1718T	CTTGAGTCAGAGG	.	PASS	Atlas-SNP
PHLDB3	653583	hgsc.bcm.edu	37	19	44001345	44001345	+	Silent	SNP	C	C	T	rs7257767	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	36	75	0	0.444444	0	C|0.843;T|0.157	0.157	strong	.	PHLDB3	30	.	NM_198850	exon6	c.G750A	p.E250E	CCGATCCTCCTCC	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242157228	242157228	+	Silent	SNP	G	G	T	rs78605785	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	51	128	0	0.46789	0	C|0.028;G|0.842;T|0.131	0.131	strong	.	ANO7	136	.	NM_001001891	exon20	c.G2262T	p.P754P	GCGCCCGGTGGCC	.	PASS	Atlas-SNP
SKAP1	8631	hgsc.bcm.edu	37	17	46266849	46266849	+	Silent	SNP	G	G	A	rs66753385	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	52	105	0	0.472727	0	G|0.965;A|0.035	0.035	strong	.	SKAP1	41	.	NM_003726	exon5	c.C294T	p.I98I	TTTTACGATGTCT	.	PASS	Atlas-SNP
BRD1	23774	hgsc.bcm.edu	37	22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	rs35331092	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	59	110	0	0.59	0	C|0.936;T|0.064	0.064	strong	.	BRD1	144	.	NM_014577	exon6	c.G2188A	p.A730T	TCATAGCGCAGGT	.	PASS	Atlas-SNP
SLC4A11	83959	hgsc.bcm.edu	37	20	3214895	3214895	+	Silent	SNP	C	C	T	rs34460295	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	58	104	0	0.464	0	C|0.974;T|0.026	0.026	strong	.	SLC4A11	188	.	NM_001174090	exon5	c.G486A	p.A162A	GGCCTGCGCCAGG	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123512627	123512627	+	Missense_Mutation	SNP	G	G	T	rs28497577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	39	97	0	0.397959	0	G|0.819;T|0.181	0.181	strong	.	MYLK	224	.	NM_053025	exon4	c.C62A	p.P21H	CTTGAGGGATCCA	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100504575	100504575	+	Missense_Mutation	SNP	G	G	C	rs2306986	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	283	136	317	0	0.480565	0	G|0.897;C|0.103	0.103	strong	.	MTTP	127	.	NM_000253	exon4	c.G294C	p.E98D	AGGAGAGAAGAGC	.	PASS	Atlas-SNP
MDGA1	266727	hgsc.bcm.edu	37	6	37626142	37626142	+	Silent	SNP	C	C	T	rs2273110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	23	83	0	0.46	0	C|0.849;T|0.151	0.151	strong	.	MDGA1	104	.	NM_153487	exon3	c.G261A	p.S87S	GAACACCGATGTC	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	98943545	98943545	+	Silent	SNP	A	A	G	rs2290471	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	57	47	0	1	0	A|0.787;G|0.213	0.213	strong	MATN2_ENST00000520016,NS,carcinoma,+1,2	MATN2	165	2	NM_002380	exon3	c.A507G	p.T169T	CGTGACAGATGGG	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	37	7	24742436	24742436	+	Silent	SNP	T	T	C	rs17149912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	72	63	0	0.734694	0	T|0.828;C|0.172	0.172	strong	DFNA5,NS,carcinoma,-2,2	DFNA5	51	2	NM_001127453	exon9	c.A1200G	p.A400A	AGCTGCTGCGCTA	.	PASS	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11420773	11420773	+	Missense_Mutation	SNP	C	C	T	rs200940772	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	7	116	6	0.0648148	0.0517241	C|0.998;T|0.002	0.002	weak	PRB3,NS,carcinoma,0,2	PRB3	84	2	NM_006249	exon3	c.G410A	p.R137H	CCCGGACGAGGCG	.	scavenged	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626529	140626529	+	Silent	SNP	C	C	T	rs61742867	byfrequency;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	43	89	0	0.390909	0	C|0.029;G|0.971	.	alt	.	PCDHB15	138	.	NM_018935	exon1	c.C1383T	p.R461R	CGTCCGCGAGAAC	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21225753	21225753	+	Missense_Mutation	SNP	C	C	T	rs1042031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	45	120	0	0.416667	0	C|0.848;T|0.152	0.152	strong	.	APOB	761	.	NM_000384	exon29	c.G12541A	p.E4181K	GGAATTCTTGAGT	.	PASS	Atlas-SNP
CTRC	11330	hgsc.bcm.edu	37	1	15772212	15772212	+	Missense_Mutation	SNP	C	C	T	rs121909293	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	10	63	0	0.27027	0	C|0.997;T|0.003	0.003	strong	.	CTRC	28	.	NM_007272	exon7	c.C760T	p.R254W	TACACCCGGGTGT	.	PASS	Atlas-SNP
ITIH2	3698	hgsc.bcm.edu	37	10	7774358	7774358	+	Missense_Mutation	SNP	C	C	G	rs7084817	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	26	114	0	0.333333	0	C|0.965;G|0.035	0.035	strong	.	ITIH2	144	.	NM_002216	exon14	c.C1705G	p.L569V	GATTTTCTATCGA	.	PASS	Atlas-SNP
LGALS14	56891	hgsc.bcm.edu	37	19	40196611	40196611	+	Missense_Mutation	SNP	C	C	T	rs35541195	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	124	231	0	0.534483	0	C|0.907;T|0.093	0.093	strong	.	LGALS14	38	.	NM_203471	exon2	c.C64T	p.R22C	GTGTGCCGCTTCT	.	PASS	Atlas-SNP
SLC30A8	169026	hgsc.bcm.edu	37	8	118184783	118184783	+	Missense_Mutation	SNP	C	C	T	rs13266634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	62	117	0	0.389937	0	C|0.758;T|0.242	0.242	strong	.	SLC30A8	102	.	NM_173851	exon8	c.C973T	p.R325W	GCCAGCCGGGACA	.	PASS	Atlas-SNP
TUBB1	81027	hgsc.bcm.edu	37	20	57599402	57599402	+	Missense_Mutation	SNP	G	G	A	rs6070697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	27	48	0	0.509434	0	G|0.852;A|0.148	0.148	strong	.	TUBB1	42	.	NM_030773	exon4	c.G920A	p.R307H	TCCGCCGTGGCCG	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152191225	152191225	+	Silent	SNP	G	G	A	rs147277587	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	367	148	285	0	0.40327	0	G|0.999;A|0.001	0.001	strong	.	HRNR	403	.	NM_001009931	exon3	c.C2880T	p.H960H	AGAGCCGTGTTGT	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91630620	91630620	+	Missense_Mutation	SNP	G	G	T	rs6964587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	94	72	0	0.989474	0	G|0.608;T|0.392	0.392	strong	.	AKAP9	788	.	NM_005751	exon8	c.G1389T	p.M463I	GGAAATGAAAACA	.	PASS	Atlas-SNP
OR6Q1	219952	hgsc.bcm.edu	37	11	57798723	57798723	+	Missense_Mutation	SNP	A	A	G	rs921135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	390	197	441	2	0.505128	0.00453515	A|0.655;G|0.345	0.345	strong	.	OR6Q1	58	.	NM_001005186	exon1	c.A299G	p.D100G	ATGCTGATTGCCT	.	PASS	Atlas-SNP
DCST1	149095	hgsc.bcm.edu	37	1	155019710	155019710	+	Missense_Mutation	SNP	A	A	C	rs11264300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	6	194	1	0.0225564	0.00515464	A|0.559;C|0.441	0.441	strong	DCST1,rectum,carcinoma,0,1	DCST1	69	1	NM_152494	exon14	c.A1534C	p.M512L	GACTCCATGCTAG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512742	195512742	+	Silent	SNP	G	G	A	rs113755990	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	615	80	390	0	0.130081	0	G|0.992;A|0.008	0.008	strong	MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,6	MUC4	1505	6	NM_018406	exon2	c.C5709T	p.T1903T	AAGAGGGGTGGTG	.	PASS	Atlas-SNP
ZNF721	170960	hgsc.bcm.edu	37	4	437221	437221	+	Missense_Mutation	SNP	G	G	A	rs114734668	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	32	86	0	0.450704	0	G|0.977;A|0.023	0.023	strong	.	ZNF721	205	.	NM_133474	exon3	c.A1035T	p.R345S	GTTTGCGGACTGT	.	PASS	Atlas-SNP
ZNF333	84449	hgsc.bcm.edu	37	19	14829749	14829749	+	Missense_Mutation	SNP	C	C	T	rs3764626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	55	145	0	0.426357	0	C|0.613;T|0.387	0.387	strong	.	ZNF333	76	.	NM_032433	exon12	c.C1610T	p.A537V	AGTGCGCGACTTG	.	PASS	Atlas-SNP
SGOL2	151246	hgsc.bcm.edu	37	2	201437328	201437328	+	Silent	SNP	C	C	A	rs35987478	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	65	129	0	0.783133	0	C|0.760;A|0.240	0.240	strong	.	SGOL2	126	.	NM_001160046	exon7	c.C2259A	p.I753I	GGAAATCATCCCT	.	PASS	Atlas-SNP
AQPEP	0	hgsc.bcm.edu	37	5	115338958	115338958	+	Missense_Mutation	SNP	G	G	T	rs17138632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	46	104	0	0.418182	0	G|0.972;T|0.028	0.028	strong	FLJ90650,NS,carcinoma,0,1	.	.	1	NM_173800	exon12	c.G1918T	p.V640F	ATGCAAGTTTCAG	.	PASS	Atlas-SNP
ZAK	0	hgsc.bcm.edu	37	2	174128513	174128513	+	Missense_Mutation	SNP	C	C	T	rs3769148	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	119	157	1	0.983471	0.00636943	C|0.702;T|0.298	0.298	strong	.	ZAK	62	.	NM_016653	exon19	c.C1592T	p.S531L	TCCATTCGATTCA	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170070172	170070172	+	Missense_Mutation	SNP	C	C	T	rs4667596	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	81	196	0	0.435484	0	C|0.980;T|0.020	0.020	strong	.	LRP2	751	.	NM_004525	exon36	c.G6035A	p.R2012K	CTGCGTCTGTGAT	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2750477	2750477	+	Silent	SNP	A	A	G	rs2304859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	73	122	0	0.62931	0	G|0.336;N|0.000	0.336	strong	SMCHD1,colon,carcinoma,+1,3	SMCHD1	88	3	NM_015295	exon32	c.A4137G	p.A1379A	AGATGCATCCTTC	.	PASS	Atlas-SNP
ZC3H11A	9877	hgsc.bcm.edu	37	1	203818973	203818973	+	Silent	SNP	C	C	A	rs41299639	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	492	486	341	1	0.987805	0.00293255	C|0.815;A|0.185	0.185	strong	.	ZC3H11A	71	.	NM_014827	exon17	c.C1758A	p.A586A	TGTAGCCTCTTGC	.	PASS	Atlas-SNP
PIK3C2A	5286	hgsc.bcm.edu	37	11	17158120	17158120	+	Missense_Mutation	SNP	C	C	T	rs61733866	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	39	104	0	0.506494	0	C|0.992;T|0.008	0.008	strong	.	PIK3C2A	148	.	NM_002645	exon8	c.G1757A	p.S586N	AAAGCACTACAGA	.	PASS	Atlas-SNP
ZNF234	10780	hgsc.bcm.edu	37	19	44660967	44660967	+	Silent	SNP	A	A	G	rs12609635	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	74	126	0	0.48366	0	A|0.448;G|0.552	0.552	strong	.	ZNF234	132	.	NM_006630	exon6	c.A798G	p.G266G	ATGTGGAAGGGCC	.	PASS	Atlas-SNP
PLCL1	5334	hgsc.bcm.edu	37	2	198950029	198950029	+	Silent	SNP	A	A	G	rs2228135	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	54	138	0	0.469565	0	A|0.767;G|0.233	0.233	strong	.	PLCL1	358	.	NM_006226	exon2	c.A1788G	p.Q596Q	TGTTCAATACAGG	.	PASS	Atlas-SNP
TARM1	441864	hgsc.bcm.edu	37	19	54577419	54577419	+	Silent	SNP	G	G	A	rs145288894	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	97	251	0	0.427313	0	G|0.993;A|0.007	0.007	strong	.	TARM1	10	.	NM_001135686	exon4	c.C411T	p.T137T	ACCTGCGGTCACT	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49106995	49106995	+	Missense_Mutation	SNP	G	G	A	rs3745728	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7	2	13	0	0.285714	0	G|0.814;A|0.186	0.186	strong	FAM83E,NS,NS,0,1	FAM83E	34	1	NM_017708	exon4	c.C932T	p.P311L	CGGTGCGGGCTGC	.	scavenged	Atlas-SNP
AK4	205	hgsc.bcm.edu	37	1	65690461	65690461	+	Silent	SNP	G	G	A	rs4915685	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	110	230	0	0.738255	0	G|0.726;A|0.274	0.274	strong	.	AK4	22	.	NM_203464	exon5	c.G465A	p.P155P	TGAACCGTTAGTC	.	PASS	Atlas-SNP
ELL2	22936	hgsc.bcm.edu	37	5	95234377	95234377	+	Silent	SNP	C	C	T	rs3777203	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	293	287	392	1	0.979522	0.00255102	C|0.691;T|0.309	0.309	strong	.	ELL2	63	.	NM_012081	exon8	c.G1092A	p.P364P	GGGCAGCGGGAGG	.	PASS	Atlas-SNP
AMDHD2	51005	hgsc.bcm.edu	37	16	2577943	2577943	+	Missense_Mutation	SNP	A	A	C	rs182580356	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	10	39	0	0.555556	0	A|0.999;C|0.001	0.001	strong	.	AMDHD2	33	.	NM_001145815	exon5	c.A585C	p.E195D	CCACGAAGTGATC	.	PASS	Atlas-SNP
NOLC1	9221	hgsc.bcm.edu	37	10	103919738	103919738	+	Silent	SNP	G	G	A	rs143372447	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	16	53	0	0.219178	0	G|0.998;A|0.002	0.002	strong	.	NOLC1	61	.	NM_004741	exon8	c.G945A	p.K315K	GGAGAAGCAGCAG	.	PASS	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134898742	134898742	+	Silent	SNP	C	C	T	rs1042787	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	277	110	264	0	0.397112	0	C|0.508;T|0.492	0.492	strong	.	EPHB1	519	.	NM_004441	exon10	c.C1800T	p.Y600Y	CACTTACGAGGAT	.	PASS	Atlas-SNP
PHACTR4	65979	hgsc.bcm.edu	37	1	28800380	28800380	+	Missense_Mutation	SNP	C	C	A	rs61785974	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	48	52	0	0.872727	0	C|0.726;A|0.274	0.274	strong	.	PHACTR4	64	.	NM_023923	exon6	c.C1168A	p.L390I	TTAGATCTACACC	.	PASS	Atlas-SNP
DAPK1	1612	hgsc.bcm.edu	37	9	90322238	90322238	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	4	150	0	0.0224719	0	.	.	none	DAPK1_ENST00000408954,colon,carcinoma,0,2	DAPK1	329	2	NM_004938	exon26	c.G4252A	p.G1418S	AACAGCGGCACCT	.	scavenged	Atlas-SNP
SLC7A14	57709	hgsc.bcm.edu	37	3	170198898	170198898	+	Silent	SNP	C	C	T	rs3732449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	42	104	0	0.403846	0	C|0.688;T|0.312	0.312	strong	.	SLC7A14	110	.	NM_020949	exon7	c.G1173A	p.S391S	GAACCCCGACACG	.	PASS	Atlas-SNP
MAP3K4	4216	hgsc.bcm.edu	37	6	161508880	161508880	+	Missense_Mutation	SNP	A	A	C	rs35533223	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	60	101	0	0.517241	0	A|0.976;C|0.024	0.024	strong	.	MAP3K4	364	.	NM_006724	exon10	c.A2717C	p.H906P	CCAAGCACGGTGA	.	PASS	Atlas-SNP
BACH2	60468	hgsc.bcm.edu	37	6	90642358	90642358	+	Silent	SNP	G	G	A	rs3798789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	32	84	0	0.450704	0	G|0.877;A|0.123	0.123	strong	.	BACH2	224	.	NM_001170794	exon7	c.C2295T	p.N765N	GGGCACGTTTTCC	.	PASS	Atlas-SNP
GLS2	27165	hgsc.bcm.edu	37	12	56865338	56865338	+	Missense_Mutation	SNP	A	A	G	rs2657879	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	67	110	0	0.458904	0	A|0.864;G|0.136	0.136	strong	.	GLS2	42	.	NM_013267	exon18	c.T1742C	p.L581P	TCAGAGAGTGTGT	.	PASS	Atlas-SNP
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987528	154987528	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	3	82	0	0.0265487	0	.	.	none	ZBTB7B,NS,carcinoma,0,1	ZBTB7B	69	1	NM_001252406	exon4	c.C494T	p.P165L	AGATCCCGTGTGT	.	scavenged	Atlas-SNP
PABPC4L	132430	hgsc.bcm.edu	37	4	135121066	135121066	+	Missense_Mutation	SNP	T	T	G	rs11099273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	45	63	0	0.725806	0	T|0.365;G|0.635	0.635	strong	.	PABPC4L	60	.	NM_001114734	exon2	c.A1283C	p.H428P	TCCTAGTGTCTCT	.	PASS	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	37	17	33749758	33749758	+	Missense_Mutation	SNP	A	A	G	rs138003670	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	53	146	0	0.452991	0	A|0.998;G|0.002	0.002	strong	.	SLFN12	56	.	NM_018042	exon2	c.T290C	p.M97T	TTCTGCATGAAGT	.	PASS	Atlas-SNP
TECRL	253017	hgsc.bcm.edu	37	4	65180425	65180425	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	440	5	459	0	0.0113636	0	.	.	none	TECRL,NS,carcinoma,-2,1	TECRL	106	1	NM_001010874	exon5	c.G492A	p.R164R	TGGGATCCTCAAA	.	scavenged	Atlas-SNP
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	60	106	0	0.555556	0	A|0.634;G|0.366	0.366	strong	.	ZNF879	41	.	NM_001136116	exon5	c.A334G	p.T112A	GATGGCACATTTG	.	PASS	Atlas-SNP
ELK3	2004	hgsc.bcm.edu	37	12	96641452	96641452	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	9	24	0	0.473684	0	.	.	none	.	ELK3	36	.	NM_005230	exon3	c.C942T	p.I314I	CTCCATCGCCCTC	.	PASS	Atlas-SNP
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959773	45959773	+	Silent	SNP	C	C	T	rs79593866		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	15	118	3	0.10274	0.0254237	.	.	weak	KRTAP10-1,NS,carcinoma,0,1	KRTAP10-1	34	1	NM_198691	exon1	c.G261A	p.P87P	GCAAGCCGGCTGG	.	scavenged	Atlas-SNP
SERAC1	84947	hgsc.bcm.edu	37	6	158571611	158571611	+	Missense_Mutation	SNP	A	A	T	rs112780453	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	35	76	0	0.522388	0	A|0.981;T|0.019	0.019	strong	.	SERAC1	31	.	NM_032861	exon4	c.T139A	p.F47I	TAAGAAATAAAGA	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43822171	43822171	+	Missense_Mutation	SNP	G	G	A	rs7310011	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	96	204	0	0.461538	0	G|0.974;A|0.026	0.026	strong	.	ADAMTS20	635	.	NM_025003	exon26	c.C3818T	p.S1273F	ACAGGGGAACTAG	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24423090	24423090	+	Silent	SNP	A	A	G	rs2273944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	72	67	0	0.972973	0	A|0.694;G|0.306	0.306	strong	.	DHRS4	22	.	NM_021004	exon1	c.A93G	p.A31A	GCTCGCAAATAAG	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169512093	169512093	+	Silent	SNP	A	A	G	rs6017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	202	185	0	1	0	A|0.760;G|0.240	0.240	strong	.	F5	301	.	NM_000130	exon13	c.T2235C	p.N745N	TTCCTGATTCAAT	.	PASS	Atlas-SNP
CPM	1368	hgsc.bcm.edu	37	12	69260779	69260779	+	Silent	SNP	C	C	T	rs33925480	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	139	244	0	0.549407	0	C|0.903;T|0.097	0.097	strong	.	CPM	30	.	NM_001005502	exon7	c.G837A	p.T279T	CTCCAACGTAATT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489791	32489791	+	Silent	SNP	A	A	G	rs41550412	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	16	12	2	0	0.75	0	G|0.633;A|0.367	0.633	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.T261C	p.A87A	GTACTCAGCGTCA	.	PASS	Atlas-SNP
PFKFB2	5208	hgsc.bcm.edu	37	1	207238419	207238419	+	Silent	SNP	C	C	T	rs72741390	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	75	175	0	0.362319	0	C|0.815;T|0.185	0.185	strong	.	PFKFB2	70	.	NM_001018053	exon8	c.C546T	p.N182N	AAGGAACAGAGAG	.	PASS	Atlas-SNP
TRIM56	81844	hgsc.bcm.edu	37	7	100730707	100730707	+	Silent	SNP	T	T	C	rs372702476		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	20	60	0	0.298507	0	.	.	weak	.	TRIM56	123	.	NM_030961	exon3	c.T114C	p.H38H	CCTGCATACCTAC	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	37	2	203155936	203155936	+	Silent	SNP	A	A	C	rs3731700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	63	159	0	0.663158	0	A|0.904;C|0.096	0.096	strong	.	NOP58	41	.	NM_015934	exon8	c.A723C	p.S241S	GATATCAATGGGA	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21232195	21232195	+	Silent	SNP	G	G	A	rs693	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	99	207	1	0.490099	0.00483092	G|0.665;N|0.000	.	strong	.	APOB	761	.	NM_000384	exon26	c.C7545T	p.T2515T	TTCTAGGGTCTCT	.	PASS	Atlas-SNP
TRPA1	8989	hgsc.bcm.edu	37	8	72967973	72967973	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	461	5	364	0	0.010846	0	.	.	none	TRPA1,NS,carcinoma,+2,2	TRPA1	256	2	NM_007332	exon11	c.T1312C	p.S438P	GAATGGACACATT	.	scavenged	Atlas-SNP
PCNXL4	64430	hgsc.bcm.edu	37	14	60581863	60581863	+	Silent	SNP	G	G	A	rs219314	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	247	228	0	0.995968	0	G|0.258;A|0.742	0.742	strong	.	.	.	.	NM_022495	exon3	c.G339A	p.P113P	TGGTCCGGAAAAA	.	PASS	Atlas-SNP
DHRS4L2	317749	hgsc.bcm.edu	37	14	24459493	24459493	+	Silent	SNP	G	G	A	rs60865462	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	274	267	324	3	0.974453	0.00925926	G|0.911;A|0.089	0.089	strong	DHRS4L2,NS,carcinoma,0,1	DHRS4L2	29	1	NM_198083	exon2	c.G231A	p.Q77Q	GCTGCAGGGGGAG	.	scavenged	Atlas-SNP
POLR3D	661	hgsc.bcm.edu	37	8	22107986	22107986	+	Silent	SNP	A	A	G	rs75142930	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	53	124	0	0.284946	0	A|0.958;G|0.042	0.042	strong	POLR3D,NS,adenoma,0,2	POLR3D	26	2	NM_001722	exon9	c.A1152G	p.V384V	ACTTGTATGTTCC	.	PASS	Atlas-SNP
IGDCC3	9543	hgsc.bcm.edu	37	15	65621441	65621441	+	Missense_Mutation	SNP	C	C	A	rs12907128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	13	139	1	0.160494	0.00719424	C|0.461;A|0.539	0.539	strong	IGDCC3,NS,carcinoma,0,1	IGDCC3	82	1	NM_004884	exon14	c.G2251T	p.V751L	GCAGCACGGAGAG	.	scavenged	Atlas-SNP
MAPK8IP1	9479	hgsc.bcm.edu	37	11	45924057	45924057	+	Missense_Mutation	SNP	C	C	T	rs117665789	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	37	114	0	0.513889	0	C|0.993;T|0.007	0.007	strong	.	MAPK8IP1	51	.	NM_005456	exon5	c.C739T	p.P247S	ATGGCACCTCCGG	.	PASS	Atlas-SNP
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	rs150395462	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	54	77	0	0.54	0	G|0.996;C|0.004	0.004	strong	.	ZKSCAN5	63	.	NM_145102	exon7	c.G2392C	p.E798Q	ACTGGTGAGAAAC	.	PASS	Atlas-SNP
REPS1	85021	hgsc.bcm.edu	37	6	139266402	139266402	+	Silent	SNP	G	G	A	rs1569238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	55	110	3	0.470085	0.0272727	G|0.897;A|0.103	0.103	strong	REPS1,NS,carcinoma,0,1	REPS1	58	1	NM_001128617	exon4	c.C582T	p.L194L	TCCCGCGAGAGGC	.	scavenged	Atlas-SNP
SEPT14	346288	hgsc.bcm.edu	37	7	55902230	55902230	+	Missense_Mutation	SNP	T	T	C	rs146004414	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	67	136	0	0.408537	0	T|0.988;C|0.012	0.012	strong	.	SEPT14	58	.	NM_207366	exon6	c.A608G	p.D203G	TGTAAATCATTTT	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6635274	6635274	+	Missense_Mutation	SNP	G	G	A	rs10849482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	46	85	0	0.474227	0	G|0.854;A|0.146	0.146	strong	.	NCAPD2	99	.	NM_014865	exon19	c.G2389A	p.V797M	ACACTGGTGAGCA	.	PASS	Atlas-SNP
TMEM176A	55365	hgsc.bcm.edu	37	7	150501455	150501455	+	Missense_Mutation	SNP	G	G	T	rs10378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	64	119	1	0.984615	0.00840336	G|0.847;T|0.153	0.153	strong	.	TMEM176A	35	.	NM_018487	exon6	c.G561T	p.L187F	GGCCTTGTTCAGA	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92600266	92600266	+	Silent	SNP	G	G	A	rs75649640	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	136	81	0	0.814371	0	A|0.048;G|0.952	0.048	strong	FAT3_ENST00000409404,colon,carcinoma,0,7	FAT3	1822	7	NM_001008781	exon21	c.G12018A	p.A4006A	CTTCGCGGAGGTG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8160334	8160334	+	Missense_Mutation	SNP	G	G	A	rs12608849	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	81	222	0	0.487952	0	G|0.757;A|0.243	0.243	strong	.	FBN3	300	.	NM_032447	exon45	c.C5710T	p.L1904F	TGTTGAGGCAATG	.	PASS	Atlas-SNP
FAM25A	643161	hgsc.bcm.edu	37	10	88782100	88782100	+	Missense_Mutation	SNP	G	G	C	rs7079587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	11	6	26	0	0.545455	0	G|0.964;C|0.036	0.036	strong	.	FAM25A	4	.	NM_001146157	exon2	c.G103C	p.V35L	AAGGAGGTGGTGG	.	PASS	Atlas-SNP
ZNF445	353274	hgsc.bcm.edu	37	3	44489880	44489880	+	Missense_Mutation	SNP	T	T	C	rs11710965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	106	345	0	0.458874	0	T|0.903;C|0.097	0.097	strong	.	ZNF445	91	.	NM_181489	exon8	c.A1283G	p.Y428C	TAGTCATAGTGGT	.	PASS	Atlas-SNP
USP19	10869	hgsc.bcm.edu	37	3	49156473	49156473	+	Missense_Mutation	SNP	C	C	G	rs11552724	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	79	192	0	0.42246	0	C|0.905;G|0.095	0.095	strong	.	USP19	158	.	NM_001199160	exon2	c.G106C	p.D36H	CTCCATCCTTGCT	.	PASS	Atlas-SNP
MFI2	4241	hgsc.bcm.edu	37	3	196742290	196742290	+	Silent	SNP	T	T	C	rs9855410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	65	154	0	0.464286	0	T|0.712;C|0.288	0.288	strong	.	MFI2	88	.	NM_005929	exon9	c.A1179G	p.P393P	GATCTCTGGCTTG	.	PASS	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20897676	20897676	+	Missense_Mutation	SNP	T	T	C	rs1953225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	52	70	0	0.530612	0	T|0.747;C|0.253	0.253	strong	.	KLHL33	37	.	NM_001109997	exon3	c.A1034G	p.E345G	TTGAGCTCAGGGT	.	PASS	Atlas-SNP
IGDCC4	57722	hgsc.bcm.edu	37	15	65676617	65676617	+	Silent	SNP	T	T	C	rs2292933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	45	119	0	0.737705	0	T|0.516;C|0.484	0.484	strong	IGDCC4,caecum,carcinoma,-1,1	IGDCC4	95	1	NM_020962	exon20	c.A3483G	p.P1161P	AGCCTCTGGAGGC	.	PASS	Atlas-SNP
ANKRD13A	88455	hgsc.bcm.edu	37	12	110474070	110474070	+	Missense_Mutation	SNP	T	T	C	rs2287174	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	120	236	0	0.55814	0	T|0.923;C|0.077	0.077	strong	.	ANKRD13A	39	.	NM_033121	exon14	c.T1514C	p.L505P	AGGAACTTTCAGG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379752	31379752	+	Silent	SNP	C	C	T	rs17206680	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	46	108	0	0.393162	0	C|0.967;T|0.033	0.033	strong	.	MICA	21	.	NM_001177519	exon4	c.C642T	p.S214S	CCGCAGCGAGGCC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47855876	47855876	+	Silent	SNP	A	A	G	rs17371795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	78	159	0	0.6	0	A|0.881;G|0.119	0.119	strong	.	PCNT	283	.	NM_006031	exon39	c.A8811G	p.T2937T	GCAGACAGTGAGA	.	PASS	Atlas-SNP
RASSF4	83937	hgsc.bcm.edu	37	10	45480313	45480313	+	Silent	SNP	C	C	T	rs35521977	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	49	249	0	0.30625	0	C|0.987;T|0.013	0.013	strong	.	RASSF4	33	.	NM_032023	exon6	c.C426T	p.D142D	GAGCGACGCCAGT	.	PASS	Atlas-SNP
RFTN1	23180	hgsc.bcm.edu	37	3	16419238	16419238	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	37	101	0	0.274074	0	.	.	none	.	RFTN1	79	.	NM_015150	exon5	c.G813C	p.E271D	GAGTGGCTCTTCA	.	PASS	Atlas-SNP
CCDC79	283847	hgsc.bcm.edu	37	16	66792714	66792714	+	Missense_Mutation	SNP	T	T	C	rs363156	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	5	79	0	0.0892857	0	T|0.651;C|0.349	0.349	strong	.	CCDC79	32	.	NM_001136505	exon18	c.A1958G	p.Q653R	AGTCGTTGTCTTC	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4876057	4876057	+	Missense_Mutation	SNP	C	C	T	rs3763384	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	36	99	0	0.439024	0	C|0.745;T|0.255	0.255	strong	.	RADIL	110	.	NM_018059	exon3	c.G715A	p.D239N	TGGCGTCGGGGCC	.	PASS	Atlas-SNP
FURIN	5045	hgsc.bcm.edu	37	15	91424029	91424029	+	Silent	SNP	C	C	T	rs142489043	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	30	195	0	0.20979	0	C|0.997;T|0.003	0.003	strong	.	FURIN	85	.	NM_002569	exon14	c.C1665T	p.S555S	CACCAGCGAAGCC	.	PASS	Atlas-SNP
KCNT1	57582	hgsc.bcm.edu	37	9	138662273	138662273	+	Silent	SNP	G	G	A	rs17038714	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	39	107	0	0.386139	0	G|0.695;A|0.305	0.305	strong	.	KCNT1	139	.	NM_020822	exon17	c.G1749A	p.A583A	CTACGCGGCCTTC	.	PASS	Atlas-SNP
SCEL	8796	hgsc.bcm.edu	37	13	78216915	78216915	+	Silent	SNP	C	C	T	rs2813739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	59	155	0	0.504274	0	C|0.851;T|0.149	0.149	strong	.	SCEL	85	.	NM_144777	exon32	c.C2022T	p.H674H	AATACACTGTGAA	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113386779	113386779	+	Missense_Mutation	SNP	C	C	G	rs2285933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	85	198	0	0.433673	0	C|0.724;G|0.276	0.276	strong	OAS3,brain,glioma,0,1	OAS3	63	1	NM_006187	exon6	c.C1143G	p.S381R	AGGGAGCAAACCT	.	PASS	Atlas-SNP
ADAM15	8751	hgsc.bcm.edu	37	1	155033308	155033308	+	Silent	SNP	G	G	A	rs11589479	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	25	14	53	0	0.56	0	G|0.889;A|0.111	0.111	strong	.	ADAM15	92	.	NM_001261464	exon19	c.G2307A	p.K769K	CACTAAGGTGAGT	.	PASS	Atlas-SNP
ZFR2	23217	hgsc.bcm.edu	37	19	3831765	3831765	+	Missense_Mutation	SNP	G	G	A	rs2240235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	57	153	0	0.483051	0	G|0.600;A|0.400	0.400	strong	ZFR2,NS,carcinoma,0,1	ZFR2	63	1	NM_015174	exon4	c.C491T	p.S164L	TATCCCGAGGACA	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52192595	52192595	+	Missense_Mutation	SNP	C	C	T	rs61748378	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	82	197	1	0.522293	0.00507614	C|0.976;T|0.024	0.024	strong	.	ZNF217	227	.	NM_006526	exon3	c.G2708A	p.R903Q	GCACTCCGATTAC	.	PASS	Atlas-SNP
SMG1	23049	hgsc.bcm.edu	37	16	18846429	18846429	+	Silent	SNP	G	G	A	rs56079655	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	69	137	0	0.522727	0	G|0.972;A|0.028	0.028	strong	.	SMG1	401	.	NM_015092	exon49	c.C8115T	p.A2705A	TTCAGTGGCAGTG	.	PASS	Atlas-SNP
TMEM183B	653659	hgsc.bcm.edu	37	1	202977809	202977809	+	Missense_Mutation	SNP	G	G	A	rs6678040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	172	204	0	0.618705	0	G|0.897;A|0.103	0.103	strong	.	.	.	.	NM_001079809	exon3	c.G238A	p.A80T	GTTCCTGCAGAGG	.	PASS	Atlas-SNP
TEKT1	83659	hgsc.bcm.edu	37	17	6704121	6704121	+	Missense_Mutation	SNP	C	C	T	rs2271233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	148	232	0	0.515679	0	C|0.951;T|0.049	0.049	strong	TEKT1,rectum,carcinoma,+2,1	TEKT1	49	1	NM_053285	exon7	c.G994A	p.V332I	GTGCGACATCACG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276149	152276149	+	Missense_Mutation	SNP	C	C	T	rs77422831	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	444	170	353	1	0.382883	0.00283286	C|0.841;T|0.159	0.159	strong	.	FLG	900	.	NM_002016	exon3	c.G11213A	p.R3738H	TCGTGGCGGGATC	.	PASS	Atlas-SNP
CARD16	114769	hgsc.bcm.edu	37	11	104912221	104912221	+	Missense_Mutation	SNP	T	T	A	rs542571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	46	105	0	0.291139	0	T|0.776;A|0.224	0.224	strong	.	CARD16	29	.	NM_001017534	exon3	c.A500T	p.N167I	AGTATGTTCCTCC	.	PASS	Atlas-SNP
FUT2	2524	hgsc.bcm.edu	37	19	49206603	49206603	+	Silent	SNP	C	C	T	rs281377	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	36	63	0	0.514286	0	C|0.559;T|0.441	0.441	strong	.	FUT2	30	.	NM_001097638	exon2	c.C390T	p.N130N	CCTGAACGACTGG	.	PASS	Atlas-SNP
DGCR6	8214	hgsc.bcm.edu	37	22	18893902	18893902	+	Silent	SNP	G	G	C	rs408469	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	8	60	0	0.296296	0	G|0.967;C|0.033	0.033	strong	.	DGCR6	12	.	NM_005675	exon1	c.G15C	p.A5A	CTACGCGGGCGCC	.	PASS	Atlas-SNP
GPR146	115330	hgsc.bcm.edu	37	7	1097394	1097394	+	Silent	SNP	T	T	C	rs11767527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	12	76	1	0.387097	0.0131579	T|0.898;C|0.102	0.102	strong	GPR146,NS,carcinoma,0,3	GPR146	20	3	NM_138445	exon1	c.T243C	p.P81P	GGCCCCTGTGCAC	.	scavenged	Atlas-SNP
CEP250	11190	hgsc.bcm.edu	37	20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	rs56259282	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40	19	43	0	0.475	0	G|0.993;A|0.007	0.007	strong	.	CEP250	141	.	NM_007186	exon30	c.G5879A	p.R1960Q	CTGCCCGGGCCCG	.	PASS	Atlas-SNP
MROH2B	133558	hgsc.bcm.edu	37	5	41033163	41033163	+	Missense_Mutation	SNP	T	T	C	rs10067611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	364	155	393	1	0.425824	0.00254453	T|0.963;C|0.037	0.037	strong	.	.	.	.	NM_173489	exon23	c.A2341G	p.M781V	TCAGCATCTCCTT	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100139161	100139161	+	Silent	SNP	A	A	G	rs11581	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	24	59	0	0.461538	0	A|0.654;G|0.346	0.346	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon37	c.A5091G	p.Q1697Q	TATCCAAGGCCTG	.	PASS	Atlas-SNP
FERMT1	55612	hgsc.bcm.edu	37	20	6078246	6078246	+	Silent	SNP	C	C	T	rs149893089	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	74	159	0	0.471338	0	C|0.999;T|0.001	0.001	strong	.	FERMT1	106	.	NM_017671	exon7	c.G882A	p.E294E	GGCTTGCTCATAG	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68053807	68053807	+	Missense_Mutation	SNP	T	T	G	rs118013098	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	255	159	199	0	0.623529	0	T|0.997;G|0.003	0.003	strong	.	PLEKHH1	118	.	NM_020715	exon29	c.T3950G	p.F1317C	CTACCTTCATCAT	.	PASS	Atlas-SNP
CPXCR1	53336	hgsc.bcm.edu	37	X	88008807	88008807	+	Missense_Mutation	SNP	G	G	A	rs5984611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	57	151	0	1	0	0|0.003;A|0.269	0.269	strong	.	CPXCR1	83	.	NM_001184771	exon3	c.G392A	p.R131H	AAACTCGTTTTCG	.	PASS	Atlas-SNP
PSMD8	5714	hgsc.bcm.edu	37	19	38872778	38872778	+	Silent	SNP	C	C	T	rs1131182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	18	34	0	0.461538	0	C|0.918;T|0.082	0.082	strong	.	PSMD8	31	.	NM_002812	exon6	c.C825T	p.I275I	GTGCATCGAGAAG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90372574	90372574	+	Missense_Mutation	SNP	A	A	C	rs36040566	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	309	150	332	0	0.485437	0	A|0.909;C|0.091	0.091	strong	.	MDN1	478	.	NM_014611	exon86	c.T14349G	p.D4783E	CTCCTCATCATCA	.	PASS	Atlas-SNP
MYO1G	64005	hgsc.bcm.edu	37	7	45016621	45016621	+	Missense_Mutation	SNP	C	C	T	rs61739531	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	101	132	0	0.587209	0	C|0.817;T|0.183	0.183	strong	MYO1G,bladder,carcinoma,+2,1	MYO1G	86	1	NM_033054	exon2	c.G145A	p.V49M	GGTTCACGGACAC	.	PASS	Atlas-SNP
C9orf96	169436	hgsc.bcm.edu	37	9	136270538	136270538	+	Missense_Mutation	SNP	T	T	G	rs41302673	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	19	24	0	0.542857	0	T|0.932;G|0.068	0.068	strong	C9orf96_ENST00000371957,NS,carcinoma,0,1	C9orf96	77	1	NM_153710	exon18	c.T2036G	p.L679R	GGGGACTGGAATA	.	PASS	Atlas-SNP
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077765	19077765	+	Missense_Mutation	SNP	T	T	C	rs10833049	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	38	89	0	0.513514	0	C|0.329;G|0.000;T|0.671	0.329	strong	MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	NM_054030	exon2	c.A185G	p.N62S	AAGGCGTTCCTGC	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188401	140188401	+	Silent	SNP	A	A	G	rs2879086	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	5	79	0	0.192308	0	A|0.414;G|0.586	0.586	strong	.	PCDHA4	419	.	NM_031500	exon1	c.A1629G	p.P543P	CGTGCCACCTCTG	.	PASS	Atlas-SNP
RNASE1	6035	hgsc.bcm.edu	37	14	21269990	21269990	+	Missense_Mutation	SNP	C	C	G	rs142457376	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	274	105	258	0	0.383212	0	C|0.998;G|0.002	0.002	strong	.	RNASE1	14	.	NM_198235	exon3	c.G238C	p.V80L	CATCTACCAGGGG	.	PASS	Atlas-SNP
ARID3C	138715	hgsc.bcm.edu	37	9	34622389	34622389	+	Missense_Mutation	SNP	A	A	C	rs3808869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	47	118	0	0.5	0	A|0.428;C|0.572	0.572	strong	.	ARID3C	33	.	NM_001017363	exon5	c.T1003G	p.C335G	GCATGCAAGGTCG	.	PASS	Atlas-SNP
OR51I1	390063	hgsc.bcm.edu	37	11	5461861	5461861	+	Missense_Mutation	SNP	C	C	G	rs76233016	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	75	149	0	0.6	0	C|0.994;G|0.006	0.006	strong	.	OR51I1	66	.	NM_001005288	exon1	c.G884C	p.S295T	TTCACACTGTAGA	.	PASS	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1811603	1811603	+	Missense_Mutation	SNP	C	C	T	rs7250872	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	35	85	0	0.625	0	C|0.614;T|0.386	0.386	strong	.	ATP8B3	108	.	NM_138813	exon2	c.G133A	p.G45R	CACCTCCGCGGAT	.	PASS	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51792232	51792232	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	2	199	0	0.0130719	0	.	.	none	DMXL2,NS,carcinoma,-1,2	DMXL2	262	2	NM_001174116	exon18	c.T3189C	p.S1063S	CACTGTACTGCTA	.	scavenged	Atlas-SNP
GRIN1	2902	hgsc.bcm.edu	37	9	140051376	140051376	+	Silent	SNP	G	G	A	rs1126442	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	85	175	0	0.57047	0	G|0.800;A|0.200	0.200	strong	.	GRIN1	51	.	NM_001185091	exon7	c.G918A	p.V306V	CGCCGTGGGCGTG	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487169	32487169	+	Silent	SNP	C	C	T	rs34555743	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	5	81	2	0.0561798	0.0246914	C|0.100;T|0.900	0.900	weak	HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	NM_002125	exon3	c.G630A	p.T210T	AGGGCTCGTCACG	.	scavenged	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	37	8	130789767	130789767	+	Missense_Mutation	SNP	G	G	A	rs10090835	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	72	70	0	0.642857	0	G|0.973;A|0.027	0.027	strong	.	GSDMC	71	.	NM_031415	exon2	c.C67T	p.P23S	TGACAGGTGTCAG	.	PASS	Atlas-SNP
TRPC3	7222	hgsc.bcm.edu	37	4	122824052	122824052	+	Silent	SNP	C	C	T	rs11732666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	110	220	1	0.982143	0.00454545	C|0.721;T|0.279	0.279	strong	.	TRPC3	201	.	NM_001130698	exon9	c.G2418A	p.R806R	CTGAAGCCTTCTC	.	PASS	Atlas-SNP
ZNF705A	440077	hgsc.bcm.edu	37	12	8329700	8329700	+	Missense_Mutation	SNP	A	A	C	rs10743253	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	329	155	374	4	0.471125	0.0106952	A|0.528;C|0.471	0.471	strong	ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	NM_001004328	exon5	c.A424C	p.K142Q	GGAAAGAAACCCT	.	scavenged	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107602666	107602666	+	Silent	SNP	C	C	T	rs2246841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	115	230	0	0.477178	0	C|0.866;T|0.134	0.134	strong	.	ABCA1	244	.	NM_005502	exon9	c.G948A	p.G316G	CTTCAGCCCCCCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508722	195508722	+	Silent	SNP	G	G	T	rs201248411	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	11	147	2	0.0647059	0.0136054	.	.	weak	MUC4_ENST00000463781,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9729A	p.T3243T	ATGACCGGTGGAT	.	scavenged	Atlas-SNP
CSHL1	1444	hgsc.bcm.edu	37	17	61987570	61987570	+	Missense_Mutation	SNP	G	G	T	rs2727307	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	440	163	600	5	0.370455	0.00833333	G|0.670;T|0.330	0.330	strong	CSHL1_ENST00000561003,bladder,carcinoma,-2,4	CSHL1	42	4	NM_022579	exon4	c.C423A	p.D141E	GTGATAGTCATCG	.	scavenged	Atlas-SNP
SLC12A3	6559	hgsc.bcm.edu	37	16	56933519	56933519	+	Missense_Mutation	SNP	G	G	A	rs11643718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	80	95	0	0.792079	0	G|0.914;A|0.086	0.086	strong	SLC12A3,NS,carcinoma,+1,1	SLC12A3	99	1	NM_000339	exon23	c.G2738A	p.R913Q	ACCCTCGGGCTGA	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	994014	994014	+	Silent	SNP	C	C	T	rs10849577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	305	142	300	0	0.465574	0	C|0.885;T|0.115	0.115	strong	.	WNK1	403	.	NM_001184985	exon19	c.C4824T	p.T1608T	CCCAACCACAGCA	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86790936	86790936	+	Silent	SNP	C	C	T	rs371409529	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	80	135	0	0.761905	0	.	.	alt	AGBL1,bladder,carcinoma,0,1	AGBL1	151	1	NM_152336	exon6	c.C423T	p.Y141Y	AGGCTACGTCACC	.	PASS	Atlas-SNP
OR1A2	26189	hgsc.bcm.edu	37	17	3101691	3101691	+	Missense_Mutation	SNP	G	G	T	rs12150427	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	107	118	1	1	0.00847458	G|0.697;N|0.000	.	strong	OR1A2,NS,carcinoma,0,1	OR1A2	52	1	NM_012352	exon1	c.G879T	p.W293C	AAATTGGGATATG	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119686	19119686	+	Silent	SNP	C	C	T	rs1052756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	43	89	0	0.413462	0	C|0.851;A|0.001	.	strong	.	TSSK2	29	.	NM_053006	exon1	c.C774T	p.S258S	CGTCAGCCAGCGG	.	PASS	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32193185	32193185	+	Missense_Mutation	SNP	G	G	A	rs41263977	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	58	108	0	0.74359	0	G|0.994;A|0.006	0.006	strong	.	BAI2	128	.	NM_001703	exon33	c.C4594T	p.R1532C	TGGGGCGCTCCCC	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22848028	22848028	+	Missense_Mutation	SNP	G	G	C	rs78240139		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	793	200	836	0	0.252207	0	G|0.500;C|0.500	0.500	weak	ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	NM_020855	exon4	c.G1557C	p.K519N	TGCAAAGATTTCC	.	scavenged	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57758732	57758732	+	Missense_Mutation	SNP	C	C	A	rs2923144	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	49	46	0	0.777778	0	C|0.891;A|0.109	0.109	strong	.	CCDC135	97	.	NM_032269	exon12	c.C1743A	p.N581K	GTCAAACCCCCGG	.	PASS	Atlas-SNP
TOR2A	27433	hgsc.bcm.edu	37	9	130495633	130495633	+	Missense_Mutation	SNP	C	C	G	rs564754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	95	103	1	0.989583	0.00970874	C|0.370;G|0.630	0.630	strong	.	TOR2A	26	.	NM_130459	exon3	c.G624C	p.W208C	GCCCCCCCACTGT	.	PASS	Atlas-SNP
EFTUD1	79631	hgsc.bcm.edu	37	15	82444437	82444437	+	Silent	SNP	A	A	G	rs905450	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	173	251	1	1	0.00398406	A|0.199;G|0.801	0.801	strong	.	EFTUD1	74	.	NM_024580	exon18	c.T2358C	p.G786G	ATTTTCACCCTCA	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228479642	228479642	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	381	5	261	2	0.0131234	0.00766284	.	.	none	OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	NM_001271223	exon44	c.C11670T	p.A3890A	AGAGGCCGTGGAA	.	scavenged	Atlas-SNP
LYZL2	119180	hgsc.bcm.edu	37	10	30918597	30918597	+	Missense_Mutation	SNP	T	T	C	rs74551644	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	11	175	1	0.092437	0.00571429	.	.	weak	LYZL2,NS,carcinoma,0,1	LYZL2	33	1	NM_183058	exon1	c.A38G	p.K13R	CTCCACTTAGTCG	.	scavenged	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140475763	140475763	+	Silent	SNP	C	C	G	rs61742867	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	26	131	0	0.211382	0	C|0.029;G|0.971	0.971	strong	PCDHB2,NS,carcinoma,+2,2	PCDHB2	163	2	NM_018936	exon1	c.C1389G	p.R463R	CGTCCGCGAGAAC	.	scavenged	Atlas-SNP
ZIM3	114026	hgsc.bcm.edu	37	19	57649884	57649884	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	5	171	0	0.0367647	0	.	.	none	ZIM3,NS,carcinoma,-1,1	ZIM3	107	1	NM_052882	exon3	c.A98G	p.Y33C	TCCCTGTACAAGT	.	scavenged	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20850093	20850093	+	Missense_Mutation	SNP	C	C	T	rs1713456	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	116	75	1	0.966667	0.0133333	C|0.754;A|0.001	.	strong	TEP1,NS,carcinoma,+1,1	TEP1	224	1	NM_007110	exon30	c.G4403A	p.C1468Y	ACGAGGCAGGCAA	.	scavenged	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90340446	90340446	+	Missense_Mutation	SNP	C	C	T	rs61739327	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	23	54	0	0.479167	0	C|0.907;T|0.093	0.093	strong	.	ANKRD6	51	.	NM_001242809	exon16	c.C1907T	p.P636L	AGCAACCCGCAGC	.	PASS	Atlas-SNP
ITGB1	3688	hgsc.bcm.edu	37	10	33214802	33214802	+	Silent	SNP	A	A	G	rs2298141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	42	83	0	0.777778	0	A|0.852;G|0.148	0.148	strong	.	ITGB1	156	.	NM_002211	exon6	c.T783C	p.C261C	TACTCCACAAACT	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6500544	6500544	+	Missense_Mutation	SNP	C	C	T	rs1057091	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	47	140	0	0.256831	0	C|0.750;T|0.250	0.250	strong	.	MCPH1	65	.	NM_024596	exon14	c.C2482T	p.P828S	TGTGCCCCTGAAA	.	PASS	Atlas-SNP
KLRC4	8302	hgsc.bcm.edu	37	12	10560957	10560957	+	Missense_Mutation	SNP	T	T	C	rs2617170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	192	207	1	0.989691	0.00483092	T|0.395;C|0.605	0.605	strong	KLRC4,caecum,carcinoma,0,1	KLRC4	23	1	NM_013431	exon3	c.A311G	p.N104S	GAAAAATTGTTCT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9065510	9065510	+	Silent	SNP	G	G	A	rs1867692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	32	54	0	0.533333	0	G|0.825;A|0.175	0.175	strong	.	MUC16	4315	.	NM_024690	exon3	c.C21936T	p.F7312F	AGTAGGGAACTTA	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61730553	61730553	+	Missense_Mutation	SNP	T	T	C	rs17185413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	78	156	1	0.467066	0.00641026	T|0.906;C|0.094	0.094	strong	BEST1_ENST00000449131,colon,carcinoma,-1,2	BEST1	85	2	NM_001139443	exon9	c.T1747C	p.S583P	AAGTGTTCGGGAC	.	scavenged	Atlas-SNP
L3MBTL4	91133	hgsc.bcm.edu	37	18	5956238	5956238	+	Missense_Mutation	SNP	C	C	T	rs3737353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	179	178	2	0.98895	0.011236	C|0.627;T|0.373	0.373	strong	L3MBTL4,colon,carcinoma,0,1	L3MBTL4	87	1	NM_173464	exon20	c.G1853A	p.G618D	TCTTGGCCTGAGG	.	scavenged	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379807	31379807	+	Missense_Mutation	SNP	C	C	T	rs1051798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	38	126	0	0.319328	0	C|0.730;T|0.270	0.270	strong	.	MICA	21	.	NM_001177519	exon4	c.C697T	p.R233W	TATCCCCGGAATA	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167319011	167319011	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	59	137	0	0.526786	0	.	.	none	.	SCN7A	410	.	NM_002976	exon9	c.A971T	p.K324I	CCAGCTTTTACAC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45016116	45016116	+	Missense_Mutation	SNP	A	A	G	rs8100718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	87	222	2	0.520958	0.00900901	A|0.633;G|0.366	0.366	strong	CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	NM_001102600	exon10	c.T1534C	p.C512R	TATTGCAATACTC	.	scavenged	Atlas-SNP
ADAM12	8038	hgsc.bcm.edu	37	10	127753388	127753388	+	Silent	SNP	C	C	T	rs2279091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	49	82	0	0.515789	0	C|0.908;T|0.092	0.092	strong	.	ADAM12	388	.	NM_021641	exon14	c.G1605A	p.T535T	CCAGAGCGTGACA	.	PASS	Atlas-SNP
SLC43A2	124935	hgsc.bcm.edu	37	17	1494567	1494567	+	Silent	SNP	G	G	A	rs12953268	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	34	63	0	0.641509	0	A|0.422;C|0.000;G|0.578	0.422	strong	SLC43A2,NS,carcinoma,0,1	SLC43A2	37	1	NM_152346	exon8	c.C927T	p.A309A	ACCTGCGGCATCC	.	PASS	Atlas-SNP
PNP	4860	hgsc.bcm.edu	37	14	20940626	20940626	+	Silent	SNP	C	C	T	rs1130650	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	49	119	0	0.340278	0	C|0.786;T|0.214	0.214	strong	PNP,NS,carcinoma,+2,2	PNP	21	2	NM_000270	exon2	c.C171T	p.P57P	CTTTCCCCGAAGT	.	PASS	Atlas-SNP
SLC22A11	55867	hgsc.bcm.edu	37	11	64336209	64336209	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	226	3	235	0	0.0132743	0	.	.	none	SLC22A11,colon,carcinoma,0,1	SLC22A11	54	1	NM_018484	exon8	c.C1341T	p.C447C	AACCTGCCTCACC	.	scavenged	Atlas-SNP
CELA1	1990	hgsc.bcm.edu	37	12	51737562	51737562	+	Missense_Mutation	SNP	T	T	C	rs17860300	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	53	130	1	0.386861	0.00769231	T|0.788;C|0.212	0.212	strong	CELA1,NS,carcinoma,+2,1	CELA1	39	1	NM_001971	exon3	c.A175G	p.M59V	CTGTCATCACCCA	.	scavenged	Atlas-SNP
USP32	84669	hgsc.bcm.edu	37	17	58288421	58288421	+	Missense_Mutation	SNP	C	C	T	rs146577219	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	650	108	418	1	0.166154	0.00239234	C|0.926;T|0.073	0.073	strong	USP32,NS,carcinoma,0,5	USP32	128	5	NM_032582	exon21	c.G2377A	p.E793K	AAAGTTCCTGCAC	.	scavenged	Atlas-SNP
FAM47A	158724	hgsc.bcm.edu	37	X	34148877	34148877	+	Missense_Mutation	SNP	C	C	G	rs5973088	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	14	145	0	0.264151	0	C|0.996;G|0.004	0.004	strong	.	FAM47A	249	.	NM_203408	exon1	c.G1519C	p.E507Q	GAGGCTCCGAGCG	.	PASS	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236748397	236748397	+	Silent	SNP	A	A	G	rs41304149	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	86	163	0	0.40566	0	A|0.984;G|0.016	0.016	strong	.	HEATR1	197	.	NM_018072	exon17	c.T2169C	p.F723F	AAATGGAAAGTGG	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21245813	21245813	+	Silent	SNP	G	G	A	rs1801700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	100	195	0	0.478469	0	G|0.970;A|0.030	0.030	strong	.	APOB	761	.	NM_000384	exon18	c.C2706T	p.N902N	GTTGGTGTTCATC	.	PASS	Atlas-SNP
TECPR2	9895	hgsc.bcm.edu	37	14	102901201	102901201	+	Missense_Mutation	SNP	A	A	G	rs10149146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	32	40	0	0.627451	0	A|0.744;G|0.256	0.256	strong	.	TECPR2	114	.	NM_001172631	exon9	c.A2047G	p.I683V	CAGGACATCCTAA	.	PASS	Atlas-SNP
CLVS1	157807	hgsc.bcm.edu	37	8	62370916	62370916	+	Silent	SNP	T	T	G	rs72657068	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	8	47	0	0.333333	0	T|0.998;G|0.002	0.002	strong	.	CLVS1	74	.	NM_173519	exon5	c.T792G	p.P264P	ACACCCTGAATTT	.	PASS	Atlas-SNP
ACADSB	36	hgsc.bcm.edu	37	10	124800853	124800853	+	Silent	SNP	C	C	T	rs1140591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	76	132	0	0.59375	0	A|0.000;C|0.783;G|0.000;T|0.217	0.217	strong	.	ACADSB	45	.	NM_001609	exon5	c.C639T	p.H213H	TGAGCACGCAGGG	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54849481	54849481	+	Silent	SNP	T	T	G	rs7256494	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	54	154	1	0.369863	0.00649351	T|0.611;G|0.389	0.389	strong	LILRA4,colon,carcinoma,0,4	LILRA4	91	4	NM_012276	exon4	c.A381C	p.A127A	TGGCAGTGCGGAC	.	scavenged	Atlas-SNP
KIAA0391	9692	hgsc.bcm.edu	37	14	35735967	35735967	+	Missense_Mutation	SNP	A	A	G	rs11156878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	272	158	258	1	0.580882	0.00387597	A|0.882;G|0.118	0.118	strong	.	KIAA0391	35	.	NM_014672	exon6	c.A1310G	p.N437S	AACGGAATCTGCG	.	PASS	Atlas-SNP
HTR3B	9177	hgsc.bcm.edu	37	11	113803666	113803666	+	Missense_Mutation	SNP	G	G	A	rs17116138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	42	124	0	0.244186	0	G|0.955;A|0.045	0.045	strong	.	HTR3B	50	.	NM_006028	exon6	c.G547A	p.V183I	GAAGACGTAGACC	.	PASS	Atlas-SNP
FLNB	2317	hgsc.bcm.edu	37	3	58081888	58081888	+	Silent	SNP	T	T	C	rs1522384	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	73	105	0	0.973333	0	T|0.536;C|0.464	0.464	strong	.	FLNB	430	.	NM_001457	exon6	c.T927C	p.S309S	TGACAGTGACAAG	.	PASS	Atlas-SNP
HIST1H4G	8369	hgsc.bcm.edu	37	6	26247198	26247198	+	Missense_Mutation	SNP	A	A	G	rs41266821	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	23	49	0	0.469388	0	A|0.903;G|0.097	0.097	strong	.	HIST1H4G	18	.	NM_003547	exon1	c.T8C	p.V3A	CCCCGAACAGACA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680490	100680490	+	Missense_Mutation	SNP	A	A	G	rs199605653		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	17	152	0	0.085	0	A|0.999;G|0.001	0.001	weak	.	MUC17	804	.	NM_001040105	exon3	c.A5793G	p.I1931M	AAGTATACCTGTC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29913037	29913037	+	Missense_Mutation	SNP	G	G	A	rs1137631	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	49	246	0	0.310127	0	G|0.829;A|0.171	0.171	strong	HLA-A,caecum,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon7	c.G1072A	p.V358M	TCTGATGTGTCCC	.	PASS	Atlas-SNP
DNMT3B	1789	hgsc.bcm.edu	37	20	31386449	31386449	+	Silent	SNP	T	T	C	rs2424922	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	41	93	0	0.525641	0	T|0.354;C|0.646	0.646	strong	.	DNMT3B	196	.	NM_006892	exon15	c.T1674C	p.Y558Y	TGAATATGTAAGC	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111665215	111665215	+	Silent	SNP	A	A	C	rs35054425	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	50	133	0	0.423729	0	A|0.990;C|0.010	0.010	strong	.	IKBKAP	122	.	NM_003640	exon16	c.T1758G	p.P586P	CAGAGAAGGTGAC	.	PASS	Atlas-SNP
FAM209B	388799	hgsc.bcm.edu	37	20	55111371	55111371	+	Silent	SNP	G	G	A	rs2296130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	71	172	0	0.44375	0	G|0.585;A|0.415	0.415	strong	.	.	.	.	NM_001013646	exon2	c.G393A	p.Q131Q	AGTGCAGAATCTT	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22575488	22575488	+	Silent	SNP	C	C	T	rs7247735	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281	111	403	1	0.395018	0.00248139	C|0.551;T|0.449	0.449	strong	.	ZNF98	230	.	NM_001098626	exon4	c.G549A	p.K183K	TTTACACTTGAAA	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377086	49377086	+	Missense_Mutation	SNP	T	T	C	rs611251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	23	71	0	0.38983	0	T|0.735;G|0.004	.	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.T596C	p.V199A	AAGCTGTAAAGAA	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	56000471	56000471	+	Missense_Mutation	SNP	G	G	A	rs11227599	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	47	122	0	0.460784	0	G|0.820;A|0.180	0.180	strong	OR5T2,NS,carcinoma,0,1	OR5T2	107	1	NM_001004746	exon1	c.C191T	p.T64I	AAGATAGTCTGCA	.	PASS	Atlas-SNP
CSDE1	7812	hgsc.bcm.edu	37	1	115269685	115269685	+	Silent	SNP	A	A	G	rs150190370	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	5	181	0	0.0595238	0	A|0.997;G|0.003	0.003	strong	.	CSDE1	145	.	NM_001242891	exon14	c.T1521C	p.Y507Y	GTCATCATAAGCA	.	PASS	Atlas-SNP
UPF3A	65110	hgsc.bcm.edu	37	13	115064423	115064423	+	Missense_Mutation	SNP	G	G	A	rs3752107	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	371	158	382	3	0.425876	0.0078534	G|0.949;A|0.051	0.051	strong	UPF3A,colon,carcinoma,0,1	UPF3A	47	1	NM_023011	exon8	c.G955A	p.A319T	CCCGGTGCAGTCG	.	scavenged	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2029199	2029199	+	Silent	SNP	G	G	A	rs10964471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	78	146	0	0.513158	0	G|0.913;A|0.086	0.086	strong	.	SMARCA2	313	.	NM_139045	exon2	c.G177A	p.T59T	GCCGACGATGGGG	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801917	185801917	+	Silent	SNP	A	A	G	rs728534	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	41	86	0	0.506173	0	A|0.840;G|0.160	0.160	strong	.	ZNF804A	322	.	NM_194250	exon4	c.A1794G	p.K598K	GAAAAAAAGAAAA	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9922167	9922167	+	Missense_Mutation	SNP	C	C	T	rs16890979	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	59	186	0	0.361963	0	C|0.737;T|0.263	0.263	strong	.	SLC2A9	158	.	NM_020041	exon7	c.G844A	p.V282I	GGGAAACGTCTGC	.	PASS	Atlas-SNP
KIAA1432	57589	hgsc.bcm.edu	37	9	5774225	5774225	+	Silent	SNP	T	T	G	rs3739648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	53	114	1	0.481818	0.00877193	T|0.717;G|0.283	0.283	strong	KIAA1432,NS,carcinoma,+2,1	KIAA1432	97	1	NM_020829	exon26	c.T4251G	p.T1417T	TGGGACTTACGAC	.	scavenged	Atlas-SNP
NLRP14	338323	hgsc.bcm.edu	37	11	7091569	7091569	+	Missense_Mutation	SNP	C	C	T	rs17280682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	77	180	0	0.455621	0	C|0.850;T|0.150	0.150	strong	.	NLRP14	187	.	NM_176822	exon11	c.C3028T	p.L1010F	TCTGCTCTTATCT	.	PASS	Atlas-SNP
ATP5F1	515	hgsc.bcm.edu	37	1	111998734	111998734	+	Missense_Mutation	SNP	A	A	G	rs151112830	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	7	64	0	0.184211	0	A|0.998;G|0.002	0.002	strong	.	ATP5F1	20	.	NM_001688	exon4	c.A250G	p.I84V	GGGCTTATCTTGT	.	PASS	Atlas-SNP
RBM11	54033	hgsc.bcm.edu	37	21	15599340	15599340	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	471	21	368	6	0.044586	0.0163043	.	.	none	RBM11,NS,carcinoma,0,1	RBM11	41	1	NM_144770	exon5	c.A572G	p.H191R	GGACTCACCAACA	.	scavenged	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	37	1	16259813	16259813	+	Missense_Mutation	SNP	A	A	G	rs848210	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	16	97	0	0.246154	0	A|0.346;G|0.654	0.654	strong	.	SPEN	374	.	NM_015001	exon11	c.A7078G	p.N2360D	GAATCCAACCAAG	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	76990178	76990178	+	Silent	SNP	C	C	G	rs4727366	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	81	205	0	0.334711	0	C|0.688;G|0.312	0.312	strong	PION,caecum,carcinoma,0,1	PION	74	1	NM_017439	exon14	c.G990C	p.G330G	GTGTGACCCAACA	.	PASS	Atlas-SNP
ALDH8A1	64577	hgsc.bcm.edu	37	6	135239758	135239758	+	Missense_Mutation	SNP	G	G	C	rs41286234	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	133	258	0	0.478417	0	G|0.981;C|0.019	0.019	strong	.	ALDH8A1	68	.	NM_022568	exon7	c.C1259G	p.A420G	GTAGCCGCCAGCC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1266537	1266537	+	Silent	SNP	G	G	T	rs199659189	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	322	90	572	5	0.279503	0.00874126	G|0.790;T|0.211	0.211	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.G8427T	p.L2809L	AGCCCTGTCCAGC	.	scavenged	Atlas-SNP
AQP12A	375318	hgsc.bcm.edu	37	2	241631499	241631499	+	Silent	SNP	G	G	A	rs200769008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	49	191	0	0.445455	0	G|0.998;A|0.002	0.002	weak	AQP12A,NS,carcinoma,+1,1	AQP12A	32	1	NM_198998	exon2	c.G132A	p.T44T	GAGGACGCTGGTC	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104059542	104059542	+	Missense_Mutation	SNP	G	G	A	rs2243682	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	40	86	0	0.597015	0	G|0.855;A|0.145	0.145	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon39	c.C6269T	p.T2090M	CTTTCCGTAAGGT	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42571346	42571346	+	Silent	SNP	A	A	T	rs16895863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	48	52	0	1	0	A|0.793;T|0.207	0.207	strong	.	UBR2	134	.	NM_001184801	exon5	c.A552T	p.S184S	TTTATCAGAAGAT	.	PASS	Atlas-SNP
IL21R	50615	hgsc.bcm.edu	37	16	27460436	27460436	+	Silent	SNP	C	C	T	rs3093408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	55	131	0	0.52381	0	C|0.999;T|0.001	0.001	strong	.	IL21R	95	.	NM_181079	exon10	c.C1515T	p.A505A	CCTGGCCGGCCTG	.	PASS	Atlas-SNP
ABCA5	23461	hgsc.bcm.edu	37	17	67304447	67304447	+	Missense_Mutation	SNP	C	C	T	rs11544715	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	70	71	0	1	0	C|0.866;T|0.134	0.134	strong	ABCA5,NS,carcinoma,0,1	ABCA5	162	1	NM_018672	exon4	c.G532A	p.A178T	TGGATGCTTGTAA	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17366313	17366313	+	Missense_Mutation	SNP	C	C	T	rs12459398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	31	89	0	0.54386	0	C|0.765;T|0.235	0.235	strong	.	USHBP1	85	.	NM_031941	exon10	c.G1573A	p.V525M	GGAGCACGTGAGC	.	PASS	Atlas-SNP
OR5D13	390142	hgsc.bcm.edu	37	11	55541284	55541284	+	Missense_Mutation	SNP	G	G	A	rs11230983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	397	154	421	1	0.387909	0.0023753	G|0.898;A|0.102	0.102	strong	OR5D13,caecum,carcinoma,0,2	OR5D13	96	2	NM_001001967	exon1	c.G371A	p.R124H	ATGACCGTTTTGT	.	PASS	Atlas-SNP
FAM179B	23116	hgsc.bcm.edu	37	14	45478260	45478260	+	Missense_Mutation	SNP	A	A	G	rs139225809	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	106	105	0	0.666667	0	A|0.999;G|0.001	0.001	strong	.	FAM179B	115	.	NM_015091	exon6	c.A3049G	p.N1017D	TCACCAAACATCA	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56373462	56373462	+	Missense_Mutation	SNP	G	G	A	rs12462372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	91	167	1	0.558282	0.00598802	G|0.927;A|0.073	0.073	strong	NLRP4_ENST00000301295,colon,carcinoma,+1,7	NLRP4	331	7	NM_134444	exon5	c.G2123A	p.R708H	TCTCTCGTGATGA	.	scavenged	Atlas-SNP
ETFB	2109	hgsc.bcm.edu	37	19	51857738	51857738	+	Missense_Mutation	SNP	G	G	A	rs79338777	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	38	92	0	0.463415	0	G|0.937;A|0.063	0.063	strong	.	ETFB	46	.	NM_001014763	exon1	c.C155T	p.P52L	GGCAGGGGCAGGT	.	PASS	Atlas-SNP
ABAT	18	hgsc.bcm.edu	37	16	8844389	8844389	+	Silent	SNP	C	C	T	rs2229157	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	76	187	0	0.506667	0	C|0.901;T|0.099	0.099	strong	.	ABAT	46	.	NM_001127448	exon5	c.C309T	p.V103V	CTCTGTCCCCATA	.	PASS	Atlas-SNP
ZCCHC3	85364	hgsc.bcm.edu	37	20	278806	278806	+	Silent	SNP	C	C	T	rs1057189	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	16	29	0	0.533333	0	C|0.780;T|0.220	0.220	strong	.	ZCCHC3	20	.	NM_033089	exon1	c.C579T	p.S193S	GCGCTCCATCGGC	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21792811	21792811	+	Silent	SNP	G	G	A	rs9322965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	61	96	0	0.458647	0	G|0.856;A|0.144	0.144	strong	.	RPGRIP1	213	.	NM_020366	exon14	c.G1797A	p.P599P	CCGACCGTTGTCG	.	PASS	Atlas-SNP
DDI2	84301	hgsc.bcm.edu	37	1	15959977	15959977	+	Silent	SNP	C	C	T	rs3795763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	17	96	0	0.265625	0	C|0.707;T|0.293	0.293	strong	.	DDI2	38	.	NM_032341	exon4	c.C549T	p.A183A	CCGAGCCCGGAGA	.	PASS	Atlas-SNP
NAV3	89795	hgsc.bcm.edu	37	12	78400884	78400884	+	Silent	SNP	G	G	A	rs34276383	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	14	47	0	0.451613	0	G|0.867;A|0.133	0.133	strong	NAV3,NS,carcinoma,0,1	NAV3	506	1	NM_014903	exon8	c.G1566A	p.P522P	AATTCCGTCTTCC	.	PASS	Atlas-SNP
PHF17	79960	hgsc.bcm.edu	37	4	129792873	129792873	+	Missense_Mutation	SNP	A	A	G	rs6855813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	21	128	0	0.21875	0	A|0.972;G|0.028	0.028	strong	.	PHF17	63	.	NM_199320	exon11	c.A1985G	p.N662S	GAGACAATCGTTT	.	PASS	Atlas-SNP
USP21	27005	hgsc.bcm.edu	37	1	161132777	161132777	+	Missense_Mutation	SNP	G	G	A	rs17356051	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	91	155	0	0.411765	0	G|0.960;A|0.040	0.040	strong	.	USP21	63	.	NM_012475	exon6	c.G962A	p.G321D	GCCGAGGCCGCCG	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17273444	17273444	+	Silent	SNP	G	G	A	rs7545185	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	5	122	0	0.128205	0	G|0.809;A|0.191	0.191	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon17	c.G2472A	p.T824T	CCCCACGCTGCGC	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22952111	22952111	+	Missense_Mutation	SNP	A	A	G	rs34726149	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	85	191	0	0.438144	0	A|0.809;G|0.191	0.191	strong	ZNF99,NS,carcinoma,0,1	ZNF99	273	1	NM_001080409	exon2	c.T19C	p.W7R	CATCCCAAAATGT	.	PASS	Atlas-SNP
SPATA2	9825	hgsc.bcm.edu	37	20	48524827	48524827	+	Silent	SNP	A	A	G	rs2769982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	55	127	0	0.443548	0	A|0.584;G|0.416	0.416	strong	.	SPATA2	36	.	NM_006038	exon2	c.T201C	p.Y67Y	CACCTCATAGAAC	.	PASS	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236729965	236729965	+	Missense_Mutation	SNP	G	G	A	rs61736343	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	38	87	0	0.324786	0	G|0.985;A|0.015	0.015	strong	HEATR1,caecum,carcinoma,0,1	HEATR1	197	1	NM_018072	exon30	c.C4289T	p.A1430V	GCAGCCGCCAGCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677974	100677974	+	Missense_Mutation	SNP	A	A	G	rs113876641	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	890	178	209	0	0.2	0	A|0.998;G|0.002	0.002	strong	.	MUC17	804	.	NM_001040105	exon3	c.A3277G	p.T1093A	ATGCCAACCTCAA	.	PASS	Atlas-SNP
ATG12	9140	hgsc.bcm.edu	37	5	115177207	115177207	+	Missense_Mutation	SNP	T	T	C	rs74844425	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	39	107	0	0.433333	0	A|0.000;C|0.019;T|0.980	0.019	strong	.	ATG12	14	.	NM_004707	exon1	c.A43G	p.I15V	CAGCAATTGAAGT	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136573412	136573412	+	Silent	SNP	G	G	A	rs2073815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	67	58	0	1	0	G|0.539;A|0.461	0.461	strong	SARDH,NS,carcinoma,0,2	SARDH	112	2	NM_007101	exon11	c.C1467T	p.H489H	TACCTCGTGCAGC	.	PASS	Atlas-SNP
FKBP1A	2280	hgsc.bcm.edu	37	20	1350709	1350709	+	Silent	SNP	T	T	C	rs8392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	43	87	0	0.488636	0	T|0.408;G|0.125;C|0.192;A|0.276	0.192	strong	.	FKBP1A	6	.	NM_001199786	exon4	c.A258G	p.P86P	CCTCCATGGCAGA	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173474429	173474429	+	Silent	SNP	T	T	C	rs12026637	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	51	122	0	0.309091	0	T|0.805;C|0.195	0.195	strong	.	.	.	.	NM_178527	exon26	c.A3267G	p.Q1089Q	AGATGCTTGGATT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911317	29911317	+	Missense_Mutation	SNP	A	A	G	rs41557913	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	44	118	0	0.218905	0	A|0.991;G|0.010	0.010	strong	.	HLA-A	89	.	NM_001242758	exon3	c.A616G	p.T206A	CAGCGCACGGGTA	.	PASS	Atlas-SNP
KDM1B	221656	hgsc.bcm.edu	37	6	18161563	18161563	+	Silent	SNP	G	G	A	rs4716224	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	28	77	0	0.482759	0	G|0.683;A|0.317	0.317	strong	.	KDM1B	58	.	NM_153042	exon4	c.G93A	p.K31K	GGCGAAGAAGAAA	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208252777	208252777	+	Missense_Mutation	SNP	G	G	C	rs17011882	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	63	77	0	0.572727	0	G|0.972;C|0.028	0.028	strong	PLXNA2,NS,carcinoma,+1,1	PLXNA2	178	1	NM_025179	exon12	c.C2414G	p.A805G	TGGGCTGCACACT	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	34015013	34015013	+	Silent	SNP	G	G	A	rs2293027	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	28	148	0	0.337349	0	G|0.841;A|0.159	0.159	strong	RYR3,NS,carcinoma,+2,1	RYR3	760	1	NM_001243996	exon44	c.G6717A	p.G2239G	AAACGGGCTCTTG	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49721532	49721532	+	Missense_Mutation	SNP	G	G	A	rs3197999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	441	202	480	2	0.45805	0.00416667	G|0.749;A|0.251	0.251	strong	MST1,NS,carcinoma,0,1	MST1	84	1	NM_020998	exon18	c.C2107T	p.R703C	GCCAGCGGGACCT	.	scavenged	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44118191	44118191	+	Missense_Mutation	SNP	G	G	A	rs34163641	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	20	36	0	0.465116	0	G|0.784;A|0.216	0.216	strong	.	SRRM5	38	.	NM_001145641	exon1	c.G1918A	p.D640N	GAGAGCGACCCCA	.	PASS	Atlas-SNP
POLR1D	51082	hgsc.bcm.edu	37	13	28240021	28240021	+	Silent	SNP	C	C	T	rs41291680	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	33	70	0	0.471429	0	A|0.000;C|0.983;T|0.017	0.017	strong	.	POLR1D	31	.	NM_152705	exon3	c.C300T	p.S100S	AGGTTCCGCCAGT	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505179	37505179	+	Silent	SNP	T	T	C	rs57914746	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	33	243	0	0.203704	0	T|0.822;C|0.178	0.178	strong	.	ANKRD30A	448	.	NM_052997	exon32	c.T2772C	p.D924D	AAAAGATCACTGT	.	PASS	Atlas-SNP
GBP4	115361	hgsc.bcm.edu	37	1	89655787	89655787	+	Silent	SNP	T	T	C	rs41305862	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	158	306	0	0.951807	0	T|0.977;C|0.023	0.023	strong	.	GBP4	89	.	NM_052941	exon7	c.A1131G	p.E377E	AATGGCTTCCCTC	.	PASS	Atlas-SNP
TDP1	55775	hgsc.bcm.edu	37	14	90458308	90458308	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	15	80	0	0.168539	0	.	.	none	.	TDP1	47	.	NM_018319	exon13	c.T1414C	p.W472R	CAGAATTGGCTGC	.	PASS	Atlas-SNP
ZMYM5	9205	hgsc.bcm.edu	37	13	20425948	20425948	+	Missense_Mutation	SNP	T	T	C	rs9579718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	74	187	0	0.411111	0	T|0.901;C|0.099	0.099	strong	.	ZMYM5	73	.	NM_001039650	exon3	c.A373G	p.I125V	TTTCTATGTCCTC	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2819196	2819196	+	Silent	SNP	G	G	C	rs150110237	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	22	83	0	0.285714	0	G|0.998;C|0.002	0.002	strong	.	SRRM2	263	.	NM_016333	exon12	c.G7932C	p.S2644S	CTCCTCGTCGTCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276871	152276871	+	Silent	SNP	A	A	G	rs3126066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	433	136	322	1	0.314088	0.00310559	A|0.703;G|0.297	0.297	strong	.	FLG	900	.	NM_002016	exon3	c.T10491C	p.D3497D	GGAGCCATCTCCT	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789312	117789312	+	Missense_Mutation	SNP	C	C	A	rs200637340	by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	5	173	0	0.0189394	0	C|1.000;T|0.000	.	alt	TMPRSS13_ENST00000445164,NS,NS,0,3	TMPRSS13	75	3	NM_001206790	exon2	c.G263T	p.R88L	GATGCCCGGGCTG	.	scavenged	Atlas-SNP
NKX2-2	4821	hgsc.bcm.edu	37	20	21494184	21494184	+	Missense_Mutation	SNP	C	C	T	rs8192562	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	17	54	0	0.548387	0	C|0.952;T|0.048	0.048	strong	.	NKX2-2	49	.	NM_002509	exon1	c.G124A	p.A42T	TCTTGGCTGGCTC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679754	100679754	+	Missense_Mutation	SNP	C	C	G	rs4992073	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	120	141	0	0.652174	0	C|0.973;G|0.027	0.027	strong	.	MUC17	804	.	NM_001040105	exon3	c.C5057G	p.T1686S	CTTATACTGAAGG	.	PASS	Atlas-SNP
C7orf26	79034	hgsc.bcm.edu	37	7	6639953	6639953	+	Silent	SNP	G	G	A	rs34300529	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	26	64	0	0.52	0	G|0.883;A|0.117	0.117	strong	C7orf26,NS,carcinoma,0,1	C7orf26	33	1	NM_024067	exon4	c.G1074A	p.V358V	GCAGGTGGCCATG	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150054	11150054	+	Missense_Mutation	SNP	C	C	T	rs79420812	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	53	115	1	0.53	0.00869565	C|0.838;T|0.162	0.162	strong	TAS2R20,NS,carcinoma,0,1	TAS2R20	17	1	NM_176889	exon1	c.G421A	p.V141I	GACAAACCAAAAA	.	scavenged	Atlas-SNP
GSTA2	2939	hgsc.bcm.edu	37	6	52617738	52617738	+	Missense_Mutation	SNP	G	G	A	rs2234951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	111	195	1	0.536232	0.00512821	G|0.960;A|0.040	0.040	strong	.	GSTA2	33	.	NM_000846	exon5	c.C328T	p.P110S	TAAAGGGCAGAAG	.	PASS	Atlas-SNP
ZNF460	10794	hgsc.bcm.edu	37	19	57802806	57802806	+	Silent	SNP	C	C	T	rs2041109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	37	112	0	0.41573	0	C|0.799;T|0.201	0.201	strong	.	ZNF460	59	.	NM_006635	exon3	c.C897T	p.N299N	GCATAACAAGAGC	.	PASS	Atlas-SNP
ZNF433	163059	hgsc.bcm.edu	37	19	12126128	12126128	+	Silent	SNP	C	C	T	rs79356451	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	84	163	1	0.54902	0.00613497	C|0.999;T|0.001	0.001	strong	ZNF433,colon,carcinoma,-1,2	ZNF433	49	2	NM_001080411	exon4	c.G1554A	p.S518S	GGAGCTCGAACAG	.	scavenged	Atlas-SNP
WDR41	55255	hgsc.bcm.edu	37	5	76728996	76728996	+	Silent	SNP	T	T	C	rs72769029	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	219	218	2	0.99095	0.00917431	T|0.979;C|0.021	0.021	strong	.	WDR41	29	.	NM_018268	exon13	c.A1344G	p.K448K	CTCTAATTTTTGA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	17	120	0	0.142857	0	.	.	weak	HLA-A,NS,carcinoma,0,5	HLA-A	89	5	NM_001242758	exon2	c.G147C	p.V49V	CGCCGTGGGCTAC	.	PASS	Atlas-SNP
REM2	161253	hgsc.bcm.edu	37	14	23354066	23354066	+	Missense_Mutation	SNP	G	G	C	rs8014119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	66	80	0	0.589286	0	G|0.884;C|0.116	0.116	strong	.	REM2	21	.	NM_173527	exon2	c.G287C	p.G96A	CCTCTGGCTCGTC	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120608031	120608031	+	Silent	SNP	A	A	G	rs2286050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	75	187	0	0.449102	0	A|0.709;G|0.291	0.291	strong	.	GCN1L1	207	.	NM_006836	exon15	c.T1461C	p.T487T	CCCTTCAGTGATG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179395573	179395573	+	Missense_Mutation	SNP	C	C	T	rs56324595	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	383	158	437	1	0.412533	0.00228833	C|0.988;T|0.012	0.012	strong	.	TTN	18412	.	NM_001267550	exon358	c.G105769A	p.E35257K	AAGGTTCTGGAGA	.	PASS	Atlas-SNP
P2RX3	5024	hgsc.bcm.edu	37	11	57137371	57137371	+	Silent	SNP	G	G	A	rs2276039	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	69	155	0	0.405882	0	G|0.664;A|0.336	0.336	strong	P2RX3,NS,adenoma,0,1	P2RX3	55	1	NM_002559	exon12	c.G1095A	p.T365T	GACTACGCTGAAA	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124748226	124748226	+	Silent	SNP	G	G	A	rs2860440	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	32	63	0	0.516129	0	G|0.528;A|0.472	0.472	strong	HEG1,colon,carcinoma,0,1	HEG1	109	1	NM_020733	exon2	c.C423T	p.G141G	CATCACGCCCTCT	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12887174	12887174	+	Missense_Mutation	SNP	C	C	T	rs75703556		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	13	3	29	2	0.230769	0.0689655	C|0.833;T|0.167	0.167	weak	PRAMEF11,extremity,malignant_melanoma,0,1	PRAMEF11	72	1	NM_001146344	exon3	c.G683A	p.R228H	AGGCAGCGCAGCT	.	scavenged	Atlas-SNP
OSMR	9180	hgsc.bcm.edu	37	5	38919158	38919158	+	Missense_Mutation	SNP	G	G	A	rs10941412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	91	179	0	0.489247	0	G|0.831;A|0.169	0.169	strong	.	OSMR	133	.	NM_003999	exon11	c.G1579A	p.E527K	GACCCCGAAAACA	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10941955	10941955	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	698	8	450	0	0.0114613	0	.	.	none	TPTE_ENST00000361285,NS,carcinoma,+1,2	TPTE	513	2	NM_199261	exon14	c.T748C	p.S250P	GAAATGACATAGC	.	scavenged	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152082376	152082376	+	Missense_Mutation	SNP	C	C	A	rs200755879	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	4	143	2	0.0192308	0.013986	.	.	weak	TCHH,left_upper_lobe,carcinoma,-1,1	TCHH	275	1	NM_007113	exon3	c.G3317T	p.R1106L	CTCTCCCGCTCCT	.	scavenged	Atlas-SNP
CHD2	1106	hgsc.bcm.edu	37	15	93552488	93552488	+	Silent	SNP	C	C	T	rs34315566	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	17	91	0	0.257576	0	C|0.967;T|0.033	0.033	strong	.	CHD2	280	.	NM_001271	exon35	c.C4527T	p.I1509I	GAAAATCGGAGAC	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158534381	158534381	+	Silent	SNP	G	G	C	rs59980573	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	53	116	0	0.679487	0	G|0.740;C|0.260	0.260	strong	.	ESYT2	70	.	NM_020728	exon17	c.C2082G	p.P694P	CTCAGGGGGCTGG	.	PASS	Atlas-SNP
PGLS	25796	hgsc.bcm.edu	37	19	17631821	17631821	+	Silent	SNP	G	G	A	rs148164602	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	64	192	0	0.438356	0	G|0.977;A|0.023	0.023	strong	.	PGLS	12	.	NM_012088	exon5	c.G708A	p.L236L	GAAACTGTGCTGG	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82834299	82834299	+	Missense_Mutation	SNP	G	G	A	rs188703	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	43	107	0	0.505882	0	G|0.623;A|0.377	0.377	strong	VCAN,NS,carcinoma,-1,1	VCAN	498	1	NM_004385	exon8	c.G5477A	p.R1826H	TCCCACGTAGTCC	.	PASS	Atlas-SNP
ZCCHC6	79670	hgsc.bcm.edu	37	9	88959938	88959938	+	Silent	SNP	C	C	T	rs791323	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	105	266	0	0.492958	0	C|0.379;N|0.000	.	strong	ZCCHC6,colon,carcinoma,0,1	ZCCHC6	105	1	NM_024617	exon5	c.G951A	p.L317L	AATTTCCAGCCTC	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50528569	50528569	+	Missense_Mutation	SNP	A	A	T	rs12628964	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14	9	27	0	0.642857	0	A|0.756;T|0.244	0.244	strong	.	MOV10L1	238	.	NM_018995	exon1	c.A52T	p.T18S	GCGGACACCCCTA	.	PASS	Atlas-SNP
CLEC19A	728276	hgsc.bcm.edu	37	16	19297219	19297219	+	Missense_Mutation	SNP	T	T	G	rs179196	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	52	127	0	0.416	0	T|0.805;G|0.195	0.195	strong	.	CLEC19A	4	.	NM_001256720	exon1	c.T46G	p.S16A	CTCCACTCTGCAC	.	PASS	Atlas-SNP
ZNF335	63925	hgsc.bcm.edu	37	20	44596545	44596545	+	Silent	SNP	G	G	A	rs3848719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	53	93	0	0.445378	0	G|0.728;A|0.272	0.272	strong	ZNF335,NS,carcinoma,0,1	ZNF335	115	1	NM_022095	exon5	c.C642T	p.S214S	CGGGGAGCTGGGC	.	PASS	Atlas-SNP
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43632536	43632536	+	Missense_Mutation	SNP	C	C	T	rs7163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	13	104	0	0.178082	0	C|0.805;T|0.195	0.195	strong	.	EBNA1BP2	37	.	NM_001159936	exon8	c.G833A	p.R278H	TTCTTGCGCTGTG	.	PASS	Atlas-SNP
INTS3	65123	hgsc.bcm.edu	37	1	153736314	153736314	+	Silent	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	4	295	0	0.0126582	0	.	.	none	INTS3,NS,carcinoma,+1,1	INTS3	83	1	NM_023015	exon17	c.G1773T	p.T591T	TGATACGGAGGCC	.	scavenged	Atlas-SNP
OR4C16	219428	hgsc.bcm.edu	37	11	55340379	55340379	+	Missense_Mutation	SNP	T	T	C	rs559449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	365	168	400	1	0.460274	0.0025	T|0.517;C|0.483	0.483	strong	.	OR4C16	104	.	NM_001004701	exon1	c.T776C	p.L259P	CATGCCTTGCAAC	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121616250	121616250	+	Silent	SNP	G	G	A	rs4629793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	51	93	0	0.75	0	G|0.681;A|0.319	0.319	strong	.	PTPRZ1	605	.	NM_001206838	exon5	c.G480A	p.A160A	TGATGCGGACCGA	.	PASS	Atlas-SNP
USP32	84669	hgsc.bcm.edu	37	17	58285542	58285542	+	Missense_Mutation	SNP	G	G	A	rs76478630		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	635	146	575	1	0.229921	0.00173913	.	.	weak	USP32,NS,malignant_melanoma,0,2	USP32	128	2	NM_032582	exon24	c.C2803T	p.R935W	CATACCGTACAGG	.	scavenged	Atlas-SNP
NOX3	50508	hgsc.bcm.edu	37	6	155761246	155761246	+	Missense_Mutation	SNP	G	G	T	rs3749930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	16	37	0	0.432432	0	G|0.878;T|0.122	0.122	strong	.	NOX3	93	.	NM_015718	exon6	c.C512A	p.T171K	GCTATTGTCCTTA	.	PASS	Atlas-SNP
TTC4	7268	hgsc.bcm.edu	37	1	55182300	55182300	+	Missense_Mutation	SNP	T	T	A	rs1147990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	43	46	0	0.977273	0	T|0.395;A|0.605	0.605	strong	TTC4,NS,carcinoma,-2,1	TTC4	21	1	NM_004623	exon2	c.T139A	p.S47T	TTTATGTCGAGAG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284505	152284505	+	Missense_Mutation	SNP	C	C	G	rs201137357	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	463	32	340	1	0.0691145	0.00294118	.	.	weak	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.G2857C	p.E953Q	GTCCCTCACTGTC	.	scavenged	Atlas-SNP
RAI14	26064	hgsc.bcm.edu	37	5	34757666	34757666	+	Missense_Mutation	SNP	G	G	A	rs17521570	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	15	39	0	0.625	0	G|0.906;A|0.094	0.094	strong	.	RAI14	100	.	NM_001145525	exon5	c.G139A	p.A47T	AAGGGGGCCAGTG	.	PASS	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49721798	49721798	+	Silent	SNP	C	C	A	rs13085791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	349	180	277	0	0.515759	0	C|0.725;A|0.275	0.275	strong	.	MST1	84	.	NM_020998	exon17	c.G1965T	p.R655R	ACTCTCCCGCACA	.	PASS	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	37	16	3254972	3254972	+	Silent	SNP	T	T	C	rs2075851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	167	226	2	1	0.00884956	T|0.618;C|0.382	0.382	strong	.	OR1F1	36	.	NM_012360	exon1	c.T726C	p.G242G	CTGTGGTTCTCAC	.	PASS	Atlas-SNP
ABHD16B	140701	hgsc.bcm.edu	37	20	62492922	62492922	+	Missense_Mutation	SNP	T	T	A	rs2281534	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	61	97	0	0.539823	0	T|0.942;A|0.058	0.058	strong	.	ABHD16B	22	.	NM_080622	exon1	c.T29A	p.L10Q	AGGCGCTGGTGCG	.	PASS	Atlas-SNP
KRT10	3858	hgsc.bcm.edu	37	17	38978462	38978462	+	Missense_Mutation	SNP	C	C	T	rs77919366	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	51	128	1	0.485714	0.0078125	C|0.838;T|0.162	0.162	strong	KRT10,NS,carcinoma,0,1	KRT10	56	1	NM_000421	exon1	c.G376A	p.G126S	CAAAGCCGCCTCC	.	scavenged	Atlas-SNP
PAPSS1	9061	hgsc.bcm.edu	37	4	108575989	108575989	+	Silent	SNP	G	G	A	rs3733633	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	233	125	188	0	0.536481	0	G|0.759;A|0.241	0.241	strong	.	PAPSS1	57	.	NM_005443	exon8	c.C963T	p.D321D	ACAGCCGTCCAGC	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197499	39197499	+	Nonsense_Mutation	SNP	G	G	A	rs3213755	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	84	186	0	0.446809	0	G|0.804;A|0.196	0.196	strong	.	KRTAP1-1	23	.	NM_030967	exon1	c.C151T	p.Q51X	TGGTCTGGCAGCA	.	PASS	Atlas-SNP
ATF5	22809	hgsc.bcm.edu	37	19	50435862	50435862	+	Missense_Mutation	SNP	C	C	T	rs283526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	107	105	3	0.89916	0.0285714	C|0.351;T|0.649	0.649	strong	ATF5,NS,carcinoma,0,1	ATF5	27	1	NM_012068	exon4	c.C362T	p.P121L	CCCCGCCCCTCCC	.	scavenged	Atlas-SNP
CHPF2	54480	hgsc.bcm.edu	37	7	150935430	150935430	+	Missense_Mutation	SNP	G	G	C	rs3748098	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	10	69	0	0.25641	0	G|0.948;C|0.052	0.052	strong	.	CHPF2	52	.	NM_019015	exon4	c.G1982C	p.G661A	CTATAGGGGGGAG	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	37	15	74703022	74703022	+	Silent	SNP	G	G	A	rs2075592	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	78	181	1	0.702703	0.00552486	G|0.857;A|0.143	0.143	strong	.	SEMA7A	58	.	NM_003612	exon14	c.C1944T	p.A648A	GGAGGCGGCCAGG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467576	10467576	+	Silent	SNP	T	T	C	rs4840499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	87	193	0	0.388393	0	T|0.566;C|0.434	0.434	strong	.	RP1L1	453	.	NM_178857	exon4	c.A4032G	p.T1344T	TCCTTCTGTTTCT	.	PASS	Atlas-SNP
OR52N4	390072	hgsc.bcm.edu	37	11	5776484	5776484	+	Nonsense_Mutation	SNP	A	A	T	rs4910844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	156	187	0	0.993631	0	A|0.784;T|0.216	0.216	strong	.	OR52N4	55	.	NM_001005175	exon1	c.A514T	p.R172X	TACTGCAGAGGCA	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127597518	127597518	+	Silent	SNP	G	G	A	rs10070365	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	93	213	1	0.502703	0.00469484	G|0.871;A|0.129	0.129	strong	.	FBN2	858	.	NM_001999	exon64	c.C8274T	p.S2758S	TTCTGGGGACAGA	.	PASS	Atlas-SNP
ATE1	11101	hgsc.bcm.edu	37	10	123549691	123549691	+	Silent	SNP	T	T	G	rs35350755	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	52	105	0	0.468468	0	T|0.544;G|0.456	0.456	strong	.	ATE1	67	.	NM_001001976	exon11	c.A1371C	p.P457P	TGCTTCTGGGTCC	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907275	12907275	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	2	247	0	0.0138889	0	.	.	none	HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.C868G	p.Q290E	CATCCTGGCCATT	.	scavenged	Atlas-SNP
SBSN	374897	hgsc.bcm.edu	37	19	36015652	36015652	+	Silent	SNP	C	C	T	rs17705633	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	61	103	0	0.525862	0	C|0.874;T|0.126	0.126	strong	.	SBSN	58	.	NM_001166034	exon3	c.G1710A	p.S570S	GTTGACCGAGGCC	.	PASS	Atlas-SNP
EMC3	55831	hgsc.bcm.edu	37	3	10028294	10028294	+	Silent	SNP	G	G	A	rs11551739	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	63	128	0	0.456522	0	G|0.941;A|0.059	0.059	strong	.	EMC3	2	.	NM_018447	exon1	c.C52T	p.L18L	TGGGTAGGACCAC	.	PASS	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13176312	13176312	+	Silent	SNP	C	C	T	rs2274856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256	138	269	1	0.539062	0.00371747	C|0.613;T|0.387	0.387	strong	.	MPDZ	324	.	NM_003829	exon20	c.G2754A	p.S918S	GTCCACCGAAGGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680370	100680370	+	Silent	SNP	C	C	T	rs10257974	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	233	228	163	0	0.978541	0	C|0.861;T|0.139	0.139	strong	.	MUC17	804	.	NM_001040105	exon3	c.C5673T	p.P1891P	AACTCCCGCTGTC	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238283605	238283605	+	Silent	SNP	G	G	A	rs12622093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	27	73	0	0.36	0	G|0.795;A|0.205	0.205	strong	COL6A3_ENST00000392004,NS,carcinoma,0,2	COL6A3	608	2	NM_004369	exon8	c.C3129T	p.G1043G	AGGGAAGCCGCTC	.	PASS	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	37	12	52827740	52827740	+	Missense_Mutation	SNP	G	G	C	rs2232386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	118	235	0	0.495798	0	G|0.888;C|0.112	0.112	strong	.	KRT75	75	.	NM_004693	exon1	c.C349G	p.P117A	CAGGGGGACACAC	.	PASS	Atlas-SNP
ZNF235	9310	hgsc.bcm.edu	37	19	44793278	44793278	+	Missense_Mutation	SNP	A	A	G	rs141976678	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	62	133	0	0.512397	0	A|0.999;G|0.001	0.001	strong	.	ZNF235	60	.	NM_004234	exon5	c.T310C	p.S104P	AGCATGAAAGCTC	.	PASS	Atlas-SNP
KRT24	192666	hgsc.bcm.edu	37	17	38855721	38855721	+	Missense_Mutation	SNP	G	G	A	rs148215930	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	2	199	0	0.0101523	0	G|1.000;A|0.000	0.000	weak	KRT24,NS,carcinoma,+1,1	KRT24	60	1	NM_019016	exon6	c.C1336T	p.R446C	GGCGGCGGTAGGT	.	scavenged	Atlas-SNP
BLVRA	644	hgsc.bcm.edu	37	7	43843423	43843423	+	Silent	SNP	G	G	A	rs1131372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	33	71	0	0.347368	0	G|0.908;A|0.092	0.092	strong	BLVRA,NS,carcinoma,0,1	BLVRA	26	1	NM_001253823	exon8	c.G609A	p.V203V	GACAGTGTGTCTG	.	PASS	Atlas-SNP
ZNF471	57573	hgsc.bcm.edu	37	19	57037103	57037103	+	Missense_Mutation	SNP	C	C	G	rs16987303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	33	73	0	0.471429	0	C|0.882;G|0.118	0.118	strong	.	ZNF471	99	.	NM_020813	exon5	c.C1667G	p.S556C	AAACTTCCAATCT	.	PASS	Atlas-SNP
PGR	5241	hgsc.bcm.edu	37	11	100922202	100922202	+	Silent	SNP	G	G	A	rs1042839	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	399	118	231	0	0.295739	0	G|0.892;A|0.108	0.108	strong	.	PGR	115	.	NM_000926	exon5	c.C2310T	p.H770H	ACTGACGTGTTTG	.	PASS	Atlas-SNP
RFX4	5992	hgsc.bcm.edu	37	12	107141265	107141265	+	Missense_Mutation	SNP	G	G	A	rs61743416	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	64	118	0	0.516129	0	G|0.990;A|0.010	0.010	strong	.	RFX4	218	.	NM_001206691	exon16	c.G1711A	p.A571T	ACGGCTGCTGGGT	.	PASS	Atlas-SNP
DNPEP	23549	hgsc.bcm.edu	37	2	220251685	220251685	+	Missense_Mutation	SNP	T	T	G	rs11539909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	57	108	0	0.791667	0	T|0.980;G|0.020	0.020	strong	.	DNPEP	40	.	NM_012100	exon3	c.A148C	p.N50H	GGCGGTTGCGGCA	.	PASS	Atlas-SNP
CDKL3	51265	hgsc.bcm.edu	37	5	133655067	133655067	+	Silent	SNP	C	C	T	rs373913998		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	21	23	0	0.5	0	.	.	weak	.	CDKL3	76	.	NM_001113575	exon6	c.G774A	p.L258L	TGCCAACAATCCA	.	PASS	Atlas-SNP
ZMYM1	79830	hgsc.bcm.edu	37	1	35570214	35570214	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	3	206	0	0.0238095	0	.	.	none	ZMYM1,NS,carcinoma,+1,1	ZMYM1	86	1	NM_024772	exon6	c.C651T	p.C217C	TGCCTGCCTTTCA	.	scavenged	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	37	13	24868919	24868919	+	Silent	SNP	T	T	C	rs35793500	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	43	98	0	0.398148	0	T|0.961;C|0.039	0.039	strong	.	SPATA13	92	.	NM_001166271	exon10	c.T3123C	p.N1041N	GAAGAATGTGGCC	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110850842	110850842	+	Silent	SNP	A	A	G	rs995224	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	43	95	0	0.413462	0	T|0.000;G|0.240;C|0.000;A|0.760	0.240	strong	.	COL4A1	372	.	NM_001845	exon21	c.T1257C	p.P419P	GGGCCCAGGGGAA	.	PASS	Atlas-SNP
EPS15	2060	hgsc.bcm.edu	37	1	51826921	51826921	+	Missense_Mutation	SNP	T	T	C	rs17567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	89	234	0	0.689922	0	T|0.702;C|0.298	0.298	strong	.	EPS15	72	.	NM_001981	exon24	c.A2466G	p.I822M	ACAAAATATTTCA	.	PASS	Atlas-SNP
LAD1	3898	hgsc.bcm.edu	37	1	201355943	201355943	+	Silent	SNP	C	C	T	rs2799677	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	70	175	0	0.295359	0	C|0.459;T|0.541	0.541	strong	.	LAD1	42	.	NM_005558	exon3	c.G546A	p.K182K	GGAGGACTTCTCC	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139263158	139263158	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	74	122	0	0.540146	0	.	.	none	.	FAM135B	423	.	NM_015912	exon6	c.C468A	p.F156L	ATAGTCGAACATG	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	108011971	108011971	+	Silent	SNP	G	G	A	rs56296886	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	28	82	0	0.4375	0	G|0.996;A|0.004	0.004	strong	.	BTBD11	122	.	NM_001018072	exon10	c.G2268A	p.K756K	AGAGAAGGAGAAG	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176482	57176482	+	Missense_Mutation	SNP	C	C	T	rs12462469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	88	113	1	1	0.00884956	C|0.621;T|0.379	0.379	strong	.	ZNF835	106	.	NM_001005850	exon2	c.G85A	p.E29K	GGTTTTCCTGCAG	.	PASS	Atlas-SNP
WDR20	91833	hgsc.bcm.edu	37	14	102675350	102675350	+	Silent	SNP	G	G	C	rs6575900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	59	129	0	0.353293	0	G|0.664;C|0.336	0.336	strong	.	WDR20	35	.	NM_001242417	exon4	c.G936C	p.G312G	AGGTGGGGAGGAC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168041152	168041152	+	Splice_Site	SNP	T	T	C	rs16853169	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	91	202	0	0.486631	0	T|0.904;C|0.096	0.096	strong	.	XIRP2	914	.	NM_001199143	exon4	c.661+2T>C	.	TATTTGTAAGGTT	.	PASS	Atlas-SNP
OR5P3	120066	hgsc.bcm.edu	37	11	7847472	7847472	+	Silent	SNP	C	C	T	rs1482793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	25	62	0	0.403226	0	C|0.504;T|0.496	0.496	strong	.	OR5P3	44	.	NM_153445	exon1	c.G48A	p.G16G	AGATAACCCCAAA	.	PASS	Atlas-SNP
DBX2	440097	hgsc.bcm.edu	37	12	45444426	45444426	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	21	84	0	0.308824	0	.	.	none	.	DBX2	45	.	NM_001004329	exon1	c.C285T	p.A95A	CGCCCCGGCGGGG	.	PASS	Atlas-SNP
CPSF4	10898	hgsc.bcm.edu	37	7	99047978	99047978	+	Silent	SNP	T	T	C	rs883403	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	47	135	0	0.29375	0	T|0.639;C|0.361	0.361	strong	.	CPSF4	24	.	NM_001081559	exon4	c.T387C	p.R129R	TGACCGTGGCTTC	.	PASS	Atlas-SNP
TMEM259	91304	hgsc.bcm.edu	37	19	1014377	1014377	+	Silent	SNP	A	A	G	rs1058506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	53	202	1	0.424	0.00495049	A|0.821;G|0.179	0.179	strong	C19orf6,NS,carcinoma,-1,2	.	.	2	NM_033420	exon2	c.T321C	p.R107R	GCCCTCACGCGGC	.	scavenged	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55873096	55873096	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	3	222	0	0.0123457	0	.	.	none	OR8H2,larynx,carcinoma,+1,1	OR8H2	117	1	NM_001005200	exon1	c.A578G	p.Y193C	ATACATACAACAC	.	scavenged	Atlas-SNP
SYNRG	11276	hgsc.bcm.edu	37	17	35956391	35956391	+	Missense_Mutation	SNP	G	G	C	rs12944821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	49	116	1	0.415254	0.00862069	G|0.825;C|0.175	0.175	strong	SYNRG,rectum,carcinoma,0,1	SYNRG	101	1	NM_001163544	exon3	c.C119G	p.A40G	AGGCCTGCTGAAA	.	scavenged	Atlas-SNP
LILRA3	11026	hgsc.bcm.edu	37	19	54803750	54803750	+	Missense_Mutation	SNP	G	G	T	rs149807835	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	2	37	0	0.0194175	0	G|0.970;T|0.030	0.030	strong	LILRA3,NS,haematopoietic_neoplasm,0,3	LILRA3	65	3	NM_001172654	exon3	c.C74A	p.P25H	GGGAGGGGCCCTG	.	scavenged	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49690627	49690627	+	Missense_Mutation	SNP	G	G	A	rs35762866	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	25	40	0	0.531915	0	G|0.940;A|0.060	0.060	strong	.	BSN	272	.	NM_003458	exon5	c.G3638A	p.G1213D	CCCATGGCGGCCC	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88787673	88787673	+	Missense_Mutation	SNP	G	G	A	rs35159887	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	16	69	0	0.213333	0	G|0.825;A|0.175	0.175	strong	PIEZO1,NS,carcinoma,0,1	PIEZO1	79	1	NM_001142864	exon39	c.C5569T	p.P1857S	CTTGGGGTTCTGG	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	37	22	18301693	18301693	+	Missense_Mutation	SNP	T	T	C	rs8135914	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	20	86	0	0.363636	0	T|0.774;C|0.226	0.226	strong	.	MICAL3	53	.	NM_015241	exon26	c.A3734G	p.Q1245R	GGTGGCTGGGGCT	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44118353	44118353	+	Missense_Mutation	SNP	G	G	A	rs2302421	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	44	119	0	0.494382	0	G|0.833;A|0.167	0.167	strong	.	SRRM5	38	.	NM_001145641	exon1	c.G2080A	p.D694N	CAAGCCGACGCCA	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258336	25258336	+	Missense_Mutation	SNP	C	C	T	rs150756150		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	401	5	357	1	0.0124688	0.00280112	C|1.000;T|0.000	0.000	weak	ZKSCAN2,rectum,carcinoma,-1,1	ZKSCAN2	90	1	NM_001012981	exon5	c.G1181A	p.R394Q	TTGGTTCGACACT	.	scavenged	Atlas-SNP
PHLPP1	23239	hgsc.bcm.edu	37	18	60645509	60645509	+	Silent	SNP	C	C	T	rs34061095	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	90	110	0	1	0	C|0.951;T|0.049	0.049	strong	.	PHLPP1	164	.	NM_194449	exon17	c.C3999T	p.N1333N	GGTGAACGGAGTG	.	PASS	Atlas-SNP
MEPE	56955	hgsc.bcm.edu	37	4	88767008	88767008	+	Missense_Mutation	SNP	G	G	A	rs17013285	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	23	37	0	0.534884	0	G|0.854;A|0.146	0.146	strong	.	MEPE	86	.	NM_020203	exon4	c.G988A	p.V330I	GATGCTGTTGATG	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	99006748	99006748	+	Silent	SNP	C	C	T	rs11559201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	58	118	0	0.379085	0	C|0.872;T|0.128	0.128	strong	.	MATN2	165	.	NM_002380	exon7	c.C1122T	p.H374H	TCAGCACGAGTGT	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31848706	31848706	+	Silent	SNP	A	A	G	rs3213709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	30	103	1	0.283019	0.00970874	A|0.792;G|0.208	0.208	strong	PDE1C_ENST00000396193,NS,carcinoma,-2,8	PDE1C	465	8	NM_001191058	exon17	c.T2010C	p.G670G	ATTTTTACCATCT	.	scavenged	Atlas-SNP
FLNA	2316	hgsc.bcm.edu	37	X	153581932	153581932	+	Silent	SNP	A	A	G	rs2070825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	96	157	0	1	0	A|0.755;0|0.006	.	strong	.	FLNA	373	.	NM_001110556	exon36	c.T5850C	p.A1950A	GACCCGAGCAGTG	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	89989779	89989779	+	Silent	SNP	G	G	A	rs16876822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	154	170	0	0.987179	0	G|0.672;A|0.328	0.328	strong	.	GPR98	605	.	NM_032119	exon33	c.G7206A	p.E2402E	AATGGAGGAAGGT	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13395475	13395475	+	Missense_Mutation	SNP	G	G	C	rs2280085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	226	104	271	0	0.460177	0	G|0.807;C|0.193	0.193	strong	.	NUP210	182	.	NM_024923	exon17	c.C2461G	p.P821A	GCTCAGGCTCGAT	.	PASS	Atlas-SNP
ZDHHC20	253832	hgsc.bcm.edu	37	13	21976996	21976996	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	32	41	0	0.627451	0	.	.	none	.	ZDHHC20	36	.	NM_153251	exon5	c.A380G	p.Y127C	TCACAATATCTGA	.	PASS	Atlas-SNP
LRRC16A	55604	hgsc.bcm.edu	37	6	25472737	25472737	+	Silent	SNP	C	C	T	rs41271815	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	59	146	0	0.508621	0	C|0.935;T|0.065	0.065	strong	.	LRRC16A	168	.	NM_001173977	exon11	c.C862T	p.L288L	AACCCACTGGAGG	.	PASS	Atlas-SNP
FAM13B	51306	hgsc.bcm.edu	37	5	137278682	137278682	+	Missense_Mutation	SNP	T	T	C	rs33956817	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	37	82	0	0.440476	0	T|0.960;C|0.040	0.040	strong	.	FAM13B	46	.	NM_016603	exon21	c.A2404G	p.M802V	TCAACATATCACC	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113363466	113363466	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	20	80	0	0.224719	0	.	.	none	.	CSMD3	2325	.	NM_198123	exon40	c.C6263T	p.S2088F	ATGTGAGAGTGAC	.	PASS	Atlas-SNP
RAET1E	135250	hgsc.bcm.edu	37	6	150210681	150210681	+	Missense_Mutation	SNP	G	G	A	rs9371533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	305	137	320	2	0.44918	0.00625	G|0.403;A|0.597	0.597	strong	RAET1E,NS,carcinoma,+1,2	RAET1E	20	2	NM_139165	exon3	c.C425T	p.T142I	CCATTGGTGGCGA	.	scavenged	Atlas-SNP
ASTN2	23245	hgsc.bcm.edu	37	9	119770495	119770495	+	Silent	SNP	G	G	A	rs61736198	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	101	189	0	0.448889	0	G|0.994;A|0.006	0.006	strong	.	ASTN2	307	.	NM_014010	exon6	c.C1314T	p.S438S	CCAGTCGGAGATG	.	PASS	Atlas-SNP
UBN1	29855	hgsc.bcm.edu	37	16	4925291	4925291	+	Silent	SNP	T	T	G	rs17137364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	45	84	0	0.517241	0	T|0.912;G|0.088	0.088	strong	.	UBN1	88	.	NM_001079514	exon15	c.T2880G	p.V960V	GCCTGTTTCCCAG	.	PASS	Atlas-SNP
CAPS2	84698	hgsc.bcm.edu	37	12	75715330	75715330	+	Missense_Mutation	SNP	C	C	A	rs10879901	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	78	161	0	0.4875	0	C|0.808;A|0.192	0.192	strong	CAPS2_ENST00000409445,NS,carcinoma,0,1	CAPS2	96	1	NM_032606	exon6	c.G375T	p.L125F	TGCTGGCAAATTT	.	PASS	Atlas-SNP
CYP27C1	339761	hgsc.bcm.edu	37	2	127956964	127956964	+	Silent	SNP	G	G	A	rs149542135	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	72	175	0	0.510638	0	G|0.999;A|0.001	0.001	strong	.	CYP27C1	52	.	NM_001001665	exon4	c.C540T	p.A180A	GACGCCGGCCAGC	.	PASS	Atlas-SNP
IL18R1	8809	hgsc.bcm.edu	37	2	103013177	103013177	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	294	4	333	0	0.0136054	0	.	.	none	IL18R1,NS,carcinoma,0,1	IL18R1	72	1	NM_003855	exon10	c.C1457T	p.P486L	TCTTGCCCCAATC	.	scavenged	Atlas-SNP
ZAK	0	hgsc.bcm.edu	37	2	174055646	174055646	+	Silent	SNP	T	T	C	rs35853276	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	35	97	0	0.538462	0	T|0.858;C|0.142	0.142	strong	.	ZAK	62	.	NM_133646	exon6	c.T439C	p.L147L	GGAGTATTGAAGG	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122649482	122649482	+	Silent	SNP	A	A	G	rs2289337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	21	78	0	0.333333	0	T|0.005;G|0.229	0.229	strong	WDR11,NS,carcinoma,0,1	WDR11	95	1	NM_018117	exon18	c.A2304G	p.A768A	AATAGCAATGTAC	.	PASS	Atlas-SNP
ABCG8	64241	hgsc.bcm.edu	37	2	44102491	44102491	+	Silent	SNP	C	C	T	rs4148221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	34	85	0	0.43038	0	C|0.850;T|0.150	0.150	strong	.	ABCG8	98	.	NM_022437	exon11	c.C1695T	p.A565A	CAATGCCCTCTAC	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73179672	73179672	+	Silent	SNP	C	C	T	rs3749645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	36	74	0	0.461538	0	C|0.820;T|0.180	0.180	strong	.	.	.	.	NM_001080479	exon24	c.C3018T	p.Y1006Y	AAAATACCCTGTC	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76472768	76472768	+	Silent	SNP	G	G	A	rs7405830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	270	143	269	0	0.52963	0	G|0.641;A|0.359	0.359	strong	.	DNAH17	347	.	NM_173628	exon52	c.C8040T	p.L2680L	GCGGACGAGGTCC	.	PASS	Atlas-SNP
DISP1	84976	hgsc.bcm.edu	37	1	223116474	223116474	+	Missense_Mutation	SNP	G	G	T	rs2789975	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	132	169	0	0.650246	0	G|0.844;T|0.156	0.156	strong	.	DISP1	145	.	NM_032890	exon4	c.G309T	p.E103D	TCCCGAGGCTGGC	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53856702	53856702	+	Missense_Mutation	SNP	G	G	A	rs200114728		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	189	14	197	1	0.0740741	0.00507614	.	.	weak	ZNF845,NS,carcinoma,0,6	ZNF845	101	6	NM_138374	exon4	c.G2774A	p.R925H	CCTTCCGTCACAA	.	scavenged	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152083806	152083806	+	Silent	SNP	C	C	T	rs200947543	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206	127	136	0	0.616505	0	C|0.993;T|0.007	0.007	strong	.	TCHH	275	.	NM_007113	exon3	c.G1887A	p.R629R	CTGGCGCCTCTCT	.	PASS	Atlas-SNP
MTNR1A	4543	hgsc.bcm.edu	37	4	187455329	187455329	+	Silent	SNP	G	G	A	rs8192549	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	13	83	0	0.2	0	G|0.977;A|0.023	0.023	strong	.	MTNR1A	46	.	NM_005958	exon2	c.C567T	p.I189I	CACGGCGATGGTG	.	PASS	Atlas-SNP
ZBED4	9889	hgsc.bcm.edu	37	22	50277968	50277968	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	2	134	0	0.0181818	0	.	.	none	ZBED4,NS,carcinoma,0,1	ZBED4	102	1	NM_014838	exon2	c.G658T	p.D220Y	TCCCCCGATCGAA	.	scavenged	Atlas-SNP
HMG20A	10363	hgsc.bcm.edu	37	15	77750802	77750802	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	5	88	0	0.0793651	0	.	.	none	.	HMG20A	48	.	NM_018200	exon3	c.A53G	p.D18G	ATGAAGACGGTTC	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	117	230	1	0.485477	0.00434783	G|0.860;A|0.140	0.140	strong	HNF1A,brain,glioma,0,4	HNF1A	302	4	NM_000545	exon8	c.G1545A	p.T515T	CCACACGGGCCTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679809	100679809	+	Silent	SNP	C	C	T	rs4992074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	186	146	1	0.994652	0.00684932	C|0.823;T|0.177	0.177	strong	.	MUC17	804	.	NM_001040105	exon3	c.C5112T	p.S1704S	GGCCAGCTCTGCA	.	PASS	Atlas-SNP
CP	1356	hgsc.bcm.edu	37	3	148904434	148904434	+	Silent	SNP	T	T	G	rs1053709	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	137	288	0	0.520913	0	T|0.962;G|0.038	0.038	strong	.	CP	112	.	NM_000096	exon11	c.A1950C	p.G650G	CTCATTTCCGGCG	.	PASS	Atlas-SNP
GUCA1C	9626	hgsc.bcm.edu	37	3	108639384	108639384	+	Missense_Mutation	SNP	T	T	C	rs6804162	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	318	315	362	0	0.990566	0	T|0.647;C|0.353	0.353	strong	.	GUCA1C	39	.	NM_005459	exon2	c.A253G	p.M85V	CTTGCATGATTAG	.	PASS	Atlas-SNP
FAM189A1	23359	hgsc.bcm.edu	37	15	29416901	29416901	+	Missense_Mutation	SNP	A	A	G	rs2279482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	26	48	0	0.8125	0	A|0.843;G|0.157	0.157	strong	.	FAM189A1	20	.	NM_015307	exon10	c.T1292C	p.V431A	CCAGGCACAGCCT	.	PASS	Atlas-SNP
KHSRP	8570	hgsc.bcm.edu	37	19	6416627	6416627	+	Silent	SNP	C	C	T	rs149214856	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	74	139	1	0.587302	0.00719424	C|0.998;T|0.002	0.002	strong	KHSRP,NS,carcinoma,-1,1	KHSRP	51	1	NM_003685	exon14	c.G1362A	p.T454T	GGCTCCCGTCTGC	.	scavenged	Atlas-SNP
PPYR1	5540	hgsc.bcm.edu	37	10	47087609	47087609	+	Missense_Mutation	SNP	G	G	A	rs79871698	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	16	67	0	0.216216	0	G|0.938;A|0.062	0.062	strong	.	PPYR1	54	.	NM_005972	exon3	c.G826A	p.V276M	TTTGCTGTGCTCT	.	PASS	Atlas-SNP
ZNF649	65251	hgsc.bcm.edu	37	19	52394736	52394736	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	354	5	354	5	0.0141243	0.0141243	.	.	none	ZNF649,NS,carcinoma,0,2	ZNF649	72	2	NM_023074	exon5	c.A653G	p.K218R	CTGTACTTCTTGT	.	scavenged	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100803982	100803982	+	Silent	SNP	C	C	T	rs79213484	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211	56	126	0	0.265403	0	C|0.983;T|0.017	0.017	strong	.	ARHGAP42	32	.	NM_152432	exon7	c.C693T	p.N231N	GTTCAACTTGCAG	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109367844	109367844	+	Missense_Mutation	SNP	T	T	G	rs2693126		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1919	20	1915	10	0.0104221	0.00522193	.	.	weak	RANBP2_ENST00000283195,NS,carcinoma,0,6	RANBP2	488	6	NM_006267	exon10	c.T1398G	p.H466Q	GCCCCATGAAACC	.	scavenged	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228135631	228135631	+	Missense_Mutation	SNP	C	C	T	rs28381984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	59	145	0	0.766234	0	C|0.604;T|0.396	0.396	strong	COL4A3_ENST00000328380,NS,carcinoma,-1,2	COL4A3	293	2	NM_000091	exon25	c.C1721T	p.P574L	GAACTCCGGGAGT	.	PASS	Atlas-SNP
CLHC1	130162	hgsc.bcm.edu	37	2	55449464	55449464	+	Silent	SNP	T	T	C	rs17852670	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	198	244	1	0.970588	0.00409836	T|0.796;C|0.204	0.204	strong	.	.	.	.	NM_152385	exon3	c.A84G	p.Q28Q	GTATCTTTGCACA	.	PASS	Atlas-SNP
THADA	63892	hgsc.bcm.edu	37	2	43625184	43625184	+	Missense_Mutation	SNP	T	T	A	rs33979934	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	101	203	1	0.487923	0.00492611	A|0.209;T|0.791	0.209	strong	THADA,NS,carcinoma,0,1	THADA	131	1	NM_001083953	exon29	c.A4153T	p.T1385S	ACAGAGTTCGAAT	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679760	100679760	+	Missense_Mutation	SNP	G	G	A	rs73168394	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	52	138	1	0.282609	0.00724638	G|0.989;A|0.011	0.011	strong	MUC17,caecum,carcinoma,0,2	MUC17	804	2	NM_001040105	exon3	c.G5063A	p.G1688E	CTGAAGGAAGAAC	.	scavenged	Atlas-SNP
COL21A1	81578	hgsc.bcm.edu	37	6	56035495	56035495	+	Silent	SNP	G	G	A	rs41271846	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	53	118	0	0.469027	0	G|0.997;A|0.003	0.003	strong	.	COL21A1	201	.	NM_030820	exon5	c.C978T	p.S326S	AATTACGCTGGTT	.	PASS	Atlas-SNP
CHRNA2	1135	hgsc.bcm.edu	37	8	27328511	27328511	+	Missense_Mutation	SNP	G	G	A	rs2472553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	81	180	0	0.385714	0	G|0.819;A|0.181	0.181	strong	.	CHRNA2	48	.	NM_000742	exon2	c.C65T	p.T22I	GCTGGGGTCAGAA	.	PASS	Atlas-SNP
ACAD9	28976	hgsc.bcm.edu	37	3	128627933	128627933	+	Silent	SNP	C	C	T	rs876755	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	60	160	0	0.444444	0	C|0.723;T|0.277	0.277	strong	.	ACAD9	51	.	NM_014049	exon14	c.C1476T	p.P492P	GCACCCCAGTCTT	.	PASS	Atlas-SNP
KRT76	51350	hgsc.bcm.edu	37	12	53164848	53164848	+	Silent	SNP	G	G	A	rs7313832	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	69	151	1	0.433962	0.00662252	G|0.510;A|0.490	0.490	strong	KRT76,NS,adenoma,0,1	KRT76	72	1	NM_015848	exon7	c.C1419T	p.N473N	CTTGACGTTCATC	.	scavenged	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32363816	32363816	+	Missense_Mutation	SNP	T	T	C	rs2076530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	33	61	0	0.4125	0	T|0.628;C|0.372	0.372	strong	.	BTNL2	50	.	NM_019602	exon5	c.A1078G	p.S360G	TCTTACTTACCAC	.	PASS	Atlas-SNP
NOD2	64127	hgsc.bcm.edu	37	16	50745583	50745583	+	Silent	SNP	T	T	G	rs1861759	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	86	106	0	0.966292	0	T|0.709;G|0.291	0.291	strong	.	NOD2	118	.	NM_022162	exon4	c.T1761G	p.R587R	GGTGCGTGCCAAA	.	PASS	Atlas-SNP
SYK	6850	hgsc.bcm.edu	37	9	93641175	93641175	+	Silent	SNP	C	C	T	rs2306041	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	89	216	0	0.505682	0	C|0.822;T|0.178	0.178	strong	.	SYK	132	.	NM_003177	exon11	c.C1521T	p.Y507Y	ACATTACGCCAAG	.	PASS	Atlas-SNP
CCDC79	283847	hgsc.bcm.edu	37	16	66812797	66812797	+	Silent	SNP	C	C	T	rs363162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	17	112	0	0.168317	0	C|0.441;T|0.559	0.559	strong	.	CCDC79	32	.	NM_001136505	exon10	c.G822A	p.T274T	AGTCTTCGTCACA	.	PASS	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27784497	27784497	+	Missense_Mutation	SNP	G	G	A	rs117316062	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	34	40	0	0.576271	0	G|0.983;A|0.017	0.017	strong	.	KIAA0556	348	.	NM_015202	exon23	c.G4276A	p.E1426K	TATGACGAGCGAG	.	PASS	Atlas-SNP
IGFN1	91156	hgsc.bcm.edu	37	1	201183424	201183424	+	Missense_Mutation	SNP	G	G	A	rs41304263	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	84	97	0	0.661417	0	G|0.960;A|0.040	0.040	strong	.	IGFN1	220	.	NM_001164586	exon13	c.G8848A	p.V2950I	GATGGCGTCAAGG	.	PASS	Atlas-SNP
EEPD1	80820	hgsc.bcm.edu	37	7	36327317	36327317	+	Missense_Mutation	SNP	C	C	T	rs196594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	154	190	0	0.618474	0	C|0.925;T|0.075	0.075	strong	.	EEPD1	47	.	NM_030636	exon6	c.C1246T	p.P416S	GAGAATCCCAGCA	.	PASS	Atlas-SNP
PTPN23	25930	hgsc.bcm.edu	37	3	47453659	47453659	+	Silent	SNP	G	G	T	rs147959396	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259	140	175	0	0.540541	0	G|0.997;T|0.003	0.003	strong	.	PTPN23	85	.	NM_015466	exon22	c.G4149T	p.P1383P	GCGGCCGCTGCAC	.	PASS	Atlas-SNP
OLFML2B	25903	hgsc.bcm.edu	37	1	161993192	161993192	+	Missense_Mutation	SNP	T	T	C	rs12130792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	72	167	0	0.313043	0	T|0.895;C|0.105	0.105	strong	.	OLFML2B	114	.	NM_015441	exon1	c.A29G	p.Y10C	GCGAAGTAGAGAA	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215848641	215848641	+	Silent	SNP	T	T	C	rs2797235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268	265	214	1	0.988806	0.0046729	T|0.265;C|0.735	0.735	strong	USH2A,NS,carcinoma,0,1	USH2A	1168	1	NM_206933	exon63	c.A12612G	p.T4204T	CTGGATTGTCTGA	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13445208	13445208	+	Silent	SNP	C	C	T	rs2248069	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	123	139	1	0.991935	0.00719424	C|0.375;T|0.625	0.625	strong	.	CACNA1A	715	.	NM_001127221	exon8	c.G1182A	p.E394E	GATCCACTCCATG	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91811749	91811749	+	Silent	SNP	G	G	A	rs3743444	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	64	196	0	0.673684	0	G|0.848;A|0.152	0.152	strong	.	SV2B	98	.	NM_014848	exon10	c.G1287A	p.V429V	GAAGGTGTTTTTT	.	PASS	Atlas-SNP
TEPP	374739	hgsc.bcm.edu	37	16	58019396	58019396	+	Missense_Mutation	SNP	G	G	A	rs9934227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	212	253	1	0.990654	0.00395257	G|0.164;A|0.836	0.836	strong	.	TEPP	30	.	NM_199046	exon6	c.G779A	p.S260N	GCCTCAGCCAGAA	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140503155	140503155	+	Silent	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252	4	251	0	0.015873	0	.	.	none	PCDHB4,caecum,carcinoma,+1,1	PCDHB4	177	1	NM_018938	exon1	c.G1575T	p.A525A	GCAGGCGTTCGAG	.	scavenged	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549264	158549264	+	Silent	SNP	G	G	A	rs863360	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	460	247	354	3	0.536957	0.00847458	G|0.489;A|0.511	0.511	strong	OR10X1,NS,carcinoma,0,1	OR10X1	96	1	NM_001004477	exon1	c.C426T	p.I142I	GTTACAGATGGCC	.	scavenged	Atlas-SNP
ZNF454	285676	hgsc.bcm.edu	37	5	178391860	178391860	+	Missense_Mutation	SNP	G	G	A	rs6867221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	83	182	1	0.549669	0.00549451	G|0.733;A|0.267	0.267	strong	.	ZNF454	99	.	NM_001178089	exon5	c.G455A	p.C152Y	AGGAATGTGATGA	.	PASS	Atlas-SNP
CDCA2	157313	hgsc.bcm.edu	37	8	25364331	25364331	+	Missense_Mutation	SNP	G	G	A	rs4872318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	38	45	0	0.633333	0	G|0.761;A|0.239	0.239	strong	.	CDCA2	78	.	NM_152562	exon15	c.G2149A	p.V717I	GCTTCTGTAACTG	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249605	71249605	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	13	129	0	0.0955882	0	.	.	none	.	KRTAP5-8	28	.	NM_021046	exon1	c.C504T	p.C168C	CTGCTGCAAGCCC	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72358722	72358722	+	Missense_Mutation	SNP	T	T	C	rs28933375	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	59	124	0	0.766234	0	T|0.994;C|0.006	0.006	strong	.	PRF1	64	.	NM_001083116	exon3	c.A755G	p.N252S	ACCTCGTTGTCCG	.	PASS	Atlas-SNP
KIAA1009	22832	hgsc.bcm.edu	37	6	84904604	84904604	+	Missense_Mutation	SNP	G	G	C	rs17790493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	63	211	0	0.45	0	G|0.983;C|0.017	0.017	strong	KIAA1009,NS,carcinoma,0,1	KIAA1009	119	1	NM_014895	exon10	c.C1025G	p.S342C	TTACCAGATTCCA	.	PASS	Atlas-SNP
DHRS4L1	728635	hgsc.bcm.edu	37	14	24517940	24517940	+	Silent	SNP	T	T	C	rs200157408		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1886	474	1050	0	0.251326	0	.	.	weak	.	.	.	.	NM_001082488	exon8	c.T595C	p.L199L	AAGACCTTGGCCA	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48603503	48603503	+	Missense_Mutation	SNP	C	C	T	rs9890721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	62	118	0	0.488189	0	C|0.507;N|0.000	.	strong	.	MYCBPAP	135	.	NM_032133	exon14	c.C2173T	p.R725W	CCTCAGCGGAAGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678740	100678740	+	Missense_Mutation	SNP	T	T	C	rs4269454	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	223	180	1	0.952991	0.00555556	T|0.821;C|0.179	0.179	strong	.	MUC17	804	.	NM_001040105	exon3	c.T4043C	p.L1348P	CCACACTGGTGGC	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102567207	102567207	+	Missense_Mutation	SNP	T	T	A	rs1276286	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	254	67	194	1	0.26378	0.00515464	T|0.600;A|0.400	0.400	strong	MMP27,NS,carcinoma,0,1	MMP27	84	1	NM_022122	exon6	c.A797T	p.E266V	GCAGGTTCCTTAG	.	scavenged	Atlas-SNP
PCDHA12	56137	hgsc.bcm.edu	37	5	140256920	140256920	+	Silent	SNP	G	G	C	rs115718636	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298	150	368	1	0.503356	0.00271739	G|0.959;C|0.041	0.041	strong	PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	NM_018903	exon1	c.G1863C	p.P621P	CATCCCGTTCCAC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47851796	47851796	+	Silent	SNP	G	G	A	rs9983522	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	38	44	0	0.678571	0	G|0.887;A|0.113	0.113	strong	.	PCNT	283	.	NM_006031	exon38	c.G8418A	p.A2806A	GCAAGCGATGCTT	.	PASS	Atlas-SNP
C15orf41	84529	hgsc.bcm.edu	37	15	36989578	36989578	+	Silent	SNP	C	C	T	rs117638434	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	84	196	0	0.763636	0	C|0.992;T|0.008	0.008	strong	.	C15orf41	24	.	NM_001130010	exon8	c.C531T	p.N177N	GAAAAACCTGTCC	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062023	64062023	+	Missense_Mutation	SNP	A	A	C	rs10878073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	64	171	0	0.412903	0	A|0.717;C|0.283	0.283	strong	.	DPY19L2	97	.	NM_173812	exon1	c.T151G	p.S51A	TCCAGGAGCCCCT	.	PASS	Atlas-SNP
OR52A5	390054	hgsc.bcm.edu	37	11	5153261	5153261	+	Silent	SNP	A	A	G	rs2472530	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	55	130	0	0.462185	0	A|0.815;G|0.185	0.185	strong	.	OR52A5	80	.	NM_001005160	exon1	c.T612C	p.F204F	GGCAACAAATAGG	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128312463	128312463	+	Missense_Mutation	SNP	C	C	G	rs74343948	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	10	83	0	0.185185	0	C|0.884;G|0.116	0.116	strong	.	FAM71F2	19	.	NM_001012454	exon1	c.C12G	p.I4M	TAAAATCAGGGGC	.	PASS	Atlas-SNP
ZNF554	115196	hgsc.bcm.edu	37	19	2834808	2834808	+	Silent	SNP	T	T	C	rs8102063	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	24	65	0	0.333333	0	C|0.395;N|0.000	0.395	strong	.	ZNF554	47	.	NM_001102651	exon5	c.T1575C	p.C525C	TGACTGTGGGAAA	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112309230	112309230	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	4	132	0	0.045977	0	.	.	none	.	DDX20	50	.	NM_007204	exon11	c.C2184T	p.S728S	GGCTAGCCAGAGA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129903465	129903465	+	Silent	SNP	A	A	G	rs2857028	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	322	179	296	0	0.555901	0	T|0.007;G|0.212	0.212	strong	.	MKI67	363	.	NM_002417	exon13	c.T6639C	p.H2213H	TTTCTCATGAGTC	.	PASS	Atlas-SNP
POLD1	5424	hgsc.bcm.edu	37	19	50905042	50905042	+	Silent	SNP	G	G	A	rs20582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	30	92	0	0.625	0	A|0.170;G|0.829;T|0.000	0.170	strong	.	POLD1	174	.	NM_002691	exon4	c.G324A	p.A108A	CCCAGCGCAGCCT	.	PASS	Atlas-SNP
ZMYM5	9205	hgsc.bcm.edu	37	13	20413021	20413021	+	Missense_Mutation	SNP	T	T	C	rs41292167	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	96	271	0	0.413793	0	T|0.903;C|0.097	0.097	strong	.	ZMYM5	73	.	NM_001039650	exon5	c.A691G	p.T231A	GGGCTGTAGGCTG	.	PASS	Atlas-SNP
OR51A2	401667	hgsc.bcm.edu	37	11	4976291	4976291	+	Missense_Mutation	SNP	G	G	A	rs55889636	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	521	161	38	1	0.309021	0.0263158	G|0.661;A|0.339	0.339	strong	OR51A2,NS,carcinoma,0,1	OR51A2	40	1	NM_001004748	exon1	c.C653T	p.S218F	GTGTAAGACACAG	.	scavenged	Atlas-SNP
OR5L2	26338	hgsc.bcm.edu	37	11	55594868	55594868	+	Silent	SNP	C	C	T	rs150337368		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	4	242	0	0.0158103	0	C|1.000;T|0.000	0.000	weak	OR5L2,right_upper_lobe,carcinoma,0,1	OR5L2	135	1	NM_001004739	exon1	c.C174T	p.P58P	CACCCCCGTGTAC	.	scavenged	Atlas-SNP
PKD2L1	9033	hgsc.bcm.edu	37	10	102089663	102089663	+	Missense_Mutation	SNP	C	C	T	rs569511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	108	255	1	0.666667	0.00392157	C|0.882;T|0.118	0.118	strong	.	PKD2L1	103	.	NM_001253837	exon1	c.G35A	p.C12Y	GCTGGACACCTGG	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82837631	82837631	+	Missense_Mutation	SNP	G	G	T	rs160277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	40	82	0	0.519481	0	G|0.618;T|0.382	0.382	strong	.	VCAN	498	.	NM_004385	exon8	c.G8809T	p.D2937Y	AAAACCGATGGTC	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3886721	3886721	+	Silent	SNP	C	C	A	rs3749350	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	70	146	0	0.518519	0	C|0.758;A|0.242	0.242	strong	.	LRRN1	82	.	NM_020873	exon2	c.C396A	p.T132T	GATTACCGAGATG	.	PASS	Atlas-SNP
ALPL	249	hgsc.bcm.edu	37	1	21894735	21894735	+	Missense_Mutation	SNP	T	T	C	rs3200254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	48	109	0	0.727273	0	A|0.131;C|0.169	0.169	strong	.	ALPL	50	.	NM_000478	exon7	c.T787C	p.Y263H	CCGAGATACAAGG	.	PASS	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	7170006	7170006	+	Missense_Mutation	SNP	G	G	A	rs7022348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	58	155	0	0.522523	0	G|0.846;A|0.154	0.154	strong	.	KDM4C	186	.	NM_001146694	exon21	c.G3110A	p.S1037N	AAAAAAGCCAATG	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46847364	46847364	+	Missense_Mutation	SNP	C	C	A	rs2032844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	315	150	327	1	0.47619	0.0030581	C|0.755;A|0.245	0.245	strong	.	TTLL6	113	.	NM_001130918	exon14	c.G2136T	p.E712D	ACTGTACTCAGAG	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2558186	2558186	+	Silent	SNP	G	G	A	rs1544514	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	47	164	0	0.47	0	G|0.860;A|0.140	0.140	strong	CACNA1C_ENST00000344100,colon,carcinoma,+1,2	CACNA1C	1023	2	NM_001129831	exon4	c.G522A	p.A174A	GGAAGCGTTTTTA	.	PASS	Atlas-SNP
OR5K4	403278	hgsc.bcm.edu	37	3	98073313	98073313	+	Missense_Mutation	SNP	A	A	G	rs9822460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	90	144	0	0.573248	0	A|0.782;G|0.218	0.218	strong	.	OR5K4	75	.	NM_001005517	exon1	c.A616G	p.I206V	ATACCAATTCAAA	.	PASS	Atlas-SNP
RBM48	84060	hgsc.bcm.edu	37	7	92158154	92158154	+	Silent	SNP	G	G	A	rs117787377	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	167	172	0	0.62782	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_032120	exon1	c.G27A	p.G9G	GCTAGGGAGTTTA	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	37	16	81929488	81929488	+	Silent	SNP	C	C	T	rs1143688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	108	133	1	0.892562	0.0075188	C|0.594;N|0.000	.	strong	.	PLCG2	276	.	NM_002661	exon13	c.C1149T	p.D383D	GTTTGACGACGTC	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89424765	89424765	+	Missense_Mutation	SNP	C	C	T	rs140982817	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	21	112	0	0.3	0	C|0.998;T|0.002	0.002	strong	HAPLN3,caecum,carcinoma,0,1	HAPLN3	43	1	NM_178232	exon3	c.G316A	p.G106R	TCAGCCCGATGGC	.	PASS	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31347399	31347399	+	Missense_Mutation	SNP	C	C	T	rs4949184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	37	129	0	0.72549	0	C|0.795;T|0.205	0.205	strong	.	SDC3	45	.	NM_014654	exon4	c.G907A	p.D303N	GCTCATCCCGGAT	.	PASS	Atlas-SNP
IFNA21	3452	hgsc.bcm.edu	37	9	21166423	21166423	+	Silent	SNP	C	C	T	rs1053884	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	121	243	0	0.521552	0	C|0.996;T|0.004	0.004	strong	.	IFNA21	25	.	NM_002175	exon1	c.G189A	p.Q63Q	CTCCTCCTGGGGG	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	37	11	4825225	4825225	+	Missense_Mutation	SNP	A	A	G	rs7941731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	36	78	0	0.473684	0	A|0.629;G|0.371	0.371	strong	.	OR52R1	81	.	NM_001005177	exon1	c.T386C	p.I129T	AAGCAGATAGCCA	.	PASS	Atlas-SNP
SCEL	8796	hgsc.bcm.edu	37	13	78188078	78188078	+	Missense_Mutation	SNP	A	A	G	rs8002725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	113	242	1	0.530516	0.00413223	A|0.790;G|0.209	0.209	strong	.	SCEL	85	.	NM_144777	exon24	c.A1439G	p.K480R	CTGTCAAAAACAC	.	PASS	Atlas-SNP
GGT5	2687	hgsc.bcm.edu	37	22	24628928	24628928	+	Silent	SNP	G	G	A	rs762276	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	24	67	0	0.585366	0	G|0.864;A|0.136	0.136	strong	.	GGT5	61	.	NM_001099781	exon4	c.C459T	p.R153R	GCCATGGCGGCGG	.	PASS	Atlas-SNP
SIM2	6493	hgsc.bcm.edu	37	21	38117040	38117040	+	Silent	SNP	G	G	A	rs2073416	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	31	68	0	0.344444	0	G|0.736;A|0.264	0.264	strong	.	SIM2	55	.	NM_005069	exon10	c.G1179A	p.S393S	CAGCTCGTTCCAA	.	PASS	Atlas-SNP
FAM47E-STBD1	0	hgsc.bcm.edu	37	4	77192868	77192868	+	Missense_Mutation	SNP	G	G	A	rs3733250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	119	130	0	0.991667	0	G|0.650;A|0.350	0.350	strong	.	.	.	.	NM_001242939	exon5	c.G817A	p.E273K	CTGCAGGAGACAG	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	21145648	21145648	+	Silent	SNP	C	C	T	rs11074483	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	30	85	0	0.375	0	C|0.759;T|0.241	0.241	strong	DNAH3_ENST00000261383,NS,carcinoma,0,2	DNAH3	1142	2	NM_017539	exon7	c.G1014A	p.K338K	GTTCCACTTCTTG	.	PASS	Atlas-SNP
ART5	116969	hgsc.bcm.edu	37	11	3659993	3659993	+	Missense_Mutation	SNP	G	G	T	rs2271586	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	66	126	0	0.511628	0	G|0.689;T|0.311	0.311	strong	.	ART5	38	.	NM_053017	exon4	c.C851A	p.T284K	CTCTTCGTCATAT	.	PASS	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159398633	159398633	+	Silent	SNP	T	T	C	rs3756988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	76	200	0	0.469136	0	T|0.844;C|0.156	0.156	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon8	c.A1620G	p.E540E	TAAGAGTTCTCTC	.	PASS	Atlas-SNP
HACE1	57531	hgsc.bcm.edu	37	6	105198267	105198267	+	Silent	SNP	A	A	G	rs7752614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	78	202	2	0.438202	0.00990099	A|0.805;G|0.195	0.195	strong	HACE1,NS,adenoma,0,1	HACE1	96	1	NM_020771	exon20	c.T2292C	p.F764F	CATATGAAAGCCC	.	scavenged	Atlas-SNP
MASP1	5648	hgsc.bcm.edu	37	3	186953808	186953808	+	Silent	SNP	C	C	T	rs850312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	41	90	0	0.539474	0	T|0.232;G|0.004	0.232	strong	MASP1_ENST00000296280,NS,carcinoma,0,1	MASP1	240	1	NM_139125	exon11	c.G1851A	p.L617L	ATACTGCAGGACA	.	PASS	Atlas-SNP
NIPAL1	152519	hgsc.bcm.edu	37	4	48037926	48037926	+	Missense_Mutation	SNP	A	A	G	rs13116684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	343	172	360	0	0.501458	0	A|0.792;G|0.208	0.208	strong	.	NIPAL1	29	.	NM_207330	exon6	c.A970G	p.I324V	TCTGCCATCTTAT	.	PASS	Atlas-SNP
ZNF679	168417	hgsc.bcm.edu	37	7	63726993	63726993	+	Missense_Mutation	SNP	G	G	A	rs10949885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	45	61	0	0.642857	0	G|0.853;A|0.147	0.147	strong	.	ZNF679	80	.	NM_153363	exon5	c.G982A	p.E328K	TGTGAAGAATGTG	.	PASS	Atlas-SNP
RTP2	344892	hgsc.bcm.edu	37	3	187419816	187419816	+	Missense_Mutation	SNP	T	T	C	rs61754877	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	124	264	1	0.469697	0.00378788	T|0.832;C|0.168	0.168	strong	.	RTP2	38	.	NM_001004312	exon1	c.A101G	p.N34S	TTGAGGTTGGGGT	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197432036	197432036	+	Missense_Mutation	SNP	C	C	T	rs61743568	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	45	63	0	0.661765	0	C|0.929;T|0.071	0.071	strong	.	KIAA0226	136	.	NM_014687	exon3	c.G230A	p.R77H	GTCTGGCGGCGGC	.	PASS	Atlas-SNP
ZNF543	125919	hgsc.bcm.edu	37	19	57838018	57838018	+	Missense_Mutation	SNP	C	C	G	rs6510057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	43	123	0	0.434343	0	C|0.496;G|0.504	0.504	strong	.	ZNF543	61	.	NM_213598	exon3	c.C163G	p.P55A	TTCAAACCAGAGC	.	PASS	Atlas-SNP
OR6F1	343169	hgsc.bcm.edu	37	1	247875608	247875608	+	Silent	SNP	C	C	G	rs6587382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	89	101	1	0.669173	0.00990099	C|0.661;G|0.339	0.339	strong	OR6F1,NS,carcinoma,-2,3	OR6F1	88	3	NM_001005286	exon1	c.G450C	p.V150V	ACCACACACCCAG	.	scavenged	Atlas-SNP
ALG12	79087	hgsc.bcm.edu	37	22	50301476	50301476	+	Silent	SNP	T	T	C	rs8135963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	69	163	0	0.511111	0	T|0.617;C|0.383	0.383	strong	ALG12,NS,carcinoma,0,1	ALG12	35	1	NM_024105	exon7	c.A885G	p.A295A	GCCCAGTGCCAGC	.	PASS	Atlas-SNP
ALX4	60529	hgsc.bcm.edu	37	11	44296946	44296946	+	Silent	SNP	C	C	T	rs11037928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	74	174	1	0.451219	0.00574713	C|0.915;T|0.085	0.085	strong	ALX4,NS,carcinoma,-1,1	ALX4	58	1	NM_021926	exon2	c.G729A	p.A243A	TTCCCGCGCATAC	.	scavenged	Atlas-SNP
CAPN3	825	hgsc.bcm.edu	37	15	42702836	42702836	+	Silent	SNP	C	C	T	rs147774793	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	20	116	0	0.224719	0	C|0.999;T|0.001	0.001	strong	.	CAPN3	172	.	NM_000070	exon21	c.C2235T	p.Y745Y	CAGCTACGAGATG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284854	152284854	+	Silent	SNP	A	A	G	rs3120653	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	449	147	360	1	0.327394	0.00277778	A|0.687;G|0.313	0.313	strong	FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.T2508C	p.D836D	CTGACCATCTTGG	.	PASS	Atlas-SNP
ZBTB46	140685	hgsc.bcm.edu	37	20	62407104	62407104	+	Silent	SNP	C	C	T	rs3827026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	60	152	0	0.444444	0	C|0.909;T|0.091	0.091	strong	.	ZBTB46	72	.	NM_025224	exon3	c.G1149A	p.L383L	GGCCTTCAGCGAC	.	PASS	Atlas-SNP
KANK4	163782	hgsc.bcm.edu	37	1	62703977	62703977	+	Missense_Mutation	SNP	G	G	A	rs34591898	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	72	350	0	0.272727	0	G|0.975;A|0.025	0.025	strong	KANK4,bladder,carcinoma,-1,2	KANK4	135	2	NM_181712	exon10	c.C2960T	p.A987V	TGCTCCGCGTGGG	.	PASS	Atlas-SNP
TNFSF11	8600	hgsc.bcm.edu	37	13	43148565	43148565	+	Silent	SNP	T	T	C	rs2296533	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	9	13	0	0.375	0	T|0.545;C|0.455	0.455	strong	.	TNFSF11	43	.	NM_003701	exon1	c.T126C	p.P42P	GCCCCCTGCCGCC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777502	52777502	+	Silent	SNP	A	A	G	rs1945297	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	71	211	0	0.387978	0	A|0.586;G|0.414	0.414	strong	.	KRT84	61	.	NM_033045	exon2	c.T627C	p.N209N	CTCCAGATTGCTC	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	37	2	220285309	220285309	+	Silent	SNP	C	C	T	rs1058261	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	95	159	0	0.785124	0	C|0.634;T|0.366	0.366	strong	.	DES	53	.	NM_001927	exon4	c.C828T	p.D276D	CAGGGACATCCGG	.	PASS	Atlas-SNP
ZNF777	27153	hgsc.bcm.edu	37	7	149129829	149129829	+	Missense_Mutation	SNP	C	C	T	rs17852167	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	50	78	0	1	0	C|0.898;T|0.102	0.102	strong	.	ZNF777	63	.	NM_015694	exon6	c.G1534A	p.A512T	TCACTGCGGGGTT	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43237016	43237016	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	4	178	1	0.0246914	0.00561798	.	.	none	PSG3,caecum,carcinoma,0,1	PSG3	82	1	NM_021016	exon3	c.A629G	p.Y210C	GCAGTGTACTTTG	.	scavenged	Atlas-SNP
AIM1L	55057	hgsc.bcm.edu	37	1	26650661	26650661	+	Silent	SNP	A	A	G	rs41305769	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	14	114	0	0.28	0	A|0.972;G|0.028	0.028	strong	.	AIM1L	98	.	NM_001039775	exon18	c.T4719C	p.D1573D	CAGCCCATCCTCG	.	PASS	Atlas-SNP
ACSM4	341392	hgsc.bcm.edu	37	12	7463241	7463241	+	Silent	SNP	A	A	T	rs7968241	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	96	77	0	0.989691	0	A|0.570;T|0.430	0.430	strong	.	ACSM4	98	.	NM_001080454	exon3	c.A519T	p.P173P	GGCCCCAGCGGTG	.	PASS	Atlas-SNP
CIAPIN1	57019	hgsc.bcm.edu	37	16	57464236	57464236	+	Silent	SNP	G	G	A	rs170358	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	82	141	0	0.845361	0	G|0.978;A|0.022	0.022	strong	CIAPIN1,colon,carcinoma,-1,1	CIAPIN1	17	1	NM_020313	exon8	c.C762T	p.A254A	TTCTTCGGCAAGG	.	PASS	Atlas-SNP
NHSL1	57224	hgsc.bcm.edu	37	6	138745299	138745299	+	Silent	SNP	G	G	A	rs9495082	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	17	39	0	0.586207	0	G|0.893;A|0.107	0.107	strong	.	NHSL1	99	.	NM_020464	exon7	c.C4752T	p.P1584P	AGGGCCGGGGGCC	.	PASS	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20296004	20296004	+	Missense_Mutation	SNP	C	C	T	rs2318279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	467	260	876	1	0.556745	0.00114155	C|0.753;T|0.247	0.247	strong	OR4N2,NS,carcinoma,0,1	OR4N2	125	1	NM_001004723	exon1	c.C397T	p.P133S	CACTATCCTACTG	.	PASS	Atlas-SNP
MYO1G	64005	hgsc.bcm.edu	37	7	45015107	45015107	+	Silent	SNP	G	G	A	rs61738857	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	284	164	181	1	0.577465	0.00552486	G|0.831;A|0.169	0.169	strong	.	MYO1G	86	.	NM_033054	exon4	c.C540T	p.H180H	GTGGATGTGTCCT	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	37	15	101567971	101567971	+	Silent	SNP	C	C	T	rs41535348	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	31	183	0	0.24031	0	C|0.995;T|0.005	0.005	strong	.	LRRK1	310	.	NM_024652	exon19	c.C2655T	p.N885N	CGACAACGACATC	.	PASS	Atlas-SNP
NTN5	126147	hgsc.bcm.edu	37	19	49168005	49168005	+	Silent	SNP	G	G	A	rs17851884	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	96	116	0	0.648649	0	G|0.937;A|0.063	0.063	strong	.	NTN5	27	.	NM_145807	exon3	c.C651T	p.H217H	TCGGGCGTGCTGG	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13409407	13409407	+	Missense_Mutation	SNP	C	C	T	rs16024	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	58	141	0	0.47541	0	C|0.997;T|0.003	0.003	strong	.	CACNA1A	715	.	NM_001127221	exon19	c.G3043A	p.E1015K	CCCCCTCGTACGT	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183713573	183713573	+	Silent	SNP	C	C	T	rs80197208	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	25	189	0	0.240385	0	C|0.987;T|0.013	0.013	strong	.	.	.	.	NM_001080477	exon25	c.C5748T	p.N1916N	ATACAACCCCCCG	.	PASS	Atlas-SNP
RNF157	114804	hgsc.bcm.edu	37	17	74162548	74162548	+	Missense_Mutation	SNP	C	C	T	rs11539879	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	32	86	0	0.463768	0	C|0.968;T|0.032	0.032	strong	.	RNF157	66	.	NM_052916	exon6	c.G622A	p.G208R	CGTCTCCTTCATC	.	PASS	Atlas-SNP
TJP3	27134	hgsc.bcm.edu	37	19	3731985	3731985	+	Silent	SNP	G	G	A	rs1879040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	35	56	0	0.538462	0	G|0.686;A|0.314	0.314	strong	TJP3,colon,carcinoma,0,2	TJP3	79	2	NM_001267561	exon6	c.G693A	p.S231S	AGATTCGGGCCTG	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121208894	121208894	+	Missense_Mutation	SNP	T	T	C	rs3218636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	40	66	0	0.588235	0	T|0.970;C|0.030	0.030	strong	.	POLQ	273	.	NM_199420	exon16	c.A2884G	p.S962G	CTCTACTTTTATT	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169512120	169512120	+	Silent	SNP	G	G	A	rs6016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	241	206	1	1	0.00485437	G|0.758;A|0.242	0.242	strong	.	F5	301	.	NM_000130	exon13	c.C2208T	p.I736I	TGACCTGATTCCT	.	PASS	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20295778	20295778	+	Silent	SNP	C	C	A	rs11621883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	285	156	647	2	0.547368	0.00309119	A|0.114;C|0.886;T|0.000	0.114	strong	.	OR4N2	125	.	NM_001004723	exon1	c.C171A	p.A57A	CACAGCCCCCCTC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9070402	9070402	+	Missense_Mutation	SNP	G	G	T	rs12150888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	412	203	382	1	0.492718	0.0026178	G|0.815;T|0.185	0.185	strong	MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	NM_024690	exon3	c.C17044A	p.P5682T	TTACGGGCTCTGG	.	PASS	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	37	3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	rs7632072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	32	104	0	0.444444	0	A|0.950;G|0.050	0.050	strong	.	PARP14	242	.	NM_017554	exon6	c.A1891G	p.T631A	CCAAACACTGTAA	.	PASS	Atlas-SNP
SAA1	6288	hgsc.bcm.edu	37	11	18290866	18290866	+	Silent	SNP	T	T	C	rs71469385	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	57	100	18	0.419118	0.18	C|1.000;|0.000	1.000	weak	SAA1,NS,carcinoma,0,1	SAA1	14	1	NM_199161	exon3	c.T216C	p.A72A	CTGGGCTGCAGAA	.	scavenged	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236719135	236719135	+	Silent	SNP	T	T	C	rs1885532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	77	194	0	0.318182	0	T|0.153;C|0.847	0.847	strong	.	HEATR1	197	.	NM_018072	exon39	c.A5619G	p.E1873E	CAGGGCTTCCAGG	.	PASS	Atlas-SNP
THEM6	51337	hgsc.bcm.edu	37	8	143816828	143816828	+	Missense_Mutation	SNP	G	G	A	rs11540544	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	66	99	0	0.47482	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_016647	exon2	c.G598A	p.G200R	GAGAGTGGGCTCA	.	PASS	Atlas-SNP
CECR5	27440	hgsc.bcm.edu	37	22	17640045	17640045	+	Missense_Mutation	SNP	G	G	A	rs7287672	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4	4	1	0	1	0	G|0.785;A|0.215	0.215	strong	.	CECR5	46	.	NM_033070	exon1	c.C97T	p.R33C	ACCTGCGGGCGGG	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2721137	2721137	+	Silent	SNP	C	C	T	rs216008	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	64	190	0	0.418301	0	C|0.730;T|0.270	0.270	strong	Q6YL47_HUMAN,NS,carcinoma,+2,4	CACNA1C	1023	4	NM_199460	exon30	c.C3846T	p.F1282F	CCTCTTCACCGTG	.	PASS	Atlas-SNP
MYH7	4625	hgsc.bcm.edu	37	14	23902753	23902753	+	Silent	SNP	G	G	A	rs2069540	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	70	53	0	1	0	G|0.488;A|0.512	0.512	strong	.	MYH7	349	.	NM_000257	exon3	c.C189T	p.T63T	ATACTCGGTCTCG	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156884584	156884584	+	Silent	SNP	C	C	T	rs56260937	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	148	113	0	0.993289	0	C|0.824;T|0.176	0.176	strong	PEAR1,colon,carcinoma,+2,1	PEAR1	118	1	NM_001080471	exon23	c.C3108T	p.D1036D	CCAGGACCGTTGA	.	PASS	Atlas-SNP
DYDC2	84332	hgsc.bcm.edu	37	10	82126541	82126541	+	Missense_Mutation	SNP	C	C	G	rs36027713	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	55	171	0	0.714286	0	C|0.982;G|0.018	0.018	strong	DYDC2,NS,carcinoma,+1,1	DYDC2	18	1	NM_001270042	exon4	c.C410G	p.P137R	TCCTGCCAGGTAC	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187088903	187088903	+	Silent	SNP	C	C	A	rs1533595	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	47	138	0	0.447619	0	C|0.669;A|0.331	0.331	strong	.	RTP4	20	.	NM_022147	exon2	c.C483A	p.I161I	GGGCATCTGTGGA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388635	1388635	+	Silent	SNP	T	T	C	rs74518227	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	80	147	1	0.747664	0.00680272	T|0.937;C|0.063	0.063	strong	CRIPAK,rectum,carcinoma,0,4	CRIPAK	185	4	NM_175918	exon1	c.T336C	p.C112C	CCCATGTGGAGTG	.	PASS	Atlas-SNP
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150167	39150167	+	Silent	SNP	G	G	A	rs12452295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	352	186	332	0	0.528409	0	G|0.777;A|0.223	0.223	strong	KRTAP3-3,NS,carcinoma,0,1	KRTAP3-3	11	1	NM_033185	exon1	c.C183T	p.C61C	GGGCACGCAGGGC	.	PASS	Atlas-SNP
ACAA2	10449	hgsc.bcm.edu	37	18	47318626	47318626	+	Missense_Mutation	SNP	T	T	C	rs11549285	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	87	176	0	0.517857	0	T|0.970;C|0.030	0.030	strong	.	ACAA2	29	.	NM_006111	exon6	c.A649G	p.M217V	CCTGCATTGTCTG	.	PASS	Atlas-SNP
CCP110	9738	hgsc.bcm.edu	37	16	19548152	19548152	+	Silent	SNP	T	T	C	rs179050	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	106	220	1	0.507177	0.00454545	T|0.896;C|0.104	0.104	strong	CCP110,NS,adenoma,0,1	CCP110	57	1	NM_001199022	exon4	c.T1161C	p.H387H	GTGTCATATACTT	.	PASS	Atlas-SNP
NEBL	10529	hgsc.bcm.edu	37	10	21108377	21108377	+	Silent	SNP	C	C	T	rs1006363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	115	197	1	0.746753	0.00507614	C|0.789;T|0.211	0.211	strong	.	NEBL	199	.	NM_006393	exon20	c.G2031A	p.R677R	GTTTCGCCTCACT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149515796	149515796	+	Silent	SNP	C	C	T	rs1557956	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	4	51	0	0.108108	0	C|0.816;T|0.184	0.184	strong	.	.	.	.	NM_198455	exon83	c.C11697T	p.P3899P	GGACCCCGCTCGC	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878589	190878589	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	524	46	553	0	0.0877863	0	.	.	none	FRG1,NS,carcinoma,0,1	FRG1	76	1	NM_004477	exon6	c.A469G	p.I157V	TGCTTTATTAGAT	.	PASS	Atlas-SNP
AKR1C3	8644	hgsc.bcm.edu	37	10	5136651	5136651	+	Missense_Mutation	SNP	C	C	G	rs12529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	119	167	1	0.983471	0.00598802	C|0.511;G|0.489	0.489	strong	.	AKR1C3	21	.	NM_001253909	exon1	c.C15G	p.H5Q	CAAACACCAGTGT	.	PASS	Atlas-SNP
ACP2	53	hgsc.bcm.edu	37	11	47270255	47270255	+	Missense_Mutation	SNP	C	C	T	rs2167079	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	65	156	0	0.496183	0	C|0.559;T|0.441	0.441	strong	.	ACP2	36	.	NM_001610	exon1	c.G86A	p.R29Q	CGGGCCCGGGTGG	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790396	4790396	+	Missense_Mutation	SNP	G	G	A	rs17324609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	95	169	0	0.519126	0	G|0.915;A|0.085	0.085	strong	.	OR51F1	60	.	NM_001004752	exon1	c.C752T	p.A251V	AAGAAAGCAACTG	.	PASS	Atlas-SNP
KANK1	23189	hgsc.bcm.edu	37	9	712137	712137	+	Silent	SNP	G	G	C	rs912175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	34	58	3	0.566667	0.0517241	G|0.771;C|0.229	0.229	strong	KANK1,NS,carcinoma,0,1	KANK1	231	1	NM_001256876	exon7	c.G1371C	p.L457L	TGAGCTGCAACAG	.	scavenged	Atlas-SNP
OR4D1	26689	hgsc.bcm.edu	37	17	56232675	56232675	+	Missense_Mutation	SNP	G	G	A	rs12602205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	59	151	0	0.472	0	G|0.932;A|0.068	0.068	strong	.	OR4D1	48	.	NM_012374	exon1	c.G161A	p.R54Q	ACTGCCGGCTCCA	.	PASS	Atlas-SNP
ZNF22	7570	hgsc.bcm.edu	37	10	45499272	45499272	+	Silent	SNP	C	C	G	rs3740092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	12	62	0	0.324324	0	C|0.960;G|0.040	0.040	strong	ZNF22,colon,carcinoma,0,1	ZNF22	28	1	NM_006963	exon2	c.C456G	p.S152S	GAGCTCCCACCTT	.	PASS	Atlas-SNP
EYA3	2140	hgsc.bcm.edu	37	1	28304899	28304899	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	40	253	0	0.258065	0	.	.	none	.	EYA3	38	.	NM_001990	exon17	c.A1627G	p.I543V	CTGCAATTTCTTC	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46652929	46652929	+	Silent	SNP	G	G	A	rs6008365	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	35	83	0	0.492958	0	G|0.739;A|0.261	0.261	strong	.	PKDREJ	195	.	NM_006071	exon1	c.C6291T	p.S2097S	ATACACGGACACA	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145508637	145508637	+	Silent	SNP	A	A	C	rs61732382	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	88	122	0	0.988764	0	A|0.808;C|0.192	0.192	strong	LARS,NS,carcinoma,0,1	LARS	100	1	NM_020117	exon26	c.T2673G	p.V891V	TTCATTAACAGGA	.	PASS	Atlas-SNP
KANSL2	54934	hgsc.bcm.edu	37	12	49061511	49061511	+	Missense_Mutation	SNP	T	T	C	rs17238800	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	44	73	0	0.52381	0	T|0.984;C|0.016	0.016	strong	.	.	.	.	NM_017822	exon7	c.A938G	p.N313S	GACTGATTGGAAC	.	PASS	Atlas-SNP
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58335626	58335626	+	Missense_Mutation	SNP	A	A	T	rs3751325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	31	78	0	0.418919	0	A|0.640;T|0.360	0.360	strong	XRCC6BP1,NS,carcinoma,0,1	XRCC6BP1	22	1	NM_033276	exon1	c.A142T	p.S48C	TTCACCAGCAACC	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777580	52777580	+	Silent	SNP	A	A	C	rs1613929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	43	122	0	0.387387	0	A|0.686;C|0.314	0.314	strong	.	KRT84	61	.	NM_033045	exon2	c.T549G	p.V183V	GAACCGAACCTAA	.	PASS	Atlas-SNP
GGA2	23062	hgsc.bcm.edu	37	16	23489711	23489711	+	Missense_Mutation	SNP	C	C	G	rs1135045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	104	130	0	1	0	C|0.272;G|0.728	0.728	strong	.	GGA2	49	.	NM_015044	exon13	c.G1270C	p.A424P	GCTGTGCTGAGAG	.	PASS	Atlas-SNP
ARSB	411	hgsc.bcm.edu	37	5	78135201	78135201	+	Silent	SNP	C	C	T	rs25413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	103	193	0	0.565934	0	C|0.727;T|0.273	0.273	strong	ARSB,NS,carcinoma,-1,1	ARSB	47	1	NM_198709	exon7	c.G1191A	p.P397P	GAAGTTCGGGTCA	.	PASS	Atlas-SNP
C20orf166	128826	hgsc.bcm.edu	37	20	61162267	61162267	+	Missense_Mutation	SNP	T	T	C	rs6062251	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20	7	37	0	0.35	0	T|0.451;C|0.549	0.549	strong	.	C20orf166	17	.	NM_178463	exon3	c.T80C	p.V27A	AGCAGGTGGCGCG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911124	29911124	+	Silent	SNP	C	C	T	rs3173418	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	70	200	0	0.421687	0	C|0.930;T|0.070	0.070	strong	.	HLA-A	89	.	NM_001242758	exon3	c.C423T	p.A141A	GGACGCCTACGAC	.	PASS	Atlas-SNP
KIAA1586	57691	hgsc.bcm.edu	37	6	56917538	56917538	+	Missense_Mutation	SNP	G	G	A	rs6926980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	19	47	0	0.358491	0	G|0.762;A|0.238	0.238	strong	.	KIAA1586	59	.	NM_020931	exon4	c.G241A	p.V81M	TTAAATGTGAAGA	.	PASS	Atlas-SNP
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077904	19077904	+	Missense_Mutation	SNP	T	T	G	rs11024970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	58	104	0	0.504348	0	T|0.899;G|0.101	0.101	strong	.	MRGPRX2	42	.	NM_054030	exon2	c.A46C	p.N16H	TTCCATTCACTGT	.	PASS	Atlas-SNP
TDRD10	126668	hgsc.bcm.edu	37	1	154516578	154516578	+	Missense_Mutation	SNP	G	G	A	rs3811448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	188	178	0	1	0	G|0.821;A|0.179	0.179	strong	.	TDRD10	48	.	NM_182499	exon9	c.G643A	p.V215I	ATGCACGTCACTG	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107049714	107049714	+	Missense_Mutation	SNP	C	C	G	rs79619029		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	845	364	751	3	0.430769	0.00399467	C|0.250;G|0.750	0.750	weak	RGPD3_ENST00000304514,right_upper_lobe,carcinoma,0,2	RGPD3	316	2	NM_001144013	exon16	c.G2233C	p.E745Q	GCATCTCTTTTAC	.	scavenged	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152529260	152529260	+	Silent	SNP	G	G	A	rs3798756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	52	117	0	0.536082	0	G|0.854;A|0.146	0.146	strong	.	SYNE1	3227	.	NM_182961	exon125	c.C22671T	p.I7557I	GTCAATGATCCCC	.	PASS	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17292074	17292074	+	Silent	SNP	G	G	C	rs28709752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	39	74	0	0.513158	0	G|0.846;C|0.154	0.154	strong	.	XYLT1	147	.	NM_022166	exon5	c.C1284G	p.P428P	CCTGATGGGGTAG	.	PASS	Atlas-SNP
GATAD2A	54815	hgsc.bcm.edu	37	19	19612027	19612027	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	226	108	228	1	0.477876	0.00438596	.	.	none	GATAD2A_ENST00000360315,colon,carcinoma,+2,2	GATAD2A	81	2	NM_017660	exon9	c.C1302T	p.G434G	GAGCGGCGCCATC	.	PASS	Atlas-SNP
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43816735	43816735	+	Missense_Mutation	SNP	G	G	C	rs200986004	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	660	101	775	0	0.15303	0	A|0.002;C|0.002;G|0.995	0.002	strong	CNTNAP3B,right_lower_lobe,carcinoma,-2,1	CNTNAP3B	37	1	NM_001201380	exon6	c.G841C	p.D281H	CTCCTCGACACGC	.	scavenged	Atlas-SNP
PTPN4	5775	hgsc.bcm.edu	37	2	120734589	120734589	+	Silent	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	51	119	0	0.383459	0	.	.	none	PTPN4,NS,carcinoma,+2,1	PTPN4	89	1	NM_002830	exon27	c.T2724A	p.I908I	AGCTATTTTGAAA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1269655	1269655	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	341	98	219	0	0.28739	0	.	.	none	.	MUC5B	473	.	NM_002458	exon31	c.T11545G	p.S3849A	ACCGGCTCTGTGG	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955885	57955885	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	3	239	2	0.0152284	0.0083682	.	.	none	ZNF749,right_upper_lobe,carcinoma,0,14	ZNF749	75	14	NM_001023561	exon3	c.C1369G	p.Q457E	CAGCACCAGAAAA	.	scavenged	Atlas-SNP
LMAN1L	79748	hgsc.bcm.edu	37	15	75113023	75113023	+	Silent	SNP	G	G	A	rs145422132	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	13	66	0	0.309524	0	G|0.980;A|0.020	0.020	strong	.	LMAN1L	43	.	NM_021819	exon8	c.G822A	p.R274R	GGCGAGGCAGCTG	.	PASS	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792171	8792171	+	Silent	SNP	T	T	C	rs11650737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	10	10	14	0	1	0	T|0.722;C|0.278	0.278	strong	PIK3R5,NS,carcinoma,0,1	PIK3R5	79	1	NM_001142633	exon10	c.A933G	p.L311L	CTGGAGTAGCTCC	.	scavenged	Atlas-SNP
RSC1A1	6248	hgsc.bcm.edu	37	1	15986547	15986547	+	Missense_Mutation	SNP	T	T	C	rs3766163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	19	93	0	0.306452	0	T|0.708;C|0.292	0.292	strong	.	RSC1A1	29	.	NM_006511	exon1	c.T184C	p.F62L	GCTGAATTCCAGC	.	PASS	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	37	5	96130836	96130836	+	Missense_Mutation	SNP	T	T	C	rs26618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	46	91	0	0.516854	0	T|0.783;C|0.217	0.217	strong	.	ERAP1	59	.	NM_001198541	exon5	c.A828G	p.I276M	TTGATTTATCTTG	.	PASS	Atlas-SNP
R3HDM4	91300	hgsc.bcm.edu	37	19	899444	899444	+	Silent	SNP	C	C	T	rs2965284	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	59	125	0	0.464567	0	C|0.877;T|0.123	0.123	strong	C19orf22,NS,carcinoma,0,1	.	.	1	NM_138774	exon7	c.G699A	p.S233S	ACTGGCCGAGATG	.	PASS	Atlas-SNP
MED12	9968	hgsc.bcm.edu	37	X	70351982	70351982	+	Silent	SNP	A	A	C	rs376058351		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	207	429	0	0.971831	0	.	.	weak	.	MED12	984	.	NM_005120	exon30	c.A4179C	p.S1393S	ACAGTCAGCAGAG	.	PASS	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41857303	41857303	+	Silent	SNP	T	T	C	rs2277536	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	32	67	0	0.680851	0	T|0.736;C|0.264	0.264	strong	.	TYRO3	169	.	NM_006293	exon6	c.T747C	p.A249A	AGGTGCTGATGGC	.	PASS	Atlas-SNP
MICAL2	9645	hgsc.bcm.edu	37	11	12229655	12229655	+	Silent	SNP	T	T	G	rs2279390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211	113	229	0	0.535545	0	G|0.341;N|0.000	0.341	strong	.	MICAL2	114	.	NM_014632	exon5	c.T558G	p.V186V	GAAGGTTCTAGAG	.	PASS	Atlas-SNP
FRMD1	79981	hgsc.bcm.edu	37	6	168479568	168479568	+	Silent	SNP	G	G	A	rs78152017	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	17	40	0	0.404762	0	G|0.913;A|0.087	0.087	strong	.	FRMD1	52	.	NM_024919	exon1	c.C207T	p.A69A	CCCCACGGCCAGC	.	PASS	Atlas-SNP
TEKT5	146279	hgsc.bcm.edu	37	16	10775855	10775855	+	Silent	SNP	G	G	A	rs71389065	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	67	164	2	0.443709	0.0121951	ATG|0.500;GTC|0.500	.	alt	TEKT5,pharynx,carcinoma,-2,1	TEKT5	66	1	NM_144674	exon4	c.C858T	p.D286D	CGTGCCGTCAATT	.	scavenged	Atlas-SNP
EVI5	7813	hgsc.bcm.edu	37	1	93073228	93073228	+	Missense_Mutation	SNP	C	C	A	rs11808092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	116	162	0	1	0	C|0.826;A|0.174	0.174	strong	.	EVI5	94	.	NM_005665	exon15	c.G1836T	p.Q612H	TTTCTCCTGTAGG	.	PASS	Atlas-SNP
CIB2	10518	hgsc.bcm.edu	37	15	78401620	78401620	+	Silent	SNP	C	C	T	rs77370542	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	16	186	1	0.186047	0.00537634	C|0.978;T|0.022	0.022	strong	CIB2,NS,carcinoma,-1,1	CIB2	24	1	NM_006383	exon4	c.G303A	p.S101S	GGGAGCCGACTCG	.	scavenged	Atlas-SNP
C1orf43	25912	hgsc.bcm.edu	37	1	154184993	154184993	+	Missense_Mutation	SNP	G	G	A	rs144385115	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	84	168	0	0.538462	0	G|0.994;A|0.006	0.006	strong	.	C1orf43	36	.	NM_001098616	exon5	c.C448T	p.R150C	CTTTGCGTACACC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179432185	179432185	+	Missense_Mutation	SNP	A	A	G	rs12463674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	50	109	0	0.454545	0	A|0.847;G|0.153	0.153	strong	.	TTN	18412	.	NM_001267550	exon326	c.T78674C	p.I26225T	CACTCAATGGTAG	.	PASS	Atlas-SNP
CTSW	1521	hgsc.bcm.edu	37	11	65650883	65650883	+	Silent	SNP	A	A	G	rs35841983	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	32	79	0	0.426667	0	A|0.975;G|0.025	0.025	strong	.	CTSW	18	.	NM_001335	exon9	c.A1008G	p.Q336Q	GGCCCAATGGGGA	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57768743	57768743	+	Missense_Mutation	SNP	C	C	T	rs56057707	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	40	85	0	0.465116	0	C|0.821;T|0.179	0.179	strong	.	ZNF831	287	.	NM_178457	exon1	c.C2669T	p.A890V	CTGCTGCTTCTGT	.	PASS	Atlas-SNP
HTR3B	9177	hgsc.bcm.edu	37	11	113803108	113803108	+	Missense_Mutation	SNP	A	A	C	rs72466469	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	345	220	245	1	0.637681	0.00408163	A|0.996;C|0.004	0.004	strong	.	HTR3B	50	.	NM_006028	exon5	c.A466C	p.S156R	GCGTGCAGTTTAG	.	PASS	Atlas-SNP
RAG1	5896	hgsc.bcm.edu	37	11	36597313	36597313	+	Missense_Mutation	SNP	A	A	G	rs2227973	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	51	114	0	0.504951	0	A|0.820;G|0.180	0.180	strong	.	RAG1	151	.	NM_000448	exon2	c.A2459G	p.K820R	TGTATAAGAATCC	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83998922	83998922	+	Silent	SNP	G	G	A	rs146347192		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	28	4	35	0	0.142857	0	G|1.000;A|0.000	0.000	weak	OSGIN1,NS,carcinoma,+2,1	OSGIN1	33	1	NM_182981	exon6	c.G744A	p.T248T	AGGCACGTTCGAC	.	scavenged	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102265815	102265815	+	Silent	SNP	A	A	G	rs2295773	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	76	159	0	0.730769	0	A|0.807;G|0.193	0.193	strong	SEC31B,colon,carcinoma,-2,1	SEC31B	84	1	NM_015490	exon9	c.T1026C	p.H342H	TCTCATATGCTGG	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	11	133	0	0.174603	0	A|0.976;G|0.024	0.024	strong	PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	NM_031500	exon1	c.A1584G	p.L528L	GGAGCTAGAGCTG	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155577823	155577823	+	Silent	SNP	C	C	T	rs1571766	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	91	176	0	0.522988	0	C|0.328;T|0.672	0.672	strong	.	TIAM2	161	.	NM_012454	exon26	c.C4674T	p.A1558A	TTTTGCCGACAAT	.	PASS	Atlas-SNP
OR4D2	124538	hgsc.bcm.edu	37	17	56247306	56247306	+	Missense_Mutation	SNP	G	G	C	rs80043692	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	20	78	0	0.37037	0	G|0.898;C|0.102	0.102	strong	OR4D2,NS,haematopoietic_neoplasm,0,1	OR4D2	48	1	NM_001004707	exon1	c.G290C	p.C97S	AGGGCTGCATGGG	.	PASS	Atlas-SNP
ZNF254	9534	hgsc.bcm.edu	37	19	24310032	24310032	+	Missense_Mutation	SNP	A	A	T	rs61737180	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	65	109	0	0.555556	0	A|0.852;T|0.148	0.148	strong	ZNF254_ENST00000357002,colon,carcinoma,0,1	ZNF254	88	1	NM_203282	exon4	c.A1230T	p.E410D	TGAAGAATGCGGC	.	PASS	Atlas-SNP
HOMEZ	57594	hgsc.bcm.edu	37	14	23744829	23744829	+	Silent	SNP	C	C	T	rs79723196	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	26	27	0	0.166667	0	.	.	weak	.	HOMEZ	80	.	NM_020834	exon2	c.G1608A	p.E536E	ATCTTCCTCCTCC	.	PASS	Atlas-SNP
CNTROB	116840	hgsc.bcm.edu	37	17	7847955	7847955	+	Missense_Mutation	SNP	C	C	A	rs11650083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	83	80	1	1	0.0125	C|0.491;A|0.509	0.509	strong	CNTROB,colon,carcinoma,0,1	CNTROB	61	1	NM_001037144	exon12	c.C1733A	p.P578Q	ACCCTCCAGTACG	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9059181	9059181	+	Missense_Mutation	SNP	G	G	A	rs12459532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	102	146	0	0.6	0	G|0.977;A|0.023	0.023	strong	.	MUC16	4315	.	NM_024690	exon3	c.C28265T	p.P9422L	GGGCTTGGCCATG	.	PASS	Atlas-SNP
TRIM55	84675	hgsc.bcm.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	A	G	rs7843605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15	14	33	0	0.933333	0	A|0.741;G|0.259	0.259	strong	TRIM55,NS,carcinoma,0,1	TRIM55	91	1	NM_184086	exon8	c.A1028G	p.K343R	GAGAAAAAGAAGG	.	PASS	Atlas-SNP
PCSK5	5125	hgsc.bcm.edu	37	9	78853916	78853916	+	Missense_Mutation	SNP	G	G	C	rs17062264	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	50	166	0	0.37594	0	G|0.882;C|0.118	0.118	strong	.	PCSK5	329	.	NM_001190482	exon23	c.G2908C	p.G970R	GAGTGTGGAGATA	.	PASS	Atlas-SNP
SEC14L4	284904	hgsc.bcm.edu	37	22	30901592	30901592	+	Missense_Mutation	SNP	T	T	C	rs9608956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	24	88	0	0.888889	0	T|0.801;C|0.199	0.199	strong	.	SEC14L4	43	.	NM_001161368	exon1	c.A7G	p.S3G	CTCGGCTGCTCAT	.	PASS	Atlas-SNP
RGSL1	353299	hgsc.bcm.edu	37	1	182496829	182496829	+	Missense_Mutation	SNP	A	A	G	rs7535533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	137	227	1	0.590517	0.00440529	A|0.661;G|0.339	0.339	strong	.	RGSL1	111	.	NM_001137669	exon11	c.A2047G	p.I683V	ATCAGTATAGAGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678820	100678820	+	Missense_Mutation	SNP	T	T	C	rs4367469	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	170	141	0	0.982659	0	T|0.834;C|0.166	0.166	strong	.	MUC17	804	.	NM_001040105	exon3	c.T4123C	p.C1375R	GAAGCCTGTTCAT	.	PASS	Atlas-SNP
FAM81B	153643	hgsc.bcm.edu	37	5	94749723	94749723	+	Silent	SNP	G	G	A	rs7726891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	53	136	0	0.469027	0	G|0.759;A|0.241	0.241	strong	.	FAM81B	51	.	NM_152548	exon4	c.G366A	p.A122A	CCAGGCGCGTACC	.	PASS	Atlas-SNP
IARS	3376	hgsc.bcm.edu	37	9	94985637	94985637	+	Missense_Mutation	SNP	T	T	C	rs556155	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	85	124	0	0.555556	0	A|0.007;C|0.130	0.130	strong	IARS,rectum,carcinoma,0,1	IARS	74	1	NM_013417	exon32	c.A3544G	p.K1182E	GTGGCTTTGCATT	.	PASS	Atlas-SNP
ZFR	51663	hgsc.bcm.edu	37	5	32400266	32400266	+	Missense_Mutation	SNP	A	A	G	rs1051489	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	73	134	0	0.521429	0	A|0.734;G|0.266	0.266	strong	.	ZFR	98	.	NM_016107	exon9	c.T1559C	p.I520T	CCTTTTATGTCTT	.	PASS	Atlas-SNP
ZNF665	79788	hgsc.bcm.edu	37	19	53668697	53668697	+	Missense_Mutation	SNP	T	T	C	rs45499997	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	80	140	0	0.597015	0	T|0.958;C|0.042	0.042	strong	.	ZNF665	136	.	NM_024733	exon4	c.A1046G	p.N349S	CATTCATTACATT	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160735174	160735174	+	Missense_Mutation	SNP	C	C	T	rs147820690	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	220	125	209	0	0.568182	0	C|0.998;T|0.002	0.002	strong	.	LY75	151	.	NM_002349	exon10	c.G1574A	p.G525E	TTTGTTCCAAAAG	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36869516	36869516	+	Missense_Mutation	SNP	C	C	A	rs1205434	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	40	46	0	0.533333	0	C|0.710;A|0.290	0.290	strong	.	KIAA1755	145	.	NM_001029864	exon3	c.G1017T	p.K339N	TTCTGGCTTTGTG	.	PASS	Atlas-SNP
C20orf111	51526	hgsc.bcm.edu	37	20	42826350	42826350	+	Missense_Mutation	SNP	A	A	C	rs9346	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	48	57	0	0.979592	0	T|0.004;G|0.002	.	strong	.	C20orf111	28	.	NM_016470	exon4	c.T221G	p.V74G	GTTCTCACTGCTC	.	PASS	Atlas-SNP
DNAJC1	64215	hgsc.bcm.edu	37	10	22048330	22048330	+	Silent	SNP	C	C	T	rs9045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	83	137	0	0.805825	0	C|0.861;T|0.139	0.139	strong	DNAJC1,colon,carcinoma,0,2	DNAJC1	42	2	NM_022365	exon11	c.G1365A	p.A455A	CGGCTTCGCTGTA	.	PASS	Atlas-SNP
VPS41	27072	hgsc.bcm.edu	37	7	38829465	38829465	+	Silent	SNP	C	C	T	rs1001476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	84	153	0	0.446809	0	T|0.138;G|0.005	0.138	strong	.	VPS41	102	.	NM_014396	exon10	c.G720A	p.V240V	TGAGCACACCTGG	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145519821	145519821	+	Silent	SNP	G	G	A	rs17493851	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	195	255	2	1	0.00784314	G|0.799;A|0.201	0.201	strong	LARS,colon,carcinoma,0,2	LARS	100	2	NM_020117	exon21	c.C2094T	p.D698D	CCATTTGTCACTT	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26462790	26462790	+	Silent	SNP	G	G	A	rs3740232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	22	110	0	0.282051	0	G|0.681;A|0.319	0.319	strong	MYO3A,colon,carcinoma,0,2	MYO3A	371	2	NM_017433	exon30	c.G3597A	p.E1199E	GGAAGAGGTTAAG	.	PASS	Atlas-SNP
CCDC66	285331	hgsc.bcm.edu	37	3	56628033	56628033	+	Nonsense_Mutation	SNP	C	C	T	rs150364083	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	51	163	0	0.408	0	C|0.996;T|0.004	0.004	strong	.	CCDC66	145	.	NM_001141947	exon10	c.C1381T	p.R461X	AGACGACGACAAA	.	PASS	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56423893	56423893	+	Silent	SNP	G	G	A	rs303998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	110	122	1	0.956522	0.00819672	G|0.379;A|0.621	0.621	strong	NLRP13,NS,malignant_melanoma,-1,1	NLRP13	220	1	NM_176810	exon5	c.C1290T	p.T430T	ACATACGGTCCAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912108	29912108	+	Missense_Mutation	SNP	G	G	C	rs75766454		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	55	205	0	0.284974	0	.	.	weak	.	HLA-A	89	.	NM_001242758	exon4	c.G829C	p.E277Q	TCTGGAGAGGAGC	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2740714	2740714	+	Silent	SNP	A	A	G	rs12327477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	40	71	0	0.421053	0	A|0.701;G|0.299	0.299	strong	.	SMCHD1	88	.	NM_015295	exon28	c.A3528G	p.T1176T	AATTACAGATCAG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129909929	129909929	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	28	85	0	0.41791	0	.	.	none	.	MKI67	363	.	NM_002417	exon11	c.A2240C	p.D747A	TTAAAGTCCATTT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9075346	9075346	+	Missense_Mutation	SNP	T	T	A	rs2591592	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	336	165	325	1	0.491071	0.00307692	T|0.558;A|0.442	0.442	strong	.	MUC16	4315	.	NM_024690	exon3	c.A12100T	p.I4034F	AGATAATACTTGT	.	PASS	Atlas-SNP
ACPT	93650	hgsc.bcm.edu	37	19	51297825	51297825	+	Missense_Mutation	SNP	G	G	A	rs55716643	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	40	85	0	0.470588	0	G|0.751;A|0.249	0.249	strong	.	ACPT	43	.	NM_033068	exon9	c.G973A	p.A325T	AATCCCGCCAAAG	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50339754	50339754	+	Missense_Mutation	SNP	G	G	T	rs73302786	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	74	139	1	0.74	0.00719424	G|0.844;T|0.156	0.156	strong	.	FAM170B	20	.	NM_001164484	exon2	c.C756A	p.D252E	CTGTTGGTCATGT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152278555	152278555	+	Missense_Mutation	SNP	T	T	C	rs80221306	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1432	193	843	9	0.134777	0.0106762	T|0.972;C|0.028	0.028	strong	FLG,NS,haematopoietic_neoplasm,0,2	FLG	900	2	NM_002016	exon3	c.A8807G	p.D2936G	GCTCTGTCTTCTT	.	scavenged	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187692908	187692908	+	Silent	SNP	T	T	G	rs17852916	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	123	285	0	0.464151	0	T|0.838;G|0.162	0.162	strong	.	ZSWIM2	119	.	NM_182521	exon9	c.A1705C	p.R569R	TTGATCTCTTGTT	.	PASS	Atlas-SNP
MAS1	4142	hgsc.bcm.edu	37	6	160328620	160328620	+	Silent	SNP	C	C	T	rs220721	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	62	103	0	0.492063	0	C|0.695;T|0.305	0.305	strong	.	MAS1	42	.	NM_002377	exon1	c.C633T	p.V211V	CTTGGTCGTGAAG	.	PASS	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117076875	117076875	+	Silent	SNP	G	G	A	rs62001039	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	438	80	215	0	0.182648	0	G|0.934;A|0.066	0.066	strong	.	PCSK7	59	.	NM_004716	exon17	c.C2196T	p.D732D	CACTTCGTCTGGA	.	PASS	Atlas-SNP
SRSF1	6426	hgsc.bcm.edu	37	17	56083705	56083705	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	56	197	0	0.321839	0	.	.	none	.	SRSF1	41	.	NM_006924	exon2	c.T378C	p.S126S	CTCACCAGAGACA	.	PASS	Atlas-SNP
COQ9	57017	hgsc.bcm.edu	37	16	57490480	57490480	+	Missense_Mutation	SNP	A	A	C	rs191446011	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	24	163	0	0.137143	0	A|1.000;C|0.000	0.000	strong	.	COQ9	30	.	NM_020312	exon4	c.A443C	p.H148P	TACTGCATTTTGT	.	PASS	Atlas-SNP
CHI3L2	1117	hgsc.bcm.edu	37	1	111783982	111783982	+	Silent	SNP	C	C	A	rs13721	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	60	101	0	0.779221	0	A|0.280;C|0.697;T|0.022	0.280	strong	.	CHI3L2	38	.	NM_004000	exon9	c.C952A	p.R318R	ATCACGCGGCTCC	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33688855	33688855	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	71	92	0	0.622807	0	.	.	none	.	URB1	176	.	NM_014825	exon38	c.C6556T	p.R2186W	CTGCCCGGCCCTG	.	PASS	Atlas-SNP
D2HGDH	728294	hgsc.bcm.edu	37	2	242690745	242690745	+	Missense_Mutation	SNP	C	C	T	rs1105273	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	57	155	0	0.419118	0	C|0.817;T|0.183	0.183	strong	D2HGDH,NS,carcinoma,-1,1	D2HGDH	39	1	NM_152783	exon8	c.C1082T	p.A361V	AGCACGCGCTGGG	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48598785	48598785	+	Missense_Mutation	SNP	G	G	A	rs1380657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	153	163	0	0.987097	0	G|0.199;A|0.801	0.801	strong	.	MYCBPAP	135	.	NM_032133	exon9	c.G1270A	p.A424T	GACACAGCATACT	.	PASS	Atlas-SNP
KCNG4	93107	hgsc.bcm.edu	37	16	84256410	84256410	+	Missense_Mutation	SNP	C	C	T	rs7196482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	18	106	0	0.2	0	C|0.810;T|0.190	0.190	strong	.	KCNG4	71	.	NM_172347	exon3	c.G973A	p.G325R	AGCTCCCGCTCGG	.	PASS	Atlas-SNP
TMEM45A	55076	hgsc.bcm.edu	37	3	100287764	100287764	+	Silent	SNP	T	T	C	rs28722928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	112	276	0	0.482759	0	T|0.783;C|0.217	0.217	strong	.	TMEM45A	35	.	NM_018004	exon5	c.T687C	p.Y229Y	GCATTATGCAGTA	.	PASS	Atlas-SNP
TTBK2	146057	hgsc.bcm.edu	37	15	43170793	43170793	+	Missense_Mutation	SNP	A	A	G	rs6493068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	24	154	0	0.235294	0	A|0.525;G|0.475	0.475	strong	.	TTBK2	82	.	NM_173500	exon2	c.T23C	p.L8P	ATATCCAGCTGCT	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125889526	125889526	+	Missense_Mutation	SNP	C	C	T	rs3740909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	51	113	0	0.251232	0	C|0.896;N|0.000	.	strong	CDON,NS,carcinoma,0,1	CDON	137	1	NM_016952	exon4	c.G484A	p.E162K	AATGTTCCAGCCA	.	PASS	Atlas-SNP
RPL13A	23521	hgsc.bcm.edu	37	19	49993535	49993535	+	Silent	SNP	C	C	G	rs1064257	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	35	42	0	0.583333	0	C|0.964;G|0.036	0.036	strong	.	RPL13A	13	.	NM_012423	exon3	c.C135G	p.G45G	TTCTGGCAATTTC	.	PASS	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	37	5	167858372	167858372	+	Missense_Mutation	SNP	T	T	G	rs3822659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	29	94	0	0.439394	0	T|0.868;G|0.132	0.132	strong	.	WWC1	98	.	NM_015238	exon15	c.T2203G	p.S735A	TCCATGTCCTATC	.	PASS	Atlas-SNP
ST3GAL5	8869	hgsc.bcm.edu	37	2	86088311	86088311	+	Missense_Mutation	SNP	T	T	C	rs1138484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	60	90	0	0.5	0	T|0.829;C|0.171	0.171	strong	.	ST3GAL5	51	.	NM_003896	exon3	c.A311G	p.H104R	TTTACATGGTCAG	.	PASS	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48745035	48745035	+	Silent	SNP	A	A	C	rs11568601	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	45	80	0	0.45	0	A|0.984;C|0.016	0.016	strong	.	ABCC3	138	.	NM_003786	exon12	c.A1552C	p.R518R	GGCATCAGGCAGG	.	PASS	Atlas-SNP
CANT1	124583	hgsc.bcm.edu	37	17	76993546	76993546	+	Silent	SNP	A	A	G	rs8077024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	34	137	0	0.343434	0	A|0.572;G|0.428	0.428	strong	.	CANT1	39	.	NM_001159772	exon4	c.T159C	p.A53A	GATGGCAGCACCC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152277184	152277184	+	Missense_Mutation	SNP	T	T	C	rs146234375	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	415	119	352	0	0.286747	0	T|0.999;C|0.001	0.001	strong	.	FLG	900	.	NM_002016	exon3	c.A10178G	p.H3393R	TGTTCATGAGTGC	.	PASS	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2175733	2175733	+	Silent	SNP	A	A	G	rs2022302	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	99	163	0	0.596386	0	A|0.714;G|0.286	0.286	strong	.	POLN	82	.	NM_181808	exon9	c.T1323C	p.H441H	AATGGCATGGCTT	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	37	16	347184	347184	+	Silent	SNP	A	A	G	rs214252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	33	84	0	0.540984	0	A|0.746;G|0.254	0.254	strong	.	AXIN1	290	.	NM_181050	exon7	c.T1827C	p.A609A	CGACTCAGCCTTC	.	PASS	Atlas-SNP
QARS	5859	hgsc.bcm.edu	37	3	49141116	49141116	+	Silent	SNP	G	G	A	rs5030795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	47	95	0	0.479592	0	G|0.924;A|0.076	0.076	strong	.	QARS	55	.	NM_005051	exon4	c.C399T	p.H133H	GGGCCGGTGCCTG	.	PASS	Atlas-SNP
CDC23	8697	hgsc.bcm.edu	37	5	137533901	137533901	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	48	80	0	0.516129	0	.	.	none	.	CDC23	46	.	NM_004661	exon9	c.G999A	p.T333T	ACAGCACGTTTCT	.	PASS	Atlas-SNP
TTI2	80185	hgsc.bcm.edu	37	8	33369944	33369944	+	Missense_Mutation	SNP	T	T	C	rs2304748	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	102	132	0	0.60355	0	C|0.548;N|0.000	0.548	strong	C8orf41,NS,carcinoma,-1,1	.	.	1	NM_001265581	exon2	c.A188G	p.E63G	TCAAATTCTGTGG	.	PASS	Atlas-SNP
RNF111	54778	hgsc.bcm.edu	37	15	59368167	59368167	+	Silent	SNP	G	G	A	rs7178935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	35	68	0	0.76087	0	G|0.595;A|0.405	0.405	strong	.	RNF111	179	.	NM_017610	exon7	c.G1701A	p.V567V	GCCAGTGGACCTG	.	PASS	Atlas-SNP
KCNK10	54207	hgsc.bcm.edu	37	14	88693725	88693725	+	Silent	SNP	G	G	C	rs2277524	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	105	102	1	1	0.00980392	G|0.690;C|0.310	0.310	strong	.	KCNK10	273	.	NM_138318	exon4	c.C675G	p.V225V	TCGAAAGACCTTC	.	PASS	Atlas-SNP
SPATA22	84690	hgsc.bcm.edu	37	17	3352331	3352331	+	Missense_Mutation	SNP	C	C	T	rs1488690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	103	275	0	0.459821	0	C|0.767;T|0.233	0.233	strong	.	SPATA22	49	.	NM_032598	exon6	c.G442A	p.V148M	AACTCACTGGACA	.	PASS	Atlas-SNP
CYP51A1	1595	hgsc.bcm.edu	37	7	91743150	91743150	+	Silent	SNP	A	A	G	rs7797834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	63	62	0	0.984375	0	A|0.620;G|0.380	0.380	strong	.	CYP51A1	30	.	NM_000786	exon10	c.T1359C	p.H453H	ACAACGATGACGC	.	PASS	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156918850	156918850	+	Missense_Mutation	SNP	C	C	T	rs2287749	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	62	136	0	0.455882	0	C|0.911;T|0.089	0.089	strong	.	ADAM19	216	.	NM_033274	exon17	c.G1979A	p.G660D	CCATGGCCATTGC	.	PASS	Atlas-SNP
CNPPD1	27013	hgsc.bcm.edu	37	2	220037444	220037444	+	Missense_Mutation	SNP	G	G	A	rs17655123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	25	118	0	0.263158	0	A|0.093;G|0.907;T|0.000	0.093	strong	.	CNPPD1	22	.	NM_015680	exon8	c.C1097T	p.P366L	TACCAGGGGCTGG	.	PASS	Atlas-SNP
POM121C	100101267	hgsc.bcm.edu	37	7	75051375	75051375	+	Silent	SNP	T	T	C	rs398016	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	178	222	12	0.89	0.0540541	T|0.701;C|0.299	0.299	strong	POM121C,NS,carcinoma,0,1	POM121C	46	1	NM_001099415	exon13	c.A2160G	p.P720P	AAGGGCTGGCTTG	.	scavenged	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23544515	23544515	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	37	115	0	0.333333	0	.	.	none	ZNF91_ENST00000300619,NS,lymphoid_neoplasm,-1,2	ZNF91	349	2	NM_003430	exon4	c.T1266A	p.T422T	ATGTATAGTAAGA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150931082	150931082	+	Silent	SNP	C	C	G	rs55719915	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	105	214	0	0.454545	0	C|0.987;G|0.013	0.013	strong	FAT2,colon,carcinoma,-1,1	FAT2	465	1	NM_001447	exon6	c.G4242C	p.S1414S	ATAGTTCGACCTT	.	PASS	Atlas-SNP
CD163L1	283316	hgsc.bcm.edu	37	12	7585971	7585971	+	Silent	SNP	A	A	G	rs10845159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	101	209	0	0.517949	0	A|0.625;G|0.375	0.375	strong	.	CD163L1	238	.	NM_174941	exon3	c.T444C	p.Y148Y	CTTACCATAACAG	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158536345	158536345	+	Missense_Mutation	SNP	A	A	G	rs2305475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	39	110	0	0.65	0	A|0.737;C|0.000;G|0.262;T|0.000	0.262	strong	.	ESYT2	70	.	NM_020728	exon16	c.T1750C	p.S584P	CCAGGGAACACTG	.	PASS	Atlas-SNP
C9orf96	169436	hgsc.bcm.edu	37	9	136269143	136269143	+	Missense_Mutation	SNP	G	G	A	rs17150554	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	58	178	0	0.43609	0	G|0.947;A|0.053	0.053	strong	C9orf96_ENST00000371957,NS,carcinoma,0,2	C9orf96	77	2	NM_153710	exon16	c.G1703A	p.R568Q	CCTACCGGGGACT	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23862710	23862710	+	Silent	SNP	C	C	T	rs145274612	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	422	277	306	1	0.656398	0.00326797	C|0.992;T|0.008	0.008	strong	.	MYH6	274	.	NM_002471	exon23	c.G2946A	p.E982E	CATCTCCTCTGTT	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44118188	44118188	+	Missense_Mutation	SNP	A	A	C	rs3815422	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	23	37	0	0.511111	0	A|0.799;C|0.201	0.201	strong	SRRM5,NS,carcinoma,0,1	SRRM5	38	1	NM_001145641	exon1	c.A1915C	p.S639R	AAGGAGAGCGACC	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	37	8	24333985	24333985	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	37	69	0	0.359223	0	.	.	none	ADAM7,NS,carcinoma,-1,4	ADAM7	165	4	NM_003817	exon8	c.C673T	p.R225X	AGGAACCGAATTT	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129807714	129807714	+	Silent	SNP	G	G	A	rs2229850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	104	207	1	0.533333	0.00483092	A|0.356;G|0.644;T|0.000	0.356	strong	.	LAMA2	481	.	NM_000426	exon56	c.G7845A	p.P2615P	AGAGCCGAATCTG	.	PASS	Atlas-SNP
KLRG2	346689	hgsc.bcm.edu	37	7	139138950	139138950	+	Missense_Mutation	SNP	C	C	G	rs17160911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	22	47	0	1	0	C|0.832;G|0.166	0.166	strong	KLRG2,NS,carcinoma,0,3	KLRG2	22	3	NM_198508	exon4	c.G1016C	p.G339A	TATCTGCCCAGGA	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34723988	34723988	+	Missense_Mutation	SNP	C	C	A	rs147591106	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	39	101	0	0.65	0	C|0.886;A|0.114	0.114	strong	.	FAM205A	45	.	NM_001141917	exon4	c.G3249T	p.R1083S	TGCTGGCCTCTGG	.	PASS	Atlas-SNP
CCDC169-SOHLH2	100526761	hgsc.bcm.edu	37	13	36744800	36744800	+	Silent	SNP	G	G	A	rs2296967	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	119	230	0	0.533632	0	G|0.916;A|0.084	0.084	strong	SOHLH2,NS,carcinoma,0,1	.	.	1	NM_001198910	exon15	c.C1356T	p.Y452Y	TGCATCGTAGGAA	.	PASS	Atlas-SNP
CPNE3	8895	hgsc.bcm.edu	37	8	87540872	87540872	+	Silent	SNP	G	G	A	rs10956871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	49	126	0	0.300613	0	G|0.775;A|0.225	0.225	strong	.	CPNE3	65	.	NM_003909	exon3	c.G99A	p.L33L	TGTGTTGTTTTTG	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23904298	23904298	+	Missense_Mutation	SNP	T	T	G	rs34382952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	50	85	0	0.403226	0	T|0.997;G|0.003	0.003	strong	.	SACS	871	.	NM_014363	exon10	c.A13717C	p.N4573H	TAAAATTTTCAAG	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2434799	2434799	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	392	126	388	1	0.321429	0.00257732	.	.	none	.	TRPM5	86	.	NM_014555	exon13	c.G1910T	p.W637L	CCCCACCAGATCC	.	PASS	Atlas-SNP
IKZF1	10320	hgsc.bcm.edu	37	7	50459542	50459542	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	4	83	0	0.05	0	.	.	none	.	IKZF1	613	.	NM_006060	exon7	c.T831C	p.S277S	GAGCTCTATGCCT	.	PASS	Atlas-SNP
PHKG1	5260	hgsc.bcm.edu	37	7	56149939	56149939	+	Silent	SNP	G	G	A	rs13238521	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	44	43	0	0.647059	0	G|0.924;A|0.076	0.076	strong	.	PHKG1	38	.	NM_001258459	exon8	c.C651T	p.C217C	GGTCCCGCAGACC	.	PASS	Atlas-SNP
SCNN1D	6339	hgsc.bcm.edu	37	1	1220954	1220954	+	Silent	SNP	G	G	A	rs12751100	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	28	165	0	0.28866	0	G|0.609;A|0.391	0.391	strong	.	SCNN1D	60	.	NM_001130413	exon6	c.G468A	p.S156S	TAGATCGCCTGGG	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72998296	72998296	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	50	199	0	0.314465	0	.	.	none	.	TSHZ1	104	.	NM_005786	exon2	c.T799C	p.C267R	ATGTACTGTGGAC	.	PASS	Atlas-SNP
RARB	5915	hgsc.bcm.edu	37	3	25635200	25635200	+	Splice_Site	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	2	154	0	0.0127389	0	.	.	none	RARB_ENST00000404969,NS,carcinoma,+2,2	RARB	123	2	NM_016152	exon6	c.655+2T>C	.	TGGAGGTACCAAC	.	scavenged	Atlas-SNP
ZNF468	90333	hgsc.bcm.edu	37	19	53344701	53344701	+	Silent	SNP	A	A	G	rs10420793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	55	95	1	0.528846	0.0105263	A|0.649;G|0.351	0.351	strong	ZNF468,NS,carcinoma,0,1	ZNF468	46	1	NM_001008801	exon4	c.T846C	p.H282H	TGAATTATGACCA	.	scavenged	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51914401	51914401	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	2	189	0	0.0103627	0	.	.	none	SIGLEC12_ENST00000439889,bladder,carcinoma,-1,2	SIGLEC10	112	2	NM_033130	exon11	c.G2046A	p.R682R	GGGCATCCGGGCC	.	scavenged	Atlas-SNP
DISP2	85455	hgsc.bcm.edu	37	15	40655845	40655845	+	Missense_Mutation	SNP	C	C	G	rs1898883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	35	78	0	0.853659	0	C|0.308;G|0.692	0.692	strong	.	DISP2	86	.	NM_033510	exon2	c.C139G	p.P47A	GCTGTGCCCCCTG	.	PASS	Atlas-SNP
AKNA	80709	hgsc.bcm.edu	37	9	117124731	117124731	+	Missense_Mutation	SNP	G	G	A	rs3748176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	28	56	0	0.491228	0	G|0.599;A|0.401	0.401	strong	AKNA,NS,carcinoma,0,1	AKNA	119	1	NM_030767	exon8	c.C1871T	p.P624L	GCAAGCGGCTGGG	.	PASS	Atlas-SNP
IMPAD1	54928	hgsc.bcm.edu	37	8	57906042	57906042	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	8	6	11	0	0.75	0	.	.	none	.	IMPAD1	27	.	NM_017813	exon1	c.C103T	p.R35C	TGAAGCGGCCGGC	.	PASS	Atlas-SNP
BCLAF1	9774	hgsc.bcm.edu	37	6	136589425	136589425	+	Missense_Mutation	SNP	G	G	T	rs77081633	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	220	40	250	0	0.181818	0	G|0.976;T|0.024	0.024	strong	.	BCLAF1	203	.	NM_014739	exon10	c.C2272A	p.P758T	AAGAAGGTGATGC	.	PASS	Atlas-SNP
ITPA	3704	hgsc.bcm.edu	37	20	3193978	3193978	+	Silent	SNP	G	G	A	rs8362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	66	143	0	0.445946	0	G|0.607;A|0.393	0.393	strong	.	ITPA	16	.	NM_033453	exon3	c.G138A	p.Q46Q	GTACCAGGGGGAG	.	PASS	Atlas-SNP
ABCB5	340273	hgsc.bcm.edu	37	7	20698270	20698270	+	Missense_Mutation	SNP	A	A	G	rs2301641	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	50	90	0	0.384615	0	A|0.625;G|0.375	0.375	strong	.	ABCB5	357	.	NM_001163941	exon14	c.A1678G	p.K560E	GAAAGCAAGTCAG	.	PASS	Atlas-SNP
HECTD2	143279	hgsc.bcm.edu	37	10	93221018	93221018	+	Missense_Mutation	SNP	G	G	A	rs61754655	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	76	176	0	0.752475	0	G|0.997;A|0.003	0.003	strong	.	HECTD2	60	.	NM_173497	exon4	c.G415A	p.V139I	GAAGATGTAGAAA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149522162	149522162	+	Missense_Mutation	SNP	G	G	T	rs62617122	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	12	102	0	0.176471	0	G|0.840;T|0.160	0.160	strong	.	.	.	.	NM_198455	exon96	c.G13949T	p.C4650F	GAGGCTGCCGGGA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104627	168104627	+	Missense_Mutation	SNP	G	G	A	rs61750760	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	110	236	1	0.493274	0.00423729	G|0.842;A|0.158	0.158	strong	XIRP2,NS,carcinoma,+1,1	XIRP2	914	1	NM_152381	exon9	c.G6725A	p.R2242Q	AAAAGCGGGAGAC	.	PASS	Atlas-SNP
KANK3	256949	hgsc.bcm.edu	37	19	8399272	8399272	+	Silent	SNP	G	G	A	rs8106699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	45	128	0	0.463918	0	G|0.859;A|0.141	0.141	strong	.	KANK3	35	.	NM_198471	exon4	c.C1359T	p.D453D	TGTGCCGTCTCTC	.	PASS	Atlas-SNP
CEP72	55722	hgsc.bcm.edu	37	5	637637	637637	+	Missense_Mutation	SNP	A	A	G	rs62000999	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	91	221	0	0.471503	0	A|0.989;G|0.011	0.011	strong	.	CEP72	53	.	NM_018140	exon7	c.A910G	p.M304V	GACTCCATGGATA	.	PASS	Atlas-SNP
NAPSA	9476	hgsc.bcm.edu	37	19	50863023	50863023	+	Silent	SNP	A	A	G	rs638294	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	133	124	1	0.985185	0.00806452	A|0.662;G|0.338	0.338	strong	.	NAPSA	38	.	NM_004851	exon6	c.T765C	p.P255P	GTAGGCAGGGACC	.	PASS	Atlas-SNP
APOL3	80833	hgsc.bcm.edu	37	22	36537671	36537671	+	Silent	SNP	T	T	G	rs132619	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	29	52	0	0.644444	0	T|0.997;G|0.003	0.003	strong	APOL3_ENST00000349314,NS,malignant_melanoma,-1,2	APOL3	60	2	NM_145640	exon3	c.A786C	p.R262R	CTTCAATCGGTCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677502	100677502	+	Silent	SNP	G	G	A	rs10267904	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	563	198	182	1	0.351687	0.00549451	G|0.969;A|0.031	0.031	strong	MUC17,right_upper_lobe,carcinoma,+2,1	MUC17	804	1	NM_001040105	exon3	c.G2805A	p.P935P	CACGCCGGTAGTC	.	scavenged	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2833605	2833605	+	Nonsense_Mutation	SNP	C	C	T	rs111939179	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	17	156	0	0.195402	0	C|0.999;T|0.001	0.001	strong	.	ARSD	47	.	NM_001669	exon6	c.G992A	p.W331X	ATGAGCCAGTCCA	.	PASS	Atlas-SNP
RDH12	145226	hgsc.bcm.edu	37	14	68193731	68193731	+	Missense_Mutation	SNP	G	G	A	rs17852293	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	52	102	0	0.342105	0	G|0.882;A|0.118	0.118	strong	RDH12,brain,glioma,0,1	RDH12	43	1	NM_152443	exon7	c.G482A	p.R161Q	TGGAGCGGCTAAA	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47805773	47805773	+	Silent	SNP	T	T	C	rs61735805	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	42	124	0	0.333333	0	T|0.972;C|0.028	0.028	strong	.	PCNT	283	.	NM_006031	exon17	c.T3339C	p.S1113S	CTTAAGTCACGAG	.	PASS	Atlas-SNP
ALS2CR8	79800	hgsc.bcm.edu	37	2	203846817	203846817	+	Missense_Mutation	SNP	A	A	T	rs72932557	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	35	196	0	0.265152	0	A|0.910;T|0.090	0.090	strong	ALS2CR8,rectum,carcinoma,-1,1	ALS2CR8	56	1	NM_024744	exon16	c.A1712T	p.Y571F	CAAGGTACACCTC	.	PASS	Atlas-SNP
CEP68	23177	hgsc.bcm.edu	37	2	65296798	65296798	+	Missense_Mutation	SNP	G	G	A	rs7572857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	45	97	0	0.436893	0	G|0.877;A|0.122	0.122	strong	CEP68,NS,carcinoma,0,1	CEP68	69	1	NM_015147	exon2	c.G220A	p.G74S	CCTGGCGGCCCCT	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102593273	102593273	+	Silent	SNP	T	T	G	rs12803000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	579	141	343	0	0.243523	0	T|0.966;G|0.034	0.034	strong	MMP8,face,malignant_melanoma,-2,1	MMP8	68	1	NM_002424	exon2	c.A234C	p.P78P	CTCATTTGGCTTC	.	PASS	Atlas-SNP
HOXD10	3236	hgsc.bcm.edu	37	2	176983923	176983923	+	Silent	SNP	G	G	C	rs33913965	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	77	128	0	0.484277	0	G|0.984;C|0.016	0.016	strong	.	HOXD10	65	.	NM_002148	exon2	c.G987C	p.R329R	GAACCGGATCCGA	.	PASS	Atlas-SNP
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	75	183	0	0.480769	0	A|0.634;C|0.366	0.366	strong	ZNF879,NS,carcinoma,0,2	ZNF879	41	2	NM_001136116	exon5	c.A477C	p.E159D	TGTTGAATTTGGG	.	PASS	Atlas-SNP
TREX1	11277	hgsc.bcm.edu	37	3	48508585	48508585	+	Silent	SNP	C	C	T	rs11797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	80	210	1	0.567376	0.0047619	C|0.642;T|0.358	0.358	strong	.	TREX1	17	.	NM_016381	exon1	c.C696T	p.Y232Y	GAGCTACAGCCTA	.	PASS	Atlas-SNP
ENPP1	5167	hgsc.bcm.edu	37	6	132172368	132172368	+	Missense_Mutation	SNP	A	A	C	rs1044498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	40	100	0	0.430108	0	A|0.655;C|0.345	0.345	strong	.	ENPP1	108	.	NM_006208	exon4	c.A517C	p.K173Q	AAGGACAAGGGCG	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93433289	93433289	+	Silent	SNP	A	A	G	rs374656563		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236	142	137	0	0.601695	0	.	.	weak	.	KIAA1731	173	.	NM_033395	exon15	c.A5211G	p.T1737T	ACAAACAGCATTG	.	PASS	Atlas-SNP
EXO5	64789	hgsc.bcm.edu	37	1	40980668	40980668	+	Missense_Mutation	SNP	T	T	C	rs35672330	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	71	149	1	0.71	0.00671141	T|0.958;C|0.042	0.042	strong	.	.	.	.	NM_022774	exon3	c.T452C	p.L151P	ACATACTTTTGCT	.	PASS	Atlas-SNP
KIAA1586	57691	hgsc.bcm.edu	37	6	56911574	56911574	+	Silent	SNP	A	A	G	rs9382680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	90	407	1	0.362903	0.002457	A|0.824;G|0.176	0.176	strong	.	KIAA1586	59	.	NM_020931	exon1	c.A21G	p.E7E	GTCGGAAGTGAGT	.	PASS	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	37	1	179972337	179972337	+	Silent	SNP	A	A	C	rs17371159	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	108	141	0	0.631579	0	A|0.930;C|0.070	0.070	strong	.	CEP350	418	.	NM_014810	exon7	c.A1047C	p.R349R	GATTCGAACACCT	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	rs147123517	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281	94	156	0	0.33452	0	C|0.996;T|0.004	0.004	strong	.	.	.	.	NM_174913	exon6	c.C1237T	p.R413C	GCCTGTCGCAGAG	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187088399	187088399	+	Missense_Mutation	SNP	G	G	T	rs111681837	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	48	276	0	0.290909	0	G|0.995;T|0.005	0.005	strong	.	FAM149A	52	.	NM_001006655	exon12	c.G1358T	p.G453V	GGACAGGTCAAAG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104988	168104988	+	Missense_Mutation	SNP	G	G	T	rs59889092	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	43	98	0	0.505882	0	G|0.860;T|0.140	0.140	strong	.	XIRP2	914	.	NM_152381	exon9	c.G7086T	p.M2362I	ATCGATGTTTCTG	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	37	8	24356818	24356818	+	Missense_Mutation	SNP	A	A	C	rs13259668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	84	83	0	0.672	0	A|0.694;C|0.306	0.306	strong	.	ADAM7	165	.	NM_003817	exon17	c.A1912C	p.N638H	CAGTGCAATGAAA	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	37	11	4825010	4825010	+	Missense_Mutation	SNP	T	T	A	rs6578533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	36	83	0	0.444444	0	A|0.369;N|0.000	0.369	strong	.	OR52R1	81	.	NM_001005177	exon1	c.A601T	p.N201Y	GCCCATTCCCACG	.	PASS	Atlas-SNP
IQGAP3	128239	hgsc.bcm.edu	37	1	156518379	156518379	+	Missense_Mutation	SNP	G	G	A	rs744224	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	178	136	1	0.983425	0.00735294	G|0.683;A|0.317	0.317	strong	IQGAP3,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	IQGAP3	146	1	NM_178229	exon17	c.C1987T	p.R663C	CTGGACGCTGTTT	.	PASS	Atlas-SNP
G6PC2	57818	hgsc.bcm.edu	37	2	169764176	169764176	+	Missense_Mutation	SNP	G	G	C	rs492594	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	412	178	485	3	0.432039	0.00618557	G|0.584;C|0.416	0.416	strong	G6PC2,NS,carcinoma,0,1	G6PC2	44	1	NM_021176	exon5	c.G655C	p.V219L	TTTGCAGTTGGCT	.	scavenged	Atlas-SNP
FAM110A	83541	hgsc.bcm.edu	37	20	826334	826334	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	3	81	0	0.0344828	0	.	.	none	FAM110A,NS,carcinoma,0,1	FAM110A	18	1	NM_207121	exon2	c.A887G	p.X296W	AAGGCTAGGCGCC	.	scavenged	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	37	17	33805150	33805150	+	Missense_Mutation	SNP	T	T	C	rs2304968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	37	120	1	0.381443	0.00833333	T|0.242;C|0.758	0.758	strong	SLFN12L_ENST00000449046,NS,carcinoma,0,6	SLFN12L	140	6	NM_001195790	exon3	c.A1148G	p.Y383C	AGAGGATAACTCT	.	scavenged	Atlas-SNP
SLC2A14	144195	hgsc.bcm.edu	37	12	7966958	7966958	+	Missense_Mutation	SNP	C	C	T	rs10845981	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	138	365	2	0.77095	0.00547945	C|0.760;T|0.240	0.240	strong	SLC2A14,NS,carcinoma,0,1	SLC2A14	78	1	NM_153449	exon12	c.G1517A	p.G506E	TTCATCCCCATGA	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	rs77329757	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	250	50	144	0	0.2	0	C|0.996;T|0.004	0.004	strong	PSPH,rectum,carcinoma,0,1	PSPH	23	1	NM_004577	exon4	c.G4A	p.V2I	GGGAGACCATCGC	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367132	107367132	+	Silent	SNP	G	G	A	rs10820679	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	117	255	0	0.483471	0	G|0.791;A|0.209	0.209	strong	.	OR13C2	46	.	NM_001004481	exon1	c.C777T	p.Y259Y	CTTCATGTACATG	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31769293	31769293	+	Missense_Mutation	SNP	T	T	C	rs143453460	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	108	209	1	0.542714	0.00478469	T|0.991;C|0.009	0.009	strong	TSHZ3_ENST00000240587,NS,carcinoma,+1,2	TSHZ3	549	2	NM_020856	exon2	c.A1406G	p.E469G	TTGACCTCCACAT	.	PASS	Atlas-SNP
KRT73	319101	hgsc.bcm.edu	37	12	53005051	53005051	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	290	3	266	0	0.0103448	0	.	.	none	KRT73,neck,malignant_melanoma,-2,1	KRT73	101	1	NM_175068	exon6	c.G1047A	p.E349E	TGAGATCTCATTT	.	scavenged	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57767727	57767727	+	Silent	SNP	T	T	A	rs61743785	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	8	4	11	0	0.5	0	T|0.939;A|0.061	0.061	strong	.	ZNF831	287	.	NM_178457	exon1	c.T1653A	p.T551T	CTCGACTGACGTT	.	PASS	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102269085	102269085	+	Missense_Mutation	SNP	C	C	A	rs3793706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	71	163	1	0.806818	0.00613497	C|0.796;A|0.204	0.204	strong	.	SEC31B	84	.	NM_015490	exon4	c.G387T	p.L129F	AGGATTCAAGTCG	.	PASS	Atlas-SNP
WDR59	79726	hgsc.bcm.edu	37	16	74942865	74942865	+	Silent	SNP	T	T	C	rs141093453	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	19	77	0	0.218391	0	T|0.973;C|0.027	0.027	strong	.	WDR59	66	.	NM_030581	exon17	c.A1653G	p.V551V	GAAATATACCAGG	.	PASS	Atlas-SNP
IGFN1	91156	hgsc.bcm.edu	37	1	201174215	201174215	+	Missense_Mutation	SNP	C	C	A	rs11584104	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	101	93	0	0.60119	0	C|0.971;A|0.029	0.029	strong	.	IGFN1	220	.	NM_001164586	exon11	c.C922A	p.P308T	GCCATCCCCCCAA	.	PASS	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45820196	45820196	+	Missense_Mutation	SNP	C	C	T	rs35288229	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	139	171	1	0.65566	0.00584795	C|0.968;T|0.032	0.032	strong	TRPM2,NS,carcinoma,-1,1	TRPM2	196	1	NM_003307	exon15	c.C2263T	p.R755C	CTGTGGCGTGTGA	.	PASS	Atlas-SNP
TCP1	6950	hgsc.bcm.edu	37	6	160201577	160201577	+	Missense_Mutation	SNP	G	G	C	rs148556538	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	101	209	1	0.515306	0.00478469	G|0.999;C|0.001	0.001	strong	.	TCP1	37	.	NM_030752	exon9	c.C995G	p.A332G	AAATTGGCCAGGG	.	PASS	Atlas-SNP
ZNF543	125919	hgsc.bcm.edu	37	19	57839150	57839150	+	Missense_Mutation	SNP	A	A	G	rs8100491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	136	125	0	1	0	A|0.278;G|0.722	0.722	strong	ZNF543,NS,lymphoid_neoplasm,+1,2	ZNF543	61	2	NM_213598	exon4	c.A320G	p.Q107R	AGGAACAACTGAC	.	PASS	Atlas-SNP
ANKRD33	341405	hgsc.bcm.edu	37	12	52282060	52282060	+	Silent	SNP	C	C	T	rs697634	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	67	162	0	0.471831	0	C|0.719;T|0.281	0.281	strong	.	ANKRD33	33	.	NM_182608	exon1	c.C90T	p.R30R	GCTCCGCGGAGCC	.	PASS	Atlas-SNP
C2orf71	388939	hgsc.bcm.edu	37	2	29296870	29296870	+	Silent	SNP	C	C	T	rs62132765	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	617	275	630	3	0.445705	0.0047619	C|0.825;T|0.175	0.175	strong	C2orf71,rectum,carcinoma,-1,1	C2orf71	146	1	NM_001029883	exon1	c.G258A	p.R86R	ATCTTTCCTTTTG	.	scavenged	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3753874	3753874	+	Silent	SNP	G	G	A	rs34868972	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	17	60	0	0.447368	0	G|0.908;A|0.092	0.092	strong	.	APBA3	28	.	NM_004886	exon6	c.C900T	p.I300I	GCAGCCGATGTCG	.	PASS	Atlas-SNP
ZNF735	730291	hgsc.bcm.edu	37	7	63680099	63680099	+	Missense_Mutation	SNP	C	C	A	rs4320434	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	70	146	0	0.357143	0	C|0.813;A|0.187	0.187	strong	.	.	.	.	NM_001159524	exon4	c.C670A	p.H224N	TTTAACCACTCCT	.	PASS	Atlas-SNP
UBN2	254048	hgsc.bcm.edu	37	7	138967814	138967814	+	Silent	SNP	G	G	A	rs61995684	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	12	86	0	0.169014	0	G|0.927;A|0.073	0.073	strong	.	UBN2	90	.	NM_173569	exon15	c.G2163A	p.V721V	CCTGGTGGCTTCG	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238244923	238244923	+	Silent	SNP	C	C	T	rs11683438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	24	62	0	0.45283	0	C|0.933;G|0.000;T|0.067	0.067	strong	.	COL6A3	608	.	NM_004369	exon40	c.G8820A	p.T2940T	CGCTGCCGTTGCT	.	PASS	Atlas-SNP
MMP25	64386	hgsc.bcm.edu	37	16	3100095	3100095	+	Silent	SNP	C	C	T	rs10431961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	32	78	0	0.542373	0	C|0.727;T|0.273	0.273	strong	.	MMP25	35	.	NM_022468	exon3	c.C318T	p.R106R	GCGTCGCCGGTAC	.	PASS	Atlas-SNP
PMVK	10654	hgsc.bcm.edu	37	1	154904840	154904840	+	Silent	SNP	T	T	C	rs1891805	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	151	159	0	0.634454	0	T|0.769;C|0.231	0.231	strong	.	PMVK	17	.	NM_006556	exon2	c.A147G	p.E49E	ATACTGTTCCTTG	.	PASS	Atlas-SNP
CCBL1	883	hgsc.bcm.edu	37	9	131600394	131600394	+	Missense_Mutation	SNP	A	A	G	rs371451324		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	99	234	1	0.502538	0.0042735	.	.	weak	.	CCBL1	36	.	NM_001122671	exon5	c.T374C	p.F125S	CAGTCAAAAAAGG	.	PASS	Atlas-SNP
FMNL2	114793	hgsc.bcm.edu	37	2	153405594	153405594	+	Silent	SNP	G	G	A	rs1155779	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	55	184	0	0.392857	0	G|0.375;A|0.625	0.625	strong	.	FMNL2	75	.	NM_052905	exon4	c.G342A	p.L114L	TTCTTTGAGAACT	.	PASS	Atlas-SNP
LRRD1	401387	hgsc.bcm.edu	37	7	91779971	91779971	+	Missense_Mutation	SNP	T	T	G	rs6465353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	109	82	0	1	0	T|0.575;G|0.425	0.425	strong	.	LRRD1	35	.	NM_001161528	exon3	c.A2155C	p.I719L	AAAAAATATTGTA	.	PASS	Atlas-SNP
ANGEL1	23357	hgsc.bcm.edu	37	14	77269788	77269788	+	Missense_Mutation	SNP	A	A	C	rs2075773	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	46	88	0	0.335766	0	A|0.875;C|0.125	0.125	strong	ANGEL1,NS,carcinoma,0,1	ANGEL1	63	1	NM_015305	exon7	c.T1544G	p.F515C	AAGCGGAAACGTA	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117113653	117113653	+	Silent	SNP	T	T	C	rs615199	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	93	165	0	0.494681	0	C|0.301;N|0.000	0.301	strong	GPRC6A,NS,carcinoma,0,1	GPRC6A	152	1	NM_148963	exon6	c.A2433G	p.P811P	CACAGCTGGTACA	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642827	1642827	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	16	157	0	0.0924855	0	.	.	none	KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	NM_001012709	exon1	c.C497G	p.S166C	GAGGAGGAGCAGC	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848826	54848826	+	Missense_Mutation	SNP	C	C	T	rs145556773	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	95	205	0	0.542857	0	C|0.997;T|0.003	0.003	strong	.	LILRA4	91	.	NM_012276	exon5	c.G797A	p.R266H	CCAGGGCGCTGGG	.	PASS	Atlas-SNP
C15orf52	388115	hgsc.bcm.edu	37	15	40629995	40629995	+	Missense_Mutation	SNP	G	G	A	rs149438052	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	18	93	0	0.375	0	A|0.001;G|0.999	0.001	strong	.	C15orf52	47	.	NM_207380	exon6	c.C745T	p.R249C	CGAGGCGGGCTAG	.	PASS	Atlas-SNP
SRP72	6731	hgsc.bcm.edu	37	4	57333859	57333859	+	Missense_Mutation	SNP	C	C	T	rs111673705	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	85	174	0	0.562914	0	C|0.997;G|0.000;T|0.003	0.003	strong	.	SRP72	59	.	NM_006947	exon1	c.C58T	p.R20W	GTGAACCGGTATG	.	PASS	Atlas-SNP
C20orf201	198437	hgsc.bcm.edu	37	20	62714783	62714783	+	Silent	SNP	C	C	G	rs6010717	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	36	64	0	0.553846	0	C|0.368;G|0.632	0.632	strong	C20orf201,NS,carcinoma,0,1	C20orf201	4	1	NM_001007125	exon2	c.G678C	p.A226A	CTCAGTCGCCGTC	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124732618	124732618	+	Missense_Mutation	SNP	A	A	G	rs6790837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	95	179	0	0.497382	0	A|0.568;G|0.432	0.432	strong	.	HEG1	109	.	NM_020733	exon6	c.T1805C	p.F602S	GCATGAAAAAAGG	.	PASS	Atlas-SNP
CLDN8	9073	hgsc.bcm.edu	37	21	31587859	31587859	+	Missense_Mutation	SNP	T	T	C	rs685967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	72	112	0	0.553846	0	T|0.908;C|0.092	0.092	strong	CLDN8,NS,adenocarcinoma,+2,1	CLDN8	40	1	NM_199328	exon1	c.A385G	p.T129A	TGCCCGTGATGAT	.	PASS	Atlas-SNP
LRRC8B	23507	hgsc.bcm.edu	37	1	90048248	90048248	+	Silent	SNP	C	C	T	rs12130207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	127	196	0	0.976923	0	C|0.814;T|0.186	0.186	strong	LRRC8B,NS,neuroblastoma,+2,1	LRRC8B	49	1	NM_015350	exon5	c.C39T	p.A13A	AGATGCCCAGTCA	.	PASS	Atlas-SNP
SYK	6850	hgsc.bcm.edu	37	9	93637015	93637015	+	Silent	SNP	C	C	T	rs2290890	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	39	107	0	0.40625	0	C|0.825;T|0.175	0.175	strong	.	SYK	132	.	NM_003177	exon9	c.C1065T	p.P355P	GGACCCCGAGGAG	.	PASS	Atlas-SNP
ASIC4	55515	hgsc.bcm.edu	37	2	220402665	220402665	+	Missense_Mutation	SNP	C	C	A	rs6436153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	24	68	0	0.705882	0	C|0.841;A|0.159	0.159	strong	.	.	.	.	NM_182847	exon9	c.C1841A	p.P614Q	CCTGCCCGAGCCG	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176096	57176096	+	Missense_Mutation	SNP	C	C	G	rs77114013	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	18	102	0	0.5	0	C|0.972;G|0.028	0.028	strong	.	ZNF835	106	.	NM_001005850	exon2	c.G471C	p.Q157H	CGTGCGCTGGTGC	.	PASS	Atlas-SNP
PDIA2	64714	hgsc.bcm.edu	37	16	336396	336396	+	Missense_Mutation	SNP	G	G	A	rs400037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	105	225	0	0.456522	0	G|0.810;A|0.190	0.190	strong	.	PDIA2	51	.	NM_006849	exon8	c.G1163A	p.R388Q	ATCAGCGGCCAGT	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Silent	SNP	C	C	T	rs371465078	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	618	20	280	1	0.0323625	0.00357143	.	.	weak	SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	NM_001135844	exon2	c.G243A	p.Q81Q	TTCTTTCTGATTG	.	scavenged	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573508	140573508	+	Silent	SNP	C	C	G	rs61742867	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	24	109	2	0.27907	0.0183486	C|0.029;G|0.971	0.971	strong	PCDHB10,NS,carcinoma,+2,2	PCDHB10	177	2	NM_018930	exon1	c.C1383G	p.R461R	CGTCCGCGAGAAC	.	scavenged	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7034508	7034508	+	Missense_Mutation	SNP	T	T	G	rs566655	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	88	195	0	0.473118	0	T|0.807;G|0.193	0.193	strong	.	LAMA1	458	.	NM_005559	exon14	c.A2021C	p.N674T	TTGTAGTTGGCTC	.	PASS	Atlas-SNP
TRAP1	10131	hgsc.bcm.edu	37	16	3724365	3724365	+	Missense_Mutation	SNP	C	C	T	rs145715008	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	90	138	0	0.552147	0	C|0.999;T|0.001	0.001	strong	TRAP1,colon,carcinoma,-1,1	TRAP1	53	1	NM_016292	exon9	c.G1019A	p.R340H	ATGCTGCGGATGT	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220348751	220348751	+	Missense_Mutation	SNP	C	C	T	rs10755037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	9	75	1	0.209302	0.0133333	A|0.000;C|0.753;G|0.000;T|0.247	0.247	strong	SPEG,NS,carcinoma,0,2	SPEG	272	2	NM_005876	exon30	c.C6566T	p.P2189L	GTACCCCTAAGTC	.	scavenged	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55872657	55872657	+	Missense_Mutation	SNP	A	A	C	rs61729740	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	106	308	0	0.436214	0	A|0.582;C|0.418	0.418	strong	OR8H2,NS,carcinoma,0,1	OR8H2	117	1	NM_001005200	exon1	c.A139C	p.I47L	GGGATGATATTGA	.	PASS	Atlas-SNP
INSL4	3641	hgsc.bcm.edu	37	9	5231712	5231712	+	Silent	SNP	T	T	A	rs12720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	45	110	0	0.36	0	T|0.613;A|0.387	0.387	strong	INSL4,bladder,carcinoma,+2,1	INSL4	20	1	NM_002195	exon1	c.T189A	p.R63R	TGGACGTCCCAAA	.	PASS	Atlas-SNP
ZNF718	255403	hgsc.bcm.edu	37	4	59350	59350	+	Missense_Mutation	SNP	A	A	G	rs6834707	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	863	41	659	0	0.0475087	0	A|0.997;G|0.003	0.003	strong	.	.	.	.	NM_001039127	exon2	c.A31G	p.I11V	GTGGCCATAGAAT	.	PASS	Atlas-SNP
HELQ	113510	hgsc.bcm.edu	37	4	84374480	84374480	+	Missense_Mutation	SNP	C	C	T	rs1494961	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	130	210	0	0.522088	0	C|0.384;N|0.000	.	strong	.	HELQ	95	.	NM_133636	exon2	c.G916A	p.V306I	ACTCAACTGTTTT	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	37	17	8381675	8381675	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	2	132	0	0.0163934	0	.	.	none	MYH10,colon,carcinoma,+1,2	MYH10	148	2	NM_001256012	exon41	c.C5687T	p.A1896V	TGGTCCGCGTGTC	.	scavenged	Atlas-SNP
GALNT15	117248	hgsc.bcm.edu	37	3	16268974	16268974	+	Silent	SNP	T	T	A	rs15767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	114	106	1	1	0.00943396	T|0.600;A|0.400	0.400	strong	GALNTL2,colon,carcinoma,0,4	.	.	4	NM_054110	exon10	c.T1887A	p.R629R	GTGGCGTTTTGAC	.	PASS	Atlas-SNP
XPO5	57510	hgsc.bcm.edu	37	6	43496662	43496662	+	Silent	SNP	A	A	C	rs1106841	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	46	79	1	1	0.0126582	A|0.635;C|0.365	0.365	strong	XPO5,colon,carcinoma,0,2	XPO5	79	2	NM_020750	exon24	c.T2679G	p.R893R	AAAGACACGTGCT	.	scavenged	Atlas-SNP
SIPA1	6494	hgsc.bcm.edu	37	11	65417434	65417434	+	Silent	SNP	G	G	A	rs746429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	30	81	0	0.422535	0	G|0.736;A|0.264	0.264	strong	.	SIPA1	45	.	NM_006747	exon13	c.G2760A	p.A920A	GGAGGCGGGCAGT	.	PASS	Atlas-SNP
PPFIA2	8499	hgsc.bcm.edu	37	12	81769581	81769581	+	Silent	SNP	C	C	T	rs10862301	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	89	182	0	0.511494	0	C|0.573;N|0.000	.	strong	.	PPFIA2	207	.	NM_001220476	exon9	c.G1125A	p.L375L	CTGCCGCAGGATA	.	PASS	Atlas-SNP
FPR2	2358	hgsc.bcm.edu	37	19	52272903	52272903	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	3	114	0	0.0285714	0	.	.	none	FPR2,NS,carcinoma,+1,1	FPR2	66	1	NM_001005738	exon2	c.C992T	p.P331L	CAGCCCCAACTAA	.	scavenged	Atlas-SNP
SON	6651	hgsc.bcm.edu	37	21	34945721	34945721	+	Silent	SNP	T	T	C	rs3174808	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	73	129	0	0.442424	0	T|0.696;C|0.304	0.304	strong	.	SON	343	.	NM_138927	exon9	c.T6993C	p.N2331N	AGGCAATAAGGAA	.	PASS	Atlas-SNP
CHMP4A	29082	hgsc.bcm.edu	37	14	24679877	24679877	+	Missense_Mutation	SNP	C	C	T	rs2295322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	81	172	0	0.3375	0	C|0.594;T|0.406	0.406	strong	.	CHMP4A	20	.	NM_014169	exon4	c.G586A	p.G196R	CATCTCCAAAGCC	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	37	11	46564235	46564235	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	3	180	0	0.0176471	0	.	.	none	AMBRA1_ENST00000458649,NS,carcinoma,-1,2	AMBRA1	201	2	NM_001267783	exon8	c.G1062A	p.S354S	ACTCACCGAAGAG	.	scavenged	Atlas-SNP
NBPF7	343505	hgsc.bcm.edu	37	1	120387120	120387120	+	Silent	SNP	G	G	A	rs12405228	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	36	63	0	0.413793	0	G|0.564;A|0.436	0.436	strong	.	NBPF7	46	.	NM_001047980	exon1	c.C39T	p.T13T	AGAAGAGGTGGAG	.	PASS	Atlas-SNP
ADHFE1	137872	hgsc.bcm.edu	37	8	67380528	67380528	+	Missense_Mutation	SNP	T	T	C	rs1060242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	24	124	0	0.289157	0	T|0.441;C|0.559	0.559	strong	.	ADHFE1	83	.	NM_144650	exon14	c.T1345C	p.C449R	GCACCCTGTCCCC	.	PASS	Atlas-SNP
TBC1D28	254272	hgsc.bcm.edu	37	17	18542519	18542519	+	Missense_Mutation	SNP	T	T	G	rs74452761	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	312	126	569	2	0.403846	0.00351494	T|0.485;G|0.515	0.515	strong	.	TBC1D28	14	.	NM_001039397	exon6	c.A167C	p.E56A	GGCAGCTCCATCT	.	PASS	Atlas-SNP
TPO	7173	hgsc.bcm.edu	37	2	1418192	1418192	+	Silent	SNP	C	C	G	rs9678281	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	122	194	0	0.945736	0	C|0.654;G|0.346;T|0.000	0.346	strong	TPO,colon,carcinoma,0,1	TPO	224	1	NM_175719	exon2	c.C12G	p.L4L	AGCGCTCGCTGTG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152282917	152282917	+	Missense_Mutation	SNP	G	G	T	rs11204978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	449	148	359	1	0.329621	0.00278552	G|0.836;T|0.164	0.164	strong	.	FLG	900	.	NM_002016	exon3	c.C4445A	p.S1482Y	TCTTGGGATGCTG	.	PASS	Atlas-SNP
ARRB1	408	hgsc.bcm.edu	37	11	74994352	74994352	+	Silent	SNP	G	G	A	rs877711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	45	83	0	0.523256	0	G|0.862;A|0.138	0.138	strong	.	ARRB1	37	.	NM_020251	exon5	c.C333T	p.H111H	GTAAGCGTGCTCG	.	PASS	Atlas-SNP
CRHR1	1394	hgsc.bcm.edu	37	17	43884402	43884402	+	Silent	SNP	C	C	T	rs12936511	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	33	69	0	0.478261	0	C|0.970;T|0.030	0.030	strong	.	CRHR1	48	.	NM_001145148	exon2	c.C60T	p.P20P	GAACCCCGTCTCT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168107155	168107155	+	Missense_Mutation	SNP	G	G	A	rs16853331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	64	118	0	0.450704	0	G|0.816;A|0.184	0.184	strong	.	XIRP2	914	.	NM_152381	exon9	c.G9253A	p.A3085T	CAAGTAGCAGCTC	.	PASS	Atlas-SNP
SBNO2	22904	hgsc.bcm.edu	37	19	1109595	1109595	+	Silent	SNP	G	G	T	rs185032569	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	63	132	0	0.508065	0	G|0.995;T|0.005	0.005	strong	.	SBNO2	112	.	NM_014963	exon28	c.C3126A	p.I1042I	CACGCTGATCTGC	.	PASS	Atlas-SNP
GM2A	2760	hgsc.bcm.edu	37	5	150647012	150647012	+	Silent	SNP	A	A	G	rs1048723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	64	155	0	0.481203	0	A|0.762;G|0.238;T|0.000	0.238	strong	.	GM2A	24	.	NM_000405	exon4	c.A582G	p.X194X	CATATAACATGGC	.	PASS	Atlas-SNP
SOAT1	6646	hgsc.bcm.edu	37	1	179319541	179319541	+	Silent	SNP	C	C	G	rs3753526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	502	498	372	0	0.992032	0	C|0.891;G|0.109	0.109	strong	.	SOAT1	53	.	NM_003101	exon14	c.C1425G	p.L475L	CGTGCTCTTCGTG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910602	29910602	+	Missense_Mutation	SNP	G	G	T	rs41552219	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	25	113	0	0.229358	0	A|0.043;G|0.955;T|0.002	0.002	strong	HLA-A,NS,carcinoma,-2,4	HLA-A	89	4	NM_001242758	exon2	c.G142T	p.A48S	TTCATCGCCGTGG	.	PASS	Atlas-SNP
UBASH3B	84959	hgsc.bcm.edu	37	11	122646967	122646967	+	Missense_Mutation	SNP	G	G	A	rs12790613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	73	40	0	0.776596	0	G|0.779;A|0.221	0.221	strong	UBASH3B,NS,carcinoma,0,1	UBASH3B	73	1	NM_032873	exon2	c.G202A	p.A68T	GTTCAGGCAGCAT	.	PASS	Atlas-SNP
USP43	124739	hgsc.bcm.edu	37	17	9580092	9580092	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256	28	264	0	0.109375	0	.	.	none	.	USP43	65	.	NM_001267576	exon5	c.C863G	p.S288C	TCCCCTCTAAGAG	.	PASS	Atlas-SNP
LGALS8	3964	hgsc.bcm.edu	37	1	236706300	236706300	+	Nonsense_Mutation	SNP	T	T	A	rs2273865	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259	73	193	0	0.281853	0	T|0.899;A|0.101	0.101	strong	.	LGALS8	42	.	NM_006499	exon9	c.T635A	p.L212X	ACACTTTGACTTG	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642823	1642823	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	16	156	0	0.0924855	0	.	.	none	KRTAP5-4,colon,carcinoma,0,1	KRTAP5-4	78	1	NM_001012709	exon1	c.C501T	p.S167S	ACCTGAGGAGGAG	.	PASS	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110763875	110763875	+	Missense_Mutation	SNP	A	A	G	rs723685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	51	72	0	0.566667	0	A|0.905;G|0.095	0.095	strong	.	SLC22A16	81	.	NM_033125	exon4	c.T755C	p.V252A	GTTCCAACTGCAA	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112512905	112512905	+	Silent	SNP	G	G	A	rs2072021	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	64	120	0	0.423841	0	G|0.735;A|0.265	0.265	strong	.	LAMA4	227	.	NM_001105206	exon6	c.C651T	p.T217T	GAATCCGGTGGTG	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126239986	126239986	+	Missense_Mutation	SNP	C	C	T	rs1039808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	38	221	0	0.267606	0	C|0.580;T|0.420	0.420	strong	.	FAT4	1752	.	NM_024582	exon1	c.C2420T	p.A807V	ACGTGGCGCTGGG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169294859	169294859	+	Silent	SNP	C	C	T	rs13133439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	51	373	0	0.242857	0	C|0.979;T|0.021	0.021	strong	DDX60L,NS,carcinoma,-2,1	DDX60L	116	1	NM_001012967	exon35	c.G4734A	p.G1578G	TGTGTTCCCCGAA	.	PASS	Atlas-SNP
PCDH19	57526	hgsc.bcm.edu	37	X	99663194	99663194	+	Silent	SNP	G	G	T	rs41300169	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	78	197	0	1	0	G|0.871;T|0.129	0.129	strong	.	PCDH19	269	.	NM_001184880	exon1	c.C402A	p.I134I	CAGCTCGATCTGT	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129324703	129324703	+	Silent	SNP	G	G	C	rs139286065	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	74	206	0	0.427746	0	G|0.998;C|0.002	0.002	strong	.	PLXND1	149	.	NM_015103	exon1	c.C780G	p.S260S	GTCGTCGGAGGGG	.	PASS	Atlas-SNP
CDR2L	30850	hgsc.bcm.edu	37	17	73000061	73000061	+	Silent	SNP	A	A	G	rs3744203	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	109	126	0	1	0	A|0.528;G|0.472	0.472	strong	HUMPPA,NS,carcinoma,0,1	.	.	1	NM_014603	exon5	c.A1290G	p.E430E	GCTGGAACAGAGC	.	PASS	Atlas-SNP
TRIM56	81844	hgsc.bcm.edu	37	7	100732321	100732321	+	Silent	SNP	C	C	T	rs11760747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17	17	18	0	1	0	C|0.857;T|0.143	0.143	strong	.	TRIM56	123	.	NM_030961	exon3	c.C1728T	p.N576N	CCCCAACGGCGAA	.	PASS	Atlas-SNP
P2RX3	5024	hgsc.bcm.edu	37	11	57137424	57137424	+	Missense_Mutation	SNP	C	C	T	rs2276038	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	59	121	0	0.437037	0	C|0.650;T|0.349	0.349	strong	.	P2RX3	55	.	NM_002559	exon12	c.C1148T	p.A383V	CCACAGCGGAGAA	.	PASS	Atlas-SNP
RAB8B	51762	hgsc.bcm.edu	37	15	63548787	63548787	+	Silent	SNP	G	G	A	rs10851726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	16	87	0	0.266667	0	G|0.814;A|0.186	0.186	strong	.	RAB8B	23	.	NM_016530	exon5	c.G408A	p.G136G	AAGAGGGGAGAAG	.	PASS	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62257036	62257036	+	Missense_Mutation	SNP	A	A	C	rs1286823	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	10	80	0	0.217391	0	A|0.923;C|0.077	0.077	strong	.	INADL	179	.	NM_176877	exon9	c.A1085C	p.E362A	TTTTTGAAACTTA	.	PASS	Atlas-SNP
DCAF4	26094	hgsc.bcm.edu	37	14	73425462	73425462	+	Silent	SNP	G	G	A	rs12882409	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	32	77	0	0.405063	0	G|0.844;A|0.156	0.156	strong	.	DCAF4	40	.	NM_015604	exon14	c.G1437A	p.P479P	CGCGCCGGGGCTG	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167262939	167262939	+	Silent	SNP	A	A	G	rs33953730	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	351	176	369	0	0.501424	0	A|0.948;G|0.052	0.052	strong	SCN7A_ENST00000409855,NS,carcinoma,-1,2	SCN7A	410	2	NM_002976	exon25	c.T4200C	p.Y1400Y	AAAATTATACATT	.	PASS	Atlas-SNP
FPGT	8790	hgsc.bcm.edu	37	1	74665493	74665493	+	Silent	SNP	G	G	A	rs792310	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	44	107	0	0.77193	0	G|0.577;A|0.423	0.423	strong	.	FPGT	77	.	NM_001199329	exon2	c.G228A	p.V76V	TTTTGTGGATCCT	.	PASS	Atlas-SNP
POM121L12	285877	hgsc.bcm.edu	37	7	53103425	53103425	+	Missense_Mutation	SNP	C	C	A	rs10229800	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	65	103	0	0.601852	0	C|0.870;A|0.130	0.130	strong	.	POM121L12	146	.	NM_182595	exon1	c.C61A	p.P21T	GGAGAACCCCTGC	.	PASS	Atlas-SNP
LGALS16	148003	hgsc.bcm.edu	37	19	40151098	40151098	+	Missense_Mutation	SNP	A	A	C	rs181925874	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	9	23	0	0.310345	0	A|1.000;C|0.000	0.000	strong	.	LGALS16	6	.	NM_001190441	exon4	c.A367C	p.M123L	GTGAAGATGATTC	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	89988504	89988504	+	Missense_Mutation	SNP	A	A	G	rs2366926	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	243	276	1	0.991837	0.00362319	A|0.667;G|0.333	0.333	strong	GPR98,NS,carcinoma,0,1	GPR98	605	1	NM_032119	exon32	c.A7034G	p.N2345S	CTGCCAATGATGA	.	PASS	Atlas-SNP
LPHN1	22859	hgsc.bcm.edu	37	19	14288369	14288369	+	Silent	SNP	C	C	T	rs146417164	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	62	140	0	0.521008	0	C|0.992;T|0.008	0.008	strong	.	LPHN1	107	.	NM_001008701	exon3	c.G258A	p.P86P	GGCGTCCGGCAGG	.	PASS	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32713706	32713706	+	Missense_Mutation	SNP	A	A	T	rs2366894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	309	151	320	3	0.488673	0.009375	A|0.424;T|0.576	0.576	strong	BIRC6_ENST00000421745,NS,carcinoma,0,3	BIRC6	838	3	NM_016252	exon42	c.A8020T	p.T2674S	AGTTCAACTGGAA	.	scavenged	Atlas-SNP
MDH2	4191	hgsc.bcm.edu	37	7	75695613	75695613	+	Missense_Mutation	SNP	A	A	G	rs10256	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	44	76	0	0.571429	0	A|0.969;G|0.031	0.031	strong	.	MDH2	35	.	NM_005918	exon9	c.A902G	p.K301R	TCGAGAAGAACCT	.	PASS	Atlas-SNP
XRCC4	7518	hgsc.bcm.edu	37	5	82648977	82648977	+	Silent	SNP	T	T	G	rs1056503	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252	115	292	0	0.456349	0	T|0.685;G|0.315	0.315	strong	.	XRCC4	37	.	NM_022406	exon8	c.T927G	p.S309S	GACGTCTAAAAAG	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36788597	36788597	+	Missense_Mutation	SNP	G	G	C	rs190224798	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	61	156	0	0.279817	0	G|1.000;C|0.000	0.000	strong	.	KCNU1	359	.	NM_001031836	exon25	c.G2865C	p.L955F	GCTCTTGTCTGGA	.	PASS	Atlas-SNP
SRP72	6731	hgsc.bcm.edu	37	4	57366826	57366826	+	Silent	SNP	G	G	A	rs143643243	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	78	121	0	0.661017	0	G|0.998;A|0.002	0.002	strong	.	SRP72	59	.	NM_006947	exon18	c.G1803A	p.G601G	AAAAGGGACCCAG	.	PASS	Atlas-SNP
SMCHD1	23347	hgsc.bcm.edu	37	18	2707619	2707619	+	Missense_Mutation	SNP	G	G	A	rs2276092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	300	141	329	0	0.47	0	G|0.319;A|0.681	0.681	strong	.	SMCHD1	88	.	NM_015295	exon16	c.G2122A	p.V708I	AATGAGGTTAGGC	.	PASS	Atlas-SNP
TANGO6	79613	hgsc.bcm.edu	37	16	68893953	68893953	+	Silent	SNP	T	T	C	rs4597312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	212	301	2	0.851406	0.00664452	T|0.895;C|0.105	0.105	strong	.	.	.	.	NM_024562	exon2	c.T261C	p.S87S	AAACTCTGTGGAT	.	PASS	Atlas-SNP
SERPINI2	5276	hgsc.bcm.edu	37	3	167184878	167184878	+	Missense_Mutation	SNP	T	T	C	rs9841174	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	61	102	0	0.480315	0	C|0.395;N|0.001	0.395	strong	.	SERPINI2	85	.	NM_001012303	exon4	c.A473G	p.E158G	ATCATCTCTGCAC	.	PASS	Atlas-SNP
MLLT4	4301	hgsc.bcm.edu	37	6	168315978	168315978	+	Silent	SNP	G	G	C	rs3213590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	79	196	0	0.395	0	G|0.880;C|0.120	0.120	strong	.	MLLT4	351	.	NM_001040000	exon18	c.G2409C	p.V803V	ATTGGTGACCGAC	.	PASS	Atlas-SNP
MMEL1	79258	hgsc.bcm.edu	37	1	2535613	2535613	+	Silent	SNP	C	C	A	rs4648562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	31	265	0	0.221429	0	C|0.594;A|0.406	0.406	strong	.	MMEL1	64	.	NM_033467	exon10	c.G924T	p.V308V	CTCCAGCACCTGC	.	PASS	Atlas-SNP
CFB	629	hgsc.bcm.edu	37	6	31915614	31915614	+	Missense_Mutation	SNP	G	G	A	rs4151651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	47	130	0	0.439252	0	G|0.978;A|0.022	0.022	strong	.	CFB	33	.	NM_001710	exon5	c.G754A	p.G252S	GGGCACGGCCCAG	.	PASS	Atlas-SNP
C10orf53	282966	hgsc.bcm.edu	37	10	50901938	50901938	+	Silent	SNP	C	C	T	rs1133837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	74	202	0	0.732673	0	C|0.595;T|0.405	0.405	strong	.	C10orf53	19	.	NM_182554	exon2	c.C216T	p.F72F	GGAGTTCGGTAAG	.	PASS	Atlas-SNP
ANKRD13C	81573	hgsc.bcm.edu	37	1	70820008	70820008	+	Silent	SNP	C	C	T	rs61782675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	7	70	0	0.241379	0	C|0.928;T|0.072	0.072	strong	.	ANKRD13C	36	.	NM_030816	exon1	c.G84A	p.E28E	CGCTTCCTCATCC	.	PASS	Atlas-SNP
ASPHD1	253982	hgsc.bcm.edu	37	16	29917177	29917177	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	56	111	0	0.565657	0	.	.	none	.	ASPHD1	28	.	NM_181718	exon3	c.G1132A	p.E378K	GGGGCTGAGCGCC	.	PASS	Atlas-SNP
MGMT	4255	hgsc.bcm.edu	37	10	131565064	131565064	+	Missense_Mutation	SNP	A	A	G	rs2308321	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	64	129	0	0.447552	0	A|0.927;G|0.073	0.073	strong	.	MGMT	32	.	NM_002412	exon5	c.A520G	p.I174V	ATCCTCATCCCGT	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672703	238672703	+	Missense_Mutation	SNP	C	C	G	rs3739038	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	69	118	0	0.530769	0	C|0.687;G|0.312	0.312	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.C2347G	p.H783D	CCAGGGCACTTCA	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100105782	100105782	+	Missense_Mutation	SNP	C	C	G	rs2061634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	34	89	0	0.425	0	C|0.698;G|0.302	0.302	strong	.	.	.	.	NM_020893	exon19	c.C2567G	p.S856C	ACACTTCCAGTGC	.	PASS	Atlas-SNP
CPED1	79974	hgsc.bcm.edu	37	7	120737809	120737809	+	Missense_Mutation	SNP	C	C	T	rs144805034	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	73	171	0	0.820225	0	C|0.996;T|0.004	0.004	strong	.	.	.	.	NM_001105533	exon5	c.C673T	p.P225S	TTAAAGCCGAGTA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895889	1895889	+	Missense_Mutation	SNP	G	G	C	rs72620874	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	24	377	0	0.115942	0	G|0.689;C|0.311	0.311	strong	SIRPA,right_upper_lobe,carcinoma,+1,3	SIRPA	83	3	NM_001040022	exon3	c.G224C	p.G75A	GACCAGGCCGGGA	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112926755	112926755	+	Silent	SNP	G	G	A	rs2303718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	47	102	0	0.5	0	G|0.869;T|0.001	.	strong	YTHDC2,NS,carcinoma,+1,1	YTHDC2	118	1	NM_022828	exon27	c.G3843A	p.S1281S	TCCTTCGCCAAGA	.	PASS	Atlas-SNP
NAT16	375607	hgsc.bcm.edu	37	7	100815816	100815816	+	Silent	SNP	C	C	T	rs12540617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7	4	10	0	0.571429	0	C|0.940;T|0.060	0.060	strong	.	.	.	.	NM_198571	exon4	c.G654A	p.E218E	GCCTGCCTCGGAC	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158534372	158534372	+	Silent	SNP	G	G	A	rs57686648	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	47	104	1	0.661972	0.00961538	G|0.759;A|0.241	0.241	strong	ESYT2,NS,malignant_melanoma,-1,1	ESYT2	70	1	NM_020728	exon17	c.C2091T	p.A697A	AGGGCCGGCCTCA	.	scavenged	Atlas-SNP
IQCC	55721	hgsc.bcm.edu	37	1	32672908	32672908	+	Missense_Mutation	SNP	T	T	G	rs3903683	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	88	157	0	0.8	0	T|0.842;G|0.158	0.158	strong	.	IQCC	46	.	NM_001160042	exon5	c.T866G	p.F289C	GCGTGTTCCTAGA	.	PASS	Atlas-SNP
PEBP4	157310	hgsc.bcm.edu	37	8	22571018	22571018	+	Silent	SNP	A	A	G	rs1047398	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	122	138	0	0.600985	0	A|0.697;G|0.303	0.303	strong	.	PEBP4	23	.	NM_144962	exon7	c.T549C	p.R183R	GTGGAAACGGTTC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20845521	20845521	+	Silent	SNP	A	A	C	rs2229101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	95	111	0	0.659722	0	A|0.936;C|0.064	0.064	strong	.	TEP1	224	.	NM_007110	exon41	c.T6006G	p.L2002L	GGACTGAAGGGAG	.	PASS	Atlas-SNP
NREP	9315	hgsc.bcm.edu	37	5	111066697	111066697	+	Missense_Mutation	SNP	T	T	C	rs11559	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	58	115	0	0.527273	0	T|0.940;C|0.060	0.060	strong	C5orf13_ENST00000395634,brain,glioma,0,2	.	.	2	NM_001142475	exon4	c.A260G	p.E87G	TTTGTCTCATCGT	.	PASS	Atlas-SNP
MAP3K9	4293	hgsc.bcm.edu	37	14	71204973	71204973	+	Silent	SNP	C	C	T	rs7153601	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	82	209	0	0.336066	0	C|0.823;T|0.177	0.177	strong	.	MAP3K9	109	.	NM_033141	exon8	c.G1833A	p.S611S	ATCTCCCGAGGCA	.	PASS	Atlas-SNP
OR9Q1	219956	hgsc.bcm.edu	37	11	57947264	57947264	+	Silent	SNP	C	C	G	rs11229273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	354	351	364	1	0.991525	0.00274725	C|0.747;G|0.253	0.253	strong	.	OR9Q1	60	.	NM_001005212	exon3	c.C348G	p.A116A	CTTGGCCCTCATG	.	PASS	Atlas-SNP
OR56A4	120793	hgsc.bcm.edu	37	11	6023928	6023928	+	Missense_Mutation	SNP	C	C	T	rs374569889	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	2	162	0	0.0127389	0	.	.	alt	OR56A4,NS,carcinoma,+2,1	OR56A4	66	1	NM_001005179	exon1	c.G451A	p.A151T	AGCAGGCTGGGAA	.	scavenged	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48595988	48595988	+	Missense_Mutation	SNP	G	G	C	rs8064455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	57	110	0	0.483051	0	G|0.721;C|0.279	0.279	strong	.	MYCBPAP	135	.	NM_032133	exon5	c.G684C	p.E228D	AGAAGAGAAGAGA	.	PASS	Atlas-SNP
CDC25C	995	hgsc.bcm.edu	37	5	137665323	137665323	+	Missense_Mutation	SNP	G	G	A	rs3734166	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	72	177	0	0.507042	0	A|0.359;C|0.003	0.359	strong	.	CDC25C	37	.	NM_001790	exon3	c.C208T	p.R70C	GGCAACGTTTTGG	.	PASS	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87229702	87229702	+	Silent	SNP	A	A	G	rs4546639	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	57	123	0	0.581633	0	A|0.858;G|0.142	0.142	strong	.	SLC7A13	97	.	NM_138817	exon3	c.T1176C	p.Y392Y	TACCTTATAAGGT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912333	29912333	+	Missense_Mutation	SNP	C	C	T	rs3179982	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	114	338	0	0.450593	0	C|0.487;T|0.513	0.513	strong	.	HLA-A	89	.	NM_001242758	exon5	c.C952T	p.L318F	GTTCTCCTTGGAG	.	PASS	Atlas-SNP
TSR1	55720	hgsc.bcm.edu	37	17	2238152	2238152	+	Missense_Mutation	SNP	T	T	C	rs79597880	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	25	57	0	0.462963	0	T|0.987;C|0.013	0.013	strong	.	TSR1	57	.	NM_018128	exon5	c.A595G	p.K199E	TTTGTTTCTTCAG	.	PASS	Atlas-SNP
HIF3A	64344	hgsc.bcm.edu	37	19	46823803	46823803	+	Missense_Mutation	SNP	C	C	T	rs61755707	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	15	54	0	0.441176	0	C|0.981;T|0.019	0.019	strong	.	HIF3A	154	.	NM_152795	exon9	c.C1129T	p.P377S	CCTAACCCTGGGG	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169435713	169435713	+	Silent	SNP	A	A	C	rs2287727	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	283	143	332	0	0.5053	0	A|0.770;C|0.230	0.230	strong	.	DOCK2	389	.	NM_004946	exon32	c.A3195C	p.L1065L	ACGGCTAATTGGC	.	PASS	Atlas-SNP
VSIG1	340547	hgsc.bcm.edu	37	X	107320447	107320447	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	4	127	0	0.056338	0	.	.	none	.	VSIG1	126	.	NM_001170553	exon8	c.C1108T	p.P370S	CCTGCCCCAGGAT	.	PASS	Atlas-SNP
OR5AS1	219447	hgsc.bcm.edu	37	11	55798278	55798278	+	Silent	SNP	C	C	T	rs148523609	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	295	136	335	1	0.461017	0.00298507	C|0.993;T|0.007	0.007	strong	.	OR5AS1	121	.	NM_001001921	exon1	c.C384T	p.N128N	CTGCAACCCACTG	.	PASS	Atlas-SNP
MAATS1	89876	hgsc.bcm.edu	37	3	119421963	119421963	+	Silent	SNP	C	C	T	rs7612861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	56	122	0	0.470588	0	C|0.824;T|0.176	0.176	strong	C3orf15,NS,carcinoma,0,1	.	.	1	NM_033364	exon1	c.C18T	p.T6T	AGTAACCATCGAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072296	9072296	+	Silent	SNP	G	G	T	rs7254970	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	59	102	0	0.491667	0	G|0.815;T|0.185	0.185	strong	.	MUC16	4315	.	NM_024690	exon3	c.C15150A	p.T5050T	AGGTGTGGTCATT	.	PASS	Atlas-SNP
OLFM4	10562	hgsc.bcm.edu	37	13	53608632	53608632	+	Silent	SNP	C	C	T	rs2298231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	71	96	0	1	0	C|0.494;T|0.506	0.506	strong	.	OLFM4	94	.	NM_006418	exon2	c.C354T	p.S118S	ACTTTCCAAAGTA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	561	143	346	0	0.254902	0	T|0.872;G|0.128	0.128	strong	FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.A6462C	p.Q2154H	TTGCTCTTGGTGG	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2816519	2816519	+	Missense_Mutation	SNP	G	G	A	rs138447860	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	48	87	0	0.484848	0	G|0.997;A|0.003	0.003	strong	.	SRRM2	263	.	NM_016333	exon11	c.G5990A	p.R1997H	GATCTCGCACATC	.	PASS	Atlas-SNP
DOK7	285489	hgsc.bcm.edu	37	4	3494826	3494826	+	Silent	SNP	A	A	C	rs6811856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	28	80	0	0.56	0	A|0.734;C|0.266	0.266	strong	.	DOK7	44	.	NM_173660	exon7	c.A1113C	p.S371S	GGGCTCACTGCTC	.	PASS	Atlas-SNP
MR1	3140	hgsc.bcm.edu	37	1	181021483	181021483	+	Silent	SNP	C	C	T	rs35223984	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	110	119	1	0.628571	0.00840336	C|0.978;T|0.022	0.022	strong	MR1,colon,NS,0,2	MR1	46	2	NM_001531	exon5	c.C717T	p.N239N	GAAAAACGGGGAA	.	scavenged	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145006143	145006143	+	Missense_Mutation	SNP	T	T	C	rs189137260	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	83	114	0	0.538961	0	T|0.995;C|0.005	0.005	strong	.	PLEC	1144	.	NM_201380	exon18	c.A2551G	p.I851V	CCTCGATACAGCA	.	PASS	Atlas-SNP
LRIG3	121227	hgsc.bcm.edu	37	12	59279660	59279660	+	Silent	SNP	A	A	T	rs11172796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	21	83	0	0.538462	0	A|0.833;T|0.167	0.167	strong	LRIG3,NS,haematopoietic_neoplasm,-1,1	LRIG3	120	1	NM_153377	exon10	c.T1197A	p.R399R	AATAGAACGGATC	.	PASS	Atlas-SNP
SLC52A1	55065	hgsc.bcm.edu	37	17	4936898	4936898	+	Missense_Mutation	SNP	C	C	T	rs2304445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	36	79	0	0.48	0	C|0.783;T|0.217	0.217	strong	GPR172B,caecum,carcinoma,0,1	.	.	1	NM_017986	exon3	c.G886A	p.V296M	GCAGCACGCCATT	.	PASS	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18377981	18377981	+	Silent	SNP	C	C	G	rs61740692	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	94	208	0	0.484536	0	C|0.984;G|0.016	0.016	strong	.	KIAA1683	190	.	NM_001145304	exon3	c.G369C	p.L123L	GGAAATCAGCTTC	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156873727	156873727	+	Silent	SNP	G	G	A	rs12407843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	26	66	0	0.393939	0	G|0.842;A|0.158	0.158	strong	.	PEAR1	118	.	NM_001080471	exon2	c.G9A	p.P3P	GTCACCGCCTCTG	.	PASS	Atlas-SNP
ZC3H11A	9877	hgsc.bcm.edu	37	1	203787702	203787702	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	3	80	0	0.0283019	0	.	.	none	ZC3H11A,NS,carcinoma,+1,1	ZC3H11A	71	1	NM_014827	exon6	c.A59G	p.D20G	AGGGTGACAGCTG	.	scavenged	Atlas-SNP
STON2	85439	hgsc.bcm.edu	37	14	81743718	81743718	+	Missense_Mutation	SNP	C	C	T	rs34323725	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	122	163	0	0.681564	0	C|0.900;T|0.100	0.100	strong	.	STON2	94	.	NM_001256430	exon6	c.G1937A	p.R646H	TGGAAACGGCACT	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167269629	167269629	+	Silent	SNP	T	T	G	rs33922582	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	328	137	367	0	0.417683	0	T|0.945;G|0.055	0.055	strong	.	SCN7A	410	.	NM_002976	exon21	c.A3417C	p.A1139A	AAATGTTGCCTGT	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27190655	27190655	+	Missense_Mutation	SNP	G	G	A	rs1334811	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	84	247	0	0.477273	0	G|0.928;A|0.072	0.072	strong	.	TEK	250	.	NM_000459	exon10	c.G1456A	p.V486I	AAACCCGTTAATC	.	PASS	Atlas-SNP
YPEL3	83719	hgsc.bcm.edu	37	16	30106716	30106716	+	Missense_Mutation	SNP	C	C	A	rs184524218	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	24	44	0	0.648649	0	C|0.995;A|0.005	0.005	strong	.	YPEL3	5	.	NM_031477	exon1	c.G88T	p.V30L	GCCCCACGCGGGG	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790575	4790575	+	Silent	SNP	A	A	G	rs12788102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	306	149	306	0	0.486928	0	A|0.911;G|0.089	0.089	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T573C	p.C191C	GTCTGAACATGCT	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124358498	124358498	+	Missense_Mutation	SNP	T	T	G	rs144489236	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	68	147	1	0.618182	0.00680272	T|0.976;G|0.024	0.024	strong	DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	NM_007329	exon26	c.T3165G	p.I1055M	ACCCATTGTCCTG	.	scavenged	Atlas-SNP
EML3	256364	hgsc.bcm.edu	37	11	62378660	62378660	+	Silent	SNP	G	G	A	rs12808829	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	22	26	0	1	0	G|0.761;A|0.239	0.239	strong	.	EML3	61	.	NM_153265	exon3	c.C351T	p.S117S	GGTCCCGCTAGGC	.	PASS	Atlas-SNP
OR51B4	79339	hgsc.bcm.edu	37	11	5322520	5322520	+	Silent	SNP	G	G	A	rs12283334	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	83	79	0	0.988095	0	G|0.775;A|0.225	0.225	strong	.	OR51B4	64	.	NM_033179	exon1	c.C657T	p.L219L	TGTCTTGAGGATT	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62253954	62253954	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	8	168	0	0.0733945	0	.	.	none	.	VPS13C	506	.	NM_020821	exon35	c.C3742A	p.P1248T	TAACCGGTGCTTT	.	PASS	Atlas-SNP
MOK	5891	hgsc.bcm.edu	37	14	102729881	102729881	+	Splice_Site	SNP	A	A	G	rs56377169	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	31	88	0	0.322917	0	A|0.954;G|0.046	0.046	strong	.	.	.	.	NM_014226	exon5	c.283+2T>C	.	CTACGTACCTCGT	.	PASS	Atlas-SNP
SRBD1	55133	hgsc.bcm.edu	37	2	45640374	45640374	+	Missense_Mutation	SNP	C	C	A	rs3755073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	182	206	1	0.98913	0.00485437	C|0.818;A|0.182	0.182	strong	.	SRBD1	107	.	NM_018079	exon19	c.G2392T	p.V798F	CCTCAACGTCTGC	.	PASS	Atlas-SNP
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31838085	31838085	+	Silent	SNP	G	G	A	rs5997988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	61	185	0	0.442029	0	G|0.611;A|0.389	0.389	strong	.	EIF4ENIF1	80	.	NM_019843	exon17	c.C2226T	p.S742S	TACAGAGCTGGAT	.	PASS	Atlas-SNP
ABI3	51225	hgsc.bcm.edu	37	17	47297633	47297633	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	269	3	324	1	0.0111524	0.00308642	.	.	none	ABI3,right_upper_lobe,carcinoma,0,1	ABI3	35	1	NM_016428	exon6	c.C747T	p.A249A	AGCAGCCGTCGAG	.	scavenged	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197401952	197401952	+	Silent	SNP	T	T	C	rs28562770	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	32	96	0	0.385542	0	T|0.811;C|0.189	0.189	strong	.	KIAA0226	136	.	NM_014687	exon20	c.A2856G	p.S952S	GTAGTCTGACAGG	.	PASS	Atlas-SNP
SCAF4	57466	hgsc.bcm.edu	37	21	33068937	33068937	+	Missense_Mutation	SNP	C	C	A	rs78537042	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	104	84	0	0.645963	0	C|0.947;A|0.053	0.053	strong	.	SCAF4	142	.	NM_020706	exon8	c.G904T	p.V302L	CAGGCACGGTGGC	.	PASS	Atlas-SNP
MICALCL	84953	hgsc.bcm.edu	37	11	12315848	12315848	+	Silent	SNP	C	C	T	rs1493952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	16	45	0	0.457143	0	C|0.576;T|0.424	0.424	strong	.	MICALCL	59	.	NM_032867	exon3	c.C870T	p.G290G	TGAAGGCGGGAAG	.	PASS	Atlas-SNP
SDC1	6382	hgsc.bcm.edu	37	2	20403949	20403949	+	Silent	SNP	C	C	T	rs2230924	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	9	24	0	0.3	0	T|0.225;G|0.000;C|0.775	0.225	strong	.	SDC1	32	.	NM_002997	exon3	c.G252A	p.E84E	TGTAGCCTCCAGG	.	PASS	Atlas-SNP
ZXDC	79364	hgsc.bcm.edu	37	3	126191011	126191011	+	Silent	SNP	G	G	A	rs62264721	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	27	49	0	0.482143	0	G|0.982;A|0.018	0.018	strong	.	ZXDC	87	.	NM_025112	exon2	c.C1045T	p.L349L	TCCGCAGGTGAAT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168106246	168106246	+	Missense_Mutation	SNP	G	G	A	rs16853330	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	64	156	0	0.467153	0	G|0.774;A|0.225	0.225	strong	XIRP2,NS,carcinoma,-1,1	XIRP2	914	1	NM_152381	exon9	c.G8344A	p.V2782I	GTGACAGTACAAT	.	PASS	Atlas-SNP
MORN2	729967	hgsc.bcm.edu	37	2	39109558	39109558	+	Missense_Mutation	SNP	G	G	A	rs3099950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	41	68	0	0.546667	0	G|0.919;A|0.081	0.081	strong	.	MORN2	3	.	NM_001145450	exon5	c.G142A	p.E48K	AGGGTGGAAGGTG	.	PASS	Atlas-SNP
HPSE	10855	hgsc.bcm.edu	37	4	84227453	84227453	+	Missense_Mutation	SNP	C	C	T	rs138882001	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	40	95	1	0.444444	0.0105263	C|0.999;T|0.001	0.001	strong	HPSE,right_upper_lobe,carcinoma,0,1	HPSE	55	1	NM_001098540	exon9	c.G1109A	p.G370D	GACAGGCCCAATT	.	scavenged	Atlas-SNP
OR7A5	26659	hgsc.bcm.edu	37	19	14938616	14938616	+	Silent	SNP	T	T	C	rs2190686	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	78	177	0	0.527027	0	T|0.505;C|0.495	0.495	strong	.	OR7A5	43	.	NM_017506	exon1	c.A438G	p.L146L	GGATGCTAGAACC	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33768199	33768199	+	Silent	SNP	G	G	A	rs56321651		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	77	167	0	0.516779	0	.	.	weak	SLFN13,NS,carcinoma,0,1	SLFN13	79	1	NM_144682	exon6	c.C2109T	p.D703D	AAAGTAGTCCAGA	.	PASS	Atlas-SNP
TES	26136	hgsc.bcm.edu	37	7	115897392	115897392	+	Silent	SNP	G	G	C	rs4710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	76	167	0	0.324786	0	T|0.000;G|0.669;C|0.331	0.331	strong	TES_ENST00000257721,colon,carcinoma,+1,2	TES	68	2	NM_015641	exon7	c.G1122C	p.R374R	GCAGCGGGTGACC	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2812647	2812647	+	Silent	SNP	C	C	T	rs2240142	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	33	78	1	0.471429	0.0128205	C|0.826;T|0.174	0.174	strong	SRRM2,NS,lymphoid_neoplasm,0,1	SRRM2	263	1	NM_016333	exon11	c.C2118T	p.S706S	TAGAAGCTTAGTT	.	scavenged	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157009	26157009	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	35	103	0	0.321101	0	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.C391T	p.P131S	AAGAAGCCAGCAG	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777513	52777513	+	Missense_Mutation	SNP	T	T	C	rs2245203	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	73	206	0	0.392473	0	T|0.684;C|0.316	0.316	strong	.	KRT84	61	.	NM_033045	exon2	c.A616G	p.I206V	TCCTGATACATTT	.	PASS	Atlas-SNP
CCDC101	112869	hgsc.bcm.edu	37	16	28603012	28603012	+	Silent	SNP	A	A	G	rs3194168	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	38	71	0	0.475	0	A|0.894;G|0.106	0.106	strong	.	CCDC101	24	.	NM_138414	exon10	c.A867G	p.E289E	TAAGGAACCCAAG	.	PASS	Atlas-SNP
MS4A14	84689	hgsc.bcm.edu	37	11	60183159	60183159	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	5	209	0	0.0246305	0	.	.	none	MS4A14,NS,carcinoma,0,1	MS4A14	120	1	NM_001261828	exon6	c.T817C	p.S273P	CTTCCATCTCCCA	.	scavenged	Atlas-SNP
BSPRY	54836	hgsc.bcm.edu	37	9	116132092	116132092	+	Missense_Mutation	SNP	G	G	C	rs818711	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	40	98	0	0.350877	0	G|0.930;C|0.070	0.070	strong	.	BSPRY	21	.	NM_017688	exon6	c.G879C	p.Q293H	TGTCCAGAACAGT	.	PASS	Atlas-SNP
NELL1	4745	hgsc.bcm.edu	37	11	20805335	20805335	+	Silent	SNP	C	C	T	rs2280363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	59	124	0	0.551402	0	C|0.716;T|0.284	0.284	strong	NELL1,NS,carcinoma,0,1	NELL1	179	1	NM_006157	exon3	c.C294T	p.S98S	GCCATCCACTTCA	.	PASS	Atlas-SNP
IFNGR1	3459	hgsc.bcm.edu	37	6	137519588	137519588	+	Silent	SNP	A	A	C	rs11914	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	39	102	0	0.371429	0	A|0.874;C|0.126	0.126	strong	.	IFNGR1	46	.	NM_000416	exon7	c.T1050G	p.S350S	TATACTAGAAAGT	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112823998	112823998	+	Silent	SNP	C	C	T	rs348943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	80	87	0	0.963855	0	C|0.505;T|0.495	0.495	strong	.	MCC	234	.	NM_001085377	exon1	c.G114A	p.E38E	CATCCTCTCCTCC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9060915	9060915	+	Missense_Mutation	SNP	C	C	T	rs59168469	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206	104	210	1	0.504854	0.0047619	C|0.974;T|0.026	0.026	strong	.	MUC16	4315	.	NM_024690	exon3	c.G26531A	p.R8844H	GATGGGCGGCTTG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2161796	2161796	+	Silent	SNP	G	G	A	rs75510884	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	28	60	0	0.54902	0	G|0.854;A|0.146	0.146	strong	PKD1,colon,carcinoma,-2,1	PKD1	184	1	NM_000296	exon15	c.C3372T	p.A1124A	CAGGGAGGCGCGC	.	PASS	Atlas-SNP
FBXO7	25793	hgsc.bcm.edu	37	22	32875190	32875190	+	Missense_Mutation	SNP	G	G	A	rs11107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	66	219	0	0.390533	0	G|0.577;N|0.000	.	strong	.	FBXO7	131	.	NM_012179	exon2	c.G345A	p.M115I	TAGCATGCAGGAT	.	PASS	Atlas-SNP
C19orf53	28974	hgsc.bcm.edu	37	19	13885309	13885309	+	Silent	SNP	C	C	T	rs1128749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	54	90	0	0.5	0	A|0.000;C|0.661;G|0.000;T|0.338	0.338	strong	C19orf53,NS,carcinoma,0,1	C19orf53	14	1	NM_014047	exon1	c.C18T	p.R6R	GCAGCGCAAGTTT	.	PASS	Atlas-SNP
VAV2	7410	hgsc.bcm.edu	37	9	136643994	136643994	+	Missense_Mutation	SNP	T	T	C	rs602990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	34	79	0	0.523077	0	T|0.441;C|0.559	0.559	strong	VAV2,NS,carcinoma,0,1	VAV2	165	1	NM_001134398	exon22	c.A1780G	p.M594V	TCTGCATGGCCAC	.	PASS	Atlas-SNP
HRCT1	646962	hgsc.bcm.edu	37	9	35906624	35906624	+	Missense_Mutation	SNP	G	G	A	rs75458097	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40	15	57	1	0.375	0.0175439	G|0.954;A|0.046	0.046	strong	HRCT1,NS,haematopoietic_neoplasm,0,1	HRCT1	14	1	NM_001039792	exon1	c.G340A	p.A114T	CGCCACGCTCGCT	.	scavenged	Atlas-SNP
XKR8	55113	hgsc.bcm.edu	37	1	28290155	28290155	+	Silent	SNP	G	G	A	rs142513353	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	16	201	0	0.125	0	G|0.997;A|0.003	0.003	strong	.	XKR8	15	.	NM_018053	exon2	c.G441A	p.T147T	GCTCACGCTGGTG	.	PASS	Atlas-SNP
MCHR1	2847	hgsc.bcm.edu	37	22	41075543	41075543	+	Missense_Mutation	SNP	A	A	G	rs133072	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	108	186	1	1	0.00537634	A|0.330;G|0.670	0.670	strong	.	MCHR1	45	.	NM_005297	exon1	c.A94G	p.N32D	CTTCCCAACTGCG	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	55999950	55999950	+	Missense_Mutation	SNP	G	G	C	rs12221615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	101	226	0	0.452915	0	G|0.901;C|0.099	0.099	strong	OR5T2,right_upper_lobe,carcinoma,+2,3	OR5T2	107	3	NM_001004746	exon1	c.C712G	p.L238V	AGAAGAGTAGAAG	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111653574	111653574	+	Silent	SNP	C	C	G	rs1063110	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	51	89	0	0.463636	0	G|0.357;C|0.643	0.357	strong	.	IKBKAP	122	.	NM_003640	exon28	c.G3069C	p.L1023L	ACATGTCAGAAAG	.	PASS	Atlas-SNP
MYBPC3	4607	hgsc.bcm.edu	37	11	47354787	47354787	+	Silent	SNP	C	C	T	rs1052373	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	143	164	0	0.972789	0	C|0.557;T|0.443	0.443	strong	.	MYBPC3	102	.	NM_000256	exon29	c.G3288A	p.E1096E	CCAGAGCTCCGTG	.	PASS	Atlas-SNP
MADD	8567	hgsc.bcm.edu	37	11	47306628	47306628	+	Missense_Mutation	SNP	G	G	A	rs3736101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	37	94	0	0.377551	0	G|0.922;A|0.078	0.078	strong	.	MADD	172	.	NM_130470	exon13	c.G2294A	p.R765Q	TGCGCCGGCGAAT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790857	4790857	+	Silent	SNP	A	A	G	rs11033797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	60	134	0	0.545455	0	A|0.713;G|0.287	0.287	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T291C	p.Y97Y	GCAGCTATATAGA	.	PASS	Atlas-SNP
RBMXL2	27288	hgsc.bcm.edu	37	11	7110548	7110548	+	Missense_Mutation	SNP	C	C	T	rs11041170	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	45	79	0	0.5	0	C|0.795;T|0.205	0.205	strong	.	RBMXL2	47	.	NM_014469	exon1	c.C197T	p.A66V	CCGCCGCCAGAGA	.	PASS	Atlas-SNP
GHSR	2693	hgsc.bcm.edu	37	3	172165757	172165757	+	Silent	SNP	G	G	C	rs2232169	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	56	134	0	0.448	0	G|0.963;C|0.037	0.037	strong	GHSR_ENST00000427970,NS,carcinoma,-2,1	GHSR	104	1	NM_198407	exon1	c.C447G	p.L149L	GGCCCGGAGTGGG	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31770009	31770009	+	Silent	SNP	C	C	T	rs28609894	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	66	80	0	0.970588	0	C|0.717;T|0.283	0.283	strong	.	TSHZ3	549	.	NM_020856	exon2	c.G690A	p.T230T	GTGCACCGTCAAC	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43074434	43074434	+	Missense_Mutation	SNP	C	C	T	rs2936817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	105	115	1	0.990566	0.00869565	C|0.535;T|0.465	0.465	strong	.	FAM198A	23	.	NM_001129908	exon2	c.C679T	p.H227Y	GGAGCTCATCAGT	.	PASS	Atlas-SNP
GAPVD1	26130	hgsc.bcm.edu	37	9	128117027	128117027	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	3	132	0	0.0344828	0	.	.	none	GAPVD1,NS,carcinoma,0,2	GAPVD1	124	2	NM_015635	exon23	c.C3745T	p.R1249W	GTTTTGCGGGACA	.	scavenged	Atlas-SNP
ZNF155	7711	hgsc.bcm.edu	37	19	44501518	44501518	+	Silent	SNP	G	G	A	rs446016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	36	108	0	0.5	0	G|0.668;A|0.332	0.332	strong	.	ZNF155	30	.	NM_001260488	exon6	c.G1542A	p.P514P	CCAGCCGAGAGAC	.	PASS	Atlas-SNP
CCDC81	60494	hgsc.bcm.edu	37	11	86123467	86123467	+	Silent	SNP	G	G	A	rs3741006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	209	127	0	0.985849	0	G|0.678;A|0.322	0.322	strong	.	CCDC81	89	.	NM_001156474	exon11	c.G1257A	p.A419A	TCCTGCGCTTAAT	.	PASS	Atlas-SNP
FBN1	2200	hgsc.bcm.edu	37	15	48797307	48797307	+	Silent	SNP	A	A	G	rs25458	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	49	129	0	0.7	0	A|0.747;G|0.253	0.253	strong	.	FBN1	310	.	NM_000138	exon16	c.T1875C	p.N625N	ACGCCCATTCATG	.	PASS	Atlas-SNP
KLHL31	401265	hgsc.bcm.edu	37	6	53519857	53519857	+	Silent	SNP	G	G	A	rs12210809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	106	181	0	0.509615	0	G|0.516;A|0.484	0.484	strong	.	KLHL31	48	.	NM_001003760	exon2	c.C214T	p.L72L	CACATAGGAAGTT	.	PASS	Atlas-SNP
HERPUD2	64224	hgsc.bcm.edu	37	7	35709842	35709842	+	Missense_Mutation	SNP	C	C	T	rs3779234	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	158	120	1	0.981366	0.00833333	C|0.703;T|0.297	0.297	strong	.	HERPUD2	47	.	NM_022373	exon4	c.G322A	p.A108T	TGGATGCCAATGC	.	PASS	Atlas-SNP
SLC45A1	50651	hgsc.bcm.edu	37	1	8395560	8395560	+	Missense_Mutation	SNP	G	G	T	rs7535752	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	28	56	0	0.756757	0	G|0.849;T|0.151	0.151	strong	.	SLC45A1	85	.	NM_001080397	exon5	c.G1507T	p.A503S	GAGCGCGCGGAGC	.	PASS	Atlas-SNP
CD1B	910	hgsc.bcm.edu	37	1	158299358	158299358	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	396	231	325	0	0.583333	0	.	.	none	CD1B,colon,carcinoma,+1,1	CD1B	78	1	NM_001764	exon4	c.T688C	p.Y230H	TTGGGTAGAATCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677378	100677378	+	Missense_Mutation	SNP	C	C	A	rs143956720	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	291	77	142	0	0.264605	0	C|0.958;A|0.042	0.042	strong	MUC17,NS,lymphoid_neoplasm,0,1	MUC17	804	1	NM_001040105	exon3	c.C2681A	p.T894K	CCAGCACACCTGT	.	PASS	Atlas-SNP
TMPO	7112	hgsc.bcm.edu	37	12	98927830	98927830	+	Missense_Mutation	SNP	C	C	G	rs17459334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	35	88	0	0.460526	0	C|0.934;G|0.066	0.066	strong	TMPO_ENST00000266732,rectum,carcinoma,0,1	TMPO	111	1	NM_003276	exon4	c.C1795G	p.Q599E	ATTAGTCAAGCTG	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39598616	39598616	+	Silent	SNP	G	G	A	rs61945763	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	64	213	0	0.418301	0	G|0.909;A|0.091	0.091	strong	.	.	.	.	NM_025138	exon7	c.C558T	p.S186S	TGGTTTGGATGGC	.	PASS	Atlas-SNP
SETD8	387893	hgsc.bcm.edu	37	12	123875311	123875311	+	Silent	SNP	C	C	T	rs74356260		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	2	169	0	0.0113636	0	.	.	weak	SETD8,NS,carcinoma,0,6	SETD8	35	6	NM_020382	exon3	c.C267T	p.A89A	ATTAGCCGGAATC	.	scavenged	Atlas-SNP
SLC39A13	91252	hgsc.bcm.edu	37	11	47431764	47431764	+	Missense_Mutation	SNP	G	G	A	rs35741412	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	54	131	0	0.55102	0	G|0.984;A|0.016	0.016	strong	.	SLC39A13	18	.	NM_152264	exon2	c.G119A	p.R40Q	GGAGCCGGGGGAC	.	PASS	Atlas-SNP
EPB41L3	23136	hgsc.bcm.edu	37	18	5416221	5416221	+	Missense_Mutation	SNP	C	C	T	rs9966357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	68	148	0	0.475524	0	C|0.945;T|0.055	0.055	strong	.	EPB41L3	222	.	NM_012307	exon13	c.G1663A	p.A555T	CCAAGGCGGGCTC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379773	31379773	+	Silent	SNP	C	C	T	rs56319010		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	39	126	0	0.351351	0	.	.	weak	.	MICA	21	.	NM_001177519	exon4	c.C663T	p.I221I	CAACATCACCGTG	.	PASS	Atlas-SNP
OR5P3	120066	hgsc.bcm.edu	37	11	7847208	7847208	+	Silent	SNP	T	T	C	rs1482791	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	67	134	0	0.503759	0	T|0.476;C|0.524	0.524	strong	.	OR5P3	44	.	NM_153445	exon1	c.A312G	p.V104V	CGTCACTACAGAA	.	PASS	Atlas-SNP
ZBTB45	84878	hgsc.bcm.edu	37	19	59028427	59028427	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	3	180	1	0.0159574	0.00555556	.	.	none	ZBTB45,NS,carcinoma,0,1	ZBTB45	37	1	NM_032792	exon2	c.A614G	p.D205G	CCTCGGTCATCAG	.	scavenged	Atlas-SNP
ZNF135	7694	hgsc.bcm.edu	37	19	58572959	58572959	+	Silent	SNP	G	G	A	rs2288274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	106	263	0	0.432653	0	G|0.716;A|0.284	0.284	strong	ZNF135_ENST00000401053,colon,carcinoma,+1,3	ZNF135	159	3	NM_007134	exon2	c.G81A	p.T27T	AGTGACGTTTGAG	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43510437	43510437	+	Missense_Mutation	SNP	A	A	G	rs17114359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	90	180	1	0.4	0.00555556	A|0.735;C|0.140;G|0.124	0.124	strong	UMODL1_ENST00000408989,colon,carcinoma,0,2	UMODL1	186	2	NM_173568	exon6	c.A820G	p.N274D	GAGCTCAATGCCT	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677995	100677995	+	Missense_Mutation	SNP	A	A	G	rs149287079	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	909	157	220	0	0.172717	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.A3298G	p.S1100G	GAAGGAAGCACTC	.	PASS	Atlas-SNP
CALCOCO2	10241	hgsc.bcm.edu	37	17	46939658	46939658	+	Missense_Mutation	SNP	C	C	G	rs10278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	93	170	0	0.460396	0	C|0.673;G|0.327	0.327	strong	.	CALCOCO2	29	.	NM_001261390	exon13	c.C1237G	p.P413A	TCTTCCCCCAGCC	.	PASS	Atlas-SNP
SLC6A18	348932	hgsc.bcm.edu	37	5	1225676	1225676	+	Silent	SNP	C	C	T	rs33978774	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	61	141	0	0.535088	0	C|0.893;T|0.107	0.107	strong	.	SLC6A18	84	.	NM_182632	exon1	c.C84T	p.L28L	GTACCTCCTGAGC	.	PASS	Atlas-SNP
KRT7	3855	hgsc.bcm.edu	37	12	52635360	52635360	+	Silent	SNP	G	G	A	rs999665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	111	130	0	0.982301	0	G|0.514;A|0.486	0.486	strong	KRT7,NS,carcinoma,0,1	KRT7	48	1	NM_005556	exon5	c.G798A	p.A266A	CAAGGCGCAGTAT	.	PASS	Atlas-SNP
GLYATL3	389396	hgsc.bcm.edu	37	6	49485266	49485266	+	Missense_Mutation	SNP	C	C	A	rs9367358	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	79	210	0	0.409326	0	C|0.732;A|0.268	0.268	strong	.	GLYATL3	19	.	NM_001010904	exon4	c.C310A	p.Q104K	CAAATACAAGGTG	.	PASS	Atlas-SNP
TKTL2	84076	hgsc.bcm.edu	37	4	164393117	164393117	+	Missense_Mutation	SNP	T	T	A	rs11735477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	36	175	0	0.262774	0	A|0.186;N|0.000	0.186	strong	TKTL2,NS,carcinoma,0,1	TKTL2	130	1	NM_032136	exon1	c.A1770T	p.Q590H	TGCCAGTTGATGA	.	PASS	Atlas-SNP
IL22RA1	58985	hgsc.bcm.edu	37	1	24447943	24447943	+	Silent	SNP	G	G	A	rs34967816	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	80	133	1	0.941176	0.0075188	G|0.880;A|0.120	0.120	strong	.	IL22RA1	62	.	NM_021258	exon7	c.C1077T	p.V359V	GGGCCCGACCTCA	.	PASS	Atlas-SNP
NLRC4	58484	hgsc.bcm.edu	37	2	32475109	32475109	+	Silent	SNP	G	G	A	rs455060	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	90	195	1	0.459184	0.00512821	G|0.383;A|0.617	0.617	strong	NLRC4,NS,carcinoma,0,1	NLRC4	165	1	NM_001199138	exon4	c.C1824T	p.A608A	GTCCAGGGCACTT	.	scavenged	Atlas-SNP
OR2W5	441932	hgsc.bcm.edu	37	1	247654916	247654916	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	4	173	0	0.0164609	0	.	.	none	OR2W5,NS,adenocarcinoma,-2,1	OR2W5	97	1	NM_001004698	exon1	c.A487G	p.T163A	CCTCAGACGATGC	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416784	105416784	+	Silent	SNP	A	A	G	rs59373922	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	380	164	250	1	0.431579	0.004	A|0.835;G|0.165	0.165	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T5004C	p.F1668F	CACCCCAAATGAT	.	PASS	Atlas-SNP
USP2	9099	hgsc.bcm.edu	37	11	119229964	119229964	+	Silent	SNP	G	G	A	rs2241646	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	283	203	162	0	0.717314	0	G|0.310;A|0.690	0.690	strong	.	USP2	71	.	NM_004205	exon5	c.C1038T	p.Y346Y	CGGTGCGTATCTC	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836060	2836060	+	Silent	SNP	G	G	A	rs113318393	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	36	82	0	0.433735	0	G|0.930;A|0.070	0.070	strong	.	ARSD	47	.	NM_001669	exon5	c.C648T	p.A216A	CTGGCCGGCAGCC	.	PASS	Atlas-SNP
KLC4	89953	hgsc.bcm.edu	37	6	43039340	43039340	+	Missense_Mutation	SNP	C	C	T	rs41274918	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	134	280	2	0.533865	0.00714286	C|0.999;T|0.001	0.001	strong	KLC4,colon,carcinoma,0,1	KLC4	89	1	NM_201523	exon10	c.C1345T	p.R449W	GAGGAGCGGGAGG	.	scavenged	Atlas-SNP
ZNF521	25925	hgsc.bcm.edu	37	18	22775185	22775185	+	Silent	SNP	C	C	T	rs1140026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	93	110	0	1	0	C|0.786;T|0.214	0.214	strong	.	ZNF521	269	.	NM_015461	exon5	c.G3597A	p.K1199K	CTGACACTTGATG	.	PASS	Atlas-SNP
NAT2	10	hgsc.bcm.edu	37	8	18258103	18258103	+	Missense_Mutation	SNP	G	G	A	rs1799930	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	37	52	0	0.402174	0	G|0.742;A|0.258	0.258	strong	.	NAT2	34	.	NM_000015	exon2	c.G590A	p.R197Q	AACCTCGAACAAT	.	PASS	Atlas-SNP
CD44	960	hgsc.bcm.edu	37	11	35222681	35222681	+	Silent	SNP	C	C	T	rs35356320	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	33	94	0	0.515625	0	C|0.956;T|0.044	0.044	strong	.	CD44	48	.	NM_000610	exon8	c.C975T	p.T325T	CTGGACCCAGTGG	.	PASS	Atlas-SNP
CC2D2A	57545	hgsc.bcm.edu	37	4	15569018	15569018	+	Silent	SNP	G	G	A	rs73125627	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	437	213	474	1	0.487414	0.0021097	G|0.819;A|0.181	0.181	strong	CC2D2A,NS,carcinoma,0,1	CC2D2A	158	1	NM_001080522	exon26	c.G3201A	p.S1067S	GCCGTCGAGGTCT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152192395	152192395	+	Silent	SNP	G	G	A	rs61814946	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	332	116	234	0	0.349398	0	G|0.895;A|0.105	0.105	strong	HRNR,NS,carcinoma,0,1	HRNR	403	1	NM_001009931	exon3	c.C1710T	p.S570S	GCCACGGCTTGAA	.	PASS	Atlas-SNP
ITIH4	3700	hgsc.bcm.edu	37	3	52864635	52864635	+	Silent	SNP	A	A	G	rs2276818	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	53	123	0	0.46087	0	A|0.880;G|0.120	0.120	strong	ITIH4,NS,adenocarcinoma,-1,1	ITIH4	74	1	NM_001166449	exon1	c.T24C	p.R8R	GCAGGTACGGACA	.	PASS	Atlas-SNP
WIPF3	644150	hgsc.bcm.edu	37	7	29924072	29924072	+	Missense_Mutation	SNP	A	A	G	rs3750092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256	90	252	0	0.351562	0	A|0.914;G|0.086	0.086	strong	WIPF3,NS,carcinoma,0,1	WIPF3	46	1	NM_001080529	exon5	c.A962G	p.E321G	GCAGTGAAACTCC	.	PASS	Atlas-SNP
HOOK2	29911	hgsc.bcm.edu	37	19	12876964	12876964	+	Missense_Mutation	SNP	G	G	C	rs897804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14	12	41	0	0.857143	0	G|0.729;C|0.271	0.271	strong	HOOK2,NS,carcinoma,0,1	HOOK2	73	1	NM_001100176	exon15	c.C1464G	p.H488Q	CTCCAGGTGGCGC	.	PASS	Atlas-SNP
TAGLN	6876	hgsc.bcm.edu	37	11	117074109	117074109	+	Silent	SNP	G	G	A	rs12970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	305	80	173	0	0.262295	0	G|0.941;A|0.059	0.059	strong	.	TAGLN	17	.	NM_001001522	exon3	c.G267A	p.K89K	CTTCAAGCAGATG	.	PASS	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108367020	108367020	+	Silent	SNP	C	C	T	rs7082289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	9	104	0	0.163636	0	C|0.839;T|0.161	0.161	strong	.	SORCS1	534	.	NM_001206572	exon23	c.G3069A	p.A1023A	GAGCACCGCCACC	.	PASS	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32196453	32196453	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	4	85	0	0.102564	0	.	.	none	BAI2,colon,carcinoma,0,1	BAI2	128	1	NM_001703	exon29	c.G4328A	p.R1443Q	ATGGTCCGGCTGC	.	PASS	Atlas-SNP
CCDC138	165055	hgsc.bcm.edu	37	2	109408159	109408159	+	Missense_Mutation	SNP	G	G	T	rs35794776	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	37	88	0	0.578125	0	G|0.942;T|0.058	0.058	strong	.	CCDC138	49	.	NM_144978	exon4	c.G295T	p.D99Y	TTCCATGATTTGA	.	PASS	Atlas-SNP
TPM1	7168	hgsc.bcm.edu	37	15	63351840	63351840	+	Silent	SNP	C	C	A	rs1071646	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	5	61	0	0.135135	0	C|0.339;A|0.661	0.661	strong	.	TPM1	59	.	NM_001018007	exon4	c.C453A	p.A151A	AGAGGCCAAGCAC	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149265875	149265875	+	Silent	SNP	G	G	A	rs61733360	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	79	159	0	0.484663	0	G|0.969;A|0.031	0.031	strong	PDE6A,NS,carcinoma,0,1	PDE6A	98	1	NM_000440	exon14	c.C1791T	p.F597F	ATGGCAGAAAGCA	.	PASS	Atlas-SNP
ADNP	23394	hgsc.bcm.edu	37	20	49509184	49509184	+	Silent	SNP	G	G	A	rs17790938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	82	200	0	0.5125	0	G|0.899;A|0.100	0.100	strong	.	ADNP	106	.	NM_015339	exon5	c.C2067T	p.G689G	TCCAACGCCCCTG	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66432424	66432424	+	Silent	SNP	C	C	T	rs3826229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	123	142	1	1	0.00704225	A|0.000;C|0.632;G|0.000;T|0.368	0.368	strong	CDH5,NS,carcinoma,+1,2	CDH5	111	2	NM_001795	exon10	c.C1551T	p.I517I	ATTCATCTTGAAT	.	PASS	Atlas-SNP
GRHL2	79977	hgsc.bcm.edu	37	8	102570987	102570987	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	2	117	0	0.0114286	0	.	.	none	GRHL2,colon,carcinoma,-1,1	GRHL2	68	1	NM_024915	exon4	c.C625T	p.R209C	GACCAGCGCAGCA	.	scavenged	Atlas-SNP
OR8J3	81168	hgsc.bcm.edu	37	11	55904382	55904382	+	Missense_Mutation	SNP	A	A	C	rs17150102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	257	124	266	0	0.48249	0	A|0.900;C|0.100	0.100	strong	OR8J3,NS,carcinoma,0,1	OR8J3	112	1	NM_001004064	exon1	c.T813G	p.D271E	CATCTTATCAGTA	.	PASS	Atlas-SNP
MUL1	79594	hgsc.bcm.edu	37	1	20827216	20827216	+	Silent	SNP	C	C	T	rs595980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	24	98	0	0.282353	0	C|0.864;T|0.136	0.136	strong	MUL1,colon,carcinoma,-1,1	MUL1	34	1	NM_024544	exon4	c.G1026A	p.A342A	GGTGATCGCCTGT	.	PASS	Atlas-SNP
NSUN7	79730	hgsc.bcm.edu	37	4	40810663	40810663	+	Missense_Mutation	SNP	A	A	G	rs4861066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	106	126	1	1	0.00793651	A|0.808;G|0.192	0.192	strong	.	NSUN7	70	.	NM_024677	exon12	c.A1864G	p.T622A	AAGAACACTTGTC	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42852497	42852497	+	Missense_Mutation	SNP	C	C	T	rs12329760	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	133	202	0	0.658416	0	C|0.744;T|0.256	0.256	strong	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	NM_001135099	exon6	c.G589A	p.V197M	AGTACACCTGAAG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50533841	50533841	+	Missense_Mutation	SNP	G	G	C	rs11101094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	7	75	0	0.109375	0	G|0.907;C|0.093	0.093	strong	.	C10orf71	179	.	NM_001135196	exon3	c.G3251C	p.G1084A	CCCCTGGAGGACC	.	PASS	Atlas-SNP
EGF	1950	hgsc.bcm.edu	37	4	110902111	110902111	+	Missense_Mutation	SNP	A	A	T	rs11569017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	64	158	0	0.477612	0	A|0.932;T|0.068	0.068	strong	EGF,NS,adenoma,0,1	EGF	113	1	NM_001963	exon15	c.A2351T	p.D784V	CTCTGGATGGTCA	.	PASS	Atlas-SNP
OPTC	26254	hgsc.bcm.edu	37	1	203472112	203472112	+	Missense_Mutation	SNP	T	T	C	rs79523790	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	115	130	0	0.595855	0	T|0.915;C|0.085	0.085	strong	OPTC,NS,carcinoma,0,1	OPTC	50	1	NM_014359	exon6	c.T803C	p.L268P	TGCCCCTGAGCCT	.	PASS	Atlas-SNP
OR6C70	390327	hgsc.bcm.edu	37	12	55863381	55863381	+	Missense_Mutation	SNP	A	A	G	rs10747756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	48	124	0	0.484848	0	A|0.170;G|0.830	0.830	strong	.	OR6C70	35	.	NM_001005499	exon1	c.T542C	p.L181P	AGGATAAGAGAAA	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103082558	103082558	+	Silent	SNP	A	A	G	rs17394217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	115	87	0	0.732484	0	A|0.913;G|0.087	0.087	strong	.	DYNC2H1	246	.	NM_001377	exon54	c.A8580G	p.E2860E	CCATGAATCTTGT	.	PASS	Atlas-SNP
HNRNPL	3191	hgsc.bcm.edu	37	19	39331198	39331198	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	30	94	0	0.333333	0	.	.	none	.	HNRNPL	67	.	NM_001533	exon7	c.T882A	p.G294G	AGGGTCACCTGTG	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42845374	42845374	+	Silent	SNP	G	G	A	rs2298659	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	131	178	1	0.651741	0.00561798	G|0.780;A|0.220	0.220	strong	TMPRSS2_ENST00000454499,NS,carcinoma,0,3	TMPRSS2	148	3	NM_001135099	exon9	c.C888T	p.G296G	GCTCTCGCCGCCC	.	PASS	Atlas-SNP
IPPK	64768	hgsc.bcm.edu	37	9	95405048	95405048	+	Silent	SNP	A	A	C	rs35248147	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	68	199	0	0.485714	0	A|0.966;C|0.034	0.034	strong	.	IPPK	34	.	NM_022755	exon7	c.T549G	p.L183L	GAGATCAAGGGGA	.	PASS	Atlas-SNP
ATXN2	6311	hgsc.bcm.edu	37	12	111907956	111907956	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	54	183	0	0.310345	0	.	.	none	.	ATXN2	99	.	NM_002973	exon20	c.C3272G	p.S1091X	GTTGCTGAAGAAG	.	PASS	Atlas-SNP
SWT1	54823	hgsc.bcm.edu	37	1	185135745	185135745	+	Silent	SNP	A	A	G	rs950327	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	185	207	1	0.984043	0.00483092	A|0.680;G|0.320	0.320	strong	.	SWT1	88	.	NM_017673	exon3	c.A126G	p.S42S	TAGTTCATCTTCT	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76069902	76069902	+	Missense_Mutation	SNP	G	G	C	rs1804905	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	350	42	197	0	0.12	0	G|0.500;C|0.500	0.500	weak	.	ZP3	32	.	NM_001110354	exon7	c.G1034C	p.R345T	GGTCCAGGTCTGC	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39835817	39835817	+	Missense_Mutation	SNP	A	A	G	rs2296172	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	38	77	0	1	0	A|0.855;G|0.145	0.145	strong	.	MACF1	909	.	NM_012090	exon47	c.A6868G	p.M2290V	ACTTCTATGAGTG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2140010	2140010	+	Silent	SNP	A	A	G	rs7203729	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	102	126	0	1	0	A|0.688;G|0.312	0.312	strong	.	PKD1	184	.	NM_001009944	exon46	c.T12630C	p.P4210P	GGGCTCAGGCTCA	.	PASS	Atlas-SNP
SPATA3	130560	hgsc.bcm.edu	37	2	231861057	231861057	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	14	158	0	0.164706	0	.	.	none	SPATA3,NS,carcinoma,-2,4	SPATA3	52	4	NM_139073	exon1	c.C109T	p.P37S	TCCACACCACAGC	.	PASS	Atlas-SNP
EPS8L3	79574	hgsc.bcm.edu	37	1	110301260	110301260	+	Missense_Mutation	SNP	C	C	T	rs6693815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	16	86	0	0.2	0	C|0.668;T|0.332	0.332	strong	.	EPS8L3	73	.	NM_139053	exon7	c.G490A	p.G164S	CCTGGCCTGGCTG	.	PASS	Atlas-SNP
ESRRG	2104	hgsc.bcm.edu	37	1	216692669	216692669	+	Silent	SNP	C	C	T	rs945453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	81	108	0	0.686441	0	C|0.442;T|0.558	0.558	strong	.	ESRRG	111	.	NM_001243518	exon7	c.G993A	p.S331S	CTCAAACGAAAGA	.	PASS	Atlas-SNP
HEPH	9843	hgsc.bcm.edu	37	X	65427040	65427040	+	Silent	SNP	T	T	C	rs806607	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	106	196	1	1	0.00510204	0|0.020;C|0.435	0.435	strong	.	HEPH	224	.	NM_138737	exon14	c.T2457C	p.Y819Y	TAGTTATGGTTAC	.	PASS	Atlas-SNP
ASTN1	460	hgsc.bcm.edu	37	1	177001896	177001896	+	Silent	SNP	C	C	G	rs2076069	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	75	61	0	0.986842	0	C|0.864;G|0.136	0.136	strong	.	ASTN1	314	.	NM_004319	exon3	c.G561C	p.P187P	GGGCTGCGGGACC	.	PASS	Atlas-SNP
MMP9	4318	hgsc.bcm.edu	37	20	44642833	44642833	+	Silent	SNP	A	A	C	rs13969	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	8	8	45	0	1	0	A|0.580;C|0.420	0.420	strong	.	MMP9	84	.	NM_004994	exon11	c.A1821C	p.G607G	CCTGGGAGCCGAC	.	PASS	Atlas-SNP
RFTN1	23180	hgsc.bcm.edu	37	3	16364919	16364919	+	Silent	SNP	A	A	C	rs690216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	48	119	0	0.396694	0	A|0.402;C|0.598	0.598	strong	.	RFTN1	79	.	NM_015150	exon9	c.T1296G	p.P432P	TAGACAAGGTCTC	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94476388	94476388	+	Silent	SNP	C	C	G	rs1801574	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	14	133	0	0.197183	0	C|0.758;G|0.242	0.242	strong	ABCA4,NS,carcinoma,0,1	ABCA4	275	1	NM_000350	exon40	c.G5682C	p.L1894L	GACCAGCAGGGTC	.	PASS	Atlas-SNP
ARF3	377	hgsc.bcm.edu	37	12	49333799	49333799	+	Silent	SNP	G	G	A	rs2228417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	107	245	1	0.521951	0.00408163	G|0.954;A|0.046	0.046	strong	.	ARF3	11	.	NM_001659	exon3	c.C240T	p.H80H	GAAGTAGTGTCTC	.	PASS	Atlas-SNP
HOXB1	3211	hgsc.bcm.edu	37	17	46607817	46607817	+	Silent	SNP	C	C	T	rs7207109	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	134	120	0	0.992593	0	C|0.838;T|0.162	0.162	strong	.	HOXB1	67	.	NM_002144	exon1	c.G450A	p.A150A	AAAGCTCGCGGTC	.	PASS	Atlas-SNP
BCAR1	9564	hgsc.bcm.edu	37	16	75263816	75263816	+	Silent	SNP	G	G	A	rs145141523	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	35	72	0	0.853659	0	G|0.993;A|0.007	0.007	strong	BCAR1_ENST00000393420,NS,carcinoma,0,2	BCAR1	184	2	NM_001170714	exon8	c.C2344T	p.L782L	GCCCCAGGCCGCC	.	PASS	Atlas-SNP
ITGA6	3655	hgsc.bcm.edu	37	2	173339808	173339808	+	Missense_Mutation	SNP	G	G	A	rs11895564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	74	116	0	0.493333	0	G|0.714;A|0.286	0.286	strong	ITGA6,NS,NS,-1,1	ITGA6	171	1	NM_001079818	exon7	c.G1138A	p.A380T	GGCATTGCAGTAA	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140579358	140579358	+	Missense_Mutation	SNP	A	A	G	rs3756323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	25	62	0	0.454545	0	A|0.818;G|0.182	0.182	strong	.	PCDHB11	162	.	NM_018931	exon1	c.A11G	p.Q4R	AGAACCAAGGGAC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412363	105412363	+	Missense_Mutation	SNP	T	T	C	rs201377363	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	12	134	1	0.0810811	0.00746269	T|0.760;C|0.240	0.240	strong	AHNAK2_ENST00000333244,NS,NS,0,1	AHNAK2	719	1	NM_138420	exon7	c.A9425G	p.K3142R	TTGAACTTGCTGT	.	scavenged	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132241682	132241682	+	Missense_Mutation	SNP	C	C	T	rs145242123	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	70	138	0	0.56	0	C|0.998;T|0.002	0.002	strong	.	DNAJC13	253	.	NM_015268	exon49	c.C5684T	p.T1895M	GAATTACGTTAAT	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	34017106	34017106	+	Missense_Mutation	SNP	C	C	T	rs1785506	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	64	184	0	0.441379	0	C|0.374;T|0.626	0.626	strong	UBAP2,bladder,carcinoma,-1,2	UBAP2	82	2	NM_018449	exon2	c.G41A	p.R14Q	TTTTCCCGAGCAC	.	PASS	Atlas-SNP
FLT3	2322	hgsc.bcm.edu	37	13	28623525	28623525	+	Silent	SNP	G	G	A	rs146983744	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	74	145	0	0.556391	0	G|0.999;A|0.001	0.001	strong	.	FLT3	15525	.	NM_004119	exon8	c.C1032T	p.I344I	ACCTACGATGGTA	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30887972	30887972	+	Silent	SNP	C	C	T	rs2285319	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	70	176	0	0.451613	0	C|0.745;T|0.255	0.255	strong	.	VARS2	60	.	NM_001167734	exon13	c.C1362T	p.S454S	GACCTCCCTCTGC	.	PASS	Atlas-SNP
MMP10	4319	hgsc.bcm.edu	37	11	102650389	102650389	+	Missense_Mutation	SNP	C	C	T	rs17293607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	78	195	0	0.310757	0	C|0.912;T|0.088	0.088	strong	.	MMP10	44	.	NM_002425	exon2	c.G193A	p.G65R	GCATTCCTTGGAT	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	37	18	21123523	21123523	+	Missense_Mutation	SNP	C	C	T	rs375047023		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15	9	21	0	0.6	0	.	.	weak	.	NPC1	114	.	NM_000271	exon14	c.G2141A	p.R714H	TGAAGACGTTCAT	.	PASS	Atlas-SNP
PIP5K1C	23396	hgsc.bcm.edu	37	19	3633473	3633473	+	Missense_Mutation	SNP	C	C	T	rs35014191	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	53	111	0	0.557895	0	C|0.992;T|0.008	0.008	strong	PIP5K1C_ENST00000335312,NS,carcinoma,+1,1	PIP5K1C	63	1	NM_012398	exon17	c.G1966A	p.A656T	CCTGGGCGCTATA	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30831181	30831181	+	Missense_Mutation	SNP	C	C	T	rs12672119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	50	102	0	0.406504	0	C|0.935;T|0.065	0.065	strong	.	FAM188B	62	.	NM_032222	exon5	c.C1064T	p.A355V	AGCCCGCACCTGT	.	PASS	Atlas-SNP
ERMP1	79956	hgsc.bcm.edu	37	9	5801283	5801283	+	Missense_Mutation	SNP	T	T	A	rs147318623	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	100	184	0	0.510204	0	T|0.993;A|0.007	0.007	strong	.	ERMP1	63	.	NM_024896	exon11	c.A1960T	p.T654S	TTAAAGTTAGCAT	.	PASS	Atlas-SNP
POLR2B	5431	hgsc.bcm.edu	37	4	57889677	57889677	+	Silent	SNP	C	C	T	rs1056364	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	129	125	1	1	0.008	C|0.436;T|0.564	0.564	strong	POLR2B,NS,carcinoma,0,1	POLR2B	108	1	NM_000938	exon19	c.C2697T	p.S899S	AACTAGCGAGACG	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789367	117789367	+	Missense_Mutation	SNP	A	A	G	rs200485169		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	8	138	0	0.0361991	0	.	.	weak	TMPRSS13_ENST00000445164,NS,carcinoma,0,3	TMPRSS13	75	3	NM_001206790	exon2	c.T208C	p.S70P	CTGGAGATGCCCG	.	scavenged	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18735465	18735465	+	Missense_Mutation	SNP	G	G	A	rs11024769	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	86	209	0	0.462366	0	G|0.963;A|0.037	0.037	strong	.	IGSF22	211	.	NM_173588	exon14	c.C2029T	p.L677F	GGATGAGGCCGCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677355	100677355	+	Silent	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	302	23	162	0	0.0761589	0	.	.	none	.	MUC17	804	.	NM_001040105	exon3	c.A2658C	p.S886S	CCTTTCAACAACT	.	PASS	Atlas-SNP
GPR63	81491	hgsc.bcm.edu	37	6	97247547	97247547	+	Missense_Mutation	SNP	C	C	T	rs35358396	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	65	123	0	0.580357	0	C|0.974;T|0.026	0.026	strong	GPR63,right_upper_lobe,carcinoma,+2,1	GPR63	60	1	NM_030784	exon2	c.G61A	p.V21M	CATACACGACAAA	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1004710	1004710	+	Missense_Mutation	SNP	C	C	T	rs4807399	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	12	8	19	0	0.666667	0	C|0.586;T|0.414	0.414	strong	.	GRIN3B	46	.	NM_138690	exon3	c.C1210T	p.R404W	TCTGCACGGCCCC	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145323667	145323667	+	Missense_Mutation	SNP	C	C	G	rs199626421		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	4	130	0	0.0223464	0	.	.	weak	NBPF10,NS,carcinoma,0,6	NBPF10	221	6	NM_001039703	exon27	c.C3504G	p.D1168E	AAAGGACGAAGAA	.	scavenged	Atlas-SNP
PNKP	11284	hgsc.bcm.edu	37	19	50364914	50364914	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	4	25	0	0.166667	0	.	.	none	.	PNKP	71	.	NM_007254	exon15	c.G1337A	p.R446H	AAGCAGCGGCAGG	.	PASS	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	37	4	3446091	3446091	+	Missense_Mutation	SNP	G	G	T	rs3748034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	37	56	0	0.596774	0	G|0.878;T|0.122	0.122	strong	.	HGFAC	69	.	NM_001528	exon6	c.G652T	p.A218S	CGCTGGGCCCGCG	.	PASS	Atlas-SNP
CHAT	1103	hgsc.bcm.edu	37	10	50854637	50854637	+	Missense_Mutation	SNP	G	G	A	rs8178991	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	104	141	0	1	0	G|0.986;A|0.014	0.014	strong	.	CHAT	162	.	NM_020549	exon8	c.G1198A	p.D400N	CTCAGCGACACCC	.	PASS	Atlas-SNP
SBDS	51119	hgsc.bcm.edu	37	7	66453460	66453460	+	Silent	SNP	G	G	A	rs73151675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	44	120	0	0.295302	0	G|0.962;A|0.038	0.038	strong	.	SBDS	20	.	NM_016038	exon5	c.C651T	p.F217F	TTCTCGGAAGCAG	.	PASS	Atlas-SNP
INMT	11185	hgsc.bcm.edu	37	7	30791847	30791847	+	Silent	SNP	C	C	T	rs2240822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	41	132	0	0.29927	0	C|0.981;T|0.019	0.019	strong	.	INMT	38	.	NM_001199219	exon1	c.C81T	p.F27F	CAGCTTCGATGGC	.	PASS	Atlas-SNP
GLTPD2	388323	hgsc.bcm.edu	37	17	4692559	4692559	+	Missense_Mutation	SNP	G	G	T	rs2304969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	29	42	0	0.58	0	G|0.753;T|0.247	0.247	strong	.	GLTPD2	15	.	NM_001014985	exon2	c.G145T	p.V49F	CCCTGCGTTCCAG	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91691601	91691601	+	Silent	SNP	C	C	T	rs10236397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	185	145	0	1	0	C|0.605;T|0.395	0.395	strong	.	AKAP9	788	.	NM_005751	exon24	c.C5778T	p.G1926G	TGATGGCTATGCA	.	PASS	Atlas-SNP
C10orf67	256815	hgsc.bcm.edu	37	10	23633566	23633566	+	Silent	SNP	C	C	A	rs2036917	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	56	118	0	0.608696	0	C|0.343;A|0.657	0.657	strong	C10orf67,NS,carcinoma,0,1	C10orf67	21	1	NM_153714	exon1	c.G141T	p.R47R	GCAGACCCGCAGC	.	PASS	Atlas-SNP
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238453	71238453	+	Missense_Mutation	SNP	G	G	C	rs147685834	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252	121	277	1	0.480159	0.00361011	G|0.807;C|0.193	0.193	strong	KRTAP5-7,NS,carcinoma,0,1	KRTAP5-7	23	1	NM_001012503	exon1	c.G107C	p.C36S	GCTGCTGTGTGCC	.	PASS	Atlas-SNP
ACADM	34	hgsc.bcm.edu	37	1	76227022	76227022	+	Silent	SNP	A	A	G	rs1061337	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	54	111	0	0.782609	0	A|0.777;G|0.223	0.223	strong	.	ACADM	50	.	NM_001127328	exon11	c.A1173G	p.V391V	TCCTGTAGAAAAA	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197427557	197427557	+	Silent	SNP	A	A	G	rs28394098	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	76	192	0	0.422222	0	A|0.885;G|0.115	0.115	strong	.	KIAA0226	136	.	NM_014687	exon7	c.T1188C	p.T396T	GGTGACAGTGAGT	.	PASS	Atlas-SNP
C9orf96	169436	hgsc.bcm.edu	37	9	136268912	136268912	+	Silent	SNP	A	A	G	rs28510482	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	68	102	1	0.985507	0.00980392	A|0.830;G|0.170	0.170	strong	.	C9orf96	77	.	NM_153710	exon15	c.A1563G	p.A521A	AATGGCAGAAGCC	.	PASS	Atlas-SNP
ANKDD1A	348094	hgsc.bcm.edu	37	15	65236875	65236875	+	Silent	SNP	T	T	C	rs2414865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	95	148	0	0.989583	0	T|0.460;C|0.540	0.540	strong	.	ANKDD1A	47	.	NM_182703	exon12	c.T1092C	p.A364A	AGTGGCTGTCCGC	.	PASS	Atlas-SNP
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	rs77807247	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	47	111	0	0.333333	0	C|0.969;T|0.031	0.031	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.G134A	p.R45H	GATGGGCGGCAGC	.	PASS	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	37	8	27301725	27301725	+	Silent	SNP	C	C	G	rs1128435	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	52	120	0	0.353741	0	C|0.913;G|0.087	0.087	strong	PTK2B_ENST00000544172,bladder,carcinoma,+1,3	PTK2B	304	3	NM_173174	exon28	c.C2151G	p.P717P	CCAGCCCAGCCGA	.	PASS	Atlas-SNP
MS4A5	64232	hgsc.bcm.edu	37	11	60197299	60197299	+	Missense_Mutation	SNP	G	G	A	rs34169848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	28	10	30	0	0.357143	0	G|0.965;A|0.035	0.035	strong	.	MS4A5	35	.	NM_023945	exon1	c.G152A	p.G51E	TCTTAGGGGTAAG	.	PASS	Atlas-SNP
UNC13A	23025	hgsc.bcm.edu	37	19	17741047	17741047	+	Silent	SNP	A	A	G	rs10413821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	67	110	0	0.492647	0	A|0.571;G|0.429	0.429	strong	.	UNC13A	299	.	NM_001080421	exon29	c.T3576C	p.V1192V	GGAGAAAACATCC	.	PASS	Atlas-SNP
KPNB1	3837	hgsc.bcm.edu	37	17	45734285	45734285	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	46	146	0	0.414414	0	.	.	none	.	KPNB1	58	.	NM_002265	exon4	c.C342C	p.H114H	TGTGGCTGGTATT	.	PASS	Atlas-SNP
TSSK1B	83942	hgsc.bcm.edu	37	5	112769997	112769997	+	Silent	SNP	C	C	T	rs34936289	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	43	91	1	0.488636	0.010989	C|0.896;T|0.104	0.104	strong	TSSK1B_ENST00000390666,colon,carcinoma,-1,2	TSSK1B	89	2	NM_032028	exon1	c.G540A	p.A180A	CGCATACGCTGGT	.	scavenged	Atlas-SNP
SLC26A2	1836	hgsc.bcm.edu	37	5	149361221	149361221	+	Missense_Mutation	SNP	A	A	T	rs3776070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	27	74	0	0.482143	0	A|0.811;T|0.190	0.190	strong	.	SLC26A2	48	.	NM_000112	exon3	c.A2065T	p.T689S	AATCCCACTGTGA	.	PASS	Atlas-SNP
ZFP69	339559	hgsc.bcm.edu	37	1	40961603	40961603	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	3	190	0	0.0247934	0	.	.	none	ZNF642,NS,carcinoma,0,1	.	.	1	NM_198494	exon6	c.C1453A	p.H485N	AAAAAACATCAGA	.	scavenged	Atlas-SNP
ZNF395	55893	hgsc.bcm.edu	37	8	28210808	28210808	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	11	139	11	0.0611111	0.0791367	.	.	none	ZNF395,rectum,carcinoma,0,1	ZNF395	54	1	NM_018660	exon5	c.A701C	p.H234P	TGGGGGTGGGGGG	.	scavenged	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	37	3	113376113	113376113	+	Silent	SNP	C	C	T	rs62265537		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	3	106	0	0.0434783	0	.	.	weak	KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	NM_001009899	exon7	c.G4416A	p.Q1472Q	CTGTTGCTGCTGC	.	scavenged	Atlas-SNP
MYEOV	26579	hgsc.bcm.edu	37	11	69063726	69063726	+	Missense_Mutation	SNP	G	G	T	rs142581206	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	57	107	0	0.487179	0	G|0.998;T|0.002	0.002	strong	MYEOV,NS,carcinoma,-1,1	MYEOV	42	1	NM_138768	exon3	c.G809T	p.G270V	CCCTGGGGGGGTG	.	PASS	Atlas-SNP
SOCS6	9306	hgsc.bcm.edu	37	18	67992432	67992432	+	Silent	SNP	C	C	T	rs2231563	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	34	75	0	0.515152	0	C|0.949;T|0.051	0.051	strong	.	SOCS6	54	.	NM_004232	exon2	c.C528T	p.H176H	TTTCCACGACCTC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9006749	9006749	+	Missense_Mutation	SNP	C	C	T	rs75444444	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	277	276	254	1	0.99639	0.00393701	C|0.824;T|0.176	0.176	strong	.	MUC16	4315	.	NM_024690	exon44	c.G39499A	p.V13167M	ATGGCACCAGGAG	.	PASS	Atlas-SNP
CNTN4	152330	hgsc.bcm.edu	37	3	3067850	3067850	+	Silent	SNP	A	A	G	rs7629924	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	93	241	0	0.5	0	A|0.847;G|0.153	0.153	strong	.	CNTN4	335	.	NM_175607	exon15	c.A1551G	p.L517L	TGTTTTACCGTGC	.	PASS	Atlas-SNP
TAOK1	57551	hgsc.bcm.edu	37	17	27835138	27835138	+	Silent	SNP	C	C	T	rs508706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	19	87	0	0.387755	0	C|0.135;A|0.007	.	strong	.	TAOK1	151	.	NM_025142	exon14	c.C1563T	p.A521A	GGCTGCCATGGAG	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88791458	88791458	+	Missense_Mutation	SNP	G	G	A	rs11645197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	44	202	0	0.309859	0	G|0.827;A|0.173	0.173	strong	.	PIEZO1	79	.	NM_001142864	exon30	c.C4193T	p.P1398L	CTCCGTGGCGGGG	.	PASS	Atlas-SNP
RIPK4	54101	hgsc.bcm.edu	37	21	43187167	43187167	+	Missense_Mutation	SNP	G	G	C	rs6586239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	28	55	1	0.666667	0.0181818	G|0.846;C|0.154	0.154	strong	RIPK4_ENST00000352483,colon,carcinoma,0,2	RIPK4	151	2	NM_020639	exon1	c.C35G	p.A12G	AGCAGCGCCAGGG	.	scavenged	Atlas-SNP
TOM1	10043	hgsc.bcm.edu	37	22	35742925	35742925	+	Silent	SNP	T	T	G	rs743810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	33	53	1	0.52381	0.0188679	T|0.655;G|0.345	0.345	strong	TOM1,NS,carcinoma,0,1	TOM1	43	1	NM_001135732	exon14	c.T1287G	p.G429G	CCAGGGTAATGAT	.	scavenged	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513635	72513635	+	Missense_Mutation	SNP	C	C	A	rs12774070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	57	90	0	0.982759	0	A|0.174;C|0.826;G|0.000	0.174	strong	ADAMTS14,NS,carcinoma,0,2	ADAMTS14	148	2	NM_139155	exon19	c.C2818A	p.L940M	TGCCTGCTGCCCC	.	PASS	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	37	20	57769140	57769140	+	Missense_Mutation	SNP	G	G	C	rs55786258	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	14	47	0	0.451613	0	G|0.829;C|0.171	0.171	strong	.	ZNF831	287	.	NM_178457	exon1	c.G3066C	p.L1022F	ACAGTTGGGGGGG	.	PASS	Atlas-SNP
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493794	77493794	+	Silent	SNP	T	T	C	rs28718623	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	12	0	0	0.666667	.	.	.	weak	.	IRF2BPL	40	.	NM_024496	exon1	c.A342G	p.Q114Q	CTGCTGTTGCTGC	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111983157	111983157	+	Silent	SNP	G	G	A	rs62276974	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	70	176	0	0.47619	0	G|0.803;A|0.197	0.197	strong	.	.	.	.	NM_183061	exon9	c.C912T	p.L304L	CACCATGAGAAAA	.	PASS	Atlas-SNP
CHD1	1105	hgsc.bcm.edu	37	5	98199204	98199204	+	Silent	SNP	C	C	T	rs161941	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	69	159	0	0.522727	0	C|0.658;T|0.342	0.342	strong	.	CHD1	137	.	NM_001270	exon31	c.G4335A	p.E1445E	AGTATGCTCTAGT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744195	54744195	+	Missense_Mutation	SNP	G	G	A	rs1132604	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	360	117	319	1	0.325	0.0031348	G|0.954;A|0.046	0.046	strong	LILRA6,colon,carcinoma,+1,1	LILRA6	75	1	NM_024318	exon6	c.C1213T	p.H405Y	GCAGGTGGGGGTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228520973	228520973	+	Missense_Mutation	SNP	C	C	G	rs369909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	46	90	0	0.345865	0	C|0.669;G|0.331	0.331	strong	.	OBSCN	2142	.	NM_001271223	exon69	c.C18676G	p.L6226V	AGAGACCTCCAGG	.	PASS	Atlas-SNP
RGS11	8786	hgsc.bcm.edu	37	16	319511	319511	+	Missense_Mutation	SNP	A	A	G	rs739999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	81	260	2	0.413265	0.00769231	A|0.720;G|0.280	0.280	strong	RGS11,colon,carcinoma,0,1	RGS11	29	1	NM_183337	exon16	c.T1280C	p.M427T	CTCTTCATCTCCA	.	scavenged	Atlas-SNP
ZFR2	23217	hgsc.bcm.edu	37	19	3820191	3820191	+	Missense_Mutation	SNP	C	C	T	rs2301843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	35	61	0	0.507246	0	C|0.594;T|0.406	0.406	strong	.	ZFR2	63	.	NM_015174	exon11	c.G1729A	p.A577T	GTGGGGCGCTGGC	.	PASS	Atlas-SNP
ACOT4	122970	hgsc.bcm.edu	37	14	74060487	74060487	+	Missense_Mutation	SNP	G	G	C	rs45522539	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	72	105	0	0.376963	0	G|0.983;C|0.017	0.017	strong	.	ACOT4	25	.	NM_152331	exon2	c.G539C	p.G180A	TTGCTGGCCATGG	.	PASS	Atlas-SNP
KIRREL	55243	hgsc.bcm.edu	37	1	158064439	158064439	+	Silent	SNP	C	C	A	rs41273465	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	27	39	0	0.6	0	C|0.924;A|0.076	0.076	strong	.	KIRREL	346	.	NM_018240	exon15	c.C1803A	p.P601P	GGACCCCACCAAT	.	PASS	Atlas-SNP
TNFRSF14	8764	hgsc.bcm.edu	37	1	2488153	2488153	+	Missense_Mutation	SNP	A	A	G	rs4870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	9	134	0	0.126761	0	A|0.440;G|0.560	0.560	strong	.	TNFRSF14	89	.	NM_003820	exon1	c.A50G	p.K17R	CCCCCAAAACCGA	.	PASS	Atlas-SNP
CREBBP	1387	hgsc.bcm.edu	37	16	3808872	3808872	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	44	136	0	0.312057	0	.	.	none	.	CREBBP	546	.	NM_004380	exon17	c.C3352T	p.Q1118X	GGAGCTGGGGATC	.	PASS	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140221139	140221139	+	Missense_Mutation	SNP	G	G	A	rs3756331	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	26	55	0	0.5	0	G|0.466;A|0.534	0.534	strong	PCDHA8_ENST00000531613,NS,carcinoma,0,2	PCDHA8	366	2	NM_031856	exon1	c.G233A	p.S78N	AGGTAAGTCTGCA	.	scavenged	Atlas-SNP
KLHL23	151230	hgsc.bcm.edu	37	2	170606041	170606041	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	4	252	1	0.0151515	0.00396825	.	.	none	KLHL23,colon,carcinoma,+2,1	KLHL23	52	1	NM_144711	exon4	c.T1476C	p.A492A	GATAGCTCCCATG	.	scavenged	Atlas-SNP
USP33	23032	hgsc.bcm.edu	37	1	78201745	78201745	+	Silent	SNP	G	G	T	rs2296227	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	107	214	0	0.981651	0	G|0.550;T|0.450	0.450	strong	.	USP33	87	.	NM_201626	exon7	c.C543A	p.A181A	ACCTCTGGCCCTA	.	PASS	Atlas-SNP
ZNF543	125919	hgsc.bcm.edu	37	19	57840547	57840547	+	Missense_Mutation	SNP	A	A	G	rs10410649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	73	164	0	0.5	0	A|0.737;G|0.263	0.263	strong	.	ZNF543	61	.	NM_213598	exon4	c.A1717G	p.M573V	CCTTTTATGACTG	.	PASS	Atlas-SNP
TMEM39B	55116	hgsc.bcm.edu	37	1	32557486	32557486	+	Silent	SNP	A	A	G	rs744455	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	55	139	0	0.670732	0	A|0.849;G|0.151	0.151	strong	.	TMEM39B	66	.	NM_018056	exon6	c.A801G	p.S267S	CCTGTCACCCAGC	.	PASS	Atlas-SNP
DACT1	51339	hgsc.bcm.edu	37	14	59113537	59113537	+	Silent	SNP	C	C	G	rs61755641	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	22	66	0	0.349206	0	C|0.956;G|0.044	0.044	strong	.	DACT1	119	.	NM_016651	exon4	c.C2196G	p.S732S	CGAGTCCCTGTTC	.	PASS	Atlas-SNP
OR1N2	138882	hgsc.bcm.edu	37	9	125316028	125316028	+	Missense_Mutation	SNP	T	T	C	rs41297203	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	83	215	0	0.474286	0	T|0.920;C|0.080	0.080	strong	.	OR1N2	51	.	NM_001004457	exon1	c.T580C	p.F194L	CCTCATTTCTATT	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7435443	7435443	+	Silent	SNP	G	G	A	rs6843370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	41	92	0	0.493976	0	G|0.886;A|0.114	0.114	strong	.	PSAPL1	51	.	NM_001085382	exon1	c.C1164T	p.D388D	CTCCGCGTCCCAC	.	PASS	Atlas-SNP
RPL3	6122	hgsc.bcm.edu	37	22	39714490	39714490	+	Silent	SNP	C	C	T	rs6509	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	89	64	0	0.978022	0	C|0.625;T|0.375	0.375	strong	.	RPL3	29	.	NM_001033853	exon2	c.G111A	p.P37P	CTTGGACGGGTCA	.	PASS	Atlas-SNP
MLL2	8085	hgsc.bcm.edu	37	12	49445028	49445028	+	Missense_Mutation	SNP	G	G	A	rs75226229	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	81	153	0	0.465517	0	G|0.971;A|0.029	0.029	strong	.	MLL2	1173	.	NM_003482	exon10	c.C2438T	p.P813L	AGGTGCGGCTCCT	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77416972	77416972	+	Silent	SNP	C	C	T	rs11144089	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	63	191	0	0.409091	0	C|0.911;T|0.089	0.089	strong	.	TRPM6	377	.	NM_017662	exon16	c.G1851A	p.L617L	TTTCATCAGCACA	.	PASS	Atlas-SNP
SLC46A2	57864	hgsc.bcm.edu	37	9	115652836	115652836	+	Silent	SNP	G	G	A	rs3802492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	53	67	0	0.963636	0	G|0.682;A|0.318	0.318	strong	.	SLC46A2	30	.	NM_033051	exon1	c.C126T	p.L42L	CACCACGAGGAGT	.	PASS	Atlas-SNP
COL3A1	1281	hgsc.bcm.edu	37	2	189852846	189852846	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	299	3	326	0	0.0100334	0	.	.	none	COL3A1,mucosal,malignant_melanoma,0,1	COL3A1	292	1	NM_000090	exon6	c.C568T	p.H190Y	TCTGGTCATCCTG	.	scavenged	Atlas-SNP
ZC3H11A	9877	hgsc.bcm.edu	37	1	203821314	203821314	+	Silent	SNP	G	G	A	rs79145608		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	318	280	238	1	0.880503	0.00420168	.	.	weak	.	ZC3H11A	71	.	NM_014827	exon20	c.G2220A	p.P740P	ACCCCCGGAGGTG	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269699	43269699	+	Missense_Mutation	SNP	C	C	T	rs7260508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	11	50	0	0.37931	0	C|0.620;T|0.380	0.380	strong	PSG8_ENST00000404209,NS,carcinoma,-1,2	PSG8	101	2	NM_001130168	exon1	c.G35A	p.R12H	GTGATGCGCTGTG	.	PASS	Atlas-SNP
FMO4	2329	hgsc.bcm.edu	37	1	171303626	171303626	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	51	133	0	0.3	0	.	.	none	FMO4,caecum,carcinoma,0,1	FMO4	64	1	NM_002022	exon8	c.G904A	p.V302M	ACCAGCGTGATTG	.	PASS	Atlas-SNP
SYTL1	84958	hgsc.bcm.edu	37	1	27676925	27676925	+	Silent	SNP	G	G	A	rs6702341	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	30	72	0	0.769231	0	G|0.711;A|0.289	0.289	strong	.	SYTL1	57	.	NM_001193308	exon10	c.G954A	p.K318K	GCGCAAGACGGCG	.	PASS	Atlas-SNP
KNTC1	9735	hgsc.bcm.edu	37	12	123042027	123042027	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	4	175	1	0.030303	0.00571429	.	.	none	KNTC1,NS,carcinoma,-2,1	KNTC1	182	1	NM_014708	exon17	c.G1369A	p.D457N	GTAGACGACGCTA	.	scavenged	Atlas-SNP
C14orf37	145407	hgsc.bcm.edu	37	14	58605734	58605734	+	Missense_Mutation	SNP	T	T	C	rs61741497	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	140	153	1	0.660377	0.00653595	T|0.995;C|0.005	0.005	strong	.	C14orf37	87	.	NM_001001872	exon2	c.A343G	p.T115A	ACTCAGTAGGTGT	.	PASS	Atlas-SNP
CELSR3	1951	hgsc.bcm.edu	37	3	48691316	48691316	+	Missense_Mutation	SNP	T	T	C	rs12107252	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	108	178	0	0.519231	0	T|0.781;C|0.219	0.219	strong	.	CELSR3	237	.	NM_001407	exon8	c.A5273G	p.Q1758R	CTAAGCTGACAGT	.	PASS	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38043904	38043904	+	Silent	SNP	T	T	C	rs9843296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	34	54	0	0.53125	0	T|0.803;C|0.197	0.197	strong	VILL,NS,carcinoma,0,1	VILL	61	1	NM_015873	exon13	c.T1497C	p.H499H	GCACCATGGAAAG	.	PASS	Atlas-SNP
TFAP4	7023	hgsc.bcm.edu	37	16	4310468	4310468	+	Missense_Mutation	SNP	C	C	G	rs251732	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	82	205	1	0.438503	0.00487805	C|0.381;G|0.619	0.619	strong	TFAP4,colon,carcinoma,0,1	TFAP4	31	1	NM_003223	exon5	c.G654C	p.Q218H	CCGCAGCTGCTGC	.	scavenged	Atlas-SNP
HEXIM1	10614	hgsc.bcm.edu	37	17	43226887	43226887	+	Silent	SNP	A	A	G	rs12051846	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	32	85	0	0.516129	0	A|0.803;G|0.197	0.197	strong	.	HEXIM1	25	.	NM_006460	exon1	c.A330G	p.E110E	AGTGGAACCGACG	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56549510	56549510	+	Missense_Mutation	SNP	T	T	C	rs16986899	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	104	222	2	0.464286	0.00900901	T|0.731;C|0.269	0.269	strong	NLRP5,NS,carcinoma,0,1	NLRP5	217	1	NM_153447	exon10	c.T2735C	p.M912T	GAGTAATGCCTCT	.	scavenged	Atlas-SNP
CRISP3	10321	hgsc.bcm.edu	37	6	49701439	49701439	+	Missense_Mutation	SNP	C	C	A	rs1864312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	58	154	0	0.504348	0	C|0.618;A|0.382	0.382	strong	.	CRISP3	67	.	NM_001190986	exon5	c.G469T	p.A157S	CCACTGCGTTGGG	.	PASS	Atlas-SNP
ZNF177	7730	hgsc.bcm.edu	37	19	9492141	9492141	+	Silent	SNP	C	C	T	rs3826783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	68	170	0	0.433121	0	C|0.431;T|0.569	0.569	strong	.	ZNF177	57	.	NM_001172651	exon6	c.C1134T	p.I378I	CTTCATCGATCAG	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113170289	113170289	+	Missense_Mutation	SNP	C	C	T	rs143931457	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	33	104	0	0.423077	0	C|0.996;T|0.004	0.004	strong	.	SVEP1	326	.	NM_153366	exon38	c.G7591A	p.E2531K	GACCTTCGAGCCG	.	PASS	Atlas-SNP
HSPD1	3329	hgsc.bcm.edu	37	2	198363504	198363504	+	Silent	SNP	A	A	G	rs1050347	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	290	128	306	1	0.441379	0.00326797	A|0.813;G|0.187	0.187	strong	.	HSPD1	68	.	NM_002156	exon2	c.T69C	p.T23T	AGCCCGAGTGAGA	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45024535	45024535	+	Missense_Mutation	SNP	T	T	C	rs200961907	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	43	70	0	0.5	0	T|0.996;C|0.004	0.004	weak	.	CEACAM20	31	.	NM_001102600	exon5	c.A1003G	p.S335G	GCTCACTCCGGGC	.	PASS	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51748684	51748684	+	Missense_Mutation	SNP	G	G	A	rs77235195		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20	17	13	0	0.85	0	A|1.000;|0.000	1.000	weak	AGAP6,NS,carcinoma,0,1	AGAP6	53	1	NM_001077665	exon1	c.G209A	p.R70Q	GTGACCGGGAGAT	.	scavenged	Atlas-SNP
SCN3A	6328	hgsc.bcm.edu	37	2	165987772	165987772	+	Silent	SNP	T	T	G	rs62174900	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	93	207	0	0.465	0	T|0.828;G|0.172	0.172	strong	.	SCN3A	544	.	NM_006922	exon16	c.A2547C	p.V849V	TCGCAGTACAGAC	.	PASS	Atlas-SNP
ABCB1	5243	hgsc.bcm.edu	37	7	87229440	87229440	+	Missense_Mutation	SNP	T	T	C	rs9332385		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	59	164	1	0.375796	0.00609756	.	.	weak	ABCB1,NS,adenoma,0,1	ABCB1	263	1	NM_000927	exon3	c.A61G	p.N21D	TTTTATTGTTCAG	.	scavenged	Atlas-SNP
C14orf177	283598	hgsc.bcm.edu	37	14	99182626	99182626	+	Missense_Mutation	SNP	T	T	C	rs4905757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	98	86	0	0.510417	0	T|0.973;C|0.027	0.027	strong	.	C14orf177	37	.	NM_182560	exon3	c.T98C	p.V33A	CATCAGTGAGCCA	.	PASS	Atlas-SNP
KIAA0825	285600	hgsc.bcm.edu	37	5	93753017	93753017	+	Missense_Mutation	SNP	C	C	T	rs29910	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	139	143	0	1	0	C|0.811;T|0.189	0.189	strong	KIAA0825_ENST00000513200,NS,carcinoma,0,2	KIAA0825	172	2	NM_001145678	exon15	c.G2551A	p.A851T	AGATGGCTTCCAT	.	PASS	Atlas-SNP
RTKN2	219790	hgsc.bcm.edu	37	10	63977980	63977980	+	Missense_Mutation	SNP	C	C	T	rs61850830	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	5	56	0	0.119048	0	C|0.913;T|0.087	0.087	strong	.	RTKN2	68	.	NM_145307	exon8	c.G862A	p.A288T	CAAATGCATCCTC	.	PASS	Atlas-SNP
ZNF107	51427	hgsc.bcm.edu	37	7	64166802	64166802	+	Missense_Mutation	SNP	G	G	T	rs73138709	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	143	193	0	0.586066	0	G|0.969;T|0.031	0.031	strong	.	ZNF107	107	.	NM_016220	exon7	c.G120T	p.E40D	ATATGAGAATTTA	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24424346	24424346	+	Silent	SNP	G	G	A	rs4981491		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	432	92	324	0	0.212963	0	.	.	weak	.	DHRS4	22	.	NM_021004	exon2	c.G231A	p.Q77Q	GCTGCAGGGGGAG	.	PASS	Atlas-SNP
AK7	122481	hgsc.bcm.edu	37	14	96871104	96871104	+	Missense_Mutation	SNP	G	G	A	rs2275554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	48	95	0	0.403361	0	G|0.770;A|0.230	0.230	strong	.	AK7	69	.	NM_152327	exon3	c.G305A	p.R102Q	TCTCTCGAGAAGA	.	PASS	Atlas-SNP
OR6C70	390327	hgsc.bcm.edu	37	12	55863398	55863398	+	Silent	SNP	G	G	A	rs12313730	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	45	127	0	0.459184	0	G|0.814;A|0.186	0.186	strong	.	OR6C70	35	.	NM_001005499	exon1	c.C525T	p.F175F	ACAAATGAAATGA	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43097710	43097710	+	Silent	SNP	A	A	G	rs664628	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	131	155	0	0.963235	0	A|0.589;G|0.411	0.411	strong	.	FAM198A	23	.	NM_001129908	exon5	c.A1560G	p.L520L	GTGTCTACAGAAC	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155256177	155256177	+	Silent	SNP	A	A	G	rs6858157	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	17	130	1	0.178947	0.00769231	A|0.668;G|0.332	0.332	strong	DCHS2_ENST00000339452,NS,carcinoma,0,3	DCHS2	594	3	NM_001142552	exon4	c.T2556C	p.G852G	GAGCCCACCACCG	.	scavenged	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136522274	136522274	+	Missense_Mutation	SNP	C	C	T	rs6271	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	98	205	0	0.480392	0	C|0.956;T|0.044	0.044	strong	.	DBH	86	.	NM_000787	exon11	c.C1645T	p.R549C	TTCAACCGCGACG	.	PASS	Atlas-SNP
REV1	51455	hgsc.bcm.edu	37	2	100055506	100055506	+	Missense_Mutation	SNP	A	A	G	rs3087386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	56	83	0	0.513761	0	A|0.422;G|0.578	0.578	strong	.	REV1	100	.	NM_001037872	exon6	c.T770C	p.F257S	TGGGAAAAGGCTG	.	PASS	Atlas-SNP
SPATA3	130560	hgsc.bcm.edu	37	2	231861059	231861059	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	18	161	1	0.204545	0.00621118	.	.	none	SPATA3,NS,carcinoma,0,4	SPATA3	52	4	NM_139073	exon1	c.A111T	p.P37P	CACACCACAGCAG	.	scavenged	Atlas-SNP
ZFP36L1	677	hgsc.bcm.edu	37	14	69259662	69259662	+	Silent	SNP	C	C	A	rs1051533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	43	69	0	0.43	0	C|0.791;A|0.209	0.209	strong	.	ZFP36L1	47	.	NM_001244701	exon2	c.G201T	p.T67T	CCTGTGCGTTCGC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276659	152276659	+	Missense_Mutation	SNP	T	T	C	rs7532285	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	376	29	398	0	0.0771277	0	T|0.993;C|0.007	0.007	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.A10703G	p.Q3568R	TGCTCCTGAGCAG	.	PASS	Atlas-SNP
WDR49	151790	hgsc.bcm.edu	37	3	167217964	167217964	+	Missense_Mutation	SNP	A	A	G	rs13060964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	40	86	0	0.588235	0	A|0.662;G|0.338	0.338	strong	.	WDR49	188	.	NM_178824	exon14	c.T1952C	p.L651P	GCCTCCAGAATTT	.	PASS	Atlas-SNP
C19orf40	91442	hgsc.bcm.edu	37	19	33467576	33467576	+	Silent	SNP	G	G	A	rs7258185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	40	117	0	0.454545	0	G|0.753;A|0.247	0.247	strong	.	C19orf40	21	.	NM_152266	exon5	c.G636A	p.T212T	CTTCACGCAGCCC	.	PASS	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236750709	236750709	+	Missense_Mutation	SNP	C	C	T	rs56242514	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	401	126	338	0	0.314214	0	C|0.985;T|0.015	0.015	strong	.	HEATR1	197	.	NM_018072	exon14	c.G1708A	p.G570R	ATTCTCCATTCTT	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31382911	31382911	+	Missense_Mutation	SNP	A	A	G	rs1882	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	39	94	0	0.327731	0	A|0.320;G|0.680	0.680	strong	.	MICA	21	.	NM_000247	exon7	c.A1147G	p.T383A	GAGGGCACCTAGA	.	PASS	Atlas-SNP
PON1	5444	hgsc.bcm.edu	37	7	94946084	94946084	+	Missense_Mutation	SNP	A	A	T	rs854560	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	44	180	0	0.291391	0	A|0.717;T|0.283	0.283	strong	.	PON1	55	.	NM_000446	exon3	c.T163A	p.L55M	TCTCCAAGTCTTC	.	PASS	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236723108	236723108	+	Missense_Mutation	SNP	C	C	T	rs6661946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	61	144	0	0.333333	0	C|0.848;T|0.152	0.152	strong	.	HEATR1	197	.	NM_018072	exon34	c.G4676A	p.S1559N	ACTGCACTGATAT	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54120025	54120025	+	Missense_Mutation	SNP	A	A	T	rs805408	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	79	146	0	0.509677	0	A|0.713;T|0.287	0.287	strong	.	PSME4	247	.	NM_014614	exon36	c.T4111A	p.S1371T	CATGTGAATCTGC	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92616452	92616452	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	2	36	0	0.025974	0	.	.	none	FAT3_ENST00000409404,bladder,carcinoma,-1,3	FAT3	1822	3	NM_001008781	exon23	c.G12830A	p.R4277Q	CAGCCCGGCGGGG	.	scavenged	Atlas-SNP
RFX2	5990	hgsc.bcm.edu	37	19	6013057	6013057	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	25	42	0	0.446429	0	.	.	none	.	RFX2	60	.	NM_000635	exon8	c.G839A	p.R280Q	TGCAGCCGGTTCA	.	PASS	Atlas-SNP
NEK1	4750	hgsc.bcm.edu	37	4	170398454	170398454	+	Missense_Mutation	SNP	T	T	C	rs34099167	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	21	146	0	0.244186	0	T|0.885;C|0.115	0.115	strong	NEK1,NS,carcinoma,0,1	NEK1	203	1	NM_001199397	exon26	c.A2255G	p.E752G	TCATCTTCTTGAG	.	PASS	Atlas-SNP
CRISP3	10321	hgsc.bcm.edu	37	6	49698883	49698883	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	3	246	0	0.0131004	0	.	.	none	CRISP3,colon,carcinoma,0,1	CRISP3	67	1	NM_001190986	exon7	c.A672G	p.G224G	GCATAGTCCATCG	.	scavenged	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171154959	171154959	+	Missense_Mutation	SNP	A	A	G	rs2020870	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	77	131	0	0.361502	0	A|0.919;G|0.081	0.081	strong	.	FMO2	66	.	NM_001460	exon2	c.A107G	p.D36G	CTGAAGATATTGG	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123847473	123847473	+	Missense_Mutation	SNP	A	A	G	rs55944888	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	115	106	0	0.66474	0	A|0.862;G|0.138	0.138	strong	.	OR10S1	78	.	NM_001004474	exon1	c.T926C	p.V309A	TGCTTCACCTCCT	.	PASS	Atlas-SNP
VN1R2	317701	hgsc.bcm.edu	37	19	53761857	53761857	+	Missense_Mutation	SNP	G	G	T	rs112986288	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	22	65	0	0.4	0	G|0.994;T|0.006	0.006	strong	.	VN1R2	71	.	NM_173856	exon1	c.G229T	p.V77F	TCTCTTGTCTCTG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388724	1388724	+	Missense_Mutation	SNP	C	C	G	rs76728908	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	20	54	1	0.645161	0.0185185	C|0.500;G|0.500	0.500	weak	CRIPAK,NS,other,0,1	CRIPAK	185	1	NM_175918	exon1	c.C425G	p.P142R	CGTGCCCATGCGG	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1272245	1272245	+	Missense_Mutation	SNP	C	C	T	rs2943511	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	523	255	471	0	0.487572	0	C|0.930;T|0.070	0.070	strong	MUC5B,colon,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.C14135T	p.T4712M	CCAGCACGGCCAC	.	PASS	Atlas-SNP
MAN2A2	4122	hgsc.bcm.edu	37	15	91452566	91452566	+	Silent	SNP	G	G	A	rs148266546	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	6	101	0	0.0967742	0	G|1.000;A|0.000	0.000	strong	.	MAN2A2	99	.	NM_006122	exon8	c.G1206A	p.L402L	AGCCCTGCTTCTG	.	PASS	Atlas-SNP
DBN1	1627	hgsc.bcm.edu	37	5	176893942	176893942	+	Missense_Mutation	SNP	C	C	T	rs146597348	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21	11	42	0	0.52381	0	C|0.990;T|0.010	0.010	strong	DBN1,NS,lymphoid_neoplasm,0,1	DBN1	122	1	NM_080881	exon8	c.G683A	p.R228Q	CGCTCCCGGTAGC	.	PASS	Atlas-SNP
CCPG1	9236	hgsc.bcm.edu	37	15	55664220	55664220	+	Silent	SNP	G	G	A	rs3203152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	40	84	0	0.97561	0	G|0.852;A|0.148	0.148	strong	.	CCPG1	74	.	NM_020739	exon6	c.C477T	p.D159D	TTCATCGTCACTA	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42385446	42385446	+	Missense_Mutation	SNP	T	T	C	rs9562353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	56	102	0	0.533333	0	T|0.931;C|0.069	0.069	strong	KIAA0564,lymph_node,lymphoid_neoplasm,0,1	.	.	1	NM_015058	exon17	c.A1978G	p.R660G	GTTGTCTGGTAGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509722	195509722	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	520	83	327	0	0.159615	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C8729A	p.T2910N	GGCGTGGTGTCAC	.	PASS	Atlas-SNP
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956194	18956194	+	Silent	SNP	T	T	C	rs2014931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	101	129	0	0.990196	0	T|0.636;C|0.364	0.364	strong	MRGPRX1,caecum,carcinoma,-2,3	MRGPRX1	84	3	NM_147199	exon1	c.A138G	p.A46A	CACAACTGCGTTT	.	PASS	Atlas-SNP
WDR88	126248	hgsc.bcm.edu	37	19	33635761	33635761	+	Silent	SNP	C	C	T	rs3848596	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	84	241	1	0.48	0.00414938	C|0.574;N|0.000	.	strong	.	WDR88	50	.	NM_173479	exon3	c.C399T	p.D133D	GGTGGACGGTTCT	.	PASS	Atlas-SNP
BMP2	650	hgsc.bcm.edu	37	20	6759595	6759595	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	3	201	0	0.0172414	0	.	.	none	BMP2,NS,carcinoma,0,1	BMP2	45	1	NM_001200	exon3	c.C1050T	p.N350N	GGTCAACTCTGTT	.	scavenged	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78599562	78599562	+	Silent	SNP	C	C	G	rs17848685	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	81	131	0	0.48503	0	C|0.836;G|0.164	0.164	strong	RPTOR,right_lower_lobe,carcinoma,+1,1	RPTOR	122	1	NM_001163034	exon2	c.C234G	p.T78T	GAAGACCACGCCC	.	PASS	Atlas-SNP
CNGA1	1259	hgsc.bcm.edu	37	4	47945295	47945295	+	Missense_Mutation	SNP	C	C	T	rs28642966	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	45	85	0	0.459184	0	C|0.787;T|0.213	0.213	strong	.	CNGA1	74	.	NM_001142564	exon7	c.G559A	p.D187N	TTTTATCATCTGA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281948	152281948	+	Missense_Mutation	SNP	G	G	A	rs12405241	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	424	154	299	1	0.363208	0.00334448	G|0.839;A|0.161	0.161	strong	.	FLG	900	.	NM_002016	exon3	c.C5414T	p.A1805V	TGGGACGCTGAGT	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34725116	34725116	+	Silent	SNP	G	G	A	rs62547038	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	550	163	518	1	0.296364	0.0019305	G|0.858;A|0.142	0.142	strong	.	FAM205A	45	.	NM_001141917	exon4	c.C2121T	p.V707V	TGCCAGGACCCCA	.	PASS	Atlas-SNP
CENPQ	55166	hgsc.bcm.edu	37	6	49459978	49459978	+	Missense_Mutation	SNP	A	A	G	rs2501968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	51	79	0	0.980769	0	A|0.545;C|0.003	.	strong	CENPQ,colon,carcinoma,0,2	CENPQ	23	2	NM_018132	exon9	c.A797G	p.D266G	AACTGGATGCATC	.	PASS	Atlas-SNP
BLVRA	644	hgsc.bcm.edu	37	7	43830888	43830888	+	Silent	SNP	T	T	C	rs1802846	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	59	173	0	0.324176	0	T|0.890;C|0.110	0.110	strong	BLVRA,NS,carcinoma,0,1	BLVRA	26	1	NM_001253823	exon5	c.T175C	p.L59L	ATTTCTTTGGAGG	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68701948	68701948	+	Silent	SNP	C	C	T	rs11228413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	88	217	0	0.483516	0	C|0.805;T|0.195	0.195	strong	IGHMBP2,colon,carcinoma,+2,3	IGHMBP2	83	3	NM_002180	exon11	c.C1554T	p.V518V	CCTCGTCAGTTTG	.	PASS	Atlas-SNP
FAM151B	167555	hgsc.bcm.edu	37	5	79817898	79817898	+	Silent	SNP	A	A	G	rs2431224	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	63	112	0	0.529412	0	A|0.954;G|0.046	0.046	strong	.	FAM151B	25	.	NM_205548	exon5	c.A612G	p.R204R	TGTCAGAGCAGCA	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34542872	34542872	+	Silent	SNP	C	C	G	rs17236798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211	154	326	0	0.729858	0	C|0.822;G|0.178	0.178	strong	.	SLC12A6	205	.	NM_133647	exon11	c.G1551C	p.P517P	ACCAATCGGAATA	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	89990324	89990324	+	Missense_Mutation	SNP	A	A	G	rs1878878	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	156	180	1	0.987342	0.00555556	A|0.209;G|0.791	0.791	strong	.	GPR98	605	.	NM_032119	exon33	c.A7751G	p.N2584S	TCTACAATATTAG	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138602417	138602417	+	Missense_Mutation	SNP	G	G	A	rs2774960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	30	44	0	1	0	G|0.595;A|0.405	0.405	strong	KIAA1549_ENST00000422774,NS,carcinoma,+1,3	KIAA1549	314	3	NM_020910	exon2	c.C1955T	p.P652L	TCACTCGGCATCA	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982428	75982428	+	Silent	SNP	C	C	T	rs7182906	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	97	161	3	0.97	0.0186335	C|0.702;T|0.298	0.298	strong	CSPG4,NS,carcinoma,0,1	CSPG4	175	1	NM_001897	exon3	c.G978A	p.G326G	ATCCAGCCCCCCG	.	scavenged	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143452	55143452	+	Missense_Mutation	SNP	T	T	C	rs1061680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	72	140	1	0.533333	0.00714286	T|0.567;C|0.433	0.433	strong	LILRB1,NS,carcinoma,-1,1	LILRB1	140	1	NM_001081637	exon5	c.T425C	p.I142T	ATGTAATCCTCCA	.	scavenged	Atlas-SNP
PTPN3	5774	hgsc.bcm.edu	37	9	112166845	112166845	+	Silent	SNP	G	G	A	rs34302609	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	51	110	0	0.463636	0	G|0.978;A|0.022	0.022	strong	.	PTPN3	106	.	NM_002829	exon19	c.C1836T	p.N612N	AAGCTGGTTCAGT	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104117191	104117191	+	Silent	SNP	A	A	G	rs2290943	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	41	69	0	0.43617	0	A|0.848;G|0.152	0.152	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon4	c.T243C	p.T81T	AAATATAGTACCT	.	PASS	Atlas-SNP
ZNF839	55778	hgsc.bcm.edu	37	14	102807671	102807671	+	Missense_Mutation	SNP	C	C	T	rs9464	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	347	130	312	0	0.37464	0	T|0.080;G|0.001	0.080	strong	.	ZNF839	41	.	NM_018335	exon8	c.C1939T	p.P647S	TCCCCTCCAGTAA	.	PASS	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	37	6	168376951	168376951	+	Missense_Mutation	SNP	T	T	C	rs71305246	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	524	83	425	0	0.158397	0	CTC|0.500;TTA|0.500	.	alt	.	.	.	.	NM_001129895	exon1	c.A382G	p.M128V	GGGTCATTACCCC	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	994452	994452	+	Silent	SNP	C	C	T	rs3755954	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	96	240	1	0.434389	0.00416667	C|0.784;T|0.216	0.216	strong	.	IDUA	33	.	NM_000203	exon3	c.C352T	p.L118L	GGGTACCTGGACC	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242396209	242396209	+	Missense_Mutation	SNP	C	C	A	rs145630778	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	258	120	266	1	0.465116	0.0037594	C|1.000;A|0.000	0.000	strong	.	FARP2	92	.	NM_014808	exon14	c.C1459A	p.P487T	AAGAGCCCCCTGA	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74497009	74497009	+	Missense_Mutation	SNP	A	A	G	rs2351528	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	35	69	1	0.522388	0.0144928	A|0.597;G|0.403	0.403	strong	CD109,caecum,carcinoma,0,1	CD109	170	1	NM_133493	exon21	c.A2390G	p.N797S	CTTCAAATGAAAT	.	scavenged	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50944294	50944294	+	Missense_Mutation	SNP	C	C	T	rs374005339		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	12	178	0	0.0591133	0	.	.	weak	.	MYBPC2	103	.	NM_004533	exon8	c.C730T	p.R244W	CTGAAGCGGCTGA	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	37	12	49950251	49950251	+	Missense_Mutation	SNP	C	C	G	rs113209368	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	70	134	0	0.460526	0	C|0.951;G|0.049	0.049	strong	.	KCNH3	88	.	NM_012284	exon13	c.C2567G	p.P856R	CCTCCCCTGGACC	.	PASS	Atlas-SNP
MORC3	23515	hgsc.bcm.edu	37	21	37692589	37692589	+	Silent	SNP	A	A	T	rs2236433	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	39	82	0	0.46988	0	A|0.762;T|0.238	0.238	strong	.	MORC3	78	.	NM_015358	exon1	c.A27T	p.I9I	CGGGATACGCCTC	.	PASS	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56423074	56423074	+	Silent	SNP	C	C	G	rs977070	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	82	106	2	1	0.0188679	C|0.480;G|0.520	0.520	strong	NLRP13,NS,carcinoma,0,1	NLRP13	220	1	NM_176810	exon5	c.G2109C	p.L703L	TCACTCCAGAATT	.	scavenged	Atlas-SNP
ASB10	136371	hgsc.bcm.edu	37	7	150873331	150873331	+	Silent	SNP	C	C	T	rs104886486	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	98	273	0	0.695035	0	C|0.992;T|0.008	0.008	strong	.	ASB10	99	.	NM_001142459	exon5	c.G1272A	p.S424S	CTGCAGCGACCTG	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121742307	121742307	+	Silent	SNP	C	C	T	rs13008360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	47	126	1	0.559524	0.00793651	C|0.984;T|0.016	0.016	strong	GLI2,NS,carcinoma,0,1	GLI2	187	1	NM_005270	exon11	c.C1944T	p.T648T	CAAGACCGAGAGC	.	scavenged	Atlas-SNP
EXD3	54932	hgsc.bcm.edu	37	9	140201433	140201433	+	Missense_Mutation	SNP	G	G	A	rs118011827	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	30	81	0	0.638298	0	G|0.996;A|0.004	0.004	strong	.	EXD3	86	.	NM_017820	exon22	c.C2600T	p.P867L	GGGGCTGGGCTCG	.	PASS	Atlas-SNP
TMEM119	338773	hgsc.bcm.edu	37	12	108985945	108985945	+	Missense_Mutation	SNP	A	A	G	rs7975237	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	106	260	1	0.504762	0.00384615	A|0.417;G|0.583	0.583	strong	.	TMEM119	31	.	NM_181724	exon2	c.T215C	p.I72T	AGGGTTATGGGCT	.	PASS	Atlas-SNP
C1orf110	339512	hgsc.bcm.edu	37	1	162825457	162825457	+	Missense_Mutation	SNP	C	C	A	rs77227460	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	428	148	309	1	0.345794	0.00323625	C|0.875;A|0.125	0.125	strong	.	C1orf110	22	.	NM_178550	exon3	c.G279T	p.R93S	CTTCTGCCTTCCC	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406626	3406626	+	Missense_Mutation	SNP	G	G	A	rs11648783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	50	107	0	0.46729	0	G|0.723;A|0.277	0.277	strong	.	OR2C1	38	.	NM_012368	exon1	c.G686A	p.R229H	AAATCCGCTCTGC	.	PASS	Atlas-SNP
HOXB8	3218	hgsc.bcm.edu	37	17	46690777	46690777	+	Silent	SNP	A	A	G	rs45441492	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	180	221	1	0.989011	0.00452489	A|0.924;G|0.076	0.076	strong	.	HOXB8	26	.	NM_024016	exon2	c.T519C	p.R173R	CCGCTTACGAGTC	.	PASS	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	37	13	67800419	67800419	+	Silent	SNP	C	C	G	rs41283952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	77	196	0	0.469512	0	C|0.970;G|0.030	0.030	strong	.	PCDH9	252	.	NM_203487	exon2	c.G2154C	p.V718V	TCCACTCACTATA	.	PASS	Atlas-SNP
TMEM245	23731	hgsc.bcm.edu	37	9	111881927	111881927	+	Silent	SNP	T	T	C	rs6825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	34	105	0	0.43038	0	T|0.679;C|0.321	0.321	strong	C9orf5,NS,carcinoma,0,1	.	.	1	NM_032012	exon1	c.A267G	p.L89L	GCCGCATAGCACG	.	PASS	Atlas-SNP
MTIF2	4528	hgsc.bcm.edu	37	2	55490788	55490788	+	Silent	SNP	T	T	C	rs1134722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	18	36	0	0.473684	0	T|0.941;C|0.059	0.059	strong	MTIF2,NS,carcinoma,0,1	MTIF2	64	1	NM_002453	exon4	c.A207G	p.L69L	TGTTACTAGAAGC	.	PASS	Atlas-SNP
SLC10A6	345274	hgsc.bcm.edu	37	4	87769929	87769929	+	Missense_Mutation	SNP	T	T	C	rs13106574	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	56	144	0	0.388889	0	T|0.854;C|0.146	0.146	strong	.	SLC10A6	40	.	NM_197965	exon1	c.A340G	p.I114V	TGAAAATGTTAGA	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125434716	125434716	+	Silent	SNP	G	G	A	rs4078216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	121	122	0	0.98374	0	G|0.776;N|0.000	.	strong	DHX37,NS,carcinoma,0,1	DHX37	114	1	NM_032656	exon24	c.C3195T	p.A1065A	GAACCGGGCAAAG	.	PASS	Atlas-SNP
PARD3	56288	hgsc.bcm.edu	37	10	34630575	34630575	+	Silent	SNP	T	T	A	rs141191270	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	69	118	0	0.784091	0	T|0.999;A|0.001	0.001	strong	.	PARD3	131	.	NM_001184787	exon16	c.A2397T	p.A799A	ACTGATTGCAGCC	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156879580	156879580	+	Silent	SNP	C	C	T	rs3737224	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	72	142	0	0.382979	0	C|0.847;T|0.153	0.153	strong	.	PEAR1	118	.	NM_001080471	exon12	c.C1449T	p.P483P	CCCACCCGGAACC	.	PASS	Atlas-SNP
SWSAP1	126074	hgsc.bcm.edu	37	19	11486354	11486354	+	Missense_Mutation	SNP	C	C	A	rs146815699	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	25	70	0	0.378788	0	C|0.997;A|0.003	0.003	strong	.	.	.	.	NM_175871	exon2	c.C352A	p.L118I	GCCTTACTTCTAG	.	PASS	Atlas-SNP
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12252955	12252955	+	Missense_Mutation	SNP	T	T	G	rs1061622	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	12	68	1	0.272727	0.0147059	T|0.792;G|0.208	0.208	strong	TNFRSF1B,NS,carcinoma,0,1	TNFRSF1B	28	1	NM_001066	exon6	c.T587G	p.M196R	CAAGCATGGATGC	.	scavenged	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011718	46011718	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	345	29	235	0	0.084058	0	.	.	none	KRTAP10-6,caecum,carcinoma,-2,1	KRTAP10-6	57	1	NM_198688	exon1	c.A648G	p.P216P	GCAAGTTGGCTGG	.	scavenged	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37153871	37153871	+	Missense_Mutation	SNP	G	G	T	rs77014998	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	34	122	0	0.377778	0	G|0.992;T|0.008	0.008	strong	.	C5orf42	422	.	NM_023073	exon41	c.C8182A	p.P2728T	TTTCAGGCTTGGG	.	PASS	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	37	8	100874154	100874154	+	Missense_Mutation	SNP	G	G	A	rs149318176	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	28	61	0	0.337349	0	G|0.998;A|0.002	0.002	strong	.	VPS13B	811	.	NM_017890	exon58	c.G11270A	p.R3757Q	TGTCCCGGCTGGG	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656607	46656607	+	Silent	SNP	G	G	A	rs8143066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	67	153	0	0.503759	0	G|0.722;A|0.278	0.278	strong	.	PKDREJ	195	.	NM_006071	exon1	c.C2613T	p.I871I	CTGGTTGATACCC	.	PASS	Atlas-SNP
KIF4B	285643	hgsc.bcm.edu	37	5	154395458	154395458	+	Missense_Mutation	SNP	G	G	A	rs17116710	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	108	256	0	0.448133	0	G|0.829;A|0.171	0.171	strong	.	KIF4B	307	.	NM_001099293	exon1	c.G2039A	p.R680H	GAGACCGTAAGAG	.	PASS	Atlas-SNP
ALG6	29929	hgsc.bcm.edu	37	1	63902524	63902524	+	Missense_Mutation	SNP	C	C	G	rs41285372	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	135	275	0	0.75	0	C|0.987;G|0.013	0.013	strong	.	ALG6	33	.	NM_013339	exon15	c.C1357G	p.L453V	GTGCTTCTGACGT	.	PASS	Atlas-SNP
IFNA1	3439	hgsc.bcm.edu	37	9	21440916	21440916	+	Missense_Mutation	SNP	C	C	T	rs2230050	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	634	176	714	0	0.277603	0	C|0.946;T|0.054	0.054	strong	IFNA1,NS,carcinoma,-1,1	IFNA1	21	1	NM_024013	exon1	c.C410T	p.A137V	TGAATGCGGACTC	.	scavenged	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	37	16	1555505	1555505	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	61	102	0	0.465649	0	.	.	none	.	TELO2	44	.	NM_016111	exon16	c.C1937T	p.P646L	GCCTGCCAGAGGC	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	37	5	73207372	73207372	+	Missense_Mutation	SNP	T	T	A	rs1478453	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	64	111	0	0.507937	0	T|0.663;A|0.337	0.337	strong	.	.	.	.	NM_001080479	exon35	c.T4920A	p.H1640Q	TTTCCATGAAAGC	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102595579	102595579	+	Missense_Mutation	SNP	G	G	C	rs17099450	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	335	80	200	0	0.238806	0	G|0.946;C|0.054	0.054	strong	.	MMP8	68	.	NM_002424	exon1	c.C8G	p.S3C	TTCAGGGAGAACA	.	PASS	Atlas-SNP
RPS6KB2	6199	hgsc.bcm.edu	37	11	67200812	67200812	+	Missense_Mutation	SNP	C	C	T	rs55987642	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	30	69	0	0.517241	0	C|0.963;T|0.037	0.037	strong	.	RPS6KB2	92	.	NM_003952	exon10	c.C800T	p.P267L	TCCAGCCGCCCTT	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	37	8	24359068	24359068	+	Silent	SNP	G	G	A	rs13277171	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	74	124	0	0.621849	0	G|0.743;A|0.257	0.257	strong	ADAM7,colon,carcinoma,0,1	ADAM7	165	1	NM_003817	exon20	c.G2187A	p.L729L	AATCCTGCCAGAA	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12428803	12428803	+	Missense_Mutation	SNP	G	G	A	rs848016	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	59	104	0	0.536364	0	G|0.324;A|0.676	0.676	strong	.	VWDE	123	.	NM_001135924	exon3	c.C425T	p.S142F	TATACAGAAAAGT	.	PASS	Atlas-SNP
PAXIP1	22976	hgsc.bcm.edu	37	7	154760666	154760666	+	Silent	SNP	C	C	T	rs61752011	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	14	82	0	0.222222	0	C|0.784;T|0.216	0.216	strong	PAXIP1_ENST00000397192,NS,carcinoma,0,2	PAXIP1	150	2	NM_007349	exon7	c.G1245A	p.P415P	TAAAACCGGGTGC	.	PASS	Atlas-SNP
GUSB	2990	hgsc.bcm.edu	37	7	65429359	65429359	+	Silent	SNP	G	G	A	rs41406646		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	93	101	0	0.6	0	G|1.000;|0.000	.	weak	.	GUSB	52	.	NM_000181	exon11	c.C1740T	p.Y580Y	AACCACGTATTTT	.	PASS	Atlas-SNP
ASPG	374569	hgsc.bcm.edu	37	14	104559852	104559852	+	Silent	SNP	T	T	C	rs941953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	89	112	0	0.581699	0	T|0.625;C|0.375	0.375	strong	.	ASPG	34	.	NM_001080464	exon3	c.T216C	p.I72I	GAGGATTCTCTAC	.	PASS	Atlas-SNP
SCN3A	6328	hgsc.bcm.edu	37	2	166003479	166003479	+	Silent	SNP	G	G	A	rs16850131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	114	230	0	0.467213	0	G|0.756;A|0.244	0.244	strong	.	SCN3A	544	.	NM_001081676	exon12	c.C1441T	p.L481L	CCAACAGCTCTCC	.	PASS	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	37	18	43496539	43496539	+	Missense_Mutation	SNP	G	G	A	rs78339727	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	28	56	0	0.528302	0	G|0.979;A|0.021	0.021	strong	.	EPG5	199	.	NM_020964	exon18	c.C3248T	p.S1083L	AGATGCGATAAAA	.	PASS	Atlas-SNP
EFTUD1	79631	hgsc.bcm.edu	37	15	82456227	82456227	+	Missense_Mutation	SNP	T	T	C	rs1128431	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	16	168	0	0.177778	0	T|0.838;C|0.162	0.162	strong	.	EFTUD1	74	.	NM_024580	exon16	c.A1849G	p.I617V	TCACAATAGGAGT	.	PASS	Atlas-SNP
AK1	203	hgsc.bcm.edu	37	9	130634103	130634103	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	2	81	0	0.03125	0	.	.	none	AK1,NS,carcinoma,0,1	AK1	13	1	NM_000476	exon5	c.G323A	p.R108Q	CTTACCCGTCGCT	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681172	100681172	+	Missense_Mutation	SNP	A	A	G	rs28555173	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	222	219	161	1	0.986486	0.00621118	A|0.823;G|0.177	0.177	strong	.	MUC17	804	.	NM_001040105	exon3	c.A6475G	p.R2159G	AGTGACAGAAGAA	.	PASS	Atlas-SNP
TBC1D10C	374403	hgsc.bcm.edu	37	11	67172911	67172911	+	Silent	SNP	C	C	T	rs61734600	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	54	116	0	0.461538	0	C|0.948;T|0.052	0.052	strong	.	TBC1D10C	42	.	NM_001256508	exon4	c.C294T	p.R98R	CCTGCGCGCCCGA	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836047	2836047	+	Missense_Mutation	SNP	C	C	T	rs67359049	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	38	95	0	0.447059	0	C|0.938;T|0.062	0.062	strong	.	ARSD	47	.	NM_001669	exon5	c.G661A	p.G221S	AGAAACCGCAGGT	.	PASS	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41383134	41383134	+	Silent	SNP	A	A	G	rs147847954	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	66	227	0	0.392857	0	A|0.978;G|0.022	0.022	strong	.	CYP2A7	71	.	NM_000764	exon7	c.T1122C	p.V374V	CTTTTTAACCCTG	.	PASS	Atlas-SNP
RRM2	6241	hgsc.bcm.edu	37	2	10262859	10262859	+	Silent	SNP	G	G	A	rs72542787	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	96	234	0	0.564706	0	G|0.956;A|0.044	0.044	strong	.	RRM2	63	.	NM_001165931	exon1	c.G114A	p.G38G	TGAGGGGTCGCCC	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215848587	215848587	+	Silent	SNP	T	T	C	rs2797234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	97	218	0	0.395918	0	T|0.680;C|0.320	0.320	strong	USH2A,NS,carcinoma,0,2	USH2A	1168	2	NM_206933	exon63	c.A12666G	p.T4222T	CATAAATGTATTC	.	PASS	Atlas-SNP
CNR2	1269	hgsc.bcm.edu	37	1	24201448	24201448	+	Silent	SNP	C	C	T	rs3003336	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	50	65	0	1	0	C|0.364;T|0.636	0.636	strong	CNR2,NS,carcinoma,0,1	CNR2	78	1	NM_001841	exon2	c.G660A	p.V220V	GCTGGCCACATGC	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120589064	120589064	+	Silent	SNP	G	G	C	rs2286045	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	50	130	0	0.37037	0	G|0.685;C|0.315	0.315	strong	GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	NM_006836	exon34	c.C4194G	p.A1398A	GCCATAGGCGGCC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149473614	149473614	+	Missense_Mutation	SNP	A	A	G	rs117048984	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	30	78	0	0.810811	0	A|0.980;G|0.020	0.020	strong	.	.	.	.	NM_198455	exon2	c.A230G	p.Y77C	CTATCTACAAGTG	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22942061	22942061	+	Missense_Mutation	SNP	A	A	C	rs61753878	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17	12	25	0	0.705882	0	A|0.910;C|0.090	0.090	strong	.	ZNF99	273	.	NM_001080409	exon4	c.T650G	p.I217S	TGTTTAATAAGGG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8212263	8212263	+	Silent	SNP	G	G	A	rs11878432	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	68	78	0	1	0	G|0.760;A|0.240	0.240	strong	.	FBN3	300	.	NM_032447	exon1	c.C102T	p.D34D	GGCCCCGTCCCAG	.	PASS	Atlas-SNP
DNAJB8	165721	hgsc.bcm.edu	37	3	128182074	128182074	+	Silent	SNP	G	G	A	rs2981026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	94	240	1	0.463054	0.00416667	G|0.724;A|0.276	0.276	strong	.	DNAJB8	34	.	NM_153330	exon3	c.C15T	p.Y5Y	CACTTCGTAGTAG	.	PASS	Atlas-SNP
ATP5SL	55101	hgsc.bcm.edu	37	19	41944237	41944237	+	Missense_Mutation	SNP	T	T	C	rs2231940	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	78	173	0	0.47561	0	T|0.640;C|0.360	0.360	strong	ATP5SL,NS,carcinoma,0,1	ATP5SL	20	1	NM_001167867	exon2	c.A119G	p.N40S	TTCTGATTGCCCT	.	PASS	Atlas-SNP
SCARB1	949	hgsc.bcm.edu	37	12	125302137	125302137	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	3	112	0	0.0263158	0	.	.	none	SCARB1,colon,carcinoma,0,1	SCARB1	40	1	NM_005505	exon2	c.C243T	p.G81G	CTTCTCGCCCTTC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152277055	152277055	+	Missense_Mutation	SNP	C	C	G	rs2065955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	388	131	253	0	0.337629	0	C|0.615;G|0.385	0.385	strong	.	FLG	900	.	NM_002016	exon3	c.G10307C	p.G3436A	GGGTGTCCACGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506982	195506982	+	Silent	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	13	173	9	0.083871	0.0520231	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11469G	p.T3823T	AAGAGGGGTGGTG	.	scavenged	Atlas-SNP
SLC39A8	64116	hgsc.bcm.edu	37	4	103228734	103228734	+	Silent	SNP	C	C	T	rs35411892	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	351	169	344	1	0.481481	0.00290698	C|0.841;T|0.159	0.159	strong	.	SLC39A8	24	.	NM_022154	exon3	c.G411A	p.T137T	AATAATCGTCACT	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36270130	36270130	+	Missense_Mutation	SNP	C	C	A	rs12199580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	49	106	1	0.4375	0.00943396	C|0.661;A|0.339	0.339	strong	PNPLA1,back,malignant_melanoma,-1,1	PNPLA1	92	1	NM_001145717	exon6	c.C1268A	p.P423H	CTTCACCCAGGCC	.	scavenged	Atlas-SNP
KCNG2	26251	hgsc.bcm.edu	37	18	77659553	77659553	+	Silent	SNP	C	C	T	rs75339189	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	279	124	263	0	0.444444	0	C|0.926;T|0.074	0.074	strong	.	KCNG2	48	.	NM_012283	exon2	c.C1138T	p.L380L	CGCAGCCTGCCCG	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55268916	55268916	+	Silent	SNP	C	C	T	rs2293347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252	85	206	0	0.337302	0	C|0.894;T|0.106	0.106	strong	.	EGFR	20426	.	NM_005228	exon25	c.C2982T	p.D994D	TACAGACTCCAAC	.	PASS	Atlas-SNP
OR11H6	122748	hgsc.bcm.edu	37	14	20691962	20691962	+	Missense_Mutation	SNP	C	C	G	rs9323693	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	376	136	296	1	0.361702	0.00337838	C|0.918;G|0.082	0.082	strong	.	OR11H6	60	.	NM_001004480	exon1	c.C94G	p.L32V	TTTGTCCTCCTGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149528262	149528262	+	Nonsense_Mutation	SNP	C	C	T	rs10261977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	41	307	0	0.238372	0	C|0.823;T|0.177	0.177	strong	.	.	.	.	NM_198455	exon108	c.C15178T	p.R5060X	GAGCTTCGAAACT	.	PASS	Atlas-SNP
GLRA4	441509	hgsc.bcm.edu	37	X	102978806	102978806	+	Silent	SNP	G	G	C	rs5945807	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	306	299	650	1	0.977124	0.00153846	0|0.009;C|0.169	0.169	strong	.	GLRA4	86	.	NM_001024452	exon5	c.C555G	p.T185T	CGTGCAGGTCTGG	.	PASS	Atlas-SNP
ABCG5	64240	hgsc.bcm.edu	37	2	44040401	44040401	+	Missense_Mutation	SNP	G	G	C	rs6720173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	53	155	0	0.456897	0	G|0.792;C|0.208	0.208	strong	.	ABCG5	72	.	NM_022436	exon13	c.C1810G	p.Q604E	TTCCTTGAGTGAA	.	PASS	Atlas-SNP
SSUH2	51066	hgsc.bcm.edu	37	3	8675447	8675447	+	Missense_Mutation	SNP	C	C	T	rs112366230	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	96	157	0	0.527473	0	C|0.986;T|0.014	0.014	strong	.	.	.	.	NM_001256748	exon4	c.G244A	p.A82T	GGAGGGCTTCCCG	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100122291	100122291	+	Missense_Mutation	SNP	T	T	C	rs3747495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	79	173	1	0.481707	0.00578035	T|0.807;C|0.193	0.193	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon26	c.T3523C	p.F1175L	CTCAGCTTCGTCC	.	scavenged	Atlas-SNP
KLHL1	57626	hgsc.bcm.edu	37	13	70681598	70681598	+	Silent	SNP	T	T	C	rs3751427	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	48	149	0	0.48	0	T|0.866;C|0.134	0.134	strong	.	KLHL1	164	.	NM_020866	exon1	c.A234G	p.S78S	GGACGATGAAGAG	.	PASS	Atlas-SNP
SUPT16H	11198	hgsc.bcm.edu	37	14	21831419	21831419	+	Silent	SNP	C	C	T	rs61746713	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	58	80	0	0.617021	0	C|0.925;T|0.075	0.075	strong	SUPT16H,NS,carcinoma,-1,1	SUPT16H	84	1	NM_007192	exon12	c.G1368A	p.R456R	TGCTGCCCGAGAA	.	PASS	Atlas-SNP
NKAIN4	128414	hgsc.bcm.edu	37	20	61878950	61878950	+	Missense_Mutation	SNP	A	A	C	rs872808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	288	122	304	1	0.423611	0.00328947	A|0.529;C|0.471	0.471	strong	NKAIN4,NS,carcinoma,0,1	NKAIN4	23	1	NM_152864	exon4	c.T451G	p.C151G	GCAGGCAACTGTG	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17273396	17273396	+	Silent	SNP	A	A	G	rs7537468	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	14	184	1	0.208955	0.00543478	A|0.845;G|0.155	0.155	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon17	c.A2424G	p.L808L	CTCCCTACGAGTG	.	scavenged	Atlas-SNP
LPL	4023	hgsc.bcm.edu	37	8	19810826	19810826	+	Silent	SNP	G	G	A	rs248	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	30	96	0	0.275229	0	G|0.944;A|0.056	0.056	strong	.	LPL	78	.	NM_000237	exon4	c.G435A	p.E145E	GGAGGAGTTTAAC	.	PASS	Atlas-SNP
DCAF5	8816	hgsc.bcm.edu	37	14	69521345	69521345	+	Silent	SNP	G	G	A	rs61741172	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	61	99	0	0.5	0	G|0.761;A|0.239	0.239	strong	.	DCAF5	67	.	NM_003861	exon9	c.C2058T	p.T686T	CTCCCCGGTCACC	.	PASS	Atlas-SNP
POMT1	10585	hgsc.bcm.edu	37	9	134385435	134385435	+	Nonsense_Mutation	SNP	C	C	T	rs3887873	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	118	107	1	0.991597	0.00934579	C|0.904;T|0.096	0.096	strong	.	POMT1	59	.	NM_007171	exon8	c.C751T	p.Q251X	CAGATGCAGATGT	.	PASS	Atlas-SNP
TPO	7173	hgsc.bcm.edu	37	2	1497803	1497803	+	Silent	SNP	C	C	T	rs1126797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	58	83	0	0.557692	0	A|0.000;C|0.646;G|0.000;T|0.354	0.354	strong	.	TPO	224	.	NM_001206744	exon11	c.C1998T	p.D666D	GCGGGACGGTGAC	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91825027	91825027	+	Silent	SNP	C	C	T	rs1117388	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	43	159	1	0.767857	0.00628931	C|0.652;T|0.348	0.348	strong	.	SV2B	98	.	NM_014848	exon11	c.C1443T	p.D481D	TGAAGACGTAACA	.	PASS	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038450	22038450	+	Silent	SNP	G	G	A	rs11626669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	143	109	1	0.979452	0.00917431	G|0.547;A|0.453	0.453	strong	.	OR10G3	40	.	NM_001005465	exon1	c.C426T	p.S142S	CAAGGCGCTCAGC	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29364815	29364815	+	Missense_Mutation	SNP	C	C	G	rs2073154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	246	313	0	0.995951	0	C|0.628;G|0.372	0.372	strong	.	OR12D2	42	.	NM_013936	exon1	c.C339G	p.F113L	GTTGTTCGCCGTG	.	PASS	Atlas-SNP
SUPT3H	8464	hgsc.bcm.edu	37	6	44982593	44982593	+	Silent	SNP	G	G	A	rs12528232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	62	192	0	0.421769	0	G|0.873;A|0.127	0.127	strong	.	SUPT3H	75	.	NM_181356	exon7	c.C342T	p.I114I	GTCTCGGATAAAC	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90020923	90020923	+	Silent	SNP	T	T	G	rs16869042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	121	143	0	0.98374	0	G|0.336;N|0.001	0.336	strong	GPR98,NS,carcinoma,0,2	GPR98	605	2	NM_032119	exon47	c.T9927G	p.P3309P	AAATCCTAAAACT	.	PASS	Atlas-SNP
TRAF7	84231	hgsc.bcm.edu	37	16	2222286	2222286	+	Silent	SNP	C	C	T	rs11547311	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	60	120	0	0.472441	0	C|0.945;T|0.055	0.055	strong	.	TRAF7	158	.	NM_032271	exon8	c.C570T	p.H190H	CCGGCACGGCTGC	.	PASS	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	37	16	3254418	3254418	+	Missense_Mutation	SNP	C	C	G	rs61731432	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	97	237	0	0.427313	0	C|0.968;G|0.032	0.032	strong	.	OR1F1	36	.	NM_012360	exon1	c.C172G	p.P58A	CACACCCCCATGT	.	PASS	Atlas-SNP
CAMSAP1	157922	hgsc.bcm.edu	37	9	138742077	138742077	+	Silent	SNP	C	C	G	rs35981196	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	43	72	0	0.462366	0	C|0.836;G|0.164	0.164	strong	.	CAMSAP1	142	.	NM_015447	exon7	c.G951C	p.P317P	AACATTCGGCTAA	.	PASS	Atlas-SNP
SARS	6301	hgsc.bcm.edu	37	1	109779073	109779073	+	Missense_Mutation	SNP	G	G	A	rs140717526	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	59	140	0	0.686047	0	G|0.989;A|0.011	0.011	strong	.	SARS	43	.	NM_006513	exon9	c.G1160A	p.G387E	GCTCAGGAGCCTT	.	PASS	Atlas-SNP
HEATR2	54919	hgsc.bcm.edu	37	7	796430	796430	+	Silent	SNP	C	C	T	rs73036225	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	67	95	0	0.536	0	C|0.850;T|0.150	0.150	strong	.	HEATR2	62	.	NM_017802	exon6	c.C1269T	p.S423S	CAGATCCGCAGAG	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126372742	126372742	+	Missense_Mutation	SNP	G	G	A	rs1567047	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	112	178	0	0.957265	0	G|0.769;A|0.231	0.231	strong	.	FAT4	1752	.	NM_024582	exon9	c.G10571A	p.G3524D	GGCCAGGCACTTT	.	PASS	Atlas-SNP
CABIN1	23523	hgsc.bcm.edu	37	22	24567795	24567795	+	Missense_Mutation	SNP	C	C	T	rs145513360	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	94	141	0	0.5875	0	C|0.999;T|0.001	0.001	strong	.	CABIN1	153	.	NM_001199281	exon34	c.C5872T	p.R1958W	GTCCAGCGGCCCA	.	PASS	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45003746	45003746	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	38	113	0	0.506667	0	.	.	none	B2M,caecum,carcinoma,-1,17	B2M	99	17	NM_004048	exon1	c.T2G	p.M1R	CCGAGATGTCTCG	.	PASS	Atlas-SNP
OR1A2	26189	hgsc.bcm.edu	37	17	3100827	3100827	+	Silent	SNP	T	T	C	rs2241093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	85	89	0	0.977012	0	T|0.693;C|0.307	0.307	strong	OR1A2,NS,carcinoma,0,1	OR1A2	52	1	NM_012352	exon1	c.T15C	p.N5N	AGAAAATCAATCC	.	PASS	Atlas-SNP
IMPACT	55364	hgsc.bcm.edu	37	18	22020467	22020467	+	Missense_Mutation	SNP	T	T	A	rs582234	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	102	117	0	1	0	T|0.899;A|0.101	0.101	strong	.	IMPACT	37	.	NM_018439	exon6	c.T375A	p.D125E	CCCAGATGTAAAG	.	PASS	Atlas-SNP
CASR	846	hgsc.bcm.edu	37	3	122003757	122003757	+	Missense_Mutation	SNP	G	G	T	rs1801725	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259	113	275	0	0.436293	0	G|0.904;T|0.096	0.096	strong	.	CASR	190	.	NM_001178065	exon7	c.G2986T	p.A996S	AAGAACGCCATGG	.	PASS	Atlas-SNP
PPP1R42	286187	hgsc.bcm.edu	37	8	67926717	67926717	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	60	127	0	0.821918	0	.	.	none	.	PPP1R42	2	.	NM_001013626	exon3	c.A240G	p.Q80Q	ATTGTTTTGTAGG	.	PASS	Atlas-SNP
HIST2H2AB	317772	hgsc.bcm.edu	37	1	149859287	149859287	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	293	3	257	2	0.0102389	0.0077821	.	.	none	HIST2H2AB,NS,carcinoma,-1,1	HIST2H2AB	49	1	NM_175065	exon1	c.C180T	p.T60T	TTCCGCGGTCAGG	.	scavenged	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94631496	94631496	+	Silent	SNP	C	C	T	rs2230755	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	12	82	0	0.222222	0	C|0.929;T|0.071	0.071	strong	.	PLXNC1	135	.	NM_005761	exon10	c.C2037T	p.N679N	AAGCAACGTGATA	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91641928	91641928	+	Silent	SNP	A	A	G	rs13245393	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	72	100	0	0.986301	0	A|0.589;G|0.411	0.411	strong	.	AKAP9	788	.	NM_005751	exon9	c.A3504G	p.E1168E	GTTAGAACTACAG	.	PASS	Atlas-SNP
CDK18	5129	hgsc.bcm.edu	37	1	205492679	205492679	+	Missense_Mutation	SNP	G	G	A	rs4623769	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	326	115	267	0	0.352761	0	G|0.915;A|0.085	0.085	strong	.	CDK18	75	.	NM_212503	exon3	c.G199A	p.G67R	GACAGCGGGGAGG	.	PASS	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19654517	19654517	+	Missense_Mutation	SNP	G	G	A	rs146711114	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	68	220	0	0.441558	0	G|0.998;A|0.002	0.002	strong	.	CILP2	84	.	NM_153221	exon8	c.G1163A	p.R388Q	ACCCCCGGCCCCG	.	PASS	Atlas-SNP
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20740252	20740252	+	Nonsense_Mutation	SNP	C	C	A	rs199807662	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	146	304	2	0.993197	0.00657895	.	.	weak	.	GOLGA6L6	37	.	NM_001145004	exon8	c.G1498T	p.E500X	CCTGCTCGTGCAT	.	PASS	Atlas-SNP
FAM162B	221303	hgsc.bcm.edu	37	6	117086378	117086378	+	Missense_Mutation	SNP	C	C	A	rs654128	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	25	8	33	0	0.32	0	C|0.895;A|0.105	0.105	strong	.	FAM162B	19	.	NM_001085480	exon2	c.G213T	p.Q71H	GTCGAACTGCGAA	.	PASS	Atlas-SNP
CCAR1	55749	hgsc.bcm.edu	37	10	70513684	70513684	+	Silent	SNP	A	A	G	rs5030887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	123	253	1	0.672131	0.00395257	A|0.900;G|0.100	0.100	strong	.	CCAR1	118	.	NM_018237	exon11	c.A1194G	p.Q398Q	TGCTCAATTTACA	.	PASS	Atlas-SNP
LDHA	3939	hgsc.bcm.edu	37	11	18422487	18422487	+	Silent	SNP	C	C	A	rs6498	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	63	146	0	0.470149	0	C|0.911;A|0.089	0.089	strong	.	LDHA	118	.	NM_001165414	exon4	c.C435A	p.I145I	GAACATCTTTAAA	.	PASS	Atlas-SNP
PCDP1	0	hgsc.bcm.edu	37	2	120383248	120383248	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	36	134	0	0.318584	0	.	.	none	.	.	.	.	NM_001271049	exon15	c.A1500G	p.K500K	AGCAAAACAATCG	.	PASS	Atlas-SNP
TSPAN32	10077	hgsc.bcm.edu	37	11	2325427	2325427	+	Missense_Mutation	SNP	T	T	C	rs61744929	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	14	36	0	0.388889	0	T|0.992;C|0.008	0.008	strong	.	TSPAN32	19	.	NM_139022	exon3	c.T272C	p.M91T	GCCTCATGGCAGG	.	PASS	Atlas-SNP
DUSP27	92235	hgsc.bcm.edu	37	1	167096931	167096931	+	Missense_Mutation	SNP	A	A	C	rs267746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	141	105	0	0.979167	0	A|0.780;C|0.220	0.220	strong	.	DUSP27	235	.	NM_001080426	exon5	c.A2563C	p.K855Q	GAGTACAAAATGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684573	100684573	+	Silent	SNP	G	G	A	rs144023476	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	22	169	0	0.10628	0	G|0.984;A|0.016	0.016	strong	MUC17,NS,haematopoietic_neoplasm,0,1	MUC17	804	1	NM_001040105	exon3	c.G9876A	p.T3292T	CACAACGGTGGCC	.	scavenged	Atlas-SNP
SCFD2	152579	hgsc.bcm.edu	37	4	53751932	53751932	+	Silent	SNP	C	C	T	rs2306600	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	357	161	425	0	0.45098	0	C|0.864;T|0.136	0.136	strong	SCFD2,colon,carcinoma,0,3	SCFD2	78	3	NM_152540	exon8	c.G1944A	p.S648S	CTTCAACGATGCC	.	PASS	Atlas-SNP
PRR14	78994	hgsc.bcm.edu	37	16	30666367	30666367	+	Missense_Mutation	SNP	C	C	T	rs3747481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	10	37	0	0.416667	0	C|0.701;T|0.299	0.299	strong	.	PRR14	45	.	NM_024031	exon8	c.C1076T	p.P359L	CACGGCCGCGGCG	.	PASS	Atlas-SNP
ZNF175	7728	hgsc.bcm.edu	37	19	52085095	52085095	+	Silent	SNP	G	G	A	rs35431178	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	35	112	0	0.393258	0	G|0.916;A|0.084	0.084	strong	.	ZNF175	65	.	NM_007147	exon4	c.G255A	p.P85P	GGAGCCGCGTGTG	.	PASS	Atlas-SNP
CRELD2	79174	hgsc.bcm.edu	37	22	50313438	50313438	+	Silent	SNP	T	T	C	rs9616388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	87	152	0	0.617021	0	T|0.754;C|0.246	0.246	strong	CRELD2_ENST00000404488,NS,carcinoma,0,3	CRELD2	57	3	NM_024324	exon3	c.T273C	p.N91N	ATGCAATCAGATG	.	PASS	Atlas-SNP
DERL3	91319	hgsc.bcm.edu	37	22	24179922	24179922	+	Missense_Mutation	SNP	G	G	C	rs3177243	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	66	209	1	0.455172	0.00478469	G|0.825;C|0.175	0.175	strong	DERL3,NS,carcinoma,0,1	DERL3	14	1	NM_001135751	exon5	c.C447G	p.F149L	TGCCTGGAAAGTG	.	scavenged	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	37	6	168377092	168377092	+	Missense_Mutation	SNP	G	G	T	rs199609073		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	354	23	228	0	0.0649718	0	.	.	weak	.	.	.	.	NM_001129895	exon1	c.C241A	p.H81N	CAGTGTGGGGGGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682156	100682156	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268	13	214	0	0.0485075	0	.	.	none	MUC17,bladder,carcinoma,-2,2	MUC17	804	2	NM_001040105	exon3	c.A7459G	p.M2487V	ACACCTATGACCA	.	scavenged	Atlas-SNP
CPZ	8532	hgsc.bcm.edu	37	4	8603117	8603117	+	Missense_Mutation	SNP	A	A	T	rs35993494	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	11	5	9	0	0.454545	0	A|0.884;T|0.116	0.116	strong	.	CPZ	95	.	NM_001014447	exon3	c.A389T	p.Q130L	TCTGCCAGCCCGC	.	PASS	Atlas-SNP
ASAP3	55616	hgsc.bcm.edu	37	1	23763449	23763449	+	Silent	SNP	G	G	A	rs115515935	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	71	132	0	0.788889	0	G|0.932;A|0.068	0.068	strong	.	ASAP3	65	.	NM_017707	exon15	c.C1431T	p.R477R	CTGCATGCGCGAA	.	PASS	Atlas-SNP
ZNF697	90874	hgsc.bcm.edu	37	1	120166528	120166528	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	40	158	0	0.246914	0	.	.	none	.	ZNF697	26	.	NM_001080470	exon3	c.T438C	p.H146H	GGAGAGATGTCGC	.	PASS	Atlas-SNP
TFG	10342	hgsc.bcm.edu	37	3	100455433	100455433	+	Silent	SNP	T	T	G	rs12562	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256	132	244	0	0.515625	0	T|0.993;G|0.007	0.007	strong	.	TFG	42	.	NM_006070	exon6	c.T594G	p.A198A	CAGTGCTCCTGCA	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207833983	207833983	+	Silent	SNP	A	A	G	rs7582305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	71	168	0	0.612069	0	A|0.685;G|0.315	0.315	strong	CPO,NS,carcinoma,+2,1	CPO	42	1	NM_173077	exon9	c.A948G	p.T316T	TGGAACATATGGG	.	PASS	Atlas-SNP
FMO4	2329	hgsc.bcm.edu	37	1	171303810	171303810	+	Missense_Mutation	SNP	C	C	T	rs144578261	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	63	111	1	0.403846	0.00900901	C|1.000;T|0.000	0.000	weak	FMO4,NS,NS,-1,1	FMO4	64	1	NM_002022	exon8	c.C1088T	p.A363V	AGAGAGCGACATT	.	scavenged	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347398	140347398	+	Silent	SNP	C	C	T	rs12153295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	53	78	0	0.546392	0	C|0.881;T|0.119	0.119	strong	.	PCDHAC2	142	.	NM_031883	exon1	c.C1047T	p.C349C	TCACTGCAAGGTG	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43528921	43528921	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	359	27	310	0	0.0752089	0	.	.	none	PSG11,NS,carcinoma,+2,1	PSG11	57	1	NM_002785	exon2	c.G352C	p.G118R	AGGATCCTGCGTC	.	scavenged	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693003	187693003	+	Missense_Mutation	SNP	A	A	T	rs10195632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	123	239	0	0.55157	0	A|0.813;T|0.187	0.187	strong	.	ZSWIM2	119	.	NM_182521	exon9	c.T1610A	p.F537Y	GTGTGAAATTTTC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379931	31379931	+	Missense_Mutation	SNP	G	G	A	rs1063635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	69	97	0	0.547619	0	G|0.488;A|0.512	0.512	strong	.	MICA	21	.	NM_001177519	exon4	c.G821A	p.R274Q	TTTGCCGAGGAGA	.	PASS	Atlas-SNP
EI24	9538	hgsc.bcm.edu	37	11	125452313	125452313	+	Missense_Mutation	SNP	A	A	G	rs4627097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	52	60	0	0.641975	0	A|0.658;G|0.342	0.342	strong	.	EI24	33	.	NM_001007277	exon9	c.A745G	p.I249V	CAAAGCATAGTAA	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46657261	46657261	+	Silent	SNP	A	A	G	rs6007747	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	25	63	0	0.438596	0	A|0.721;G|0.279	0.279	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T1959C	p.D653D	TAGAGAATCATAG	.	PASS	Atlas-SNP
RAB23	51715	hgsc.bcm.edu	37	6	57055354	57055354	+	Missense_Mutation	SNP	C	C	T	rs1040461	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	76	167	0	0.463415	0	C|0.892;T|0.108	0.108	strong	.	RAB23	22	.	NM_016277	exon7	c.G619A	p.G207S	GGGTACCTGAATT	.	PASS	Atlas-SNP
ZDHHC4	55146	hgsc.bcm.edu	37	7	6621277	6621277	+	Missense_Mutation	SNP	G	G	A	rs11559146	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	333	136	247	1	0.408408	0.00404858	G|0.691;A|0.309	0.309	strong	.	ZDHHC4	36	.	NM_018106	exon4	c.G157A	p.V53M	AGAGCCGTGCATG	.	PASS	Atlas-SNP
CCDC102B	79839	hgsc.bcm.edu	37	18	66678326	66678326	+	Silent	SNP	T	T	C	rs3763951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	142	150	0	1	0	T|0.949;C|0.051	0.051	strong	.	CCDC102B	92	.	NM_001093729	exon9	c.T1419C	p.N473N	ACTCAATCAAAAA	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20435262	20435262	+	Silent	SNP	T	T	G	rs12103211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	75	183	0	0.493421	0	T|0.853;G|0.147	0.147	strong	.	ACSM5	101	.	NM_017888	exon6	c.T792G	p.S264S	CGAATCTGACATC	.	PASS	Atlas-SNP
MUT	4594	hgsc.bcm.edu	37	6	49425446	49425446	+	Silent	SNP	T	T	C	rs138085432	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	46	69	0	0.393162	0	T|0.991;C|0.009	0.009	strong	.	MUT	70	.	NM_000255	exon3	c.A711G	p.P237P	CATGGATGGTTCT	.	PASS	Atlas-SNP
ZNF555	148254	hgsc.bcm.edu	37	19	2852744	2852744	+	Silent	SNP	C	C	T	rs35627030	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	29	64	0	0.426471	0	C|0.893;T|0.107	0.107	strong	.	ZNF555	61	.	NM_152791	exon4	c.C681T	p.T227T	GAAAACCTACGAA	.	PASS	Atlas-SNP
SSH1	54434	hgsc.bcm.edu	37	12	109198832	109198832	+	Silent	SNP	G	G	A	rs140151008	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	63	132	0	0.477273	0	G|0.996;A|0.004	0.004	strong	.	SSH1	144	.	NM_001161331	exon9	c.C987T	p.L329L	TCTTACGAGATAA	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4870284	4870284	+	Missense_Mutation	SNP	G	G	C	rs35918613	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	143	336	0	0.498258	0	G|0.898;C|0.102	0.102	strong	.	OR51S1	83	.	NM_001004758	exon1	c.C155G	p.T52S	AGGATGGTGCCAT	.	PASS	Atlas-SNP
TRMU	55687	hgsc.bcm.edu	37	22	46731689	46731689	+	Missense_Mutation	SNP	G	G	T	rs11090865	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17	9	16	0	0.529412	0	G|0.890;T|0.110	0.110	strong	.	TRMU	23	.	NM_018006	exon1	c.G28T	p.A10S	GTGTGCGCCCTGT	.	PASS	Atlas-SNP
GNA14	9630	hgsc.bcm.edu	37	9	80040566	80040566	+	Silent	SNP	C	C	T	rs1801259	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	121	153	1	0.960317	0.00653595	C|0.894;T|0.106	0.106	strong	.	GNA14	50	.	NM_004297	exon6	c.G789A	p.S263S	CACAGACGAATTC	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124351424	124351424	+	Silent	SNP	T	T	C	rs1660038	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	118	126	0	0.991597	0	T|0.326;C|0.674	0.674	strong	.	KALRN	556	.	NM_001024660	exon35	c.T5334C	p.L1778L	TCGGCTTAACAGC	.	PASS	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20897064	20897064	+	Missense_Mutation	SNP	C	C	T	rs7145318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	306	181	246	1	0.591503	0.00406504	C|0.365;N|0.001	.	strong	.	KLHL33	37	.	NM_001109997	exon4	c.G1546A	p.A516T	GCACAGCGGGCAG	.	PASS	Atlas-SNP
IFRD1	3475	hgsc.bcm.edu	37	7	112112279	112112279	+	Silent	SNP	G	G	A	rs2074796	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	88	134	1	0.553459	0.00746269	G|0.736;A|0.264	0.264	strong	IFRD1,NS,carcinoma,+1,2	IFRD1	46	2	NM_001007245	exon11	c.G1047A	p.R349R	GGAACGGGATTTT	.	scavenged	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92537388	92537388	+	Missense_Mutation	SNP	T	T	C	rs12896589	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	26	51	0	0.448276	0	T|0.928;C|0.072	0.072	strong	.	ATXN3	46	.	NM_001164778	exon6	c.A397G	p.K133E	CTGCTTTTGCTGC	.	PASS	Atlas-SNP
CABS1	85438	hgsc.bcm.edu	37	4	71201943	71201943	+	Silent	SNP	A	A	G	rs13039	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	46	134	0	0.38983	0	A|0.812;G|0.188	0.188	strong	.	CABS1	75	.	NM_033122	exon1	c.A1187G	p.X396X	TGATTTAAAAGCA	.	PASS	Atlas-SNP
GPR1	2825	hgsc.bcm.edu	37	2	207041441	207041441	+	Silent	SNP	G	G	A	rs3732082	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	43	111	0	0.796296	0	G|0.626;A|0.374	0.374	strong	.	GPR1	38	.	NM_001098199	exon3	c.C531T	p.D177D	CACAGTGTCCCGG	.	PASS	Atlas-SNP
SLC7A2	6542	hgsc.bcm.edu	37	8	17396415	17396415	+	Missense_Mutation	SNP	G	G	A	rs13259978	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	76	96	0	0.628099	0	A|0.011;C|0.200;G|0.789	0.011	strong	.	SLC7A2	157	.	NM_001164771	exon1	c.G82A	p.D28N	GTTTGCGACAGCA	.	PASS	Atlas-SNP
CCR4	1233	hgsc.bcm.edu	37	3	32995928	32995928	+	Silent	SNP	C	C	T	rs2228428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	96	191	0	0.5	0	C|0.799;T|0.201	0.201	strong	.	CCR4	36	.	NM_005508	exon2	c.C1014T	p.Y338Y	AATTTACTCTGCT	.	PASS	Atlas-SNP
SUSD1	64420	hgsc.bcm.edu	37	9	114820741	114820741	+	Silent	SNP	G	G	A	rs2296213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	44	84	0	0.453608	0	G|0.966;A|0.034	0.034	strong	.	SUSD1	51	.	NM_022486	exon14	c.C2076T	p.C692C	TATAATGCAGTAA	.	PASS	Atlas-SNP
KCNQ3	3786	hgsc.bcm.edu	37	8	133184914	133184914	+	Silent	SNP	G	G	C	rs17575754	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	44	74	0	0.483516	0	G|0.954;C|0.046	0.046	strong	.	KCNQ3	164	.	NM_004519	exon7	c.C1071G	p.L357L	CACCTTGAGGGCC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs55790575		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	20	42	0	0.416667	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.C1758A	p.D586E	ACACACGTCGACC	.	PASS	Atlas-SNP
ZNF197	10168	hgsc.bcm.edu	37	3	44683454	44683454	+	Missense_Mutation	SNP	G	G	C	rs148794995	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	57	136	0	0.463415	0	G|0.998;C|0.002	0.002	strong	.	ZNF197	81	.	NM_006991	exon6	c.G832C	p.D278H	AGAGCAGACTCTC	.	PASS	Atlas-SNP
FAM196A	642938	hgsc.bcm.edu	37	10	128974621	128974621	+	Silent	SNP	C	C	T	rs2489386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	58	50	0	0.95082	0	C|0.469;T|0.531	0.531	strong	.	FAM196A	55	.	NM_001039762	exon4	c.G39A	p.T13T	CTCCGACGTTGTG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145008560	145008560	+	Silent	SNP	A	A	G	rs11783799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	250	138	180	0	0.552	0	A|0.702;G|0.298	0.298	strong	.	PLEC	1144	.	NM_201380	exon11	c.T1506C	p.D502D	CTCCACATCCAGC	.	PASS	Atlas-SNP
KIF2C	11004	hgsc.bcm.edu	37	1	45218895	45218895	+	Silent	SNP	A	A	T	rs3795713	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	22	123	1	0.244444	0.00813008	A|0.741;T|0.259	0.259	strong	KIF2C,NS,carcinoma,+2,1	KIF2C	68	1	NM_006845	exon6	c.A531T	p.R177R	CATCCGAGGCAGC	.	scavenged	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61730183	61730183	+	Silent	SNP	C	C	T	rs1800008	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	22	83	0	0.309859	0	C|0.846;T|0.154	0.154	strong	BEST1_ENST00000449131,NS,carcinoma,+1,2	BEST1	85	2	NM_004183	exon10	c.C1557T	p.S519S	AGAGAGCGATGGG	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235383188	235383188	+	Silent	SNP	A	A	G	rs4659654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	374	241	301	3	0.644385	0.00996678	A|0.549;G|0.451	0.451	strong	ARID4B_ENST00000264183,NS,carcinoma,0,1	ARID4B	142	1	NM_016374	exon16	c.T1503C	p.D501D	TTTGTCATCCAGA	.	scavenged	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137686951	137686951	+	Silent	SNP	G	G	A	rs41310207	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	49	79	0	0.526882	0	G|0.975;A|0.025	0.025	strong	COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	NM_000093	exon33	c.G2724A	p.P908P	AGGACCGCGGGGG	.	PASS	Atlas-SNP
MRAP2	112609	hgsc.bcm.edu	37	6	84799185	84799185	+	Silent	SNP	C	C	T	rs2875382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	59	117	1	0.546296	0.00854701	C|0.654;T|0.346	0.346	strong	MRAP2,NS,carcinoma,0,1	MRAP2	40	1	NM_138409	exon4	c.C603T	p.H201H	CTCACACAAAGAC	.	scavenged	Atlas-SNP
USP25	29761	hgsc.bcm.edu	37	21	17181168	17181168	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	15	55	0	0.1875	0	.	.	none	.	USP25	156	.	NM_013396	exon8	c.T821G	p.L274X	ATTGGTTAGAAGA	.	PASS	Atlas-SNP
CWC27	10283	hgsc.bcm.edu	37	5	64097145	64097145	+	Missense_Mutation	SNP	C	C	G	rs7735338	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	62	131	0	0.476923	0	C|0.646;G|0.354	0.354	strong	.	CWC27	47	.	NM_005869	exon9	c.C766G	p.P256A	GATGCACCAGATT	.	PASS	Atlas-SNP
MYLK4	340156	hgsc.bcm.edu	37	6	2749381	2749381	+	Missense_Mutation	SNP	C	C	T	rs2296356	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	46	112	0	0.469388	0	C|0.865;T|0.135	0.135	strong	.	MYLK4	74	.	NM_001012418	exon2	c.G148A	p.G50R	TATGTCCAGATCT	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088811	56088811	+	Missense_Mutation	SNP	T	T	C	rs78599516	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	401	116	214	0	0.289277	0	T|0.746;C|0.254	0.254	strong	.	PSPH	23	.	NM_004577	exon4	c.A95G	p.D32G	AGCTCATCGATTC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	66204945	66204945	+	Missense_Mutation	SNP	G	G	A	rs12193967	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	47	133	0	0.435185	0	A|0.168;G|0.832	0.168	strong	.	EYS	527	.	NM_001142801	exon4	c.C359T	p.T120M	TCTTCCGTTGTGG	.	PASS	Atlas-SNP
TAMM41	132001	hgsc.bcm.edu	37	3	11887993	11887993	+	Missense_Mutation	SNP	G	G	A	rs144232229	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	65	187	0	0.439189	0	G|0.984;A|0.016	0.016	strong	.	.	.	.	NM_138807	exon1	c.C118T	p.P40S	AACTCGGCCCTGC	.	PASS	Atlas-SNP
SEMA4B	10509	hgsc.bcm.edu	37	15	90771704	90771704	+	Silent	SNP	G	G	A	rs3751656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	29	37	0	0.966667	0	G|0.746;A|0.254	0.254	strong	.	SEMA4B	51	.	NM_020210	exon15	c.G2343A	p.P781P	CACCCCGCTCGAT	.	PASS	Atlas-SNP
DUSP22	56940	hgsc.bcm.edu	37	6	350829	350829	+	Silent	SNP	G	G	A	rs1129085	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	314	73	317	0	0.232484	0	G|0.581;A|0.419	0.419	strong	.	DUSP22	55	.	NM_020185	exon8	c.G516A	p.P172P	CGCTCCGGGAATT	.	PASS	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92549586	92549586	+	Silent	SNP	G	G	A	rs16999141	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	72	60	0	0.986301	0	G|0.463;A|0.537	0.537	strong	ATXN3,NS,carcinoma,0,1	ATXN3	46	1	NM_004993	exon7	c.C492T	p.V164V	CTTAACGACAAAT	.	PASS	Atlas-SNP
LIPG	9388	hgsc.bcm.edu	37	18	47093864	47093864	+	Missense_Mutation	SNP	C	C	T	rs2000813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	56	107	0	0.504505	0	C|0.760;T|0.240	0.240	strong	.	LIPG	47	.	NM_006033	exon3	c.C332T	p.T111I	TGCACACAAGAGA	.	PASS	Atlas-SNP
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99128904	99128904	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	4	185	0	0.0160643	0	.	.	none	ZKSCAN5,colon,carcinoma,-1,1	ZKSCAN5	63	1	NM_145102	exon7	c.A1552G	p.M518V	ATTCCCATGAAAG	.	scavenged	Atlas-SNP
KRT77	374454	hgsc.bcm.edu	37	12	53090181	53090181	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	27	51	1	0.482143	0.0196078	.	.	none	KRT77,NS,carcinoma,0,1	KRT77	58	1	NM_175078	exon3	c.C792T	p.S264S	ATTCTCGCTGCCA	.	scavenged	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43557559	43557559	+	Silent	SNP	T	T	A	rs3819141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	62	187	0	0.26383	0	T|0.652;A|0.348	0.348	strong	.	UMODL1	186	.	NM_173568	exon21	c.T4170A	p.P1390P	GCCTCCTCATGCA	.	PASS	Atlas-SNP
ARHGEF39	84904	hgsc.bcm.edu	37	9	35662251	35662251	+	Missense_Mutation	SNP	T	T	C	rs2297879	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	59	168	0	0.450382	0	T|0.720;C|0.280	0.280	strong	.	.	.	.	NM_032818	exon8	c.A917G	p.H306R	TTCTCATGAGGGA	.	PASS	Atlas-SNP
SLC25A13	10165	hgsc.bcm.edu	37	7	95800820	95800820	+	Silent	SNP	T	T	C	rs2301629	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	168	191	1	0.688525	0.0052356	T|0.645;C|0.355	0.355	strong	SLC25A13,caecum,carcinoma,0,1	SLC25A13	131	1	NM_001160210	exon12	c.A1197G	p.L399L	TCCCAATAACTGT	.	PASS	Atlas-SNP
PTPRJ	5795	hgsc.bcm.edu	37	11	48145166	48145166	+	Silent	SNP	G	G	A	rs2270993	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	39	75	0	0.527027	0	G|0.843;A|0.157	0.157	strong	PTPRJ,NS,carcinoma,0,1	PTPRJ	225	1	NM_001098503	exon5	c.G618A	p.E206E	AATAGAGCCGATC	.	PASS	Atlas-SNP
ACVR2B	93	hgsc.bcm.edu	37	3	38524664	38524664	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	2	233	2	0.0106383	0.00858369	.	.	none	ACVR2B_ENST00000352511,NS,carcinoma,0,2	ACVR2B	88	2	NM_001106	exon11	c.C1380T	p.C460C	GGAGTGCTGGGAC	.	scavenged	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100971024	100971024	+	Silent	SNP	G	G	A	rs148143158	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	121	243	0	0.493878	0	G|0.996;A|0.004	0.004	strong	TBC1D2_ENST00000375063,NS,carcinoma,0,2	TBC1D2	70	2	NM_001267571	exon9	c.C2076T	p.P692P	CTTGTCGGGGAAG	.	PASS	Atlas-SNP
KRT5	3852	hgsc.bcm.edu	37	12	52908872	52908872	+	Missense_Mutation	SNP	C	C	T	rs11549949	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	27	76	0	0.369863	0	T|0.147;G|0.000;C|0.853;A|0.000	0.147	strong	.	KRT5	88	.	NM_000424	exon9	c.G1627A	p.G543S	CACCACCTAGGCC	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104086631	104086631	+	Silent	SNP	C	C	T	rs703651	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	110	237	0	0.536585	0	C|0.546;T|0.453	0.453	strong	STAB2,rectum,carcinoma,0,2	STAB2	370	2	NM_017564	exon31	c.C3339T	p.N1113N	GGACAACGCAGCC	.	PASS	Atlas-SNP
CCDC107	203260	hgsc.bcm.edu	37	9	35660990	35660990	+	Missense_Mutation	SNP	A	A	G	rs1339374	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	109	111	0	0.981982	0	A|0.226;G|0.774	0.774	strong	.	CCDC107	12	.	NM_174923	exon5	c.A658G	p.I220V	GAGGAGATTGGTG	.	PASS	Atlas-SNP
NKAPL	222698	hgsc.bcm.edu	37	6	28227436	28227436	+	Missense_Mutation	SNP	A	A	G	rs12000	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	31	59	0	0.402597	0	A|0.613;G|0.387	0.387	strong	.	NKAPL	72	.	NM_001007531	exon1	c.A287G	p.Y96C	ATCGCTACCATCG	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78369573	78369573	+	Missense_Mutation	SNP	C	C	T	rs75922333	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	47	106	0	0.447619	0	C|0.990;T|0.010	0.010	strong	.	.	.	.	NM_001098816	exon34	c.G7840A	p.V2614M	TATCCACCCCATC	.	PASS	Atlas-SNP
SF3A2	8175	hgsc.bcm.edu	37	19	2248185	2248185	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15	10	24	0	0.666667	0	.	.	none	SF3A2,colon,carcinoma,0,1	SF3A2	22	1	NM_007165	exon9	c.A1035T	p.P345P	TCACCCACCAGCC	.	scavenged	Atlas-SNP
PDE9A	5152	hgsc.bcm.edu	37	21	44189166	44189166	+	Silent	SNP	T	T	C	rs1045382	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	267	76	203	0	0.284644	0	T|0.555;C|0.445	0.445	strong	.	PDE9A	69	.	NM_002606	exon17	c.T1491C	p.P497P	CCTTCCTGTGGCA	.	PASS	Atlas-SNP
TAGLN3	29114	hgsc.bcm.edu	37	3	111719786	111719786	+	Silent	SNP	A	A	T	rs2292583	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	33	77	0	0.55	0	A|0.919;T|0.081	0.081	strong	.	TAGLN3	44	.	NM_001008272	exon3	c.A348T	p.L116L	GGATCTATGGGAA	.	PASS	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106999822	106999822	+	Missense_Mutation	SNP	G	G	A	rs2297970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	46	188	0	0.359375	0	G|0.768;A|0.232	0.232	strong	AIM1,NS,carcinoma,0,1	AIM1	161	1	NM_001624	exon12	c.G4184A	p.C1395Y	AAAATTGTAAGAT	.	PASS	Atlas-SNP
NFXL1	152518	hgsc.bcm.edu	37	4	47901476	47901476	+	Missense_Mutation	SNP	G	G	A	rs12651301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	93	199	0	0.537572	0	G|0.647;A|0.353	0.353	strong	.	NFXL1	79	.	NM_152995	exon6	c.C737T	p.P246L	AGCCACGGATCTA	.	PASS	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106196819	106196819	+	Missense_Mutation	SNP	G	G	T	rs142312318	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	95	263	0	0.475	0	G|0.999;T|0.001	0.001	strong	TET2,NS,lymphoid_neoplasm,0,8	TET2	1762	8	NM_001127208	exon11	c.G5152T	p.V1718L	CATCATGTAGGGA	.	PASS	Atlas-SNP
SDCBP2	27111	hgsc.bcm.edu	37	20	1293149	1293149	+	Silent	SNP	C	C	T	rs55648421	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	51	108	0	0.459459	0	C|0.993;T|0.007	0.007	strong	SDCBP2_ENST00000381812,NS,carcinoma,-1,3	SDCBP2	78	3	NM_080489	exon7	c.G564A	p.P188P	CTGGAACGGCCTG	.	PASS	Atlas-SNP
ERO1LB	56605	hgsc.bcm.edu	37	1	236381825	236381825	+	Missense_Mutation	SNP	G	G	C	rs1055851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	303	183	281	1	0.60396	0.00355872	G|0.530;C|0.470	0.470	strong	.	ERO1LB	48	.	NM_019891	exon16	c.C1395G	p.H465Q	CCTACTGTGTTGT	.	PASS	Atlas-SNP
YAF2	10138	hgsc.bcm.edu	37	12	42554505	42554505	+	Silent	SNP	A	A	G	rs1059360	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	135	168	1	0.985401	0.00595238	A|0.654;G|0.346	0.346	strong	.	YAF2	16	.	NM_001190979	exon5	c.T501C	p.A167A	TGCAGAAGCAGCA	.	PASS	Atlas-SNP
BRCA1	672	hgsc.bcm.edu	37	17	41246481	41246481	+	Missense_Mutation	SNP	T	T	C	rs1799950	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	81	145	0	0.515924	0	T|0.960;C|0.040	0.040	strong	.	BRCA1	304	.	NM_007300	exon10	c.A1067G	p.Q356R	AGTTTCTGCTTAT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268579	1268579	+	Missense_Mutation	SNP	T	T	G	rs190148881	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	393	33	516	2	0.0839695	0.00387597	T|0.984;G|0.016	0.016	strong	MUC5B,NS,carcinoma,0,5	MUC5B	473	5	NM_002458	exon31	c.T10469G	p.V3490G	CCACGGTGACTTC	.	scavenged	Atlas-SNP
ITPA	3704	hgsc.bcm.edu	37	20	3204084	3204084	+	Silent	SNP	G	G	A	rs9101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	30	65	0	0.517241	0	G|0.729;A|0.271	0.271	strong	ITPA,NS,carcinoma,0,1	ITPA	16	1	NM_033453	exon8	c.G561A	p.E187E	GCAGGAGTACTTT	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	37	11	108106435	108106435	+	Missense_Mutation	SNP	A	A	G	rs148590073	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	64	135	0	0.301887	0	A|0.997;G|0.003	0.003	strong	.	ATM	1657	.	NM_000051	exon5	c.A370G	p.I124V	AATTATATCATGG	.	PASS	Atlas-SNP
AIM1L	55057	hgsc.bcm.edu	37	1	26673076	26673076	+	Missense_Mutation	SNP	G	G	A	rs11247924	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	14	77	0	0.254545	0	G|0.828;A|0.172	0.172	strong	.	AIM1L	98	.	NM_001039775	exon2	c.C73T	p.R25W	GGGGCCGCTGCCG	.	PASS	Atlas-SNP
SPARCL1	8404	hgsc.bcm.edu	37	4	88416188	88416188	+	Missense_Mutation	SNP	G	G	T	rs13051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	259	329	2	0.977359	0.00607903	G|0.474;T|0.526	0.526	strong	SPARCL1,NS,carcinoma,0,1	SPARCL1	59	1	NM_004684	exon3	c.C146A	p.A49D	TCTTCAGCTTCAG	.	scavenged	Atlas-SNP
PAPOLB	56903	hgsc.bcm.edu	37	7	4901385	4901385	+	Missense_Mutation	SNP	A	A	C	rs3750009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	15	46	0	0.319149	0	A|0.534;C|0.466	0.466	strong	.	PAPOLB	93	.	NM_020144	exon1	c.T57G	p.N19K	GTAGCGATTCGGC	.	PASS	Atlas-SNP
SAMD15	161394	hgsc.bcm.edu	37	14	77844592	77844592	+	Silent	SNP	T	T	A	rs10133824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	27	44	0	0.529412	0	T|0.848;A|0.152	0.152	strong	.	SAMD15	60	.	NM_001010860	exon1	c.T831A	p.G277G	GGCAGGTCTAGAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677405	100677405	+	Missense_Mutation	SNP	G	G	A	rs141963257		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	330	73	133	0	0.221212	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.G2708A	p.R903H	AAGCCCGTTCGTC	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124036328	124036328	+	Missense_Mutation	SNP	G	G	A	rs11200524	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	68	143	1	0.49635	0.00699301	G|0.959;A|0.041	0.041	strong	BTBD16,NS,carcinoma,0,1	BTBD16	44	1	NM_144587	exon3	c.G41A	p.R14Q	AACGCCGGGTCAC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	640	36	367	0	0.05625	0	.	.	weak	FLG,NS,malignant_melanoma,+1,1	FLG	900	1	NM_002016	exon3	c.T6671A	p.L2224Q	CCCACCAGTGAGT	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2054066	2054066	+	Silent	SNP	A	A	G	rs17684416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	87	171	0	0.359504	0	A|0.843;G|0.157	0.157	strong	.	MYOM2	251	.	NM_003970	exon22	c.A2769G	p.Q923Q	TGAACAAGGCAAC	.	PASS	Atlas-SNP
NEIL2	252969	hgsc.bcm.edu	37	8	11640784	11640784	+	Silent	SNP	A	A	G	rs8191642	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	484	154	413	1	0.318182	0.00242131	A|0.751;G|0.249	0.249	strong	.	NEIL2	14	.	NM_001135746	exon4	c.A564G	p.P188P	TTCCCCAGTGGTC	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324237	39324237	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	2	71	0	0.0229885	0	.	.	none	KRTAP4-3,NS,carcinoma,-1,1	KRTAP4-3	40	1	NM_033187	exon1	c.G188C	p.S63T	CAGCAGCTGGGTT	.	scavenged	Atlas-SNP
ATP8B2	57198	hgsc.bcm.edu	37	1	154316434	154316434	+	Silent	SNP	C	C	T	rs2274988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	102	76	0	1	0	C|0.774;T|0.226	0.226	strong	ATP8B2,colon,carcinoma,0,1	ATP8B2	158	1	NM_020452	exon18	c.C1923T	p.Y641Y	GTACTACGAGGAG	.	PASS	Atlas-SNP
CSF2RB	1439	hgsc.bcm.edu	37	22	37329999	37329999	+	Silent	SNP	C	C	T	rs1801117	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	32	69	0	0.516129	0	C|0.793;T|0.207	0.207	strong	.	CSF2RB	104	.	NM_000395	exon10	c.C1278T	p.S426S	CTGGAGCGAGTGG	.	PASS	Atlas-SNP
ZNF805	390980	hgsc.bcm.edu	37	19	57764770	57764770	+	Missense_Mutation	SNP	G	G	A	rs10421632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	130	141	0	1	0	G|0.634;A|0.366	0.366	strong	.	ZNF805	30	.	NM_001023563	exon4	c.G583A	p.V195I	AATCCAGTTATTC	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	42	83	0	0.446809	0	G|0.878;C|0.122	0.122	strong	.	UTP20	222	.	NM_014503	exon59	c.G7834C	p.E2612Q	AAGGAAGAGCTCG	.	PASS	Atlas-SNP
OR2G3	81469	hgsc.bcm.edu	37	1	247769752	247769752	+	Missense_Mutation	SNP	A	A	G	rs61730407	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	159	149	0	0.97546	0	A|0.629;G|0.371	0.371	strong	.	OR2G3	108	.	NM_001001914	exon1	c.A865G	p.I289V	CCTATCATCTATA	.	PASS	Atlas-SNP
SIK3	23387	hgsc.bcm.edu	37	11	116719841	116719841	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	461	306	326	1	0.663774	0.00306748	.	.	none	.	SIK3	112	.	NM_025164	exon21	c.G3496A	p.A1166T	CATAAGCATCGTC	.	PASS	Atlas-SNP
FLRT2	23768	hgsc.bcm.edu	37	14	86088573	86088573	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	2	159	0	0.0100503	0	.	.	none	FLRT2,NS,carcinoma,0,1	FLRT2	168	1	NM_013231	exon2	c.C715T	p.R239C	ATTGTACGTAATT	.	scavenged	Atlas-SNP
GPR161	23432	hgsc.bcm.edu	37	1	168059866	168059866	+	Silent	SNP	A	A	G	rs275149	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	48	133	2	0.360902	0.0150376	A|0.580;G|0.420	0.420	strong	GPR161,colon,carcinoma,0,2	GPR161	56	2	NM_001267609	exon5	c.T1200C	p.G400G	CTGTCCACCTGCC	.	scavenged	Atlas-SNP
PFKP	5214	hgsc.bcm.edu	37	10	3172145	3172145	+	Silent	SNP	C	C	T	rs1052337	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	47	93	2	0.854545	0.0215054	C|0.856;G|0.000;T|0.144	0.144	strong	PFKP_ENST00000381075,colon,carcinoma,0,2	PFKP	182	2	NM_002627	exon17	c.C1818T	p.F606F	CATTTTCGAAGAG	.	scavenged	Atlas-SNP
DNTTIP2	30836	hgsc.bcm.edu	37	1	94343023	94343023	+	Silent	SNP	A	A	G	rs2391322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	58	107	0	1	0	A|0.587;G|0.413	0.413	strong	.	DNTTIP2	59	.	NM_014597	exon2	c.T468C	p.P156P	TTCTGTAGGAAGC	.	PASS	Atlas-SNP
JMY	133746	hgsc.bcm.edu	37	5	78610361	78610361	+	Silent	SNP	C	C	T	rs61751239	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	110	243	0	0.468085	0	C|0.983;T|0.017	0.017	strong	.	JMY	82	.	NM_152405	exon9	c.C2346T	p.P782P	GCCTCCCACTATA	.	PASS	Atlas-SNP
EIF5B	9669	hgsc.bcm.edu	37	2	99978048	99978048	+	Silent	SNP	G	G	A	rs12233086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	133	241	0	0.501887	0	G|0.842;A|0.158	0.158	strong	.	EIF5B	95	.	NM_015904	exon4	c.G684A	p.V228V	GACAGTGGCCCAA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1896060	1896060	+	Missense_Mutation	SNP	T	T	C	rs114499682	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	26	434	1	0.116071	0.00230415	T|0.684;C|0.317	0.317	strong	SIRPA,caecum,carcinoma,+1,2	SIRPA	83	2	NM_001040022	exon3	c.T395C	p.V132A	ATGACGTGGAGTT	.	scavenged	Atlas-SNP
INSL3	3640	hgsc.bcm.edu	37	19	17932138	17932138	+	Missense_Mutation	SNP	T	T	C	rs6523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	6	48	0	0.333333	0	T|0.225;G|0.175	.	strong	INSL3,NS,carcinoma,0,1	INSL3	8	1	NM_005543	exon1	c.A178G	p.T60A	CTCCGGTCGCAGG	.	PASS	Atlas-SNP
SERPINI2	5276	hgsc.bcm.edu	37	3	167189607	167189607	+	Missense_Mutation	SNP	A	A	C	rs17246389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	34	67	0	0.557377	0	A|0.830;C|0.170	0.170	strong	.	SERPINI2	85	.	NM_001012303	exon3	c.T46G	p.L16V	TCCACAAGAAGAT	.	PASS	Atlas-SNP
SENP3	26168	hgsc.bcm.edu	37	17	7468277	7468277	+	Silent	SNP	C	C	T	rs35596387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	22	56	0	0.478261	0	C|0.976;T|0.024	0.024	strong	.	SENP3	18	.	NM_015670	exon4	c.C957T	p.S319S	ACCAGGCATCTTG	.	PASS	Atlas-SNP
NETO1	81832	hgsc.bcm.edu	37	18	70526301	70526301	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	51	144	0	0.34	0	.	.	none	.	NETO1	178	.	NM_001201465	exon4	c.A229G	p.R77G	ACTGTCTTGGAGC	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531374	140531374	+	Silent	SNP	T	T	C	rs17844437	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	94	221	0	0.502674	0	T|0.924;C|0.076	0.076	strong	.	PCDHB6	161	.	NM_018939	exon1	c.T1536C	p.F512F	CCTGTTTGCCCTC	.	PASS	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221054571	221054571	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	272	4	193	0	0.0147059	0	.	.	none	HLX,NS,carcinoma,-1,1	HLX	67	1	NM_021958	exon2	c.G628A	p.G210R	CCCGCCGGGGTGC	.	scavenged	Atlas-SNP
TRAK1	22906	hgsc.bcm.edu	37	3	42251263	42251263	+	Silent	SNP	C	C	T	rs2290134	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	22	52	0	0.564103	0	C|0.503;T|0.497	0.497	strong	.	TRAK1	188	.	NM_001265608	exon14	c.C1749T	p.S583S	AGGTTCCGCCACA	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22940827	22940827	+	Silent	SNP	T	T	C	rs142615427	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	31	75	0	0.596154	0	T|0.921;C|0.079	0.079	strong	.	ZNF99	273	.	NM_001080409	exon4	c.A1884G	p.K628K	AAAAGCTTTGCCA	.	PASS	Atlas-SNP
GANC	2595	hgsc.bcm.edu	37	15	42643538	42643538	+	Missense_Mutation	SNP	A	A	G	rs7180279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	19	153	0	0.195876	0	A|0.898;G|0.102	0.102	strong	.	GANC	57	.	NM_198141	exon23	c.A2543G	p.Q848R	CTGACCAGAGGGG	.	PASS	Atlas-SNP
SPATA3	130560	hgsc.bcm.edu	37	2	231861071	231861071	+	Silent	SNP	T	T	C	rs61738380	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	49	159	1	0.556818	0.00628931	T|0.222;C|0.778	0.778	strong	SPATA3,colon,carcinoma,0,2	SPATA3	52	2	NM_139073	exon1	c.T123C	p.S41S	GCCTAGTCCTGAA	.	scavenged	Atlas-SNP
MRGPRF	116535	hgsc.bcm.edu	37	11	68773403	68773403	+	Silent	SNP	G	G	A	rs11544722	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	19	35	0	0.558824	0	G|0.763;A|0.237	0.237	strong	.	MRGPRF	22	.	NM_001098515	exon3	c.C375T	p.C125C	GAACATGCAGAGC	.	PASS	Atlas-SNP
CCDC37	348807	hgsc.bcm.edu	37	3	126137558	126137558	+	Silent	SNP	C	C	T	rs4679242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	40	95	0	0.454545	0	C|0.760;T|0.240	0.240	strong	.	CCDC37	69	.	NM_182628	exon7	c.C591T	p.A197A	GGACGCCGCCTTG	.	PASS	Atlas-SNP
HOXA1	3198	hgsc.bcm.edu	37	7	27135096	27135096	+	Missense_Mutation	SNP	G	G	T	rs45571645	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	48	83	0	0.393443	0	G|0.988;T|0.012	0.012	strong	.	HOXA1	64	.	NM_005522	exon1	c.C436A	p.H146N	CCTGGTGGTGGTG	.	PASS	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56424443	56424443	+	Missense_Mutation	SNP	T	T	C	rs303997	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	140	134	2	1	0.0149254	C|0.641;N|0.000	0.641	strong	NLRP13,colon,carcinoma,0,2	NLRP13	220	2	NM_176810	exon5	c.A740G	p.Q247R	ATAGCCTGCATTG	.	scavenged	Atlas-SNP
RBP5	83758	hgsc.bcm.edu	37	12	7281317	7281317	+	Missense_Mutation	SNP	C	C	T	rs10963	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	101	256	0	0.487923	0	C|0.823;T|0.177	0.177	strong	.	RBP5	20	.	NM_031491	exon1	c.G55A	p.D19N	GGTAGTCCTCCAT	.	PASS	Atlas-SNP
SEPT1	1731	hgsc.bcm.edu	37	16	30393147	30393147	+	Missense_Mutation	SNP	C	C	A	rs34518080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	125	146	0	0.976562	0	C|0.975;A|0.025	0.025	strong	.	SEPT1	34	.	NM_052838	exon5	c.G380T	p.G127V	TTCACACCCCCTT	.	PASS	Atlas-SNP
APBA2	321	hgsc.bcm.edu	37	15	29368269	29368269	+	Silent	SNP	G	G	A	rs149285403	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	76	138	0	0.8	0	G|0.999;A|0.001	0.001	strong	.	APBA2	132	.	NM_005503	exon5	c.G1044A	p.V348V	GAAGGTGGCATCA	.	PASS	Atlas-SNP
SYNPO	11346	hgsc.bcm.edu	37	5	149998128	149998128	+	Missense_Mutation	SNP	G	G	A	rs6579797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	120	209	0	0.526316	0	G|0.850;A|0.150	0.150	strong	SYNPO_ENST00000394243,colon,carcinoma,0,1	SYNPO	147	1	NM_001166209	exon2	c.G199A	p.D67N	GGGGACGACTCTG	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21607296	21607296	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	4	70	0	0.056338	0	.	.	none	ZNF493_ENST00000392288,NS,carcinoma,0,4	ZNF493	178	4	NM_001076678	exon4	c.G1835A	p.R612Q	TTAACCGATCTTC	.	scavenged	Atlas-SNP
PLK2	10769	hgsc.bcm.edu	37	5	57753149	57753149	+	Silent	SNP	A	A	G	rs17767072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	32	41	0	0.457143	0	A|0.871;G|0.129	0.129	strong	.	PLK2	71	.	NM_006622	exon7	c.T867C	p.Y289Y	GCACCTATAAGTT	.	PASS	Atlas-SNP
SACM1L	22908	hgsc.bcm.edu	37	3	45754685	45754685	+	Silent	SNP	A	A	G	rs2271619	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	19	31	0	0.59375	0	A|0.856;G|0.144	0.144	strong	.	SACM1L	38	.	NM_014016	exon6	c.A540G	p.P180P	ACAGCCAGAGGTA	.	PASS	Atlas-SNP
GLOD4	51031	hgsc.bcm.edu	37	17	663472	663472	+	Missense_Mutation	SNP	C	C	A	rs77166377	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	36	94	0	0.418605	0	C|0.975;A|0.025	0.025	strong	.	GLOD4	12	.	NM_016080	exon9	c.G838T	p.A280S	CTGCTGCCATTGC	.	PASS	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152328282	152328282	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	375	8	303	6	0.0213333	0.019802	.	.	none	FLG2,NS,carcinoma,0,4	FLG2	431	4	NM_001014342	exon3	c.A1980G	p.S660S	TGAGCCTGATCCA	.	scavenged	Atlas-SNP
CNIH4	29097	hgsc.bcm.edu	37	1	224553602	224553602	+	Missense_Mutation	SNP	G	G	A	rs74546314	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	546	184	425	0	0.336996	0	G|0.997;A|0.003	0.003	strong	.	CNIH4	17	.	NM_014184	exon3	c.G160A	p.G54S	TTGATTGGCCATA	.	PASS	Atlas-SNP
PTCHD3	374308	hgsc.bcm.edu	37	10	27702688	27702688	+	Silent	SNP	C	C	T	rs7087552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	15	125	0	0.192308	0	C|0.764;T|0.236	0.236	strong	.	PTCHD3	140	.	NM_001034842	exon1	c.G492A	p.E164E	GTCTTCCTCTTCG	.	PASS	Atlas-SNP
CD300A	11314	hgsc.bcm.edu	37	17	72469966	72469966	+	Missense_Mutation	SNP	G	G	A	rs78031008	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	104	275	0	0.427984	0	.	.	weak	.	CD300A	40	.	NM_007261	exon2	c.G332A	p.R111Q	GGCTCCGAGACTT	.	PASS	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2160894	2160894	+	Silent	SNP	C	C	T	rs10488836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	68	178	0	0.489209	0	C|0.840;T|0.160	0.160	strong	.	POLN	82	.	NM_181808	exon12	c.G1599A	p.L533L	GTATTCCAAAATT	.	PASS	Atlas-SNP
FAM160A1	729830	hgsc.bcm.edu	37	4	152577473	152577473	+	Nonsense_Mutation	SNP	C	C	T	rs367582779		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	122	278	1	0.674033	0.00359712	.	.	weak	.	FAM160A1	60	.	NM_001109977	exon12	c.C2641T	p.Q881X	ATTACTCAGCTAG	.	PASS	Atlas-SNP
DFNB31	25861	hgsc.bcm.edu	37	9	117169033	117169033	+	Missense_Mutation	SNP	A	A	G	rs942519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	55	87	0	0.466102	0	A|0.511;G|0.489	0.489	strong	.	DFNB31	100	.	NM_001173425	exon9	c.T1838C	p.M613T	GAAGGCATGGAGG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118537074	118537074	+	Silent	SNP	A	A	G	rs12031260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	42	124	0	0.7	0	A|0.919;G|0.081	0.081	strong	.	SPAG17	263	.	NM_206996	exon35	c.T5133C	p.P1711P	ATTAGGAGGGACA	.	PASS	Atlas-SNP
KDM5A	5927	hgsc.bcm.edu	37	12	406292	406292	+	Silent	SNP	G	G	A	rs2229351	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	33	88	0	0.428571	0	T|0.139;G|0.444;C|0.211;A|0.206	0.206	strong	KDM5A_ENST00000399788,trunk,malignant_melanoma,-1,2	KDM5A	307	2	NM_001042603	exon25	c.C4149T	p.S1383S	CTCCTCGGATTTG	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238280553	238280553	+	Silent	SNP	G	G	A	rs35114079	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	28	127	0	0.363636	0	G|0.994;A|0.006	0.006	strong	.	COL6A3	608	.	NM_004369	exon9	c.C4107T	p.I1369I	CCTGGCGATCGTG	.	PASS	Atlas-SNP
VSIG10L	147645	hgsc.bcm.edu	37	19	51837171	51837171	+	Silent	SNP	A	A	G	rs7255306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	44	77	0	0.517647	0	A|0.563;G|0.437	0.437	strong	.	VSIG10L	40	.	NM_001163922	exon9	c.T2448C	p.P816P	GGTAGAAGGATGC	.	PASS	Atlas-SNP
CCDC154	645811	hgsc.bcm.edu	37	16	1493909	1493909	+	Missense_Mutation	SNP	C	C	T	rs34470360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	58	98	0	0.637363	0	C|0.950;T|0.050	0.050	strong	CCDC154,lymph_node,lymphoid_neoplasm,0,1	CCDC154	27	1	NM_001143980	exon2	c.G112A	p.E38K	AGGGCTCGGGGCT	.	PASS	Atlas-SNP
PTPRK	5796	hgsc.bcm.edu	37	6	128388799	128388799	+	Silent	SNP	G	G	T	rs35030557	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	89	92	0	0.936842	0	T|0.314;G|0.686;C|0.000	0.314	strong	.	PTPRK	330	.	NM_001135648	exon12	c.C2022A	p.L674L	CGGGGGGAGTTCT	.	PASS	Atlas-SNP
CDC14A	8556	hgsc.bcm.edu	37	1	100949860	100949860	+	Silent	SNP	G	G	A	rs2270694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	10	39	0	0.285714	0	G|0.905;A|0.095	0.095	strong	.	CDC14A	65	.	NM_033313	exon11	c.G990A	p.S330S	AGCATCGTTGTGG	.	PASS	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102269206	102269206	+	Missense_Mutation	SNP	A	A	G	rs3763695	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	41	71	0	0.745455	0	A|0.809;G|0.191	0.191	strong	.	SEC31B	84	.	NM_015490	exon4	c.T266C	p.V89A	CCGCCAACAATAA	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78921117	78921117	+	Silent	SNP	C	C	T	rs4969231	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	126	153	1	0.976744	0.00653595	C|0.763;T|0.237	0.237	strong	RPTOR,colon,carcinoma,0,1	RPTOR	122	1	NM_020761	exon27	c.C3231T	p.N1077N	TCTGAACGGCCAG	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19725280	19725280	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	297	3	205	0	0.010101	0	.	.	none	TMPRSS15,extremity,malignant_melanoma,0,1	TMPRSS15	189	1	NM_002772	exon10	c.G1111A	p.G371R	TGCTTCCCTGAAT	.	scavenged	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155451352	155451352	+	Missense_Mutation	SNP	G	G	A	rs931312	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	37	63	0	0.544118	0	G|0.815;A|0.185	0.185	strong	.	TIAM2	161	.	NM_012454	exon3	c.G995A	p.R332H	GCAACCGTGTCTC	.	PASS	Atlas-SNP
FAM98A	25940	hgsc.bcm.edu	37	2	33820635	33820635	+	Silent	SNP	C	C	T	rs72785999	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	94	133	0	0.549708	0	C|0.995;T|0.005	0.005	strong	.	FAM98A	42	.	NM_015475	exon2	c.G123A	p.E41E	GGTAAACTCGGGG	.	PASS	Atlas-SNP
LASP1	3927	hgsc.bcm.edu	37	17	37070658	37070658	+	Silent	SNP	A	A	G	rs525989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	197	223	0	0.980099	0	A|0.285;G|0.715	0.715	strong	LASP1,colon,carcinoma,0,3	LASP1	24	3	NM_006148	exon5	c.A438G	p.S146S	GGATTCACAGGAC	.	PASS	Atlas-SNP
HDHD1	8226	hgsc.bcm.edu	37	X	6995417	6995417	+	Silent	SNP	C	C	T	rs2379207	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	93	175	0	0.96875	0	C|0.748;0|0.031	.	strong	.	HDHD1	21	.	NM_001135565	exon4	c.G423A	p.A141A	GAACGACGCGGAC	.	PASS	Atlas-SNP
MTHFSD	64779	hgsc.bcm.edu	37	16	86565882	86565882	+	Missense_Mutation	SNP	G	G	C	rs3751802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	19	179	0	0.141791	0	G|0.733;C|0.267	0.267	strong	.	MTHFSD	52	.	NM_001159377	exon8	c.C887G	p.S296C	GGTGGGGAGCCAG	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72360197	72360197	+	Silent	SNP	T	T	C	rs116554195	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	92	235	0	0.730159	0	T|0.987;C|0.013	0.013	strong	.	PRF1	64	.	NM_001083116	exon2	c.A462G	p.A154A	GTTGGCTGCCTGT	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16872940	16872940	+	Silent	SNP	G	G	A	rs773852	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	79	102	1	0.9875	0.00980392	G|0.570;A|0.430	0.430	strong	.	NWD1	303	.	NM_001007525	exon8	c.G2124A	p.L708L	GAACTTGGACCGA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093481	1093481	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	20	72	0	0.289855	0	.	.	none	.	MUC2	614	.	NM_002457	exon30	c.C5300T	p.T1767M	CAACCACGGTACT	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385184	16385184	+	Silent	SNP	G	G	A	rs75273615	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	393	145	906	3	0.368957	0.00331126	G|0.740;A|0.260	0.260	strong	FAM131C,NS,haematopoietic_neoplasm,0,1	FAM131C	21	1	NM_182623	exon7	c.C591T	p.S197S	GGGAAGGCTGTCC	.	scavenged	Atlas-SNP
TRIP6	7205	hgsc.bcm.edu	37	7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	rs2437100	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	73	71	0	0.695238	0	G|0.985;A|0.015	0.015	strong	.	TRIP6	45	.	NM_003302	exon3	c.G332A	p.R111Q	GGGGTCGGGGTCA	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107040985	107040985	+	Silent	SNP	T	T	C	rs140856347	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	8	8	33	1	1	0.030303	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	NM_001144013	exon20	c.A3438G	p.R1146R	TGCCAATCGCTCT	.	scavenged	Atlas-SNP
FCRL4	83417	hgsc.bcm.edu	37	1	157559122	157559122	+	Missense_Mutation	SNP	C	C	T	rs11582663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	594	594	437	0	1	0	C|0.911;T|0.089	0.089	strong	.	FCRL4	95	.	NM_031282	exon3	c.G179A	p.R60Q	TAGTGCCGATGAT	.	PASS	Atlas-SNP
COX10	1352	hgsc.bcm.edu	37	17	14005439	14005439	+	Silent	SNP	G	G	A	rs2159132	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	39	125	0	0.336207	0	G|0.468;A|0.532	0.532	strong	.	COX10	36	.	NM_001303	exon4	c.G504A	p.L168L	AGCTCTGGTTGTA	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36663795	36663795	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	2	130	0	0.0110497	0	.	.	none	KCNU1_ENST00000399881,NS,carcinoma,+2,2	KCNU1	359	2	NM_001031836	exon5	c.A477T	p.A159A	TATGGCAGCTGAT	.	scavenged	Atlas-SNP
GNB5	10681	hgsc.bcm.edu	37	15	52446260	52446260	+	Silent	SNP	C	C	T	rs35581121	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	6	51	0	0.230769	0	C|0.973;T|0.027	0.027	strong	.	GNB5	28	.	NM_016194	exon4	c.G252A	p.A84A	CCGCTCCGCCACC	.	PASS	Atlas-SNP
C1orf106	55765	hgsc.bcm.edu	37	1	200880869	200880869	+	Missense_Mutation	SNP	A	A	C	rs45547233	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	47	180	0	0.297468	0	A|0.921;C|0.079	0.079	strong	C1orf106,caecum,carcinoma,0,1	C1orf106	59	1	NM_018265	exon9	c.A1545C	p.R515S	CAGCAGAGAGCTG	.	PASS	Atlas-SNP
GTPBP10	85865	hgsc.bcm.edu	37	7	90001496	90001496	+	Missense_Mutation	SNP	G	G	C	rs35001814	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	58	114	0	0.54717	0	G|0.908;C|0.092	0.092	strong	.	GTPBP10	31	.	NM_033107	exon5	c.G492C	p.L164F	CTCTTTGCTAAGT	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1003158	1003158	+	Silent	SNP	C	C	T	rs35163060	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	54	110	0	0.469565	0	C|0.875;T|0.125	0.125	strong	.	GRIN3B	46	.	NM_138690	exon2	c.C456T	p.A152A	CTGGGCCAGCCCC	.	PASS	Atlas-SNP
IFNA1	3439	hgsc.bcm.edu	37	9	21440535	21440535	+	Missense_Mutation	SNP	T	T	C	rs35960747	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	80	309	0	0.375587	0	T|0.954;C|0.046	0.046	strong	.	IFNA1	21	.	NM_024013	exon1	c.T29C	p.V10A	TGATGGTCCTGGT	.	PASS	Atlas-SNP
CCDC40	55036	hgsc.bcm.edu	37	17	78023722	78023722	+	Silent	SNP	C	C	T	rs2289531	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	40	107	0	0.425532	0	C|0.893;T|0.107	0.107	strong	CCDC40,NS,carcinoma,0,1	CCDC40	198	1	NM_017950	exon6	c.C873T	p.F291F	AAGATTCCAGGCT	.	PASS	Atlas-SNP
ZNF480	147657	hgsc.bcm.edu	37	19	52825235	52825235	+	Silent	SNP	A	A	G	rs8102373	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	44	127	0	0.372881	0	A|0.449;G|0.551	0.551	strong	ZNF480_ENST00000468240,NS,carcinoma,+1,2	ZNF480	123	2	NM_144684	exon5	c.A732G	p.S244S	CAATTCACACCTT	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151171439	151171439	+	Missense_Mutation	SNP	A	A	C	rs7619322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	65	134	0	0.451389	0	A|0.276;C|0.724	0.724	strong	.	IGSF10	279	.	NM_178822	exon3	c.T448G	p.Y150D	GCCCATAAAAAAC	.	PASS	Atlas-SNP
ST14	6768	hgsc.bcm.edu	37	11	130058047	130058047	+	Silent	SNP	A	A	G	rs62642510	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	128	137	0	0.719101	0	A|0.885;G|0.115	0.115	strong	.	ST14	82	.	NM_021978	exon2	c.A120G	p.P40P	CCTGCCAGTCAAC	.	PASS	Atlas-SNP
RORA	6095	hgsc.bcm.edu	37	15	60803741	60803741	+	Silent	SNP	C	C	T	rs61740274	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	27	234	0	0.184932	0	C|0.924;T|0.076	0.076	strong	.	RORA	114	.	NM_134260	exon6	c.G603A	p.Q201Q	GCGCTGCTGCTGC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224746	248224746	+	Missense_Mutation	SNP	G	G	T	rs74579079		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	365	203	290	1	0.556164	0.00344828	.	.	weak	.	OR2L3	97	.	NM_001004687	exon1	c.G763T	p.V255F	CCTTTTGTCTACA	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580772	140580772	+	Silent	SNP	T	T	C	rs57636116	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	77	163	0	0.516779	0	T|0.869;C|0.131	0.131	strong	.	PCDHB11	162	.	NM_018931	exon1	c.T1425C	p.A475A	CAGCGCTACAGAC	.	PASS	Atlas-SNP
GBP7	388646	hgsc.bcm.edu	37	1	89613280	89613280	+	Silent	SNP	G	G	A	rs115454072	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	158	300	0	0.993711	0	G|0.976;A|0.024	0.024	strong	.	GBP7	57	.	NM_207398	exon8	c.C1335T	p.D445D	TGTATAGTCCTGT	.	PASS	Atlas-SNP
C14orf80	283643	hgsc.bcm.edu	37	14	105965155	105965155	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	566	9	500	4	0.0159011	0.008	.	.	none	C14orf80_ENST00000392522,NS,carcinoma,-2,2	C14orf80	19	2	NM_001134875	exon8	c.A1153G	p.T385A	ATCAGGACGCTGA	.	scavenged	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2140454	2140454	+	Silent	SNP	T	T	C	rs3087632	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	81	91	0	0.975904	0	T|0.696;C|0.304	0.304	strong	.	PKD1	184	.	NM_001009944	exon45	c.A12276G	p.A4092A	CCGCAGTGCCCAG	.	PASS	Atlas-SNP
SCFD1	23256	hgsc.bcm.edu	37	14	31099738	31099738	+	Missense_Mutation	SNP	A	A	G	rs229150	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	57	106	0	0.38	0	G|0.519;N|0.000	0.519	strong	SCFD1,NS,carcinoma,0,1	SCFD1	43	1	NM_016106	exon3	c.A188G	p.K63R	CTGTGAAGGAGCT	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234713	45234713	+	Silent	SNP	T	T	C	rs139751753		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	347	40	282	3	0.115274	0.0106383	.	.	weak	CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	NM_001114091	exon6	c.A513G	p.T171T	TAAAGATGTGAAT	.	scavenged	Atlas-SNP
SEC23A	10484	hgsc.bcm.edu	37	14	39517925	39517925	+	Silent	SNP	T	T	C	rs11556216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	11	25	0	0.37931	0	T|0.741;C|0.259	0.259	strong	.	SEC23A	73	.	NM_006364	exon15	c.A1668G	p.K556K	TCCAAATTTCTGA	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104082349	104082349	+	Silent	SNP	C	C	T	rs2251634	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	93	216	1	0.513812	0.00462963	T|0.446;G|0.001	0.446	strong	.	CENPE	253	.	NM_001813	exon20	c.G2025A	p.Q675Q	CTCCAACTGGCTT	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242371101	242371101	+	Missense_Mutation	SNP	C	C	T	rs757978	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	41	118	0	0.518987	0	C|0.901;T|0.099	0.099	strong	.	FARP2	92	.	NM_014808	exon9	c.C779T	p.T260I	GCACCACCAAAAT	.	PASS	Atlas-SNP
MRPL43	84545	hgsc.bcm.edu	37	10	102746503	102746503	+	Silent	SNP	C	C	T	rs2863095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	10	65	0	0.196078	0	C|0.704;T|0.296	0.296	strong	.	MRPL43	16	.	NM_032112	exon3	c.G468A	p.V156V	TGCTTGCACCTGG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910622	29910622	+	Silent	SNP	C	C	T	rs199501996	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	20	139	0	0.142857	0	C|0.998;T|0.002	0.002	strong	HLA-A,NS,carcinoma,0,4	HLA-A	89	4	NM_001242758	exon2	c.C162T	p.D54D	GGACGACACGCAG	.	PASS	Atlas-SNP
ACSL1	2180	hgsc.bcm.edu	37	4	185724503	185724503	+	Missense_Mutation	SNP	C	C	T	rs114493597	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	64	126	0	0.688172	0	C|0.998;T|0.002	0.002	strong	.	ACSL1	77	.	NM_001995	exon2	c.G166A	p.D56N	AGAGGTCGCATGG	.	PASS	Atlas-SNP
UMOD	7369	hgsc.bcm.edu	37	16	20359831	20359831	+	Silent	SNP	C	C	T	rs13335818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	23	25	0	0.621622	0	C|0.866;T|0.134	0.134	strong	.	UMOD	128	.	NM_003361	exon3	c.G792A	p.V264V	GGCCTTCACCTGG	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43327793	43327793	+	Silent	SNP	C	C	T	rs3746904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	30	68	0	0.4	0	C|0.655;T|0.345	0.345	strong	C2CD2,NS,carcinoma,0,1	C2CD2	47	1	NM_015500	exon9	c.G1119A	p.S373S	CAGCACCGAGCTG	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76111835	76111835	+	Silent	SNP	G	G	A	rs4236506	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	282	169	262	0	0.599291	0	G|0.795;A|0.205	0.205	strong	DTX2,rectum,carcinoma,0,2	DTX2	64	2	NM_001102596	exon2	c.G279A	p.R93R	CATGCGGGCTGTG	.	PASS	Atlas-SNP
C18orf8	29919	hgsc.bcm.edu	37	18	21109997	21109997	+	Silent	SNP	C	C	T	rs34136453	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	109	201	0	0.536946	0	C|0.993;T|0.007	0.007	strong	.	C18orf8	58	.	NM_013326	exon17	c.C1500T	p.Y500Y	GCATTACCTACAT	.	PASS	Atlas-SNP
LURAP1L	286343	hgsc.bcm.edu	37	9	12775880	12775880	+	Missense_Mutation	SNP	T	T	G	rs201963967	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14	3	11	0	0.214286	0	.	.	weak	C9orf150,caecum,carcinoma,0,3	.	.	3	NM_203403	exon1	c.T166G	p.C56G	GGCGGCTGCAGTA	.	scavenged	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124746049	124746049	+	Missense_Mutation	SNP	A	A	G	rs2981546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	39	81	0	0.4875	0	A|0.534;G|0.466	0.466	strong	.	HEG1	109	.	NM_020733	exon3	c.T913C	p.S305P	ACTCACATGAGGA	.	PASS	Atlas-SNP
ADAMTSL2	9719	hgsc.bcm.edu	37	9	136412296	136412296	+	Silent	SNP	C	C	T	rs2073877	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	34	88	0	0.507463	0	C|0.895;T|0.105	0.105	strong	.	ADAMTSL2	40	.	NM_014694	exon9	c.C900T	p.I300I	GTACATCGTGGCA	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7435901	7435901	+	Missense_Mutation	SNP	C	C	T	rs56269914	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	49	72	0	0.576471	0	C|0.986;T|0.014	0.014	strong	.	PSAPL1	51	.	NM_001085382	exon1	c.G706A	p.D236N	CTTGGTCAGCAGG	.	PASS	Atlas-SNP
FCGR3B	2215	hgsc.bcm.edu	37	1	161596072	161596072	+	Missense_Mutation	SNP	T	T	C	rs71632959	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	662	29	235	2	0.0438066	0.00851064	T|0.500;C|0.500	0.500	weak	FCGR3B,colon,carcinoma,-1,2	FCGR3B	35	2	NM_001244753	exon4	c.A548G	p.D183G	TTCCTGTCTTTGC	.	scavenged	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879340	39879340	+	Missense_Mutation	SNP	G	G	C	rs141110458	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	37	140	0	0.606557	0	G|0.990;C|0.010	0.010	strong	.	KIAA0754	93	.	NM_015038	exon1	c.G3403C	p.A1135P	CCAGCTGCTGCAG	.	PASS	Atlas-SNP
NUF2	83540	hgsc.bcm.edu	37	1	163297322	163297322	+	Silent	SNP	A	A	C	rs16852612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	181	199	0	0.754167	0	A|0.888;C|0.112	0.112	strong	.	NUF2	138	.	NM_145697	exon3	c.A168C	p.V56V	AATAGTATATGGA	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121605355	121605355	+	Missense_Mutation	SNP	G	G	A	rs7958311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	100	187	0	0.49505	0	A|0.265;G|0.735;N|0.000	0.265	strong	P2RX7,NS,carcinoma,0,1	P2RX7	53	1	NM_002562	exon8	c.G809A	p.R270H	ACTGCCGTCCCAA	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71277083	71277083	+	Silent	SNP	C	C	T	rs146926834	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	123	210	1	0.532468	0.0047619	C|0.959;T|0.041	0.041	strong	.	KRTAP5-10	37	.	NM_001012710	exon1	c.C450T	p.C150C	CTGCTGCTCCTCA	.	PASS	Atlas-SNP
CELSR2	1952	hgsc.bcm.edu	37	1	109793034	109793034	+	Silent	SNP	C	C	T	rs142746289	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	24	47	0	0.75	0	C|0.989;T|0.011	0.011	strong	.	CELSR2	228	.	NM_001408	exon1	c.C333T	p.P111P	CTGCCCCTGGAGC	.	PASS	Atlas-SNP
NDC80	10403	hgsc.bcm.edu	37	18	2595443	2595443	+	Missense_Mutation	SNP	G	G	T	rs12456560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	75	197	0	0.405405	0	G|0.900;N|0.000	.	strong	.	NDC80	62	.	NM_006101	exon11	c.G1044T	p.E348D	ACAGGAGAACACT	.	PASS	Atlas-SNP
PER2	8864	hgsc.bcm.edu	37	2	239162318	239162318	+	Silent	SNP	G	G	A	rs10195959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	34	128	0	0.441558	0	G|0.950;A|0.050	0.050	strong	PER2,NS,carcinoma,0,1	PER2	85	1	NM_022817	exon19	c.C2346T	p.S782S	TATTCCGGAAGTA	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46496910	46496910	+	Silent	SNP	G	G	A	rs145526650	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	80	196	0	0.496894	0	G|0.998;A|0.002	0.002	strong	LTF,NS,carcinoma,0,1	LTF	98	1	NM_002343	exon5	c.C522T	p.A174A	ACAGCTGGCTGAG	.	PASS	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	37	4	184192231	184192231	+	Splice_Site	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	3	144	0	0.0441176	0	.	.	none	WWC2,NS,carcinoma,0,1	WWC2	78	1	NM_024949	exon16	c.2401-2A>G	.	TTACATAGGCTGG	.	scavenged	Atlas-SNP
TTC16	158248	hgsc.bcm.edu	37	9	130489558	130489558	+	Silent	SNP	A	A	G	rs472144	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	136	131	0	0.992701	0	A|0.377;G|0.623	0.623	strong	TTC16,NS,carcinoma,0,1	TTC16	55	1	NM_144965	exon12	c.A1578G	p.K526K	GCTTAAACGGCAC	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158624528	158624528	+	Missense_Mutation	SNP	G	G	T	rs35948326	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	41	72	0	0.506173	0	G|0.972;T|0.028	0.028	strong	SPTA1,NS,carcinoma,-1,1	SPTA1	720	1	NM_003126	exon21	c.C2909A	p.A970D	GGTGCAGCCTGTT	.	PASS	Atlas-SNP
CERKL	375298	hgsc.bcm.edu	37	2	182468803	182468803	+	Missense_Mutation	SNP	T	T	G	rs61750041	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40	20	61	0	0.5	0	T|0.866;G|0.134	0.134	strong	.	CERKL	138	.	NM_001160277	exon2	c.A242C	p.D81A	TTAGAATCACCTG	.	PASS	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44560337	44560337	+	Silent	SNP	G	G	T	rs3744864	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	53	119	0	0.434426	0	G|0.992;T|0.008	0.008	strong	TCEB3B,NS,carcinoma,-1,1	TCEB3B	141	1	NM_016427	exon1	c.C1299A	p.V433V	TTCCTGGACAGGA	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186381115	186381115	+	Missense_Mutation	SNP	G	G	T	rs7699687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	15	107	0	0.1875	0	G|0.564;T|0.436	0.436	strong	.	CCDC110	78	.	NM_152775	exon6	c.C626A	p.P209Q	ACATTTGGAGGTG	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238249108	238249108	+	Silent	SNP	T	T	C	rs61729844	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	26	49	0	0.472727	0	A|0.000;C|0.070;T|0.930	0.070	strong	.	COL6A3	608	.	NM_004369	exon38	c.A8451G	p.P2817P	GAAGGATGGCAAC	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47917087	47917087	+	Silent	SNP	C	C	T	rs72601626	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	74	113	0	0.513889	0	C|0.942;T|0.058	0.058	strong	.	PKD1L1	328	.	NM_138295	exon22	c.G3663A	p.P1221P	ACGTACCGGTTTT	.	PASS	Atlas-SNP
DKKL1	27120	hgsc.bcm.edu	37	19	49867913	49867913	+	Missense_Mutation	SNP	G	G	A	rs919364	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	220	108	230	0	0.490909	0	G|0.704;A|0.296	0.296	strong	.	DKKL1	23	.	NM_014419	exon2	c.G85A	p.A29T	CCCTCCGCTGCAG	.	PASS	Atlas-SNP
KLRG1	10219	hgsc.bcm.edu	37	12	9161648	9161648	+	Silent	SNP	T	T	C	rs3026251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	74	231	0	0.37	0	T|0.754;C|0.246	0.246	strong	.	KLRG1	16	.	NM_005810	exon4	c.T435C	p.D145D	GGAAGATGGATCA	.	PASS	Atlas-SNP
NLRP9	338321	hgsc.bcm.edu	37	19	56249672	56249672	+	Silent	SNP	A	A	G	rs56211941	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	76	143	0	0.481013	0	A|0.852;G|0.148	0.148	strong	NLRP9,colon,carcinoma,0,1	NLRP9	163	1	NM_176820	exon1	c.T69C	p.F23F	TTTCCAAAACTCT	.	PASS	Atlas-SNP
HFE	3077	hgsc.bcm.edu	37	6	26091185	26091185	+	Missense_Mutation	SNP	A	A	T	rs1800730	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	105	260	1	0.443038	0.00384615	A|0.990;T|0.010	0.010	strong	.	HFE	37	.	NM_139006	exon2	c.A193T	p.S65C	CATGAGAGTCGCC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113221247	113221247	+	Missense_Mutation	SNP	T	T	C	rs7038903	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	65	174	0	0.414013	0	T|0.828;C|0.172	0.172	strong	.	SVEP1	326	.	NM_153366	exon19	c.A3469G	p.I1157V	CTGTGATGGATCT	.	PASS	Atlas-SNP
OR9G4	283189	hgsc.bcm.edu	37	11	56511160	56511160	+	Missense_Mutation	SNP	A	A	G	rs11228763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	18	63	0	0.367347	0	A|0.905;G|0.095	0.095	strong	OR9G4,NS,carcinoma,0,1	OR9G4	73	1	NM_001005284	exon1	c.T128C	p.F43S	ACTCCAAATAGAA	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11015165	11015165	+	Missense_Mutation	SNP	A	A	G	rs75130475	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	43	106	0	0.781818	0	A|0.843;G|0.157	0.157	strong	.	C1orf127	134	.	NM_001170754	exon9	c.T857C	p.I286T	TCCTCAATGTAGG	.	PASS	Atlas-SNP
RAET1E	135250	hgsc.bcm.edu	37	6	150211100	150211100	+	Silent	SNP	T	T	C	rs3798763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	189	99	191	0	0.52381	0	T|0.790;C|0.210	0.210	strong	.	RAET1E	20	.	NM_139165	exon2	c.A267G	p.E89E	GGTCAATTCTCCC	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862731	5862731	+	Missense_Mutation	SNP	A	A	G	rs61743084	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	91	243	2	0.425234	0.00823045	A|0.622;G|0.378	0.378	strong	OR52E6,NS,carcinoma,+2,2	OR52E6	70	2	NM_001005167	exon1	c.T397C	p.W133R	TGTACCAAAGAGG	.	scavenged	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	49	106	0	0.462264	0	G|0.744;A|0.256	0.256	strong	ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	NM_001007231	exon6	c.G756A	p.Q252Q	GAGCCAGTACGAA	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008695	11008695	+	Silent	SNP	T	T	C	rs17036032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	32	79	0	0.695652	0	T|0.858;C|0.142	0.142	strong	.	C1orf127	134	.	NM_001170754	exon12	c.A1497G	p.P499P	CAAGACTGGACGT	.	PASS	Atlas-SNP
ETV3L	440695	hgsc.bcm.edu	37	1	157069134	157069134	+	Missense_Mutation	SNP	G	G	A	rs61730132	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	94	150	0	0.406926	0	G|0.994;A|0.006	0.006	strong	.	ETV3L	73	.	NM_001004341	exon2	c.C95T	p.S32L	GGGGACGACTCGG	.	PASS	Atlas-SNP
VTCN1	79679	hgsc.bcm.edu	37	1	117753455	117753455	+	Missense_Mutation	SNP	A	A	G	rs34957002	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	36	106	0	0.734694	0	A|0.983;G|0.017	0.017	strong	.	VTCN1	26	.	NM_001253850	exon1	c.T23C	p.L8P	CAGAAGAGGATCT	.	PASS	Atlas-SNP
LIPF	8513	hgsc.bcm.edu	37	10	90429652	90429652	+	Missense_Mutation	SNP	A	A	G	rs814628	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	72	189	0	0.774194	0	A|0.851;G|0.149	0.149	strong	.	LIPF	62	.	NM_001198829	exon6	c.A511G	p.T171A	AAGAAAACTGGAC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678932	100678932	+	Missense_Mutation	SNP	A	A	G	rs114941002		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	31	128	0	0.142202	0	.	.	weak	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.A4235G	p.E1412G	GTTCTGAGGCTAG	.	scavenged	Atlas-SNP
MOCOS	55034	hgsc.bcm.edu	37	18	33848581	33848581	+	Missense_Mutation	SNP	T	T	C	rs1057251	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	102	222	1	0.453333	0.0045045	T|0.921;C|0.079	0.079	strong	.	MOCOS	84	.	NM_017947	exon15	c.T2600C	p.V867A	TCCCTGTGTTGAA	.	PASS	Atlas-SNP
IL20RA	53832	hgsc.bcm.edu	37	6	137323213	137323213	+	Missense_Mutation	SNP	G	G	A	rs1342642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	72	193	0	0.455696	0	G|0.794;N|0.001	.	strong	.	IL20RA	54	.	NM_014432	exon7	c.C1144T	p.L382F	GGGTGAGAGAAGT	.	PASS	Atlas-SNP
ALAD	210	hgsc.bcm.edu	37	9	116153891	116153891	+	Missense_Mutation	SNP	C	C	G	rs1800435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	60	161	0	0.41958	0	C|0.938;G|0.062	0.062	strong	.	ALAD	36	.	NM_000031	exon4	c.G177C	p.K59N	CAGCCGCTTCACA	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	37	22	18300879	18300879	+	Silent	SNP	G	G	A	rs11704809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	60	118	0	0.451128	0	G|0.800;A|0.200	0.200	strong	.	MICAL3	53	.	NM_015241	exon26	c.C4548T	p.S1516S	CTCCACGCTCTCC	.	PASS	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4228418	4228418	+	Silent	SNP	G	G	A	rs199644487		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	25	8	56	0	0.32	0	G|0.994;A|0.006	0.006	weak	OTOP1,NS,haematopoietic_neoplasm,0,1	OTOP1	118	1	NM_177998	exon1	c.C174T	p.A58A	CATCTCGGCCAGT	.	scavenged	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156639636	156639636	+	Silent	SNP	G	G	A	rs11549292	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	47	98	0	0.367188	0	G|0.773;A|0.227	0.227	strong	NES,NS,carcinoma,0,1	NES	196	1	NM_006617	exon4	c.C4344T	p.A1448A	ACTCAGGGCCTGG	.	PASS	Atlas-SNP
CENPW	387103	hgsc.bcm.edu	37	6	126661502	126661502	+	Missense_Mutation	SNP	G	G	T	rs41285260	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	54	121	0	0.482143	0	G|0.937;T|0.063	0.063	strong	.	CENPW	7	.	NM_001012507	exon1	c.G83T	p.R28L	TCAAGCGAAAGAA	.	PASS	Atlas-SNP
TMEM89	440955	hgsc.bcm.edu	37	3	48659009	48659009	+	Missense_Mutation	SNP	G	G	T	rs9834639	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	98	207	0	0.538462	0	G|0.878;T|0.122	0.122	strong	.	TMEM89	10	.	NM_001008269	exon1	c.C181A	p.P61T	CTCCAGGGCCCAG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388379	1388379	+	Missense_Mutation	SNP	G	G	A	rs56109734	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	45	210	4	0.236842	0.0190476	G|0.996;A|0.004	0.004	strong	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.G80A	p.C27Y	GCTCATGTGCCCA	.	scavenged	Atlas-SNP
LRBA	987	hgsc.bcm.edu	37	4	151207127	151207127	+	Missense_Mutation	SNP	C	C	T	rs3749574	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	118	277	0	0.702381	0	C|0.798;T|0.202	0.202	strong	.	LRBA	253	.	NM_006726	exon55	c.G8110A	p.A2704T	ACACCGCAGCACA	.	PASS	Atlas-SNP
PML	5371	hgsc.bcm.edu	37	15	74336656	74336656	+	Silent	SNP	C	C	T	rs61751122	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40	32	64	0	0.8	0	C|0.967;T|0.033	0.033	strong	.	PML	169	.	NM_033238	exon9	c.C1956T	p.A652A	CAAGGCCGTGTCC	.	PASS	Atlas-SNP
C3orf58	205428	hgsc.bcm.edu	37	3	143691672	143691672	+	Silent	SNP	C	C	T	rs151261436	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	19	56	0	0.527778	0	C|0.989;T|0.011	0.011	strong	.	C3orf58	36	.	NM_173552	exon1	c.C498T	p.D166D	GTCGGACCTGGTG	.	PASS	Atlas-SNP
TPPP	11076	hgsc.bcm.edu	37	5	678087	678087	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	303	14	352	0	0.0462046	0	.	.	none	TPPP,NS,carcinoma,0,1	TPPP	24	1	NM_007030	exon2	c.G89A	p.R30K	GACAGCCTCTTGG	.	scavenged	Atlas-SNP
FGFBP2	83888	hgsc.bcm.edu	37	4	15964574	15964574	+	Missense_Mutation	SNP	C	C	T	rs62617788	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	13	24	0	0.481481	0	C|0.978;T|0.022	0.022	strong	.	FGFBP2	22	.	NM_031950	exon1	c.G179A	p.R60H	TCGACACGAAGCC	.	PASS	Atlas-SNP
CRISPLD1	83690	hgsc.bcm.edu	37	8	75927053	75927053	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	4	85	0	0.036036	0	.	.	none	CRISPLD1,colon,carcinoma,+2,1	CRISPLD1	94	1	NM_031461	exon6	c.C633T	p.N211N	GGGAAACTGGTGG	.	scavenged	Atlas-SNP
CPA1	1357	hgsc.bcm.edu	37	7	130023539	130023539	+	Silent	SNP	C	C	T	rs12706927	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	26	145	0	0.25	0	C|0.903;T|0.097	0.097	strong	.	CPA1	73	.	NM_001868	exon6	c.C600T	p.Y200Y	AGACTACGGGCAG	.	PASS	Atlas-SNP
CGNL1	84952	hgsc.bcm.edu	37	15	57839587	57839587	+	Missense_Mutation	SNP	A	A	G	rs16977594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	15	116	0	0.230769	0	A|0.914;G|0.086	0.086	strong	CGNL1,NS,carcinoma,0,1	CGNL1	125	1	NM_032866	exon19	c.A3808G	p.M1270V	GATGACATGGATG	.	PASS	Atlas-SNP
CHRNA2	1135	hgsc.bcm.edu	37	8	27324822	27324822	+	Missense_Mutation	SNP	T	T	C	rs891398	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	244	233	1	0.987854	0.00429185	T|0.402;C|0.598	0.598	strong	.	CHRNA2	48	.	NM_000742	exon5	c.A373G	p.T125A	AATCAGTGGGGTT	.	PASS	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693104	187693104	+	Silent	SNP	C	C	T	rs10172225	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	72	133	0	0.517986	0	C|0.805;T|0.195	0.195	strong	.	ZSWIM2	119	.	NM_182521	exon9	c.G1509A	p.V503V	AAATGACACAGTG	.	PASS	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43836173	43836173	+	Missense_Mutation	SNP	T	T	A	rs2301366	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	117	279	0	0.471774	0	T|0.724;A|0.276	0.276	strong	SEMG1,NS,carcinoma,-2,3	SEMG1	71	3	NM_003007	exon2	c.T235A	p.S79T	GACCAGTCCCGAA	.	PASS	Atlas-SNP
ARID4A	5926	hgsc.bcm.edu	37	14	58831995	58831995	+	Missense_Mutation	SNP	A	A	G	rs377087834		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	42	84	0	0.424242	0	.	.	weak	.	ARID4A	222	.	NM_002892	exon20	c.A3188G	p.Q1063R	TTGTACAAGAGAG	.	PASS	Atlas-SNP
IL17RB	55540	hgsc.bcm.edu	37	3	53892830	53892830	+	Missense_Mutation	SNP	T	T	C	rs2232346	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	18	80	0	0.290323	0	T|0.982;C|0.018	0.018	strong	.	IL17RB	27	.	NM_018725	exon9	c.T832C	p.F278L	GTCCCTTTCCCTC	.	PASS	Atlas-SNP
GJA9	81025	hgsc.bcm.edu	37	1	39340504	39340504	+	Silent	SNP	T	T	G	rs41270783	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	35	283	0	0.205882	0	T|0.935;G|0.065	0.065	strong	.	GJA9	55	.	NM_030772	exon2	c.A1267C	p.R423R	TAGCTCTAAGCCA	.	PASS	Atlas-SNP
PAG1	55824	hgsc.bcm.edu	37	8	81897200	81897200	+	Silent	SNP	C	C	T	rs7006101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	529	177	381	1	0.334594	0.00262467	C|0.853;T|0.147	0.147	strong	.	PAG1	39	.	NM_018440	exon7	c.G687A	p.S229S	GTCCACCGAGGCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678622	100678622	+	Missense_Mutation	SNP	G	G	A	rs77299546	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	90	157	0	0.340909	0	G|0.936;A|0.064	0.064	strong	.	MUC17	804	.	NM_001040105	exon3	c.G3925A	p.V1309M	GGTCCTGTGGTCA	.	PASS	Atlas-SNP
TNFSF9	8744	hgsc.bcm.edu	37	19	6534728	6534728	+	Missense_Mutation	SNP	G	G	C	rs61750000	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	55	154	0	0.5	0	G|0.997;C|0.003	0.003	strong	.	TNFSF9	17	.	NM_003811	exon3	c.G416C	p.G139A	AGGCTGGAGTCTA	.	PASS	Atlas-SNP
ZC3H11A	9877	hgsc.bcm.edu	37	1	203821334	203821334	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	362	3	264	1	0.00828729	0.00378788	.	.	none	ZC3H11A,NS,carcinoma,0,1	ZC3H11A	71	1	NM_014827	exon20	c.C2240T	p.S747L	CTTCCTCATCCCA	.	scavenged	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	37	12	52818377	52818377	+	Missense_Mutation	SNP	C	C	T	rs61730614	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	84	201	1	0.461538	0.00497512	C|0.848;T|0.152	0.152	strong	KRT75,rectum,NS,0,2	KRT75	75	2	NM_004693	exon9	c.G1580A	p.R527Q	AAGCCCCGGTTGC	.	scavenged	Atlas-SNP
BMP5	653	hgsc.bcm.edu	37	6	55739553	55739553	+	Silent	SNP	A	A	G	rs3734444	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	41	69	0	0.518987	0	A|0.533;G|0.467	0.467	strong	.	BMP5	94	.	NM_021073	exon1	c.T111C	p.S37S	AATAAAACTGGAG	.	PASS	Atlas-SNP
TMEM170B	100113407	hgsc.bcm.edu	37	6	11538534	11538534	+	Silent	SNP	C	C	T	rs821443	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	19	20	0	1	0	C|0.787;T|0.213	0.213	strong	.	TMEM170B	9	.	NM_001100829	exon1	c.C24T	p.H8H	CGACCACTCCATG	.	PASS	Atlas-SNP
TOLLIP	54472	hgsc.bcm.edu	37	11	1309956	1309956	+	Silent	SNP	C	C	T	rs3750920	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	82	152	2	0.532468	0.0131579	C|0.625;T|0.375	0.375	strong	TOLLIP,NS,carcinoma,0,1	TOLLIP	25	1	NM_019009	exon4	c.G417A	p.P139P	GGACTCCGGGATG	.	scavenged	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777578	52777578	+	Missense_Mutation	SNP	C	C	T	rs1613931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	44	128	0	0.389381	0	C|0.686;T|0.314	0.314	strong	KRT84,colon,carcinoma,0,1	KRT84	61	1	NM_033045	exon2	c.G551A	p.R184Q	AGGAACCGAACCT	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39623363	39623363	+	Missense_Mutation	SNP	T	T	C	rs3744786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	56	123	0	0.474576	0	C|0.286;N|0.000	0.286	strong	.	KRT32	57	.	NM_002278	exon1	c.A215G	p.Q72R	GCTGCCTGGCAGG	.	PASS	Atlas-SNP
PBK	55872	hgsc.bcm.edu	37	8	27667969	27667969	+	Silent	SNP	C	C	G	rs2294092	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	129	157	1	0.638614	0.00636943	C|0.567;G|0.433	0.433	strong	.	PBK	29	.	NM_018492	exon8	c.G822C	p.A274A	TCCCAACGCTGCA	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12888397	12888397	+	Missense_Mutation	SNP	C	C	T	rs78478513		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	351	79	505	102	0.225071	0.20198	C|0.250;T|0.750	0.750	weak	PRAMEF11,NS,other,0,1	PRAMEF11	72	1	NM_001146344	exon2	c.G127A	p.D43N	GCCCATCGAGCAC	.	scavenged	Atlas-SNP
PDE4A	5141	hgsc.bcm.edu	37	19	10577843	10577843	+	Missense_Mutation	SNP	C	C	A	rs1051738	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	113	117	0	0.982609	0	A|0.205;C|0.795	0.205	strong	PDE4A,NS,carcinoma,0,1	PDE4A	236	1	NM_001111307	exon15	c.C2207A	p.A736E	TGACTGCGCAGGG	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187078745	187078745	+	Missense_Mutation	SNP	A	A	G	rs113168248	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	5	41	0	0.131579	0	A|0.995;G|0.005	0.005	strong	.	FAM149A	52	.	NM_001006655	exon7	c.A601G	p.K201E	ACATTGAAAGTGG	.	PASS	Atlas-SNP
PAK7	57144	hgsc.bcm.edu	37	20	9523244	9523244	+	Missense_Mutation	SNP	C	C	T	rs150828790	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	189	96	159	0	0.507937	0	C|0.999;T|0.001	0.001	strong	.	PAK7	194	.	NM_177990	exon9	c.G1993A	p.D665N	GTAGGTCCTTCAC	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193080414	193080414	+	Missense_Mutation	SNP	C	C	G	rs6797429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	78	128	0	0.503226	0	C|0.453;G|0.547	0.547	strong	.	ATP13A5	171	.	NM_198505	exon4	c.G397C	p.E133Q	GCACTTCCATGCA	.	PASS	Atlas-SNP
KLHL34	257240	hgsc.bcm.edu	37	X	21675125	21675125	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	83	203	0	0.954023	0	.	.	none	.	KLHL34	76	.	NM_153270	exon1	c.C782T	p.T261M	GAGGGCGTCGTGT	.	PASS	Atlas-SNP
HS3ST2	9956	hgsc.bcm.edu	37	16	22826339	22826339	+	Silent	SNP	A	A	G	rs208951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	56	120	0	0.41791	0	A|0.600;G|0.400	0.400	strong	.	HS3ST2	59	.	NM_006043	exon1	c.A408G	p.V136V	CCGAGTACACCCG	.	PASS	Atlas-SNP
GANC	2595	hgsc.bcm.edu	37	15	42643529	42643529	+	Missense_Mutation	SNP	T	T	C	rs7181742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	20	146	0	0.212766	0	T|0.702;C|0.298	0.298	strong	.	GANC	57	.	NM_198141	exon23	c.T2534C	p.F845S	CCAGTTTTGCTGA	.	PASS	Atlas-SNP
MYO9A	4649	hgsc.bcm.edu	37	15	72180440	72180440	+	Silent	SNP	C	C	T	rs148060237	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	16	103	0	0.280702	0	C|0.983;T|0.017	0.017	strong	.	MYO9A	203	.	NM_006901	exon27	c.G5160A	p.S1720S	AACTGACGAAAAT	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3165949	3165949	+	Silent	SNP	G	G	C	rs141170475	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	288	104	208	0	0.361111	0	A|0.000;C|0.004;G|0.996	0.004	strong	.	CSMD1	1469	.	NM_033225	exon24	c.C3708G	p.T1236T	AGTGTCGGTAAAG	.	PASS	Atlas-SNP
KCNK16	83795	hgsc.bcm.edu	37	6	39284148	39284148	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	46	89	0	0.516854	0	.	.	none	.	KCNK16	59	.	NM_001135106	exon5	c.G732A	p.L244L	CCACGCCAGGCCC	.	PASS	Atlas-SNP
MYBPC1	4604	hgsc.bcm.edu	37	12	102069077	102069077	+	Silent	SNP	A	A	G	rs764291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	89	232	0	0.451777	0	A|0.807;G|0.193	0.193	strong	.	MYBPC1	235	.	NM_206819	exon26	c.A2817G	p.P939P	CCGTCCAGGTCCA	.	PASS	Atlas-SNP
DISC1	27185	hgsc.bcm.edu	37	1	232144598	232144598	+	Missense_Mutation	SNP	A	A	T	rs821616	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	49	126	0	0.365672	0	A|0.747;T|0.253	0.253	strong	.	DISC1	207	.	NM_001164537	exon12	c.A2206T	p.S736C	ATCCAGAGCCTAC	.	PASS	Atlas-SNP
UBP1	7342	hgsc.bcm.edu	37	3	33434831	33434831	+	Silent	SNP	G	G	A	rs2293250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	48	125	0	0.428571	0	G|0.490;N|0.001	.	strong	.	UBP1	42	.	NM_014517	exon14	c.C1506T	p.T502T	AATACCGGTGGGA	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29246044	29246044	+	Missense_Mutation	SNP	T	T	C	rs6721861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206	87	238	2	0.42233	0.00840336	T|0.456;C|0.544	0.544	strong	FAM179A,NS,carcinoma,0,1	FAM179A	106	1	NM_199280	exon12	c.T1604C	p.V535A	GCTTGGTGGTGAC	.	scavenged	Atlas-SNP
ELMO3	79767	hgsc.bcm.edu	37	16	67233266	67233266	+	Missense_Mutation	SNP	A	A	C	rs12923138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	7	54	0	0.162791	0	A|0.448;C|0.552	0.552	strong	.	ELMO3	41	.	NM_024712	exon1	c.A196C	p.K66Q	GCCATCAAGATGC	.	PASS	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170169688	170169688	+	Missense_Mutation	SNP	A	A	G	rs61738268	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	25	77	0	0.409836	0	A|0.991;G|0.009	0.009	strong	.	C6orf70	63	.	NM_018341	exon12	c.A1112G	p.H371R	GAGATCATTTAAG	.	PASS	Atlas-SNP
CSRP2BP	57325	hgsc.bcm.edu	37	20	18168099	18168099	+	Missense_Mutation	SNP	G	G	A	rs376874386		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	29	66	0	0.446154	0	.	.	weak	.	CSRP2BP	80	.	NM_020536	exon10	c.G2345A	p.R782H	TCCGGCGCTGATG	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4870139	4870139	+	Silent	SNP	G	G	A	rs11602455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	120	126	0	0.967742	0	G|0.691;A|0.309	0.309	strong	.	OR51S1	83	.	NM_001004758	exon1	c.C300T	p.V100V	GGCAGGGACAGTG	.	PASS	Atlas-SNP
HS1BP3	64342	hgsc.bcm.edu	37	2	20818764	20818764	+	Missense_Mutation	SNP	C	C	T	rs3732149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	70	160	0	0.391061	0	C|0.834;T|0.166	0.166	strong	.	HS1BP3	33	.	NM_022460	exon7	c.G1162A	p.A388T	TGGGGGCGGCCTG	.	PASS	Atlas-SNP
VCAM1	7412	hgsc.bcm.edu	37	1	101203698	101203698	+	Silent	SNP	C	C	T	rs3176878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	78	225	0	0.696429	0	C|0.854;T|0.146	0.146	strong	.	VCAM1	111	.	NM_001078	exon9	c.C2079T	p.D693D	CAAAGACTATTTT	.	PASS	Atlas-SNP
TRIM22	10346	hgsc.bcm.edu	37	11	5730294	5730294	+	Silent	SNP	C	C	T	rs61735276	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	51	130	0	0.504951	0	C|0.969;T|0.031	0.031	strong	.	TRIM22	66	.	NM_006074	exon8	c.C913T	p.L305L	GTGATGCTGAATC	.	PASS	Atlas-SNP
DDX31	64794	hgsc.bcm.edu	37	9	135521303	135521303	+	Silent	SNP	C	C	T	rs306537	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	39	83	0	0.506494	0	C|0.927;T|0.073	0.073	strong	.	DDX31	76	.	NM_022779	exon13	c.G1674A	p.L558L	GCCATGCAGCCGT	.	PASS	Atlas-SNP
UTP15	84135	hgsc.bcm.edu	37	5	72868447	72868447	+	Silent	SNP	T	T	C	rs16870610	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	23	71	0	0.418182	0	T|0.945;C|0.055	0.055	strong	.	UTP15	30	.	NM_032175	exon7	c.T807C	p.D269D	ACTGGATAGGTTG	.	PASS	Atlas-SNP
ZNF709	163051	hgsc.bcm.edu	37	19	12575152	12575152	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	3	128	3	0.0326087	0.0234375	.	.	none	ZNF709_ENST00000397732,NS,carcinoma,0,4	ZNF709	80	4	NM_152601	exon4	c.G1584A	p.G528G	TTTCTCCCCAGTG	.	scavenged	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	99006736	99006736	+	Silent	SNP	C	C	T	rs11559202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	62	128	0	0.397436	0	C|0.872;T|0.128	0.128	strong	.	MATN2	165	.	NM_002380	exon7	c.C1110T	p.H370H	TAATCACGGATGT	.	PASS	Atlas-SNP
ISOC2	79763	hgsc.bcm.edu	37	19	55967848	55967848	+	Silent	SNP	C	C	T	rs11555784	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	42	103	0	0.518519	0	C|0.939;T|0.061	0.061	strong	.	ISOC2	16	.	NM_001136202	exon2	c.G6A	p.A2A	GGCAGCCGCCATT	.	PASS	Atlas-SNP
CECR1	51816	hgsc.bcm.edu	37	22	17669306	17669306	+	Missense_Mutation	SNP	T	T	C	rs2231495	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	74	93	0	0.986667	0	T|0.627;C|0.373	0.373	strong	.	CECR1	77	.	NM_017424	exon6	c.A1004G	p.H335R	TAGTCATGCAAGG	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4869906	4869906	+	Missense_Mutation	SNP	A	A	C	rs7117260	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	92	117	0	0.989247	0	A|0.479;C|0.521	0.521	strong	.	OR51S1	83	.	NM_001004758	exon1	c.T533G	p.L178R	TGTGGGAGGCAGT	.	PASS	Atlas-SNP
PPP4R1	9989	hgsc.bcm.edu	37	18	9570320	9570320	+	Missense_Mutation	SNP	T	T	C	rs329003	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	60	172	0	0.4	0	T|0.940;C|0.060	0.060	strong	.	PPP4R1	63	.	NM_001042388	exon11	c.A1408G	p.I470V	GCTCTATGTCTAG	.	PASS	Atlas-SNP
CXorf65	158830	hgsc.bcm.edu	37	X	70324157	70324157	+	Silent	SNP	C	C	T	rs1130009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	104	175	1	0.936937	0.00571429	0|0.002;T|0.182	0.182	strong	.	CXorf65	23	.	NM_001025265	exon5	c.G417A	p.A139A	GACACTCGCAGGG	.	PASS	Atlas-SNP
APBB2	323	hgsc.bcm.edu	37	4	40818179	40818179	+	Missense_Mutation	SNP	T	T	C	rs112788816	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	107	338	0	0.451477	0	T|0.991;C|0.009	0.009	strong	.	APBB2	61	.	NM_004307	exon18	c.A2210G	p.N737S	TTTACATTGGTTG	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33493200	33493200	+	Missense_Mutation	SNP	G	G	A	rs200623446	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	22	167	3	0.120879	0.0179641	G|0.935;A|0.065	0.065	strong	RHPN2,caecum,carcinoma,-1,17	RHPN2	107	17	NM_033103	exon9	c.C1058T	p.A353V	AGGGCCGCGTAGT	.	scavenged	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16351275	16351275	+	Missense_Mutation	SNP	A	A	G	rs10927887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	89	167	0	0.780702	0	A|0.397;G|0.603	0.603	strong	.	CLCNKA	56	.	NM_004070	exon4	c.A247G	p.R83G	CTGTACAGGGAGA	.	PASS	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108863591	108863591	+	Missense_Mutation	SNP	G	G	A	rs1805388	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	41	116	0	0.5125	0	G|0.856;N|0.000	.	strong	.	LIG4	91	.	NM_206937	exon3	c.C26T	p.T9I	GCAACAGTTTGTG	.	PASS	Atlas-SNP
ABCB1	5243	hgsc.bcm.edu	37	7	87178735	87178735	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	3	207	1	0.0118577	0.00483092	.	.	none	ABCB1,NS,carcinoma,+2,1	ABCB1	263	1	NM_000927	exon15	c.C1654T	p.L552F	GCAGGAGGATCTT	.	scavenged	Atlas-SNP
ZNF618	114991	hgsc.bcm.edu	37	9	116812084	116812084	+	Silent	SNP	C	C	T	rs7856141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	52	89	0	0.485981	0	C|0.923;T|0.077	0.077	strong	.	ZNF618	184	.	NM_133374	exon14	c.C2223T	p.N741N	CATCAACGAGGTG	.	PASS	Atlas-SNP
TRIM71	131405	hgsc.bcm.edu	37	3	32933036	32933036	+	Silent	SNP	G	G	A	rs13096271	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	30	86	0	0.441176	0	G|0.873;A|0.127	0.127	strong	TRIM71,NS,meningioma,+1,1	TRIM71	73	1	NM_001039111	exon4	c.G2340A	p.S780S	CCAGTCGGCACGC	.	PASS	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	37	17	80159665	80159665	+	Silent	SNP	G	G	A	rs11653797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	226	117	189	0	0.517699	0	G|0.859;A|0.141	0.141	strong	.	CCDC57	102	.	NM_198082	exon2	c.C156T	p.C52C	CTGCAGGCACCGC	.	PASS	Atlas-SNP
MLX	6945	hgsc.bcm.edu	37	17	40722162	40722162	+	Silent	SNP	G	G	A	rs1474040	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	68	176	1	0.377778	0.00568182	G|0.827;A|0.173	0.173	strong	MLX,colon,carcinoma,+1,1	MLX	17	1	NM_170607	exon7	c.G801A	p.A267A	GTCAGCGTGTGTC	.	scavenged	Atlas-SNP
RASGRF1	5923	hgsc.bcm.edu	37	15	79298523	79298523	+	Silent	SNP	G	G	A	rs894780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	52	79	0	0.764706	0	G|0.921;T|0.000	.	strong	.	RASGRF1	168	.	NM_002891	exon15	c.C2119T	p.L707L	ACCTCAGCCACCT	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848145	54848145	+	Missense_Mutation	SNP	G	G	A	rs75547479	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	19	235	0	0.104396	0	A|0.005;G|0.995	0.005	strong	.	LILRA4	91	.	NM_012276	exon6	c.C1222T	p.H408Y	TGGGGTGAGACAG	.	PASS	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	37	5	96129543	96129543	+	Missense_Mutation	SNP	C	C	T	rs27895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	119	262	1	0.48374	0.00381679	C|0.903;T|0.097	0.097	strong	.	ERAP1	59	.	NM_001198541	exon6	c.G1037A	p.G346D	GTGATGCCAAGCT	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116931666	116931666	+	Missense_Mutation	SNP	A	A	T	rs2567705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	24	50	0	0.375	0	A|0.648;T|0.352	0.352	strong	.	COL27A1	200	.	NM_032888	exon3	c.A1831T	p.I611F	TATTCGATCTTCC	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1817367	1817367	+	Silent	SNP	G	G	A	rs7003969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	279	85	278	0	0.304659	0	G|0.777;A|0.223	0.223	strong	.	ARHGEF10	255	.	NM_014629	exon7	c.G630A	p.E210E	TCCAGAGGAAGCA	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13399786	13399786	+	Missense_Mutation	SNP	G	G	A	rs6795271	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	81	179	0	0.455056	0	G|0.734;A|0.266	0.266	strong	.	NUP210	182	.	NM_024923	exon16	c.C2264T	p.A755V	ACAGGCGCGAGGG	.	PASS	Atlas-SNP
ZNF431	170959	hgsc.bcm.edu	37	19	21326358	21326358	+	Missense_Mutation	SNP	A	A	G	rs17445374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	68	175	0	0.489209	0	A|0.836;G|0.164	0.164	strong	.	ZNF431	71	.	NM_133473	exon2	c.A8G	p.D3G	AGGACGACTTGAA	.	PASS	Atlas-SNP
HSPA12A	259217	hgsc.bcm.edu	37	10	118435989	118435989	+	Silent	SNP	C	C	A	rs11197793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	45	84	0	0.548781	0	C|0.991;A|0.009	0.009	strong	.	HSPA12A	81	.	NM_025015	exon11	c.G1311T	p.S437S	CCCCTGCGAGGAC	.	PASS	Atlas-SNP
GPR151	134391	hgsc.bcm.edu	37	5	145894882	145894882	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	32	94	0	0.283186	0	.	.	none	.	GPR151	35	.	NM_194251	exon1	c.C795T	p.P265P	CCATTCGGGGAGC	.	PASS	Atlas-SNP
TUBA3D	113457	hgsc.bcm.edu	37	2	132238286	132238286	+	Silent	SNP	C	C	T	rs111626841	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	50	143	0	0.362319	0	C|0.831;T|0.169	0.169	strong	.	TUBA3D	60	.	NM_080386	exon4	c.C1020T	p.T340T	GCGCACCATCCAG	.	PASS	Atlas-SNP
AP5B1	91056	hgsc.bcm.edu	37	11	65547333	65547333	+	Missense_Mutation	SNP	G	G	A	rs12146493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	365	166	356	2	0.454795	0.00561798	G|0.644;A|0.356	0.356	strong	AP5B1_ENST00000532090,NS,carcinoma,0,2	AP5B1	40	2	NM_138368	exon2	c.C631T	p.L211F	CCGTGAGCAGTCC	.	scavenged	Atlas-SNP
ECT2L	345930	hgsc.bcm.edu	37	6	139206937	139206937	+	Silent	SNP	A	A	G	rs17067993	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	41	93	0	0.450549	0	A|0.902;G|0.098	0.098	strong	.	ECT2L	75	.	NM_001195037	exon17	c.A2229G	p.Q743Q	TGACCAAATCAAA	.	PASS	Atlas-SNP
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60021761	60021761	+	Missense_Mutation	SNP	C	C	T	rs35211496	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15	7	25	0	0.466667	0	C|0.883;T|0.117	0.117	strong	TNFRSF11A,NS,carcinoma,0,1	TNFRSF11A	51	1	NM_001270951	exon4	c.C421T	p.H141Y	GCCCAGCACCCGT	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84229892	84229892	+	Missense_Mutation	SNP	C	C	T	rs141742506	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	11	120	0	0.105769	0	C|0.991;T|0.009	0.009	strong	.	ADAD2	46	.	NM_139174	exon9	c.C1688T	p.T563I	CTGACACCTGCCG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388693	1388693	+	Missense_Mutation	SNP	C	C	G	rs78906219	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	35	76	1	0.777778	0.0131579	G|1.000;|0.000	1.000	weak	CRIPAK,caecum,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.C394G	p.H132D	CGTGCCCATGCGG	.	scavenged	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50532812	50532812	+	Missense_Mutation	SNP	A	A	G	rs11101093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	35	232	0	0.213415	0	A|0.908;G|0.092	0.092	strong	.	C10orf71	179	.	NM_001135196	exon3	c.A2222G	p.D741G	CATTTGATGATCA	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11014118	11014118	+	Missense_Mutation	SNP	C	C	T	rs45537241	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	105	315	0	0.7	0	C|0.852;T|0.148	0.148	strong	.	C1orf127	134	.	NM_001170754	exon10	c.G1057A	p.A353T	CCGGGGCAGCCAT	.	PASS	Atlas-SNP
SCML4	256380	hgsc.bcm.edu	37	6	108029109	108029109	+	Silent	SNP	T	T	C	rs3734754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	56	171	3	0.466667	0.0175439	T|0.784;C|0.216	0.216	strong	SCML4_ENST00000369020,colon,carcinoma,0,1	SCML4	65	1	NM_198081	exon7	c.A1080G	p.P360P	AGCCTGTGGGTCG	.	scavenged	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145001588	145001588	+	Missense_Mutation	SNP	C	C	T	rs11136334	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4	4	6	0	1	0	C|0.706;T|0.294	0.294	strong	PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	NM_201380	exon27	c.G4157A	p.R1386Q	TCCTGCCGCAGCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152286002	152286002	+	Missense_Mutation	SNP	T	T	C	rs2011331	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	466	170	336	0	0.364807	0	T|0.667;C|0.333	0.333	strong	.	FLG	900	.	NM_002016	exon3	c.A1360G	p.T454A	CACGTGTGGACTC	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361642	107361642	+	Missense_Mutation	SNP	G	G	A	rs41430948	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	417	154	501	1	0.369305	0.00199601	G|1.000;|0.000	.	weak	.	OR13C5	60	.	NM_001004482	exon1	c.C53T	p.S18F	TGACCAGAAAGTC	.	PASS	Atlas-SNP
FBXL4	26235	hgsc.bcm.edu	37	6	99374400	99374400	+	Silent	SNP	G	G	A	rs1011676	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	54	155	0	0.394161	0	G|0.955;A|0.045	0.045	strong	.	FBXL4	54	.	NM_012160	exon3	c.C465T	p.L155L	ACAAGCGAGAATT	.	PASS	Atlas-SNP
UMOD	7369	hgsc.bcm.edu	37	16	20359633	20359633	+	Silent	SNP	C	C	T	rs28544423	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	28	77	0	0.4	0	C|0.858;T|0.142	0.142	strong	.	UMOD	128	.	NM_003361	exon4	c.G885A	p.G295G	ACACGTCCCCTCC	.	PASS	Atlas-SNP
NLRP10	338322	hgsc.bcm.edu	37	11	7981521	7981521	+	Silent	SNP	C	C	T	rs11608118	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	47	113	0	0.419643	0	C|0.930;T|0.070	0.070	strong	.	NLRP10	146	.	NM_176821	exon2	c.G1638A	p.K546K	AAAATGCTTCAGA	.	PASS	Atlas-SNP
KANK3	256949	hgsc.bcm.edu	37	19	8389405	8389405	+	Silent	SNP	G	G	A	rs12981073	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	68	175	0	0.43871	0	G|0.840;A|0.159	0.159	strong	.	KANK3	35	.	NM_198471	exon10	c.C2310T	p.A770A	CTCCAGGGCGATG	.	PASS	Atlas-SNP
DIS3L2	129563	hgsc.bcm.edu	37	2	233201328	233201328	+	Silent	SNP	A	A	G	rs3811578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	26	49	0	0.382353	0	A|0.797;G|0.203	0.203	strong	.	DIS3L2	77	.	NM_152383	exon21	c.A2646G	p.S882S	GGACTCAAGCACC	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43638457	43638457	+	Silent	SNP	T	T	A	rs1782387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	16	183	0	0.246154	0	T|0.803;A|0.197	0.197	strong	.	WDR65	76	.	NM_152498	exon2	c.T33A	p.V11V	GCATGTTTTTGGT	.	PASS	Atlas-SNP
FNBP4	23360	hgsc.bcm.edu	37	11	47745589	47745589	+	Missense_Mutation	SNP	T	T	C	rs34242224	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	47	58	0	0.559524	0	T|0.943;C|0.057	0.057	strong	.	FNBP4	99	.	NM_015308	exon14	c.A2455G	p.I819V	TAGCTATAGCTGA	.	PASS	Atlas-SNP
PIEZO2	63895	hgsc.bcm.edu	37	18	10681711	10681711	+	Missense_Mutation	SNP	C	C	T	rs3748428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	66	137	0	0.578947	0	C|0.882;T|0.118	0.118	strong	.	.	.	.	NM_022068	exon47	c.G7387A	p.V2463I	CCATAACTTTCAA	.	PASS	Atlas-SNP
GPR97	222487	hgsc.bcm.edu	37	16	57707249	57707249	+	Silent	SNP	C	C	T	rs73552781	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	170	193	1	0.880829	0.00518135	C|0.957;T|0.043	0.043	strong	.	GPR97	74	.	NM_170776	exon2	c.C75T	p.T25T	GCCCACCGAAGGG	.	PASS	Atlas-SNP
PODN	127435	hgsc.bcm.edu	37	1	53535499	53535499	+	Missense_Mutation	SNP	C	C	T	rs17107831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	19	168	0	0.260274	0	C|0.933;T|0.067	0.067	strong	.	PODN	86	.	NM_153703	exon2	c.C116T	p.A39V	CAGGCGCATCTGA	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89498428	89498428	+	Silent	SNP	G	G	A	rs1398197	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	332	151	313	0	0.454819	0	G|0.889;A|0.111	0.111	strong	.	EPHA3	501	.	NM_005233	exon14	c.G2400A	p.K800K	CCGCAAGTTCACG	.	PASS	Atlas-SNP
PLCL2	23228	hgsc.bcm.edu	37	3	17053613	17053613	+	Silent	SNP	C	C	T	rs61751588	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	22	70	0	0.431373	0	C|0.987;T|0.013	0.013	strong	.	PLCL2	145	.	NM_015184	exon2	c.C2397T	p.P799P	CCAGCCCCCTATA	.	PASS	Atlas-SNP
KCNA10	3744	hgsc.bcm.edu	37	1	111060669	111060669	+	Silent	SNP	T	T	C	rs1281175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	83	149	1	1	0.00671141	T|0.326;C|0.674	0.674	strong	.	KCNA10	92	.	NM_005549	exon1	c.A741G	p.L247L	CACCTTTAGCTCC	.	PASS	Atlas-SNP
ABCF2	10061	hgsc.bcm.edu	37	7	150912786	150912786	+	Silent	SNP	T	T	C	rs7786151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	17	144	0	0.151786	0	T|0.901;C|0.099	0.099	strong	.	ABCF2	54	.	NM_007189	exon13	c.A1434G	p.S478S	CAAAGGTGAGAGA	.	PASS	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	37	19	41008049	41008049	+	Silent	SNP	A	A	G	rs814526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	36	76	0	0.590164	0	A|0.581;G|0.419	0.419	strong	.	SPTBN4	213	.	NM_020971	exon9	c.A912G	p.V304V	CCAGGTATTGGAG	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216248820	216248820	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	19	114	0	0.267606	0	.	.	none	.	FN1	521	.	NM_212482	exon30	c.C4817A	p.T1606N	GTGATGGTATAAT	.	PASS	Atlas-SNP
HHLA1	10086	hgsc.bcm.edu	37	8	133092138	133092138	+	Missense_Mutation	SNP	G	G	A	rs2403730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	580	351	471	3	0.605172	0.00636943	G|0.754;A|0.246	0.246	strong	HHLA1,NS,carcinoma,0,1	HHLA1	35	1	NM_001145095	exon10	c.C752T	p.P251L	TGTCCGGGGCTTG	.	scavenged	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17794494	17794494	+	Silent	SNP	G	G	A	rs3734234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	50	102	0	0.446429	0	G|0.609;A|0.391	0.391	strong	.	KIF13A	276	.	NM_001105567	exon25	c.C3208T	p.L1070L	TGTCCAGCCCTCT	.	PASS	Atlas-SNP
CCDC108	255101	hgsc.bcm.edu	37	2	219900068	219900068	+	Missense_Mutation	SNP	C	C	T	rs17852959	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	7	91	0	0.118644	0	C|0.904;T|0.096	0.096	strong	CCDC108_ENST00000295729,NS,carcinoma,0,1	CCDC108	208	1	NM_152389	exon4	c.G481A	p.V161M	ACTGCACGTATTT	.	scavenged	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115710	168115710	+	Missense_Mutation	SNP	T	T	G	rs3749006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	33	101	0	0.358696	0	T|0.808;G|0.192	0.192	strong	XIRP2_ENST00000409728,NS,carcinoma,0,1	XIRP2	914	1	NM_001199143	exon11	c.T2753G	p.V918G	GGCATGTTGAAAC	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55494320	55494320	+	Silent	SNP	G	G	A	rs61735078		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	73	183	0	0.51773	0	G|0.987;A|0.013	0.013	weak	.	NLRP2	161	.	NM_017852	exon6	c.G1254A	p.P418P	GGACCCGGTCCCC	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66660242	66660242	+	Missense_Mutation	SNP	A	A	G	rs71563185		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	57	229	1	0.293814	0.00436681	A|0.500;G|0.500	0.500	weak	TYW1,NS,carcinoma,0,1	TYW1	71	1	NM_018264	exon15	c.A1895G	p.H632R	TTGTCCACGAGTT	.	scavenged	Atlas-SNP
CTDNEP1	23399	hgsc.bcm.edu	37	17	7154582	7154582	+	Missense_Mutation	SNP	T	T	C	rs3744399	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	50	119	1	0.45045	0.00840336	T|0.898;C|0.102	0.102	strong	CTDNEP1,NS,carcinoma,0,2	CTDNEP1	26	2	NM_001143775	exon1	c.A34G	p.T12A	CGAACGTGCGCAG	.	scavenged	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228492044	228492044	+	Silent	SNP	G	G	A	rs1150910	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	40	91	0	0.353982	0	G|0.636;A|0.364	0.364	strong	.	OBSCN	2142	.	NM_001271223	exon53	c.G14043A	p.E4681E	CCAGGAGGCCAGA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389161	1389161	+	Missense_Mutation	SNP	A	A	G	rs71614973	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	30	150	1	0.909091	0.00666667	G|1.000;|0.000	1.000	weak	.	CRIPAK	185	.	NM_175918	exon1	c.A862G	p.S288G	ATGTGGAGTGCCC	.	PASS	Atlas-SNP
U2AF2	11338	hgsc.bcm.edu	37	19	56181019	56181019	+	Silent	SNP	C	C	T	rs147666260	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	81	151	0	0.5	0	C|0.994;T|0.006	0.006	strong	.	U2AF2	62	.	NM_007279	exon11	c.C1254T	p.P418P	GATCCCCCGGCCT	.	PASS	Atlas-SNP
MYO1H	283446	hgsc.bcm.edu	37	12	109848567	109848567	+	Silent	SNP	T	T	C	rs7315991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	25	51	0	0.454545	0	T|0.459;C|0.541	0.541	strong	MYO1H,NS,carcinoma,+1,1	MYO1H	98	1	NM_001101421	exon12	c.T1356C	p.S452S	CATATCTATTCTG	.	PASS	Atlas-SNP
TYR	7299	hgsc.bcm.edu	37	11	88911696	88911696	+	Missense_Mutation	SNP	C	C	A	rs1042602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	124	107	0	0.681319	0	C|0.751;A|0.249	0.249	strong	TYR,NS,carcinoma,0,1	TYR	130	1	NM_000372	exon1	c.C575A	p.S192Y	GGGGATCTGAAAT	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22586192	22586192	+	Silent	SNP	A	A	G	rs71333875	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	56	247	0	0.405797	0	G|1.000;|0.000	1.000	weak	.	ZNF98	230	.	NM_001098626	exon2	c.T153C	p.F51F	ACCCACAAAGACC	.	PASS	Atlas-SNP
CHN2	1124	hgsc.bcm.edu	37	7	29519929	29519929	+	Missense_Mutation	SNP	A	A	G	rs3750103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	375	136	261	0	0.362667	0	A|0.901;G|0.099	0.099	strong	.	CHN2	98	.	NM_004067	exon7	c.A611G	p.H204R	TCACACACAACGA	.	PASS	Atlas-SNP
CLEC4M	10332	hgsc.bcm.edu	37	19	7831628	7831628	+	Missense_Mutation	SNP	G	G	A	rs2277998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	95	191	1	0.542857	0.0052356	G|0.787;A|0.213	0.213	strong	CLEC4M,right_lower_lobe,carcinoma,-2,2	CLEC4M	58	2	NM_014257	exon5	c.G871A	p.D291N	TGGCACGACTCCG	.	PASS	Atlas-SNP
VMO1	284013	hgsc.bcm.edu	37	17	4689313	4689313	+	Missense_Mutation	SNP	G	G	C	rs2279961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	47	123	0	0.47	0	G|0.901;C|0.099	0.099	strong	.	VMO1	19	.	NM_182566	exon2	c.C230G	p.T77S	AGTGCAGTGTCGT	.	PASS	Atlas-SNP
VEGFC	7424	hgsc.bcm.edu	37	4	177713326	177713326	+	Missense_Mutation	SNP	T	T	A	rs55728985	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15	4	25	0	0.266667	0	T|0.996;A|0.004	0.004	strong	VEGFC,NS,carcinoma,-1,1	VEGFC	94	1	NM_005429	exon1	c.A140T	p.E47V	GTGGCCTCGCCCG	.	PASS	Atlas-SNP
SLC22A14	9389	hgsc.bcm.edu	37	3	38355225	38355225	+	Missense_Mutation	SNP	G	G	A	rs73064822	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	11	59	0	0.314286	0	G|0.825;A|0.175	0.175	strong	.	SLC22A14	64	.	NM_004803	exon7	c.G1171A	p.V391I	TTTACCGTCAGTT	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46894377	46894377	+	Missense_Mutation	SNP	A	A	C	rs3959442	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	9	35	0	0.346154	0	T|0.000;G|0.000;C|0.278;A|0.721	0.278	strong	.	TTLL6	113	.	NM_001130918	exon1	c.T58G	p.W20G	TAGTCCAGCTTGC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144997656	144997656	+	Silent	SNP	C	C	T	rs7016416	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	18	38	0	0.818182	0	C|0.718;T|0.282	0.282	strong	PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	NM_201380	exon31	c.G6852A	p.A2284A	CCGCCGCGCCGCC	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43638436	43638436	+	Silent	SNP	G	G	T	rs6695238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	53	175	0	0.768116	0	G|0.920;T|0.080	0.080	strong	.	WDR65	76	.	NM_152498	exon2	c.G12T	p.V4V	AGCCGTGGTAGCT	.	PASS	Atlas-SNP
ZNF277	11179	hgsc.bcm.edu	37	7	111981007	111981007	+	Missense_Mutation	SNP	G	G	A	rs11539696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	138	177	0	0.579832	0	G|0.943;A|0.057	0.057	strong	.	ZNF277	46	.	NM_021994	exon11	c.G1090A	p.V364M	TGCCATGTGAAGT	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242373714	242373714	+	Missense_Mutation	SNP	C	C	T	rs372818608		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	4	121	0	0.0444444	0	.	.	weak	.	FARP2	92	.	NM_014808	exon10	c.C1009T	p.R337W	TTCAGCCGGGGCT	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	93994	93994	+	Missense_Mutation	SNP	A	A	G	rs71634631	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	42	280	0	0.188341	0	A|1.000;|0.000	.	weak	.	TUBB8	62	.	NM_177987	exon4	c.T338C	p.M113T	GACTCCATCAGCT	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103027234	103027234	+	Missense_Mutation	SNP	A	A	G	rs17301750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	117	105	0	0.764706	0	A|0.912;G|0.088	0.088	strong	.	DYNC2H1	246	.	NM_001377	exon26	c.A3862G	p.T1288A	AGTCGAACTATGA	.	PASS	Atlas-SNP
ZNF732	654254	hgsc.bcm.edu	37	4	289877	289877	+	Missense_Mutation	SNP	G	G	T	rs62619793	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	291	138	326	1	0.474227	0.00306748	G|0.958;T|0.042	0.042	strong	.	ZNF732	117	.	NM_001137608	exon1	c.C68A	p.A23D	TGCTGGGCAGGGT	.	PASS	Atlas-SNP
KIAA1217	56243	hgsc.bcm.edu	37	10	24813454	24813454	+	Missense_Mutation	SNP	G	G	A	rs10828663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	33	97	0	0.717391	0	G|0.760;A|0.240	0.240	strong	KIAA1217,colon,carcinoma,0,2	KIAA1217	235	2	NM_019590	exon13	c.G2659A	p.A887T	CGCCACGCGCAGA	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	rs10890850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211	60	152	0	0.28436	0	T|0.967;A|0.033	0.033	strong	.	EXPH5	193	.	NM_015065	exon6	c.A2674T	p.N892Y	AAGAATTCTTTGA	.	PASS	Atlas-SNP
ST8SIA2	8128	hgsc.bcm.edu	37	15	92987938	92987938	+	Silent	SNP	C	C	G	rs2305561	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	17	132	0	0.175258	0	C|0.758;G|0.242	0.242	strong	.	ST8SIA2	41	.	NM_006011	exon5	c.C621G	p.P207P	GAACCCCTCGGTC	.	PASS	Atlas-SNP
ZNF440	126070	hgsc.bcm.edu	37	19	11943713	11943713	+	Silent	SNP	G	G	A	rs56167415	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	20	47	0	0.344828	0	G|0.863;A|0.137	0.137	strong	.	ZNF440	56	.	NM_152357	exon4	c.G1722A	p.R574R	TGTAAGGAATGTG	.	PASS	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98221978	98221978	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	2	180	0	0.0115607	0	.	.	none	PTCH1_ENST00000430669,NS,lymphoid_neoplasm,+2,4	PTCH1	1850	4	NM_000264	exon17	c.C2791A	p.P931T	CGACGGGGTCGTT	.	scavenged	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116346118	116346118	+	Missense_Mutation	SNP	G	G	A	rs41305473	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	41	87	0	0.401961	0	G|0.884;A|0.116	0.116	strong	.	RGS3	251	.	NM_144488	exon21	c.G2426A	p.R809Q	CCACCCGGGACCT	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113312231	113312231	+	Missense_Mutation	SNP	G	G	C	rs61751937	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	95	213	0	0.505319	0	G|0.954;C|0.046	0.046	strong	.	SVEP1	326	.	NM_153366	exon2	c.C685G	p.R229G	GCTCTCGAATGTT	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2836041	2836041	+	Missense_Mutation	SNP	A	A	T	rs67272620	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	37	98	0	0.425287	0	A|0.500;T|0.500	0.500	strong	.	ARSD	47	.	NM_001669	exon5	c.T667A	p.F223I	CAGAGAAGAAACC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228526665	228526665	+	Silent	SNP	T	T	C	rs505629	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	340	127	291	1	0.373529	0.00343643	T|0.479;C|0.521	0.521	strong	.	OBSCN	2142	.	NM_001271223	exon80	c.T20067C	p.A6689A	CATAGCTGTGGCC	.	PASS	Atlas-SNP
GUCY2F	2986	hgsc.bcm.edu	37	X	108708552	108708552	+	Missense_Mutation	SNP	A	A	G	rs12008095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	108	207	1	1	0.00483092	A|0.790;0|0.012	.	strong	.	GUCY2F	178	.	NM_001522	exon3	c.T851C	p.L284P	TAGAGCAGGGCAT	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	37	3	47043622	47043622	+	Silent	SNP	G	G	A	rs2305635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	51	94	0	0.621951	0	G|0.685;A|0.315	0.315	strong	.	NBEAL2	267	.	NM_015175	exon31	c.G4995A	p.V1665V	GCTGGTGCCACTG	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53994083	53994083	+	Silent	SNP	T	T	C	rs150664026	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	5	331	0	0.0192308	0	T|0.999;C|0.001	0.001	strong	ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	NM_001004301	exon4	c.T597C	p.S199S	GAATTCTTCGTTA	.	scavenged	Atlas-SNP
FAM210B	116151	hgsc.bcm.edu	37	20	54941140	54941140	+	Missense_Mutation	SNP	C	C	T	rs6099115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	45	109	0	0.378151	0	C|0.729;T|0.271	0.271	strong	.	.	.	.	NM_080821	exon3	c.C376T	p.P126S	GACATGCCTGCAA	.	PASS	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204199614	204199614	+	Missense_Mutation	SNP	C	C	T	rs10900562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	221	141	0	0.991031	0	C|0.466;T|0.534	0.534	strong	PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	NM_014935	exon18	c.G2510A	p.R837K	TTCTCCCTCATGG	.	PASS	Atlas-SNP
OR5J2	282775	hgsc.bcm.edu	37	11	55944474	55944474	+	Silent	SNP	G	G	A	rs4489763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	443	181	498	1	0.408578	0.00200803	G|0.903;A|0.097	0.097	strong	OR5J2,NS,carcinoma,0,1	OR5J2	98	1	NM_001005492	exon1	c.G381A	p.V127V	CATTGTGAGTCCC	.	PASS	Atlas-SNP
FRMD4A	55691	hgsc.bcm.edu	37	10	13735947	13735947	+	Silent	SNP	A	A	G	rs2296596	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	20	92	0	0.294118	0	A|0.869;G|0.131	0.131	strong	.	FRMD4A	108	.	NM_018027	exon15	c.T1068C	p.G356G	CTTGCTACCCATG	.	PASS	Atlas-SNP
PSMF1	9491	hgsc.bcm.edu	37	20	1115919	1115919	+	Missense_Mutation	SNP	A	A	G	rs2235587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	46	77	0	0.429907	0	A|0.849;G|0.151	0.151	strong	.	PSMF1	27	.	NM_006814	exon4	c.A521G	p.H174R	CTCCACACCACCC	.	PASS	Atlas-SNP
ANKRD20A1	84210	hgsc.bcm.edu	37	9	67938633	67938633	+	Missense_Mutation	SNP	G	G	T	rs200989194	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	257	7	617	3	0.0272374	0.00486224	G|0.990;T|0.010	0.010	strong	ANKRD20A1,bladder,carcinoma,0,3	ANKRD20A1	16	3	NM_032250	exon6	c.G768T	p.K256N	TAAAAAGAAGATA	.	scavenged	Atlas-SNP
ZNF705A	440077	hgsc.bcm.edu	37	12	8329652	8329652	+	Missense_Mutation	SNP	A	A	G	rs10743251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298	105	392	4	0.352349	0.0102041	A|0.527;G|0.473	0.473	strong	ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	NM_001004328	exon5	c.A376G	p.T126A	GATTGCACTCACA	.	scavenged	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380515	186380515	+	Missense_Mutation	SNP	G	G	A	rs11132306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	7	116	0	0.1	0	G|0.562;A|0.438	0.438	strong	.	CCDC110	78	.	NM_152775	exon6	c.C1226T	p.S409F	TTTTCAGATATTA	.	PASS	Atlas-SNP
PCDHA3	56145	hgsc.bcm.edu	37	5	140181734	140181734	+	Missense_Mutation	SNP	A	A	G	rs3733708	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	66	116	0	0.640777	0	G|0.521;N|0.000	0.521	strong	.	PCDHA3	396	.	NM_031497	exon1	c.A952G	p.I318V	TATGAAATCCAGG	.	PASS	Atlas-SNP
MYO5B	4645	hgsc.bcm.edu	37	18	47363963	47363963	+	Missense_Mutation	SNP	T	T	C	rs112417235	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	334	109	354	0	0.326347	0	T|0.979;C|0.021	0.021	strong	.	MYO5B	178	.	NM_001080467	exon37	c.A5062G	p.M1688V	TGATCATGTAGAA	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145323666	145323666	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	4	129	0	0.0227273	0	.	.	none	NBPF10,NS,carcinoma,-1,6	NBPF10	221	6	NM_001039703	exon27	c.A3503G	p.D1168G	AAAAGGACGAAGA	.	scavenged	Atlas-SNP
C20orf111	51526	hgsc.bcm.edu	37	20	42825929	42825929	+	Silent	SNP	C	C	T	rs8268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	150	157	0	0.986842	0	C|0.766;T|0.234	0.234	strong	.	C20orf111	28	.	NM_016470	exon4	c.G642A	p.V214V	GGAATACACTTCC	.	PASS	Atlas-SNP
FAM183A	440585	hgsc.bcm.edu	37	1	43618596	43618596	+	Silent	SNP	G	G	A	rs12074551	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	24	158	0	0.166667	0	G|0.838;A|0.162	0.162	strong	.	FAM183A	28	.	NM_001101376	exon3	c.G291A	p.E97E	CTTAGAGCCCTTG	.	PASS	Atlas-SNP
ALDH5A1	7915	hgsc.bcm.edu	37	6	24503590	24503590	+	Missense_Mutation	SNP	C	C	T	rs2760118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	28	42	0	0.965517	0	C|0.656;T|0.344	0.344	strong	.	ALDH5A1	42	.	NM_001080	exon3	c.C538T	p.H180Y	ATTATCCACACCC	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	123946895	123946895	+	Silent	SNP	G	G	A	rs2293641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	250	118	284	0	0.472	0	G|0.891;A|0.109	0.109	strong	.	KALRN	556	.	NM_003947	exon2	c.G126A	p.K42K	GGAAAAGGTGGCC	.	PASS	Atlas-SNP
INTS10	55174	hgsc.bcm.edu	37	8	19677915	19677915	+	Silent	SNP	G	G	A	rs7822495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	122	160	0	0.616162	0	G|0.763;A|0.237	0.237	strong	.	INTS10	46	.	NM_018142	exon4	c.G327A	p.R109R	TGGTCGGGTCCAG	.	PASS	Atlas-SNP
PARP9	83666	hgsc.bcm.edu	37	3	122259640	122259640	+	Missense_Mutation	SNP	T	T	C	rs28365795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	222	95	278	1	0.427928	0.00359712	T|0.867;C|0.133	0.133	strong	.	PARP9	72	.	NM_031458	exon8	c.A1549G	p.I517V	GATTGATGGCAGG	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	37	1	222802376	222802376	+	Missense_Mutation	SNP	A	A	G	rs2936052	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	76	104	0	0.622951	0	A|0.758;G|0.242	0.242	strong	MIA3,NS,carcinoma,0,2	MIA3	167	2	NM_198551	exon4	c.A1814G	p.K605R	GGGCCAAACTGCA	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465748	10465748	+	Missense_Mutation	SNP	T	T	C	rs11783478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	59	65	0	0.584158	0	T|0.395;C|0.605	0.605	strong	RP1L1,NS,carcinoma,0,1	RP1L1	453	1	NM_178857	exon4	c.A5860G	p.T1954A	GCTGGGTCTGCCC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47821588	47821588	+	Missense_Mutation	SNP	A	A	G	rs6518291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	83	121	0	0.628788	0	A|0.679;G|0.321	0.321	strong	.	PCNT	283	.	NM_006031	exon26	c.A4915G	p.I1639V	CCAGAAATACAGT	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44109474	44109474	+	Missense_Mutation	SNP	G	G	A	rs7220988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	58	118	0	0.47541	0	G|0.694;A|0.306	0.306	strong	.	.	.	.	NM_001193466	exon14	c.C3029T	p.P1010L	TGTCGCGGAGTGT	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93430474	93430474	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	79	117	0	0.344978	0	.	.	none	.	KIAA1731	173	.	NM_033395	exon15	c.C2396G	p.P799R	CTCTGCCTGTTAA	.	PASS	Atlas-SNP
COPB1	1315	hgsc.bcm.edu	37	11	14515829	14515829	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	55	112	0	0.443548	0	.	.	none	.	COPB1	81	.	NM_001144062	exon3	c.A248G	p.E83G	ACAATTTCCCAAA	.	PASS	Atlas-SNP
CH25H	9023	hgsc.bcm.edu	37	10	90966996	90966996	+	Silent	SNP	C	C	G	rs10887932	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	21	118	0	0.2625	0	C|0.834;G|0.166	0.166	strong	.	CH25H	19	.	NM_003956	exon1	c.G54C	p.L18L	CAGGAACAGCTGC	.	PASS	Atlas-SNP
ZNF281	23528	hgsc.bcm.edu	37	1	200378495	200378495	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	26	43	0	0.684211	0	.	.	none	.	ZNF281	74	.	NM_012482	exon2	c.G339A	p.S113S	CCTCTGCGAGGGG	.	PASS	Atlas-SNP
CNNM1	26507	hgsc.bcm.edu	37	10	101122084	101122084	+	Silent	SNP	C	C	T	rs117724968	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	93	252	1	0.704545	0.00396825	C|0.997;T|0.003	0.003	strong	.	CNNM1	101	.	NM_020348	exon4	c.C1959T	p.N653N	GAAGAACAAGAAG	.	PASS	Atlas-SNP
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2920666	2920666	+	Missense_Mutation	SNP	C	C	T	rs365605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	125	124	1	0.968992	0.00806452	C|0.393;T|0.607	0.607	strong	.	SLC22A18AS	7	.	NM_007105	exon3	c.G266A	p.G89D	AAGCCACCTCTCC	.	PASS	Atlas-SNP
UTP18	51096	hgsc.bcm.edu	37	17	49350802	49350802	+	Silent	SNP	A	A	C	rs2318789	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	61	95	0	0.983871	0	A|0.569;C|0.431	0.431	strong	.	UTP18	28	.	NM_016001	exon5	c.A702C	p.G234G	AAGAGGAATCTTG	.	PASS	Atlas-SNP
CSN1S1	1446	hgsc.bcm.edu	37	4	70807771	70807771	+	Missense_Mutation	SNP	C	C	T	rs10030475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	291	290	267	1	0.996564	0.00374532	C|0.659;T|0.341	0.341	strong	.	CSN1S1	20	.	NM_001890	exon13	c.C350T	p.A117V	AAGCTGCCCATGC	.	PASS	Atlas-SNP
GHRL	51738	hgsc.bcm.edu	37	3	10328453	10328453	+	Missense_Mutation	SNP	T	T	A	rs4684677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	54	146	0	0.495413	0	T|0.950;A|0.050	0.050	strong	.	GHRL	8	.	NM_016362	exon4	c.A269T	p.Q90L	TGGTACTGAACCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679390	100679390	+	Missense_Mutation	SNP	A	A	G	rs150982179		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	330	34	189	1	0.10303	0.00529101	.	.	weak	MUC17,NS,carcinoma,-2,1	MUC17	804	1	NM_001040105	exon3	c.A4693G	p.T1565A	ATGCAAACCTCAA	.	scavenged	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88779132	88779132	+	Missense_Mutation	SNP	C	C	T	rs2290895	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	29	208	0	0.13242	0	C|0.860;T|0.140	0.140	strong	.	CTU2	66	.	NM_001012759	exon7	c.C556T	p.H186Y	CAGCAGCATGTGC	.	PASS	Atlas-SNP
KCNK16	83795	hgsc.bcm.edu	37	6	39290200	39290200	+	Silent	SNP	C	C	T	rs3734619	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	37	79	0	0.435294	0	C|0.591;T|0.409	0.409	strong	KCNK16_ENST00000425054,NS,carcinoma,-1,2	KCNK16	59	2	NM_001135106	exon1	c.G117A	p.A39A	AGCCTCCGCCTGC	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790410	4790410	+	Silent	SNP	A	A	G	rs1030724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	98	151	0	0.521277	0	A|0.707;G|0.293	0.293	strong	OR51F1,right_upper_lobe,carcinoma,-2,1	OR51F1	60	1	NM_001004752	exon1	c.T738C	p.H246H	TCCCACATGGGAG	.	PASS	Atlas-SNP
C17orf62	79415	hgsc.bcm.edu	37	17	80404555	80404555	+	Missense_Mutation	SNP	G	G	A	rs72857481	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	31	66	0	0.424658	0	G|0.989;A|0.011	0.011	strong	.	C17orf62	23	.	NM_001193657	exon5	c.C145T	p.L49F	AGAAGAGCTTCCA	.	PASS	Atlas-SNP
TAAR5	9038	hgsc.bcm.edu	37	6	132910634	132910634	+	Silent	SNP	C	C	T	rs3813354	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	57	124	1	0.581633	0.00806452	C|0.845;T|0.155	0.155	strong	TAAR5,NS,carcinoma,-1,1	TAAR5	53	1	NM_003967	exon1	c.G192A	p.A64A	GTGAAGCGCTTTG	.	scavenged	Atlas-SNP
RIMS4	140730	hgsc.bcm.edu	37	20	43386414	43386414	+	Splice_Site	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	26	81	0	0.325	0	.	.	none	.	RIMS4	47	.	NM_001205317	exon5	c.353-2A>T	.	ATCCCCTGGAAGA	.	PASS	Atlas-SNP
TRDN	10345	hgsc.bcm.edu	37	6	123869607	123869607	+	Missense_Mutation	SNP	G	G	C	rs9490809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	101	121	0	1	0	G|0.614;C|0.386	0.386	strong	TRDN,NS,carcinoma,-1,1	TRDN	88	1	NM_001256022	exon3	c.C383G	p.T128S	TTATCAGTATCTT	.	PASS	Atlas-SNP
DGCR6	8214	hgsc.bcm.edu	37	22	18893995	18893995	+	Silent	SNP	C	C	G	rs409155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	14	50	0	0.291667	0	C|0.969;G|0.031	0.031	strong	.	DGCR6	12	.	NM_005675	exon1	c.C108G	p.P36P	GTTGCCCAGGTAC	.	PASS	Atlas-SNP
LARP4B	23185	hgsc.bcm.edu	37	10	909711	909711	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	10	112	0	0.142857	0	.	.	none	.	LARP4B	110	.	NM_015155	exon5	c.T402C	p.Y134Y	AGAGTCATATTCT	.	PASS	Atlas-SNP
USH1C	10083	hgsc.bcm.edu	37	11	17531146	17531146	+	Silent	SNP	G	G	A	rs17776775	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	27	35	0	0.627907	0	A|0.048;G|0.952	0.048	strong	.	USH1C	157	.	NM_153676	exon18	c.C1770T	p.A590A	GGATGAGGCGCTC	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	304670	304670	+	Missense_Mutation	SNP	C	C	T	rs146490788	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	30	67	0	0.517241	0	C|0.999;T|0.001	0.001	strong	.	DOCK8	401	.	NM_203447	exon5	c.C494T	p.S165L	TTGAGTCGGAAAC	.	PASS	Atlas-SNP
GPRIN2	9721	hgsc.bcm.edu	37	10	46999922	46999922	+	Missense_Mutation	SNP	G	G	T	rs4926046	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	26	120	1	0.265306	0.00833333	G|0.634;T|0.366	0.366	strong	GPRIN2,colon,carcinoma,0,1	GPRIN2	94	1	NM_014696	exon3	c.G1042T	p.V348L	AAGGCTGTGGCCA	.	scavenged	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891009	44891009	+	Silent	SNP	C	C	T	rs139913772	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	84	236	0	0.42	0	C|0.999;T|0.001	0.001	strong	ZNF285,NS,carcinoma,0,2	ZNF285	86	2	NM_152354	exon4	c.G1398A	p.A466A	GCTATACGCAAAA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129905896	129905896	+	Missense_Mutation	SNP	T	T	A	rs3740423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252	122	268	1	0.484127	0.00373134	T|0.852;A|0.148	0.148	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.A4208T	p.E1403V	GAGAGCTCCTTCT	.	PASS	Atlas-SNP
AP3B2	8120	hgsc.bcm.edu	37	15	83378366	83378366	+	Silent	SNP	G	G	A	rs200226421	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	12	10	10	0	0.833333	0	.	.	weak	.	AP3B2	103	.	NM_004644	exon1	c.C93T	p.I31I	GGAGAAGATGCCG	.	PASS	Atlas-SNP
PRSS41	360226	hgsc.bcm.edu	37	16	2849372	2849372	+	Missense_Mutation	SNP	C	C	A	rs201777593		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	54	128	0	0.482143	0	.	.	weak	.	.	.	.	NM_001135086	exon3	c.C382A	p.R128S	AGCAGTCGTTACA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682097	100682097	+	Missense_Mutation	SNP	C	C	T	rs138703892	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	8	201	0	0.0325203	0	C|1.000;T|0.000	0.000	strong	MUC17,colon,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.C7400T	p.P2467L	CCACGCCGGTGGT	.	scavenged	Atlas-SNP
BFSP1	631	hgsc.bcm.edu	37	20	17477592	17477592	+	Missense_Mutation	SNP	C	C	T	rs6080719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	29	61	0	0.557692	0	C|0.784;T|0.216	0.216	strong	.	BFSP1	55	.	NM_001195	exon7	c.G1033A	p.G345S	TCCCACCGGATCC	.	PASS	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5068297	5068297	+	Missense_Mutation	SNP	G	G	A	rs58664826	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	379	173	461	1	0.456464	0.0021692	G|0.894;A|0.106	0.106	strong	.	OR52J3	77	.	NM_001001916	exon1	c.G542A	p.C181Y	CCTACTGTGAGCA	.	PASS	Atlas-SNP
C11orf30	56946	hgsc.bcm.edu	37	11	76257215	76257215	+	Silent	SNP	T	T	C	rs3753051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	56	110	1	0.491228	0.00909091	T|0.755;C|0.245	0.245	strong	C11orf30,NS,carcinoma,0,1	C11orf30	123	1	NM_020193	exon20	c.T3648C	p.T1216T	ATCCACTGTTGGC	.	scavenged	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	26	60	0	1	0	G|0.754;C|0.246	0.246	strong	HNF1A,brain,glioma,0,1	HNF1A	302	1	NM_000545	exon4	c.G864C	p.G288G	CAGCGGGCCCCCC	.	PASS	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	37	2	15378808	15378808	+	Silent	SNP	C	C	G	rs34080125	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	49	94	0	0.532609	0	C|0.967;G|0.033	0.033	strong	.	NBAS	246	.	NM_015909	exon45	c.G5727C	p.L1909L	CACAGACAGCTTA	.	PASS	Atlas-SNP
PI4KA	5297	hgsc.bcm.edu	37	22	21066789	21066789	+	Silent	SNP	A	A	G	rs5996654	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	359	138	412	3	0.384401	0.00728155	A|0.618;G|0.382	0.382	strong	PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	NM_058004	exon50	c.T5787C	p.T1929T	GGCCAGAGTGGAC	.	scavenged	Atlas-SNP
DCST1	149095	hgsc.bcm.edu	37	1	155019698	155019698	+	Missense_Mutation	SNP	G	G	A	rs200041699	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	144	184	0	0.56917	0	G|0.999;A|0.001	0.001	weak	.	DCST1	69	.	NM_152494	exon14	c.G1522A	p.G508R	AAGGTCGGGGGAG	.	PASS	Atlas-SNP
CA10	56934	hgsc.bcm.edu	37	17	49713300	49713300	+	Silent	SNP	G	G	A	rs11870209	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	125	152	0	1	0	G|0.606;A|0.394	0.394	strong	CA10,NS,carcinoma,0,2	CA10	84	2	NM_001082534	exon8	c.C705T	p.Y235Y	CCCATCGTAAGTG	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61528044	61528044	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	53	91	0	0.486239	0	.	.	none	.	DIDO1	321	.	NM_080797	exon7	c.C1893T	p.S631S	AGCAGCGGAGCCA	.	PASS	Atlas-SNP
SLC8A3	6547	hgsc.bcm.edu	37	14	70634801	70634801	+	Silent	SNP	T	T	C	rs17765575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	354	130	281	0	0.367232	0	T|0.893;C|0.107	0.107	strong	.	SLC8A3	234	.	NM_183002	exon2	c.A339G	p.T113T	CTTAATTGTCACC	.	PASS	Atlas-SNP
RBM17	84991	hgsc.bcm.edu	37	10	6139078	6139078	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	5	174	0	0.0423729	0	.	.	none	.	RBM17	45	.	NM_001145547	exon2	c.A50G	p.E17G	AAACAGAAGGCTG	.	PASS	Atlas-SNP
ZNF146	7705	hgsc.bcm.edu	37	19	36727365	36727365	+	Missense_Mutation	SNP	G	G	A	rs2070132	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	56	102	0	0.565657	0	G|0.622;A|0.378	0.378	strong	.	ZNF146	32	.	NM_001099638	exon3	c.G23A	p.R8K	AGCAGAGAATTTA	.	PASS	Atlas-SNP
ZSCAN25	221785	hgsc.bcm.edu	37	7	99217424	99217424	+	Silent	SNP	G	G	A	rs10282706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	43	111	0	0.352459	0	G|0.735;A|0.265	0.265	strong	.	.	.	.	NM_145115	exon4	c.G195A	p.E65E	CCAGGAGCTCTGT	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169127097	169127097	+	Silent	SNP	C	C	A	rs2112703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	86	164	0	0.569536	0	C|0.852;A|0.148	0.148	strong	.	DOCK2	389	.	NM_004946	exon13	c.C1212A	p.T404T	CAGGACCACCGTG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017575	1017575	+	Silent	SNP	C	C	T	rs76222533	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	678	57	906	88	0.0840708	0.0971302	C|0.500;T|0.500	0.500	strong	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G5226A	p.T1742T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
ZNF33B	7582	hgsc.bcm.edu	37	10	43089370	43089370	+	Missense_Mutation	SNP	T	T	A	rs71505625	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	23	215	0	0.174242	0	T|0.998;A|0.002	0.002	strong	.	ZNF33B	78	.	NM_006955	exon5	c.A1028T	p.H343L	GTGAGATGTGACT	.	PASS	Atlas-SNP
HTRA1	5654	hgsc.bcm.edu	37	10	124249118	124249118	+	Silent	SNP	C	C	T	rs17624021	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	55	113	0	0.533981	0	C|0.966;T|0.034	0.034	strong	.	HTRA1	40	.	NM_002775	exon3	c.C753T	p.I251I	AGACATCGCACTC	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113345147	113345147	+	Missense_Mutation	SNP	A	A	G	rs6533616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	12	100	0	0.230769	0	A|0.920;G|0.080	0.080	strong	.	ALPK1	125	.	NM_001102406	exon6	c.A523G	p.N175D	AGCAACAATGGAG	.	PASS	Atlas-SNP
HKDC1	80201	hgsc.bcm.edu	37	10	71010375	71010375	+	Silent	SNP	C	C	T	rs5030948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	24	55	1	0.648649	0.0181818	C|0.835;T|0.165	0.165	strong	HKDC1,NS,carcinoma,+1,1	HKDC1	98	1	NM_025130	exon12	c.C1803T	p.F601F	CACATTCTCATTT	.	scavenged	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788188	3788188	+	Silent	SNP	C	C	T	rs3803135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	77	181	0	0.475309	0	C|0.862;T|0.138	0.138	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.G417A	p.K139K	ATACACCTTCTCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678481	100678481	+	Missense_Mutation	SNP	A	A	T	rs73168389	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	300	89	143	0	0.296667	0	A|0.973;T|0.027	0.027	strong	.	MUC17	804	.	NM_001040105	exon3	c.A3784T	p.T1262S	CCTACAACCGCTG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78263486	78263486	+	Missense_Mutation	SNP	T	T	C	rs17853989	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	48	120	0	0.489796	0	T|0.759;C|0.241	0.241	strong	RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	NM_001256071	exon6	c.T962C	p.M321T	ACGAGATGGCTGC	.	PASS	Atlas-SNP
COL10A1	1300	hgsc.bcm.edu	37	6	116446576	116446576	+	Missense_Mutation	SNP	A	A	G	rs1064583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	243	258	1	0.995902	0.00387597	A|0.536;G|0.464	0.464	strong	.	COL10A1	51	.	NM_000493	exon2	c.T80C	p.M27T	GTGGGCATTTGGT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281007	152281007	+	Missense_Mutation	SNP	A	A	G	rs7512553	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	750	204	383	2	0.272	0.00522193	A|0.030;G|0.970	0.970	strong	FLG,brain,glioma,+2,1	FLG	900	1	NM_002016	exon3	c.T6355C	p.Y2119H	GATCATAATGGGA	.	scavenged	Atlas-SNP
CCL23	6368	hgsc.bcm.edu	37	17	34340284	34340284	+	Missense_Mutation	SNP	C	C	T	rs1003645	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	140	125	0	1	0	C|0.421;T|0.579	0.579	strong	.	CCL23	17	.	NM_005064	exon4	c.G367A	p.V123M	TTCTCACGCAAAC	.	PASS	Atlas-SNP
QRSL1	55278	hgsc.bcm.edu	37	6	107113715	107113715	+	Silent	SNP	G	G	A	rs2015205	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	177	164	1	0.983333	0.00609756	G|0.595;A|0.405	0.405	strong	.	QRSL1	30	.	NM_018292	exon11	c.G1425A	p.L475L	AGGACTGCAGTTT	.	PASS	Atlas-SNP
FCHO2	115548	hgsc.bcm.edu	37	5	72348272	72348272	+	Missense_Mutation	SNP	A	A	G	rs185435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	213	282	0	0.995327	0	A|0.768;G|0.232	0.232	strong	.	FCHO2	96	.	NM_138782	exon13	c.A1111G	p.M371V	CACACAATGGCTT	.	PASS	Atlas-SNP
MROH7	374977	hgsc.bcm.edu	37	1	55166842	55166842	+	Silent	SNP	C	C	T	rs1065173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	26	152	0	0.285714	0	C|0.744;T|0.256	0.256	strong	HEATR8_ENST00000421030,NS,carcinoma,0,2	.	.	2	NM_001039464	exon19	c.C3132T	p.P1044P	CCTGCCCTCCATG	.	PASS	Atlas-SNP
AP1B1	162	hgsc.bcm.edu	37	22	29755888	29755888	+	Silent	SNP	T	T	C	rs2072051	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	142	158	0	0.993007	0	T|0.337;C|0.663	0.663	strong	.	AP1B1	72	.	NM_001127	exon4	c.A204G	p.L68L	GTATACTAGCTTC	.	PASS	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	37	2	211456639	211456639	+	Silent	SNP	C	C	T	rs2229589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	21	105	0	0.3	0	C|0.408;T|0.592	0.592	strong	.	CPS1	485	.	NM_001122633	exon11	c.C1050T	p.T350T	CAACACCCTCCCT	.	PASS	Atlas-SNP
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071060	6071060	+	Silent	SNP	G	G	A	rs4724769	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	132	162	0	0.66	0	G|0.600;A|0.400	0.400	strong	.	.	.	.	NM_001271700	exon1	c.G54A	p.K18K	TGCCAAGTCCCTG	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215901492	215901492	+	Silent	SNP	C	C	T	rs2820718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	269	182	194	0	0.67658	0	C|0.836;T|0.164	0.164	strong	.	USH2A	1168	.	NM_206933	exon61	c.G11946A	p.L3982L	ATTCAACAGAACT	.	PASS	Atlas-SNP
STXBP2	6813	hgsc.bcm.edu	37	19	7712050	7712050	+	Silent	SNP	C	C	T	rs146425381	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	15	57	0	0.3	0	C|0.999;T|0.001	0.001	strong	.	STXBP2	63	.	NM_001272034	exon17	c.C1488T	p.D496D	CCAGGACGCCGTG	.	PASS	Atlas-SNP
LRIG3	121227	hgsc.bcm.edu	37	12	59313248	59313248	+	Silent	SNP	G	G	A	rs12426969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	39	103	0	0.433333	0	G|0.903;A|0.097	0.097	strong	.	LRIG3	120	.	NM_001136051	exon1	c.C16T	p.L6L	ACAACAGAAGTAC	.	PASS	Atlas-SNP
SLITRK3	22865	hgsc.bcm.edu	37	3	164906800	164906800	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	15	111	0	0.172414	0	.	.	none	.	SLITRK3	263	.	NM_014926	exon2	c.C1819A	p.L607M	CTTCCAGCTCAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515305	195515305	+	Missense_Mutation	SNP	G	G	A	rs13077555	by2hit2allele;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	10	177	1	0.0581395	0.00564972	G|0.750;T|0.250	.	alt	MUC4_ENST00000463781,NS,carcinoma,+1,2	MUC4	1505	2	NM_018406	exon2	c.C3146T	p.A1049V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
RSPH6A	81492	hgsc.bcm.edu	37	19	46318312	46318312	+	Silent	SNP	C	C	T	rs45598433	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	42	91	0	0.531646	0	C|0.987;T|0.013	0.013	strong	.	RSPH6A	70	.	NM_030785	exon1	c.G123A	p.E41E	CCTCTCCTCGGGG	.	PASS	Atlas-SNP
KLHL17	339451	hgsc.bcm.edu	37	1	899824	899824	+	Silent	SNP	C	C	T	rs201807567	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	38	88	0	0.791667	0	C|0.996;T|0.004	0.004	strong	.	KLHL17	31	.	NM_198317	exon11	c.C1614T	p.N538N	GGGCAACGACGGC	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107040572	107040572	+	Missense_Mutation	SNP	T	T	C	rs3870235		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	151	1233	2	0.932099	0.00162206	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,4	RGPD3	316	4	NM_001144013	exon20	c.A3851G	p.H1284R	TCAAAGTGGAAAA	.	scavenged	Atlas-SNP
ME3	10873	hgsc.bcm.edu	37	11	86153911	86153911	+	Silent	SNP	G	G	A	rs7548	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	113	67	1	0.991228	0.0149254	G|0.594;T|0.036	.	strong	ME3,NS,carcinoma,0,1	ME3	70	1	NM_006680	exon14	c.C1605T	p.Y535Y	TGGTGGGTAGAGT	.	scavenged	Atlas-SNP
TK1	7083	hgsc.bcm.edu	37	17	76178748	76178748	+	Silent	SNP	T	T	C	rs1143697	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	21	37	0	0.6	0	T|0.400;G|0.007	.	strong	TK1_ENST00000301634,NS,carcinoma,0,1	TK1	23	1	NM_003258	exon4	c.A225G	p.A75A	GGGCAGTGCCTCC	.	PASS	Atlas-SNP
EP300	2033	hgsc.bcm.edu	37	22	41546158	41546158	+	Missense_Mutation	SNP	C	C	A	rs148884710	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	33	59	0	0.568965	0	C|0.995;A|0.005	0.005	strong	EP300,NS,lymphoid_neoplasm,0,1	EP300	367	1	NM_001429	exon14	c.C2773A	p.P925T	TCTGTTCCTACCC	.	PASS	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	37	5	140262492	140262492	+	Silent	SNP	A	A	T	rs11744560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	46	100	0	0.511111	0	A|0.877;T|0.123	0.123	strong	.	PCDHA13	213	.	NM_031865	exon1	c.A639T	p.T213T	ACTGACAGCCAGT	.	PASS	Atlas-SNP
MEP1B	4225	hgsc.bcm.edu	37	18	29788107	29788107	+	Silent	SNP	G	G	A	rs4799640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	222	89	274	0	0.400901	0	G|0.778;A|0.222	0.222	strong	.	MEP1B	54	.	NM_005925	exon9	c.G792A	p.S264S	GGACTCGTGCAGT	.	PASS	Atlas-SNP
SLAIN1	122060	hgsc.bcm.edu	37	13	78320801	78320801	+	Missense_Mutation	SNP	C	C	G	rs144139933	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	95	181	0	0.524862	0	C|0.999;G|0.001	0.001	strong	.	SLAIN1	43	.	NM_001242868	exon4	c.C1069G	p.P357A	CCACCACCTCAGC	.	PASS	Atlas-SNP
ATRNL1	26033	hgsc.bcm.edu	37	10	117486763	117486763	+	Silent	SNP	G	G	T	rs2254619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	13	41	0	0.382353	0	G|0.735;T|0.265	0.265	strong	.	ATRNL1	219	.	NM_207303	exon27	c.G3801T	p.L1267L	GCAACTGCTTCGA	.	PASS	Atlas-SNP
PYCRL	65263	hgsc.bcm.edu	37	8	144689146	144689146	+	Missense_Mutation	SNP	C	C	T	rs2242089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	72	208	0	0.284585	0	C|0.785;T|0.215	0.215	strong	PYCRL,NS,carcinoma,0,1	PYCRL	14	1	NM_023078	exon3	c.G349A	p.V117M	GAGACACCCCAGC	.	PASS	Atlas-SNP
REXO4	57109	hgsc.bcm.edu	37	9	136277482	136277482	+	Missense_Mutation	SNP	T	T	C	rs2285487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	58	138	0	0.537037	0	T|0.944;C|0.056	0.056	strong	.	REXO4	27	.	NM_020385	exon4	c.A847G	p.T283A	GCTCAGTTGGTTT	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90368380	90368380	+	Silent	SNP	G	G	A	rs34732313	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	96	261	0	0.450704	0	G|0.886;A|0.114	0.114	strong	.	MDN1	478	.	NM_014611	exon89	c.C14970T	p.A4990A	TTCATCGGCTTCC	.	PASS	Atlas-SNP
PLB1	151056	hgsc.bcm.edu	37	2	28761981	28761981	+	Missense_Mutation	SNP	G	G	C	rs6753929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	106	210	0	0.517073	0	A|0.000;C|0.213;G|0.787	0.213	strong	.	PLB1	255	.	NM_001170585	exon11	c.G667C	p.V223L	GCATTTGTAAACC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9066580	9066580	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	4	219	1	0.0203046	0.00456621	.	.	none	MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	NM_024690	exon3	c.A20866G	p.T6956A	TGCTGGTCTCTCT	.	scavenged	Atlas-SNP
AMPH	273	hgsc.bcm.edu	37	7	38431415	38431415	+	Silent	SNP	C	C	T	rs55969455	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	101	122	0	0.647436	0	C|0.987;T|0.013	0.013	strong	.	AMPH	157	.	NM_001635	exon19	c.G1812A	p.G604G	AGCAGCCCCCATG	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43664218	43664218	+	Silent	SNP	C	C	T	rs603123	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	83	151	0	0.976471	0	C|0.742;T|0.258	0.258	strong	.	WDR65	76	.	NM_152498	exon8	c.C1329T	p.H443H	TGGACACTTCATT	.	PASS	Atlas-SNP
PGM2L1	283209	hgsc.bcm.edu	37	11	74109166	74109166	+	Missense_Mutation	SNP	A	A	G	rs12049823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	50	87	0	0.47619	0	A|0.843;G|0.157	0.157	strong	PGM2L1,NS,carcinoma,0,1	PGM2L1	59	1	NM_173582	exon1	c.T41C	p.L14P	GCGTGGAGCAGGT	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17612518	17612518	+	Missense_Mutation	SNP	A	A	G	rs61733696	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	61	115	0	0.685393	0	A|0.971;G|0.029	0.029	strong	.	MTUS1	144	.	NM_001001924	exon2	c.T799C	p.S267P	CTGAAGAACATGC	.	PASS	Atlas-SNP
MST1R	4486	hgsc.bcm.edu	37	3	49928866	49928866	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	4	218	0	0.0196078	0	.	.	none	MST1R_ENST00000296474,NS,neuroblastoma,-1,2	MST1R	205	2	NM_002447	exon16	c.G3500A	p.G1167D	AGGTCACCGTGGC	.	scavenged	Atlas-SNP
OR10X1	128367	hgsc.bcm.edu	37	1	158549420	158549420	+	Silent	SNP	C	C	T	rs863361	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	257	154	154	2	0.599222	0.012987	C|0.471;T|0.529	0.529	strong	OR10X1,face,carcinoma,-2,1	OR10X1	96	1	NM_001004477	exon1	c.G270A	p.T90T	GGTCAGCGTATAG	.	scavenged	Atlas-SNP
CD300A	11314	hgsc.bcm.edu	37	17	72469958	72469958	+	Silent	SNP	A	A	G	rs1127737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	107	279	1	0.406844	0.00358423	A|0.418;G|0.582	0.582	strong	.	CD300A	40	.	NM_007261	exon2	c.A324G	p.P108P	TACACCATGGCTC	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126241565	126241565	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	54	154	0	0.580645	0	.	.	none	FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	2	NM_024582	exon1	c.C3999T	p.L1333L	TGAACTCGTGTCC	.	PASS	Atlas-SNP
PLAUR	5329	hgsc.bcm.edu	37	19	44153100	44153100	+	Missense_Mutation	SNP	A	A	G	rs4760	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	68	173	0	0.459459	0	A|0.908;G|0.092	0.092	strong	.	PLAUR	71	.	NM_002659	exon7	c.T950C	p.L317P	ATGGTGAGGCTGA	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8229140	8229140	+	Missense_Mutation	SNP	G	G	T	rs141562329	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	40	97	0	0.430108	0	G|0.999;T|0.001	0.001	strong	.	SH3TC1	105	.	NM_018986	exon12	c.G1719T	p.R573S	CAGGAGGCTCAAG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912348	29912348	+	Missense_Mutation	SNP	A	A	G	rs1137078	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	108	334	1	0.448133	0.00299401	A|0.761;G|0.239	0.239	strong	.	HLA-A	89	.	NM_001242758	exon5	c.A967G	p.T323A	GTGATCACTGGAG	.	PASS	Atlas-SNP
COPE	11316	hgsc.bcm.edu	37	19	19023853	19023853	+	Silent	SNP	T	T	C	rs3177137	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	42	65	0	0.56	0	T|0.586;C|0.414	0.414	strong	COPE,NS,adenoma,0,1	COPE	26	1	NM_007263	exon2	c.A129G	p.L43L	GCTTGATAGCTGT	.	PASS	Atlas-SNP
NDUFA2	4695	hgsc.bcm.edu	37	5	140026868	140026868	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	3	150	0	0.02	0	.	.	none	NDUFA2,colon,carcinoma,+2,1	NDUFA2	13	1	NM_001185012	exon2	c.G181A	p.V61M	GCTGCACATCGGA	.	scavenged	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	101094554	101094554	+	Silent	SNP	A	A	G	rs239239	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	72	218	0	0.361809	0	A|0.438;G|0.562	0.562	strong	.	ASCC3	205	.	NM_006828	exon22	c.T3570C	p.P1190P	TGTGATAGGCTGA	.	PASS	Atlas-SNP
PARP15	165631	hgsc.bcm.edu	37	3	122296638	122296638	+	Missense_Mutation	SNP	G	G	A	rs1875272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	60	154	1	0.566038	0.00649351	G|0.744;A|0.256	0.256	strong	PARP15_ENST00000464300,NS,carcinoma,0,1	PARP15	115	1	NM_001113523	exon1	c.G124A	p.V42M	GGGAGCGTGCTGC	.	scavenged	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3806147	3806147	+	Missense_Mutation	SNP	T	T	C	rs9788233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	20	49	1	0.588235	0.0204082	T|0.870;C|0.130	0.130	strong	EFCAB4B_ENST00000444507,NS,carcinoma,+2,8	EFCAB4B	100	8	NM_001144958	exon4	c.A19G	p.R7G	CTACCCTCCCGTC	.	scavenged	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1005531	1005531	+	Silent	SNP	G	G	C	rs12973948	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	43	104	0	0.452632	0	C|0.264;G|0.736;T|0.000	0.264	strong	.	GRIN3B	46	.	NM_138690	exon3	c.G2031C	p.L677L	GGAGCTGTCGGGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	rs147173571		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	753	89	206	0	0.118194	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.T3335C	p.L1112P	CCAGGCTGGTGGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678442	100678442	+	Missense_Mutation	SNP	C	C	G	rs4729653	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	258	67	141	0	0.25969	0	C|0.918;G|0.082	0.082	strong	.	MUC17	804	.	NM_001040105	exon3	c.C3745G	p.P1249A	AGCACACCTGTGA	.	PASS	Atlas-SNP
UGT2B4	7363	hgsc.bcm.edu	37	4	70346565	70346565	+	Missense_Mutation	SNP	A	A	T	rs13119049	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	83	194	0	0.494048	0	A|0.853;T|0.147	0.147	strong	.	UGT2B4	105	.	NM_021139	exon6	c.T1374A	p.D458E	TGCTCGATCAAGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149518961	149518961	+	Silent	SNP	T	T	C	rs1008335	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	40	238	0	0.229885	0	T|0.554;C|0.446	0.446	strong	.	.	.	.	NM_198455	exon90	c.T12765C	p.A4255A	TGAGGCTTGGACG	.	PASS	Atlas-SNP
LGR4	55366	hgsc.bcm.edu	37	11	27406844	27406844	+	Silent	SNP	G	G	A	rs6484295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	43	119	0	0.494253	0	G|0.665;A|0.335	0.335	strong	.	LGR4	87	.	NM_018490	exon5	c.C573T	p.S191S	AGGGATGCTTGAG	.	PASS	Atlas-SNP
LAMC1	3915	hgsc.bcm.edu	37	1	183091040	183091040	+	Missense_Mutation	SNP	G	G	A	rs147401305	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	88	103	1	0.60274	0.00970874	G|0.999;A|0.001	0.001	strong	LAMC1,NS,carcinoma,0,1	LAMC1	176	1	NM_002293	exon12	c.G2173A	p.A725T	CTTTGCGCCTGCA	.	scavenged	Atlas-SNP
FAM200B	285550	hgsc.bcm.edu	37	4	15689928	15689928	+	Missense_Mutation	SNP	G	G	A	rs4235380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	97	185	0	0.527174	0	G|0.679;A|0.321	0.321	strong	.	FAM200B	56	.	NM_001145191	exon2	c.G1328A	p.S443N	AACTGAGTTTAAA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092973	1092973	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	5	70	0	0.078125	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	NM_002457	exon30	c.C4792T	p.P1598S	CCAACACCCACCG	.	scavenged	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39764176	39764176	+	Missense_Mutation	SNP	G	G	C	rs17855896	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	335	198	249	0	0.591045	0	G|0.960;C|0.040	0.040	strong	.	CTAGE5	75	.	NM_001247989	exon8	c.G630C	p.K210N	ACTGAAGATAGCA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62212781	62212781	+	Silent	SNP	T	T	C	rs17238189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	33	310	0	0.197605	0	T|0.930;C|0.070	0.070	strong	.	VPS13C	506	.	NM_020821	exon56	c.A7128G	p.Q2376Q	TGCCATTTGTGGC	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24424367	24424367	+	Silent	SNP	G	G	A	rs12147221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	398	270	293	0	0.678392	0	G|0.796;A|0.204	0.204	strong	.	DHRS4	22	.	NM_021004	exon2	c.G252A	p.T84T	CGTGACGGGCACC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678610	100678610	+	Missense_Mutation	SNP	A	A	T	rs78010183	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	85	150	0	0.35124	0	A|0.943;T|0.057	0.057	strong	.	MUC17	804	.	NM_001040105	exon3	c.A3913T	p.T1305S	GTTGACACTAAAG	.	PASS	Atlas-SNP
C9orf40	55071	hgsc.bcm.edu	37	9	77563087	77563087	+	Silent	SNP	C	C	T	rs2769058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	61	170	0	0.491935	0	C|0.688;T|0.312	0.312	strong	C9orf40,NS,carcinoma,0,1	C9orf40	5	1	NM_017998	exon2	c.G462A	p.Q154Q	CCAGTACTGGAAG	.	PASS	Atlas-SNP
SUCLG2	8801	hgsc.bcm.edu	37	3	67579535	67579535	+	Missense_Mutation	SNP	T	T	C	rs74675534	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	57	129	0	0.558824	0	T|0.993;C|0.007	0.007	strong	.	SUCLG2	95	.	NM_001177599	exon3	c.A302G	p.K101R	CCTCCTTTCAAAC	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324547	31324547	+	Missense_Mutation	SNP	G	G	C	rs1065386	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	57	145	2	0.354037	0.0137931	G|0.668;C|0.332	0.332	strong	HLA-B,NS,lymphoid_neoplasm,-2,2	HLA-B	54	2	NM_005514	exon2	c.C261G	p.N87K	CTGTGTGTTCCGG	.	scavenged	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380295	186380295	+	Silent	SNP	A	A	G	rs36007437	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	15	104	0	0.205479	0	A|0.623;G|0.377	0.377	strong	.	CCDC110	78	.	NM_152775	exon6	c.T1446C	p.N482N	AACCAGATTCTTA	.	PASS	Atlas-SNP
UNC45B	146862	hgsc.bcm.edu	37	17	33513337	33513337	+	Missense_Mutation	SNP	T	T	A	rs11654824	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	69	97	0	0.507353	0	T|0.948;A|0.052	0.052	strong	.	UNC45B	133	.	NM_173167	exon20	c.T2555A	p.I852N	TGGAGATCCTCCA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114282496	114282496	+	Missense_Mutation	SNP	C	C	T	rs2075387	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	33	55	0	0.673469	0	C|0.781;T|0.219	0.219	strong	.	RBM19	117	.	NM_001146699	exon23	c.G2762A	p.R921Q	GTCTTCCGCCGCA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4513549	4513549	+	Silent	SNP	G	G	A	rs146566557	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	47	80	0	0.52809	0	G|0.998;A|0.002	0.002	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C381T	p.S127S	GACCCCGCTGGAC	.	PASS	Atlas-SNP
METTL25	84190	hgsc.bcm.edu	37	12	82792792	82792792	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	11	48	0	0.354839	0	.	.	none	.	.	.	.	NM_032230	exon4	c.T750G	p.N250K	GCAAAATAAAGTT	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168711107	168711107	+	Silent	SNP	G	G	A	rs111574499	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	136	233	4	0.513208	0.0171674	G|0.968;A|0.032	0.032	strong	DACT2_ENST00000366795,NS,carcinoma,0,1	DACT2	46	1	NM_214462	exon3	c.C399T	p.D133D	TCCACCGTCGCTC	.	scavenged	Atlas-SNP
TEDDM1	127670	hgsc.bcm.edu	37	1	182369078	182369078	+	Silent	SNP	G	G	A	rs6698722	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	357	227	236	1	0.635854	0.00423729	G|0.154;A|0.846	0.846	strong	.	TEDDM1	32	.	NM_172000	exon1	c.C543T	p.P181P	AGAGACGGGTCTG	.	PASS	Atlas-SNP
KIAA1024	23251	hgsc.bcm.edu	37	15	79748603	79748603	+	Silent	SNP	C	C	T	rs7183867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	22	186	0	0.226804	0	C|0.813;T|0.187	0.187	strong	.	KIAA1024	146	.	NM_015206	exon2	c.C114T	p.F38F	CCGGTTCGACCTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680120	100680120	+	Missense_Mutation	SNP	C	C	A	rs147991653	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	338	49	202	1	0.14497	0.00495049	C|0.975;A|0.025	0.025	strong	MUC17,extremity,malignant_melanoma,0,2	MUC17	804	2	NM_001040105	exon3	c.C5423A	p.T1808N	GAATGACTCCATT	.	scavenged	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	37	3	47036756	47036756	+	Missense_Mutation	SNP	C	C	G	rs11720139	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	32	97	0	0.52459	0	C|0.687;G|0.313	0.313	strong	NBEAL2_ENST00000450053,NS,carcinoma,0,4	NBEAL2	267	4	NM_015175	exon13	c.C1531G	p.R511G	GAGGCCCGCTGCC	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43826204	43826204	+	Missense_Mutation	SNP	C	C	T	rs7297737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	70	191	1	0.419162	0.0052356	C|0.968;T|0.032	0.032	strong	ADAMTS20_ENST00000389420,colon,carcinoma,-1,1	ADAMTS20	635	1	NM_025003	exon21	c.G2999A	p.R1000H	GCAAGACGATGGC	.	scavenged	Atlas-SNP
REXO1	57455	hgsc.bcm.edu	37	19	1819125	1819125	+	Missense_Mutation	SNP	T	T	C	rs2396359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	78	174	0	0.464286	0	T|0.668;C|0.332	0.332	strong	REXO1,NS,carcinoma,0,1	REXO1	55	1	NM_020695	exon8	c.A2656G	p.S886G	GGCCACTGGTTTC	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28934408	28934408	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217	3	223	0	0.0138249	0	.	.	none	DSG1,NS,carcinoma,-1,1	DSG1	176	1	NM_001942	exon15	c.C2249T	p.T750I	TGGATACCCTGGG	.	scavenged	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11651057	11651057	+	Missense_Mutation	SNP	A	A	G	rs3744581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	42	109	1	0.428571	0.00917431	A|0.779;G|0.221	0.221	strong	DNAH9,colon,carcinoma,0,1	DNAH9	695	1	NM_001372	exon32	c.A6584G	p.N2195S	TCATCAATCCAGC	.	scavenged	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43504228	43504228	+	Silent	SNP	T	T	C	rs7278485	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	170	134	1	0.982659	0.00746269	T|0.347;C|0.653	0.653	strong	UMODL1_ENST00000408989,NS,carcinoma,+1,4	UMODL1	186	4	NM_173568	exon3	c.T354C	p.P118P	AAGACCTGGGGCC	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880818	39880818	+	Silent	SNP	C	C	T	rs41338344	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	15	80	0	0.277778	0	C|0.975;T|0.025	0.025	strong	.	THBS1	106	.	NM_003246	exon10	c.C1563T	p.N521N	CAACAACCCCACA	.	PASS	Atlas-SNP
GLIS2	84662	hgsc.bcm.edu	37	16	4382351	4382351	+	Silent	SNP	C	C	A	rs34543395	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	47	116	0	0.435185	0	C|0.993;A|0.007	0.007	strong	.	GLIS2	29	.	NM_032575	exon1	c.C70A	p.R24R	GAGAAGCGGGAGA	.	PASS	Atlas-SNP
ZSWIM1	90204	hgsc.bcm.edu	37	20	44511627	44511627	+	Silent	SNP	C	C	T	rs11086984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	124	247	0	0.5	0	C|0.930;T|0.070	0.070	strong	.	ZSWIM1	35	.	NM_080603	exon2	c.C396T	p.F132F	AGTATTCAAGAAG	.	PASS	Atlas-SNP
PDZRN4	29951	hgsc.bcm.edu	37	12	41967677	41967677	+	Silent	SNP	G	G	A	rs3747556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	54	128	0	0.509434	0	G|0.870;A|0.130	0.130	strong	.	PDZRN4	346	.	NM_001164595	exon10	c.G3096A	p.S1032S	CTTGTCGGTGACC	.	PASS	Atlas-SNP
KIF18B	146909	hgsc.bcm.edu	37	17	43004436	43004436	+	Missense_Mutation	SNP	G	G	A	rs61739617	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	41	97	0	0.44086	0	G|0.965;A|0.035	0.035	strong	.	KIF18B	63	.	NM_001264573	exon14	c.C2323T	p.P775S	ACAGGGGCACAGG	.	PASS	Atlas-SNP
C6orf170	221322	hgsc.bcm.edu	37	6	121401996	121401996	+	Missense_Mutation	SNP	T	T	G	rs56300302	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	113	164	0	0.582474	0	T|0.984;G|0.016	0.016	strong	C6orf170,NS,carcinoma,-1,1	C6orf170	146	1	NM_152730	exon32	c.A3695C	p.E1232A	ATGTATTCAAAAT	.	PASS	Atlas-SNP
HIST1H1T	3010	hgsc.bcm.edu	37	6	26108168	26108168	+	Missense_Mutation	SNP	G	G	A	rs2051542	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	80	178	0	0.451977	0	G|0.838;A|0.162	0.162	strong	.	HIST1H1T	40	.	NM_005323	exon1	c.C154T	p.L52F	CTGAAAGGGCCTC	.	PASS	Atlas-SNP
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118231317	118231317	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	86	233	0	0.43	0	.	.	none	.	PNLIPRP3	101	.	NM_001011709	exon10	c.C1098T	p.S366S	TGGAAGCGAAGTC	.	PASS	Atlas-SNP
HNRNPU	3192	hgsc.bcm.edu	37	1	245027349	245027349	+	Silent	SNP	C	C	T	rs6675421	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	18	41	0	0.473684	0	C|0.723;T|0.277	0.277	strong	.	HNRNPU	64	.	NM_004501	exon1	c.G261A	p.E87E	CTCTTCCTCCTCC	.	PASS	Atlas-SNP
USPL1	10208	hgsc.bcm.edu	37	13	31233063	31233063	+	Missense_Mutation	SNP	G	G	A	rs3742302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	131	135	1	0.992424	0.00740741	G|0.506;N|0.000	.	strong	.	USPL1	82	.	NM_005800	exon9	c.G2849A	p.S950N	TTGCCAGTGAGTC	.	PASS	Atlas-SNP
TMEM259	91304	hgsc.bcm.edu	37	19	1012120	1012120	+	Silent	SNP	G	G	A	rs7145	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	44	130	0	0.40367	0	G|0.868;A|0.132	0.132	strong	C19orf6,NS,carcinoma,0,1	.	.	1	NM_033420	exon5	c.C786T	p.Y262Y	GTCATCGTAGCCC	.	PASS	Atlas-SNP
OR5H2	79310	hgsc.bcm.edu	37	3	98002587	98002587	+	Missense_Mutation	SNP	A	A	G	rs16839611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	46	102	0	0.403509	0	A|0.567;G|0.433	0.433	strong	.	OR5H2	63	.	NM_001005482	exon1	c.A856G	p.I286V	ACAATCATAATTC	.	PASS	Atlas-SNP
DFNB31	25861	hgsc.bcm.edu	37	9	117186712	117186712	+	Missense_Mutation	SNP	C	C	T	rs4978584	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	70	132	1	0.411765	0.00757576	C|0.802;T|0.198	0.198	strong	DFNB31,colon,carcinoma,0,1	DFNB31	100	1	NM_001173425	exon6	c.G1318A	p.A440T	TGGTGGCGTGTTC	.	scavenged	Atlas-SNP
LY6H	4062	hgsc.bcm.edu	37	8	144240257	144240257	+	Silent	SNP	C	C	G	rs9694368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	123	190	2	0.574766	0.0105263	C|0.620;G|0.380	0.380	strong	LY6H,NS,carcinoma,0,1	LY6H	12	1	NM_001135655	exon3	c.G213C	p.T71T	ACACACCGTGTCG	.	scavenged	Atlas-SNP
SCNN1G	6340	hgsc.bcm.edu	37	16	23200761	23200761	+	Silent	SNP	T	T	C	rs5734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	70	83	0	0.972222	0	T|0.744;C|0.256	0.256	strong	.	SCNN1G	82	.	NM_001039	exon3	c.T387C	p.Y129Y	CCTGTATGGCTTT	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79041057	79041057	+	Missense_Mutation	SNP	A	A	G	rs12514461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	78	150	0	0.509804	0	A|0.904;G|0.096	0.096	strong	.	CMYA5	643	.	NM_153610	exon4	c.A10747G	p.K3583E	TGTAGTAAAAATG	.	PASS	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21976289	21976289	+	Silent	SNP	C	C	T	rs141127873	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	42	189	0	0.257669	0	C|0.996;T|0.004	0.004	strong	.	RAP1GAP	119	.	NM_001145658	exon2	c.G45A	p.G15G	GTCCACCCTGAAA	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84227713	84227713	+	Missense_Mutation	SNP	C	C	T	rs78344060	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	30	137	0	0.218978	0	C|0.975;T|0.025	0.025	strong	ADAD2,caecum,carcinoma,0,1	ADAD2	46	1	NM_139174	exon2	c.C520T	p.R174C	GGGTGGCGTGGGC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284549	152284549	+	Missense_Mutation	SNP	G	G	C	rs141646551	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	546	31	412	3	0.0567766	0.00728155	G|0.989;C|0.011	0.011	strong	FLG,rectum,NS,0,1	FLG	900	1	NM_002016	exon3	c.C2813G	p.T938R	CTGCTTGTCCTGG	.	scavenged	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9305473	9305473	+	Silent	SNP	T	T	C	rs10771357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	162	170	1	0.993865	0.00588235	T|0.362;C|0.638	0.638	strong	.	PZP	422	.	NM_002864	exon31	c.A4068G	p.Q1356Q	GCAAGTTTGGGGC	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	30143499	30143499	+	Silent	SNP	G	G	C	rs4358080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4	4	0	0	1	.	G|0.120;C|0.880	0.880	strong	.	ALK	533	.	NM_004304	exon1	c.C27G	p.L9L	CGGCAGGAGCCAC	.	PASS	Atlas-SNP
PFKM	5213	hgsc.bcm.edu	37	12	48539482	48539482	+	Silent	SNP	T	T	G	rs8716	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	78	108	0	0.987342	0	T|0.746;G|0.254	0.254	strong	.	PFKM	117	.	NM_001166686	exon25	c.T2547G	p.A849A	GGAAGCTGCCGTC	.	PASS	Atlas-SNP
PHYHIP	9796	hgsc.bcm.edu	37	8	22084503	22084503	+	Silent	SNP	C	C	T	rs11547656	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	50	59	0	0.617284	0	T|0.357;G|0.000;C|0.642	0.357	strong	.	PHYHIP	24	.	NM_014759	exon3	c.G201A	p.P67P	GGGCAGCGGCACT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511790	195511790	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	358	4	452	1	0.0111732	0.00221239	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+2,1	MUC4	1505	1	NM_018406	exon2	c.C6661T	p.H2221Y	TGGCGTGACCTGT	.	scavenged	Atlas-SNP
MARCH7	64844	hgsc.bcm.edu	37	2	160604452	160604452	+	Silent	SNP	C	C	T	rs11555185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	305	162	342	2	0.531148	0.00584795	C|0.761;T|0.239	0.239	strong	MARCH7,colon,carcinoma,0,2	MARCH7	48	2	NM_022826	exon5	c.C651T	p.D217D	TAGGGACTCCAGA	.	scavenged	Atlas-SNP
CTAGE4	100128553	hgsc.bcm.edu	37	7	143882673	143882673	+	Missense_Mutation	SNP	C	C	T	rs62484795		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	72	158	1	0.334884	0.00632911	.	.	weak	CTAGE4,NS,carcinoma,0,1	CTAGE4	10	1	NM_198495	exon1	c.C2077T	p.L693F	CCTGGCCTTATTC	.	scavenged	Atlas-SNP
IL12B	3593	hgsc.bcm.edu	37	5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	rs3213096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	29	57	0	0.460317	0	C|0.994;T|0.006	0.006	strong	.	IL12B	30	.	NM_002187	exon3	c.G97A	p.V33I	ATTCTACGACATA	.	PASS	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	37	17	48625928	48625928	+	Missense_Mutation	SNP	C	C	G	rs8076632	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	21	40	0	0.552632	0	C|0.583;G|0.417	0.417	strong	SPATA20,NS,carcinoma,0,1	SPATA20	59	1	NM_022827	exon4	c.C310G	p.Q104E	TGGGGACAGGAAG	.	PASS	Atlas-SNP
ZNF16	7564	hgsc.bcm.edu	37	8	146157265	146157265	+	Missense_Mutation	SNP	C	C	T	rs80044147	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	48	137	0	0.301887	0	C|0.998;T|0.002	0.002	strong	.	ZNF16	80	.	NM_006958	exon3	c.G908A	p.S303N	TTCTGGCTGAAGG	.	PASS	Atlas-SNP
FBXL7	23194	hgsc.bcm.edu	37	5	15936591	15936591	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	2	100	0	0.0229885	0	.	.	none	FBXL7,colon,carcinoma,0,3	FBXL7	138	3	NM_012304	exon4	c.C772T	p.R258W	TTGACCCGGGAGG	.	scavenged	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140559679	140559679	+	Silent	SNP	C	C	G	rs17844507	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	34	72	0	0.618182	0	C|0.863;G|0.137	0.137	strong	.	PCDHB8	199	.	NM_019120	exon1	c.C2064G	p.T688T	TCTCACCGTCTAC	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101587518	101587518	+	Missense_Mutation	SNP	C	C	T	rs1709189	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	73	213	0	0.442424	0	C|0.745;T|0.255	0.255	strong	.	SLC5A8	102	.	NM_145913	exon5	c.G577A	p.V193I	TCCCAACTTGAAA	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25259006	25259006	+	Missense_Mutation	SNP	G	G	T	rs2228976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	57	121	0	0.448819	0	G|0.833;T|0.167	0.167	strong	PYGB,NS,carcinoma,0,2	PYGB	84	2	NM_002862	exon8	c.G907T	p.A303S	GTGGCCGCCACGC	.	PASS	Atlas-SNP
UGT3A2	167127	hgsc.bcm.edu	37	5	36039683	36039683	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	2	177	1	0.0151515	0.00564972	.	.	none	UGT3A2,rectum,carcinoma,-1,1	UGT3A2	117	1	NM_174914	exon5	c.C971T	p.P324L	CCTTGGGGTAGGT	.	scavenged	Atlas-SNP
CENPO	79172	hgsc.bcm.edu	37	2	25022598	25022598	+	Missense_Mutation	SNP	A	A	G	rs1550116	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	52	115	0	0.45614	0	A|0.859;G|0.141	0.141	strong	.	CENPO	18	.	NM_024322	exon3	c.A101G	p.Q34R	GTAAACAGTCTGA	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219602499	219602499	+	Missense_Mutation	SNP	G	G	C	rs3731877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	32	167	0	0.283186	0	G|0.525;C|0.475	0.475	strong	TTLL4,brain,glioma,0,1	TTLL4	96	1	NM_014640	exon3	c.G100C	p.E34Q	CCACCTGAGAAAC	.	PASS	Atlas-SNP
SPSB1	80176	hgsc.bcm.edu	37	1	9416346	9416346	+	Silent	SNP	C	C	T	rs3795309	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	28	64	0	0.717949	0	C|0.763;T|0.237	0.237	strong	.	SPSB1	22	.	NM_025106	exon2	c.C396T	p.L132L	AACCCTCGTGGGG	.	PASS	Atlas-SNP
LSS	4047	hgsc.bcm.edu	37	21	47614443	47614443	+	Silent	SNP	A	A	G	rs2254522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	76	100	0	0.539007	0	A|0.712;C|0.002	.	strong	.	LSS	50	.	NM_001001438	exon20	c.T1950C	p.H650H	TGTGTTATGGATC	.	PASS	Atlas-SNP
AIM1L	55057	hgsc.bcm.edu	37	1	26673108	26673108	+	Missense_Mutation	SNP	C	C	T	rs11247925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	18	97	0	0.285714	0	C|0.834;T|0.166	0.166	strong	.	AIM1L	98	.	NM_001039775	exon2	c.G41A	p.R14Q	ACCACTCGGGCCT	.	PASS	Atlas-SNP
CAST	831	hgsc.bcm.edu	37	5	96031569	96031569	+	Silent	SNP	A	A	G	rs9667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	90	181	0	0.48913	0	A|0.818;G|0.182	0.182	strong	.	CAST	58	.	NM_001042440	exon3	c.A168G	p.Q56Q	CAGTCAATCCTCC	.	PASS	Atlas-SNP
SH3BGR	6450	hgsc.bcm.edu	37	21	40871810	40871810	+	Missense_Mutation	SNP	T	T	C	rs9974333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	74	90	1	0.691589	0.0111111	T|0.476;C|0.524	0.524	strong	SH3BGR,NS,carcinoma,-1,2	SH3BGR	29	2	NM_007341	exon4	c.T563C	p.V188A	AAGATGTGGGCAA	.	scavenged	Atlas-SNP
ADAMTS17	170691	hgsc.bcm.edu	37	15	100636586	100636586	+	Silent	SNP	G	G	A	rs4965583	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	25	46	0	0.581395	0	G|0.801;A|0.199	0.199	strong	.	ADAMTS17	127	.	NM_139057	exon15	c.C2112T	p.G704G	GAAGTCGCCCTTC	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129813053	129813053	+	Missense_Mutation	SNP	A	A	G	rs2244008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	27	60	2	0.529412	0.0333333	A|0.905;C|0.001	.	strong	LAMA2,NS,carcinoma,0,1	LAMA2	481	1	NM_000426	exon57	c.A7906G	p.T2636A	ATCTTTACAGTTC	.	scavenged	Atlas-SNP
PDLIM7	9260	hgsc.bcm.edu	37	5	176916516	176916516	+	Silent	SNP	C	C	T	rs335462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	37	94	1	0.685185	0.0106383	C|0.555;T|0.445	0.445	strong	PDLIM7,NS,carcinoma,0,1	PDLIM7	32	1	NM_005451	exon9	c.G747A	p.P249P	CGTGGCCGGCTGG	.	scavenged	Atlas-SNP
FUK	197258	hgsc.bcm.edu	37	16	70503095	70503095	+	Missense_Mutation	SNP	A	A	G	rs113497209	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	21	108	0	0.221053	0	A|0.989;G|0.011	0.011	strong	.	FUK	72	.	NM_145059	exon10	c.A824G	p.N275S	CTGAGAACGTGAC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	T	G	rs7863519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	108	168	0	0.556701	0	T|0.684;G|0.316	0.316	strong	SVEP1,NS,carcinoma,0,2	SVEP1	326	2	NM_153366	exon26	c.A4330C	p.M1444L	GGAGCATGCCATC	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238155	31238155	+	Missense_Mutation	SNP	G	G	A	rs1050328	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	117	195	1	0.444867	0.00512821	G|0.695;A|0.305	0.305	strong	HLA-C,colon,carcinoma,+1,1	HLA-C	92	1	NM_002117	exon4	c.C727T	p.R243W	CATCCCGCTGCCA	.	scavenged	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87229890	87229890	+	Missense_Mutation	SNP	G	G	A	rs72688509	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	65	107	0	0.477941	0	G|0.979;A|0.021	0.021	strong	.	SLC7A13	97	.	NM_138817	exon3	c.C988T	p.L330F	TATTAAGTGTATT	.	PASS	Atlas-SNP
C7orf63	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	56	144	1	0.299465	0.00694444	C|0.602;T|0.398	0.398	strong	C7orf63_ENST00000389297,colon,carcinoma,+2,2	C7orf63	158	2	NM_001039706	exon11	c.C1116T	p.N372N	ATTCAACGTAATT	.	scavenged	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	13	156	0	0.0962963	0	.	.	none	KRTAP1-1,NS,malignant_melanoma,0,1	KRTAP1-1	23	1	NM_030967	exon1	c.A346G	p.I116V	ACCTGATACGGGT	.	PASS	Atlas-SNP
DCAF8L1	139425	hgsc.bcm.edu	37	X	27999146	27999146	+	Silent	SNP	C	C	T	rs41311803	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	114	253	0	0.974359	0	C|0.904;T|0.096	0.096	strong	.	DCAF8L1	121	.	NM_001017930	exon1	c.G306A	p.E102E	TTCTTCCTCCTCC	.	PASS	Atlas-SNP
ZNF345	25850	hgsc.bcm.edu	37	19	37369032	37369032	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	56	97	0	0.554455	0	.	.	none	.	ZNF345	68	.	NM_001242476	exon4	c.G1300C	p.A434P	GGGAAGGCTTTTT	.	PASS	Atlas-SNP
TPSD1	23430	hgsc.bcm.edu	37	16	1306680	1306680	+	Silent	SNP	C	C	T	rs1969653	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	81	170	0	0.515924	0	C|0.850;T|0.150	0.150	strong	.	TPSD1	47	.	NM_012217	exon2	c.C246T	p.C82C	GCACTGCGTGGAA	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6585670	6585670	+	Silent	SNP	C	C	T	rs16915423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	116	205	0	0.489451	0	C|0.905;T|0.095	0.095	strong	.	DNHD1	198	.	NM_144666	exon32	c.C10392T	p.D3464D	ACTGGACGAGTGG	.	PASS	Atlas-SNP
IQCE	23288	hgsc.bcm.edu	37	7	2644519	2644519	+	Missense_Mutation	SNP	C	C	T	rs2293404	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	27	70	0	0.325301	0	C|0.622;T|0.378	0.378	strong	IQCE,NS,carcinoma,0,1	IQCE	66	1	NM_152558	exon19	c.C1637T	p.A546V	AGGCGGCTGTGGT	.	PASS	Atlas-SNP
PTCH2	8643	hgsc.bcm.edu	37	1	45294295	45294295	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	4	102	0	0.0597015	0	.	.	none	.	PTCH2	96	.	NM_001166292	exon12	c.G1473A	p.M491I	CTCGCCCATGCGC	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924507	70924507	+	Silent	SNP	A	A	C	rs3751524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	73	170	1	0.301653	0.00588235	A|0.780;C|0.220	0.220	strong	ADAM21,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.A291C	p.A97A	CCGTGCACTCCTG	.	scavenged	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19433449	19433449	+	Silent	SNP	A	A	G	rs6426677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	120	258	0	0.764331	0	A|0.311;G|0.689	0.689	strong	.	UBR4	415	.	NM_020765	exon82	c.T12117C	p.V4039V	GGCCTCAACGGGG	.	PASS	Atlas-SNP
BCOR	54880	hgsc.bcm.edu	37	X	39932808	39932808	+	Silent	SNP	G	G	A	rs144606152	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	36	90	0	0.947368	0	G|0.963;A|0.037	0.037	strong	.	BCOR	351	.	NM_001123385	exon4	c.C1791T	p.H597H	GCCCACGTGCTGA	.	PASS	Atlas-SNP
SELL	6402	hgsc.bcm.edu	37	1	169676486	169676486	+	Missense_Mutation	SNP	A	A	G	rs1131498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	310	240	2	0.981013	0.00833333	A|0.861;G|0.139	0.139	strong	.	SELL	43	.	NM_000655	exon4	c.T616C	p.F206L	TACCAAACTGACA	.	PASS	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28559120	28559120	+	Silent	SNP	G	G	C	rs17486417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	33	86	0	0.492537	0	G|0.870;C|0.128	0.128	strong	.	TTC28	84	.	NM_001145418	exon6	c.C1401G	p.L467L	GTCCTTGAGATCC	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2140554	2140554	+	Missense_Mutation	SNP	G	G	A	rs3209986	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	21	50	0	0.538462	0	G|0.950;A|0.050	0.050	strong	.	PKD1	184	.	NM_001009944	exon45	c.C12176T	p.A4059V	GCCTGGGCCACGC	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101560328	101560328	+	Missense_Mutation	SNP	C	C	A	rs164365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	51	125	0	0.435897	0	C|0.767;A|0.233	0.233	strong	.	SLC5A8	102	.	NM_145913	exon12	c.G1470T	p.M490I	GGTTGTCATCAAA	.	PASS	Atlas-SNP
ARAP2	116984	hgsc.bcm.edu	37	4	36230634	36230634	+	Missense_Mutation	SNP	G	G	A	rs141442791	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	43	82	0	0.457447	0	G|0.998;A|0.002	0.002	strong	.	ARAP2	210	.	NM_015230	exon2	c.C475T	p.P159S	GGTGTGGTTCCTC	.	PASS	Atlas-SNP
PNP	4860	hgsc.bcm.edu	37	14	20940606	20940606	+	Missense_Mutation	SNP	G	G	A	rs1049564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	62	152	0	0.346369	0	G|0.786;A|0.214	0.214	strong	PNP,NS,carcinoma,0,1	PNP	21	1	NM_000270	exon2	c.G151A	p.G51S	GACTACGGTGAAA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144921924	144921924	+	Silent	SNP	G	G	A	rs71664015	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	412	119	382	1	0.288835	0.0026178	A|0.001;C|0.795	0.001	strong	.	PDE4DIP	817	.	NM_001002811	exon5	c.C1594T	p.L532L	CAGCCAGTTGGCG	.	PASS	Atlas-SNP
VRK1	7443	hgsc.bcm.edu	37	14	97321689	97321689	+	Silent	SNP	C	C	T	rs2230532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	66	108	0	0.578947	0	C|0.650;T|0.350	0.350	strong	.	VRK1	34	.	NM_003384	exon8	c.C705T	p.G235G	CAATGGCGTGGGT	.	PASS	Atlas-SNP
STIM1	6786	hgsc.bcm.edu	37	11	4103524	4103524	+	Silent	SNP	A	A	G	rs2304891	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	144	170	0	0.972973	0	A|0.576;G|0.424	0.424	strong	STIM1,NS,carcinoma,0,2	STIM1	55	2	NM_003156	exon8	c.A1080G	p.Q360Q	GGTGCAATATTAC	.	PASS	Atlas-SNP
CEP63	80254	hgsc.bcm.edu	37	3	134225969	134225969	+	Silent	SNP	T	T	C	rs9827878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	72	119	0	0.514286	0	T|0.841;C|0.159	0.159	strong	.	CEP63	56	.	NM_001042383	exon3	c.T63C	p.C21C	ATCTTGTGAAGCA	.	PASS	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	37	9	139905141	139905141	+	Silent	SNP	G	G	A	rs112887513	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	378	194	330	0	0.513228	0	A|0.055;C|0.000;G|0.945	0.055	strong	.	ABCA2	113	.	NM_212533	exon40	c.C6195T	p.A2065A	CTCACTGGCCACG	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55541738	55541738	+	Missense_Mutation	SNP	A	A	C	rs147009600	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	15	184	0	0.15	0	A|0.999;C|0.001	0.001	strong	.	RP1	429	.	NM_006269	exon4	c.A5296C	p.N1766H	TGTGGCAATGCAG	.	PASS	Atlas-SNP
PPHLN1	51535	hgsc.bcm.edu	37	12	42839923	42839923	+	Missense_Mutation	SNP	G	G	A	rs201876048	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	47	92	0	0.505376	0	.	.	weak	.	PPHLN1	101	.	NM_016488	exon12	c.G1181A	p.R394H	GGGTTCGTCGGAC	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62191558	62191558	+	Silent	SNP	G	G	A	rs3810479	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	26	56	0	0.52	0	G|0.863;A|0.137	0.137	strong	.	.	.	.	NM_001037335	exon18	c.C7623T	p.A2541A	CACCCCGGCGATG	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45021210	45021210	+	Missense_Mutation	SNP	G	G	A	rs10414398	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	24	47	0	0.387097	0	G|0.836;A|0.164	0.164	strong	.	CEACAM20	31	.	NM_001102600	exon6	c.C1106T	p.S369F	AGGCTGGAGTTGA	.	PASS	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	37	6	168377135	168377135	+	Silent	SNP	T	T	C	rs372663828		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	418	24	286	0	0.0574163	0	.	.	weak	.	.	.	.	NM_001129895	exon1	c.A198G	p.Q66Q	AGTGTGTTGGGAG	.	PASS	Atlas-SNP
AGXT2	64902	hgsc.bcm.edu	37	5	35037115	35037115	+	Missense_Mutation	SNP	C	C	T	rs37369	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	47	123	0	0.38843	0	C|0.692;T|0.308	0.308	strong	.	AGXT2	89	.	NM_031900	exon4	c.G418A	p.V140I	AGAAGACGGTGCT	.	PASS	Atlas-SNP
KIAA0195	9772	hgsc.bcm.edu	37	17	73493874	73493874	+	Silent	SNP	G	G	C	rs12949173	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	52	94	0	0.5	0	G|0.863;C|0.137	0.137	strong	.	KIAA0195	102	.	NM_014738	exon27	c.G3420C	p.L1140L	TCTGCTGGGGAAG	.	PASS	Atlas-SNP
PLXNB1	5364	hgsc.bcm.edu	37	3	48461313	48461313	+	Silent	SNP	C	C	G	rs2362450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	104	211	0	0.45815	0	C|0.517;G|0.483	0.483	strong	PLXNB1,colon,carcinoma,-2,1	PLXNB1	150	1	NM_001130082	exon11	c.G2382C	p.P794P	CTCTGACGGTGAC	.	PASS	Atlas-SNP
AOC3	8639	hgsc.bcm.edu	37	17	41003914	41003914	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	3	187	0	0.0153846	0	.	.	none	AOC3,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	AOC3	88	1	NM_003734	exon1	c.A554G	p.N185S	TCTTCAACAGAGA	.	scavenged	Atlas-SNP
GDPD5	81544	hgsc.bcm.edu	37	11	75150971	75150971	+	Silent	SNP	G	G	A	rs115438239	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	62	115	0	0.529915	0	G|0.997;A|0.003	0.003	strong	.	GDPD5	49	.	NM_030792	exon15	c.C1509T	p.A503A	CAGGTCGGCAGTG	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79897117	79897117	+	Silent	SNP	G	G	A	rs11145366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	153	201	1	0.987097	0.00497512	G|0.898;A|0.102	0.102	strong	VPS13A_ENST00000376634,NS,carcinoma,+1,3	VPS13A	735	3	NM_001018038	exon29	c.G3045A	p.P1015P	CCTTCCGCAATCA	.	PASS	Atlas-SNP
AQPEP	0	hgsc.bcm.edu	37	5	115351066	115351066	+	Silent	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	3	31	0	0.0857143	0	.	.	none	FLJ90650,caecum,carcinoma,0,1	.	.	1	NM_173800	exon17	c.T2568A	p.I856I	AAAGATTCAACTT	.	scavenged	Atlas-SNP
HHLA2	11148	hgsc.bcm.edu	37	3	108081247	108081247	+	Silent	SNP	G	G	A	rs16854512	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	35	116	0	0.37234	0	G|0.836;A|0.164	0.164	strong	.	HHLA2	95	.	NM_007072	exon7	c.G1062A	p.A354A	CTCTGCGATTTTG	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165664562	165664562	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	23	100	0	0.232323	0	.	.	none	.	ALDH9A1	75	.	NM_000696	exon2	c.C254T	p.A85V	TTAAAAGCAGCCT	.	PASS	Atlas-SNP
SBDS	51119	hgsc.bcm.edu	37	7	66459316	66459316	+	Silent	SNP	G	G	A	rs113993989	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	33	94	0	0.375	0	G|0.989;A|0.011	0.011	strong	.	SBDS	20	.	NM_016038	exon2	c.C141T	p.L47L	TTCATCGAGGTCT	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234727	45234727	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	323	13	250	3	0.0402477	0.012	.	.	none	CDC27_ENST00000531206,NS,carcinoma,+2,10	CDC27	337	10	NM_001114091	exon6	c.A499T	p.T167S	TAAATGTTTGGTC	.	scavenged	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489749	32489749	+	Silent	SNP	G	G	C	rs1064594	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	25	2	0	0.961538	0	G|0.339;C|0.661	0.661	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.C303G	p.R101R	CGCGGCGCGCCTG	.	PASS	Atlas-SNP
OR4A16	81327	hgsc.bcm.edu	37	11	55111238	55111238	+	Missense_Mutation	SNP	C	C	A	rs11229158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	304	162	337	1	0.532895	0.00296736	C|0.584;A|0.416	0.416	strong	.	OR4A16	120	.	NM_001005274	exon1	c.C562A	p.L188I	TTGTGCCTTGACA	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88965021	88965021	+	Missense_Mutation	SNP	G	G	A	rs10487075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	107	163	0	0.622093	0	G|0.916;A|0.084	0.084	strong	.	ZNF804B	322	.	NM_181646	exon4	c.G2725A	p.E909K	CCTTCAGAAACCA	.	PASS	Atlas-SNP
ZNF341	84905	hgsc.bcm.edu	37	20	32371640	32371640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	2	114	0	0.017094	0	.	.	none	ZNF341,NS,carcinoma,-1,1	ZNF341	73	1	NM_032819	exon12	c.T1801C	p.Y601H	GAGCATTATCTCA	.	scavenged	Atlas-SNP
DIAPH3	81624	hgsc.bcm.edu	37	13	60240961	60240961	+	Silent	SNP	C	C	T	rs9538494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	286	283	293	1	0.98951	0.00341297	C|0.820;T|0.180	0.180	strong	.	DIAPH3	139	.	NM_001042517	exon28	c.G3339A	p.L1113L	TTCTGTCAACTGC	.	PASS	Atlas-SNP
ECM1	1893	hgsc.bcm.edu	37	1	150484987	150484987	+	Missense_Mutation	SNP	G	G	A	rs13294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	118	183	1	0.551402	0.00546448	A|0.317;C|0.005	0.317	strong	.	ECM1	96	.	NM_001202858	exon8	c.G1324A	p.G442S	GACATCGGTCGAG	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76332530	76332530	+	Silent	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	8	163	0	0.0506329	0	.	.	none	AGGF1,NS,carcinoma,+2,1	AGGF1	71	1	NM_018046	exon4	c.T666G	p.G222G	CACTGGTTTCTAT	.	scavenged	Atlas-SNP
OR56A5	390084	hgsc.bcm.edu	37	11	5989415	5989415	+	Missense_Mutation	SNP	C	C	T	rs7114672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	72	143	0	0.48	0	A|0.039;C|0.419;T|0.541	0.541	strong	.	.	.	.	NM_001146033	exon1	c.G310A	p.V104M	TGAACACCTGAAG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239108	31239108	+	Missense_Mutation	SNP	T	T	A	rs1131118	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	15	68	1	0.333333	0.0147059	T|0.768;A|0.232	0.232	strong	HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	NM_002117	exon3	c.A361T	p.R121W	ACATCCTCTGGAG	.	scavenged	Atlas-SNP
TCERG1L	256536	hgsc.bcm.edu	37	10	132961454	132961454	+	Missense_Mutation	SNP	C	C	T	rs118074196	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	18	28	0	0.514286	0	C|0.983;T|0.017	0.017	strong	.	TCERG1L	91	.	NM_174937	exon6	c.G965A	p.G322E	CCTCCCCCCAGCA	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2833628	2833628	+	Silent	SNP	A	A	C	rs373216270	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	25	187	0	0.263158	0	.	.	weak	.	ARSD	47	.	NM_001669	exon6	c.T969G	p.G323G	ATTATCACCATAT	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324911	31324911	+	Missense_Mutation	SNP	C	C	G	rs1050462	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	8	110	0	0.0661157	0	C|0.792;G|0.208	0.208	strong	HLA-B,cerebellum,glioma,0,1	HLA-B	54	1	NM_005514	exon1	c.G25C	p.V9L	GGAGGACGGTTCG	.	scavenged	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77436641	77436641	+	Silent	SNP	G	G	A	rs7018994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	42	86	0	0.47191	0	G|0.701;A|0.299	0.299	strong	.	TRPM6	377	.	NM_017662	exon8	c.C954T	p.G318G	ACCTGTGCCCTCA	.	PASS	Atlas-SNP
FBXO25	26260	hgsc.bcm.edu	37	8	381344	381344	+	Missense_Mutation	SNP	C	C	G	rs28438773	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	56	134	0	0.4	0	C|0.860;G|0.140	0.140	strong	.	FBXO25	25	.	NM_183420	exon3	c.C138G	p.I46M	CAGTATCTTAAAT	.	PASS	Atlas-SNP
MKX	283078	hgsc.bcm.edu	37	10	27964470	27964470	+	Silent	SNP	G	G	A	rs2253230	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	122	203	0	0.99187	0	G|0.693;A|0.307	0.307	strong	.	MKX	43	.	NM_001242702	exon6	c.C852T	p.N284N	GGATCCGTTTTCC	.	PASS	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55655597	55655597	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	814	59	850	52	0.0724816	0.0611765	.	.	none	SPRYD5_ENST00000327733,NS,carcinoma,+2,2	.	.	2	NM_032681	exon4	c.A597G	p.E199E	CTTGGAAAGGCTG	.	scavenged	Atlas-SNP
RAD9A	5883	hgsc.bcm.edu	37	11	67160961	67160961	+	Missense_Mutation	SNP	A	A	G	rs2066496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	63	122	0	0.492188	0	A|0.819;G|0.181	0.181	strong	.	RAD9A	15	.	NM_001243224	exon1	c.A1G	p.M1V	TATCCCATGCAGT	.	PASS	Atlas-SNP
CTCFL	140690	hgsc.bcm.edu	37	20	56099114	56099114	+	Missense_Mutation	SNP	C	C	G	rs6070128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	85	181	0	0.548387	0	C|0.675;G|0.325	0.325	strong	CTCFL,caecum,carcinoma,0,1	CTCFL	97	1	NM_001269044	exon1	c.G148C	p.E50Q	TACGCTCGGCCTC	.	PASS	Atlas-SNP
EGF	1950	hgsc.bcm.edu	37	4	110883121	110883121	+	Missense_Mutation	SNP	G	G	A	rs11568943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	73	204	0	0.384211	0	G|0.845;A|0.155	0.155	strong	.	EGF	113	.	NM_001963	exon8	c.G1292A	p.R431K	TTGAGAGAGATGG	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22942335	22942335	+	Missense_Mutation	SNP	G	G	A	rs61740110	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	61	185	0	0.429577	0	G|0.915;A|0.085	0.085	strong	ZNF99,right_upper_lobe,carcinoma,+2,2	ZNF99	273	2	NM_001080409	exon4	c.C376T	p.H126Y	CTTCGTGCATCTT	.	PASS	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	37	3	126735453	126735453	+	Silent	SNP	C	C	T	rs9858521	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	86	162	0	0.518072	0	C|0.897;T|0.103	0.103	strong	.	PLXNA1	185	.	NM_032242	exon15	c.C3108T	p.T1036T	GCTCACCAACCCT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790758	4790758	+	Silent	SNP	G	G	A	rs11033796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	72	141	0	0.496552	0	G|0.690;A|0.310	0.310	strong	.	OR51F1	60	.	NM_001004752	exon1	c.C390T	p.D130D	CAGAGGGTCACAG	.	PASS	Atlas-SNP
LYPD5	284348	hgsc.bcm.edu	37	19	44306482	44306482	+	Silent	SNP	C	C	T	rs11879355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	39	75	0	0.52	0	C|0.728;T|0.272	0.272	strong	LYPD5_ENST00000377950,colon,carcinoma,-1,1	LYPD5	22	1	NM_001031749	exon1	c.G51A	p.A17A	GCAGAGCGCAGCC	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96091414	96091414	+	Missense_Mutation	SNP	C	C	T	rs34585936	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	35	108	0	0.388889	0	C|0.983;T|0.017	0.017	strong	.	UNC5C	141	.	NM_003728	exon15	c.G2521A	p.A841T	TGAAAGCACTGGG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144992900	144992900	+	Silent	SNP	G	G	A	rs17062686	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	52	112	0	0.382353	0	G|0.970;A|0.030	0.030	strong	.	PLEC	1144	.	NM_201380	exon32	c.C11500T	p.L3834L	CGGGCAGGTAGAC	.	PASS	Atlas-SNP
PTPRO	5800	hgsc.bcm.edu	37	12	15661564	15661564	+	Missense_Mutation	SNP	G	G	A	rs71459181	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	109	198	0	0.550505	0	G|0.991;A|0.009	0.009	strong	.	PTPRO	148	.	NM_002848	exon7	c.G1327A	p.V443I	GTCCACGTTTTAA	.	PASS	Atlas-SNP
ACTR1B	10120	hgsc.bcm.edu	37	2	98275354	98275354	+	Missense_Mutation	SNP	G	G	A	rs11692435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	41	81	0	0.61194	0	G|0.950;A|0.050	0.050	strong	ACTR1B,NS,adenoma,0,1	ACTR1B	34	1	NM_005735	exon5	c.C428T	p.A143V	AGCACAGCCTGCA	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43828141	43828141	+	Missense_Mutation	SNP	T	T	A	rs7302446	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	61	174	0	0.398693	0	T|0.974;A|0.026	0.026	strong	.	ADAMTS20	635	.	NM_025003	exon19	c.A2627T	p.K876M	TCACTCTTATGTA	.	PASS	Atlas-SNP
TUBA1C	84790	hgsc.bcm.edu	37	12	49663751	49663751	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	3	181	0	0.0137615	0	.	.	none	TUBA1C,NS,carcinoma,0,1	TUBA1C	32	1	NM_032704	exon3	c.C367T	p.R123C	CGAATTCGCAAGC	.	scavenged	Atlas-SNP
CRLF1	9244	hgsc.bcm.edu	37	19	18705145	18705145	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	4	130	0	0.0377358	0	.	.	none	CRLF1,bladder,carcinoma,+1,1	CRLF1	32	1	NM_004750	exon7	c.A1124G	p.K375R	TGCTTCTTGAGCC	.	scavenged	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879435	39879435	+	Silent	SNP	C	C	A	rs112569629	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	44	200	0	0.594595	0	C|0.995;A|0.005	0.005	weak	.	KIAA0754	93	.	NM_015038	exon1	c.C3498A	p.P1166P	CACCCCCGAGGAA	.	PASS	Atlas-SNP
ENG	2022	hgsc.bcm.edu	37	9	130605385	130605385	+	Silent	SNP	C	C	T	rs11545664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	27	51	0	0.5	0	C|0.852;T|0.148	0.148	strong	.	ENG	44	.	NM_001114753	exon2	c.G207A	p.L69L	GAACTCCAGGAAG	.	PASS	Atlas-SNP
OR51B2	79345	hgsc.bcm.edu	37	11	5344592	5344592	+	Missense_Mutation	SNP	A	A	C	rs11036814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	58	136	0	0.464	0	A|0.880;C|0.120	0.120	strong	OR51B2,NS,carcinoma,0,1	OR51B2	69	1	NM_033180	exon1	c.T936G	p.S312R	AGTTTAACTACTA	.	PASS	Atlas-SNP
PBK	55872	hgsc.bcm.edu	37	8	27685663	27685663	+	Silent	SNP	C	C	T	rs55973425	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	41	69	0	0.42268	0	C|0.998;T|0.002	0.002	strong	.	PBK	29	.	NM_018492	exon3	c.G111A	p.K37K	GCCAAGCTTCTGC	.	PASS	Atlas-SNP
ATP9A	10079	hgsc.bcm.edu	37	20	50346491	50346491	+	Missense_Mutation	SNP	C	C	A	rs142435125	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	27	46	0	0.473684	0	C|0.997;A|0.003	0.003	strong	.	ATP9A	135	.	NM_006045	exon2	c.G95T	p.G32V	CCTCCACCGCAGC	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117560058	117560058	+	Missense_Mutation	SNP	C	C	G	rs17235773	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	18	187	0	0.204545	0	C|0.944;G|0.056	0.056	strong	.	CD101	95	.	NM_001256109	exon5	c.C1575G	p.S525R	TCTGAGCTGGACT	.	PASS	Atlas-SNP
HCN1	348980	hgsc.bcm.edu	37	5	45262443	45262443	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	3	125	0	0.0272727	0	.	.	none	HCN1,right_upper_lobe,carcinoma,0,1	HCN1	298	1	NM_021072	exon8	c.G2253A	p.P751P	CGGGGACGGCTGC	.	scavenged	Atlas-SNP
ZNF772	400720	hgsc.bcm.edu	37	19	57984918	57984918	+	Silent	SNP	A	A	G	rs2074058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	62	79	0	0.584906	0	A|0.659;G|0.341	0.341	strong	.	ZNF772	42	.	NM_001024596	exon5	c.T1194C	p.S398S	ATGAACACTCCAA	.	PASS	Atlas-SNP
ATP6V0A1	535	hgsc.bcm.edu	37	17	40632729	40632729	+	Silent	SNP	C	C	T	rs41283429	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	38	69	0	0.527778	0	C|0.969;T|0.031	0.031	strong	.	ATP6V0A1	67	.	NM_001130020	exon8	c.C699T	p.G233G	CCAAGGCGATCAG	.	PASS	Atlas-SNP
CD207	50489	hgsc.bcm.edu	37	2	71062648	71062648	+	Missense_Mutation	SNP	G	G	A	rs10489990	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	55	120	0	0.404412	0	G|0.716;A|0.284	0.284	strong	CD207,NS,carcinoma,0,1	CD207	47	1	NM_015717	exon2	c.C164T	p.A55V	ACGGAGGCGACCA	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72998886	72998886	+	Silent	SNP	T	T	C	rs3809997	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	16	50	0	0.380952	0	T|0.630;C|0.370	0.370	strong	.	TSHZ1	104	.	NM_005786	exon2	c.T1389C	p.P463P	GCCGCCTGTGGCT	.	PASS	Atlas-SNP
TNRC6A	27327	hgsc.bcm.edu	37	16	24834233	24834233	+	Silent	SNP	C	C	T	rs2303085	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	69	150	0	0.453947	0	C|0.816;T|0.184	0.184	strong	TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	NM_014494	exon24	c.C5412T	p.H1804H	GCAGCACGGCCCG	.	PASS	Atlas-SNP
FAR2	55711	hgsc.bcm.edu	37	12	29423460	29423460	+	Silent	SNP	G	G	A	rs2216854	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	69	184	0	0.420732	0	G|0.554;A|0.446	0.446	strong	FAR2,NS,carcinoma,0,1	FAR2	60	1	NM_018099	exon2	c.G78A	p.L26L	AGTGCTGATGGAG	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77765398	77765398	+	Missense_Mutation	SNP	A	A	G	rs16919452	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	152	191	0	0.633333	0	A|0.927;G|0.073	0.073	strong	.	ZFHX4	878	.	NM_024721	exon10	c.A6241G	p.I2081V	CCTTCCATTATGA	.	PASS	Atlas-SNP
COX5B	1329	hgsc.bcm.edu	37	2	98264478	98264478	+	Silent	SNP	C	C	T	rs142899936		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	58	182	0	0.384106	0	C|1.000;T|0.000	0.000	weak	.	COX5B	9	.	NM_001862	exon4	c.C297T	p.S99S	TACCAGCGTCGTC	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66660247	66660247	+	Silent	SNP	T	T	C	rs71563186		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	56	224	1	0.302703	0.00446429	T|0.500;C|0.500	0.500	weak	TYW1,NS,carcinoma,0,1	TYW1	71	1	NM_018264	exon15	c.T1900C	p.L634L	CACGAGTTGGTGG	.	scavenged	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238247734	238247734	+	Missense_Mutation	SNP	C	C	G	rs36104025	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	22	47	0	0.415094	0	C|0.942;G|0.058	0.058	strong	.	COL6A3	608	.	NM_004369	exon39	c.G8491C	p.D2831H	TGATATCTGGGGA	.	PASS	Atlas-SNP
ZNF276	92822	hgsc.bcm.edu	37	16	89799950	89799950	+	Silent	SNP	C	C	T	rs17177891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	33	282	2	0.165	0.0070922	C|0.932;T|0.068	0.068	strong	ZNF276_ENST00000443381,colon,carcinoma,0,2	ZNF276	70	2	NM_001113525	exon8	c.C1341T	p.G447G	CCGAGGCGCTGAC	.	scavenged	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145543972	145543972	+	Silent	SNP	G	G	A	rs3763373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	217	296	2	0.990868	0.00675676	G|0.801;A|0.199	0.199	strong	LARS,NS,carcinoma,0,1	LARS	100	1	NM_020117	exon6	c.C495T	p.G165G	AGACAGGCCAAGG	.	PASS	Atlas-SNP
CBX5	23468	hgsc.bcm.edu	37	12	54639963	54639963	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	73	191	0	0.459119	0	.	.	none	.	CBX5	24	.	NM_012117	exon4	c.C361T	p.L121L	GTTCCAGTCCTCT	.	PASS	Atlas-SNP
TFAP2D	83741	hgsc.bcm.edu	37	6	50683009	50683009	+	Missense_Mutation	SNP	T	T	C	rs78648104	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	111	265	0	0.523585	0	T|0.925;C|0.075	0.075	strong	.	TFAP2D	144	.	NM_172238	exon2	c.T220C	p.F74L	CAGTCCTTCCATT	.	PASS	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504794	227504794	+	Silent	SNP	T	T	C	rs11804613	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	324	202	222	0	0.623457	0	T|0.768;C|0.232	0.232	strong	.	CDC42BPA	528	.	NM_003607	exon1	c.A90G	p.T30T	CAGTAATGTCTCC	.	PASS	Atlas-SNP
ZNF679	168417	hgsc.bcm.edu	37	7	63727212	63727212	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	33	46	0	0.767442	0	.	.	none	.	ZNF679	80	.	NM_153363	exon5	c.A1201T	p.M401L	AAGAGTATGCATA	.	PASS	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1811547	1811547	+	Silent	SNP	A	A	G	rs12609187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	57	92	0	0.966102	0	A|0.151;G|0.849	0.849	strong	.	ATP8B3	108	.	NM_138813	exon2	c.T189C	p.P63P	CCTCTCAGGTGCC	.	PASS	Atlas-SNP
H1FNT	341567	hgsc.bcm.edu	37	12	48723324	48723324	+	Missense_Mutation	SNP	C	C	G	rs2732441	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	77	79	0	0.9625	0	C|0.798;G|0.202	0.202	strong	H1FNT,NS,carcinoma,0,2	H1FNT	30	2	NM_181788	exon1	c.C250G	p.R84G	GAGCTCCGAAACG	.	PASS	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	37	4	3451109	3451109	+	Missense_Mutation	SNP	G	G	A	rs2498323	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	282	135	263	1	0.478723	0.00380228	G|0.909;A|0.091	0.091	strong	HGFAC,NS,carcinoma,0,1	HGFAC	69	1	NM_001528	exon14	c.G1931A	p.R644Q	ACGACCGGATACG	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	76984961	76984961	+	Missense_Mutation	SNP	T	T	C	rs375426636		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	106	112	0	0.650307	0	.	.	weak	.	PION	74	.	NM_017439	exon15	c.A1031G	p.Y344C	ACATAATAGTCTA	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130282383	130282383	+	Missense_Mutation	SNP	C	C	A	rs114511272	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	91	232	1	0.439614	0.00431034	C|0.992;A|0.008	0.008	strong	COL6A6_ENST00000358511,colon,carcinoma,-1,3	COL6A6	497	3	NM_001102608	exon2	c.C536A	p.T179K	TGGCCACGTCTCA	.	PASS	Atlas-SNP
SH3RF1	57630	hgsc.bcm.edu	37	4	170037572	170037572	+	Missense_Mutation	SNP	G	G	A	rs3811813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	17	130	1	0.193182	0.00769231	G|0.906;A|0.094	0.094	strong	SH3RF1,NS,carcinoma,+2,1	SH3RF1	60	1	NM_020870	exon10	c.C1987T	p.P663S	TCAGTGGAGCAGC	.	scavenged	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78261730	78261730	+	Silent	SNP	G	G	A	rs17853714	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	62	149	0	0.476923	0	G|0.861;A|0.139	0.139	strong	.	RNF213	766	.	NM_001256071	exon4	c.G378A	p.P126P	AAACCCGTGGCCT	.	PASS	Atlas-SNP
OGFOD3	79701	hgsc.bcm.edu	37	17	80373377	80373377	+	Missense_Mutation	SNP	G	G	T	rs8072110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	32	101	0	0.507937	0	G|0.944;T|0.056	0.056	strong	C17orf101_ENST00000313056,NS,carcinoma,-2,2	.	.	2	NM_175902	exon2	c.C201A	p.D67E	CCCGTCGTCGGCC	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56485023	56485023	+	Missense_Mutation	SNP	T	T	C	rs35497571	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	39	100	0	0.464286	0	T|0.983;C|0.017	0.017	strong	.	DST	1427	.	NM_001723	exon23	c.A3809G	p.K1270R	TTATTTTTTTGTT	.	PASS	Atlas-SNP
PSMB8	5696	hgsc.bcm.edu	37	6	32811629	32811629	+	Missense_Mutation	SNP	G	G	T	rs2071543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	19	49	0	0.38	0	G|0.865;T|0.135	0.135	strong	.	PSMB8	42	.	NM_148919	exon1	c.C145A	p.Q49K	CGACCTGCATTCC	.	PASS	Atlas-SNP
THOC5	8563	hgsc.bcm.edu	37	22	29908072	29908072	+	Missense_Mutation	SNP	C	C	T	rs1049534	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	247	264	0	0.991968	0	C|0.771;T|0.229	0.229	strong	.	THOC5	58	.	NM_001002878	exon19	c.G1735A	p.V579I	GGAAAACAGGTGG	.	PASS	Atlas-SNP
NDUFS1	4719	hgsc.bcm.edu	37	2	207008763	207008763	+	Silent	SNP	C	C	A	rs1127566	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	36	99	0	0.782609	0	C|0.495;A|0.505	0.505	strong	NDUFS1,NS,carcinoma,0,1	NDUFS1	82	1	NM_001199984	exon10	c.G1008T	p.A336A	AGAGAGCGCATCC	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	71	139	1	0.342995	0.00719424	C|0.213;N|0.000	0.213	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon7	c.A880G	p.I294V	TACTGATGTTTGA	.	scavenged	Atlas-SNP
CCDC169	728591	hgsc.bcm.edu	37	13	36871782	36871782	+	Silent	SNP	G	G	T	rs201215750	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	26	61	0	0.433333	0	G|0.993;T|0.007	0.007	strong	.	CCDC169	20	.	NM_001144981	exon1	c.C75A	p.V25V	CTTGCGGACTTCT	.	PASS	Atlas-SNP
AGPHD1	123688	hgsc.bcm.edu	37	15	78825562	78825562	+	Silent	SNP	C	C	T	rs12906951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	42	144	1	0.666667	0.00694444	C|0.733;T|0.267	0.267	strong	AGPHD1,NS,carcinoma,0,1	AGPHD1	22	1	NM_001013619	exon5	c.C672T	p.H224H	CAATCACGGAGAT	.	scavenged	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160676427	160676427	+	Missense_Mutation	SNP	C	C	A	rs12692566	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	91	142	1	0.98913	0.00704225	C|0.148;A|0.852	0.852	strong	.	LY75	151	.	NM_002349	exon29	c.G3963T	p.K1321N	AAGAGACTTATCT	.	PASS	Atlas-SNP
AFF3	3899	hgsc.bcm.edu	37	2	100218080	100218080	+	Silent	SNP	G	G	A	rs4851214	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	19	11	0	1	0	G|0.776;A|0.224	0.224	strong	.	AFF3	164	.	NM_001025108	exon13	c.C1263T	p.A421A	GACCACGGCGCTG	.	PASS	Atlas-SNP
GMNC	647309	hgsc.bcm.edu	37	3	190578566	190578566	+	Missense_Mutation	SNP	A	A	G	rs13075089	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	137	172	0	0.985611	0	A|0.589;G|0.411	0.411	strong	.	GMNC	12	.	NM_001146686	exon2	c.T85C	p.S29P	CACTAGATTCTGA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238244781	238244781	+	Missense_Mutation	SNP	T	T	C	rs11690358	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	44	74	0	0.5	0	T|0.934;C|0.066	0.066	strong	.	COL6A3	608	.	NM_004369	exon40	c.A8962G	p.M2988V	TACCCATGGGCTT	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3148653	3148653	+	Missense_Mutation	SNP	T	T	G	rs1143646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	99	218	0	0.464789	0	T|0.968;G|0.032	0.032	strong	.	HTT	221	.	NM_002111	exon25	c.T3273G	p.I1091M	TTTGATTTTGGCC	.	PASS	Atlas-SNP
KIF7	374654	hgsc.bcm.edu	37	15	90188392	90188392	+	Silent	SNP	A	A	T	rs72750755	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	17	32	0	0.653846	0	A|0.976;T|0.024	0.024	strong	.	KIF7	130	.	NM_198525	exon10	c.T2043A	p.V681V	CCCACCAACTGCT	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151165678	151165678	+	Silent	SNP	T	T	C	rs9871952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217	217	246	0	1	0	T|0.213;C|0.787	0.787	strong	.	IGSF10	279	.	NM_178822	exon4	c.A2091G	p.Q697Q	ACGGAGTTGTGCA	.	PASS	Atlas-SNP
RBM5	10181	hgsc.bcm.edu	37	3	50144951	50144951	+	Silent	SNP	T	T	C	rs1061474	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	109	240	1	0.465812	0.00416667	T|0.327;C|0.673	0.673	strong	.	RBM5	76	.	NM_005778	exon12	c.T990C	p.A330A	CAGCGCTTTCTCT	.	PASS	Atlas-SNP
AP3D1	8943	hgsc.bcm.edu	37	19	2138654	2138654	+	Silent	SNP	T	T	G	rs25672	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	43	103	0	0.614286	0	T|0.695;G|0.304;N|0.000;A|0.000	0.304	strong	.	AP3D1	81	.	NM_001261826	exon2	c.A156C	p.I52I	CACCGCTATGTTG	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58750604	58750604	+	Silent	SNP	G	G	A	rs1058192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	9	103	0	0.1125	0	G|0.286;A|0.714	0.714	strong	GOT2,NS,carcinoma,0,1	GOT2	42	1	NM_002080	exon7	c.C816T	p.C272C	GCAGAGGCAAACA	.	PASS	Atlas-SNP
FLNB	2317	hgsc.bcm.edu	37	3	58109162	58109162	+	Missense_Mutation	SNP	G	G	A	rs1131356	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	74	98	0	0.961039	0	G|0.596;A|0.404	0.404	strong	.	FLNB	430	.	NM_001457	exon21	c.G3469A	p.D1157N	AGCGTCGACTGCT	.	PASS	Atlas-SNP
RAC2	5880	hgsc.bcm.edu	37	22	37622815	37622815	+	Silent	SNP	A	A	G	rs1064498	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	22	70	0	0.37931	0	T|0.000;G|0.229;A|0.771	0.229	strong	.	RAC2	22	.	NM_002872	exon6	c.T477C	p.A159A	GGTGAGAGCTGAG	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187089031	187089031	+	Missense_Mutation	SNP	C	C	A	rs1003995	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	13	43	0	0.433333	0	C|0.721;A|0.278	0.278	strong	.	RTP4	20	.	NM_022147	exon2	c.C611A	p.A204D	AGTCAGCTGAGGC	.	PASS	Atlas-SNP
VARS	7407	hgsc.bcm.edu	37	6	31748675	31748675	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	2	108	0	0.0165289	0	.	.	none	VARS,NS,carcinoma,+1,1	VARS	76	1	NM_006295	exon23	c.G2690A	p.S897N	ACCTCGCTGGGAT	.	scavenged	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72137561	72137561	+	Silent	SNP	G	G	A	rs2240243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	163	164	1	0.993902	0.00609756	G|0.533;A|0.467	0.467	strong	.	DHX38	91	.	NM_014003	exon13	c.G1698A	p.T566T	GCTGACGCAGTAC	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220353532	220353532	+	Missense_Mutation	SNP	C	C	A	rs13026308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	127	268	0	0.738372	0	C|0.913;A|0.087	0.087	strong	.	SPEG	272	.	NM_005876	exon34	c.C8059A	p.P2687T	GAGGTACCCCAGA	.	PASS	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	37	8	95541459	95541459	+	Missense_Mutation	SNP	A	A	C	rs76706433	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	269	167	222	1	0.620818	0.0045045	A|0.989;C|0.011	0.011	strong	.	KIAA1429	176	.	NM_015496	exon7	c.T719G	p.V240G	TCTTCTACTTCTC	.	PASS	Atlas-SNP
C1orf159	54991	hgsc.bcm.edu	37	1	1021346	1021346	+	Silent	SNP	A	A	G	rs10907177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	31	99	0	0.659574	0	A|0.814;G|0.186	0.186	strong	.	C1orf159	9	.	NM_017891	exon7	c.T357C	p.I119I	GGAGCTAATGAAG	.	PASS	Atlas-SNP
TOMM40	10452	hgsc.bcm.edu	37	19	45397229	45397229	+	Silent	SNP	G	G	A	rs1160983	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	51	105	0	0.447368	0	G|0.950;A|0.050	0.050	strong	.	TOMM40	13	.	NM_001128917	exon5	c.G549A	p.S183S	GCAGTCGAAGTTT	.	PASS	Atlas-SNP
MEGF11	84465	hgsc.bcm.edu	37	15	66214785	66214785	+	Silent	SNP	G	G	A	rs11637551	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	50	139	0	0.735294	0	G|0.950;A|0.050	0.050	strong	.	MEGF11	70	.	NM_032445	exon15	c.C1848T	p.H616H	GCAGCCGTGGCCA	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120602208	120602208	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	4	107	0	0.0425532	0	.	.	none	.	GCN1L1	207	.	NM_006836	exon18	c.T1780C	p.S594P	CAAGAGAGGACAG	.	PASS	Atlas-SNP
MS4A6E	245802	hgsc.bcm.edu	37	11	60102507	60102507	+	Missense_Mutation	SNP	G	G	T	rs2304933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	100	184	0	0.549451	0	G|0.705;T|0.295	0.295	strong	.	MS4A6E	22	.	NM_139249	exon1	c.G139T	p.V47F	GTCAAAGTTATTG	.	PASS	Atlas-SNP
OR4A16	81327	hgsc.bcm.edu	37	11	55111584	55111584	+	Missense_Mutation	SNP	A	A	T	rs10896659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	24	62	0	0.428571	0	A|0.589;T|0.411	0.411	strong	.	OR4A16	120	.	NM_001005274	exon1	c.A908T	p.K303M	GTGAAAAGTTAAG	.	PASS	Atlas-SNP
C19orf48	84798	hgsc.bcm.edu	37	19	51301395	51301395	+	Missense_Mutation	SNP	C	C	T	rs4801853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	37	76	0	0.521127	0	C|0.714;N|0.001	.	strong	.	C19orf48	11	.	NM_199249	exon5	c.G311A	p.G104E	TTCACCCCTGGAG	.	PASS	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	37	2	15372562	15372562	+	Missense_Mutation	SNP	C	C	T	rs6710817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	31	77	2	0.397436	0.025974	C|0.899;T|0.101	0.101	strong	NBAS,NS,carcinoma,0,1	NBAS	246	1	NM_015909	exon47	c.G6220A	p.A2074T	CACTGGCGTGGAC	.	scavenged	Atlas-SNP
KRT72	140807	hgsc.bcm.edu	37	12	52981627	52981627	+	Missense_Mutation	SNP	A	A	T	rs7310138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	31	82	0	0.469697	0	A|0.813;T|0.187	0.187	strong	.	KRT72	70	.	NM_001146225	exon7	c.T1098A	p.D366E	CTCCAGATCGGCA	.	PASS	Atlas-SNP
DHRS4L2	317749	hgsc.bcm.edu	37	14	24470138	24470138	+	Nonsense_Mutation	SNP	C	C	T	rs55972438		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1347	637	639	1	0.472903	0.00156495	.	.	weak	DHRS4L2,NS,carcinoma,-1,1	DHRS4L2	29	1	NM_198083	exon4	c.C475T	p.R159X	GAGAAACGAGGGT	.	PASS	Atlas-SNP
ZNF668	79759	hgsc.bcm.edu	37	16	31072912	31072912	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20	9	20	0	0.45	0	.	.	none	.	ZNF668	121	.	NM_001172669	exon4	c.C1406T	p.P469L	GCTGCCGGGGCGG	.	PASS	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	37	1	180080290	180080290	+	Silent	SNP	T	T	A	rs12126496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	111	165	0	0.581152	0	T|0.938;A|0.062	0.062	strong	.	CEP350	418	.	NM_014810	exon38	c.T9348A	p.L3116L	GCTACTTGTGTGA	.	PASS	Atlas-SNP
CHD4	1108	hgsc.bcm.edu	37	12	6709059	6709059	+	Silent	SNP	G	G	A	rs11539542	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	91	224	1	0.459596	0.00446429	G|0.872;A|0.128	0.128	strong	.	CHD4	539	.	NM_001273	exon10	c.C1362T	p.V454V	CTTGCAGACCCGA	.	PASS	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134911655	134911655	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	296	3	300	0	0.0101351	0	.	.	none	EPHB1_ENST00000398015,colon,carcinoma,-1,7	EPHB1	519	7	NM_004441	exon11	c.C2120T	p.S707F	TGGATTCTTTCCT	.	scavenged	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10942756	10942756	+	Nonsense_Mutation	SNP	G	G	A	rs1810540	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	640	224	411	3	0.35	0.00729927	G|0.905;A|0.095	0.095	strong	TPTE_ENST00000361285,NS,carcinoma,+1,4	TPTE	513	4	NM_199261	exon13	c.C685T	p.R229X	TGTATCGCCTTTT	.	scavenged	Atlas-SNP
PDF	64146	hgsc.bcm.edu	37	16	69364030	69364030	+	Silent	SNP	G	G	A	rs3852691	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	10	55	0	0.163934	0	G|0.930;A|0.070	0.070	strong	PDF,NS,carcinoma,0,1	PDF	4	1	NM_022341	exon1	c.C444T	p.F148F	CAGGGGGAAGGGC	.	PASS	Atlas-SNP
KCNE1	3753	hgsc.bcm.edu	37	21	35821821	35821821	+	Missense_Mutation	SNP	T	T	C	rs199809486	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	50	94	0	0.344828	0	.	.	weak	.	KCNE1	23	.	NM_001127669	exon3	c.A112G	p.S38G	CGTCACTGCTGCG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11017141	11017141	+	Silent	SNP	G	G	A	rs75810903	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	29	40	0	0.557692	0	G|0.996;A|0.004	0.004	strong	.	C1orf127	134	.	NM_001170754	exon8	c.C717T	p.L239L	TGGCAGGAGCTCA	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50530501	50530501	+	Missense_Mutation	SNP	A	A	T	rs9617066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	118	266	1	0.517544	0.0037594	A|0.776;T|0.224	0.224	strong	MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	NM_018995	exon2	c.A169T	p.M57L	GATGATATGATCT	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129571330	129571330	+	Missense_Mutation	SNP	G	G	A	rs3816665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	57	93	0	0.575758	0	G|0.744;A|0.256	0.256	strong	.	LAMA2	481	.	NM_000426	exon13	c.G1856A	p.R619H	CAGAACGTGTTCT	.	PASS	Atlas-SNP
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797919	31797919	+	Silent	SNP	G	G	A	rs73356706	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	61	108	0	0.356725	0	G|0.975;A|0.025	0.025	strong	.	KRTAP13-3	47	.	NM_181622	exon1	c.C312T	p.S104S	GCTATTGGATCCA	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32638550	32638550	+	Missense_Mutation	SNP	C	C	T	rs2070418	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	49	100	0	0.401639	0	C|0.874;A|0.001	.	strong	.	TIAM1	522	.	NM_003253	exon5	c.G739A	p.G247R	GCCCCCCGTTTGC	.	PASS	Atlas-SNP
ITGA2	3673	hgsc.bcm.edu	37	5	52351413	52351413	+	Silent	SNP	G	G	A	rs1062535	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	97	127	1	1	0.00787402	G|0.627;A|0.373	0.373	strong	.	ITGA2	211	.	NM_002203	exon8	c.G825A	p.T275T	TGCTACGAAAGTA	.	PASS	Atlas-SNP
CPB2	1361	hgsc.bcm.edu	37	13	46648094	46648094	+	Missense_Mutation	SNP	C	C	T	rs3742264	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	26	59	0	0.440678	0	C|0.653;T|0.347	0.347	strong	.	CPB2	60	.	NM_001872	exon6	c.G505A	p.A169T	TGGCTGCTTGTTC	.	PASS	Atlas-SNP
SLAMF1	6504	hgsc.bcm.edu	37	1	160616703	160616703	+	Missense_Mutation	SNP	G	G	T	rs2295612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	285	169	228	1	0.592982	0.00438596	G|0.877;T|0.123	0.123	strong	SLAMF1,colon,carcinoma,0,1	SLAMF1	74	1	NM_003037	exon1	c.C33A	p.F11L	CAGCACGAAGGTC	.	PASS	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	37	9	136324239	136324239	+	Silent	SNP	C	C	A	rs1055432	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	73	108	0	0.52518	0	C|0.769;A|0.231	0.231	strong	.	ADAMTS13	113	.	NM_139025	exon29	c.C4221A	p.T1407T	CTGGACCCTCCAA	.	PASS	Atlas-SNP
TTC5	91875	hgsc.bcm.edu	37	14	20770036	20770036	+	Missense_Mutation	SNP	T	T	C	rs3742945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	364	136	292	2	0.373626	0.00684932	T|0.243;C|0.757	0.757	strong	TTC5,NS,adenoma,0,1	TTC5	34	1	NM_138376	exon2	c.A140G	p.Q47R	TCCTTCTGCACAT	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179440029	179440029	+	Silent	SNP	G	G	A	rs12464787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	80	152	0	0.544218	0	G|0.832;A|0.168	0.168	strong	.	TTN	18412	.	NM_001267550	exon326	c.C70830T	p.S23610S	CCCCGCGCTGTTC	.	PASS	Atlas-SNP
SIVA1	10572	hgsc.bcm.edu	37	14	105222037	105222037	+	Silent	SNP	C	C	T	rs1132975	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	146	75	0	1	0	C|0.646;T|0.354	0.354	strong	.	SIVA1	12	.	NM_006427	exon2	c.C189T	p.A63A	CTGTGCCGTCGTT	.	PASS	Atlas-SNP
ZNF195	7748	hgsc.bcm.edu	37	11	3380678	3380678	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	3	94	3	0.0319149	0.0319149	.	.	none	ZNF195,NS,carcinoma,0,4	ZNF195	77	4	NM_001130520	exon6	c.G1560A	p.K520K	GTAGGGCTTCTCT	.	scavenged	Atlas-SNP
SLC13A4	26266	hgsc.bcm.edu	37	7	135376041	135376041	+	Missense_Mutation	SNP	G	G	A	rs36004833	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	27	158	0	0.313953	0	G|0.976;A|0.024	0.024	strong	.	SLC13A4	56	.	NM_012450	exon13	c.C1351T	p.P451S	TGATGGGCTCGGT	.	PASS	Atlas-SNP
HIVEP3	59269	hgsc.bcm.edu	37	1	42046613	42046613	+	Silent	SNP	G	G	T	rs12132697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	63	103	0	0.732558	0	G|0.838;T|0.162	0.162	strong	HIVEP3,NS,carcinoma,0,1	HIVEP3	235	1	NM_024503	exon4	c.C3856A	p.R1286R	GTAGCCGGATGTC	.	PASS	Atlas-SNP
RTEL1	51750	hgsc.bcm.edu	37	20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	rs190887884	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	13	53	0	0.382353	0	G|0.994;A|0.006	0.006	strong	.	RTEL1	114	.	NM_032957	exon27	c.G2618A	p.G873D	GCCCTGGCGAGGA	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109377070	109377070	+	Missense_Mutation	SNP	C	C	A	rs12060255	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	27	64	0	0.75	0	C|0.870;A|0.130	0.130	strong	.	AKNAD1	83	.	NM_152763	exon9	c.G1745T	p.G582V	ATTACCCCAGAGT	.	PASS	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	452	15	173	4	0.0331858	0.0231214	.	.	weak	PRB1,NS,carcinoma,0,2	PRB1	33	2	NM_199353	exon4	c.A350G	p.K117R	TGAGGTTTGTTGC	.	scavenged	Atlas-SNP
SLC25A48	153328	hgsc.bcm.edu	37	5	135178142	135178142	+	Silent	SNP	A	A	G	rs6596270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	72	128	0	0.549618	0	A|0.820;G|0.180	0.180	strong	.	SLC25A48	37	.	NM_145282	exon2	c.A84G	p.T28T	GGACACAGTCAAG	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14992031	14992031	+	Missense_Mutation	SNP	A	A	G	rs10405129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	27	102	0	0.375	0	A|0.747;G|0.253	0.253	strong	.	OR7A17	37	.	NM_030901	exon1	c.T137C	p.I46T	GCCAGGATGATGA	.	PASS	Atlas-SNP
PNPLA2	57104	hgsc.bcm.edu	37	11	823809	823809	+	Silent	SNP	C	C	G	rs1135628	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	26	52	0	0.509804	0	C|0.796;G|0.204	0.204	strong	.	PNPLA2	26	.	NM_020376	exon7	c.C873G	p.P291P	GCTGCCCGGAGAA	.	PASS	Atlas-SNP
CRADD	8738	hgsc.bcm.edu	37	12	94243853	94243853	+	Silent	SNP	C	C	T	rs56944668	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	61	160	0	0.717647	0	C|0.825;T|0.175	0.175	strong	CRADD,colon,carcinoma,0,1	CRADD	21	1	NM_003805	exon3	c.C406T	p.L136L	ATGGTGCTGTCTC	.	PASS	Atlas-SNP
SMURF1	57154	hgsc.bcm.edu	37	7	98645367	98645367	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	3	146	0	0.0184049	0	.	.	none	SMURF1,NS,carcinoma,0,1	SMURF1	58	1	NM_020429	exon11	c.G1170A	p.S390S	CTGAAGCGACAGT	.	scavenged	Atlas-SNP
GIPC1	10755	hgsc.bcm.edu	37	19	14590279	14590279	+	Missense_Mutation	SNP	G	G	C	rs45458894	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	33	118	0	0.532258	0	G|0.904;C|0.096	0.096	strong	.	GIPC1	21	.	NM_202468	exon6	c.C713G	p.T238S	CGGCCAGTGCCCA	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	20089944	20089944	+	Silent	SNP	T	T	C	rs1442710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	47	89	0	0.505376	0	T|0.724;C|0.276	0.276	strong	.	NAV2	255	.	NM_001244963	exon24	c.T5151C	p.N1717N	AGCAAATGTAAGT	.	PASS	Atlas-SNP
TMEM259	91304	hgsc.bcm.edu	37	19	1010406	1010406	+	Silent	SNP	G	G	A	rs62131162	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14	11	16	0	0.785714	0	G|0.903;A|0.097	0.097	strong	.	.	.	.	NM_001033026	exon11	c.C1806T	p.G602G	AGGCCCGCCTACC	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145523105	145523105	+	Silent	SNP	G	G	A	rs11540217	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	42	56	0	1	0	G|0.794;A|0.206	0.206	strong	.	LARS	100	.	NM_020117	exon19	c.C1747T	p.L583L	AAGGCAGGTGAGT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149519184	149519184	+	Missense_Mutation	SNP	C	C	T	rs1008336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15	4	32	0	0.266667	0	C|0.831;T|0.169	0.169	strong	.	.	.	.	NM_198455	exon90	c.C12988T	p.R4330C	GCCTCTCGCTCTG	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	37	22	50722167	50722167	+	Missense_Mutation	SNP	T	T	C	rs28470336	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	43	80	0	0.632353	0	T|0.968;C|0.032	0.032	strong	.	PLXNB2	172	.	NM_012401	exon15	c.A2434G	p.T812A	GGCCCGTCTCAGG	.	PASS	Atlas-SNP
WDR33	55339	hgsc.bcm.edu	37	2	128464116	128464116	+	Silent	SNP	G	G	A	rs34550770	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	31	57	0	0.5	0	G|0.935;A|0.065	0.065	strong	.	WDR33	136	.	NM_018383	exon22	c.C3792T	p.G1264G	TCCTGGGCCCCCT	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187088812	187088812	+	Missense_Mutation	SNP	C	C	T	rs3821812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	76	152	0	0.45509	0	C|0.657;N|0.000	.	strong	.	RTP4	20	.	NM_022147	exon2	c.C392T	p.T131M	ATGGCACGAGGAA	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107620867	107620867	+	Missense_Mutation	SNP	C	C	T	rs2230806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	65	181	0	0.384615	0	C|0.587;T|0.413	0.413	strong	ABCA1,NS,carcinoma,0,1	ABCA1	244	1	NM_005502	exon7	c.G656A	p.R219K	TTCTCCCTTGGTA	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34726182	34726182	+	Missense_Mutation	SNP	A	A	G	rs62547040		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	262	554	1	0.988679	0.00180505	.	.	weak	.	FAM205A	45	.	NM_001141917	exon4	c.T1055C	p.F352S	GTCTCAAATCTAT	.	PASS	Atlas-SNP
KCNH6	81033	hgsc.bcm.edu	37	17	61607708	61607708	+	Silent	SNP	T	T	C	rs7221517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	48	101	0	0.457143	0	T|0.671;C|0.329	0.329	strong	.	KCNH6	122	.	NM_030779	exon4	c.T480C	p.H160H	CTCTCATGGCAGG	.	PASS	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223567803	223567803	+	Missense_Mutation	SNP	G	G	A	rs10907376	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	58	146	0	0.394558	0	G|0.814;A|0.186	0.186	strong	C1orf65,NS,carcinoma,0,4	C1orf65	71	4	NM_152610	exon1	c.G986A	p.G329D	AGCGCGGCCTGCG	.	PASS	Atlas-SNP
XRCC4	7518	hgsc.bcm.edu	37	5	82648943	82648943	+	Splice_Site	SNP	G	G	A	rs1805377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	73	196	0	0.445122	0	G|0.679;A|0.321	0.321	strong	.	XRCC4	37	.	NM_022406	exon8	c.894-1G>A	.	TTTTCAGTTCTAG	.	PASS	Atlas-SNP
SYT14	255928	hgsc.bcm.edu	37	1	210334081	210334081	+	Silent	SNP	T	T	C	rs17188183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	53	116	0	0.401515	0	T|0.914;C|0.086	0.086	strong	.	SYT14	89	.	NM_001146261	exon10	c.T1554C	p.Y518Y	TACATATGTTAAG	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912002	45912002	+	Missense_Mutation	SNP	A	A	C	rs735482	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	18	49	0	0.382979	0	A|0.771;C|0.229	0.229	strong	.	CD3EAP	27	.	NM_012099	exon3	c.A776C	p.K259T	AAGGGAAAGAAAC	.	PASS	Atlas-SNP
OR4D2	124538	hgsc.bcm.edu	37	17	56247454	56247454	+	Silent	SNP	A	A	G	rs9912728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	41	73	0	0.493976	0	A|0.890;G|0.110	0.110	strong	.	OR4D2	48	.	NM_001004707	exon1	c.A438G	p.V146V	GGTGGTAGCCACC	.	PASS	Atlas-SNP
OR6P1	128366	hgsc.bcm.edu	37	1	158533140	158533140	+	Silent	SNP	A	A	G	rs12080815	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	60	84	0	0.618557	0	A|0.465;G|0.535	0.535	strong	OR6P1,NS,carcinoma,0,1	OR6P1	47	1	NM_001160325	exon1	c.T255C	p.F85F	GGTAAGAAAGGCT	.	PASS	Atlas-SNP
FAM179B	23116	hgsc.bcm.edu	37	14	45481271	45481271	+	Silent	SNP	C	C	T	rs144530053	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	107	141	0	0.629412	0	C|0.990;T|0.010	0.010	strong	.	FAM179B	115	.	NM_015091	exon7	c.C3231T	p.P1077P	AAGCCCCAGTGCA	.	PASS	Atlas-SNP
OR2G3	81469	hgsc.bcm.edu	37	1	247769062	247769062	+	Missense_Mutation	SNP	A	A	G	rs61748963	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	560	346	459	1	0.617857	0.00217865	A|0.914;G|0.086	0.086	strong	OR2G3,NS,carcinoma,-2,2	OR2G3	108	2	NM_001001914	exon1	c.A175G	p.M59V	ACCCCAATGTACT	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195448	18195448	+	Silent	SNP	C	C	T	rs4630269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	65	97	1	0.532787	0.0103093	C|0.710;T|0.290	0.290	strong	MRGPRX4,NS,adenoma,0,1	MRGPRX4	68	1	NM_054032	exon1	c.C645T	p.Y215Y	GCTGTACGTGACC	.	scavenged	Atlas-SNP
DOCK11	139818	hgsc.bcm.edu	37	X	117722176	117722176	+	Silent	SNP	G	G	A	rs41312765	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	84	182	0	1	0	G|0.917;A|0.083	0.083	strong	.	DOCK11	185	.	NM_144658	exon17	c.G1872A	p.E624E	TGAAGAGTTTGTT	.	PASS	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879410	39879410	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	9	206	0	0.155172	0	.	.	none	KIAA0754_ENST00000530275,NS,carcinoma,-1,2	KIAA0754	93	2	NM_015038	exon1	c.C3473T	p.S1158F	CCGCCTCCGCAGC	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149516881	149516881	+	Missense_Mutation	SNP	G	G	T	rs1005603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	17	110	0	0.293103	0	G|0.799;T|0.201	0.201	strong	.	.	.	.	NM_198455	exon85	c.G12083T	p.S4028I	TGAGAAGCCGCAG	.	PASS	Atlas-SNP
TAP2	6891	hgsc.bcm.edu	37	6	32798548	32798548	+	Silent	SNP	G	G	A	rs200734705		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	59	113	0	0.526786	0	.	.	weak	.	TAP2	98	.	NM_018833	exon8	c.C1308T	p.N436N	TCCCACGTTGCTG	.	PASS	Atlas-SNP
SLC6A11	6538	hgsc.bcm.edu	37	3	10885920	10885920	+	Silent	SNP	T	T	C	rs2304725	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	172	177	2	0.99422	0.0112994	T|0.655;C|0.345	0.345	strong	SLC6A11,NS,adenoma,0,1	SLC6A11	87	1	NM_014229	exon5	c.T645C	p.S215S	CATCTCTGACGGG	.	scavenged	Atlas-SNP
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774076	140774076	+	Missense_Mutation	SNP	G	G	T	rs367855808		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	83	172	0	0.456044	0	.	.	weak	.	PCDHGA8	146	.	NM_014004	exon1	c.G1696T	p.A566S	TACCCCGCCCTCC	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133899008	133899008	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	72	76	0	0.423529	0	.	.	none	.	TG	416	.	NM_003235	exon9	c.C1391A	p.P464Q	CCAACCCAAAGAG	.	PASS	Atlas-SNP
PCGF3	10336	hgsc.bcm.edu	37	4	755129	755129	+	Silent	SNP	C	C	T	rs2242234	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	72	198	0	0.444444	0	C|0.930;T|0.070	0.070	strong	.	PCGF3	23	.	NM_006315	exon9	c.C525T	p.R175R	GATCCGCTGCTCA	.	PASS	Atlas-SNP
KCNK10	54207	hgsc.bcm.edu	37	14	88652389	88652389	+	Silent	SNP	C	C	T	rs3742692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	42	101	0	0.461538	0	C|0.786;T|0.214	0.214	strong	KCNK10_ENST00000319231,NS,carcinoma,0,3	KCNK10	273	3	NM_138318	exon7	c.G1122A	p.A374A	GGTGGCCGCCCGC	.	PASS	Atlas-SNP
MYBPC3	4607	hgsc.bcm.edu	37	11	47365164	47365164	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	4	89	0	0.0412371	0	.	.	none	.	MYBPC3	102	.	NM_000256	exon13	c.A1102G	p.K368E	CCAGCTTCTTCTG	.	PASS	Atlas-SNP
MTX3	345778	hgsc.bcm.edu	37	5	79282798	79282798	+	Missense_Mutation	SNP	G	G	C	rs9293796	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	55	91	0	0.495495	0	G|0.925;C|0.075	0.075	strong	.	MTX3	29	.	NM_001010891	exon7	c.C714G	p.S238R	ATAACTGCTCAGG	.	PASS	Atlas-SNP
UCN3	114131	hgsc.bcm.edu	37	10	5415954	5415954	+	Missense_Mutation	SNP	A	A	G	rs10904481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	35	51	0	0.945946	0	A|0.639;G|0.361	0.361	strong	.	UCN3	13	.	NM_053049	exon2	c.A271G	p.R91G	GGAGCCAGAGGCA	.	PASS	Atlas-SNP
VN1R1	57191	hgsc.bcm.edu	37	19	57967049	57967049	+	Missense_Mutation	SNP	G	G	T	rs61744949	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	321	142	415	0	0.442368	0	G|0.675;T|0.325	0.325	strong	.	VN1R1	48	.	NM_020633	exon1	c.C806A	p.A269D	GCTCTGGCTTCCT	.	PASS	Atlas-SNP
ZBTB1	22890	hgsc.bcm.edu	37	14	64988924	64988924	+	Silent	SNP	T	T	C	rs10133411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	77	112	0	0.611111	0	T|0.831;C|0.169	0.169	strong	ZBTB1_ENST00000394712,adrenal_gland,adrenal_cortical_adenoma,0,2	ZBTB1	93	2	NM_014950	exon2	c.T702C	p.H234H	TGAGCATGTGCTA	.	PASS	Atlas-SNP
GANAB	23193	hgsc.bcm.edu	37	11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	rs76572368	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	92	205	0	0.403509	0	T|0.974;C|0.026	0.026	strong	.	GANAB	110	.	NM_198335	exon16	c.A1846G	p.M616V	GTTCCATGCCCCC	.	PASS	Atlas-SNP
UGGT2	55757	hgsc.bcm.edu	37	13	96638651	96638651	+	Missense_Mutation	SNP	C	C	T	rs12863903	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	34	58	0	0.586207	0	C|0.894;T|0.106	0.106	strong	.	UGGT2	127	.	NM_020121	exon9	c.G967A	p.A323T	CTGGAGCGGACAT	.	PASS	Atlas-SNP
PTCHD3	374308	hgsc.bcm.edu	37	10	27702725	27702725	+	Missense_Mutation	SNP	A	A	G	rs6482626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	13	113	0	0.2	0	A|0.769;G|0.231	0.231	strong	.	PTCHD3	140	.	NM_001034842	exon1	c.T455C	p.L152P	GTGCCCAGCGCGG	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33602757	33602757	+	Silent	SNP	C	C	T	rs10420258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	56	151	0	0.380952	0	C|0.829;T|0.171	0.171	strong	.	GPATCH1	79	.	NM_018025	exon12	c.C1713T	p.H571H	CACTCACGCCAAG	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140532165	140532165	+	Missense_Mutation	SNP	G	G	A	rs17844444	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	114	218	0	0.493506	0	G|0.864;A|0.136	0.136	strong	.	PCDHB6	161	.	NM_018939	exon1	c.G2327A	p.G776D	CTCAGGGCACTGA	.	PASS	Atlas-SNP
LPAR1	1902	hgsc.bcm.edu	37	9	113637854	113637854	+	Silent	SNP	G	G	A	rs3739709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	122	212	1	0.519149	0.00471698	G|0.863;A|0.137	0.137	strong	LPAR1,NS,carcinoma,-1,2	LPAR1	48	2	NM_001401	exon4	c.C942T	p.R314R	TTTGTCGCGGTAG	.	PASS	Atlas-SNP
FAM134A	79137	hgsc.bcm.edu	37	2	220046840	220046840	+	Missense_Mutation	SNP	G	G	A	rs3210652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	20	96	0	0.289855	0	G|0.902;A|0.098	0.098	strong	.	FAM134A	34	.	NM_024293	exon9	c.G1121A	p.R374H	TAGGCCGTCCTCA	.	PASS	Atlas-SNP
SIK1	150094	hgsc.bcm.edu	37	21	44846016	44846016	+	Missense_Mutation	SNP	C	C	T	rs3746951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	19	65	0	0.296875	0	C|0.827;T|0.173	0.173	strong	.	SIK1	65	.	NM_173354	exon2	c.G43A	p.G15S	CCTGACCCTGGCC	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119545	19119545	+	Silent	SNP	C	C	T	rs45604134	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	56	93	0	0.478632	0	C|0.846;T|0.154	0.154	strong	.	TSSK2	29	.	NM_053006	exon1	c.C633T	p.C211C	GGTCTGCGGCTCC	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51917968	51917968	+	Silent	SNP	T	T	G	rs4715271	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	38	101	0	0.376238	0	T|0.921;G|0.079	0.079	strong	PKHD1_ENST00000340994,NS,malignant_melanoma,-1,4	PKHD1	927	4	NM_170724	exon21	c.A2046C	p.P682P	CAGCACTGGGGAG	.	PASS	Atlas-SNP
RPSA	3921	hgsc.bcm.edu	37	3	39453160	39453160	+	Silent	SNP	G	G	A	rs2269350	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	22	67	0	0.407407	0	G|0.745;A|0.255	0.255	strong	.	RPSA	15	.	NM_001012321	exon4	c.G519A	p.L173L	GGGTTTGATGTGG	.	PASS	Atlas-SNP
STYK1	55359	hgsc.bcm.edu	37	12	10783729	10783729	+	Silent	SNP	A	A	G	rs2290717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	111	130	0	0.965217	0	A|0.701;G|0.299	0.299	strong	.	STYK1	55	.	NM_018423	exon5	c.T366C	p.S122S	GCTACCACTGCAA	.	PASS	Atlas-SNP
PGM1	5236	hgsc.bcm.edu	37	1	64114301	64114301	+	Missense_Mutation	SNP	T	T	C	rs11208257	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	6	78	0	0.136364	0	T|0.809;C|0.191	0.191	strong	PGM1_ENST00000371083,NS,carcinoma,0,2	PGM1	75	2	NM_001172818	exon8	c.T1312C	p.Y438H	CAAAAGTATGGCC	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887936	9887936	+	Missense_Mutation	SNP	G	G	C	rs17805544	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	294	141	286	0	0.479592	0	G|0.916;C|0.084	0.084	strong	.	TXNDC2	168	.	NM_001098529	exon2	c.G1460C	p.R487T	CCATCAGACCATT	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103141351	103141351	+	Silent	SNP	G	G	A	rs2229862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	182	168	0	0.983784	0	T|0.003;G|0.860;C|0.102;A|0.035	0.035	strong	.	RELN	593	.	NM_173054	exon53	c.C8508T	p.F2836F	CTGATAGAACCTA	.	PASS	Atlas-SNP
ADI1	55256	hgsc.bcm.edu	37	2	3504687	3504687	+	Silent	SNP	A	A	G	rs9950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	76	194	2	0.463415	0.0103093	A|0.473;G|0.527	0.527	strong	ADI1,NS,carcinoma,0,1	ADI1	12	1	NM_018269	exon3	c.T318C	p.D106D	CCTCACATCGAAG	.	scavenged	Atlas-SNP
CLEC19A	728276	hgsc.bcm.edu	37	16	19310092	19310092	+	Silent	SNP	T	T	C	rs1548450	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	54	124	0	0.385714	0	T|0.566;C|0.434	0.434	strong	CLEC19A_ENST00000465414,NS,carcinoma,0,2	CLEC19A	4	2	NM_001256720	exon2	c.T186C	p.A62A	CTGGGCTGAGGCC	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4935985	4935985	+	Missense_Mutation	SNP	C	C	G	rs35869286	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	51	78	0	0.542553	0	C|0.942;G|0.058	0.058	strong	PPL,NS,carcinoma,0,1	PPL	168	1	NM_002705	exon22	c.G2671C	p.E891Q	ACGCCTCCTCCAC	.	PASS	Atlas-SNP
SEMA4A	64218	hgsc.bcm.edu	37	1	156146218	156146218	+	Silent	SNP	C	C	T	rs12401573	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	124	109	0	0.992	0	C|0.508;T|0.492	0.492	strong	.	SEMA4A	75	.	NM_001193300	exon15	c.C1716T	p.P572P	TGTCCCCAACTCC	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218683257	218683257	+	Silent	SNP	A	A	G	rs2571442	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	110	174	1	0.973451	0.00574713	T|0.000;G|0.418;A|0.582	0.418	strong	.	TNS1	251	.	NM_022648	exon24	c.T3486C	p.A1162A	AGCTCGAGCCTGG	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50502526	50502526	+	Silent	SNP	A	A	G	rs11568187	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	39	190	0	0.253247	0	A|0.894;G|0.106	0.106	strong	.	MLC1	48	.	NM_015166	exon11	c.T996C	p.S332S	CCTTGCACTGACC	.	PASS	Atlas-SNP
SLCO1B7	338821	hgsc.bcm.edu	37	12	21176135	21176135	+	Missense_Mutation	SNP	T	T	C	rs1546308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	427	425	506	1	0.995316	0.00197628	T|0.041;C|0.959	0.959	strong	.	SLCO1B7	85	.	NM_001009562	exon5	c.T500C	p.V167A	TGAATGTAATGGG	.	PASS	Atlas-SNP
NRG2	9542	hgsc.bcm.edu	37	5	139422232	139422232	+	Silent	SNP	G	G	A	rs144634106	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	37	90	0	0.578125	0	G|0.965;A|0.035	0.035	strong	.	NRG2	69	.	NM_013982	exon1	c.C423T	p.A141A	GCCGCCGGCTGGG	.	PASS	Atlas-SNP
SYTL5	94122	hgsc.bcm.edu	37	X	37935844	37935844	+	Silent	SNP	G	G	A	rs12558731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	40	146	0	0.97561	0	G|0.993;A|0.007	0.007	strong	.	SYTL5	72	.	NM_001163334	exon5	c.G579A	p.S193S	CAGATCGGCAACC	.	PASS	Atlas-SNP
MEF2A	4205	hgsc.bcm.edu	37	15	100252892	100252892	+	Silent	SNP	A	A	G	rs34851361	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	22	180	0	0.211538	0	A|0.949;G|0.051	0.051	strong	.	MEF2A	138	.	NM_005587	exon11	c.A1416G	p.P472P	TTCTCCAATTGTG	.	PASS	Atlas-SNP
FASN	2194	hgsc.bcm.edu	37	17	80045086	80045086	+	Silent	SNP	G	G	C	rs4485435	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	44	120	0	0.423077	0	G|0.762;C|0.238	0.238	strong	.	FASN	154	.	NM_004104	exon21	c.C3267G	p.A1089A	GCCTCCGGCCACT	.	PASS	Atlas-SNP
STIL	6491	hgsc.bcm.edu	37	1	47746678	47746678	+	Silent	SNP	G	G	C	rs10789505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	113	282	1	0.719745	0.0035461	G|0.817;C|0.183	0.183	strong	.	STIL	91	.	NM_003035	exon12	c.C1452G	p.S484S	TCTCAAGGAAGGC	.	PASS	Atlas-SNP
GLI3	2737	hgsc.bcm.edu	37	7	42004600	42004600	+	Silent	SNP	G	G	A	rs34089404	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	44	114	0	0.305556	0	G|0.927;A|0.073	0.073	strong	.	GLI3	312	.	NM_000168	exon15	c.C4071T	p.Y1357Y	CCCTTGGTAGATG	.	PASS	Atlas-SNP
OR5D18	219438	hgsc.bcm.edu	37	11	55587914	55587914	+	Missense_Mutation	SNP	A	A	G	rs55832853	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	56	127	1	0.486957	0.00787402	A|0.774;G|0.226	0.226	strong	OR5D18,NS,carcinoma,-1,1	OR5D18	121	1	NM_001001952	exon1	c.A809G	p.H270R	CCAGGCACACAGT	.	scavenged	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40363926	40363926	+	Missense_Mutation	SNP	C	C	G	rs3746013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	89	178	0	0.494444	0	C|0.746;G|0.254	0.254	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon31	c.G14716C	p.D4906H	GGAGATCTCCAGC	.	PASS	Atlas-SNP
SLC1A4	6509	hgsc.bcm.edu	37	2	65245365	65245365	+	Missense_Mutation	SNP	G	G	A	rs759458	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	41	120	0	0.37963	0	G|0.791;N|0.001	.	strong	SLC1A4,NS,carcinoma,-2,1	SLC1A4	33	1	NM_003038	exon6	c.G1195A	p.V399I	AACAACGTAGAGC	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151166058	151166058	+	Missense_Mutation	SNP	G	G	A	rs17204557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	330	155	382	0	0.469697	0	G|0.971;A|0.029	0.029	strong	.	IGSF10	279	.	NM_178822	exon4	c.C1711T	p.P571S	CCAAAGGTTCTAC	.	PASS	Atlas-SNP
BCL9L	283149	hgsc.bcm.edu	37	11	118769604	118769604	+	Silent	SNP	C	C	T	rs61751532	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	327	221	200	1	0.675841	0.005	C|0.941;T|0.059	0.059	strong	.	BCL9L	254	.	NM_182557	exon8	c.G4020A	p.Q1340Q	GAAGTACTGGAGG	.	PASS	Atlas-SNP
NUFIP2	57532	hgsc.bcm.edu	37	17	27613677	27613677	+	Silent	SNP	G	G	A	rs12452857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	77	134	0	0.542253	0	G|0.815;A|0.185	0.185	strong	.	NUFIP2	60	.	NM_020772	exon2	c.C1335T	p.P445P	AGAGATGGGTGTT	.	PASS	Atlas-SNP
TOMM5	401505	hgsc.bcm.edu	37	9	37592452	37592452	+	Silent	SNP	G	G	A	rs7021977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	57	133	0	0.448819	0	G|0.834;A|0.166	0.166	strong	.	TOMM5	3	.	NM_001134485	exon1	c.C78T	p.S26S	TATGGAGGAGATC	.	PASS	Atlas-SNP
PHC2	1912	hgsc.bcm.edu	37	1	33790496	33790496	+	Silent	SNP	G	G	A	rs11554674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	25	99	0	0.352113	0	G|0.830;A|0.170	0.170	strong	.	PHC2	78	.	NM_198040	exon14	c.C2547T	p.Y849Y	GCGGGCGTAGATC	.	PASS	Atlas-SNP
SNX13	23161	hgsc.bcm.edu	37	7	17854532	17854532	+	Silent	SNP	G	G	T	rs2723501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	66	69	0	0.985075	0	G|0.331;T|0.669	0.669	strong	.	SNX13	113	.	NM_015132	exon20	c.C1989A	p.P663P	TAAAGCGGGGGAT	.	PASS	Atlas-SNP
ARHGEF11	9826	hgsc.bcm.edu	37	1	156909695	156909695	+	Silent	SNP	G	G	A	rs2275199	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17	16	11	0	0.941176	0	G|0.817;A|0.183	0.183	strong	.	ARHGEF11	168	.	NM_198236	exon37	c.C3741T	p.N1247N	TCGCAGGTTCTCC	.	PASS	Atlas-SNP
TXNDC16	57544	hgsc.bcm.edu	37	14	52981664	52981664	+	Missense_Mutation	SNP	G	G	C	rs117463339	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	37	67	0	0.37	0	G|0.979;C|0.021	0.021	strong	.	TXNDC16	59	.	NM_020784	exon8	c.C539G	p.A180G	ACAAAAGCGGCTT	.	PASS	Atlas-SNP
DISC1	27185	hgsc.bcm.edu	37	1	231902975	231902975	+	Missense_Mutation	SNP	C	C	T	rs28930675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	32	108	0	0.258065	0	C|0.998;T|0.002	0.002	strong	.	DISC1	207	.	NM_001164537	exon6	c.C1454T	p.T485M	CCATCACGAGACG	.	PASS	Atlas-SNP
KDR	3791	hgsc.bcm.edu	37	4	55973911	55973911	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	2	174	0	0.0124224	0	.	.	none	KDR,NS,carcinoma,0,1	KDR	307	1	NM_002253	exon10	c.G1405A	p.E469K	TGGGCTCGTTGGC	.	scavenged	Atlas-SNP
AVPR1B	553	hgsc.bcm.edu	37	1	206225260	206225260	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	39	144	0	0.205263	0	.	.	none	.	AVPR1B	47	.	NM_000707	exon1	c.C820G	p.R274G	ATCTCACGGGCCA	.	PASS	Atlas-SNP
PRTG	283659	hgsc.bcm.edu	37	15	55970041	55970041	+	Silent	SNP	A	A	G	rs11854213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	27	117	0	0.287234	0	A|0.787;G|0.213	0.213	strong	.	PRTG	110	.	NM_173814	exon8	c.T1335C	p.N445N	GTCTGAATTATAA	.	PASS	Atlas-SNP
PRTG	283659	hgsc.bcm.edu	37	15	55972797	55972797	+	Missense_Mutation	SNP	T	T	C	rs16976466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	29	244	0	0.205674	0	C|0.201;N|0.000	0.201	strong	.	PRTG	110	.	NM_173814	exon5	c.A706G	p.T236A	TAATTGTTGGTGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681920	100681920	+	Missense_Mutation	SNP	C	C	T	rs140211048	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	314	16	210	0	0.0509554	0	C|1.000;T|0.000	0.000	strong	MUC17,NS,carcinoma,-1,1	MUC17	804	1	NM_001040105	exon3	c.C7223T	p.P2408L	CCATGCCGGTGGT	.	PASS	Atlas-SNP
GLG1	2734	hgsc.bcm.edu	37	16	74490556	74490556	+	Silent	SNP	G	G	A	rs9945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	79	108	0	0.822917	0	T|0.028;G|0.674;C|0.146;A|0.153	0.153	strong	.	GLG1	106	.	NM_001145667	exon25	c.C3363T	p.Y1121Y	TGCTGCGTAACTC	.	PASS	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65310489	65310489	+	Silent	SNP	T	T	C	rs2230588	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	79	152	0	0.738318	0	T|0.670;C|0.330	0.330	strong	.	JAK1	209	.	NM_002227	exon16	c.A2199G	p.P733P	GATGAATGGGCCA	.	PASS	Atlas-SNP
C20orf85	128602	hgsc.bcm.edu	37	20	56735761	56735761	+	Silent	SNP	C	C	T	rs61749694	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	36	90	0	0.45	0	C|0.997;T|0.003	0.003	strong	.	C20orf85	35	.	NM_178456	exon4	c.C297T	p.I99I	CTTCATCGGCTGG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8154990	8154990	+	Silent	SNP	C	C	T	rs35002391	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	53	102	0	0.509615	0	C|0.668;T|0.332	0.332	strong	.	FBN3	300	.	NM_032447	exon48	c.G6177A	p.E2059E	GCTGCCCTCCTGG	.	PASS	Atlas-SNP
RNF39	80352	hgsc.bcm.edu	37	6	30041009	30041009	+	Missense_Mutation	SNP	A	A	G	rs2074479	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	73	167	0	0.462025	0	A|0.808;G|0.192	0.192	strong	RNF39_ENST00000244360,NS,carcinoma,+1,1	RNF39	27	1	NM_025236	exon3	c.T607C	p.S203P	ACTTGGATGTTGG	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2833643	2833643	+	Missense_Mutation	SNP	C	C	A	rs115332247	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	28	194	0	0.294737	0	.	.	strong	.	ARSD	47	.	NM_001669	exon6	c.G954T	p.Q318H	GCCATGCTGACTT	.	PASS	Atlas-SNP
ITGA2B	3674	hgsc.bcm.edu	37	17	42453065	42453065	+	Missense_Mutation	SNP	A	A	C	rs5911	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	33	87	0	0.485294	0	A|0.621;C|0.379	0.379	strong	ITGA2B,NS,carcinoma,0,1	ITGA2B	88	1	NM_000419	exon26	c.T2621G	p.I874S	CTGGGGATGGGCA	.	PASS	Atlas-SNP
DNAJB3	414061	hgsc.bcm.edu	37	2	234652347	234652347	+	Silent	SNP	C	C	G	rs13009407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	50	114	0	0.50505	0	C|0.867;G|0.133	0.133	strong	.	.	.	.	NM_001001394	exon1	c.G216C	p.G72G	CTCCGCCCCCGCC	.	PASS	Atlas-SNP
DNMT1	1786	hgsc.bcm.edu	37	19	10265593	10265593	+	Silent	SNP	G	G	T	rs2228613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	59	121	0	0.508621	0	T|0.063;G|0.937;C|0.000	0.063	strong	.	DNMT1	148	.	NM_001130823	exon20	c.C1632A	p.I544I	CTTGTTGATCAGG	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102584104	102584104	+	Missense_Mutation	SNP	T	T	G	rs35866072	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	68	154	0	0.328502	0	T|0.907;G|0.093	0.093	strong	.	MMP8	68	.	NM_002424	exon10	c.A1379C	p.K460T	AGCCATTTATTGC	.	PASS	Atlas-SNP
SORT1	6272	hgsc.bcm.edu	37	1	109897103	109897103	+	Silent	SNP	A	A	G	rs11142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	76	129	0	0.974359	0	A|0.257;G|0.743	0.743	strong	SORT1,colon,carcinoma,0,1	SORT1	48	1	NM_002959	exon5	c.T594C	p.F198F	TGATCTAAAGATT	.	PASS	Atlas-SNP
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105897003	105897003	+	Silent	SNP	G	G	A	rs2241799	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	90	219	0	0.403587	0	G|0.853;A|0.147	0.147	strong	.	TGFBRAP1	70	.	NM_004257	exon6	c.C1299T	p.N433N	GACCTCGTTCAGG	.	PASS	Atlas-SNP
GYS1	2997	hgsc.bcm.edu	37	19	49485548	49485548	+	Silent	SNP	G	G	A	rs5464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	66	143	0	0.528	0	G|0.713;A|0.287	0.287	strong	.	GYS1	59	.	NM_002103	exon7	c.C1026T	p.F342F	CTCCAGGAAGACG	.	PASS	Atlas-SNP
TNFAIP8	25816	hgsc.bcm.edu	37	5	118728953	118728953	+	Silent	SNP	G	G	C	rs3203922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	76	214	0	0.436782	0	G|0.745;C|0.255	0.255	strong	.	TNFAIP8	12	.	NM_014350	exon2	c.G474C	p.V158V	TAATGTGTTTGAT	.	PASS	Atlas-SNP
C1orf35	79169	hgsc.bcm.edu	37	1	228290223	228290223	+	Silent	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	66	148	0	0.377143	0	.	.	none	.	C1orf35	17	.	NM_024319	exon4	c.C330G	p.P110P	CTCCTCGGGGTCG	.	PASS	Atlas-SNP
OLFML1	283298	hgsc.bcm.edu	37	11	7509566	7509566	+	Missense_Mutation	SNP	A	A	T	rs12805648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	50	117	0	0.47619	0	A|0.833;T|0.167	0.167	strong	OLFML1,NS,carcinoma,+1,3	OLFML1	54	3	NM_198474	exon2	c.A338T	p.E113V	GCATCGAATCAGA	.	PASS	Atlas-SNP
ZNF556	80032	hgsc.bcm.edu	37	19	2877426	2877426	+	Missense_Mutation	SNP	C	C	T	rs34849844	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	36	94	0	0.553846	0	C|0.987;T|0.013	0.013	strong	.	ZNF556	73	.	NM_024967	exon4	c.C470T	p.T157I	TCTTCACCCATTC	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73568055	73568055	+	Silent	SNP	C	C	T	rs1661714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	40	89	0	0.547945	0	C|0.747;T|0.253	0.253	strong	.	LLGL2	155	.	NM_004524	exon19	c.C2370T	p.P790P	CCTTCCCGAGCCC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230408	23230408	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	38	164	0	0.262069	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.A175C	p.S59R	GGAAGCAGCCGAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508982	195508982	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	15	188	0	0.0627615	0	.	.	none	MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G9469A	p.D3157N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
DNAAF1	123872	hgsc.bcm.edu	37	16	84209815	84209815	+	Missense_Mutation	SNP	C	C	G	rs2288021	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	94	143	1	0.770492	0.00699301	C|0.848;G|0.152	0.152	strong	.	DNAAF1	81	.	NM_178452	exon11	c.C1975G	p.L659V	GGCCAGCTACTGA	.	PASS	Atlas-SNP
CHRNA1	1134	hgsc.bcm.edu	37	2	175614716	175614716	+	Silent	SNP	G	G	A	rs2229957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	110	280	1	0.482456	0.00357143	T|0.025;G|0.730;C|0.169;A|0.077	0.077	strong	.	CHRNA1	92	.	NM_001039523	exon8	c.C1035T	p.H345H	TGAGCGGTGGTGT	.	PASS	Atlas-SNP
GBP4	115361	hgsc.bcm.edu	37	1	89655994	89655994	+	Silent	SNP	C	C	T	rs1410871	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	84	120	0	0.976744	0	C|0.898;T|0.102	0.102	strong	.	GBP4	89	.	NM_052941	exon7	c.G924A	p.G308G	CAGAGTCCCCAGC	.	PASS	Atlas-SNP
CHIA	27159	hgsc.bcm.edu	37	1	111854889	111854889	+	Missense_Mutation	SNP	A	A	G	rs41282492	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	11	226	0	0.100917	0	A|0.881;G|0.119	0.119	strong	CHIA_ENST00000369740,NS,carcinoma,-1,1	CHIA	115	1	NM_201653	exon4	c.A133G	p.N45D	CCTGACAACATCG	.	PASS	Atlas-SNP
LRRC37A3	374819	hgsc.bcm.edu	37	17	62892031	62892031	+	Missense_Mutation	SNP	C	C	T	rs3893633		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	367	51	470	3	0.138965	0.00638298	T|1.000;|0.000	1.000	weak	LRRC37A3,NS,carcinoma,0,4	LRRC37A3	75	4	NM_199340	exon3	c.G1345A	p.V449I	GTTCTACATCATT	.	scavenged	Atlas-SNP
ABR	29	hgsc.bcm.edu	37	17	970419	970419	+	Silent	SNP	G	G	A	rs199545490	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	40	66	1	0.547945	0.0151515	G|0.999;A|0.001	0.001	weak	ABR,colon,carcinoma,0,1	ABR	119	1	NM_021962	exon10	c.C1080T	p.P360P	CTCCTCGGGGGAT	.	scavenged	Atlas-SNP
USB1	79650	hgsc.bcm.edu	37	16	58035429	58035429	+	Silent	SNP	C	C	A	rs3743559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	166	179	0	0.902174	0	C|0.939;A|0.061	0.061	strong	.	.	.	.	NM_024598	exon1	c.C42A	p.S14S	CGGCTCCGAGGAT	.	PASS	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	37	1	201285712	201285712	+	Silent	SNP	C	C	T	rs7514146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	329	110	256	0	0.334347	0	C|0.863;T|0.137	0.137	strong	.	PKP1	127	.	NM_001005337	exon4	c.C733T	p.L245L	AGTGGGCTGACCA	.	PASS	Atlas-SNP
TMEM132C	92293	hgsc.bcm.edu	37	12	129190480	129190480	+	Silent	SNP	G	G	A	rs7316019	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	34	81	0	0.441558	0	G|0.870;A|0.130	0.130	strong	.	TMEM132C	142	.	NM_001136103	exon9	c.G2967A	p.P989P	GCCGCCGCCCCAG	.	PASS	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879405	39879405	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	20	206	0	0.363636	0	.	.	none	.	KIAA0754	93	.	NM_015038	exon1	c.C3468T	p.S1156S	GGAATCCGCCTCC	.	PASS	Atlas-SNP
TDRD5	163589	hgsc.bcm.edu	37	1	179600001	179600001	+	Missense_Mutation	SNP	A	A	G	rs6704505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	359	132	281	0	0.367688	0	A|0.911;G|0.089	0.089	strong	.	TDRD5	149	.	NM_173533	exon7	c.A1072G	p.K358E	TTCAGGAAAGGAC	.	PASS	Atlas-SNP
MGAT4A	11320	hgsc.bcm.edu	37	2	99271976	99271976	+	Missense_Mutation	SNP	T	T	C	rs61748145	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	48	99	0	0.489796	0	T|0.993;C|0.007	0.007	strong	.	MGAT4A	51	.	NM_012214	exon8	c.A706G	p.T236A	GCTTTGTTCTCCA	.	PASS	Atlas-SNP
PIK3R1	5295	hgsc.bcm.edu	37	5	67522722	67522722	+	Silent	SNP	C	C	T	rs706713	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	78	199	0	0.448276	0	C|0.633;T|0.367	0.367	strong	.	PIK3R1	869	.	NM_181523	exon2	c.C219T	p.Y73Y	AACTTACGTAGAA	.	PASS	Atlas-SNP
HOXA7	3204	hgsc.bcm.edu	37	7	27196116	27196116	+	Missense_Mutation	SNP	C	C	T	rs78410337	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	47	116	0	0.286585	0	C|0.993;T|0.007	0.007	strong	.	HOXA7	34	.	NM_006896	exon1	c.G49A	p.G17R	AAGCCCCCGCCGT	.	PASS	Atlas-SNP
ZNF862	643641	hgsc.bcm.edu	37	7	149559465	149559465	+	Silent	SNP	C	C	T	rs2074701	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	53	89	0	1	0	C|0.500;T|0.500	0.500	strong	ZNF862,NS,carcinoma,0,1	ZNF862	97	1	NM_001099220	exon7	c.C3216T	p.G1072G	GAACGGCGTGGCC	.	PASS	Atlas-SNP
ZSWIM4	65249	hgsc.bcm.edu	37	19	13934296	13934296	+	Missense_Mutation	SNP	A	A	G	rs76549352	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	59	94	0	0.526786	0	A|0.987;G|0.013	0.013	strong	.	ZSWIM4	69	.	NM_023072	exon10	c.A1846G	p.M616V	TCCACCATGTTGA	.	PASS	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39855288	39855288	+	Silent	SNP	C	C	A	rs35383047	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	93	80	0	0.978947	0	C|0.882;A|0.118	0.118	strong	.	DAAM2	101	.	NM_015345	exon16	c.C1980A	p.I660I	AGACATCTACCTG	.	PASS	Atlas-SNP
FAM193B	54540	hgsc.bcm.edu	37	5	176963389	176963389	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	2	72	0	0.0240964	0	.	.	none	FLJ10404,NS,carcinoma,0,3	FAM193B	28	3	NM_001190946	exon4	c.C1046T	p.P349L	GAGCTCGGGGGTG	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1263523	1263523	+	Missense_Mutation	SNP	G	G	A	rs1541314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	109	223	0	0.5	0	G|0.928;A|0.072	0.072	strong	.	MUC5B	473	.	NM_002458	exon31	c.G5413A	p.G1805S	GTTGCAGGCGGGG	.	PASS	Atlas-SNP
RNF151	146310	hgsc.bcm.edu	37	16	2017772	2017772	+	Missense_Mutation	SNP	G	G	A	rs62617081	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	25	63	0	0.520833	0	G|0.972;A|0.028	0.028	strong	.	RNF151	12	.	NM_174903	exon3	c.G196A	p.V66I	AAAAAGGTTGTCC	.	PASS	Atlas-SNP
ZNF596	169270	hgsc.bcm.edu	37	8	196274	196274	+	Missense_Mutation	SNP	T	T	G	rs2072174	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	39	85	0	0.367925	0	G|0.132;N|0.001	0.132	strong	.	ZNF596	34	.	NM_173539	exon6	c.T1427G	p.V476G	CATATGTATGTCC	.	PASS	Atlas-SNP
WDR48	57599	hgsc.bcm.edu	37	3	39111140	39111140	+	Silent	SNP	C	C	A	rs2293312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	58	115	0	0.464	0	C|0.529;N|0.000	.	strong	.	WDR48	41	.	NM_020839	exon7	c.C577A	p.R193R	GTGTTACGGGTAT	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109381438	109381438	+	Silent	SNP	A	A	G	rs61748149	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	88	189	0	0.488889	0	A|0.942;G|0.058	0.058	strong	.	RANBP2	488	.	NM_006267	exon20	c.A4443G	p.G1481G	GGAAGGACAGTGG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2140680	2140680	+	Missense_Mutation	SNP	T	T	C	rs10960	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	46	78	0	1	0	T|0.709;C|0.291	0.291	strong	.	PKD1	184	.	NM_001009944	exon44	c.A12133G	p.I4045V	CCAGGATGGCCAG	.	PASS	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113527967	113527967	+	Silent	SNP	G	G	A	rs1320525	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	103	218	0	0.459821	0	G|0.623;A|0.377	0.377	strong	.	ATP11A	225	.	NM_032189	exon27	c.G3138A	p.S1046S	CTTTTCGCTTCTC	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219610433	219610433	+	Silent	SNP	A	A	G	rs586194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	18	173	0	0.216867	0	A|0.446;G|0.554	0.554	strong	.	TTLL4	96	.	NM_014640	exon7	c.A1806G	p.E602E	CTGGGAACAGAGG	.	PASS	Atlas-SNP
IP6K2	51447	hgsc.bcm.edu	37	3	48732480	48732480	+	Missense_Mutation	SNP	T	T	C	rs17080319	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	49	100	0	0.5	0	A|0.000;C|0.134;T|0.866	0.134	strong	.	IP6K2	63	.	NM_001190317	exon3	c.A419G	p.D140G	CTCACATCTCCTC	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66366659	66366659	+	Missense_Mutation	SNP	C	C	G	rs144503106	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	130	270	1	0.513834	0.0037037	C|0.988;G|0.012	0.012	strong	ARSG,rectum,carcinoma,0,1	ARSG	55	1	NM_001267727	exon8	c.C976G	p.R326G	CAAACTCGTCAAG	.	PASS	Atlas-SNP
PARK2	5071	hgsc.bcm.edu	37	6	162864492	162864492	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	35	118	0	0.271318	0	.	.	none	.	PARK2	96	.	NM_004562	exon2	c.C21G	p.F7L	GGAGTTGAACCTG	.	PASS	Atlas-SNP
TCF3	6929	hgsc.bcm.edu	37	19	1615393	1615393	+	Silent	SNP	C	C	T	rs143212973	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	37	99	0	0.5	0	C|0.997;T|0.003	0.003	strong	.	TCF3	72	.	NM_003200	exon18	c.G1713A	p.E571E	CCCCAGCTCCTTA	.	PASS	Atlas-SNP
CALU	813	hgsc.bcm.edu	37	7	128388648	128388648	+	Missense_Mutation	SNP	G	G	A	rs2290228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	17	129	0	0.17	0	G|0.841;A|0.159	0.159	strong	.	CALU	42	.	NM_001199671	exon3	c.G35A	p.R12Q	ACCTGCGACAGTT	.	PASS	Atlas-SNP
ANXA7	310	hgsc.bcm.edu	37	10	75139952	75139952	+	Missense_Mutation	SNP	C	C	T	rs10159690	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	3	89	0	0.0483871	0	C|0.994;T|0.006	0.006	strong	ANXA7,colon,carcinoma,-1,1	ANXA7	50	1	NM_004034	exon11	c.G992A	p.R331H	TCATCACGATTTC	.	scavenged	Atlas-SNP
USPL1	10208	hgsc.bcm.edu	37	13	31231806	31231806	+	Missense_Mutation	SNP	T	T	C	rs7984952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	123	138	0	1	0	T|0.507;C|0.493	0.493	strong	.	USPL1	82	.	NM_005800	exon9	c.T1592C	p.L531S	TATCTTTAACATC	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	37	8	12958025	12958025	+	Silent	SNP	C	C	A	rs3739298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	27	37	0	0.6	0	C|0.703;A|0.297	0.297	strong	.	DLC1	411	.	NM_182643	exon9	c.G1821T	p.A607A	GGGGGGCGCGTGG	.	PASS	Atlas-SNP
ADRA2B	151	hgsc.bcm.edu	37	2	96781257	96781257	+	Missense_Mutation	SNP	C	C	G	rs9333568	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252	136	216	1	0.539683	0.00462963	C|0.952;G|0.048	0.048	strong	ADRA2B_ENST00000409345,brain,glioma,-1,2	ADRA2B	115	2	NM_000682	exon1	c.G632C	p.G211A	GGCCCCCCCTTGG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76503624	76503624	+	Silent	SNP	C	C	T	rs626439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	60	152	0	0.491803	0	C|0.716;T|0.284	0.284	strong	.	DNAH17	347	.	NM_173628	exon28	c.G4500A	p.E1500E	GATGCTCTCCAGG	.	PASS	Atlas-SNP
PBLD	64081	hgsc.bcm.edu	37	10	70066553	70066553	+	Missense_Mutation	SNP	G	G	A	rs12359690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	117	264	0	1	0	G|0.961;A|0.039	0.039	strong	.	PBLD	53	.	NM_022129	exon2	c.C49T	p.R17C	TCCCACGAAATGC	.	PASS	Atlas-SNP
NKAIN4	128414	hgsc.bcm.edu	37	20	61880169	61880169	+	Missense_Mutation	SNP	T	T	G	rs1129659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	16	51	0	0.372093	0	T|0.594;G|0.406	0.406	strong	NKAIN4,NS,carcinoma,0,1	NKAIN4	23	1	NM_152864	exon3	c.A271C	p.K91Q	TCACCTTTAAGAG	.	PASS	Atlas-SNP
SH3GLB2	56904	hgsc.bcm.edu	37	9	131772399	131772399	+	Silent	SNP	G	G	A	rs11537525	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	300	145	289	2	0.483333	0.00692042	G|0.999;A|0.001	0.001	strong	SH3GLB2,NS,haematopoietic_neoplasm,0,1	SH3GLB2	32	1	NM_020145	exon8	c.C738T	p.H246H	ACTCACGTGAGTG	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677988	100677988	+	Missense_Mutation	SNP	T	T	A	rs11769696	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	929	263	218	0	0.2831	0	T|0.991;A|0.009	0.009	strong	.	MUC17	804	.	NM_001040105	exon3	c.T3291A	p.S1097R	TTATAGTGAAGGA	.	PASS	Atlas-SNP
ZEB2	9839	hgsc.bcm.edu	37	2	145156851	145156851	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	3	134	0	0.0185185	0	.	.	none	ZEB2,NS,carcinoma,0,1	ZEB2	218	1	NM_014795	exon8	c.C1903T	p.L635F	ACAAGAGGAGGGC	.	scavenged	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64496763	64496763	+	Silent	SNP	T	T	C	rs11850509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	35	87	0	0.376344	0	T|0.938;C|0.062	0.062	strong	.	SYNE2	577	.	NM_182914	exon44	c.T6865C	p.L2289L	GAAAAATTGCAGA	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19415304	19415304	+	Silent	SNP	C	C	T	rs1043899	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	106	218	0	0.726027	0	C|0.426;T|0.574	0.574	strong	.	UBR4	415	.	NM_020765	exon98	c.G14379A	p.K4793K	CATGCGCTTCTTC	.	PASS	Atlas-SNP
SPARCL1	8404	hgsc.bcm.edu	37	4	88415636	88415636	+	Missense_Mutation	SNP	G	G	C	rs1049544	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	275	273	303	1	0.992727	0.00330033	G|0.488;C|0.512	0.512	strong	SPARCL1,NS,carcinoma,0,1	SPARCL1	59	1	NM_004684	exon4	c.C316G	p.H106D	TTAAGTGACCATC	.	PASS	Atlas-SNP
PEAK1	0	hgsc.bcm.edu	37	15	77407114	77407114	+	Missense_Mutation	SNP	C	C	G	rs1867780	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	4	54	0	0.148148	0	C|0.750;G|0.250	0.250	strong	.	.	.	.	NM_024776	exon8	c.G4625C	p.S1542T	GTGGGGCTGGGCT	.	PASS	Atlas-SNP
TMEM82	388595	hgsc.bcm.edu	37	1	16069644	16069644	+	Silent	SNP	C	C	T	rs11584945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	16	96	0	0.210526	0	C|0.766;T|0.234	0.234	strong	.	TMEM82	30	.	NM_001013641	exon3	c.C291T	p.L97L	GGTGCTCGAGTTC	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32811607	32811607	+	Missense_Mutation	SNP	G	G	A	rs2806639	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	74	58	0	1	0	G|0.755;A|0.245	0.245	strong	.	FRY	312	.	NM_023037	exon44	c.G5902A	p.G1968S	ACCAGCGGCAACA	.	PASS	Atlas-SNP
SKAP1	8631	hgsc.bcm.edu	37	17	46474118	46474118	+	Silent	SNP	G	G	T	rs11079820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	25	86	0	0.384615	0	G|0.903;T|0.097	0.097	strong	.	SKAP1	41	.	NM_003726	exon2	c.C76A	p.R26R	CATTCCGCAAACC	.	PASS	Atlas-SNP
ACE	1636	hgsc.bcm.edu	37	17	61573777	61573777	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	124	245	1	0.5	0.00408163	.	.	none	.	ACE	187	.	NM_000789	exon23	c.C3403A	p.Q1135K	ATCATCCAGTTCC	.	PASS	Atlas-SNP
SLC6A15	55117	hgsc.bcm.edu	37	12	85257230	85257230	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	76	247	0	0.315353	0	.	.	none	.	SLC6A15	159	.	NM_182767	exon11	c.G1806T	p.W602C	TTCAATCCATGCG	.	PASS	Atlas-SNP
IP6K2	51447	hgsc.bcm.edu	37	3	48725707	48725707	+	Silent	SNP	C	C	T	rs1048940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	95	230	0	0.472637	0	T|0.062;G|0.000;C|0.937	0.062	strong	.	IP6K2	63	.	NM_016291	exon6	c.G1280A	p.X427X	CAAGCTCACTCCC	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103158278	103158278	+	Missense_Mutation	SNP	C	C	T	rs10895391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	352	214	232	0	0.607955	0	C|0.709;T|0.291	0.291	strong	DYNC2H1_ENST00000398093,colon,carcinoma,-1,1	DYNC2H1	246	1	NM_001080463	exon76	c.C11060T	p.A3687V	TACAGGCGCTAAG	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61832626	61832626	+	Silent	SNP	G	G	A	rs41274674	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	120	240	0	0.784314	0	G|0.957;A|0.043	0.043	strong	.	ANK3	703	.	NM_020987	exon37	c.C8013T	p.S2671S	TGGGCTGCTGGGC	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1004844	1004844	+	Silent	SNP	T	T	C	rs4806909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	10	71	0	0.212766	0	T|0.639;C|0.361	0.361	strong	GRIN3B,rectum,carcinoma,0,1	GRIN3B	46	1	NM_138690	exon3	c.T1344C	p.P448P	GGACCCTGGCACC	.	PASS	Atlas-SNP
ACOT4	122970	hgsc.bcm.edu	37	14	74060476	74060476	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	85	98	0	0.469613	0	.	.	none	.	ACOT4	25	.	NM_152331	exon2	c.C528A	p.S176R	AGCCAGCCTCCTT	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	37	17	10409241	10409241	+	Missense_Mutation	SNP	T	T	C	rs73974725	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	389	204	410	1	0.524422	0.00243902	T|0.975;C|0.025	0.025	strong	.	MYH1	403	.	NM_005963	exon19	c.A2062G	p.M688V	GCTCCATGGCACC	.	PASS	Atlas-SNP
ARHGEF7	8874	hgsc.bcm.edu	37	13	111870037	111870037	+	Silent	SNP	T	T	C	rs2296354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	114	226	1	0.476987	0.00442478	T|0.807;C|0.193	0.193	strong	.	ARHGEF7	157	.	NM_001113511	exon6	c.T543C	p.D181D	GACCGATAATAGC	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	94026	94026	+	Silent	SNP	G	G	A	rs10904032	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236	35	268	0	0.148305	0	G|0.731;A|0.269	0.269	strong	.	TUBB8	62	.	NM_177987	exon4	c.C306T	p.A102A	TCCCTTGGCCCAG	.	PASS	Atlas-SNP
CRYZ	1429	hgsc.bcm.edu	37	1	75172001	75172001	+	Silent	SNP	T	T	A	rs7527057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	172	298	2	0.988506	0.00671141	T|0.678;A|0.322	0.322	strong	.	CRYZ	28	.	NM_001889	exon9	c.A969T	p.G323G	CATTTTTCCAGTA	.	PASS	Atlas-SNP
PFKP	5214	hgsc.bcm.edu	37	10	3150973	3150973	+	Silent	SNP	C	C	T	rs1132173	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	37	259	0	0.224242	0	C|0.668;N|0.000	.	strong	.	PFKP	182	.	NM_002627	exon9	c.C951T	p.F317F	GGCATTCGACAGG	.	PASS	Atlas-SNP
PI3	5266	hgsc.bcm.edu	37	20	43803613	43803613	+	Missense_Mutation	SNP	C	C	T	rs17333103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	66	161	0	0.481752	0	C|0.864;T|0.136	0.136	strong	PI3,caecum,carcinoma,0,2	PI3	21	2	NM_002638	exon1	c.C50T	p.T17M	CTGGGACGCTGGT	.	PASS	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	37	2	149806388	149806388	+	Silent	SNP	C	C	T	rs60169973	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	67	175	0	0.432258	0	C|0.884;T|0.116	0.116	strong	.	KIF5C	166	.	NM_004522	exon9	c.C750T	p.D250D	TCTTGACGAAGCT	.	PASS	Atlas-SNP
EXOC4	60412	hgsc.bcm.edu	37	7	133689801	133689801	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	9	122	0	0.147541	0	.	.	none	EXOC4_ENST00000545148,NS,carcinoma,0,2	EXOC4	118	2	NM_021807	exon16	c.A2485G	p.S829G	GCCATGAGCGCCA	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159667972	159667972	+	Missense_Mutation	SNP	C	C	T	rs61746218	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	42	136	0	0.403846	0	C|0.995;T|0.005	0.005	strong	.	FNDC1	250	.	NM_032532	exon15	c.C4661T	p.T1554M	TACCTACGGAAGA	.	PASS	Atlas-SNP
SYTL1	84958	hgsc.bcm.edu	37	1	27679797	27679797	+	Missense_Mutation	SNP	A	A	G	rs3813795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	149	204	2	0.993333	0.00980392	A|0.473;G|0.527	0.527	strong	.	SYTL1	57	.	NM_001193308	exon14	c.A1367G	p.Q456R	ACAGCCAGGCCAG	.	PASS	Atlas-SNP
USB1	79650	hgsc.bcm.edu	37	16	58054099	58054099	+	Missense_Mutation	SNP	C	C	G	rs16959641	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	201	194	1	0.810484	0.00515464	C|0.938;G|0.062	0.062	strong	.	.	.	.	NM_024598	exon7	c.C748G	p.Q250E	ACTGAGCAAGTCC	.	PASS	Atlas-SNP
ALCAM	214	hgsc.bcm.edu	37	3	105260524	105260524	+	Silent	SNP	T	T	C	rs35271455	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	49	108	0	0.480392	0	T|0.991;C|0.009	0.009	strong	.	ALCAM	71	.	NM_001627	exon8	c.T906C	p.D302D	GACGGATGTGAGG	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156883215	156883215	+	Missense_Mutation	SNP	C	C	A	rs822442	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	60	142	0	0.375	0	C|0.841;A|0.159	0.159	strong	.	PEAR1	118	.	NM_001080471	exon20	c.C2544A	p.N848K	GCAGAACCCTGAG	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145508636	145508636	+	Missense_Mutation	SNP	T	T	C	rs61732383	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	90	124	0	0.989011	0	T|0.808;C|0.192	0.192	strong	LARS,NS,carcinoma,0,1	LARS	100	1	NM_020117	exon26	c.A2674G	p.N892D	CTTCATTAACAGG	.	PASS	Atlas-SNP
SAMD15	161394	hgsc.bcm.edu	37	14	77843971	77843971	+	Silent	SNP	C	C	T	rs45540040	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	58	64	0	0.623656	0	C|0.848;T|0.152	0.152	strong	.	SAMD15	60	.	NM_001010860	exon1	c.C210T	p.D70D	GCCAGACAGTGCT	.	PASS	Atlas-SNP
GPLD1	2822	hgsc.bcm.edu	37	6	24489652	24489652	+	Missense_Mutation	SNP	C	C	T	rs1126617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	108	145	1	0.972973	0.00689655	C|0.700;T|0.299	0.299	strong	.	GPLD1	91	.	NM_001503	exon1	c.G88A	p.V30I	TTTCTACGTGTGT	.	PASS	Atlas-SNP
RAD21L1	642636	hgsc.bcm.edu	37	20	1221038	1221038	+	Silent	SNP	T	T	C	rs16992733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	58	93	0	0.527273	0	T|0.914;C|0.086	0.086	strong	.	RAD21L1	51	.	NM_001136566	exon8	c.T816C	p.T272T	ATCAACTGAAGAG	.	PASS	Atlas-SNP
RFX4	5992	hgsc.bcm.edu	37	12	107113769	107113769	+	Silent	SNP	G	G	A	rs17038732	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	102	210	0	0.504951	0	G|0.928;A|0.072	0.072	strong	.	RFX4	218	.	NM_001206691	exon12	c.G1197A	p.E399E	GGAGGAGCAGTCT	.	PASS	Atlas-SNP
PCSK7	9159	hgsc.bcm.edu	37	11	117096652	117096652	+	Silent	SNP	G	G	A	rs2277287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	43	117	0	0.277419	0	G|0.759;A|0.241	0.241	strong	.	PCSK7	59	.	NM_004716	exon6	c.C855T	p.S285S	CCTGCAGCTGTAG	.	PASS	Atlas-SNP
PCDHGB4	8641	hgsc.bcm.edu	37	5	140768442	140768442	+	Missense_Mutation	SNP	G	G	T	rs201053346	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	33	64	0	0.428571	0	.	.	weak	.	PCDHGB4	125	.	NM_032098	exon1	c.G991T	p.V331L	TGCACAGTGGAGG	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788222	3788222	+	Missense_Mutation	SNP	G	G	A	rs242017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	71	164	0	0.507143	0	G|0.756;N|0.000	.	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.C383T	p.A128V	TCACCTGCATCTT	.	PASS	Atlas-SNP
OXNAD1	92106	hgsc.bcm.edu	37	3	16336381	16336381	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	94	216	0	0.439252	0	.	.	none	.	OXNAD1	31	.	NM_138381	exon6	c.A309G	p.P103P	TATTCCAGGAGTC	.	PASS	Atlas-SNP
PARD3B	117583	hgsc.bcm.edu	37	2	205829991	205829991	+	Silent	SNP	C	C	T	rs236843	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	78	213	1	0.764706	0.00469484	C|0.267;T|0.732	0.732	strong	PARD3B_ENST00000358768,colon,carcinoma,0,3	PARD3B	314	3	NM_205863	exon3	c.C339T	p.A113A	ACTGGCCGCATTT	.	PASS	Atlas-SNP
ELAVL1	1994	hgsc.bcm.edu	37	19	8028544	8028544	+	Silent	SNP	A	A	G	rs14394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	255	120	243	1	0.470588	0.00411523	A|0.776;G|0.224	0.224	strong	.	ELAVL1	44	.	NM_001419	exon6	c.T804C	p.G268G	GACGGCACCAAAC	.	PASS	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1731268	1731268	+	Silent	SNP	T	T	C	rs8067660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	94	85	0	1	0	T|0.294;C|0.706	0.706	strong	.	SMYD4	50	.	NM_052928	exon2	c.A21G	p.E7E	TTTCCATTCATCC	.	PASS	Atlas-SNP
SZT2	23334	hgsc.bcm.edu	37	1	43870071	43870071	+	Silent	SNP	C	C	A	rs41312024	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	68	147	0	0.819277	0	C|0.990;A|0.010	0.010	strong	.	SZT2	383	.	NM_015284	exon4	c.C348A	p.I116I	GGAGATCTTGTTT	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170088351	170088351	+	Silent	SNP	G	G	A	rs2302694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	96	211	0	0.45283	0	G|0.806;A|0.194	0.194	strong	.	LRP2	751	.	NM_004525	exon31	c.C5100T	p.S1700S	ATTCACGGCTGCA	.	PASS	Atlas-SNP
NAB1	4664	hgsc.bcm.edu	37	2	191550256	191550256	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	3	242	0	0.0147783	0	.	.	none	NAB1,NS,carcinoma,-1,2	NAB1	31	2	NM_005966	exon8	c.T1150C	p.Y384H	GCTGGCTATGAGA	.	scavenged	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46657798	46657798	+	Silent	SNP	A	A	G	rs6007748	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	49	97	0	0.510417	0	A|0.737;G|0.263	0.263	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T1422C	p.D474D	AAATCTATCAGAG	.	PASS	Atlas-SNP
CYB5RL	606495	hgsc.bcm.edu	37	1	54661150	54661150	+	Missense_Mutation	SNP	C	C	T	rs946448	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	26	68	0	0.577778	0	C|0.708;T|0.292	0.292	strong	.	CYB5RL	17	.	NM_001031672	exon3	c.G140A	p.R47K	TCCCACCTTGCCA	.	PASS	Atlas-SNP
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56736102	56736102	+	Missense_Mutation	SNP	A	A	T	rs201600248		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	690	9	900	1	0.0130435	0.00111111	.	.	weak	ZSCAN5A,trunk,malignant_melanoma,0,2	ZSCAN5A	118	2	NM_024303	exon2	c.T314A	p.M105K	TTCATCATGACTA	.	scavenged	Atlas-SNP
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350481	65350481	+	Missense_Mutation	SNP	C	C	T	rs3805466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	51	89	0	0.525773	0	C|0.936;T|0.064	0.064	strong	.	ERBB2IP	120	.	NM_001253699	exon21	c.C3335T	p.S1112L	TCCACTCAGCGGG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144991925	144991925	+	Missense_Mutation	SNP	G	G	A	rs189061273	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	63	96	0	0.617647	0	G|0.995;A|0.005	0.005	strong	PLEC_ENST00000436759,bladder,carcinoma,+2,3	PLEC	1144	3	NM_201380	exon32	c.C12475T	p.L4159F	AGATGAGCTTCCC	.	PASS	Atlas-SNP
E4F1	1877	hgsc.bcm.edu	37	16	2285357	2285357	+	Silent	SNP	C	C	T	rs26840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	43	77	0	0.573333	0	C|0.702;T|0.298	0.298	strong	.	E4F1	53	.	NM_004424	exon14	c.C2139T	p.I713I	CACCATCGCCACC	.	PASS	Atlas-SNP
FBXO7	25793	hgsc.bcm.edu	37	22	32880006	32880006	+	Silent	SNP	A	A	G	rs41311141	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	324	140	375	1	0.432099	0.00266667	A|0.969;G|0.030;T|0.000	0.030	strong	.	FBXO7	131	.	NM_012179	exon3	c.A540G	p.P180P	AGTGCCACATTCA	.	PASS	Atlas-SNP
RPL7A	6130	hgsc.bcm.edu	37	9	136216882	136216882	+	Silent	SNP	G	G	A	rs7700	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	42	101	0	0.518519	0	G|0.942;A|0.058	0.058	strong	.	RPL7A	9	.	NM_000972	exon4	c.G390A	p.T130T	CCCAACGAAGAGA	.	PASS	Atlas-SNP
ZNF805	390980	hgsc.bcm.edu	37	19	57760057	57760057	+	Missense_Mutation	SNP	G	G	A	rs3746231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	124	130	1	1	0.00769231	G|0.643;A|0.357	0.357	strong	.	ZNF805	30	.	NM_001023563	exon3	c.G242A	p.G81D	CCCAAGGCACCTG	.	PASS	Atlas-SNP
ZNF394	84124	hgsc.bcm.edu	37	7	99091599	99091599	+	Silent	SNP	C	C	T	rs78336331	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	293	105	227	0	0.358362	0	C|0.986;T|0.014	0.014	strong	ZNF394,NS,carcinoma,-1,1	ZNF394	48	1	NM_032164	exon3	c.G1239A	p.P413P	GGTGTACGGCTTC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280559	152280559	+	Missense_Mutation	SNP	T	T	C	rs150122015	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	516	65	374	0	0.125969	0	.	.	weak	.	FLG	900	.	NM_002016	exon3	c.A6803G	p.H2268R	GATCCATGATGGT	.	PASS	Atlas-SNP
NUDT12	83594	hgsc.bcm.edu	37	5	102894977	102894977	+	Silent	SNP	T	T	C	rs7734923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	51	112	0	0.447368	0	T|0.863;C|0.137	0.137	strong	.	NUDT12	27	.	NM_031438	exon3	c.A399G	p.R133R	ATTATTTCTCTTT	.	PASS	Atlas-SNP
R3HCC1	203069	hgsc.bcm.edu	37	8	23148930	23148930	+	Silent	SNP	A	A	G	rs2272762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	123	93	1	1	0.0107527	A|0.395;G|0.605	0.605	strong	R3HCC1,colon,carcinoma,0,1	R3HCC1	11	1	NM_001136108	exon5	c.A348G	p.T116T	GGACACATCCTCC	.	scavenged	Atlas-SNP
PDLIM5	10611	hgsc.bcm.edu	37	4	95496882	95496882	+	Missense_Mutation	SNP	C	C	T	rs2452600	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	107	255	0	0.465217	0	C|0.737;T|0.263	0.263	strong	.	PDLIM5	76	.	NM_006457	exon5	c.C407T	p.S136F	CTGTGTCTTCACC	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72999359	72999359	+	Missense_Mutation	SNP	T	T	C	rs55679337	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	40	123	0	0.384615	0	A|0.000;C|0.274;G|0.000;T|0.725	0.274	strong	.	TSHZ1	104	.	NM_005786	exon2	c.T1862C	p.L621P	GCTCCCTGGCCAA	.	PASS	Atlas-SNP
MPZL3	196264	hgsc.bcm.edu	37	11	118110977	118110977	+	Silent	SNP	T	T	C	rs2853006	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	375	101	207	1	0.269333	0.00483092	T|0.217;C|0.783	0.783	strong	MPZL3,NS,carcinoma,0,1	MPZL3	22	1	NM_198275	exon2	c.A189G	p.K63K	AGTAAGTTTGTCA	.	scavenged	Atlas-SNP
TMEM44	93109	hgsc.bcm.edu	37	3	194353875	194353875	+	Missense_Mutation	SNP	G	G	T	rs1675955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	55	166	0	0.518868	0	G|0.652;T|0.348	0.348	strong	.	TMEM44	42	.	NM_138399	exon1	c.C70A	p.H24N	CGCGGTGGCGGGC	.	PASS	Atlas-SNP
NMUR2	56923	hgsc.bcm.edu	37	5	151775064	151775064	+	Missense_Mutation	SNP	C	C	G	rs4958535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	116	275	2	0.493617	0.00727273	C|0.866;G|0.134	0.134	strong	NMUR2,NS,carcinoma,0,1	NMUR2	111	1	NM_020167	exon3	c.G893C	p.S298T	GATTCACTCCACT	.	scavenged	Atlas-SNP
CCDC11	220136	hgsc.bcm.edu	37	18	47788544	47788544	+	Silent	SNP	T	T	G	rs112087763	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	53	100	0	0.438017	0	T|0.997;G|0.003	0.003	strong	.	CCDC11	59	.	NM_145020	exon2	c.A115C	p.R39R	GGATTCTTTCTAG	.	PASS	Atlas-SNP
VWA5A	4013	hgsc.bcm.edu	37	11	124006993	124006993	+	Missense_Mutation	SNP	G	G	A	rs2276053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	47	95	0	0.241026	0	G|0.883;A|0.117	0.117	strong	.	VWA5A	102	.	NM_014622	exon12	c.G1517A	p.R506K	CCGGGAGGATGCC	.	PASS	Atlas-SNP
CYP17A1	1586	hgsc.bcm.edu	37	10	104596924	104596924	+	Silent	SNP	C	C	A	rs6163	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	53	144	0	0.646341	0	C|0.605;A|0.390	0.390	strong	CYP17A1,NS,carcinoma,-1,1	CYP17A1	48	1	NM_000102	exon1	c.G195T	p.S65S	ACGAACCGAATAG	.	PASS	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62516683	62516683	+	Missense_Mutation	SNP	G	G	C	rs2498982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	63	123	0	0.969231	0	G|0.424;C|0.576	0.576	strong	INADL,NS,carcinoma,0,1	INADL	179	1	NM_176877	exon31	c.G4078C	p.V1360L	GGCAGCGTCGAAG	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10943003	10943003	+	Missense_Mutation	SNP	C	C	T	rs1810856	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	525	146	281	2	0.278095	0.00711744	C|0.923;T|0.077	0.077	strong	TPTE_ENST00000361285,lower_third,carcinoma,-1,8	TPTE	513	8	NM_199261	exon12	c.G584A	p.R195Q	AGAAGTCGAAGTA	.	scavenged	Atlas-SNP
MSS51	118490	hgsc.bcm.edu	37	10	75184444	75184444	+	Missense_Mutation	SNP	A	A	G	rs11591720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	34	203	0	0.263566	0	A|0.989;G|0.011	0.011	strong	ZMYND17,bladder,carcinoma,+1,1	.	.	1	NM_001024593	exon7	c.T1250C	p.L417P	GGTTTGAGGGACA	.	PASS	Atlas-SNP
KLHL7	55975	hgsc.bcm.edu	37	7	23212627	23212627	+	Silent	SNP	A	A	G	rs118185564	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	437	278	297	0	0.636156	0	A|0.994;G|0.006	0.006	strong	.	KLHL7	102	.	NM_001031710	exon10	c.A1440G	p.K480K	TGTAAAAGACAAG	.	PASS	Atlas-SNP
TBC1D15	64786	hgsc.bcm.edu	37	12	72307616	72307616	+	Silent	SNP	A	A	G	rs3759171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	22	53	0	0.318841	0	A|0.446;G|0.554	0.554	strong	.	TBC1D15	99	.	NM_022771	exon13	c.A1362G	p.Q454Q	TGTTCAAGGAATG	.	PASS	Atlas-SNP
KRTAP21-2	337978	hgsc.bcm.edu	37	21	32119495	32119495	+	Missense_Mutation	SNP	C	C	G	rs12053674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	272	88	242	0	0.323529	0	C|0.840;G|0.160	0.160	strong	.	KRTAP21-2	16	.	NM_181617	exon1	c.G26C	p.C9S	CCACAGCAGTTTC	.	PASS	Atlas-SNP
RAET1E	135250	hgsc.bcm.edu	37	6	150210723	150210723	+	Missense_Mutation	SNP	C	C	T	rs6925151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	106	259	0	0.407692	0	C|0.693;T|0.307	0.307	strong	.	RAET1E	20	.	NM_139165	exon3	c.G383A	p.R128H	GCTTCACGTTGAC	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186671912	186671912	+	Missense_Mutation	SNP	G	G	A	rs1862066	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	91	240	0	0.455	0	G|0.479;A|0.521	0.521	strong	FSIP2_ENST00000343098,caecum,carcinoma,+1,2	FSIP2	251	2	NM_173651	exon17	c.G18146A	p.R6049H	TCCAACGTCAGGT	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89809319	89809319	+	Silent	SNP	T	T	C	rs1800358	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	14	91	0	0.142857	0	T|0.874;C|0.126	0.126	strong	.	FANCA	99	.	NM_000135	exon37	c.A3654G	p.P1218P	GGGTGCTGGGGAG	.	PASS	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167023573	167023573	+	Missense_Mutation	SNP	C	C	T	rs140166106	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	310	125	343	0	0.403226	0	C|0.989;T|0.011	0.011	strong	.	ZBBX	299	.	NM_024687	exon17	c.G1583A	p.S528N	TCCTTGCTTTCAA	.	PASS	Atlas-SNP
SF3A3	10946	hgsc.bcm.edu	37	1	38449910	38449910	+	Silent	SNP	T	T	C	rs11210870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	53	115	0	0.883333	0	T|0.718;C|0.282	0.282	strong	.	SF3A3	37	.	NM_006802	exon6	c.A399G	p.E133E	TCCCTCTTCATCT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168106085	168106085	+	Missense_Mutation	SNP	G	G	A	rs16853328	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	61	153	0	0.426573	0	G|0.837;A|0.163	0.163	strong	.	XIRP2	914	.	NM_152381	exon9	c.G8183A	p.S2728N	ACCACAGCTATGA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90408589	90408589	+	Silent	SNP	A	A	G	rs3736984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	28	66	0	0.411765	0	A|0.865;G|0.135	0.135	strong	.	MDN1	478	.	NM_014611	exon59	c.T9163C	p.L3055L	CCTTCAATGTGGA	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3224561	3224561	+	Silent	SNP	T	T	C	rs4875703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	99	140	0	0.578947	0	T|0.701;C|0.299	0.299	strong	.	CSMD1	1469	.	NM_033225	exon20	c.A3108G	p.T1036T	TGAAAATGTGATA	.	PASS	Atlas-SNP
USP20	10868	hgsc.bcm.edu	37	9	132636920	132636920	+	Silent	SNP	C	C	T	rs35899714	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	94	208	0	0.484536	0	C|0.937;T|0.063	0.063	strong	.	USP20	186	.	NM_001008563	exon18	c.C1806T	p.H602H	CAGCCACGTCTCC	.	PASS	Atlas-SNP
GPR133	283383	hgsc.bcm.edu	37	12	131620650	131620650	+	Missense_Mutation	SNP	C	C	T	rs61746588	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	82	238	0	0.416244	0	C|0.997;T|0.003	0.003	strong	.	GPR133	136	.	NM_198827	exon22	c.C2336T	p.A779V	TGCTTGCTGTCAA	.	PASS	Atlas-SNP
NECAB2	54550	hgsc.bcm.edu	37	16	84012104	84012104	+	Silent	SNP	T	T	C	rs925331	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	80	117	0	0.808081	0	T|0.692;C|0.308	0.308	strong	.	NECAB2	36	.	NM_019065	exon3	c.T282C	p.L94L	CGTCCTTAATGAG	.	PASS	Atlas-SNP
P2RY12	64805	hgsc.bcm.edu	37	3	151056616	151056616	+	Silent	SNP	G	G	A	rs6785930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	51	130	0	0.46789	0	G|0.736;A|0.264	0.264	strong	P2RY12,NS,malignant_melanoma,-1,1	P2RY12	36	1	NM_022788	exon3	c.C18T	p.N6N	GGTGAGGTTGTCG	.	PASS	Atlas-SNP
TAS2R46	259292	hgsc.bcm.edu	37	12	11214360	11214360	+	Silent	SNP	C	C	T	rs73260771	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	255	116	245	0	0.454902	0	C|0.833;T|0.167	0.167	strong	.	TAS2R46	43	.	NM_176887	exon1	c.G534A	p.T178T	GGTTACCGTTGTA	.	PASS	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22364230	22364230	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	282	100	292	1	0.35461	0.00342466	.	.	none	ZNF676,NS,carcinoma,+1,2	ZNF676	146	2	NM_001001411	exon3	c.G289T	p.G97C	TATAACCTTCTTT	.	PASS	Atlas-SNP
CTTN	2017	hgsc.bcm.edu	37	11	70253475	70253475	+	Silent	SNP	C	C	T	rs2298397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	22	105	0	0.328358	0	C|0.847;T|0.153	0.153	strong	.	CTTN	162	.	NM_001184740	exon3	c.C72T	p.T24T	GGAGACCGACCCT	.	PASS	Atlas-SNP
KRR1	11103	hgsc.bcm.edu	37	12	75900588	75900588	+	Silent	SNP	A	A	G	rs2070162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	47	126	0	0.5	0	A|0.777;G|0.223	0.223	strong	.	KRR1	37	.	NM_007043	exon3	c.T367C	p.L123L	TTGCTAACAGTTT	.	PASS	Atlas-SNP
T	6862	hgsc.bcm.edu	37	6	166571935	166571935	+	Silent	SNP	C	C	T	rs35819705	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	132	160	1	0.970588	0.00625	C|0.771;T|0.229	0.229	strong	.	T	77	.	NM_003181	exon9	c.G1176A	p.A392A	AGAGGGCGCCGAG	.	PASS	Atlas-SNP
CCRL1	51554	hgsc.bcm.edu	37	3	132319604	132319604	+	Silent	SNP	A	A	C	rs139873131	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	608	172	542	1	0.282895	0.00184502	A|0.990;C|0.010	0.010	strong	.	CCRL1	30	.	NM_178445	exon1	c.A363C	p.L121L	CACACTAAACTTT	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118693217	118693217	+	Silent	SNP	T	T	C	rs1935992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	34	269	2	0.22973	0.00743494	C|0.210;N|0.000	0.210	strong	SPAG17,NS,carcinoma,0,1	SPAG17	263	1	NM_206996	exon3	c.A264G	p.S88S	TTTAGATGAAGCA	.	scavenged	Atlas-SNP
ZBTB17	7709	hgsc.bcm.edu	37	1	16271260	16271260	+	Silent	SNP	G	G	A	rs9661939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	16	109	0	0.222222	0	G|0.802;A|0.198	0.198	strong	.	ZBTB17	45	.	NM_003443	exon8	c.C1002T	p.F334F	GCACGAGAAGGGC	.	PASS	Atlas-SNP
EIF2A	83939	hgsc.bcm.edu	37	3	150280445	150280445	+	Missense_Mutation	SNP	C	C	G	rs1132979	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	14	50	0	0.424242	0	C|0.635;G|0.365	0.365	strong	EIF2A_ENST00000487799,NS,carcinoma,0,1	EIF2A	59	1	NM_032025	exon4	c.C290G	p.T97S	CTTACACTAGTAA	.	PASS	Atlas-SNP
ZNF208	7757	hgsc.bcm.edu	37	19	22154954	22154954	+	Missense_Mutation	SNP	C	C	T	rs2214301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	55	96	0	0.539216	0	C|0.353;T|0.647	0.647	strong	.	ZNF208	817	.	NM_007153	exon4	c.G2882A	p.S961N	TGATAACTAAGGG	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77038912	77038912	+	Missense_Mutation	SNP	A	A	T	rs144785979	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256	115	251	0	0.449219	0	A|0.999;T|0.001	0.001	strong	.	NUP54	48	.	NM_017426	exon11	c.T1300A	p.L434M	ACATCAATTCATT	.	PASS	Atlas-SNP
SAAL1	113174	hgsc.bcm.edu	37	11	18127464	18127464	+	Missense_Mutation	SNP	C	C	T	rs77233279	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	21	42	0	0.4375	0	C|0.981;T|0.019	0.019	strong	SAAL1,NS,carcinoma,0,1	SAAL1	34	1	NM_138421	exon1	c.G125A	p.G42E	ATGAGTCCGCTGA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1248960	1248960	+	Silent	SNP	G	G	A	rs2075855	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	43	91	1	0.565789	0.010989	G|0.929;A|0.071	0.071	strong	MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	NM_002458	exon7	c.G723A	p.T241T	GCCCACGGAGCAG	.	scavenged	Atlas-SNP
PCED1A	64773	hgsc.bcm.edu	37	20	2816821	2816821	+	Silent	SNP	C	C	T	rs2274669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	3	256	0	0.012605	0	C|0.833;G|0.000;T|0.167	0.167	strong	FAM113A,colon,carcinoma,0,1	.	.	1	NM_022760	exon7	c.G981A	p.P327P	AGGAAGCGGGTAG	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280864	152280864	+	Silent	SNP	A	A	G	rs75034106		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	495	240	305	0	0.484848	0	.	.	weak	.	FLG	900	.	NM_002016	exon3	c.T6498C	p.S2166S	GTGATGAGACCCT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1263776	1263776	+	Missense_Mutation	SNP	C	C	T	rs2943510	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	136	256	0	0.569038	0	C|0.873;T|0.127	0.127	strong	.	MUC5B	473	.	NM_002458	exon31	c.C5666T	p.P1889L	GTACCCCAGCCAC	.	PASS	Atlas-SNP
PLCH1	23007	hgsc.bcm.edu	37	3	155301264	155301264	+	Silent	SNP	T	T	C	rs9289957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	74	171	0	0.528571	0	T|0.957;C|0.043	0.043	strong	.	PLCH1	406	.	NM_001130960	exon5	c.A732G	p.Q244Q	TACCTTTTGCTCC	.	PASS	Atlas-SNP
ANO7	50636	hgsc.bcm.edu	37	2	242151585	242151585	+	Silent	SNP	C	C	T	rs7593101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	67	134	0	0.51145	0	C|0.787;T|0.213	0.213	strong	.	ANO7	136	.	NM_001001891	exon16	c.C1800T	p.Y600Y	CTTCTACTCCTCA	.	PASS	Atlas-SNP
NUBP1	4682	hgsc.bcm.edu	37	16	10846511	10846511	+	Silent	SNP	G	G	A	rs2233535	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	72	186	0	0.447205	0	G|0.997;A|0.003	0.003	strong	.	NUBP1	31	.	NM_002484	exon4	c.G303A	p.K101K	TCCCAAGATAATG	.	PASS	Atlas-SNP
NEU4	129807	hgsc.bcm.edu	37	2	242757820	242757820	+	Missense_Mutation	SNP	G	G	A	rs11545301	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	50	109	0	0.49505	0	G|0.725;A|0.275	0.275	strong	.	NEU4	39	.	NM_001167599	exon4	c.G940A	p.G314R	GGCCCCGGGAGTC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	77	112	0	0.596899	0	T|0.764;A|0.236	0.236	strong	.	RP1L1	453	.	NM_178857	exon4	c.A5666T	p.D1889V	TCTACATCTTCTG	.	PASS	Atlas-SNP
DDX58	23586	hgsc.bcm.edu	37	9	32480251	32480251	+	Missense_Mutation	SNP	A	A	T	rs17217280	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	82	164	0	0.5125	0	A|0.906;T|0.094	0.094	strong	.	DDX58	82	.	NM_014314	exon12	c.T1740A	p.D580E	AATCTCATCGAAT	.	PASS	Atlas-SNP
ADCY3	109	hgsc.bcm.edu	37	2	25064157	25064157	+	Silent	SNP	G	G	C	rs2241758	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	47	63	0	0.580247	0	G|0.925;C|0.075	0.075	strong	.	ADCY3	114	.	NM_004036	exon5	c.C1167G	p.L389L	CCCCATGAGGATG	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77376647	77376647	+	Missense_Mutation	SNP	T	T	C	rs2274924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	261	127	249	0	0.48659	0	T|0.756;C|0.244	0.244	strong	TRPM6,caecum,carcinoma,+2,2	TRPM6	377	2	NM_017662	exon27	c.A4750G	p.K1584E	TTTTCTTTGACAG	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248084473	248084473	+	Silent	SNP	C	C	A	rs143274587	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	433	175	703	0	0.404157	0	C|0.887;A|0.113	0.113	strong	OR2T8,NS,carcinoma,-1,1	OR2T8	67	1	NM_001005522	exon1	c.C154A	p.R52R	GACCACCGGCTCC	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38122122	38122122	+	Missense_Mutation	SNP	T	T	C	rs5756795	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	31	69	0	0.5	0	T|0.609;C|0.391	0.391	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.T3559C	p.F1187L	TCCCTCTTCTTCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105413220	105413220	+	Silent	SNP	A	A	C	rs151173659	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	167	205	1	0.670683	0.00487805	A|0.994;C|0.006	0.006	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T8568G	p.L2856L	GGTCTTAAGATCC	.	PASS	Atlas-SNP
NOD2	64127	hgsc.bcm.edu	37	16	50733859	50733859	+	Silent	SNP	C	C	G	rs2067085	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	18	17	0	1	0	C|0.673;G|0.327	0.327	strong	NOD2,NS,carcinoma,0,1	NOD2	118	1	NM_022162	exon2	c.C534G	p.S178S	ACCGTCCCAGAGG	.	PASS	Atlas-SNP
CGN	57530	hgsc.bcm.edu	37	1	151491656	151491656	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	3	81	0	0.0218978	0	.	.	none	CGN,NS,carcinoma,0,1	CGN	106	1	NM_020770	exon2	c.C661T	p.R221W	CTCCCACGGGACA	.	scavenged	Atlas-SNP
FRMD6	122786	hgsc.bcm.edu	37	14	52186966	52186966	+	Silent	SNP	G	G	A	rs2277495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	74	88	0	0.660714	0	G|0.751;C|0.000;A|0.249	0.249	strong	.	FRMD6	100	.	NM_001267046	exon11	c.G1218A	p.T406T	GGACACGGGGCCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508903	195508903	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	14	180	0	0.0571429	0	.	.	none	MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C9548T	p.T3183M	AGAGGCGTGGTGT	.	scavenged	Atlas-SNP
SLC17A4	10050	hgsc.bcm.edu	37	6	25773809	25773809	+	Silent	SNP	A	A	G	rs2275906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	301	136	293	0	0.451827	0	A|0.903;G|0.097	0.097	strong	.	SLC17A4	79	.	NM_005495	exon8	c.A894G	p.L298L	CATTTTAGTCTCT	.	PASS	Atlas-SNP
HIST1H4H	8365	hgsc.bcm.edu	37	6	26285503	26285503	+	Silent	SNP	C	C	T	rs41266829	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	78	197	0	0.5	0	C|0.869;T|0.131	0.131	strong	HIST1H4H,colon,carcinoma,0,1	HIST1H4H	16	1	NM_003543	exon1	c.G225A	p.E75E	GGCGTGCTCTGTG	.	PASS	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87229739	87229739	+	Missense_Mutation	SNP	C	C	T	rs4419794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	87	157	0	0.608392	0	C|0.856;T|0.144	0.144	strong	SLC7A13,NS,carcinoma,+1,1	SLC7A13	97	1	NM_138817	exon3	c.G1139A	p.R380K	CTCCGCCTTAGTA	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49701983	49701983	+	Silent	SNP	G	G	A	rs9858542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	22	29	0	0.647059	0	G|0.749;A|0.251	0.251	strong	BSN,NS,carcinoma,+1,1	BSN	272	1	NM_003458	exon9	c.G11736A	p.T3912T	ACTGACGGAAGGT	.	PASS	Atlas-SNP
KCTD18	130535	hgsc.bcm.edu	37	2	201355106	201355106	+	Missense_Mutation	SNP	G	G	A	rs13018579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	21	81	0	0.313433	0	G|0.849;A|0.151	0.151	strong	.	KCTD18	44	.	NM_152387	exon7	c.C998T	p.A333V	ACCAGGGCCGTGG	.	PASS	Atlas-SNP
RETNLB	84666	hgsc.bcm.edu	37	3	108475974	108475974	+	Missense_Mutation	SNP	G	G	A	rs11708527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	43	89	1	0.544304	0.011236	G|0.795;A|0.205	0.205	strong	RETNLB,NS,carcinoma,+1,1	RETNLB	38	1	NM_032579	exon1	c.C59T	p.P20L	CTCCCCGGGTTGA	.	scavenged	Atlas-SNP
SDPR	8436	hgsc.bcm.edu	37	2	192711385	192711385	+	Silent	SNP	G	G	A	rs35883486	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	105	195	0	0.514706	0	G|0.977;A|0.023	0.023	strong	SDPR,caecum,carcinoma,0,1	SDPR	67	1	NM_004657	exon1	c.C267T	p.S89S	CTTCACGGAGCCC	.	PASS	Atlas-SNP
PGR	5241	hgsc.bcm.edu	37	11	100933412	100933412	+	Missense_Mutation	SNP	C	C	A	rs1042838	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	68	109	0	0.4	0	C|0.893;A|0.107	0.107	strong	.	PGR	115	.	NM_000926	exon4	c.G1978T	p.V660L	CGCCCACTGGCTG	.	PASS	Atlas-SNP
SRBD1	55133	hgsc.bcm.edu	37	2	45645512	45645512	+	Silent	SNP	C	C	T	rs2276655	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	208	232	0	0.990476	0	C|0.840;T|0.160	0.160	strong	.	SRBD1	107	.	NM_018079	exon18	c.G2325A	p.T775T	GCAAAACGTTCGG	.	PASS	Atlas-SNP
SOWAHC	65124	hgsc.bcm.edu	37	2	110373197	110373197	+	Silent	SNP	G	G	A	rs1560884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	33	77	0	0.6	0	G|0.728;A|0.272	0.272	strong	.	.	.	.	NM_023016	exon1	c.G1131A	p.K377K	GAAAAAGGCCTCC	.	PASS	Atlas-SNP
IGFN1	91156	hgsc.bcm.edu	37	1	201166383	201166383	+	Missense_Mutation	SNP	G	G	A	rs4915221	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	38	95	0	0.365385	0	G|0.289;A|0.710	0.710	strong	.	IGFN1	220	.	NM_001164586	exon5	c.G305A	p.R102H	TGTACCGCTGCAC	.	PASS	Atlas-SNP
OR51E1	143503	hgsc.bcm.edu	37	11	4674575	4674575	+	Silent	SNP	G	G	A	rs3817098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	153	131	1	0.968354	0.00763359	G|0.615;A|0.385	0.385	strong	.	OR51E1	67	.	NM_152430	exon2	c.G819A	p.P273P	CTCTCCGCTGCCC	.	PASS	Atlas-SNP
FAM26F	441168	hgsc.bcm.edu	37	6	116784797	116784797	+	Missense_Mutation	SNP	G	G	A	rs11544160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	104	220	1	0.495238	0.00454545	G|0.951;A|0.049	0.049	strong	.	FAM26F	12	.	NM_001010919	exon3	c.T877A	p.S293T	TCTACTGAAGGAG	.	PASS	Atlas-SNP
ZNF22	7570	hgsc.bcm.edu	37	10	45499009	45499009	+	Missense_Mutation	SNP	A	A	G	rs3740093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	6	47	0	0.222222	0	A|0.958;G|0.042	0.042	strong	.	ZNF22	28	.	NM_006963	exon2	c.A193G	p.S65G	AGTTTCAGTCAGA	.	PASS	Atlas-SNP
FHL3	2275	hgsc.bcm.edu	37	1	38463504	38463504	+	Silent	SNP	C	C	T	rs7366048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	70	144	0	0.795455	0	C|0.477;T|0.523	0.523	strong	.	FHL3	9	.	NM_004468	exon5	c.G540A	p.P180P	ATGCCACGGCTGA	.	PASS	Atlas-SNP
CLEC1B	51266	hgsc.bcm.edu	37	12	10150974	10150974	+	Missense_Mutation	SNP	A	A	G	rs2273986	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	77	167	0	0.442529	0	A|0.594;G|0.406	0.406	strong	.	CLEC1B	39	.	NM_016509	exon2	c.T70C	p.S24P	ATGCAGAGCCAAC	.	PASS	Atlas-SNP
CDH20	28316	hgsc.bcm.edu	37	18	59166541	59166541	+	Silent	SNP	C	C	T	rs12964819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	125	129	1	0.984252	0.00775194	C|0.363;T|0.637	0.637	strong	CDH20,NS,carcinoma,+2,1	CDH20	117	1	NM_031891	exon2	c.C369T	p.D123D	GCTCGACCGAGAG	.	PASS	Atlas-SNP
UBTFL1	642623	hgsc.bcm.edu	37	11	89819431	89819431	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	411	270	321	1	0.656934	0.00311526	.	.	none	.	.	.	.	NM_001143975	exon1	c.C314T	p.T105I	CCCTTACTGCTTA	.	PASS	Atlas-SNP
PCMT1	5110	hgsc.bcm.edu	37	6	150114745	150114745	+	Missense_Mutation	SNP	G	G	A	rs4816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	96	185	0	0.551724	0	G|0.418;A|0.582	0.582	strong	.	PCMT1	27	.	NM_005389	exon5	c.G532A	p.V178I	GACTCAGTAAATA	.	PASS	Atlas-SNP
HELQ	113510	hgsc.bcm.edu	37	4	84370091	84370091	+	Silent	SNP	A	A	G	rs13141136	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	29	50	0	0.568627	0	A|0.654;G|0.346	0.346	strong	.	HELQ	95	.	NM_133636	exon3	c.T1036C	p.L346L	AATTCAATGTTAA	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72997677	72997677	+	Silent	SNP	C	C	T	rs3826609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	32	67	0	0.470588	0	C|0.779;T|0.221	0.221	strong	.	TSHZ1	104	.	NM_005786	exon2	c.C180T	p.S60S	CGACAGCGTCTCG	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113541999	113541999	+	Silent	SNP	C	C	T	rs148186900	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	308	4	358	0	0.012987	0	C|0.997;T|0.003	0.003	strong	RASAL1,NS,carcinoma,-1,1	RASAL1	89	1	NM_001193520	exon18	c.G1938A	p.T646T	CGCCCCCGTGCCG	.	scavenged	Atlas-SNP
LATS2	26524	hgsc.bcm.edu	37	13	21562832	21562832	+	Missense_Mutation	SNP	C	C	T	rs2770928	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4	4	8	0	1	0	T|0.842;G|0.000;C|0.158;A|0.000	0.842	strong	LATS2_ENST00000382592,NS,carcinoma,0,1	LATS2	176	1	NM_014572	exon4	c.G1087A	p.G363S	TGCTGCCCAATTC	.	PASS	Atlas-SNP
NAP1L3	4675	hgsc.bcm.edu	37	X	92927728	92927728	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	5	159	0	0.0641026	0	.	.	none	.	NAP1L3	81	.	NM_004538	exon1	c.A576G	p.E192E	TTCTTCTTCCTCA	.	PASS	Atlas-SNP
KLHL13	90293	hgsc.bcm.edu	37	X	117053499	117053499	+	Silent	SNP	C	C	T	rs6645994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	129	393	0	0.977273	0	C|0.688;0|0.003	.	strong	.	KLHL13	87	.	NM_001168299	exon5	c.G564A	p.V188V	GAGAAACACTTTA	.	PASS	Atlas-SNP
CPSF4	10898	hgsc.bcm.edu	37	7	99050039	99050039	+	Silent	SNP	G	G	A	rs17854665	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	37	74	0	0.373737	0	G|0.909;A|0.091	0.091	strong	.	CPSF4	24	.	NM_001081559	exon6	c.G546A	p.P182P	ACTGCCGCAGCAG	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104385711	104385711	+	Missense_Mutation	SNP	C	C	T	rs35768024	bycluster;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	84	191	0	0.5	0	CA|0.500;TG|0.500	.	alt	.	GRIN3A	186	.	NM_133445	exon5	c.G2503A	p.D835N	CTGGATCATTCCT	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56549532	56549532	+	Silent	SNP	A	A	G	rs306447	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	97	202	0	0.468599	0	A|0.693;G|0.307	0.307	strong	NLRP5,NS,carcinoma,0,1	NLRP5	217	1	NM_153447	exon10	c.A2757G	p.R919R	CTTGAGAGTCTCC	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45029208	45029208	+	Missense_Mutation	SNP	G	G	A	rs10408247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	105	233	0	0.441176	0	G|0.725;A|0.275	0.275	strong	.	CEACAM20	31	.	NM_001102600	exon2	c.C122T	p.A41V	TGGGTGGCATCAA	.	PASS	Atlas-SNP
UPK1A	11045	hgsc.bcm.edu	37	19	36157740	36157740	+	Missense_Mutation	SNP	C	C	T	rs61741212	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	107	238	0	0.455319	0	C|0.856;T|0.144	0.144	strong	.	UPK1A	23	.	NM_007000	exon1	c.C26T	p.A9V	CGGAGGCCGAGAA	.	PASS	Atlas-SNP
BOD1L1	259282	hgsc.bcm.edu	37	4	13602793	13602793	+	Missense_Mutation	SNP	C	C	G	rs199927242	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	68	160	0	0.462585	0	.	.	weak	.	.	.	.	NM_148894	exon10	c.G5731C	p.V1911L	CTACCACAGTACC	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	37	2	220286142	220286142	+	Silent	SNP	G	G	A	rs1058284	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	64	154	1	0.719101	0.00649351	G|0.640;A|0.360	0.360	strong	DES,right_upper_lobe,carcinoma,+1,1	DES	53	1	NM_001927	exon6	c.G1104A	p.A368A	CATTGCGCGCCTG	.	PASS	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	68	147	0	0.382022	0	G|0.656;T|0.344	0.344	strong	.	OR10G3	40	.	NM_001005465	exon1	c.C351A	p.T117T	CATTAGGGTGTAG	.	PASS	Atlas-SNP
C19orf44	84167	hgsc.bcm.edu	37	19	16612011	16612011	+	Silent	SNP	T	T	C	rs728117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	35	73	0	0.538462	0	T|0.663;C|0.337	0.337	strong	.	C19orf44	47	.	NM_032207	exon2	c.T408C	p.S136S	CCTCTCTGGGGGT	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1504437	1504437	+	Silent	SNP	C	C	T	rs12935737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	53	123	0	0.46087	0	C|0.926;T|0.074	0.074	strong	CLCN7,NS,carcinoma,0,1	CLCN7	53	1	NM_001287	exon13	c.G1128A	p.P376P	GAAGACCGGGATC	.	PASS	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	37	3	38645420	38645420	+	Missense_Mutation	SNP	T	T	C	rs1805124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	71	230	1	0.362245	0.00434783	T|0.790;C|0.210	0.210	strong	SCN5A_ENST00000413689,colon,carcinoma,0,3	SCN5A	634	3	NM_001160160	exon12	c.A1673G	p.H558R	GATGTGTGGTGGC	.	scavenged	Atlas-SNP
SEMA4G	57715	hgsc.bcm.edu	37	10	102743494	102743494	+	Missense_Mutation	SNP	G	G	A	rs41291464	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	17	85	0	0.283333	0	G|0.981;A|0.019	0.019	strong	.	SEMA4G	55	.	NM_017893	exon14	c.G2138A	p.R713H	GAGGGCGCCGACG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31237858	31237858	+	Silent	SNP	T	T	C	rs34794906	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	70	245	0	0.288066	0	T|0.659;C|0.341	0.341	strong	.	HLA-C	92	.	NM_002117	exon5	c.A900G	p.P300P	GGAAGATGGCTCT	.	PASS	Atlas-SNP
ATAD3C	219293	hgsc.bcm.edu	37	1	1390875	1390875	+	Silent	SNP	C	C	T	rs1781147	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	14	177	1	0.17284	0.00564972	C|0.608;T|0.392	0.392	strong	ATAD3C,NS,carcinoma,+2,1	ATAD3C	23	1	NM_001039211	exon5	c.C414T	p.D138D	CCAGGACGTGCTG	.	scavenged	Atlas-SNP
CNR2	1269	hgsc.bcm.edu	37	1	24201919	24201919	+	Silent	SNP	T	T	C	rs35761398	bycluster;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	82	146	1	0.97619	0.00684932	CC|1.000;|0.000	.	alt	CNR2,NS,carcinoma,-1,2	CNR2	78	2	NM_001841	exon2	c.A189G	p.Q63Q	GCGGAGTTGGTGG	.	PASS	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140222641	140222641	+	Missense_Mutation	SNP	A	A	G	rs6580012	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	10	5	46	2	0.5	0.0434783	A|0.480;G|0.520	0.520	strong	PCDHA8_ENST00000531613,NS,carcinoma,0,4	PCDHA8	366	4	NM_031856	exon1	c.A1735G	p.K579E	GCGAGCAAGCTGG	.	scavenged	Atlas-SNP
GNPAT	8443	hgsc.bcm.edu	37	1	231408091	231408091	+	Missense_Mutation	SNP	A	A	G	rs11558492	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	289	288	252	1	0.99654	0.00396825	G|0.155;N|0.000	0.155	strong	.	GNPAT	73	.	NM_014236	exon11	c.A1556G	p.D519G	TACGTGATGTTTT	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126238924	126238924	+	Missense_Mutation	SNP	A	A	T	rs6847454	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	20	176	0	0.206186	0	A|0.518;T|0.482	0.482	strong	.	FAT4	1752	.	NM_024582	exon1	c.A1358T	p.Q453L	CAGTCCAGGCGCG	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71841018	71841018	+	Silent	SNP	A	A	G	rs17062695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	126	264	0	0.475472	0	A|0.907;G|0.093	0.093	strong	.	TJP2	120	.	NM_001170416	exon7	c.A1230G	p.L410L	ACAGCTAGTGGTG	.	PASS	Atlas-SNP
AKR7A2	8574	hgsc.bcm.edu	37	1	19635011	19635011	+	Missense_Mutation	SNP	C	C	T	rs1043657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	94	212	1	0.764228	0.00471698	C|0.938;T|0.062	0.062	strong	.	AKR7A2	19	.	NM_003689	exon2	c.G424A	p.A142T	CAGGTGCGTGTAG	.	PASS	Atlas-SNP
IMMT	10989	hgsc.bcm.edu	37	2	86385728	86385728	+	Silent	SNP	C	C	T	rs1131071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	63	138	0	0.557522	0	T|0.180;G|0.013	0.180	strong	.	IMMT	65	.	NM_006839	exon10	c.G1149A	p.G383G	TTTCCACCCAGGA	.	PASS	Atlas-SNP
NBPF14	25832	hgsc.bcm.edu	37	1	148004783	148004783	+	Missense_Mutation	SNP	C	C	A	rs147480284	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	412	393	529	2	0.953883	0.00378072	C|0.960;A|0.040	0.040	strong	NBPF14,NS,adenoma,0,2	NBPF14	107	2	NM_015383	exon22	c.G2531T	p.S844I	AGCATGCTGTTGA	.	scavenged	Atlas-SNP
BCAN	63827	hgsc.bcm.edu	37	1	156627996	156627996	+	Silent	SNP	T	T	C	rs2298135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	317	103	258	0	0.324921	0	T|0.928;C|0.072	0.072	strong	.	BCAN	174	.	NM_021948	exon12	c.T2370C	p.H790H	GTGGCATGATCAG	.	PASS	Atlas-SNP
VNN2	8875	hgsc.bcm.edu	37	6	133073844	133073844	+	Silent	SNP	C	C	T	rs33980664	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	45	84	0	0.473684	0	C|0.976;T|0.024	0.024	strong	.	VNN2	83	.	NM_004665	exon4	c.G582A	p.P194P	CAACTCCGGCTTT	.	PASS	Atlas-SNP
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	103	98	0	0.647799	0	A|0.817;G|0.183	0.183	strong	.	MET	412	.	NM_000245	exon7	c.A1944G	p.Q648Q	AACACAATACAGT	.	PASS	Atlas-SNP
LCP1	3936	hgsc.bcm.edu	37	13	46705031	46705031	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	3	250	0	0.012987	0	.	.	none	LCP1,colon,carcinoma,0,1	LCP1	69	1	NM_002298	exon15	c.G1669A	p.D557N	TGGCATCGATGAG	.	scavenged	Atlas-SNP
OR5AS1	219447	hgsc.bcm.edu	37	11	55798259	55798259	+	Missense_Mutation	SNP	G	G	T	rs12224086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	127	316	0	0.442509	0	A|0.000;G|0.900;T|0.099	0.099	strong	OR5AS1,NS,carcinoma,+1,5	OR5AS1	121	5	NM_001001921	exon1	c.G365T	p.R122L	ATGACCGCTATGC	.	PASS	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	37	6	3010390	3010390	+	Missense_Mutation	SNP	C	C	T	rs1143684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	113	159	0	1	0	C|0.183;T|0.817	0.817	strong	.	NQO2	21	.	NM_000904	exon3	c.C139T	p.L47F	ATGAACCTTGAGC	.	PASS	Atlas-SNP
PAPOLB	56903	hgsc.bcm.edu	37	7	4900341	4900341	+	Silent	SNP	G	G	A	rs17135247	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	342	108	218	0	0.315789	0	G|0.777;A|0.223	0.223	strong	PAPOLB_ENST00000404991,NS,carcinoma,-1,2	PAPOLB	93	2	NM_020144	exon1	c.C1101T	p.S367S	AAAGAAGCTTGGA	.	PASS	Atlas-SNP
ASB11	140456	hgsc.bcm.edu	37	X	15332558	15332558	+	Silent	SNP	A	A	G	rs5935944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	65	138	1	1	0.00724638	A|0.680;0|0.003	.	strong	.	ASB11	79	.	NM_001012428	exon1	c.T51C	p.R17R	TCTGATACGTTCT	.	PASS	Atlas-SNP
SP140	11262	hgsc.bcm.edu	37	2	231110582	231110582	+	Silent	SNP	C	C	T	rs28445040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	64	164	0	0.340426	0	C|0.854;T|0.146	0.146	strong	.	SP140	121	.	NM_007237	exon7	c.C669T	p.S223S	AGTGTCCTGTAAA	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109374952	109374952	+	Silent	SNP	A	A	G	rs826549	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	94	338	2	0.414097	0.00591716	A|0.745;G|0.255	0.255	strong	RANBP2_ENST00000283195,NS,carcinoma,0,1	RANBP2	488	1	NM_006267	exon18	c.A2550G	p.S850S	AGACTCAGTGCCT	.	scavenged	Atlas-SNP
NKX2-3	159296	hgsc.bcm.edu	37	10	101293035	101293035	+	Silent	SNP	C	C	A	rs41290504	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	20	114	0	0.227273	0	C|0.494;A|0.506	0.506	strong	NKX2-3,NS,carcinoma,0,1	NKX2-3	11	1	NM_145285	exon1	c.C147A	p.A49A	GGCCGCCGCTGAG	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238668802	238668802	+	Silent	SNP	A	A	G	rs3213868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	46	110	0	0.469388	0	A|0.676;G|0.324	0.324	strong	LRRFIP1_ENST00000392000,colon,carcinoma,+1,3	LRRFIP1	171	3	NM_001137550	exon19	c.A1413G	p.T471T	GATGACAAAAGAA	.	PASS	Atlas-SNP
ANKRD35	148741	hgsc.bcm.edu	37	1	145562087	145562087	+	Missense_Mutation	SNP	G	G	A	rs41315701	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	32	52	0	0.268908	0	G|0.837;A|0.163	0.163	strong	.	ANKRD35	96	.	NM_144698	exon10	c.G1775A	p.R592Q	GGGCTCGAGGAGA	.	PASS	Atlas-SNP
MACROD2	140733	hgsc.bcm.edu	37	20	14066276	14066276	+	Missense_Mutation	SNP	C	C	T	rs2990505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	81	174	0	0.509434	0	C|0.749;T|0.251	0.251	strong	C20orf133,NS,carcinoma,0,1	MACROD2	34	1	NM_080676	exon3	c.C173T	p.T58I	AAAATACTCAGGA	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10114740	10114740	+	Missense_Mutation	SNP	T	T	A	rs62104337	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	107	158	0	0.514423	0	T|0.838;A|0.162	0.162	strong	.	COL5A3	243	.	NM_015719	exon5	c.A676T	p.N226Y	CCAGGTTGTCACA	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216258213	216258213	+	Missense_Mutation	SNP	A	A	G	rs56222536	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	85	86	0	0.643939	0	A|0.892;G|0.108	0.108	strong	.	USH2A	1168	.	NM_206933	exon25	c.T4994C	p.I1665T	TTTTGGATTATCT	.	PASS	Atlas-SNP
STK36	27148	hgsc.bcm.edu	37	2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	rs1863704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	36	260	0	0.288	0	G|0.767;A|0.233	0.233	strong	STK36,rectum,carcinoma,0,1	STK36	111	1	NM_015690	exon25	c.G3008A	p.G1003D	TTATAGGTGTCTT	.	PASS	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	37	5	140262582	140262582	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	49	133	0	0.347518	0	.	.	none	.	PCDHA13	213	.	NM_031865	exon1	c.C729G	p.Y243X	ATTTTACCAATCC	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216219781	216219781	+	Missense_Mutation	SNP	A	A	G	rs6657250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	189	151	1	0.994737	0.00662252	A|0.338;G|0.661	0.661	strong	USH2A,NS,carcinoma,0,1	USH2A	1168	1	NM_206933	exon32	c.T6317C	p.I2106T	GTGACTATGTAGT	.	PASS	Atlas-SNP
SUPT6H	6830	hgsc.bcm.edu	37	17	27016529	27016529	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	2	147	0	0.0151515	0	.	.	none	SUPT6H,NS,carcinoma,0,1	SUPT6H	165	1	NM_003170	exon25	c.C3292T	p.R1098X	CCAGAGCGACTGA	.	scavenged	Atlas-SNP
SLC35B1	10237	hgsc.bcm.edu	37	17	47783663	47783663	+	Missense_Mutation	SNP	C	C	T	rs1135034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	66	121	0	0.47482	0	C|0.928;T|0.072	0.072	strong	.	SLC35B1	21	.	NM_005827	exon3	c.G242A	p.R81H	CGGGTACGATCCA	.	PASS	Atlas-SNP
ALX4	60529	hgsc.bcm.edu	37	11	44286566	44286566	+	Silent	SNP	G	G	A	rs3802805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	118	158	1	0.967213	0.00632911	G|0.699;A|0.301	0.301	strong	ALX4,NS,adenoma,0,1	ALX4	58	1	NM_021926	exon4	c.C1074T	p.H358H	GCCCACGTGACTG	.	PASS	Atlas-SNP
KPNA5	3841	hgsc.bcm.edu	37	6	117045491	117045491	+	Silent	SNP	T	T	C	rs2243368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	92	271	0	0.403509	0	T|0.959;C|0.041	0.041	strong	.	KPNA5	57	.	NM_002269	exon10	c.T952C	p.L318L	CCTGCATTAAGGG	.	PASS	Atlas-SNP
TJP1	7082	hgsc.bcm.edu	37	15	30008889	30008889	+	Silent	SNP	G	G	A	rs2229518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	78	134	0	1	0	G|0.213;A|0.787	0.787	strong	.	TJP1	140	.	NM_003257	exon23	c.C4128T	p.A1376A	GCTGGCGGCAATG	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167313451	167313451	+	Missense_Mutation	SNP	T	T	C	rs11888208	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	76	210	0	0.410811	0	T|0.896;C|0.104	0.104	strong	.	SCN7A	410	.	NM_002976	exon10	c.A1219G	p.I407V	TAGATATTTCACC	.	PASS	Atlas-SNP
NSUN2	54888	hgsc.bcm.edu	37	5	6604787	6604787	+	Silent	SNP	C	C	T	rs13181449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	58	133	0	0.504348	0	C|0.819;T|0.181	0.181	strong	.	NSUN2	82	.	NM_017755	exon16	c.G1749A	p.T583T	GATCCCCGTGTTA	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77353973	77353973	+	Missense_Mutation	SNP	G	G	T	rs9930984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	11	60	0	0.177419	0	G|0.434;T|0.566	0.566	strong	.	ADAMTS18	270	.	NM_199355	exon16	c.C2305A	p.L769I	GAATGAGGACCAC	.	PASS	Atlas-SNP
MICALCL	84953	hgsc.bcm.edu	37	11	12315915	12315915	+	Missense_Mutation	SNP	A	A	G	rs1493954	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	20	50	0	0.526316	0	A|0.511;C|0.004	.	strong	.	MICALCL	59	.	NM_032867	exon3	c.A937G	p.S313G	TCATTCAGCCTTC	.	PASS	Atlas-SNP
MDM1	56890	hgsc.bcm.edu	37	12	68709892	68709892	+	Missense_Mutation	SNP	C	C	T	rs17224810	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	77	172	1	0.430168	0.00581395	C|0.857;T|0.143	0.143	strong	MDM1,caecum,carcinoma,+1,1	MDM1	74	1	NM_017440	exon8	c.G1147A	p.V383I	TACTAACGGTTCC	.	scavenged	Atlas-SNP
GC	2638	hgsc.bcm.edu	37	4	72618323	72618323	+	Missense_Mutation	SNP	G	G	T	rs4588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	74	173	0	0.4625	0	G|0.785;T|0.215	0.215	strong	.	GC	132	.	NM_001204307	exon12	c.C1364A	p.T455K	AGTTCCGTGGGTG	.	PASS	Atlas-SNP
ST20	400410	hgsc.bcm.edu	37	15	80191280	80191280	+	Missense_Mutation	SNP	T	T	A	rs184575290	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	87	285	1	0.674419	0.00350877	T|0.998;A|0.002	0.002	strong	ST20,NS,carcinoma,+1,1	ST20	9	1	NM_001199757	exon3	c.A233T	p.Y78F	TAAAAGTAGAAGT	.	PASS	Atlas-SNP
NUP62	23636	hgsc.bcm.edu	37	19	50412217	50412217	+	Missense_Mutation	SNP	C	C	G	rs1062798	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	71	96	1	0.972603	0.0104167	C|0.677;G|0.323	0.323	strong	NUP62,NS,carcinoma,0,2	NUP62	50	2	NM_153719	exon3	c.G848C	p.S283T	CTGCTGCTGGTGG	.	scavenged	Atlas-SNP
RAP1GAP	5909	hgsc.bcm.edu	37	1	21940555	21940555	+	Missense_Mutation	SNP	C	C	T	rs2275363	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	71	147	1	0.959459	0.00680272	C|0.587;T|0.413	0.413	strong	.	RAP1GAP	119	.	NM_001145658	exon8	c.G511A	p.A171T	GGGCAGCGTCCAG	.	PASS	Atlas-SNP
MFI2	4241	hgsc.bcm.edu	37	3	196743130	196743130	+	Silent	SNP	T	T	C	rs6779362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	47	120	1	0.423423	0.00833333	T|0.686;C|0.314	0.314	strong	MFI2,NS,carcinoma,0,1	MFI2	88	1	NM_005929	exon8	c.A1011G	p.T337T	GGTCTGTGTGGCG	.	scavenged	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318741	21318741	+	Silent	SNP	C	C	T	rs75113504	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	12	146	0	0.102564	0	C|0.883;T|0.117	0.117	strong	KCNJ12,NS,neuroblastoma,0,2	.	.	2	NM_001194958	exon3	c.C87T	p.N29N	CGCCAACGGCTTC	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789317	117789317	+	Silent	SNP	T	T	C	rs201369736		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268	13	118	0	0.0485075	0	.	.	weak	TMPRSS13,caecum,carcinoma,0,1	TMPRSS13	75	1	NM_001206790	exon2	c.A258G	p.P86P	CCGGGCTGGAGAT	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72360224	72360224	+	Silent	SNP	C	C	T	rs115281140	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	87	226	2	0.731092	0.00884956	C|0.990;T|0.010	0.010	strong	PRF1,NS,carcinoma,-2,1	PRF1	64	1	NM_001083116	exon2	c.G435A	p.V145V	CACAGACACATGC	.	scavenged	Atlas-SNP
IL1RAP	3556	hgsc.bcm.edu	37	3	190363594	190363594	+	Silent	SNP	G	G	A	rs34879831	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	73	162	0	0.489933	0	G|0.811;A|0.189	0.189	strong	.	IL1RAP	96	.	NM_001167929	exon10	c.G1308A	p.K436K	ATACAAGCTGTGC	.	PASS	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346468	140346468	+	Silent	SNP	T	T	A	rs155364	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	30	104	0	0.483871	0	T|0.409;A|0.591	0.591	strong	PCDHAC2,NS,carcinoma,0,1	PCDHAC2	142	1	NM_031883	exon1	c.T117A	p.P39P	TGGCCCTGCGGCC	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3782647	3782647	+	Missense_Mutation	SNP	A	A	T	rs36030417	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	47	192	0	0.373016	0	A|0.861;T|0.139	0.139	strong	.	EFCAB4B	100	.	NM_001144958	exon7	c.T636A	p.H212Q	CTCCTCATGGGCT	.	PASS	Atlas-SNP
OR1K1	392392	hgsc.bcm.edu	37	9	125562527	125562527	+	Silent	SNP	T	T	C	rs10985782	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	129	250	0	0.518072	0	T|0.876;C|0.124	0.124	strong	OR1K1,NS,carcinoma,0,1	OR1K1	34	1	NM_080859	exon1	c.T126C	p.G42G	CCTGGGTAATGGA	.	PASS	Atlas-SNP
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12248942	12248942	+	Silent	SNP	A	A	G	rs945439	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	11	56	0	0.354839	0	A|0.787;G|0.213	0.213	strong	.	TNFRSF1B	28	.	NM_001066	exon2	c.A168G	p.K56K	CAGCAAATGCTCG	.	PASS	Atlas-SNP
MMEL1	79258	hgsc.bcm.edu	37	1	2526746	2526746	+	Missense_Mutation	SNP	A	A	G	rs3748816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	39	249	0	0.267123	0	A|0.529;G|0.471	0.471	strong	.	MMEL1	64	.	NM_033467	exon16	c.T1553C	p.M518T	CTGTTCATCTCCT	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43095101	43095101	+	Missense_Mutation	SNP	A	A	G	rs536119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	157	148	0	1	0	A|0.413;G|0.587	0.587	strong	.	FAM198A	23	.	NM_001129908	exon3	c.A1379G	p.Q460R	AATGCCAGAACCC	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167262353	167262353	+	Missense_Mutation	SNP	C	C	G	rs3791251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	69	186	0	0.5	0	C|0.920;G|0.080	0.080	strong	.	SCN7A	410	.	NM_002976	exon25	c.G4786C	p.V1596L	CTGAAACAACTTT	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	241979550	241979550	+	Silent	SNP	T	T	C	rs7571117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	46	111	0	0.365079	0	T|0.554;C|0.446	0.446	strong	.	SNED1	76	.	NM_001080437	exon7	c.T1104C	p.N368N	GGAGAATGGCTCT	.	PASS	Atlas-SNP
TRAF3	7187	hgsc.bcm.edu	37	14	103336727	103336727	+	Silent	SNP	G	G	A	rs142350527	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	37	82	0	0.397849	0	G|0.996;A|0.004	0.004	strong	.	TRAF3	60	.	NM_145726	exon3	c.G189A	p.P63P	CAGCCCGAAGCAG	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138740037	138740037	+	Missense_Mutation	SNP	G	G	C	rs2297236	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	7	50	0	0.269231	0	G|0.451;C|0.549	0.549	strong	ZC3HAV1,NS,carcinoma,0,2	ZC3HAV1	75	2	NM_020119	exon10	c.C2101G	p.Q701E	CTGGCTGATGGCT	.	PASS	Atlas-SNP
CCDC67	159989	hgsc.bcm.edu	37	11	93129483	93129483	+	Missense_Mutation	SNP	G	G	C	rs12288277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	60	141	0	0.237154	0	C|0.236;G|0.764	0.236	strong	.	CCDC67	57	.	NM_181645	exon11	c.G1318C	p.E440Q	CCCGGAGAATACA	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184290348	184290348	+	Silent	SNP	G	G	A	rs9862375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	85	165	0	0.497076	0	G|0.918;A|0.082	0.082	strong	.	EPHB3	114	.	NM_004443	exon3	c.G240A	p.V80V	CCAGGTGTGTAAT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60897104	60897104	+	Missense_Mutation	SNP	C	C	T	rs141208202	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40	17	47	0	0.425	0	C|0.973;T|0.027	0.027	strong	.	LAMA5	268	.	NM_005560	exon48	c.G6467A	p.G2156E	ACAGGCCCGCCTG	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153421912	153421912	+	Silent	SNP	T	T	C	rs1065439	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	352	345	695	2	0.980114	0.0028777	0|0.004;C|0.185	0.185	strong	.	OPN1LW	87	.	NM_020061	exon5	c.T888C	p.G296G	CCCTGGTTACGCC	.	PASS	Atlas-SNP
SNF8	11267	hgsc.bcm.edu	37	17	47007963	47007963	+	Silent	SNP	C	C	T	rs2270576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	17	35	0	0.472222	0	C|0.747;T|0.253	0.253	strong	.	SNF8	15	.	NM_007241	exon8	c.G651A	p.L217L	TTCCTTCAGCAGG	.	PASS	Atlas-SNP
OR8D2	283160	hgsc.bcm.edu	37	11	124189729	124189729	+	Missense_Mutation	SNP	C	C	T	rs2512219	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	39	65	0	0.345133	0	C|0.749;T|0.250	0.250	strong	.	OR8D2	65	.	NM_001002918	exon1	c.G365A	p.R122H	ACATAACGGTCAT	.	PASS	Atlas-SNP
HCAR3	8843	hgsc.bcm.edu	37	12	123200937	123200937	+	Silent	SNP	T	T	G	rs1696352	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	91	104	1	1	0.00961538	T|0.468;G|0.532	0.532	strong	.	HCAR3	49	.	NM_006018	exon1	c.A348C	p.I116I	GAGGAATATGATG	.	PASS	Atlas-SNP
SLC17A5	26503	hgsc.bcm.edu	37	6	74354175	74354175	+	Silent	SNP	C	C	T	rs472294	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	138	141	1	0.992806	0.0070922	C|0.888;T|0.112	0.112	strong	.	SLC17A5	42	.	NM_012434	exon2	c.G246A	p.A82A	TGGACACGCCTTG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76433899	76433899	+	Missense_Mutation	SNP	G	G	A	rs61742072	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	63	126	0	0.583333	0	G|0.865;A|0.135	0.135	strong	DNAH17,NS,carcinoma,+1,1	DNAH17	347	1	NM_173628	exon74	c.C11857T	p.H3953Y	TGTAGTGCTCCAG	.	PASS	Atlas-SNP
MDH1B	130752	hgsc.bcm.edu	37	2	207619779	207619779	+	Silent	SNP	A	A	G	rs59358632	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	28	159	0	0.225806	0	A|0.884;G|0.116	0.116	strong	.	MDH1B	89	.	NM_001039845	exon5	c.T864C	p.G288G	CGCTTCACCTTCC	.	PASS	Atlas-SNP
ATP5J2-PTCD1	100526740	hgsc.bcm.edu	37	7	99017737	99017737	+	Silent	SNP	G	G	A	rs114658645	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	64	104	0	0.369942	0	G|0.968;A|0.032	0.032	strong	PTCD1,caecum,carcinoma,0,1	.	.	1	NM_001198879	exon9	c.C2103T	p.D701D	GAAGCCGTCAATC	.	PASS	Atlas-SNP
DNA2	1763	hgsc.bcm.edu	37	10	70178965	70178965	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	19	49	0	0.5	0	.	.	none	.	DNA2	76	.	NM_001080449	exon19	c.A2793G	p.G931G	ACTGCATCCAGCC	.	PASS	Atlas-SNP
ITGA7	3679	hgsc.bcm.edu	37	12	56092682	56092682	+	Silent	SNP	C	C	T	rs3847675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	25	48	0	0.403226	0	C|0.941;T|0.059	0.059	strong	ITGA7_ENST00000553804,rectum,carcinoma,0,2	ITGA7	194	2	NM_001144996	exon6	c.G822A	p.G274G	ACCTTTCCCCGAG	.	PASS	Atlas-SNP
PRPF4B	8899	hgsc.bcm.edu	37	6	4044109	4044109	+	Silent	SNP	G	G	A	rs12195092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	56	163	0	0.470588	0	G|0.982;A|0.018	0.018	strong	.	PRPF4B	140	.	NM_003913	exon6	c.G1713A	p.Q571Q	CCCCCAGAGCAGT	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73567846	73567846	+	Missense_Mutation	SNP	C	C	T	rs1661715	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	39	55	0	0.549296	0	C|0.622;T|0.378	0.378	strong	LLGL2_ENST00000167462,rectum,carcinoma,0,6	LLGL2	155	6	NM_004524	exon18	c.C2275T	p.P759S	GATGAGCCTGTGC	.	PASS	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	37	7	4050731	4050731	+	Silent	SNP	C	C	T	rs61752593	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	44	57	0	0.578947	0	C|0.882;T|0.118	0.118	strong	.	SDK1	361	.	NM_152744	exon15	c.C2265T	p.S755S	GTACAGCGCCGAG	.	PASS	Atlas-SNP
KLK6	5653	hgsc.bcm.edu	37	19	51465096	51465096	+	Silent	SNP	C	C	G	rs1701950	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	60	84	0	0.526316	0	C|0.883;G|0.117	0.117	strong	.	KLK6	35	.	NM_001012964	exon5	c.G486C	p.L162L	GGACACCAGGTGG	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77359919	77359919	+	Missense_Mutation	SNP	A	A	T	rs11640912	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	22	121	0	0.166667	0	A|0.625;T|0.375	0.375	strong	.	ADAMTS18	270	.	NM_199355	exon13	c.T1876A	p.L626I	AGAATAAGCCACC	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1500501	1500501	+	Silent	SNP	C	C	T	rs117461525	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	37	90	0	0.560606	0	C|0.940;T|0.060	0.060	strong	.	CLCN7	53	.	NM_001287	exon17	c.G1614A	p.A538A	CACCGCCGCCCCC	.	PASS	Atlas-SNP
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969507	99969507	+	Missense_Mutation	SNP	C	C	T	rs35122894	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	20	107	0	0.333333	0	C|0.980;T|0.020	0.020	strong	.	R3HCC1L	3	.	NM_001256620	exon4	c.C1636T	p.P546S	TCTTTTCCTGATA	.	PASS	Atlas-SNP
TAT	6898	hgsc.bcm.edu	37	16	71602660	71602660	+	Missense_Mutation	SNP	G	G	A	rs142634310	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	32	148	0	0.205128	0	G|0.999;A|0.001	0.001	strong	.	TAT	80	.	NM_000353	exon11	c.C1178T	p.T393M	CGCTCCGTGAACT	.	PASS	Atlas-SNP
TRPV2	51393	hgsc.bcm.edu	37	17	16336992	16336992	+	Silent	SNP	C	C	G	rs14039	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	58	130	1	0.426471	0.00769231	T|0.000;G|0.355;C|0.645	0.355	strong	TRPV2,NS,carcinoma,0,1	TRPV2	74	1	NM_016113	exon13	c.C2094G	p.P698P	CAGCCCCGATGAG	.	scavenged	Atlas-SNP
SP110	3431	hgsc.bcm.edu	37	2	231077676	231077676	+	Missense_Mutation	SNP	G	G	A	rs11556887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	269	141	278	0	0.524164	0	G|0.925;A|0.075	0.075	strong	SP110,NS,carcinoma,0,1	SP110	105	1	NM_001185015	exon5	c.C401T	p.A134V	CCTTCTGCTAGGC	.	PASS	Atlas-SNP
ACE	1636	hgsc.bcm.edu	37	17	61574642	61574642	+	Missense_Mutation	SNP	G	G	A	rs200754517	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	18	47	0	0.666667	0	.	.	weak	.	ACE	187	.	NM_000789	exon25	c.G3836A	p.R1279Q	GCCAGCGGCTCTT	.	PASS	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	62	211	0	0.446043	0	G|0.957;A|0.043	0.043	strong	.	PCDHA10	358	.	NM_031859	exon1	c.G1525A	p.V509M	GTGTCGGTGCACG	.	PASS	Atlas-SNP
GAD2	2572	hgsc.bcm.edu	37	10	26575277	26575277	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	15	84	0	0.267857	0	.	.	none	.	GAD2	116	.	NM_000818	exon13	c.T1240C	p.L414L	TAGGGATTGATGC	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89398553	89398553	+	Missense_Mutation	SNP	C	C	A	rs35430524	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	54	105	0	0.683544	0	C|0.901;A|0.099	0.099	strong	ACAN,NS,carcinoma,0,1	ACAN	220	1	NM_001135	exon12	c.C2737A	p.P913T	GGCCTGCCTGTGG	.	PASS	Atlas-SNP
ZNF480	147657	hgsc.bcm.edu	37	19	52825032	52825032	+	Missense_Mutation	SNP	C	C	T	rs13343641	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	311	128	349	0	0.411576	0	C|0.820;T|0.180	0.180	strong	.	ZNF480	123	.	NM_144684	exon5	c.C529T	p.P177S	AAAACCCCCATTT	.	PASS	Atlas-SNP
SLAMF1	6504	hgsc.bcm.edu	37	1	160580549	160580549	+	Missense_Mutation	SNP	G	G	T	rs3796504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	416	233	364	0	0.560096	0	G|0.945;T|0.055	0.055	strong	.	SLAMF1	74	.	NM_003037	exon7	c.C997A	p.P333T	TCTCTGGAAGTGT	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380243	186380243	+	Missense_Mutation	SNP	A	A	C	rs59319722	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	8	55	0	0.195122	0	A|0.548;C|0.452	0.452	strong	.	CCDC110	78	.	NM_152775	exon6	c.T1498G	p.Y500D	TGCTGTATTCTTC	.	PASS	Atlas-SNP
ZNF300	91975	hgsc.bcm.edu	37	5	150275835	150275835	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	26	126	0	0.254902	0	.	.	none	.	ZNF300	69	.	NM_001172831	exon7	c.G1014T	p.E338D	AGGTTTCTCCCCA	.	PASS	Atlas-SNP
MAP1B	4131	hgsc.bcm.edu	37	5	71495041	71495041	+	Silent	SNP	T	T	C	rs3805452	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	49	53	0	0.960784	0	T|0.749;C|0.251	0.251	strong	.	MAP1B	243	.	NM_005909	exon5	c.T5859C	p.G1953G	AGAGGGTGGGTAC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144875979	144875979	+	Silent	SNP	G	G	C	rs71664005	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	64	144	0	0.372093	0	G|0.216;C|0.784	0.784	strong	.	PDE4DIP	817	.	NM_014644	exon29	c.C4701G	p.L1567L	TTACCTGAGGGCC	.	PASS	Atlas-SNP
PDE2A	5138	hgsc.bcm.edu	37	11	72288599	72288599	+	Silent	SNP	G	G	A	rs1980091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	14	27	0	0.4375	0	G|0.707;A|0.293	0.293	strong	PDE2A,NS,adenoma,0,1	PDE2A	156	1	NM_002599	exon31	c.C2655T	p.Y885Y	GCGCTCGTACAGC	.	scavenged	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518333	161518333	+	Missense_Mutation	SNP	A	A	C	rs10127939	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	903	365	596	1	0.404208	0.00167785	T|0.013;C|0.046;A|0.941	0.046	strong	.	FCGR3A	38	.	NM_000569	exon3	c.T305G	p.L102R	GAGATGAGGCTCT	.	PASS	Atlas-SNP
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119945484	119945484	+	Missense_Mutation	SNP	A	A	G	rs144062067	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	3	101	0	0.0263158	0	A|1.000;G|0.000	0.000	strong	TNFRSF11B,NS,carcinoma,0,1	TNFRSF11B	87	1	NM_002546	exon2	c.T86C	p.L29P	TAATGAAGGTACT	.	scavenged	Atlas-SNP
EXOC6B	23233	hgsc.bcm.edu	37	2	72958333	72958333	+	Silent	SNP	T	T	C	rs61736520	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	387	184	397	0	0.475452	0	T|0.816;C|0.184	0.184	strong	.	EXOC6B	93	.	NM_015189	exon4	c.A369G	p.Q123Q	TCTCTGTTGTAGT	.	PASS	Atlas-SNP
NDST3	9348	hgsc.bcm.edu	37	4	119161795	119161795	+	Silent	SNP	G	G	A	rs617430	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	24	192	0	0.275862	0	G|0.732;A|0.268	0.268	strong	NDST3,NS,carcinoma,0,1	NDST3	107	1	NM_004784	exon11	c.G2235A	p.P745P	GGTCCCGGGGTGG	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83999033	83999033	+	Silent	SNP	A	A	G	rs173776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21	19	24	0	0.904762	0	A|0.701;G|0.299	0.299	strong	.	OSGIN1	33	.	NM_182981	exon6	c.A855G	p.S285S	GGCCTCAGACCCT	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15841773	15841773	+	Silent	SNP	G	G	A	rs12931799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	47	73	0	0.52809	0	G|0.917;A|0.083	0.083	strong	.	MYH11	520	.	NM_001040114	exon19	c.C2229T	p.I743I	TTTGGGGATGGCA	.	PASS	Atlas-SNP
GRAMD1C	54762	hgsc.bcm.edu	37	3	113594377	113594377	+	Silent	SNP	A	A	G	rs13079383	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	40	99	0	0.454545	0	A|0.724;G|0.276	0.276	strong	.	GRAMD1C	71	.	NM_017577	exon4	c.A306G	p.L102L	ACGACTATACCTT	.	PASS	Atlas-SNP
CAPN1	823	hgsc.bcm.edu	37	11	64950970	64950970	+	Silent	SNP	C	C	T	rs17583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	86	177	1	0.502924	0.00564972	C|0.734;T|0.266	0.266	strong	CAPN1,colon,carcinoma,0,1	CAPN1	44	1	NM_001198869	exon4	c.C363T	p.I121I	GGCCATCGCCTCC	.	scavenged	Atlas-SNP
H2AFV	94239	hgsc.bcm.edu	37	7	44874131	44874131	+	Missense_Mutation	SNP	A	A	G	rs114398265	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	5	139	0	0.026738	0	A|0.999;G|0.001	0.001	weak	H2AFV,NS,carcinoma,0,1	H2AFV	14	1	NM_012412	exon5	c.T356C	p.I119T	TTTCCAATCAGAG	.	scavenged	Atlas-SNP
MCM8	84515	hgsc.bcm.edu	37	20	5933108	5933108	+	Missense_Mutation	SNP	C	C	A	rs236110	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	110	222	0	0.493274	0	C|0.763;A|0.237	0.237	strong	.	MCM8	125	.	NM_032485	exon3	c.C187A	p.Q63K	ACCCCACAGTCAA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856817	144856817	+	Missense_Mutation	SNP	T	T	C	rs3844239	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	8	109	2	0.0592593	0.0183486	.	.	weak	PDE4DIP_ENST00000369356,caecum,carcinoma,0,4	PDE4DIP	817	4	NM_014644	exon40	c.A6668G	p.E2223G	ATTACCTCTGTGC	.	scavenged	Atlas-SNP
OR4X2	119764	hgsc.bcm.edu	37	11	48266736	48266736	+	Nonsense_Mutation	SNP	C	C	G	rs7120775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	94	242	2	0.494737	0.00826446	C|0.823;G|0.176;T|0.002	0.176	strong	OR4X2,NS,carcinoma,0,1	OR4X2	65	1	NM_001004727	exon1	c.C81G	p.Y27X	CTTGTACACAGCA	.	scavenged	Atlas-SNP
ANKRD36	375248	hgsc.bcm.edu	37	2	97909661	97909661	+	Silent	SNP	A	A	C	rs2595357		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1099	90	947	5	0.0818926	0.00527983	.	.	weak	ANKRD36_ENST00000420699,right_lower_lobe,carcinoma,0,2	ANKRD36	170	2	NM_001164315	exon70	c.A4464C	p.I1488I	AAGAATAACAGAA	.	scavenged	Atlas-SNP
TTC39A	22996	hgsc.bcm.edu	37	1	51767352	51767352	+	Silent	SNP	G	G	A	rs41287290	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	29	121	0	0.329545	0	A|0.083;C|0.000;G|0.917	0.083	strong	TTC39A,colon,carcinoma,0,2	TTC39A	40	2	NM_001144832	exon12	c.C957T	p.F319F	GTGGTGGAACTGC	.	PASS	Atlas-SNP
KRT5	3852	hgsc.bcm.edu	37	12	52912909	52912909	+	Missense_Mutation	SNP	G	G	T	rs641615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	34	186	0	0.269841	0	G|0.790;T|0.210	0.210	strong	.	KRT5	88	.	NM_000424	exon2	c.C591A	p.D197E	CTTGGTGTCCAGA	.	PASS	Atlas-SNP
GTSE1	51512	hgsc.bcm.edu	37	22	46704243	46704243	+	Silent	SNP	C	C	T	rs6008598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	35	70	0	0.603448	0	C|0.821;T|0.179	0.179	strong	.	GTSE1	100	.	NM_016426	exon4	c.C165T	p.F55F	CTTCTTCGGACCC	.	PASS	Atlas-SNP
PLIN3	10226	hgsc.bcm.edu	37	19	4852137	4852137	+	Silent	SNP	C	C	T	rs1055919	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	57	157	1	0.452381	0.00636943	C|0.557;T|0.443	0.443	strong	PLIN3,colon,carcinoma,0,1	PLIN3	36	1	NM_001164189	exon5	c.G525A	p.S175S	CATGACCGATTGG	.	scavenged	Atlas-SNP
HOXD10	3236	hgsc.bcm.edu	37	2	176982173	176982173	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	3	107	0	0.03125	0	.	.	none	HOXD10,NS,carcinoma,0,1	HOXD10	65	1	NM_002148	exon1	c.C612T	p.P204P	CGAGCCCGTGAGC	.	scavenged	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28459393	28459393	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	45	82	0	0.849057	0	.	.	none	.	HERC2	501	.	NM_004667	exon41	c.G6384A	p.V2128V	CGGGCGCACCCTG	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82363340	82363340	+	Silent	SNP	C	C	A	rs7069048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	15	123	0	0.197368	0	C|0.624;A|0.376	0.376	strong	SH2D4B,NS,carcinoma,-1,2	SH2D4B	44	2	NM_207372	exon5	c.C649A	p.R217R	GTGCGCCGGTCCA	.	PASS	Atlas-SNP
TNFRSF19	55504	hgsc.bcm.edu	37	13	24243204	24243204	+	Missense_Mutation	SNP	G	G	A	rs3751362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	45	119	0	0.46875	0	G|0.874;A|0.126	0.126	strong	TNFRSF19,NS,carcinoma,0,1	TNFRSF19	52	1	NM_018647	exon9	c.G1213A	p.V405I	GGTGCTGTCATCC	.	PASS	Atlas-SNP
PRB2	653247	hgsc.bcm.edu	37	12	11546309	11546309	+	Missense_Mutation	SNP	C	C	G	rs201308939		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	591	10	623	6	0.0169205	0.00963082	.	.	weak	PRB2_ENST00000389362,trunk,malignant_melanoma,0,2	PRB2	168	2	NM_006248	exon3	c.G703C	p.A235P	ATCGGGCACTTTG	.	scavenged	Atlas-SNP
PPID	5481	hgsc.bcm.edu	37	4	159631991	159631991	+	Missense_Mutation	SNP	G	G	T	rs9410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	48	101	0	0.716418	0	G|0.586;T|0.237	0.237	strong	.	PPID	22	.	NM_005038	exon8	c.C904A	p.L302I	GGTCTAGTTCAAG	.	PASS	Atlas-SNP
NPY2R	4887	hgsc.bcm.edu	37	4	156135676	156135676	+	Silent	SNP	C	C	T	rs1047214	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	76	124	0	0.767677	0	C|0.329;N|0.000	.	strong	.	NPY2R	87	.	NM_000910	exon2	c.C585T	p.I195I	GATCATCCCGGAC	.	PASS	Atlas-SNP
TRPV4	59341	hgsc.bcm.edu	37	12	110240838	110240838	+	Silent	SNP	T	T	G	rs3825394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	40	110	0	0.330579	0	T|0.359;G|0.641	0.641	strong	.	TRPV4	88	.	NM_001177433	exon3	c.A670C	p.R224R	ACTCCCTCATGTT	.	PASS	Atlas-SNP
SLC6A15	55117	hgsc.bcm.edu	37	12	85277561	85277561	+	Missense_Mutation	SNP	T	T	A	rs17183577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	175	188	0	1	0	T|0.862;A|0.138	0.138	strong	.	SLC6A15	159	.	NM_018057	exon5	c.A833T	p.D278V	CAGAAATCTGTAA	.	PASS	Atlas-SNP
SPNS2	124976	hgsc.bcm.edu	37	17	4434031	4434031	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	103	201	0	0.502439	0	.	.	none	SPNS2,colon,carcinoma,+1,1	SPNS2	24	1	NM_001124758	exon4	c.G678A	p.T226T	GAACACGCGTACG	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136536679	136536679	+	Silent	SNP	G	G	A	rs129932	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	104	250	1	0.462222	0.004	G|0.464;A|0.536	0.536	strong	.	SARDH	112	.	NM_007101	exon18	c.C2304T	p.I768I	GGAGTCGATGGCG	.	PASS	Atlas-SNP
OR10R2	343406	hgsc.bcm.edu	37	1	158450382	158450382	+	Missense_Mutation	SNP	C	C	T	rs1418843	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	131	175	1	0.617925	0.00571429	C|0.554;N|0.000	.	strong	.	OR10R2	81	.	NM_001004472	exon1	c.C715T	p.L239F	TCTTATCTCTGCA	.	PASS	Atlas-SNP
CCDC108	255101	hgsc.bcm.edu	37	2	219890814	219890814	+	Missense_Mutation	SNP	C	C	T	rs114017706	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	47	230	0	0.286585	0	C|0.989;T|0.011	0.011	strong	CCDC108,right_upper_lobe,carcinoma,+1,1	CCDC108	208	1	NM_194302	exon14	c.G2279A	p.R760Q	CGTGCCCGCACCG	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24424420	24424420	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	57	205	0	0.205036	0	.	.	none	DHRS4,NS,carcinoma,0,5	DHRS4	22	5	NM_021004	exon2	c.C305T	p.T102M	TGGCCACGGTGAG	.	scavenged	Atlas-SNP
OR6F1	343169	hgsc.bcm.edu	37	1	247875415	247875415	+	Missense_Mutation	SNP	A	A	G	rs2282316	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	86	101	0	0.651515	0	A|0.635;G|0.365	0.365	strong	OR6F1,NS,carcinoma,0,1	OR6F1	88	1	NM_001005286	exon1	c.T643C	p.F215L	AGACAAAGGTGAT	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135203838	135203838	+	Silent	SNP	G	G	A	rs3739921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	40	127	0	0.412371	0	G|0.910;A|0.090	0.090	strong	.	SETX	234	.	NM_015046	exon10	c.C3147T	p.H1049H	TGAAACGTGCTGC	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47560163	47560163	+	Silent	SNP	C	C	A	rs11729411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	211	228	0	0.981395	0	C|0.779;A|0.221	0.221	strong	ATP10D,NS,carcinoma,0,1	ATP10D	168	1	NM_020453	exon12	c.C2307A	p.I769I	ACACATCCTGCCC	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124351974	124351974	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	26	90	0	0.333333	0	.	.	none	.	DMBT1	677	.	NM_007329	exon20	c.T2363G	p.F788C	CCCGGTTTGGCCA	.	PASS	Atlas-SNP
APOBEC2	10930	hgsc.bcm.edu	37	6	41029109	41029109	+	Silent	SNP	T	T	C	rs2073014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	46	118	0	0.418182	0	T|0.840;C|0.160	0.160	strong	.	APOBEC2	30	.	NM_006789	exon2	c.T174C	p.N58N	CCGGAATGTGGAG	.	PASS	Atlas-SNP
BEND7	222389	hgsc.bcm.edu	37	10	13534851	13534851	+	Silent	SNP	A	A	G	rs2251555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	54	114	0	1	0	A|0.476;G|0.524	0.524	strong	BEND7_ENST00000378605,colon,carcinoma,0,4	BEND7	85	4	NM_001100912	exon4	c.T480C	p.P160P	AATTGGAGGTTGT	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11521428	11521428	+	Silent	SNP	A	A	G	rs61996277	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	336	121	273	0	0.360119	0	A|0.946;G|0.054	0.054	strong	.	THSD7A	219	.	NM_015204	exon7	c.T2004C	p.Y668Y	ACCCGCATAGGCC	.	PASS	Atlas-SNP
ZNF667	63934	hgsc.bcm.edu	37	19	56954103	56954103	+	Silent	SNP	C	C	A	rs7253217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	20	29	0	0.625	0	C|0.825;A|0.175	0.175	strong	.	ZNF667	95	.	NM_022103	exon5	c.G261T	p.G87G	TTTAGACCCCGAG	.	PASS	Atlas-SNP
PKM	5315	hgsc.bcm.edu	37	15	72501072	72501072	+	Silent	SNP	C	C	T	rs11558376	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	64	140	1	0.752941	0.00714286	C|0.999;T|0.001	0.001	strong	PKM2,NS,neuroblastoma,-1,2	PKM	25	2	NM_001206796	exon7	c.G948A	p.A316A	GAATGACGCAAAC	.	PASS	Atlas-SNP
KIAA1324	57535	hgsc.bcm.edu	37	1	109714593	109714593	+	Silent	SNP	C	C	T	rs112023388	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	122	267	0	0.7625	0	C|0.999;T|0.001	0.001	strong	.	KIAA1324	77	.	NM_020775	exon4	c.C573T	p.F191F	TAACTTCGAATAC	.	PASS	Atlas-SNP
MYSM1	114803	hgsc.bcm.edu	37	1	59127086	59127086	+	Silent	SNP	G	G	A	rs7523134	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	79	191	0	1	0	G|0.742;A|0.258	0.258	strong	.	MYSM1	50	.	NM_001085487	exon18	c.C2262T	p.L754L	ATGGGAGAGCCTG	.	PASS	Atlas-SNP
LANCL2	55915	hgsc.bcm.edu	37	7	55433880	55433880	+	Silent	SNP	G	G	C	rs2272262	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	22	79	0	0.318841	0	G|0.685;C|0.315	0.315	strong	.	LANCL2	54	.	NM_018697	exon1	c.G162C	p.A54A	CCCGGCGACCACG	.	PASS	Atlas-SNP
GFPT2	9945	hgsc.bcm.edu	37	5	179734200	179734200	+	Silent	SNP	A	A	G	rs73343449	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	67	149	3	0.437909	0.0201342	A|0.788;G|0.212	0.212	strong	GFPT2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	GFPT2	74	1	NM_005110	exon16	c.T1650C	p.Y550Y	GGTGGCATAGTTG	.	scavenged	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158827326	158827326	+	Silent	SNP	G	G	A	rs2071624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	32	148	0	0.285714	0	G|0.742;N|0.000	.	strong	.	VIPR2	53	.	NM_003382	exon9	c.C825T	p.N275N	GTGGTCGTTTGTA	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3886847	3886847	+	Silent	SNP	G	G	C	rs3749349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	41	107	0	0.427083	0	G|0.820;C|0.180	0.180	strong	.	LRRN1	82	.	NM_020873	exon2	c.G522C	p.L174L	CCACCTGAACTCC	.	PASS	Atlas-SNP
FBXO32	114907	hgsc.bcm.edu	37	8	124525483	124525483	+	Silent	SNP	C	C	T	rs3739287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	123	168	1	0.602941	0.00595238	C|0.843;T|0.157	0.157	strong	.	FBXO32	39	.	NM_058229	exon6	c.G606A	p.T202T	GAGAATCGTCTCC	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89815152	89815152	+	Missense_Mutation	SNP	G	G	A	rs17233497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	9	74	0	0.160714	0	G|0.954;A|0.046	0.046	strong	FANCA,lymph_node,lymphoid_neoplasm,0,1	FANCA	99	1	NM_000135	exon33	c.C3263T	p.S1088F	AGGACAGACGAAG	.	PASS	Atlas-SNP
SLC35F1	222553	hgsc.bcm.edu	37	6	118588185	118588185	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	379	117	366	2	0.308707	0.00546448	.	.	none	SLC35F1,bladder,carcinoma,-2,2	SLC35F1	65	2	NM_001029858	exon4	c.G505A	p.V169M	CCAGTCGTGATTT	.	scavenged	Atlas-SNP
KIF21B	23046	hgsc.bcm.edu	37	1	200959302	200959302	+	Silent	SNP	G	G	A	rs2297911	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	770	196	712	1	0.254545	0.00140449	G|0.752;A|0.248	0.248	strong	.	KIF21B	208	.	NM_017596	exon20	c.C2994T	p.D998D	CTGGCAGTCGGTG	.	PASS	Atlas-SNP
MAP9	79884	hgsc.bcm.edu	37	4	156274377	156274377	+	Missense_Mutation	SNP	T	T	C	rs1058992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	82	198	1	0.700855	0.00505051	T|0.652;C|0.348	0.348	strong	MAP9,NS,carcinoma,0,1	MAP9	79	1	NM_001039580	exon11	c.A1496G	p.K499R	GTTTTCTTCTTGT	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44117582	44117582	+	Missense_Mutation	SNP	T	T	C	rs10410000	bycluster;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	35	83	1	0.426829	0.0120482	C|1.000;|0.000	1.000	weak	SRRM5,colon,carcinoma,0,3	SRRM5	38	3	NM_001145641	exon1	c.T1309C	p.C437R	AGAGATTGCAGCC	.	scavenged	Atlas-SNP
ZNF615	284370	hgsc.bcm.edu	37	19	52505463	52505463	+	Silent	SNP	C	C	T	rs151263298	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	104	193	0	0.547368	0	C|0.966;T|0.034	0.034	strong	.	ZNF615	111	.	NM_001199324	exon4	c.G87A	p.Q29Q	GTCCTTCTGAGCA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2161793	2161793	+	Silent	SNP	G	G	A	rs74331768	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	29	60	0	0.604167	0	G|0.856;A|0.144	0.144	strong	.	PKD1	184	.	NM_000296	exon15	c.C3375T	p.S1125S	GGGCAGGGAGGCG	.	PASS	Atlas-SNP
PLCH1	23007	hgsc.bcm.edu	37	3	155200563	155200563	+	Silent	SNP	G	G	T	rs1816522	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	58	160	0	0.446154	0	A|0.000;G|0.948;T|0.052	0.052	strong	PLCH1_ENST00000340059,NS,adenoma,0,2	PLCH1	406	2	NM_001130960	exon23	c.C3276A	p.P1092P	AGGATCGGGAGCC	.	PASS	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	37	17	80059690	80059690	+	Silent	SNP	G	G	A	rs61735692	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	49	121	0	0.485149	0	G|0.975;A|0.025	0.025	strong	.	CCDC57	102	.	NM_198082	exon17	c.C2616T	p.G872G	GGCAATGCCTGCC	.	PASS	Atlas-SNP
PARP2	10038	hgsc.bcm.edu	37	14	20824181	20824181	+	Silent	SNP	T	T	C	rs3093930	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	193	162	0	0.989744	0	T|0.445;C|0.555	0.555	strong	.	PARP2	92	.	NM_005484	exon11	c.T1131C	p.Y377Y	AAGTTATGAGTTC	.	PASS	Atlas-SNP
ZBTB16	7704	hgsc.bcm.edu	37	11	113934473	113934473	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	3	60	0	0.0326087	0	.	.	none	ZBTB16_ENST00000335953,NS,carcinoma,-1,1	ZBTB16	101	1	NM_006006	exon2	c.C451T	p.R151W	AAGGCTCGGTACC	.	scavenged	Atlas-SNP
GRIN1	2902	hgsc.bcm.edu	37	9	140051238	140051238	+	Silent	SNP	A	A	G	rs6293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	39	143	0	0.458824	0	A|0.831;G|0.169	0.169	strong	GRIN1,NS,carcinoma,0,2	GRIN1	51	2	NM_001185091	exon6	c.A852G	p.P284P	CGCCCCAGACGGT	.	PASS	Atlas-SNP
FAM22A	728118	hgsc.bcm.edu	37	10	88988232	88988232	+	Missense_Mutation	SNP	G	G	A	rs200425300	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	360	3	457	2	0.00833333	0.00437637	G|0.996;A|0.004	0.004	strong	FAM22D,NS,carcinoma,-1,2	FAM22A	20	2	NM_001099338	exon2	c.G595A	p.G199R	GGGGCCGGGGCTT	.	scavenged	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	658993	658993	+	Silent	SNP	C	C	T	rs73592377	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	138	293	1	0.549801	0.00341297	C|0.925;T|0.075	0.075	strong	.	B4GALNT3	64	.	NM_173593	exon10	c.C912T	p.H304H	CAGCCACGTGGAC	.	PASS	Atlas-SNP
PHACTR2	9749	hgsc.bcm.edu	37	6	144074943	144074943	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	2	138	0	0.0168067	0	.	.	none	PHACTR2_ENST00000440869,rectum,carcinoma,0,2	PHACTR2	99	2	NM_001100165	exon4	c.C348T	p.I116I	ACCCATCGGAGAG	.	scavenged	Atlas-SNP
UQCRB	7381	hgsc.bcm.edu	37	8	97243720	97243720	+	Silent	SNP	G	G	A	rs2292835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7	7	5	0	1	0	G|0.748;A|0.252	0.252	strong	.	UQCRB	17	.	NM_001254752	exon4	c.C282T	p.H94H	AGCAGAGTGCAGA	.	PASS	Atlas-SNP
OR8J3	81168	hgsc.bcm.edu	37	11	55905078	55905078	+	Missense_Mutation	SNP	C	C	T	rs61742348	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	87	173	1	0.517857	0.00578035	C|0.901;T|0.099	0.099	strong	OR8J3,NS,carcinoma,0,2	OR8J3	112	2	NM_001004064	exon1	c.G117A	p.M39I	CCCTGCCATGGTC	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911218	29911218	+	Missense_Mutation	SNP	G	G	A	rs1059526	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	73	144	0	0.450617	0	A|0.067;G|0.933	0.067	strong	.	HLA-A	89	.	NM_001242758	exon3	c.G517A	p.A173T	TGGGAGGCGGCCC	.	PASS	Atlas-SNP
XRCC3	7517	hgsc.bcm.edu	37	14	104174950	104174950	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	46	83	0	0.319444	0	.	.	none	.	XRCC3	16	.	NM_005432	exon5	c.C102A	p.D34E	CTTCAAGTCTGGT	.	PASS	Atlas-SNP
B4GALT7	11285	hgsc.bcm.edu	37	5	177035964	177035964	+	Silent	SNP	T	T	C	rs729459	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	14	27	0	0.518519	0	T|0.401;C|0.599	0.599	strong	.	B4GALT7	21	.	NM_007255	exon5	c.T777C	p.H259H	CCTGCATGACCCA	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118657952	118657952	+	Missense_Mutation	SNP	C	C	T	rs12133381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	85	183	0	0.758929	0	C|0.932;T|0.068	0.068	strong	.	SPAG17	263	.	NM_206996	exon4	c.G428A	p.R143Q	TCCCGTCGCTGTT	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17764530	17764530	+	Silent	SNP	C	C	T	rs9371018	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	67	169	0	0.406061	0	C|0.684;T|0.316	0.316	strong	.	KIF13A	276	.	NM_022113	exon39	c.G5229A	p.E1743E	TTTTCCCTCTGAC	.	PASS	Atlas-SNP
PATL1	219988	hgsc.bcm.edu	37	11	59410479	59410479	+	Silent	SNP	A	A	T	rs77793148	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	52	115	0	0.472727	0	A|0.995;G|0.000;T|0.005	0.005	strong	.	PATL1	92	.	NM_152716	exon16	c.T1923A	p.S641S	AAGGAGAGAGAAG	.	PASS	Atlas-SNP
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017397	26017397	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	125	292	1	0.498008	0.00342466	.	.	none	.	HIST1H1A	25	.	NM_005325	exon1	c.G564C	p.K188N	TACAGCCTTAGCT	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78263514	78263514	+	Silent	SNP	G	G	A	rs17853713	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	43	123	0	0.447917	0	G|0.760;A|0.240	0.240	strong	RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	NM_001256071	exon6	c.G990A	p.K330K	CGGTAAGAATGAA	.	PASS	Atlas-SNP
AIPL1	23746	hgsc.bcm.edu	37	17	6331817	6331817	+	Missense_Mutation	SNP	C	C	T	rs62619924	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	40	64	0	0.547945	0	C|0.985;T|0.015	0.015	strong	.	AIPL1	34	.	NM_014336	exon3	c.G286A	p.V96I	GGTAGACCCCCGT	.	PASS	Atlas-SNP
CDK12	51755	hgsc.bcm.edu	37	17	37627387	37627387	+	Silent	SNP	A	A	G	rs56158954	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	33	68	0	0.559322	0	A|0.987;G|0.013	0.013	strong	CDK12,NS,carcinoma,0,1	CDK12	161	1	NM_016507	exon2	c.A1302G	p.S434S	CAGTTCAGTAGAG	.	PASS	Atlas-SNP
SAMD15	161394	hgsc.bcm.edu	37	14	77844265	77844265	+	Missense_Mutation	SNP	G	G	A	rs45527334	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	31	31	0	0.553571	0	G|0.848;A|0.152	0.152	strong	.	SAMD15	60	.	NM_001010860	exon1	c.G504A	p.M168I	AACCATGTCTGAG	.	PASS	Atlas-SNP
LSG1	55341	hgsc.bcm.edu	37	3	194387300	194387300	+	Silent	SNP	C	C	T	rs1675943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	33	84	0	0.492537	0	C|0.573;T|0.427	0.427	strong	.	LSG1	38	.	NM_018385	exon3	c.G228A	p.E76E	AAGTTTCTCTGTT	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6580495	6580495	+	Silent	SNP	G	G	A	rs72901756	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	64	142	0	0.492308	0	G|0.957;A|0.043	0.043	strong	.	DNHD1	198	.	NM_144666	exon28	c.G9501A	p.Q3167Q	ACAGCAGCTGAAA	.	PASS	Atlas-SNP
TOP3B	8940	hgsc.bcm.edu	37	22	22318671	22318671	+	Silent	SNP	G	G	A	rs9610729	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	58	134	0	0.464	0	G|0.896;A|0.104	0.104	strong	.	TOP3B	107	.	NM_003935	exon10	c.C960T	p.H320H	CATGGCGTGCTGC	.	PASS	Atlas-SNP
CD101	9398	hgsc.bcm.edu	37	1	117568217	117568217	+	Missense_Mutation	SNP	G	G	A	rs17229382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	25	43	0	0.78125	0	G|0.987;A|0.013	0.013	strong	.	CD101	95	.	NM_001256109	exon8	c.G2515A	p.V839I	GAGAGTGTAGGCA	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11189591	11189591	+	Missense_Mutation	SNP	C	C	T	rs62488717	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	39	125	1	0.19403	0.008	.	.	weak	AMAC1L2,NS,carcinoma,-1,1	.	.	1	NM_054028	exon1	c.C976T	p.R326W	ACAGCCCGGAACC	.	scavenged	Atlas-SNP
CHAD	1101	hgsc.bcm.edu	37	17	48545596	48545596	+	Silent	SNP	G	G	A	rs34864120	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	79	152	0	0.5	0	G|0.767;A|0.233	0.233	strong	.	CHAD	36	.	NM_001267	exon1	c.C579T	p.D193D	CTCCACGTCGTCC	.	PASS	Atlas-SNP
ZNF705A	440077	hgsc.bcm.edu	37	12	8329833	8329833	+	Missense_Mutation	SNP	G	G	A	rs11043758	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	100	316	2	0.431034	0.00632911	G|0.506;A|0.494	0.494	strong	ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	NM_001004328	exon5	c.G557A	p.R186H	GCTTTCGCCTTAG	.	scavenged	Atlas-SNP
CRYBB3	1417	hgsc.bcm.edu	37	22	25603052	25603052	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	51	150	0	0.401575	0	.	.	none	.	CRYBB3	13	.	NM_004076	exon6	c.T509G	p.V170G	GGCGCCAGTACGT	.	PASS	Atlas-SNP
CCDC129	223075	hgsc.bcm.edu	37	7	31682829	31682829	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	26	68	0	0.285714	0	.	.	none	.	CCDC129	127	.	NM_001257968	exon11	c.G1923C	p.E641D	CTCTGAGGCCCCA	.	PASS	Atlas-SNP
HS6ST1	9394	hgsc.bcm.edu	37	2	129025800	129025800	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	5	140	0	0.0520833	0	.	.	none	.	HS6ST1	31	.	NM_004807	exon2	c.A1172G	p.D391G	TCGGCATCCTCCC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912087	29912087	+	Missense_Mutation	SNP	G	G	T	rs2231093	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	50	219	0	0.252525	0	G|0.860;T|0.140	0.140	strong	.	HLA-A	89	.	NM_001242758	exon4	c.G808T	p.A270S	TGGGCGGCTGTGG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149521544	149521544	+	Silent	SNP	C	C	T	rs12673475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20	4	52	0	0.2	0	C|0.845;T|0.155	0.155	strong	.	.	.	.	NM_198455	exon95	c.C13623T	p.S4541S	GCCCAGCGCCCTG	.	PASS	Atlas-SNP
NPAT	4863	hgsc.bcm.edu	37	11	108044204	108044204	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	386	99	207	0	0.256477	0	.	.	none	.	NPAT	124	.	NM_002519	exon13	c.G1507C	p.D503H	GCTGATCAGGCTG	.	PASS	Atlas-SNP
SPTBN5	51332	hgsc.bcm.edu	37	15	42145049	42145049	+	Silent	SNP	C	C	T	rs55978013	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	26	181	0	0.292135	0	C|0.936;T|0.064	0.064	strong	.	SPTBN5	171	.	NM_016642	exon60	c.G10215A	p.E3405E	GAGTCCCTCCCAG	.	PASS	Atlas-SNP
GGT6	124975	hgsc.bcm.edu	37	17	4463796	4463796	+	Silent	SNP	G	G	A	rs7216474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	16	39	0	0.484848	0	G|0.838;A|0.162	0.162	strong	.	GGT6	22	.	NM_001122890	exon1	c.C21T	p.P7P	GACCACGGGCTCT	.	PASS	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134898789	134898789	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	261	3	264	0	0.0114943	0	.	.	none	EPHB1_ENST00000398015,rectum,carcinoma,0,2	EPHB1	519	2	NM_004441	exon10	c.T1847C	p.V616A	TTGATGTATCTTT	.	scavenged	Atlas-SNP
SLC1A1	6505	hgsc.bcm.edu	37	9	4576680	4576680	+	Silent	SNP	T	T	C	rs301430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	117	252	1	0.473684	0.00396825	T|0.604;C|0.396	0.396	strong	.	SLC1A1	43	.	NM_004170	exon10	c.T1110C	p.T370T	TGGGACTGCGCTC	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48313510	48313510	+	Missense_Mutation	SNP	A	A	G	rs17547830	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	157	137	0	1	0	A|0.781;G|0.219	0.219	strong	.	ABCA13	1192	.	NM_152701	exon17	c.A4247G	p.H1416R	AAGGTCATCTTCA	.	PASS	Atlas-SNP
ZNF283	284349	hgsc.bcm.edu	37	19	44351836	44351836	+	Silent	SNP	G	G	A	rs957569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	56	114	0	0.474576	0	G|0.328;A|0.672	0.672	strong	.	ZNF283	83	.	NM_181845	exon7	c.G1083A	p.Q361Q	CTATCAGCTTACT	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186671357	186671357	+	Missense_Mutation	SNP	G	G	A	rs17826534	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	68	171	0	0.386364	0	G|0.487;A|0.513	0.513	strong	FSIP2_ENST00000343098,caecum,carcinoma,+1,2	FSIP2	251	2	NM_173651	exon17	c.G17591A	p.R5864Q	ACCAACGAGAAAG	.	PASS	Atlas-SNP
ADCK1	57143	hgsc.bcm.edu	37	14	78399654	78399654	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268	122	217	0	0.455224	0	.	.	none	.	ADCK1	81	.	NM_020421	exon11	c.C1492T	p.L498F	CATGAGCTCATCC	.	PASS	Atlas-SNP
FAM78B	149297	hgsc.bcm.edu	37	1	166039898	166039898	+	Silent	SNP	C	C	G	rs41269662	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	32	74	0	0.31068	0	C|0.820;G|0.180	0.180	strong	.	FAM78B	51	.	NM_001017961	exon2	c.G366C	p.V122V	CAGGGTCACAGTT	.	PASS	Atlas-SNP
MMAB	326625	hgsc.bcm.edu	37	12	109994870	109994870	+	Missense_Mutation	SNP	A	A	T	rs9593	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	102	96	0	1	0	A|0.431;T|0.569	0.569	strong	MMAB,rectum,carcinoma,+1,1	MMAB	16	1	NM_052845	exon9	c.T716A	p.M239K	TTTTTCATGTATA	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102563739	102563739	+	Silent	SNP	C	C	T	rs1276289	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	57	94	0	0.349693	0	C|0.594;T|0.406	0.406	strong	MMP27,NS,carcinoma,0,1	MMP27	84	1	NM_022122	exon9	c.G1227A	p.G409G	CGGGAACCCTTTG	.	PASS	Atlas-SNP
DMWD	1762	hgsc.bcm.edu	37	19	46289009	46289009	+	Missense_Mutation	SNP	G	G	A	rs146577305	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	51	115	0	0.5	0	G|0.986;A|0.014	0.014	strong	.	DMWD	46	.	NM_004943	exon3	c.C1745T	p.A582V	CACAGCGCAGTGC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910604	29910604	+	Silent	SNP	C	C	A	rs12721675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	14	118	2	0.125	0.0169492	A|0.361;C|0.639	0.361	strong	HLA-A,NS,carcinoma,0,4	HLA-A	89	4	NM_001242758	exon2	c.C144A	p.A48A	CATCGCCGTGGGC	.	scavenged	Atlas-SNP
GTSE1	51512	hgsc.bcm.edu	37	22	46719100	46719100	+	Missense_Mutation	SNP	C	C	G	rs6008684	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	80	192	0	0.484848	0	C|0.856;G|0.144	0.144	strong	.	GTSE1	100	.	NM_016426	exon8	c.C1446G	p.D482E	CCCGGACAGCTCA	.	PASS	Atlas-SNP
CYP2F1	1572	hgsc.bcm.edu	37	19	41628014	41628014	+	Missense_Mutation	SNP	G	G	C	rs75405062	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	12	74	8	0.179104	0.108108	G|0.250;C|0.750	0.750	weak	CYP2F1,NS,carcinoma,+2,1	CYP2F1	60	1	NM_000774	exon6	c.G798C	p.Q266H	CATCCAGTGCTTC	.	scavenged	Atlas-SNP
KIAA0556	23247	hgsc.bcm.edu	37	16	27761040	27761040	+	Missense_Mutation	SNP	C	C	T	rs61734902	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	59	157	0	0.453846	0	C|0.951;T|0.049	0.049	strong	.	KIAA0556	348	.	NM_015202	exon16	c.C2759T	p.P920L	AGCTCCCGGGGGA	.	PASS	Atlas-SNP
AHNAK	79026	hgsc.bcm.edu	37	11	62284888	62284888	+	Silent	SNP	G	G	A	rs11555628	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	67	189	0	0.465278	0	G|0.966;C|0.000;A|0.034	0.034	strong	.	AHNAK	532	.	NM_001620	exon5	c.C17001T	p.T5667T	AGAGAAGGTAAAT	.	PASS	Atlas-SNP
GRM8	2918	hgsc.bcm.edu	37	7	126542667	126542667	+	Missense_Mutation	SNP	A	A	T	rs78124913	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	31	177	0	0.238462	0	A|0.896;T|0.104	0.104	strong	GRM8,NS,carcinoma,0,1	GRM8	377	1	NM_000845	exon5	c.T1085A	p.F362Y	TCCCAGAATTCTG	.	PASS	Atlas-SNP
UGT2A1	10941	hgsc.bcm.edu	37	4	70512773	70512773	+	Missense_Mutation	SNP	A	A	G	rs41292307	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	45	89	0	0.436893	0	A|0.882;G|0.118	0.118	strong	.	UGT2A1	131	.	NM_001252274	exon2	c.T590C	p.L197S	TCTGATAAAACAG	.	PASS	Atlas-SNP
ABCC5	10057	hgsc.bcm.edu	37	3	183660585	183660585	+	Silent	SNP	G	G	A	rs3749442	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	48	139	0	0.403361	0	G|0.765;A|0.235	0.235	strong	.	ABCC5	142	.	NM_005688	exon25	c.C3624T	p.L1208L	TAGGACGAGAGGG	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	37	15	74703929	74703929	+	Silent	SNP	T	T	C	rs741761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	46	93	0	0.836364	0	T|0.582;C|0.418	0.418	strong	.	SEMA7A	58	.	NM_003612	exon12	c.A1545G	p.Q515Q	GCGGCCTTGGTCC	.	PASS	Atlas-SNP
TYR	7299	hgsc.bcm.edu	37	11	88911218	88911218	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	2	123	0	0.010101	0	.	.	none	TYR,NS,carcinoma,-2,2	TYR	130	2	NM_000372	exon1	c.A97G	p.K33E	ATGGAGAAGGAAT	.	scavenged	Atlas-SNP
NPAS3	64067	hgsc.bcm.edu	37	14	34247747	34247747	+	Silent	SNP	C	C	T	rs147070037	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	108	133	0	0.650602	0	C|0.999;T|0.001	0.001	strong	.	NPAS3	266	.	NM_001164749	exon9	c.C1122T	p.D374D	TGAAGACGTGGAG	.	PASS	Atlas-SNP
CTDSP1	58190	hgsc.bcm.edu	37	2	219267781	219267781	+	Silent	SNP	C	C	T	rs2227255	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	166	267	2	0.982249	0.00749064	C|0.533;T|0.467	0.467	strong	CTDSP1,colon,carcinoma,0,1	CTDSP1	19	1	NM_021198	exon5	c.C402T	p.H134H	TCCTCACGTGGAT	.	scavenged	Atlas-SNP
HMMR	3161	hgsc.bcm.edu	37	5	162901156	162901156	+	Missense_Mutation	SNP	G	G	A	rs2303078	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	314	156	321	1	0.496815	0.00311526	G|0.961;A|0.039	0.039	strong	.	HMMR	64	.	NM_001142556	exon10	c.G998A	p.R333H	AGGAACGTGAAAA	.	PASS	Atlas-SNP
EMC1	23065	hgsc.bcm.edu	37	1	19566881	19566881	+	Silent	SNP	C	C	T	rs12084825	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	91	214	0	0.784483	0	C|0.864;T|0.136	0.136	strong	.	.	.	.	NM_001271427	exon7	c.G696A	p.E232E	GACAGCCTCATCC	.	PASS	Atlas-SNP
UGGT2	55757	hgsc.bcm.edu	37	13	96555149	96555149	+	Missense_Mutation	SNP	C	C	T	rs33949518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	49	111	0	0.556818	0	C|0.858;T|0.142	0.142	strong	.	UGGT2	127	.	NM_020121	exon21	c.G2461A	p.A821T	AAATAGCTGTAGC	.	PASS	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76335109	76335109	+	Silent	SNP	A	A	G	rs17706535	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	39	64	0	0.5	0	A|0.921;G|0.079	0.079	strong	.	LMO7	334	.	NM_005358	exon5	c.A408G	p.G136G	GATTGGATTGAAA	.	PASS	Atlas-SNP
CCDC8	83987	hgsc.bcm.edu	37	19	46915091	46915091	+	Missense_Mutation	SNP	T	T	C	rs74516985	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	103	164	0	0.556757	0	T|0.980;C|0.020	0.020	strong	CCDC8,NS,haematopoietic_neoplasm,0,1	CCDC8	56	1	NM_032040	exon1	c.A977G	p.D326G	CCCTGGTCAGCTG	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128367241	128367241	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	5	253	0	0.0213675	0	.	.	none	MYO7B_ENST00000428314,NS,carcinoma,+1,2	MYO7B	359	2	NM_001080527	exon23	c.G2975A	p.R992Q	TCCGGCGGCCCCT	.	scavenged	Atlas-SNP
CRHR2	1395	hgsc.bcm.edu	37	7	30695202	30695202	+	Silent	SNP	C	C	T	rs2240403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	33	80	0	0.33	0	C|0.902;T|0.098	0.098	strong	.	CRHR2	104	.	NM_001202475	exon11	c.G1128A	p.S376S	CTGGAACGACTGC	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	151112568	151112568	+	Silent	SNP	G	G	A	rs3732768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	24	52	0	0.545455	0	G|0.724;A|0.276	0.276	strong	MED12L,NS,carcinoma,+1,2	MED12L	271	2	NM_053002	exon37	c.G5628A	p.S1876S	CACATCGCAGCAG	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81242102	81242102	+	Missense_Mutation	SNP	G	G	A	rs6420424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	8	59	0	0.123077	0	G|0.437;A|0.563	0.563	strong	.	PKD1L2	361	.	NM_001076780	exon4	c.C754T	p.R252W	CTTCCCGGCACTG	.	PASS	Atlas-SNP
DBNDD1	79007	hgsc.bcm.edu	37	16	90075226	90075226	+	Silent	SNP	C	C	T	rs4362387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	15	72	0	0.245902	0	C|0.947;T|0.053	0.053	strong	.	DBNDD1	9	.	NM_024043	exon3	c.G345A	p.S115S	GTCGTCCGAGTCA	.	PASS	Atlas-SNP
GPR108	56927	hgsc.bcm.edu	37	19	6733582	6733582	+	Missense_Mutation	SNP	G	G	A	rs201134279	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	129	159	1	1	0.00628931	G|0.995;A|0.005	0.005	strong	.	GPR108	35	.	NM_001080452	exon8	c.C722T	p.T241M	CTCACCGTGATGT	.	PASS	Atlas-SNP
NFKBIB	4793	hgsc.bcm.edu	37	19	39399416	39399416	+	Missense_Mutation	SNP	C	C	T	rs17886215	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	58	109	0	0.456693	0	C|0.998;T|0.002	0.002	strong	.	NFKBIB	23	.	NM_002503	exon6	c.C1015T	p.R339W	CAAACCCGGCTGC	.	PASS	Atlas-SNP
C4orf21	55345	hgsc.bcm.edu	37	4	113524723	113524723	+	Missense_Mutation	SNP	G	G	A	rs17669218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	19	210	0	0.211111	0	G|0.937;A|0.063	0.063	strong	.	C4orf21	223	.	NM_018392	exon10	c.C2933T	p.T978I	TCTGGTGTCTCTG	.	PASS	Atlas-SNP
ACRV1	56	hgsc.bcm.edu	37	11	125547897	125547897	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	376	4	232	1	0.0106383	0.00431034	.	.	none	ACRV1,caecum,carcinoma,-1,1	ACRV1	21	1	NM_001612	exon2	c.A348G	p.G116G	CTGTTCTCCTGAA	.	scavenged	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218682771	218682771	+	Silent	SNP	A	A	G	rs3796026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	46	78	0	0.978723	0	A|0.689;G|0.311	0.311	strong	.	TNS1	251	.	NM_022648	exon24	c.T3972C	p.G1324G	ATAGCCACCATAG	.	PASS	Atlas-SNP
GHRHR	2692	hgsc.bcm.edu	37	7	31011677	31011677	+	Silent	SNP	C	C	T	rs740336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	52	116	0	0.305882	0	C|0.943;T|0.057	0.057	strong	.	GHRHR	55	.	NM_000823	exon6	c.C564T	p.H188H	TTTCCACAGCGAC	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238068	31238068	+	Missense_Mutation	SNP	C	C	T	rs1050276	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	222	75	198	0	0.337838	0	C|0.963;T|0.037	0.037	strong	.	HLA-C	92	.	NM_002117	exon4	c.G814A	p.V272M	GCACCACCACAGC	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33579128	33579128	+	Silent	SNP	T	T	C	rs7259333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	69	142	0	0.46	0	T|0.549;C|0.451	0.451	strong	.	GPATCH1	79	.	NM_018025	exon2	c.T162C	p.S54S	CTTTAGTGGAGGT	.	PASS	Atlas-SNP
CNOT11	55571	hgsc.bcm.edu	37	2	101879023	101879023	+	Silent	SNP	G	G	A	rs1007752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	128	247	0	0.537815	0	G|0.972;A|0.028	0.028	strong	.	.	.	.	NM_017546	exon3	c.G702A	p.T234T	GCCAACGCAAAGC	.	PASS	Atlas-SNP
CEACAM6	4680	hgsc.bcm.edu	37	19	42260569	42260569	+	Silent	SNP	G	G	A	rs55738855		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	129	229	1	0.539749	0.00436681	.	.	weak	CEACAM6,NS,carcinoma,0,1	CEACAM6	52	1	NM_002483	exon2	c.G126A	p.P42P	CACGCCGTTCAAT	.	PASS	Atlas-SNP
CEP112	201134	hgsc.bcm.edu	37	17	64023624	64023624	+	Missense_Mutation	SNP	T	T	C	rs17704679	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	127	228	0	0.557018	0	C|0.474;N|0.000	0.474	strong	.	CEP112	192	.	NM_001199165	exon16	c.A1651G	p.K551E	CCTTTTTTTCATA	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26810777	26810777	+	Silent	SNP	T	T	C	rs2291264	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	103	226	0	0.447826	0	T|0.606;C|0.394	0.394	strong	.	ITPR2	270	.	NM_002223	exon18	c.A2055G	p.S685S	GTCATCTGAAAGG	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	102991197	102991197	+	Missense_Mutation	SNP	C	C	T	rs17301182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	102	98	0	0.744526	0	C|0.912;N|0.001	.	strong	.	DYNC2H1	246	.	NM_001377	exon7	c.C1021T	p.H341Y	ACAATTCATGAGA	.	PASS	Atlas-SNP
RPS15	6209	hgsc.bcm.edu	37	19	1440068	1440068	+	Missense_Mutation	SNP	G	G	C	rs61746286	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	7	49	1	0.179487	0.0204082	G|0.442;C|0.558	0.558	strong	RPS15,extremity,malignant_melanoma,0,1	RPS15	11	1	NM_001018	exon3	c.G140C	p.R47P	TGAACCGGGGCCT	.	scavenged	Atlas-SNP
OXER1	165140	hgsc.bcm.edu	37	2	42990336	42990336	+	Silent	SNP	T	T	G	rs1992286	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	77	134	1	0.475309	0.00746269	G|0.690;N|0.002	0.690	strong	OXER1,NS,carcinoma,0,1	OXER1	33	1	NM_148962	exon1	c.A984C	p.R328R	CAGGGATCGGCAG	.	scavenged	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1896059	1896059	+	Missense_Mutation	SNP	G	G	A	rs115287948	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	25	435	4	0.109649	0.0091954	G|0.679;A|0.321	0.321	strong	SIRPA,caecum,carcinoma,0,2	SIRPA	83	2	NM_001040022	exon3	c.G394A	p.V132M	GATGACGTGGAGT	.	scavenged	Atlas-SNP
OR4B1	119765	hgsc.bcm.edu	37	11	48238880	48238880	+	Silent	SNP	C	C	T	rs10838833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	272	140	312	0	0.514706	0	C|0.829;T|0.171	0.171	strong	.	OR4B1	52	.	NM_001005470	exon1	c.C519T	p.D173D	GATTGACCACTAT	.	PASS	Atlas-SNP
RDH13	112724	hgsc.bcm.edu	37	19	55559715	55559715	+	Silent	SNP	G	G	A	rs2305543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	57	154	0	0.478992	0	G|0.701;A|0.299	0.299	strong	.	RDH13	43	.	NM_001145971	exon5	c.C640T	p.L214L	GGCTCAGCTCCTT	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33014876	33014876	+	Silent	SNP	C	C	T	rs375820695		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	51	89	0	0.414634	0	.	.	weak	.	AKAP6	308	.	NM_004274	exon4	c.C1017T	p.P339P	TCAACCCTCCTCT	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2046700	2046700	+	Missense_Mutation	SNP	C	C	T	rs2294066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	25	80	0	0.280899	0	C|0.846;N|0.000	.	strong	.	MYOM2	251	.	NM_003970	exon19	c.C2327T	p.T776M	GCTTGACGGAAGG	.	PASS	Atlas-SNP
NUDT6	11162	hgsc.bcm.edu	37	4	123814308	123814308	+	Missense_Mutation	SNP	C	C	T	rs1048201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	13	81	0	0.224138	0	C|0.825;T|0.175	0.175	strong	NUDT6_ENST00000304430,NS,carcinoma,0,3	NUDT6	50	3	NM_007083	exon5	c.G626A	p.R209Q	TGTTGCCGAATAC	.	PASS	Atlas-SNP
CACNA1B	774	hgsc.bcm.edu	37	9	140773613	140773613	+	Splice_Site	SNP	T	T	A	rs201604190		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	10	59	2	0.147059	0.0338983	.	.	weak	CACNA1B,colon,carcinoma,0,8	CACNA1B	266	8	NM_001243812	exon2	c.390+2T>A	.	GGCTGGTGAGTGC	.	scavenged	Atlas-SNP
VEZT	55591	hgsc.bcm.edu	37	12	95694111	95694111	+	Missense_Mutation	SNP	T	T	G	rs17855934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	69	125	0	0.46	0	T|0.924;G|0.076	0.076	strong	.	VEZT	106	.	NM_017599	exon12	c.T2002G	p.S668A	GAAAACTCTCTAG	.	PASS	Atlas-SNP
MYT1	4661	hgsc.bcm.edu	37	20	62850358	62850358	+	Silent	SNP	C	C	T	rs41279348	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	67	115	0	0.515385	0	C|0.907;T|0.093	0.093	strong	.	MYT1	152	.	NM_004535	exon12	c.C1941T	p.L647L	GAACCTCAGCACG	.	PASS	Atlas-SNP
CST5	1473	hgsc.bcm.edu	37	20	23860178	23860178	+	Missense_Mutation	SNP	A	A	G	rs1799841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	70	145	1	0.530303	0.00689655	A|0.455;G|0.545	0.545	strong	CST5,NS,carcinoma,0,1	CST5	24	1	NM_001900	exon1	c.T136C	p.C46R	GGGCACACTGCAC	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1265987	1265987	+	Missense_Mutation	SNP	C	C	G	rs3021158	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	262	138	258	1	0.526718	0.00387597	C|0.873;G|0.127	0.127	strong	MUC5AC,brain,glioma,0,1	MUC5B	473	1	NM_002458	exon31	c.C7877G	p.T2626R	CAGGGACGGCACG	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023444	25023444	+	Missense_Mutation	SNP	G	G	T	rs201546887		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	380	45	350	0	0.118421	0	.	.	weak	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon12	c.G1066T	p.A356S	CTCCGGGCCCAGA	.	scavenged	Atlas-SNP
FMNL1	752	hgsc.bcm.edu	37	17	43316360	43316360	+	Silent	SNP	G	G	A	rs12940312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	289	142	300	0	0.491349	0	G|0.919;A|0.081	0.081	strong	.	FMNL1	78	.	NM_005892	exon11	c.G1008A	p.S336S	ACATTCGGTGGAG	.	PASS	Atlas-SNP
COG3	83548	hgsc.bcm.edu	37	13	46104849	46104849	+	Silent	SNP	C	C	T	rs62637564	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	61	106	0	0.5	0	C|0.964;T|0.036	0.036	strong	.	COG3	52	.	NM_031431	exon22	c.C2391T	p.H797H	GTTCCACGCTCTG	.	PASS	Atlas-SNP
HDAC9	9734	hgsc.bcm.edu	37	7	18687542	18687542	+	Silent	SNP	A	A	T	rs35614472	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	34	90	0	0.386364	0	A|0.992;T|0.008	0.008	strong	.	HDAC9	560	.	NM_178425	exon9	c.A1170T	p.P390P	AAAGCCACCCAAC	.	PASS	Atlas-SNP
LPCAT2	54947	hgsc.bcm.edu	37	16	55562466	55562466	+	Missense_Mutation	SNP	G	G	A	rs837550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	418	71	369	0	0.169856	0	G|0.457;A|0.543	0.543	strong	.	LPCAT2	35	.	NM_017839	exon3	c.G489A	p.M163I	TTCTATGGTATCT	.	PASS	Atlas-SNP
ADAT3	113179	hgsc.bcm.edu	37	19	1912934	1912934	+	Silent	SNP	T	T	C	rs12984675	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	10	41	0	0.454545	0	T|0.727;C|0.273	0.273	strong	.	ADAT3	15	.	NM_138422	exon2	c.T888C	p.T296T	GTGCACTGGCTAC	.	PASS	Atlas-SNP
ZNF205	7755	hgsc.bcm.edu	37	16	3170188	3170188	+	Silent	SNP	C	C	T	rs12032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	22	45	0	0.611111	0	C|0.639;T|0.361	0.361	strong	.	ZNF205	42	.	NM_003456	exon7	c.C1527T	p.C509C	GTTGTGCGGCAAG	.	PASS	Atlas-SNP
CCDC149	91050	hgsc.bcm.edu	37	4	24836619	24836619	+	Silent	SNP	C	C	T	rs16876194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	101	141	1	1	0.0070922	C|0.904;T|0.096	0.096	strong	.	CCDC149	41	.	NM_173463	exon9	c.G771A	p.Q257Q	TTTACCCTGGCCC	.	PASS	Atlas-SNP
MCTP1	79772	hgsc.bcm.edu	37	5	94278129	94278129	+	Silent	SNP	T	T	C	rs293035	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	80	106	1	1	0.00943396	T|0.746;C|0.254	0.254	strong	.	MCTP1	110	.	NM_024717	exon4	c.A984G	p.V328V	GTCAAATACCTGA	.	PASS	Atlas-SNP
GLIS1	148979	hgsc.bcm.edu	37	1	54060248	54060248	+	Missense_Mutation	SNP	T	T	C	rs4307514	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	66	149	1	0.717391	0.00671141	T|0.751;C|0.249	0.249	strong	GLIS1,NS,carcinoma,0,1	GLIS1	52	1	NM_147193	exon3	c.A328G	p.T110A	CTCCCGTCAGAGG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79025157	79025157	+	Missense_Mutation	SNP	A	A	G	rs10942901	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	110	172	0	0.536585	0	A|0.832;G|0.162	0.162	strong	.	CMYA5	643	.	NM_153610	exon2	c.A569G	p.D190G	TTTATGATAAAGC	.	PASS	Atlas-SNP
CDH4	1002	hgsc.bcm.edu	37	20	60503350	60503350	+	Missense_Mutation	SNP	A	A	G	rs6142884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	26	41	0	0.509804	0	A|0.508;G|0.492	0.492	strong	.	CDH4	172	.	NM_001794	exon12	c.A1874G	p.K625R	GCGAGAAGCCCAA	.	PASS	Atlas-SNP
OPN1LW	5956	hgsc.bcm.edu	37	X	153420176	153420176	+	Missense_Mutation	SNP	A	A	G	rs78093925	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	319	314	639	1	0.984326	0.00156495	A|0.814;G|0.186	0.186	strong	.	OPN1LW	87	.	NM_020061	exon4	c.A706G	p.M236V	ATCATCATGCTCT	.	PASS	Atlas-SNP
ALDH1L1	10840	hgsc.bcm.edu	37	3	125826003	125826003	+	Missense_Mutation	SNP	T	T	C	rs4646750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	39	71	0	0.506494	0	T|0.919;C|0.081	0.081	strong	.	ALDH1L1	138	.	NM_001270364	exon21	c.A2464G	p.I822V	GAGAGATGATCAT	.	PASS	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552086	178552086	+	Missense_Mutation	SNP	T	T	G	rs376054177		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	4	215	3	0.0229885	0.0139535	.	.	weak	ADAMTS2,NS,malignant_melanoma,0,1	ADAMTS2	190	1	NM_014244	exon19	c.A2846C	p.N949T	GTGGTGTTGTCGT	.	scavenged	Atlas-SNP
CELSR3	1951	hgsc.bcm.edu	37	3	48699519	48699519	+	Silent	SNP	C	C	T	rs3733086	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	33	86	0	0.434211	0	C|0.885;T|0.115	0.115	strong	.	CELSR3	237	.	NM_001407	exon1	c.G549A	p.K183K	CACCGGCTTGGGA	.	PASS	Atlas-SNP
KHNYN	23351	hgsc.bcm.edu	37	14	24901433	24901433	+	Silent	SNP	C	C	T	rs17795094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	96	138	0	0.596273	0	C|0.904;T|0.096	0.096	strong	.	KHNYN	46	.	NM_015299	exon3	c.C966T	p.H322H	TGTCCACCGTGAG	.	PASS	Atlas-SNP
INS-IGF2	723961	hgsc.bcm.edu	37	11	2169014	2169014	+	Missense_Mutation	SNP	A	A	G	rs10770125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	44	161	0	0.382609	0	A|0.652;G|0.348	0.348	strong	.	INS-IGF2	8	.	NM_001042376	exon4	c.T431C	p.L144P	CACACAAGCTCGG	.	PASS	Atlas-SNP
YIPF7	285525	hgsc.bcm.edu	37	4	44626641	44626641	+	Silent	SNP	A	A	G	rs60959366	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	391	160	411	1	0.409207	0.00243309	A|0.499;G|0.501	0.501	strong	.	YIPF7	33	.	NM_182592	exon5	c.T657C	p.G219G	GGCGCAACCAGAC	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130150310	130150310	+	Missense_Mutation	SNP	A	A	C	rs61744488	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	43	88	0	0.573333	0	A|0.971;C|0.029	0.029	strong	.	COL6A5	205	.	NM_153264	exon33	c.A5250C	p.E1750D	TCTAGAAAAATGT	.	PASS	Atlas-SNP
GUCY1A2	2977	hgsc.bcm.edu	37	11	106558291	106558291	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	3	103	0	0.016129	0	.	.	none	GUCY1A2,colon,carcinoma,0,2	GUCY1A2	180	2	NM_001256424	exon9	c.G2276T	p.R759L	GTCTCCCGGAGGA	.	scavenged	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48768486	48768486	+	Silent	SNP	A	A	G	rs1051640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	58	122	0	0.42963	0	A|0.876;G|0.124	0.124	strong	.	ABCC3	138	.	NM_003786	exon31	c.A4509G	p.E1503E	AGCTGAATTTGAT	.	PASS	Atlas-SNP
MMP10	4319	hgsc.bcm.edu	37	11	102650424	102650424	+	Missense_Mutation	SNP	C	C	T	rs486055	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	125	157	0	0.65445	0	C|0.916;T|0.084	0.084	strong	.	MMP10	44	.	NM_002425	exon2	c.G158A	p.R53K	TCCTTTCTTCTAA	.	PASS	Atlas-SNP
ALKBH8	91801	hgsc.bcm.edu	37	11	107375703	107375703	+	Missense_Mutation	SNP	C	C	T	rs139390837	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	36	91	0	0.270677	0	C|0.998;T|0.002	0.002	strong	.	ALKBH8	88	.	NM_138775	exon12	c.G1676A	p.R559H	TTAATGCGGGGGA	.	PASS	Atlas-SNP
ICT1	3396	hgsc.bcm.edu	37	17	73016621	73016621	+	Silent	SNP	C	C	T	rs1044228	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	108	124	0	0.972973	0	C|0.689;T|0.311	0.311	strong	.	ICT1	17	.	NM_001545	exon5	c.C405T	p.L135L	GATCCTCACCTCT	.	PASS	Atlas-SNP
TJP3	27134	hgsc.bcm.edu	37	19	3740658	3740658	+	Silent	SNP	T	T	G	rs10416362	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	19	88	0	0.387755	0	T|0.478;G|0.522	0.522	strong	TJP3,NS,carcinoma,0,1	TJP3	79	1	NM_001267561	exon14	c.T1767G	p.L589L	GGGTCTTCGTCGA	.	PASS	Atlas-SNP
SLC25A37	51312	hgsc.bcm.edu	37	8	23423669	23423669	+	Missense_Mutation	SNP	A	A	G	rs2942194	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	69	67	0	1	0	A|0.818;G|0.182	0.182	strong	.	SLC25A37	27	.	NM_016612	exon2	c.A259G	p.I87V	ACAAGTATCTACG	.	PASS	Atlas-SNP
EBF1	1879	hgsc.bcm.edu	37	5	158139318	158139318	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	3	162	0	0.0175439	0	.	.	none	EBF1,colon,carcinoma,+2,1	EBF1	110	1	NM_024007	exon14	c.G1393A	p.V465I	GTGATACGCTGCT	.	scavenged	Atlas-SNP
CPT2	1376	hgsc.bcm.edu	37	1	53668099	53668099	+	Missense_Mutation	SNP	C	C	T	rs74315294	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	78	162	0	0.634146	0	C|0.999;T|0.001	0.001	strong	CPT2,right_upper_lobe,carcinoma,0,1	CPT2	34	1	NM_000098	exon3	c.C338T	p.S113L	ACATTTCGGGTAG	.	PASS	Atlas-SNP
REXO1	57455	hgsc.bcm.edu	37	19	1827565	1827565	+	Missense_Mutation	SNP	A	A	G	rs10415018	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	10	126	0	0.196078	0	A|0.781;G|0.219	0.219	strong	REXO1,NS,carcinoma,0,1	REXO1	55	1	NM_020695	exon2	c.T1223C	p.V408A	TTCTCCACAGGCC	.	PASS	Atlas-SNP
NAGK	55577	hgsc.bcm.edu	37	2	71297695	71297695	+	Silent	SNP	T	T	C	rs2287328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	43	131	0	0.467391	0	T|0.851;C|0.149	0.149	strong	.	NAGK	34	.	NM_017567	exon2	c.T231C	p.D77D	AGCAGATGGACTG	.	PASS	Atlas-SNP
B4GALT3	8703	hgsc.bcm.edu	37	1	161141691	161141691	+	Missense_Mutation	SNP	C	C	T	rs111614721	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	6	132	1	0.0320856	0.00757576	C|0.998;T|0.002	0.002	strong	B4GALT3,NS,carcinoma,0,1	B4GALT3	39	1	NM_003779	exon8	c.G1097A	p.R366H	TCTTGACGGAAGG	.	scavenged	Atlas-SNP
ZNF727	442319	hgsc.bcm.edu	37	7	63538777	63538777	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	3	104	1	0.0234375	0.00961538	.	.	none	ZNF727,NS,carcinoma,0,1	ZNF727	35	1	NM_001159522	exon4	c.G1350A	p.K450K	AGAGAAGCCCTAC	.	scavenged	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190873335	190873335	+	Missense_Mutation	SNP	C	C	T	rs191989708	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	14	154	6	0.106061	0.038961	.	.	weak	FRG1,trunk,malignant_melanoma,0,1	FRG1	76	1	NM_004477	exon3	c.C152T	p.T51I	CAGTAACAAACTT	.	scavenged	Atlas-SNP
CELSR3	1951	hgsc.bcm.edu	37	3	48681053	48681053	+	Silent	SNP	C	C	T	rs9868809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	44	87	0	0.478261	0	C|0.880;T|0.120	0.120	strong	CELSR3,NS,carcinoma,0,1	CELSR3	237	1	NM_001407	exon28	c.G8223A	p.G2741G	CAGGAGCCCAAAG	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208390155	208390155	+	Silent	SNP	C	C	T	rs4844657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	88	100	0	0.647059	0	C|0.856;T|0.144	0.144	strong	.	PLXNA2	178	.	NM_025179	exon2	c.G1113A	p.L371L	GGACTGCAGGCGC	.	PASS	Atlas-SNP
RNASEL	6041	hgsc.bcm.edu	37	1	182554557	182554557	+	Missense_Mutation	SNP	C	C	T	rs486907	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	432	260	351	0	0.601852	0	C|0.737;T|0.263	0.263	strong	.	RNASEL	83	.	NM_021133	exon2	c.G1385A	p.R462Q	ACATTTCGGGCAA	.	PASS	Atlas-SNP
ZSWIM4	65249	hgsc.bcm.edu	37	19	13941022	13941022	+	Missense_Mutation	SNP	A	A	C	rs56177954	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	32	44	0	0.542373	0	A|0.984;C|0.016	0.016	strong	.	ZSWIM4	69	.	NM_023072	exon13	c.A2128C	p.N710H	CTGATGAATATCA	.	PASS	Atlas-SNP
RFWD3	55159	hgsc.bcm.edu	37	16	74664698	74664698	+	Silent	SNP	A	A	G	rs78796563	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	16	91	0	0.183908	0	A|0.981;G|0.019	0.019	strong	RFWD3,NS,carcinoma,0,1	RFWD3	49	1	NM_018124	exon10	c.T1735C	p.L579L	CTACTAACTCCTG	.	PASS	Atlas-SNP
SAGE1	55511	hgsc.bcm.edu	37	X	134990000	134990000	+	Missense_Mutation	SNP	C	C	T	rs41301507	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	187	424	0	0.979058	0	C|0.937;T|0.063	0.063	strong	.	SAGE1	160	.	NM_018666	exon10	c.C1159T	p.H387Y	GATCAGCGTAAGT	.	PASS	Atlas-SNP
SCRIB	23513	hgsc.bcm.edu	37	8	144885669	144885669	+	Missense_Mutation	SNP	G	G	C	rs138257744	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15	9	21	0	0.6	0	G|0.999;C|0.001	0.001	strong	.	SCRIB	192	.	NM_015356	exon24	c.C3487G	p.Q1163E	GGCTCTGCTGGTT	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100070351	100070351	+	Silent	SNP	G	G	C	rs12683119	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	45	133	0	0.432692	0	G|0.813;C|0.187	0.187	strong	.	.	.	.	NM_020893	exon2	c.G138C	p.S46S	GATGTCGTCAGTG	.	PASS	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158603839	158603839	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	13	224	4	0.0541667	0.0178571	.	.	none	RNF145,NS,carcinoma,0,4	RNF145	110	4	NM_001199380	exon5	c.T512C	p.M171T	GTTTTCATGACAC	.	scavenged	Atlas-SNP
KIAA1024	23251	hgsc.bcm.edu	37	15	79749447	79749447	+	Missense_Mutation	SNP	G	G	T	rs11634652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	21	76	0	0.3	0	G|0.866;T|0.134	0.134	strong	.	KIAA1024	146	.	NM_015206	exon2	c.G958T	p.V320F	TCCCCGGTTCCTG	.	PASS	Atlas-SNP
FPR3	2359	hgsc.bcm.edu	37	19	52327479	52327479	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	97	258	0	0.399177	0	.	.	none	.	FPR3	66	.	NM_002030	exon2	c.A478T	p.N160Y	TTACCAAATTTCA	.	PASS	Atlas-SNP
DIS3L2	129563	hgsc.bcm.edu	37	2	232879671	232879671	+	Missense_Mutation	SNP	C	C	T	rs723044	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	35	54	0	0.479452	0	C|0.930;T|0.070	0.070	strong	.	DIS3L2	77	.	NM_001257282	exon2	c.C34T	p.P12S	CTCCGGCCCCTGG	.	PASS	Atlas-SNP
FAM160A2	84067	hgsc.bcm.edu	37	11	6238960	6238960	+	Missense_Mutation	SNP	C	C	A	rs3750943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	42	62	0	0.575342	0	C|0.853;A|0.147	0.147	strong	.	FAM160A2	100	.	NM_032127	exon9	c.G1898T	p.R633L	CCAGCCCGCCCCC	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	37	5	70858194	70858194	+	Silent	SNP	C	C	T	rs277941	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	96	125	1	0.989691	0.008	C|0.662;T|0.338	0.338	strong	.	BDP1	204	.	NM_018429	exon38	c.C7590T	p.R2530R	GAAACGCCTAAAA	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50515273	50515273	+	Silent	SNP	G	G	A	rs6010165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	53	73	0	0.616279	0	G|0.884;A|0.116	0.116	strong	.	MLC1	48	.	NM_015166	exon7	c.C594T	p.Y198Y	TACTGAGTAAGAT	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17612846	17612846	+	Silent	SNP	T	T	C	rs3739408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	89	163	0	0.413953	0	T|0.855;C|0.145	0.145	strong	.	MTUS1	144	.	NM_001001924	exon2	c.A471G	p.L157L	TTGGTTTAGCTCC	.	PASS	Atlas-SNP
MLKL	197259	hgsc.bcm.edu	37	16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	rs144526386	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	25	126	0	0.204918	0	C|0.986;A|0.014	0.014	strong	.	MLKL	51	.	NM_001142497	exon4	c.G605T	p.G202V	GCTGAGCCAGTCT	.	PASS	Atlas-SNP
GPR1	2825	hgsc.bcm.edu	37	2	207041053	207041053	+	Missense_Mutation	SNP	T	T	C	rs3732083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	86	150	0	0.86	0	T|0.502;C|0.498	0.498	strong	.	GPR1	38	.	NM_001098199	exon3	c.A919G	p.I307V	TACTAATTAGGAC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280170	152280170	+	Missense_Mutation	SNP	C	C	G	rs76133835	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	452	137	353	0	0.303097	0	C|0.500;G|0.500	0.500	weak	.	FLG	900	.	NM_002016	exon3	c.G7192C	p.E2398Q	TGGACTCTTGGTG	.	PASS	Atlas-SNP
PCDHA3	56145	hgsc.bcm.edu	37	5	140181892	140181892	+	Silent	SNP	T	T	C	rs3733707	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	76	149	1	0.477987	0.00671141	T|0.403;C|0.597	0.597	strong	PCDHA3_ENST00000522353,rectum,carcinoma,+2,2	PCDHA3	396	2	NM_031497	exon1	c.T1110C	p.A370A	CATCGCTCTGATC	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681444	100681444	+	Silent	SNP	A	A	C	rs201002287	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	16	157	5	0.0695652	0.0318471	A|0.999;C|0.001	0.001	weak	MUC17,caecum,carcinoma,0,2	MUC17	804	2	NM_001040105	exon3	c.A6747C	p.T2249T	CAGCACACCTGTG	.	scavenged	Atlas-SNP
OR6K3	391114	hgsc.bcm.edu	37	1	158687896	158687896	+	Missense_Mutation	SNP	C	C	T	rs857705	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	62	108	0	0.335135	0	C|0.776;T|0.224	0.224	strong	.	OR6K3	101	.	NM_001005327	exon1	c.G10A	p.G4R	GGTTTCCGCTCTC	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733127	52733127	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	518	28	400	0	0.0540541	0	.	.	none	.	PCMTD1	73	.	NM_052937	exon6	c.C858T	p.N286N	GTAAGTGTTAATT	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145296373	145296373	+	Missense_Mutation	SNP	G	G	T	rs3969711	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	12	48	1	0.0851064	0.0208333	G|0.700;T|0.300	0.300	strong	NBPF10,NS,carcinoma,0,3	NBPF10	221	3	NM_001039703	exon3	c.G295T	p.V99F	GTCCTAGTTCACT	.	scavenged	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54127041	54127041	+	Silent	SNP	C	C	T	rs805423	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	285	136	352	0	0.477193	0	C|0.452;T|0.548	0.548	strong	.	PSME4	247	.	NM_014614	exon29	c.G3399A	p.Q1133Q	CTTTTCCTGTTGG	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75836079	75836079	+	Missense_Mutation	SNP	A	A	G	rs200450866	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	40	100	0	0.47619	0	.	.	weak	.	COL12A1	385	.	NM_004370	exon39	c.T6448C	p.Y2150H	GCTTATATACTAT	.	PASS	Atlas-SNP
FBXW5	54461	hgsc.bcm.edu	37	9	139836694	139836694	+	Silent	SNP	C	C	T	rs34391108	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7	6	40	0	0.857143	0	C|0.975;T|0.025	0.025	strong	.	FBXW5	36	.	NM_018998	exon6	c.G900A	p.E300E	CAAGCCCTCCTTG	.	PASS	Atlas-SNP
CMTM1	113540	hgsc.bcm.edu	37	16	66600479	66600479	+	Silent	SNP	G	G	A	rs7193473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	25	150	0	0.19084	0	G|0.721;A|0.279	0.279	strong	.	CMTM1	34	.	NM_181271	exon1	c.G63A	p.P21P	ACAACCGGAGACT	.	PASS	Atlas-SNP
EPHA2	1969	hgsc.bcm.edu	37	1	16475126	16475126	+	Silent	SNP	C	C	T	rs6678618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	10	49	0	0.238095	0	C|0.748;T|0.252	0.252	strong	EPHA2,NS,adenoma,0,1	EPHA2	102	1	NM_004431	exon3	c.G570A	p.A190A	GAGCAGCGCCACA	.	PASS	Atlas-SNP
SLC1A6	6511	hgsc.bcm.edu	37	19	15083555	15083555	+	Silent	SNP	G	G	A	rs115001292	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	57	133	0	0.518182	0	G|0.993;A|0.007	0.007	strong	.	SLC1A6	111	.	NM_001272087	exon4	c.C168T	p.N56N	GAAGGCGTTTCGG	.	PASS	Atlas-SNP
BTN2A2	10385	hgsc.bcm.edu	37	6	26388405	26388405	+	Missense_Mutation	SNP	G	G	A	rs62617839	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	58	181	0	0.42029	0	G|0.941;A|0.059	0.059	strong	.	BTN2A2	87	.	NM_001197238	exon4	c.G607A	p.G203S	GCTGACGGCCTCT	.	PASS	Atlas-SNP
MLLT6	4302	hgsc.bcm.edu	37	17	36868976	36868976	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	34	107	0	0.276423	0	.	.	none	.	MLLT6	80	.	NM_005937	exon8	c.G753A	p.K251K	GCAGAAGCACAAG	.	PASS	Atlas-SNP
COL4A2	1284	hgsc.bcm.edu	37	13	111160304	111160304	+	Silent	SNP	G	G	A	rs391859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	80	127	0	0.512821	0	G|0.890;A|0.110	0.110	strong	.	COL4A2	178	.	NM_001846	exon47	c.G4617A	p.A1539A	CCTGGCGCGGTTC	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132561987	132561987	+	Silent	SNP	C	C	T	rs12311898	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	74	186	0	0.448485	0	C|0.932;T|0.068	0.068	strong	.	EP400	370	.	NM_015409	exon53	c.C9141T	p.A3047A	GGCGGCCGGGCAG	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	31	82	0	0.238462	0	G|0.965;A|0.035	0.035	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.G730A	p.A244T	CAGGCCGCCACGC	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194827	18194827	+	Missense_Mutation	SNP	C	C	G	rs2468774	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	85	148	0	0.494186	0	C|0.699;G|0.301	0.301	strong	.	MRGPRX4	68	.	NM_054032	exon1	c.C24G	p.F8L	AGTCTTCGGTACA	.	PASS	Atlas-SNP
PROM1	8842	hgsc.bcm.edu	37	4	16077401	16077401	+	Silent	SNP	G	G	A	rs10033086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	71	148	0	0.510791	0	G|0.912;A|0.088	0.088	strong	PROM1,bladder,carcinoma,-2,1	PROM1	91	1	NM_001145847	exon2	c.C129T	p.T43T	GTCTTGGGTCTCA	.	PASS	Atlas-SNP
KCNA7	3743	hgsc.bcm.edu	37	19	49573438	49573438	+	Missense_Mutation	SNP	A	A	G	rs1017219	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	46	76	0	0.5	0	A|0.619;G|0.381	0.381	strong	.	KCNA7	30	.	NM_031886	exon2	c.T1253C	p.M418T	GGCTGCATGTCCA	.	PASS	Atlas-SNP
ARPC1B	10095	hgsc.bcm.edu	37	7	98984354	98984354	+	Missense_Mutation	SNP	G	G	C	rs1045012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	67	95	0	0.429487	0	G|0.926;C|0.074	0.074	strong	.	ARPC1B	41	.	NM_005720	exon3	c.G111C	p.K37N	TGAAAAGAGCGGT	.	PASS	Atlas-SNP
GAK	2580	hgsc.bcm.edu	37	4	843536	843536	+	Silent	SNP	G	G	A	rs55904229	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268	132	279	0	0.492537	0	G|0.997;A|0.003	0.003	strong	.	GAK	104	.	NM_005255	exon28	c.C3861T	p.H1287H	CTTGGCGTGCTGC	.	PASS	Atlas-SNP
ITGA10	8515	hgsc.bcm.edu	37	1	145536082	145536082	+	Missense_Mutation	SNP	G	G	A	rs2274616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	304	191	231	0	0.628289	0	G|0.869;A|0.131	0.131	strong	ITGA10,NS,carcinoma,-1,1	ITGA10	131	1	NM_003637	exon17	c.G2174A	p.R725Q	CCCCTCGGAGGCT	.	PASS	Atlas-SNP
ATF7IP2	80063	hgsc.bcm.edu	37	16	10575824	10575824	+	Silent	SNP	C	C	A	rs1970817	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	97	107	0	1	0	C|0.529;A|0.471	0.471	strong	ATF7IP2_ENST00000396560,NS,adenoma,0,1	ATF7IP2	40	1	NM_024997	exon12	c.C1767A	p.P589P	CAGACCCAATGGC	.	PASS	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71344769	71344769	+	Missense_Mutation	SNP	G	G	A	rs199591952	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	34	88	0	0.507463	0	A|0.000;G|1.000	0.000	strong	.	SDK2	219	.	NM_001144952	exon44	c.C6134T	p.T2045M	TTCTCCGTCAGGC	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1412681	1412681	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	250	3	392	0	0.012	0	.	.	none	ATAD3B_ENST00000378741,right_upper_lobe,carcinoma,-1,2	ATAD3B	68	2	NM_031921	exon2	c.C233T	p.A78V	ATCTGGCGCAGAT	.	scavenged	Atlas-SNP
KIAA1671	85379	hgsc.bcm.edu	37	22	25586744	25586744	+	Silent	SNP	T	T	G	rs2330986	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	33	84	0	0.4125	0	T|0.952;G|0.048	0.048	strong	.	KIAA1671	28	.	NM_001145206	exon10	c.T5418G	p.V1806V	CCAAGTTTGACCA	.	PASS	Atlas-SNP
SYT15	83849	hgsc.bcm.edu	37	10	46968665	46968665	+	Silent	SNP	G	G	A	rs200814731	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	12	58	0	0.230769	0	G|0.911;A|0.089	0.089	strong	SYT15_ENST00000416127,colon,carcinoma,0,15	SYT15	165	15	NM_031912	exon3	c.C271T	p.L91L	TGTGCAGGGGCAC	.	PASS	Atlas-SNP
HMP19	0	hgsc.bcm.edu	37	5	173491300	173491300	+	Silent	SNP	G	G	A	rs17076802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	44	86	0	0.53012	0	G|0.924;A|0.075	0.075	strong	.	HMP19	21	.	NM_015980	exon3	c.G195A	p.P65P	GGTGCCGAAAATC	.	PASS	Atlas-SNP
PRPF4	9128	hgsc.bcm.edu	37	9	116045007	116045007	+	Missense_Mutation	SNP	A	A	C	rs148684386	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	61	162	0	0.480315	0	A|0.999;C|0.001	0.001	strong	.	PRPF4	56	.	NM_004697	exon4	c.A477C	p.K159N	GTCCAAAGAAGAG	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239038912	239038912	+	Silent	SNP	T	T	C	rs57813708	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	86	227	0	0.434343	0	T|0.748;C|0.252	0.252	strong	.	ESPNL	63	.	NM_194312	exon9	c.T1557C	p.L519L	GCAGCTTCGGCGC	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72139184	72139184	+	Silent	SNP	C	C	A	rs2074626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	91	91	1	1	0.010989	C|0.529;A|0.471	0.471	strong	DHX38,NS,carcinoma,0,2	DHX38	91	2	NM_014003	exon17	c.C2316A	p.A772A	GCCTGCCCTGGCT	.	scavenged	Atlas-SNP
TTLL3	26140	hgsc.bcm.edu	37	3	9876987	9876987	+	Silent	SNP	G	G	A	rs1057281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	45	78	0	0.529412	0	G|0.873;A|0.127	0.127	strong	.	TTLL3	51	.	NM_001025930	exon13	c.G2562A	p.R854R	CCAGAGGCGCAGG	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656805	46656805	+	Silent	SNP	G	G	A	rs6519994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	69	194	0	0.403509	0	G|0.732;A|0.268	0.268	strong	PKDREJ,caecum,carcinoma,0,1	PKDREJ	195	1	NM_006071	exon1	c.C2415T	p.I805I	ACTCACGATTTCT	.	PASS	Atlas-SNP
BPI	671	hgsc.bcm.edu	37	20	36932676	36932676	+	Silent	SNP	G	G	C	rs1341024	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	95	109	1	0.959596	0.00917431	G|0.549;C|0.451	0.451	strong	.	BPI	67	.	NM_001725	exon1	c.G63C	p.L21L	GGTGCTGGTCGCC	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558528	140558528	+	Missense_Mutation	SNP	A	A	G	rs3733694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	82	305	0	0.383178	0	G|0.146;N|0.001	0.146	strong	.	PCDHB8	199	.	NM_019120	exon1	c.A913G	p.K305E	CGACTAAAGAAAC	.	PASS	Atlas-SNP
FAM81B	153643	hgsc.bcm.edu	37	5	94756010	94756010	+	Missense_Mutation	SNP	C	C	T	rs11555275	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	48	86	0	0.457143	0	C|0.978;T|0.022	0.022	strong	.	FAM81B	51	.	NM_152548	exon5	c.C560T	p.A187V	TAAGAGCTCGAGA	.	PASS	Atlas-SNP
NBEAL1	65065	hgsc.bcm.edu	37	2	203990789	203990789	+	Silent	SNP	T	T	G	rs72934556	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	44	400	0	0.203704	0	T|0.923;G|0.077	0.077	strong	.	NBEAL1	266	.	NM_001114132	exon20	c.T2871G	p.V957V	TGGAGTTGCAACT	.	PASS	Atlas-SNP
NQO1	1728	hgsc.bcm.edu	37	16	69745145	69745145	+	Missense_Mutation	SNP	G	G	A	rs1800566	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	19	152	1	0.159664	0.00657895	G|0.761;A|0.239	0.239	strong	NQO1,NS,carcinoma,0,1	NQO1	21	1	NM_000903	exon6	c.C559T	p.P187S	GTTGAGGTTCTAA	.	scavenged	Atlas-SNP
POLR3B	55703	hgsc.bcm.edu	37	12	106838340	106838340	+	Silent	SNP	T	T	C	rs10861607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	118	122	1	1	0.00819672	T|0.752;C|0.248	0.248	strong	POLR3B,caecum,carcinoma,0,1	POLR3B	123	1	NM_018082	exon19	c.T2055C	p.Y685Y	CACTTATCAGTGT	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125873796	125873796	+	Splice_Site	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	5	60	0	0.0515464	0	.	.	none	.	CDON	137	.	NM_001243597	exon11	c.2026+1G>A	.	CACTCACCTTTGC	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186670780	186670780	+	Missense_Mutation	SNP	T	T	A	rs16827154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	61	103	0	0.580952	0	T|0.513;A|0.487	0.487	strong	FSIP2_ENST00000343098,colon,carcinoma,0,2	FSIP2	251	2	NM_173651	exon17	c.T17014A	p.Y5672N	GAGATATACACAC	.	PASS	Atlas-SNP
LRP3	4037	hgsc.bcm.edu	37	19	33698448	33698448	+	Silent	SNP	G	G	A	rs3745973	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	28	67	0	0.5	0	G|0.910;C|0.000;A|0.090	0.090	strong	.	LRP3	46	.	NM_002333	exon7	c.G2280A	p.E760E	GCTGGAGGCCAGC	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29364835	29364835	+	Missense_Mutation	SNP	T	T	G	rs2073153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	226	300	2	0.9869	0.00666667	T|0.650;G|0.350	0.350	strong	.	OR12D2	42	.	NM_013936	exon1	c.T359G	p.L120R	TTGACCTCTCTGT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9048342	9048342	+	Missense_Mutation	SNP	C	C	T	rs10854118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	85	147	0	0.57047	0	C|0.570;T|0.430	0.430	strong	MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	NM_024690	exon5	c.G33289A	p.V11097M	TCACCACTCCTGA	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169511734	169511734	+	Missense_Mutation	SNP	T	T	C	rs4525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	375	369	329	0	0.984	0	T|0.758;C|0.242	0.242	strong	F5,NS,carcinoma,-1,1	F5	301	1	NM_000130	exon13	c.A2594G	p.H865R	CCCTTATGCTTAG	.	PASS	Atlas-SNP
CR2	1380	hgsc.bcm.edu	37	1	207653364	207653364	+	Missense_Mutation	SNP	A	A	G	rs17618	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	296	111	191	0	0.375	0	A|0.932;G|0.068	0.068	strong	.	CR2	164	.	NM_001006658	exon18	c.A3154G	p.I1052V	ATTGTCATTACCT	.	PASS	Atlas-SNP
ZNF560	147741	hgsc.bcm.edu	37	19	9579809	9579809	+	Missense_Mutation	SNP	C	C	A	rs61737643	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	85	251	0	0.438144	0	C|0.997;A|0.003	0.003	strong	.	ZNF560	162	.	NM_152476	exon9	c.G584T	p.C195F	TTTAAACAAAAAT	.	PASS	Atlas-SNP
WDR12	55759	hgsc.bcm.edu	37	2	203765756	203765756	+	Missense_Mutation	SNP	T	T	C	rs35212307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	20	133	0	0.215054	0	T|0.919;C|0.081	0.081	strong	.	WDR12	35	.	NM_018256	exon3	c.A223G	p.I75V	ATGAGATGTTCTC	.	PASS	Atlas-SNP
C16orf96	342346	hgsc.bcm.edu	37	16	4625938	4625938	+	Missense_Mutation	SNP	A	A	T	rs2450386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	23	80	0	0.522727	0	A|0.865;T|0.135	0.135	strong	C16orf96,NS,carcinoma,0,1	C16orf96	28	1	NM_001145011	exon5	c.A1457T	p.D486V	GCAAGGATGGGGT	.	PASS	Atlas-SNP
UBE2J1	51465	hgsc.bcm.edu	37	6	90047956	90047956	+	Silent	SNP	G	G	A	rs35213866	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	52	134	0	0.379562	0	G|0.993;A|0.007	0.007	strong	.	UBE2J1	28	.	NM_016021	exon5	c.C396T	p.Y132Y	AGGAGTGTAATCT	.	PASS	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	37	17	38955173	38955173	+	Silent	SNP	G	G	A	rs7222207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	267	123	290	1	0.460674	0.00344828	G|0.838;A|0.162	0.162	strong	.	KRT28	65	.	NM_181535	exon2	c.C529T	p.L177L	ACTTTAGCCTGAA	.	PASS	Atlas-SNP
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100482866	100482866	+	Missense_Mutation	SNP	G	G	A	rs17851246	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	55	149	0	0.447154	0	G|0.954;A|0.046	0.046	strong	.	UHRF1BP1L	144	.	NM_015054	exon8	c.C848T	p.T283I	ACTACTGTAGAGC	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117050998	117050998	+	Missense_Mutation	SNP	G	G	A	rs10982134	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	56	150	0	0.434109	0	G|0.655;A|0.345	0.345	strong	COL27A1,NS,carcinoma,+1,1	COL27A1	200	1	NM_032888	exon43	c.G4061A	p.R1354Q	GTGATCGAGGAGA	.	PASS	Atlas-SNP
ELL2	22936	hgsc.bcm.edu	37	5	95236459	95236459	+	Missense_Mutation	SNP	C	C	T	rs3815768	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	149	179	0	0.986755	0	C|0.695;T|0.305	0.305	strong	.	ELL2	63	.	NM_012081	exon7	c.G892A	p.A298T	TGCCTGCAGCATT	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74921072	74921072	+	Silent	SNP	G	G	C	rs3889145	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	65	91	2	0.481481	0.021978	G|0.785;C|0.215	0.215	strong	MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	NM_198955	exon8	c.G1083C	p.R361R	AGGCCGGGGAAGC	.	scavenged	Atlas-SNP
LAMTOR5	10542	hgsc.bcm.edu	37	1	110950439	110950439	+	Missense_Mutation	SNP	C	C	T	rs6674775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	78	152	1	0.735849	0.00657895	C|0.604;T|0.396	0.396	strong	HBXIP,colon,carcinoma,0,1	.	.	1	NM_006402	exon1	c.G50A	p.S17N	CGAAGGCTTGGGC	.	PASS	Atlas-SNP
CCM2	83605	hgsc.bcm.edu	37	7	45104131	45104131	+	Missense_Mutation	SNP	G	G	A	rs11552377	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	16	54	0	0.296296	0	G|0.879;A|0.121	0.121	strong	.	CCM2	42	.	NM_001029835	exon4	c.G421A	p.V141I	TACAACGTCAAGC	.	PASS	Atlas-SNP
PLXNA2	5362	hgsc.bcm.edu	37	1	208390162	208390162	+	Missense_Mutation	SNP	T	T	C	rs4844658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	95	100	0	0.655172	0	T|0.865;C|0.135	0.135	strong	.	PLXNA2	178	.	NM_025179	exon2	c.A1106G	p.E369G	AGGCGCTCCTTGA	.	PASS	Atlas-SNP
CYP2W1	54905	hgsc.bcm.edu	37	7	1023013	1023013	+	Silent	SNP	C	C	T	rs2272375	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	18	26	0	0.75	0	C|0.645;T|0.355	0.355	strong	.	CYP2W1	28	.	NM_017781	exon1	c.C166T	p.L56L	CGGTCCCTGATGG	.	PASS	Atlas-SNP
DEFB129	140881	hgsc.bcm.edu	37	20	210061	210061	+	Silent	SNP	G	G	A	rs13045643	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	39	65	0	0.493671	0	G|0.710;A|0.289	0.289	strong	DEFB129,NS,carcinoma,0,1	DEFB129	24	1	NM_080831	exon2	c.G201A	p.L67L	CTACCTGCAATAT	.	PASS	Atlas-SNP
FAM167B	84734	hgsc.bcm.edu	37	1	32713199	32713199	+	Silent	SNP	A	A	G	rs2291063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	84	190	1	0.717949	0.00526316	A|0.870;G|0.130	0.130	strong	.	FAM167B	18	.	NM_032648	exon1	c.A177G	p.Q59Q	GGCCCAAGCCAAA	.	PASS	Atlas-SNP
ALDH4A1	8659	hgsc.bcm.edu	37	1	19212007	19212007	+	Missense_Mutation	SNP	G	G	A	rs139640415	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	32	98	0	0.727273	0	G|0.999;A|0.001	0.001	strong	ALDH4A1_ENST00000375341,NS,carcinoma,+1,2	ALDH4A1	72	2	NM_003748	exon5	c.C413T	p.P138L	CTGCGCGGCCCAC	.	PASS	Atlas-SNP
DVL2	1856	hgsc.bcm.edu	37	17	7129840	7129840	+	Silent	SNP	T	T	C	rs35594616	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	68	60	0	0.985507	0	T|0.449;C|0.551	0.551	strong	.	DVL2	49	.	NM_004422	exon14	c.A1662G	p.Q554Q	AGGGTATTGGTAG	.	PASS	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	37	5	167858371	167858371	+	Missense_Mutation	SNP	G	G	T	rs3822660	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	29	96	0	0.432836	0	G|0.927;T|0.073	0.073	strong	.	WWC1	98	.	NM_015238	exon15	c.G2202T	p.M734I	ATCCATGTCCTAT	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788145	3788145	+	Missense_Mutation	SNP	C	C	T	rs242018	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	70	163	0	0.4375	0	C|0.763;T|0.237	0.237	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.G460A	p.E154K	CATCTTCGCCCAT	.	PASS	Atlas-SNP
DDX54	79039	hgsc.bcm.edu	37	12	113596866	113596866	+	Missense_Mutation	SNP	G	G	A	rs1048889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	36	117	0	0.418605	0	G|0.963;A|0.037	0.037	strong	.	DDX54	73	.	NM_001111322	exon20	c.C2465T	p.P822L	AGTTCCGGGCGGA	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88781040	88781040	+	Missense_Mutation	SNP	A	A	G	rs8059048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	120	208	1	0.833333	0.00480769	A|0.751;G|0.249	0.249	strong	CTU2_ENST00000453996,NS,carcinoma,0,4	CTU2	66	4	NM_001012759	exon12	c.A1247G	p.Q416R	TCTCCCAGATGCA	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54756246	54756246	+	Missense_Mutation	SNP	A	A	G	rs117421142	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	82	203	0	0.455556	0	A|0.985;G|0.015	0.015	strong	.	LILRB5	176	.	NM_001081442	exon11	c.T1559C	p.I520T	TCCTGGATGTCAG	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225533684	225533684	+	Missense_Mutation	SNP	A	A	G	rs6667999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	106	131	0	0.679487	0	A|0.507;G|0.493	0.493	strong	.	DNAH14	300	.	NM_001373	exon68	c.A10420G	p.K3474E	GATGACAAAATTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684593	100684593	+	Missense_Mutation	SNP	G	G	A	rs35988443	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	182	155	0	0.978495	0	G|0.888;A|0.112	0.112	strong	.	MUC17	804	.	NM_001040105	exon3	c.G9896A	p.S3299N	AAACGAGCACCCT	.	PASS	Atlas-SNP
TGM5	9333	hgsc.bcm.edu	37	15	43531411	43531411	+	Missense_Mutation	SNP	G	G	C	rs28756768	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	10	81	0	0.2	0	G|0.789;C|0.211	0.211	strong	.	TGM5	88	.	NM_201631	exon8	c.C1055G	p.A352G	CCATATGCAGGGG	.	PASS	Atlas-SNP
NTRK3	4916	hgsc.bcm.edu	37	15	88576185	88576185	+	Silent	SNP	G	G	C	rs2229910	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	14	149	2	0.191781	0.0134228	G|0.647;C|0.353	0.353	strong	NTRK3_ENST00000360948,NS,carcinoma,-1,4	NTRK3	587	4	NM_001012338	exon14	c.C1488G	p.A496A	GGGCCCGGCATCC	.	scavenged	Atlas-SNP
SOCS5	9655	hgsc.bcm.edu	37	2	46986716	46986716	+	Silent	SNP	C	C	G	rs41489952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	125	181	1	0.578704	0.00552486	C|0.935;G|0.065	0.065	strong	.	SOCS5	62	.	NM_144949	exon2	c.C1047G	p.T349T	CCATACCCATGTT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537475	88537475	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	453	7	416	1	0.0154525	0.00240385	.	.	none	DSPP,colon,carcinoma,-1,1	DSPP	174	1	NM_014208	exon5	c.G3661A	p.D1221N	AGCAGCGACAGCA	.	scavenged	Atlas-SNP
TTLL9	164395	hgsc.bcm.edu	37	20	30527065	30527065	+	Silent	SNP	T	T	C	rs6061043	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	30	71	0	0.47619	0	T|0.572;C|0.428	0.428	strong	TTLL9,NS,carcinoma,0,1	TTLL9	95	1	NM_001008409	exon14	c.T1239C	p.H413H	CACACATCTCGGT	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138602523	138602523	+	Missense_Mutation	SNP	T	T	C	rs2774962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	44	80	1	0.956522	0.0125	T|0.509;C|0.491	0.491	strong	KIAA1549_ENST00000422774,colon,carcinoma,0,3	KIAA1549	314	3	NM_020910	exon2	c.A1849G	p.R617G	CACCTCTGGGTTT	.	scavenged	Atlas-SNP
FXYD3	5349	hgsc.bcm.edu	37	19	35612159	35612159	+	Missense_Mutation	SNP	C	C	G	rs2290649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	121	278	1	0.504167	0.00359712	C|0.741;G|0.259	0.259	strong	.	FXYD3	15	.	NM_001136010	exon5	c.C107G	p.P36R	AGAGCCCGTGCCC	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100512412	100512412	+	Silent	SNP	T	T	C	rs982424	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	60	148	0	0.46875	0	T|0.855;C|0.145	0.145	strong	.	MTTP	127	.	NM_000253	exon6	c.T522C	p.C174C	AAATTGTAAAGTG	.	PASS	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	37	8	17824674	17824674	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	82	144	0	0.61194	0	.	.	none	PCM1,colon,carcinoma,0,1	PCM1	120	1	NM_006197	exon21	c.C3407T	p.A1136V	CATTTGCACCAGG	.	PASS	Atlas-SNP
HSD3B1	3283	hgsc.bcm.edu	37	1	120056849	120056849	+	Silent	SNP	C	C	T	rs141977722	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	65	128	0	0.371429	0	C|0.998;T|0.002	0.002	strong	.	HSD3B1	53	.	NM_000862	exon4	c.C703T	p.L235L	CACATTCTGGCCT	.	PASS	Atlas-SNP
JARID2	3720	hgsc.bcm.edu	37	6	15468876	15468876	+	Silent	SNP	C	C	G	rs7768621	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	64	143	0	0.470588	0	C|0.903;G|0.096;T|0.000	0.096	strong	.	JARID2	135	.	NM_004973	exon5	c.C597G	p.T199T	AGCCACCAACAAT	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15519029	15519029	+	Silent	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	272	32	295	0	0.117647	0	.	.	none	.	CDRT1	83	.	NM_006382	exon2	c.T600G	p.T200T	GTGCTGAGTTTTG	.	PASS	Atlas-SNP
CASP9	842	hgsc.bcm.edu	37	1	15850613	15850613	+	Missense_Mutation	SNP	G	G	A	rs1052571	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	29	60	0	0.966667	0	G|0.387;A|0.613	0.613	strong	.	CASP9	40	.	NM_001229	exon1	c.C83T	p.A28V	AGCAGGGCGTCCC	.	PASS	Atlas-SNP
CLEC16A	23274	hgsc.bcm.edu	37	16	11272330	11272330	+	Missense_Mutation	SNP	G	G	A	rs72650689	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	44	106	0	0.458333	0	A|0.006;G|0.994	0.006	strong	.	CLEC16A	101	.	NM_015226	exon23	c.G2945A	p.S982N	CCCCCAGCCTCGT	.	PASS	Atlas-SNP
HEATR6	63897	hgsc.bcm.edu	37	17	58153586	58153586	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	12	15	0	0.5	0	.	.	none	.	HEATR6	98	.	NM_022070	exon2	c.C232G	p.L78V	CAAGAAGAGCACT	.	PASS	Atlas-SNP
HEATR2	54919	hgsc.bcm.edu	37	7	810219	810219	+	Missense_Mutation	SNP	T	T	C	rs4720951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	81	148	0	0.426316	0	T|0.578;C|0.422	0.422	strong	HEATR2,colon,carcinoma,-1,1	HEATR2	62	1	NM_017802	exon9	c.T1895C	p.V632A	CCACCGTGCTGCT	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36982754	36982754	+	Missense_Mutation	SNP	G	G	A	rs36015492	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	51	75	0	0.573034	0	G|0.988;A|0.012	0.012	strong	.	LBP	60	.	NM_004139	exon4	c.G439A	p.E147K	GGCAGCGAGTCCT	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	76991935	76991935	+	Missense_Mutation	SNP	C	C	T	rs1527263	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	71	154	0	0.298319	0	C|0.675;N|0.000	.	strong	PION,colon,carcinoma,+1,4	PION	74	4	NM_017439	exon13	c.G914A	p.G305E	ATTTGTCCCCAAG	.	PASS	Atlas-SNP
TRUB1	142940	hgsc.bcm.edu	37	10	116702425	116702425	+	Missense_Mutation	SNP	A	A	C	rs34393297	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	29	84	0	0.47541	0	A|0.977;C|0.023	0.023	strong	.	TRUB1	30	.	NM_139169	exon2	c.A308C	p.E103A	CTCCAGAATGGAC	.	PASS	Atlas-SNP
EPB41L3	23136	hgsc.bcm.edu	37	18	5478334	5478334	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	301	5	331	0	0.0166113	0	.	.	none	EPB41L3,rectum,carcinoma,+1,1	EPB41L3	222	1	NM_012307	exon3	c.T287C	p.L96P	CGAGAGAGTTTAC	.	scavenged	Atlas-SNP
EPHA2	1969	hgsc.bcm.edu	37	1	16475123	16475123	+	Silent	SNP	C	C	T	rs6678616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	10	48	0	0.232558	0	C|0.740;T|0.260	0.260	strong	.	EPHA2	102	.	NM_004431	exon3	c.G573A	p.L191L	GGAGAGCAGCGCC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103395769	103395769	+	Silent	SNP	G	G	C	rs117896704	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	103	241	0	0.507389	0	G|0.986;C|0.014	0.014	strong	.	.	.	.	NM_001146197	exon4	c.C7278G	p.T2426T	CAGTTTGGTTTTT	.	PASS	Atlas-SNP
NUP98	4928	hgsc.bcm.edu	37	11	3723941	3723941	+	Silent	SNP	C	C	T	rs35488940	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	87	228	0	0.488764	0	C|0.951;T|0.049	0.049	strong	.	NUP98	149	.	NM_016320	exon23	c.G3264A	p.P1088P	TTTCAACGGAACC	.	PASS	Atlas-SNP
TSPAN13	27075	hgsc.bcm.edu	37	7	16823095	16823095	+	Silent	SNP	G	G	A	rs11491	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	51	81	0	0.53125	0	T|0.000;G|0.537;C|0.000;A|0.463	0.463	strong	TSPAN13,NS,carcinoma,0,1	TSPAN13	13	1	NM_014399	exon6	c.G594A	p.A198A	CCGCGCGAATCCT	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94496602	94496602	+	Silent	SNP	G	G	T	rs1801666	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	19	131	0	0.223529	0	T|0.019;G|0.979;A|0.002	0.019	strong	.	ABCA4	275	.	NM_000350	exon28	c.C4203A	p.P1401P	CAAAGCGGGGTAT	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156878531	156878531	+	Silent	SNP	T	T	C	rs11264580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	20	105	0	0.246914	0	T|0.780;C|0.220	0.220	strong	PEAR1,colon,carcinoma,0,1	PEAR1	118	1	NM_001080471	exon10	c.T1200C	p.H400H	CACGCATGGGCCA	.	PASS	Atlas-SNP
PLK2	10769	hgsc.bcm.edu	37	5	57753116	57753116	+	Silent	SNP	C	C	T	rs17710502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	28	43	0	0.459016	0	C|0.868;T|0.132	0.132	strong	.	PLK2	71	.	NM_006622	exon7	c.G900A	p.P300P	TGAGGACGGCATT	.	PASS	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806863	33806863	+	Silent	SNP	G	G	A	rs12451746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	94	154	0	0.54023	0	G|0.626;A|0.374	0.374	strong	SLFN12L_ENST00000449046,NS,carcinoma,0,1	SLFN12L	140	1	NM_001195790	exon2	c.C366T	p.H122H	AAAAATGTGAAAG	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216462662	216462662	+	Missense_Mutation	SNP	T	T	A	rs1805048	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	131	190	0	0.582222	0	T|0.942;A|0.058	0.058	strong	.	USH2A	1168	.	NM_007123	exon11	c.A1931T	p.D644V	ACTGTATCACAGT	.	PASS	Atlas-SNP
FAM21A	387680	hgsc.bcm.edu	37	10	51853633	51853633	+	Missense_Mutation	SNP	C	C	T	rs199520696	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	762	217	645	3	0.284777	0.00465116	C|0.796;T|0.205	0.205	strong	FAM21A,NS,carcinoma,0,4	FAM21A	32	4	NM_001005751	exon13	c.C1136T	p.T379M	TCTTCACGGAAGC	.	scavenged	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4720469	4720469	+	Missense_Mutation	SNP	C	C	T	rs1052748	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	73	204	0	0.405556	0	C|0.670;T|0.330	0.330	strong	.	PLD2	138	.	NM_001243108	exon17	c.C1730T	p.T577I	CTCCCACATACCC	.	PASS	Atlas-SNP
SEMA3C	10512	hgsc.bcm.edu	37	7	80380645	80380645	+	Silent	SNP	G	G	T	rs138526129		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	151	210	0	0.601594	0	G|1.000;T|0.000	0.000	weak	.	SEMA3C	106	.	NM_006379	exon16	c.C1651A	p.R551R	GTCTTCGGCTCCT	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71851969	71851969	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	68	155	0	0.459459	0	.	.	none	.	TJP2	120	.	NM_001170416	exon14	c.T2189C	p.L730P	AGAACCTGAGGAA	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	98943598	98943598	+	Missense_Mutation	SNP	C	C	T	rs2290472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	30	44	0	0.576923	0	C|0.889;T|0.111	0.111	strong	MATN2_ENST00000520016,NS,carcinoma,-1,2	MATN2	165	2	NM_002380	exon3	c.C560T	p.T187M	GGGACACGGGCAT	.	PASS	Atlas-SNP
CIDEB	27141	hgsc.bcm.edu	37	14	24775287	24775287	+	Silent	SNP	G	G	A	rs139893717	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	53	53	0	0.638554	0	G|0.995;A|0.005	0.005	strong	.	CIDEB	17	.	NM_014430	exon6	c.C393T	p.I131I	TCGGGCGATGTCC	.	PASS	Atlas-SNP
GABRB1	2560	hgsc.bcm.edu	37	4	47408709	47408709	+	Silent	SNP	A	A	G	rs6289	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	80	200	0	0.470588	0	A|0.721;G|0.279	0.279	strong	.	GABRB1	107	.	NM_000812	exon8	c.A846G	p.T282T	CACGACAGTGCTT	.	PASS	Atlas-SNP
FAM161A	84140	hgsc.bcm.edu	37	2	62067433	62067433	+	Missense_Mutation	SNP	T	T	C	rs17513722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	88	269	0	0.387665	0	T|0.844;C|0.156	0.156	strong	FAM161A_ENST00000405894,colon,carcinoma,+2,3	FAM161A	200	3	NM_032180	exon3	c.A706G	p.I236V	CTGTAATTGTGGG	.	PASS	Atlas-SNP
MMAB	326625	hgsc.bcm.edu	37	12	110011230	110011230	+	Missense_Mutation	SNP	C	C	T	rs10774775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	32	77	0	0.603774	0	C|0.693;T|0.307	0.307	strong	.	MMAB	16	.	NM_052845	exon1	c.G56A	p.R19H	CACCCGCGCAGGC	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158536267	158536267	+	Missense_Mutation	SNP	T	T	C	rs2305473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	94	163	0	0.770492	0	T|0.712;C|0.288	0.288	strong	.	ESYT2	70	.	NM_020728	exon16	c.A1828G	p.S610G	AGTTACTGAGCTG	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88387557	88387557	+	Missense_Mutation	SNP	A	A	C	rs1542087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298	130	275	0	0.436242	0	A|0.865;C|0.135	0.135	strong	.	SMYD1	95	.	NM_198274	exon3	c.A491C	p.Q164P	GCCAGCAGTTCAG	.	PASS	Atlas-SNP
TAPBPL	55080	hgsc.bcm.edu	37	12	6562285	6562285	+	Silent	SNP	C	C	T	rs2041384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	53	123	0	0.524752	0	C|0.782;G|0.000;T|0.218	0.218	strong	.	TAPBPL	21	.	NM_018009	exon2	c.C117T	p.C39C	AGACTGCTTCCTG	.	PASS	Atlas-SNP
EFTUD1	79631	hgsc.bcm.edu	37	15	82444663	82444663	+	Missense_Mutation	SNP	T	T	C	rs2292071	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	12	92	0	0.244898	0	T|0.844;C|0.156	0.156	strong	.	EFTUD1	74	.	NM_024580	exon18	c.A2132G	p.K711R	TGCTGTTTGCCTA	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	89943571	89943571	+	Missense_Mutation	SNP	G	G	T	rs2366777	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	34	19	0	1	0	G|0.206;T|0.794	0.794	strong	.	GPR98	605	.	NM_032119	exon17	c.G3279T	p.L1093F	CCTCTTGAATTCA	.	PASS	Atlas-SNP
SMCO4	0	hgsc.bcm.edu	37	11	93212254	93212254	+	Silent	SNP	C	C	T	rs2658797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	128	117	0	0.962406	0	C|0.421;T|0.579	0.579	strong	.	.	.	.	NM_020179	exon3	c.G102A	p.V34V	GGGCAGCACCACT	.	PASS	Atlas-SNP
SAMD11	148398	hgsc.bcm.edu	37	1	879317	879317	+	Silent	SNP	C	C	T	rs7523549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	20	129	0	0.253165	0	C|0.908;T|0.092	0.092	strong	SAMD11,colon,carcinoma,0,2	SAMD11	34	2	NM_152486	exon14	c.C1830T	p.Y610Y	TTTCTACGTGGCC	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33635910	33635910	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	11	17	0	0.611111	0	.	.	none	.	KL	106	.	NM_004795	exon4	c.T2694C	p.A898A	CGAAGCTCTCAAA	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89807233	89807233	+	Silent	SNP	C	C	G	rs11649210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	226	24	261	0	0.106195	0	C|0.892;G|0.108	0.108	strong	.	FANCA	99	.	NM_000135	exon38	c.G3807C	p.L1269L	TGACGACAGCAGG	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55494638	55494638	+	Silent	SNP	T	T	C	rs61735084	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	21	108	0	0.276316	0	T|0.987;C|0.013	0.013	strong	.	NLRP2	161	.	NM_017852	exon6	c.T1572C	p.D524D	AGAGGATAGGGAC	.	PASS	Atlas-SNP
RHBDF2	79651	hgsc.bcm.edu	37	17	74475975	74475975	+	Missense_Mutation	SNP	C	C	A	rs3809694	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	44	87	0	0.458333	0	C|0.600;A|0.400	0.400	strong	RHBDF2,colon,carcinoma,+1,1	RHBDF2	57	1	NM_024599	exon4	c.G199T	p.A67S	TGTGTGCAGCCCA	.	PASS	Atlas-SNP
SPATA22	84690	hgsc.bcm.edu	37	17	3343519	3343519	+	Silent	SNP	T	T	C	rs17822627	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	345	150	418	1	0.434783	0.00239234	T|0.774;C|0.226	0.226	strong	.	SPATA22	49	.	NM_032598	exon9	c.A1014G	p.E338E	TTTTTGTTCAGAA	.	PASS	Atlas-SNP
MYH13	8735	hgsc.bcm.edu	37	17	10236465	10236465	+	Silent	SNP	G	G	A	rs2240579	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	49	50	0	1	0	G|0.544;A|0.455	0.455	strong	MYH13_ENST00000252172,NS,carcinoma,0,2	MYH13	533	2	NM_003802	exon19	c.C2100T	p.N700N	GACCCCGTTACAG	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520259	72520259	+	Missense_Mutation	SNP	C	C	T	rs61573157	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	27	49	0	0.771429	0	C|0.925;T|0.075	0.075	strong	.	ADAMTS14	148	.	NM_139155	exon22	c.C3331T	p.P1111S	CCTGGCCCAACCT	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	37	5	32074099	32074099	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	2	169	0	0.0117647	0	.	.	none	PDZD2,NS,carcinoma,-2,1	PDZD2	306	1	NM_178140	exon17	c.G2887T	p.G963C	AAGGTAGGCTGCT	.	scavenged	Atlas-SNP
NDN	4692	hgsc.bcm.edu	37	15	23931507	23931507	+	Silent	SNP	G	G	A	rs2192206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	8	67	0	0.266667	0	G|0.810;A|0.190	0.190	strong	.	NDN	79	.	NM_002487	exon1	c.C858T	p.D286D	CTGGGGGTCTTTC	.	PASS	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41862801	41862801	+	Splice_Site	SNP	G	G	T	rs200684350	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	6	92	3	0.0952381	0.0326087	G|0.985;T|0.015	0.015	strong	TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	NM_006293	exon12	c.1484-1G>T	.	CCCACAGTGGACA	.	scavenged	Atlas-SNP
S1PR4	8698	hgsc.bcm.edu	37	19	3179021	3179021	+	Silent	SNP	G	G	A	rs34728133	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	21	63	0	0.6	0	G|0.953;A|0.047	0.047	strong	.	S1PR4	31	.	NM_003775	exon1	c.G231A	p.S77S	GCGGTCGCGACGC	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202276494	202276494	+	Silent	SNP	C	C	T	rs896551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	302	301	246	2	0.996689	0.00813008	C|0.532;T|0.468	0.468	strong	.	LGR6	102	.	NM_001017403	exon14	c.C1245T	p.P415P	CCACCCCGAGGCC	.	PASS	Atlas-SNP
RMDN1	51115	hgsc.bcm.edu	37	8	87519315	87519315	+	Missense_Mutation	SNP	T	T	G	rs6980476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	47	106	0	0.330986	0	T|0.790;G|0.210	0.210	strong	.	.	.	.	NM_016033	exon2	c.A156C	p.K52N	GCCTCTTTTGAAA	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011719	46011719	+	Missense_Mutation	SNP	G	G	A	rs202022037		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	344	28	234	0	0.0813954	0	.	.	weak	KRTAP10-6,caecum,carcinoma,-1,1	KRTAP10-6	57	1	NM_198688	exon1	c.C647T	p.P216L	CAAGTTGGCTGGC	.	scavenged	Atlas-SNP
ODF3L2	284451	hgsc.bcm.edu	37	19	464310	464310	+	Missense_Mutation	SNP	A	A	G	rs34551779	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	44	119	0	0.423077	0	A|0.527;G|0.473	0.473	strong	.	ODF3L2	18	.	NM_182577	exon4	c.T404C	p.V135A	TGGCGCACAGGGG	.	PASS	Atlas-SNP
ANKS3	124401	hgsc.bcm.edu	37	16	4776685	4776685	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	5	91	0	0.0490196	0	.	.	none	.	ANKS3	44	.	NM_133450	exon5	c.G466A	p.D156N	CACTGTCCAAGAG	.	PASS	Atlas-SNP
ZNF100	163227	hgsc.bcm.edu	37	19	21910125	21910125	+	Nonsense_Mutation	SNP	G	G	T	rs138292237	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	12	32	0	0.413793	0	G|0.990;T|0.010	0.010	strong	.	ZNF100	62	.	NM_173531	exon5	c.C989A	p.S330X	AGGTGTGAGGACC	.	PASS	Atlas-SNP
C6orf223	221416	hgsc.bcm.edu	37	6	43968412	43968412	+	Missense_Mutation	SNP	C	C	T	rs35703624	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	64	180	0	0.412903	0	C|0.993;T|0.007	0.007	strong	.	C6orf223	14	.	NM_153246	exon1	c.C56T	p.T19M	CAGCAACGGAGTG	.	PASS	Atlas-SNP
C5orf34	375444	hgsc.bcm.edu	37	5	43505993	43505993	+	Silent	SNP	A	A	G	rs7710628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	73	139	0	0.52518	0	A|0.526;G|0.474	0.474	strong	.	C5orf34	47	.	NM_198566	exon4	c.T789C	p.N263N	GATTTTATTATGA	.	PASS	Atlas-SNP
TEKT5	146279	hgsc.bcm.edu	37	16	10769958	10769958	+	Missense_Mutation	SNP	T	T	C	rs2719710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	47	94	0	0.435185	0	T|0.469;C|0.531	0.531	strong	.	TEKT5	66	.	NM_144674	exon5	c.A944G	p.Q315R	CGCAGCTGGATGG	.	PASS	Atlas-SNP
LYZL2	119180	hgsc.bcm.edu	37	10	30918549	30918549	+	Missense_Mutation	SNP	G	G	C	rs201069868	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	28	159	1	0.220472	0.00628931	G|0.894;C|0.106	0.106	strong	LYZL2,NS,adenoma,0,2	LYZL2	33	2	NM_183058	exon1	c.C86G	p.A29G	CCTGCCGCAGAGG	.	scavenged	Atlas-SNP
NDUFA13	51079	hgsc.bcm.edu	37	19	19627083	19627083	+	Silent	SNP	G	G	C	rs11552886	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	112	262	2	0.460905	0.00763359	.	.	alt	NDUFA13,NS,carcinoma,0,1	NDUFA13	17	1	NM_015965	exon1	c.G36C	p.P12P	GCCTCCGCCGGGG	.	scavenged	Atlas-SNP
AGR2	10551	hgsc.bcm.edu	37	7	16834597	16834597	+	Silent	SNP	A	A	G	rs6842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	229	178	0	0.991342	0	T|0.132;G|0.313;C|0.057;A|0.498	0.313	strong	.	AGR2	14	.	NM_006408	exon7	c.T441C	p.N147N	GAGACGATTTGAA	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21225281	21225281	+	Missense_Mutation	SNP	C	C	T	rs1042034	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	119	137	1	0.991667	0.00729927	C|0.265;T|0.735	0.735	strong	.	APOB	761	.	NM_000384	exon29	c.G13013A	p.S4338N	TAATCACTGAAGA	.	PASS	Atlas-SNP
WDR16	146845	hgsc.bcm.edu	37	17	9515777	9515777	+	Missense_Mutation	SNP	G	G	A	rs6503235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	53	75	1	1	0.0133333	G|0.383;A|0.617	0.617	strong	WDR16,NS,carcinoma,0,1	WDR16	67	1	NM_145054	exon8	c.G1006A	p.E336K	GCTGTCGAGGATA	.	scavenged	Atlas-SNP
KLRC2	3822	hgsc.bcm.edu	37	12	10588530	10588530	+	Missense_Mutation	SNP	C	C	G	rs75545535	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	564	231	513	2	0.409574	0.00389864	C|0.745;G|0.255	0.255	strong	KLRC2,NS,carcinoma,0,1	KLRC2	29	1	NM_002260	exon1	c.G56C	p.R19P	TGCTGCCGCTTTG	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186381165	186381165	+	Silent	SNP	G	G	A	rs7699724	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	26	159	0	0.238532	0	G|0.547;A|0.453	0.453	strong	.	CCDC110	78	.	NM_152775	exon6	c.C576T	p.D192D	CAAGATGTCAGAA	.	PASS	Atlas-SNP
DERL1	79139	hgsc.bcm.edu	37	8	124031541	124031541	+	Missense_Mutation	SNP	T	T	C	rs2272722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	56	131	0	0.380952	0	T|0.926;C|0.074	0.074	strong	.	DERL1	27	.	NM_024295	exon7	c.A511G	p.I171V	CATTGATTACCCT	.	PASS	Atlas-SNP
FRMPD4	9758	hgsc.bcm.edu	37	X	12720127	12720127	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	39	101	0	1	0	.	.	none	.	FRMPD4	214	.	NM_014728	exon10	c.C1068T	p.I356I	ATACATCGAGTAA	.	PASS	Atlas-SNP
CLIP4	79745	hgsc.bcm.edu	37	2	29356669	29356669	+	Silent	SNP	A	A	G	rs3100232	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	54	97	0	0.469565	0	A|0.551;G|0.449	0.449	strong	.	CLIP4	69	.	NM_024692	exon5	c.A516G	p.T172T	GAAAACATCGAAA	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134659573	134659573	+	Silent	SNP	G	G	A	rs34588833	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	29	99	0	0.42029	0	G|0.936;A|0.064	0.064	strong	.	TTC40	100	.	NM_001200049	exon44	c.C6426T	p.A2142A	CACGGCGGCCAGC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264808	1264808	+	Missense_Mutation	SNP	T	T	G	rs2943528	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	445	153	448	1	0.34382	0.00223214	T|0.921;G|0.079	0.079	strong	.	MUC5B	473	.	NM_002458	exon31	c.T6698G	p.V2233G	CCACGGTGACTTC	.	PASS	Atlas-SNP
IQGAP3	128239	hgsc.bcm.edu	37	1	156499969	156499969	+	Silent	SNP	T	T	C	rs1171566	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	173	122	0	0.982955	0	T|0.489;C|0.511	0.511	strong	IQGAP3,NS,carcinoma,0,1	IQGAP3	146	1	NM_178229	exon34	c.A4332G	p.L1444L	TCGGCGTAGGTTC	.	PASS	Atlas-SNP
CDHR2	54825	hgsc.bcm.edu	37	5	176011889	176011889	+	Silent	SNP	G	G	A	rs4868660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	110	221	0	0.464135	0	G|0.727;A|0.273	0.273	strong	.	CDHR2	152	.	NM_017675	exon19	c.G2607A	p.A869A	AGTGGCGGCCAAC	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	101296389	101296389	+	Missense_Mutation	SNP	G	G	A	rs9390698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	63	182	0	0.411765	0	G|0.688;A|0.312	0.312	strong	ASCC3,NS,carcinoma,0,1	ASCC3	205	1	NM_006828	exon4	c.C436T	p.L146F	CAGTAAGATCATC	.	PASS	Atlas-SNP
OR5K3	403277	hgsc.bcm.edu	37	3	98109640	98109640	+	Missense_Mutation	SNP	G	G	A	rs13068323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	422	213	476	1	0.504739	0.00210084	G|0.846;A|0.154	0.154	strong	OR5K3,rectum,carcinoma,-1,1	OR5K3	60	1	NM_001005516	exon1	c.G131A	p.G44D	ACATTGGTTTGGT	.	PASS	Atlas-SNP
DDX51	317781	hgsc.bcm.edu	37	12	132626668	132626668	+	Missense_Mutation	SNP	T	T	C	rs1133690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	41	114	0	0.455556	0	T|0.404;C|0.596	0.596	strong	.	DDX51	33	.	NM_175066	exon5	c.A884G	p.Q295R	ACCTGCTGGGCCA	.	PASS	Atlas-SNP
MROH2B	133558	hgsc.bcm.edu	37	5	41054934	41054934	+	Silent	SNP	A	A	G	rs325874	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	61	109	0	0.521368	0	A|0.778;G|0.222	0.222	strong	.	.	.	.	NM_173489	exon11	c.T1042C	p.L348L	CCCTCAACCTGGG	.	PASS	Atlas-SNP
TSNAX	7257	hgsc.bcm.edu	37	1	231665038	231665038	+	Silent	SNP	C	C	T	rs138421350	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	67	143	0	0.352632	0	C|0.999;T|0.001	0.001	strong	.	TSNAX	14	.	NM_005999	exon2	c.C54T	p.F18F	CAATTTCCCACAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281690	152281690	+	Missense_Mutation	SNP	C	C	T	rs12407748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	467	152	351	0	0.325482	0	C|0.851;T|0.149	0.149	strong	.	FLG	900	.	NM_002016	exon3	c.G5672A	p.R1891Q	TCGGCCCGAGAGG	.	PASS	Atlas-SNP
ODF4	146852	hgsc.bcm.edu	37	17	8243598	8243598	+	Missense_Mutation	SNP	C	C	T	rs73250854	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	65	113	0	0.541667	0	C|0.881;T|0.119	0.119	strong	ODF4,colon,carcinoma,0,1	ODF4	23	1	NM_153007	exon1	c.C229T	p.R77C	AGCTTCCGCTGGA	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	17113563	17113563	+	Silent	SNP	C	C	T	rs1801225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	4	31	0	0.181818	0	C|0.657;T|0.343	0.343	strong	.	CUBN	515	.	NM_001081	exon19	c.G2487A	p.S829S	AAAAGGCGAGCGA	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656511	46656511	+	Silent	SNP	A	A	G	rs9627324	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	65	126	0	0.481481	0	A|0.733;G|0.267	0.267	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T2709C	p.I903I	TGTAGAAATGGGA	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134108453	134108453	+	Silent	SNP	C	C	T	rs2069568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	131	194	0	0.582222	0	C|0.629;T|0.371	0.371	strong	.	TG	416	.	NM_003235	exon43	c.C7408T	p.L2470L	CAGCTCCTGGCCG	.	PASS	Atlas-SNP
RHBG	57127	hgsc.bcm.edu	37	1	156351699	156351699	+	Missense_Mutation	SNP	G	G	A	rs3748569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	412	260	321	2	0.631068	0.00623053	G|0.472;A|0.528	0.528	strong	.	RHBG	133	.	NM_020407	exon6	c.G943A	p.G315R	TTGGCTGGGACTG	.	PASS	Atlas-SNP
CLTCL1	8218	hgsc.bcm.edu	37	22	19175133	19175133	+	Silent	SNP	C	C	A	rs187075533	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	108	278	0	0.502326	0	C|0.999;A|0.001	0.001	strong	.	CLTCL1	115	.	NM_007098	exon29	c.G4542T	p.L1514L	CTTGTACAGATAG	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53854397	53854397	+	Missense_Mutation	SNP	G	G	C	rs10415799	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	229	272	0	0.991342	0	G|0.643;C|0.357	0.357	strong	ZNF845,NS,carcinoma,0,6	ZNF845	101	6	NM_138374	exon4	c.G469C	p.E157Q	CAGACCGAAGGGA	.	PASS	Atlas-SNP
ASUN	55726	hgsc.bcm.edu	37	12	27064232	27064232	+	Silent	SNP	C	C	T	rs3210635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	132	165	0	0.977778	0	C|0.475;T|0.525	0.525	strong	.	.	.	.	NM_018164	exon15	c.G1824A	p.E608E	TCCACGCTCTAAG	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120591143	120591143	+	Silent	SNP	A	A	G	rs12312562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	46	128	0	0.38983	0	A|0.657;G|0.343	0.343	strong	GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	NM_006836	exon33	c.T3936C	p.Y1312Y	AGCATCATAGCTG	.	PASS	Atlas-SNP
NINL	22981	hgsc.bcm.edu	37	20	25456698	25456698	+	Missense_Mutation	SNP	C	C	T	rs35666277	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	95	251	1	0.5	0.00398406	C|0.953;T|0.047	0.047	strong	.	NINL	148	.	NM_025176	exon17	c.G3229A	p.D1077N	TCAAATCTACATG	.	PASS	Atlas-SNP
TLR8	51311	hgsc.bcm.edu	37	X	12937513	12937513	+	Silent	SNP	C	C	T	rs2159377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	68	159	1	0.971429	0.00628931	C|0.738;0|0.006	.	strong	.	TLR8	134	.	NM_138636	exon2	c.C354T	p.D118D	CACAGACGGGGCA	.	PASS	Atlas-SNP
KRTAP6-1	337966	hgsc.bcm.edu	37	21	31986163	31986163	+	Missense_Mutation	SNP	C	C	T	rs138494765	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	383	158	267	0	0.412533	0	C|1.000;T|0.000	0.000	weak	.	KRTAP6-1	21	.	NM_181602	exon1	c.G61A	p.G21R	GGCCTCCATAGCC	.	PASS	Atlas-SNP
EPS8L1	54869	hgsc.bcm.edu	37	19	55587822	55587822	+	Missense_Mutation	SNP	G	G	A	rs12609976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	274	150	310	3	0.547445	0.00967742	G|0.878;A|0.122	0.122	strong	EPS8L1,NS,carcinoma,0,1	EPS8L1	122	1	NM_133180	exon2	c.G10A	p.A4T	AGCACCGCCACAG	.	scavenged	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103292201	103292201	+	Missense_Mutation	SNP	G	G	A	rs78008536	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	71	102	0	0.435583	0	G|0.990;A|0.010	0.010	strong	.	RELN	593	.	NM_173054	exon15	c.C1799T	p.S600F	GACCAGGAGCGCC	.	PASS	Atlas-SNP
ZNF471	57573	hgsc.bcm.edu	37	19	57036012	57036012	+	Missense_Mutation	SNP	G	G	T	rs11667052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	28	49	0	0.56	0	G|0.792;T|0.208	0.208	strong	.	ZNF471	99	.	NM_020813	exon5	c.G576T	p.M192I	TTCTATGGTAATA	.	PASS	Atlas-SNP
TUBB6	84617	hgsc.bcm.edu	37	18	12308793	12308793	+	Silent	SNP	G	G	C	rs11267036	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	55	86	0	0.45082	0	G|0.887;C|0.113	0.113	strong	.	TUBB6	35	.	NM_032525	exon2	c.G165C	p.S55S	GTCATCGTGTGAG	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104642422	104642422	+	Silent	SNP	A	A	G	rs3742947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21	7	30	0	0.333333	0	A|0.697;G|0.303	0.303	strong	.	KIF26A	84	.	NM_015656	exon12	c.A3297G	p.A1099A	GGGGGCAGCCTGG	.	PASS	Atlas-SNP
MOK	5891	hgsc.bcm.edu	37	14	102698131	102698131	+	Silent	SNP	G	G	A	rs7152550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	46	78	0	0.425926	0	G|0.951;A|0.049	0.049	strong	.	.	.	.	NM_014226	exon10	c.C894T	p.S298S	TCTGTGGCTGCCC	.	PASS	Atlas-SNP
C1orf87	127795	hgsc.bcm.edu	37	1	60503762	60503762	+	Silent	SNP	T	T	C	rs17560663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	31	77	0	0.939394	0	T|0.897;C|0.103	0.103	strong	.	C1orf87	55	.	NM_152377	exon6	c.A765G	p.L255L	CCAGAGTAGCTTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507251	195507251	+	Missense_Mutation	SNP	G	G	T	rs201456607	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	419	43	308	14	0.102625	0.0454545	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11200A	p.P3734T	AGGAAGGGCTGGT	.	scavenged	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	37	1	180000542	180000542	+	Missense_Mutation	SNP	G	G	T	rs12125245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	456	297	388	1	0.651316	0.00257732	G|0.929;T|0.071	0.071	strong	.	CEP350	418	.	NM_014810	exon15	c.G3638T	p.G1213V	AATCTGGGACCAG	.	PASS	Atlas-SNP
OR8K5	219453	hgsc.bcm.edu	37	11	55927584	55927584	+	Missense_Mutation	SNP	A	A	T	rs141612231	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	99	177	0	0.512953	0	A|0.998;T|0.002	0.002	strong	.	OR8K5	82	.	NM_001004058	exon1	c.T210A	p.D70E	ACCAAGATCAACA	.	PASS	Atlas-SNP
PRDM2	7799	hgsc.bcm.edu	37	1	14105139	14105139	+	Missense_Mutation	SNP	T	T	A	rs2076324	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	13	98	0	0.22807	0	T|0.662;A|0.338	0.338	strong	.	PRDM2	147	.	NM_015866	exon8	c.T849A	p.D283E	AGAAGATGATGAT	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52115645	52115645	+	Missense_Mutation	SNP	G	G	C	rs3829655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	54	145	0	0.486486	0	G|0.577;C|0.423	0.423	strong	.	SIGLEC5	67	.	NM_003830	exon9	c.C1495G	p.P499A	CTCCGGGGCTGTC	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561340	32561340	+	Missense_Mutation	SNP	G	G	A	rs78337553	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	11	134	0	0.06875	0	G|0.999;A|0.001	0.001	weak	ARHGAP5,NS,carcinoma,0,1	ARHGAP5	166	1	NM_001173	exon2	c.G1465A	p.E489K	AAAGAAGAGTTTC	.	PASS	Atlas-SNP
TCN1	6947	hgsc.bcm.edu	37	11	59623433	59623433	+	Silent	SNP	G	G	A	rs1042613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	86	194	0	0.477778	0	G|0.704;A|0.296	0.296	strong	TCN1,NS,carcinoma,0,1	TCN1	64	1	NM_001062	exon6	c.C846T	p.S282S	TGGATTGCTGAAT	.	PASS	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	81006629	81006629	+	Silent	SNP	C	C	T	rs7406119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	88	195	0	0.546584	0	C|0.782;T|0.218	0.218	strong	.	B3GNTL1	40	.	NM_001009905	exon2	c.G93A	p.P31P	CAGCCACGGTTCA	.	PASS	Atlas-SNP
GTSE1	51512	hgsc.bcm.edu	37	22	46712077	46712077	+	Silent	SNP	C	C	T	rs9615947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	34	100	0	0.373626	0	C|0.933;T|0.067	0.067	strong	.	GTSE1	100	.	NM_016426	exon7	c.C1200T	p.V400V	GCGGGTCGATGTT	.	PASS	Atlas-SNP
ZNF460	10794	hgsc.bcm.edu	37	19	57802824	57802824	+	Silent	SNP	G	G	A	rs2041110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	46	151	0	0.422018	0	G|0.806;A|0.194	0.194	strong	.	ZNF460	59	.	NM_006635	exon3	c.G915A	p.K305K	TGAGAAGAAACCC	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4722785	4722785	+	Silent	SNP	G	G	A	rs1052751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	57	97	0	0.513514	0	G|0.863;A|0.137	0.137	strong	.	PLD2	138	.	NM_001243108	exon23	c.G2370A	p.L790L	CGTGCTGATCGAG	.	PASS	Atlas-SNP
PTGDR	5729	hgsc.bcm.edu	37	14	52735108	52735108	+	Silent	SNP	C	C	T	rs34968651	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	41	75	0	0.394231	0	C|0.932;T|0.068	0.068	strong	.	PTGDR	58	.	NM_000953	exon1	c.C576T	p.G192G	GGAGGGCTCGCTG	.	PASS	Atlas-SNP
ZNF468	90333	hgsc.bcm.edu	37	19	53344919	53344919	+	Missense_Mutation	SNP	T	T	G	rs58239286	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	82	186	0	0.503067	0	T|0.795;G|0.205	0.205	strong	.	ZNF468	46	.	NM_001008801	exon4	c.A628C	p.M210L	CTCTCATGTGTAC	.	PASS	Atlas-SNP
TMEM132D	121256	hgsc.bcm.edu	37	12	129559421	129559421	+	Missense_Mutation	SNP	C	C	T	rs73159540	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	99	214	1	0.515625	0.0046729	C|0.919;T|0.081	0.081	strong	.	TMEM132D	299	.	NM_133448	exon9	c.G2299A	p.V767I	CCTTGACCAGGGT	.	PASS	Atlas-SNP
ADORA3	140	hgsc.bcm.edu	37	1	112043139	112043139	+	Silent	SNP	G	G	A	rs2789537	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	18	124	0	0.253521	0	G|0.981;A|0.019	0.019	strong	.	ADORA3	104	.	NM_000677	exon2	c.C390T	p.A130A	GCCCAGGGCCAGC	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71347333	71347333	+	Missense_Mutation	SNP	C	C	T	rs72655156	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	409	185	398	1	0.452323	0.00251256	C|0.985;T|0.015	0.015	strong	.	MUC7	91	.	NM_001145007	exon4	c.C872T	p.T291I	CAACTACACCAGC	.	PASS	Atlas-SNP
EPHX1	2052	hgsc.bcm.edu	37	1	226019633	226019633	+	Missense_Mutation	SNP	T	T	C	rs1051740	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	120	86	0	0.991736	0	C|0.290;N|0.000	0.290	strong	.	EPHX1	57	.	NM_001136018	exon3	c.T337C	p.Y113H	AACAGATACCCTC	.	PASS	Atlas-SNP
IL17RD	54756	hgsc.bcm.edu	37	3	57136585	57136585	+	Missense_Mutation	SNP	C	C	T	rs17057718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	141	192	1	1	0.00520833	C|0.840;T|0.160	0.160	strong	.	IL17RD	93	.	NM_017563	exon10	c.G901A	p.V301M	TGGCCACGGCTCT	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95076771	95076771	+	Silent	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	24	98	0	0.266667	0	.	.	none	.	NOL8	118	.	NM_017948	exon7	c.T2136G	p.S712S	TGAATCAGACCGC	.	PASS	Atlas-SNP
SLC25A15	10166	hgsc.bcm.edu	37	13	41379272	41379272	+	Silent	SNP	C	C	T	rs9577152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	52	103	0	0.55914	0	C|0.883;T|0.117	0.117	strong	SLC25A15,NS,carcinoma,0,1	SLC25A15	30	1	NM_014252	exon4	c.C333T	p.A111A	TGCAGCCGCCGGT	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145539996	145539996	+	Silent	SNP	T	T	G	rs11540214	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	172	128	0	0.99422	0	T|0.793;G|0.207	0.207	strong	LARS,NS,carcinoma,0,2	LARS	100	2	NM_020117	exon7	c.A648C	p.S216S	GACAAATGAATCA	.	PASS	Atlas-SNP
EPSTI1	94240	hgsc.bcm.edu	37	13	43462435	43462435	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	4	229	3	0.0177778	0.0131004	.	.	none	EPSTI1,NS,carcinoma,+1,1	EPSTI1	47	1	NM_001002264	exon13	c.A1184G	p.E395G	ATGAGTTCAGGAA	.	scavenged	Atlas-SNP
C4orf36	132989	hgsc.bcm.edu	37	4	87809020	87809020	+	Missense_Mutation	SNP	C	C	G	rs72613147	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	60	126	0	0.48	0	C|0.864;G|0.136	0.136	strong	C4orf36,NS,carcinoma,0,1	C4orf36	10	1	NM_144645	exon4	c.G247C	p.V83L	GCTTCACTTCATA	.	PASS	Atlas-SNP
ANKAR	150709	hgsc.bcm.edu	37	2	190569908	190569908	+	Missense_Mutation	SNP	G	G	A	rs116660656	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	110	306	0	0.468085	0	G|0.983;A|0.017	0.017	strong	.	ANKAR	184	.	NM_144708	exon8	c.G1868A	p.C623Y	CTCTCTGTAGGAA	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs56376819		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	18	49	0	0.367347	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.A1778G	p.H593R	GCCAGATGAAGAG	.	PASS	Atlas-SNP
MICAL1	64780	hgsc.bcm.edu	37	6	109767396	109767396	+	Missense_Mutation	SNP	G	G	A	rs199541635	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	3	154	0	0.0205479	0	.	.	weak	MICAL1,NS,carcinoma,+1,1	MICAL1	79	1	NM_022765	exon19	c.C2524T	p.R842C	CGTGGCGGGCCAA	.	scavenged	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388553	1388553	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	14	251	3	0.061674	0.0119522	.	.	none	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.A254G	p.H85R	GTGCCCACCTGCT	.	scavenged	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170068086	170068086	+	Missense_Mutation	SNP	C	C	T	rs41265385	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	34	87	0	0.515152	0	C|0.840;T|0.160	0.160	strong	.	WDR27	129	.	NM_182552	exon5	c.G652A	p.G218S	TAAAGCCTCTGTC	.	PASS	Atlas-SNP
KIAA1279	26128	hgsc.bcm.edu	37	10	70748784	70748784	+	Missense_Mutation	SNP	G	G	A	rs2255607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	16	11	27	0	0.6875	0	G|0.584;A|0.416	0.416	strong	.	KIAA1279	35	.	NM_015634	exon1	c.G196A	p.G66S	GAGGACGGCCCGG	.	PASS	Atlas-SNP
YARS	8565	hgsc.bcm.edu	37	1	33245802	33245802	+	Silent	SNP	C	C	G	rs699005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	14	118	0	0.197183	0	C|0.899;G|0.101	0.101	strong	.	YARS	34	.	NM_003680	exon11	c.G1218C	p.L406L	CTGTACCAGGCCG	.	PASS	Atlas-SNP
NDUFA6	4700	hgsc.bcm.edu	37	22	42486723	42486723	+	Missense_Mutation	SNP	G	G	A	rs1801311	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	100	111	0	0.961538	0	G|0.625;A|0.375	0.375	strong	.	NDUFA6	13	.	NM_002490	exon1	c.C104T	p.A35V	GAAGTAGCTTGGC	.	PASS	Atlas-SNP
STON2	85439	hgsc.bcm.edu	37	14	81743565	81743565	+	Missense_Mutation	SNP	T	T	C	rs36017951	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	66	163	0	0.336735	0	T|0.961;C|0.039	0.039	strong	.	STON2	94	.	NM_001256430	exon6	c.A2090G	p.N697S	GCCCCATTGACAC	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062052	64062052	+	Missense_Mutation	SNP	G	G	A	rs10878074	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	60	160	0	0.410959	0	G|0.718;A|0.282	0.282	strong	.	DPY19L2	97	.	NM_173812	exon1	c.C122T	p.A41V	CCTAGGGCCGACT	.	PASS	Atlas-SNP
TUSC5	286753	hgsc.bcm.edu	37	17	1183612	1183612	+	Missense_Mutation	SNP	T	T	C	rs72816260	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	70	92	0	0.551181	0	T|0.994;C|0.006	0.006	strong	.	TUSC5	25	.	NM_172367	exon1	c.T317C	p.I106T	ACCTCATCCTGGC	.	PASS	Atlas-SNP
GLIS3	169792	hgsc.bcm.edu	37	9	4286248	4286248	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	55	149	0	0.37931	0	.	.	none	.	GLIS3	152	.	NM_001042413	exon2	c.C178A	p.L60I	TCTTGAGATGGAG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76488794	76488794	+	Silent	SNP	G	G	A	rs76641546	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	68	137	0	0.527132	0	G|0.994;A|0.006	0.006	strong	.	DNAH17	347	.	NM_173628	exon42	c.C6462T	p.A2154A	GTCCACGGCGACC	.	PASS	Atlas-SNP
KIAA1407	57577	hgsc.bcm.edu	37	3	113720517	113720517	+	Missense_Mutation	SNP	T	T	A	rs6784095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	310	310	355	0	1	0	T|0.883;A|0.117	0.117	strong	.	KIAA1407	80	.	NM_020817	exon13	c.A2088T	p.E696D	CTGACGTTCCTCC	.	PASS	Atlas-SNP
QSOX1	5768	hgsc.bcm.edu	37	1	180148012	180148012	+	Missense_Mutation	SNP	G	G	C	rs17855475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	97	131	0	0.617834	0	G|0.866;C|0.134	0.134	strong	.	QSOX1	79	.	NM_002826	exon5	c.G599C	p.G200A	ACCTGGGTAGAGA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150945483	150945483	+	Missense_Mutation	SNP	C	C	T	rs3734055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	68	160	0	0.492754	0	C|0.544;T|0.456	0.456	strong	.	FAT2	465	.	NM_001447	exon1	c.G3010A	p.G1004S	TCCCACCATCACT	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104123911	104123911	+	Silent	SNP	C	C	T	rs10778281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	22	76	0	0.44898	0	C|0.717;T|0.283	0.283	strong	.	STAB2	370	.	NM_017564	exon49	c.C5100T	p.N1700N	TATAAACAATAAG	.	PASS	Atlas-SNP
SCARF1	8578	hgsc.bcm.edu	37	17	1538669	1538669	+	Missense_Mutation	SNP	C	C	T	rs36108564	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	59	94	0	0.967213	0	C|0.913;T|0.087	0.087	strong	.	SCARF1	46	.	NM_003693	exon11	c.G1876A	p.G626S	CAGGACCCGACTG	.	PASS	Atlas-SNP
WIPF3	644150	hgsc.bcm.edu	37	7	29927688	29927688	+	Silent	SNP	C	C	T	rs61750796	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	16	42	0	0.202532	0	C|0.979;T|0.021	0.021	strong	.	WIPF3	46	.	NM_001080529	exon6	c.C1104T	p.A368A	AGGGGCCGGTGGG	.	PASS	Atlas-SNP
SP110	3431	hgsc.bcm.edu	37	2	231077110	231077110	+	Missense_Mutation	SNP	C	C	T	rs9061	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206	110	274	0	0.533981	0	C|0.895;T|0.105	0.105	strong	SP110,NS,carcinoma,0,1	SP110	105	1	NM_001185015	exon6	c.G637A	p.E213K	CTTCTTCCGCATT	.	PASS	Atlas-SNP
C12orf71	728858	hgsc.bcm.edu	37	12	27235381	27235381	+	Silent	SNP	G	G	A	rs708168	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	451	211	495	2	0.467849	0.0040404	G|0.820;A|0.180	0.180	strong	.	C12orf71	20	.	NM_001080406	exon1	c.C36T	p.D12D	GCTGTCGTCCTCT	.	PASS	Atlas-SNP
SPHKAP	80309	hgsc.bcm.edu	37	2	228855866	228855866	+	Missense_Mutation	SNP	G	G	C	rs16824283	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	70	149	0	0.411765	0	G|0.803;C|0.197	0.197	strong	SPHKAP_ENST00000392056,colon,carcinoma,0,2	SPHKAP	750	2	NM_001142644	exon11	c.C4809G	p.S1603R	CTGGGGGCTGGCT	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173516903	173516903	+	Silent	SNP	A	A	G	rs10494490	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	71	124	0	0.342995	0	A|0.637;G|0.363	0.363	strong	SLC9A11,NS,carcinoma,-2,1	.	.	1	NM_178527	exon13	c.T1482C	p.N494N	CATATCATTATGT	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595802	140595802	+	Missense_Mutation	SNP	T	T	C	rs17844618	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	37	83	0	0.480519	0	T|0.856;C|0.144	0.144	strong	.	PCDHB13	142	.	NM_018933	exon1	c.T2107C	p.F703L	TTCCTCTTTTCGG	.	PASS	Atlas-SNP
RASL12	51285	hgsc.bcm.edu	37	15	65357558	65357558	+	Silent	SNP	A	A	G	rs36045000	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	18	144	0	0.178218	0	A|0.987;G|0.013	0.013	strong	.	RASL12	32	.	NM_016563	exon2	c.T157C	p.L53L	TACCCAAGTTGGG	.	PASS	Atlas-SNP
ZNF345	25850	hgsc.bcm.edu	37	19	37368535	37368535	+	Missense_Mutation	SNP	G	G	C	rs112729744	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	70	123	0	0.534351	0	G|0.993;C|0.007	0.007	strong	.	ZNF345	68	.	NM_001242476	exon4	c.G803C	p.S268T	CCTTTAGTTTTGG	.	PASS	Atlas-SNP
FOXR1	283150	hgsc.bcm.edu	37	11	118851327	118851327	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	4	92	0	0.0307692	0	.	.	none	FOXR1,NS,carcinoma,-1,1	FOXR1	30	1	NM_181721	exon5	c.C739T	p.R247X	CGGCCTCGATCTT	.	scavenged	Atlas-SNP
OLA1	29789	hgsc.bcm.edu	37	2	174946760	174946760	+	Missense_Mutation	SNP	T	T	C	rs11558990	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	37	84	0	0.445783	0	T|0.841;C|0.159	0.159	strong	.	OLA1	37	.	NM_013341	exon8	c.A761G	p.Y254C	GGGTCATACTTGT	.	PASS	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	81	127	0	0.582734	0	A|0.692;G|0.308	0.308	strong	.	HBS1L	75	.	NM_006620	exon17	c.T1977C	p.F659F	CTCTTTAAAGTCT	.	PASS	Atlas-SNP
HDLBP	3069	hgsc.bcm.edu	37	2	242179134	242179134	+	Silent	SNP	G	G	A	rs10153800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	54	98	0	0.534653	0	G|0.800;A|0.200	0.200	strong	.	HDLBP	118	.	NM_005336	exon19	c.C2493T	p.G831G	CACCCCGCCATAC	.	PASS	Atlas-SNP
PJA2	9867	hgsc.bcm.edu	37	5	108714329	108714329	+	Missense_Mutation	SNP	C	C	T	rs144230886	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	3	180	2	0.017341	0.0111111	C|1.000;A|0.000	.	alt	PJA2,NS,carcinoma,+2,1	PJA2	53	1	NM_014819	exon4	c.G859A	p.A287T	CACAGGCTGCATC	.	scavenged	Atlas-SNP
SLC16A5	9121	hgsc.bcm.edu	37	17	73089852	73089852	+	Silent	SNP	T	T	C	rs4788863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	143	177	0	1	0	T|0.323;C|0.677	0.677	strong	SLC16A5_ENST00000450736,NS,carcinoma,0,2	SLC16A5	80	2	NM_001271765	exon3	c.T121C	p.L41L	ACTGAATTGCAAT	.	PASS	Atlas-SNP
CDH1	999	hgsc.bcm.edu	37	16	68855966	68855966	+	Missense_Mutation	SNP	G	G	A	rs35187787	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	21	171	0	0.130435	0	A|0.003;G|0.997	0.003	strong	CDH1,NS,carcinoma,0,4	CDH1	535	4	NM_004360	exon12	c.G1774A	p.A592T	GACAACGCCCCCA	.	PASS	Atlas-SNP
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18504916	18504916	+	Silent	SNP	T	T	A	rs2277160	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	40	38	0	0.930233	0	T|0.415;A|0.585	0.585	strong	.	ADAMTSL1	306	.	NM_052866	exon2	c.T153A	p.G51G	CGGGGGTGGGGCC	.	PASS	Atlas-SNP
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331625	21331625	+	Silent	SNP	C	C	T	rs2291075	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	192	226	1	0.994819	0.00442478	C|0.548;T|0.452	0.452	strong	SLCO1B1,NS,carcinoma,+2,1	SLCO1B1	151	1	NM_006446	exon6	c.C597T	p.F199F	TGATTTCGCTAAA	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39424253	39424253	+	Missense_Mutation	SNP	C	C	G	rs9548506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	47	124	0	0.456311	0	C|0.913;G|0.087	0.087	strong	.	FREM2	385	.	NM_207361	exon9	c.C6458G	p.T2153S	ATAGGACTGGGGA	.	PASS	Atlas-SNP
TYK2	7297	hgsc.bcm.edu	37	19	10463118	10463118	+	Missense_Mutation	SNP	G	G	C	rs34536443	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	160	213	1	0.615385	0.00469484	G|0.975;C|0.025	0.025	strong	.	TYK2	126	.	NM_003331	exon23	c.C3310G	p.P1104A	TGGGGGGGCTCTG	.	PASS	Atlas-SNP
VPS53	55275	hgsc.bcm.edu	37	17	534812	534812	+	Missense_Mutation	SNP	G	G	A	rs138639431	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	47	98	0	0.431193	0	G|1.000;A|0.000	0.000	strong	.	VPS53	109	.	NM_001128159	exon8	c.C665T	p.A222V	GGAAACGCTTCTT	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	37	7	78119109	78119109	+	Silent	SNP	C	C	T	rs3735442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259	159	245	1	0.6139	0.00408163	C|0.670;T|0.330	0.330	strong	.	MAGI2	246	.	NM_012301	exon6	c.G1014A	p.K338K	TTTAGCCTTTTTC	.	PASS	Atlas-SNP
PHTF2	57157	hgsc.bcm.edu	37	7	77569559	77569559	+	Silent	SNP	C	C	T	rs1064040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	55	165	0	0.308989	0	C|0.980;T|0.020	0.020	strong	.	PHTF2	104	.	NM_001127357	exon12	c.C1578T	p.R526R	GGTTCGCGTGTCT	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130189719	130189719	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	2	104	0	0.0215054	0	.	.	none	FLJ35880,rectum,carcinoma,+1,4	COL6A5	205	4	NM_153264	exon39	c.C7482T	p.A2494A	AGGTGCCATCAAC	.	scavenged	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79954545	79954545	+	Silent	SNP	T	T	C	rs7025532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	105	147	0	0.981308	0	T|0.818;C|0.182	0.182	strong	.	VPS13A	735	.	NM_001018038	exon48	c.T6492C	p.D2164D	TCACGATTGGAAA	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48315930	48315930	+	Missense_Mutation	SNP	G	G	C	rs74859514	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	148	141	0	1	0	G|0.939;C|0.061	0.061	strong	.	ABCA13	1192	.	NM_152701	exon17	c.G6667C	p.A2223P	CAGGAAGCAGCTT	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5444150	5444150	+	Silent	SNP	C	C	T	rs118011081	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	74	154	0	0.573643	0	C|0.985;T|0.015	0.015	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.C720T	p.L240L	TGCCCTCAATAAC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280759	152280759	+	Silent	SNP	A	A	G	rs2338554	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	641	104	349	2	0.162246	0.00573066	A|0.718;G|0.282	0.282	strong	FLG,NS,carcinoma,-2,2	FLG	900	2	NM_002016	exon3	c.T6603C	p.D2201D	AGAGCCATCTCCT	.	scavenged	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105344293	105344293	+	Silent	SNP	C	C	T	rs61995995	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	82	95	0	0.602941	0	C|0.592;T|0.408	0.408	strong	.	.	.	.	NM_001112726	exon4	c.C267T	p.F89F	CCGCTTCGGCTAC	.	PASS	Atlas-SNP
BHLHE40	8553	hgsc.bcm.edu	37	3	5024771	5024771	+	Silent	SNP	T	T	C	rs908078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	51	59	0	1	0	T|0.855;C|0.145	0.145	strong	.	BHLHE40	35	.	NM_003670	exon5	c.T633C	p.G211G	CAAAGGTTCGGAA	.	PASS	Atlas-SNP
TMPRSS11E	28983	hgsc.bcm.edu	37	4	69337325	69337325	+	Missense_Mutation	SNP	C	C	G	rs2603188	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	321	156	397	1	0.485981	0.00251889	C|0.887;G|0.113	0.113	strong	.	TMPRSS11E	40	.	NM_014058	exon5	c.C474G	p.H158Q	TCCTCACTCAGTT	.	PASS	Atlas-SNP
CNTN4	152330	hgsc.bcm.edu	37	3	3067853	3067853	+	Silent	SNP	G	G	A	rs7639977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	93	248	0	0.486911	0	G|0.858;A|0.142	0.142	strong	.	CNTN4	335	.	NM_175607	exon15	c.G1554A	p.P518P	TTTACCGTGCCAG	.	PASS	Atlas-SNP
DNMT3L	29947	hgsc.bcm.edu	37	21	45670770	45670770	+	Missense_Mutation	SNP	T	T	C	rs7354779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	138	196	0	0.613333	0	T|0.786;C|0.214	0.214	strong	.	DNMT3L	33	.	NM_013369	exon10	c.A832G	p.R278G	AGGGCCTGGGGCT	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127230891	127230891	+	Missense_Mutation	SNP	G	G	A	rs10760365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	66	132	0	0.481752	0	G|0.465;A|0.535	0.535	strong	.	GPR144	33	.	NM_001161808	exon14	c.G2248A	p.V750M	AGGAAGGTGGTAG	.	PASS	Atlas-SNP
TSGA13	114960	hgsc.bcm.edu	37	7	130368440	130368440	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	2	203	0	0.0148148	0	.	.	none	TSGA13,NS,carcinoma,+1,1	TSGA13	35	1	NM_052933	exon3	c.A94G	p.S32G	CTTTGCTATTGAC	.	scavenged	Atlas-SNP
RBM46	166863	hgsc.bcm.edu	37	4	155720274	155720274	+	Silent	SNP	T	T	C	rs156502	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	24	142	0	0.26087	0	T|0.395;C|0.605	0.605	strong	.	RBM46	76	.	NM_144979	exon4	c.T960C	p.N320N	TCTTAATGGTCAG	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152188847	152188847	+	Missense_Mutation	SNP	A	A	G	rs145667921		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	985	82	1390	64	0.0832487	0.0460432	.	.	weak	HRNR,NS,carcinoma,0,1	HRNR	403	1	NM_001009931	exon3	c.T5258C	p.V1753A	CCAAAGACAGAAG	.	scavenged	Atlas-SNP
BNC2	54796	hgsc.bcm.edu	37	9	16435714	16435714	+	Silent	SNP	T	T	C	rs3739715	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	87	216	1	0.480663	0.00462963	T|0.903;C|0.097	0.097	strong	.	BNC2	166	.	NM_017637	exon6	c.A2478G	p.L826L	AGAACATAGGTCA	.	PASS	Atlas-SNP
SLC16A8	23539	hgsc.bcm.edu	37	22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	rs75640043	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	44	94	0	0.956522	0	G|0.951;A|0.049	0.049	strong	SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	NM_013356	exon4	c.C770T	p.A257V	GTGACGGCGTACA	.	PASS	Atlas-SNP
KRT5	3852	hgsc.bcm.edu	37	12	52911401	52911401	+	Silent	SNP	T	T	G	rs4761924	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	49	108	0	0.515789	0	T|0.856;G|0.144	0.144	strong	.	KRT5	88	.	NM_000424	exon5	c.A1065C	p.T355T	GGCTTCTGTCCGG	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38121152	38121152	+	Missense_Mutation	SNP	C	C	A	rs9610841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	74	206	1	0.496644	0.00485437	C|0.623;A|0.377	0.377	strong	TRIOBP_ENST00000344404,NS,carcinoma,+1,1	TRIOBP	262	1	NM_001039141	exon7	c.C2589A	p.N863K	AGACAACCCTGGA	.	PASS	Atlas-SNP
CNKSR3	154043	hgsc.bcm.edu	37	6	154763401	154763401	+	Silent	SNP	G	G	A	rs6557351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	38	104	0	0.457831	0	G|0.660;A|0.340	0.340	strong	CNKSR3,NS,carcinoma,0,1	CNKSR3	56	1	NM_173515	exon3	c.C240T	p.N80N	CTTCATGTTATCA	.	PASS	Atlas-SNP
ANGPT4	51378	hgsc.bcm.edu	37	20	854940	854940	+	Silent	SNP	T	T	C	rs944110	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	269	132	288	1	0.490706	0.00347222	T|0.549;C|0.451	0.451	strong	ANGPT4,colon,carcinoma,0,2	ANGPT4	77	2	NM_015985	exon8	c.A1338G	p.Q446Q	CATCACTTGGGCA	.	PASS	Atlas-SNP
ITGA4	3676	hgsc.bcm.edu	37	2	182395345	182395345	+	Missense_Mutation	SNP	G	G	A	rs1143676	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	233	229	205	1	0.982833	0.00487805	G|0.258;A|0.742	0.742	strong	.	ITGA4	142	.	NM_000885	exon24	c.G2633A	p.R878Q	TAGTCCGGTTCTT	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197432029	197432029	+	Silent	SNP	C	C	A	rs60457064	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	45	72	0	0.661765	0	C|0.877;A|0.123	0.123	strong	.	KIAA0226	136	.	NM_014687	exon3	c.G237T	p.T79T	GTAATCCGTCTGG	.	PASS	Atlas-SNP
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77510008	77510008	+	Silent	SNP	C	C	A	rs35763299	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	19	111	0	0.292308	0	T|0.009;C|0.980;A|0.010	0.010	strong	.	ST6GALNAC5	59	.	NM_030965	exon3	c.C381A	p.P127P	CGCCCCCACACGC	.	PASS	Atlas-SNP
CASP8	841	hgsc.bcm.edu	37	2	202149589	202149589	+	Missense_Mutation	SNP	G	G	C	rs1045485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	29	185	0	0.254386	0	G|0.901;C|0.099	0.099	strong	.	CASP8	272	.	NM_001080125	exon8	c.G1030C	p.D344H	CCCCACGATGACT	.	PASS	Atlas-SNP
KLHL36	79786	hgsc.bcm.edu	37	16	84695280	84695280	+	Silent	SNP	A	A	G	rs17755815	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	103	123	1	0.837398	0.00813008	A|0.757;G|0.243	0.243	strong	KLHL36,NS,carcinoma,0,1	KLHL36	51	1	NM_024731	exon5	c.A1392G	p.L464L	CCTGCTATGCTAC	.	PASS	Atlas-SNP
TINAG	27283	hgsc.bcm.edu	37	6	54173413	54173413	+	Missense_Mutation	SNP	A	A	G	rs2297980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	77	174	0	0.531034	0	A|0.911;G|0.089	0.089	strong	.	TINAG	102	.	NM_014464	exon1	c.A65G	p.Q22R	AGAAGCAGTATTT	.	PASS	Atlas-SNP
ABHD12B	145447	hgsc.bcm.edu	37	14	51370852	51370852	+	Missense_Mutation	SNP	C	C	G	rs34800262	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	336	197	267	1	0.58631	0.00374532	C|0.912;G|0.088	0.088	strong	ABHD12B_ENST00000337334,right_upper_lobe,carcinoma,-1,2	ABHD12B	53	2	NM_001206673	exon12	c.C1003G	p.P335A	ATCTTTCCTCCTG	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91726927	91726927	+	Silent	SNP	A	A	C	rs1063243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	259	223	1	0.984791	0.00448431	A|0.588;C|0.412	0.412	strong	AKAP9_ENST00000356239,NS,carcinoma,-1,2	AKAP9	788	2	NM_005751	exon42	c.A10426C	p.R3476R	AGTGATAGAACTA	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21607253	21607253	+	Missense_Mutation	SNP	A	A	G	rs150159158		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	11	75	0	0.169231	0	.	.	weak	.	ZNF493	178	.	NM_001076678	exon4	c.A1792G	p.K598E	ACTGATAAGAAAC	.	PASS	Atlas-SNP
ZNF80	7634	hgsc.bcm.edu	37	3	113955753	113955753	+	Missense_Mutation	SNP	C	C	T	rs146464395	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	61	128	0	0.54955	0	C|0.991;T|0.009	0.009	strong	.	ZNF80	75	.	NM_007136	exon1	c.G169A	p.V57M	TAAACACGCTCCC	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2816224	2816224	+	Missense_Mutation	SNP	C	C	T	rs151100831	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	2	116	0	0.0163934	0	C|0.999;A|0.001	.	alt	SRRM2,colon,carcinoma,0,1	SRRM2	263	1	NM_016333	exon11	c.C5695T	p.R1899W	CGGAGACGGTCAA	.	scavenged	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10447168	10447168	+	Missense_Mutation	SNP	C	C	G	rs66538112	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	43	103	0	0.477778	0	C|0.795;G|0.205	0.205	strong	.	ZNF518B	116	.	NM_053042	exon3	c.G785C	p.G262A	GAGAAACCTGACA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1075850	1075850	+	Silent	SNP	G	G	A	rs11825969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	63	113	0	0.557522	0	G|0.844;A|0.156	0.156	strong	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon2	c.G276A	p.E92E	GGTGGAGTCCATC	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86909493	86909493	+	Silent	SNP	C	C	T	rs2390059	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	14	99	0	0.225806	0	T|0.113;G|0.000;C|0.887	0.113	strong	.	CLCA2	102	.	NM_006536	exon10	c.C1512T	p.V504V	AAATGTCAAACCT	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218674614	218674614	+	Silent	SNP	C	C	T	rs13417442	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	178	300	0	0.946809	0	C|0.934;T|0.066	0.066	strong	.	TNS1	251	.	NM_022648	exon30	c.G4893A	p.T1631T	AGCTGGCGTGGGG	.	PASS	Atlas-SNP
ABHD5	51099	hgsc.bcm.edu	37	3	43732496	43732496	+	Silent	SNP	G	G	A	rs141365045	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	18	27	0	0.666667	0	G|0.979;A|0.021	0.021	strong	.	ABHD5	33	.	NM_016006	exon1	c.G12A	p.E4E	GGCGGAGGAGGAG	.	PASS	Atlas-SNP
GLRX3	10539	hgsc.bcm.edu	37	10	131959150	131959150	+	Missense_Mutation	SNP	C	C	T	rs2274217	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	33	73	0	0.52381	0	C|0.799;T|0.201	0.201	strong	TXNL2,colon,carcinoma,0,2	GLRX3	39	2	NM_006541	exon4	c.C367T	p.P123S	TTCCTACCCAGCG	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169511555	169511555	+	Missense_Mutation	SNP	T	T	C	rs6032	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	237	184	1	1	0.00543478	T|0.758;C|0.242	0.242	strong	F5,colon,carcinoma,+2,1	F5	301	1	NM_000130	exon13	c.A2773G	p.K925E	GGTCCTTCCAGGG	.	PASS	Atlas-SNP
XPO7	23039	hgsc.bcm.edu	37	8	21847855	21847855	+	Silent	SNP	G	G	C	rs56062629	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	75	159	0	0.303644	0	G|0.938;C|0.062	0.062	strong	.	XPO7	79	.	NM_015024	exon17	c.G1869C	p.G623G	CTTCACGTACAGT	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118198	93118198	+	Silent	SNP	C	C	T	rs3814830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	55	110	0	0.639535	0	C|0.764;T|0.236	0.236	strong	.	RIN3	81	.	NM_024832	exon6	c.C804T	p.A268A	TGATGCCACCTCA	.	PASS	Atlas-SNP
SIGLEC15	284266	hgsc.bcm.edu	37	18	43422149	43422149	+	Silent	SNP	G	G	A	rs143689799	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	61	131	0	0.530435	0	G|0.997;A|0.003	0.003	strong	.	SIGLEC15	10	.	NM_213602	exon6	c.G984A	p.P328P	CTCACCGTGAGGA	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104066461	104066461	+	Missense_Mutation	SNP	A	A	G	rs2615542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	38	64	0	0.475	0	A|0.848;G|0.152	0.152	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon32	c.T4603C	p.F1535L	TATTAAATTGTTC	.	PASS	Atlas-SNP
MROH7	374977	hgsc.bcm.edu	37	1	55119144	55119144	+	Missense_Mutation	SNP	A	A	G	rs11206407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	78	142	0	0.987342	0	A|0.655;G|0.344	0.344	strong	HEATR8_ENST00000421030,colon,carcinoma,0,2	.	.	2	NM_001039464	exon3	c.A545G	p.H182R	GGCACCATTCCAG	.	PASS	Atlas-SNP
PGR	5241	hgsc.bcm.edu	37	11	100998771	100998771	+	Missense_Mutation	SNP	C	C	G	rs3740753	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	23	10	48	0	0.434783	0	C|0.884;G|0.116	0.116	strong	.	PGR	115	.	NM_000926	exon1	c.G1031C	p.S344T	GGTGAACTCCGCG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168103304	168103304	+	Missense_Mutation	SNP	G	G	A	rs16853309	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	83	199	0	0.434555	0	G|0.820;A|0.180	0.180	strong	.	XIRP2	914	.	NM_152381	exon9	c.G5402A	p.R1801H	TTGAACGTACTGT	.	PASS	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	37	13	25440318	25440318	+	Missense_Mutation	SNP	G	G	A	rs9507425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	160	332	1	0.506329	0.00301205	G|0.778;A|0.222	0.222	strong	.	RNF17	259	.	NM_031277	exon30	c.G4138A	p.E1380K	GAAGAGGAACAAT	.	PASS	Atlas-SNP
SULT1A2	6799	hgsc.bcm.edu	37	16	28607196	28607196	+	Missense_Mutation	SNP	G	G	A	rs10797300	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	273	137	142	0	0.501832	0	G|0.903;A|0.097	0.097	strong	.	SULT1A2	27	.	NM_001054	exon2	c.C56T	p.P19L	ATGAGCGGGACCC	.	PASS	Atlas-SNP
ESR2	2100	hgsc.bcm.edu	37	14	64724051	64724051	+	Silent	SNP	C	C	T	rs1256049	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	57	125	0	0.339286	0	C|0.909;T|0.091	0.091	strong	ESR2,NS,carcinoma,0,1	ESR2	82	1	NM_001214902	exon5	c.G984A	p.V328V	GAGCCGCACTTGG	.	PASS	Atlas-SNP
CFHR5	81494	hgsc.bcm.edu	37	1	196967354	196967354	+	Missense_Mutation	SNP	G	G	A	rs35662416	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	315	204	281	1	0.647619	0.00355872	G|0.979;A|0.021	0.021	strong	CFHR5_ENST00000367414,NS,carcinoma,+1,2	CFHR5	150	2	NM_030787	exon7	c.G1067A	p.R356H	GAATACGTTACAG	.	PASS	Atlas-SNP
TRIM22	10346	hgsc.bcm.edu	37	11	5729419	5729419	+	Silent	SNP	T	T	C	rs112606816	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	26	103	0	0.45614	0	A|0.000;C|0.006;T|0.993	0.006	strong	.	TRIM22	66	.	NM_006074	exon6	c.T790C	p.L264L	TGGACATTGAAGA	.	PASS	Atlas-SNP
SPNS3	201305	hgsc.bcm.edu	37	17	4391152	4391152	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	3	178	1	0.0198676	0.00561798	.	.	none	SPNS3,NS,carcinoma,-1,1	SPNS3	52	1	NM_182538	exon12	c.T1502C	p.L501P	AAGGCCTACTTTC	.	scavenged	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115004914	115004914	+	Silent	SNP	C	C	T	rs2296971	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	76	86	0	0.938272	0	C|0.562;T|0.438	0.438	strong	.	CDC16	50	.	NM_003903	exon5	c.C330T	p.D110D	GAAGGACGAAAGT	.	PASS	Atlas-SNP
BANP	54971	hgsc.bcm.edu	37	16	88066717	88066717	+	Missense_Mutation	SNP	C	C	T	rs74992447	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	54	318	0	0.188153	0	C|0.875;T|0.125	0.125	strong	BANP,rectum,carcinoma,-1,1	BANP	67	1	NM_001173542	exon9	c.C1066T	p.P356S	ACAGAGCCGATGA	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22940659	22940659	+	Silent	SNP	C	C	T	rs59621958	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	28	75	0	0.466667	0	C|0.826;T|0.174	0.174	strong	.	ZNF99	273	.	NM_001080409	exon4	c.G2052A	p.K684K	AAAAGCCTTGCCA	.	PASS	Atlas-SNP
JSRP1	126306	hgsc.bcm.edu	37	19	2252990	2252990	+	Missense_Mutation	SNP	C	C	G	rs80043033	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	34	110	0	0.485714	0	C|0.842;G|0.158	0.158	strong	.	JSRP1	18	.	NM_144616	exon6	c.G449C	p.G150A	GCCTCCCCAGGGA	.	PASS	Atlas-SNP
CLRN2	645104	hgsc.bcm.edu	37	4	17524570	17524570	+	Missense_Mutation	SNP	C	C	G	rs13147559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	63	141	0	0.5	0	C|0.904;G|0.095	0.095	strong	.	CLRN2	40	.	NM_001079827	exon2	c.C337G	p.L113V	CTGGCTCTGGTCA	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39263023	39263023	+	Silent	SNP	C	C	T	rs12874397	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	37	67	0	0.587302	0	C|0.841;T|0.159	0.159	strong	.	FREM2	385	.	NM_207361	exon1	c.C1542T	p.A514A	GGCAGCCGGCCAG	.	PASS	Atlas-SNP
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56704101	56704101	+	Silent	SNP	G	G	A	rs61747508	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	706	272	645	1	0.385269	0.00155039	G|0.869;A|0.131	0.131	strong	.	ZSCAN5B	160	.	NM_001080456	exon1	c.C321T	p.N107N	CACACCGTTCACC	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32598656	32598656	+	Silent	SNP	C	C	T	rs2290214	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	110	164	1	0.617977	0.00609756	C|0.781;T|0.219	0.219	strong	.	AVL9	66	.	NM_015060	exon10	c.C795T	p.S265S	TGCATCCACTGCT	.	PASS	Atlas-SNP
SERPINE2	5270	hgsc.bcm.edu	37	2	224866387	224866387	+	Silent	SNP	G	G	A	rs12138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	42	94	0	0.494118	0	T|0.040;G|0.683;C|0.156;A|0.120	0.120	strong	.	SERPINE2	103	.	NM_001136530	exon2	c.C267T	p.L89L	CATGGCGAGCTGC	.	PASS	Atlas-SNP
KLRC3	3823	hgsc.bcm.edu	37	12	10573094	10573094	+	Missense_Mutation	SNP	C	C	G	rs34195537	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211	140	176	1	0.663507	0.00568182	C|0.500;G|0.500	0.500	weak	.	KLRC3	25	.	NM_007333	exon1	c.G56C	p.W19S	TGCTGCCACTTTG	.	PASS	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98244242	98244242	+	Silent	SNP	T	T	C	rs1805154	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	45	106	0	0.473684	0	T|0.976;C|0.024	0.024	strong	.	PTCH1	1850	.	NM_000264	exon5	c.A735G	p.T245T	GTATGCTGTCCCA	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52863564	52863564	+	Silent	SNP	C	C	T	rs3894847	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	92	269	1	0.453202	0.00371747	C|0.788;T|0.212	0.212	strong	.	KRT6C	55	.	NM_173086	exon7	c.G1314A	p.K438K	GTCCTGCTTGGCC	.	PASS	Atlas-SNP
CYP26C1	340665	hgsc.bcm.edu	37	10	94824166	94824166	+	Missense_Mutation	SNP	G	G	A	rs11187265	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	29	116	0	0.305263	0	G|0.914;A|0.086	0.086	strong	.	CYP26C1	25	.	NM_183374	exon4	c.G734A	p.R245Q	TGCATCGGCACCT	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52193088	52193088	+	Missense_Mutation	SNP	C	C	T	rs6063966	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	43	125	1	0.373913	0.008	C|0.859;T|0.141	0.141	strong	ZNF217,NS,carcinoma,0,1	ZNF217	227	1	NM_006526	exon3	c.G2215A	p.V739I	TATGAACGTCAGG	.	scavenged	Atlas-SNP
ZNF283	284349	hgsc.bcm.edu	37	19	44351694	44351694	+	Missense_Mutation	SNP	C	C	T	rs2195980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	77	143	0	0.578947	0	C|0.206;T|0.794	0.794	strong	.	ZNF283	83	.	NM_181845	exon7	c.C941T	p.T314I	TTCATACTGGTGT	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1729958	1729958	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	59	67	0	0.621053	0	.	.	none	.	TACC3	69	.	NM_006342	exon4	c.G829T	p.A277S	TGCCCTGCGGGTG	.	PASS	Atlas-SNP
LTA4H	4048	hgsc.bcm.edu	37	12	96408716	96408716	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	8	148	0	0.0432432	0	.	.	none	.	LTA4H	38	.	NM_000895	exon12	c.A1121G	p.D374G	TCAGGGTCTATAT	.	PASS	Atlas-SNP
KDM4B	23030	hgsc.bcm.edu	37	19	5110794	5110794	+	Silent	SNP	A	A	G	rs2613739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	26	104	0	0.342105	0	A|0.406;G|0.594	0.594	strong	.	KDM4B	120	.	NM_015015	exon10	c.A1080G	p.A360A	GAGTGCATCCCGG	.	PASS	Atlas-SNP
TRIM6-TRIM34	445372	hgsc.bcm.edu	37	11	5664831	5664831	+	Silent	SNP	C	C	A	rs3740998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	130	247	0	0.534979	0	C|0.716;A|0.284	0.284	strong	.	TRIM6-TRIM34	68	.	NM_001003819	exon14	c.C2421A	p.G807G	CCATGGCTCCCTC	.	PASS	Atlas-SNP
SAMM50	25813	hgsc.bcm.edu	37	22	44372632	44372632	+	Silent	SNP	C	C	T	rs17850259		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	66	152	0	0.415094	0	.	.	weak	SAMM50,NS,carcinoma,0,1	SAMM50	30	1	NM_015380	exon9	c.C780T	p.H260H	TCAGCACGCCATG	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183721088	183721088	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	5	198	0	0.049505	0	.	.	none	.	.	.	.	NM_001080477	exon27	c.C7684T	p.L2562L	GGCACGCTGCGGT	.	PASS	Atlas-SNP
KIAA1549L	25758	hgsc.bcm.edu	37	11	33581306	33581306	+	Silent	SNP	G	G	A	rs2281380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	88	213	0	0.458333	0	G|0.613;A|0.387	0.387	strong	.	.	.	.	NM_012194	exon6	c.G2976A	p.T992T	GAGCACGTCCAAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682094	100682094	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	8	198	0	0.0321285	0	.	.	none	MUC17,NS,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.C7397G	p.T2466R	GCACCACGCCGGT	.	scavenged	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248834	48248834	+	Silent	SNP	T	T	C	rs10404034	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	58	162	0	0.467742	0	A|0.000;C|0.097;T|0.903	0.097	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.T18C	p.S6S	AGGCAGTGGCGTT	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90500067	90500067	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	6	114	0	0.0461538	0	.	.	none	.	MDN1	478	.	NM_014611	exon6	c.G909A	p.V303V	AACCAGCACATAA	.	PASS	Atlas-SNP
NPEPL1	79716	hgsc.bcm.edu	37	20	57282190	57282190	+	Silent	SNP	G	G	A	rs41310841	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	85	192	1	0.467033	0.00520833	G|0.947;A|0.053	0.053	strong	NPEPL1,NS,carcinoma,0,1	NPEPL1	36	1	NM_024663	exon7	c.G834A	p.P278P	CATGCCGGGGATG	.	scavenged	Atlas-SNP
ZCCHC2	54877	hgsc.bcm.edu	37	18	60231851	60231851	+	Silent	SNP	A	A	G	rs12956093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	87	188	0	0.537037	0	A|0.878;G|0.122	0.122	strong	.	ZCCHC2	64	.	NM_017742	exon10	c.A1734G	p.G578G	GAAAGGAAAGCCA	.	PASS	Atlas-SNP
ITIH2	3698	hgsc.bcm.edu	37	10	7759736	7759736	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	86	154	0	0.704918	0	.	.	none	.	ITIH2	144	.	NM_002216	exon6	c.G615A	p.L205L	ACGGCTGGCCAAA	.	PASS	Atlas-SNP
ZCCHC11	23318	hgsc.bcm.edu	37	1	52956410	52956410	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	3	246	0	0.0192308	0	.	.	none	ZCCHC11,NS,carcinoma,0,2	ZCCHC11	151	2	NM_015269	exon8	c.G1382A	p.R461Q	CTTTTTCGATCTC	.	scavenged	Atlas-SNP
ASTN1	460	hgsc.bcm.edu	37	1	176992553	176992553	+	Silent	SNP	A	A	G	rs172917	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	280	278	204	1	0.992857	0.00490196	A|0.423;G|0.577	0.577	strong	.	ASTN1	314	.	NM_004319	exon7	c.T1425C	p.C475C	GGGGTCACATTGG	.	PASS	Atlas-SNP
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156027	39156027	+	Missense_Mutation	SNP	G	G	A	rs3829598	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	136	240	1	0.555102	0.00416667	G|0.865;A|0.135	0.135	strong	.	KRTAP3-2	11	.	NM_031959	exon1	c.C79T	p.R27C	CACAGCGGCAGGA	.	PASS	Atlas-SNP
DDX54	79039	hgsc.bcm.edu	37	12	113600940	113600940	+	Missense_Mutation	SNP	C	C	T	rs11564	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	45	101	0	0.436893	0	C|0.954;T|0.046	0.046	strong	.	DDX54	73	.	NM_024072	exon16	c.G2078A	p.R693Q	CACCCCCGCTCGC	.	PASS	Atlas-SNP
SERPINF1	5176	hgsc.bcm.edu	37	17	1674429	1674429	+	Silent	SNP	T	T	C	rs8074840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	44	115	1	0.407407	0.00869565	T|0.735;C|0.265	0.265	strong	SERPINF1,NS,carcinoma,0,1	SERPINF1	31	1	NM_002615	exon4	c.T390C	p.T130T	GGTCACTGCCCCC	.	scavenged	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151970797	151970797	+	Silent	SNP	A	A	T	rs141993954	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	827	120	909	2	0.145103	0.00220022	A|0.985;T|0.015	0.015	strong	MLL3_ENST00000355193,NS,adenoma,0,4	MLL3	1564	4	NM_170606	exon7	c.T1005A	p.P335P	TCTTTCAGGAGCT	.	scavenged	Atlas-SNP
PTCHD3	374308	hgsc.bcm.edu	37	10	27702169	27702169	+	Silent	SNP	C	C	T	rs6482625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	18	146	0	0.222222	0	C|0.765;T|0.235	0.235	strong	.	PTCHD3	140	.	NM_001034842	exon1	c.G1011A	p.V337V	GCTCTGCACGTCG	.	PASS	Atlas-SNP
OR1C1	26188	hgsc.bcm.edu	37	1	247921412	247921412	+	Silent	SNP	G	G	C	rs41304163	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	94	137	0	0.594937	0	G|0.952;C|0.048	0.048	strong	.	OR1C1	86	.	NM_012353	exon1	c.C297G	p.T99T	GAGCTGGGTGAGG	.	PASS	Atlas-SNP
RNF121	55298	hgsc.bcm.edu	37	11	71701763	71701763	+	Silent	SNP	G	G	A	rs35844388	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	58	152	0	0.483333	0	G|0.972;A|0.028	0.028	strong	.	RNF121	19	.	NM_018320	exon6	c.G627A	p.G209G	CATAGGGGTAAGT	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50502469	50502469	+	Silent	SNP	A	A	G	rs11568190	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	12	166	0	0.131868	0	A|0.901;G|0.099	0.099	strong	MLC1,caecum,carcinoma,0,2	MLC1	48	2	NM_015166	exon11	c.T1053C	p.A351A	CTCCCCAGCCAGG	.	PASS	Atlas-SNP
CCDC101	112869	hgsc.bcm.edu	37	16	28602991	28602991	+	Silent	SNP	A	A	G	rs11401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	44	82	0	0.488889	0	A|0.832;G|0.168	0.168	strong	.	CCDC101	24	.	NM_138414	exon10	c.A846G	p.R282R	TCAGAGATACGTG	.	PASS	Atlas-SNP
CDC42BPB	9578	hgsc.bcm.edu	37	14	103440473	103440473	+	Silent	SNP	G	G	C	rs8009219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	28	55	0	0.282828	0	G|0.410;C|0.589	0.589	strong	.	CDC42BPB	123	.	NM_006035	exon12	c.C1521G	p.L507L	TCGCTCGAGCCTG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264772	1264772	+	Missense_Mutation	SNP	T	T	C	rs2943500	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	375	15	391	1	0.04	0.00255754	.	.	weak	MUC5B,NS,neuroblastoma,0,3	MUC5B	473	3	NM_002458	exon31	c.T6662C	p.I2221T	CGGGCATCTTGGG	.	scavenged	Atlas-SNP
OR4L1	122742	hgsc.bcm.edu	37	14	20528496	20528496	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	2	126	0	0.0105263	0	.	.	none	OR4L1,NS,carcinoma,+1,1	OR4L1	98	1	NM_001004717	exon1	c.T293A	p.V98E	GCTGCGTGACCCA	.	scavenged	Atlas-SNP
QSOX2	169714	hgsc.bcm.edu	37	9	139115921	139115921	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	4	152	0	0.0239521	0	.	.	none	QSOX2,NS,carcinoma,0,1	QSOX2	63	1	NM_181701	exon4	c.G516A	p.M172I	GTCAATCATCGTC	.	scavenged	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8168545	8168545	+	Missense_Mutation	SNP	C	C	T	rs33967815	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	109	221	0	0.547739	0	C|0.769;T|0.231	0.231	strong	.	FBN3	300	.	NM_032447	exon38	c.G4840A	p.G1614S	AGATGCCGGAGTG	.	PASS	Atlas-SNP
TNIP1	10318	hgsc.bcm.edu	37	5	150410219	150410219	+	Missense_Mutation	SNP	C	C	A	rs2233311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	34	70	0	0.478873	0	G|0.000;C|0.890;A|0.109	0.109	strong	.	TNIP1	51	.	NM_001252393	exon18	c.G1892T	p.R631I	GGCAATCTGAGAT	.	PASS	Atlas-SNP
ADSSL1	122622	hgsc.bcm.edu	37	14	105211221	105211221	+	Silent	SNP	C	C	T	rs12432802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	43	122	0	0.257485	0	C|0.882;T|0.118	0.118	strong	.	ADSSL1	37	.	NM_199165	exon11	c.C1275T	p.N425N	GCTGAACGGGAAA	.	PASS	Atlas-SNP
C14orf79	122616	hgsc.bcm.edu	37	14	105457923	105457923	+	Missense_Mutation	SNP	T	T	A	rs61745867	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	69	116	0	0.433962	0	T|0.990;A|0.010	0.010	strong	.	C14orf79	13	.	NM_174891	exon3	c.T665A	p.F222Y	AGAACTTCTTTCT	.	PASS	Atlas-SNP
TAPBPL	55080	hgsc.bcm.edu	37	12	6562836	6562836	+	Silent	SNP	G	G	A	rs2041388	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	30	84	0	0.491803	0	G|0.800;A|0.200	0.200	strong	.	TAPBPL	21	.	NM_018009	exon3	c.G519A	p.P173P	GCACCCGACGCTG	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	107712880	107712880	+	Silent	SNP	C	C	T	rs10082935	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	39	65	0	0.629032	0	C|0.868;T|0.132	0.132	strong	.	BTBD11	122	.	NM_001018072	exon1	c.C163T	p.L55L	CCGCCTCTAGCTG	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790482	4790482	+	Silent	SNP	T	T	C	rs12792898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	95	184	0	0.492228	0	T|0.909;C|0.091	0.091	strong	OR51F1,NS,carcinoma,-2,1	OR51F1	60	1	NM_001004752	exon1	c.A666G	p.L222L	AATAATTAAGATA	.	PASS	Atlas-SNP
LRBA	987	hgsc.bcm.edu	37	4	151793903	151793903	+	Missense_Mutation	SNP	T	T	C	rs72719663	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	22	149	0	0.205607	0	T|0.983;C|0.017	0.017	strong	.	LRBA	253	.	NM_006726	exon18	c.A2170G	p.I724V	TGTAGATAACACT	.	PASS	Atlas-SNP
TRIP6	7205	hgsc.bcm.edu	37	7	100465747	100465747	+	Missense_Mutation	SNP	G	G	T	rs139351872	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	71	180	0	0.334906	0	C|0.000;G|0.999;T|0.001	0.001	strong	.	TRIP6	45	.	NM_003302	exon3	c.G255T	p.R85S	AGACAGGGGGGGC	.	PASS	Atlas-SNP
METTL25	84190	hgsc.bcm.edu	37	12	82752559	82752559	+	Missense_Mutation	SNP	T	T	G	rs113882703	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	92	293	0	0.37247	0	T|0.939;G|0.061	0.061	strong	.	.	.	.	NM_032230	exon1	c.T215G	p.L72R	AGGCCCTGCCCTC	.	PASS	Atlas-SNP
TMEM86B	255043	hgsc.bcm.edu	37	19	55739689	55739689	+	Silent	SNP	G	G	A	rs10413828	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	45	89	0	0.608108	0	G|0.620;A|0.380	0.380	strong	.	TMEM86B	12	.	NM_173804	exon2	c.C168T	p.P56P	GAGGACGGGCAGG	.	PASS	Atlas-SNP
CPSF1	29894	hgsc.bcm.edu	37	8	145624559	145624559	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	36	103	0	0.235294	0	.	.	none	.	CPSF1	92	.	NM_013291	exon15	c.G1426A	p.A476T	CATTGGCACAGGG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104370	168104370	+	Silent	SNP	A	A	C	rs61748715	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	42	93	0	0.525	0	A|0.860;C|0.140	0.140	strong	.	XIRP2	914	.	NM_152381	exon9	c.A6468C	p.T2156T	TGATACACAAAGC	.	PASS	Atlas-SNP
SCNN1D	6339	hgsc.bcm.edu	37	1	1223385	1223385	+	Missense_Mutation	SNP	G	G	C	rs2228579	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	8	177	0	0.0987654	0	G|0.717;C|0.283	0.283	strong	.	SCNN1D	60	.	NM_001130413	exon12	c.G1630C	p.E544Q	GAGGTGGAGCTGC	.	PASS	Atlas-SNP
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	50	90	0	0.561798	0	G|0.691;T|0.309	0.309	strong	.	DNAJC25	20	.	NM_001015882	exon3	c.G702T	p.G234G	AAAGGGGGGCTAT	.	PASS	Atlas-SNP
PTPRU	10076	hgsc.bcm.edu	37	1	29618535	29618535	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	2	101	0	0.0338983	0	.	.	none	PTPRU_ENST00000460170,colon,carcinoma,0,4	PTPRU	374	4	NM_005704	exon16	c.C2503T	p.R835W	AGCACCCGGGGTG	.	scavenged	Atlas-SNP
STPG1	90529	hgsc.bcm.edu	37	1	24706269	24706269	+	Silent	SNP	A	A	G	rs1064842	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	55	157	1	0.647059	0.00636943	A|0.589;G|0.411	0.411	strong	C1orf201_ENST00000374409,colon,carcinoma,0,2	.	.	2	NM_001199012	exon5	c.T336C	p.N112N	GTATGCATTCGCT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149521183	149521183	+	Missense_Mutation	SNP	G	G	A	rs4389841	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	9	112	0	0.12	0	G|0.848;A|0.152	0.152	strong	.	.	.	.	NM_198455	exon94	c.G13523A	p.R4508Q	AATGCCGGCGTGG	.	PASS	Atlas-SNP
UBE4A	9354	hgsc.bcm.edu	37	11	118253436	118253436	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	76	85	0	0.690909	0	.	.	none	.	UBE4A	97	.	NM_004788	exon13	c.T2163C	p.Y721Y	TCAGTATGCACCC	.	PASS	Atlas-SNP
MANBA	4126	hgsc.bcm.edu	37	4	103555992	103555992	+	Silent	SNP	A	A	G	rs2272697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	179	194	1	0.983516	0.00515464	A|0.447;G|0.553	0.553	strong	MANBA,NS,carcinoma,0,2	MANBA	78	2	NM_005908	exon16	c.T2368C	p.L790L	AGGACAAGAAGTG	.	PASS	Atlas-SNP
DISP2	85455	hgsc.bcm.edu	37	15	40660566	40660566	+	Silent	SNP	G	G	A	rs72733420	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	31	41	0	1	0	G|0.847;A|0.153	0.153	strong	DISP2,NS,carcinoma,0,1	DISP2	86	1	NM_033510	exon8	c.G2253A	p.A751A	CGACGCGGAGTAT	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152919	103152919	+	Silent	SNP	G	G	A	rs12574626	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	53	44	0	0.726027	0	G|0.808;A|0.192	0.192	strong	.	DYNC2H1	246	.	NM_001080463	exon73	c.G10794A	p.T3598T	GGATACGTTTACA	.	PASS	Atlas-SNP
CD1C	911	hgsc.bcm.edu	37	1	158261015	158261015	+	Silent	SNP	C	C	T	rs3138099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	400	219	278	0	0.5475	0	C|0.928;T|0.072	0.072	strong	.	CD1C	100	.	NM_001765	exon2	c.C153T	p.D51D	GCTGGACGAGTTG	.	PASS	Atlas-SNP
MGAT4C	25834	hgsc.bcm.edu	37	12	86373221	86373221	+	Missense_Mutation	SNP	G	G	C	rs17855890	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	54	137	0	0.482143	0	G|0.927;C|0.073	0.073	strong	.	MGAT4C	110	.	NM_013244	exon7	c.C1283G	p.T428S	AAGTAAGTAGAAC	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813785	248813785	+	Missense_Mutation	SNP	A	A	T	rs200036975	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	610	210	321	1	0.344262	0.00311526	A|0.863;T|0.137	0.137	strong	OR2T27,bladder,carcinoma,0,1	OR2T27	52	1	NM_001001824	exon1	c.T401A	p.V134D	ATGAGGACAGGAT	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506597	195506597	+	Missense_Mutation	SNP	G	G	A	rs200685331		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	10	111	0	0.227273	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,9	MUC4	1505	9	NM_018406	exon2	c.C11854T	p.P3952S	GAAGAGGGGTGGT	.	scavenged	Atlas-SNP
C18orf56	494514	hgsc.bcm.edu	37	18	658064	658064	+	Missense_Mutation	SNP	G	G	C	rs2853533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	17	44	0	0.5	0	G|0.684;C|0.316	0.316	strong	.	C18orf56	2	.	NM_001012716	exon1	c.C184G	p.R62G	TCCTGCGAGGGAG	.	PASS	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110763935	110763935	+	Missense_Mutation	SNP	T	T	C	rs41288594	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	52	91	0	0.485981	0	T|0.985;C|0.015	0.015	strong	.	SLC22A16	81	.	NM_033125	exon4	c.A695G	p.E232G	ATGAATTCCATCA	.	PASS	Atlas-SNP
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58350631	58350631	+	Silent	SNP	C	C	T	rs10122	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	47	90	0	0.484536	0	C|0.485;T|0.515	0.515	strong	.	XRCC6BP1	22	.	NM_033276	exon6	c.C699T	p.H233H	TGCTCACAGAGAC	.	PASS	Atlas-SNP
RPE65	6121	hgsc.bcm.edu	37	1	68914353	68914353	+	Silent	SNP	A	A	G	rs62642581	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	25	158	0	0.257732	0	A|1.000;G|0.000	0.000	strong	.	RPE65	87	.	NM_000329	exon2	c.T48C	p.F16F	AGTTTCAAACAGT	.	PASS	Atlas-SNP
IQCA1	79781	hgsc.bcm.edu	37	2	237300677	237300677	+	Missense_Mutation	SNP	T	T	C	rs10204742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	86	219	0	0.51497	0	T|0.926;C|0.074	0.074	strong	.	IQCA1	170	.	NM_001270585	exon11	c.A1376G	p.K459R	GCTAGCTTTAAGT	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124096041	124096041	+	Silent	SNP	T	T	C	rs1129973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	51	116	1	0.432203	0.00862069	T|0.621;C|0.379	0.379	strong	BTBD16,NS,lymphoid_neoplasm,0,1	BTBD16	44	1	NM_144587	exon15	c.T1296C	p.S432S	TCCCTCTGCGGTC	.	scavenged	Atlas-SNP
SHKBP1	92799	hgsc.bcm.edu	37	19	41096189	41096189	+	Silent	SNP	A	A	G	rs396118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	41	75	0	0.953488	0	A|0.421;G|0.579	0.579	strong	SHKBP1,NS,carcinoma,0,2	SHKBP1	68	2	NM_138392	exon16	c.A1629G	p.T543T	CACGACAGCCTTC	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32363955	32363955	+	Silent	SNP	T	T	C	rs2076529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	70	142	0	0.48951	0	T|0.636;C|0.364	0.364	strong	.	BTNL2	50	.	NM_019602	exon5	c.A939G	p.V313V	CACCAGTACAGTC	.	PASS	Atlas-SNP
ARHGEF12	23365	hgsc.bcm.edu	37	11	120328858	120328858	+	Silent	SNP	T	T	C	rs766894	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	303	86	218	2	0.283828	0.00917431	T|0.833;C|0.167	0.167	strong	ARHGEF12,NS,carcinoma,+2,1	ARHGEF12	133	1	NM_015313	exon25	c.T2295C	p.D765D	GACAGATCCACCC	.	scavenged	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124746347	124746347	+	Silent	SNP	T	T	C	rs4404487	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	61	125	0	0.448529	0	T|0.270;C|0.730	0.730	strong	.	HEG1	109	.	NM_020733	exon3	c.A615G	p.S205S	ACTTTCTGAGGCT	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76455218	76455218	+	Silent	SNP	G	G	A	rs2289754	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	49	91	1	0.441441	0.010989	G|0.835;A|0.165	0.165	strong	DNAH17,NS,lymphoid_neoplasm,-1,2	DNAH17	347	2	NM_173628	exon61	c.C9726T	p.C3242C	CCAGGAGCACAGG	.	scavenged	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	37	3	126726705	126726705	+	Silent	SNP	A	A	G	rs9876615	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	30	81	0	0.447761	0	A|0.893;G|0.107	0.107	strong	PLXNA1,NS,carcinoma,0,1	PLXNA1	185	1	NM_032242	exon8	c.A2061G	p.T687T	GTGCACACACAAC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129906980	129906980	+	Missense_Mutation	SNP	C	C	T	rs2152143	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	148	326	2	0.515679	0.00613497	T|0.208;G|0.007	0.208	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.G3124A	p.G1042S	ACTTGCCGACTGC	.	scavenged	Atlas-SNP
ELL2	22936	hgsc.bcm.edu	37	5	95234392	95234392	+	Silent	SNP	A	A	C	rs3777202	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	299	297	408	0	0.993311	0	A|0.674;C|0.326	0.326	strong	ELL2,NS,carcinoma,-1,1	ELL2	63	1	NM_012081	exon8	c.T1077G	p.S359S	TGCAGCAGATTTT	.	PASS	Atlas-SNP
RBM23	55147	hgsc.bcm.edu	37	14	23371268	23371268	+	Silent	SNP	A	A	G	rs56708790	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	11	60	0	0.234043	0	A|0.887;G|0.113	0.113	strong	RBM23,NS,carcinoma,0,3	RBM23	44	3	NM_001077351	exon12	c.T1167C	p.A389A	GGCGGCAGCAGCA	.	PASS	Atlas-SNP
PPP1R3C	5507	hgsc.bcm.edu	37	10	93390158	93390158	+	Silent	SNP	C	C	T	rs35530640	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	27	43	0	0.84375	0	C|0.974;T|0.026	0.026	strong	.	PPP1R3C	30	.	NM_005398	exon2	c.G480A	p.E160E	GCAGTTCTCCAGA	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62254989	62254989	+	Missense_Mutation	SNP	T	T	C	rs3784635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	29	214	0	0.223077	0	T|0.948;C|0.052	0.052	strong	.	VPS13C	506	.	NM_020821	exon33	c.A3394G	p.I1132V	CAATAATATTTTC	.	PASS	Atlas-SNP
OR6F1	343169	hgsc.bcm.edu	37	1	247875314	247875314	+	Silent	SNP	C	C	A	rs41268353	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	77	105	0	0.611111	0	C|0.948;A|0.052	0.052	strong	.	OR6F1	88	.	NM_001005286	exon1	c.G744T	p.V248V	AATGAGCACCACG	.	PASS	Atlas-SNP
GPA33	10223	hgsc.bcm.edu	37	1	167042762	167042762	+	Missense_Mutation	SNP	C	C	T	rs2274531	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	131	108	0	1	0	C|0.905;T|0.095	0.095	strong	.	GPA33	50	.	NM_005814	exon2	c.G58A	p.D20N	TGGCATCGACGGT	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964000	88964000	+	Silent	SNP	C	C	T	rs801839	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	62	62	0	0.613861	0	C|0.493;T|0.507	0.507	strong	.	ZNF804B	322	.	NM_181646	exon4	c.C1704T	p.F568F	TACTTTCAGTGCA	.	PASS	Atlas-SNP
CPEB2	132864	hgsc.bcm.edu	37	4	15005641	15005641	+	Silent	SNP	C	C	T	rs142927413	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	16	52	0	0.444444	0	C|0.977;T|0.023	0.023	strong	.	CPEB2	77	.	NM_001177381	exon1	c.C1344T	p.G448G	GAACGGCTTCTAC	.	PASS	Atlas-SNP
DHRS12	79758	hgsc.bcm.edu	37	13	52343391	52343391	+	Missense_Mutation	SNP	C	C	T	rs10676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21	10	22	0	0.47619	0	C|0.885;T|0.115	0.115	strong	.	DHRS12	28	.	NM_001270424	exon9	c.G745A	p.G249R	GGTCCCCGAACCT	.	PASS	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156640308	156640308	+	Silent	SNP	C	C	T	rs3748571	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	40	88	1	0.296296	0.0113636	C|0.788;T|0.212	0.212	strong	NES,rectum,carcinoma,0,1	NES	196	1	NM_006617	exon4	c.G3672A	p.T1224T	GGTGTACGTTGGG	.	scavenged	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	37	19	41354533	41354533	+	Missense_Mutation	SNP	A	A	T	rs1801272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	48	110	0	0.475248	0	A|0.983;T|0.017	0.017	strong	.	CYP2A6	69	.	NM_000762	exon3	c.T479A	p.L160H	CCCCGGAGGGCGT	.	PASS	Atlas-SNP
EXOC1	55763	hgsc.bcm.edu	37	4	56737278	56737278	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	77	198	0	0.487342	0	.	.	none	.	EXOC1	103	.	NM_018261	exon7	c.C843G	p.D281E	CATGGACTTGGCC	.	PASS	Atlas-SNP
PLEKHO2	80301	hgsc.bcm.edu	37	15	65158047	65158047	+	Missense_Mutation	SNP	G	G	A	rs77456635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17	13	24	0	0.764706	0	G|0.982;A|0.018	0.018	strong	.	PLEKHO2	50	.	NM_025201	exon6	c.G1433A	p.R478Q	AGAAGCGGAAGGA	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29747417	29747417	+	Silent	SNP	C	C	T	rs1887465	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	8	90	0	0.142857	0	C|0.733;T|0.267	0.267	strong	.	SVIL	226	.	NM_021738	exon37	c.G6504A	p.P2168P	CCCCTCCGGGAGT	.	PASS	Atlas-SNP
EFEMP1	2202	hgsc.bcm.edu	37	2	56144930	56144930	+	Silent	SNP	T	T	C	rs14282	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	48	97	0	0.475248	0	T|0.979;C|0.021	0.021	strong	.	EFEMP1	81	.	NM_001039349	exon4	c.A387G	p.E129E	CTGCATTTCAGGG	.	PASS	Atlas-SNP
PLEKHM2	23207	hgsc.bcm.edu	37	1	16056364	16056364	+	Silent	SNP	G	G	A	rs3817269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	9	72	0	0.214286	0	G|0.678;A|0.322	0.322	strong	.	PLEKHM2	94	.	NM_015164	exon14	c.G2148A	p.T716T	CCTGACGGATGCC	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46877017	46877017	+	Silent	SNP	C	C	T	rs201225285	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	63	189	0	0.425676	0	C|0.996;T|0.004	0.004	strong	.	TTLL6	113	.	NM_001130918	exon6	c.G717A	p.V239V	TTCTTTCACTGTC	.	PASS	Atlas-SNP
COQ9	57017	hgsc.bcm.edu	37	16	57484980	57484980	+	Silent	SNP	G	G	A	rs223864	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	86	86	0	0.877551	0	G|0.973;A|0.027	0.027	strong	.	COQ9	30	.	NM_020312	exon2	c.G102A	p.P34P	GGTGCCGCGTGCC	.	PASS	Atlas-SNP
OXR1	55074	hgsc.bcm.edu	37	8	107754473	107754473	+	Silent	SNP	G	G	A	rs1681904	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	289	287	230	2	0.99308	0.00869565	G|0.627;A|0.373	0.373	strong	.	OXR1	190	.	NM_001198532	exon14	c.G2343A	p.E781E	ATCTGAGCCACTG	.	PASS	Atlas-SNP
HPS5	11234	hgsc.bcm.edu	37	11	18303533	18303533	+	Missense_Mutation	SNP	G	G	A	rs61884288	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	73	215	0	0.394595	0	G|0.975;A|0.025	0.025	strong	HPS5,NS,meningioma,0,1	HPS5	70	1	NM_181507	exon22	c.C3293T	p.T1098I	TCGCAGGTTCTGG	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21790040	21790040	+	Missense_Mutation	SNP	G	G	T	rs10151259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	56	111	0	0.327485	0	A|0.059;C|0.298	.	strong	.	RPGRIP1	213	.	NM_020366	exon13	c.G1639T	p.A547S	ACAAAAGCTGACA	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8159362	8159362	+	Missense_Mutation	SNP	G	G	T	rs7245429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	41	81	0	0.532468	0	G|0.603;T|0.397	0.397	strong	.	FBN3	300	.	NM_032447	exon46	c.C5873A	p.P1958H	AAGCCAGGGGGAC	.	PASS	Atlas-SNP
EML4	27436	hgsc.bcm.edu	37	2	42515437	42515437	+	Missense_Mutation	SNP	A	A	G	rs28651764	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	24	63	1	0.380952	0.015873	A|0.717;G|0.283	0.283	strong	EML4_ENST00000318522,NS,carcinoma,-1,2	EML4	92	2	NM_019063	exon11	c.A1193G	p.K398R	GGCAGAAGAAAGC	.	scavenged	Atlas-SNP
ATAD3A	55210	hgsc.bcm.edu	37	1	1455652	1455652	+	Missense_Mutation	SNP	G	G	T	rs75466946		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	30	345	2	0.211268	0.0057971	.	.	weak	ATAD3A,NS,carcinoma,0,4	ATAD3A	35	4	NM_018188	exon6	c.G790T	p.A264S	AAGGCGGCCGAGC	.	scavenged	Atlas-SNP
TP53TG5	27296	hgsc.bcm.edu	37	20	44005936	44005936	+	Missense_Mutation	SNP	C	C	T	rs2231616	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	79	98	0	0.975309	0	C|0.863;T|0.137	0.137	strong	.	TP53TG5	36	.	NM_014477	exon3	c.G170A	p.R57H	ATCCGGCGGTTTG	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139370217	139370217	+	Silent	SNP	G	G	A	rs76562693	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	44	72	0	0.571429	0	G|0.965;A|0.035	0.035	strong	SEC16A_NM_014866.1,NS,haematopoietic_neoplasm,0,2	SEC16A	249	2	NM_014866	exon3	c.C1851T	p.H617H	AACTAAGTGAGAT	.	PASS	Atlas-SNP
NF1	4763	hgsc.bcm.edu	37	17	29553485	29553485	+	Silent	SNP	G	G	A	rs2285892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	25	50	0	0.5	0	G|0.568;A|0.432	0.432	strong	.	NF1	1586	.	NM_000267	exon18	c.G2034A	p.P678P	CCCCCCGATTTGC	.	PASS	Atlas-SNP
RALGPS2	55103	hgsc.bcm.edu	37	1	178861391	178861391	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	498	5	364	0	0.0100402	0	.	.	none	RALGPS2,NS,carcinoma,-1,1	RALGPS2	69	1	NM_152663	exon15	c.C1274T	p.P425L	TCGGCCCGGTGAC	.	scavenged	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	37	19	41356246	41356246	+	Missense_Mutation	SNP	C	C	T	rs28399435	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	330	166	341	1	0.50303	0.00293255	C|0.975;T|0.025	0.025	strong	.	CYP2A6	69	.	NM_000762	exon1	c.G86A	p.S29N	CCCTTGCTCTTCC	.	PASS	Atlas-SNP
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350044	65350044	+	Silent	SNP	A	A	G	rs35278406	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	33	97	0	0.351064	0	A|0.974;G|0.026	0.026	strong	.	ERBB2IP	120	.	NM_001253699	exon21	c.A2898G	p.Q966Q	CCCACAATCTGCA	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088789	56088789	+	Silent	SNP	G	G	A	rs199851385	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	313	90	169	0	0.28754	0	G|0.750;A|0.250	0.250	strong	.	PSPH	23	.	NM_004577	exon4	c.C117T	p.G39G	CTCAACGCCACAG	.	PASS	Atlas-SNP
ACTL7B	10880	hgsc.bcm.edu	37	9	111617341	111617341	+	Silent	SNP	A	A	G	rs3750467	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	55	150	0	0.436508	0	A|0.890;G|0.110	0.110	strong	.	ACTL7B	57	.	NM_006686	exon1	c.T870C	p.T290T	GCCAATAGTGATG	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1502864	1502864	+	Silent	SNP	A	A	G	rs12926669	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	47	142	0	0.439252	0	A|0.912;G|0.088	0.088	strong	.	CLCN7	53	.	NM_001287	exon15	c.T1245C	p.I415I	GGCCTCAATCACC	.	PASS	Atlas-SNP
CCDC67	159989	hgsc.bcm.edu	37	11	93129484	93129484	+	Missense_Mutation	SNP	A	A	G	rs12282288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	250	60	140	0	0.24	0	A|0.801;G|0.199	0.199	strong	.	CCDC67	57	.	NM_181645	exon11	c.A1319G	p.E440G	CCGGAGAATACAT	.	PASS	Atlas-SNP
LATS2	26524	hgsc.bcm.edu	37	13	21562948	21562948	+	Missense_Mutation	SNP	G	G	A	rs558614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21	18	28	0	0.857143	0	G|0.298;A|0.702	0.702	strong	LATS2_ENST00000382592,NS,carcinoma,0,2	LATS2	176	2	NM_014572	exon4	c.C971T	p.A324V	TGGGCCGCGGGAC	.	PASS	Atlas-SNP
ACYP1	97	hgsc.bcm.edu	37	14	75520272	75520272	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	5	183	0	0.021645	0	.	.	none	ACYP1,NS,carcinoma,+2,1	ACYP1	6	1	NM_001107	exon3	c.G175T	p.V59L	GACGCACCTTGGA	.	scavenged	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227216775	227216775	+	Missense_Mutation	SNP	C	C	T	rs1929860	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	33	41	0	0.589286	0	T|0.301;C|0.699	0.301	strong	.	CDC42BPA	528	.	NM_003607	exon29	c.G3910A	p.V1304I	AAGTTACGGTTTG	.	PASS	Atlas-SNP
SIX4	51804	hgsc.bcm.edu	37	14	61187111	61187111	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	308	4	254	1	0.012987	0.00393701	.	.	none	SIX4,NS,carcinoma,0,1	SIX4	69	1	NM_017420	exon2	c.G916A	p.D306N	ATAAATCCTCATG	.	scavenged	Atlas-SNP
TTLL12	23170	hgsc.bcm.edu	37	22	43579083	43579083	+	Missense_Mutation	SNP	G	G	A	rs138951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	124	187	0	0.579439	0	G|0.927;A|0.073	0.073	strong	.	TTLL12	50	.	NM_015140	exon2	c.C250T	p.R84W	CCTCCCGGGCTGC	.	PASS	Atlas-SNP
OR4X1	390113	hgsc.bcm.edu	37	11	48285906	48285906	+	Missense_Mutation	SNP	C	C	T	rs16905753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	85	200	0	0.454545	0	C|0.822;T|0.178	0.178	strong	OR4X1,NS,adenoma,-1,2	OR4X1	75	2	NM_001004726	exon1	c.C494T	p.P165L	AGCTCCCGTTCTG	.	PASS	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56468225	56468225	+	Missense_Mutation	SNP	G	G	A	rs148651508	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298	76	289	2	0.255034	0.00692042	G|1.000;A|0.000	0.000	weak	OR9G1,NS,carcinoma,0,1	.	.	1	NM_001013358	exon1	c.G362A	p.R121H	ATGACCGCTACGT	.	scavenged	Atlas-SNP
UGT2B4	7363	hgsc.bcm.edu	37	4	70346564	70346564	+	Silent	SNP	G	G	T	rs67904882	bycluster;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	83	193	0	0.491124	0	TT|1.000;|0.000	.	alt	UGT2B4,NS,carcinoma,0,1	UGT2B4	105	1	NM_021139	exon6	c.C1375A	p.R459R	CTGCTCGATCAAG	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789327	117789327	+	Missense_Mutation	SNP	T	T	C	rs61900346	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	25	108	1	0.093985	0.00925926	T|0.814;C|0.186	0.186	strong	TMPRSS13_ENST00000445164,NS,carcinoma,0,4	TMPRSS13	75	4	NM_001206790	exon2	c.A248G	p.Q83R	GATGCCTGGGCTG	.	scavenged	Atlas-SNP
MYEOV	26579	hgsc.bcm.edu	37	11	69063527	69063527	+	Missense_Mutation	SNP	C	C	T	rs150423809	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	78	154	0	0.478528	0	C|0.998;T|0.002	0.002	strong	.	MYEOV	42	.	NM_138768	exon3	c.C610T	p.R204C	GCTCTGCGCTCAC	.	PASS	Atlas-SNP
APPL2	55198	hgsc.bcm.edu	37	12	105600935	105600935	+	Silent	SNP	G	G	A	rs2293643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	42	75	0	0.506024	0	G|0.836;A|0.164	0.164	strong	.	APPL2	69	.	NM_001251904	exon8	c.C543T	p.H181H	GGAGAGGTGCTGC	.	PASS	Atlas-SNP
SERPINB5	5268	hgsc.bcm.edu	37	18	61170721	61170721	+	Silent	SNP	T	T	C	rs1455556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	107	189	0	0.557292	0	T|0.435;C|0.565	0.565	strong	.	SERPINB5	35	.	NM_002639	exon7	c.T894C	p.S298S	CTTCAGTGAAGAC	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124089075	124089075	+	Missense_Mutation	SNP	G	G	A	rs986178	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	22	50	1	0.423077	0.02	G|0.902;A|0.098	0.098	strong	BTBD16,NS,carcinoma,0,1	BTBD16	44	1	NM_144587	exon11	c.G992A	p.G331D	TGCACGGCATCAC	.	scavenged	Atlas-SNP
PLAT	5327	hgsc.bcm.edu	37	8	42044965	42044965	+	Missense_Mutation	SNP	G	G	A	rs2020921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	35	37	0	0.583333	0	G|0.987;A|0.013	0.013	strong	PLAT,NS,carcinoma,+1,1	PLAT	62	1	NM_000930	exon6	c.C490T	p.R164W	GCCTCCGCCCGCT	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43547873	43547873	+	Missense_Mutation	SNP	G	G	A	rs220159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	269	117	222	0	0.434944	0	G|0.638;N|0.000	.	strong	UMODL1_ENST00000408989,colon,carcinoma,0,2	UMODL1	186	2	NM_173568	exon19	c.G4006A	p.D1336N	ATCAACGACTCCA	.	PASS	Atlas-SNP
ZNF701	55762	hgsc.bcm.edu	37	19	53085813	53085813	+	Silent	SNP	T	T	C	rs3745101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	71	185	0	0.470199	0	T|0.704;C|0.296	0.296	strong	.	ZNF701	44	.	NM_001172655	exon5	c.T699C	p.A233A	GAAGGCTATCAAC	.	PASS	Atlas-SNP
GIT2	9815	hgsc.bcm.edu	37	12	110385079	110385079	+	Silent	SNP	G	G	T	rs2063388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	125	270	0	0.555556	0	G|0.922;T|0.078	0.078	strong	.	GIT2	81	.	NM_001135214	exon15	c.C1623A	p.L541L	GGGCTGGAGTCTC	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	995919	995919	+	Silent	SNP	G	G	C	rs6830825	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	18	39	0	0.514286	0	G|0.815;C|0.185	0.185	strong	IDUA,NS,carcinoma,0,1	IDUA	33	1	NM_000203	exon7	c.G942C	p.A314A	GAGGGCGGACGTG	.	PASS	Atlas-SNP
SCRT2	85508	hgsc.bcm.edu	37	20	656181	656181	+	Missense_Mutation	SNP	G	G	A	rs76595598	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	34	101	0	0.441558	0	G|0.950;A|0.050	0.050	strong	SCRT2,NS,carcinoma,0,1	SCRT2	16	1	NM_033129	exon1	c.C65T	p.A22V	GTGGGGGCCGGCA	.	PASS	Atlas-SNP
SEZ6	124925	hgsc.bcm.edu	37	17	27284443	27284443	+	Missense_Mutation	SNP	A	A	G	rs12941884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	78	161	0	0.509804	0	A|0.847;G|0.153	0.153	strong	.	SEZ6	61	.	NM_001098635	exon12	c.T2417C	p.M806T	CTGCCCATCAGCA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392182	40392182	+	Missense_Mutation	SNP	T	T	G	rs202122337	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	728	28	558	15	0.0384615	0.0268817	T|0.985;G|0.015	0.015	strong	FCGBP,NS,other,0,1	FCGBP	416	1	NM_003890	exon17	c.A8204C	p.Q2735P	CTGTTCTGAGGGC	.	scavenged	Atlas-SNP
ELTD1	64123	hgsc.bcm.edu	37	1	79392756	79392756	+	Missense_Mutation	SNP	C	C	A	rs12754818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	10	106	0	0.15873	0	C|0.374;A|0.625	0.625	strong	.	ELTD1	143	.	NM_022159	exon8	c.G898T	p.V300L	AATATACAAATGC	.	PASS	Atlas-SNP
ARL2	402	hgsc.bcm.edu	37	11	64789194	64789194	+	Missense_Mutation	SNP	T	T	C	rs664226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	17	46	0	0.459459	0	T|0.439;C|0.561	0.561	strong	ARL2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ARL2	11	1	NM_001667	exon5	c.T422C	p.V141A	CCCAGGTCCTGGA	.	PASS	Atlas-SNP
CELA2B	51032	hgsc.bcm.edu	37	1	15808767	15808767	+	Missense_Mutation	SNP	G	G	A	rs3820071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	65	105	1	0.984848	0.00952381	G|0.706;A|0.294	0.294	strong	CELA2B_ENST00000422901,NS,carcinoma,-1,6	CELA2B	37	6	NM_015849	exon4	c.G235A	p.G79R	TCCTCCGGGATCT	.	PASS	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983602	97983602	+	Silent	SNP	T	T	C	rs75354046	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	8	282	0	0.0316206	0	T|0.898;C|0.102	0.102	strong	OR5H6,adrenal_gland,adrenal_cortical_adenoma,0,1	OR5H6	89	1	NM_001005479	exon1	c.T474C	p.I158I	ATGCATTCAGCTA	.	scavenged	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154388363	154388363	+	Missense_Mutation	SNP	C	C	T	rs78441178	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	93	218	0	0.678832	0	.	.	weak	.	KIAA0922	214	.	NM_001131007	exon2	c.C125T	p.A42V	CTGCAGCGATTGA	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144620855	144620855	+	Missense_Mutation	SNP	C	C	A	rs4873802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	20	29	0	0.408163	0	C|0.858;A|0.142	0.142	strong	.	ZC3H3	75	.	NM_015117	exon2	c.G682T	p.A228S	AGCTCGCCTTGAC	.	PASS	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40909695	40909695	+	Silent	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	56	159	0	0.482759	0	.	.	none	.	PRX	151	.	NM_181882	exon5	c.A102C	p.V34V	GCCCGCTACGTTG	.	PASS	Atlas-SNP
PABPC1L	80336	hgsc.bcm.edu	37	20	43566787	43566787	+	Silent	SNP	A	A	G	rs11780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	63	140	0	0.470149	0	A|0.569;G|0.428	0.428	strong	.	PABPC1L	59	.	NM_001124756	exon13	c.A1731G	p.S577S	CAACTCAGAGCTG	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160453978	160453978	+	Silent	SNP	A	A	G	rs1570070	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	74	58	0	1	0	A|0.643;G|0.357	0.357	strong	.	IGF2R	251	.	NM_000876	exon9	c.A1050G	p.S350S	AGGTTCATCCTAT	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887394	9887394	+	Silent	SNP	C	C	T	rs2240910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	47	70	0	0.580247	0	C|0.531;T|0.469	0.469	strong	TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.C918T	p.A306A	GGAAGCCATCCAG	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40574434	40574434	+	Missense_Mutation	SNP	T	T	C	rs144295288	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	55	115	0	0.364238	0	T|0.997;C|0.003	0.003	strong	.	BRWD1	325	.	NM_018963	exon38	c.A4402G	p.I1468V	GAATTATTTTTGT	.	PASS	Atlas-SNP
PVR	5817	hgsc.bcm.edu	37	19	45153113	45153113	+	Missense_Mutation	SNP	G	G	C	rs35959395	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	60	155	0	0.451128	0	G|0.999;C|0.001	0.001	strong	.	PVR	23	.	NM_001135769	exon3	c.G460C	p.V154L	CAGAAGGTCCAGC	.	PASS	Atlas-SNP
DFNB31	25861	hgsc.bcm.edu	37	9	117266965	117266965	+	Silent	SNP	C	C	T	rs2297815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	13	47	0	0.590909	0	C|0.706;T|0.294	0.294	strong	.	DFNB31	100	.	NM_001173425	exon1	c.G117A	p.V39V	CTGGCGCACGTTG	.	PASS	Atlas-SNP
DDB1	1642	hgsc.bcm.edu	37	11	61099072	61099072	+	Silent	SNP	G	G	A	rs2230356	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	96	166	0	0.48731	0	G|0.928;A|0.072	0.072	strong	.	DDB1	100	.	NM_001923	exon2	c.C153T	p.P51P	TTTGACGGGCCGA	.	PASS	Atlas-SNP
ABCA8	10351	hgsc.bcm.edu	37	17	66878099	66878099	+	Missense_Mutation	SNP	C	C	T	rs34987539	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	64	93	0	0.542373	0	C|0.992;T|0.008	0.008	strong	.	ABCA8	213	.	NM_007168	exon29	c.G3731A	p.C1244Y	CGTAGACAGCTGG	.	PASS	Atlas-SNP
MAP3K10	4294	hgsc.bcm.edu	37	19	40719076	40719076	+	Silent	SNP	T	T	C	rs1129156	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	25	58	0	0.543478	0	T|0.250;C|0.750	0.750	strong	MAP3K10,NS,carcinoma,0,1	MAP3K10	70	1	NM_002446	exon8	c.T1818C	p.F606F	TGGCTTTGCCAGC	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31090094	31090094	+	Missense_Mutation	SNP	G	G	A	rs78522165	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	52	119	0	0.452174	0	A|0.052;C|0.000;G|0.948	0.052	strong	.	ZNF646	133	.	NM_014699	exon2	c.G2449A	p.A817T	TGGCAGGCTGGGG	.	PASS	Atlas-SNP
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802629	31802629	+	Silent	SNP	C	C	T	rs73356729	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	79	181	0	0.329167	0	C|0.963;T|0.037	0.037	strong	.	KRTAP13-4	46	.	NM_181600	exon1	c.C36T	p.S12S	CTCCTCCCGCTCC	.	PASS	Atlas-SNP
DEFB129	140881	hgsc.bcm.edu	37	20	210306	210306	+	Missense_Mutation	SNP	C	C	G	rs1053783	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	50	89	0	0.510204	0	C|0.798;G|0.202	0.202	strong	.	DEFB129	24	.	NM_080831	exon2	c.C446G	p.T149S	GTAACACCAAAGA	.	PASS	Atlas-SNP
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100452832	100452832	+	Silent	SNP	C	C	T	rs11832216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	127	264	0	0.51417	0	C|0.936;T|0.064	0.064	strong	UHRF1BP1L,caecum,carcinoma,-1,1	UHRF1BP1L	144	1	NM_015054	exon14	c.G2223A	p.P741P	AGTCTGCGGCTCT	.	PASS	Atlas-SNP
CCDC74A	90557	hgsc.bcm.edu	37	2	132289293	132289293	+	Missense_Mutation	SNP	T	T	C	rs2599962	bycluster;byfrequency;bysubmitter;by2hit2allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	31	203	2	0.27193	0.00985222	T|0.300;C|0.700	0.700	strong	CCDC74A,NS,carcinoma,-2,1	CCDC74A	44	1	NM_001258304	exon4	c.T727C	p.S243P	GACGTCTCCCAGA	.	scavenged	Atlas-SNP
C19orf48	84798	hgsc.bcm.edu	37	19	51301456	51301456	+	Missense_Mutation	SNP	G	G	A	rs4802741	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	38	93	0	0.436782	0	G|0.713;A|0.287	0.287	strong	.	C19orf48	11	.	NM_199249	exon5	c.C250T	p.R84C	GGTGGCGTATGGA	.	PASS	Atlas-SNP
PRKD1	5587	hgsc.bcm.edu	37	14	30066929	30066929	+	Silent	SNP	A	A	G	rs2230505	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	32	39	0	0.450704	0	T|0.088;G|0.396;C|0.100;A|0.416	0.396	strong	.	PRKD1	316	.	NM_002742	exon16	c.T2202C	p.I734I	CTCTCCAATGATC	.	PASS	Atlas-SNP
RTTN	25914	hgsc.bcm.edu	37	18	67755252	67755252	+	Missense_Mutation	SNP	C	C	G	rs376382612		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	26	70	0	0.440678	0	.	.	weak	.	RTTN	184	.	NM_173630	exon31	c.G4275C	p.Q1425H	TTCTGACTGGTCC	.	PASS	Atlas-SNP
PADI4	23569	hgsc.bcm.edu	37	1	17668563	17668563	+	Missense_Mutation	SNP	G	G	A	rs35903413	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	21	159	0	0.196262	0	G|0.908;A|0.092	0.092	strong	.	PADI4	70	.	NM_012387	exon7	c.G778A	p.D260N	GACACCGACTTCC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9068990	9068990	+	Missense_Mutation	SNP	G	G	T	rs35092547	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	619	307	620	0	0.495961	0	G|0.981;T|0.019	0.019	strong	.	MUC16	4315	.	NM_024690	exon3	c.C18456A	p.H6152Q	GGTCTTGTGTGTA	.	PASS	Atlas-SNP
SLC9C2	284525	hgsc.bcm.edu	37	1	173516871	173516871	+	Missense_Mutation	SNP	G	G	C	rs16846206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	226	80	147	0	0.353982	0	G|0.763;C|0.237	0.237	strong	.	.	.	.	NM_178527	exon13	c.C1514G	p.A505G	ATTAAAGCTTCAT	.	PASS	Atlas-SNP
MSI2	124540	hgsc.bcm.edu	37	17	55752389	55752389	+	Missense_Mutation	SNP	G	G	A	rs116924898	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	57	142	0	0.475	0	A|0.007;C|0.000;G|0.992	0.007	strong	.	MSI2	52	.	NM_138962	exon12	c.G847A	p.A283T	CCTGTCGCCGATC	.	PASS	Atlas-SNP
LRRTM1	347730	hgsc.bcm.edu	37	2	80529918	80529918	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	3	143	1	0.0222222	0.00699301	.	.	none	LRRTM1_ENST00000295057,colon,carcinoma,+1,2	LRRTM1	251	2	NM_178839	exon2	c.G1027A	p.A343T	GGCTGGCGCACTG	.	scavenged	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50502544	50502544	+	Silent	SNP	G	G	A	rs11568186	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	52	185	0	0.320988	0	G|0.891;A|0.109	0.109	strong	.	MLC1	48	.	NM_015166	exon11	c.C978T	p.C326C	GCGCACGCACTGG	.	PASS	Atlas-SNP
C1orf52	148423	hgsc.bcm.edu	37	1	85724328	85724328	+	Silent	SNP	C	C	T	rs4949926	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	241	116	0	0.987705	0	C|0.810;T|0.190	0.190	strong	.	C1orf52	16	.	NM_198077	exon2	c.G354A	p.P118P	TGGAGGCGGAGGC	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862532	5862532	+	Missense_Mutation	SNP	A	A	C	rs10742809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	51	115	0	0.418033	0	A|0.670;C|0.330	0.330	strong	.	OR52E6	70	.	NM_001005167	exon1	c.T596G	p.M199R	CCAAACATAATGT	.	PASS	Atlas-SNP
PPIG	9360	hgsc.bcm.edu	37	2	170493103	170493103	+	Missense_Mutation	SNP	T	T	A	rs1050354	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	67	146	0	0.446667	0	A|0.574;N|0.000	0.574	strong	PPIG,NS,carcinoma,0,1	PPIG	100	1	NM_004792	exon14	c.T1335A	p.D445E	AAAAGATGACAAG	.	PASS	Atlas-SNP
VPREB1	7441	hgsc.bcm.edu	37	22	22599674	22599674	+	Silent	SNP	C	C	T	rs5995719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	16	17	1	0.888889	0.0588235	C|0.808;T|0.192	0.192	strong	VPREB1,NS,carcinoma,+1,1	VPREB1	20	1	NM_007128	exon2	c.C363T	p.S121S	CCGCAGCTCGGAG	.	scavenged	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64518321	64518321	+	Missense_Mutation	SNP	A	A	G	rs11628107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	52	103	0	0.356164	0	A|0.970;G|0.030	0.030	strong	.	SYNE2	577	.	NM_182914	exon48	c.A7690G	p.I2564V	AAATTCATAGCAT	.	PASS	Atlas-SNP
KCNK6	9424	hgsc.bcm.edu	37	19	38817876	38817876	+	Missense_Mutation	SNP	G	G	A	rs34989303	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	42	126	0	0.488372	0	G|0.865;A|0.135	0.135	strong	.	KCNK6	37	.	NM_004823	exon3	c.G775A	p.V259M	CGCCACGTGTCCG	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36595436	36595436	+	Missense_Mutation	SNP	A	A	C	rs1008328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	42	120	1	0.5	0.00833333	A|0.255;C|0.745	0.745	strong	WDR62,NS,carcinoma,0,1	WDR62	102	1	NM_001083961	exon31	c.A4170C	p.L1390F	TCTGTTACAGGGC	.	scavenged	Atlas-SNP
DHFRL1	200895	hgsc.bcm.edu	37	3	93780109	93780109	+	Missense_Mutation	SNP	G	G	C	rs61739170	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	110	238	0	0.470085	0	G|0.833;C|0.167	0.167	strong	DHFRL1,NS,carcinoma,0,1	DHFRL1	25	1	NM_001195643	exon2	c.C247G	p.P83A	GTGGAGGTTCCTT	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	994414	994414	+	Missense_Mutation	SNP	G	G	A	rs3755955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	103	236	1	0.481308	0.00423729	G|0.859;A|0.141	0.141	strong	.	IDUA	33	.	NM_000203	exon3	c.G314A	p.R105Q	CTGGACGGGGCCT	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150945699	150945699	+	Silent	SNP	G	G	A	rs10085060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259	123	295	0	0.474903	0	G|0.529;A|0.471	0.471	strong	.	FAT2	465	.	NM_001447	exon1	c.C2794T	p.L932L	CCTTCAGCCTGTT	.	PASS	Atlas-SNP
GPNMB	10457	hgsc.bcm.edu	37	7	23313171	23313171	+	Silent	SNP	T	T	C	rs2268748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	163	213	0	0.654619	0	T|0.909;G|0.000	.	strong	.	GPNMB	88	.	NM_001005340	exon10	c.T1497C	p.S499S	AAACAGTGCCCTG	.	PASS	Atlas-SNP
TOP3B	8940	hgsc.bcm.edu	37	22	22318538	22318538	+	Missense_Mutation	SNP	C	C	T	rs9610728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	124	191	0	0.54386	0	C|0.880;T|0.120	0.120	strong	.	TOP3B	107	.	NM_003935	exon10	c.G1093A	p.D365N	CCGTGTCGGCCCA	.	PASS	Atlas-SNP
DMRT2	10655	hgsc.bcm.edu	37	9	1057204	1057204	+	Silent	SNP	A	A	G	rs4741029	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	45	121	0	0.445545	0	A|0.784;G|0.216	0.216	strong	.	DMRT2	70	.	NM_181872	exon4	c.A1617G	p.E539E	GAATGAACCACTG	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29161503	29161503	+	Missense_Mutation	SNP	A	A	G	rs11080134	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	28	12	38	0	0.428571	0	A|0.786;G|0.214	0.214	strong	.	ATAD5	150	.	NM_024857	exon2	c.A404G	p.E135G	CAATTGAAATTAG	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11511457	11511457	+	Silent	SNP	C	C	T	rs11078022	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	67	96	0	1	0	C|0.626;N|0.000	.	strong	.	DNAH9	695	.	NM_001372	exon2	c.C429T	p.P143P	TCTACCCGTCCTG	.	PASS	Atlas-SNP
GBP1	2633	hgsc.bcm.edu	37	1	89523911	89523911	+	Missense_Mutation	SNP	C	C	T	rs75161612	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	27	55	0	1	0	C|0.981;T|0.019	0.019	strong	.	GBP1	68	.	NM_002053	exon6	c.G638A	p.S213N	TTTTGACTGGTAC	.	PASS	Atlas-SNP
HSD17B12	51144	hgsc.bcm.edu	37	11	43702530	43702530	+	Silent	SNP	A	A	G	rs56168061	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	25	80	1	0.462963	0.0125	A|0.873;G|0.127	0.127	strong	HSD17B12,NS,carcinoma,0,1	HSD17B12	25	1	NM_016142	exon1	c.A153G	p.E51E	CGGAGAATGGGCA	.	scavenged	Atlas-SNP
AQP10	89872	hgsc.bcm.edu	37	1	154296076	154296076	+	Silent	SNP	T	T	C	rs1194610	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	190	116	0	0.994764	0	T|0.702;C|0.298	0.298	strong	AQP10,NS,carcinoma,0,1	AQP10	44	1	NM_080429	exon5	c.T501C	p.T167T	GGGCACTGGGATG	.	PASS	Atlas-SNP
PRDM10	56980	hgsc.bcm.edu	37	11	129785594	129785594	+	Silent	SNP	G	G	A	rs3734073	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	270	80	156	0	0.296296	0	G|0.729;A|0.271	0.271	strong	PRDM10,colon,carcinoma,0,1	PRDM10	120	1	NM_020228	exon17	c.C2499T	p.P833P	GCAGACGGGAGGG	.	PASS	Atlas-SNP
SLC9A9	285195	hgsc.bcm.edu	37	3	143293012	143293012	+	Silent	SNP	A	A	G	rs6763202	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	124	255	1	0.504065	0.00392157	A|0.684;G|0.316	0.316	strong	.	SLC9A9	117	.	NM_173653	exon8	c.T918C	p.C306C	GAACTCACACAGC	.	PASS	Atlas-SNP
HFE	3077	hgsc.bcm.edu	37	6	26091179	26091179	+	Missense_Mutation	SNP	C	C	G	rs1799945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	129	272	1	0.53527	0.00367647	C|0.898;G|0.102	0.102	strong	.	HFE	37	.	NM_139006	exon2	c.C187G	p.H63D	TATGATCATGAGA	.	PASS	Atlas-SNP
WDR55	54853	hgsc.bcm.edu	37	5	140048707	140048707	+	Missense_Mutation	SNP	A	A	G	rs35983033	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	71	102	0	0.518248	0	A|0.936;G|0.064	0.064	strong	.	WDR55	27	.	NM_017706	exon6	c.A704G	p.Y235C	CCATCTACCTCTT	.	PASS	Atlas-SNP
CKM	1158	hgsc.bcm.edu	37	19	45815163	45815163	+	Missense_Mutation	SNP	G	G	A	rs17357122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	58	189	0	0.381579	0	G|0.995;A|0.005	0.005	strong	.	CKM	40	.	NM_001824	exon5	c.C497T	p.T166M	TCGCCCGTCAGGC	.	PASS	Atlas-SNP
SIPA1L1	26037	hgsc.bcm.edu	37	14	72138078	72138078	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	3	112	0	0.0181818	0	.	.	none	SIPA1L1,colon,carcinoma,0,1	SIPA1L1	219	1	NM_015556	exon8	c.C2498T	p.P833L	AGTTTCCGTTCAT	.	scavenged	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	37	12	125900095	125900095	+	Silent	SNP	T	T	A	rs3809261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	111	139	1	0.982301	0.00719424	T|0.901;A|0.099	0.099	strong	.	TMEM132B	207	.	NM_052907	exon3	c.T963A	p.G321G	AGCAGGTGTGAAG	.	PASS	Atlas-SNP
CLIP4	79745	hgsc.bcm.edu	37	2	29383256	29383256	+	Missense_Mutation	SNP	G	G	T	rs3100246	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	64	144	0	0.48855	0	G|0.905;T|0.095	0.095	strong	.	CLIP4	69	.	NM_024692	exon12	c.G1457T	p.R486L	AACTCCGCCTCGG	.	PASS	Atlas-SNP
APOD	347	hgsc.bcm.edu	37	3	195306289	195306289	+	Missense_Mutation	SNP	A	A	G	rs5952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	24	50	0	0.45283	0	A|0.996;G|0.004	0.004	strong	.	APOD	28	.	NM_001647	exon2	c.T44C	p.F15S	GCACCGAAGAGGC	.	PASS	Atlas-SNP
CEP112	201134	hgsc.bcm.edu	37	17	64025331	64025331	+	Silent	SNP	A	A	G	rs11652766	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	115	230	0	0.491453	0	A|0.507;G|0.493	0.493	strong	.	CEP112	192	.	NM_001199165	exon14	c.T1413C	p.N471N	ATAATCATTTACA	.	PASS	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84611367	84611367	+	Missense_Mutation	SNP	G	G	C	rs34047645	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	31	53	0	0.939394	0	G|0.892;C|0.108	0.108	strong	ADAMTSL3,NS,carcinoma,-2,2	ADAMTSL3	290	2	NM_207517	exon18	c.G2137C	p.G713R	TCTTGGGGGCCCT	.	PASS	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56467945	56467945	+	Missense_Mutation	SNP	G	G	T	rs36184181	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	49	198	0	0.255208	0	G|0.646;T|0.354	0.354	strong	.	.	.	.	NM_001013358	exon1	c.G82T	p.V28L	CTCTTCGTGGTGT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093324	1093324	+	Missense_Mutation	SNP	G	G	A	rs201143282		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	4	67	0	0.0645161	0	.	.	weak	MUC2_ENST00000441003,uveal_tract,malignant_melanoma,0,2	MUC2	614	2	NM_002457	exon30	c.G5143A	p.G1715S	CCCACCGGCACAC	.	PASS	Atlas-SNP
KERA	11081	hgsc.bcm.edu	37	12	91449984	91449984	+	Silent	SNP	C	C	T	rs12320366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	66	118	0	0.825	0	C|0.758;T|0.242	0.242	strong	.	KERA	62	.	NM_007035	exon2	c.G75A	p.Q25Q	ATAGACCTGCCTC	.	PASS	Atlas-SNP
STRN	6801	hgsc.bcm.edu	37	2	37152342	37152342	+	Missense_Mutation	SNP	C	C	T	rs200160777	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	14	167	14	0.0689655	0.0838323	C|0.719;T|0.281	0.281	strong	STRN,NS,other,0,2	STRN	71	2	NM_003162	exon2	c.G244A	p.A82T	GGAAGGCAATCTG	.	scavenged	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14991963	14991963	+	Missense_Mutation	SNP	C	C	A	rs10404119	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	54	126	0	0.432	0	C|0.711;A|0.289	0.289	strong	.	OR7A17	37	.	NM_030901	exon1	c.G205T	p.A69S	TGTCTGCAAAGGA	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33875262	33875262	+	Missense_Mutation	SNP	T	T	A	rs8073060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	25	78	0	0.462963	0	T|0.694;A|0.306	0.306	strong	.	SLFN14	43	.	NM_001129820	exon4	c.A2735T	p.Y912F	TTTCAGTAGGCTG	.	PASS	Atlas-SNP
CCDC138	165055	hgsc.bcm.edu	37	2	109408208	109408208	+	Missense_Mutation	SNP	G	G	A	rs6740879	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	19	44	0	0.513514	0	G|0.747;A|0.253	0.253	strong	CCDC138,NS,carcinoma,0,1	CCDC138	49	1	NM_144978	exon4	c.G344A	p.R115K	ATTATAGAGTTAG	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38345455	38345455	+	Silent	SNP	A	A	G	rs12242343	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	17	102	0	0.257576	0	A|0.968;G|0.032	0.032	strong	.	ZNF33A	103	.	NM_006954	exon5	c.A2403G	p.G801G	CTGTGGAGAAAGC	.	PASS	Atlas-SNP
ITGA2	3673	hgsc.bcm.edu	37	5	52347369	52347369	+	Silent	SNP	C	C	T	rs1126643	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	142	154	0	0.993007	0	C|0.629;T|0.371	0.371	strong	.	ITGA2	211	.	NM_002203	exon7	c.C759T	p.F253F	CACATTCGGAGCA	.	PASS	Atlas-SNP
AMPH	273	hgsc.bcm.edu	37	7	38431511	38431511	+	Silent	SNP	C	C	T	rs2229922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	64	102	0	0.457143	0	C|0.919;T|0.081	0.081	strong	AMPH,NS,carcinoma,-1,1	AMPH	157	1	NM_001635	exon19	c.G1716A	p.A572A	AGGAGCCGCGTCC	.	PASS	Atlas-SNP
PVRIG	79037	hgsc.bcm.edu	37	7	99817585	99817585	+	Nonsense_Mutation	SNP	G	G	T	rs7786505	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	379	146	296	1	0.385224	0.00337838	G|0.814;T|0.186	0.186	strong	.	PVRIG	20	.	NM_024070	exon2	c.G52T	p.E18X	GGACTGGAGGGGG	.	PASS	Atlas-SNP
ELL2	22936	hgsc.bcm.edu	37	5	95236415	95236415	+	Silent	SNP	G	G	A	rs17085249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	174	216	0	0.983051	0	G|0.697;A|0.303	0.303	strong	ELL2,NS,carcinoma,0,1	ELL2	63	1	NM_012081	exon7	c.C936T	p.D312D	TACAGCGTCTCTA	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72998004	72998004	+	Silent	SNP	T	T	C	rs3744908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	45	86	0	0.5	0	T|0.690;C|0.310	0.310	strong	.	TSHZ1	104	.	NM_005786	exon2	c.T507C	p.Y169Y	CTCGTATGGGCTG	.	PASS	Atlas-SNP
OTOP1	133060	hgsc.bcm.edu	37	4	4199760	4199760	+	Silent	SNP	G	G	A	rs17697262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	106	262	2	0.434426	0.00763359	G|0.855;A|0.145	0.145	strong	OTOP1,NS,carcinoma,-2,1	OTOP1	118	1	NM_177998	exon5	c.C801T	p.I267I	GTAGTAGATCCCG	.	scavenged	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60776186	60776186	+	Missense_Mutation	SNP	C	C	T	rs11230562	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	41	106	0	0.539474	0	C|0.852;T|0.148	0.148	strong	.	CD6	122	.	NM_006725	exon4	c.C650T	p.T217M	ACTTCACGCCCGG	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	15	118	0	0.16129	0	G|0.572;A|0.428	0.428	strong	WWP2,NS,carcinoma,0,1	WWP2	88	1	NM_001270454	exon24	c.G2595A	p.E865E	GACCGAGGGCTTT	.	PASS	Atlas-SNP
ELL	8178	hgsc.bcm.edu	37	19	18562438	18562438	+	Missense_Mutation	SNP	C	C	T	rs2303694	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	41	90	0	0.37963	0	C|0.865;T|0.135	0.135	strong	.	ELL	52	.	NM_006532	exon7	c.G890A	p.S297N	CCAGTGCTCTGTG	.	PASS	Atlas-SNP
GLIS3	169792	hgsc.bcm.edu	37	9	4118111	4118111	+	Missense_Mutation	SNP	G	G	T	rs6415788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	11	17	0	0.578947	0	G|0.313;T|0.687	0.687	strong	.	GLIS3	152	.	NM_001042413	exon4	c.C1367A	p.P456Q	GGGCCTGGGGGCG	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43531264	43531264	+	Missense_Mutation	SNP	C	C	G	rs111772429	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	47	121	0	0.370079	0	A|0.003;C|0.996;G|0.000	0.000	strong	.	UMODL1	186	.	NM_173568	exon11	c.C1932G	p.D644E	GATGGACCAGGGG	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48608717	48608717	+	Silent	SNP	T	T	C	rs1064055	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	93	137	0	1	0	T|0.195;C|0.805	0.805	strong	.	MYCBPAP	135	.	NM_032133	exon19	c.T2883C	p.T961T	GGTGACTGACCTG	.	PASS	Atlas-SNP
PPM1F	9647	hgsc.bcm.edu	37	22	22288560	22288560	+	Missense_Mutation	SNP	G	G	A	rs9610645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	39	53	0	0.58209	0	G|0.900;A|0.100	0.100	strong	PPM1F,colon,carcinoma,0,1	PPM1F	34	1	NM_014634	exon4	c.C394T	p.R132C	AAAGGCGGTTAAA	.	PASS	Atlas-SNP
SLC9B2	133308	hgsc.bcm.edu	37	4	103964529	103964529	+	Missense_Mutation	SNP	A	A	C	rs2276976	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	36	65	0	0.5	0	A|0.893;C|0.107	0.107	strong	.	.	.	.	NM_178833	exon9	c.T1070G	p.F357C	AAACCAAAATGCA	.	PASS	Atlas-SNP
C15orf52	388115	hgsc.bcm.edu	37	15	40627845	40627845	+	Silent	SNP	G	G	A	rs55641696	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	50	78	0	0.806452	0	G|0.836;A|0.164	0.164	strong	.	C15orf52	47	.	NM_207380	exon11	c.C1119T	p.S373S	CATCCCGCTCTGC	.	PASS	Atlas-SNP
ITGB2	3689	hgsc.bcm.edu	37	21	46330229	46330229	+	Silent	SNP	C	C	T	rs35903905	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	56	158	0	0.256881	0	C|0.987;T|0.013	0.013	strong	.	ITGB2	107	.	NM_000211	exon3	c.G117A	p.S39S	GGGCCCCGACTCG	.	PASS	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5749171	5749171	+	Missense_Mutation	SNP	A	A	G	rs72983139	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	34	90	0	0.453333	0	A|0.957;G|0.043	0.043	strong	.	.	.	.	NM_152784	exon11	c.A964G	p.I322V	CTGGGCATCGTGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678527	100678527	+	Missense_Mutation	SNP	G	G	T	rs73402889	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	314	109	149	0	0.347134	0	G|0.918;T|0.082	0.082	strong	MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	NM_001040105	exon3	c.G3830T	p.S1277I	AAGGAAGTACTCT	.	PASS	Atlas-SNP
MSLN	10232	hgsc.bcm.edu	37	16	816977	816977	+	Missense_Mutation	SNP	G	G	A	rs35935235	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	62	94	0	0.53913	0	G|0.968;A|0.032	0.032	strong	.	MSLN	109	.	NM_013404	exon14	c.G1490A	p.G497E	TGAACGGGTCCGA	.	PASS	Atlas-SNP
ULBP2	80328	hgsc.bcm.edu	37	6	150267527	150267527	+	Silent	SNP	A	A	C	rs61730070	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	89	255	0	0.46114	0	A|0.889;C|0.111	0.111	strong	.	ULBP2	22	.	NM_025217	exon3	c.A369C	p.A123A	GCAGGCAAGGATG	.	PASS	Atlas-SNP
RIN2	54453	hgsc.bcm.edu	37	20	19970705	19970705	+	Silent	SNP	C	C	T	rs2076584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	69	164	0	0.453947	0	C|0.570;T|0.430	0.430	strong	.	RIN2	126	.	NM_001242581	exon9	c.C1965T	p.H655H	GGGGCACGTGGAG	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	71029733	71029733	+	Missense_Mutation	SNP	C	C	T	rs2584021	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	335	168	328	0	0.501493	0	C|0.773;T|0.227	0.227	strong	.	PTPRB	676	.	NM_001109754	exon2	c.G169A	p.D57N	TTTCATCCTCAGT	.	PASS	Atlas-SNP
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43636484	43636484	+	Silent	SNP	C	C	G	rs1049276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	23	150	0	0.27381	0	C|0.799;G|0.201	0.201	strong	.	EBNA1BP2	37	.	NM_001159936	exon5	c.G555C	p.T185T	TCGCTTCGTAGGG	.	PASS	Atlas-SNP
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703248	56703248	+	Missense_Mutation	SNP	G	G	A	rs527025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	51	122	0	0.554348	0	G|0.725;A|0.275	0.275	strong	.	ZSCAN5B	160	.	NM_001080456	exon2	c.C559T	p.P187S	CCCTGGGCAGGAT	.	PASS	Atlas-SNP
FAM118A	55007	hgsc.bcm.edu	37	22	45719125	45719125	+	Silent	SNP	C	C	T	rs138980075	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	83	165	0	0.474286	0	C|0.997;T|0.003	0.003	strong	.	FAM118A	32	.	NM_017911	exon3	c.C117T	p.S39S	CGTCAGCGCAGCA	.	PASS	Atlas-SNP
ETS1	2113	hgsc.bcm.edu	37	11	128333503	128333503	+	Silent	SNP	T	T	C	rs2230004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	77	76	0	0.675439	0	T|0.524;C|0.476	0.476	strong	.	ETS1	123	.	NM_001143820	exon9	c.A1143G	p.L381L	CTGCCATAGCTGG	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982185	75982185	+	Silent	SNP	T	T	C	rs77341302	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	29	130	4	0.5	0.0307692	T|0.983;C|0.018	0.018	strong	CSPG4,NS,carcinoma,-2,1	CSPG4	175	1	NM_001897	exon3	c.A1221G	p.P407P	CATGGCTGGCCAA	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678029	100678029	+	Missense_Mutation	SNP	G	G	C	rs142558659		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	766	95	212	0	0.124021	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.G3332C	p.R1111T	GCACCAGGCTGGT	.	PASS	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	99690450	99690450	+	Silent	SNP	T	T	C	rs12222337	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	37	127	0	0.177033	0	C|0.101;T|0.899	0.101	strong	.	CNTN5	324	.	NM_001243270	exon3	c.T231C	p.Y77Y	TTATTATTCCCCC	.	PASS	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	37	6	168376840	168376840	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	30	321	0	0.10453	0	.	.	none	.	.	.	.	NM_001129895	exon1	c.A493G	p.T165A	TGTGTGTGGGGAG	.	PASS	Atlas-SNP
STAG3	10734	hgsc.bcm.edu	37	7	99778285	99778285	+	Missense_Mutation	SNP	A	A	C	rs2272343	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	36	93	0	0.295082	0	A|0.837;C|0.163	0.163	strong	STAG3,NS,carcinoma,0,1	STAG3	121	1	NM_012447	exon2	c.A106C	p.T36P	AACCATACCTCAG	.	PASS	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113508839	113508839	+	Silent	SNP	G	G	C	rs9549573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	26	47	0	0.541667	0	G|0.292;C|0.708	0.708	strong	.	ATP11A	225	.	NM_032189	exon19	c.G2238C	p.L746L	CAACCTGTCCGGG	.	PASS	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138377498	138377498	+	Missense_Mutation	SNP	G	G	T	rs34151777	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	25	56	0	0.431034	0	G|0.956;T|0.044	0.044	strong	.	.	.	.	NM_014811	exon4	c.G1142T	p.R381L	AAACACGCAAGGA	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85450426	85450426	+	Missense_Mutation	SNP	G	G	A	rs74720621	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	46	118	0	0.464646	0	G|0.992;A|0.008	0.008	strong	.	LRRIQ1	512	.	NM_001079910	exon8	c.G1855A	p.E619K	ACATCAGAAAATT	.	PASS	Atlas-SNP
SLC12A3	6559	hgsc.bcm.edu	37	16	56919235	56919235	+	Silent	SNP	G	G	A	rs5802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	57	61	0	0.826087	0	A|0.069;C|0.000;G|0.931	0.069	strong	.	SLC12A3	99	.	NM_001126108	exon15	c.G1884A	p.S628S	CTACTCGGTGGGC	.	PASS	Atlas-SNP
TBL3	10607	hgsc.bcm.edu	37	16	2028402	2028402	+	Silent	SNP	A	A	C	rs8460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	13	74	0	0.302326	0	A|0.592;C|0.408	0.408	strong	TBL3,NS,carcinoma,0,1	TBL3	54	1	NM_006453	exon21	c.A2223C	p.R741R	GAGGCGAGAGGCC	.	PASS	Atlas-SNP
SH3TC2	79628	hgsc.bcm.edu	37	5	148386525	148386525	+	Silent	SNP	T	T	G	rs6871030	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	126	212	1	0.477273	0.00471698	C|0.005;G|0.447;T|0.549	0.447	strong	.	SH3TC2	178	.	NM_024577	exon16	c.A3594C	p.P1198P	CAGCCATGGTGGA	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37230734	37230734	+	Silent	SNP	C	C	T	rs17497654	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	44	122	0	0.444444	0	C|0.834;T|0.166	0.166	strong	.	HEATR5B	185	.	NM_019024	exon31	c.G5001A	p.Q1667Q	TACTATCTGTTGT	.	PASS	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	37	5	9190404	9190404	+	Silent	SNP	G	G	A	rs1806095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	44	97	0	0.431373	0	G|0.771;A|0.229	0.229	strong	.	SEMA5A	236	.	NM_003966	exon11	c.C1248T	p.L416L	GTGGACGAGCGCT	.	PASS	Atlas-SNP
WNT8B	7479	hgsc.bcm.edu	37	10	102222957	102222957	+	Missense_Mutation	SNP	G	G	C	rs3793771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	60	165	0	0.582524	0	G|0.799;C|0.201	0.201	strong	.	WNT8B	31	.	NM_003393	exon1	c.G32C	p.C11S	ACATCTGTCTTTT	.	PASS	Atlas-SNP
OSMR	9180	hgsc.bcm.edu	37	5	38904082	38904082	+	Missense_Mutation	SNP	T	T	C	rs35117676	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	365	171	387	1	0.468493	0.00258398	T|0.991;C|0.009	0.009	strong	.	OSMR	133	.	NM_003999	exon8	c.T1090C	p.Y364H	TTCACATATTTGT	.	PASS	Atlas-SNP
AS3MT	57412	hgsc.bcm.edu	37	10	104638723	104638723	+	Missense_Mutation	SNP	T	T	C	rs11191439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	54	125	0	0.72	0	T|0.914;C|0.086	0.086	strong	.	AS3MT	17	.	NM_020682	exon9	c.T860C	p.M287T	AACTAATGTTTGA	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33493201	33493201	+	Missense_Mutation	SNP	C	C	T	rs201601538	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	20	167	3	0.112994	0.0179641	C|0.929;T|0.070	0.070	strong	RHPN2,caecum,carcinoma,0,17	RHPN2	107	17	NM_033103	exon9	c.G1057A	p.A353T	GGGCCGCGTAGTG	.	scavenged	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	37	2	209168942	209168942	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	42	93	0	0.711864	0	.	.	none	.	PIKFYVE	223	.	NM_015040	exon11	c.C1368T	p.N456N	AGTGAACTCCGTG	.	PASS	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	37	12	126137060	126137060	+	Missense_Mutation	SNP	C	C	T	rs61021440	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	112	245	1	0.425856	0.00408163	C|0.759;T|0.241	0.241	strong	TMEM132B,NS,carcinoma,-1,1	TMEM132B	207	1	NM_052907	exon8	c.C1973T	p.A658V	CCATCGCGGAGCT	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123848121	123848121	+	Missense_Mutation	SNP	T	T	C	rs17686210	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	99	96	0	0.568965	0	T|0.785;C|0.215	0.215	strong	.	OR10S1	78	.	NM_001004474	exon1	c.A278G	p.K93R	ATGACCTTGGGCA	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14992045	14992045	+	Silent	SNP	C	C	T	rs10404335	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	32	106	0	0.421053	0	C|0.713;T|0.287	0.287	strong	.	OR7A17	37	.	NM_030901	exon1	c.G123A	p.G41G	CAGATTCCCGAGC	.	PASS	Atlas-SNP
RNF43	54894	hgsc.bcm.edu	37	17	56436109	56436109	+	Missense_Mutation	SNP	C	C	T	rs34523089	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	21	57	0	0.446809	0	C|0.912;T|0.088	0.088	strong	RNF43,NS,carcinoma,0,1	RNF43	157	1	NM_017763	exon9	c.G1028A	p.R343H	TGCTGGCGAATGA	.	PASS	Atlas-SNP
MYBPC3	4607	hgsc.bcm.edu	37	11	47370041	47370041	+	Missense_Mutation	SNP	T	T	C	rs3729989	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	75	146	0	0.547445	0	T|0.916;C|0.084	0.084	strong	.	MYBPC3	102	.	NM_000256	exon6	c.A706G	p.S236G	GGTAGCTGCCAGT	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386217	7386217	+	Missense_Mutation	SNP	T	T	C	rs200349946	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	44	216	0	0.158273	0	T|0.734;C|0.266	0.266	strong	POLR2A_ENST00000412468,NS,carcinoma,0,3	.	.	3	NM_001102614	exon2	c.T914C	p.V305A	AGACTGTGGCACC	.	PASS	Atlas-SNP
EIF2B3	8891	hgsc.bcm.edu	37	1	45444038	45444038	+	Silent	SNP	G	G	A	rs11556200	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	22	171	0	0.229167	0	G|0.714;A|0.286	0.286	strong	.	EIF2B3	43	.	NM_020365	exon3	c.C243T	p.D81D	GTCAGCGTCATCA	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	51	110	0	0.573034	0	G|0.888;A|0.112	0.112	strong	.	UTP20	222	.	NM_014503	exon10	c.G1143A	p.P381P	CTTGCCGGAGACC	.	PASS	Atlas-SNP
CAPN2	824	hgsc.bcm.edu	37	1	223954080	223954080	+	Missense_Mutation	SNP	A	A	C	rs17599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	75	156	1	0.388601	0.00641026	A|0.649;C|0.175;G|0.031;T|0.145	0.175	strong	CAPN2,NS,carcinoma,0,1	CAPN2	69	1	NM_001748	exon16	c.A1702C	p.K568Q	GATATCAAGTCAG	.	scavenged	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101732655	101732655	+	Silent	SNP	C	C	T	rs56265469	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	108	247	0	0.484305	0	C|0.766;T|0.234	0.234	strong	.	UTP20	222	.	NM_014503	exon31	c.C3933T	p.S1311S	TCTCAGCAAAACC	.	PASS	Atlas-SNP
MED12	9968	hgsc.bcm.edu	37	X	70349947	70349947	+	Silent	SNP	A	A	C	rs5030619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	224	456	1	0.973913	0.00219298	A|0.853;0|0.007	.	strong	.	MED12	984	.	NM_005120	exon28	c.A3930C	p.P1310P	AGACCCAGTGTTG	.	PASS	Atlas-SNP
BCAM	4059	hgsc.bcm.edu	37	19	45316588	45316588	+	Missense_Mutation	SNP	G	G	A	rs28399654	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	38	88	0	0.535211	0	G|0.983;A|0.017	0.017	strong	.	BCAM	53	.	NM_001013257	exon5	c.G586A	p.V196I	GTGCCCGTAGAGA	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225586274	225586274	+	Missense_Mutation	SNP	G	G	T	rs41304131	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	77	157	0	0.32906	0	G|0.985;T|0.015	0.015	strong	.	DNAH14	300	.	NM_001373	exon83	c.G13238T	p.G4413V	TCGAGGGGGCAAG	.	PASS	Atlas-SNP
PPT1	5538	hgsc.bcm.edu	37	1	40557033	40557033	+	Missense_Mutation	SNP	A	A	G	rs1800205	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	7	82	0	0.137255	0	A|0.952;G|0.048	0.048	strong	.	PPT1	18	.	NM_000310	exon4	c.T401C	p.I134T	AGATTGATCATGG	.	PASS	Atlas-SNP
CNOT4	4850	hgsc.bcm.edu	37	7	135098310	135098310	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	72	242	0	0.541353	0	.	.	none	.	CNOT4	146	.	NM_001190850	exon6	c.G614A	p.C205Y	TTTGGACACTGCA	.	PASS	Atlas-SNP
LAMC1	3915	hgsc.bcm.edu	37	1	183079729	183079729	+	Missense_Mutation	SNP	C	C	T	rs142614579	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	122	162	0	0.600985	0	C|0.999;T|0.001	0.001	strong	.	LAMC1	176	.	NM_002293	exon4	c.C961T	p.P321S	TGTCTTCCTTTCT	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	37	15	52635394	52635394	+	Missense_Mutation	SNP	T	T	A	rs61731219	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	48	152	0	0.857143	0	T|0.955;A|0.045	0.045	strong	.	MYO5A	145	.	NM_000259	exon31	c.A3960T	p.R1320S	AGATGATCTTCCA	.	PASS	Atlas-SNP
PDILT	204474	hgsc.bcm.edu	37	16	20371972	20371972	+	Missense_Mutation	SNP	A	A	C	rs4500734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232	111	217	0	0.478448	0	A|0.975;C|0.025	0.025	strong	.	PDILT	120	.	NM_174924	exon11	c.T1424G	p.L475R	TTATACAGGACAG	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190883051	190883051	+	Missense_Mutation	SNP	G	G	A	rs1803593	bycluster;bysubmitter	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	45	241	40	0.266272	0.165975	G|1.000;|0.000	.	weak	FRG1,NS,carcinoid-endocrine_tumour,0,1	FRG1	76	1	NM_004477	exon8	c.G704A	p.R235Q	AGGCTCGGAAAGA	.	scavenged	Atlas-SNP
RASSF7	8045	hgsc.bcm.edu	37	11	562219	562219	+	Missense_Mutation	SNP	C	C	G	rs2242183	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	72	143	0	0.464516	0	C|0.930;G|0.070	0.070	strong	.	RASSF7	22	.	NM_001143994	exon3	c.C265G	p.P89A	ACAGGGCCCAGCC	.	PASS	Atlas-SNP
OR52E8	390079	hgsc.bcm.edu	37	11	5878458	5878458	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	4	191	0	0.0206186	0	.	.	none	OR52E8,NS,carcinoma,0,1	OR52E8	54	1	NM_001005168	exon1	c.C475T	p.L159L	TGTACAGGCTCCT	.	scavenged	Atlas-SNP
ATN1	1822	hgsc.bcm.edu	37	12	7047143	7047143	+	Silent	SNP	C	C	A	rs7969685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	28	36	0	0.965517	0	C|0.802;A|0.198	0.198	strong	.	ATN1	95	.	NM_001007026	exon6	c.C2430A	p.R810R	GCAGCGCGCGCGC	.	PASS	Atlas-SNP
PRRC2C	23215	hgsc.bcm.edu	37	1	171486912	171486912	+	Missense_Mutation	SNP	G	G	A	rs10913157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	94	103	0	0.681159	0	G|0.869;A|0.131	0.131	strong	.	.	.	.	NM_015172	exon6	c.G703A	p.A235T	CAGCAGGCTGCTC	.	PASS	Atlas-SNP
WRN	7486	hgsc.bcm.edu	37	8	31024638	31024638	+	Silent	SNP	C	C	T	rs1801196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	310	172	219	0	0.554839	0	C|0.728;T|0.272	0.272	strong	.	WRN	116	.	NM_000553	exon34	c.C4083T	p.S1361S	TGACAGCGGACTT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681917	100681917	+	Missense_Mutation	SNP	T	T	G	rs111633703	bycluster;byfrequency;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	326	16	217	0	0.0490798	0	T|0.996;C|0.004	.	alt	.	MUC17	804	.	NM_001040105	exon3	c.T7220G	p.M2407R	GCACCATGCCGGT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276626	152276626	+	Missense_Mutation	SNP	G	G	C	rs3126075	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	413	46	483	3	0.11138	0.00621118	G|0.716;C|0.284	0.284	strong	FLG,colon,carcinoma,-1,1	FLG	900	1	NM_002016	exon3	c.C10736G	p.T3579R	TGGGACGTGGGGT	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093344	1093344	+	Silent	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	7	88	0	0.0909091	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.G5163T	p.P1721P	AACCCCGACACCC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389005	1389005	+	Missense_Mutation	SNP	T	T	C	rs71614970	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	13	8	121	0	0.615385	0	C|1.000;|0.000	1.000	weak	CRIPAK,rectum,NS,0,1	CRIPAK	185	1	NM_175918	exon1	c.T706C	p.C236R	TGCCGATGCGGAG	.	PASS	Atlas-SNP
KCNH3	23416	hgsc.bcm.edu	37	12	49951528	49951528	+	Missense_Mutation	SNP	C	C	T	rs144397719	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	60	126	0	0.491803	0	C|0.982;T|0.018	0.018	strong	.	KCNH3	88	.	NM_012284	exon15	c.C3044T	p.P1015L	GCACCCCTGCCTC	.	PASS	Atlas-SNP
POPDC2	64091	hgsc.bcm.edu	37	3	119379186	119379186	+	Missense_Mutation	SNP	C	C	T	rs4688023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	45	94	0	0.409091	0	C|0.615;T|0.385	0.385	strong	.	POPDC2	36	.	NM_022135	exon1	c.G85A	p.V29I	GGTAGACAGCCCC	.	PASS	Atlas-SNP
PER2	8864	hgsc.bcm.edu	37	2	239157721	239157721	+	Silent	SNP	G	G	A	rs35873326	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	46	64	0	0.489362	0	G|0.950;A|0.050	0.050	strong	.	PER2	85	.	NM_022817	exon22	c.C3600T	p.P1200P	GGCTGCGGGCAGG	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48597114	48597114	+	Silent	SNP	C	C	T	rs28498091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	29	85	0	0.439394	0	C|0.802;T|0.198	0.198	strong	.	MYCBPAP	135	.	NM_032133	exon7	c.C1011T	p.H337H	CACTCACATCAGG	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002421	36002421	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	6	35	0	0.0833333	0	.	.	none	DMKN,colon,carcinoma,0,1	DMKN	116	1	NM_001126058	exon5	c.T810C	p.G270G	GCTGCCACCACTG	.	PASS	Atlas-SNP
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461116	141461116	+	Silent	SNP	C	C	T	rs34457678	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	62	67	0	0.476923	0	C|0.912;T|0.088	0.088	strong	.	TRAPPC9	114	.	NM_031466	exon2	c.G651A	p.G217G	CTGCAGCCCGAAG	.	PASS	Atlas-SNP
SERPINE2	5270	hgsc.bcm.edu	37	2	224866576	224866576	+	Silent	SNP	C	C	A	rs12436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	18	56	1	0.473684	0.0178571	C|0.805;A|0.195	0.195	strong	SERPINE2_ENST00000447280,NS,carcinoma,-1,2	SERPINE2	103	2	NM_001136530	exon2	c.G78T	p.T26T	AGGCAGCGTCACA	.	scavenged	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	80992932	80992932	+	Silent	SNP	A	A	C	rs16940609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	78	190	0	0.481481	0	A|0.794;C|0.206	0.206	strong	.	B3GNTL1	40	.	NM_001009905	exon4	c.T321G	p.S107S	AAGGTAAGACCCT	.	PASS	Atlas-SNP
P4HA3	283208	hgsc.bcm.edu	37	11	73988167	73988167	+	Missense_Mutation	SNP	C	C	T	rs2282488	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	172	175	0	0.982857	0	C|0.847;T|0.153	0.153	strong	.	P4HA3	43	.	NM_182904	exon9	c.G1198A	p.D400N	TTGGGTCAACAGT	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22941617	22941617	+	Missense_Mutation	SNP	T	T	C	rs58653025	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	30	62	2	0.447761	0.0322581	T|0.811;C|0.189	0.189	strong	ZNF99,NS,carcinoma,0,1	ZNF99	273	1	NM_001080409	exon4	c.A1094G	p.E365G	TTCTCTTCAGTAT	.	scavenged	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24426581	24426581	+	Missense_Mutation	SNP	G	G	A	rs140804905	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	32	82	0	0.415584	0	G|0.999;A|0.001	0.001	strong	.	ITSN2	224	.	NM_006277	exon40	c.C5008T	p.R1670C	GTCGGCGGGTCAT	.	PASS	Atlas-SNP
CCND1	595	hgsc.bcm.edu	37	11	69457987	69457987	+	Silent	SNP	C	C	T	rs371689281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	18	47	0	0.428571	0	.	.	weak	.	CCND1	107	.	NM_053056	exon2	c.C387T	p.D129D	CACCGACAACTCC	.	PASS	Atlas-SNP
SMTN	6525	hgsc.bcm.edu	37	22	31487146	31487146	+	Silent	SNP	C	C	T	rs143316150		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	4	228	0	0.0192308	0	C|1.000;T|0.000	0.000	weak	SMTN_ENST00000404496,NS,carcinoma,0,3	SMTN	219	3	NM_001207018	exon9	c.C1305T	p.S435S	CTCCAGCGGCTCC	.	scavenged	Atlas-SNP
KCNH2	3757	hgsc.bcm.edu	37	7	150645534	150645534	+	Missense_Mutation	SNP	T	T	G	rs1805123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	33	46	0	0.970588	0	T|0.855;G|0.145	0.145	strong	KCNH2,colon,carcinoma,0,1	KCNH2	157	1	NM_000238	exon11	c.A2690C	p.K897T	TCACCCTTGTCCG	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243329211	243329211	+	Missense_Mutation	SNP	G	G	T	rs2728430		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	329	42	221	0	0.12766	0	.	.	weak	CEP170,NS,carcinoma,-1,1	CEP170	153	1	NM_014812	exon13	c.C2051A	p.T684K	ACCTGTGTAGGTG	.	scavenged	Atlas-SNP
COQ4	51117	hgsc.bcm.edu	37	9	131094453	131094453	+	Missense_Mutation	SNP	G	G	A	rs34043652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	42	133	0	0.428571	0	G|0.995;A|0.005	0.005	strong	.	COQ4	20	.	NM_016035	exon5	c.G424A	p.A142T	ACCCGAGCACCCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680939	100680939	+	Missense_Mutation	SNP	C	C	A	rs36120435	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	143	114	1	0.993056	0.00877193	C|0.880;A|0.120	0.120	strong	.	MUC17	804	.	NM_001040105	exon3	c.C6242A	p.A2081D	CTGAAGCCAGTTC	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24423007	24423007	+	Missense_Mutation	SNP	G	G	A	rs17099455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	79	80	0	1	0	G|0.795;A|0.205	0.205	strong	.	DHRS4	22	.	NM_021004	exon1	c.G10A	p.A4T	CACAAGGCGGGGC	.	PASS	Atlas-SNP
ALS2CR12	130540	hgsc.bcm.edu	37	2	202154200	202154200	+	Silent	SNP	C	C	T	rs17468277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	40	235	0	0.28777	0	C|0.910;T|0.090	0.090	strong	.	ALS2CR12	54	.	NM_139163	exon14	c.G1191A	p.T397T	CTCTTCCGTCAGG	.	PASS	Atlas-SNP
CSHL1	1444	hgsc.bcm.edu	37	17	61987576	61987576	+	Silent	SNP	G	G	A	rs2246207	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	436	165	591	4	0.37844	0.00676819	G|0.566;A|0.434	0.434	strong	CSHL1_ENST00000561003,NS,adenoma,0,2	CSHL1	42	2	NM_022579	exon4	c.C417T	p.S139S	GTCATCGCTGTCC	.	scavenged	Atlas-SNP
CUEDC2	79004	hgsc.bcm.edu	37	10	104184081	104184081	+	Silent	SNP	G	G	A	rs1044476	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	79	118	0	0.951807	0	G|0.898;A|0.102	0.102	strong	CUEDC2,NS,carcinoma,0,1	CUEDC2	22	1	NM_024040	exon5	c.C351T	p.P117P	CATTTCGGGCCGC	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108133967	108133967	+	Silent	SNP	A	A	G	rs2229085	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	288	287	259	1	0.996528	0.003861	A|0.801;G|0.199	0.199	strong	.	FER	100	.	NM_005246	exon3	c.A84G	p.V28V	AACAGTAAAGAAA	.	PASS	Atlas-SNP
AOX1	316	hgsc.bcm.edu	37	2	201526330	201526330	+	Missense_Mutation	SNP	A	A	G	rs55754655	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	23	168	0	0.232323	0	A|0.848;G|0.152	0.152	strong	.	AOX1	152	.	NM_001159	exon30	c.A3404G	p.N1135S	GCATTAACCTTTC	.	PASS	Atlas-SNP
CNGA2	1260	hgsc.bcm.edu	37	X	150909307	150909307	+	Missense_Mutation	SNP	G	G	T	rs35350051	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	93	201	1	0.978947	0.00497512	G|0.898;T|0.102	0.102	strong	.	CNGA2	136	.	NM_005140	exon5	c.G416T	p.W139L	GGGATTGGTACTA	.	PASS	Atlas-SNP
MBD3L3	653657	hgsc.bcm.edu	37	19	7056590	7056590	+	Missense_Mutation	SNP	C	C	T	rs76391970		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	314	57	349	6	0.181529	0.017192	.	.	weak	MBD3L3,NS,haematopoietic_neoplasm,0,1	MBD3L3	12	1	NM_001164425	exon2	c.G370A	p.G124S	ATTCACCGGCCGT	.	scavenged	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561316	32561316	+	Nonsense_Mutation	SNP	G	G	T	rs200628183	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	7	117	0	0.0538462	0	G|0.996;T|0.004	0.004	strong	ARHGAP5,uveal_tract,malignant_melanoma,0,1	ARHGAP5	166	1	NM_001173	exon2	c.G1441T	p.E481X	CAGCGAGAAATAG	.	PASS	Atlas-SNP
TPP1	1200	hgsc.bcm.edu	37	11	6637577	6637577	+	Silent	SNP	G	G	A	rs35706972	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	39	70	0	0.448276	0	G|0.992;A|0.008	0.008	strong	.	TPP1	71	.	NM_000391	exon8	c.C1044T	p.A348A	CCGAGCGGCAGCC	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21606719	21606719	+	Missense_Mutation	SNP	C	C	G	rs201385477		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	29	52	0	0.491525	0	.	.	weak	.	ZNF493	178	.	NM_001076678	exon4	c.C1258G	p.L420V	TCACACCTTACTA	.	PASS	Atlas-SNP
SLC10A2	6555	hgsc.bcm.edu	37	13	103705050	103705050	+	Silent	SNP	G	G	A	rs41281678	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	51	127	0	0.41129	0	G|0.972;A|0.028	0.028	strong	.	SLC10A2	67	.	NM_000452	exon3	c.C505T	p.L169L	AAACCAGAGATGT	.	PASS	Atlas-SNP
R3HCC1	203069	hgsc.bcm.edu	37	8	23148940	23148940	+	Missense_Mutation	SNP	G	G	A	rs2272761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	136	105	1	1	0.00952381	G|0.401;A|0.599	0.599	strong	.	R3HCC1	11	.	NM_001136108	exon5	c.G358A	p.V120M	TCCTTCGTGGAGG	.	PASS	Atlas-SNP
LEPRE1	64175	hgsc.bcm.edu	37	1	43212926	43212926	+	Missense_Mutation	SNP	G	G	A	rs67014447	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	11	65	0	0.244444	0	G|0.936;A|0.064	0.064	strong	.	LEPRE1	130	.	NM_001146289	exon14	c.C2072T	p.A691V	TCACCCGCTCGAG	.	PASS	Atlas-SNP
TRPV4	59341	hgsc.bcm.edu	37	12	110252569	110252569	+	Silent	SNP	C	C	A	rs56092423	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	16	7	22	0	0.4375	0	C|0.996;A|0.004	0.004	strong	.	TRPV4	88	.	NM_001177433	exon1	c.G33T	p.G11G	CCCGGGCCCCGCG	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77377410	77377410	+	Missense_Mutation	SNP	C	C	T	rs3750425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	41	100	0	0.418367	0	C|0.855;T|0.145	0.145	strong	.	TRPM6	377	.	NM_017662	exon26	c.G4177A	p.V1393I	AGACAACTGGGGT	.	PASS	Atlas-SNP
CEP170B	283638	hgsc.bcm.edu	37	14	105346632	105346632	+	Silent	SNP	G	G	A	rs72700176	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	39	88	0	0.375	0	G|0.971;A|0.029	0.029	strong	.	.	.	.	NM_001112726	exon6	c.G342A	p.K114K	TGAAAAGTACACC	.	PASS	Atlas-SNP
CNTNAP4	85445	hgsc.bcm.edu	37	16	76482747	76482747	+	Missense_Mutation	SNP	C	C	G	rs34251012	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	39	224	0	0.157895	0	C|0.967;G|0.033	0.033	strong	.	CNTNAP4	600	.	NM_138994	exon6	c.C751G	p.L251V	TCAGTGCTCATCC	.	PASS	Atlas-SNP
SLC3A1	6519	hgsc.bcm.edu	37	2	44502977	44502977	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	2	163	1	0.0117647	0.00613497	.	.	none	SLC3A1,NS,carcinoma,0,1	SLC3A1	62	1	NM_000341	exon1	c.C303T	p.I101I	GCTCATCGCGGCC	.	scavenged	Atlas-SNP
CD93	22918	hgsc.bcm.edu	37	20	23065879	23065879	+	Silent	SNP	G	G	A	rs34170527	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	117	236	1	0.549296	0.00423729	G|0.958;A|0.042	0.042	strong	.	CD93	84	.	NM_012072	exon1	c.C951T	p.C317C	CAGGACGCACGTG	.	PASS	Atlas-SNP
HK3	3101	hgsc.bcm.edu	37	5	176314459	176314459	+	Silent	SNP	G	G	A	rs2278492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	53	112	0	0.552083	0	G|0.694;A|0.306	0.306	strong	.	HK3	210	.	NM_002115	exon11	c.C1593T	p.D531D	GCTGCCGTCAGGG	.	PASS	Atlas-SNP
NOBOX	135935	hgsc.bcm.edu	37	7	144096068	144096068	+	Missense_Mutation	SNP	C	C	T	rs2525702	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	64	329	1	0.285714	0.00303951	C|0.876;T|0.124	0.124	strong	NOBOX_ENST00000467773,NS,carcinoma,0,2	NOBOX	130	2	NM_001080413	exon8	c.G1444A	p.G482S	AGGGGCCGTCCTT	.	scavenged	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107456763	107456763	+	Missense_Mutation	SNP	T	T	C	rs10991359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	71	140	0	0.470199	0	T|0.800;C|0.200	0.200	strong	OR13D1,NS,carcinoma,0,1	OR13D1	42	1	NM_001004484	exon1	c.T61C	p.F21L	GTCCTTTTCTATA	.	PASS	Atlas-SNP
SLC5A4	6527	hgsc.bcm.edu	37	22	32631021	32631021	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	3	174	1	0.0214286	0.00574713	.	.	none	SLC5A4,NS,carcinoma,+2,2	SLC5A4	82	2	NM_014227	exon8	c.T724C	p.S242P	CTACGGATGGGGT	.	scavenged	Atlas-SNP
DEFA3	1668	hgsc.bcm.edu	37	8	6873603	6873603	+	Missense_Mutation	SNP	T	T	G	rs2230231	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	328	31	1031	19	0.0945122	0.0184287	T|0.167;G|0.833	0.833	strong	DEFA3,NS,carcinoma,0,1	DEFA3	7	1	NM_005217	exon3	c.A194C	p.D65A	TAGCAGTCCATGT	.	scavenged	Atlas-SNP
HCAR3	8843	hgsc.bcm.edu	37	12	123200354	123200354	+	Missense_Mutation	SNP	G	G	A	rs200905183	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	258	92	292	0	0.356589	0	G|0.884;A|0.116	0.116	strong	HCAR3_ENST00000528880,colon,carcinoma,+1,3	HCAR3	49	3	NM_006018	exon1	c.C931T	p.R311C	GGCAGCGGTTGAT	.	scavenged	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	151150568	151150568	+	Silent	SNP	G	G	A	rs142871635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	90	173	0	0.542169	0	G|0.997;A|0.003	0.003	strong	.	MED12L	271	.	NM_053002	exon43	c.G6414A	p.P2138P	GACTCCGTATGGG	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133253180	133253180	+	Missense_Mutation	SNP	A	A	T	rs139075637	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	91	223	0	0.54491	0	A|0.999;T|0.001	0.001	strong	.	POLE	416	.	NM_006231	exon9	c.T861A	p.D287E	CTCAGCATCAGGA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47968927	47968927	+	Missense_Mutation	SNP	C	C	A	rs2686817	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	243	273	2	0.975904	0.00732601	C|0.513;A|0.487	0.487	strong	.	PKD1L1	328	.	NM_138295	exon7	c.G934T	p.V312F	TATGAACACGGAA	.	PASS	Atlas-SNP
LILRA3	11026	hgsc.bcm.edu	37	19	54804167	54804167	+	Missense_Mutation	SNP	G	G	A	rs11574606	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	115	97	0	0.566502	0	G|0.907;A|0.093	0.093	strong	.	LILRA3	65	.	NM_001172654	exon1	c.C7T	p.P3S	GGATGGGGGTCAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152285930	152285930	+	Missense_Mutation	SNP	G	G	A	rs11584340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	440	172	313	1	0.390909	0.00319489	G|0.785;A|0.215	0.215	strong	.	FLG	900	.	NM_002016	exon3	c.C1432T	p.P478S	AGTCAGGCTGTTC	.	PASS	Atlas-SNP
SLC17A3	10786	hgsc.bcm.edu	37	6	25850845	25850845	+	Missense_Mutation	SNP	C	C	T	rs56027330	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	38	63	0	0.603175	0	C|0.910;T|0.090	0.090	strong	SLC17A3,NS,carcinoma,+1,1	SLC17A3	95	1	NM_001098486	exon8	c.G835A	p.G279R	AAGACCCGACCTG	.	PASS	Atlas-SNP
ATP13A1	57130	hgsc.bcm.edu	37	19	19758522	19758522	+	Silent	SNP	T	T	C	rs142259293	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	41	161	0	0.5	0	T|0.989;C|0.011	0.011	strong	ATP13A1,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	ATP13A1	82	2	NM_020410	exon20	c.A2679G	p.R893R	CCGCCGTCGCCGC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225393787	225393787	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	34	79	0	0.330097	0	.	.	none	.	DNAH14	300	.	NM_001373	exon39	c.T6026G	p.I2009R	AGAGAATAGCTTT	.	PASS	Atlas-SNP
PLA2G7	7941	hgsc.bcm.edu	37	6	46672943	46672943	+	Missense_Mutation	SNP	A	A	G	rs1051931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	109	124	1	1	0.00806452	A|0.223;G|0.777	0.777	strong	.	PLA2G7	49	.	NM_005084	exon11	c.T1136C	p.V379A	ATAGCTACATTTG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118530796	118530796	+	Silent	SNP	C	C	T	rs12040811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	56	176	0	0.608696	0	C|0.915;T|0.085	0.085	strong	.	SPAG17	263	.	NM_206996	exon39	c.G5553A	p.Q1851Q	CAAAGACTGCTTG	.	PASS	Atlas-SNP
UBE2U	148581	hgsc.bcm.edu	37	1	64672525	64672525	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	189	3	293	0	0.015873	0	.	.	none	UBE2U,caecum,carcinoma,0,2	UBE2U	16	2	NM_152489	exon3	c.C227T	p.P76L	CAATTCCGTTTCA	.	scavenged	Atlas-SNP
SEZ6	124925	hgsc.bcm.edu	37	17	27284515	27284515	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	2	122	0	0.015748	0	.	.	none	SEZ6,colon,carcinoma,0,1	SEZ6	61	1	NM_001098635	exon12	c.G2345A	p.R782H	ATGAGGCGTCGGC	.	scavenged	Atlas-SNP
RFPL4A	342931	hgsc.bcm.edu	37	19	56274453	56274453	+	Missense_Mutation	SNP	G	G	A	rs75239380	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	46	187	0	0.239583	0	G|0.760;A|0.240	0.240	strong	ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	NM_001145014	exon3	c.G776A	p.G259E	AACGTGGAAGTCA	.	scavenged	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912343	45912343	+	Missense_Mutation	SNP	A	A	G	rs762562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	13	53	0	0.342105	0	A|0.774;G|0.226	0.226	strong	CD3EAP,NS,carcinoma,0,1	CD3EAP	27	1	NM_012099	exon3	c.A1117G	p.K373E	GGAGCGAAGCCTC	.	PASS	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5068431	5068431	+	Missense_Mutation	SNP	G	G	A	rs17350764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	444	230	518	4	0.518018	0.00772201	G|0.792;A|0.208	0.208	strong	OR52J3,right_upper_lobe,carcinoma,-2,1	OR52J3	77	1	NM_001001916	exon1	c.G676A	p.V226I	CGTGCTGTCTTCC	.	scavenged	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	37	4	30725987	30725987	+	Silent	SNP	G	G	A	rs977931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	50	74	0	0.526316	0	A|0.158;C|0.004	0.158	strong	.	PCDH7	215	.	NM_032457	exon1	c.G2943A	p.R981R	ATACAGGTCCGTT	.	PASS	Atlas-SNP
SLIT1	6585	hgsc.bcm.edu	37	10	98806512	98806512	+	Silent	SNP	G	G	C	rs17112342	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	28	4	48	0	0.142857	0	G|0.955;C|0.045	0.045	strong	.	SLIT1	154	.	NM_003061	exon18	c.C1752G	p.A584A	CTCGAAGGCCCCA	.	PASS	Atlas-SNP
ZNF385A	25946	hgsc.bcm.edu	37	12	54767812	54767812	+	Silent	SNP	G	G	A	rs2887875	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	54	94	0	0.574468	0	G|0.827;C|0.000;A|0.173	0.173	strong	.	ZNF385A	45	.	NM_001130967	exon4	c.C366T	p.D122D	AGCTGGGTCTCCA	.	PASS	Atlas-SNP
UTP6	55813	hgsc.bcm.edu	37	17	30200750	30200750	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	4	69	0	0.0784314	0	.	.	none	.	UTP6	46	.	NM_018428	exon15	c.C1328T	p.S443F	GCCCAGGAAATCC	.	PASS	Atlas-SNP
SIGLEC12	89858	hgsc.bcm.edu	37	19	52004878	52004878	+	Missense_Mutation	SNP	C	C	T	rs148809065	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	51	144	0	0.439655	0	C|0.988;T|0.012	0.012	strong	.	SIGLEC12	243	.	NM_053003	exon1	c.G110A	p.G37D	CACAGGCCCTCCT	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196529917	196529917	+	Silent	SNP	A	A	G	rs183020057	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	10	180	0	0.046729	0	A|1.000;G|0.000	0.000	strong	.	PAK2	113	.	NM_002577	exon4	c.A318G	p.L106L	ATTACTACAGACC	.	PASS	Atlas-SNP
SLC22A20	440044	hgsc.bcm.edu	37	11	64981853	64981853	+	Missense_Mutation	SNP	G	G	T	rs239259	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	45	69	1	0.592105	0.0144928	G|0.667;T|0.333	0.333	strong	SLC22A20,NS,carcinoma,0,4	SLC22A20	36	4	NM_001004326	exon2	c.G438T	p.M146I	CTACATGGCCGGG	.	scavenged	Atlas-SNP
ME3	10873	hgsc.bcm.edu	37	11	86159223	86159223	+	Silent	SNP	C	C	T	rs34662182	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	117	122	0	0.672414	0	C|0.946;T|0.054	0.054	strong	ME3,NS,carcinoma,0,1	ME3	70	1	NM_006680	exon11	c.G1206A	p.V402V	CCTCACCACCTCC	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951488	130951488	+	Silent	SNP	A	A	G	rs2443644	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	58	189	0	0.233871	0	A|0.985;G|0.015	0.015	strong	TUBA3E,right_upper_lobe,carcinoma,-1,1	TUBA3E	73	1	NM_207312	exon4	c.T927C	p.H309H	CTTGCCATGGCGA	.	scavenged	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159398700	159398700	+	Missense_Mutation	SNP	C	C	T	rs3756987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	74	187	0	0.445783	0	C|0.842;T|0.158	0.158	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon8	c.G1553A	p.G518D	AGGTAGCCTCCAT	.	PASS	Atlas-SNP
C10orf90	118611	hgsc.bcm.edu	37	10	128193368	128193368	+	Missense_Mutation	SNP	C	C	T	rs11245008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	57	104	0	0.606383	0	C|0.781;T|0.219	0.219	strong	.	C10orf90	121	.	NM_001004298	exon3	c.G401A	p.R134H	CCTCTGCGGGGGC	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067099	79067099	+	Silent	SNP	G	G	C	rs142017909	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	9	71	0	0.121622	0	G|0.970;C|0.030	0.030	strong	ADAMTS7,NS,carcinoma,0,3	ADAMTS7	142	3	NM_014272	exon12	c.C1743G	p.R581R	GCGCTTGCGCTCA	.	PASS	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13150531	13150531	+	Silent	SNP	T	T	C	rs10756457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	59	127	0	0.421429	0	T|0.540;C|0.460	0.460	strong	.	MPDZ	324	.	NM_003829	exon25	c.A3609G	p.K1203K	TCCAGGTTTCAAG	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92257991	92257991	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	123	134	0	0.615	0	.	.	none	.	FAT3	1822	.	NM_001008781	exon2	c.C3484A	p.P1162T	AACTCTCCAAAGG	.	PASS	Atlas-SNP
SCAMP5	192683	hgsc.bcm.edu	37	15	75308976	75308976	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	33	118	0	0.492537	0	.	.	none	.	SCAMP5	34	.	NM_001178111	exon5	c.C179T	p.A60V	GTCTCGCGTGGCT	.	PASS	Atlas-SNP
DRG2	1819	hgsc.bcm.edu	37	17	18003919	18003919	+	Missense_Mutation	SNP	G	G	A	rs143296623	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	51	83	0	0.5	0	G|0.996;A|0.004	0.004	strong	.	DRG2	27	.	NM_001388	exon7	c.G577A	p.V193I	TCGACAGTCACGC	.	PASS	Atlas-SNP
HSDL1	83693	hgsc.bcm.edu	37	16	84158248	84158248	+	Missense_Mutation	SNP	G	G	C	rs4378600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	19	159	0	0.11875	0	G|0.737;C|0.263	0.263	strong	.	HSDL1	23	.	NM_031463	exon6	c.C980G	p.S327C	GTGCAGGATAAGG	.	PASS	Atlas-SNP
DEPDC5	9681	hgsc.bcm.edu	37	22	32205632	32205632	+	Silent	SNP	A	A	C	rs5998135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	14	56	0	0.264151	0	A|0.906;C|0.094	0.094	strong	.	DEPDC5	266	.	NM_001242897	exon19	c.A1323C	p.T441T	TGATACATGTGAG	.	PASS	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	37	7	4172006	4172006	+	Silent	SNP	C	C	T	rs13224870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	80	104	0	0.661157	0	C|0.720;T|0.280	0.280	strong	SDK1,NS,malignant_melanoma,+1,1	SDK1	361	1	NM_152744	exon28	c.C4179T	p.S1393S	CACCTCCGTGCGG	.	PASS	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2176454	2176454	+	Missense_Mutation	SNP	G	G	A	rs9328764	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	87	245	1	0.488764	0.00408163	G|0.682;A|0.318	0.318	strong	.	POLN	82	.	NM_181808	exon8	c.C1273T	p.R425C	AAGTACGAAATAG	.	PASS	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2577809	2577809	+	Missense_Mutation	SNP	G	G	A	rs375916445		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	53	65	0	0.736111	0	.	.	weak	.	BRAT1	57	.	NM_152743	exon14	c.C2360T	p.T787M	GCCAGCGTGCTCC	.	PASS	Atlas-SNP
MFGE8	4240	hgsc.bcm.edu	37	15	89450003	89450003	+	Silent	SNP	G	G	A	rs2271714	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	15	132	0	0.192308	0	G|0.826;A|0.174	0.174	strong	MFGE8,NS,carcinoma,0,1	MFGE8	60	1	NM_001114614	exon4	c.C394T	p.L132L	GCAGCAGGTTCAC	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12391319	12391319	+	Missense_Mutation	SNP	G	G	T	rs6967385	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	51	106	0	0.525773	0	G|0.378;T|0.622	0.622	strong	.	VWDE	123	.	NM_001135924	exon19	c.C3766A	p.Q1256K	TAAATTGATTTAC	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3789452	3789452	+	Missense_Mutation	SNP	C	C	T	rs17836273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	89	201	0	0.502825	0	C|0.866;T|0.134	0.134	strong	.	EFCAB4B	100	.	NM_001144958	exon5	c.G292A	p.A98T	CATCAGCATCCAG	.	PASS	Atlas-SNP
SLC2A4	6517	hgsc.bcm.edu	37	17	7187123	7187123	+	Silent	SNP	T	T	C	rs5435	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	119	109	1	1	0.00917431	C|0.701;N|0.001	0.701	strong	.	SLC2A4	44	.	NM_001042	exon4	c.T390C	p.N130N	GGCCAATGCTGCT	.	PASS	Atlas-SNP
CUL4A	8451	hgsc.bcm.edu	37	13	113909008	113909008	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	53	98	0	0.509615	0	.	.	none	.	CUL4A	50	.	NM_001008895	exon17	c.G1754A	p.G585E	TCCAGGGGAAGAA	.	PASS	Atlas-SNP
ARHGEF40	55701	hgsc.bcm.edu	37	14	21542753	21542753	+	Silent	SNP	G	G	A	rs1243472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	22	26	0	0.666667	0	G|0.741;A|0.259	0.259	strong	.	ARHGEF40	84	.	NM_018071	exon3	c.G864A	p.A288A	CCGGGCGTGGATG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910693	29910693	+	Missense_Mutation	SNP	A	A	G	rs41559716	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	14	192	0	0.0682927	0	A|0.979;G|0.021	0.021	strong	HLA-A,bladder,carcinoma,0,8	HLA-A	89	8	NM_001242758	exon2	c.A233G	p.Q78R	TAGAGCAGGAGGG	.	PASS	Atlas-SNP
DCAF12	25853	hgsc.bcm.edu	37	9	34107505	34107505	+	Missense_Mutation	SNP	C	C	T	rs11557154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	79	168	0	0.448864	0	C|0.846;T|0.154	0.154	strong	DCAF12,colon,carcinoma,+1,1	DCAF12	37	1	NM_015397	exon3	c.G392A	p.R131Q	GGCTCCCGGTCTT	.	PASS	Atlas-SNP
COG8	84342	hgsc.bcm.edu	37	16	69373414	69373414	+	Silent	SNP	T	T	C	rs11542583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	37	55	0	1	0	T|0.711;C|0.289	0.289	strong	.	COG8	32	.	NM_032382	exon1	c.A42G	p.T14T	CGCTGCTGTGGCC	.	PASS	Atlas-SNP
IRS1	3667	hgsc.bcm.edu	37	2	227660544	227660544	+	Missense_Mutation	SNP	C	C	T	rs1801278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	40	79	0	0.740741	0	T|0.061;C|0.939	0.061	strong	.	IRS1	141	.	NM_005544	exon1	c.G2911A	p.G971R	CAGCCCCGGGAGG	.	PASS	Atlas-SNP
SH3PXD2B	285590	hgsc.bcm.edu	37	5	171849471	171849471	+	Silent	SNP	G	G	A	rs17074773	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	9	25	0	0.375	0	G|0.692;A|0.308	0.308	strong	.	SH3PXD2B	91	.	NM_001017995	exon2	c.C105T	p.S35S	GGAGCCGCTGGAC	.	PASS	Atlas-SNP
NR0B1	190	hgsc.bcm.edu	37	X	30326983	30326983	+	Silent	SNP	C	C	T	rs2269345	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	28	26	66	0	0.928571	0	C|0.621;T|0.379	0.379	strong	.	NR0B1	61	.	NM_000475	exon1	c.G498A	p.R166R	CCCTGGCCGTGCC	.	PASS	Atlas-SNP
SLC23A2	9962	hgsc.bcm.edu	37	20	4880308	4880308	+	Silent	SNP	G	G	A	rs1776964	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	104	155	1	1	0.00645161	G|0.545;A|0.455	0.455	strong	.	SLC23A2	62	.	NM_203327	exon6	c.C375T	p.A125A	GGCATCGGCCAAC	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186678633	186678633	+	Missense_Mutation	SNP	C	C	T	rs17826666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	112	246	0	0.486957	0	C|0.944;T|0.056	0.056	strong	.	FSIP2	251	.	NM_173651	exon18	c.C20456T	p.T6819I	AAAGTACTGAAGC	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487265	32487265	+	Missense_Mutation	SNP	C	C	G	rs139485758	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	18	91	9	0.159292	0.0989011	A|0.003;C|0.930;G|0.067	0.067	strong	HLA-DRB5,NS,NS,0,1	HLA-DRB5	31	1	NM_002125	exon3	c.G534C	p.Q178H	TCCATTCTGAATC	.	scavenged	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7033037	7033037	+	Silent	SNP	G	G	A	rs621993	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	45	71	1	1	0.0140845	G|0.542;A|0.458	0.458	strong	LAMA1,brain,glioma,-1,1	LAMA1	458	1	NM_005559	exon15	c.C2109T	p.A703A	ATCAGCGGCCACC	.	scavenged	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380396	107380396	+	Silent	SNP	T	T	G	rs36091517	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	371	162	402	0	0.436658	0	T|0.792;G|0.208	0.208	strong	.	OR13C9	42	.	NM_001001956	exon1	c.A90C	p.L30L	GAAGATTAGCACA	.	PASS	Atlas-SNP
THBS4	7060	hgsc.bcm.edu	37	5	79351852	79351852	+	Silent	SNP	A	A	T	rs71594659	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	42	128	0	0.42	0	ACAGGTAGG|0.500;TCAGGTAAA|0.500	.	alt	THBS4,NS,carcinoma,0,1	THBS4	82	1	NM_003248	exon3	c.A537T	p.P179P	GAAGCCACAGGTA	.	PASS	Atlas-SNP
RAD9B	144715	hgsc.bcm.edu	37	12	110960196	110960196	+	Missense_Mutation	SNP	G	G	A	rs34513555	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	113	245	1	0.530516	0.00408163	G|0.924;A|0.076	0.076	strong	.	RAD9B	50	.	NM_152442	exon10	c.G1105A	p.G369R	GTGCCAGGGTCTC	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158536334	158536334	+	Silent	SNP	G	G	A	rs2305474	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	46	114	0	0.686567	0	G|0.846;A|0.154	0.154	strong	.	ESYT2	70	.	NM_020728	exon16	c.C1761T	p.N587N	CTTCAGGTTCCCC	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169512027	169512027	+	Silent	SNP	T	T	C	rs6021	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	186	160	1	0.994652	0.00625	T|0.763;C|0.237	0.237	strong	.	F5	301	.	NM_000130	exon13	c.A2301G	p.S767S	TGTGTTTGAAGAA	.	PASS	Atlas-SNP
C1orf53	388722	hgsc.bcm.edu	37	1	197874949	197874949	+	Silent	SNP	T	T	C	rs2270763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	363	362	290	2	0.997245	0.00689655	T|0.659;C|0.341	0.341	strong	.	C1orf53	18	.	NM_001024594	exon2	c.T288C	p.D96D	TGTGGATCCAGCT	.	PASS	Atlas-SNP
FAM178A	55719	hgsc.bcm.edu	37	10	102716222	102716222	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	4	127	0	0.0408163	0	.	.	none	.	FAM178A	9	.	NM_001136123	exon18	c.A3345G	p.L1115L	TGTGCTACTCTGT	.	PASS	Atlas-SNP
GPER	2852	hgsc.bcm.edu	37	7	1131411	1131411	+	Missense_Mutation	SNP	C	C	T	rs11544331	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	121	170	1	0.633508	0.00588235	C|0.808;T|0.192	0.192	strong	.	GPER	25	.	NM_001505	exon2	c.C47T	p.P16L	TGTACCCAGGCAC	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55485899	55485899	+	Silent	SNP	G	G	A	rs2217659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	28	75	0	0.388889	0	G|0.829;A|0.171	0.171	strong	.	NLRP2	161	.	NM_001174082	exon3	c.G312A	p.K104K	AAGGAAGCCTCTA	.	PASS	Atlas-SNP
HHLA3	11147	hgsc.bcm.edu	37	1	70820880	70820880	+	Silent	SNP	G	G	A	rs55863806	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	8	53	0	0.181818	0	G|0.926;A|0.074	0.074	strong	.	HHLA3	11	.	NM_001036645	exon1	c.G246A	p.A82A	AAAAGCGGAGGCG	.	PASS	Atlas-SNP
SEL1L2	80343	hgsc.bcm.edu	37	20	13912309	13912309	+	Missense_Mutation	SNP	G	G	A	rs41275404	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	65	167	0	0.422078	0	G|0.910;A|0.090	0.090	strong	SEL1L2,colon,carcinoma,0,1	SEL1L2	103	1	NM_001271539	exon3	c.C223T	p.R75C	TTTTACGTTGATT	.	PASS	Atlas-SNP
GLMN	11146	hgsc.bcm.edu	37	1	92754667	92754667	+	Missense_Mutation	SNP	C	C	T	rs61754623	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	49	84	0	0.844828	0	C|0.996;T|0.004	0.004	strong	.	GLMN	37	.	NM_053274	exon6	c.G436A	p.A146T	ACAATGCTAATCC	.	PASS	Atlas-SNP
CAMKMT	79823	hgsc.bcm.edu	37	2	44942450	44942450	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	45	99	0	0.424528	0	.	.	none	.	CAMKMT	20	.	NM_024766	exon7	c.A581G	p.N194S	CAAGGAATCAGAA	.	PASS	Atlas-SNP
CEP135	9662	hgsc.bcm.edu	37	4	56874517	56874517	+	Missense_Mutation	SNP	A	A	C	rs3214045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	83	112	1	0.976471	0.00892857	A|0.815;C|0.185;G|0.000	0.185	strong	.	CEP135	115	.	NM_025009	exon18	c.A2305C	p.I769L	ATGAAGATAATGA	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242407588	242407588	+	Missense_Mutation	SNP	G	G	A	rs41342147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	72	133	0	0.473684	0	G|0.892;A|0.108	0.108	strong	FARP2,rectum,carcinoma,-2,1	FARP2	92	1	NM_014808	exon18	c.G1927A	p.V643I	GACGAGGTCCTAA	.	PASS	Atlas-SNP
PEX11G	92960	hgsc.bcm.edu	37	19	7542118	7542118	+	Silent	SNP	G	G	A	rs7256275	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	29	92	0	0.568627	0	G|0.870;A|0.130	0.130	strong	.	PEX11G	16	.	NM_080662	exon5	c.C696T	p.A232A	GCCGCCGGCCCGG	.	PASS	Atlas-SNP
OPN4	94233	hgsc.bcm.edu	37	10	88422028	88422028	+	Missense_Mutation	SNP	C	C	G	rs34191521	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	84	165	1	0.785047	0.00606061	C|0.977;G|0.023	0.023	strong	.	OPN4	61	.	NM_001030015	exon9	c.C1126G	p.L376V	CAGCACCTGCCCT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677556	100677556	+	Silent	SNP	A	A	C	rs4373459	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	534	174	176	2	0.325843	0.0113636	A|0.947;C|0.053	0.053	strong	MUC17,colon,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.A2859C	p.T953T	CAGCACACCTGTG	.	scavenged	Atlas-SNP
OR2L8	391190	hgsc.bcm.edu	37	1	248112915	248112915	+	Silent	SNP	A	A	G	rs77641372		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	372	120	291	1	0.322581	0.00343643	.	.	weak	OR2L8,right_upper_lobe,carcinoma,+1,1	OR2L8	92	1	NM_001001963	exon1	c.A756G	p.A252A	CTATGCACCTTTT	.	scavenged	Atlas-SNP
FAM126A	84668	hgsc.bcm.edu	37	7	23015831	23015831	+	Silent	SNP	T	T	C	rs3735231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	72	56	0	1	0	T|0.643;C|0.357	0.357	strong	FAM126A,NS,carcinoma,-1,1	FAM126A	53	1	NM_032581	exon7	c.A624G	p.S208S	TTACCTTGAACAA	.	PASS	Atlas-SNP
ZNF16	7564	hgsc.bcm.edu	37	8	146157339	146157339	+	Silent	SNP	T	T	C	rs3735787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	47	150	0	0.252688	0	T|0.784;C|0.216	0.216	strong	ZNF16,NS,adenoma,0,1	ZNF16	80	1	NM_006958	exon3	c.A834G	p.S278S	AAAGTCTGAGTGC	.	PASS	Atlas-SNP
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959776	45959776	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	10	114	1	0.070922	0.00877193	.	.	none	KRTAP10-1,NS,carcinoma,0,1	KRTAP10-1	34	1	NM_198691	exon1	c.G258T	p.Q86H	AGCCGGCTGGCAG	.	scavenged	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76126737	76126737	+	Missense_Mutation	SNP	C	C	T	rs145964625		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	632	91	477	1	0.143987	0.00209644	.	.	weak	DTX2,NS,haematopoietic_neoplasm,0,3	DTX2	64	3	NM_001102594	exon6	c.C1093T	p.R365C	GCCTCCCGTCTGG	.	scavenged	Atlas-SNP
USP34	9736	hgsc.bcm.edu	37	2	61415492	61415492	+	Silent	SNP	A	A	G	rs14170	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	38	85	0	0.417582	0	A|0.525;G|0.475	0.475	strong	.	USP34	334	.	NM_014709	exon80	c.T10386C	p.A3462A	TTCCTCAGCTAGG	.	PASS	Atlas-SNP
CEP128	145508	hgsc.bcm.edu	37	14	80971261	80971261	+	Missense_Mutation	SNP	C	C	T	rs61744330	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	20	54	0	0.322581	0	C|0.923;T|0.077	0.077	strong	.	CEP128	146	.	NM_152446	exon23	c.G3175A	p.V1059M	AGTTCACGTATGA	.	PASS	Atlas-SNP
ADAMTS6	11174	hgsc.bcm.edu	37	5	64756136	64756136	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	8	113	0	0.0701754	0	.	.	none	.	ADAMTS6	174	.	NM_197941	exon4	c.G492A	p.E164E	AAAATACTCTTCA	.	PASS	Atlas-SNP
SAMD4A	23034	hgsc.bcm.edu	37	14	55226987	55226987	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	32	45	0	0.695652	0	.	.	none	.	SAMD4A	68	.	NM_015589	exon6	c.C1285T	p.R429C	GCTCGCCGCCGGG	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56572832	56572832	+	Missense_Mutation	SNP	G	G	A	rs10409555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	120	226	1	0.56338	0.00442478	G|0.645;A|0.355	0.355	strong	.	NLRP5	217	.	NM_153447	exon15	c.G3541A	p.V1181I	CCCCGAGTCGTAA	.	PASS	Atlas-SNP
C2orf71	388939	hgsc.bcm.edu	37	2	29294754	29294754	+	Missense_Mutation	SNP	G	G	C	rs17744093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	44	99	0	0.44	0	G|0.836;C|0.164	0.164	strong	.	C2orf71	146	.	NM_001029883	exon1	c.C2374G	p.L792V	TTTTGAGAGATTC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129900918	129900918	+	Silent	SNP	C	C	A	rs201914667	by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	274	3	290	0	0.0109489	0	C|1.000;T|0.000	.	alt	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.G9186T	p.A3062A	CTCTTCCGCAGGT	.	scavenged	Atlas-SNP
OR4D1	26689	hgsc.bcm.edu	37	17	56233234	56233234	+	Silent	SNP	C	C	T	rs62636635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	143	295	0	0.498258	0	C|0.961;T|0.039	0.039	strong	.	OR4D1	48	.	NM_012374	exon1	c.C720T	p.C240C	CACCTGCACCACC	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128315889	128315889	+	Missense_Mutation	SNP	A	A	T	rs6971819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	11	66	0	0.611111	0	A|0.892;T|0.108	0.108	strong	.	FAM71F2	19	.	NM_001012454	exon2	c.A341T	p.D114V	CTGGTGACGCCCC	.	PASS	Atlas-SNP
KRTAP24-1	643803	hgsc.bcm.edu	37	21	31654809	31654809	+	Missense_Mutation	SNP	C	C	T	rs77638540	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	277	155	233	0	0.559567	0	C|0.951;T|0.049	0.049	strong	.	KRTAP24-1	44	.	NM_001085455	exon1	c.G442A	p.G148S	TGGAACCGTTGCG	.	PASS	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74516497	74516497	+	Silent	SNP	G	G	A	rs34076068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	279	187	223	1	0.670251	0.00448431	G|0.885;A|0.115	0.115	strong	.	.	.	.	NM_025057	exon8	c.G885A	p.L295L	AAACTTGGAGACT	.	PASS	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219513782	219513782	+	Silent	SNP	T	T	C	rs4674322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	12	62	0	0.285714	0	T|0.861;C|0.139	0.139	strong	.	ZNF142	190	.	NM_001105537	exon6	c.A849G	p.P283P	GGGTAATGGCTCT	.	PASS	Atlas-SNP
PPAP2C	8612	hgsc.bcm.edu	37	19	282753	282753	+	Missense_Mutation	SNP	G	G	A	rs1138439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	19	65	0	0.339286	0	T|0.071;G|0.466;C|0.124;A|0.339	0.339	strong	PPAP2C_ENST00000269812,caecum,carcinoma,0,5	PPAP2C	38	5	NM_177543	exon4	c.C602T	p.A201V	CTCACCGCCAAGA	.	PASS	Atlas-SNP
PHYH	5264	hgsc.bcm.edu	37	10	13330402	13330402	+	Silent	SNP	T	T	C	rs473407	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	12	119	0	0.196721	0	T|0.728;C|0.272	0.272	strong	.	PHYH	50	.	NM_006214	exon6	c.A636G	p.T212T	CTTGTGTGTGCCT	.	PASS	Atlas-SNP
RNF39	80352	hgsc.bcm.edu	37	6	30039240	30039240	+	Missense_Mutation	SNP	G	G	T	rs2301753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17	10	29	0	0.588235	0	G|0.804;T|0.196	0.196	strong	.	RNF39	27	.	NM_025236	exon4	c.C911A	p.A304E	TCGTCCGCATCCT	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79095417	79095417	+	Missense_Mutation	SNP	C	C	T	rs10043986	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	72	141	0	0.525547	0	C|0.938;T|0.062	0.062	strong	.	CMYA5	643	.	NM_153610	exon13	c.C12188T	p.P4063L	AGCCCCCGGATTC	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123846252	123846252	+	Missense_Mutation	SNP	G	G	A	rs201709460	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	51	106	0	0.428571	0	G|0.999;A|0.001	0.001	strong	.	TACC2	271	.	NM_206862	exon4	c.G4237A	p.A1413T	CACATCGCCAAGA	.	PASS	Atlas-SNP
MMAB	326625	hgsc.bcm.edu	37	12	110011229	110011229	+	Silent	SNP	G	G	T	rs36013132	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	32	78	0	0.592593	0	.	.	alt	.	MMAB	16	.	NM_052845	exon1	c.C57A	p.R19R	GCACCCGCGCAGG	.	PASS	Atlas-SNP
SYNRG	11276	hgsc.bcm.edu	37	17	35896123	35896123	+	Silent	SNP	T	T	C	rs1045000	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	58	136	0	0.42963	0	T|0.778;C|0.222	0.222	strong	.	SYNRG	101	.	NM_007247	exon19	c.A3624G	p.V1208V	ATTCCATACTTTA	.	PASS	Atlas-SNP
RBM6	10180	hgsc.bcm.edu	37	3	50005855	50005855	+	Missense_Mutation	SNP	G	G	A	rs143972186	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	106	219	1	0.517073	0.00456621	G|0.997;A|0.003	0.003	strong	.	RBM6	85	.	NM_005777	exon3	c.G997A	p.E333K	AAGGGAGAATTTG	.	PASS	Atlas-SNP
GTF2A1	2957	hgsc.bcm.edu	37	14	81662494	81662494	+	Silent	SNP	T	T	C	rs34999597	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212	107	180	0	0.504717	0	T|0.998;C|0.002	0.002	strong	.	GTF2A1	34	.	NM_015859	exon6	c.A570G	p.P190P	CATTTGTGGTATA	.	PASS	Atlas-SNP
ZNF215	7762	hgsc.bcm.edu	37	11	6962879	6962879	+	Missense_Mutation	SNP	C	C	T	rs141940336	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	40	83	0	0.45977	0	C|1.000;T|0.000	0.000	strong	.	ZNF215	72	.	NM_013250	exon4	c.C478T	p.P160S	GGCAAACCACAGG	.	PASS	Atlas-SNP
POLR1B	84172	hgsc.bcm.edu	37	2	113308516	113308516	+	Silent	SNP	T	T	A	rs2304555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	273	366	0	0.982014	0	T|0.369;A|0.631	0.631	strong	POLR1B,NS,carcinoma,+1,1	POLR1B	95	1	NM_019014	exon5	c.T699A	p.T233T	TGGCACTGTTATG	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214805928	214805928	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	2	108	0	0.0126582	0	.	.	none	CENPF,colon,carcinoma,-1,1	CENPF	321	1	NM_016343	exon10	c.C1429T	p.L477L	AATGAGCTGAGGA	.	scavenged	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2195024	2195024	+	Missense_Mutation	SNP	T	T	G	rs10018786	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	83	227	0	0.432292	0	T|0.710;G|0.290	0.290	strong	.	POLN	82	.	NM_181808	exon5	c.A928C	p.M310L	ATTTCATTGTTTG	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32029431	32029431	+	Missense_Mutation	SNP	G	G	A	rs12524664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	2	117	1	0.020202	0.00854701	G|0.894;A|0.106	0.106	strong	TNXB_ENST00000375247,NS,carcinoma,+1,2	TNXB	553	2	NM_019105	exon21	c.C7235T	p.P2412L	AGGAGCGGCTCCT	.	scavenged	Atlas-SNP
SYNGR4	23546	hgsc.bcm.edu	37	19	48879375	48879375	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	38	147	0	0.258503	0	.	.	none	SYNGR4,NS,carcinoma,-2,3	SYNGR4	31	3	NM_012451	exon5	c.C505T	p.R169X	GACCTCCGAAATG	.	PASS	Atlas-SNP
MAMLD1	10046	hgsc.bcm.edu	37	X	149638920	149638920	+	Missense_Mutation	SNP	C	C	T	rs41313406	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	68	106	0	0.985507	0	C|0.927;T|0.073	0.073	strong	.	MAMLD1	263	.	NM_005491	exon3	c.C1075T	p.P359S	CCACCCCCATTCA	.	PASS	Atlas-SNP
MMP14	4323	hgsc.bcm.edu	37	14	23312594	23312594	+	Missense_Mutation	SNP	G	G	A	rs1042704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	49	71	0	0.680556	0	G|0.873;A|0.127	0.127	strong	.	MMP14	40	.	NM_004995	exon5	c.G817A	p.D273N	CTGCCCGATGATG	.	PASS	Atlas-SNP
YIPF7	285525	hgsc.bcm.edu	37	4	44652030	44652030	+	Missense_Mutation	SNP	C	C	T	rs2348353	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	87	175	0	0.572368	0	C|0.816;T|0.184	0.184	strong	.	YIPF7	33	.	NM_182592	exon2	c.G160A	p.A54T	CATAGGCATTAGA	.	PASS	Atlas-SNP
SP2	6668	hgsc.bcm.edu	37	17	45994154	45994154	+	Silent	SNP	G	G	A	rs2229358	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	38	89	0	0.5	0	G|0.545;A|0.455	0.455	strong	.	SP2	38	.	NM_003110	exon3	c.G717A	p.P239P	AACCCCGCTGTCT	.	PASS	Atlas-SNP
CEP68	23177	hgsc.bcm.edu	37	2	65298839	65298839	+	Silent	SNP	A	A	G	rs17849707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	33	96	0	0.434211	0	A|0.773;G|0.227	0.227	strong	.	CEP68	69	.	NM_015147	exon3	c.A609G	p.T203T	CTCCACAGGCAGC	.	PASS	Atlas-SNP
ZNF721	170960	hgsc.bcm.edu	37	4	438067	438067	+	Silent	SNP	C	C	T	rs73070365	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	69	224	0	0.445161	0	C|0.943;T|0.057	0.057	strong	.	ZNF721	205	.	NM_133474	exon3	c.A189A	p.V63V	AACTCCCTTCTGC	.	PASS	Atlas-SNP
CTTNBP2NL	55917	hgsc.bcm.edu	37	1	112991698	112991698	+	Silent	SNP	T	T	C	rs2256883	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	100	129	0	0.980392	0	T|0.457;C|0.543	0.543	strong	CTTNBP2NL,NS,carcinoma,0,1	CTTNBP2NL	65	1	NM_018704	exon4	c.T234C	p.N78N	CACAAATCCACTC	.	PASS	Atlas-SNP
ZNRF4	148066	hgsc.bcm.edu	37	19	5455976	5455976	+	Silent	SNP	C	C	T	rs61740902	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	25	14	30	0	0.56	0	C|0.851;T|0.149	0.149	strong	.	ZNRF4	59	.	NM_181710	exon1	c.C474T	p.I158I	CGCCATCGTGCTG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9082514	9082514	+	Missense_Mutation	SNP	C	C	A	rs17000871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	387	190	419	0	0.490956	0	A|0.158;C|0.841;T|0.000	0.158	strong	.	MUC16	4315	.	NM_024690	exon1	c.G9301T	p.A3101S	CTTCTGCAATGGT	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25016911	25016911	+	Missense_Mutation	SNP	C	C	T	rs199703506	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	429	17	378	0	0.039627	0	C|0.996;T|0.004	0.004	strong	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon9	c.C607T	p.R203W	GTGCTTCGGGAGG	.	scavenged	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6610889	6610889	+	Missense_Mutation	SNP	G	G	A	rs61733402	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	74	165	0	0.4625	0	G|0.936;A|0.064	0.064	strong	.	MAN2B2	80	.	NM_015274	exon12	c.G1870A	p.G624R	GTCAACGGGGATG	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	37	11	119052826	119052826	+	Missense_Mutation	SNP	C	C	A	rs4245191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	119	128	0	0.653846	0	C|0.378;A|0.622	0.622	strong	.	NLRX1	128	.	NM_024618	exon9	c.C2378A	p.A793E	TGACGGCGGCAGG	.	PASS	Atlas-SNP
PRKAA1	5562	hgsc.bcm.edu	37	5	40765280	40765280	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	306	131	277	0	0.428105	0	.	.	none	.	PRKAA1	27	.	NM_206907	exon8	c.T927C	p.Y309Y	TGAACTATATGAT	.	PASS	Atlas-SNP
DEFB104B	503618	hgsc.bcm.edu	37	8	7694034	7694034	+	Missense_Mutation	SNP	A	A	G	rs2680507	bycluster;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1448	369	2087	5	0.254834	0.00239578	A|0.250;G|0.750	0.750	weak	DEFB104A,NS,other,0,1	.	.	1	NM_001040702	exon1	c.A28G	p.I10V	TTAGCCATTTCTC	.	scavenged	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118509191	118509191	+	Missense_Mutation	SNP	G	G	A	rs7307331	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	66	165	0	0.437086	0	G|0.472;A|0.528	0.528	strong	.	VSIG10	41	.	NM_019086	exon6	c.C1303T	p.H435Y	TATAATGCAACAG	.	PASS	Atlas-SNP
MYO1G	64005	hgsc.bcm.edu	37	7	45005795	45005795	+	Silent	SNP	G	G	A	rs2269969	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	70	86	0	0.603448	0	G|0.848;A|0.152	0.152	strong	.	MYO1G	86	.	NM_033054	exon16	c.C2034T	p.H678H	CAGCCCGTGCTGC	.	PASS	Atlas-SNP
FBXO30	84085	hgsc.bcm.edu	37	6	146126419	146126419	+	Missense_Mutation	SNP	C	C	T	rs9373475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	94	275	0	0.489583	0	C|0.663;N|0.000	.	strong	.	FBXO30	56	.	NM_032145	exon2	c.G1123A	p.V375M	TCTTCACGTCCCC	.	PASS	Atlas-SNP
TECPR2	9895	hgsc.bcm.edu	37	14	102901023	102901023	+	Silent	SNP	G	G	A	rs45605932	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	32	97	0	0.280702	0	G|0.880;A|0.120	0.120	strong	.	TECPR2	114	.	NM_001172631	exon9	c.G1869A	p.G623G	TCCTGGGGCGCAT	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1003374	1003374	+	Silent	SNP	G	G	A	rs34585248	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4	4	0	0	1	.	G|0.966;A|0.034	0.034	strong	.	GRIN3B	46	.	NM_138690	exon2	c.G672A	p.A224A	GGCGGCGCCAGTG	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080696	194080696	+	Silent	SNP	G	G	A	rs9682541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	131	222	1	0.543568	0.0045045	G|0.844;A|0.156	0.156	strong	.	LRRC15	137	.	NM_001135057	exon3	c.C1095T	p.N365N	GAAGACGTTCCCG	.	PASS	Atlas-SNP
CASP10	843	hgsc.bcm.edu	37	2	202074207	202074207	+	Missense_Mutation	SNP	A	A	G	rs17860405	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	7	131	0	0.0909091	0	A|0.973;G|0.027	0.027	strong	.	CASP10	95	.	NM_032977	exon9	c.A1337G	p.Y446C	CAGGCTATGTATC	.	PASS	Atlas-SNP
SRMS	6725	hgsc.bcm.edu	37	20	62172244	62172244	+	Missense_Mutation	SNP	C	C	G	rs33933649	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	27	77	0	0.465517	0	C|0.979;G|0.021	0.021	strong	.	SRMS	48	.	NM_080823	exon8	c.G1394C	p.S465T	GGGCTGCTCCTCC	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169174484	169174484	+	Silent	SNP	A	A	G	rs13155521	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	33	118	0	0.388235	0	A|0.957;G|0.043	0.043	strong	.	DOCK2	389	.	NM_004946	exon23	c.A2352G	p.Q784Q	AAGTCAATACAAA	.	PASS	Atlas-SNP
TCEB2	6923	hgsc.bcm.edu	37	16	2821525	2821525	+	Missense_Mutation	SNP	G	G	A	rs4036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	75	185	0	0.462963	0	G|0.812;A|0.188	0.188	strong	.	TCEB2	6	.	NM_207013	exon5	c.C434T	p.T145M	TCCCTCGTTGAAC	.	PASS	Atlas-SNP
FAM13A	10144	hgsc.bcm.edu	37	4	89772301	89772301	+	Missense_Mutation	SNP	C	C	A	rs7680970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	41	69	0	0.640625	0	C|0.918;A|0.082	0.082	strong	.	FAM13A	181	.	NM_014883	exon7	c.G877T	p.A293S	TGTGGGCCTGAAT	.	PASS	Atlas-SNP
PHF17	79960	hgsc.bcm.edu	37	4	129792787	129792787	+	Silent	SNP	A	A	G	rs6850940	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	22	117	0	0.255814	0	A|0.972;G|0.028	0.028	strong	.	PHF17	63	.	NM_199320	exon11	c.A1899G	p.L633L	GGGTTTAGAAAAG	.	PASS	Atlas-SNP
HDHD1	8226	hgsc.bcm.edu	37	X	6995438	6995438	+	Silent	SNP	C	C	T	rs1803675	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	97	156	0	0.989796	0	C|0.723;T|0.277	0.277	strong	.	HDHD1	21	.	NM_001135565	exon4	c.G402A	p.L134L	GGTGGCCAGTGCA	.	PASS	Atlas-SNP
TSPAN6	7105	hgsc.bcm.edu	37	X	99890204	99890204	+	Missense_Mutation	SNP	C	C	T	rs1802288	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	103	225	0	0.962617	0	0|0.015;T|0.099	0.099	strong	.	TSPAN6	23	.	NM_003270	exon3	c.G322A	p.A108T	CGATGGCAGCGAC	.	PASS	Atlas-SNP
SPARCL1	8404	hgsc.bcm.edu	37	4	88412806	88412806	+	Missense_Mutation	SNP	T	T	C	rs1130643	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	70	154	0	0.530303	0	T|0.777;C|0.223	0.223	strong	.	SPARCL1	59	.	NM_004684	exon5	c.A1255G	p.T419A	TTGACGTTTCCTC	.	PASS	Atlas-SNP
AMICA1	120425	hgsc.bcm.edu	37	11	118074337	118074337	+	Missense_Mutation	SNP	A	A	G	rs1793174	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	61	133	0	0.251029	0	A|0.202;G|0.798	0.798	strong	AMICA1,NS,carcinoma,0,1	AMICA1	49	1	NM_001098526	exon6	c.T578C	p.V193A	TACTCCACAGACA	.	PASS	Atlas-SNP
COX6C	1345	hgsc.bcm.edu	37	8	100899793	100899793	+	Silent	SNP	G	G	A	rs1130569	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	44	75	0	0.536585	0	G|0.733;A|0.267	0.267	strong	COX6C_ENST00000520468,NS,carcinoma,0,1	COX6C	25	1	NM_004374	exon3	c.C168T	p.Y56Y	GACATCGTAGTTT	.	PASS	Atlas-SNP
OR4A5	81318	hgsc.bcm.edu	37	11	51411918	51411918	+	Missense_Mutation	SNP	C	C	T	rs150995059	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	72	143	0	0.486486	0	C|0.993;T|0.007	0.007	strong	.	OR4A5	116	.	NM_001005272	exon1	c.G478A	p.V160M	TGTACACAACAAT	.	PASS	Atlas-SNP
ZNF75D	7626	hgsc.bcm.edu	37	X	134421168	134421168	+	Silent	SNP	C	C	T	rs1129093	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	146	270	1	0.986486	0.0037037	0|0.005;T|0.219	0.219	strong	.	ZNF75D	65	.	NM_007131	exon6	c.G1434A	p.T478T	GCTACACGTATAA	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50572473	50572473	+	Missense_Mutation	SNP	G	G	A	rs2340601	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	66	153	0	0.532258	0	G|0.776;A|0.224	0.224	strong	MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	NM_018995	exon14	c.G1948A	p.V650I	GAACACGTCATCC	.	PASS	Atlas-SNP
MAP6	4135	hgsc.bcm.edu	37	11	75298468	75298468	+	Missense_Mutation	SNP	A	A	C	rs61895095	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	87	185	0	0.5	0	A|0.960;C|0.040	0.040	strong	.	MAP6	45	.	NM_033063	exon4	c.T2078G	p.V693G	TCGTGAACCTTTG	.	PASS	Atlas-SNP
C2orf74	339804	hgsc.bcm.edu	37	2	61389737	61389737	+	Missense_Mutation	SNP	T	T	G	rs1729674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	95	143	0	0.568862	0	T|0.583;G|0.417	0.417	strong	.	C2orf74	22	.	NM_001143959	exon1	c.T109G	p.Y37D	TTTTTATATAAAT	.	PASS	Atlas-SNP
RXRG	6258	hgsc.bcm.edu	37	1	165389129	165389129	+	Silent	SNP	G	G	A	rs1128977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	115	127	0	0.61828	0	G|0.737;A|0.263	0.263	strong	.	RXRG	91	.	NM_006917	exon3	c.C420T	p.A140A	ACAGATGGCACAG	.	PASS	Atlas-SNP
SLC26A6	65010	hgsc.bcm.edu	37	3	48669447	48669447	+	Missense_Mutation	SNP	C	C	T	rs13324142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	73	179	0	0.424419	0	C|0.888;T|0.112	0.112	strong	.	SLC26A6	45	.	NM_022911	exon6	c.G616A	p.V206M	TGACCACGAAGCC	.	PASS	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22941591	22941591	+	Missense_Mutation	SNP	A	A	T	rs62119159	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	30	81	0	0.357143	0	A|0.911;T|0.089	0.089	strong	ZNF99,NS,carcinoma,0,1	ZNF99	273	1	NM_001080409	exon4	c.T1120A	p.C374S	TGCCGCATTCTTC	.	PASS	Atlas-SNP
ACOX1	51	hgsc.bcm.edu	37	17	73949540	73949540	+	Missense_Mutation	SNP	G	G	C	rs1135640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	222	97	229	0	0.436937	0	G|0.477;C|0.523	0.523	strong	.	ACOX1	85	.	NM_007292	exon7	c.C936G	p.I312M	TGGCTTGATTTCA	.	PASS	Atlas-SNP
SLC26A7	115111	hgsc.bcm.edu	37	8	92364100	92364100	+	Silent	SNP	T	T	C	rs10109254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	51	121	0	0.314815	0	T|0.739;C|0.261	0.261	strong	.	SLC26A7	207	.	NM_134266	exon10	c.T1203C	p.L401L	TTTGCTTTACTGG	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22846623	22846623	+	Missense_Mutation	SNP	G	G	A	rs71355986	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	10	91	0	0.181818	0	G|0.827;A|0.173	0.173	strong	ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	NM_020855	exon4	c.G152A	p.R51Q	TTGCCCGAGACCT	.	scavenged	Atlas-SNP
KIAA1522	57648	hgsc.bcm.edu	37	1	33235651	33235651	+	Missense_Mutation	SNP	A	A	G	rs12730560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	14	135	0	0.2	0	A|0.838;G|0.162	0.162	strong	KIAA1522,colon,carcinoma,0,1	KIAA1522	68	1	NM_020888	exon6	c.A871G	p.M291V	GAGGCCATGCTGC	.	PASS	Atlas-SNP
VPS39	23339	hgsc.bcm.edu	37	15	42459034	42459034	+	Silent	SNP	T	T	C	rs1619030	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	21	145	0	0.265823	0	T|0.694;C|0.306	0.306	strong	.	VPS39	53	.	NM_015289	exon14	c.A1455G	p.L485L	CTTCTTTAGCACG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169348435	169348435	+	Silent	SNP	T	T	C	rs2712120	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	97	181	0	0.740458	0	T|0.783;C|0.217	0.217	strong	DDX60L,NS,carcinoma,0,1	DDX60L	116	1	NM_001012967	exon14	c.A1716G	p.K572K	TGACTTTTTCTTA	.	PASS	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547096	132547096	+	Silent	SNP	G	G	A	rs74479394	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	4	93	1	0.027972	0.0107527	.	.	weak	EP400,colon,carcinoma,0,3	EP400	370	3	NM_015409	exon47	c.G8184A	p.Q2728Q	ACAACAGCAGCAG	.	scavenged	Atlas-SNP
HIP1	3092	hgsc.bcm.edu	37	7	75171262	75171262	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	317	72	256	0	0.227129	0	.	.	none	HIP1,NS,carcinoma,-2,1	HIP1	91	1	NM_005338	exon29	c.C2928T	p.I976I	GCGTTTGATCTGT	.	PASS	Atlas-SNP
FAM171A1	221061	hgsc.bcm.edu	37	10	15256368	15256368	+	Missense_Mutation	SNP	C	C	T	rs143772901	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	21	94	0	0.362069	0	C|1.000;T|0.000	0.000	weak	.	FAM171A1	252	.	NM_001010924	exon8	c.G1219A	p.E407K	CCCCTTCGCCGCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677625	100677625	+	Silent	SNP	G	G	A	rs115078078	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	625	151	196	1	0.2416	0.00510204	G|0.964;A|0.036	0.036	strong	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G2928A	p.S976S	AACCTCGACTCCT	.	scavenged	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327906	16327906	+	Missense_Mutation	SNP	C	C	A	rs376233432		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	19	70	1	0.228916	0.0142857	.	.	weak	ATXN1,colon,carcinoma,0,3	ATXN1	117	3	NM_001128164	exon7	c.G636T	p.Q212H	CTGCTGCTGATGC	.	scavenged	Atlas-SNP
NUBP2	10101	hgsc.bcm.edu	37	16	1838703	1838703	+	Silent	SNP	G	G	A	rs11540961	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	37	49	0	0.544118	0	G|0.949;A|0.051	0.051	strong	NUBP2,NS,carcinoma,+2,2	NUBP2	25	2	NM_012225	exon7	c.G804A	p.A268A	GCCCGCGTGCCTC	.	PASS	Atlas-SNP
TRIM4	89122	hgsc.bcm.edu	37	7	99490190	99490190	+	Missense_Mutation	SNP	G	G	A	rs35432946	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	59	159	0	0.317204	0	G|0.942;A|0.058	0.058	strong	.	TRIM4	33	.	NM_033017	exon7	c.C1099T	p.P367S	CACAGGGTAAGTG	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21232804	21232804	+	Silent	SNP	G	G	A	rs1041968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	69	156	0	0.475862	0	G|0.640;A|0.360	0.360	strong	APOB,NS,malignant_melanoma,-2,1	APOB	761	1	NM_000384	exon26	c.C6936T	p.D2312D	AAGAATGTCATTT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680017	100680017	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	11	145	0	0.0536585	0	.	.	none	MUC17,right_lower_lobe,carcinoma,-1,1	MUC17	804	1	NM_001040105	exon3	c.A5320G	p.I1774V	ACTCCTATTGACA	.	scavenged	Atlas-SNP
FRMPD1	22844	hgsc.bcm.edu	37	9	37733752	37733752	+	Missense_Mutation	SNP	G	G	A	rs140800271	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	64	109	0	0.507937	0	G|0.997;A|0.003	0.003	strong	.	FRMPD1	237	.	NM_014907	exon12	c.G1148A	p.R383H	AGCTACGTTTAAA	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32638549	32638549	+	Missense_Mutation	SNP	C	C	A	rs2070417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	49	102	0	0.401639	0	C|0.874;A|0.119	0.119	strong	.	TIAM1	522	.	NM_003253	exon5	c.G740T	p.G247V	GGCCCCCCGTTTG	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235383742	235383742	+	Missense_Mutation	SNP	C	C	G	rs148132837	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	487	158	405	0	0.324435	0	C|0.999;G|0.001	0.001	strong	.	ARID4B	142	.	NM_016374	exon15	c.G1282C	p.V428L	CCTTAACTTTTAT	.	PASS	Atlas-SNP
ELMOD1	55531	hgsc.bcm.edu	37	11	107535758	107535758	+	Silent	SNP	G	G	A	rs647756	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	41	79	0	0.30597	0	G|0.697;A|0.303	0.303	strong	.	ELMOD1	40	.	NM_018712	exon12	c.G840A	p.L280L	CTATTTGATGCAT	.	PASS	Atlas-SNP
ACTRT2	140625	hgsc.bcm.edu	37	1	2938989	2938989	+	Missense_Mutation	SNP	G	G	A	rs3795263	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	35	92	0	0.744681	0	G|0.842;A|0.158	0.158	strong	.	ACTRT2	69	.	NM_080431	exon1	c.G739A	p.G247R	CCCGACGGGAACA	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	37	11	119050906	119050906	+	Missense_Mutation	SNP	G	G	A	rs45450295	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	428	99	234	0	0.231308	0	G|0.988;A|0.012	0.012	strong	.	NLRX1	128	.	NM_024618	exon7	c.G2176A	p.A726T	AGGCATGCCCTGG	.	PASS	Atlas-SNP
SMYD3	64754	hgsc.bcm.edu	37	1	246021858	246021858	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	3	158	0	0.0136986	0	.	.	none	SMYD3_ENST00000388985,right_lower_lobe,carcinoma,+1,2	SMYD3	77	2	NM_001167740	exon10	c.T1016C	p.I339T	AGGTTGATGCAGG	.	scavenged	Atlas-SNP
KIAA0319L	79932	hgsc.bcm.edu	37	1	35972375	35972375	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	29	161	0	0.281553	0	.	.	none	.	KIAA0319L	156	.	NM_024874	exon3	c.T504A	p.A168A	GAGTGCAGCTCTG	.	PASS	Atlas-SNP
SLC39A12	221074	hgsc.bcm.edu	37	10	18254606	18254606	+	Silent	SNP	C	C	A	rs691513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	39	101	0	0.722222	0	C|0.672;A|0.328	0.328	strong	.	SLC39A12	181	.	NM_152725	exon4	c.C738A	p.T246T	GAATACCCTCCGC	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	37	12	6935977	6935977	+	Missense_Mutation	SNP	A	A	G	rs11612427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	97	81	0	0.989796	0	A|0.801;G|0.199	0.199	strong	.	GPR162	55	.	NM_019858	exon5	c.A1375G	p.R459G	GGACAAAGACACA	.	PASS	Atlas-SNP
ARFGAP2	84364	hgsc.bcm.edu	37	11	47188411	47188411	+	Missense_Mutation	SNP	C	C	T	rs3740691	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	37	68	0	0.430233	0	C|0.607;T|0.393	0.393	strong	.	ARFGAP2	43	.	NM_032389	exon13	c.G1232A	p.S411N	CTCCGGCTCTCCA	.	PASS	Atlas-SNP
SSPN	8082	hgsc.bcm.edu	37	12	26377232	26377232	+	Silent	SNP	T	T	C	rs34624361	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	92	207	1	0.44878	0.00483092	T|0.919;C|0.081	0.081	strong	SSPN,NS,carcinoma,0,1	SSPN	19	1	NM_005086	exon2	c.T286C	p.L96L	GTCTGCTTAGTGG	.	scavenged	Atlas-SNP
SLC25A23	79085	hgsc.bcm.edu	37	19	6458240	6458240	+	Silent	SNP	G	G	C	rs2289784	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	11	51	0	0.305556	0	G|0.946;C|0.054	0.054	strong	SLC25A23,NS,carcinoma,0,1	SLC25A23	43	1	NM_024103	exon2	c.C252G	p.L84L	AAACATGAGCAGC	.	PASS	Atlas-SNP
RBBP7	5931	hgsc.bcm.edu	37	X	16887655	16887655	+	Missense_Mutation	SNP	C	C	T	rs67984110	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	143	310	0	0.966216	0	C|0.769;T|0.231	0.231	strong	.	RBBP7	58	.	NM_001198719	exon1	c.G110A	p.R37H	GCTGCGCGACCCA	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156877797	156877797	+	Silent	SNP	C	C	A	rs77235035	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	286	90	218	2	0.314685	0.00917431	C|0.810;A|0.190	0.190	strong	PEAR1,NS,carcinoma,0,2	PEAR1	118	2	NM_001080471	exon8	c.C856A	p.R286R	TGTGACCGATTCA	.	scavenged	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81208515	81208515	+	Missense_Mutation	SNP	G	G	A	rs12596941	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	16	65	0	0.246154	0	G|0.789;A|0.211	0.211	strong	.	PKD1L2	361	.	NM_001076780	exon16	c.C2588T	p.A863V	CCGAGTGCCACCT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155241572	155241572	+	Missense_Mutation	SNP	G	G	A	rs11935573	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	31	254	0	0.196203	0	G|0.746;A|0.254	0.254	strong	DCHS2,NS,carcinoma,0,2	DCHS2	594	2	NM_017639	exon14	c.C3614T	p.S1205L	TTTCCTGAGAGGA	.	PASS	Atlas-SNP
FZD8	8325	hgsc.bcm.edu	37	10	35929131	35929131	+	Silent	SNP	G	G	A	rs74989785	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	30	54	0	0.769231	0	G|0.962;A|0.038	0.038	strong	.	FZD8	41	.	NM_031866	exon1	c.C1227T	p.A409A	GGAGCTGGCCATG	.	PASS	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2194953	2194953	+	Silent	SNP	G	G	A	rs10002583	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	88	246	0	0.468085	0	G|0.735;A|0.265	0.265	strong	.	POLN	82	.	NM_181808	exon5	c.C999T	p.G333G	ATCATTGCCAAAA	.	PASS	Atlas-SNP
MMP19	4327	hgsc.bcm.edu	37	12	56236136	56236136	+	Splice_Site	SNP	C	C	T	rs145293054	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	117	227	1	0.508696	0.00440529	C|0.999;T|0.001	0.001	strong	.	MMP19	61	.	NM_002429	exon3	c.173+1G>A	.	TTCTCACCTCAGA	.	PASS	Atlas-SNP
SCN2A	6326	hgsc.bcm.edu	37	2	166245230	166245230	+	Silent	SNP	T	T	A	rs75650659		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	84	198	0	0.466667	0	.	.	weak	SCN2A_ENST00000375437,colon,carcinoma,+2,2	SCN2A	589	2	NM_001040143	exon26	c.T4914A	p.R1638R	CCTACGTCTGATC	.	PASS	Atlas-SNP
MAD2L1BP	9587	hgsc.bcm.edu	37	6	43608220	43608220	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	30	100	0	0.29703	0	.	.	none	.	MAD2L1BP	12	.	NM_001003690	exon4	c.G871A	p.D291N	TGGGAAGACTACA	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216242917	216242917	+	Silent	SNP	T	T	A	rs1132741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	31	67	0	0.939394	0	T|0.728;A|0.272	0.272	strong	FN1,NS,carcinoma,0,1	FN1	521	1	NM_212482	exon35	c.A5691T	p.G1897G	GACAACTCCCTGA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388350	1388350	+	Silent	SNP	G	G	A	rs77782813	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	83	218	0	0.406863	0	G|0.858;A|0.142	0.142	strong	.	CRIPAK	185	.	NM_175918	exon1	c.G51A	p.T17T	TCACACGTGCCCA	.	PASS	Atlas-SNP
ISOC1	51015	hgsc.bcm.edu	37	5	128430757	128430757	+	Silent	SNP	T	T	C	rs1127827	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	30	10	53	0	0.333333	0	T|0.232;C|0.768	0.768	strong	.	ISOC1	26	.	NM_016048	exon1	c.T298C	p.L100L	GTGCCGTTGCAGA	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66648157	66648157	+	Silent	SNP	C	C	T	rs4145350	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	82	127	0	0.640625	0	C|0.778;T|0.222	0.222	strong	.	TYW1	71	.	NM_018264	exon14	c.C1743T	p.N581N	ATGGAACGTGGAC	.	PASS	Atlas-SNP
ZNF16	7564	hgsc.bcm.edu	37	8	146171437	146171437	+	Silent	SNP	A	A	G	rs3735785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	38	113	0	0.260274	0	A|0.773;G|0.227	0.227	strong	.	ZNF16	80	.	NM_006958	exon2	c.T156C	p.D52D	CTCAGTATCACTA	.	PASS	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	37	2	149799216	149799216	+	Silent	SNP	T	T	C	rs61734995	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	88	167	0	0.458333	0	T|0.860;C|0.140	0.140	strong	.	KIF5C	166	.	NM_004522	exon7	c.T531C	p.P177P	GAGCCCTGAGGAA	.	PASS	Atlas-SNP
KIF26B	55083	hgsc.bcm.edu	37	1	245772617	245772617	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	283	3	209	0	0.0106007	0	.	.	none	KIF26B_ENST00000407071,NS,carcinoma,0,2	KIF26B	343	2	NM_018012	exon8	c.C1701T	p.G567G	CCTGGGCATCATT	.	scavenged	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79891006	79891006	+	Missense_Mutation	SNP	T	T	C	rs78048112	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	16	53	0	0.421053	0	T|0.980;C|0.020	0.020	strong	.	VPS13A	735	.	NM_001018038	exon26	c.T2693C	p.V898A	ACCTTGTTGGAGA	.	PASS	Atlas-SNP
GXYLT1	283464	hgsc.bcm.edu	37	12	42503467	42503467	+	Silent	SNP	T	T	C	rs7312933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	83	91	0	1	0	T|0.670;C|0.330	0.330	strong	.	GXYLT1	47	.	NM_173601	exon4	c.A513G	p.T171T	ATTAAATGTTTGT	.	PASS	Atlas-SNP
DCAF6	55827	hgsc.bcm.edu	37	1	167973976	167973976	+	Silent	SNP	C	C	T	rs1060041	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	130	176	1	0.588235	0.00568182	C|0.821;T|0.179	0.179	strong	.	DCAF6	99	.	NM_001198956	exon10	c.C1323T	p.D441D	TCCAGACAGTGAA	.	PASS	Atlas-SNP
R3HDM2	22864	hgsc.bcm.edu	37	12	57649840	57649840	+	Silent	SNP	C	C	T	rs4075325	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	285	284	295	2	0.996491	0.00677966	C|0.612;T|0.388	0.388	strong	.	R3HDM2	125	.	NM_014925	exon21	c.G2523A	p.K841K	TCCATGCTTCAGT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9088722	9088722	+	Silent	SNP	G	G	A	rs17000948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	117	236	1	0.483471	0.00423729	G|0.860;A|0.140	0.140	strong	.	MUC16	4315	.	NM_024690	exon1	c.C3093T	p.G1031G	CATAGAGCCTGGG	.	PASS	Atlas-SNP
SCAF4	57466	hgsc.bcm.edu	37	21	33044408	33044408	+	Silent	SNP	A	A	G	rs73201506	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	24	65	0	0.292683	0	A|0.972;G|0.028	0.028	strong	.	SCAF4	142	.	NM_020706	exon20	c.T2748C	p.V916V	AGGCCTAACAAAG	.	PASS	Atlas-SNP
CLCN3	1182	hgsc.bcm.edu	37	4	170634390	170634390	+	Silent	SNP	C	C	T	rs1058868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	49	181	0	0.335616	0	C|0.879;T|0.121	0.121	strong	CLCN3,NS,carcinoma,+1,2	CLCN3	85	2	NM_001829	exon12	c.C2310T	p.I770I	GGAGATCGTGGTG	.	PASS	Atlas-SNP
GOLIM4	27333	hgsc.bcm.edu	37	3	167747022	167747022	+	Missense_Mutation	SNP	C	C	T	rs61743591	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	116	117	0	0.983051	0	C|0.956;T|0.044	0.044	strong	GOLIM4,NS,carcinoma,-1,1	GOLIM4	71	1	NM_014498	exon11	c.G1502A	p.G501E	TCCTCTCCTTGGA	.	PASS	Atlas-SNP
NKAIN3	286183	hgsc.bcm.edu	37	8	63659635	63659635	+	Missense_Mutation	SNP	G	G	A	rs4739003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	13	121	0	0.178082	0	G|0.768;A|0.231	0.231	strong	.	NKAIN3	32	.	NM_173688	exon4	c.G418A	p.V140I	TGCATCGTTGACT	.	PASS	Atlas-SNP
METTL25	84190	hgsc.bcm.edu	37	12	82792666	82792666	+	Silent	SNP	C	C	T	rs10506872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	32	89	0	0.477612	0	C|0.955;T|0.045	0.045	strong	.	.	.	.	NM_032230	exon4	c.C624T	p.T208T	AAATACCAATACT	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855647	12855647	+	Silent	SNP	C	C	T	rs200536957		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	26	442	29	0.111111	0.0656109	C|0.999;T|0.001	0.001	weak	PRAMEF1,NS,carcinoma,+2,2	PRAMEF1	78	2	NM_023013	exon4	c.C927T	p.D309D	AGAAGACATGAAG	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264767	1264767	+	Silent	SNP	G	G	A	rs74447707	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	366	14	364	0	0.0382514	0	.	.	weak	MUC5B,NS,neuroblastoma,0,2	MUC5B	473	2	NM_002458	exon31	c.G6657A	p.S2219S	CACCTCGGGCATC	.	scavenged	Atlas-SNP
IVD	3712	hgsc.bcm.edu	37	15	40705225	40705225	+	Silent	SNP	C	C	T	rs2229312	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	68	148	0	0.68	0	C|0.887;T|0.113	0.113	strong	.	IVD	29	.	NM_002225	exon7	c.C732T	p.D244D	GCTGGACAAGCTG	.	PASS	Atlas-SNP
UPK3BL	100134938	hgsc.bcm.edu	37	7	102279621	102279621	+	Missense_Mutation	SNP	C	C	T	rs56365279		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1349	294	576	4	0.217939	0.00694444	.	.	weak	UPK3BL,NS,carcinoma,0,4	UPK3BL	6	4	NM_001114403	exon4	c.G511A	p.E171K	GTCCTTCGTCATT	.	scavenged	Atlas-SNP
ORC4	5000	hgsc.bcm.edu	37	2	148730367	148730367	+	Missense_Mutation	SNP	G	G	C	rs2307397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206	122	223	0	0.592233	0	G|0.964;C|0.036	0.036	strong	.	ORC4	40	.	NM_002552	exon4	c.C166G	p.L56V	CATGGAGAGCAGT	.	PASS	Atlas-SNP
MADCAM1	8174	hgsc.bcm.edu	37	19	501900	501900	+	Missense_Mutation	SNP	C	C	A	rs3745925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	28	76	0	0.509091	0	C|0.760;A|0.240	0.240	strong	.	MADCAM1	29	.	NM_130760	exon4	c.C899A	p.P300H	CTGGGCCCACGCA	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140552558	140552558	+	Silent	SNP	T	T	C	rs17096945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	90	171	1	0.5	0.00584795	T|0.860;C|0.140	0.140	strong	PCDHB7,NS,carcinoma,-2,1	PCDHB7	231	1	NM_018940	exon1	c.T142C	p.L48L	ACCAACTTGGCAA	.	scavenged	Atlas-SNP
A1CF	29974	hgsc.bcm.edu	37	10	52573698	52573698	+	Silent	SNP	G	G	A	rs41274048	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	134	327	0	0.705263	0	G|0.908;A|0.092	0.092	strong	.	A1CF	190	.	NM_001198819	exon12	c.C1290T	p.L430L	GTCATAGAGTTTG	.	PASS	Atlas-SNP
PPAN-P2RY11	692312	hgsc.bcm.edu	37	19	10224526	10224526	+	Missense_Mutation	SNP	C	C	T	rs3745600	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	43	112	0	0.452632	0	C|0.631;T|0.369	0.369	strong	PPAN-P2RY11,caecum,carcinoma,+2,2	PPAN-P2RY11	81	2	NM_001198690	exon13	c.C1559T	p.P520L	CTGCGCCCTGACG	.	PASS	Atlas-SNP
GPR18	2841	hgsc.bcm.edu	37	13	99907341	99907341	+	Silent	SNP	G	G	A	rs3742130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	88	154	0	0.488889	0	G|0.849;A|0.151	0.151	strong	.	GPR18	23	.	NM_001098200	exon2	c.C786T	p.N262N	GTAACTGTTCTCC	.	PASS	Atlas-SNP
SPECC1	92521	hgsc.bcm.edu	37	17	20013802	20013802	+	Silent	SNP	G	G	A	rs3764436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	284	127	320	0	0.447183	0	G|0.892;A|0.108	0.108	strong	.	SPECC1	100	.	NM_001033553	exon3	c.G210A	p.V70V	GGGGGTGGTTCGC	.	PASS	Atlas-SNP
EPHA4	2043	hgsc.bcm.edu	37	2	222301160	222301160	+	Silent	SNP	G	G	T	rs56159060		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	16	106	0	0.225352	0	.	.	weak	.	EPHA4	263	.	NM_004438	exon13	c.C2305A	p.R769R	GCACTCGGGACAT	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243329075	243329075	+	Silent	SNP	T	T	C	rs61833876	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	322	42	206	0	0.130435	0	T|0.500;C|0.500	0.500	weak	.	CEP170	153	.	NM_014812	exon13	c.A2187G	p.K729K	TTTCTCTTTTCCA	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124949044	124949044	+	Silent	SNP	C	C	T	rs33932952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	354	233	216	0	0.658192	0	C|0.814;T|0.186	0.186	strong	SLC37A2,NS,carcinoma,0,1	SLC37A2	105	1	NM_001145290	exon5	c.C351T	p.Y117Y	TTACTACCTCTCA	.	PASS	Atlas-SNP
SPATA18	132671	hgsc.bcm.edu	37	4	52946023	52946023	+	Silent	SNP	G	G	A	rs79854970	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	98	261	0	0.443439	0	G|0.995;A|0.005	0.005	strong	SPATA18_ENST00000295213,NS,carcinoma,0,2	SPATA18	222	2	NM_145263	exon9	c.G1293A	p.Q431Q	AATGCAGGCCTTA	.	PASS	Atlas-SNP
C11orf35	256329	hgsc.bcm.edu	37	11	556584	556584	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	28	67	0	0.622222	0	.	.	none	.	C11orf35	22	.	NM_173573	exon9	c.C981T	p.L327L	TTTCTGGAGATCT	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102439	22102439	+	Missense_Mutation	SNP	C	C	G	rs41361344	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	429	154	473	4	0.358974	0.00845666	C|0.586;G|0.414	0.414	strong	OR10G2,NS,carcinoma,0,2	OR10G2	35	2	NM_001005466	exon1	c.G560C	p.R187P	ACTGCGCGGATGT	.	scavenged	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	37	1	65312342	65312342	+	Silent	SNP	G	G	A	rs17127063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	56	137	0	0.682927	0	G|0.944;A|0.056	0.056	strong	JAK1,NS,malignant_melanoma,-1,1	JAK1	209	1	NM_002227	exon14	c.C1977T	p.R659R	CACGTCGCGGACA	.	PASS	Atlas-SNP
SPECC1	92521	hgsc.bcm.edu	37	17	20108184	20108184	+	Missense_Mutation	SNP	C	C	G	rs9908032	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	35	67	0	0.514706	0	C|0.883;G|0.117	0.117	strong	.	SPECC1	100	.	NM_001033553	exon4	c.C822G	p.S274R	CAGCAGCTGCCCA	.	PASS	Atlas-SNP
GNAI1	2770	hgsc.bcm.edu	37	7	79842157	79842157	+	Silent	SNP	T	T	C	rs10241877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	65	190	0	0.318627	0	T|0.917;C|0.083	0.083	strong	.	GNAI1	44	.	NM_002069	exon7	c.T846C	p.P282P	GAGCCCTCTCACT	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88502208	88502208	+	Missense_Mutation	SNP	A	A	T	rs3812954	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	54	80	0	0.857143	0	A|0.944;T|0.056	0.056	strong	.	ZNF469	121	.	NM_001127464	exon2	c.A8246T	p.D2749V	CGGAGGACAGCAG	.	PASS	Atlas-SNP
STT3A	3703	hgsc.bcm.edu	37	11	125479363	125479363	+	Silent	SNP	G	G	A	rs2241502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	438	291	291	1	0.664384	0.00343643	G|0.582;A|0.418	0.418	strong	STT3A,NS,carcinoma,+1,1	STT3A	52	1	NM_152713	exon10	c.G996A	p.S332S	CTACTCGCTGCTG	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50502491	50502491	+	Missense_Mutation	SNP	T	T	C	rs11568188	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	14	186	0	0.116667	0	T|0.905;C|0.095	0.095	strong	MLC1,rectum,carcinoma,0,2	MLC1	48	2	NM_015166	exon11	c.A1031G	p.N344S	GGGCCGTTCTGGG	.	PASS	Atlas-SNP
PARD3	56288	hgsc.bcm.edu	37	10	34620220	34620220	+	Silent	SNP	C	C	T	rs3781128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	35	84	0	0.714286	0	C|0.459;T|0.541	0.541	strong	.	PARD3	131	.	NM_001184787	exon19	c.G2667A	p.S889S	CTCCAACGAGCTT	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92568149	92568149	+	Missense_Mutation	SNP	A	A	G	rs75651194	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	50	118	0	0.273224	0	A|0.991;G|0.009	0.009	strong	.	FAT3	1822	.	NM_001008781	exon14	c.A9985G	p.I3329V	GTCAACATCAACC	.	PASS	Atlas-SNP
EHD4	30844	hgsc.bcm.edu	37	15	42235316	42235316	+	Missense_Mutation	SNP	C	C	T	rs11549015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	12	78	0	0.24	0	C|0.899;T|0.101	0.101	strong	EHD4,NS,carcinoma,0,1	EHD4	46	1	NM_139265	exon3	c.G460A	p.V154I	CGATGACGCTGAT	.	PASS	Atlas-SNP
PSORS1C2	170680	hgsc.bcm.edu	37	6	31106065	31106065	+	Missense_Mutation	SNP	C	C	T	rs2233950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	36	71	0	0.473684	0	C|0.957;T|0.043	0.043	strong	.	PSORS1C2	11	.	NM_014069	exon2	c.G74A	p.G25D	GGGTGGCCCTCGC	.	PASS	Atlas-SNP
ZNF33B	7582	hgsc.bcm.edu	37	10	43089278	43089278	+	Missense_Mutation	SNP	T	T	C	rs71505624	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	33	200	0	0.189655	0	T|0.998;C|0.002	0.002	strong	.	ZNF33B	78	.	NM_006955	exon5	c.A1120G	p.K374E	GATGTTTAGTGAG	.	PASS	Atlas-SNP
DAPK1	1612	hgsc.bcm.edu	37	9	90265015	90265015	+	Silent	SNP	C	C	T	rs3818584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	21	75	0	0.456522	0	C|0.634;T|0.365	0.365	strong	DAPK1_ENST00000408954,NS,carcinoma,0,4	DAPK1	329	4	NM_004938	exon16	c.C1608T	p.D536D	AGCCGACCTTAAT	.	PASS	Atlas-SNP
LLGL2	3993	hgsc.bcm.edu	37	17	73566561	73566561	+	Silent	SNP	G	G	A	rs2305525	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	18	43	0	0.5	0	G|0.868;A|0.132	0.132	strong	.	LLGL2	155	.	NM_004524	exon16	c.G2007A	p.P669P	GCACCCGGCTGGC	.	PASS	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102247526	102247526	+	Silent	SNP	G	G	C	rs2298074	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	52	140	0	0.58427	0	G|0.833;C|0.167	0.167	strong	.	SEC31B	84	.	NM_015490	exon26	c.C3387G	p.L1129L	CTCATGGAGCCCA	.	PASS	Atlas-SNP
BTN2A2	10385	hgsc.bcm.edu	37	6	26384092	26384092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	6	125	0	0.048	0	.	.	none	BTN2A2_ENST00000432533,bladder,carcinoma,-1,2	BTN2A2	87	2	NM_181531	exon2	c.C43T	p.L15F	GCCTCCCTCCTCC	.	scavenged	Atlas-SNP
NOX5	79400	hgsc.bcm.edu	37	15	69328226	69328226	+	Missense_Mutation	SNP	C	C	T	rs12907196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	80	146	1	0.987654	0.00684932	C|0.650;T|0.350	0.350	strong	.	NOX5	60	.	NM_024505	exon7	c.C1138T	p.L380F	CTCCTCCTCATGT	.	PASS	Atlas-SNP
RNF151	146310	hgsc.bcm.edu	37	16	2018554	2018554	+	Silent	SNP	G	G	T	rs114840677	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	77	153	0	0.52027	0	G|0.970;T|0.030	0.030	strong	.	RNF151	12	.	NM_174903	exon4	c.G366T	p.V122V	GCAGGTGCCGCGT	.	PASS	Atlas-SNP
SLC17A9	63910	hgsc.bcm.edu	37	20	61595636	61595636	+	Silent	SNP	C	C	T	rs2248900	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	292	150	307	0	0.513699	0	C|0.831;T|0.169	0.169	strong	SLC17A9,caecum,carcinoma,0,1	SLC17A9	54	1	NM_022082	exon8	c.C879T	p.S293S	ATTCAGCGGGTTT	.	PASS	Atlas-SNP
ASIC4	55515	hgsc.bcm.edu	37	2	220399951	220399951	+	Silent	SNP	A	A	G	rs2276643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	49	114	0	0.844828	0	A|0.731;G|0.268	0.268	strong	.	.	.	.	NM_182847	exon5	c.A1458G	p.T486T	CCTGACACGCTAT	.	PASS	Atlas-SNP
ST3GAL1	6482	hgsc.bcm.edu	37	8	134488007	134488007	+	Silent	SNP	G	G	A	rs2230542	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	173	143	1	1	0.00699301	G|0.495;A|0.505	0.505	strong	ST3GAL1,NS,carcinoma,0,1	ST3GAL1	39	1	NM_173344	exon5	c.C261T	p.T87T	CTGGGCGGTCAGC	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56392875	56392875	+	Silent	SNP	T	T	G	rs302456	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	28	61	0	0.54902	0	T|0.716;G|0.284	0.284	strong	NLRP4_ENST00000301295,colon,carcinoma,+2,2	NLRP4	331	2	NM_134444	exon10	c.T2907G	p.L969L	GGCACTTCTGACG	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124739892	124739892	+	Silent	SNP	G	G	A	rs6438874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	106	249	1	0.475336	0.00401606	G|0.510;A|0.490	0.490	strong	.	HEG1	109	.	NM_020733	exon4	c.C996T	p.A332A	CACGGTGGCAACA	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53995004	53995004	+	Silent	SNP	G	G	A	rs2708845	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	73	202	3	0.429412	0.0148515	G|0.248;A|0.752	0.752	strong	ZNF813_ENST00000396403,colon,carcinoma,+1,1	ZNF813	81	1	NM_001004301	exon4	c.G1518A	p.R506R	TAATCGGAAAACA	.	scavenged	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	37	4	3446132	3446132	+	Missense_Mutation	SNP	C	C	G	rs1987546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	74	79	0	0.973684	0	C|0.293;G|0.707	0.707	strong	.	HGFAC	69	.	NM_001528	exon6	c.C693G	p.F231L	GTGCTTCGGGGGC	.	PASS	Atlas-SNP
DPYD	1806	hgsc.bcm.edu	37	1	97915624	97915624	+	Silent	SNP	A	A	G	rs17376848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	67	165	0	0.697917	0	A|0.951;G|0.049	0.049	strong	.	DPYD	219	.	NM_000110	exon14	c.T1896C	p.F632F	GTCTGGAAAGTCA	.	PASS	Atlas-SNP
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259822	71259822	+	Missense_Mutation	SNP	A	A	G	rs10792769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	120	225	0	0.495868	0	A|0.819;G|0.181	0.181	strong	.	KRTAP5-9	19	.	NM_005553	exon1	c.A119G	p.Y40C	CCGTCTACTGCTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678407	100678407	+	Missense_Mutation	SNP	G	G	A	rs4729649	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	244	68	135	1	0.278689	0.00740741	G|0.948;A|0.052	0.052	strong	MUC17,caecum,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.G3710A	p.S1237N	AGGCTAGCACCCT	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681345	100681345	+	Missense_Mutation	SNP	T	T	G	rs142097516	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	23	177	0	0.0923695	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.T6648G	p.S2216R	TCCTAGTGAAGGA	.	PASS	Atlas-SNP
PTPRN	5798	hgsc.bcm.edu	37	2	220162015	220162015	+	Silent	SNP	C	C	G	rs17847406	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	31	164	0	0.242188	0	C|0.921;G|0.079	0.079	strong	PTPRN,NS,carcinoma,-1,1	PTPRN	138	1	NM_002846	exon14	c.G2028C	p.P676P	CCAGGACGGGGTG	.	PASS	Atlas-SNP
COL9A3	1299	hgsc.bcm.edu	37	20	61463522	61463522	+	Missense_Mutation	SNP	C	C	A	rs751557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	70	209	1	0.443038	0.00478469	T|0.003;G|0.006	.	strong	COL9A3,caecum,carcinoma,0,1	COL9A3	70	1	NM_001853	exon25	c.C1304A	p.A435E	GTGCCGCAGGCCC	.	scavenged	Atlas-SNP
OR10Z1	128368	hgsc.bcm.edu	37	1	158577109	158577109	+	Missense_Mutation	SNP	A	A	C	rs857685	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	129	161	0	0.575893	0	A|0.766;C|0.234	0.234	strong	.	OR10Z1	99	.	NM_001004478	exon1	c.A881C	p.N294T	TAAGGAATAGGGC	.	PASS	Atlas-SNP
TMEM52B	120939	hgsc.bcm.edu	37	12	10339178	10339178	+	Silent	SNP	C	C	T	rs4764308	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	33	58	0	0.358696	0	C|0.970;T|0.030	0.030	strong	.	.	.	.	NM_153022	exon3	c.C237T	p.S79S	CCAGAGCACTATC	.	PASS	Atlas-SNP
FAM189A1	23359	hgsc.bcm.edu	37	15	29421054	29421054	+	Missense_Mutation	SNP	C	C	T	rs2306933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	29	63	0	0.644444	0	C|0.877;T|0.123	0.123	strong	.	FAM189A1	20	.	NM_015307	exon8	c.G941A	p.G314D	TGCTGACCTATAC	.	PASS	Atlas-SNP
CNGB1	1258	hgsc.bcm.edu	37	16	57996932	57996932	+	Silent	SNP	G	G	A	rs17821448	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	74	95	0	0.961039	0	G|0.665;A|0.334	0.334	strong	.	CNGB1	105	.	NM_001297	exon5	c.C327T	p.G109G	CTCTACGCCCTTC	.	PASS	Atlas-SNP
PRR5L	79899	hgsc.bcm.edu	37	11	36472800	36472800	+	Silent	SNP	A	A	G	rs3740958	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	134	245	0	0.482014	0	A|0.833;G|0.167	0.167	strong	.	PRR5L	35	.	NM_024841	exon9	c.A627G	p.Q209Q	TTTGCAACTGGAG	.	PASS	Atlas-SNP
TBPL2	387332	hgsc.bcm.edu	37	14	55907172	55907172	+	Missense_Mutation	SNP	C	C	G	rs8019270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	54	117	0	0.402985	0	C|0.350;G|0.650	0.650	strong	TBPL2,NS,carcinoma,0,2	TBPL2	27	2	NM_199047	exon1	c.G92C	p.R31P	ATGGACCGTAATC	.	PASS	Atlas-SNP
RRM1	6240	hgsc.bcm.edu	37	11	4154851	4154851	+	Missense_Mutation	SNP	T	T	C	rs145770432	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	40	118	0	0.357143	0	T|0.999;C|0.001	0.001	strong	.	RRM1	31	.	NM_001033	exon17	c.T1964C	p.M655T	AAGAGATGAAAAA	.	PASS	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	37	9	136287582	136287582	+	Missense_Mutation	SNP	C	C	T	rs34024143	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	34	74	1	0.53125	0.0135135	C|0.905;T|0.095	0.095	strong	ADAMTS13,colon,carcinoma,-2,1	ADAMTS13	113	1	NM_139026	exon1	c.C19T	p.R7W	CACCCCCGGGCAA	.	scavenged	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22940694	22940694	+	Missense_Mutation	SNP	C	C	T	rs62119157	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	32	96	0	0.426667	0	C|0.913;T|0.087	0.087	strong	ZNF99,NS,carcinoma,0,1	ZNF99	273	1	NM_001080409	exon4	c.G2017A	p.E673K	TCTCTTCAGTATG	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52192637	52192637	+	Missense_Mutation	SNP	T	T	C	rs34323943	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	84	192	0	0.587413	0	T|0.918;C|0.082;A|0.000	0.082	strong	.	ZNF217	227	.	NM_006526	exon3	c.A2666G	p.D889G	GGGCTGTCGTTCT	.	PASS	Atlas-SNP
RANBP17	64901	hgsc.bcm.edu	37	5	170626735	170626735	+	Silent	SNP	A	A	G	rs35724654	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	35	47	0	0.479452	0	A|0.890;G|0.110	0.110	strong	.	RANBP17	108	.	NM_022897	exon19	c.A2100G	p.V700V	AACAGTATTACAA	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21319488	21319488	+	Silent	SNP	C	C	T	rs77176173	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	25	220	28	0.131579	0.127273	C|0.625;T|0.375	0.375	strong	KCNJ12,NS,carcinoma,0,1	.	.	1	NM_001194958	exon3	c.C834T	p.S278S	GGCCAGCCCGCTC	.	scavenged	Atlas-SNP
IMPG1	3617	hgsc.bcm.edu	37	6	76640781	76640781	+	Missense_Mutation	SNP	C	C	T	rs3734313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	70	173	0	0.443038	0	C|0.826;T|0.174	0.174	strong	IMPG1,NS,carcinoma,-1,1	IMPG1	143	1	NM_001563	exon15	c.G2132A	p.R711H	TTGCAGCGACACT	.	PASS	Atlas-SNP
TRPM8	79054	hgsc.bcm.edu	37	2	234905078	234905078	+	Silent	SNP	C	C	T	rs11563208	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	250	140	315	0	0.56	0	C|0.795;N|0.000	.	strong	.	TRPM8	146	.	NM_024080	exon22	c.C3048T	p.I1016I	CTTCATCGTCTTC	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733164	52733164	+	Missense_Mutation	SNP	G	G	C	rs149898988		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	579	27	458	0	0.0466321	0	.	.	weak	PCMTD1,NS,carcinoma,0,3	PCMTD1	73	3	NM_052937	exon6	c.C821G	p.P274R	CTTTTGGGTGGAG	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104102563	104102563	+	Silent	SNP	T	T	C	rs17217250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	423	178	443	3	0.420804	0.00677201	T|0.840;C|0.160	0.160	strong	CENPE,NS,carcinoma,0,1	CENPE	253	1	NM_001813	exon12	c.A1014G	p.V338V	AGTTGATACCTCA	.	scavenged	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149242788	149242788	+	Silent	SNP	G	G	A	rs4705390	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	220	95	218	2	0.431818	0.00917431	A|0.027;G|0.973;T|0.000	0.027	strong	PDE6A,NS,carcinoma,-2,1	PDE6A	98	1	NM_000440	exon21	c.C2400T	p.D800D	GATCCCGTCCAAC	.	scavenged	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	93987	93987	+	Silent	SNP	T	T	C	rs72651751		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	42	277	0	0.190045	0	T|0.500;C|0.500	0.500	weak	.	TUBB8	62	.	NM_177987	exon4	c.A345G	p.S115S	CATCACTGACTCC	.	PASS	Atlas-SNP
GPR1	2825	hgsc.bcm.edu	37	2	207041602	207041602	+	Missense_Mutation	SNP	T	T	C	rs138365581	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	24	108	0	0.252632	0	T|0.996;C|0.004	0.004	strong	.	GPR1	38	.	NM_001098199	exon3	c.A370G	p.S124G	AAACACTGGCAAA	.	PASS	Atlas-SNP
SP2	6668	hgsc.bcm.edu	37	17	45994094	45994094	+	Silent	SNP	T	T	C	rs2228251	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	37	78	0	0.45679	0	T|0.467;C|0.533	0.533	strong	.	SP2	38	.	NM_003110	exon3	c.T657C	p.L219L	CAACCTTGTGAAC	.	PASS	Atlas-SNP
TULP2	7288	hgsc.bcm.edu	37	19	49391404	49391404	+	Missense_Mutation	SNP	C	C	T	rs8112811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	70	143	0	0.538462	0	C|0.790;T|0.210	0.210	strong	.	TULP2	60	.	NM_003323	exon8	c.G751A	p.D251N	TATGGTCGCTGTC	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362669	32362669	+	Silent	SNP	T	T	G	rs41449245	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	64	143	0	0.450704	0	T|0.859;G|0.141	0.141	strong	.	BTNL2	50	.	NM_019602	exon6	c.A1212C	p.S404S	GGAAGATGATGGT	.	PASS	Atlas-SNP
CHMP4C	92421	hgsc.bcm.edu	37	8	82670412	82670412	+	Silent	SNP	G	G	A	rs62514262	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	92	143	1	0.557576	0.00699301	G|0.966;A|0.034	0.034	strong	CHMP4C,NS,carcinoma,0,1	CHMP4C	28	1	NM_152284	exon4	c.G519A	p.Q173Q	GGAACAGGAGGAA	.	scavenged	Atlas-SNP
PPP1R9A	55607	hgsc.bcm.edu	37	7	94539536	94539536	+	Silent	SNP	C	C	T	rs12536183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	78	141	0	0.440678	0	C|0.915;T|0.085	0.085	strong	.	PPP1R9A	264	.	NM_017650	exon2	c.C111T	p.P37P	CAAACCCAAGTCA	.	PASS	Atlas-SNP
FRG2	448831	hgsc.bcm.edu	37	4	190947916	190947916	+	Silent	SNP	C	C	T	rs4863310		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	50	265	34	0.234742	0.128302	.	.	weak	FRG2,NS,carcinoma,0,1	FRG2	12	1	NM_001005217	exon2	c.G183A	p.S61S	GGGCTCCGATCCT	.	scavenged	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33725931	33725931	+	Missense_Mutation	SNP	G	G	A	rs1785928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	107	227	0	0.455319	0	G|0.656;A|0.344	0.344	strong	ELP2,colon,carcinoma,0,1	ELP2	70	1	NM_001242875	exon11	c.G1108A	p.V370M	CAGCCAGTGAGAT	.	PASS	Atlas-SNP
DQX1	165545	hgsc.bcm.edu	37	2	74746757	74746757	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	3	169	0	0.0165746	0	.	.	none	DQX1_ENST00000404568,NS,malignant_melanoma,+1,2	DQX1	95	2	NM_133637	exon10	c.T1732C	p.S578P	GTAGGGACAAGGG	.	scavenged	Atlas-SNP
SLC1A4	6509	hgsc.bcm.edu	37	2	65217089	65217089	+	Silent	SNP	G	G	C	rs7559202	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	33	37	0	1	0	G|0.815;C|0.185	0.185	strong	.	SLC1A4	33	.	NM_003038	exon1	c.G312C	p.S104S	CGCCTCGCTCGAT	.	PASS	Atlas-SNP
ZNF28	7576	hgsc.bcm.edu	37	19	53303890	53303890	+	Missense_Mutation	SNP	C	C	G	rs57548937	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	35	71	0	0.443038	0	C|0.898;G|0.102	0.102	strong	.	ZNF28	191	.	NM_006969	exon4	c.G1208C	p.R403T	TGAATCCTCTTAT	.	PASS	Atlas-SNP
PAPD7	11044	hgsc.bcm.edu	37	5	6753013	6753013	+	Silent	SNP	C	C	T	rs28381429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	89	219	0	0.42381	0	C|0.979;T|0.021	0.021	strong	.	PAPD7	69	.	NM_001171805	exon12	c.C1297T	p.L433L	CCGACCCTAGGGG	.	PASS	Atlas-SNP
PRSS57	400668	hgsc.bcm.edu	37	19	687112	687112	+	Missense_Mutation	SNP	G	G	A	rs72618588	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	99	225	1	0.538043	0.00444444	G|0.929;A|0.071	0.071	strong	.	PRSS57	18	.	NM_214710	exon4	c.C458T	p.A153V	GTCCCCGCTGTGG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129903016	129903016	+	Missense_Mutation	SNP	T	T	C	rs7071768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	346	167	364	1	0.482659	0.00274725	T|0.519;C|0.481	0.481	strong	.	MKI67	363	.	NM_002417	exon13	c.A7088G	p.N2363S	CTGAGGTTTCTCT	.	PASS	Atlas-SNP
DHRS9	10170	hgsc.bcm.edu	37	2	169952233	169952233	+	Silent	SNP	T	T	C	rs1059261	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	74	152	0	0.45679	0	T|0.732;C|0.268	0.268	strong	.	DHRS9	29	.	NM_005771	exon8	c.T916C	p.L306L	TTTTTATTGTTGA	.	PASS	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170058374	170058374	+	Missense_Mutation	SNP	C	C	T	rs3800544	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	101	199	1	0.554945	0.00502513	C|0.910;T|0.090	0.090	strong	.	WDR27	129	.	NM_182552	exon13	c.G1400A	p.R467H	TGACCACGTCGCT	.	PASS	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38047680	38047680	+	Silent	SNP	G	G	A	rs11707277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	63	143	0	0.5625	0	G|0.881;A|0.119	0.119	strong	VILL,NS,carcinoma,+1,2	VILL	61	2	NM_015873	exon17	c.G2142A	p.P714P	CCACCCGTCCCAC	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218682757	218682757	+	Missense_Mutation	SNP	G	G	A	rs140104262	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	37	73	0	0.948718	0	G|0.999;A|0.001	0.001	strong	TNS1,NS,carcinoma,+1,1	TNS1	251	1	NM_022648	exon24	c.C3986T	p.P1329L	TCCTCCGGGGTAG	.	PASS	Atlas-SNP
QDPR	5860	hgsc.bcm.edu	37	4	17506042	17506042	+	Silent	SNP	G	G	A	rs12645938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	98	215	1	0.4689	0.00465116	G|0.963;A|0.037	0.037	strong	.	QDPR	22	.	NM_000320	exon3	c.C255T	p.C85C	AGCAACGCAAAGA	.	PASS	Atlas-SNP
MAP3K10	4294	hgsc.bcm.edu	37	19	40712040	40712040	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	80	168	0	0.555556	0	.	.	none	.	MAP3K10	70	.	NM_002446	exon5	c.G1411A	p.G471S	GAAGGCGGCAGCC	.	PASS	Atlas-SNP
CBS	875	hgsc.bcm.edu	37	21	44485590	44485590	+	Silent	SNP	C	C	T	rs73906420	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	55	115	1	0.410448	0.00869565	C|0.993;T|0.007	0.007	strong	CBS_ENST00000398168,NS,carcinoma,0,2	CBS	85	2	NM_000071	exon7	c.G573A	p.T191T	GGTGGGCGTCCTC	.	scavenged	Atlas-SNP
PLK3	1263	hgsc.bcm.edu	37	1	45270024	45270024	+	Silent	SNP	G	G	C	rs11211036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	30	171	0	0.280374	0	G|0.828;C|0.172	0.172	strong	.	PLK3	41	.	NM_004073	exon12	c.G1356C	p.P452P	GAACCCGGCCCCC	.	PASS	Atlas-SNP
YIF1B	90522	hgsc.bcm.edu	37	19	38800165	38800165	+	Silent	SNP	C	C	T	rs3900981	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	78	203	0	0.428571	0	C|0.803;T|0.197	0.197	strong	.	YIF1B	47	.	NM_001039672	exon2	c.G177A	p.L59L	ATAACTCAGGCCA	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411619	105411619	+	Missense_Mutation	SNP	T	T	C	rs200461684	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	96	156	0	0.390244	0	T|0.999;C|0.001	0.001	weak	.	AHNAK2	719	.	NM_138420	exon7	c.A10169G	p.H3390R	GGCAGGTGCCCTT	.	PASS	Atlas-SNP
ND1	10625	hgsc.bcm.edu	37	MT	4153	4153	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	12	8	5	0	0.666667	0	.	.	none	.	.	.	.	ENST00000361390	exon1	c.G847A	p.D283N	CGCTACGACCAAC	.	PASS	Atlas-SNP
SNAP23	8773	hgsc.bcm.edu	37	15	42820589	42820589	+	Silent	SNP	G	G	A	rs1060291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	60	144	1	1	0.00694444	G|0.678;A|0.322	0.322	strong	SNAP23,colon,carcinoma,+1,1	SNAP23	15	1	NM_003825	exon6	c.G396A	p.T132T	AACAACGGGAGCA	.	PASS	Atlas-SNP
HERC5	51191	hgsc.bcm.edu	37	4	89390360	89390360	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	2	158	0	0.0125786	0	.	.	none	HERC5,NS,carcinoma,+1,1	HERC5	114	1	NM_016323	exon9	c.T1187C	p.V396A	GGACTGTAAAGAG	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179395554	179395554	+	Missense_Mutation	SNP	G	G	A	rs66961115	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	323	130	387	2	0.402477	0.00516796	G|0.993;A|0.007	0.007	strong	TTN_ENST00000359218,NS,carcinoma,+1,5	TTN	18412	5	NM_001267550	exon358	c.C105788T	p.A35263V	GATACGGCTTTCG	.	scavenged	Atlas-SNP
RBM6	10180	hgsc.bcm.edu	37	3	50005373	50005373	+	Missense_Mutation	SNP	C	C	T	rs142246877	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	49	112	0	0.480392	0	C|0.997;T|0.003	0.003	strong	.	RBM6	85	.	NM_005777	exon3	c.C515T	p.P172L	CTCCTCCATCTGA	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	147038089	147038089	+	Missense_Mutation	SNP	G	G	T	rs61748896	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	42	117	0	0.538462	0	G|0.941;T|0.059	0.059	strong	.	ADGB	93	.	NM_024694	exon15	c.G1812T	p.E604D	AAGAGAGATAGTC	.	PASS	Atlas-SNP
STK36	27148	hgsc.bcm.edu	37	2	219555262	219555262	+	Missense_Mutation	SNP	G	G	A	rs1344642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	23	145	0	0.244681	0	G|0.530;A|0.470	0.470	strong	.	STK36	111	.	NM_015690	exon14	c.G1748A	p.R583Q	CTTTGCGGAGGGA	.	PASS	Atlas-SNP
FAM21B	55747	hgsc.bcm.edu	37	10	47909792	47909792	+	Missense_Mutation	SNP	C	C	T	rs201373575	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	9	827	1	0.0608108	0.00120919	C|0.949;T|0.051	0.051	strong	FAM21B_ENST00000358474,NS,carcinoma,0,2	FAM21B	31	2	NM_018232	exon11	c.C889T	p.R297W	CAGGATCGGCAAG	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684550	100684550	+	Missense_Mutation	SNP	A	A	G	rs35090328	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	185	192	0	0.848624	0	A|0.904;G|0.096	0.096	strong	.	MUC17	804	.	NM_001040105	exon3	c.A9853G	p.S3285G	TTAACAAGTATGC	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175105996	175105996	+	Missense_Mutation	SNP	C	C	T	rs2072036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	81	92	0	0.669421	0	C|0.889;T|0.111	0.111	strong	TNN,bladder,carcinoma,-1,1	TNN	297	1	NM_022093	exon17	c.C3467T	p.A1156V	CTCCAGCGCGGTA	.	PASS	Atlas-SNP
CLGN	1047	hgsc.bcm.edu	37	4	141313500	141313500	+	Silent	SNP	G	G	A	rs34492995	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	117	223	0	0.717791	0	G|0.992;A|0.008	0.008	strong	.	CLGN	76	.	NM_001130675	exon14	c.C1524T	p.T508T	TATGTCGGTTTTT	.	PASS	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106967185	106967185	+	Missense_Mutation	SNP	A	A	C	rs1159148	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	34	79	0	0.586207	0	A|0.787;C|0.213	0.213	strong	.	AIM1	161	.	NM_001624	exon2	c.A878C	p.Q293P	GAGGCCAAAGGAA	.	PASS	Atlas-SNP
HIVEP1	3096	hgsc.bcm.edu	37	6	12164308	12164308	+	Missense_Mutation	SNP	G	G	A	rs181056704	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	58	120	0	0.495726	0	G|0.999;A|0.001	0.001	strong	.	HIVEP1	242	.	NM_002114	exon9	c.G7771A	p.A2591T	GCCAGCGCAAACC	.	PASS	Atlas-SNP
ALDH1L1	10840	hgsc.bcm.edu	37	3	125865766	125865766	+	Missense_Mutation	SNP	C	C	A	rs2886059	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	49	66	0	0.960784	0	C|0.771;N|0.000	.	strong	.	ALDH1L1	138	.	NM_001270364	exon9	c.G1018T	p.V340F	GCCAAACACTCTG	.	PASS	Atlas-SNP
RNASET2	8635	hgsc.bcm.edu	37	6	167344583	167344583	+	Silent	SNP	A	A	G	rs13213697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	56	121	0	0.5	0	A|0.780;G|0.220	0.220	strong	.	RNASET2	18	.	NM_003730	exon8	c.T516C	p.L172L	TCTGGCAAGGGCA	.	PASS	Atlas-SNP
CPT2	1376	hgsc.bcm.edu	37	1	53679229	53679229	+	Missense_Mutation	SNP	A	A	G	rs1799822	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	42	63	0	0.711864	0	A|0.854;G|0.146	0.146	strong	.	CPT2	34	.	NM_000098	exon5	c.A1939G	p.M647V	GAAGACATGTTTG	.	PASS	Atlas-SNP
FAM47A	158724	hgsc.bcm.edu	37	X	34148882	34148882	+	Missense_Mutation	SNP	C	C	T	rs5973089	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	7	151	0	0.12963	0	C|1.000;T|0.000	0.000	strong	.	FAM47A	249	.	NM_203408	exon1	c.G1514A	p.R505H	TCCGAGCGGAGAC	.	PASS	Atlas-SNP
NMT1	4836	hgsc.bcm.edu	37	17	43176804	43176804	+	Silent	SNP	C	C	T	rs2239923	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	324	149	315	0	0.459877	0	C|0.780;T|0.220	0.220	strong	.	NMT1	31	.	NM_021079	exon8	c.C916T	p.L306L	CGGAAGCTGATTG	.	PASS	Atlas-SNP
DIS3L	115752	hgsc.bcm.edu	37	15	66618342	66618342	+	Missense_Mutation	SNP	A	A	G	rs3803412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	87	133	1	1	0.0075188	A|0.760;G|0.240	0.240	strong	.	DIS3L	175	.	NM_001143688	exon12	c.A1841G	p.D614G	ACTTGGATGAGAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910335	29910335	+	Missense_Mutation	SNP	C	C	T	rs200058378		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	5	159	1	0.0322581	0.00628931	C|0.999;T|0.001	0.001	weak	HLA-A,NS,carcinoma,-1,1	HLA-A	89	1	NM_001242758	exon1	c.C5T	p.A2V	GGATGGCCGTCAT	.	scavenged	Atlas-SNP
IPO11	51194	hgsc.bcm.edu	37	5	61772535	61772535	+	Silent	SNP	G	G	T	rs26635	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	352	351	475	4	0.997159	0.00842105	G|0.567;T|0.433	0.433	strong	IPO11,NS,carcinoma,0,1	IPO11	76	1	NM_001134779	exon9	c.G903T	p.V301V	TAATGTGTGTAGA	.	scavenged	Atlas-SNP
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651057	84651057	+	Missense_Mutation	SNP	G	G	A	rs140206840	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	53	107	0	0.84127	0	G|0.980;A|0.020	0.020	strong	.	ADAMTSL3	290	.	NM_207517	exon21	c.G2677A	p.E893K	CTTGGTGAGCAGG	.	PASS	Atlas-SNP
ARHGEF25	115557	hgsc.bcm.edu	37	12	58005682	58005682	+	Missense_Mutation	SNP	G	G	A	rs60586224	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	13	7	9	0	0.538462	0	G|0.777;A|0.223	0.223	strong	.	ARHGEF25	111	.	NM_182947	exon1	c.G5A	p.R2Q	CCATGCGGGGGGG	.	PASS	Atlas-SNP
INTS2	57508	hgsc.bcm.edu	37	17	59969000	59969000	+	Silent	SNP	T	T	C	rs753765	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	51	134	0	0.459459	0	T|0.903;C|0.097	0.097	strong	INTS2,NS,carcinoma,0,1	INTS2	89	1	NM_020748	exon14	c.A1773G	p.Q591Q	AAGTAATTGAGGA	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	92	188	0	0.505495	0	A|0.976;G|0.024	0.024	strong	.	ADGB	93	.	NM_024694	exon8	c.A876G	p.K292K	CCTGAAAGAAATA	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36689434	36689434	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	4	75	0	0.04	0	.	.	none	.	MYH9	225	.	NM_002473	exon30	c.G4036A	p.E1346K	CCTCCTCCAGCTG	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115030714	115030714	+	Silent	SNP	T	T	C	rs8809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	66	174	0	0.464789	0	T|0.661;C|0.339	0.339	strong	.	CDC16	50	.	NM_003903	exon17	c.T1602C	p.I534I	TTATATTGGTAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512302	195512302	+	Missense_Mutation	SNP	G	G	A	rs201164821	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	405	52	296	4	0.128395	0.0135135	A|0.008;G|0.989;T|0.002	0.008	strong	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.C6149T	p.P2050L	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2577781	2577781	+	Silent	SNP	T	T	C	rs1043291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	21	73	0	0.259259	0	T|0.555;C|0.445	0.445	strong	BRAT1,NS,carcinoma,0,4	BRAT1	57	4	NM_152743	exon14	c.A2388G	p.E796E	ACTCTTTTCCACG	.	PASS	Atlas-SNP
ANKEF1	63926	hgsc.bcm.edu	37	20	10030188	10030188	+	Missense_Mutation	SNP	T	T	A	rs652633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	49	99	0	0.4375	0	T|0.761;A|0.239	0.239	strong	.	.	.	.	NM_198798	exon6	c.T971A	p.L324Q	ATCCACTGTGGGC	.	PASS	Atlas-SNP
TAPBPL	55080	hgsc.bcm.edu	37	12	6562823	6562823	+	Missense_Mutation	SNP	C	C	T	rs2041387	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	42	97	0	0.538462	0	C|0.744;N|0.000	.	strong	.	TAPBPL	21	.	NM_018009	exon3	c.C506T	p.A169V	ATGAGGCGCTCTG	.	PASS	Atlas-SNP
ERMAP	114625	hgsc.bcm.edu	37	1	43296195	43296195	+	Missense_Mutation	SNP	C	C	T	rs33953680	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	60	137	0	0.740741	0	C|0.807;T|0.193	0.193	strong	.	ERMAP	30	.	NM_001017922	exon3	c.C76T	p.H26Y	TCTGTGCATGTGT	.	PASS	Atlas-SNP
EXT1	2131	hgsc.bcm.edu	37	8	118847782	118847782	+	Silent	SNP	G	G	A	rs11546829	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	43	93	0	0.37069	0	G|0.774;A|0.226	0.226	strong	EXT1,NS,carcinoma,0,1	EXT1	98	1	NM_000127	exon3	c.C1065T	p.C355C	AGGGACGCAGGCA	.	PASS	Atlas-SNP
HDGFL1	154150	hgsc.bcm.edu	37	6	22570064	22570064	+	Missense_Mutation	SNP	C	C	T	rs2076506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	15	39	0	0.625	0	C|0.862;T|0.138	0.138	strong	.	HDGFL1	33	.	NM_138574	exon1	c.C260T	p.T87M	ACCCCACGGTCCA	.	PASS	Atlas-SNP
WRAP73	49856	hgsc.bcm.edu	37	1	3551792	3551792	+	Silent	SNP	G	G	A	rs2296034	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	69	167	0	0.627273	0	G|0.949;A|0.051	0.051	strong	.	WRAP73	43	.	NM_017818	exon7	c.C670T	p.L224L	TGCCCAGGGACCA	.	PASS	Atlas-SNP
SIDT1	54847	hgsc.bcm.edu	37	3	113320477	113320477	+	Missense_Mutation	SNP	C	C	T	rs33990195	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	88	222	0	0.478261	0	C|0.924;T|0.076	0.076	strong	SIDT1,colon,carcinoma,-1,1	SIDT1	99	1	NM_017699	exon11	c.C1088T	p.T363I	CCAGCACACCCGA	.	PASS	Atlas-SNP
FAM32A	26017	hgsc.bcm.edu	37	19	16301759	16301759	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	53	127	0	0.40458	0	.	.	none	FAM32A,NS,carcinoma,0,1	FAM32A	6	1	NM_014077	exon4	c.C332T	p.T111M	GCTGGACGAAGTA	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29364838	29364838	+	Missense_Mutation	SNP	C	C	G	rs2073152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	220	304	1	0.977778	0.00328947	C|0.763;G|0.237	0.237	strong	.	OR12D2	42	.	NM_013936	exon1	c.C362G	p.S121C	ACCTCTCTGTGGC	.	PASS	Atlas-SNP
TUBB1	81027	hgsc.bcm.edu	37	20	57598808	57598808	+	Missense_Mutation	SNP	G	G	A	rs41303899	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	59	113	0	0.475806	0	G|0.999;A|0.001	0.001	strong	TUBB1,mucosal,malignant_melanoma,+1,1	TUBB1	42	1	NM_030773	exon4	c.G326A	p.G109E	CGGAGGGAGCCGA	.	PASS	Atlas-SNP
TRIM58	25893	hgsc.bcm.edu	37	1	248023966	248023966	+	Silent	SNP	C	C	T	rs3737277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	52	120	0	0.327044	0	C|0.716;T|0.284	0.284	strong	.	TRIM58	143	.	NM_015431	exon2	c.C468T	p.D156D	GGAGGACGCCTTG	.	PASS	Atlas-SNP
AKAP13	11214	hgsc.bcm.edu	37	15	86287867	86287867	+	Missense_Mutation	SNP	G	G	A	rs2614668	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	50	95	0	0.746269	0	G|0.842;A|0.158	0.158	strong	.	AKAP13	394	.	NM_006738	exon37	c.G8413A	p.A2805T	GGTCCCGCGTCAG	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112889374	112889374	+	Missense_Mutation	SNP	G	G	A	rs10071816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	44	128	0	0.473118	0	G|0.681;A|0.319	0.319	strong	.	YTHDC2	118	.	NM_022828	exon14	c.G1955A	p.S652N	CTGACAGTACACA	.	PASS	Atlas-SNP
CNNM2	54805	hgsc.bcm.edu	37	10	104678801	104678801	+	Silent	SNP	C	C	T	rs117691462	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	62	134	0	0.826667	0	C|0.996;T|0.004	0.004	strong	.	CNNM2	119	.	NM_199076	exon1	c.C564T	p.S188S	CAAGTCCTATTAC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20837033	20837033	+	Missense_Mutation	SNP	T	T	C	rs2104978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	155	239	0	0.596154	0	T|0.957;C|0.043	0.043	strong	.	TEP1	224	.	NM_007110	exon54	c.A7685G	p.H2562R	AGCACATGGAGGG	.	PASS	Atlas-SNP
ZNF304	57343	hgsc.bcm.edu	37	19	57863052	57863052	+	Missense_Mutation	SNP	T	T	C	rs117111481	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	51	135	0	0.459459	0	T|0.985;C|0.015	0.015	strong	.	ZNF304	74	.	NM_020657	exon1	c.T20C	p.M7T	TGCTGATGGACCG	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229623338	229623338	+	Missense_Mutation	SNP	T	T	C	rs1065674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	30	52	0	0.365854	0	T|0.691;C|0.309	0.309	strong	.	NUP133	111	.	NM_018230	exon10	c.A1217G	p.Q406R	GTCAACTGACACA	.	PASS	Atlas-SNP
CTH	1491	hgsc.bcm.edu	37	1	70904800	70904800	+	Missense_Mutation	SNP	G	G	T	rs1021737	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	92	209	0	0.676471	0	G|0.779;T|0.221	0.221	strong	.	CTH	48	.	NM_001902	exon12	c.G1208T	p.S403I	GTGGAAGTCACAG	.	PASS	Atlas-SNP
CPSF6	11052	hgsc.bcm.edu	37	12	69646914	69646914	+	Silent	SNP	G	G	A	rs2305641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	300	136	318	0	0.453333	0	G|0.568;A|0.432	0.432	strong	.	CPSF6	96	.	NM_007007	exon3	c.G354A	p.R118R	AAATCGGGCAAAT	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76069811	76069811	+	Missense_Mutation	SNP	T	T	C	rs2906999	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	288	182	240	1	0.631944	0.00416667	T|0.444;C|0.556	0.556	strong	.	ZP3	32	.	NM_001110354	exon7	c.T943C	p.S315P	GAAGGCTCGGCTG	.	PASS	Atlas-SNP
CLEC4D	338339	hgsc.bcm.edu	37	12	8667897	8667897	+	Missense_Mutation	SNP	A	A	G	rs4304840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	286	120	329	0	0.41958	0	A|0.678;G|0.322	0.322	strong	.	CLEC4D	46	.	NM_080387	exon2	c.A94G	p.S32G	CTTCTCAGTGTCT	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51227000	51227000	+	Silent	SNP	A	A	G	rs4901055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	21	44	0	0.328125	0	A|0.812;G|0.188	0.188	strong	.	NIN	475	.	NM_020921	exon17	c.T1974C	p.H658H	GTTCTCATGCCTT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152279729	152279729	+	Missense_Mutation	SNP	C	C	T	rs3126072	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	401	151	295	2	0.376559	0.00677966	C|0.682;T|0.318	0.318	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.G7633A	p.G2545R	AGTGTCCAGAGCT	.	scavenged	Atlas-SNP
RBM5	10181	hgsc.bcm.edu	37	3	50153356	50153356	+	Silent	SNP	T	T	C	rs1138536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	55	101	0	0.639535	0	T|0.328;C|0.672	0.672	strong	.	RBM5	76	.	NM_005778	exon22	c.T2037C	p.Y679Y	CATCTATCGACGA	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23091371	23091371	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	15	248	0	0.0568182	0	.	.	none	.	USP31	122	.	NM_020718	exon13	c.C2072T	p.P691L	CTCCACGGGGACC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152277822	152277822	+	Silent	SNP	T	T	C	rs3126069	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	442	22	479	0	0.0497738	0	T|0.777;C|0.223	0.223	strong	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.A9540G	p.S3180S	GTGACGTGACACT	.	scavenged	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792093	8792093	+	Silent	SNP	G	G	A	rs16957702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	37	51	0	0.973684	0	G|0.734;A|0.266	0.266	strong	.	PIK3R5	79	.	NM_001142633	exon10	c.C1011T	p.D337D	GTGCCCGTCAGTT	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104373829	104373829	+	Silent	SNP	C	C	A	rs75200561	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	284	8	258	0	0.028169	0	.	.	weak	TDG,pharynx,carcinoma,0,1	TDG	43	1	NM_003211	exon3	c.C387A	p.T129T	TTTGACCTTCAAT	.	scavenged	Atlas-SNP
CAPN10	11132	hgsc.bcm.edu	37	2	241526428	241526428	+	Missense_Mutation	SNP	C	C	G	rs138005500	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	55	109	0	0.585106	0	C|0.991;G|0.009	0.009	strong	.	CAPN10	105	.	NM_023085	exon1	c.C100G	p.L34V	ACGCCGCTGGCCC	.	PASS	Atlas-SNP
SOAT1	6646	hgsc.bcm.edu	37	1	179312752	179312752	+	Silent	SNP	C	C	T	rs10753191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	134	123	0	0.992593	0	C|0.768;N|0.000	.	strong	.	SOAT1	53	.	NM_003101	exon10	c.C969T	p.V323V	TTATGTCGCTATG	.	PASS	Atlas-SNP
ANKRD33	341405	hgsc.bcm.edu	37	12	52284500	52284500	+	Missense_Mutation	SNP	A	A	G	rs34494292	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	26	27	0	0.962963	0	A|0.845;G|0.155	0.155	strong	.	ANKRD33	33	.	NM_182608	exon5	c.A770G	p.Q257R	TTAGCCAGCACTA	.	PASS	Atlas-SNP
OR6Q1	219952	hgsc.bcm.edu	37	11	57798942	57798942	+	Missense_Mutation	SNP	A	A	G	rs2513726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	103	305	0	0.420408	0	A|0.653;G|0.347	0.347	strong	.	OR6Q1	58	.	NM_001005186	exon1	c.A518G	p.Y173C	CATTTTATGGCCC	.	PASS	Atlas-SNP
SLC26A9	115019	hgsc.bcm.edu	37	1	205884508	205884508	+	Missense_Mutation	SNP	C	C	T	rs147005854	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	254	88	180	0	0.346457	0	C|0.999;T|0.001	0.001	strong	.	SLC26A9	176	.	NM_134325	exon21	c.G2353A	p.A785T	TCTCTGCGTGAAA	.	PASS	Atlas-SNP
FBXO47	494188	hgsc.bcm.edu	37	17	37093510	37093510	+	Missense_Mutation	SNP	T	T	C	rs113358400	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	51	104	0	0.463636	0	T|0.981;C|0.019	0.019	strong	.	FBXO47	34	.	NM_001008777	exon11	c.A1277G	p.N426S	AACAAATTCAAAA	.	PASS	Atlas-SNP
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43630156	43630156	+	Silent	SNP	A	A	C	rs11559311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	87	148	0	0.731092	0	A|0.912;C|0.088	0.088	strong	.	EBNA1BP2	37	.	NM_001159936	exon10	c.T1044G	p.P348P	TTTTCCAGGTCTC	.	PASS	Atlas-SNP
SLC14A2	8170	hgsc.bcm.edu	37	18	43246156	43246156	+	Missense_Mutation	SNP	G	G	A	rs9960464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	59	135	0	0.556604	0	G|0.615;A|0.385	0.385	strong	SLC14A2,NS,carcinoma,0,1	SLC14A2	121	1	NM_001242692	exon13	c.G1529A	p.R510Q	CCTATCGATACCG	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40138676	40138676	+	Missense_Mutation	SNP	A	A	G	rs2271395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	110	201	1	0.531401	0.00497512	A|0.918;G|0.082	0.082	strong	.	N4BP2	166	.	NM_018177	exon14	c.A4759G	p.T1587A	TCTCATACTGGCC	.	PASS	Atlas-SNP
TECPR1	25851	hgsc.bcm.edu	37	7	97847040	97847040	+	Silent	SNP	G	G	A	rs2279676	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	67	103	1	0.712766	0.00970874	G|0.772;A|0.228	0.228	strong	TECPR1,colon,carcinoma,0,1	TECPR1	77	1	NM_015395	exon25	c.C3348T	p.H1116H	GGGCTCGTGAGGC	.	scavenged	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384999	16384999	+	Missense_Mutation	SNP	G	G	A	rs1807284	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	9	4	18	0	0.444444	0	G|0.717;A|0.283	0.283	strong	FAM131C,NS,carcinoma,0,2	FAM131C	21	2	NM_182623	exon7	c.C776T	p.P259L	CCCGGGGGGTGGG	.	scavenged	Atlas-SNP
SORT1	6272	hgsc.bcm.edu	37	1	109878903	109878903	+	Missense_Mutation	SNP	C	C	G	rs2228606	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	102	210	0	0.784615	0	C|0.986;G|0.014	0.014	strong	.	SORT1	48	.	NM_002959	exon11	c.G1330C	p.E444Q	TGTTTTCAGGCTT	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100105735	100105735	+	Silent	SNP	T	T	C	rs1947717	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	104	112	0	0.971963	0	T|0.445;C|0.555	0.555	strong	.	.	.	.	NM_020893	exon19	c.T2520C	p.C840C	GCATTGTAGGAAG	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27279852	27279852	+	Missense_Mutation	SNP	T	T	C	rs2235233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	82	105	0	0.942529	0	T|0.762;C|0.238	0.238	strong	.	POM121L2	61	.	NM_033482	exon1	c.A98G	p.Q33R	AGGGGCTGAGGTG	.	PASS	Atlas-SNP
SERPINA6	866	hgsc.bcm.edu	37	14	94776219	94776219	+	Silent	SNP	C	C	T	rs2228542	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	89	128	1	0.597315	0.0078125	C|0.758;T|0.242	0.242	strong	SERPINA6_ENST00000341584,NS,adenoma,0,1	SERPINA6	102	1	NM_001756	exon3	c.G738A	p.S246S	GAGCTCCGAGTCA	.	scavenged	Atlas-SNP
PIAS1	8554	hgsc.bcm.edu	37	15	68479959	68479959	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	16	272	0	0.0935673	0	.	.	none	PIAS1,NS,carcinoma,-1,1	PIAS1	42	1	NM_016166	exon14	c.T1742C	p.F581S	GGTTTTTCCCGTA	.	PASS	Atlas-SNP
KLC1	3831	hgsc.bcm.edu	37	14	104143806	104143806	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	35	98	0	0.277778	0	.	.	none	.	KLC1	54	.	NM_182923	exon12	c.C1434T	p.G478G	TCAAGGCAAATTT	.	PASS	Atlas-SNP
MTL5	9633	hgsc.bcm.edu	37	11	68512543	68512543	+	Missense_Mutation	SNP	A	A	G	rs12365708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	84	198	0	0.525	0	A|0.925;G|0.075	0.075	strong	.	MTL5	37	.	NM_001039656	exon4	c.T667C	p.C223R	CTATACATAGCAT	.	PASS	Atlas-SNP
ZBTB45	84878	hgsc.bcm.edu	37	19	59028407	59028407	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	2	165	0	0.011236	0	.	.	none	ZBTB45,NS,carcinoma,0,1	ZBTB45	37	1	NM_032792	exon2	c.G634A	p.E212K	TTTCCTCGTCATC	.	scavenged	Atlas-SNP
RBM44	375316	hgsc.bcm.edu	37	2	238742968	238742968	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	262	128	297	1	0.48855	0.003367	.	.	none	.	RBM44	167	.	NM_001080504	exon15	c.G3083A	p.G1028D	ATAAAGGTTTTCT	.	PASS	Atlas-SNP
SFN	2810	hgsc.bcm.edu	37	1	27190196	27190196	+	Missense_Mutation	SNP	A	A	T	rs77755255	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37	6	59	0	0.162162	0	.	.	weak	.	SFN	20	.	NM_006142	exon1	c.A493T	p.T165S	CCGCCCACCAACC	.	PASS	Atlas-SNP
LAD1	3898	hgsc.bcm.edu	37	1	201355522	201355522	+	Missense_Mutation	SNP	T	T	C	rs4128458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	51	117	0	0.329032	0	T|0.405;C|0.595	0.595	strong	.	LAD1	42	.	NM_005558	exon3	c.A967G	p.K323E	CCTGCTTTGCCAA	.	PASS	Atlas-SNP
TNFAIP6	7130	hgsc.bcm.edu	37	2	152226570	152226570	+	Missense_Mutation	SNP	A	A	G	rs1046668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	39	80	0	0.557143	0	A|0.810;G|0.190	0.190	strong	.	TNFAIP6	98	.	NM_007115	exon4	c.A431G	p.Q144R	CAAAGCAAATTTT	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150947719	150947719	+	Silent	SNP	C	C	T	rs3734060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	68	135	1	0.462585	0.00740741	C|0.527;T|0.473	0.473	strong	FAT2,colon,carcinoma,0,2	FAT2	465	2	NM_001447	exon1	c.G774A	p.S258S	CACCACCGAAGCA	.	scavenged	Atlas-SNP
SYVN1	84447	hgsc.bcm.edu	37	11	64898226	64898226	+	Silent	SNP	C	C	T	rs9971407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	6	25	0	0.25	0	C|0.844;T|0.156	0.156	strong	SYVN1,NS,lymphoid_neoplasm,0,1	SYVN1	55	1	NM_172230	exon11	c.G1011A	p.S337S	TGGCAGCGATGCA	.	PASS	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55722882	55722882	+	Nonsense_Mutation	SNP	C	C	A	rs57809907	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	75	108	1	1	0.00925926	C|0.819;A|0.181	0.181	strong	DYX1C1,NS,carcinoma,+2,1	DYX1C1	54	1	NM_130810	exon10	c.G1249T	p.E417X	TTAGTTCTGTTCC	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	33971740	33971740	+	Silent	SNP	A	A	G	rs3739690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	49	91	0	0.480392	0	A|0.762;G|0.238	0.238	strong	.	UBAP2	82	.	NM_018449	exon8	c.T588C	p.P196P	GTCTGCAGGATTA	.	PASS	Atlas-SNP
LTK	4058	hgsc.bcm.edu	37	15	41805237	41805237	+	Missense_Mutation	SNP	C	C	T	rs2305030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	29	68	0	0.659091	0	C|0.858;T|0.142	0.142	strong	.	LTK	117	.	NM_001135685	exon2	c.G125A	p.R42Q	GGGTCCCGGGGGC	.	PASS	Atlas-SNP
AGAP11	119385	hgsc.bcm.edu	37	10	88768423	88768423	+	Silent	SNP	A	A	G	rs2641562	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	73	102	0	0.784946	0	A|0.567;G|0.433	0.433	strong	.	.	.	.	NM_133447	exon12	c.A414G	p.T138T	GAAGACATGGAAA	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104641612	104641612	+	Silent	SNP	T	T	C	rs4906422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	45	50	0	0.714286	0	T|0.708;C|0.292	0.292	strong	KIF26A,NS,carcinoma,0,1	KIF26A	84	1	NM_015656	exon12	c.T2487C	p.G829G	CAAGGGTCCCCGA	.	PASS	Atlas-SNP
ELMSAN1	91748	hgsc.bcm.edu	37	14	74205878	74205878	+	Silent	SNP	C	C	T	rs17782128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	59	130	0	0.35119	0	C|0.861;T|0.139	0.139	strong	C14orf43,bladder,carcinoma,-1,1	.	.	1	NM_194278	exon2	c.G834A	p.P278P	TTGCTGCGGCATG	.	PASS	Atlas-SNP
STAC	6769	hgsc.bcm.edu	37	3	36422216	36422216	+	Silent	SNP	T	T	C	rs73052248	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	33	94	0	0.515625	0	T|0.823;C|0.177	0.177	strong	STAC,caecum,carcinoma,0,1	STAC	78	1	NM_003149	exon1	c.T81C	p.S27S	GCCCTCTCCTGCA	.	PASS	Atlas-SNP
CCDC170	80129	hgsc.bcm.edu	37	6	151939181	151939181	+	Missense_Mutation	SNP	G	G	A	rs3734804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	75	227	0	0.369458	0	G|0.473;A|0.527	0.527	strong	.	.	.	.	NM_025059	exon11	c.G2047A	p.V683I	AGATTGGTCCATT	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29274704	29274704	+	Silent	SNP	C	C	T	rs61749512	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167	73	195	0	0.437126	0	C|0.785;T|0.215	0.215	strong	.	FAM179A	106	.	NM_199280	exon20	c.C2805T	p.T935T	GAACACCGCCACC	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76922868	76922868	+	Silent	SNP	C	C	T	rs41298757	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	28	52	0	0.54902	0	C|0.975;T|0.025	0.025	strong	.	MYO7A	164	.	NM_000260	exon46	c.C6240T	p.S2080S	ATAGTCCATCGTC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379794	31379794	+	Silent	SNP	C	C	T	rs1051797	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	39	122	0	0.330508	0	C|0.698;T|0.302	0.302	strong	.	MICA	21	.	NM_001177519	exon4	c.C684T	p.S228S	GGCTTCCAGCTTC	.	PASS	Atlas-SNP
SPRY4	81848	hgsc.bcm.edu	37	5	141693948	141693948	+	Silent	SNP	G	G	A	rs145360326	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	108	251	0	0.471616	0	G|0.999;A|0.001	0.001	strong	SPRY4,rectum,carcinoma,0,2	SPRY4	31	2	NM_030964	exon3	c.C795T	p.S265S	CACCACGGAGAGA	.	PASS	Atlas-SNP
MEF2A	4205	hgsc.bcm.edu	37	15	100250918	100250918	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	71	139	0	0.731959	0	.	.	none	.	MEF2A	138	.	NM_005587	exon10	c.G1071A	p.S357S	GGTGTCGGCCTGG	.	PASS	Atlas-SNP
GAS8	2622	hgsc.bcm.edu	37	16	90106746	90106746	+	Silent	SNP	C	C	T	rs61734731	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	5	38	0	0.108696	0	C|0.963;T|0.037	0.037	strong	GAS8,NS,carcinoma,0,1	GAS8	29	1	NM_001481	exon9	c.C1050T	p.T350T	GTTCACCGCAGCC	.	PASS	Atlas-SNP
PRSS57	400668	hgsc.bcm.edu	37	19	687078	687078	+	Silent	SNP	G	G	A	rs72618587	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	262	130	275	1	0.496183	0.00363636	G|0.928;A|0.072	0.072	strong	.	PRSS57	18	.	NM_214710	exon4	c.C492T	p.F164F	AGACACGAAGCCC	.	PASS	Atlas-SNP
TEKT3	64518	hgsc.bcm.edu	37	17	15215660	15215660	+	Silent	SNP	T	T	C	rs2286516	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	97	233	1	0.431111	0.00429185	T|0.770;C|0.230	0.230	strong	.	TEKT3	64	.	NM_031898	exon7	c.A1017G	p.Q339Q	GTTGAATTGATTC	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769276	43769276	+	Silent	SNP	T	T	C	rs10880473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	61	193	1	0.388535	0.00518135	T|0.747;C|0.253	0.253	strong	ADAMTS20_ENST00000389420,neck,malignant_melanoma,-2,1	ADAMTS20	635	1	NM_025003	exon36	c.A5352G	p.R1784R	TTCCCTTCTACTC	.	scavenged	Atlas-SNP
ABCF2	10061	hgsc.bcm.edu	37	7	150912750	150912750	+	Silent	SNP	G	G	T	rs12538823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	22	160	0	0.178862	0	G|0.939;T|0.061	0.061	strong	.	ABCF2	54	.	NM_007189	exon13	c.C1470A	p.I490I	CTCCTTGATCTCT	.	PASS	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1373518	1373518	+	Missense_Mutation	SNP	T	T	C	rs9905106	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	123	132	1	1	0.00757576	T|0.270;C|0.730	0.730	strong	MYO1C,NS,carcinoma,0,2	MYO1C	57	2	NM_001080779	exon24	c.A2477G	p.Q826R	ACATTCTGGGGCA	.	PASS	Atlas-SNP
MAD1L1	8379	hgsc.bcm.edu	37	7	2020125	2020125	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	3	84	0	0.0306122	0	.	.	none	MAD1L1,NS,carcinoma,0,1	MAD1L1	81	1	NM_003550	exon15	c.A1468G	p.S490G	GGAAGCTCTGTTC	.	scavenged	Atlas-SNP
METTL21A	151194	hgsc.bcm.edu	37	2	208478055	208478055	+	Silent	SNP	A	A	G	rs17520056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	43	92	0	0.704918	0	A|0.705;G|0.295	0.295	strong	METTL21A,NS,carcinoma,0,1	METTL21A	24	1	NM_145280	exon4	c.T372C	p.T124T	TCCCCAAGTCAGC	.	PASS	Atlas-SNP
LRRC42	115353	hgsc.bcm.edu	37	1	54432019	54432019	+	Silent	SNP	G	G	A	rs2294514	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	70	223	0	0.679612	0	G|0.708;A|0.292	0.292	strong	.	LRRC42	29	.	NM_052940	exon7	c.G978A	p.E326E	ACGGGAGACCTCG	.	PASS	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92734358	92734358	+	Silent	SNP	G	G	A	rs200454238	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	68	128	0	0.343434	0	G|0.999;A|0.001	0.001	weak	.	SAMD9	239	.	NM_001193307	exon2	c.C1053T	p.D351D	CGTAATGTCCTTA	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1887245	1887245	+	Silent	SNP	G	G	A	rs28575980	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	57	87	0	0.982759	0	G|0.777;A|0.223	0.223	strong	KIAA1751,NS,carcinoma,0,1	KIAA1751	92	1	NM_001080484	exon18	c.C2061T	p.A687A	GGTGGCGGCTTTG	.	PASS	Atlas-SNP
ADH4	127	hgsc.bcm.edu	37	4	100047812	100047812	+	Silent	SNP	G	G	A	rs1126672	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	59	150	0	0.42446	0	G|0.824;A|0.176	0.176	strong	ADH4,NS,carcinoma,0,1	ADH4	35	1	NM_000670	exon8	c.C1051T	p.L351L	TCACCAGTGCATC	.	PASS	Atlas-SNP
KISS1	3814	hgsc.bcm.edu	37	1	204159922	204159922	+	Missense_Mutation	SNP	T	T	C	rs35431622	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	26	113	0	0.204724	0	T|0.941;C|0.059	0.059	strong	.	KISS1	6	.	NM_002256	exon3	c.A107G	p.Q36R	AGCTGCTGGCCTA	.	PASS	Atlas-SNP
RHBDF2	79651	hgsc.bcm.edu	37	17	74473329	74473329	+	Missense_Mutation	SNP	C	C	T	rs140433374	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	74	158	0	0.536232	0	C|0.999;T|0.001	0.001	strong	.	RHBDF2	57	.	NM_024599	exon8	c.G940A	p.A314T	AGCTGGCAGAGAG	.	PASS	Atlas-SNP
TBC1D26	353149	hgsc.bcm.edu	37	17	15640806	15640806	+	Missense_Mutation	SNP	A	A	C	rs3852810	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	323	20	71	1	0.0619195	0.0140845	A|0.500;C|0.500	0.500	strong	TBC1D26,trunk,malignant_melanoma,0,1	TBC1D26	16	1	NM_178571	exon5	c.A167C	p.E56A	AGATGGAGCTGCC	.	scavenged	Atlas-SNP
VILL	50853	hgsc.bcm.edu	37	3	38047954	38047954	+	Missense_Mutation	SNP	G	G	C	rs9816693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	67	202	1	0.352632	0.00495049	G|0.800;C|0.200	0.200	strong	VILL,NS,carcinoma,0,1	VILL	61	1	NM_015873	exon18	c.G2220C	p.L740F	CAACTTGCGGCTA	.	scavenged	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34824107	34824107	+	Missense_Mutation	SNP	A	A	C	rs16894945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	62	148	0	0.4	0	A|0.884;C|0.116	0.116	strong	.	UHRF1BP1	102	.	NM_017754	exon10	c.A1212C	p.K404N	GAGCAAAATGGAG	.	PASS	Atlas-SNP
SLC15A4	121260	hgsc.bcm.edu	37	12	129293346	129293346	+	Silent	SNP	C	C	T	rs11059924	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	33	130	0	0.370787	0	C|0.525;T|0.475	0.475	strong	.	SLC15A4	41	.	NM_145648	exon5	c.G1245A	p.S415S	AAAGGCCGAGCAC	.	PASS	Atlas-SNP
PRDM10	56980	hgsc.bcm.edu	37	11	129830796	129830796	+	Missense_Mutation	SNP	C	C	T	rs11221912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	34	113	0	0.255639	0	C|0.776;T|0.224	0.224	strong	PRDM10,NS,carcinoma,0,1	PRDM10	120	1	NM_020228	exon2	c.G64A	p.A22T	CCTGTGCGGCATT	.	PASS	Atlas-SNP
PLEKHA1	59338	hgsc.bcm.edu	37	10	124189197	124189197	+	Missense_Mutation	SNP	A	A	G	rs1045216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	102	109	1	0.980769	0.00917431	A|0.314;G|0.686	0.686	strong	.	PLEKHA1	33	.	NM_021622	exon12	c.A958G	p.T320A	GCAGCCACCGCCA	.	PASS	Atlas-SNP
RNF121	55298	hgsc.bcm.edu	37	11	71706544	71706544	+	Silent	SNP	A	A	G	rs34075366	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	108	257	1	0.493151	0.00389105	A|0.964;G|0.036	0.036	strong	.	RNF121	19	.	NM_018320	exon8	c.A810G	p.Q270Q	GAAGCAAACGTGT	.	PASS	Atlas-SNP
ZCCHC14	23174	hgsc.bcm.edu	37	16	87493737	87493737	+	Missense_Mutation	SNP	T	T	C	rs11648852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	115	174	0	0.732484	0	T|0.873;C|0.127	0.127	strong	.	ZCCHC14	87	.	NM_015144	exon2	c.A160G	p.I54V	GAGTGATCTGAGG	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2092803	2092803	+	Silent	SNP	A	A	G	rs1063523	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	29	67	0	0.367089	0	A|0.741;G|0.259	0.259	strong	.	MYOM2	251	.	NM_003970	exon37	c.A4296G	p.T1432T	CGTGACAGTGAGC	.	PASS	Atlas-SNP
SESTD1	91404	hgsc.bcm.edu	37	2	179979930	179979930	+	Silent	SNP	T	T	C	rs2289993	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	98	180	0	0.544444	0	T|0.810;C|0.190	0.190	strong	.	SESTD1	66	.	NM_178123	exon16	c.A1701G	p.Q567Q	CAAAGATTGGCAT	.	PASS	Atlas-SNP
MTHFSD	64779	hgsc.bcm.edu	37	16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	rs34005514	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	113	130	0	0.795775	0	G|0.968;C|0.032	0.032	strong	.	MTHFSD	52	.	NM_001159377	exon3	c.C133G	p.L45V	AAGCCAGATAAGA	.	PASS	Atlas-SNP
SUSD4	55061	hgsc.bcm.edu	37	1	223465859	223465859	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	296	3	239	0	0.0101351	0	.	.	none	SUSD4_ENST00000343846,NS,carcinoma,+2,2	SUSD4	82	2	NM_017982	exon3	c.A283G	p.T95A	TCTTTGTAGCGCC	.	scavenged	Atlas-SNP
LPAR2	9170	hgsc.bcm.edu	37	19	19737992	19737992	+	Silent	SNP	G	G	A	rs150741448	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	35	66	0	0.466667	0	G|0.997;A|0.003	0.003	strong	.	LPAR2	28	.	NM_004720	exon2	c.C102T	p.V34V	CACCACGACCACA	.	PASS	Atlas-SNP
ZNF283	284349	hgsc.bcm.edu	37	19	44352665	44352665	+	Missense_Mutation	SNP	T	T	C	rs2356437	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	52	114	0	0.485981	0	T|0.341;C|0.659	0.659	strong	ZNF283_ENST00000324461,colon,carcinoma,0,1	ZNF283	83	1	NM_181845	exon7	c.T1912C	p.C638R	TTTACTTGTGGCT	.	PASS	Atlas-SNP
INF2	64423	hgsc.bcm.edu	37	14	105180785	105180785	+	Missense_Mutation	SNP	C	C	T	rs34251364	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	75	107	0	0.6	0	C|0.946;T|0.054	0.054	strong	.	INF2	148	.	NM_022489	exon21	c.C3286T	p.P1096S	CCCCAGCCCTTGG	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023459	25023459	+	Missense_Mutation	SNP	G	G	C	rs138813205	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	338	27	322	0	0.0798817	0	C|0.014;G|0.986	0.014	strong	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon12	c.G1081C	p.D361H	TCTGACGACACCA	.	scavenged	Atlas-SNP
PI4KA	5297	hgsc.bcm.edu	37	22	21066897	21066897	+	Silent	SNP	G	G	A	rs60856465		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	285	56	432	1	0.196491	0.00231481	A|1.000;|0.000	1.000	weak	PI4KA_ENST00000255882,NS,carcinoma,0,2	PI4KA	313	2	NM_058004	exon50	c.C5679T	p.C1893C	CACCCCGCACTAG	.	scavenged	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	rs117833529	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	35	59	0	0.507246	0	C|0.976;T|0.024	0.024	strong	.	LRRC16B	120	.	NM_138360	exon33	c.C3184T	p.R1062W	CGGCCCCGGAGCT	.	PASS	Atlas-SNP
MCM10	55388	hgsc.bcm.edu	37	10	13239651	13239651	+	Missense_Mutation	SNP	A	A	G	rs2274110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	36	101	0	0.734694	0	A|0.880;G|0.120	0.120	strong	MCM10,NS,carcinoma,0,1	MCM10	76	1	NM_182751	exon15	c.A2006G	p.K669R	GGGCAAAAGGCCA	.	PASS	Atlas-SNP
TPX2	22974	hgsc.bcm.edu	37	20	30382315	30382315	+	Silent	SNP	A	A	G	rs3203770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	103	107	0	1	0	A|0.722;G|0.278	0.278	strong	.	TPX2	61	.	NM_012112	exon15	c.A1797G	p.R599R	TGACAGAAGAGGT	.	PASS	Atlas-SNP
HYI	81888	hgsc.bcm.edu	37	1	43917637	43917637	+	Silent	SNP	G	G	A	rs2251802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	32	183	0	0.248062	0	G|0.679;A|0.321	0.321	strong	.	HYI	23	.	NM_001243526	exon5	c.C549T	p.D183D	CTGGGGGTCAGTG	.	PASS	Atlas-SNP
GIT2	9815	hgsc.bcm.edu	37	12	110383141	110383141	+	Missense_Mutation	SNP	G	G	A	rs11068997	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	13	41	0	0.382353	0	G|0.941;A|0.059	0.059	strong	.	GIT2	81	.	NM_057169	exon16	c.C1655T	p.A552V	ACAAGTGCACTCC	.	PASS	Atlas-SNP
FAM21A	387680	hgsc.bcm.edu	37	10	51827934	51827934	+	Missense_Mutation	SNP	G	G	A	rs55875820	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	54	43	0	0.964286	0	G|0.689;A|0.311	0.311	strong	FAM21A,NS,carcinoma,0,1	FAM21A	32	1	NM_001005751	exon2	c.G73A	p.V25M	TGGTCGGTGGAGG	.	PASS	Atlas-SNP
IBTK	25998	hgsc.bcm.edu	37	6	82933309	82933309	+	Silent	SNP	C	C	T	rs9361904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	44	92	0	0.453608	0	C|0.756;T|0.244	0.244	strong	IBTK,NS,carcinoma,0,1	IBTK	128	1	NM_015525	exon8	c.G972A	p.K324K	TACACACTTTTCT	.	PASS	Atlas-SNP
SCFD2	152579	hgsc.bcm.edu	37	4	54011576	54011576	+	Silent	SNP	T	T	C	rs79628372	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	84	153	0	0.556291	0	T|0.942;C|0.058	0.058	strong	SCFD2,NS,carcinoma,0,1	SCFD2	78	1	NM_152540	exon5	c.A1485G	p.E495E	TTTTTCTTCTGCT	.	PASS	Atlas-SNP
ZNF808	388558	hgsc.bcm.edu	37	19	53057479	53057479	+	Missense_Mutation	SNP	G	G	A	rs61746334	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	41	87	0	0.532468	0	G|0.924;A|0.076	0.076	strong	.	ZNF808	81	.	NM_001039886	exon5	c.G1310A	p.S437N	TTTTCAGTCAGAA	.	PASS	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	37	1	16256007	16256007	+	Missense_Mutation	SNP	T	T	C	rs848209	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	42	254	0	0.285714	0	T|0.347;C|0.653	0.653	strong	.	SPEN	374	.	NM_015001	exon11	c.T3272C	p.L1091P	GAGAACTAGCAGG	.	PASS	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20295779	20295779	+	Missense_Mutation	SNP	C	C	G	rs11621884	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281	152	645	0	0.540925	0	C|0.886;G|0.114	0.114	strong	OR4N2,NS,carcinoma,-2,1	OR4N2	125	1	NM_001004723	exon1	c.C172G	p.P58A	ACAGCCCCCCTCT	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26357747	26357747	+	Silent	SNP	C	C	T	rs35379457	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	20	100	0	0.263158	0	C|0.552;T|0.448	0.448	strong	MYO3A,brain,glioma,0,3	MYO3A	371	3	NM_017433	exon12	c.C1104T	p.Y368Y	GATCTACGTCTAT	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135602581	135602581	+	Silent	SNP	A	A	G	rs3739425	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	119	89	0	1	0	A|0.709;G|0.291	0.291	strong	.	ZFAT	265	.	NM_020863	exon8	c.T2493C	p.S831S	AGGACAAGAATAA	.	PASS	Atlas-SNP
DNAJB8	165721	hgsc.bcm.edu	37	3	128181537	128181537	+	Silent	SNP	C	C	T	rs2953129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	64	170	0	0.435374	0	C|0.820;T|0.180	0.180	strong	.	DNAJB8	34	.	NM_153330	exon3	c.G552A	p.S184S	GGTGGACGACATC	.	PASS	Atlas-SNP
PCDHA12	56137	hgsc.bcm.edu	37	5	140256807	140256807	+	Missense_Mutation	SNP	T	T	A	rs199811254	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	117	295	0	0.522321	0	T|0.999;A|0.001	0.001	strong	PCDHA12,NS,carcinoma,-1,2	PCDHA12	196	2	NM_018903	exon1	c.T1750A	p.S584T	CCGCGGTCGGTGG	.	PASS	Atlas-SNP
OR5AN1	390195	hgsc.bcm.edu	37	11	59132798	59132798	+	Missense_Mutation	SNP	G	G	C	rs7941190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	25	51	0	0.446429	0	G|0.358;C|0.642	0.642	strong	.	OR5AN1	49	.	NM_001004729	exon1	c.G867C	p.L289F	TCCCTTGATTTAC	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23874507	23874507	+	Silent	SNP	G	G	T	rs2277473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	131	136	0	0.606481	0	A|0.000;C|0.007	.	strong	.	MYH6	274	.	NM_002471	exon5	c.C427A	p.R143R	TGCCCCGGTAGGC	.	PASS	Atlas-SNP
CYLC1	1538	hgsc.bcm.edu	37	X	83116204	83116204	+	Missense_Mutation	SNP	G	G	C	rs142474490	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	138	269	0	0.992806	0	G|0.992;C|0.008	0.008	strong	.	CYLC1	272	.	NM_021118	exon1	c.G14C	p.R5T	TTCCAAGGTTGTA	.	PASS	Atlas-SNP
KIF2C	11004	hgsc.bcm.edu	37	1	45226084	45226084	+	Silent	SNP	G	G	A	rs1140279	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	10	106	0	0.204082	0	G|0.834;A|0.166	0.166	strong	KIF2C,NS,carcinoma,+2,1	KIF2C	68	1	NM_006845	exon15	c.G1500A	p.A500A	AGGCGCGGACACT	.	PASS	Atlas-SNP
ZNF451	26036	hgsc.bcm.edu	37	6	57012930	57012930	+	Silent	SNP	C	C	T	rs3734738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	65	176	0	0.411392	0	C|0.753;T|0.247	0.247	strong	.	ZNF451	181	.	NM_001031623	exon10	c.C2047T	p.L683L	GCATTTCTGAGTC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682117	100682117	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	15	187	0	0.0630252	0	.	.	none	MUC17,right_upper_lobe,carcinoma,-2,1	MUC17	804	1	NM_001040105	exon3	c.G7420A	p.G2474S	GAGGCTGGCACCC	.	scavenged	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	rs191412861	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217	73	149	0	0.336406	0	A|0.997;C|0.003	0.003	strong	.	PKHD1L1	522	.	NM_177531	exon67	c.A10792C	p.S3598R	ATCATGAGTTACA	.	PASS	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72413874	72413874	+	Silent	SNP	T	T	C	rs61749860	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	360	148	492	6	0.411111	0.0121951	T|0.500;C|0.500	0.500	weak	POM121_ENST00000395270,bladder,carcinoma,+1,2	POM121	131	2	NM_172020	exon11	c.T2547C	p.N849N	GATCAATGTGGCC	.	scavenged	Atlas-SNP
GP6	51206	hgsc.bcm.edu	37	19	55525818	55525818	+	Missense_Mutation	SNP	C	C	T	rs41275822	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	44	124	0	0.458333	0	C|0.977;T|0.023	0.023	strong	GP6,caecum,carcinoma,+2,1	GP6	55	1	NM_001083899	exon8	c.G1495A	p.G499S	TTAGACCGCAGTG	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26446312	26446312	+	Missense_Mutation	SNP	G	G	A	rs3758449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	21	212	1	0.177966	0.00471698	G|0.512;N|0.000	.	strong	MYO3A,rectum,carcinoma,0,6	MYO3A	371	6	NM_017433	exon26	c.G2867A	p.S956N	CAAATAGTGAGCG	.	scavenged	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201009182	201009182	+	Missense_Mutation	SNP	A	A	G	rs12139527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211	78	134	0	0.369668	0	A|0.756;G|0.244	0.244	strong	.	CACNA1S	249	.	NM_000069	exon44	c.T5399C	p.L1800S	GCTGCCAAGGTGC	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	70928616	70928616	+	Silent	SNP	G	G	A	rs3752703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	92	108	1	1	0.00925926	G|0.613;A|0.387	0.387	strong	PTPRB_ENST00000334414,colon,carcinoma,0,3	PTPRB	676	3	NM_001109754	exon30	c.C6201T	p.C2067C	TACACCGCATATC	.	PASS	Atlas-SNP
JAG2	3714	hgsc.bcm.edu	37	14	105617042	105617042	+	Missense_Mutation	SNP	C	C	T	rs1057744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	64	128	0	0.64	0	C|0.423;T|0.577	0.577	strong	JAG2,NS,carcinoma,0,1	JAG2	69	1	NM_002226	exon12	c.G1501A	p.E501K	CACACTCGTCTCG	.	PASS	Atlas-SNP
LSG1	55341	hgsc.bcm.edu	37	3	194387253	194387253	+	Missense_Mutation	SNP	A	A	G	rs34423045	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	75	181	0	0.513699	0	A|0.940;G|0.060	0.060	strong	.	LSG1	38	.	NM_018385	exon3	c.T275C	p.L92P	AAAGACAGTAGTC	.	PASS	Atlas-SNP
CPNE6	9362	hgsc.bcm.edu	37	14	24543808	24543808	+	Silent	SNP	G	G	C	rs2070343	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	123	97	0	0.97619	0	G|0.789;C|0.211	0.211	strong	.	CPNE6	40	.	NM_006032	exon6	c.G567C	p.L189L	TCAGCTGGTCTGG	.	PASS	Atlas-SNP
ZNF366	167465	hgsc.bcm.edu	37	5	71756670	71756670	+	Silent	SNP	C	C	T	rs2278600	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	49	133	0	0.411765	0	C|0.757;T|0.243	0.243	strong	ZNF366,NS,carcinoma,-2,1	ZNF366	108	1	NM_152625	exon2	c.G654A	p.E218E	CTGGGGCTCGGCT	.	PASS	Atlas-SNP
SERPINE1	5054	hgsc.bcm.edu	37	7	100771717	100771717	+	Missense_Mutation	SNP	G	G	A	rs6092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	51	50	0	0.614458	0	G|0.914;A|0.086	0.086	strong	.	SERPINE1	60	.	NM_000602	exon2	c.G43A	p.A15T	GGCCTGGCCCTTG	.	PASS	Atlas-SNP
TSPYL5	85453	hgsc.bcm.edu	37	8	98289721	98289721	+	Missense_Mutation	SNP	C	C	T	rs118032326	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	50	94	0	0.403226	0	C|0.994;T|0.006	0.006	strong	.	TSPYL5	48	.	NM_033512	exon1	c.G352A	p.A118T	TGTCTGCGGCCAG	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	360	15	669	0	0.0416667	0	.	.	weak	SIRPA,brain,glioma,0,4	SIRPA	83	4	NM_001040022	exon3	c.C300A	p.N100K	GAGAAACAACATG	.	scavenged	Atlas-SNP
PADI2	11240	hgsc.bcm.edu	37	1	17410253	17410253	+	Nonsense_Mutation	SNP	G	G	A	rs142403504	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	35	219	0	0.289256	0	G|0.998;A|0.002	0.002	strong	.	PADI2	72	.	NM_007365	exon9	c.C1018T	p.Q340X	GGTACTGGAAGCA	.	PASS	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43837278	43837278	+	Missense_Mutation	SNP	G	G	A	rs79500955	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	127	247	1	0.488462	0.00404858	G|0.996;A|0.004	0.004	strong	SEMG1,colon,carcinoma,+1,1	SEMG1	71	1	NM_003007	exon2	c.G1340A	p.R447H	GTGATCGTCATTT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115158	168115158	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	37	88	0	0.435294	0	.	.	none	.	XIRP2	914	.	NM_001199143	exon11	c.A2201C	p.K734T	ATCATAAAGAAAA	.	PASS	Atlas-SNP
BAIAP2	10458	hgsc.bcm.edu	37	17	79089590	79089590	+	Missense_Mutation	SNP	A	A	G	rs4969391	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	49	122	0	0.494949	0	A|0.843;G|0.157	0.157	strong	BAIAP2_ENST00000321300,colon,carcinoma,0,1	BAIAP2	74	1	NM_001144888	exon14	c.A1556G	p.Q519R	ACGTCCAGCTGAA	.	PASS	Atlas-SNP
DMPK	1760	hgsc.bcm.edu	37	19	46273740	46273740	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	45	157	0	0.473684	0	.	.	none	.	DMPK	74	.	NM_001081562	exon15	c.A1877G	p.X626W	CAGTTCTAGGGTT	.	PASS	Atlas-SNP
CACNA2D1	781	hgsc.bcm.edu	37	7	81635083	81635083	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	475	107	380	0	0.225263	0	.	.	none	.	CACNA2D1	191	.	NM_000722	exon17	c.A1513G	p.T505A	TTACTGTAAAACG	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58616984	58616984	+	Silent	SNP	T	T	C	rs17854029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	209	231	1	1	0.004329	T|0.709;C|0.291	0.291	strong	CNOT1_ENST00000441024,NS,carcinoma,0,2	CNOT1	359	2	NM_206999	exon9	c.A909G	p.G303G	TGTTAATCCTGAA	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3248333	3248333	+	Silent	SNP	T	T	C	rs372395776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	171	397	2	0.971591	0.00503778	.	.	weak	.	MXRA5	815	.	NM_015419	exon4	c.A435G	p.Q145Q	GAAAGCTTGAGGG	.	PASS	Atlas-SNP
TSPAN13	27075	hgsc.bcm.edu	37	7	16816000	16816000	+	Silent	SNP	T	T	C	rs2290837	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	166	212	0	0.62406	0	T|0.608;C|0.392	0.392	strong	.	TSPAN13	13	.	NM_014399	exon2	c.T228C	p.F76F	GCTATTTTTTGTA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149484798	149484798	+	Missense_Mutation	SNP	C	C	T	rs62490656	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	12	57	0	0.666667	0	C|0.826;T|0.174	0.174	strong	.	.	.	.	NM_198455	exon25	c.C3620T	p.A1207V	GTGGGGCGCTGCT	.	PASS	Atlas-SNP
APOBEC3F	200316	hgsc.bcm.edu	37	22	39438955	39438955	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	318	4	335	0	0.0125786	0	.	.	none	APOBEC3F_ENST00000381565,brain,glioma,0,2	APOBEC3F	37	2	NM_145298	exon2	c.C31T	p.R11X	GTGGAGCGAATGT	.	scavenged	Atlas-SNP
MS4A13	503497	hgsc.bcm.edu	37	11	60291413	60291413	+	Missense_Mutation	SNP	C	C	T	rs6591595	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	53	91	0	1	0	C|0.236;T|0.764	0.764	strong	.	MS4A13	27	.	NM_001100909	exon4	c.C173T	p.P58L	AGTATCCGACTCG	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	37	22	50722408	50722408	+	Missense_Mutation	SNP	T	T	C	rs79966207	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	23	23	25	0	1	0	T|0.908;C|0.092	0.092	strong	PLXNB2,brain,glioma,0,1	PLXNB2	172	1	NM_012401	exon14	c.A2275G	p.N759D	AGCAGTTGTAGAG	.	PASS	Atlas-SNP
TBC1D25	4943	hgsc.bcm.edu	37	X	48418659	48418659	+	Missense_Mutation	SNP	G	G	A	rs235836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	105	227	2	0.963303	0.00881057	G|0.441;A|0.559	0.559	strong	.	TBC1D25	70	.	NM_002536	exon6	c.G1363A	p.A455T	GCAGACGCTGGTT	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29365241	29365241	+	Silent	SNP	T	T	C	rs2073150	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	280	280	335	0	1	0	T|0.623;C|0.377	0.377	strong	.	OR12D2	42	.	NM_013936	exon1	c.T765C	p.L255L	TGTTCTTTTCACC	.	PASS	Atlas-SNP
DVL2	1856	hgsc.bcm.edu	37	17	7133162	7133162	+	Silent	SNP	G	G	A	rs222836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	86	78	0	1	0	G|0.552;A|0.448	0.448	strong	.	DVL2	49	.	NM_004422	exon5	c.C621T	p.S207S	CCCCAGGCTGGTA	.	PASS	Atlas-SNP
ISLR	3671	hgsc.bcm.edu	37	15	74467856	74467856	+	Silent	SNP	G	G	A	rs1052622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	58	55	0	1	0	G|0.400;A|0.600	0.600	strong	ISLR,NS,carcinoma,0,1	ISLR	49	1	NM_201526	exon2	c.G657A	p.T219T	GGGTACGCCGCTG	.	PASS	Atlas-SNP
TMEM132D	121256	hgsc.bcm.edu	37	12	129566469	129566469	+	Silent	SNP	C	C	T	rs77363876	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	108	221	2	0.553846	0.00904977	C|0.970;T|0.030	0.030	strong	TMEM132D,NS,carcinoma,-2,1	TMEM132D	299	1	NM_133448	exon7	c.G1758A	p.E586E	GGCCGCCTCAGCC	.	scavenged	Atlas-SNP
PDE8A	5151	hgsc.bcm.edu	37	15	85610349	85610349	+	Silent	SNP	C	C	T	rs35666574	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	62	105	0	0.849315	0	C|0.976;T|0.024	0.024	strong	.	PDE8A	50	.	NM_173454	exon3	c.C348T	p.V116V	GGCTGTCCTTGCC	.	PASS	Atlas-SNP
FBXO16	157574	hgsc.bcm.edu	37	8	28309958	28309958	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	3	169	0	0.0133333	0	.	.	none	FBXO16_ENST00000380254,lower_third,carcinoma,-2,1	FBXO16	29	1	NM_172366	exon6	c.T543C	p.V181V	TAGTTGAACGTCA	.	scavenged	Atlas-SNP
ARHGAP29	9411	hgsc.bcm.edu	37	1	94643531	94643531	+	Silent	SNP	T	T	C	rs1048854	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	72	117	0	0.782609	0	T|0.826;C|0.174	0.174	strong	.	ARHGAP29	132	.	NM_004815	exon21	c.A2673G	p.Q891Q	TTGTGGTTGTAGG	.	PASS	Atlas-SNP
RHOBTB3	22836	hgsc.bcm.edu	37	5	95115959	95115959	+	Missense_Mutation	SNP	C	C	T	rs41276257	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	120	282	0	0.461538	0	C|0.934;T|0.066	0.066	strong	RHOBTB3,NS,carcinoma,-1,1	RHOBTB3	43	1	NM_014899	exon9	c.C1286T	p.T429M	CAGGTACGACAGT	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31768416	31768416	+	Silent	SNP	A	A	G	rs3745784	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	56	137	0	0.421053	0	A|0.717;G|0.283	0.283	strong	.	TSHZ3	549	.	NM_020856	exon2	c.T2283C	p.A761A	CACAGCAGCCTTC	.	PASS	Atlas-SNP
CNGB1	1258	hgsc.bcm.edu	37	16	57937788	57937788	+	Missense_Mutation	SNP	T	T	C	rs2303785	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	145	134	0	0.833333	0	T|0.922;C|0.078	0.078	strong	.	CNGB1	105	.	NM_001297	exon27	c.A2732G	p.K911R	ACGGACTTGGGGA	.	PASS	Atlas-SNP
ZNF607	84775	hgsc.bcm.edu	37	19	38189555	38189555	+	Missense_Mutation	SNP	T	T	C	rs61910733	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	49	172	0	0.422414	0	T|0.992;C|0.008	0.008	strong	ZNF607,bladder,carcinoma,+1,1	ZNF607	82	1	NM_032689	exon5	c.A1477G	p.T493A	GTATAGTGAGTTT	.	PASS	Atlas-SNP
MYOT	9499	hgsc.bcm.edu	37	5	137221770	137221770	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	2	189	0	0.0114286	0	.	.	none	MYOT,NS,carcinoma,-1,1	MYOT	50	1	NM_006790	exon8	c.A1058G	p.Y353C	TTATCTACAAACC	.	scavenged	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54133744	54133744	+	Silent	SNP	T	T	C	rs805316	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	89	195	2	0.429952	0.0102564	T|0.784;C|0.216	0.216	strong	PSME4,NS,carcinoma,0,1	PSME4	247	1	NM_014614	exon26	c.A2934G	p.S978S	ACTGTATGAACTT	.	scavenged	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64026685	64026685	+	Silent	SNP	C	C	T	rs28395882	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	13	13	17	0	1	0	C|0.817;T|0.183	0.183	strong	PLCB3,NS,carcinoma,0,1	PLCB3	103	1	NM_000932	exon13	c.C1494T	p.S498S	GAGCTCCGCGGCC	.	PASS	Atlas-SNP
PRDM7	11105	hgsc.bcm.edu	37	16	90130136	90130136	+	Missense_Mutation	SNP	C	C	T	rs2078478	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	270	26	307	0	0.0962963	0	C|0.693;T|0.307	0.307	strong	.	PRDM7	53	.	NM_001098173	exon5	c.G392A	p.R131K	AATTCTCTCAAAC	.	PASS	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12376811	12376811	+	Missense_Mutation	SNP	A	A	C	rs2192828	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	125	210	0	0.541126	0	A|0.306;C|0.694	0.694	strong	.	VWDE	123	.	NM_001135924	exon25	c.T4454G	p.F1485C	TTTTGGAATCTCC	.	PASS	Atlas-SNP
ANKEF1	63926	hgsc.bcm.edu	37	20	10030452	10030452	+	Missense_Mutation	SNP	G	G	A	rs524625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	18	36	0	0.428571	0	G|0.769;A|0.231	0.231	strong	.	.	.	.	NM_198798	exon6	c.G1235A	p.G412E	CGTATGGACCTAA	.	PASS	Atlas-SNP
HMOX2	3163	hgsc.bcm.edu	37	16	4556911	4556911	+	Silent	SNP	G	G	A	rs25685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	52	117	0	0.485981	0	G|0.921;A|0.079	0.079	strong	.	HMOX2	22	.	NM_001127205	exon3	c.G102A	p.S34S	CCTCTCGGAGCTC	.	PASS	Atlas-SNP
C15orf59	388135	hgsc.bcm.edu	37	15	74032783	74032783	+	Silent	SNP	A	A	G	rs28594180	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	43	81	0	0.977273	0	A|0.610;G|0.390;T|0.000	0.390	strong	C15orf59,NS,carcinoma,0,1	C15orf59	38	1	NM_001039614	exon2	c.T357C	p.S119S	GGGGGTAGAGACG	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	37	16	4933907	4933907	+	Silent	SNP	T	T	C	rs17137389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	90	158	0	0.548781	0	T|0.902;C|0.098	0.098	strong	.	PPL	168	.	NM_002705	exon22	c.A4749G	p.Q1583Q	TTCCGATTGGAGC	.	PASS	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92537387	92537387	+	Missense_Mutation	SNP	T	T	G	rs12896588	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	28	51	0	0.474576	0	T|0.921;G|0.079	0.079	strong	.	ATXN3	46	.	NM_004993	exon10	c.A883C	p.K295Q	GCTGCTTTTGCTG	.	PASS	Atlas-SNP
HMHA1	23526	hgsc.bcm.edu	37	19	1079959	1079959	+	Missense_Mutation	SNP	G	G	A	rs36084354	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	52	109	0	0.604651	0	G|0.948;A|0.052	0.052	strong	HMHA1,NS,carcinoma,0,2	HMHA1	78	2	NM_001258328	exon13	c.G1593A	p.M531I	GCATATGCAGACG	.	PASS	Atlas-SNP
ZNF781	163115	hgsc.bcm.edu	37	19	38160565	38160565	+	Missense_Mutation	SNP	C	C	T	rs113316386	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	40	80	0	0.506329	0	C|0.977;T|0.023	0.023	strong	.	ZNF781	66	.	NM_152605	exon4	c.G485A	p.S162N	CTGATGCTGAATA	.	PASS	Atlas-SNP
USP53	54532	hgsc.bcm.edu	37	4	120181724	120181724	+	Silent	SNP	A	A	G	rs35372126	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	30	187	0	0.243902	0	A|0.753;G|0.247	0.247	strong	.	USP53	69	.	NM_019050	exon10	c.A738G	p.T246T	TGTTACAATTGGT	.	PASS	Atlas-SNP
UGT1A8	54576	hgsc.bcm.edu	37	2	234526871	234526871	+	Missense_Mutation	SNP	C	C	G	rs1042597	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	97	186	0	0.524324	0	C|0.755;G|0.245	0.245	strong	.	UGT1A8	69	.	NM_019076	exon1	c.C518G	p.A173G	GAATAGCTTGCCA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9074265	9074265	+	Missense_Mutation	SNP	G	G	A	rs10406209	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	372	187	357	0	0.502688	0	G|0.826;A|0.174	0.174	strong	.	MUC16	4315	.	NM_024690	exon3	c.C13181T	p.T4394I	GCTCCAGTAGGAC	.	PASS	Atlas-SNP
TMC5	79838	hgsc.bcm.edu	37	16	19451987	19451987	+	Silent	SNP	C	C	T	rs148052684	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	60	125	0	0.504202	0	C|0.992;T|0.008	0.008	strong	.	TMC5	169	.	NM_001105249	exon3	c.C627T	p.G209G	TCCAGGCGCTGAC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678988	100678988	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	12	120	0	0.0585366	0	.	.	none	MUC17,NS,carcinoma,0,2	MUC17	804	2	NM_001040105	exon3	c.G4291A	p.A1431T	ACTTCTGCTGAAG	.	scavenged	Atlas-SNP
CXorf64	100130613	hgsc.bcm.edu	37	X	125954753	125954753	+	Silent	SNP	C	C	T	rs41309538	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	132	264	1	0.970588	0.00378788	C|0.953;T|0.047	0.047	strong	.	.	.	.	NM_001122716	exon2	c.C132T	p.D44D	GGATGACGCAGAG	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	37	6	158502527	158502527	+	Silent	SNP	C	C	T	rs1744177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	73	172	0	0.506944	0	C|0.911;T|0.089	0.089	strong	.	SYNJ2	111	.	NM_003898	exon20	c.C2850T	p.D950D	CCTGGACGTGGAC	.	PASS	Atlas-SNP
TXNDC16	57544	hgsc.bcm.edu	37	14	52937255	52937255	+	Missense_Mutation	SNP	C	C	T	rs7155490	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	69	149	0	0.350254	0	C|0.787;N|0.000	.	strong	.	TXNDC16	59	.	NM_020784	exon15	c.G1456A	p.E486K	GATCTTCGGTTCC	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580941	140580941	+	Missense_Mutation	SNP	G	G	A	rs138686663	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	46	286	0	0.22549	0	G|0.970;A|0.030	0.030	strong	PCDHB11,NS,carcinoma,0,3	PCDHB11	162	3	NM_018931	exon1	c.G1594A	p.G532S	CGCGTGGGCGCCA	.	PASS	Atlas-SNP
KCNQ4	9132	hgsc.bcm.edu	37	1	41296828	41296828	+	Missense_Mutation	SNP	T	T	G	rs34287852	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	138	311	2	0.673171	0.00643087	T|0.858;G|0.142	0.142	strong	.	KCNQ4	58	.	NM_004700	exon10	c.T1365G	p.H455Q	GCAGCATCTGGCA	.	PASS	Atlas-SNP
FARSA	2193	hgsc.bcm.edu	37	19	13035006	13035006	+	Silent	SNP	G	G	A	rs1045913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	23	40	0	0.71875	0	G|0.920;A|0.080	0.080	strong	.	FARSA	46	.	NM_004461	exon12	c.C1347T	p.P449P	GTTCTCGGGAAGC	.	PASS	Atlas-SNP
CCDC51	79714	hgsc.bcm.edu	37	3	48474249	48474249	+	Silent	SNP	A	A	G	rs2279077	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	50	107	0	0.485437	0	A|0.636;G|0.364	0.364	strong	.	CCDC51	34	.	NM_024661	exon4	c.T805C	p.L269L	CCCTCAAGTCCAC	.	PASS	Atlas-SNP
VAMP1	6843	hgsc.bcm.edu	37	12	6575044	6575044	+	Silent	SNP	G	G	T	rs2072375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	69	140	0	0.556452	0	G|0.728;T|0.272	0.272	strong	.	VAMP1	6	.	NM_014231	exon3	c.C252A	p.A84A	TAGCTTGGCAGCA	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11305161	11305161	+	Silent	SNP	A	A	G	rs754529	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	20	54	0	0.465116	0	A|0.932;G|0.068	0.068	strong	.	KANK2	47	.	NM_015493	exon1	c.T27C	p.A9A	GAAGGGAGCAGGC	.	PASS	Atlas-SNP
SLC29A3	55315	hgsc.bcm.edu	37	10	73082563	73082563	+	Missense_Mutation	SNP	A	A	G	rs2277257	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	77	143	1	0.740385	0.00699301	A|0.527;G|0.473	0.473	strong	.	SLC29A3	51	.	NM_018344	exon2	c.A52G	p.R18G	ACCTACAGAACCA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238277573	238277573	+	Silent	SNP	C	C	A	rs2645774	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	40	71	0	0.547945	0	C|0.757;A|0.243	0.243	strong	.	COL6A3	608	.	NM_004369	exon10	c.G4533T	p.G1511G	TGGGGACCCCCCT	.	PASS	Atlas-SNP
NUP160	23279	hgsc.bcm.edu	37	11	47833936	47833936	+	Silent	SNP	C	C	T	rs61756071	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	97	249	0	0.449074	0	C|0.989;T|0.011	0.011	strong	.	NUP160	116	.	NM_015231	exon16	c.G1998A	p.R666R	TGGGTTCCTAATC	.	PASS	Atlas-SNP
EEF1B2	1933	hgsc.bcm.edu	37	2	207025366	207025366	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	3	208	1	0.0181818	0.00480769	.	.	none	EEF1B2,NS,carcinoma,0,19	EEF1B2	58	19	NM_021121	exon3	c.G135A	p.P45P	CCCACCGCCTGCC	.	scavenged	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20295763	20295763	+	Silent	SNP	C	C	T	rs11621854	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	186	663	0	0.588608	0	C|0.764;T|0.236	0.236	strong	.	OR4N2	125	.	NM_001004723	exon1	c.C156T	p.D52D	GTCAGACCCTGGG	.	PASS	Atlas-SNP
KCNK6	9424	hgsc.bcm.edu	37	19	38817486	38817486	+	Silent	SNP	T	T	C	rs3745951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	31	67	0	0.584906	0	T|0.836;C|0.164	0.164	strong	.	KCNK6	37	.	NM_004823	exon2	c.T576C	p.F192F	GATCTTTGCCCAC	.	PASS	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	37	5	35641582	35641582	+	Missense_Mutation	SNP	A	A	C	rs6897513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	126	134	0	0.992126	0	A|0.372;C|0.621	0.621	strong	.	SPEF2	324	.	NM_024867	exon3	c.A211C	p.N71H	ACACTTAACCTTC	.	PASS	Atlas-SNP
KIAA0408	9729	hgsc.bcm.edu	37	6	127768762	127768762	+	Silent	SNP	G	G	A	rs6902288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	28	69	0	0.451613	0	G|0.483;A|0.517	0.517	strong	.	KIAA0408	61	.	NM_014702	exon5	c.C702T	p.N234N	CTTCCTGTTTTTC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17100550	17100550	+	Missense_Mutation	SNP	A	A	T	rs61744414	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	46	126	0	0.38983	0	A|0.967;T|0.033	0.033	strong	.	CPAMD8	192	.	NM_015692	exon13	c.T1439A	p.V480E	GCCCCCACAGGCT	.	PASS	Atlas-SNP
SPATA3	130560	hgsc.bcm.edu	37	2	231861056	231861056	+	Silent	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	13	157	6	0.154762	0.0382166	.	.	none	SPATA3,rectum,carcinoma,0,1	SPATA3	52	1	NM_139073	exon1	c.A108C	p.T36T	ATCCACACCACAG	.	scavenged	Atlas-SNP
TBK1	29110	hgsc.bcm.edu	37	12	64849716	64849716	+	Silent	SNP	T	T	C	rs41292019	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	64	178	0	0.423841	0	T|0.970;C|0.030	0.030	strong	.	TBK1	149	.	NM_013254	exon2	c.T66C	p.N22N	TGCAAATGTCTTT	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	114186003	114186003	+	Missense_Mutation	SNP	T	T	C	rs2219898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	261	143	210	0	0.547893	0	T|0.622;C|0.378	0.378	strong	.	CSMD3	2325	.	NM_052900	exon4	c.A657G	p.I219M	ATTGGCTATGCAG	.	PASS	Atlas-SNP
MTX3	345778	hgsc.bcm.edu	37	5	79286042	79286042	+	Missense_Mutation	SNP	T	T	A	rs371364933		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	349	162	380	0	0.464183	0	.	.	weak	.	MTX3	29	.	NM_001010891	exon3	c.A169T	p.T57S	CAGTTGTCAAAAT	.	PASS	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	841238	841238	+	Silent	SNP	G	G	A	rs151271197	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	41	76	0	0.518987	0	G|0.995;A|0.005	0.005	strong	.	CHTF18	52	.	NM_022092	exon8	c.G972A	p.K324K	CCGGAAGCCCAGG	.	PASS	Atlas-SNP
HSPH1	10808	hgsc.bcm.edu	37	13	31725260	31725260	+	Silent	SNP	A	A	G	rs11556147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	96	172	0	0.533333	0	A|0.653;G|0.347	0.347	strong	.	HSPH1	65	.	NM_006644	exon7	c.T732C	p.F244F	TGCACAAAAATGT	.	PASS	Atlas-SNP
TOR1A	1861	hgsc.bcm.edu	37	9	132585058	132585058	+	Silent	SNP	G	G	A	rs2296793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	233	107	276	1	0.459227	0.00362319	G|0.763;A|0.237	0.237	strong	TOR1A,NS,carcinoma,0,1	TOR1A	36	1	NM_000113	exon2	c.C246T	p.A82A	AAACACGGCATTT	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	37	3	113376119	113376119	+	Silent	SNP	C	C	T	rs62265538		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	16	102	0	0.131148	0	C|0.500;T|0.500	0.500	weak	KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	NM_001009899	exon7	c.G4410A	p.Q1470Q	CTGCTGCTGCTGC	.	PASS	Atlas-SNP
FAM19A3	284467	hgsc.bcm.edu	37	1	113264930	113264930	+	Silent	SNP	C	C	G	rs35995150	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	84	125	1	0.823529	0.008	C|0.909;G|0.091	0.091	strong	.	FAM19A3	10	.	NM_001004440	exon2	c.C75G	p.T25T	GTGGACCCACCTG	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50584201	50584201	+	Silent	SNP	A	A	C	rs2272838	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	34	62	0	0.515152	0	A|0.774;C|0.226	0.226	strong	MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	NM_018995	exon19	c.A2589C	p.T863T	CACCACATGCAGC	.	PASS	Atlas-SNP
EIF3G	8666	hgsc.bcm.edu	37	19	10226256	10226256	+	Silent	SNP	A	A	G	rs7710	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	46	103	0	0.464646	0	A|0.564;G|0.436	0.436	strong	.	EIF3G	16	.	NM_003755	exon10	c.T846C	p.F282F	GAAGGCAAAGCCC	.	PASS	Atlas-SNP
TMCC3	57458	hgsc.bcm.edu	37	12	94972290	94972290	+	Silent	SNP	C	C	T	rs2270893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	21	99	1	0.313433	0.010101	C|0.474;T|0.526	0.526	strong	TMCC3,NS,carcinoma,0,1	TMCC3	63	1	NM_020698	exon3	c.G1011A	p.E337E	CTGGTCCTCCAGT	.	scavenged	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46652959	46652959	+	Silent	SNP	A	A	G	rs4508712	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	22	72	0	0.392857	0	A|0.593;G|0.407;T|0.000	0.407	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T6261C	p.P2087P	GATGCCAGGGAGG	.	PASS	Atlas-SNP
ZDHHC19	131540	hgsc.bcm.edu	37	3	195938177	195938177	+	Silent	SNP	A	A	G	rs1522394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	40	94	0	0.425532	0	A|0.742;G|0.258	0.258	strong	.	ZDHHC19	25	.	NM_001039617	exon1	c.T10C	p.L4L	CCGTTAAGAGTGT	.	PASS	Atlas-SNP
SLC41A3	54946	hgsc.bcm.edu	37	3	125726048	125726048	+	Silent	SNP	G	G	C	rs2279819	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	112	117	0	1	0	G|0.309;C|0.691	0.691	strong	.	SLC41A3	80	.	NM_017836	exon11	c.C1275G	p.L425L	TTCTGCGAGGTAC	.	PASS	Atlas-SNP
ATRN	8455	hgsc.bcm.edu	37	20	3624830	3624830	+	Silent	SNP	G	G	A	rs2246808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	86	233	0	0.447917	0	G|0.577;A|0.423	0.423	strong	.	ATRN	118	.	NM_139321	exon28	c.G4080A	p.P1360P	GGAGCCGTGTTTT	.	PASS	Atlas-SNP
C9orf72	203228	hgsc.bcm.edu	37	9	27561628	27561628	+	Missense_Mutation	SNP	T	T	C	rs17769294	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	72	128	0	0.517986	0	T|0.919;C|0.081	0.081	strong	.	C9orf72	48	.	NM_018325	exon5	c.A620G	p.N207S	TCATCATTGAGTA	.	PASS	Atlas-SNP
KMO	8564	hgsc.bcm.edu	37	1	241695792	241695792	+	Silent	SNP	T	T	C	rs3819976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	160	200	1	0.675106	0.005	T|0.910;C|0.090	0.090	strong	.	KMO	69	.	NM_003679	exon1	c.T48C	p.G16G	TGGTGGTGGCTTG	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113128051	113128051	+	Silent	SNP	G	G	T	rs13059888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	45	138	0	0.405405	0	G|0.919;T|0.081	0.081	strong	.	WDR52	151	.	NM_001164496	exon7	c.C792A	p.P264P	TAGTATGGGTTGT	.	PASS	Atlas-SNP
OR5H1	26341	hgsc.bcm.edu	37	3	97851645	97851645	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	657	16	691	0	0.0243531	0	.	.	none	OR5H1,NS,carcinoma,+1,1	OR5H1	71	1	NM_001005338	exon1	c.A104G	p.Y35C	TAATATATCTCAT	.	scavenged	Atlas-SNP
PRRG2	5639	hgsc.bcm.edu	37	19	50093248	50093248	+	Missense_Mutation	SNP	A	A	T	rs144521999	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	16	10	27	0	0.625	0	A|0.939;T|0.061	0.061	strong	.	PRRG2	13	.	NM_000951	exon6	c.A529T	p.T177S	CTCCCCACCTATG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507262	195507262	+	Missense_Mutation	SNP	T	T	G	rs367631576	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	453	54	329	7	0.119205	0.0212766	.	.	weak	MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.A11189C	p.H3730P	GTGACATGAAGAG	.	scavenged	Atlas-SNP
RSPRY1	89970	hgsc.bcm.edu	37	16	57261339	57261339	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	3	189	0	0.0182927	0	.	.	none	RSPRY1,colon,carcinoma,-1,2	RSPRY1	49	2	NM_133368	exon11	c.C1247T	p.P416L	GTAAGCCTCACAT	.	scavenged	Atlas-SNP
TREML4	285852	hgsc.bcm.edu	37	6	41196169	41196169	+	Missense_Mutation	SNP	G	G	T	rs112680060	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	46	75	0	0.541176	0	G|0.995;T|0.005	0.005	strong	.	TREML4	25	.	NM_198153	exon1	c.G4T	p.A2S	GGAATGGCCTGGG	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115002305	115002305	+	Silent	SNP	G	G	A	rs8002514	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	57	157	0	0.428571	0	G|0.678;A|0.322	0.322	strong	.	CDC16	50	.	NM_003903	exon3	c.G135A	p.Q45Q	GGCTCAGTGTCTT	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610504	38610504	+	Silent	SNP	G	G	A	rs59185302	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	34	39	0	1	0	G|0.866;A|0.134	0.134	strong	.	SIPA1L3	150	.	NM_015073	exon9	c.G2850A	p.E950E	AAGGGAGATAGTG	.	PASS	Atlas-SNP
BRD3	8019	hgsc.bcm.edu	37	9	136901254	136901254	+	Silent	SNP	G	G	A	rs448698	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	107	213	0	0.532338	0	G|0.979;A|0.021	0.021	strong	.	BRD3	82	.	NM_007371	exon10	c.C1836T	p.D612D	TATCTCGTCGGGG	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3483205	3483205	+	Silent	SNP	C	C	T	rs6767	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	101	214	0	0.467593	0	C|0.531;T|0.469	0.469	strong	.	.	.	.	NM_016030	exon12	c.C2181T	p.F727F	CAGCTTCAACACA	.	PASS	Atlas-SNP
PNPLA7	375775	hgsc.bcm.edu	37	9	140357943	140357943	+	Silent	SNP	G	G	A	rs78550888	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	79	64	0	1	0	G|0.958;A|0.042	0.042	strong	.	PNPLA7	124	.	NM_001098537	exon29	c.C3267T	p.S1089S	GTAACCGGACAGG	.	PASS	Atlas-SNP
CNOT4	4850	hgsc.bcm.edu	37	7	135082953	135082953	+	Missense_Mutation	SNP	G	G	C	rs77841106	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	45	110	0	0.803571	0	G|0.933;C|0.067	0.067	strong	.	CNOT4	146	.	NM_001190850	exon8	c.C847G	p.L283V	TACTGAGAGAATC	.	PASS	Atlas-SNP
ZFYVE26	23503	hgsc.bcm.edu	37	14	68257352	68257352	+	Missense_Mutation	SNP	T	T	A	rs17192170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	356	218	298	0	0.61236	0	T|0.932;A|0.068	0.068	strong	.	ZFYVE26	223	.	NM_015346	exon15	c.A2692T	p.T898S	GAATGGTGCTGCT	.	PASS	Atlas-SNP
EPHA5	2044	hgsc.bcm.edu	37	4	66509085	66509085	+	Missense_Mutation	SNP	T	T	G	rs33932471	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	83	201	0	0.463687	0	T|0.959;G|0.041	0.041	strong	.	EPHA5	315	.	NM_004439	exon2	c.A242C	p.N81T	ACCCCATTTTTTG	.	PASS	Atlas-SNP
GNAO1	2775	hgsc.bcm.edu	37	16	56377748	56377748	+	Silent	SNP	A	A	G	rs1799917	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	99	142	1	0.825	0.00704225	A|0.609;G|0.391	0.391	strong	.	GNAO1	95	.	NM_138736	exon8	c.A951G	p.K317K	CCACAAAGAGATC	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2833631	2833631	+	Silent	SNP	A	A	G	rs377542415		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	26	192	0	0.276596	0	.	.	weak	.	ARSD	47	.	NM_001669	exon6	c.T966C	p.Y322Y	ATCACCATATAAG	.	PASS	Atlas-SNP
TSC2	7249	hgsc.bcm.edu	37	16	2138269	2138269	+	Silent	SNP	T	T	C	rs1748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	71	123	0	0.601695	0	T|0.695;G|0.000;C|0.305;A|0.000	0.305	strong	.	TSC2	364	.	NM_000548	exon41	c.T5202C	p.D1734D	CACCGATATCTAC	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34724987	34724987	+	Silent	SNP	A	A	G	rs201739024	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	363	97	305	1	0.267218	0.00327869	A|0.870;G|0.130	0.130	strong	FAM205A_ENST00000378788,colon,carcinoma,-1,2	FAM205A	45	2	NM_001141917	exon4	c.T2250C	p.A750A	TGGTAAAGCCTGT	.	scavenged	Atlas-SNP
TBC1D15	64786	hgsc.bcm.edu	37	12	72307637	72307637	+	Silent	SNP	C	C	G	rs11178983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	33	79	0	0.354839	0	C|0.947;G|0.053	0.053	strong	.	TBC1D15	99	.	NM_022771	exon13	c.C1383G	p.S461S	ACTTTCCCCTCTT	.	PASS	Atlas-SNP
SPACA3	124912	hgsc.bcm.edu	37	17	31322691	31322691	+	Missense_Mutation	SNP	A	A	G	rs28963	bycluster;byfrequency;bysubmitter;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	101	245	0	0.497537	0	A|0.998;G|0.002	0.002	strong	.	SPACA3	35	.	NM_173847	exon2	c.A299G	p.H100R	TGCTACATGACTT	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786440	75786440	+	Silent	SNP	C	C	T	rs6790146	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	33	57	5	0.767442	0.0877193	C|0.603;T|0.397	0.397	strong	ZNF717,NS,carcinoma,0,1	ZNF717	160	1	NM_001128223	exon5	c.G2334A	p.G778G	GTGAGTCCCCTGA	.	scavenged	Atlas-SNP
ASPA	443	hgsc.bcm.edu	37	17	3397702	3397702	+	Silent	SNP	C	C	T	rs12948217	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	52	128	0	0.416	0	C|0.732;T|0.268	0.268	strong	.	ASPA	37	.	NM_000049	exon5	c.C693T	p.Y231Y	TGATTACCCCCGG	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52777439	52777439	+	Silent	SNP	A	A	G	rs1614888	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	60	157	0	0.451128	0	A|0.686;G|0.314	0.314	strong	.	KRT84	61	.	NM_033045	exon2	c.T690C	p.S230S	CTGATCACTGACC	.	PASS	Atlas-SNP
MRGPRF	116535	hgsc.bcm.edu	37	11	68772925	68772925	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	2	137	0	0.0145985	0	.	.	none	MRGPRF,rectum,carcinoma,+2,1	MRGPRF	22	1	NM_001098515	exon3	c.A853G	p.S285G	TGGCGCTGCTGTT	.	scavenged	Atlas-SNP
CYFIP1	23191	hgsc.bcm.edu	37	15	22969232	22969232	+	Missense_Mutation	SNP	G	G	A	rs7170637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	44	114	1	0.709677	0.00877193	G|0.704;A|0.296	0.296	strong	CYFIP1_ENST00000435939,colon,carcinoma,0,2	CYFIP1	159	2	NM_014608	exon22	c.G2458A	p.G820S	CTGGACGGCTTCG	.	scavenged	Atlas-SNP
USP4	7375	hgsc.bcm.edu	37	3	49343175	49343175	+	Silent	SNP	G	G	A	rs2230929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	112	227	0	0.511416	0	G|0.864;C|0.000;A|0.136	0.136	strong	USP4,NS,carcinoma,0,1	USP4	72	1	NM_003363	exon9	c.C1101T	p.D367D	ATGGGCGTCCCTT	.	PASS	Atlas-SNP
SLC12A5	57468	hgsc.bcm.edu	37	20	44680412	44680412	+	Silent	SNP	C	C	T	rs3746522	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	46	94	0	0.522727	0	C|0.824;T|0.176	0.176	strong	SLC12A5,caecum,carcinoma,0,1	SLC12A5	181	1	NM_001134771	exon18	c.C2349T	p.S783S	CCAGTCCGGGGGC	.	PASS	Atlas-SNP
HHIPL1	84439	hgsc.bcm.edu	37	14	100129327	100129327	+	Silent	SNP	G	G	A	rs34890784	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249	172	181	1	0.690763	0.00552486	G|0.944;A|0.056	0.056	strong	HHIPL1,NS,malignant_melanoma,+2,1	HHIPL1	86	1	NM_032425	exon6	c.G1617A	p.P539P	CTACCCGTACATC	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124066731	124066731	+	Silent	SNP	T	T	G	rs7100442	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	70	169	0	0.469799	0	T|0.906;G|0.094	0.094	strong	.	BTBD16	44	.	NM_144587	exon10	c.T819G	p.L273L	CCATCTTCTGAAA	.	PASS	Atlas-SNP
FCRLA	84824	hgsc.bcm.edu	37	1	161681780	161681780	+	Missense_Mutation	SNP	A	A	G	rs2275603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	76	154	0	0.365385	0	A|0.595;G|0.405	0.405	strong	.	FCRLA	101	.	NM_001184866	exon5	c.A625G	p.S209G	GCAGGAAGCCCCA	.	PASS	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	37	17	16068463	16068463	+	Missense_Mutation	SNP	C	C	T	rs74453660	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	488	66	346	0	0.135246	0	.	.	weak	NCOR1,NS,carcinoma,0,2	NCOR1	240	2	NM_001190440	exon4	c.G448A	p.G150R	TGCCTCCGAATGC	.	PASS	Atlas-SNP
RASGRP1	10125	hgsc.bcm.edu	37	15	38794566	38794566	+	Silent	SNP	A	A	G	rs12324402	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	61	131	0	0.7625	0	A|0.833;G|0.167	0.167	strong	.	RASGRP1	50	.	NM_005739	exon12	c.T1485C	p.F495F	CTTTTCAAATTCT	.	PASS	Atlas-SNP
CHST13	166012	hgsc.bcm.edu	37	3	126260995	126260995	+	Silent	SNP	C	C	T	rs7614066	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	11	16	0	0.611111	0	C|0.956;T|0.044	0.044	strong	.	CHST13	21	.	NM_152889	exon3	c.C600T	p.Y200Y	GCGCTACGGTGCA	.	PASS	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	37	5	14304588	14304588	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	81	151	0	0.482143	0	.	.	none	.	TRIO	305	.	NM_007118	exon8	c.T1387G	p.S463A	GTGGATTCATGGT	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81232294	81232294	+	Missense_Mutation	SNP	T	T	C	rs61734110	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	88	122	0	0.807339	0	T|0.956;C|0.044	0.044	strong	.	PKD1L2	361	.	NM_001076780	exon7	c.A1516G	p.I506V	GGCAAATCCCAAA	.	PASS	Atlas-SNP
TIFA	92610	hgsc.bcm.edu	37	4	113199075	113199075	+	Silent	SNP	A	A	G	rs701759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	63	110	0	1	0	A|0.344;G|0.656	0.656	strong	.	TIFA	15	.	NM_052864	exon2	c.T498C	p.Y166Y	GAGCGAATAAGTG	.	PASS	Atlas-SNP
RHPN1	114822	hgsc.bcm.edu	37	8	144462841	144462841	+	Silent	SNP	G	G	A	rs117282246	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	95	233	0	0.452381	0	G|0.994;A|0.006	0.006	strong	.	RHPN1	76	.	NM_052924	exon11	c.G1299A	p.V433V	CGAGGTGGACCTG	.	PASS	Atlas-SNP
AGMAT	79814	hgsc.bcm.edu	37	1	15909850	15909850	+	Missense_Mutation	SNP	C	C	G	rs6429757	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	64	99	0	1	0	C|0.348;G|0.652	0.652	strong	.	AGMAT	25	.	NM_024758	exon2	c.G313C	p.G105R	CTGTCCCAAGCAT	.	PASS	Atlas-SNP
PRND	23627	hgsc.bcm.edu	37	20	4705718	4705718	+	Missense_Mutation	SNP	C	C	T	rs2245220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	31	69	0	0.424658	0	C|0.492;T|0.508	0.508	strong	PRND,caecum,carcinoma,0,1	PRND	34	1	NM_012409	exon2	c.C521T	p.T174M	GGCTCACGGTGAA	.	PASS	Atlas-SNP
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777422	18777422	+	Silent	SNP	G	G	A	rs45579937	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	57	81	0	0.626374	0	G|0.884;A|0.116	0.116	strong	ADAMTSL1_ENST00000380548,NS,carcinoma,0,1	ADAMTSL1	306	1	NM_001040272	exon19	c.G3195A	p.L1065L	GCTCCTGCACCTG	.	PASS	Atlas-SNP
KAT2A	2648	hgsc.bcm.edu	37	17	40265751	40265751	+	Silent	SNP	C	C	T	rs147642400	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	15	35	0	0.277778	0	C|0.998;T|0.002	0.002	strong	.	KAT2A	54	.	NM_021078	exon18	c.G2430A	p.P810P	GCTGTCCGGGGGG	.	PASS	Atlas-SNP
PIK3C2B	5287	hgsc.bcm.edu	37	1	204434438	204434438	+	Missense_Mutation	SNP	G	G	A	rs45492196	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	513	306	376	0	0.596491	0	G|0.963;A|0.037	0.037	strong	.	PIK3C2B	142	.	NM_002646	exon4	c.C943T	p.R315W	GGGGCCGGGAGCC	.	PASS	Atlas-SNP
TBC1D2B	23102	hgsc.bcm.edu	37	15	78369815	78369815	+	Silent	SNP	G	G	A	rs9047	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	19	38	0	0.612903	0	G|0.810;A|0.190	0.190	strong	.	TBC1D2B	104	.	NM_144572	exon1	c.C180T	p.F60F	CGCGTCGAACACG	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151161112	151161112	+	Missense_Mutation	SNP	A	A	G	rs12487205	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	35	123	0	0.448718	0	A|0.969;G|0.031	0.031	strong	.	IGSF10	279	.	NM_178822	exon5	c.T5623C	p.Y1875H	CCCAGTAAACGCT	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49749976	49749976	+	Missense_Mutation	SNP	G	G	A	rs34823813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	74	177	0	0.503401	0	G|0.933;A|0.067	0.067	strong	.	RNF123	100	.	NM_022064	exon27	c.G2561A	p.R854H	GTGATCGCACAGG	.	PASS	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170047902	170047902	+	Missense_Mutation	SNP	T	T	A	rs61740334	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	120	202	1	0.528634	0.00495049	T|0.912;A|0.088	0.088	strong	.	WDR27	129	.	NM_182552	exon16	c.A1624T	p.T542S	TGCAGGTGGGGGC	.	PASS	Atlas-SNP
TCF25	22980	hgsc.bcm.edu	37	16	89965055	89965055	+	Silent	SNP	G	G	A	rs11648433	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	15	53	0	0.254237	0	G|0.932;A|0.068	0.068	strong	.	TCF25	61	.	NM_014972	exon10	c.G1113A	p.L371L	CATCCTGAGGTGA	.	PASS	Atlas-SNP
C6orf170	221322	hgsc.bcm.edu	37	6	121642851	121642851	+	Missense_Mutation	SNP	C	C	T	rs7767455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281	128	315	1	0.455516	0.0031746	C|0.826;T|0.174	0.174	strong	.	C6orf170	146	.	NM_152730	exon2	c.G245A	p.R82Q	TGATTCCGATCAG	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89857935	89857935	+	Missense_Mutation	SNP	G	G	A	rs11646374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	21	79	0	0.247059	0	G|0.932;A|0.068	0.068	strong	.	FANCA	99	.	NM_000135	exon14	c.C1235T	p.A412V	AAACGCGCCACCC	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129899778	129899778	+	Missense_Mutation	SNP	G	G	C	rs11106	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217	103	219	1	0.474654	0.00456621	G|0.569;C|0.431	0.431	strong	.	MKI67	363	.	NM_002417	exon14	c.C9449G	p.T3150S	TTCTCAGTGACTT	.	PASS	Atlas-SNP
MYT1L	23040	hgsc.bcm.edu	37	2	1893133	1893133	+	Silent	SNP	C	C	T	rs75247762	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	51	100	0	0.472222	0	C|0.930;T|0.070	0.070	strong	.	MYT1L	241	.	NM_015025	exon16	c.G2394A	p.Q798Q	TGCCTGCTGCTGG	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175087729	175087729	+	Missense_Mutation	SNP	T	T	C	rs6696455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	179	148	0	0.98895	0	T|0.488;C|0.512	0.512	strong	.	TNN	297	.	NM_022093	exon11	c.T2419C	p.W807R	ACTGACTGGGTGA	.	PASS	Atlas-SNP
CASP1	834	hgsc.bcm.edu	37	11	104900488	104900488	+	Silent	SNP	G	G	A	rs580253	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	492	137	317	0	0.278455	0	G|0.867;A|0.133	0.133	strong	.	CASP1	53	.	NM_001257118	exon6	c.C766T	p.L256L	GTTGTAGTATATC	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118629599	118629599	+	Silent	SNP	G	G	A	rs12142616	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	52	108	0	0.776119	0	G|0.923;A|0.077	0.077	strong	.	SPAG17	263	.	NM_206996	exon11	c.C1392T	p.P464P	CAGACTGGGTGGG	.	PASS	Atlas-SNP
C5orf64	285668	hgsc.bcm.edu	37	5	60999768	60999768	+	Missense_Mutation	SNP	C	C	T	rs436696	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	89	214	1	0.468421	0.0046729	C|0.769;T|0.231	0.231	strong	C5orf64,caecum,carcinoma,0,2	C5orf64	9	2	NM_173667	exon4	c.C301T	p.R101W	GAGGAACGGAAAG	.	PASS	Atlas-SNP
IGF1R	3480	hgsc.bcm.edu	37	15	99456369	99456369	+	Silent	SNP	G	G	A	rs2228531	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	22	138	0	0.338462	0	G|0.990;A|0.010	0.010	strong	.	IGF1R	147	.	NM_000875	exon8	c.G1686A	p.V562V	GGACGTGGAGCCC	.	PASS	Atlas-SNP
PRRC2B	84726	hgsc.bcm.edu	37	9	134351770	134351770	+	Silent	SNP	G	G	A	rs78591540	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	63	70	0	0.940298	0	A|0.104;C|0.000;G|0.895	0.104	strong	.	PRRC2B	266	.	NM_013318	exon15	c.G4254A	p.K1418K	GGCCAAGAGGAGC	.	PASS	Atlas-SNP
OMG	4974	hgsc.bcm.edu	37	17	29623288	29623288	+	Missense_Mutation	SNP	C	C	T	rs11080149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	79	181	0	0.490683	0	C|0.931;T|0.069	0.069	strong	.	OMG	30	.	NM_002544	exon2	c.G62A	p.G21D	AAAATACCAGGTG	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62020348	62020348	+	Missense_Mutation	SNP	T	T	C	rs2058194	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	413	183	406	4	0.443099	0.00985222	T|0.407;C|0.593	0.593	strong	SCN4A,NS,carcinoma,0,1	SCN4A	205	1	NM_000334	exon23	c.A4126G	p.N1376D	TCTGGTTGTCTGT	.	scavenged	Atlas-SNP
GUCY2D	3000	hgsc.bcm.edu	37	17	7918754	7918754	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	2	95	0	0.0204082	0	.	.	none	GUCY2D_ENST00000254854,NS,carcinoma,0,2	GUCY2D	82	2	NM_000180	exon15	c.G2878A	p.V960M	AGTGCCGTGGGCA	.	scavenged	Atlas-SNP
FAM160B2	64760	hgsc.bcm.edu	37	8	21955116	21955116	+	Silent	SNP	C	C	T	rs11352	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281	161	244	1	0.572954	0.00409836	C|0.639;T|0.361	0.361	strong	.	FAM160B2	35	.	NM_022749	exon4	c.C387T	p.V129V	CAGCGTCCACAGG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379795	31379795	+	Missense_Mutation	SNP	A	A	G	rs1131898	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	37	122	0	0.313559	0	A|0.700;G|0.300	0.300	strong	.	MICA	21	.	NM_001177519	exon4	c.A685G	p.S229G	GCTTCCAGCTTCT	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52774305	52774305	+	Silent	SNP	A	A	G	rs1732293	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	55	127	0	0.470085	0	A|0.682;G|0.318	0.318	strong	.	KRT84	61	.	NM_033045	exon7	c.T1266C	p.D422D	TTTGGCATCACTG	.	PASS	Atlas-SNP
ATRN	8455	hgsc.bcm.edu	37	20	3564672	3564672	+	Silent	SNP	C	C	T	rs235540	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	134	223	1	0.570213	0.00448431	C|0.239;T|0.761	0.761	strong	.	ATRN	118	.	NM_139321	exon17	c.C2892T	p.Y964Y	TGCCTACGTGGCC	.	PASS	Atlas-SNP
ACOT8	10005	hgsc.bcm.edu	37	20	44483868	44483868	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	2	55	0	0.0363636	0	.	.	none	ACOT8,NS,carcinoma,-2,1	ACOT8	29	1	NM_005469	exon2	c.G192A	p.L64L	AGCCACCAGGGCC	.	scavenged	Atlas-SNP
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68810246	68810246	+	Silent	SNP	G	G	A	rs1370840	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	71	147	0	0.486301	0	G|0.710;A|0.290	0.290	strong	TMPRSS11A,NS,carcinoma,0,1	TMPRSS11A	74	1	NM_001114387	exon3	c.C243T	p.T81T	ATTTTCGGTCGTC	.	PASS	Atlas-SNP
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	157	182	1	1	0.00549451	C|0.772;T|0.228	0.228	strong	.	ZNF17	49	.	NM_006959	exon3	c.C693T	p.S231S	CAACTCCGACCTT	.	PASS	Atlas-SNP
EXO5	64789	hgsc.bcm.edu	37	1	40980731	40980731	+	Missense_Mutation	SNP	G	G	T	rs11208299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	33	190	0	0.259843	0	G|0.508;T|0.492	0.492	strong	.	.	.	.	NM_022774	exon3	c.G515T	p.G172V	GGGAAGGGGAGGG	.	PASS	Atlas-SNP
OR2AK2	391191	hgsc.bcm.edu	37	1	248128929	248128929	+	Missense_Mutation	SNP	G	G	A	rs6664332	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	84	157	0	0.373333	0	G|0.663;A|0.337	0.337	strong	.	OR2AK2	90	.	NM_001004491	exon1	c.G296A	p.S99N	CAGTCAGCTTCCT	.	PASS	Atlas-SNP
CSF3R	1441	hgsc.bcm.edu	37	1	36937106	36937106	+	Missense_Mutation	SNP	C	C	T	rs3918019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	50	105	0	0.684932	0	C|0.996;T|0.004	0.004	strong	.	CSF3R	157	.	NM_156039	exon10	c.G1213A	p.E405K	CCACCTCCTGGGC	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	995305	995305	+	Silent	SNP	T	T	C	rs6815946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	39	86	0	0.458824	0	T|0.821;C|0.179	0.179	strong	.	IDUA	33	.	NM_000203	exon5	c.T543C	p.N181N	GTGGAATGAGCCA	.	PASS	Atlas-SNP
CNDP1	84735	hgsc.bcm.edu	37	18	72238472	72238472	+	Missense_Mutation	SNP	C	C	A	rs73973908	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	349	344	372	3	0.985673	0.00806452	C|0.848;A|0.152	0.152	strong	CNDP1,NS,carcinoma,0,1	CNDP1	98	1	NM_032649	exon7	c.C808A	p.H270N	ATCCTTCATGAAC	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20847202	20847202	+	Silent	SNP	A	A	G	rs938887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	64	170	0	0.342246	0	A|0.719;C|0.001	.	strong	.	TEP1	224	.	NM_007110	exon36	c.T5190C	p.D1730D	GAGTGTATCATCG	.	PASS	Atlas-SNP
SLC16A13	201232	hgsc.bcm.edu	37	17	6943266	6943266	+	Silent	SNP	G	G	A	rs4796576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	39	58	0	0.481481	0	G|0.412;A|0.588	0.588	strong	.	SLC16A13	28	.	NM_201566	exon4	c.G1266A	p.G422G	GGAGGGGCTGGAA	.	PASS	Atlas-SNP
OSCP1	127700	hgsc.bcm.edu	37	1	36898067	36898067	+	Missense_Mutation	SNP	T	T	C	rs34409118	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	80	180	0	0.8	0	T|0.800;C|0.200	0.200	strong	OSCP1_ENST00000354267,colon,carcinoma,0,4	OSCP1	48	4	NM_145047	exon3	c.A391G	p.T131A	GGATGGTTGGGGA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149515103	149515103	+	Silent	SNP	C	C	T	rs10250401	bycluster;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	5	95	0	0.113636	0	C|0.840;T|0.160	0.160	strong	.	.	.	.	NM_198455	exon80	c.C11493T	p.G3831G	GCTGGGCACCCGT	.	PASS	Atlas-SNP
OR13G1	441933	hgsc.bcm.edu	37	1	247835779	247835779	+	Missense_Mutation	SNP	C	C	G	rs56096718	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	130	217	0	0.567686	0	C|0.956;G|0.044	0.044	strong	.	OR13G1	78	.	NM_001005487	exon1	c.G565C	p.V189L	TTCTTACAGGGCT	.	PASS	Atlas-SNP
DLG4	1742	hgsc.bcm.edu	37	17	7099811	7099811	+	Silent	SNP	G	G	A	rs17203281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	63	195	0	0.45	0	G|0.742;A|0.258	0.258	strong	.	DLG4	110	.	NM_001365	exon12	c.C1296T	p.I432I	CTGAGCGATGATC	.	PASS	Atlas-SNP
PDGFD	80310	hgsc.bcm.edu	37	11	103780455	103780455	+	Silent	SNP	A	A	G	rs10791649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	296	204	237	1	0.689189	0.00421941	A|0.527;G|0.473	0.473	strong	.	PDGFD	125	.	NM_025208	exon7	c.T1080C	p.C360C	ACAATCACATCGT	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76918411	76918411	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	72	112	0	0.610169	0	.	.	none	.	MYO7A	164	.	NM_000260	exon42	c.A5820G	p.S1940S	GTCCTCAGAGGGA	.	PASS	Atlas-SNP
NAT2	10	hgsc.bcm.edu	37	8	18258316	18258316	+	Missense_Mutation	SNP	G	G	A	rs1208	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	47	42	0	0.959184	0	G|0.370;A|0.630	0.630	strong	.	NAT2	34	.	NM_000015	exon2	c.G803A	p.R268K	TGCTGAGAAATAT	.	PASS	Atlas-SNP
ANKZF1	55139	hgsc.bcm.edu	37	2	220100787	220100787	+	Missense_Mutation	SNP	C	C	T	rs2293079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	15	118	0	0.214286	0	C|0.912;T|0.088	0.088	strong	.	ANKZF1	45	.	NM_001042410	exon13	c.C2027T	p.P676L	CCTCTCCAATCCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679136	100679136	+	Missense_Mutation	SNP	T	T	C	rs7780935	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	208	156	1	0.967442	0.00641026	T|0.875;C|0.125	0.125	strong	.	MUC17	804	.	NM_001040105	exon3	c.T4439C	p.V1480A	CTCCTGTTGACTC	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52409421	52409421	+	Missense_Mutation	SNP	A	A	G	rs56002041	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	15	29	0	0.428571	0	A|0.943;G|0.057	0.057	strong	.	DNAH1	534	.	NM_015512	exon45	c.A7151G	p.N2384S	TGGGCAACTGGTT	.	PASS	Atlas-SNP
BFSP1	631	hgsc.bcm.edu	37	20	17475217	17475217	+	Silent	SNP	C	C	T	rs6136118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	87	180	0	0.514793	0	C|0.697;T|0.303	0.303	strong	.	BFSP1	55	.	NM_001195	exon8	c.G1500A	p.A500A	GTCTTCCGCAACA	.	PASS	Atlas-SNP
SYT10	341359	hgsc.bcm.edu	37	12	33538179	33538179	+	Silent	SNP	C	C	T	rs11052670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	45	113	0	0.511364	0	C|0.958;T|0.042	0.042	strong	.	SYT10	109	.	NM_198992	exon4	c.G1125A	p.P375P	AGCCGTCGGTAGG	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269704	43269704	+	Silent	SNP	T	T	C	rs62112127	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	13	53	0	0.40625	0	T|0.624;C|0.376	0.376	strong	.	PSG8	101	.	NM_001130168	exon1	c.A30G	p.T10T	GCGCTGTGTGCAG	.	PASS	Atlas-SNP
HEATR6	63897	hgsc.bcm.edu	37	17	58156228	58156228	+	Silent	SNP	C	C	T	rs116476597	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	52	93	0	0.590909	0	C|0.996;T|0.004	0.004	strong	.	HEATR6	98	.	NM_022070	exon1	c.G48A	p.R16R	TGCCTCCCGCGGC	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124731485	124731485	+	Missense_Mutation	SNP	C	C	G	rs10804567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	104	256	0	0.452174	0	C|0.293;G|0.707	0.707	strong	.	HEG1	109	.	NM_020733	exon6	c.G2938C	p.V980L	AGGACACTGTTGT	.	PASS	Atlas-SNP
PALD1	27143	hgsc.bcm.edu	37	10	72291172	72291172	+	Missense_Mutation	SNP	G	G	A	rs61737673	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	13	92	0	0.240741	0	G|0.979;A|0.021	0.021	strong	.	.	.	.	NM_014431	exon5	c.G595A	p.V199I	CCCGGGGTCCGGG	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982119	75982119	+	Silent	SNP	G	G	T	rs199778089	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	15	134	0	0.170455	0	G|0.997;T|0.003	0.003	strong	CSPG4,NS,neuroblastoma,0,1	CSPG4	175	1	NM_001897	exon3	c.C1287A	p.T429T	CAGCTGGGTGAAA	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183549831	183549831	+	Silent	SNP	T	T	G	rs74199039	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	91	248	0	0.7	0	T|0.912;G|0.088	0.088	strong	.	.	.	.	NM_001080477	exon4	c.T777G	p.G259G	AACAGGTACAACG	.	PASS	Atlas-SNP
COQ3	51805	hgsc.bcm.edu	37	6	99825348	99825348	+	Missense_Mutation	SNP	T	T	C	rs11548336	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	23	50	0	0.469388	0	T|0.701;C|0.299	0.299	strong	.	COQ3	19	.	NM_017421	exon4	c.A400G	p.K134E	TTGTTTTCAGAAG	.	PASS	Atlas-SNP
SLC22A20	440044	hgsc.bcm.edu	37	11	64981472	64981472	+	Silent	SNP	G	G	C	rs239258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	33	83	0	0.5	0	G|0.614;C|0.386	0.386	strong	SLC22A20,NS,carcinoma,0,6	SLC22A20	36	6	NM_001004326	exon1	c.G129C	p.T43T	CTTCACGGCCGCT	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	32	102	0	0.444444	0	T|0.601;G|0.399	0.399	strong	CPAMD8,NS,carcinoma,-1,1	CPAMD8	192	1	NM_015692	exon14	c.A1665C	p.R555R	CTTGCTTCGCTGC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388324	1388324	+	Missense_Mutation	SNP	A	A	C	rs74377230	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	23	212	1	0.129213	0.00471698	A|0.833;C|0.167	0.167	weak	CRIPAK,caecum,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.A25C	p.N9H	TGTGCCAATGTGG	.	scavenged	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239036270	239036270	+	Silent	SNP	C	C	T	rs13382446	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	374	200	381	1	0.534759	0.00262467	C|0.861;T|0.139	0.139	strong	.	ESPNL	63	.	NM_194312	exon7	c.C1110T	p.S370S	CATGTCCCTCAGC	.	PASS	Atlas-SNP
CCR6	1235	hgsc.bcm.edu	37	6	167549775	167549775	+	Silent	SNP	T	T	C	rs3093007	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	44	111	0	0.55	0	T|0.835;C|0.165	0.165	strong	.	CCR6	36	.	NM_004367	exon3	c.T57C	p.F19F	TTATTTTGTGTCA	.	PASS	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110777962	110777962	+	Silent	SNP	A	A	G	rs6907567	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	307	135	354	0	0.439739	0	A|0.716;G|0.284	0.284	strong	.	SLC22A16	81	.	NM_033125	exon2	c.T312C	p.N104N	CCTCTTATTCCTG	.	PASS	Atlas-SNP
RNF17	56163	hgsc.bcm.edu	37	13	25378476	25378476	+	Missense_Mutation	SNP	A	A	G	rs9511451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	56	133	0	0.482759	0	A|0.776;G|0.224	0.224	strong	RNF17_ENST00000255324,NS,carcinoma,+1,1	RNF17	259	1	NM_001184993	exon15	c.A2000G	p.H667R	CTTTACACTATCA	.	PASS	Atlas-SNP
ZNF337	26152	hgsc.bcm.edu	37	20	25666737	25666737	+	Missense_Mutation	SNP	C	C	T	rs926487	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	29	82	0	0.508772	0	C|0.838;T|0.162	0.162	strong	.	ZNF337	65	.	NM_015655	exon3	c.G49A	p.V17I	CAGTGACATCCCC	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4722876	4722876	+	Missense_Mutation	SNP	G	G	A	rs3764897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	36	56	0	0.521739	0	G|0.804;A|0.196	0.196	strong	.	PLD2	138	.	NM_002663	exon23	c.G2461A	p.G821S	TGCTTCGGGTAGA	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17367435	17367435	+	Missense_Mutation	SNP	T	T	C	rs9676419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	46	120	0	0.505495	0	T|0.693;C|0.307	0.307	strong	USHBP1,NS,carcinoma,0,2	USHBP1	85	2	NM_031941	exon9	c.A1315G	p.M439V	TCTTCATTAGAGA	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	37	5	70800475	70800475	+	Missense_Mutation	SNP	C	C	T	rs3761966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	262	320	2	0.996198	0.00625	C|0.667;T|0.333	0.333	strong	.	BDP1	204	.	NM_018429	exon16	c.C2269T	p.R757C	CAATCGCGTAAAG	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573719	140573719	+	Missense_Mutation	SNP	G	G	A	rs148484995	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	3	208	0	0.0212766	0	G|0.961;A|0.039	0.039	strong	PCDHB10,NS,lymphoid_neoplasm,-2,1	PCDHB10	177	1	NM_018930	exon1	c.G1594A	p.G532S	CGCGTGGGCGCCA	.	scavenged	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982052	240982052	+	Silent	SNP	C	C	G	rs77588089	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	19	100	2	0.231707	0.02	C|0.250;G|0.750	0.750	weak	PRR21,pharynx,carcinoma,0,4	PRR21	53	4	NM_001080835	exon1	c.G348C	p.S116S	CATGGACGAAGGG	.	scavenged	Atlas-SNP
NUDT12	83594	hgsc.bcm.edu	37	5	102895124	102895124	+	Silent	SNP	G	G	A	rs7723689	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	84	203	1	0.494118	0.00492611	G|0.869;A|0.131	0.131	strong	.	NUDT12	27	.	NM_031438	exon3	c.C252T	p.D84D	AGCAATGTCCAGT	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2694638	2694638	+	Silent	SNP	C	C	T	rs215976	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	47	87	0	0.516484	0	C|0.836;T|0.164	0.164	strong	Q6YL47_HUMAN,NS,carcinoma,0,5	CACNA1C	1023	5	NM_001129831	exon17	c.C2436T	p.D812D	GGCTGACGGAGAG	.	PASS	Atlas-SNP
MYO1H	283446	hgsc.bcm.edu	37	12	109883374	109883374	+	Missense_Mutation	SNP	T	T	C	rs3825393	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40	40	46	0	1	0	T|0.322;C|0.678	0.678	strong	.	MYO1H	98	.	NM_001101421	exon30	c.T3002C	p.L1001P	CTGGACTGGAAGA	.	PASS	Atlas-SNP
LRRC71	149499	hgsc.bcm.edu	37	1	156890672	156890672	+	Missense_Mutation	SNP	T	T	C	rs41273221	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	63	77	0	0.984375	0	T|0.793;C|0.207	0.207	strong	.	LRRC71	33	.	NM_144702	exon1	c.T77C	p.V26A	GCGCGGTGACCAA	.	PASS	Atlas-SNP
POTEH	23784	hgsc.bcm.edu	37	22	16287562	16287562	+	Missense_Mutation	SNP	G	G	C	rs202187764	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	16	467	7	0.100629	0.0149893	G|0.975;C|0.025	0.025	strong	POTEH,NS,carcinoma,0,1	POTEH	114	1	NM_001136213	exon1	c.C324G	p.C108W	CCTGCAGCAGGGG	.	scavenged	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	94025	94025	+	Missense_Mutation	SNP	T	T	C	rs143154682	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	56	268	0	0.236287	0	T|0.998;C|0.002	0.002	strong	.	TUBB8	62	.	NM_177987	exon4	c.A307G	p.K103E	GTCCCTTGGCCCA	.	PASS	Atlas-SNP
PCOLCE	5118	hgsc.bcm.edu	37	7	100205706	100205706	+	Missense_Mutation	SNP	G	G	C	rs61739556	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	28	62	0	0.325581	0	G|0.992;C|0.008	0.008	strong	.	PCOLCE	37	.	NM_002593	exon9	c.G1330C	p.A444P	GTGCGGGCTGCTG	.	PASS	Atlas-SNP
PIK3C3	5289	hgsc.bcm.edu	37	18	39623783	39623783	+	Splice_Site	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	3	119	0	0.0252101	0	.	.	none	PIK3C3,NS,carcinoma,+2,1	PIK3C3	138	1	NM_002647	exon20	c.2188+2T>C	.	CTGTGGTAAGTTT	.	scavenged	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	37	7	4026944	4026944	+	Silent	SNP	C	C	G	rs7785899	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	163	120	0	0.987879	0	C|0.566;G|0.434	0.434	strong	.	SDK1	361	.	NM_152744	exon14	c.C2121G	p.L707L	GGAGCTCTCTGAA	.	PASS	Atlas-SNP
DLEC1	9940	hgsc.bcm.edu	37	3	38125704	38125704	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	89	159	0	0.5	0	.	.	none	.	DLEC1	278	.	NM_007337	exon7	c.C1229T	p.P410L	TCCTCCCGCCTTC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093094	1093094	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	13	57	0	0.216667	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	NM_002457	exon30	c.T4913G	p.V1638G	CTACGGTGACCCC	.	PASS	Atlas-SNP
GALNT14	79623	hgsc.bcm.edu	37	2	31135184	31135184	+	Missense_Mutation	SNP	G	G	T	rs2288101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	39	79	0	0.481481	0	G|0.797;T|0.203	0.203	strong	.	GALNT14	103	.	NM_001253826	exon15	c.C1420A	p.Q474K	GGATCTGCTGGGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100695138	100695138	+	Missense_Mutation	SNP	G	G	A	rs73168398	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	182	137	0	0.98913	0	G|0.898;A|0.102	0.102	strong	.	MUC17	804	.	NM_001040105	exon9	c.G12998A	p.R4333Q	AGTACCGGGACCA	.	PASS	Atlas-SNP
CDH19	28513	hgsc.bcm.edu	37	18	64172434	64172434	+	Missense_Mutation	SNP	C	C	G	rs55874520	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	97	239	0	0.482587	0	C|0.983;G|0.017	0.017	strong	.	CDH19	141	.	NM_021153	exon12	c.G1934C	p.G645A	CCACCCCCTTCAT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104199	168104199	+	Silent	SNP	C	C	T	rs7581190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	59	159	0	0.495798	0	C|0.840;T|0.160	0.160	strong	.	XIRP2	914	.	NM_152381	exon9	c.C6297T	p.D2099D	ATCAGACAGGGCA	.	PASS	Atlas-SNP
FGD2	221472	hgsc.bcm.edu	37	6	36988364	36988364	+	Silent	SNP	C	C	T	rs831504	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	41	73	0	0.450549	0	C|0.467;T|0.533	0.533	strong	.	FGD2	65	.	NM_173558	exon10	c.C1170T	p.S390S	GGTGTCCGGGAAG	.	PASS	Atlas-SNP
CEP164	22897	hgsc.bcm.edu	37	11	117266312	117266312	+	Missense_Mutation	SNP	C	C	G	rs2305830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	259	163	0	0.996154	0	C|0.709;G|0.291	0.291	strong	.	CEP164	121	.	NM_001271933	exon23	c.C2972G	p.T991S	AGCACACCCACCT	.	PASS	Atlas-SNP
GTF3C4	9329	hgsc.bcm.edu	37	9	135546021	135546021	+	Silent	SNP	G	G	A	rs146201597	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	9	8	13	0	0.888889	0	G|0.986;A|0.014	0.014	strong	.	GTF3C4	53	.	NM_012204	exon1	c.G36A	p.A12A	GCCCGCGGACGAC	.	PASS	Atlas-SNP
ZNF470	388566	hgsc.bcm.edu	37	19	57085769	57085769	+	Missense_Mutation	SNP	G	G	C	rs10421285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	88	153	0	0.54321	0	G|0.566;C|0.434	0.434	strong	ZNF470,NS,carcinoma,0,1	ZNF470	103	1	NM_001001668	exon4	c.G67C	p.V23L	GGTTCAGTGACTT	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91713972	91713972	+	Silent	SNP	C	C	T	rs10228334	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	251	218	0	1	0	C|0.593;T|0.407	0.407	strong	.	AKAP9	788	.	NM_005751	exon34	c.C8665T	p.L2889L	CCTGAGCTAGCAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506603	195506603	+	Missense_Mutation	SNP	T	T	C	rs201602653		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	13	120	1	0.288889	0.00833333	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.A11848G	p.T3950A	GGGTGGTGTCACC	.	scavenged	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136029138	136029138	+	Silent	SNP	G	G	A	rs35902535	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	68	122	0	0.485714	0	G|0.944;A|0.056	0.056	strong	.	GBGT1	25	.	NM_021996	exon7	c.C870T	p.G290G	CATGATGCCATTG	.	PASS	Atlas-SNP
OR11H2	79334	hgsc.bcm.edu	37	14	20181502	20181502	+	Missense_Mutation	SNP	C	C	T	rs201024081	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	911	521	1699	1	0.571899	0.000588581	.	.	weak	.	.	.	.	NM_001197287	exon2	c.G574A	p.V192I	ACACAACATGGTC	.	PASS	Atlas-SNP
MGARP	84709	hgsc.bcm.edu	37	4	140188094	140188094	+	Missense_Mutation	SNP	C	C	T	rs3208941	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	23	198	0	0.165468	0	C|0.944;T|0.056	0.056	strong	.	.	.	.	NM_032623	exon4	c.G382A	p.A128T	CTGTAGCACTGGG	.	PASS	Atlas-SNP
TEKT5	146279	hgsc.bcm.edu	37	16	10788200	10788200	+	Missense_Mutation	SNP	C	C	G	rs148185751	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	28	71	0	0.430769	0	C|0.998;G|0.002	0.002	strong	.	TEKT5	66	.	NM_144674	exon1	c.G531C	p.E177D	CGCGCACTCCAGC	.	PASS	Atlas-SNP
SLC1A5	6510	hgsc.bcm.edu	37	19	47282162	47282162	+	Silent	SNP	G	G	A	rs2070246	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	56	90	0	0.565657	0	G|0.704;A|0.296	0.296	strong	.	SLC1A5	31	.	NM_005628	exon5	c.C828T	p.Y276Y	AGGGGCGTACCTG	.	PASS	Atlas-SNP
LACC1	144811	hgsc.bcm.edu	37	13	44457984	44457984	+	Silent	SNP	A	A	G	rs9533673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	98	197	0	0.49	0	A|0.903;G|0.097	0.097	strong	.	.	.	.	NM_001128303	exon4	c.A819G	p.R273R	TCAGAGAGGAGTC	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790605	4790605	+	Silent	SNP	A	A	G	rs112024216	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	126	237	1	0.508065	0.00421941	A|0.971;G|0.029	0.029	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T543C	p.C181C	ATGGTAACAATAG	.	PASS	Atlas-SNP
RPS6KA2	6196	hgsc.bcm.edu	37	6	167040463	167040463	+	Silent	SNP	A	A	G	rs10946179	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	19	39	0	0.372549	0	A|0.834;G|0.166	0.166	strong	RPS6KA2,brain,glioma,0,2	RPS6KA2	212	2	NM_021135	exon1	c.T45C	p.S15S	GTACACAGAGAAG	.	PASS	Atlas-SNP
SHC1	6464	hgsc.bcm.edu	37	1	154938235	154938235	+	Silent	SNP	G	G	C	rs1131397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	115	129	0	0.684524	0	G|0.847;C|0.153	0.153	strong	SHC1_ENST00000448116,NS,carcinoma,-2,2	SHC1	91	2	NM_001130040	exon11	c.C1410G	p.R470R	AGGCACGCGAAGA	.	PASS	Atlas-SNP
WDR27	253769	hgsc.bcm.edu	37	6	170070723	170070723	+	Missense_Mutation	SNP	A	A	G	rs4236176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	29	93	0	0.414286	0	A|0.485;G|0.515	0.515	strong	.	WDR27	129	.	NM_182552	exon4	c.T398C	p.L133P	TCATCCAGGCTCA	.	PASS	Atlas-SNP
GLRA1	2741	hgsc.bcm.edu	37	5	151208500	151208500	+	Silent	SNP	C	C	T	rs75463357	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	35	66	0	0.492958	0	C|0.983;T|0.017	0.017	strong	.	GLRA1	61	.	NM_000171	exon8	c.G1041A	p.R347R	CCGCTTCCTCCTG	.	PASS	Atlas-SNP
SPATA6	54558	hgsc.bcm.edu	37	1	48865121	48865121	+	Missense_Mutation	SNP	C	C	T	rs77303590	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	159	318	1	0.719457	0.00314465	C|0.983;T|0.017	0.017	strong	.	SPATA6	45	.	NM_019073	exon7	c.G682A	p.E228K	ATAGCTCACACAT	.	PASS	Atlas-SNP
GUCY1B3	2983	hgsc.bcm.edu	37	4	156721198	156721198	+	Silent	SNP	C	C	T	rs2229202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	43	88	0	0.914894	0	C|0.851;T|0.149	0.149	strong	GUCY1B3,NS,carcinoma,0,1	GUCY1B3	65	1	NM_000857	exon9	c.C1147T	p.L383L	AGAGCCCTGGAAG	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23811795	23811795	+	Missense_Mutation	SNP	T	T	G	rs10263079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201	109	126	0	0.542289	0	T|0.843;G|0.157	0.157	strong	.	STK31	175	.	NM_031414	exon15	c.T1863G	p.N621K	TTTAAATAAGAGT	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	37	17	8396176	8396176	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	4	125	0	0.043956	0	.	.	none	.	MYH10	148	.	NM_001256012	exon33	c.A4376G	p.E1459G	TCCAGCTCCTGCT	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84926756	84926756	+	Silent	SNP	G	G	A	rs74514752	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	38	94	0	0.447059	0	G|0.994;A|0.006	0.006	strong	.	DNAH6	194	.	NM_001370	exon48	c.G7716A	p.L2572L	GAAGCTGCACATT	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41559609	41559609	+	Silent	SNP	G	G	A	rs2304880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	73	120	0	0.570312	0	G|0.820;A|0.180	0.180	strong	.	ANK1	497	.	NM_001142446	exon21	c.C2448T	p.T816T	CACGTCGGTGACA	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207787796	207787796	+	Missense_Mutation	SNP	T	T	C	rs61822976	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	394	36	327	0	0.0913706	0	.	.	weak	CR1_ENST00000367049,NS,carcinoma,0,4	CR1	354	4	NM_000651	exon40	c.T6623C	p.M2208T	CTGGAATGAAAGC	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56543982	56543982	+	Missense_Mutation	SNP	G	G	T	rs17713875	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	66	73	1	0.503817	0.0136986	G|0.978;T|0.022	0.022	strong	NLRP5,NS,carcinoma,+1,1	NLRP5	217	1	NM_153447	exon8	c.G2282T	p.R761L	GGATGCGGGATAA	.	scavenged	Atlas-SNP
GRB10	2887	hgsc.bcm.edu	37	7	50660787	50660787	+	Silent	SNP	G	G	A	rs3807550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	99	85	0	1	0	T|0.000;G|0.913;A|0.087	0.087	strong	.	GRB10	155	.	NM_005311	exon16	c.C1647T	p.D549D	CCCGTCGTCCTCG	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140564214	140564214	+	Silent	SNP	T	T	C	rs61739446	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	39	81	0	0.557143	0	T|0.863;C|0.137	0.137	strong	.	PCDHB16	159	.	NM_020957	exon1	c.T2080C	p.L694L	GTGGCGTTGGCCT	.	PASS	Atlas-SNP
VWCE	220001	hgsc.bcm.edu	37	11	61053895	61053895	+	Silent	SNP	G	G	A	rs146572904	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	26	56	0	0.40625	0	G|0.998;A|0.002	0.002	strong	.	VWCE	84	.	NM_152718	exon5	c.C432T	p.D144D	ACATTCGTCAATG	.	PASS	Atlas-SNP
CYP2F1	1572	hgsc.bcm.edu	37	19	41622481	41622481	+	Missense_Mutation	SNP	G	G	C	rs57670668	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	52	110	0	0.5	0	G|0.992;C|0.008	0.008	strong	.	CYP2F1	60	.	NM_000774	exon3	c.G293C	p.R98P	GTGGCCGCGGTGA	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137734084	137734084	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	68	156	0	0.472222	0	.	.	none	.	COL5A1	323	.	NM_000093	exon66	c.A5452G	p.N1818D	ATGTTCAATGACT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489754	32489754	+	Missense_Mutation	SNP	T	T	C	rs41551116	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	27	2	0	0.931035	0	T|0.952;C|0.047	0.047	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.A298G	p.R100G	CGCGCCTGTCTTC	.	PASS	Atlas-SNP
CA14	23632	hgsc.bcm.edu	37	1	150234657	150234657	+	Silent	SNP	G	G	T	rs34714364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	90	101	0	0.566038	0	G|0.897;T|0.103	0.103	strong	.	CA14	37	.	NM_012113	exon4	c.G357T	p.G119G	CCCAGGGGGGTCA	.	PASS	Atlas-SNP
HMHA1	23526	hgsc.bcm.edu	37	19	1085993	1085993	+	Silent	SNP	G	G	A	rs34721728	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	50	114	0	0.47619	0	G|0.963;A|0.037	0.037	strong	.	HMHA1	78	.	NM_001258328	exon23	c.G3447A	p.P1149P	GCAGCCGGAATTC	.	PASS	Atlas-SNP
C12orf29	91298	hgsc.bcm.edu	37	12	88440676	88440676	+	Missense_Mutation	SNP	G	G	C	rs9262	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194	94	231	0	0.484536	0	G|0.510;C|0.490	0.490	strong	.	C12orf29	18	.	NM_001009894	exon6	c.G712C	p.V238L	GATCTCGTGTCCT	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239025630	239025630	+	Silent	SNP	T	T	C	rs11904159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	80	170	0	0.503145	0	T|0.803;C|0.197	0.197	strong	.	ESPNL	63	.	NM_194312	exon5	c.T942C	p.H314H	GTACCATGGACAC	.	PASS	Atlas-SNP
LHX2	9355	hgsc.bcm.edu	37	9	126783433	126783433	+	Silent	SNP	G	G	C	rs1042486	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	96	87	0	0.989691	0	G|0.625;C|0.375	0.375	strong	.	LHX2	30	.	NM_004789	exon4	c.G783C	p.P261P	ATACCCGAGCAGC	.	PASS	Atlas-SNP
CLHC1	130162	hgsc.bcm.edu	37	2	55404883	55404883	+	Silent	SNP	T	T	C	rs13032294	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	35	87	0	0.4375	0	T|0.932;C|0.068	0.068	strong	C2orf63_ENST00000407122,NS,carcinoma,0,2	.	.	2	NM_152385	exon12	c.A1419G	p.Q473Q	TTCAACTTGGGGA	.	PASS	Atlas-SNP
PI3	5266	hgsc.bcm.edu	37	20	43804522	43804522	+	Missense_Mutation	SNP	A	A	C	rs2664581	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	52	127	0	0.416	0	A|0.862;C|0.138	0.138	strong	.	PI3	21	.	NM_002638	exon2	c.A100C	p.T34P	CAAGACACTGTCA	.	PASS	Atlas-SNP
TPH2	121278	hgsc.bcm.edu	37	12	72372862	72372862	+	Silent	SNP	A	A	G	rs7305115	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	20	74	0	0.384615	0	A|0.439;G|0.561	0.561	strong	TPH2,colon,carcinoma,+1,1	TPH2	81	1	NM_173353	exon7	c.A936G	p.P312P	CACCCCAGAACCG	.	PASS	Atlas-SNP
TBC1D1	23216	hgsc.bcm.edu	37	4	38016395	38016395	+	Missense_Mutation	SNP	T	T	G	rs10501	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	17	28	0	0.5	0	T|0.448;G|0.552	0.552	strong	TBC1D1,NS,carcinoma,0,1	TBC1D1	94	1	NM_015173	exon3	c.T683G	p.V228G	AGCCTGTGCGCAG	.	PASS	Atlas-SNP
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349037	65349037	+	Silent	SNP	G	G	A	rs74684453	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	92	195	0	0.440191	0	G|0.989;A|0.011	0.011	strong	.	EHBP1L1	64	.	NM_001099409	exon9	c.G894A	p.T298T	GGACACGGCCCCC	.	PASS	Atlas-SNP
TTC7A	57217	hgsc.bcm.edu	37	2	47278901	47278901	+	Silent	SNP	G	G	A	rs3739100	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	81	150	0	0.509434	0	G|0.870;A|0.130	0.130	strong	.	TTC7A	80	.	NM_020458	exon18	c.G2034A	p.S678S	GGCTTCGTCCATC	.	PASS	Atlas-SNP
CACNA1E	777	hgsc.bcm.edu	37	1	181725110	181725110	+	Silent	SNP	T	T	C	rs4652678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	74	125	0	0.601626	0	T|0.710;C|0.290	0.290	strong	.	CACNA1E	778	.	NM_001205293	exon29	c.T4008C	p.H1336H	AGATCATGAGAAA	.	PASS	Atlas-SNP
AAAS	8086	hgsc.bcm.edu	37	12	53708910	53708910	+	Silent	SNP	A	A	G	rs11540353	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	117	212	0	0.524664	0	A|0.931;G|0.069	0.069	strong	.	AAAS	46	.	NM_015665	exon5	c.T414C	p.D138D	GATCAGATCTTCG	.	PASS	Atlas-SNP
CHEK2	11200	hgsc.bcm.edu	37	22	29130458	29130458	+	Silent	SNP	T	T	C	rs1805129	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	18	84	0	0.352941	0	T|0.954;C|0.046	0.046	strong	CHEK2,NS,carcinoma,0,1	CHEK2	438	1	NM_145862	exon2	c.A252G	p.E84E	CTCAGGTTCTTGG	.	PASS	Atlas-SNP
WDR17	116966	hgsc.bcm.edu	37	4	177100644	177100644	+	Missense_Mutation	SNP	G	G	A	rs11736872	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	131	330	0	0.770588	0	G|0.774;A|0.226	0.226	strong	.	WDR17	198	.	NM_170710	exon31	c.G3883A	p.A1295T	AAATCTGCTATCT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54743824	54743824	+	Missense_Mutation	SNP	T	T	G	rs199826565	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	55	128	3	0.387324	0.0234375	.	.	weak	LILRA6,NS,carcinoma,0,1	LILRA6	75	1	NM_024318	exon7	c.A1262C	p.H421P	CCAGAGTGTCCTG	.	scavenged	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789314	117789314	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	10	118	0	0.0378788	0	.	.	none	TMPRSS13,colon,carcinoma,0,2	TMPRSS13	75	2	NM_001206790	exon2	c.C261T	p.A87A	TGCCCGGGCTGGA	.	scavenged	Atlas-SNP
GUCY2D	3000	hgsc.bcm.edu	37	17	7906519	7906519	+	Missense_Mutation	SNP	G	G	T	rs61749665	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	18	23	0	1	0	G|0.623;T|0.377	0.377	strong	.	GUCY2D	82	.	NM_000180	exon2	c.G154T	p.A52S	CTCTCCGCCGTGT	.	PASS	Atlas-SNP
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519637	113519637	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	53	188	0	0.292818	0	.	.	none	.	PPP1R3A	317	.	NM_002711	exon4	c.G1510C	p.G504R	AAGATCCTTCTTC	.	PASS	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57732012	57732012	+	Missense_Mutation	SNP	G	G	A	rs55645458	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	18	137	0	0.169811	0	G|0.971;A|0.029	0.029	strong	.	CCDC135	97	.	NM_032269	exon2	c.G151A	p.D51N	CTCAGAGACCTGG	.	PASS	Atlas-SNP
KMO	8564	hgsc.bcm.edu	37	1	241755348	241755348	+	Missense_Mutation	SNP	C	C	T	rs1053230	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	50	105	1	0.480769	0.00952381	C|0.853;T|0.147	0.147	strong	KMO,NS,adenoma,0,1	KMO	69	1	NM_003679	exon15	c.C1354T	p.R452C	TTCCTCCGCTTGA	.	scavenged	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171240249	171240249	+	Silent	SNP	C	C	T	rs11675394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	100	105	0	0.980392	0	C|0.732;T|0.268	0.268	strong	MYO3B_ENST00000408978,rectum,carcinoma,0,6	MYO3B	320	6	NM_001083615	exon12	c.C1215T	p.R405R	GAAACGCGCCTCC	.	PASS	Atlas-SNP
LRRC37A3	374819	hgsc.bcm.edu	37	17	62892159	62892159	+	Missense_Mutation	SNP	G	G	T	rs199539333	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	830	59	923	3	0.0710843	0.00325027	.	.	weak	LRRC37A3,NS,carcinoma,0,1	LRRC37A3	75	1	NM_199340	exon3	c.C1217A	p.A406D	GGTGAAGCTAAAT	.	scavenged	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102247408	102247408	+	Missense_Mutation	SNP	C	C	A	rs2298075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	38	78	1	0.76	0.0128205	C|0.795;A|0.205	0.205	strong	SEC31B,NS,carcinoma,0,2	SEC31B	84	2	NM_015490	exon26	c.G3505T	p.A1169S	GGACAGCCTTCAG	.	scavenged	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225528189	225528189	+	Silent	SNP	C	C	T	rs115148958	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	383	189	391	0	0.493473	0	C|0.988;T|0.012	0.012	strong	.	DNAH14	300	.	NM_001373	exon67	c.C10185T	p.P3395P	CAACCCCCATTTT	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43575905	43575905	+	Missense_Mutation	SNP	C	C	T	rs77035666	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234	121	227	2	0.517094	0.00881057	C|0.904;T|0.096	0.096	strong	PSG2,NS,carcinoma,0,1	PSG2	84	1	NM_031246	exon4	c.G911A	p.R304H	GAGTTACGAACAG	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280032	152280032	+	Missense_Mutation	SNP	T	T	C	rs71625200	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	421	170	261	0	0.4038	0	T|0.803;C|0.197	0.197	strong	FLG,larynx,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.A7330G	p.K2444E	CCTGCTTGTGGTG	.	PASS	Atlas-SNP
B4GALNT1	2583	hgsc.bcm.edu	37	12	58023981	58023981	+	Missense_Mutation	SNP	C	C	A	rs715930	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	295	150	323	2	0.508475	0.00619195	C|0.771;A|0.229	0.229	strong	B4GALNT1,NS,carcinoma,0,1	B4GALNT1	53	1	NM_001478	exon6	c.G666T	p.Q222H	AGTGACCAGTTGT	.	scavenged	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3886919	3886919	+	Silent	SNP	C	C	T	rs3749348	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	39	64	0	0.557143	0	C|0.817;T|0.183	0.183	strong	.	LRRN1	82	.	NM_020873	exon2	c.C594T	p.I198I	CATGATCGGAGAA	.	PASS	Atlas-SNP
COL9A3	1299	hgsc.bcm.edu	37	20	61460124	61460124	+	Silent	SNP	G	G	A	rs2249903	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	50	89	0	0.458716	0	G|0.833;A|0.167	0.167	strong	COL9A3,right_lower_lobe,carcinoma,+1,1	COL9A3	70	1	NM_001853	exon18	c.G909A	p.P303P	CATGCCGGGCAAG	.	PASS	Atlas-SNP
SULT1C4	27233	hgsc.bcm.edu	37	2	108994808	108994808	+	Missense_Mutation	SNP	C	C	G	rs1402467	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	142	169	0	0.993007	0	C|0.602;G|0.398	0.398	strong	.	SULT1C4	41	.	NM_006588	exon1	c.C15G	p.D5E	ACACGACATGGAG	.	PASS	Atlas-SNP
TOP2A	7153	hgsc.bcm.edu	37	17	38564363	38564363	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	27	43	0	0.465517	0	.	.	none	.	TOP2A	124	.	NM_001067	exon12	c.C1356T	p.S452S	CTCAGTGGAGTTT	.	PASS	Atlas-SNP
ZNF286A	57335	hgsc.bcm.edu	37	17	15620481	15620481	+	Silent	SNP	C	C	T	rs74608540		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	141	359	0	0.979167	0	C|0.250;T|0.750	0.750	weak	ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	NM_020652	exon6	c.C1443T	p.L481L	AGCTCTCATTCAA	.	PASS	Atlas-SNP
C20orf112	140688	hgsc.bcm.edu	37	20	31044059	31044059	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	71	181	0	0.467105	0	.	.	none	.	C20orf112	39	.	NM_001256798	exon6	c.C981T	p.A327A	CTCGGCGGCCGTG	.	PASS	Atlas-SNP
C8orf22	492307	hgsc.bcm.edu	37	8	49987801	49987801	+	Missense_Mutation	SNP	A	A	G	rs72641628	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	313	115	235	0	0.367412	0	A|0.985;G|0.015	0.015	strong	.	C8orf22	20	.	NM_001007176	exon5	c.A241G	p.S81G	ATGAACAGTTGAT	.	PASS	Atlas-SNP
TOP1MT	116447	hgsc.bcm.edu	37	8	144406705	144406705	+	Missense_Mutation	SNP	C	C	T	rs11544484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	62	120	0	0.352273	0	C|0.689;T|0.311	0.311	strong	.	TOP1MT	63	.	NM_052963	exon6	c.G766A	p.V256I	TCTGAACGCTCTC	.	PASS	Atlas-SNP
PRDM7	11105	hgsc.bcm.edu	37	16	90124871	90124871	+	Missense_Mutation	SNP	G	G	T	rs7206111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	329	51	361	0	0.155015	0	G|0.923;T|0.077	0.077	strong	PRDM7,NS,carcinoma,0,1	PRDM7	53	1	NM_001098173	exon10	c.C1305A	p.N435K	CCACATGTTGACT	.	PASS	Atlas-SNP
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465094	39465094	+	Missense_Mutation	SNP	C	C	T	rs12453338	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259	6	262	0	0.023166	0	C|0.771;T|0.229	0.229	strong	KRTAP16-1,NS,carcinoma,+2,1	KRTAP16-1	12	1	NM_001146182	exon1	c.G412A	p.V138I	CACAAACGGTGGC	.	scavenged	Atlas-SNP
PTGIS	5740	hgsc.bcm.edu	37	20	48140682	48140682	+	Silent	SNP	C	C	T	rs5628	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	90	215	0	0.461538	0	C|0.897;T|0.103	0.103	strong	PTGIS,NS,carcinoma,0,1	PTGIS	60	1	NM_000961	exon6	c.G768A	p.L256L	ACTCTCCAGCCAT	.	PASS	Atlas-SNP
ISM2	145501	hgsc.bcm.edu	37	14	77942316	77942316	+	Silent	SNP	G	G	A	rs3742732	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14	7	12	0	0.5	0	G|0.930;A|0.070	0.070	strong	.	ISM2	68	.	NM_199296	exon7	c.C1338T	p.D446D	GTGCTCGTCCTGT	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76922946	76922946	+	Silent	SNP	G	G	A	rs11237123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	45	99	0	0.5	0	G|0.785;A|0.215	0.215	strong	.	MYO7A	164	.	NM_000260	exon46	c.G6318A	p.K2106K	CTTCAAGTGGCCC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45122324	45122324	+	Missense_Mutation	SNP	C	C	A	rs3735493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	61	134	0	0.398693	0	C|0.891;A|0.109	0.109	strong	.	NACAD	44	.	NM_001146334	exon2	c.G3455T	p.C1152F	TCTGGGCAGGAGT	.	PASS	Atlas-SNP
C3orf62	375341	hgsc.bcm.edu	37	3	49313978	49313978	+	Missense_Mutation	SNP	C	C	T	rs13077498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	189	82	273	0	0.433862	0	C|0.907;T|0.093	0.093	strong	.	C3orf62	23	.	NM_198562	exon1	c.G328A	p.E110K	TTCTCTCGGGGCA	.	PASS	Atlas-SNP
ADCY10	55811	hgsc.bcm.edu	37	1	167839578	167839578	+	Silent	SNP	G	G	A	rs67878347	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	103	156	0	0.609467	0	G|0.835;A|0.165	0.165	strong	ADCY10,brain,glioma,0,1	ADCY10	175	1	NM_018417	exon14	c.C1533T	p.V511V	CATTAAGACTTGG	.	PASS	Atlas-SNP
OR6M1	390261	hgsc.bcm.edu	37	11	123676388	123676388	+	Missense_Mutation	SNP	G	G	A	rs76301014	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	66	63	0	0.694737	0	G|0.859;A|0.141	0.141	strong	.	OR6M1	60	.	NM_001005325	exon1	c.C670T	p.R224C	GGATACGCAGGAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678075	100678075	+	Silent	SNP	C	C	T	rs147945988	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	529	80	191	0	0.151229	0	C|0.998;T|0.002	0.002	strong	.	MUC17	804	.	NM_001040105	exon3	c.C3378T	p.V1126V	TCCTGTCGACACC	.	PASS	Atlas-SNP
PEX11G	92960	hgsc.bcm.edu	37	19	7547074	7547074	+	Missense_Mutation	SNP	A	A	C	rs2303146	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	22	72	0	0.392857	0	A|0.557;C|0.443	0.443	strong	.	PEX11G	16	.	NM_001270539	exon3	c.T273G	p.C91W	GGAGACACAGCGG	.	PASS	Atlas-SNP
KNCN	148930	hgsc.bcm.edu	37	1	47013431	47013431	+	Missense_Mutation	SNP	G	G	A	rs61735709	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	273	61	389	0	0.223443	0	G|0.995;A|0.005	0.005	strong	.	KNCN	7	.	NM_001097611	exon3	c.C277T	p.P93S	TCCCCGGCTTCAG	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91632306	91632306	+	Silent	SNP	C	C	T	rs1989779	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	229	156	1	1	0.00641026	C|0.082;T|0.918	0.918	strong	.	AKAP9	788	.	NM_005751	exon8	c.C3075T	p.T1025T	TGTGACCATGACA	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982186	75982186	+	Missense_Mutation	SNP	G	G	A	rs199819221		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	30	131	5	0.508475	0.0381679	.	.	weak	CSPG4,NS,carcinoma,-1,1	CSPG4	175	1	NM_001897	exon3	c.C1220T	p.P407L	ATGGCTGGCCAAG	.	scavenged	Atlas-SNP
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350374	65350374	+	Silent	SNP	A	A	G	rs36303	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	63	130	0	0.492188	0	A|0.830;G|0.170	0.170	strong	.	ERBB2IP	120	.	NM_001253699	exon21	c.A3228G	p.R1076R	CCAGCGACAAAGT	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058090	79058090	+	Missense_Mutation	SNP	A	A	G	rs2929158	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	15	84	1	0.241935	0.0119048	A|0.897;G|0.103	0.103	strong	ADAMTS7,rectum,carcinoma,0,1	ADAMTS7	142	1	NM_014272	exon19	c.T4163C	p.V1388A	TCAGGGACTCTGT	.	scavenged	Atlas-SNP
LURAP1L	286343	hgsc.bcm.edu	37	9	12821695	12821695	+	Missense_Mutation	SNP	T	T	C	rs61755264	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	47	80	0	0.516484	0	T|0.992;C|0.008	0.008	strong	.	.	.	.	NM_203403	exon2	c.T623C	p.I208T	CCCTCATAGAGGA	.	PASS	Atlas-SNP
LENG9	94059	hgsc.bcm.edu	37	19	54973280	54973280	+	Missense_Mutation	SNP	C	C	G	rs10423424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	54	46	0	0.981818	0	C|0.414;G|0.586	0.586	strong	.	LENG9	46	.	NM_198988	exon1	c.G1496C	p.R499P	TCCAGGCGGATCT	.	PASS	Atlas-SNP
PTPRT	11122	hgsc.bcm.edu	37	20	40714479	40714479	+	Silent	SNP	G	G	A	rs2016647	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	64	142	0	0.516129	0	G|0.823;A|0.177	0.177	strong	.	PTPRT	372	.	NM_133170	exon29	c.C3918T	p.Y1306Y	AGGCCAGTACTGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507379	195507379	+	Missense_Mutation	SNP	G	G	C	rs371423143		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	19	120	0	0.115854	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11072G	p.T3691R	TGACCTGTGGATG	.	scavenged	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68606192	68606192	+	Missense_Mutation	SNP	C	C	T	rs368307734		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	78	158	0	0.78	0	.	.	weak	.	ITGA11	110	.	NM_001004439	exon23	c.G2807A	p.R936Q	CTGTCCCGCTCAT	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186380846	186380846	+	Missense_Mutation	SNP	A	A	T	rs7698680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	16	84	0	0.216216	0	A|0.555;T|0.445	0.445	strong	CCDC110,NS,carcinoma,0,1	CCDC110	78	1	NM_152775	exon6	c.T895A	p.L299M	CGTCCAAGTTTTC	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32598630	32598630	+	Missense_Mutation	SNP	T	T	A	rs2290213	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	117	171	1	0.661017	0.00584795	A|0.150;C|0.000;T|0.850	0.150	strong	.	AVL9	66	.	NM_015060	exon10	c.T769A	p.C257S	AACCCATGTGCAG	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813271	248813271	+	Silent	SNP	C	C	A	rs2802081	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	399	59	327	0	0.14787	0	C|0.779;A|0.221	0.221	strong	.	OR2T27	52	.	NM_001001824	exon1	c.G915T	p.V305V	CCTCCCCACAACC	.	PASS	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219508372	219508372	+	Missense_Mutation	SNP	A	A	T	rs3770213	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	29	154	0	0.292929	0	A|0.741;N|0.000	.	strong	.	ZNF142	190	.	NM_001105537	exon8	c.T2867A	p.L956H	GTGGCAAGAGGCT	.	PASS	Atlas-SNP
EIF4G2	1982	hgsc.bcm.edu	37	11	10825093	10825093	+	Silent	SNP	C	C	T	rs35388213	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	92	228	1	0.462312	0.00438596	C|0.984;T|0.016	0.016	strong	.	EIF4G2	89	.	NM_001172705	exon9	c.G747A	p.E249E	CAAATCCTCTCCC	.	PASS	Atlas-SNP
HDHD3	81932	hgsc.bcm.edu	37	9	116136262	116136262	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	75	116	0	0.517241	0	.	.	none	.	HDHD3	10	.	NM_031219	exon2	c.C373T	p.R125C	GTGTGCGGCACTC	.	PASS	Atlas-SNP
SLCO1B7	338821	hgsc.bcm.edu	37	12	21201663	21201663	+	Missense_Mutation	SNP	G	G	A	rs11045689	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	69	141	0	0.530769	0	G|0.507;A|0.493	0.493	strong	.	SLCO1B7	85	.	NM_001009562	exon8	c.G1012A	p.A338T	CTACCTGCTGTTG	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978210	45978210	+	Missense_Mutation	SNP	G	G	C	rs200250794	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	118	165	0	0.592965	0	G|0.999;C|0.001	0.001	weak	.	KRTAP10-3	17	.	NM_198696	exon1	c.C389G	p.S130C	GCCCCAGAGCAGA	.	PASS	Atlas-SNP
SLC39A12	221074	hgsc.bcm.edu	37	10	18254595	18254595	+	Missense_Mutation	SNP	C	C	T	rs62619938	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	14	106	0	0.229508	0	C|0.956;T|0.044	0.044	strong	SLC39A12,NS,carcinoma,-1,1	SLC39A12	181	1	NM_152725	exon4	c.C727T	p.R243C	TTGAATCGTACGA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280347	152280347	+	Missense_Mutation	SNP	C	C	T	rs77166567	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	295	45	217	1	0.152542	0.00460829	.	.	weak	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.G7015A	p.D2339N	AGCTGTCTGCTGA	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680438	100680438	+	Missense_Mutation	SNP	G	G	C	rs112926140	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	16	167	2	0.076555	0.011976	A|0.001;G|0.999	.	strong	MUC17,right_upper_lobe,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G5741C	p.S1914T	ACGGTAGCAGCAT	.	scavenged	Atlas-SNP
ST8SIA3	51046	hgsc.bcm.edu	37	18	55021725	55021725	+	Missense_Mutation	SNP	A	A	C	rs3745060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	49	94	0	0.563218	0	A|0.692;C|0.308	0.308	strong	.	ST8SIA3	73	.	NM_015879	exon2	c.A272C	p.K91T	AGTGGAAATTTAA	.	PASS	Atlas-SNP
USP45	85015	hgsc.bcm.edu	37	6	99883694	99883694	+	Silent	SNP	T	T	C	rs9402791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	38	105	0	0.452381	0	T|0.786;C|0.214	0.214	strong	USP45,NS,carcinoma,0,1	USP45	56	1	NM_001080481	exon18	c.A2343G	p.A781A	CTGGCCTGCTGAT	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4870261	4870261	+	Missense_Mutation	SNP	G	G	C	rs11602499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	290	290	323	0	1	0	G|0.673;C|0.327	0.327	strong	.	OR51S1	83	.	NM_001004758	exon1	c.C178G	p.Q60E	CGGGCTGCAGGGC	.	PASS	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177935050	177935050	+	Silent	SNP	T	T	A	rs1889981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	111	116	0	0.649123	0	T|0.786;A|0.214	0.214	strong	SEC16B,NS,carcinoma,0,1	SEC16B	92	1	NM_033127	exon3	c.A390T	p.P130P	CCACTGTGGGTGT	.	PASS	Atlas-SNP
MAN2A1	4124	hgsc.bcm.edu	37	5	109110537	109110537	+	Silent	SNP	T	T	A	rs6894260	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	46	84	1	0.554217	0.0119048	A|0.390;N|0.000	0.390	strong	MAN2A1,extremity,malignant_melanoma,+2,1	MAN2A1	136	1	NM_002372	exon8	c.T1245A	p.R415R	TTTTCGTACCAAA	.	scavenged	Atlas-SNP
SLC39A8	64116	hgsc.bcm.edu	37	4	103225513	103225513	+	Silent	SNP	T	T	C	rs11097773	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	103	196	1	0.565934	0.00510204	T|0.860;C|0.140	0.140	strong	.	SLC39A8	24	.	NM_022154	exon5	c.A801G	p.G267G	GATATGTCCATTA	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20432605	20432605	+	Missense_Mutation	SNP	A	A	G	rs59025904	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	34	62	0	0.465753	0	A|0.875;G|0.125	0.125	strong	.	ACSM5	101	.	NM_017888	exon5	c.A649G	p.M217V	AACTGCATGAGGA	.	PASS	Atlas-SNP
TRAP1	10131	hgsc.bcm.edu	37	16	3708193	3708193	+	Silent	SNP	G	G	A	rs1059857	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	42	145	0	0.442105	0	G|0.912;A|0.088	0.088	strong	.	TRAP1	53	.	NM_016292	exon18	c.C2052T	p.D684D	AGGGTCGTCAACA	.	PASS	Atlas-SNP
WDR5	11091	hgsc.bcm.edu	37	9	137017126	137017126	+	Silent	SNP	A	A	G	rs34523253	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	73	160	0	0.51049	0	A|0.920;G|0.080	0.080	strong	WDR5,NS,carcinoma,+1,1	WDR5	29	1	NM_052821	exon8	c.A606G	p.S202S	CGCCTCAGGCCAG	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64612858	64612858	+	Missense_Mutation	SNP	C	C	A	rs10151658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	324	98	238	1	0.302469	0.00420168	C|0.386;A|0.614	0.614	strong	SYNE2,NS,carcinoma,0,1	SYNE2	577	1	NM_182914	exon84	c.C15556A	p.L5186M	AACTGGCTGGAAG	.	scavenged	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149489540	149489540	+	Missense_Mutation	SNP	G	G	A	rs199795943	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7	5	27	0	0.714286	0	G|0.998;A|0.002	0.002	weak	.	.	.	.	NM_198455	exon37	c.G5693A	p.R1898Q	GGCCCCGACGCTG	.	PASS	Atlas-SNP
OR52J3	119679	hgsc.bcm.edu	37	11	5068662	5068662	+	Nonsense_Mutation	SNP	C	C	T	rs57026471	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	39	72	0	0.590909	0	C|0.886;T|0.114	0.114	strong	.	OR52J3	77	.	NM_001001916	exon1	c.C907T	p.R303X	CGAGAACGAGTGC	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38344895	38344895	+	Missense_Mutation	SNP	G	G	A	rs12256916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	10	73	0	0.208333	0	G|0.970;A|0.030	0.030	strong	.	ZNF33A	103	.	NM_006954	exon5	c.G1843A	p.G615R	GAATGTGGAAAAG	.	PASS	Atlas-SNP
CCDC9	26093	hgsc.bcm.edu	37	19	47774358	47774358	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	72	150	0	0.496552	0	.	.	none	.	CCDC9	37	.	NM_015603	exon11	c.G1105C	p.E369Q	CGCTGGGAGACAA	.	PASS	Atlas-SNP
F8	2157	hgsc.bcm.edu	37	X	154158285	154158285	+	Missense_Mutation	SNP	G	G	C	rs1800291	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	56	111	0	1	0	G|0.649;0|0.032	.	strong	.	F8	646	.	NM_000132	exon14	c.C3780G	p.D1260E	TGCCCCGTCATAT	.	PASS	Atlas-SNP
METTL2B	55798	hgsc.bcm.edu	37	7	128140982	128140982	+	Silent	SNP	T	T	C	rs1132651		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	137	276	0	0.774011	0	.	.	weak	.	METTL2B	34	.	NM_018396	exon8	c.T942C	p.Y314Y	TTTCTATGTGAGA	.	PASS	Atlas-SNP
CTCFL	140690	hgsc.bcm.edu	37	20	56090779	56090779	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	2	70	0	0.027027	0	.	.	none	CTCFL,colon,carcinoma,+2,2	CTCFL	97	2	NM_001269044	exon5	c.A1171G	p.T391A	AGTGCGTTCTCAT	.	scavenged	Atlas-SNP
ZNF708	7562	hgsc.bcm.edu	37	19	21477403	21477403	+	Missense_Mutation	SNP	T	T	G	rs1781872	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	58	137	0	0.43609	0	T|0.851;G|0.149	0.149	strong	.	ZNF708	66	.	NM_021269	exon4	c.A365C	p.K122T	CCTCCTTTGTGCA	.	PASS	Atlas-SNP
RPS24	6229	hgsc.bcm.edu	37	10	79814612	79814612	+	Silent	SNP	T	T	C	rs2257155	bycluster;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	67	169	0	0.712766	0	T|1.000;|0.000	.	weak	.	RPS24	23	.	NM_001142285	exon5	c.T714C	p.G238G	GGACGGTGACTTG	.	PASS	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124746182	124746182	+	Silent	SNP	C	C	A	rs2333041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	102	201	2	0.485714	0.00995025	A|0.503;C|0.497;T|0.000	0.503	strong	HEG1,NS,carcinoma,-1,1	HEG1	109	1	NM_020733	exon3	c.G780T	p.P260P	AAAGGACGGGCTC	.	scavenged	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	843815	843815	+	Silent	SNP	C	C	T	rs71591190	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	451	136	487	3	0.301552	0.00616016	C|0.856;T|0.144	0.144	strong	ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	NM_024786	exon4	c.G528A	p.S176S	TGTGGCCGAGGCC	.	scavenged	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062065	64062065	+	Missense_Mutation	SNP	T	T	C	rs10878075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	52	145	0	0.371429	0	T|0.711;C|0.289	0.289	strong	.	DPY19L2	97	.	NM_173812	exon1	c.A109G	p.M37V	TTTCCATCTCCTC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092926	1092926	+	Missense_Mutation	SNP	C	C	G	rs377100070		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	9	106	0	0.134328	0	.	.	weak	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.C4745G	p.T1582R	CCCCAACATCGAC	.	PASS	Atlas-SNP
NEK1	4750	hgsc.bcm.edu	37	4	170428901	170428901	+	Missense_Mutation	SNP	C	C	T	rs33933790	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	58	126	0	0.753247	0	C|0.961;T|0.039	0.039	strong	.	NEK1	203	.	NM_001199397	exon22	c.G1876A	p.A626T	TGTCAGCCTCTTC	.	PASS	Atlas-SNP
CECR1	51816	hgsc.bcm.edu	37	22	17662874	17662874	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	2	85	0	0.016129	0	.	.	none	CECR1_ENST00000330232,NS,lymphoid_neoplasm,-2,4	CECR1	77	4	NM_017424	exon8	c.A1278G	p.V426V	AGTGGCTACAGGG	.	scavenged	Atlas-SNP
KIRREL2	84063	hgsc.bcm.edu	37	19	36351935	36351935	+	Silent	SNP	G	G	T	rs35854130	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	18	41	0	0.666667	0	G|0.811;T|0.189	0.189	strong	.	KIRREL2	170	.	NM_199180	exon8	c.G1053T	p.A351A	TGGCGCGCAGGTA	.	PASS	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2883588	2883588	+	Missense_Mutation	SNP	C	C	A	rs17762452	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	188	97	175	0	0.515957	0	C|0.737;A|0.263	0.263	strong	.	RAP1GAP2	90	.	NM_015085	exon9	c.C604A	p.L202M	TCCAAACTGAAGA	.	PASS	Atlas-SNP
SLC26A8	116369	hgsc.bcm.edu	37	6	35960390	35960390	+	Missense_Mutation	SNP	C	C	T	rs17707331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	33	72	0	0.478261	0	C|0.898;N|0.000	.	strong	.	SLC26A8	95	.	NM_052961	exon6	c.G689A	p.S230N	TAAGCACTCATTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681303	100681303	+	Silent	SNP	T	T	C	rs143516283		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	40	160	0	0.163265	0	.	.	weak	MUC17,rectum,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.T6606C	p.P2202P	ATCTCCTACAACT	.	PASS	Atlas-SNP
CCNA1	8900	hgsc.bcm.edu	37	13	37012830	37012830	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	4	247	0	0.0185185	0	.	.	none	CCNA1,NS,carcinoma,0,1	CCNA1	91	1	NM_003914	exon5	c.C719T	p.T240M	ACATCACGGAAGG	.	scavenged	Atlas-SNP
DPP10	57628	hgsc.bcm.edu	37	2	116510817	116510817	+	Missense_Mutation	SNP	G	G	C	rs2053724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	84	257	2	0.451613	0.0077821	G|0.483;C|0.517	0.517	strong	DPP10_ENST00000410059,NS,carcinoma,0,2	DPP10	415	2	NM_001178034	exon11	c.G1030C	p.A344P	AACCGAGCTCAGA	.	scavenged	Atlas-SNP
FTCD	10841	hgsc.bcm.edu	37	21	47557222	47557222	+	Silent	SNP	G	G	A	rs10432965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	63	89	0	0.552632	0	G|0.872;A|0.128	0.128	strong	.	FTCD	59	.	NM_206965	exon13	c.C1470T	p.G490G	AAACACGCCCATC	.	PASS	Atlas-SNP
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011298	46011298	+	Silent	SNP	G	G	A	rs74695406		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	303	14	251	9	0.0462046	0.0358566	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
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526406	150526406	+	Silent	SNP	C	C	T	rs6681639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	84	96	0	0.613139	0	C|0.647;T|0.353	0.353	strong	ADAMTSL4,NS,carcinoma,0,1	ADAMTSL4	101	1	NM_019032	exon6	c.C939T	p.G313G	GCAGGGCCAAGGG	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159653544	159653544	+	Missense_Mutation	SNP	G	G	A	rs139265083	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	30	74	0	0.714286	0	G|0.979;A|0.021	0.021	strong	FNDC1,NS,haematopoietic_neoplasm,+1,2	FNDC1	250	2	NM_032532	exon11	c.G2000A	p.R667Q	AGCCCCGGCCAGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678560	100678560	+	Missense_Mutation	SNP	C	C	A	rs77199586	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	85	136	0	0.323194	0	C|0.936;A|0.064	0.064	strong	MUC17,NS,carcinoma,-1,2	MUC17	804	2	NM_001040105	exon3	c.C3863A	p.T1288K	GCACCACGCTGGT	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	37	5	7885959	7885959	+	Missense_Mutation	SNP	A	A	G	rs162036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	157	148	1	0.987421	0.00675676	A|0.774;G|0.226	0.226	strong	.	MTRR	74	.	NM_024010	exon7	c.A1130G	p.K377R	ACACAAAGAAGAA	.	PASS	Atlas-SNP
MUS81	80198	hgsc.bcm.edu	37	11	65631361	65631361	+	Missense_Mutation	SNP	C	C	T	rs34891773	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	37	80	0	0.41573	0	C|0.979;T|0.021	0.021	strong	.	MUS81	68	.	NM_025128	exon10	c.C1048T	p.R350W	CGCTTCCGGGAGC	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531606	50531606	+	Missense_Mutation	SNP	C	C	A	rs55780106	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	32	54	0	0.761905	0	C|0.803;A|0.197	0.197	strong	.	C10orf71	179	.	NM_001135196	exon3	c.C1016A	p.A339E	GACTTGCAGCAGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678013	100678013	+	Missense_Mutation	SNP	G	G	A	rs75312831	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	848	181	212	1	0.213443	0.00471698	A|0.022;G|0.978	0.022	strong	MUC17,NS,carcinoma,-2,1	MUC17	804	1	NM_001040105	exon3	c.G3316A	p.V1106M	ACAAGTGTGCCTG	.	scavenged	Atlas-SNP
CEP55	55165	hgsc.bcm.edu	37	10	95259979	95259979	+	Missense_Mutation	SNP	C	C	G	rs3740370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	33	69	0	1	0	C|0.756;G|0.244	0.244	strong	.	CEP55	35	.	NM_018131	exon2	c.C171G	p.H57Q	GAGACACAGACTT	.	PASS	Atlas-SNP
ITIH5	80760	hgsc.bcm.edu	37	10	7618501	7618501	+	Silent	SNP	A	A	G	rs2275068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	50	90	1	0.980392	0.0111111	A|0.494;G|0.506	0.506	strong	ITIH5_ENST00000397145,caecum,carcinoma,0,6	ITIH5	343	6	NM_001001851	exon10	c.T1893C	p.D631D	CAGGCCATCCATG	.	scavenged	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56538832	56538832	+	Silent	SNP	C	C	T	rs1808663	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	63	91	1	0.470149	0.010989	C|0.950;T|0.050	0.050	strong	NLRP5_ENST00000390649,NS,carcinoma,0,1	NLRP5	217	1	NM_153447	exon7	c.C1233T	p.D411D	CAGAGACGTGGGC	.	scavenged	Atlas-SNP
DFNB31	25861	hgsc.bcm.edu	37	9	117166206	117166206	+	Missense_Mutation	SNP	G	G	T	rs2274158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	32	93	0	0.581818	0	G|0.796;T|0.204	0.204	strong	.	DFNB31	100	.	NM_015404	exon10	c.C2388A	p.N796K	CCTCTCGTTCCGA	.	PASS	Atlas-SNP
KHSRP	8570	hgsc.bcm.edu	37	19	6415735	6415735	+	Silent	SNP	A	A	G	rs145698454	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	10	48	0	0.322581	0	A|0.994;G|0.006	0.006	strong	KHSRP,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	KHSRP	51	1	NM_003685	exon17	c.T1698C	p.A566A	CGCTGCAGCTGCT	.	PASS	Atlas-SNP
BOD1L1	259282	hgsc.bcm.edu	37	4	13601337	13601337	+	Missense_Mutation	SNP	G	G	A	rs3733557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	79	69	1	0.9875	0.0144928	G|0.894;A|0.106	0.106	strong	BOD1L,NS,carcinoma,0,1	.	.	1	NM_148894	exon10	c.C7187T	p.P2396L	GGACCCGGTTCTT	.	scavenged	Atlas-SNP
DUSP19	142679	hgsc.bcm.edu	37	2	183951796	183951796	+	Missense_Mutation	SNP	G	G	A	rs368865344		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	17	57	0	0.354167	0	.	.	weak	.	DUSP19	41	.	NM_080876	exon3	c.G302A	p.G101E	CATATGGAGTTGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100676409	100676409	+	Missense_Mutation	SNP	C	C	T	rs34834039	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	222	222	186	0	1	0	C|0.880;T|0.120	0.120	strong	.	MUC17	804	.	NM_001040105	exon3	c.C1712T	p.P571L	GCACTCCATTAAC	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38345409	38345409	+	Missense_Mutation	SNP	A	A	G	rs71491230	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	24	162	0	0.252632	0	A|0.998;G|0.002	0.002	strong	ZNF33A,NS,carcinoma,0,1	ZNF33A	103	1	NM_006954	exon5	c.A2357G	p.Q786R	ATTTCCAGCCACA	.	PASS	Atlas-SNP
BMP2	650	hgsc.bcm.edu	37	20	6759706	6759706	+	Silent	SNP	C	C	T	rs13037675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	31	64	0	0.484375	0	C|0.943;T|0.057	0.057	strong	.	BMP2	45	.	NM_001200	exon3	c.C1161T	p.D387D	TCAGGACATGGTT	.	PASS	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48761053	48761053	+	Missense_Mutation	SNP	G	G	A	rs11568591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	34	63	0	0.5	0	G|0.964;A|0.036	0.036	strong	ABCC3,NS,carcinoma,+1,2	ABCC3	138	2	NM_003786	exon27	c.G3890A	p.R1297H	CTGTGCGCTACCG	.	PASS	Atlas-SNP
SIM2	6493	hgsc.bcm.edu	37	21	38117505	38117505	+	Silent	SNP	C	C	T	rs2073602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	383	120	284	0	0.313316	0	C|0.739;T|0.261	0.261	strong	.	SIM2	55	.	NM_009586	exon10	c.C1644T	p.G548G	CCATGGCGGTGGG	.	PASS	Atlas-SNP
NOC3L	64318	hgsc.bcm.edu	37	10	96106240	96106240	+	Missense_Mutation	SNP	G	G	C	rs11187895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	44	161	0	0.637681	0	G|0.928;C|0.072	0.072	strong	NOC3L,NS,carcinoma,0,1	NOC3L	67	1	NM_022451	exon11	c.C1331G	p.P444R	TTTTTTGGTTTAT	.	PASS	Atlas-SNP
ARHGAP12	94134	hgsc.bcm.edu	37	10	32128611	32128611	+	Missense_Mutation	SNP	A	A	G	rs2808096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	51	59	0	1	0	G|0.199;N|0.000	0.199	strong	.	ARHGAP12	79	.	NM_001270695	exon8	c.T1325C	p.F442S	TCAGGAAAGCAGG	.	PASS	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	37	2	211481257	211481257	+	Silent	SNP	C	C	G	rs2287599	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	6	78	0	0.133333	0	C|0.357;G|0.643	0.643	strong	.	CPS1	485	.	NM_001122633	exon22	c.C2697G	p.G899G	GAAAGGCCTCAAC	.	PASS	Atlas-SNP
KRT80	144501	hgsc.bcm.edu	37	12	52579294	52579294	+	Silent	SNP	G	G	A	rs17704675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	35	44	0	1	0	G|0.920;A|0.080	0.080	strong	.	KRT80	68	.	NM_182507	exon2	c.C378T	p.F126F	GAGGTCGAAGATG	.	PASS	Atlas-SNP
RASSF4	83937	hgsc.bcm.edu	37	10	45478092	45478092	+	Missense_Mutation	SNP	A	A	G	rs870957	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	24	209	0	0.198347	0	A|0.750;G|0.250	0.250	strong	.	RASSF4	33	.	NM_032023	exon4	c.A262G	p.R88G	ATGCCCAGACGGC	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123848212	123848212	+	Missense_Mutation	SNP	C	C	T	rs17759513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	77	70	0	0.557971	0	C|0.792;N|0.000	.	strong	.	OR10S1	78	.	NM_001004474	exon1	c.G187A	p.G63S	CAGAGCCCACAGT	.	PASS	Atlas-SNP
MLLT4	4301	hgsc.bcm.edu	37	6	168343838	168343838	+	Silent	SNP	T	T	C	rs1132306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	93	214	0	0.502703	0	T|0.525;C|0.475	0.475	strong	.	MLLT4	351	.	NM_001040000	exon23	c.T3108C	p.Y1036Y	AATCTATGTGAAG	.	PASS	Atlas-SNP
EIF5B	9669	hgsc.bcm.edu	37	2	99992822	99992822	+	Missense_Mutation	SNP	A	A	C	rs7558074	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	11	16	0	0.423077	0	A|0.436;C|0.564;G|0.000;T|0.000	0.564	strong	.	EIF5B	95	.	NM_015904	exon10	c.A1565C	p.K522T	GAAACAAAGTTCA	.	PASS	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	37	6	42233518	42233518	+	Silent	SNP	C	C	T	rs17704222	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	46	102	0	0.418182	0	C|0.950;T|0.050	0.050	strong	.	TRERF1	124	.	NM_033502	exon6	c.G1455A	p.G485G	GGCTCTCCCATCA	.	PASS	Atlas-SNP
MROH9	80133	hgsc.bcm.edu	37	1	171033252	171033252	+	Missense_Mutation	SNP	T	T	C	rs190157737	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	88	142	0	0.505747	0	T|0.998;C|0.002	0.002	strong	.	.	.	.	NM_001163629	exon22	c.T2357C	p.L786P	AACGACTGCTCCG	.	PASS	Atlas-SNP
CNKSR1	10256	hgsc.bcm.edu	37	1	26515956	26515956	+	Missense_Mutation	SNP	C	C	A	rs1045105	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	31	290	0	0.191358	0	A|0.120;C|0.880;T|0.000	0.120	strong	CNKSR1,colon,carcinoma,0,3	CNKSR1	66	3	NM_006314	exon21	c.C2059A	p.H687N	TCCCCCCACTCCC	.	PASS	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	89979698	89979698	+	Missense_Mutation	SNP	C	C	T	rs4916685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	163	140	1	1	0.00714286	C|0.655;T|0.345	0.345	strong	GPR98,NS,carcinoma,0,1	GPR98	605	1	NM_032119	exon28	c.C5960T	p.P1987L	ACAGACCTGTTAA	.	PASS	Atlas-SNP
SNTB2	6645	hgsc.bcm.edu	37	16	69221510	69221510	+	Silent	SNP	C	C	G	rs10650	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	20	37	0	0.769231	0	C|0.815;G|0.185	0.185	strong	.	SNTB2	22	.	NM_006750	exon1	c.C441G	p.P147P	CTTCCCCGGGCTG	.	PASS	Atlas-SNP
NUMA1	4926	hgsc.bcm.edu	37	11	71717106	71717106	+	Silent	SNP	G	G	A	rs61745941	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	34	78	0	0.404762	0	G|0.969;A|0.031	0.031	strong	.	NUMA1	142	.	NM_006185	exon22	c.C5667T	p.A1889A	CACCCCGGCCTGG	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53990002	53990002	+	Silent	SNP	G	G	A	rs77810160	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	30	92	0	0.252101	0	G|0.500;A|0.500	0.500	strong	.	ZNF813	81	.	NM_001004301	exon3	c.G132A	p.L44L	GAACCTGGTCTCC	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130129322	130129322	+	Missense_Mutation	SNP	G	G	C	rs35886424	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	40	114	0	0.430108	0	G|0.888;C|0.112	0.112	strong	.	COL6A5	205	.	NM_153264	exon20	c.G4616C	p.S1539T	GTAGAAGTGGACA	.	PASS	Atlas-SNP
CD300C	10871	hgsc.bcm.edu	37	17	72541052	72541052	+	Silent	SNP	C	C	T	rs2292107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	49	79	0	0.521277	0	C|0.911;T|0.089	0.089	strong	CD300C,NS,carcinoma,-2,1	CD300C	41	1	NM_006678	exon2	c.G96A	p.A32A	GGGGCCCGCCACG	.	PASS	Atlas-SNP
SF3B4	10262	hgsc.bcm.edu	37	1	149895866	149895866	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	31	101	0	0.258333	0	.	.	none	.	SF3B4	37	.	NM_005850	exon5	c.C954T	p.G318G	TCCTAAGCCATGA	.	PASS	Atlas-SNP
MAK16	84549	hgsc.bcm.edu	37	8	33356074	33356074	+	Missense_Mutation	SNP	A	A	G	rs6468171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	134	212	0	0.638095	0	A|0.389;G|0.611	0.611	strong	.	MAK16	25	.	NM_032509	exon10	c.A830G	p.Q277R	CACTGCAGAGAAA	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216172380	216172380	+	Missense_Mutation	SNP	A	A	G	rs10864219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	156	101	0	0.993631	0	A|0.470;G|0.530	0.530	strong	.	USH2A	1168	.	NM_206933	exon34	c.T6506C	p.I2169T	CCACTTATTTTTC	.	PASS	Atlas-SNP
ZNF85	7639	hgsc.bcm.edu	37	19	21133078	21133078	+	Missense_Mutation	SNP	A	A	G	rs142868740	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	46	99	0	0.469388	0	A|0.999;G|0.001	0.001	strong	.	ZNF85	72	.	NM_001256171	exon5	c.A1848G	p.I616M	TAAGATAATTCAT	.	PASS	Atlas-SNP
C4orf19	55286	hgsc.bcm.edu	37	4	37592128	37592128	+	Missense_Mutation	SNP	G	G	A	rs2973275	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	73	121	0	0.462025	0	G|0.830;A|0.170	0.170	strong	.	C4orf19	17	.	NM_018302	exon3	c.G451A	p.A151T	CTGCTGGCCTCAG	.	PASS	Atlas-SNP
SNX16	64089	hgsc.bcm.edu	37	8	82727569	82727569	+	Silent	SNP	T	T	C	rs16909651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	76	99	0	0.554745	0	T|0.855;C|0.145	0.145	strong	SNX16,caecum,carcinoma,0,1	SNX16	21	1	NM_152836	exon5	c.A672G	p.E224E	GCTTTCTTCTAGG	.	PASS	Atlas-SNP
TFDP2	7029	hgsc.bcm.edu	37	3	141692893	141692893	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	3	210	0	0.0152284	0	.	.	none	TFDP2_ENST00000489671,rectum,carcinoma,0,3	TFDP2	44	3	NM_001178139	exon8	c.G660A	p.L220L	TACCTCCAGATTC	.	scavenged	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152329369	152329369	+	Missense_Mutation	SNP	C	C	G	rs2282302	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	83	144	0	0.576389	0	C|0.848;G|0.152	0.152	strong	.	FLG2	431	.	NM_001014342	exon3	c.G893C	p.C298S	GACTGACAAGAAC	.	PASS	Atlas-SNP
C10orf12	26148	hgsc.bcm.edu	37	10	98742750	98742750	+	Missense_Mutation	SNP	A	A	C	rs3829856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	13	123	0	0.206349	0	A|0.918;C|0.082	0.082	strong	.	C10orf12	94	.	NM_015652	exon1	c.A1603C	p.I535L	CTTGAAATCAAAG	.	PASS	Atlas-SNP
HK3	3101	hgsc.bcm.edu	37	5	176314639	176314639	+	Silent	SNP	G	G	A	rs6875296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	83	151	0	0.588652	0	G|0.724;A|0.276	0.276	strong	HK3_ENST00000292432,NS,carcinoma,0,2	HK3	210	2	NM_002115	exon11	c.C1413T	p.A471A	AGCCACGGCAGTC	.	PASS	Atlas-SNP
ANKMY1	51281	hgsc.bcm.edu	37	2	241463453	241463453	+	Missense_Mutation	SNP	C	C	A	rs3821348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	45	82	0	0.5	0	C|0.846;A|0.147	0.147	strong	.	ANKMY1	112	.	NM_016552	exon7	c.G1414T	p.V472L	CACACACGTTGGA	.	PASS	Atlas-SNP
KDM5A	5927	hgsc.bcm.edu	37	12	427575	427575	+	Missense_Mutation	SNP	A	A	G	rs11062385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	73	162	0	0.459119	0	A|0.651;G|0.349	0.349	strong	.	KDM5A	307	.	NM_001042603	exon19	c.T2594C	p.M865T	TCATCCATCATGG	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	37	2	203139844	203139844	+	Silent	SNP	T	T	C	rs80282360	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	150	275	0	0.806452	0	T|0.904;C|0.096	0.096	strong	NOP58,NS,carcinoma,0,1	NOP58	41	1	NM_015934	exon2	c.T54C	p.N18N	TCTAAATGAGAAG	.	PASS	Atlas-SNP
TJP1	7082	hgsc.bcm.edu	37	15	30026582	30026582	+	Missense_Mutation	SNP	T	T	C	rs2229517	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	43	135	0	0.704918	0	T|0.991;C|0.009	0.009	strong	.	TJP1	140	.	NM_175610	exon12	c.A1412G	p.N471S	ACGTTGTTTACCT	.	PASS	Atlas-SNP
N4BP3	23138	hgsc.bcm.edu	37	5	177547336	177547336	+	Missense_Mutation	SNP	G	G	A	rs3812082	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	12	8	24	0	0.666667	0	G|0.832;A|0.168	0.168	strong	N4BP3,NS,carcinoma,0,2	N4BP3	25	2	NM_015111	exon3	c.G488A	p.R163Q	GGCCCCGGGCCAG	.	scavenged	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088786	56088786	+	Silent	SNP	A	A	T	rs202027697	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	302	86	163	0	0.284768	0	A|0.749;T|0.251	0.251	strong	.	PSPH	23	.	NM_004577	exon4	c.T120A	p.V40V	GTCCTCAACGCCA	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76069886	76069886	+	Missense_Mutation	SNP	A	A	G	rs2906997	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	342	32	222	0	0.0935673	0	A|0.912;G|0.088	0.088	strong	.	ZP3	32	.	NM_001110354	exon7	c.A1018G	p.M340V	CATGTCATGAGCC	.	PASS	Atlas-SNP
SFN	2810	hgsc.bcm.edu	37	1	27190149	27190149	+	Missense_Mutation	SNP	C	C	T	rs78707984	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	11	48	0	0.268293	0	.	.	weak	.	SFN	20	.	NM_006142	exon1	c.C446T	p.S149L	CCCGGTCAGCCTA	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167262169	167262169	+	Missense_Mutation	SNP	T	T	C	rs35344714	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236	106	283	0	0.449153	0	T|0.949;C|0.051	0.051	strong	.	SCN7A	410	.	NM_002976	exon25	c.A4970G	p.D1657G	TCTCTGTCACCAT	.	PASS	Atlas-SNP
UNC80	285175	hgsc.bcm.edu	37	2	210705348	210705348	+	Silent	SNP	C	C	G	rs10178675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	93	193	0	0.688889	0	C|0.831;G|0.169	0.169	strong	.	UNC80	280	.	NM_032504	exon20	c.C3339G	p.L1113L	CCGACTCTCTTTC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6588553	6588553	+	Silent	SNP	C	C	T	rs56313830	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	34	72	0	0.4	0	C|0.870;T|0.130	0.130	strong	.	DNHD1	198	.	NM_144666	exon36	c.C11814T	p.G3938G	ATTGGGCGCTTTG	.	PASS	Atlas-SNP
NBPF14	25832	hgsc.bcm.edu	37	1	148010987	148010987	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1403	20	783	8	0.0142552	0.0102171	.	.	none	NBPF14,NS,carcinoma,0,3	NBPF14	107	3	NM_015383	exon14	c.A1635G	p.S545S	AGGAGTTGAATAA	.	scavenged	Atlas-SNP
SMC4	10051	hgsc.bcm.edu	37	3	160146646	160146646	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	4	230	0	0.0152091	0	.	.	none	SMC4,bladder,carcinoma,+1,1	SMC4	135	1	NM_005496	exon17	c.A2711G	p.D904G	AACAAGACAAACT	.	scavenged	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81241100	81241100	+	Missense_Mutation	SNP	G	G	C	rs11150370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	11	81	0	0.1375	0	G|0.506;C|0.494	0.494	strong	.	PKD1L2	361	.	NM_001076780	exon5	c.C901G	p.P301A	TCGGCGGGTTGTA	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64612845	64612845	+	Silent	SNP	C	C	T	rs11629287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	308	91	235	0	0.295455	0	C|0.567;T|0.433	0.433	strong	SYNE2,NS,carcinoma,0,1	SYNE2	577	1	NM_182914	exon84	c.C15543T	p.I5181I	ACAGATCTTGAAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506147	195506147	+	Missense_Mutation	SNP	G	G	A	rs200473856	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	10	30	6	0.263158	0.2	G|0.981;A|0.019	0.019	strong	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.C12304T	p.L4102F	AGGAAAGGCTGGT	.	scavenged	Atlas-SNP
PRDM4	11108	hgsc.bcm.edu	37	12	108140191	108140191	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	46	122	0	0.422018	0	.	.	none	PRDM4,bladder,carcinoma,-1,1	PRDM4	64	1	NM_012406	exon6	c.G1137A	p.L379L	GTCACACAGAGTA	.	PASS	Atlas-SNP
PIGB	9488	hgsc.bcm.edu	37	15	55647492	55647492	+	Silent	SNP	C	C	T	rs8043415	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	97	165	0	1	0	C|0.909;T|0.091	0.091	strong	PIGB,NS,carcinoma,+1,1	PIGB	36	1	NM_004855	exon12	c.C1527T	p.S509S	AATAAGCGCTTTC	.	PASS	Atlas-SNP
MFI2	4241	hgsc.bcm.edu	37	3	196746629	196746629	+	Silent	SNP	T	T	C	rs1056664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	76	172	0	0.496732	0	T|0.742;C|0.258	0.258	strong	.	MFI2	88	.	NM_033316	exon7	c.A756G	p.E252E	GCCTTCTTCCTCC	.	PASS	Atlas-SNP
HOXB1	3211	hgsc.bcm.edu	37	17	46607958	46607958	+	Missense_Mutation	SNP	T	T	A	rs12939811	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	11	45	0	0.314286	0	T|0.866;A|0.134	0.134	strong	.	HOXB1	67	.	NM_002144	exon1	c.A309T	p.Q103H	TTCTGATTGACCC	.	PASS	Atlas-SNP
IGFN1	91156	hgsc.bcm.edu	37	1	201190732	201190732	+	Silent	SNP	G	G	A	rs3738269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	293	101	243	0	0.34471	0	G|0.775;A|0.225	0.225	strong	IGFN1_ENST00000335211,NS,carcinoma,0,4	IGFN1	220	4	NM_001164586	exon19	c.G10059A	p.V3353V	CCATGTGGGCACC	.	PASS	Atlas-SNP
TRPV2	51393	hgsc.bcm.edu	37	17	16325968	16325968	+	Silent	SNP	A	A	G	rs8121	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	56	97	1	0.491228	0.0103093	A|0.561;G|0.439	0.439	strong	TRPV2,right_upper_lobe,carcinoma,+1,2	TRPV2	74	2	NM_016113	exon4	c.A390G	p.G130G	GGACGGAGTCAAT	.	scavenged	Atlas-SNP
NUP85	79902	hgsc.bcm.edu	37	17	73205976	73205976	+	Silent	SNP	T	T	C	rs34126097	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	36	110	0	0.423529	0	T|0.929;C|0.071	0.071	strong	.	NUP85	44	.	NM_024844	exon3	c.T186C	p.D62D	TGTAGATGTTTAC	.	PASS	Atlas-SNP
SCAF1	58506	hgsc.bcm.edu	37	19	50154607	50154607	+	Missense_Mutation	SNP	C	C	T	rs146455893	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	16	20	0	0.842105	0	A|0.000;C|0.999;T|0.001	0.001	strong	.	SCAF1	78	.	NM_021228	exon7	c.C961T	p.R321C	AGCCCCCGCCCGG	.	PASS	Atlas-SNP
OR6P1	128366	hgsc.bcm.edu	37	1	158533224	158533224	+	Silent	SNP	A	A	G	rs12081915	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	82	99	0	0.607407	0	A|0.441;G|0.558	0.558	strong	OR6P1,NS,carcinoma,-1,1	OR6P1	47	1	NM_001160325	exon1	c.T171C	p.R57R	CATGGGACGATGA	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38119894	38119894	+	Missense_Mutation	SNP	G	G	A	rs35105846	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	222	7	204	6	0.0315315	0.0294118	G|0.500;A|0.500	0.500	strong	TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	NM_001039141	exon7	c.G1331A	p.S444N	CTCCCAGTAGAGC	.	scavenged	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152328222	152328222	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	369	10	256	4	0.0271003	0.015625	.	.	none	FLG2,NS,carcinoma,0,3	FLG2	431	3	NM_001014342	exon3	c.T2040C	p.G680G	TCCAAAACCAGAG	.	scavenged	Atlas-SNP
SPAM1	6677	hgsc.bcm.edu	37	7	123594206	123594206	+	Silent	SNP	G	G	A	rs2285996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	65	127	0	0.984848	0	G|0.754;T|0.001	.	strong	.	SPAM1	195	.	NM_153189	exon3	c.G582A	p.K194K	TGAAAAGGCAGGG	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235392546	235392546	+	Silent	SNP	T	T	C	rs12731746	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214	126	163	0	0.588785	0	T|0.545;C|0.455	0.455	strong	.	ARID4B	142	.	NM_016374	exon11	c.A897G	p.E299E	ACTTACTTCTTCT	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43579679	43579679	+	Missense_Mutation	SNP	T	T	A	rs1058086	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	284	121	264	1	0.426056	0.00378788	T|0.897;A|0.103	0.103	strong	.	PSG2	84	.	NM_031246	exon3	c.A536T	p.Q179L	CACCACTGGTAGC	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152432311	152432311	+	Silent	SNP	T	T	C	rs33988153	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	49	98	0	0.445455	0	T|0.853;C|0.147	0.147	strong	.	NEB	1697	.	NM_001271208	exon107	c.A16911G	p.P5637P	GTACTTTGGCTGT	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76332463	76332463	+	Missense_Mutation	SNP	C	C	A	rs78273685	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	8	216	0	0.0333333	0	A|0.001;C|0.999	0.001	weak	AGGF1,NS,carcinoma,0,1	AGGF1	71	1	NM_018046	exon4	c.C599A	p.A200E	CAGAAGCGGCTGT	.	scavenged	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	56000451	56000451	+	Silent	SNP	G	G	A	rs11227598	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	34	105	0	0.414634	0	G|0.901;A|0.099	0.099	strong	OR5T2,colon,carcinoma,0,2	OR5T2	107	2	NM_001004746	exon1	c.C211T	p.L71L	TTGCTAGAAACAG	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964196	88964196	+	Missense_Mutation	SNP	T	T	A	rs801840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	98	126	0	0.636364	0	T|0.483;A|0.517	0.517	strong	.	ZNF804B	322	.	NM_181646	exon4	c.T1900A	p.F634I	TCTAGGTTTAAAA	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13414594	13414594	+	Silent	SNP	C	C	T	rs16016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	45	111	0	0.529412	0	C|0.834;T|0.166	0.166	strong	.	CACNA1A	715	.	NM_001127221	exon16	c.G2094A	p.T698T	AAAGAGCGTCAGT	.	PASS	Atlas-SNP
C10orf111	221060	hgsc.bcm.edu	37	10	15138696	15138696	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	3	287	0	0.0121951	0	.	.	none	C10orf111,NS,malignant_melanoma,0,1	C10orf111	11	1	NM_153244	exon2	c.G128A	p.R43K	GCAACTCTTACTG	.	scavenged	Atlas-SNP
C3	718	hgsc.bcm.edu	37	19	6702157	6702157	+	Silent	SNP	C	C	G	rs428453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	31	47	0	0.939394	0	C|0.332;G|0.668	0.668	strong	.	C3	192	.	NM_000064	exon19	c.G2421C	p.V807V	CATGCTCACAGCC	.	PASS	Atlas-SNP
FCGR3B	2215	hgsc.bcm.edu	37	1	161599571	161599571	+	Missense_Mutation	SNP	T	T	C	rs2290834	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	359	40	182	1	0.111421	0.00549451	.	.	weak	FCGR3B,NS,carcinoma,+2,1	FCGR3B	35	1	NM_001244753	exon3	c.A424G	p.I142V	CACCGATATGGAC	.	scavenged	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144993324	144993324	+	Silent	SNP	C	C	T	rs6984820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	90	121	0	0.559006	0	C|0.730;T|0.270	0.270	strong	.	PLEC	1144	.	NM_201380	exon32	c.G11076A	p.T3692T	CACCTGCGTGGTC	.	PASS	Atlas-SNP
CLDN19	149461	hgsc.bcm.edu	37	1	43201614	43201614	+	Missense_Mutation	SNP	C	C	T	rs9660973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	45	216	0	0.335821	0	C|0.945;T|0.055	0.055	strong	.	CLDN19	21	.	NM_001185117	exon3	c.G476A	p.R159Q	TGGCTCCGGGCAT	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	37	14	20852770	20852770	+	Silent	SNP	G	G	T	rs1713458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	57	155	0	0.320225	0	G|0.769;T|0.231	0.231	strong	.	TEP1	224	.	NM_007110	exon22	c.C3210A	p.I1070I	GCAGGTGATCCCT	.	PASS	Atlas-SNP
ALOXE3	59344	hgsc.bcm.edu	37	17	7999957	7999957	+	Silent	SNP	G	G	A	rs3809881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	330	162	330	3	0.490909	0.00909091	G|0.593;A|0.407	0.407	strong	ALOXE3_ENST00000318227,NS,carcinoma,0,2	ALOXE3	145	2	NM_001165960	exon16	c.C2520T	p.S840S	GGAGACGCTGTTC	.	scavenged	Atlas-SNP
DOCK9	23348	hgsc.bcm.edu	37	13	99575568	99575568	+	Silent	SNP	G	G	A	rs12428661	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	55	97	0	0.55	0	G|0.826;A|0.174	0.174	strong	DOCK9_ENST00000448493,caecum,carcinoma,0,3	DOCK9	311	3	NM_001130049	exon5	c.C477T	p.V159V	TTTGTCGACCTCC	.	PASS	Atlas-SNP
TPCN1	53373	hgsc.bcm.edu	37	12	113733830	113733830	+	Silent	SNP	C	C	T	rs61943642	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	60	158	0	0.495868	0	C|0.958;T|0.042	0.042	strong	.	TPCN1	109	.	NM_001143819	exon29	c.C2616T	p.P872P	AGCCCCCGCCGCC	.	PASS	Atlas-SNP
CPVL	54504	hgsc.bcm.edu	37	7	29152371	29152371	+	Silent	SNP	G	G	A	rs323182	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	72	164	0	0.347826	0	G|0.887;A|0.113	0.113	strong	.	CPVL	60	.	NM_019029	exon3	c.C237T	p.T79T	ATTCACGGTGAGG	.	PASS	Atlas-SNP
OR8H3	390152	hgsc.bcm.edu	37	11	55889895	55889895	+	Missense_Mutation	SNP	C	C	T	rs61751933	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	123	186	0	0.61809	0	C|0.900;T|0.100	0.100	strong	OR8H3,NS,carcinoma,0,1	OR8H3	92	1	NM_001005201	exon1	c.C47T	p.T16M	TCCTTACGGGACT	.	PASS	Atlas-SNP
DNASE1	1773	hgsc.bcm.edu	37	16	3707747	3707747	+	Missense_Mutation	SNP	G	G	A	rs1053874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	154	129	0	1	0	G|0.520;A|0.480	0.480	strong	.	DNASE1	16	.	NM_005223	exon8	c.G731A	p.R244Q	TGCTCCGAGGCGC	.	PASS	Atlas-SNP
PER2	8864	hgsc.bcm.edu	37	2	239161957	239161957	+	Missense_Mutation	SNP	C	C	T	rs35333999	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	60	138	0	0.495868	0	C|0.970;T|0.030	0.030	strong	.	PER2	85	.	NM_022817	exon19	c.G2707A	p.V903I	CCATGACAGGCGC	.	PASS	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2583328	2583328	+	Silent	SNP	C	C	T	rs61753095	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	59	130	0	0.383117	0	C|0.871;T|0.129	0.129	strong	BRAT1,NS,carcinoma,0,1	BRAT1	57	1	NM_152743	exon5	c.G699A	p.T233T	GGCTTCCGTCCAG	.	PASS	Atlas-SNP
LINS	55180	hgsc.bcm.edu	37	15	101109683	101109683	+	Silent	SNP	T	T	C	rs1047320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	53	135	0	0.946429	0	T|0.982;C|0.018	0.018	strong	.	LINS	62	.	NM_001040616	exon7	c.A2034G	p.P678P	CCTTGATGGAGGC	.	PASS	Atlas-SNP
KIF6	221458	hgsc.bcm.edu	37	6	39325078	39325078	+	Missense_Mutation	SNP	A	A	G	rs20455	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	80	154	1	0.467836	0.00649351	A|0.497;G|0.503	0.503	strong	KIF6_ENST00000287152,NS,carcinoma,0,1	KIF6	233	1	NM_145027	exon19	c.T2155C	p.W719R	GGGACCATTCATG	.	scavenged	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33600764	33600764	+	Missense_Mutation	SNP	T	T	C	rs2287679	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	32	72	0	0.507937	0	T|0.541;C|0.459	0.459	strong	.	GPATCH1	79	.	NM_018025	exon11	c.T1427C	p.L476P	CCCAGCTCTCCCC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152282267	152282267	+	Missense_Mutation	SNP	G	G	A	rs12405278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	277	109	198	0	0.393502	0	G|0.811;A|0.189	0.189	strong	FLG,colon,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.C5095T	p.R1699C	GTCTGCGCCCAGT	.	PASS	Atlas-SNP
LMNA	4000	hgsc.bcm.edu	37	1	156105059	156105059	+	Missense_Mutation	SNP	C	C	T	rs59885338	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	339	4	254	0	0.0117994	0	.	.	weak	LMNA,colon,carcinoma,0,1	LMNA	31	1	NM_170707	exon5	c.C892T	p.R298C	CGCATCCGCATCG	.	scavenged	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52825912	52825912	+	Silent	SNP	C	C	A	rs7549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	126	257	1	0.477273	0.00389105	C|0.941;A|0.059	0.059	strong	.	ITIH1	108	.	NM_002215	exon22	c.C2721A	p.V907V	TATCGTCCCCGAC	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243328887	243328887	+	Nonsense_Mutation	SNP	G	G	T	rs2728433	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	11	96	0	0.0666667	0	T|0.500;G|0.500	0.500	weak	CEP170,extremity,malignant_melanoma,0,1	CEP170	153	1	NM_014812	exon13	c.C2375A	p.S792X	TGTCCTGAATTTT	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276660	152276660	+	Missense_Mutation	SNP	G	G	C	rs7540123	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	375	31	395	0	0.0826667	0	G|0.995;C|0.005	0.005	strong	FLG,NS,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.C10702G	p.Q3568E	GCTCCTGAGCAGA	.	PASS	Atlas-SNP
SAE1	10055	hgsc.bcm.edu	37	19	47700542	47700542	+	Silent	SNP	T	T	C	rs117605411	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	74	238	0	0.389474	0	T|0.997;C|0.003	0.003	strong	.	SAE1	50	.	NM_005500	exon7	c.T786C	p.Y262Y	TACATATGAGGAA	.	PASS	Atlas-SNP
C19orf53	28974	hgsc.bcm.edu	37	19	13885484	13885484	+	Missense_Mutation	SNP	A	A	G	rs10104	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	287	147	334	0	0.512195	0	A|0.669;G|0.331	0.331	strong	.	C19orf53	14	.	NM_014047	exon2	c.A116G	p.K39R	CTCCCAAGAAGGC	.	PASS	Atlas-SNP
FAM171B	165215	hgsc.bcm.edu	37	2	187558960	187558960	+	Silent	SNP	G	G	A	rs2276562	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	17	54	0	0.548387	0	G|0.763;A|0.237	0.237	strong	.	FAM171B	146	.	NM_177454	exon1	c.G60A	p.L20L	GGTGCTGCTGAAA	.	PASS	Atlas-SNP
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493809	77493809	+	Silent	SNP	C	C	T	rs61991638	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	13	4	15	0	0.307692	0	C|0.978;T|0.022	0.022	strong	.	IRF2BPL	40	.	NM_024496	exon1	c.G327A	p.Q109Q	CTGCTGCTGCTGT	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238434249	238434249	+	Silent	SNP	C	C	T	rs2292881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	64	147	0	0.537815	0	C|0.895;T|0.105	0.105	strong	.	MLPH	41	.	NM_001042467	exon7	c.C681T	p.L227L	GTCCCTCACAGAT	.	PASS	Atlas-SNP
SPG11	80208	hgsc.bcm.edu	37	15	44943757	44943757	+	Missense_Mutation	SNP	A	A	G	rs3759871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	24	172	0	0.193548	0	A|0.523;G|0.477	0.477	strong	SPG11,NS,carcinoma,0,1	SPG11	207	1	NM_025137	exon6	c.T1388C	p.F463S	AGGGAAAAACACT	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1857548	1857548	+	Silent	SNP	T	T	C	rs2294038	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	47	88	0	0.345588	0	T|0.853;C|0.147	0.147	strong	.	ARHGEF10	255	.	NM_014629	exon18	c.T2055C	p.Y685Y	CGAGTATGGCAGC	.	PASS	Atlas-SNP
TJP3	27134	hgsc.bcm.edu	37	19	3728609	3728609	+	Missense_Mutation	SNP	G	G	A	rs2067019	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	36	72	2	0.395604	0.0277778	G|0.787;A|0.213	0.213	strong	TJP3,colon,carcinoma,0,1	TJP3	79	1	NM_001267561	exon3	c.G83A	p.R28H	ACCCCCGCCGGGG	.	scavenged	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	185	439	1	0.780591	0.0022779	G|0.751;A|0.249	0.249	strong	.	SLC12A6	205	.	NM_133647	exon4	c.C475T	p.L159L	GAGTCAGATTAGT	.	PASS	Atlas-SNP
SLC7A8	23428	hgsc.bcm.edu	37	14	23598976	23598976	+	Silent	SNP	G	G	A	rs17183863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	67	172	0	0.380682	0	G|0.901;A|0.099	0.099	strong	.	SLC7A8	54	.	NM_012244	exon9	c.C1146T	p.S382S	CATGTCGCTGGTG	.	PASS	Atlas-SNP
EIF2B4	8890	hgsc.bcm.edu	37	2	27590666	27590666	+	Silent	SNP	C	C	T	rs41288829	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	291	137	345	0	0.47079	0	C|0.981;T|0.019	0.019	strong	.	EIF2B4	48	.	NM_172195	exon7	c.G789A	p.P263P	ATTAGGCGGTGTT	.	PASS	Atlas-SNP
C8orf34	116328	hgsc.bcm.edu	37	8	69699756	69699756	+	Missense_Mutation	SNP	G	G	A	rs16935065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	82	190	1	0.689076	0.00526316	G|0.813;A|0.187	0.187	strong	.	C8orf34	170	.	NM_052958	exon12	c.G1534A	p.A512T	GTGGAAGCAGAAC	.	PASS	Atlas-SNP
AP3D1	8943	hgsc.bcm.edu	37	19	2110746	2110746	+	Silent	SNP	G	G	A	rs20567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	55	118	0	0.478261	0	G|0.672;N|0.000	.	strong	.	AP3D1	81	.	NM_001261826	exon27	c.C3135T	p.S1045S	GTGGACGGAGGAG	.	PASS	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187692983	187692983	+	Missense_Mutation	SNP	T	T	C	rs17856918	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	250	139	281	0	0.556	0	T|0.813;C|0.187	0.187	strong	.	ZSWIM2	119	.	NM_182521	exon9	c.A1630G	p.M544V	TGGTCATCCGGCT	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186437944	186437944	+	Silent	SNP	T	T	C	rs5029980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	83	164	0	0.522013	0	T|0.907;C|0.093	0.093	strong	KNG1_ENST00000265023,NS,carcinoma,0,2	KNG1	129	2	NM_000893	exon2	c.T246C	p.D82D	GGGGGATTGTCCT	.	PASS	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	37	9	137775155	137775155	+	Silent	SNP	T	T	C	rs4520243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	51	100	0	0.515152	0	T|0.642;C|0.358	0.358	strong	.	FCN2	55	.	NM_004108	exon3	c.T222C	p.R74R	AGAACGTGGCCCC	.	PASS	Atlas-SNP
POGLUT1	56983	hgsc.bcm.edu	37	3	119196166	119196166	+	Silent	SNP	T	T	C	rs3732420	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	95	226	0	0.458937	0	T|0.860;C|0.140	0.140	strong	.	POGLUT1	32	.	NM_152305	exon4	c.T327C	p.S109S	GTGTAGTGGTGTT	.	PASS	Atlas-SNP
PEX5	5830	hgsc.bcm.edu	37	12	7343153	7343153	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	6	49	2	0.0983607	0.0408163	.	.	none	PEX5_ENST00000434354,colon,carcinoma,0,3	PEX5	63	3	NM_001131023	exon2	c.A180G	p.A60A	AGGTGCAGCCTCT	.	scavenged	Atlas-SNP
AOC3	8639	hgsc.bcm.edu	37	17	41004625	41004625	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	4	301	0	0.0126582	0	.	.	none	AOC3,NS,neuroblastoma,0,1	AOC3	88	1	NM_003734	exon1	c.C1265T	p.P422L	AGGCCCCCAAGAC	.	scavenged	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48226458	48226458	+	Silent	SNP	C	C	T	rs144318062		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	116	148	0	0.822695	0	C|1.000;T|0.000	0.000	weak	.	ABCC11	177	.	NM_033151	exon19	c.G2679A	p.T893T	CAGGGCCGTGGAT	.	PASS	Atlas-SNP
C1QA	712	hgsc.bcm.edu	37	1	22965438	22965438	+	Silent	SNP	A	A	G	rs172378	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	9	83	0	0.157895	0	A|0.431;C|0.013	.	strong	.	C1QA	31	.	NM_015991	exon3	c.A276G	p.G92G	CCTCGGAGCCCGT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149485557	149485557	+	Silent	SNP	C	C	T	rs73168056	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	15	117	0	0.174419	0	C|0.986;T|0.014	0.014	strong	.	.	.	.	NM_198455	exon27	c.C3963T	p.H1321H	GCTGCACGGTGTG	.	PASS	Atlas-SNP
IHH	3549	hgsc.bcm.edu	37	2	219920565	219920565	+	Silent	SNP	C	C	T	rs3731878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20	9	66	0	0.45	0	C|0.902;T|0.098	0.098	strong	.	IHH	33	.	NM_002181	exon3	c.G600A	p.T200T	GCCGCCCGTCTTG	.	PASS	Atlas-SNP
CHD6	84181	hgsc.bcm.edu	37	20	40080586	40080586	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	346	4	348	0	0.0115607	0	.	.	none	CHD6,NS,lymphoid_neoplasm,+1,3	CHD6	312	3	NM_032221	exon22	c.C3403T	p.R1135C	GGGCACGGCAAAT	.	scavenged	Atlas-SNP
KLHL30	377007	hgsc.bcm.edu	37	2	239059610	239059610	+	Silent	SNP	C	C	T	rs61736173	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	115	189	1	0.602094	0.00529101	C|0.961;T|0.039	0.039	strong	.	KLHL30	79	.	NM_198582	exon8	c.C1641T	p.G547G	CCACGGCGCCCTG	.	PASS	Atlas-SNP
CGRRF1	10668	hgsc.bcm.edu	37	14	55005083	55005083	+	Silent	SNP	C	C	T	rs202061859	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	32	87	0	0.326531	0	C|0.999;T|0.001	0.001	weak	.	CGRRF1	30	.	NM_006568	exon6	c.C981T	p.D327D	TAAAGACAAACCG	.	PASS	Atlas-SNP
DHRS13	147015	hgsc.bcm.edu	37	17	27228198	27228198	+	Silent	SNP	G	G	A	rs4795474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281	145	283	1	0.516014	0.00353357	G|0.885;A|0.115	0.115	strong	DHRS13,NS,carcinoma,-1,1	DHRS13	22	1	NM_144683	exon4	c.C492T	p.R164R	CACCACGCGGCTA	.	PASS	Atlas-SNP
TPSAB1	7177	hgsc.bcm.edu	37	16	1291621	1291621	+	Silent	SNP	C	C	T	rs372314315		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	708	173	417	1	0.24435	0.00239808	.	.	weak	TPSAB1,NS,carcinoma,0,1	TPSAB1	24	1	NM_003294	exon4	c.C420T	p.V140V	CACGGTCACCCTG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149519742	149519742	+	Missense_Mutation	SNP	G	G	A	rs201102091	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	11	118	0	0.229167	0	.	.	weak	.	.	.	.	NM_198455	exon91	c.G13232A	p.R4411Q	ACTTCCGGCCTTG	.	PASS	Atlas-SNP
CXXC1	30827	hgsc.bcm.edu	37	18	47810351	47810351	+	Silent	SNP	A	A	G	rs7228084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	40	60	0	0.506329	0	A|0.305;G|0.695	0.695	strong	.	CXXC1	50	.	NM_001101654	exon10	c.T1338C	p.T446T	AAGGCGAGTGCGG	.	PASS	Atlas-SNP
MAP2K1	5604	hgsc.bcm.edu	37	15	66727483	66727483	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	54	141	0	0.556701	0	.	.	none	MAP2K1,NS,lymphoid_neoplasm,0,5	MAP2K1	115	5	NM_002755	exon2	c.G199A	p.D67N	GATGACGACTTTG	.	PASS	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56468440	56468440	+	Missense_Mutation	SNP	G	G	T	rs12421330	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	31	231	0	0.212329	0	G|0.625;T|0.375	0.375	strong	.	.	.	.	NM_001013358	exon1	c.G577T	p.G193C	AAGGGCGGCTATA	.	PASS	Atlas-SNP
OR11H6	122748	hgsc.bcm.edu	37	14	20691888	20691888	+	Missense_Mutation	SNP	C	C	A	rs10140652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	84	191	0	0.342857	0	C|0.909;A|0.091	0.091	strong	.	OR11H6	60	.	NM_001004480	exon1	c.C20A	p.S7Y	TTCATTCTTTGGT	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	37	1	94476467	94476467	+	Missense_Mutation	SNP	T	T	A	rs1801466	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	12	100	0	0.146341	0	T|0.956;A|0.044	0.044	strong	.	ABCA4	275	.	NM_000350	exon40	c.A5603T	p.N1868I	AACGGATTTGCAG	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50546666	50546666	+	Missense_Mutation	SNP	C	C	T	rs3810971	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	81	143	0	0.515924	0	C|0.782;T|0.218	0.218	strong	.	MOV10L1	238	.	NM_018995	exon4	c.C544T	p.R182C	TACAAGCGCGTGG	.	PASS	Atlas-SNP
C2orf62	375307	hgsc.bcm.edu	37	2	219221846	219221846	+	Silent	SNP	G	G	A	rs4324314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	22	97	0	0.289474	0	G|0.843;A|0.157	0.157	strong	.	C2orf62	28	.	NM_198559	exon2	c.G54A	p.S18S	GCCCTCGGGTCCG	.	PASS	Atlas-SNP
TTC7A	57217	hgsc.bcm.edu	37	2	47251469	47251469	+	Missense_Mutation	SNP	G	G	C	rs2304290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164	80	113	0	0.487805	0	G|0.779;C|0.221	0.221	strong	.	TTC7A	80	.	NM_020458	exon14	c.G1612C	p.V538L	CTCTATGTCTCGC	.	PASS	Atlas-SNP
NPR3	4883	hgsc.bcm.edu	37	5	32786389	32786389	+	Missense_Mutation	SNP	A	A	G	rs2270915	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	115	240	1	0.433962	0.00416667	A|0.833;G|0.167	0.167	strong	.	NPR3	65	.	NM_001204375	exon8	c.A1564G	p.N522D	GAAAGTAACCTTG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388378	1388378	+	Missense_Mutation	SNP	T	T	C	rs55884223	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	48	209	7	0.252632	0.0334928	T|0.993;C|0.007	0.007	strong	CRIPAK,NS,carcinoma,-1,1	CRIPAK	185	1	NM_175918	exon1	c.T79C	p.C27R	TGCTCATGTGCCC	.	scavenged	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176304	57176304	+	Missense_Mutation	SNP	T	T	G	rs12460400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	87	114	1	0.988636	0.00877193	T|0.628;G|0.372	0.372	strong	.	ZNF835	106	.	NM_001005850	exon2	c.A263C	p.E88A	GGGCTCTCCCCAG	.	PASS	Atlas-SNP
TRAF3IP2	10758	hgsc.bcm.edu	37	6	111913070	111913070	+	Missense_Mutation	SNP	G	G	A	rs13190932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	116	148	0	0.588832	0	G|0.954;A|0.046	0.046	strong	.	TRAF3IP2	35	.	NM_147686	exon2	c.C220T	p.R74W	CAGGCCGCTGGTG	.	PASS	Atlas-SNP
GPR158	57512	hgsc.bcm.edu	37	10	25888180	25888180	+	Missense_Mutation	SNP	A	A	G	rs10828833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	29	74	0	0.805556	0	A|0.388;G|0.612	0.612	strong	GPR158,right_upper_lobe,carcinoma,-2,1	GPR158	255	1	NM_020752	exon11	c.A3625G	p.I1209V	GAAGAGATCTGGG	.	PASS	Atlas-SNP
MTL5	9633	hgsc.bcm.edu	37	11	68514791	68514791	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	2	168	0	0.0127389	0	.	.	none	MTL5,NS,carcinoma,0,1	MTL5	37	1	NM_001039656	exon3	c.C515T	p.P172L	TCTTCCGGATTAT	.	scavenged	Atlas-SNP
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331549	21331549	+	Missense_Mutation	SNP	T	T	C	rs4149056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253	149	284	1	0.588933	0.00352113	T|0.890;C|0.110	0.110	strong	.	SLCO1B1	151	.	NM_006446	exon6	c.T521C	p.V174A	TATATGTGTTCAT	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	37	16	2329071	2329071	+	Missense_Mutation	SNP	G	G	A	rs146709251	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	67	134	0	0.468531	0	G|0.997;A|0.003	0.003	strong	.	ABCA3	176	.	NM_001089	exon29	c.C4420T	p.R1474W	TCTCCCGGCCTGT	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55496494	55496494	+	Silent	SNP	C	C	T	rs61733928	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	73	184	0	0.474026	0	C|0.980;T|0.020	0.020	strong	.	NLRP2	161	.	NM_017852	exon7	c.C2110T	p.L704L	ATGGGTCTAGCAA	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46655779	46655779	+	Missense_Mutation	SNP	G	G	C	rs36125344	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	37	91	0	0.5	0	G|0.912;C|0.088	0.088	strong	.	PKDREJ	195	.	NM_006071	exon1	c.C3441G	p.I1147M	GAGTCCGATTGTG	.	PASS	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11421004	11421004	+	Missense_Mutation	SNP	C	C	T	rs71455364	bycluster;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	27	108	0	0.369863	0	C|0.500;G|0.500	.	alt	.	PRB3	84	.	NM_006249	exon3	c.G179A	p.R60Q	GGGGGTCGTCCTT	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202287813	202287813	+	Silent	SNP	T	T	C	rs788793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	226	167	1	0.9869	0.00598802	T|0.445;C|0.555	0.555	strong	.	LGR6	102	.	NM_001017403	exon18	c.T2382C	p.F794F	CAGCTTTGCCTCC	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46652737	46652737	+	Silent	SNP	G	G	A	rs6008362	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	70	136	0	0.542636	0	G|0.737;A|0.263	0.263	strong	.	PKDREJ	195	.	NM_006071	exon1	c.C6483T	p.C2161C	CAAGACGCAGATC	.	PASS	Atlas-SNP
ZSWIM5	57643	hgsc.bcm.edu	37	1	45504720	45504720	+	Silent	SNP	G	G	C	rs7551698	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	37	78	1	0.787234	0.0128205	G|0.462;C|0.538	0.538	strong	ZSWIM5,NS,carcinoma,-1,1	ZSWIM5	72	1	NM_020883	exon8	c.C1782G	p.T594T	TGTGATGGTTGTG	.	scavenged	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29364643	29364643	+	Missense_Mutation	SNP	T	T	C	rs4987411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	257	304	0	0.988462	0	T|0.630;C|0.370	0.370	strong	.	OR12D2	42	.	NM_013936	exon1	c.T167C	p.L56P	ATTCCCTTATGTA	.	PASS	Atlas-SNP
NEK2	4751	hgsc.bcm.edu	37	1	211846876	211846876	+	Silent	SNP	A	A	G	rs701929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	94	232	0	0.353383	0	A|0.463;G|0.537	0.537	strong	.	NEK2	49	.	NM_002497	exon3	c.T504C	p.H168H	CGTGTCATGGTTT	.	PASS	Atlas-SNP
RERE	473	hgsc.bcm.edu	37	1	8425900	8425900	+	Silent	SNP	T	T	C	rs3753275	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	53	107	0	0.779412	0	T|0.771;C|0.229	0.229	strong	.	RERE	129	.	NM_012102	exon14	c.A1419G	p.T473T	GGAGGGTGTGTTG	.	PASS	Atlas-SNP
HES7	84667	hgsc.bcm.edu	37	17	8026364	8026364	+	Silent	SNP	C	C	T	rs61731639	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	114	183	0	0.527778	0	C|0.854;T|0.146	0.146	strong	.	.	.	.	NM_001165967	exon2	c.G123A	p.E41E	GGTCCGCTCCAGC	.	PASS	Atlas-SNP
MACROD1	28992	hgsc.bcm.edu	37	11	63767186	63767186	+	Silent	SNP	A	A	G	rs709594	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	9	38	0	0.375	0	A|0.619;G|0.381	0.381	strong	.	MACROD1	17	.	NM_014067	exon6	c.T714C	p.S238S	AGCCTGACTGGCG	.	PASS	Atlas-SNP
SLC41A2	84102	hgsc.bcm.edu	37	12	105199038	105199038	+	Silent	SNP	G	G	A	rs11112201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	57	137	0	0.428571	0	G|0.919;A|0.081	0.081	strong	SLC41A2,NS,carcinoma,0,1	SLC41A2	66	1	NM_032148	exon10	c.C1614T	p.S538S	GGGGATGGAGAAA	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43073761	43073761	+	Silent	SNP	G	G	A	rs658958	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	106	91	1	0.946429	0.010989	G|0.533;A|0.467	0.467	strong	FAM198A_ENST00000430121,caecum,carcinoma,0,1	FAM198A	23	1	NM_001129908	exon2	c.G6A	p.A2A	TCAGGCGTCTTGG	.	scavenged	Atlas-SNP
CCDC170	80129	hgsc.bcm.edu	37	6	151936677	151936677	+	Missense_Mutation	SNP	G	G	A	rs6929137	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	82	195	0	0.471264	0	G|0.655;A|0.345	0.345	strong	.	.	.	.	NM_025059	exon10	c.G1810A	p.V604I	ATGTCTGTCAAGT	.	PASS	Atlas-SNP
PML	5371	hgsc.bcm.edu	37	15	74328206	74328206	+	Missense_Mutation	SNP	G	G	C	rs743582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	11	38	0	0.314286	0	G|0.888;C|0.112	0.112	strong	.	PML	169	.	NM_033239	exon8	c.G2404C	p.A802P	CTGGAAGCCTCTC	.	PASS	Atlas-SNP
SOCS6	9306	hgsc.bcm.edu	37	18	67993227	67993227	+	Silent	SNP	C	C	T	rs112244149	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	66	186	0	0.364641	0	C|0.995;T|0.005	0.005	strong	.	SOCS6	54	.	NM_004232	exon2	c.C1323T	p.S441S	GTTTAGCTTTTAT	.	PASS	Atlas-SNP
VPS4A	27183	hgsc.bcm.edu	37	16	69354963	69354963	+	Silent	SNP	A	A	G	rs1127231	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	139	111	1	0.985816	0.00900901	A|0.722;G|0.278	0.278	strong	.	VPS4A	18	.	NM_013245	exon9	c.A861G	p.K287K	TGAAAAACGAATT	.	PASS	Atlas-SNP
GLRX3	10539	hgsc.bcm.edu	37	10	131934747	131934747	+	Missense_Mutation	SNP	G	G	C	rs13991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	10	67	0	0.37037	0	G|0.849;C|0.151	0.151	strong	TXNL2,NS,carcinoma,0,2	GLRX3	39	2	NM_006541	exon1	c.G63C	p.Q21H	CGGGCAGTTTGAG	.	PASS	Atlas-SNP
YAP1	10413	hgsc.bcm.edu	37	11	102094424	102094424	+	Silent	SNP	C	C	T	rs61749258	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	209	156	1	0.661392	0.00641026	C|0.995;T|0.005	0.005	strong	.	YAP1	45	.	NM_001130145	exon7	c.C1104T	p.P368P	TTCTCCCGGGATG	.	PASS	Atlas-SNP
GCAT	23464	hgsc.bcm.edu	37	22	38204089	38204089	+	Missense_Mutation	SNP	C	C	T	rs710187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	53	117	0	0.53	0	C|0.420;T|0.580	0.580	strong	GCAT,NS,carcinoma,0,1	GCAT	27	1	NM_001171690	exon1	c.C115T	p.R39C	GGCATCCGCGGAG	.	PASS	Atlas-SNP
GPR180	160897	hgsc.bcm.edu	37	13	95273447	95273447	+	Silent	SNP	G	G	A	rs12429818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	78	169	0	0.513158	0	G|0.877;A|0.123	0.123	strong	.	GPR180	24	.	NM_180989	exon6	c.G852A	p.T284T	TTCTACGCCTGCA	.	PASS	Atlas-SNP
KLK4	9622	hgsc.bcm.edu	37	19	51412666	51412666	+	Silent	SNP	C	C	A	rs1654552	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	66	129	0	0.503817	0	C|0.685;A|0.315	0.315	strong	KLK4,colon,carcinoma,0,2	KLK4	46	2	NM_004917	exon2	c.G66T	p.S22S	GACGAGCGATCCT	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88504850	88504850	+	Missense_Mutation	SNP	G	G	C	rs1105066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	7	70	0	0.125	0	G|0.601;C|0.399	0.399	strong	.	ZNF469	121	.	NM_001127464	exon2	c.G10888C	p.E3630Q	GTGTCTGAGGGGG	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1502857	1502857	+	Missense_Mutation	SNP	C	C	T	rs12926089	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	45	137	0	0.416667	0	C|0.889;T|0.111	0.111	strong	.	CLCN7	53	.	NM_001287	exon15	c.G1252A	p.V418M	CCAGCACGGCCTC	.	PASS	Atlas-SNP
CNTROB	116840	hgsc.bcm.edu	37	17	7843053	7843053	+	Silent	SNP	C	C	T	rs11078719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	59	68	0	1	0	C|0.506;T|0.494	0.494	strong	.	CNTROB	61	.	NM_001037144	exon8	c.C1150T	p.L384L	GCTCAGCTGGAAA	.	PASS	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	rs35898523	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	23	7	24	0	0.304348	0	G|0.941;T|0.059	0.059	strong	GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	NM_021996	exon7	c.C363A	p.Y121X	ATGAGTGTACCTA	.	PASS	Atlas-SNP
JHDM1D	80853	hgsc.bcm.edu	37	7	139801777	139801777	+	Silent	SNP	T	T	G	rs1062277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	108	234	0	0.701299	0	T|0.659;G|0.341	0.341	strong	.	JHDM1D	54	.	NM_030647	exon12	c.A1612C	p.R538R	CTAATCTTTTGAG	.	PASS	Atlas-SNP
CTSB	1508	hgsc.bcm.edu	37	8	11710174	11710174	+	Missense_Mutation	SNP	T	T	C	rs1803250	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	27	80	0	0.397059	0	T|0.896;C|0.103;A|0.000	0.103	strong	.	CTSB	24	.	NM_147780	exon5	c.A157G	p.S53G	AGTAGCTCATGTC	.	PASS	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187698707	187698707	+	Missense_Mutation	SNP	C	C	T	rs6434197	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	51	99	0	0.51	0	C|0.806;T|0.194	0.194	strong	.	ZSWIM2	119	.	NM_182521	exon6	c.G794A	p.C265Y	TGGCAGCAGCTAT	.	PASS	Atlas-SNP
RFC4	5984	hgsc.bcm.edu	37	3	186509517	186509517	+	Silent	SNP	G	G	A	rs187868	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	48	95	0	0.527473	0	G|0.516;A|0.484	0.484	strong	RFC4,colon,carcinoma,0,1	RFC4	54	1	NM_181573	exon8	c.C798T	p.A266A	TACCCCGGCAATG	.	PASS	Atlas-SNP
OTUD3	23252	hgsc.bcm.edu	37	1	20224152	20224152	+	Silent	SNP	G	G	A	rs61769077	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	10	92	0	0.172414	0	G|0.950;A|0.050	0.050	strong	.	OTUD3	25	.	NM_015207	exon4	c.G603A	p.T201T	CCAGACGGATGTG	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50515270	50515270	+	Silent	SNP	T	T	C	rs6010164	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	51	71	0	0.607143	0	T|0.887;C|0.113	0.113	strong	.	MLC1	48	.	NM_015166	exon7	c.A597G	p.S199S	TCTTACTGAGTAA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115797	168115797	+	Missense_Mutation	SNP	G	G	C	rs75758327	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	56	147	0	0.504505	0	G|0.922;C|0.078	0.078	strong	.	XIRP2	914	.	NM_001199143	exon11	c.G2840C	p.R947T	TTCCCAGAGTGGA	.	PASS	Atlas-SNP
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671328	238671328	+	Silent	SNP	A	A	G	rs868119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	413	200	385	1	0.484262	0.0025974	A|0.732;G|0.268	0.268	strong	.	LRRFIP1	171	.	NM_001137552	exon11	c.A972G	p.E324E	GAAAGAACAACAC	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16162039	16162039	+	Silent	SNP	C	C	T	rs8187858	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182	83	180	0	0.456044	0	C|0.953;T|0.047	0.047	strong	.	ABCC1	156	.	NM_004996	exon13	c.C1704T	p.Y568Y	CGTCTACGTGACC	.	PASS	Atlas-SNP
TECPR2	9895	hgsc.bcm.edu	37	14	102909991	102909991	+	Silent	SNP	C	C	T	rs17100923	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	31	48	0	0.378049	0	C|0.899;T|0.101	0.101	strong	.	TECPR2	114	.	NM_001172631	exon12	c.C2760T	p.S920S	TCTGAGCGTGGAT	.	PASS	Atlas-SNP
GNB5	10681	hgsc.bcm.edu	37	15	52446200	52446200	+	Silent	SNP	G	G	A	rs6493537	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	7	69	0	0.2	0	G|0.873;A|0.127	0.127	strong	.	GNB5	28	.	NM_016194	exon4	c.C312T	p.H104H	GTTCCCGTGGCCT	.	PASS	Atlas-SNP
MYRF	745	hgsc.bcm.edu	37	11	61553284	61553284	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	3	191	0	0.0131579	0	.	.	none	C11orf9,right_upper_lobe,carcinoma,-1,1	.	.	1	NM_001127392	exon26	c.C3313T	p.R1105W	TCTCACCGGTGGC	.	scavenged	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234541801	234541801	+	Silent	SNP	A	A	G	rs12073170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	328	327	296	1	0.996951	0.00337838	A|0.897;G|0.103	0.103	strong	.	TARBP1	111	.	NM_005646	exon24	c.T3837C	p.C1279C	ATTGAAACACCAC	.	PASS	Atlas-SNP
ELL2	22936	hgsc.bcm.edu	37	5	95234350	95234350	+	Silent	SNP	A	A	G	rs3777204	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	228	292	2	0.991304	0.00684932	A|0.626;G|0.374	0.374	strong	.	ELL2	63	.	NM_012081	exon8	c.T1119C	p.P373P	AGGGGTAGGGATG	.	PASS	Atlas-SNP
PKDREJ	10343	hgsc.bcm.edu	37	22	46656479	46656479	+	Missense_Mutation	SNP	A	A	G	rs6519993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	52	111	0	0.485981	0	A|0.724;G|0.276	0.276	strong	.	PKDREJ	195	.	NM_006071	exon1	c.T2741C	p.L914P	GGAAAGAGGTCAT	.	PASS	Atlas-SNP
CATSPERG	57828	hgsc.bcm.edu	37	19	38847431	38847431	+	Silent	SNP	T	T	C	rs2286475	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	220	96	238	0	0.436364	0	T|0.735;C|0.265	0.265	strong	.	CATSPERG	121	.	NM_021185	exon11	c.T1245C	p.T415T	GTATACTCTACTG	.	PASS	Atlas-SNP
FAM189A1	23359	hgsc.bcm.edu	37	15	29421014	29421014	+	Silent	SNP	G	G	C	rs2306934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	35	83	0	0.648148	0	G|0.869;C|0.131	0.131	strong	.	FAM189A1	20	.	NM_015307	exon8	c.C981G	p.T327T	AGCACTGGTGTTT	.	PASS	Atlas-SNP
EIF5B	9669	hgsc.bcm.edu	37	2	99995804	99995804	+	Silent	SNP	T	T	C	rs1376443	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	115	232	0	0.497835	0	T|0.415;C|0.585	0.585	strong	.	EIF5B	95	.	NM_015904	exon12	c.T1974C	p.D658D	ACAAGATGGTGAA	.	PASS	Atlas-SNP
SLC6A12	6539	hgsc.bcm.edu	37	12	311949	311949	+	Silent	SNP	A	A	G	rs216250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	86	121	1	0.955556	0.00826446	A|0.437;G|0.563	0.563	strong	.	SLC6A12	60	.	NM_001122848	exon5	c.T447C	p.T149T	CTCAGAAGTGAAG	.	PASS	Atlas-SNP
ARSD	414	hgsc.bcm.edu	37	X	2835964	2835964	+	Silent	SNP	G	G	A	rs73632972	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	55	213	0	0.392857	0	G|0.500;A|0.500	0.500	strong	.	ARSD	47	.	NM_001669	exon5	c.C744T	p.F248F	AAACCCGAAGGAG	.	PASS	Atlas-SNP
GJB3	2707	hgsc.bcm.edu	37	1	35250720	35250720	+	Silent	SNP	C	C	T	rs41310442	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	99	186	0	0.673469	0	C|0.936;T|0.064	0.064	strong	.	GJB3	40	.	NM_001005752	exon2	c.C357T	p.N119N	CGACAACGCAGGC	.	PASS	Atlas-SNP
EPB41L2	2037	hgsc.bcm.edu	37	6	131190838	131190838	+	Silent	SNP	G	G	A	rs17059736	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	112	216	0	0.430769	0	G|0.841;A|0.159	0.159	strong	.	EPB41L2	96	.	NM_001431	exon15	c.C2472T	p.P824P	CTCTCCGGGTATC	.	PASS	Atlas-SNP
WRAP73	49856	hgsc.bcm.edu	37	1	3551828	3551828	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	48	157	0	0.40678	0	.	.	none	WRAP73,NS,carcinoma,+1,1	WRAP73	43	1	NM_017818	exon7	c.C634T	p.R212W	ACAACCGGCCATC	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769228	43769228	+	Silent	SNP	A	A	C	rs10506226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	56	164	0	0.388889	0	A|0.790;C|0.210	0.210	strong	.	ADAMTS20	635	.	NM_025003	exon36	c.T5400G	p.T1800T	GAAAACAGTGTAT	.	PASS	Atlas-SNP
KRT81	3887	hgsc.bcm.edu	37	12	52681080	52681080	+	Silent	SNP	G	G	A	rs4761784	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	67	128	0	0.54918	0	G|0.744;A|0.256	0.256	strong	.	KRT81	46	.	NM_002281	exon7	c.C1053T	p.A351A	AGACTGGGCCACC	.	PASS	Atlas-SNP
HOXD4	3233	hgsc.bcm.edu	37	2	177016728	177016728	+	Missense_Mutation	SNP	T	T	C	rs34727427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	41	60	0	1	0	T|0.722;C|0.278	0.278	strong	HOXD4,NS,carcinoma,-1,1	HOXD4	32	1	NM_014621	exon1	c.T367C	p.S123P	CCGCCCTCCGGGA	.	PASS	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	37	8	17847418	17847418	+	Silent	SNP	A	A	G	rs145539051	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	45	79	0	0.463918	0	A|0.991;G|0.009	0.009	strong	.	PCM1	120	.	NM_006197	exon27	c.A4461G	p.Q1487Q	TGAGCAAAATGAT	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165648709	165648709	+	Silent	SNP	C	C	T	rs1143661	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	258	253	191	0	0.98062	0	C|0.910;T|0.090	0.090	strong	.	ALDH9A1	75	.	NM_000696	exon6	c.G900A	p.A300A	CATCAGCGCCCCC	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895963	1895963	+	Missense_Mutation	SNP	A	A	G	rs17855613	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	360	15	673	0	0.0416667	0	.	.	weak	SIRPA,brain,glioma,-2,4	SIRPA	83	4	NM_001040022	exon3	c.A298G	p.N100D	AAGAGAAACAACA	.	scavenged	Atlas-SNP
LIG4	3981	hgsc.bcm.edu	37	13	108863609	108863609	+	Missense_Mutation	SNP	G	G	A	rs1805389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	28	77	0	0.518519	0	G|0.955;A|0.045	0.045	strong	.	LIG4	91	.	NM_206937	exon3	c.C8T	p.A3V	TGTGAGGCAGCCA	.	PASS	Atlas-SNP
CBS	875	hgsc.bcm.edu	37	21	44483101	44483101	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	27	106	0	0.225	0	.	.	none	.	CBS	85	.	NM_000071	exon10	c.A916G	p.I306V	AGCCGATCCCTTC	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39549983	39549983	+	Silent	SNP	G	G	A	rs3736890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	16	89	0	0.266667	0	G|0.867;A|0.133	0.133	strong	.	MACF1	909	.	NM_012090	exon3	c.G93A	p.S31S	GCGGTCGGGGAGC	.	PASS	Atlas-SNP
QSOX1	5768	hgsc.bcm.edu	37	1	180144485	180144485	+	Silent	SNP	G	G	A	rs10913939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	355	221	211	1	0.622535	0.00473934	G|0.866;A|0.134	0.134	strong	.	QSOX1	79	.	NM_002826	exon3	c.G396A	p.S132S	CGGCTCGGGAGCA	.	PASS	Atlas-SNP
FTL	2512	hgsc.bcm.edu	37	19	49469087	49469087	+	Silent	SNP	T	T	C	rs2230267	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	51	89	0	0.566667	0	T|0.480;C|0.520	0.520	strong	.	FTL	19	.	NM_000146	exon2	c.T163C	p.L55L	CGCGAATTGGCCG	.	PASS	Atlas-SNP
CHAMP1	283489	hgsc.bcm.edu	37	13	115091399	115091399	+	Silent	SNP	T	T	C	rs9525332	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	50	154	0	0.442478	0	T|0.893;C|0.107	0.107	strong	.	.	.	.	NM_001164144	exon3	c.T2082C	p.S694S	TATCTCTGAAGAG	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144621084	144621084	+	Missense_Mutation	SNP	T	T	G	rs3750207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	28	107	0	0.259259	0	T|0.601;G|0.399	0.399	strong	.	ZC3H3	75	.	NM_015117	exon2	c.A453C	p.E151D	GGGGGTTTCCTCA	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	37	7	24789386	24789386	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	29	113	0	0.254386	0	.	.	none	.	DFNA5	51	.	NM_001127453	exon2	c.C8T	p.A3V	GCTTTGGCAAACA	.	PASS	Atlas-SNP
ZNF286A	57335	hgsc.bcm.edu	37	17	15604485	15604485	+	Silent	SNP	T	T	C	rs78494624	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	317	74	250	0	0.233438	0	T|0.895;C|0.105	0.105	strong	ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	NM_020652	exon3	c.T57C	p.S19S	GGATTCTCCCCAT	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24435538	24435538	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1334	116	1014	1	0.0869565	0.000986193	.	.	none	DHRS4,NS,carcinoma,0,1	DHRS4	22	1	NM_021004	exon6	c.C578A	p.T193N	GCCTGACCAAGAC	.	scavenged	Atlas-SNP
YIPF5	81555	hgsc.bcm.edu	37	5	143539969	143539969	+	Missense_Mutation	SNP	C	C	T	rs147304369	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	42	67	0	0.494118	0	C|0.993;T|0.007	0.007	strong	.	YIPF5	17	.	NM_001024947	exon6	c.G766A	p.V256I	AAAAGACGGAAAT	.	PASS	Atlas-SNP
MTTP	4547	hgsc.bcm.edu	37	4	100510903	100510903	+	Missense_Mutation	SNP	A	A	G	rs3792683	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	21	48	0	0.583333	0	A|0.901;G|0.099	0.099	strong	MTTP,NS,carcinoma,-1,1	MTTP	127	1	NM_000253	exon5	c.A497G	p.N166S	CCACCAATGAGGT	.	PASS	Atlas-SNP
DHX15	1665	hgsc.bcm.edu	37	4	24550580	24550580	+	Silent	SNP	G	G	A	rs33972724	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	39	102	0	0.423913	0	G|0.991;A|0.009	0.009	strong	.	DHX15	69	.	NM_001358	exon6	c.C1146T	p.D382D	TTTAATGTCACCA	.	PASS	Atlas-SNP
TNKS2	80351	hgsc.bcm.edu	37	10	93608142	93608142	+	Silent	SNP	G	G	A	rs3758499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	38	73	0	0.76	0	G|0.687;A|0.313	0.313	strong	.	TNKS2	103	.	NM_025235	exon19	c.G2361A	p.A787A	CTAGGCGGATGAT	.	PASS	Atlas-SNP
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	119	263	1	0.53125	0.00380228	A|0.598;G|0.402	0.402	strong	.	KRTAP3-3	11	.	NM_033185	exon1	c.T66C	p.S22S	TTTGTCAGAGGAG	.	PASS	Atlas-SNP
SLC16A13	201232	hgsc.bcm.edu	37	17	6942108	6942108	+	Silent	SNP	C	C	T	rs11078663	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	51	102	0	0.455357	0	C|0.571;T|0.429	0.429	strong	.	SLC16A13	28	.	NM_201566	exon3	c.C981T	p.S327S	CTTCTCCGTGCTG	.	PASS	Atlas-SNP
SLC16A10	117247	hgsc.bcm.edu	37	6	111493953	111493953	+	Silent	SNP	C	C	T	rs33965856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	332	165	311	1	0.496988	0.00321543	C|0.952;T|0.048	0.048	strong	.	SLC16A10	33	.	NM_018593	exon2	c.C399T	p.S133S	AGTCAGCGTCTTC	.	PASS	Atlas-SNP
KIFC1	3833	hgsc.bcm.edu	37	6	33374422	33374422	+	Silent	SNP	T	T	C	rs371316441		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231	3	222	0	0.012987	0	.	.	weak	KIFC1,rectum,carcinoma,0,1	KIFC1	47	1	NM_002263	exon9	c.T1881C	p.S627S	GAACTCTCTGGGT	.	scavenged	Atlas-SNP
EXO1	9156	hgsc.bcm.edu	37	1	242035438	242035438	+	Missense_Mutation	SNP	G	G	A	rs4149965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	379	202	296	0	0.532982	0	G|0.851;A|0.149	0.149	strong	EXO1,caecum,carcinoma,0,2	EXO1	103	2	NM_006027	exon10	c.G1372A	p.V458M	TCTGAAGTGTTTG	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30868352	30868352	+	Silent	SNP	C	C	T	rs201645679	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	48	80	0	0.489796	0	C|0.999;T|0.001	0.001	weak	.	FAM188B	62	.	NM_032222	exon6	c.C1131T	p.L377L	GCGGCTCGGTAGG	.	PASS	Atlas-SNP
IKBKB	3551	hgsc.bcm.edu	37	8	42174380	42174380	+	Silent	SNP	G	G	A	rs56230731	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	37	106	0	0.321739	0	G|0.991;A|0.009	0.009	strong	.	IKBKB	88	.	NM_001556	exon11	c.G1083A	p.L361L	GGCGTTGATCCCC	.	PASS	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45811343	45811343	+	Missense_Mutation	SNP	T	T	G	rs1556314	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	64	52	0	0.984615	0	T|0.777;G|0.223	0.223	strong	.	TRPM2	196	.	NM_003307	exon11	c.T1629G	p.D543E	GGAGGATCCCGAG	.	PASS	Atlas-SNP
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17934319	17934319	+	Silent	SNP	C	C	T	rs114551094	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	28	115	0	0.301075	0	C|0.981;T|0.019	0.019	strong	.	ARHGEF10L	219	.	NM_018125	exon7	c.C456T	p.Y152Y	GCTCTACGAGGAT	.	PASS	Atlas-SNP
SLC22A1	6580	hgsc.bcm.edu	37	6	160560845	160560845	+	Missense_Mutation	SNP	A	A	G	rs628031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	61	112	0	0.968254	0	A|0.330;G|0.669	0.669	strong	.	SLC22A1	69	.	NM_153187	exon7	c.A1222G	p.M408V	ATGGCCATGTCAA	.	PASS	Atlas-SNP
ZFYVE1	53349	hgsc.bcm.edu	37	14	73440864	73440864	+	Silent	SNP	C	C	T	rs12931	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	140	125	1	0.979021	0.008	C|0.501;T|0.499	0.499	strong	.	ZFYVE1	67	.	NM_021260	exon11	c.G2025A	p.T675T	AATGAGCGTTCCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	6	173	1	0.0384615	0.00578035	.	.	none	MUC4_ENST00000463781,NS,carcinoma,+1,2	MUC4	1505	2	NM_018406	exon2	c.C11468T	p.T3823I	AGAGGGGTGGTGT	.	scavenged	Atlas-SNP
HIST1H2AH	85235	hgsc.bcm.edu	37	6	27115084	27115084	+	Silent	SNP	G	G	C	rs147640519	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	113	218	0	0.518349	0	G|0.994;C|0.006	0.006	strong	.	HIST1H2AH	26	.	NM_080596	exon1	c.G177C	p.L59L	GTACCTGACCGCT	.	PASS	Atlas-SNP
CRELD1	78987	hgsc.bcm.edu	37	3	9985096	9985096	+	Silent	SNP	G	G	A	rs76764016	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	110	232	0	0.480349	0	G|0.991;A|0.009	0.009	strong	.	CRELD1	48	.	NM_001077415	exon10	c.G945A	p.P315P	GTGTCCGGGAGAG	.	PASS	Atlas-SNP
HEMGN	55363	hgsc.bcm.edu	37	9	100692648	100692648	+	Silent	SNP	G	G	T	rs35527067	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	267	119	242	0	0.445693	0	G|0.992;T|0.008	0.008	strong	.	HEMGN	55	.	NM_197978	exon3	c.C1029A	p.I343I	TTCTTGGATTGTT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790951	4790951	+	Missense_Mutation	SNP	A	A	G	rs11033801	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	43	103	0	0.413462	0	A|0.702;G|0.298	0.298	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T197C	p.F66S	AGCCTGAAGAGGA	.	PASS	Atlas-SNP
IMMT	10989	hgsc.bcm.edu	37	2	86400824	86400824	+	Missense_Mutation	SNP	G	G	A	rs1050301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	73	148	0	0.521429	0	T|0.038;G|0.593;C|0.070;N|0.001;A|0.299	0.299	strong	IMMT,NS,carcinoma,0,1	IMMT	65	1	NM_006839	exon4	c.C370T	p.P124S	AGGCAGGCTGTTT	.	PASS	Atlas-SNP
LIPA	3988	hgsc.bcm.edu	37	10	91007360	91007360	+	Missense_Mutation	SNP	T	T	G	rs1051338	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	23	88	0	0.638889	0	T|0.740;G|0.254	0.254	strong	.	LIPA	29	.	NM_000235	exon2	c.A46C	p.T16P	GCAGGGTCCAGAG	.	PASS	Atlas-SNP
EFCAB3	146779	hgsc.bcm.edu	37	17	60469289	60469289	+	Silent	SNP	T	T	C	rs61764063	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	323	113	346	0	0.349845	0	T|0.993;C|0.007	0.007	strong	.	EFCAB3	71	.	NM_001144933	exon6	c.T414C	p.H138H	CAAGCATGATGTC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678616	100678616	+	Missense_Mutation	SNP	G	G	A	rs113959201	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256	92	155	0	0.359375	0	G|0.941;A|0.059	0.059	strong	.	MUC17	804	.	NM_001040105	exon3	c.G3919A	p.G1307S	ACTAAAGGTCCTG	.	PASS	Atlas-SNP
ZNF317	57693	hgsc.bcm.edu	37	19	9267319	9267319	+	Missense_Mutation	SNP	G	G	T	rs3752199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	33	67	0	0.485294	0	G|0.865;T|0.135	0.135	strong	ZNF317,NS,carcinoma,0,1	ZNF317	61	1	NM_020933	exon3	c.G57T	p.Q19H	TCTCCAGGACTCA	.	PASS	Atlas-SNP
CCPG1	9236	hgsc.bcm.edu	37	15	55664110	55664110	+	Missense_Mutation	SNP	G	G	C	rs117236526	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	99	173	0	0.942857	0	G|0.947;C|0.053	0.053	strong	.	CCPG1	74	.	NM_020739	exon6	c.C587G	p.A196G	TGTTCAGCAACTA	.	PASS	Atlas-SNP
PARP3	10039	hgsc.bcm.edu	37	3	51981769	51981769	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	57	103	0	0.587629	0	.	.	none	.	PARP3	90	.	NM_001003931	exon10	c.G1311A	p.K437K	CATGAAGTGTGGG	.	PASS	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	37	11	63884747	63884747	+	Silent	SNP	C	C	T	rs35247680	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	163	174	0	0.987879	0	C|0.975;T|0.025	0.025	strong	.	FLRT1	46	.	NM_013280	exon2	c.C1008T	p.L336L	CAACCTCATGTGG	.	PASS	Atlas-SNP
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	64	141	0	0.457143	0	G|0.968;A|0.032	0.032	strong	.	SCYL1	76	.	NM_020680	exon4	c.G600A	p.K200K	AGAGAAGTGGTGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680463	100680463	+	Missense_Mutation	SNP	G	G	T	rs368849364	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	19	157	0	0.0931373	0	.	.	alt	.	MUC17	804	.	NM_001040105	exon3	c.G5766T	p.R1922S	TCCTAGGGAAGGA	.	PASS	Atlas-SNP
SCUBE1	80274	hgsc.bcm.edu	37	22	43607040	43607040	+	Silent	SNP	G	G	A	rs138988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	446	208	483	1	0.466368	0.00207039	G|0.910;A|0.090	0.090	strong	.	SCUBE1	105	.	NM_173050	exon18	c.C2271T	p.I757I	GCAGCGGATGCAG	.	PASS	Atlas-SNP
PANX2	56666	hgsc.bcm.edu	37	22	50617671	50617671	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	44	146	0	0.346457	0	.	.	none	.	PANX2	69	.	NM_052839	exon3	c.G1999A	p.E667K	TTCGACGAGCCGA	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11303943	11303943	+	Silent	SNP	A	A	G	rs3745681	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	20	31	0	0.526316	0	A|0.544;G|0.456	0.456	strong	KANK2,NS,carcinoma,0,1	KANK2	47	1	NM_015493	exon2	c.T813C	p.V271V	TTCTCGAACCCAG	.	PASS	Atlas-SNP
C1orf105	92346	hgsc.bcm.edu	37	1	172431333	172431333	+	Missense_Mutation	SNP	A	A	G	rs16844498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	338	114	250	0	0.337278	0	A|0.949;G|0.051	0.051	strong	.	C1orf105	24	.	NM_139240	exon5	c.A289G	p.M97V	AGAACAATGAAAA	.	PASS	Atlas-SNP
GNPDA1	10007	hgsc.bcm.edu	37	5	141391532	141391532	+	Silent	SNP	G	G	A	rs164080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	107	241	0	0.436735	0	G|0.454;A|0.546	0.546	strong	GNPDA1,NS,carcinoma,0,1	GNPDA1	16	1	NM_005471	exon2	c.C69T	p.R23R	GATGATGCGGTTC	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44948563	44948563	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230	117	270	0	0.508696	0	.	.	none	.	TGM4	82	.	NM_003241	exon10	c.A1198G	p.M400V	GTGAAGATGGTGA	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160493834	160493834	+	Silent	SNP	G	G	A	rs2230044	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	111	286	1	0.47234	0.0034965	G|0.958;A|0.042	0.042	strong	.	IGF2R	251	.	NM_000876	exon33	c.G4608A	p.A1536A	CAGGGCGGGATTC	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982131	240982131	+	Missense_Mutation	SNP	A	A	G	rs79839275	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	94	211	3	0.494737	0.014218	A|0.737;G|0.263	0.263	strong	PRR21,NS,carcinoma,0,2	PRR21	53	2	NM_001080835	exon1	c.T269C	p.M90T	AGAGGCATGGATG	.	scavenged	Atlas-SNP
SLCO1A2	6579	hgsc.bcm.edu	37	12	21487544	21487544	+	Missense_Mutation	SNP	A	A	G	rs10841795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	90	188	1	0.508475	0.00531915	A|0.924;G|0.076	0.076	strong	SLCO1A2,NS,carcinoma,0,1	SLCO1A2	107	1	NM_134431	exon3	c.T38C	p.I13T	CATCTTATTCTAT	.	scavenged	Atlas-SNP
HNRNPA1	3178	hgsc.bcm.edu	37	12	54676630	54676630	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	38	125	0	0.365385	0	.	.	none	.	HNRNPA1	72	.	NM_002136	exon7	c.G723A	p.G241G	CAGTGGGGATGGC	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49690496	49690496	+	Silent	SNP	C	C	T	rs11709525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	59	117	1	0.572816	0.00854701	C|0.731;G|0.000;T|0.269	0.269	strong	BSN,NS,carcinoma,0,1	BSN	272	1	NM_003458	exon5	c.C3507T	p.S1169S	ACCCTCCGGCAGC	.	scavenged	Atlas-SNP
TMEM45A	55076	hgsc.bcm.edu	37	3	100274090	100274090	+	Missense_Mutation	SNP	C	C	A	rs200878698	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	68	195	0	0.435897	0	.	.	weak	TMEM45A,NS,carcinoma,+1,1	TMEM45A	35	1	NM_018004	exon2	c.C35A	p.T12N	CTGGAACCTTCTT	.	PASS	Atlas-SNP
VANGL2	57216	hgsc.bcm.edu	37	1	160385934	160385934	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	267	5	212	0	0.0187266	0	.	.	none	VANGL2,NS,carcinoma,-2,1	VANGL2	83	1	NM_020335	exon3	c.C154T	p.P52S	GGGGAGCCCCTGC	.	scavenged	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31382882	31382882	+	Missense_Mutation	SNP	C	C	A	rs9266825	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	68	137	0	0.419753	0	C|0.666;A|0.334	0.334	strong	.	MICA	21	.	NM_000247	exon7	c.C1118A	p.A373D	TGTCAGCTCTTGG	.	PASS	Atlas-SNP
COPE	11316	hgsc.bcm.edu	37	19	19011244	19011244	+	Silent	SNP	T	T	C	rs1127821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	78	159	0	0.478528	0	T|0.421;G|0.095;C|0.305;A|0.179	0.305	strong	.	COPE	26	.	NM_007263	exon8	c.A750G	p.P250P	CGTCTCTGGGTAG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2160973	2160973	+	Missense_Mutation	SNP	A	A	G	rs116092985	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	34	136	0	0.317757	0	A|0.943;G|0.057	0.057	strong	.	PKD1	184	.	NM_000296	exon15	c.T4195C	p.W1399R	CCAGCCAGGCCTC	.	PASS	Atlas-SNP
IRF2	3660	hgsc.bcm.edu	37	4	185310218	185310218	+	Silent	SNP	C	C	T	rs1131553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	84	143	0	0.807692	0	C|0.617;T|0.383	0.383	strong	IRF2,NS,carcinoma,0,1	IRF2	53	1	NM_002199	exon9	c.G744A	p.G248G	TGGCCGCCCCTTT	.	PASS	Atlas-SNP
TMED6	146456	hgsc.bcm.edu	37	16	69381769	69381769	+	Silent	SNP	C	C	T	rs16958777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	275	34	277	0	0.123636	0	C|0.926;T|0.074	0.074	strong	.	TMED6	19	.	NM_144676	exon3	c.G411A	p.G137G	GAAGACCCCAAAG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60892538	60892538	+	Silent	SNP	G	G	A	rs146174815	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	61	164	0	0.480315	0	G|0.994;A|0.006	0.006	strong	.	LAMA5	268	.	NM_005560	exon55	c.C7374T	p.A2458A	GCTGGCGGCGAGG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467124	10467124	+	Missense_Mutation	SNP	G	G	C	rs4841399	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	30	37	0	0.555556	0	G|0.722;C|0.278	0.278	strong	RP1L1,NS,carcinoma,0,1	RP1L1	453	1	NM_178857	exon4	c.C4484G	p.P1495R	TGGGTGGGTTGGG	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518314	161518314	+	Silent	SNP	C	C	T	rs114535887	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	952	246	590	1	0.258403	0.00169492	C|0.960;T|0.040	0.040	strong	.	FCGR3A	38	.	NM_000569	exon3	c.G324A	p.S108S	GTAGCTCGAGGCC	.	PASS	Atlas-SNP
B3GALTL	145173	hgsc.bcm.edu	37	13	31891746	31891746	+	Missense_Mutation	SNP	G	G	A	rs1041073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	151	146	1	1	0.00684932	G|0.337;A|0.663	0.663	strong	.	B3GALTL	48	.	NM_194318	exon13	c.G1108A	p.E370K	TCCGGCGAGCCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515304	195515304	+	Silent	SNP	T	T	A	rs202019266		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	17	183	1	0.0955056	0.00546448	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A3147T	p.A1049A	TGTGGATGCTGAG	.	scavenged	Atlas-SNP
EYA2	2139	hgsc.bcm.edu	37	20	45717954	45717954	+	Silent	SNP	C	C	T	rs866937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	51	109	0	0.421488	0	C|0.768;T|0.232	0.232	strong	.	EYA2	85	.	NM_172110	exon8	c.C738T	p.D246D	CTCCGACGGGAAG	.	PASS	Atlas-SNP
CPNE3	8895	hgsc.bcm.edu	37	8	87567193	87567193	+	Missense_Mutation	SNP	C	C	T	rs2304789	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	45	114	0	0.328467	0	C|0.730;T|0.270	0.270	strong	.	CPNE3	65	.	NM_003909	exon15	c.C1235T	p.T412M	CAGCCACGCAACA	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225534219	225534219	+	Missense_Mutation	SNP	T	T	C	rs7527925	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	356	215	218	0	0.603933	0	T|0.500;C|0.500	0.500	strong	.	DNAH14	300	.	NM_001373	exon69	c.T10880C	p.V3627A	GCACTGTAATCAT	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55542540	55542540	+	Missense_Mutation	SNP	G	G	A	rs61739567	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	74	189	0	0.787234	0	A|0.295;G|0.705	0.295	strong	.	RP1	429	.	NM_006269	exon4	c.G6098A	p.C2033Y	GGTTTTGTATGAA	.	PASS	Atlas-SNP
HENMT1	113802	hgsc.bcm.edu	37	1	109200108	109200108	+	Missense_Mutation	SNP	C	C	T	rs36100901	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	53	111	0	0.768116	0	C|0.984;T|0.016	0.016	strong	.	HENMT1	38	.	NM_144584	exon3	c.G115A	p.V39I	TTTTAACGAACTG	.	PASS	Atlas-SNP
MCPH1	79648	hgsc.bcm.edu	37	8	6479178	6479178	+	Silent	SNP	C	C	A	rs2912016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	68	94	0	0.561983	0	C|0.615;A|0.385	0.385	strong	.	MCPH1	65	.	NM_024596	exon13	c.C2418A	p.A806A	GAAAGCCACAGTC	.	PASS	Atlas-SNP
EIF3D	8664	hgsc.bcm.edu	37	22	36912630	36912630	+	Silent	SNP	A	A	G	rs11558519	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181	80	221	0	0.441989	0	A|0.914;G|0.086	0.086	strong	.	EIF3D	37	.	NM_003753	exon12	c.T1101C	p.D367D	AATATCATCTCCA	.	PASS	Atlas-SNP
PROM1	8842	hgsc.bcm.edu	37	4	16077515	16077515	+	Silent	SNP	G	G	A	rs10033189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	56	88	0	0.643678	0	G|0.945;A|0.055	0.055	strong	.	PROM1	91	.	NM_001145847	exon2	c.C15T	p.L5L	GGAGCCGAGTACG	.	PASS	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	80923536	80923536	+	Silent	SNP	C	C	T	rs4986144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	28	58	0	0.482759	0	C|0.739;T|0.261	0.261	strong	B3GNTL1,NS,malignant_melanoma,0,2	B3GNTL1	40	2	NM_001009905	exon7	c.G591A	p.E197E	ACCTCCCTCGTTA	.	PASS	Atlas-SNP
AGBL2	79841	hgsc.bcm.edu	37	11	47711820	47711820	+	Missense_Mutation	SNP	A	A	G	rs76215382	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	108	264	1	0.439024	0.00378788	A|0.990;G|0.010	0.010	strong	.	AGBL2	73	.	NM_024783	exon10	c.T1439C	p.L480P	TTGCTAAGGATGA	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33475282	33475282	+	Missense_Mutation	SNP	C	C	T	rs2228638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	86	165	2	0.754386	0.0121212	C|0.910;T|0.090	0.090	strong	NRP1,NS,carcinoma,+2,1	NRP1	126	1	NM_003873	exon14	c.G2197A	p.V733I	TGCCGACGTGGGA	.	scavenged	Atlas-SNP
TGS1	96764	hgsc.bcm.edu	37	8	56698801	56698801	+	Missense_Mutation	SNP	C	C	T	rs76064957	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	19	68	0	0.558824	0	C|0.992;T|0.008	0.008	strong	.	TGS1	66	.	NM_024831	exon4	c.C344T	p.S115F	AGGTATCTATGAA	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243329049	243329049	+	Missense_Mutation	SNP	G	G	A	rs71627763	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	336	54	209	0	0.160714	0	G|0.167;A|0.833	0.833	weak	.	CEP170	153	.	NM_014812	exon13	c.C2213T	p.T738I	AAAGAAGTTTCCT	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194081179	194081179	+	Silent	SNP	G	G	A	rs11715737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	67	105	0	0.587719	0	G|0.830;A|0.170	0.170	strong	.	LRRC15	137	.	NM_001135057	exon3	c.C612T	p.N204N	CTGGAGGTTGCCC	.	PASS	Atlas-SNP
FAM161B	145483	hgsc.bcm.edu	37	14	74402693	74402693	+	Silent	SNP	C	C	T	rs17182699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	92	184	0	0.401747	0	C|0.935;T|0.065	0.065	strong	.	FAM161B	67	.	NM_152445	exon8	c.G1953A	p.R651R	AACAGCCCGGGTG	.	PASS	Atlas-SNP
RAD54B	25788	hgsc.bcm.edu	37	8	95419698	95419698	+	Silent	SNP	A	A	G	rs2291439	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	368	219	301	0	0.595109	0	A|0.610;C|0.003	.	strong	.	RAD54B	88	.	NM_012415	exon5	c.T750C	p.N250N	TTTGCAATTTTGG	.	PASS	Atlas-SNP
CRISP3	10321	hgsc.bcm.edu	37	6	49701523	49701523	+	Missense_Mutation	SNP	A	A	G	rs495335	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	131	157	0	0.984962	0	A|0.322;G|0.678	0.678	strong	.	CRISP3	67	.	NM_001190986	exon5	c.T385C	p.S129P	AGCTGGAGGCACT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152279019	152279019	+	Silent	SNP	G	G	A	rs57670307	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1422	244	679	4	0.171589	0.00589102	G|0.939;A|0.061	0.061	strong	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.C8343T	p.D2781D	CTGACCGTCTTGG	.	scavenged	Atlas-SNP
OR8J3	81168	hgsc.bcm.edu	37	11	55904828	55904828	+	Missense_Mutation	SNP	A	A	G	rs11227321	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218	97	214	0	0.444954	0	A|0.901;G|0.099	0.099	strong	OR8J3,NS,carcinoma,0,1	OR8J3	112	1	NM_001004064	exon1	c.T367C	p.Y123H	CCACATAGCGGTC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092954	1092954	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	3	82	1	0.0447761	0.0121951	.	.	none	MUC2_ENST00000441003,rectum,carcinoma,0,4	MUC2	614	4	NM_002457	exon30	c.G4773A	p.T1591T	CACTACGGTGACC	.	scavenged	Atlas-SNP
XKR9	389668	hgsc.bcm.edu	37	8	71646201	71646201	+	Missense_Mutation	SNP	C	C	T	rs61734026	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	461	266	365	0	0.577007	0	C|0.990;T|0.010	0.010	strong	.	XKR9	43	.	NM_001011720	exon5	c.C664T	p.L222F	GTTGTACTTCTAC	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386272	7386272	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	5	132	0	0.033557	0	.	.	none	POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	NM_001102614	exon2	c.C969T	p.I323I	CATCATCACAGCC	.	scavenged	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151845972	151845972	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	3	221	0	0.0204082	0	.	.	none	MLL3_ENST00000355193,rectum,carcinoma,-1,7	MLL3	1564	7	NM_170606	exon52	c.C13040T	p.P4347L	TTGAGCGGCCTGC	.	scavenged	Atlas-SNP
C9orf172	389813	hgsc.bcm.edu	37	9	139740436	139740436	+	Missense_Mutation	SNP	G	G	A	rs375030600		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	37	81	0	0.587302	0	.	.	weak	.	C9orf172	23	.	NM_001080482	exon1	c.G1570A	p.G524S	GGCCTGGGCCGCA	.	PASS	Atlas-SNP
SCRN3	79634	hgsc.bcm.edu	37	2	175289259	175289259	+	Missense_Mutation	SNP	G	G	T	rs41270195	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	271	148	319	0	0.546125	0	G|0.971;T|0.029	0.029	strong	.	SCRN3	76	.	NM_024583	exon7	c.G974T	p.S325I	ATACCAGTTCACC	.	PASS	Atlas-SNP
ZNF816	125893	hgsc.bcm.edu	37	19	53454543	53454543	+	Missense_Mutation	SNP	G	G	A	rs11084210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	56	176	0	0.5	0	A|0.112;C|0.000;G|0.888	0.112	strong	.	ZNF816	73	.	NM_001202457	exon4	c.C485T	p.S162L	AGATGCGAATGAA	.	PASS	Atlas-SNP
CATSPERG	57828	hgsc.bcm.edu	37	19	38827960	38827960	+	Missense_Mutation	SNP	T	T	C	rs2302182	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72	34	85	0	0.472222	0	T|0.855;C|0.145	0.145	strong	.	CATSPERG	121	.	NM_021185	exon2	c.T86C	p.L29P	CAGTGCTCCTGGC	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13368892	13368892	+	Silent	SNP	G	G	A	rs2271509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	146	159	0	0.993197	0	G|0.541;A|0.459	0.459	strong	NUP210,NS,carcinoma,0,2	NUP210	182	2	NM_024923	exon32	c.C4332T	p.C1444C	GACAACGCAGGTG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149513560	149513560	+	Silent	SNP	T	T	C	rs12674102	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	7	96	0	0.142857	0	T|0.614;C|0.386	0.386	strong	.	.	.	.	NM_198455	exon78	c.T11181C	p.S3727S	CTTCTCTGAGGGC	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39422624	39422624	+	Missense_Mutation	SNP	C	C	T	rs9548505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	68	145	0	0.566667	0	C|0.894;G|0.000;T|0.106	0.106	strong	.	FREM2	385	.	NM_207361	exon8	c.C6196T	p.R2066C	ATCAGCCGTAATT	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	54	141	0	0.312139	0	A|0.690;G|0.310	0.310	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon11	c.T1456C	p.L486L	CTTCCAAGTCTTC	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104643409	104643409	+	Silent	SNP	A	A	G	rs2487303	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7	7	2	1	1	0.5	A|0.242;G|0.758	0.758	strong	KIF26A,NS,carcinoma,0,1	KIF26A	84	1	NM_015656	exon12	c.A4284G	p.A1428A	AGAAGCAGCACAC	.	scavenged	Atlas-SNP
MBD1	4152	hgsc.bcm.edu	37	18	47796399	47796399	+	Missense_Mutation	SNP	A	A	C	rs183864846	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	5	4	5	0	0.8	0	A|0.993;C|0.007	0.007	strong	MBD1_ENST00000339998,NS,carcinoma,-1,1	MBD1	228	1	NM_001204142	exon14	c.T1635G	p.I545M	CAAATAAATTTCA	.	scavenged	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159399348	159399348	+	Missense_Mutation	SNP	A	A	G	rs768994	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	28	62	0	0.509091	0	A|0.862;G|0.138	0.138	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon7	c.T1316C	p.M439T	TCATTCATTAGCC	.	PASS	Atlas-SNP
CDH7	1005	hgsc.bcm.edu	37	18	63477206	63477206	+	Silent	SNP	G	G	A	rs17075229	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	52	159	1	0.416	0.00628931	G|0.984;A|0.016	0.016	strong	CDH7_ENST00000323011,NS,carcinoma,+2,2	CDH7	362	2	NM_004361	exon3	c.G477A	p.T159T	ATACACGGCAGGA	.	scavenged	Atlas-SNP
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586361	79586361	+	Silent	SNP	T	T	C	rs8038778	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	8	80	0	0.177778	0	T|0.315;C|0.685	0.685	strong	.	ANKRD34C	29	.	NM_001146341	exon2	c.T735C	p.P245P	TTTGCCTCAACTG	.	PASS	Atlas-SNP
HDGFL1	154150	hgsc.bcm.edu	37	6	22570245	22570245	+	Silent	SNP	G	G	A	rs6900627	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	20	102	0	0.344828	0	G|0.820;A|0.180	0.180	strong	.	HDGFL1	33	.	NM_138574	exon1	c.G441A	p.R147R	GAAGAGGAGCGCG	.	PASS	Atlas-SNP
FAM134A	79137	hgsc.bcm.edu	37	2	220046155	220046155	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	18	82	0	0.243243	0	.	.	none	FAM134A,colon,carcinoma,0,1	FAM134A	34	1	NM_024293	exon7	c.C849T	p.S283S	TGAAAGCGAGGCA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513285	195513285	+	Silent	SNP	G	G	T	rs200293322	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	531	12	444	7	0.0225989	0.0157658	G|0.988;T|0.013	0.013	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C5166A	p.S1722S	ACCTGTGGATACT	.	scavenged	Atlas-SNP
KCNG4	93107	hgsc.bcm.edu	37	16	84256103	84256103	+	Missense_Mutation	SNP	C	C	T	rs35649980	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	111	129	0	0.880952	0	C|0.935;T|0.065	0.065	strong	.	KCNG4	71	.	NM_172347	exon3	c.G1280A	p.R427H	ACACTGCGGGGCA	.	PASS	Atlas-SNP
MEP1B	4225	hgsc.bcm.edu	37	18	29782953	29782953	+	Missense_Mutation	SNP	A	A	G	rs71361372	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	24	37	0	0.615385	0	A|0.992;G|0.008	0.008	strong	.	MEP1B	54	.	NM_005925	exon6	c.A348G	p.I116M	CTATATATCAGTG	.	PASS	Atlas-SNP
NUF2	83540	hgsc.bcm.edu	37	1	163313539	163313539	+	Missense_Mutation	SNP	C	C	T	rs11802875	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	90	136	0	0.535714	0	C|0.865;N|0.000	.	strong	NUF2_ENST00000271452,NS,carcinoma,0,2	NUF2	138	2	NM_145697	exon10	c.C686T	p.S229L	AATTGTCGGTGGT	.	PASS	Atlas-SNP
QSER1	79832	hgsc.bcm.edu	37	11	32996805	32996805	+	Silent	SNP	C	C	T	rs11032076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	32	103	1	0.4	0.00970874	C|0.907;T|0.093	0.093	strong	QSER1,caecum,carcinoma,0,1	QSER1	153	1	NM_001076786	exon12	c.C4983T	p.V1661V	TGCTGTCGATCCA	.	scavenged	Atlas-SNP
LEPRE1	64175	hgsc.bcm.edu	37	1	43223489	43223489	+	Missense_Mutation	SNP	C	C	T	rs6700677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	20	170	0	0.204082	0	C|0.940;T|0.060	0.060	strong	LEPRE1_ENST00000296388,colon,carcinoma,0,8	LEPRE1	130	8	NM_001146289	exon5	c.G1045A	p.G349R	CTTCTCCAAGCAT	.	PASS	Atlas-SNP
TRPM6	140803	hgsc.bcm.edu	37	9	77415284	77415284	+	Silent	SNP	A	A	C	rs7859201	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	72	136	0	0.517986	0	A|0.532;C|0.468	0.468	strong	.	TRPM6	377	.	NM_017662	exon17	c.T2124G	p.L708L	CAGTTTAAGGCAG	.	PASS	Atlas-SNP
CHSY1	22856	hgsc.bcm.edu	37	15	101717888	101717888	+	Missense_Mutation	SNP	C	C	T	rs62621399	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79	22	130	1	0.278481	0.00769231	C|0.907;G|0.000;T|0.093	0.093	strong	CHSY1,colon,carcinoma,-1,1	CHSY1	60	1	NM_014918	exon3	c.G2114A	p.R705Q	CCCACTCGGACAA	.	scavenged	Atlas-SNP
FLRT1	23769	hgsc.bcm.edu	37	11	63885704	63885704	+	Silent	SNP	C	C	T	rs677447	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	145	142	0	0.993151	0	C|0.533;T|0.467	0.467	strong	.	FLRT1	46	.	NM_013280	exon2	c.C1965T	p.Y655Y	TGGCTACGGCACC	.	PASS	Atlas-SNP
FAM155B	27112	hgsc.bcm.edu	37	X	68725640	68725640	+	Missense_Mutation	SNP	T	T	C	rs1171942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	119	265	2	0.952	0.00754717	T|0.456;C|0.544	0.544	strong	.	FAM155B	44	.	NM_015686	exon1	c.T515C	p.L172P	ACTCCCTTTCCCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509378	195509378	+	Missense_Mutation	SNP	G	G	C	rs199889138		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	363	71	222	0	0.195592	0	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9073G	p.L3025V	CATGAAGAGGGGT	.	PASS	Atlas-SNP
OR8D2	283160	hgsc.bcm.edu	37	11	124189306	124189306	+	Missense_Mutation	SNP	G	G	A	rs2466620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	67	158	0	0.295154	0	G|0.761;A|0.239	0.239	strong	.	OR8D2	65	.	NM_001002918	exon1	c.C788T	p.P263L	CTGGAAGGGGGCT	.	PASS	Atlas-SNP
PEX10	5192	hgsc.bcm.edu	37	1	2340212	2340212	+	Silent	SNP	G	G	A	rs1143016	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	77	144	0	0.740385	0	G|0.960;A|0.040	0.040	strong	.	PEX10	18	.	NM_002617	exon3	c.C279T	p.G93G	CAGCACGCCACGG	.	PASS	Atlas-SNP
PTH1R	5745	hgsc.bcm.edu	37	3	46939456	46939456	+	Splice_Site	SNP	G	G	C	rs201472450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	49	123	0	0.333333	0	.	.	weak	.	PTH1R	49	.	NM_000316	exon6	c.424+1G>C	.	ACAAAGGTGAGGC	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789345	117789345	+	Missense_Mutation	SNP	G	G	C	rs61900347	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	27	144	0	0.111111	0	G|0.899;C|0.101	0.101	strong	TMPRSS13_ENST00000445164,NS,carcinoma,0,2	TMPRSS13	75	2	NM_001206790	exon2	c.C230G	p.A77G	GCCTGGGCTGGAG	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23908034	23908034	+	Silent	SNP	A	A	G	rs2737700	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	129	115	0	1	0	A|0.664;G|0.336	0.336	strong	.	SACS	871	.	NM_014363	exon10	c.T9981C	p.A3327A	ACAGCCAGCTTTC	.	PASS	Atlas-SNP
GTPBP10	85865	hgsc.bcm.edu	37	7	89982132	89982132	+	Silent	SNP	T	T	C	rs6972561	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	22	39	0	0.5	0	T|0.731;C|0.269	0.269	strong	.	GTPBP10	31	.	NM_001042717	exon2	c.T36C	p.Y12Y	TAAGTATGGAAAT	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89521725	89521725	+	Silent	SNP	T	T	C	rs1054750	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	65	157	2	0.511811	0.0127389	T|0.835;C|0.165	0.165	strong	EPHA3,NS,malignant_melanoma,+2,1	EPHA3	501	1	NM_005233	exon16	c.T2802C	p.G934G	CACGGGTGTGGAG	.	scavenged	Atlas-SNP
CCL24	6369	hgsc.bcm.edu	37	7	75442730	75442730	+	Missense_Mutation	SNP	T	T	G	rs2302006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	36	45	0	0.610169	0	T|0.714;G|0.286	0.286	strong	.	CCL24	11	.	NM_002991	exon2	c.A85C	p.I29L	AGGGGATGACCAC	.	PASS	Atlas-SNP
PSD3	23362	hgsc.bcm.edu	37	8	18729459	18729459	+	Silent	SNP	T	T	C	rs13273954	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	377	136	314	1	0.360743	0.00318471	C|0.267;N|0.001	0.267	strong	.	PSD3	142	.	NM_015310	exon3	c.A915G	p.E305E	CAGTATTTCCACT	.	PASS	Atlas-SNP
ANAPC15	25906	hgsc.bcm.edu	37	11	71821236	71821236	+	Silent	SNP	A	A	G	rs17161980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	84	211	0	0.442105	0	A|0.864;G|0.136	0.136	strong	.	.	.	.	NM_014042	exon5	c.T216C	p.D72D	CTCATCATCTTCA	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626724	140626724	+	Silent	SNP	T	T	G	rs3776091	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	82	324	0	0.44086	0	T|0.852;G|0.148	0.148	strong	.	PCDHB15	138	.	NM_018935	exon1	c.T1578G	p.A526A	GCAGGCTTTCGAG	.	PASS	Atlas-SNP
ADCK4	79934	hgsc.bcm.edu	37	19	41220529	41220529	+	Silent	SNP	C	C	T	rs11673492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	72	153	0	0.467532	0	C|0.854;T|0.146	0.146	strong	.	ADCK4	92	.	NM_001142555	exon2	c.G9A	p.L3L	CACCTTCAGCCAC	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	37	6	43182906	43182906	+	Silent	SNP	C	C	T	rs76552409	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	110	104	0	0.973451	0	C|0.981;T|0.019	0.019	strong	.	CUL9	248	.	NM_015089	exon30	c.C5778T	p.V1926V	AGATGTCCTCTCT	.	PASS	Atlas-SNP
MSRB2	22921	hgsc.bcm.edu	37	10	23408278	23408278	+	Silent	SNP	C	C	T	rs7427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	50	105	0	0.735294	0	C|0.746;T|0.254	0.254	strong	.	MSRB2	21	.	NM_012228	exon4	c.C342T	p.S114S	GTTTTCCGAGGCT	.	PASS	Atlas-SNP
ZNF181	339318	hgsc.bcm.edu	37	19	35232368	35232368	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	6	135	0	0.0428571	0	.	.	none	ZNF181,NS,carcinoma,0,1	ZNF181	65	1	NM_001029997	exon4	c.G1082C	p.R361T	TTCATAGGTCATC	.	scavenged	Atlas-SNP
TEKT5	146279	hgsc.bcm.edu	37	16	10775932	10775932	+	Missense_Mutation	SNP	A	A	G	rs138988373	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	85	222	0	0.414634	0	A|0.998;G|0.002	0.002	strong	.	TEKT5	66	.	NM_144674	exon4	c.T781C	p.C261R	CGATACACTGGGC	.	PASS	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178634683	178634683	+	Missense_Mutation	SNP	C	C	T	rs11750821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	35	76	0	0.492958	0	C|0.931;T|0.069	0.069	strong	ADAMTS2,right_upper_lobe,carcinoma,+1,1	ADAMTS2	190	1	NM_021599	exon4	c.G722A	p.R241H	AGGGCGCGGCTGA	.	PASS	Atlas-SNP
LRRC71	149499	hgsc.bcm.edu	37	1	156902281	156902281	+	Missense_Mutation	SNP	T	T	G	rs822431	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	241	212	1	0.975708	0.00471698	T|0.706;G|0.294	0.294	strong	LRRC71,NS,carcinoma,0,1	LRRC71	33	1	NM_144702	exon14	c.T1507G	p.S503A	CAGTTCTCCAAGG	.	PASS	Atlas-SNP
PAX8	7849	hgsc.bcm.edu	37	2	113976146	113976146	+	Silent	SNP	T	T	C	rs368201100		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	32	54	0	0.457143	0	.	.	weak	.	PAX8	42	.	NM_003466	exon12	c.A1317G	p.A439A	GGGCGGTGCACTC	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115950156	115950156	+	Missense_Mutation	SNP	G	G	A	rs10465129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	103	234	0	0.492823	0	G|0.890;A|0.110	0.110	strong	FKBP15_ENST00000238256,NS,carcinoma,0,1	FKBP15	128	1	NM_015258	exon14	c.C1300T	p.L434F	CCTGGAGCCCAGT	.	PASS	Atlas-SNP
OR51D1	390038	hgsc.bcm.edu	37	11	4661285	4661285	+	Missense_Mutation	SNP	A	A	G	rs905871	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	330	153	332	1	0.463636	0.00301205	A|0.794;G|0.206	0.206	strong	.	OR51D1	49	.	NM_001004751	exon1	c.A265G	p.I89V	TCCTCTATCACCA	.	PASS	Atlas-SNP
AKR1B15	441282	hgsc.bcm.edu	37	7	134261174	134261174	+	Missense_Mutation	SNP	A	A	G	rs2458502	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	17	91	0	0.220779	0	A|0.998;G|0.002	0.002	strong	.	AKR1B15	105	.	NM_001080538	exon9	c.A817G	p.T273A	AAAACCACAGCCC	.	PASS	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175335234	175335234	+	Silent	SNP	C	C	T	rs1385541	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	308	114	284	0	0.37013	0	C|0.809;T|0.191	0.191	strong	.	TNR	399	.	NM_003285	exon11	c.G2094A	p.S698S	GGTCTCCGAGGAG	.	PASS	Atlas-SNP
CCDC178	374864	hgsc.bcm.edu	37	18	30928852	30928852	+	Splice_Site	SNP	A	A	G	rs140419270	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	24	77	0	0.387097	0	A|0.997;G|0.003	0.003	strong	.	.	.	.	NM_001105528	exon8	c.457+2T>C	.	AACTTTACCTCTC	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	372	106	282	0	0.284946	0	G|0.761;A|0.239	0.239	strong	PDE1C_ENST00000396191,NS,carcinoma,0,2	PDE1C	465	2	NM_001191058	exon16	c.C1962T	p.A654A	CTTCTCGGCTTTG	.	PASS	Atlas-SNP
FAM69B	138311	hgsc.bcm.edu	37	9	139617836	139617836	+	Silent	SNP	C	C	T	rs6874	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	30	88	0	0.410959	0	C|0.915;T|0.085	0.085	strong	.	FAM69B	22	.	NM_152421	exon5	c.C906T	p.N302N	GGCCAACGTGGGC	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169498975	169498975	+	Missense_Mutation	SNP	T	T	C	rs6030	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	203	163	0	0.990244	0	T|0.711;C|0.288	0.288	strong	.	F5	301	.	NM_000130	exon16	c.A5290G	p.M1764V	TGTCCATAGGCAT	.	PASS	Atlas-SNP
PAGE5	90737	hgsc.bcm.edu	37	X	55247817	55247817	+	Missense_Mutation	SNP	T	T	C	rs61745114	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	272	622	0	0.978417	0	T|0.994;C|0.006	0.006	strong	.	PAGE5	20	.	NM_130467	exon2	c.T62C	p.M21T	GAGATATGAGTGA	.	PASS	Atlas-SNP
TCEAL4	79921	hgsc.bcm.edu	37	X	102842041	102842041	+	Silent	SNP	T	T	C	rs11010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	52	124	1	1	0.00806452	0|0.006;C|0.292	0.292	strong	.	TCEAL4	18	.	NM_001006935	exon3	c.T438C	p.H146H	CATACATGATATG	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28517454	28517454	+	Silent	SNP	G	G	T	rs28457230	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	43	138	0	0.364407	0	G|0.938;T|0.062	0.062	strong	.	HERC2	501	.	NM_004667	exon9	c.C990A	p.A330A	GCCCTGGGCGGAA	.	PASS	Atlas-SNP
AKR7A3	22977	hgsc.bcm.edu	37	1	19612477	19612477	+	Missense_Mutation	SNP	C	C	T	rs2231198	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	32	222	0	0.242424	0	C|0.603;T|0.397	0.397	strong	.	AKR7A3	30	.	NM_012067	exon3	c.G412A	p.V138M	GCTCCACGAACTT	.	PASS	Atlas-SNP
ZNF184	7738	hgsc.bcm.edu	37	6	27425185	27425185	+	Missense_Mutation	SNP	C	C	A	rs1883216	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	62	129	1	0.558559	0.00775194	C|0.387;A|0.613	0.613	strong	ZNF184,NS,carcinoma,+2,1	ZNF184	89	1	NM_007149	exon4	c.G79T	p.A27S	TCACCGCTTCCTG	.	scavenged	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41383137	41383137	+	Silent	SNP	C	C	T	rs148915421	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	67	243	1	0.387283	0.00411523	C|0.978;T|0.022	0.022	strong	CYP2A7,NS,carcinoma,-1,1	CYP2A7	71	1	NM_000764	exon7	c.G1119A	p.R373R	TTTAACCCTGCGG	.	scavenged	Atlas-SNP
KCNA6	3742	hgsc.bcm.edu	37	12	4920767	4920767	+	Silent	SNP	T	T	C	rs34642709	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	32	82	0	0.484848	0	T|0.987;C|0.013	0.013	strong	.	KCNA6	122	.	NM_002235	exon1	c.T1560C	p.Y520Y	GGCCTATGCAGAG	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43557698	43557698	+	Missense_Mutation	SNP	A	A	C	rs3819142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	59	175	0	0.364198	0	A|0.810;C|0.190	0.190	strong	.	UMODL1	186	.	NM_173568	exon21	c.A4309C	p.N1437H	CAGTCCAACAACT	.	PASS	Atlas-SNP
SCYL2	55681	hgsc.bcm.edu	37	12	100709420	100709420	+	Silent	SNP	C	C	T	rs10860577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	75	175	0	0.480769	0	C|0.853;T|0.147	0.147	strong	SCYL2,colon,carcinoma,-1,1	SCYL2	99	1	NM_017988	exon9	c.C1180T	p.L394L	AATGTTCTACTTA	.	PASS	Atlas-SNP
TOPAZ1	375337	hgsc.bcm.edu	37	3	44283817	44283817	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	2	144	0	0.012987	0	.	.	none	C3orf77_ENST00000309765,NS,carcinoma,-1,3	.	.	3	NM_001145030	exon1	c.C272T	p.P91L	TGAGCCCGTCAGA	.	scavenged	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489753	32489753	+	Missense_Mutation	SNP	C	C	T	rs41544215	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	25	2	0	0.925926	0	T|0.078;C|0.922	0.078	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.G299A	p.R100K	GCGCGCCTGTCTT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152191082	152191082	+	Missense_Mutation	SNP	C	C	G	rs139947063	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	100	166	0	0.436681	0	A|0.002;C|0.998;G|0.000	0.000	strong	.	HRNR	403	.	NM_001009931	exon3	c.G3023C	p.S1008T	CTAGGGCTAGGAG	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33605300	33605300	+	Missense_Mutation	SNP	A	A	G	rs10416265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	44	113	0	0.411215	0	A|0.517;G|0.483	0.483	strong	.	GPATCH1	79	.	NM_018025	exon15	c.A2171G	p.H724R	AAGAGCATGCACC	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149245754	149245754	+	Silent	SNP	A	A	G	rs17110644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	32	120	0	0.359551	0	A|0.946;G|0.054	0.054	strong	.	PDE6A	98	.	NM_000440	exon20	c.T2337C	p.F779F	GCAAACAAAGTCA	.	PASS	Atlas-SNP
PLEKHG2	64857	hgsc.bcm.edu	37	19	39905888	39905888	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	2	85	0	0.025	0	.	.	none	PLEKHG2_ENST00000409794,colon,carcinoma,+1,2	PLEKHG2	329	2	NM_022835	exon3	c.C366T	p.R122R	CCTCCGCAGCATC	.	scavenged	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9315209	9315209	+	Silent	SNP	A	A	G	rs10771381	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	84	93	0	0.988235	0	A|0.580;G|0.420	0.420	strong	.	PZP	422	.	NM_002864	exon22	c.T2772C	p.S924S	GGTCATAGAACTG	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125453115	125453115	+	Missense_Mutation	SNP	C	C	T	rs11057939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	15	48	0	0.326087	0	C|0.906;T|0.094	0.094	strong	.	DHX37	114	.	NM_032656	exon10	c.G1373A	p.R458Q	ACCTTCCGGAAGC	.	PASS	Atlas-SNP
JAKMIP3	282973	hgsc.bcm.edu	37	10	133950642	133950642	+	Silent	SNP	T	T	C	rs75996870	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	79	199	0	0.487654	0	T|0.912;C|0.088	0.088	strong	.	JAKMIP3	69	.	NM_001105521	exon6	c.T1236C	p.D412D	CATAGATGAACTG	.	PASS	Atlas-SNP
FAM98C	147965	hgsc.bcm.edu	37	19	38893856	38893856	+	Silent	SNP	G	G	C	rs3745957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	28	90	0	0.383562	0	G|0.900;C|0.100	0.100	strong	.	FAM98C	39	.	NM_174905	exon1	c.G63C	p.L21L	GGCTCTGGGGTAA	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50532588	50532588	+	Missense_Mutation	SNP	C	C	G	rs10857469	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	17	84	0	0.288136	0	C|0.906;G|0.094	0.094	strong	.	C10orf71	179	.	NM_001135196	exon3	c.C1998G	p.H666Q	GACCCACCAGCTA	.	PASS	Atlas-SNP
MADD	8567	hgsc.bcm.edu	37	11	47306585	47306585	+	Missense_Mutation	SNP	G	G	A	rs1051006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	47	70	0	0.552941	0	G|0.733;A|0.267	0.267	strong	.	MADD	172	.	NM_130474	exon13	c.G2251A	p.V751M	TCGAACGTGGACA	.	PASS	Atlas-SNP
MYOF	26509	hgsc.bcm.edu	37	10	95093619	95093619	+	Missense_Mutation	SNP	G	G	A	rs61861290	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75	20	153	1	0.266667	0.00653595	G|0.988;A|0.012	0.012	strong	MYOF,trunk,malignant_melanoma,0,1	MYOF	177	1	NM_013451	exon42	c.C4615T	p.P1539S	GTCTGGGAGGGGC	.	scavenged	Atlas-SNP
MLXIP	22877	hgsc.bcm.edu	37	12	122618131	122618131	+	Silent	SNP	A	A	G	rs36045144	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	62	107	0	0.53913	0	A|0.784;G|0.216;T|0.000	0.216	strong	.	MLXIP	46	.	NM_014938	exon9	c.A1329G	p.P443P	CGCCCCACCGCCC	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296423	39296423	+	Missense_Mutation	SNP	C	C	T	rs349790	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	11	171	0	0.0723684	0	C|0.988;T|0.012	0.012	strong	KRTAP4-6,NS,carcinoma,0,2	KRTAP4-6	46	2	NM_030976	exon1	c.G317A	p.R106H	CTGGGACGGCAGC	.	scavenged	Atlas-SNP
QPCTL	54814	hgsc.bcm.edu	37	19	46202131	46202131	+	Missense_Mutation	SNP	C	C	T	rs145016874	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	45	113	0	0.48913	0	C|0.999;T|0.001	0.001	strong	.	QPCTL	24	.	NM_017659	exon5	c.C859T	p.R287C	ACGGTCCGCTGGT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	690	58	801	61	0.084058	0.0761548	C|0.500;T|0.500	0.500	weak	MUC6,NS,carcinoma,-1,1	MUC6	408	1	NM_005961	exon31	c.G5733A	p.T1911T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
ERCC6L2	375748	hgsc.bcm.edu	37	9	98691137	98691137	+	Missense_Mutation	SNP	T	T	C	rs2274654	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	21	47	0	0.538462	0	T|0.816;C|0.184	0.184	strong	.	.	.	.	NM_001010895	exon11	c.T1775C	p.V592A	GCCTTGTCTCTAC	.	PASS	Atlas-SNP
ARHGEF37	389337	hgsc.bcm.edu	37	5	149008467	149008467	+	Missense_Mutation	SNP	C	C	A	rs3733662	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	26	90	0	0.393939	0	C|0.839;A|0.161	0.161	strong	.	ARHGEF37	45	.	NM_001001669	exon12	c.C1756A	p.P586T	AAAGACCCCCGAT	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102562700	102562700	+	Missense_Mutation	SNP	C	C	T	rs2509010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	34	107	0	0.25	0	C|0.800;T|0.200	0.200	strong	.	MMP27	84	.	NM_022122	exon10	c.G1339A	p.D447N	TAATGTCGTATTC	.	PASS	Atlas-SNP
C17orf77	146723	hgsc.bcm.edu	37	17	72588806	72588806	+	Nonsense_Mutation	SNP	C	C	A	rs545652	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133	75	121	0	0.56391	0	C|0.751;A|0.249	0.249	strong	C17orf77,colon,carcinoma,0,1	C17orf77	31	1	NM_152460	exon3	c.C621A	p.C207X	CCCATGCCCCAGG	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	64062132	64062132	+	Silent	SNP	G	G	A	rs11175111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	18	78	0	0.28125	0	G|0.957;A|0.043	0.043	strong	.	DPY19L2	97	.	NM_173812	exon1	c.C42T	p.S14S	GCGGCCGGAAGAT	.	PASS	Atlas-SNP
F2RL3	9002	hgsc.bcm.edu	37	19	17000632	17000632	+	Missense_Mutation	SNP	G	G	A	rs773902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20	8	27	0	0.4	0	G|0.677;A|0.323	0.323	strong	.	F2RL3	20	.	NM_003950	exon2	c.G358A	p.A120T	CTCGCGGCTGCTG	.	PASS	Atlas-SNP
ASXL1	171023	hgsc.bcm.edu	37	20	31024274	31024274	+	Silent	SNP	T	T	C	rs4911231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	29	53	0	0.508772	0	T|0.653;C|0.347	0.347	strong	.	ASXL1	1114	.	NM_015338	exon12	c.T3759C	p.S1253S	GGACAGTAATTCA	.	PASS	Atlas-SNP
PLEKHG1	57480	hgsc.bcm.edu	37	6	151121915	151121915	+	Silent	SNP	G	G	A	rs2073061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	87	153	0	0.524096	0	G|0.393;A|0.607	0.607	strong	PLEKHG1,NS,adenoma,0,1	PLEKHG1	97	1	NM_001029884	exon7	c.G690A	p.E230E	CAGGGAGCGTCAG	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238449023	238449023	+	Silent	SNP	T	T	C	rs3817363	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	46	134	0	0.308725	0	T|0.874;C|0.126	0.126	strong	MLPH,NS,carcinoma,0,2	MLPH	41	2	NM_024101	exon10	c.T1137C	p.D379D	GGCCGATGTAGAG	.	PASS	Atlas-SNP
POLD1	5424	hgsc.bcm.edu	37	19	50905074	50905074	+	Missense_Mutation	SNP	G	G	A	rs1726801	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	50	135	0	0.60241	0	G|0.838;A|0.162	0.162	strong	.	POLD1	174	.	NM_002691	exon4	c.G356A	p.R119H	CATCCCGCGGCTC	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42526775	42526775	+	Missense_Mutation	SNP	C	C	T	rs72552268	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	289	154	308	1	0.532872	0.00324675	C|0.996;T|0.004	0.004	strong	.	CYP2D6	104	.	NM_000106	exon1	c.G19A	p.V7M	GGGGCACCAGTGC	.	PASS	Atlas-SNP
CDH7	1005	hgsc.bcm.edu	37	18	63511176	63511176	+	Silent	SNP	T	T	C	rs2306675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	276	123	297	0	0.445652	0	T|0.756;C|0.244	0.244	strong	CDH7,NS,carcinoma,0,1	CDH7	362	1	NM_004361	exon7	c.T1110C	p.D370D	GGAAGATGTAGAT	.	PASS	Atlas-SNP
PLIN3	10226	hgsc.bcm.edu	37	19	4847868	4847868	+	Silent	SNP	G	G	A	rs10406652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	69	162	0	0.489362	0	G|0.867;A|0.132	0.132	strong	.	PLIN3	36	.	NM_001164189	exon6	c.C669T	p.V223V	GGACGCGACGTCA	.	PASS	Atlas-SNP
TMC7	79905	hgsc.bcm.edu	37	16	19041595	19041595	+	Missense_Mutation	SNP	G	G	A	rs4072393	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	144	176	0	0.96	0	G|0.443;A|0.557	0.557	strong	.	TMC7	75	.	NM_024847	exon6	c.G761A	p.G254E	TTGATGGGGTGAA	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104335682	104335682	+	Missense_Mutation	SNP	C	C	T	rs3739722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	233	118	279	1	0.506438	0.00358423	C|0.831;T|0.169	0.169	strong	.	GRIN3A	186	.	NM_133445	exon9	c.G3122A	p.R1041Q	TGGATCCGGATGC	.	PASS	Atlas-SNP
ACTR3B	57180	hgsc.bcm.edu	37	7	152511706	152511706	+	Silent	SNP	A	A	G	rs35293703	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	356	4	519	0	0.011236	0	.	.	alt	ACTR3B,brain,glioma,0,13	ACTR3B	50	13	NM_020445	exon5	c.A408G	p.V136V	TAACGTACCAGGA	.	scavenged	Atlas-SNP
HIST1H2AA	221613	hgsc.bcm.edu	37	6	25726621	25726621	+	Silent	SNP	C	C	T	rs9467583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	32	93	0	0.329897	0	C|0.749;T|0.251	0.251	strong	HIST1H2AA,NS,malignant_melanoma,0,3	HIST1H2AA	34	3	NM_170745	exon1	c.G135A	p.G45G	GCCTGCCCCTATC	.	PASS	Atlas-SNP
SOAT1	6646	hgsc.bcm.edu	37	1	179320578	179320578	+	Missense_Mutation	SNP	A	A	G	rs13306731	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	309	261	2	0.977848	0.00766284	A|0.904;G|0.095	0.095	strong	.	SOAT1	53	.	NM_003101	exon15	c.A1577G	p.Q526R	CACGTCAGCACTG	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14991643	14991643	+	Silent	SNP	G	G	A	rs10401818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	189	171	1	0.994737	0.00584795	G|0.709;A|0.291	0.291	strong	.	OR7A17	37	.	NM_030901	exon1	c.C525T	p.P175P	AAAGTGGGGGATT	.	PASS	Atlas-SNP
HNRNPA2B1	3181	hgsc.bcm.edu	37	7	26236961	26236961	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	292	3	209	0	0.010274	0	.	.	none	HNRNPA2B1_ENST00000354667,NS,carcinoma,0,2	HNRNPA2B1	70	2	NM_031243	exon4	c.G274A	p.E92K	TTGGCTCAACTAC	.	scavenged	Atlas-SNP
CAPN10	11132	hgsc.bcm.edu	37	2	241531479	241531479	+	Silent	SNP	A	A	G	rs3792269	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	106	216	0	0.464912	0	A|0.886;G|0.114	0.114	strong	.	CAPN10	105	.	NM_023085	exon4	c.A600G	p.P200P	CAGGCCAGGCCGC	.	PASS	Atlas-SNP
SRP14	6727	hgsc.bcm.edu	37	15	40330518	40330518	+	Silent	SNP	T	T	G	rs1059395	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	22	129	0	0.392857	0	T|0.867;G|0.133	0.133	strong	.	SRP14	11	.	NM_003134	exon3	c.A175C	p.R59R	TAGCTCTTAACAG	.	PASS	Atlas-SNP
EDDM3A	10876	hgsc.bcm.edu	37	14	21215923	21215923	+	Missense_Mutation	SNP	G	G	T	rs34552133	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	261	161	183	0	0.616858	0	T|0.100;G|0.900;A|0.000	0.100	strong	.	EDDM3A	15	.	NM_006683	exon2	c.G184T	p.G62C	CTGAAAGGCAAGA	.	PASS	Atlas-SNP
KCNQ3	3786	hgsc.bcm.edu	37	8	133192521	133192521	+	Silent	SNP	A	A	G	rs41272389	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	17	64	0	0.223684	0	A|0.951;G|0.049	0.049	strong	.	KCNQ3	164	.	NM_004519	exon4	c.T660C	p.N220N	CAGAACATTGCCT	.	PASS	Atlas-SNP
PEAR1	375033	hgsc.bcm.edu	37	1	156882996	156882996	+	Silent	SNP	G	G	C	rs822441	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	58	147	1	0.284314	0.00680272	G|0.714;C|0.285	0.285	strong	PEAR1,NS,carcinoma,+2,1	PEAR1	118	1	NM_001080471	exon19	c.G2433C	p.P811P	CCCTCCGAGCTAC	.	scavenged	Atlas-SNP
RBMS3	27303	hgsc.bcm.edu	37	3	30032626	30032626	+	Silent	SNP	C	C	G	rs114278295	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	294	127	302	0	0.431973	0	C|0.982;G|0.018	0.018	strong	.	RBMS3	62	.	NM_001003793	exon14	c.C1233G	p.T411T	GGACACCAGTGGT	.	PASS	Atlas-SNP
CFTR	1080	hgsc.bcm.edu	37	7	117199533	117199533	+	Missense_Mutation	SNP	G	G	A	rs213950	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	58	66	0	1	0	G|0.436;A|0.564	0.564	strong	.	CFTR	171	.	NM_000492	exon11	c.G1408A	p.V470M	CTAATGGTGATTA	.	PASS	Atlas-SNP
RPL10L	140801	hgsc.bcm.edu	37	14	47120423	47120423	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	2	111	0	0.0116959	0	.	.	none	RPL10L,bladder,carcinoma,+2,1	RPL10L	64	1	NM_080746	exon1	c.T517C	p.F173L	TCGTGAAGCCCCA	.	scavenged	Atlas-SNP
C7orf72	100130988	hgsc.bcm.edu	37	7	50180972	50180972	+	Missense_Mutation	SNP	C	C	T	rs1456908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	233	232	224	1	0.995708	0.00446429	C|0.671;T|0.329	0.329	strong	.	C7orf72	26	.	NM_001161834	exon7	c.C1073T	p.T358I	TTTATACAAACAC	.	PASS	Atlas-SNP
POLN	353497	hgsc.bcm.edu	37	4	2194946	2194946	+	Missense_Mutation	SNP	C	C	T	rs10011549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	83	219	0	0.466292	0	C|0.708;T|0.292	0.292	strong	.	POLN	82	.	NM_181808	exon5	c.G1006A	p.G336S	AACTGCCATCATT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100675376	100675376	+	Missense_Mutation	SNP	A	A	C	rs10229731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210	206	126	1	0.980952	0.00793651	A|0.825;C|0.175	0.175	strong	.	MUC17	804	.	NM_001040105	exon3	c.A679C	p.K227Q	ACCATGAAGGTGG	.	PASS	Atlas-SNP
SLC26A1	10861	hgsc.bcm.edu	37	4	983868	983868	+	Missense_Mutation	SNP	G	G	A	rs201572215	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	2	95	0	0.0273973	0	G|1.000;A|0.000	0.000	strong	SLC26A1,colon,carcinoma,0,2	SLC26A1	44	2	NM_022042	exon3	c.C859T	p.R287C	TCAGGCGGTGTCG	.	scavenged	Atlas-SNP
MFSD1	64747	hgsc.bcm.edu	37	3	158538056	158538056	+	Silent	SNP	T	T	C	rs4680469	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	113	246	0	0.515982	0	T|0.820;C|0.180	0.180	strong	.	MFSD1	88	.	NM_022736	exon9	c.T951C	p.L317L	GTGGCTTATATTT	.	PASS	Atlas-SNP
LY6H	4062	hgsc.bcm.edu	37	8	144239859	144239859	+	Silent	SNP	A	A	G	rs10109061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	67	106	1	0.57265	0.00943396	A|0.509;G|0.491	0.491	strong	LY6H,NS,carcinoma,0,1	LY6H	12	1	NM_001135655	exon4	c.T294C	p.C98C	GAAGTCACAGGAG	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179440955	179440955	+	Missense_Mutation	SNP	C	C	T	rs190421400	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	3	128	0	0.0238095	0	C|1.000;T|0.000	0.000	strong	TTN_ENST00000359218,NS,carcinoma,0,4	TTN	18412	4	NM_001267550	exon326	c.G69904A	p.V23302I	GAACAACGAACTG	.	scavenged	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3267108	3267108	+	Silent	SNP	A	A	G	rs190257069	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	38	90	0	0.372549	0	A|0.999;G|0.001	0.001	strong	.	CSMD1	1469	.	NM_033225	exon13	c.T1581C	p.C527C	ATCCCCACACCCT	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79057989	79057989	+	Missense_Mutation	SNP	C	C	T	rs200769684	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	19	144	1	0.171171	0.00694444	C|0.999;T|0.001	0.001	weak	ADAMTS7,face,carcinoma,0,3	ADAMTS7	142	3	NM_014272	exon19	c.G4264A	p.E1422K	TTGCCTCGCTCCA	.	scavenged	Atlas-SNP
MR1	3140	hgsc.bcm.edu	37	1	181018236	181018236	+	Missense_Mutation	SNP	A	A	G	rs2236410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	362	140	294	1	0.38674	0.00340136	A|0.833;G|0.167	0.167	strong	MR1,NS,carcinoma,0,1	MR1	46	1	NM_001195035	exon3	c.A116G	p.H39R	CCATCCATGGGGT	.	PASS	Atlas-SNP
TTI2	80185	hgsc.bcm.edu	37	8	33369994	33369994	+	Silent	SNP	A	A	G	rs3098657	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	69	121	0	0.547619	0	A|0.369;G|0.631	0.631	strong	.	.	.	.	NM_001265581	exon2	c.T138C	p.N46N	TTTTACATTGCCT	.	PASS	Atlas-SNP
MYO19	80179	hgsc.bcm.edu	37	17	34884029	34884029	+	Missense_Mutation	SNP	T	T	C	rs61738887	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	30	87	0	0.422535	0	T|0.931;C|0.069	0.069	strong	.	MYO19	130	.	NM_001163735	exon5	c.A17G	p.N6S	TGGCCATTGACCT	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100074446	100074446	+	Silent	SNP	C	C	T	rs3747504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	42	101	1	0.424242	0.00990099	C|0.766;T|0.234	0.234	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon4	c.C444T	p.I148I	CACCATCGCTGCC	.	scavenged	Atlas-SNP
SEC14L6	730005	hgsc.bcm.edu	37	22	30921371	30921371	+	Silent	SNP	T	T	C	rs6518698	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	203	225	1	0.995098	0.00444444	C|0.290;N|0.001	0.290	strong	.	SEC14L6	6	.	NM_001193336	exon11	c.A1047G	p.E349E	CCCATCTTCAGGC	.	PASS	Atlas-SNP
KIAA0895	23366	hgsc.bcm.edu	37	7	36366404	36366404	+	Missense_Mutation	SNP	C	C	T	rs191576648	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	100	171	0	0.406504	0	C|1.000;T|0.000	0.000	strong	.	KIAA0895	89	.	NM_001100425	exon7	c.G1528A	p.E510K	TCAGTTCATTCAC	.	PASS	Atlas-SNP
OXTR	5021	hgsc.bcm.edu	37	3	8809184	8809184	+	Silent	SNP	G	G	A	rs237902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	70	55	0	0.7	0	G|0.714;A|0.286	0.286	strong	OXTR,NS,carcinoma,0,1	OXTR	31	1	NM_000916	exon3	c.C690T	p.N230N	CCGCAAGTTCTGC	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38766701	38766701	+	Silent	SNP	C	C	T	rs6791171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	57	163	0	0.365385	0	C|0.861;T|0.139	0.139	strong	.	SCN10A	359	.	NM_006514	exon17	c.G3192A	p.T1064T	TTTCCACGTCTCA	.	PASS	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	37	5	35654711	35654711	+	Silent	SNP	C	C	T	rs2270558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	136	154	0	0.978417	0	C|0.379;A|0.004	.	strong	SPEF2,NS,carcinoma,+2,1	SPEF2	324	1	NM_024867	exon7	c.C861T	p.D287D	AGATGACGAGTAC	.	PASS	Atlas-SNP
SFTA2	389376	hgsc.bcm.edu	37	6	30899571	30899571	+	Silent	SNP	C	C	T	rs2286656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	28	74	0	0.311111	0	C|0.811;T|0.189	0.189	strong	.	SFTA2	6	.	NM_205854	exon2	c.G63A	p.G21G	ACCCGGCCCTGCG	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	rs62640905	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	43	76	0	0.811321	0	T|0.985;C|0.015	0.015	strong	.	OSGIN1	33	.	NM_182981	exon6	c.T1370C	p.V457A	GGTTTGTGCAGGG	.	PASS	Atlas-SNP
COPZ1	22818	hgsc.bcm.edu	37	12	54734289	54734289	+	Missense_Mutation	SNP	A	A	G	rs11170877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	73	181	0	0.470968	0	A|0.825;G|0.175	0.175	strong	.	COPZ1	10	.	NM_001271736	exon2	c.A1G	p.M1V	GTGGTGATGGGAG	.	PASS	Atlas-SNP
GAB3	139716	hgsc.bcm.edu	37	X	153925443	153925443	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	4	158	0	0.0540541	0	.	.	none	.	GAB3	73	.	NM_001081573	exon7	c.A1391G	p.E464G	GCATGTTCCCGGA	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50582626	50582626	+	Missense_Mutation	SNP	A	A	G	rs2272837	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	50	120	0	0.462963	0	A|0.738;G|0.262	0.262	strong	.	MOV10L1	238	.	NM_018995	exon18	c.A2459G	p.Q820R	TGCTACAGCCGGC	.	PASS	Atlas-SNP
AVPR1B	553	hgsc.bcm.edu	37	1	206230986	206230986	+	Silent	SNP	G	G	A	rs28676508	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	40	43	1	0.615385	0.0232558	G|0.775;A|0.225	0.225	strong	AVPR1B,rectum,carcinoma,0,1	AVPR1B	47	1	NM_000707	exon2	c.G1119A	p.S373S	CCTCTCGAGCCGC	.	scavenged	Atlas-SNP
TNK1	8711	hgsc.bcm.edu	37	17	7286326	7286326	+	Silent	SNP	T	T	A	rs1554948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	110	108	0	1	0	T|0.623;A|0.377	0.377	strong	.	TNK1	31	.	NM_003985	exon2	c.T81A	p.L27L	CATCCTTGAGGAG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170163816	170163816	+	Silent	SNP	G	G	T	rs34104660	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	44	110	0	0.427184	0	G|0.934;T|0.066	0.066	strong	.	LRP2	751	.	NM_004525	exon4	c.C402A	p.P134P	TCCATCGGGGCAG	.	PASS	Atlas-SNP
EPHA8	2046	hgsc.bcm.edu	37	1	22919904	22919904	+	Silent	SNP	C	C	T	rs209696	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	34	178	0	0.237762	0	C|0.706;T|0.294	0.294	strong	.	EPHA8	221	.	NM_020526	exon6	c.C1401T	p.N467N	GCCGAACGGCATC	.	PASS	Atlas-SNP
MYO16	23026	hgsc.bcm.edu	37	13	109777503	109777503	+	Missense_Mutation	SNP	A	A	G	rs157024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	301	135	292	0	0.448505	0	A|0.869;G|0.131	0.131	strong	.	MYO16	285	.	NM_001198950	exon30	c.A3579G	p.I1193M	GAGAATAAGCATC	.	PASS	Atlas-SNP
LATS1	9113	hgsc.bcm.edu	37	6	149983216	149983216	+	Silent	SNP	G	G	A	rs3924871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	57	145	0	0.431818	0	G|0.512;A|0.488	0.488	strong	.	LATS1	241	.	NM_004690	exon8	c.C3042T	p.D1014D	GGAGAAGTCAATT	.	PASS	Atlas-SNP
KIAA1586	57691	hgsc.bcm.edu	37	6	56919443	56919443	+	Missense_Mutation	SNP	A	A	G	rs61740375	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	52	126	0	0.444444	0	A|0.917;G|0.083	0.083	strong	.	KIAA1586	59	.	NM_020931	exon4	c.A2146G	p.I716V	ATGAACATAATTT	.	PASS	Atlas-SNP
BCL7A	605	hgsc.bcm.edu	37	12	122497001	122497001	+	Silent	SNP	T	T	C	rs28629903	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	106	90	0	0.963636	0	T|0.501;C|0.499	0.499	strong	.	BCL7A	31	.	NM_020993	exon6	c.T628C	p.L210L	AAGGATTTGGAAG	.	PASS	Atlas-SNP
CYP27A1	1593	hgsc.bcm.edu	37	2	219678877	219678877	+	Missense_Mutation	SNP	C	C	T	rs41272687	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	62	126	0	0.712644	0	C|0.985;T|0.015	0.015	strong	.	CYP27A1	52	.	NM_000784	exon6	c.C1151T	p.P384L	ACATGCCGTTGCT	.	PASS	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76069881	76069881	+	Missense_Mutation	SNP	A	A	G	rs2906998	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	335	31	226	0	0.0925373	0	A|0.885;G|0.115	0.115	strong	.	ZP3	32	.	NM_001110354	exon7	c.A1013G	p.H338R	AGCCTCATGTCAT	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587185	15587185	+	Missense_Mutation	SNP	C	C	T	rs733731	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	254	112	259	0	0.440945	0	C|0.637;T|0.363	0.363	strong	PGLYRP2_ENST00000292609,NS,carcinoma,0,4	PGLYRP2	116	4	NM_052890	exon2	c.G296A	p.R99Q	TCATGTCGGGCCA	.	PASS	Atlas-SNP
DNTTIP2	30836	hgsc.bcm.edu	37	1	94342564	94342564	+	Missense_Mutation	SNP	C	C	A	rs3747965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	81	112	1	0.964286	0.00892857	C|0.661;A|0.339	0.339	strong	.	DNTTIP2	59	.	NM_014597	exon2	c.G927T	p.E309D	TTTCCCCTCATCT	.	PASS	Atlas-SNP
HAS1	3036	hgsc.bcm.edu	37	19	52220351	52220351	+	Silent	SNP	G	G	A	rs11084111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	32	81	0	0.421053	0	G|0.855;A|0.145	0.145	strong	.	HAS1	61	.	NM_001523	exon3	c.C798T	p.D266D	CCGCACGTCCCCA	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41553928	41553928	+	Silent	SNP	C	C	G	rs504574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	59	115	0	0.614583	0	C|0.627;G|0.373	0.373	strong	ANK1_ENST00000265709,NS,carcinoma,0,4	ANK1	497	4	NM_001142446	exon27	c.G3036C	p.L1012L	GCTGGCCAGGCCC	.	PASS	Atlas-SNP
GFAP	2670	hgsc.bcm.edu	37	17	42992714	42992714	+	Silent	SNP	C	C	T	rs2229011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	53	132	0	0.486239	0	C|0.969;T|0.031	0.031	strong	.	GFAP	88	.	NM_001131019	exon1	c.G141A	p.P47P	CCGGGTCGGGAGT	.	PASS	Atlas-SNP
LILRA2	11027	hgsc.bcm.edu	37	19	55086873	55086873	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	7	296	5	0.0282258	0.0168919	.	.	none	LILRA2,NS,carcinoma,0,1	LILRA2	99	1	NM_001130917	exon5	c.G806A	p.W269X	CTGGTTGGCAGCC	.	scavenged	Atlas-SNP
NDST3	9348	hgsc.bcm.edu	37	4	118975189	118975189	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	60	224	1	0.487805	0.00446429	.	.	none	.	NDST3	107	.	NM_004784	exon2	c.G124T	p.E42X	GAAAATGAACTCT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	rs112900956	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	40	89	0	0.615385	0	G|0.994;A|0.006	0.006	strong	MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	NM_001130065	exon22	c.G3838A	p.G1280S	CCATGTGGCAGCC	.	PASS	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92537379	92537379	+	Missense_Mutation	SNP	T	T	C	rs12896583	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	53	61	0	0.697368	0	T|1.000;|0.000	.	strong	ATXN3,NS,carcinoma,0,1	ATXN3	46	1	NM_001164778	exon6	c.A406G	p.T136A	CTGCTGTTGCTGC	.	PASS	Atlas-SNP
ZNF618	114991	hgsc.bcm.edu	37	9	116810204	116810204	+	Silent	SNP	G	G	A	rs12378906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	56	126	0	0.424242	0	G|0.927;A|0.073	0.073	strong	.	ZNF618	184	.	NM_133374	exon13	c.G999A	p.Q333Q	CAACCAGTCCCGA	.	PASS	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	37	5	9108333	9108333	+	Silent	SNP	C	C	T	rs34874986	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211	105	216	0	0.49763	0	C|0.879;T|0.121	0.121	strong	SEMA5A,NS,carcinoma,-2,1	SEMA5A	236	1	NM_003966	exon16	c.G1992A	p.R664R	TGTGCACCGTTCC	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152286032	152286032	+	Missense_Mutation	SNP	C	C	T	rs11588170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	364	134	288	0	0.368132	0	C|0.839;T|0.161	0.161	strong	.	FLG	900	.	NM_002016	exon3	c.G1330A	p.G444R	TCAGCCCAGCCTT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489766	32489766	+	Missense_Mutation	SNP	A	A	T	rs41562819	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	28	2	0	0.875	0	G|0.474;A|0.526	.	strong	HLA-DRB5,brain,glioma,0,2	HLA-DRB5	31	2	NM_002125	exon2	c.T286A	p.F96I	CCAGGAAGTCCTT	.	PASS	Atlas-SNP
AURKC	6795	hgsc.bcm.edu	37	19	57742489	57742489	+	Splice_Site	SNP	C	C	T	rs58264281	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	35	202	1	0.897436	0.00495049	C|0.239;T|0.761	0.761	strong	.	AURKC	97	.	.	.	.	.	GTGAGGCTGCAGG	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36238357	36238357	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	3	246	0	0.0131004	0	.	.	none	PNPLA1_ENST00000394571,NS,carcinoma,0,2	PNPLA1	92	2	NM_001145717	exon1	c.C121T	p.R41W	GCCCCCCGGATGC	.	scavenged	Atlas-SNP
NDUFAF1	51103	hgsc.bcm.edu	37	15	41679685	41679685	+	Missense_Mutation	SNP	G	G	C	rs12900702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	27	146	0	0.27	0	G|0.873;C|0.127	0.127	strong	.	NDUFAF1	39	.	NM_016013	exon5	c.C941G	p.A314G	TCATAGGCAAATT	.	PASS	Atlas-SNP
SIDT2	51092	hgsc.bcm.edu	37	11	117052532	117052532	+	Silent	SNP	C	C	A	rs61729990	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	54	98	0	0.295082	0	C|0.991;A|0.009	0.009	strong	SIDT2,colon,carcinoma,+1,1	SIDT2	82	1	NM_001040455	exon3	c.C315A	p.R105R	TCAGCGCAAGTAC	.	PASS	Atlas-SNP
REXO4	57109	hgsc.bcm.edu	37	9	136279935	136279935	+	Missense_Mutation	SNP	C	C	T	rs6597630	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	101	213	1	0.531579	0.00469484	C|0.889;T|0.111	0.111	strong	.	REXO4	27	.	NM_020385	exon2	c.G422A	p.R141K	GGCGCCCTCCTGT	.	PASS	Atlas-SNP
ZNF214	7761	hgsc.bcm.edu	37	11	7022360	7022360	+	Missense_Mutation	SNP	A	A	C	rs2239734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	89	184	0	0.514451	0	A|0.909;C|0.091	0.091	strong	.	ZNF214	65	.	NM_013249	exon3	c.T554G	p.I185R	TGAACTATGAGCT	.	PASS	Atlas-SNP
UPF3A	65110	hgsc.bcm.edu	37	13	115047305	115047305	+	Missense_Mutation	SNP	G	G	A	rs3752105	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	50	110	0	0.485437	0	G|0.728;A|0.272	0.272	strong	UPF3A,NS,carcinoma,0,1	UPF3A	47	1	NM_080687	exon1	c.G191A	p.R64K	AGAAGAGGACGGC	.	PASS	Atlas-SNP
ZNF208	7757	hgsc.bcm.edu	37	19	22155918	22155918	+	Missense_Mutation	SNP	T	T	C	rs79937054	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	28	108	0	0.325581	0	T|0.500;C|0.500	0.500	strong	.	ZNF208	817	.	NM_007153	exon4	c.A1918G	p.K640E	ATTCTTTACATTT	.	PASS	Atlas-SNP
RNPEP	6051	hgsc.bcm.edu	37	1	201973565	201973565	+	Missense_Mutation	SNP	G	G	A	rs3820439	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	22	57	0	0.26506	0	G|0.707;A|0.293	0.293	strong	.	RNPEP	39	.	NM_020216	exon10	c.G1735A	p.V579I	CAAATCGTCCTTA	.	PASS	Atlas-SNP
POU4F2	5458	hgsc.bcm.edu	37	4	147561804	147561804	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	3	74	0	0.0545455	0	.	.	none	POU4F2,caecum,carcinoma,+1,1	POU4F2	83	1	NM_004575	exon2	c.C1074T	p.R358R	GAAGCGCTCGCTC	.	scavenged	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136037742	136037742	+	Missense_Mutation	SNP	G	G	A	rs2073924	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	68	195	1	0.465753	0.00512821	G|0.741;A|0.259	0.259	strong	GBGT1,NS,carcinoma,0,1	GBGT1	25	1	NM_021996	exon2	c.C58T	p.L20F	CACTGAGGCTTGT	.	scavenged	Atlas-SNP
SNX32	254122	hgsc.bcm.edu	37	11	65601560	65601560	+	Silent	SNP	G	G	C	rs17854357	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	42	82	0	0.477273	0	G|0.893;C|0.107	0.107	strong	SNX32,NS,carcinoma,0,1	SNX32	46	1	NM_152760	exon1	c.G24C	p.G8G	GGTTGGGAAGGAG	.	PASS	Atlas-SNP
NBPF4	148545	hgsc.bcm.edu	37	1	108771721	108771721	+	Missense_Mutation	SNP	T	T	C	rs79996376	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	435	167	765	1	0.383908	0.00130719	T|0.838;C|0.162	0.162	strong	.	NBPF4	4	.	NM_001143989	exon13	c.A1481G	p.Q494R	TCTGACTGGTGGT	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21607252	21607252	+	Missense_Mutation	SNP	T	T	A	rs142288436		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	11	77	0	0.166667	0	.	.	weak	.	ZNF493	178	.	NM_001076678	exon4	c.T1791A	p.D597E	TACTGATAAGAAA	.	PASS	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	37	8	95538468	95538468	+	Silent	SNP	T	T	C	rs2890827	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	351	133	287	0	0.378917	0	T|0.651;C|0.349	0.349	strong	.	KIAA1429	176	.	NM_015496	exon8	c.A2004G	p.P668P	AGGGTATGGATCA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9059307	9059307	+	Missense_Mutation	SNP	C	C	T	rs12461695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	136	223	0	0.559671	0	C|0.861;T|0.139	0.139	strong	MUC16_ENST00000397910,right_upper_lobe,carcinoma,-1,2	MUC16	4315	2	NM_024690	exon3	c.G28139A	p.G9380D	AAGGTACCCTGCG	.	PASS	Atlas-SNP
FAM25A	643161	hgsc.bcm.edu	37	10	88782084	88782084	+	Silent	SNP	A	A	G	rs3802666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	11	6	25	1	0.545455	0.04	A|0.562;G|0.438	0.438	strong	FAM25A,NS,carcinoma,0,1	FAM25A	4	1	NM_001146157	exon2	c.A87G	p.E29E	CGTGGAAGAAGTG	.	scavenged	Atlas-SNP
GTSE1	51512	hgsc.bcm.edu	37	22	46722531	46722531	+	Silent	SNP	C	C	T	rs9615949	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	38	81	0	0.558824	0	C|0.928;T|0.072	0.072	strong	.	GTSE1	100	.	NM_016426	exon9	c.C1704T	p.P568P	TGAGCCCCGCAAG	.	PASS	Atlas-SNP
EVC2	132884	hgsc.bcm.edu	37	4	5577986	5577986	+	Silent	SNP	G	G	A	rs112554914	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	59	116	0	0.433824	0	G|0.954;A|0.046	0.046	strong	.	EVC2	202	.	NM_147127	exon18	c.C3253T	p.L1085L	GCTCCAGTAATGT	.	PASS	Atlas-SNP
KRT5	3852	hgsc.bcm.edu	37	12	52912906	52912906	+	Silent	SNP	G	G	T	rs641621	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	37	187	0	0.282443	0	T|0.177;G|0.823	0.177	strong	.	KRT5	88	.	NM_000424	exon2	c.C594A	p.T198T	CCACTTGGTGTCC	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77211764	77211764	+	Silent	SNP	T	T	C	rs15350	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	28	107	0	0.518519	0	T|0.727;C|0.273	0.273	strong	.	NFATC1	105	.	NM_172390	exon6	c.T1851C	p.S617S	CCTGTCTGGCCAC	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78178916	78178916	+	Silent	SNP	C	C	T	rs61757652	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	63	125	0	0.520661	0	C|0.928;T|0.072	0.072	strong	.	CARD14	98	.	NM_024110	exon18	c.C2481T	p.P827P	CCGGCCCCGGCCT	.	PASS	Atlas-SNP
LMOD3	56203	hgsc.bcm.edu	37	3	69167851	69167851	+	Missense_Mutation	SNP	G	G	T	rs145387235	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	113	277	0	0.472803	0	G|0.988;T|0.012	0.012	strong	.	LMOD3	92	.	NM_198271	exon2	c.C1655A	p.P552H	CTTACAGGTTTAA	.	PASS	Atlas-SNP
CSF1R	1436	hgsc.bcm.edu	37	5	149457678	149457678	+	Silent	SNP	G	G	A	rs2228422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	267	266	311	3	0.996255	0.0096463	G|0.561;A|0.439	0.439	strong	CSF1R_ENST00000286301,NS,carcinoma,0,1	CSF1R	250	1	NM_005211	exon5	c.C726T	p.T242T	GACCTTGGTGTTG	.	scavenged	Atlas-SNP
SMR3A	26952	hgsc.bcm.edu	37	4	71227877	71227877	+	Silent	SNP	G	G	A	rs62322478	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	723	211	740	0	0.29184	0	G|0.881;A|0.119	0.119	strong	SMR3A,NS,carcinoma,0,1	SMR3A	35	1	NM_012390	exon2	c.G45A	p.A15A	TGCAGCGTGTTTC	.	PASS	Atlas-SNP
GLDC	2731	hgsc.bcm.edu	37	9	6589230	6589230	+	Silent	SNP	C	C	T	rs121964976	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	58	93	0	0.508772	0	T|0.021;G|0.000;C|0.978	0.021	strong	.	GLDC	118	.	NM_000170	exon12	c.G1545A	p.R515R	GCTGGTCCTCTTG	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124094467	124094467	+	Silent	SNP	T	T	C	rs10887135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69	29	73	0	0.42029	0	T|0.943;C|0.057	0.057	strong	.	BTBD16	44	.	NM_144587	exon14	c.T1236C	p.D412D	ACATGATACTACC	.	PASS	Atlas-SNP
ITGA10	8515	hgsc.bcm.edu	37	1	145533175	145533175	+	Silent	SNP	T	T	C	rs11590105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	47	91	0	0.376	0	T|0.762;C|0.238	0.238	strong	.	ITGA10	131	.	NM_003637	exon11	c.T1270C	p.L424L	CCTGCATTGCAGA	.	PASS	Atlas-SNP
LDHAL6A	160287	hgsc.bcm.edu	37	11	18487305	18487305	+	Silent	SNP	C	C	G	rs17851143	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	114	266	0	0.473029	0	C|0.890;G|0.110	0.110	strong	LDHAL6A,NS,adenoma,0,1	LDHAL6A	35	1	NM_144972	exon3	c.C366G	p.P122P	GATTCCCAATATT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910562	29910562	+	Silent	SNP	A	A	C	rs1059418	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	14	52	0	0.25	0	A|0.837;C|0.159;T|0.004	0.159	strong	.	HLA-A	89	.	NM_001242758	exon2	c.A102C	p.T34T	CTTCACATCCGTG	.	PASS	Atlas-SNP
SEMA7A	8482	hgsc.bcm.edu	37	15	74706943	74706943	+	Silent	SNP	G	G	A	rs1046146	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	108	261	0	0.734694	0	G|0.846;A|0.154	0.154	strong	.	SEMA7A	58	.	NM_003612	exon10	c.C1239T	p.V413V	GCGGTGGACGGCC	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34544468	34544468	+	Silent	SNP	C	C	T	rs2290940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	108	229	0	0.666667	0	C|0.821;T|0.179	0.179	strong	.	SLC12A6	205	.	NM_133647	exon9	c.G1236A	p.S412S	TTGACTCGAGTTA	.	PASS	Atlas-SNP
SPECC1L	23384	hgsc.bcm.edu	37	22	24717518	24717518	+	Silent	SNP	G	G	A	rs3747113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	34	52	0	0.557377	0	G|0.777;A|0.223	0.223	strong	SPECC1L,NS,carcinoma,0,1	SPECC1L	85	1	NM_001145468	exon4	c.G570A	p.T190T	TCTCACGCTGGCA	.	PASS	Atlas-SNP
HOXD1	3231	hgsc.bcm.edu	37	2	177054769	177054769	+	Missense_Mutation	SNP	G	G	A	rs6710142	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	157	164	0	0.96319	0	G|0.768;A|0.232	0.232	strong	.	HOXD1	33	.	NM_024501	exon2	c.G886A	p.A296T	GCCACGGCCATTC	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs28583670		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	480	8	608	10	0.0166667	0.0164474	.	.	weak	ENSG00000188219,NS,carcinoma,-1,1	.	.	1	NM_001083538	exon15	c.C2656A	p.P886T	GAACTGCCTGACT	.	scavenged	Atlas-SNP
RGR	5995	hgsc.bcm.edu	37	10	86012713	86012713	+	Silent	SNP	C	C	T	rs1042454	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	15	110	1	0.245902	0.00909091	C|0.502;T|0.498	0.498	strong	RGR,NS,adenoma,0,2	RGR	42	2	NM_002921	exon4	c.C471T	p.Y157Y	TCACTACGACTAT	.	scavenged	Atlas-SNP
C20orf111	51526	hgsc.bcm.edu	37	20	42826379	42826379	+	Silent	SNP	C	C	T	rs11274	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24	24	40	0	1	0	C|0.685;N|0.000	.	strong	.	C20orf111	28	.	NM_016470	exon4	c.G192A	p.G64G	TGTAGACCTAAAG	.	PASS	Atlas-SNP
SNTG2	54221	hgsc.bcm.edu	37	2	1168781	1168781	+	Missense_Mutation	SNP	C	C	A	rs28505970	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	51	96	2	0.515152	0.0208333	C|0.822;A|0.178	0.178	strong	SNTG2,NS,carcinoma,0,1	SNTG2	125	1	NM_018968	exon8	c.C503A	p.S168Y	CAGGGTCCCCAGG	.	scavenged	Atlas-SNP
LRRC71	149499	hgsc.bcm.edu	37	1	156902222	156902222	+	Missense_Mutation	SNP	G	G	A	rs12119908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	171	126	2	0.971591	0.015873	G|0.784;A|0.216	0.216	strong	LRRC71,caecum,carcinoma,0,1	LRRC71	33	1	NM_144702	exon14	c.G1448A	p.R483H	GGAACCGCATCAC	.	scavenged	Atlas-SNP
RFWD3	55159	hgsc.bcm.edu	37	16	74664743	74664743	+	Missense_Mutation	SNP	T	T	C	rs7193541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	90	120	1	0.857143	0.00833333	T|0.562;C|0.438	0.438	strong	RFWD3,NS,carcinoma,0,1	RFWD3	49	1	NM_018124	exon10	c.A1690G	p.I564V	CCAGAATTGAACC	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234429744	234429744	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	6	60	0	0.0895522	0	.	.	none	USP40_ENST00000450966,caecum,carcinoma,+2,2	USP40	174	2	NM_018218	exon16	c.G2251A	p.E751K	ATTTCTCTTCCTT	.	scavenged	Atlas-SNP
DOCK3	1795	hgsc.bcm.edu	37	3	51198110	51198110	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	2	141	0	0.0141844	0	.	.	none	DOCK3_ENST00000266037,rectum,carcinoma,0,3	DOCK3	397	3	NM_004947	exon12	c.G1014A	p.K338K	AGAAAAGGATTTT	.	scavenged	Atlas-SNP
CCR2	729230	hgsc.bcm.edu	37	3	46399226	46399226	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	353	141	380	1	0.399433	0.00263158	.	.	none	.	CCR2	103	.	NM_001123041	exon2	c.T208G	p.C70G	ATAAACTGCAAAA	.	PASS	Atlas-SNP
FAM218A	152756	hgsc.bcm.edu	37	4	165878335	165878335	+	Missense_Mutation	SNP	A	A	G	rs3733418	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	107	273	0	0.672956	0	A|0.813;G|0.187	0.187	strong	.	.	.	.	NM_153027	exon1	c.A161G	p.H54R	GCCGCCATGGCAG	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45232075	45232075	+	Missense_Mutation	SNP	A	A	T	rs199711781	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	4	91	3	0.039604	0.032967	A|0.999;T|0.001	0.001	weak	CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	NM_001114091	exon8	c.T920A	p.V307E	TCAATTACAGGAG	.	scavenged	Atlas-SNP
MMP17	4326	hgsc.bcm.edu	37	12	132325239	132325239	+	Missense_Mutation	SNP	G	G	A	rs6598163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	16	16	30	1	1	0.0333333	A|0.462;G|0.537;T|0.000	0.462	strong	MMP17_ENST00000360564,NS,carcinoma,-2,1	MMP17	77	1	NM_016155	exon4	c.G544A	p.A182T	GGCAGCGCCGCCG	.	scavenged	Atlas-SNP
SP2	6668	hgsc.bcm.edu	37	17	46002744	46002744	+	Silent	SNP	G	G	T	rs1130932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	39	65	0	0.557143	0	G|0.537;T|0.463	0.463	strong	SP2,colon,carcinoma,0,2	SP2	38	2	NM_003110	exon6	c.G1578T	p.V526V	GCACGTGTGCCAC	.	PASS	Atlas-SNP
ZNF701	55762	hgsc.bcm.edu	37	19	53086485	53086485	+	Silent	SNP	T	T	C	rs62117247	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	370	125	520	0	0.337838	0	T|0.961;C|0.039	0.039	strong	.	ZNF701	44	.	NM_001172655	exon5	c.T1371C	p.F457F	GACCTTTGTTCAA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40368330	40368330	+	Missense_Mutation	SNP	C	C	T	rs74540349	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170	28	190	2	0.164706	0.0105263	C|0.827;T|0.173	0.173	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon28	c.G13018A	p.E4340K	AGTCTTCGATGAC	.	scavenged	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14992042	14992042	+	Silent	SNP	A	A	G	rs76014757		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	31	104	0	0.407895	0	.	.	weak	.	OR7A17	37	.	NM_030901	exon1	c.T126C	p.N42N	GAGCAGATTCCCG	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247051714	247051714	+	Silent	SNP	A	A	G	rs144599339	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	565	328	477	1	0.580531	0.00209644	A|0.997;G|0.003	0.003	strong	.	AHCTF1	187	.	NM_015446	exon18	c.T2277C	p.Y759Y	AGGAGGATATTTT	.	PASS	Atlas-SNP
TTLL5	23093	hgsc.bcm.edu	37	14	76368544	76368544	+	Missense_Mutation	SNP	T	T	C	rs1133834	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	40	103	0	0.363636	0	C|0.345;N|0.000	0.345	strong	.	TTLL5	102	.	NM_015072	exon31	c.T3800C	p.F1267S	CAGCCTTTGTGCC	.	PASS	Atlas-SNP
WDHD1	11169	hgsc.bcm.edu	37	14	55448409	55448409	+	Missense_Mutation	SNP	G	G	C	rs61741224	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	80	95	0	0.583942	0	G|0.928;C|0.072	0.072	strong	.	WDHD1	82	.	NM_007086	exon16	c.C1912G	p.P638A	AACAAGGGGTACC	.	PASS	Atlas-SNP
NAPSA	9476	hgsc.bcm.edu	37	19	50865535	50865535	+	Missense_Mutation	SNP	A	A	G	rs676314	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	85	99	0	0.965909	0	A|0.618;G|0.382	0.382	strong	NAPSA,tonsil,carcinoma,0,1	NAPSA	38	1	NM_004851	exon2	c.T119C	p.I40T	TTCAGGATCCTGC	.	PASS	Atlas-SNP
RHOBTB3	22836	hgsc.bcm.edu	37	5	95084131	95084131	+	Silent	SNP	G	G	A	rs34896	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	70	181	0	0.48951	0	A|0.416;C|0.001	0.416	strong	.	RHOBTB3	43	.	NM_014899	exon4	c.G510A	p.A170A	AGGAGCGACCTAT	.	PASS	Atlas-SNP
MAST2	23139	hgsc.bcm.edu	37	1	46500613	46500613	+	Silent	SNP	T	T	C	rs17855317	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	22	183	0	0.180328	0	A|0.000;C|0.179;T|0.821	0.179	strong	MAST2_ENST00000361297,NS,carcinoma,0,1	MAST2	136	1	NM_015112	exon29	c.T4272C	p.T1424T	AGCCACTTCTCGC	.	PASS	Atlas-SNP
RTN2	6253	hgsc.bcm.edu	37	19	45998247	45998247	+	Silent	SNP	A	A	G	rs10401270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	57	82	0	0.966102	0	A|0.870;G|0.130	0.130	strong	.	RTN2	45	.	NM_206900	exon3	c.T96C	p.S32S	AAAATCAGAGTCG	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	37	19	15586672	15586672	+	Missense_Mutation	SNP	A	A	T	rs892145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	31	65	1	0.462687	0.0153846	A|0.632;T|0.368	0.368	strong	PGLYRP2_ENST00000292609,NS,carcinoma,0,4	PGLYRP2	116	4	NM_052890	exon2	c.T809A	p.M270K	AAGGCCATGGTTA	.	scavenged	Atlas-SNP
CPQ	10404	hgsc.bcm.edu	37	8	97847358	97847358	+	Silent	SNP	G	G	T	rs1864384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278	274	223	1	0.985611	0.00448431	G|0.413;T|0.587	0.587	strong	.	.	.	.	NM_016134	exon3	c.G591T	p.V197V	CAAGGTGGGGGCT	.	PASS	Atlas-SNP
INO80D	54891	hgsc.bcm.edu	37	2	206874307	206874307	+	Missense_Mutation	SNP	T	T	C	rs144598064	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	16	106	0	0.271186	0	T|0.997;C|0.003	0.003	strong	.	INO80D	134	.	NM_017759	exon9	c.A1754G	p.H585R	CGGATGTGAGAGG	.	PASS	Atlas-SNP
TMEM52B	120939	hgsc.bcm.edu	37	12	10332198	10332198	+	Missense_Mutation	SNP	G	G	T	rs140071448	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	54	163	0	0.457627	0	G|1.000;T|0.000	0.000	strong	.	.	.	.	NM_153022	exon1	c.G9T	p.W3C	GTCGTGGCGGCCT	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	2820043	2820043	+	Silent	SNP	G	G	T	rs4876056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	52	123	1	0.322981	0.00813008	G|0.871;T|0.129	0.129	strong	CSMD1_ENST00000318252,NS,carcinoma,-1,1	CSMD1	1469	1	NM_033225	exon61	c.C9573A	p.S3191S	TCTTCTGGAGGAT	.	scavenged	Atlas-SNP
CFP	5199	hgsc.bcm.edu	37	X	47483800	47483800	+	Silent	SNP	G	G	A	rs1048118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	62	131	1	0.953846	0.00763359	G|0.777;0|0.004	.	strong	.	CFP	43	.	NM_001145252	exon9	c.C1284T	p.N428N	GGTCACGTTCTTC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	19735325	19735325	+	Silent	SNP	C	C	A	rs11828836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21	9	38	0	0.428571	0	C|0.975;A|0.025	0.025	strong	.	NAV2	255	.	NM_145117	exon1	c.C84A	p.P28P	CGTGCCCCCGGCC	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561313	32561313	+	Nonsense_Mutation	SNP	C	C	T	rs201986816	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	7	116	0	0.0555556	0	C|0.998;T|0.002	0.002	strong	.	ARHGAP5	166	.	NM_001173	exon2	c.C1438T	p.R480X	CATCAGCGAGAAA	.	PASS	Atlas-SNP
ZNF492	57615	hgsc.bcm.edu	37	19	22836805	22836805	+	Missense_Mutation	SNP	G	G	A	rs200144130	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	7	95	0	0.0569106	0	.	.	weak	ZNF492_ENST00000456783,NS,carcinoma,0,4	ZNF492	129	4	NM_020855	exon3	c.G118A	p.A40T	ATGGTAGCTGAAC	.	scavenged	Atlas-SNP
CLIP1	6249	hgsc.bcm.edu	37	12	122817580	122817580	+	Missense_Mutation	SNP	A	A	G	rs17883517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241	97	291	1	0.40249	0.00343643	A|0.939;G|0.061	0.061	strong	.	CLIP1	126	.	NM_001247997	exon15	c.T2821C	p.S941P	GAGAAGAGTTATC	.	PASS	Atlas-SNP
VN1R1	57191	hgsc.bcm.edu	37	19	57967133	57967133	+	Missense_Mutation	SNP	G	G	A	rs28649880	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	109	274	1	0.456067	0.00364964	G|0.674;A|0.326	0.326	strong	VN1R1,NS,adenoma,0,1	VN1R1	48	1	NM_020633	exon1	c.C722T	p.S241F	ACCATGGAGCCAC	.	PASS	Atlas-SNP
RNGTT	8732	hgsc.bcm.edu	37	6	89614521	89614521	+	Silent	SNP	G	G	A	rs139029923		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206	103	227	0	0.5	0	G|1.000;A|0.000	0.000	weak	.	RNGTT	52	.	NM_003800	exon6	c.C597T	p.D199D	ATCTTCGTCTTCA	.	PASS	Atlas-SNP
CTIF	9811	hgsc.bcm.edu	37	18	46343666	46343666	+	Silent	SNP	C	C	T	rs3764481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	83	203	0	0.532051	0	C|0.881;T|0.119	0.119	strong	.	CTIF	102	.	NM_001142397	exon11	c.C1452T	p.C484C	CCTGTGCGAGGTC	.	PASS	Atlas-SNP
PTCHD4	442213	hgsc.bcm.edu	37	6	47847179	47847179	+	Silent	SNP	A	A	G	rs3799276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	189	152	0	0.994737	0	A|0.279;G|0.721	0.721	strong	.	.	.	.	NM_001013732	exon3	c.T1401C	p.V467V	GATGACAACAAAT	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129371106	129371106	+	Silent	SNP	C	C	T	rs1140366	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	120	249	0	0.526316	0	C|0.907;T|0.093	0.093	strong	.	LAMA2	481	.	NM_000426	exon2	c.C156T	p.I52I	TCTTATCACGACC	.	PASS	Atlas-SNP
RUFY2	55680	hgsc.bcm.edu	37	10	70143826	70143826	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	4	132	0	0.047619	0	.	.	none	.	RUFY2	58	.	NM_017987	exon9	c.A909G	p.K303K	CTGTGTTTTCATT	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225528183	225528183	+	Missense_Mutation	SNP	C	C	A	rs3856145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	366	179	376	0	0.489071	0	C|0.498;A|0.500	0.500	strong	.	DNAH14	300	.	NM_001373	exon67	c.C10179A	p.D3393E	AATAGACAACCCC	.	PASS	Atlas-SNP
CNR2	1269	hgsc.bcm.edu	37	1	24201920	24201920	+	Missense_Mutation	SNP	T	T	C	rs2501432	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	84	146	1	0.965517	0.00684932	T|0.468;C|0.532	0.532	strong	CNR2,NS,carcinoma,0,2	CNR2	78	2	NM_001841	exon2	c.A188G	p.Q63R	CGGAGTTGGTGGG	.	PASS	Atlas-SNP
PDE9A	5152	hgsc.bcm.edu	37	21	44180443	44180443	+	Silent	SNP	C	C	T	rs13047953	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	16	30	0	0.592593	0	C|0.675;T|0.325	0.325	strong	PDE9A,NS,carcinoma,0,1	PDE9A	69	1	NM_002606	exon12	c.C903T	p.C301C	GTTCTGCGTCCAC	.	PASS	Atlas-SNP
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077755	19077755	+	Silent	SNP	A	A	C	rs11024969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	40	85	0	0.512821	0	A|0.900;C|0.100	0.100	strong	MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	NM_054030	exon2	c.T195G	p.S65S	GTAGACAGAGAAG	.	PASS	Atlas-SNP
CTNNA3	29119	hgsc.bcm.edu	37	10	68535222	68535222	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	6	175	0	0.0588235	0	.	.	none	.	CTNNA3	401	.	NM_013266	exon8	c.A1108G	p.T370A	CTCTTGTCTTCTT	.	PASS	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983374	97983374	+	Silent	SNP	A	A	G	rs4857358	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	774	355	791	2	0.458656	0.00252845	A|0.785;G|0.215	0.215	strong	.	OR5H6	89	.	NM_001005479	exon1	c.A246G	p.L82L	GAGTTTAGCCTTT	.	PASS	Atlas-SNP
PCYOX1L	78991	hgsc.bcm.edu	37	5	148747902	148747902	+	Missense_Mutation	SNP	G	G	C	rs4705336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193	85	191	0	0.440415	0	G|0.877;C|0.123	0.123	strong	PCYOX1L,NS,carcinoma,0,1	PCYOX1L	32	1	NM_024028	exon6	c.G1170C	p.E390D	CCAGGAGGCAGCT	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39424254	39424254	+	Silent	SNP	T	T	C	rs9548507	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	47	122	0	0.460784	0	T|0.912;C|0.088	0.088	strong	.	FREM2	385	.	NM_207361	exon9	c.T6459C	p.T2153T	TAGGACTGGGGAT	.	PASS	Atlas-SNP
POLM	27434	hgsc.bcm.edu	37	7	44121936	44121936	+	Silent	SNP	C	C	A	rs3218655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	13	40	0	0.448276	0	C|0.841;A|0.159	0.159	strong	.	POLM	50	.	NM_013284	exon1	c.G102T	p.L34L	CTCGACCAGGTAG	.	PASS	Atlas-SNP
MAPRE1	22919	hgsc.bcm.edu	37	20	31427635	31427635	+	Silent	SNP	C	C	T	rs2070090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	59	160	0	0.475806	0	C|0.738;T|0.261	0.261	strong	.	MAPRE1	17	.	NM_012325	exon5	c.C570T	p.D190D	CGGAGACGACGAG	.	PASS	Atlas-SNP
HSH2D	84941	hgsc.bcm.edu	37	19	16265241	16265241	+	Silent	SNP	C	C	T	rs36088948	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	20	42	0	0.37037	0	C|0.927;T|0.073	0.073	strong	.	HSH2D	16	.	NM_032855	exon7	c.C414T	p.L138L	GGATCTCTTCCTC	.	PASS	Atlas-SNP
ARL13B	200894	hgsc.bcm.edu	37	3	93714763	93714763	+	Silent	SNP	C	C	T	rs146396078	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	382	208	434	0	0.544503	0	C|0.990;T|0.010	0.010	strong	.	ARL13B	52	.	NM_182896	exon2	c.C105T	p.T35T	TAAAACCGCAACA	.	PASS	Atlas-SNP
EIF4E	1977	hgsc.bcm.edu	37	4	99808254	99808254	+	Silent	SNP	G	G	A	rs62323192	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196	99	221	1	0.505102	0.00452489	G|0.819;A|0.181	0.181	strong	EIF4E,NS,carcinoma,0,1	EIF4E	18	1	NM_001130678	exon5	c.C435T	p.D145D	ATCGAGGTCACTT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46760481	46760481	+	Missense_Mutation	SNP	C	C	G	rs9615351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	52	141	0	0.440678	0	C|0.700;G|0.300	0.300	strong	CELSR1,NS,carcinoma,0,1	CELSR1	242	1	NM_014246	exon33	c.G8707C	p.E2903Q	GGTACTCTCCACG	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107379895	107379895	+	Missense_Mutation	SNP	G	G	T	rs10761054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	115	250	0	0.475207	0	G|0.786;T|0.214	0.214	strong	.	OR13C9	42	.	NM_001001956	exon1	c.C591A	p.F197L	CATGAGGAACTCA	.	PASS	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22382704	22382704	+	Missense_Mutation	SNP	G	G	C	rs62006708	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	369	35	509	0	0.0948509	0	G|0.843;C|0.157	0.157	strong	.	OR4N4	108	.	NM_001005241	exon1	c.G232C	p.A78P	ATTGTGGCTCCCA	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23098422	23098422	+	Missense_Mutation	SNP	A	A	G	rs13339649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	185	176	1	1	0.00568182	A|0.742;G|0.258	0.258	strong	.	USP31	122	.	NM_020718	exon9	c.T1613C	p.I538T	TCTACTATTGGGT	.	PASS	Atlas-SNP
FGD6	55785	hgsc.bcm.edu	37	12	95604290	95604290	+	Missense_Mutation	SNP	T	T	C	rs10507047	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	13	77	0	0.232143	0	T|0.842;C|0.158	0.158	strong	FGD6,NS,carcinoma,0,2	FGD6	127	2	NM_018351	exon2	c.A770G	p.Q257R	TCATCCTGGCAAG	.	PASS	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110760008	110760008	+	Missense_Mutation	SNP	A	A	G	rs12210538	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	63	157	0	0.4375	0	A|0.851;G|0.149	0.149	strong	.	SLC22A16	81	.	NM_033125	exon5	c.T1226C	p.M409T	TTGTCCATGGCGA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276282	152276282	+	Missense_Mutation	SNP	C	C	G	rs76133835	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	492	51	369	3	0.103659	0.00813008	C|0.500;G|0.500	0.500	weak	FLG,extremity,malignant_melanoma,0,1	FLG	900	1	NM_002016	exon3	c.G11080C	p.E3694Q	TGGACTCTTGGTG	.	scavenged	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406516	3406516	+	Silent	SNP	A	A	G	rs11643487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	105	91	0	0.981308	0	A|0.659;G|0.341	0.341	strong	.	OR2C1	38	.	NM_012368	exon1	c.A576G	p.T192T	CGACACAAGTCTC	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746701	143746701	+	Silent	SNP	A	A	G	rs3802232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	39	101	0	0.364486	0	A|0.479;G|0.521	0.521	strong	.	.	.	.	NM_003724	exon2	c.T777C	p.N259N	CCAGGCATTCCCC	.	PASS	Atlas-SNP
PATE1	160065	hgsc.bcm.edu	37	11	125617610	125617610	+	Missense_Mutation	SNP	A	A	G	rs2114084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	46	34	0	0.630137	0	A|0.675;G|0.325	0.325	strong	.	PATE1	21	.	NM_138294	exon4	c.A140G	p.Q47R	TTGTTCAGTGTAG	.	PASS	Atlas-SNP
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278203	126278203	+	Silent	SNP	T	T	C	rs2298475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	269	189	177	1	0.702602	0.00564972	T|0.925;C|0.075	0.075	strong	ST3GAL4,NS,carcinoma,0,1	ST3GAL4	25	1	NM_001254757	exon8	c.T439C	p.L147L	CCCAGATTGAACA	.	PASS	Atlas-SNP
AGPAT4	56895	hgsc.bcm.edu	37	6	161567601	161567601	+	Silent	SNP	G	G	A	rs16892215	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	36	77	0	0.473684	0	G|0.975;A|0.025	0.025	strong	.	AGPAT4	50	.	NM_020133	exon7	c.C798T	p.D266D	GTCATCGTCTTCA	.	PASS	Atlas-SNP
HYOU1	10525	hgsc.bcm.edu	37	11	118925341	118925341	+	Silent	SNP	G	G	A	rs538478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	148	104	1	0.993289	0.00961538	G|0.585;A|0.415	0.415	strong	HYOU1,NS,carcinoma,-1,1	HYOU1	88	1	NM_006389	exon7	c.C543T	p.N181N	GGCCTGGTTGAAG	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2794921	2794921	+	Missense_Mutation	SNP	G	G	A	rs71458011		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	9	136	7	0.0769231	0.0514706	G|0.500;A|0.500	0.500	weak	Q6YL47_HUMAN,NS,carcinoma,0,8	CACNA1C	1023	8	NM_199460	exon47	c.G5842A	p.E1948K	GATGACGAAAATC	.	scavenged	Atlas-SNP
ALDH1L1	10840	hgsc.bcm.edu	37	3	125856695	125856695	+	Silent	SNP	C	C	A	rs2305230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	254	252	305	1	0.992126	0.00327869	C|0.767;A|0.233	0.233	strong	.	ALDH1L1	138	.	NM_001270364	exon10	c.G1215T	p.L405L	CCCTCGCAGCTTC	.	PASS	Atlas-SNP
ZNF497	162968	hgsc.bcm.edu	37	19	58868480	58868480	+	Missense_Mutation	SNP	G	G	T	rs12609654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	96	207	0	0.516129	0	G|0.561;T|0.439	0.439	strong	.	ZNF497	22	.	NM_001207009	exon2	c.C522A	p.H174Q	CTGCGAGTGCGCG	.	PASS	Atlas-SNP
KIAA1958	158405	hgsc.bcm.edu	37	9	115421788	115421788	+	Silent	SNP	C	C	A	rs16917185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	60	141	0	0.397351	0	C|0.916;A|0.084	0.084	strong	.	KIAA1958	52	.	NM_133465	exon4	c.C1590A	p.I530I	CAACATCGTCTAC	.	PASS	Atlas-SNP
C22orf42	150297	hgsc.bcm.edu	37	22	32554997	32554997	+	Missense_Mutation	SNP	G	G	A	rs78036098	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	302	123	290	2	0.407285	0.00689655	G|0.988;A|0.012	0.012	strong	C22orf42,NS,carcinoma,-1,1	C22orf42	37	1	NM_001010859	exon1	c.C206T	p.T69M	TTCGGCGTCTTCG	.	scavenged	Atlas-SNP
CACTIN	58509	hgsc.bcm.edu	37	19	3611972	3611972	+	Silent	SNP	G	G	A	rs2158935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	57	84	0	0.537736	0	G|0.545;A|0.455	0.455	strong	.	.	.	.	NM_021231	exon10	c.C2226T	p.N742N	GATGCCGTTGGCA	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39135207	39135207	+	Missense_Mutation	SNP	A	A	G	rs150812789	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	69	131	1	0.522727	0.00763359	A|0.787;G|0.213	0.213	strong	KRT40,NS,carcinoma,+2,1	KRT40	27	1	NM_182497	exon8	c.T1045C	p.C349R	TCAGACACTGAAT	.	scavenged	Atlas-SNP
TMEM63A	9725	hgsc.bcm.edu	37	1	226055595	226055595	+	Silent	SNP	G	G	A	rs2292564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	93	82	0	0.989362	0	G|0.640;A|0.360	0.360	strong	TMEM63A,NS,carcinoma,0,1	TMEM63A	75	1	NM_014698	exon7	c.C507T	p.D169D	CAGCAAGTCCCCT	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327897	16327897	+	Missense_Mutation	SNP	C	C	A	rs184327938	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	4	73	0	0.0444444	0	C|0.926;A|0.074	0.074	strong	ATXN1,NS,carcinoma,0,3	ATXN1	117	3	NM_001128164	exon7	c.G645T	p.Q215H	CTGCTGCTGCTGC	.	PASS	Atlas-SNP
APOBEC1	339	hgsc.bcm.edu	37	12	7803646	7803646	+	Silent	SNP	G	G	A	rs10431309	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	72	138	0	0.517986	0	G|0.779;A|0.221	0.221	strong	APOBEC1,caecum,carcinoma,0,2	APOBEC1	43	2	NM_001644	exon4	c.C534T	p.Y178Y	CAGTGCGTACAAC	.	PASS	Atlas-SNP
PPP1R36	145376	hgsc.bcm.edu	37	14	65054858	65054858	+	Silent	SNP	T	T	C	rs723594	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	39	98	0	0.314516	0	T|0.940;C|0.060	0.060	strong	.	.	.	.	NM_172365	exon11	c.T927C	p.A309A	AAAAGCTATCAAC	.	PASS	Atlas-SNP
OR4N2	390429	hgsc.bcm.edu	37	14	20296010	20296010	+	Missense_Mutation	SNP	G	G	C	rs17114261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	474	265	910	0	0.559072	0	G|0.824;C|0.176	0.176	strong	.	OR4N2	125	.	NM_001004723	exon1	c.G403C	p.V135L	CCTACTGTCATGA	.	PASS	Atlas-SNP
MCF2L	23263	hgsc.bcm.edu	37	13	113739226	113739226	+	Silent	SNP	T	T	C	rs2281723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	34	114	0	0.441558	0	T|0.904;C|0.096	0.096	strong	.	MCF2L	182	.	NM_001112732	exon19	c.T2082C	p.Y694Y	GATCTATGAGAAG	.	PASS	Atlas-SNP
ULBP3	79465	hgsc.bcm.edu	37	6	150390118	150390118	+	Missense_Mutation	SNP	C	C	T	rs113233347	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186	98	206	0	0.526882	0	C|0.925;T|0.075	0.075	strong	ULBP3,NS,carcinoma,0,1	ULBP3	22	1	NM_024518	exon1	c.G85A	p.A29T	CACCGGCCCGCCC	.	PASS	Atlas-SNP
RASA2	5922	hgsc.bcm.edu	37	3	141327474	141327474	+	Silent	SNP	G	G	A	rs295323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	227	3	268	0	0.0132159	0	G|0.523;A|0.477	0.477	strong	RASA2_ENST00000286364,NS,carcinoma,0,1	RASA2	169	1	NM_006506	exon21	c.G2160A	p.L720L	GTATCTGAACGGA	.	scavenged	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86909582	86909582	+	Missense_Mutation	SNP	G	G	A	rs1413426	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	13	124	0	0.19403	0	G|0.904;A|0.096	0.096	strong	.	CLCA2	102	.	NM_006536	exon10	c.G1601A	p.G534D	CCAGTGGTCCTCC	.	PASS	Atlas-SNP
CATSPERB	79820	hgsc.bcm.edu	37	14	92159558	92159558	+	Missense_Mutation	SNP	A	A	G	rs72629402	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	89	150	0	0.574194	0	A|0.955;G|0.045	0.045	strong	.	CATSPERB	114	.	NM_024764	exon9	c.T743C	p.V248A	GTTAAAACCATAT	.	PASS	Atlas-SNP
CASR	846	hgsc.bcm.edu	37	3	122003769	122003769	+	Missense_Mutation	SNP	A	A	G	rs1042636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	239	125	274	1	0.523013	0.00364964	A|0.871;G|0.129	0.129	strong	.	CASR	190	.	NM_001178065	exon7	c.A2998G	p.R1000G	GCCCACAGGAATT	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121742124	121742124	+	Silent	SNP	G	G	A	rs61732852	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	83	206	0	0.461111	0	G|0.991;A|0.009	0.009	strong	.	GLI2	187	.	NM_005270	exon11	c.G1761A	p.T587T	GAAAACGGTCCAC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225534348	225534348	+	Missense_Mutation	SNP	G	G	A	rs7535953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236	147	168	0	0.622881	0	G|0.499;A|0.501	0.501	strong	.	DNAH14	300	.	NM_001373	exon69	c.G11009A	p.R3670K	AGTCTAGACTTAC	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	37	14	64519709	64519709	+	Missense_Mutation	SNP	A	A	T	rs34843668	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	57	130	1	0.387755	0.00769231	A|0.970;T|0.030	0.030	strong	SYNE2,NS,carcinoma,+2,1	SYNE2	577	1	NM_182914	exon48	c.A9078T	p.E3026D	ATTTGAAAAAGAA	.	scavenged	Atlas-SNP
SLC25A24	29957	hgsc.bcm.edu	37	1	108703834	108703834	+	Silent	SNP	C	C	T	rs11185293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	28	230	0	0.163743	0	C|0.947;T|0.053	0.053	strong	.	SLC25A24	65	.	NM_013386	exon4	c.G480A	p.E160E	AATTTCCTCAATG	.	PASS	Atlas-SNP
SLC27A2	11001	hgsc.bcm.edu	37	15	50474766	50474766	+	Missense_Mutation	SNP	A	A	C	rs1648348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	7	93	0	0.205882	0	A|0.412;C|0.588	0.588	strong	.	SLC27A2	50	.	NM_003645	exon1	c.A142C	p.K48Q	TACGGGAAGCGGC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134748281	134748281	+	Missense_Mutation	SNP	G	G	A	rs74460040	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	23	78	0	0.328571	0	G|0.972;A|0.028	0.028	strong	.	TTC40	100	.	NM_001200049	exon8	c.C841T	p.R281C	GAAAGCGCTGGTG	.	PASS	Atlas-SNP
C15orf39	56905	hgsc.bcm.edu	37	15	75499995	75499995	+	Missense_Mutation	SNP	T	T	G	rs28509789	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	16	112	0	0.195122	0	T|0.662;G|0.338	0.338	strong	C15orf39,bladder,carcinoma,-1,1	C15orf39	64	1	NM_015492	exon2	c.T1606G	p.S536A	CCTGACTCAGCCC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	66112409	66112409	+	Silent	SNP	A	A	G	rs974110	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	96	224	1	0.446512	0.00446429	A|0.498;G|0.502	0.502	strong	.	EYS	527	.	NM_001142801	exon7	c.T1146C	p.N382N	TGTAGCATTATTC	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40119501	40119501	+	Silent	SNP	T	T	C	rs1128372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	37	105	0	0.385417	0	T|0.851;C|0.149	0.149	strong	.	N4BP2	166	.	NM_018177	exon8	c.T1677C	p.H559H	CATTCATGGGGTA	.	PASS	Atlas-SNP
SLC2A14	144195	hgsc.bcm.edu	37	12	7966975	7966975	+	Silent	SNP	C	C	T	rs71436622		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157	33	328	0	0.210191	0	T|1.000;|0.000	1.000	weak	SLC2A14,NS,carcinoma,-2,1	SLC2A14	78	1	NM_153449	exon12	c.G1500A	p.G500G	GTCCTTCCCAGAT	.	scavenged	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274343	39274343	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	8	182	5	0.0551724	0.0274725	.	.	none	KRTAP4-11,NS,malignant_melanoma,0,2	KRTAP4-11	94	2	NM_033059	exon1	c.T225C	p.C75C	GGGGCGACAGCAG	.	scavenged	Atlas-SNP
CBX2	84733	hgsc.bcm.edu	37	17	77758691	77758691	+	Silent	SNP	G	G	A	rs3751957	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	39	74	0	0.506494	0	G|0.630;A|0.370	0.370	strong	CBX2,mucosal,malignant_melanoma,+2,1	CBX2	50	1	NM_005189	exon5	c.G1449A	p.P483P	GAACCCGTCAGTG	.	PASS	Atlas-SNP
BIRC3	330	hgsc.bcm.edu	37	11	102195297	102195297	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	442	95	315	0	0.214932	0	.	.	none	.	BIRC3	56	.	NM_001165	exon2	c.G57A	p.T19T	CAACACGTTTGAA	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs56451138		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252	16	431	2	0.0634921	0.00464037	C|0.750;T|0.250	0.250	weak	OR10G2,NS,carcinoma,0,1	OR10G2	35	1	NM_001005466	exon1	c.G706A	p.A236T	CATCAGCGGTGCG	.	scavenged	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38753732	38753732	+	Missense_Mutation	SNP	A	A	T	rs11711062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	117	224	0	0.4875	0	A|0.996;T|0.004	0.004	strong	.	SCN10A	359	.	NM_006514	exon22	c.T4009A	p.S1337T	CAGTGGAGTTTTG	.	PASS	Atlas-SNP
ARID4A	5926	hgsc.bcm.edu	37	14	58768333	58768333	+	Silent	SNP	C	C	T	rs45562837	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	169	63	120	0	0.372781	0	C|0.947;T|0.053	0.053	strong	ARID4A_ENST00000355431,colon,carcinoma,0,2	ARID4A	222	2	NM_002892	exon3	c.C42T	p.T14T	GGGAACCGATGTC	.	PASS	Atlas-SNP
GBP7	388646	hgsc.bcm.edu	37	1	89599013	89599013	+	Silent	SNP	G	G	T	rs115671591	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	274	272	473	0	0.992701	0	G|0.979;T|0.021	0.021	strong	.	GBP7	57	.	NM_207398	exon10	c.C1590A	p.L530L	CTTCTTGAGTTGA	.	PASS	Atlas-SNP
GYG1	2992	hgsc.bcm.edu	37	3	148727133	148727133	+	Silent	SNP	G	G	A	rs4938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	34	137	0	0.373626	0	G|0.703;A|0.297	0.297	strong	.	GYG1	29	.	NM_004130	exon5	c.G552A	p.P184P	CCTGCCGTTTATT	.	PASS	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48761105	48761105	+	Silent	SNP	C	C	T	rs2277624	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	21	36	0	0.428571	0	C|0.739;T|0.261	0.261	strong	.	ABCC3	138	.	NM_003786	exon27	c.C3942T	p.H1314H	TGTGCACGGTGGC	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231226371	231226371	+	Missense_Mutation	SNP	A	A	G	rs190007801	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	4	103	0	0.0449438	0	A|0.999;G|0.001	0.001	strong	.	SP140L	68	.	NM_138402	exon5	c.A482G	p.E161G	GAAAAGAAAGGGA	.	PASS	Atlas-SNP
SLC2A8	29988	hgsc.bcm.edu	37	9	130164993	130164993	+	Silent	SNP	C	C	T	rs1138739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103	102	111	1	0.990291	0.00900901	C|0.827;T|0.173	0.173	strong	.	SLC2A8	27	.	NM_014580	exon5	c.C684T	p.S228S	GGGCTCCGAGCAG	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595756	140595756	+	Silent	SNP	C	C	T	rs17844617	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	33	66	0	0.507692	0	C|0.855;T|0.145	0.145	strong	.	PCDHB13	142	.	NM_018933	exon1	c.C2061T	p.T687T	GCTCACCGTCTAC	.	PASS	Atlas-SNP
STPG1	90529	hgsc.bcm.edu	37	1	24718075	24718075	+	Silent	SNP	T	T	C	rs2294520	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	34	77	0	0.708333	0	T|0.728;C|0.272	0.272	strong	.	.	.	.	NM_001199012	exon3	c.A165G	p.Q55Q	CTTGGCTTGACTA	.	PASS	Atlas-SNP
APPL1	26060	hgsc.bcm.edu	37	3	57269608	57269608	+	Silent	SNP	A	A	G	rs11544592	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	121	274	0	0.497942	0	A|0.987;G|0.013	0.013	strong	.	APPL1	59	.	NM_012096	exon2	c.A69G	p.L23L	TTTACTAGGTGTA	.	PASS	Atlas-SNP
PHF2	5253	hgsc.bcm.edu	37	9	96407983	96407983	+	Silent	SNP	C	C	T	rs9695734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	30	55	0	0.461538	0	C|0.853;T|0.147	0.147	strong	PHF2,NS,carcinoma,0,1	PHF2	113	1	NM_005392	exon4	c.C372T	p.T124T	CTTCACCGAGCCC	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140187048	140187048	+	Silent	SNP	G	G	C	rs3822349	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	23	98	1	0.298701	0.0102041	G|0.926;C|0.074	0.074	strong	PCDHA4_ENST00000530339,NS,carcinoma,0,4	PCDHA4	419	4	NM_031500	exon1	c.G276C	p.R92R	CGACCGGGAGGAG	.	scavenged	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53856730	53856730	+	Silent	SNP	G	G	A	rs201351032		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	187	14	182	1	0.0748663	0.00549451	.	.	weak	ZNF845,NS,carcinoma,0,5	ZNF845	101	5	NM_138374	exon4	c.G2802A	p.K934K	TCATAAGACAATT	.	scavenged	Atlas-SNP
BIRC3	330	hgsc.bcm.edu	37	11	102195984	102195984	+	Silent	SNP	T	T	A	rs147757750	bycluster;by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106	20	66	0	0.188679	0	T|1.000;C|0.000	.	alt	BIRC3,colon,carcinoma,+2,2	BIRC3	56	2	NM_001165	exon2	c.T744A	p.S248S	AGTTTCTAATCTG	.	PASS	Atlas-SNP
NCKIPSD	51517	hgsc.bcm.edu	37	3	48717276	48717276	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	67	166	0	0.544715	0	.	.	none	.	NCKIPSD	52	.	NM_016453	exon7	c.C1308T	p.N436N	GAACTCGTTTCTC	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553664	140553664	+	Silent	SNP	G	G	A	rs3733695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	103	185	0	0.492823	0	G|0.819;A|0.181	0.181	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G1248A	p.E416E	CACTGAGTACAAC	.	PASS	Atlas-SNP
BCAM	4059	hgsc.bcm.edu	37	19	45315445	45315445	+	Missense_Mutation	SNP	G	G	A	rs28399653	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50	34	61	0	0.68	0	G|0.977;A|0.023	0.023	strong	.	BCAM	53	.	NM_001013257	exon3	c.G230A	p.R77H	GCCCCCGCCTAGC	.	PASS	Atlas-SNP
KIAA1244	57221	hgsc.bcm.edu	37	6	138645228	138645228	+	Silent	SNP	G	G	A	rs3734301	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	39	96	1	0.448276	0.0104167	G|0.789;A|0.211	0.211	strong	KIAA1244,NS,carcinoma,+1,1	KIAA1244	236	1	NM_020340	exon31	c.G4938A	p.A1646A	AGTGGCGGCCCCG	.	scavenged	Atlas-SNP
SEZ6L	23544	hgsc.bcm.edu	37	22	26692986	26692986	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	2	156	1	0.0135135	0.00641026	.	.	none	SEZ6L,scalp,malignant_melanoma,-1,1	SEZ6L	174	1	NM_001184777	exon4	c.T1102C	p.S368P	ACCATCTCCGTCT	.	scavenged	Atlas-SNP
OSCP1	127700	hgsc.bcm.edu	37	1	36886117	36886117	+	Missense_Mutation	SNP	C	C	T	rs2275477	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	68	140	1	0.701031	0.00714286	C|0.755;T|0.245	0.245	strong	OSCP1,NS,carcinoma,0,1	OSCP1	48	1	NM_145047	exon8	c.G919A	p.G307R	GGAATCCGGGCTC	.	scavenged	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20897065	20897065	+	Silent	SNP	G	G	A	rs368179614		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	302	123	246	0	0.407285	0	.	.	weak	.	KLHL33	37	.	NM_001109997	exon4	c.C1545T	p.P515P	CACAGCGGGCAGT	.	PASS	Atlas-SNP
ACOT12	134526	hgsc.bcm.edu	37	5	80631642	80631642	+	Missense_Mutation	SNP	C	C	T	rs10371	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204	98	221	1	0.480392	0.00452489	C|0.852;T|0.148	0.148	strong	.	ACOT12	57	.	NM_130767	exon12	c.G1207A	p.A403T	GATAAGCCAAATG	.	PASS	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	37	9	35705759	35705759	+	Silent	SNP	G	G	A	rs11541908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	39	76	0	0.619048	0	G|0.806;A|0.194	0.194	strong	.	TLN1	185	.	NM_006289	exon42	c.C5601T	p.T1867T	CTGAACGGTCACT	.	PASS	Atlas-SNP
OR4K13	390433	hgsc.bcm.edu	37	14	20502044	20502044	+	Missense_Mutation	SNP	G	G	T	rs17277025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	41	94	0	0.414141	0	G|0.933;T|0.067	0.067	strong	.	OR4K13	68	.	NM_001004714	exon1	c.C874A	p.Q292K	CCTCTTGATTTCT	.	PASS	Atlas-SNP
CHCHD6	84303	hgsc.bcm.edu	37	3	126451937	126451937	+	Missense_Mutation	SNP	G	G	T	rs2272487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229	124	251	1	0.541485	0.00398406	G|0.788;T|0.212	0.212	strong	.	CHCHD6	18	.	NM_032343	exon4	c.G283T	p.A95S	GAGCATGCTGCTA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280614	152280614	+	Missense_Mutation	SNP	C	C	G	rs3120645	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	475	13	314	0	0.0273684	0	C|0.996;G|0.003;T|0.001	0.003	strong	FLG,right_upper_lobe,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.G6748C	p.E2250Q	GTCCCTCACTGTC	.	scavenged	Atlas-SNP
OR3A2	4995	hgsc.bcm.edu	37	17	3181384	3181384	+	Silent	SNP	C	C	T	rs769434	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	70	123	0	0.492958	0	C|0.838;T|0.162	0.162	strong	.	OR3A2	36	.	NM_002551	exon1	c.G846A	p.G282G	TCCAACCCCTTTA	.	PASS	Atlas-SNP
KIAA1009	22832	hgsc.bcm.edu	37	6	84881429	84881429	+	Silent	SNP	T	T	C	rs41271603	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	66	134	0	0.458333	0	T|0.957;C|0.043	0.043	strong	KIAA1009,NS,carcinoma,-2,1	KIAA1009	119	1	NM_014895	exon17	c.A2175G	p.E725E	TAATCGTTCATTT	.	PASS	Atlas-SNP
PCIF1	63935	hgsc.bcm.edu	37	20	44575932	44575932	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	6	110	0	0.0576923	0	.	.	none	.	PCIF1	51	.	NM_022104	exon16	c.T1738C	p.S580P	CCCCTGTCCTTCA	.	PASS	Atlas-SNP
DGCR2	9993	hgsc.bcm.edu	37	22	19026613	19026613	+	Missense_Mutation	SNP	A	A	G	rs2072123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183	178	203	1	0.972678	0.00492611	T|0.004;G|0.408	0.408	strong	.	DGCR2	45	.	NM_005137	exon10	c.T1418C	p.V473A	ACCTCCACAGGCT	.	PASS	Atlas-SNP
IL17RE	132014	hgsc.bcm.edu	37	3	9952706	9952706	+	Silent	SNP	A	A	G	rs279572	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	98	112	1	0.989899	0.00892857	A|0.492;G|0.508	0.508	strong	.	IL17RE	62	.	NM_153483	exon10	c.A1080G	p.T360T	TGCCACAGCTCGA	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39622068	39622068	+	Missense_Mutation	SNP	G	G	T	rs2071561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	59	147	0	0.401361	0	G|0.553;T|0.445	0.445	strong	.	KRT32	57	.	NM_002278	exon3	c.C665A	p.S222Y	TTCAGGGACTCAA	.	PASS	Atlas-SNP
ERI2	112479	hgsc.bcm.edu	37	16	20810067	20810067	+	Missense_Mutation	SNP	T	T	C	rs3213646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	100	109	0	0.980392	0	T|0.674;C|0.326	0.326	strong	.	ERI2	50	.	NM_001142725	exon9	c.A1055G	p.Y352C	TGCATATAGATAG	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219602819	219602819	+	Silent	SNP	G	G	A	rs3731876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	11	50	0	0.407407	0	G|0.459;A|0.541	0.541	strong	.	TTLL4	96	.	NM_014640	exon3	c.G420A	p.P140P	GAGCCCGTCAGAA	.	PASS	Atlas-SNP
SAR1B	51128	hgsc.bcm.edu	37	5	133945288	133945288	+	Silent	SNP	C	C	T	rs140899111	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	56	138	0	0.386207	0	C|0.999;T|0.001	0.001	strong	.	SAR1B	19	.	NM_001033503	exon6	c.G321A	p.R107R	TAACAGCCTTTCG	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74497152	74497152	+	Missense_Mutation	SNP	G	G	A	rs5023688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	59	125	0	0.531532	0	G|0.598;A|0.402	0.402	strong	.	CD109	170	.	NM_133493	exon21	c.G2533A	p.V845I	GATGCTGTCACCC	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4869649	4869649	+	Missense_Mutation	SNP	G	G	A	rs12361955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	176	209	0	0.99435	0	G|0.658;A|0.342	0.342	strong	OR51S1,NS,carcinoma,+2,1	OR51S1	83	1	NM_001004758	exon1	c.C790T	p.L264F	CCAGGAGGATCAT	.	PASS	Atlas-SNP
POLQ	10721	hgsc.bcm.edu	37	3	121208176	121208176	+	Missense_Mutation	SNP	T	T	C	rs3218651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	97	199	0	0.598765	0	T|0.779;C|0.221	0.221	strong	.	POLQ	273	.	NM_199420	exon16	c.A3602G	p.H1201R	TGTTCATGAGATT	.	PASS	Atlas-SNP
ARHGEF3	50650	hgsc.bcm.edu	37	3	56835761	56835761	+	Silent	SNP	G	G	A	rs3732508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	114	162	0	0.991304	0	G|0.677;A|0.323	0.323	strong	ARHGEF3_ENST00000296315,NS,carcinoma,0,2	ARHGEF3	128	2	NM_019555	exon1	c.C66T	p.P22P	GGCCGGGGGTAGC	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33697576	33697576	+	Missense_Mutation	SNP	G	G	A	rs187640762	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	34	67	0	0.386364	0	G|0.995;A|0.005	0.005	strong	.	URB1	176	.	NM_014825	exon31	c.C5084T	p.S1695L	AAGTGCGAGTAGT	.	PASS	Atlas-SNP
EXOC4	60412	hgsc.bcm.edu	37	7	133749164	133749164	+	Silent	SNP	G	G	A	rs6953296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	16	81	0	0.271186	0	G|0.353;A|0.647	0.647	strong	.	EXOC4	118	.	NM_021807	exon18	c.G2808A	p.Q936Q	CAGCCAGACTGGG	.	PASS	Atlas-SNP
HOXB5	3215	hgsc.bcm.edu	37	17	46669730	46669730	+	Silent	SNP	G	G	T	rs36049616	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203	76	187	0	0.374384	0	G|0.960;T|0.040	0.040	strong	.	HOXB5	20	.	NM_002147	exon2	c.C651A	p.R217R	CAGGTAGCGGTTG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677409	100677409	+	Silent	SNP	G	G	A	rs150735476	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	334	78	131	2	0.233533	0.0152672	G|0.957;A|0.043	0.043	strong	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G2712A	p.S904S	CCGTTCGTCTCCT	.	scavenged	Atlas-SNP
VWA2	340706	hgsc.bcm.edu	37	10	116045993	116045993	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	43	117	0	0.483146	0	.	.	none	.	VWA2	64	.	NM_001272046	exon11	c.G1293A	p.E431E	GGCAGAGCGTGGC	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55539395	55539395	+	Missense_Mutation	SNP	A	A	T	rs2293869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	34	75	0	0.708333	0	A|0.687;T|0.313	0.313	strong	.	RP1	429	.	NM_006269	exon4	c.A2953T	p.N985Y	GGAGATAATCTAT	.	PASS	Atlas-SNP
PRDM6	93166	hgsc.bcm.edu	37	5	122425832	122425832	+	Silent	SNP	G	G	T	rs13182369	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	19	21	0	1	0	G|0.741;T|0.259	0.259	strong	PRDM6,NS,NS,0,1	PRDM6	26	1	NM_001136239	exon2	c.G123T	p.A41A	CGCCGCGGGTCTC	.	PASS	Atlas-SNP
MATN4	8785	hgsc.bcm.edu	37	20	43933163	43933163	+	Silent	SNP	T	T	C	rs2233094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	19	115	0	0.246753	0	T|0.676;C|0.324	0.324	strong	MATN4,NS,carcinoma,0,1	MATN4	57	1	NM_030592	exon3	c.A348G	p.A116A	CTGGATTGCCAGT	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3413868	3413868	+	Missense_Mutation	SNP	C	C	G	rs4648506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14	12	46	0	0.857143	0	C|0.736;G|0.264	0.264	strong	.	MEGF6	91	.	NM_001409	exon27	c.G3410C	p.G1137A	GCAGCGCCAGGCG	.	PASS	Atlas-SNP
RRM1	6240	hgsc.bcm.edu	37	11	4141132	4141132	+	Silent	SNP	C	C	A	rs183484	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	152	194	0	0.980645	0	C|0.614;N|0.000	.	strong	.	RRM1	31	.	NM_001033	exon9	c.C850A	p.R284R	ACAGCTCGATATG	.	PASS	Atlas-SNP
DISP1	84976	hgsc.bcm.edu	37	1	223116472	223116472	+	Missense_Mutation	SNP	G	G	A	rs71583926	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207	134	168	0	0.647343	0	AAT|0.500;GAG|0.500	.	alt	.	DISP1	145	.	NM_032890	exon4	c.G307A	p.E103K	CATCCCGAGGCTG	.	PASS	Atlas-SNP
GNB5	10681	hgsc.bcm.edu	37	15	52433397	52433397	+	Silent	SNP	C	C	T	rs17612637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	24	186	0	0.255319	0	C|0.973;G|0.000;T|0.027	0.027	strong	.	GNB5	28	.	NM_016194	exon7	c.G567A	p.K189K	AACAGACTTCTTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512531	195512531	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	677	23	353	1	0.0339734	0.00283286	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G5920A	p.A1974T	AGGAAGCGTCGGT	.	scavenged	Atlas-SNP
ADSSL1	122622	hgsc.bcm.edu	37	14	105196230	105196230	+	Missense_Mutation	SNP	A	A	C	rs80097179	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46	45	31	0	0.978261	0	A|0.640;C|0.360	0.360	strong	.	ADSSL1	37	.	NM_199165	exon1	c.A1C	p.M1L	GTCGGCATGGTGG	.	PASS	Atlas-SNP
CPVL	54504	hgsc.bcm.edu	37	7	29152416	29152416	+	Silent	SNP	G	G	A	rs2011337	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	64	157	0	0.369942	0	G|0.869;A|0.131	0.131	strong	.	CPVL	60	.	NM_019029	exon3	c.C192T	p.G64G	GAAAGGGCCGACC	.	PASS	Atlas-SNP
LINGO1	84894	hgsc.bcm.edu	37	15	77907535	77907535	+	Silent	SNP	C	C	G	rs2271396	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	111	185	1	0.991071	0.00540541	C|0.298;G|0.702	0.702	strong	.	LINGO1	76	.	NM_032808	exon2	c.G714C	p.L238L	TCGGTACAGCCTC	.	PASS	Atlas-SNP
MPHOSPH8	54737	hgsc.bcm.edu	37	13	20224387	20224387	+	Silent	SNP	A	A	G	rs9578176	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	34	99	0	0.395349	0	A|0.886;G|0.114	0.114	strong	.	MPHOSPH8	58	.	NM_017520	exon5	c.A1563G	p.A521A	CCAAGCAGATGAG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17100552	17100552	+	Silent	SNP	A	A	G	rs1973093	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	48	125	0	0.40678	0	A|0.428;G|0.572	0.572	strong	CPAMD8,colon,carcinoma,-2,1	CPAMD8	192	1	NM_015692	exon13	c.T1437C	p.P479P	CCCCACAGGCTTC	.	PASS	Atlas-SNP
TEDDM1	127670	hgsc.bcm.edu	37	1	182369233	182369233	+	Missense_Mutation	SNP	A	A	G	rs6674281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190	115	149	0	0.605263	0	A|0.364;G|0.636	0.636	strong	.	TEDDM1	32	.	NM_172000	exon1	c.T388C	p.Y130H	GAGAATAAACGTG	.	PASS	Atlas-SNP
ZNF468	90333	hgsc.bcm.edu	37	19	53344118	53344118	+	Missense_Mutation	SNP	C	C	G	rs10419826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	52	193	0	0.358621	0	C|0.485;G|0.515	0.515	strong	ZNF468,NS,carcinoma,0,1	ZNF468	46	1	NM_001008801	exon4	c.G1429C	p.G477R	TCTGACCGAAGGT	.	scavenged	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31091209	31091209	+	Silent	SNP	T	T	C	rs3751855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	49	128	0	0.445455	0	A|0.000;C|0.415;T|0.584	0.415	strong	.	ZNF646	133	.	NM_014699	exon2	c.T3564C	p.T1188T	GGAGACTGCCGAG	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	37	5	79966029	79966029	+	Silent	SNP	G	G	A	rs1805355	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	129	275	0	0.513944	0	G|0.817;A|0.183	0.183	strong	.	MSH3	129	.	NM_002439	exon4	c.G693A	p.P231P	TACGCCGCTAGAA	.	PASS	Atlas-SNP
TPSG1	25823	hgsc.bcm.edu	37	16	1271983	1271983	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236	3	258	1	0.0127119	0.00387597	.	.	none	TPSG1,face,carcinoma,-2,1	TPSG1	19	1	NM_012467	exon6	c.T771C	p.R257R	AGGGACACGAGTG	.	scavenged	Atlas-SNP
WBP1	23559	hgsc.bcm.edu	37	2	74687781	74687781	+	Silent	SNP	G	G	A	rs61733470	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	255	117	294	1	0.458824	0.00340136	G|0.970;A|0.030	0.030	strong	.	WBP1	35	.	NM_012477	exon4	c.G783A	p.L261L	GGGGCTGTCTTCC	.	PASS	Atlas-SNP
MALT1	10892	hgsc.bcm.edu	37	18	56367823	56367823	+	Missense_Mutation	SNP	A	A	G	rs74847855	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41	22	38	0	0.536585	0	A|0.975;G|0.025	0.025	strong	.	MALT1	55	.	NM_173844	exon4	c.A649G	p.R217G	TTCCAGAGTAAGT	.	PASS	Atlas-SNP
HIST1H3C	8352	hgsc.bcm.edu	37	6	26045737	26045737	+	Silent	SNP	C	C	G	rs3752418	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	43	91	0	0.565789	0	C|0.881;G|0.119	0.119	strong	.	HIST1H3C	34	.	NM_003531	exon1	c.C99G	p.T33T	GGCCACCGGTGGC	.	PASS	Atlas-SNP
ASPRV1	151516	hgsc.bcm.edu	37	2	70188676	70188676	+	Missense_Mutation	SNP	T	T	C	rs3796097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	39	105	0	0.453488	0	T|0.345;C|0.655	0.655	strong	.	ASPRV1	41	.	NM_152792	exon1	c.A145G	p.T49A	GCAGAGTGGGGAT	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389101	1389101	+	Missense_Mutation	SNP	A	A	G	rs71614971	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	43	180	0	0.977273	0	A|0.752;G|0.248	0.248	strong	.	CRIPAK	185	.	NM_175918	exon1	c.A802G	p.S268G	ATGTGGAGTGCCC	.	PASS	Atlas-SNP
THBS4	7060	hgsc.bcm.edu	37	5	79361265	79361265	+	Missense_Mutation	SNP	G	G	C	rs1866389	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	59	164	0	0.453846	0	G|0.840;C|0.160	0.160	strong	.	THBS4	82	.	NM_003248	exon9	c.G1159C	p.A387P	AATGGAGCGTGCG	.	PASS	Atlas-SNP
GRIK1	2897	hgsc.bcm.edu	37	21	31062070	31062070	+	Silent	SNP	T	T	G	rs363538	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	393	248	351	0	0.631043	0	T|0.690;G|0.310	0.310	strong	.	GRIK1	293	.	NM_175611	exon3	c.A522C	p.T174T	CACCACTGTCACT	.	PASS	Atlas-SNP
EDDM3B	64184	hgsc.bcm.edu	37	14	21238318	21238318	+	Silent	SNP	G	G	A	rs3827905	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180	105	177	1	0.583333	0.00564972	G|0.447;A|0.553	0.553	strong	.	EDDM3B	23	.	NM_022360	exon2	c.G9A	p.S3S	GGCATCGTCTCTA	.	PASS	Atlas-SNP
EEA1	8411	hgsc.bcm.edu	37	12	93202801	93202801	+	Silent	SNP	C	C	T	rs7970286	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	10	132	0	0.153846	0	C|0.618;T|0.382	0.382	strong	.	EEA1	104	.	NM_003566	exon18	c.G2331A	p.E777E	TTCCTTCTCCATT	.	PASS	Atlas-SNP
TPO	7173	hgsc.bcm.edu	37	2	1499899	1499899	+	Silent	SNP	C	C	T	rs732608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	46	85	0	0.469388	0	C|0.585;A|0.003	.	strong	TPO,NS,malignant_melanoma,+2,2	TPO	224	2	NM_001206744	exon12	c.C2145T	p.P715P	ATTCCCCGAAGAC	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	37	17	27442710	27442710	+	Silent	SNP	G	G	C	rs28587908	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	63	128	0	0.504	0	G|0.893;C|0.107	0.107	strong	.	MYO18A	217	.	NM_078471	exon12	c.C2199G	p.P733P	CTCCTCGGGGCCC	.	PASS	Atlas-SNP
CDC16	8881	hgsc.bcm.edu	37	13	115004935	115004935	+	Silent	SNP	T	T	C	rs2296970	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	60	77	0	0.967742	0	T|0.563;C|0.437	0.437	strong	.	CDC16	50	.	NM_003903	exon5	c.T351C	p.P117P	AGATCCTTCCAGC	.	PASS	Atlas-SNP
TTC38	55020	hgsc.bcm.edu	37	22	46682976	46682976	+	Missense_Mutation	SNP	C	C	T	rs55653327	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	28	68	0	0.636364	0	C|0.941;T|0.059	0.059	strong	.	TTC38	40	.	NM_017931	exon10	c.C841T	p.P281S	ATCCTTCCCAGCC	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	56000600	56000600	+	Missense_Mutation	SNP	G	G	T	rs3919907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	36	117	0	0.387097	0	G|0.810;T|0.190	0.190	strong	OR5T2,NS,carcinoma,+1,1	OR5T2	107	1	NM_001004746	exon1	c.C62A	p.S21Y	CAAAAAGAATGAA	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57175121	57175121	+	Silent	SNP	G	G	A	rs115625349	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121	58	151	0	0.479339	0	G|0.942;A|0.058	0.058	strong	.	ZNF835	106	.	NM_001005850	exon2	c.C1446T	p.A482A	GCTGAAGGCCTTC	.	PASS	Atlas-SNP
TTC17	55761	hgsc.bcm.edu	37	11	43472746	43472746	+	Silent	SNP	C	C	T	rs11551137	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	31	51	0	0.455882	0	C|0.929;T|0.071	0.071	strong	.	TTC17	112	.	NM_018259	exon21	c.C2961T	p.L987L	AAATCTCGGCAAA	.	PASS	Atlas-SNP
RCOR1	23186	hgsc.bcm.edu	37	14	103173756	103173756	+	Silent	SNP	C	C	A	rs149418829	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	51	161	0	0.314815	0	C|0.990;A|0.010	0.010	strong	.	RCOR1	39	.	NM_015156	exon5	c.C567A	p.T189T	CTTTACCCCTTTC	.	PASS	Atlas-SNP
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299467	125299467	+	Missense_Mutation	SNP	G	G	T	rs10126452	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	142	263	0	1	0	G|0.479;T|0.521	0.521	strong	.	DCAF12L2	157	.	NM_001013628	exon1	c.C441A	p.H147Q	GCCCTGGTGGGCC	.	PASS	Atlas-SNP
OXR1	55074	hgsc.bcm.edu	37	8	107719336	107719336	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	2	96	0	0.0143885	0	.	.	none	OXR1_ENST00000442977,NS,carcinoma,+1,3	OXR1	190	3	NM_001198532	exon8	c.T1590C	p.A530A	AGAAGCTAAGCAT	.	scavenged	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20673867	20673867	+	Silent	SNP	G	G	A	rs2276433	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	170	150	0	0.977012	0	G|0.601;T|0.003	.	strong	.	SLC6A5	151	.	NM_004211	exon15	c.G2103A	p.E701E	GTGGGAGCCCATG	.	PASS	Atlas-SNP
MRTO4	51154	hgsc.bcm.edu	37	1	19584004	19584004	+	Silent	SNP	G	G	A	rs1042380	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	18	56	0	0.666667	0	G|0.711;A|0.289	0.289	strong	.	MRTO4	17	.	NM_016183	exon5	c.G330A	p.E110E	AAAGGAGGAGGTG	.	PASS	Atlas-SNP
NLRP7	199713	hgsc.bcm.edu	37	19	55450696	55450696	+	Silent	SNP	G	G	A	rs775880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	23	123	0	0.133721	0	G|0.908;A|0.092	0.092	strong	.	NLRP7	411	.	NM_001127255	exon4	c.C1491T	p.I497I	GTCCCCGATGTCC	.	PASS	Atlas-SNP
FECH	2235	hgsc.bcm.edu	37	18	55247313	55247313	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	4	161	0	0.0208333	0	.	.	none	FECH,right_lower_lobe,carcinoma,0,2	FECH	42	2	NM_001012515	exon2	c.G186A	p.P62P	CTTCTGCGGTTGA	.	scavenged	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324145	31324145	+	Missense_Mutation	SNP	A	A	C	rs9266150	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	41	124	1	0.353448	0.00806452	A|0.886;C|0.114	0.114	strong	HLA-B,colon,carcinoma,+1,1	HLA-B	54	1	NM_005514	exon3	c.T418G	p.Y140D	AGGCGTACTGGTC	.	scavenged	Atlas-SNP
CHRD	8646	hgsc.bcm.edu	37	3	184099378	184099378	+	Silent	SNP	C	C	A	rs35929225	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	50	110	0	0.793651	0	C|0.808;A|0.192	0.192	strong	.	CHRD	149	.	NM_003741	exon4	c.C477A	p.G159G	GCCAGGCGCTGAG	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	37	15	24921771	24921771	+	Missense_Mutation	SNP	G	G	C	rs1563102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	32	104	1	0.516129	0.00961538	G|0.744;C|0.256	0.256	strong	C15orf2,NS,carcinoma,0,2	.	.	2	NM_018958	exon1	c.G757C	p.G253R	CATCTTGGAAAGC	.	scavenged	Atlas-SNP
SIL1	64374	hgsc.bcm.edu	37	5	138456815	138456815	+	Silent	SNP	T	T	C	rs3088052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	11	144	0	0.150685	0	T|0.513;C|0.487	0.487	strong	.	SIL1	31	.	NM_001037633	exon4	c.A153G	p.T51T	TCTCTCTGTTTCT	.	PASS	Atlas-SNP
ERMAP	114625	hgsc.bcm.edu	37	1	43296173	43296173	+	Silent	SNP	C	C	T	rs33950227	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	73	166	1	0.760417	0.0060241	C|0.814;T|0.186	0.186	strong	.	ERMAP	30	.	NM_001017922	exon3	c.C54T	p.L18L	CCCTCTCGTCTTC	.	PASS	Atlas-SNP
DTD2	112487	hgsc.bcm.edu	37	14	31922515	31922515	+	Silent	SNP	G	G	A	rs61754291	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85	83	99	0	0.976471	0	G|0.977;A|0.023	0.023	strong	.	.	.	.	NM_080664	exon2	c.C147T	p.F49F	TCCCTTGAAAAAG	.	PASS	Atlas-SNP
PKN1	5585	hgsc.bcm.edu	37	19	14581063	14581063	+	Silent	SNP	A	A	G	rs1042728	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110	43	100	0	0.390909	0	A|0.837;G|0.163	0.163	strong	.	PKN1	99	.	NM_213560	exon19	c.A2400G	p.R800R	CACGCGAGCTGTG	.	PASS	Atlas-SNP
SASH1	23328	hgsc.bcm.edu	37	6	148841011	148841011	+	Silent	SNP	C	C	T	rs13196292	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	12	9	0	0.545455	0	C|0.926;T|0.074	0.074	strong	SASH1,NS,carcinoma,0,2	SASH1	123	2	NM_015278	exon10	c.C1191T	p.L397L	GGGTCTCGGGTCC	.	PASS	Atlas-SNP
PLEKHG7	440107	hgsc.bcm.edu	37	12	93147901	93147901	+	Silent	SNP	C	C	T	rs74784157	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	30	178	0	0.23622	0	C|0.947;T|0.053	0.053	strong	.	PLEKHG7	38	.	NM_001004330	exon6	c.C351T	p.H117H	GCTCCACGTGCCA	.	PASS	Atlas-SNP
KRT1	3848	hgsc.bcm.edu	37	12	53069243	53069243	+	Missense_Mutation	SNP	T	T	C	rs77846840	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	25	8	17	0	0.32	0	T|0.500;C|0.500	0.500	weak	.	KRT1	110	.	NM_006121	exon9	c.A1669G	p.S557G	AGCTGCTACCTCC	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125448960	125448960	+	Silent	SNP	C	C	T	rs4076777	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	53	68	0	0.981481	0	C|0.671;T|0.329	0.329	strong	.	DHX37	114	.	NM_032656	exon15	c.G2025A	p.T675T	GGGCTCCGTCCGT	.	PASS	Atlas-SNP
TRDMT1	1787	hgsc.bcm.edu	37	10	17243610	17243610	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18	12	44	0	0.666667	0	.	.	none	.	TRDMT1	46	.	NM_004412	exon1	c.G24A	p.E8E	GTATAGCTCCAGC	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732457	138732457	+	Silent	SNP	G	G	A	rs3735008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	12	154	1	0.136364	0.00649351	G|0.530;A|0.470	0.470	strong	ZC3HAV1,colon,carcinoma,0,1	ZC3HAV1	75	1	NM_020119	exon13	c.C2592T	p.F864F	GCTGTCGAACTGT	.	scavenged	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101831995	101831995	+	Missense_Mutation	SNP	G	G	A	rs10519	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153	74	141	0	0.48366	0	G|0.860;A|0.140	0.140	strong	COL15A1,colon,carcinoma,0,1	COL15A1	211	1	NM_001855	exon42	c.G3994A	p.V1332I	CATGGCGTCCGCC	.	PASS	Atlas-SNP
BPIFA2	140683	hgsc.bcm.edu	37	20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	rs17304572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	58	148	0	0.460317	0	A|0.994;G|0.006	0.006	strong	.	.	.	.	NM_080574	exon4	c.A337G	p.K113E	GATGTCAAAGCTG	.	PASS	Atlas-SNP
CASZ1	54897	hgsc.bcm.edu	37	1	10713765	10713765	+	Silent	SNP	T	T	C	rs284294	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	17	77	0	0.894737	0	T|0.453;C|0.547	0.547	strong	CASZ1,colon,carcinoma,0,1	CASZ1	150	1	NM_001079843	exon11	c.A2349G	p.S783S	GGGGATTGAGCCA	.	PASS	Atlas-SNP
JAK2	3717	hgsc.bcm.edu	37	9	5072551	5072551	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	4	170	0	0.028169	0	.	.	none	JAK2,caecum,carcinoma,0,3	JAK2	35466	3	NM_004972	exon13	c.A1701G	p.V567V	AGAAGTAGGAGAC	.	scavenged	Atlas-SNP
INF2	64423	hgsc.bcm.edu	37	14	105179184	105179184	+	Missense_Mutation	SNP	G	G	A	rs142678449	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	50	121	0	0.344828	0	G|0.992;A|0.008	0.008	strong	.	INF2	148	.	NM_022489	exon18	c.G2630A	p.R877Q	CCTTCCGGGCACT	.	PASS	Atlas-SNP
MANBA	4126	hgsc.bcm.edu	37	4	103557077	103557077	+	Missense_Mutation	SNP	G	G	A	rs2866413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	126	134	1	0.984375	0.00746269	G|0.448;A|0.552	0.552	strong	MANBA,NS,adenoma,0,1	MANBA	78	1	NM_005908	exon15	c.C2102T	p.T701M	TAGAACGTGTTTT	.	PASS	Atlas-SNP
DGCR14	8220	hgsc.bcm.edu	37	22	19122665	19122665	+	Silent	SNP	C	C	T	rs2240111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	103	171	0	0.613095	0	C|0.835;A|0.001	.	strong	.	DGCR14	43	.	NM_022719	exon9	c.G1059A	p.E353E	CAGCCGCTCCCTG	.	PASS	Atlas-SNP
SLCO1C1	53919	hgsc.bcm.edu	37	12	20885931	20885931	+	Silent	SNP	A	A	G	rs16923154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206	114	208	0	0.553398	0	A|0.919;G|0.081	0.081	strong	SLCO1C1,NS,carcinoma,0,1	SLCO1C1	216	1	NM_017435	exon10	c.A1275G	p.A425A	AGCTGCAAAACTC	.	PASS	Atlas-SNP
ZBTB1	22890	hgsc.bcm.edu	37	14	64988279	64988279	+	Silent	SNP	A	A	G	rs28626711	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	87	146	0	0.540373	0	A|0.827;G|0.173	0.173	strong	.	ZBTB1	93	.	NM_014950	exon2	c.A57G	p.E19E	AAGAGAATGGGGT	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113565933	113565933	+	Missense_Mutation	SNP	G	G	A	rs34598602	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	43	62	0	0.518072	0	G|0.957;A|0.043	0.043	strong	.	RASAL1	89	.	NM_004658	exon4	c.C173T	p.T58M	TGCACCGTGTACT	.	PASS	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55873334	55873334	+	Silent	SNP	A	A	G	rs11227212	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	63	174	0	0.406452	0	A|0.902;G|0.098	0.098	strong	OR8H2,NS,carcinoma,0,1	OR8H2	117	1	NM_001005200	exon1	c.A816G	p.Q272Q	AGATCAAGTGGCT	.	PASS	Atlas-SNP
TXNDC16	57544	hgsc.bcm.edu	37	14	52923820	52923820	+	Missense_Mutation	SNP	T	T	C	rs61744423	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260	149	227	1	0.573077	0.00440529	T|0.983;C|0.017	0.017	strong	.	TXNDC16	59	.	NM_020784	exon17	c.A1691G	p.D564G	AAAACATCTTCTT	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145508340	145508340	+	Silent	SNP	A	A	G	rs2895647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	292	288	284	1	0.986301	0.00352113	A|0.799;G|0.201	0.201	strong	.	LARS	100	.	NM_020117	exon27	c.T2775C	p.T925T	TTTGTCAGTCTTC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467571	10467571	+	Missense_Mutation	SNP	C	C	T	rs200175359		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	11	189	1	0.0544554	0.00529101	.	.	weak	RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	NM_178857	exon4	c.G4037A	p.G1346E	CCTTCTCCTTCTG	.	scavenged	Atlas-SNP
SYN1	6853	hgsc.bcm.edu	37	X	47466361	47466361	+	Silent	SNP	A	A	G	rs1142636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	90	253	2	0.947368	0.00790514	T|0.141;G|0.294;C|0.097;A|0.468	0.294	strong	.	SYN1	84	.	NM_006950	exon3	c.T510C	p.N170N	CACCCCATTCCGA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384998	16384998	+	Silent	SNP	G	G	C	rs1807285	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	9	4	18	0	0.444444	0	G|0.706;C|0.294	0.294	strong	FAM131C,NS,carcinoma,-1,2	FAM131C	21	2	NM_182623	exon7	c.C777G	p.P259P	GCCCGGGGGGTGG	.	scavenged	Atlas-SNP
OGFR	11054	hgsc.bcm.edu	37	20	61444693	61444693	+	Missense_Mutation	SNP	G	G	A	rs35813009	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	6	2	31	0	0.333333	0	G|0.780;A|0.220	0.220	strong	OGFR,rectum,carcinoma,0,2	OGFR	63	2	NM_007346	exon7	c.G1726A	p.E576K	CCAGCCGAGAGCC	.	scavenged	Atlas-SNP
PSMB1	5689	hgsc.bcm.edu	37	6	170862300	170862300	+	Missense_Mutation	SNP	G	G	C	rs12717	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	22	49	0	0.52381	0	G|0.580;C|0.420	0.420	strong	.	PSMB1	12	.	NM_002793	exon1	c.C31G	p.P11A	TGCCAGGAGCCGA	.	PASS	Atlas-SNP
TBXA2R	6915	hgsc.bcm.edu	37	19	3595923	3595923	+	Silent	SNP	G	G	A	rs1131882	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	46	97	0	0.630137	0	G|0.733;A|0.267	0.267	strong	TBXA2R,NS,carcinoma,0,1	TBXA2R	31	1	NM_201636	exon3	c.C795T	p.I265I	CTGGGCGATGAAG	.	PASS	Atlas-SNP
TRIML1	339976	hgsc.bcm.edu	37	4	189060900	189060900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	2	254	1	0.0149254	0.00393701	.	.	none	TRIML1,NS,carcinoma,0,1	TRIML1	126	1	NM_178556	exon1	c.C188T	p.P63L	AGGGCCCGCATTT	.	scavenged	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8191401	8191401	+	Silent	SNP	G	G	A	rs3813778	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	33	85	1	0.55	0.0117647	G|0.684;A|0.316	0.316	strong	FBN3,NS,carcinoma,0,1	FBN3	300	1	NM_032447	exon19	c.C2505T	p.C835C	GGTGGCGCAGCAC	.	scavenged	Atlas-SNP
ATP2A3	489	hgsc.bcm.edu	37	17	3828702	3828702	+	Silent	SNP	T	T	C	rs887387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27	8	30	0	0.296296	0	T|0.680;C|0.320	0.320	strong	.	ATP2A3	148	.	NM_174955	exon22	c.A3102G	p.R1034R	CTCCACTCTGTTC	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023893	25023893	+	Missense_Mutation	SNP	G	G	A	rs201313233	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	719	147	561	1	0.204451	0.00178253	G|0.983;A|0.017	0.017	strong	GGT1,scalp,carcinoma,0,10	GGT1	68	10	NM_013430	exon13	c.G1283A	p.S428N	CTCCCAGCATCAC	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1075920	1075920	+	Missense_Mutation	SNP	G	G	A	rs11825977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	46	76	0	0.575	0	G|0.851;A|0.149	0.149	strong	.	MUC2	614	.	NM_002457	exon2	c.G346A	p.V116M	GGGGCCGTGTGAG	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82451984	82451984	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	12	60	0	0.193548	0	.	.	none	.	PCLO	1506	.	NM_014510	exon20	c.A14618C	p.E4873A	GATTTCTCAATGG	.	PASS	Atlas-SNP
SYT15	83849	hgsc.bcm.edu	37	10	46967514	46967514	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	15	141	0	0.103448	0	.	.	none	.	SYT15	165	.	NM_031912	exon4	c.A563G	p.Y188C	AGCAGGTAGAGCT	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225533931	225533931	+	Missense_Mutation	SNP	A	A	G	rs17522489	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142	79	148	0	0.556338	0	A|0.887;G|0.113	0.113	strong	.	DNAH14	300	.	NM_001373	exon68	c.A10667G	p.Q3556R	AAGAACAAGAACA	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33493188	33493188	+	Missense_Mutation	SNP	T	T	A	rs193179333	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	19	154	3	0.107955	0.0194805	T|0.902;A|0.097	0.097	strong	RHPN2,colon,carcinoma,0,9	RHPN2	107	9	NM_033103	exon9	c.A1070T	p.H357L	AAGTAGTGGGCCA	.	scavenged	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119938	19119938	+	Silent	SNP	G	G	A	rs1052773	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	44	52	0	0.977778	0	A|0.201;C|0.006	0.201	strong	.	TSSK2	29	.	NM_053006	exon1	c.G1026A	p.R342R	CTCCAGGGCCAAA	.	PASS	Atlas-SNP
MGAT1	4245	hgsc.bcm.edu	37	5	180219304	180219304	+	Missense_Mutation	SNP	C	C	T	rs7726005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	44	86	0	0.52381	0	C|0.844;T|0.156	0.156	strong	.	MGAT1	48	.	NM_001114617	exon3	c.G668A	p.R223Q	GTGGCCCGAAAGT	.	PASS	Atlas-SNP
MYEOV	26579	hgsc.bcm.edu	37	11	69063393	69063393	+	Missense_Mutation	SNP	T	T	C	rs7103126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	261	107	302	0	0.409962	0	T|0.606;C|0.394	0.394	strong	.	MYEOV	42	.	NM_138768	exon3	c.T476C	p.V159A	CAAGGGTGGTGGG	.	PASS	Atlas-SNP
CTNS	1497	hgsc.bcm.edu	37	17	3563221	3563221	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174	46	134	0	0.264368	0	.	.	none	.	CTNS	42	.	NM_001031681	exon11	c.G922A	p.G308R	TTCACCGGGGGCA	.	PASS	Atlas-SNP
ECI1	1632	hgsc.bcm.edu	37	16	2301520	2301520	+	Silent	SNP	G	G	C	rs11541763	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21	10	19	0	0.47619	0	G|0.917;C|0.083	0.083	strong	ECI1,NS,carcinoma,0,1	ECI1	20	1	NM_001178029	exon1	c.C48G	p.R16R	ACCCGCGCGGAGC	.	PASS	Atlas-SNP
OR1A2	26189	hgsc.bcm.edu	37	17	3101578	3101578	+	Missense_Mutation	SNP	G	G	T	rs2241091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	157	224	0	0.993671	0	G|0.704;T|0.295	0.295	strong	.	OR1A2	52	.	NM_012352	exon1	c.G766T	p.G256C	ACGATGGGCATGT	.	PASS	Atlas-SNP
DACT2	168002	hgsc.bcm.edu	37	6	168708763	168708763	+	Silent	SNP	C	C	A	rs149504015	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	26	68	0	0.553191	0	C|0.996;A|0.004	0.004	strong	.	DACT2	46	.	NM_214462	exon4	c.G1674T	p.G558G	GGAGCGCCCGGGT	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76121509	76121509	+	Silent	SNP	C	C	T	rs2302541	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	697	144	809	3	0.2066	0.00370828	C|1.000;|0.000	.	weak	DTX2,NS,carcinoma,0,1	DTX2	64	1	NM_001102596	exon3	c.C948T	p.S316S	AGGGAGCGTCCCT	.	scavenged	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5863113	5863113	+	Silent	SNP	G	G	A	rs10742810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	78	156	0	0.565217	0	G|0.605;A|0.395	0.395	strong	OR52E6,NS,carcinoma,0,1	OR52E6	70	1	NM_001005167	exon1	c.C15T	p.N5N	GGTGTCGTTAGCT	.	PASS	Atlas-SNP
CEP128	145508	hgsc.bcm.edu	37	14	81259254	81259254	+	Silent	SNP	A	A	T	rs45535733	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	315	179	220	1	0.568254	0.00454545	A|0.960;T|0.040	0.040	strong	.	CEP128	146	.	NM_152446	exon13	c.T1410A	p.A470A	TTTCAGAGCCTCT	.	PASS	Atlas-SNP
IRS1	3667	hgsc.bcm.edu	37	2	227662753	227662753	+	Silent	SNP	C	C	T	rs2234931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	47	99	0	0.701493	0	C|0.941;T|0.059	0.059	strong	IRS1,rectum,carcinoma,-2,1	IRS1	141	1	NM_005544	exon1	c.G702A	p.G234G	GAACTCCCCGGGC	.	PASS	Atlas-SNP
LCP2	3937	hgsc.bcm.edu	37	5	169685163	169685163	+	Silent	SNP	C	C	T	rs315717	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	134	155	0	0.978102	0	C|0.429;T|0.571	0.571	strong	.	LCP2	133	.	NM_005565	exon16	c.G978A	p.Q326Q	AGGTCTCTGATGC	.	PASS	Atlas-SNP
C9orf72	203228	hgsc.bcm.edu	37	9	27556780	27556780	+	Silent	SNP	G	G	A	rs10122902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125	64	130	0	0.512	0	G|0.789;A|0.211	0.211	strong	.	C9orf72	48	.	NM_018325	exon8	c.C870T	p.S290S	CACAAAGCTTCCA	.	PASS	Atlas-SNP
CELA1	1990	hgsc.bcm.edu	37	12	51739625	51739625	+	Missense_Mutation	SNP	C	C	T	rs74336876	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	26	66	0	0.490566	0	C|0.995;T|0.005	0.005	strong	.	CELA1	39	.	NM_001971	exon2	c.G53A	p.R18H	ACTACGCGGGCAT	.	PASS	Atlas-SNP
ANKRD61	100310846	hgsc.bcm.edu	37	7	6075823	6075823	+	Missense_Mutation	SNP	A	A	T	rs2302334	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	99	116	0	0.626582	0	A|0.619;T|0.381	0.381	strong	.	.	.	.	NM_001271700	exon3	c.A1063T	p.M355L	GGAATCATGCTAC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017797	1017797	+	Silent	SNP	C	C	G	rs76800954	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1003	67	1185	72	0.0667996	0.0607595	C|0.500;G|0.500	0.500	strong	MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	NM_005961	exon31	c.G5004C	p.A1668A	TGTTGGCGCTGTG	.	scavenged	Atlas-SNP
C9orf171	389799	hgsc.bcm.edu	37	9	135374898	135374898	+	Silent	SNP	T	T	C	rs562350	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129	65	117	2	0.503876	0.017094	T|0.356;C|0.644	0.644	strong	C9orf171,NS,carcinoma,0,2	C9orf171	53	2	NM_207417	exon4	c.T543C	p.N181N	GCTCAATGACATC	.	scavenged	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152082484	152082484	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	4	153	5	0.0180995	0.0326797	.	.	none	TCHH,NS,carcinoma,0,4	TCHH	275	4	NM_007113	exon3	c.C3209A	p.T1070K	CTTCTCGTCTCCC	.	scavenged	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22363610	22363610	+	Silent	SNP	A	A	G	rs201622264	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43	11	43	1	0.255814	0.0232558	A|0.793;G|0.207	0.207	strong	ZNF676,rectum,carcinoma,0,2	ZNF676	146	2	NM_001001411	exon3	c.T909C	p.H303H	TCCAGTATGAATT	.	scavenged	Atlas-SNP
DDX50	79009	hgsc.bcm.edu	37	10	70700944	70700944	+	Silent	SNP	A	A	G	rs5030900	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	71	177	1	0.731959	0.00564972	A|0.368;G|0.632	0.632	strong	.	DDX50	65	.	NM_024045	exon13	c.A1884G	p.G628G	GAAAGGAAATATG	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89839766	89839766	+	Missense_Mutation	SNP	G	G	C	rs17232910	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114	12	97	0	0.105263	0	G|0.936;C|0.064	0.064	strong	.	FANCA	99	.	NM_000135	exon22	c.C1927G	p.P643A	AGTTGGGTTCTGC	.	PASS	Atlas-SNP
PRUNE2	158471	hgsc.bcm.edu	37	9	79324408	79324408	+	Missense_Mutation	SNP	T	T	C	rs41289953	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	86	206	0	0.483146	0	T|0.964;C|0.036	0.036	strong	.	PRUNE2	331	.	NM_015225	exon8	c.A2782G	p.K928E	CTCCTTTCTTCAT	.	PASS	Atlas-SNP
TGIF1	7050	hgsc.bcm.edu	37	18	3457641	3457641	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	3	175	1	0.0170455	0.00571429	.	.	none	TGIF1,colon,carcinoma,0,1	TGIF1	41	1	NM_170695	exon3	c.C909T	p.C303C	GATCTGCCATACC	.	scavenged	Atlas-SNP
APOBEC2	10930	hgsc.bcm.edu	37	6	41029342	41029342	+	Missense_Mutation	SNP	T	T	C	rs2076472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	80	145	0	0.506329	0	T|0.816;C|0.184	0.184	strong	.	APOBEC2	30	.	NM_006789	exon2	c.T407C	p.I136T	GCATTATCAAAAC	.	PASS	Atlas-SNP
KIAA1107	23285	hgsc.bcm.edu	37	1	92646021	92646021	+	Silent	SNP	G	G	A	rs1483022	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	24	146	0	0.235294	0	G|0.301;A|0.699	0.699	strong	.	KIAA1107	60	.	NM_015237	exon8	c.G1467A	p.K489K	GTCAAAGAAAGGT	.	PASS	Atlas-SNP
ACPP	55	hgsc.bcm.edu	37	3	132075554	132075554	+	Silent	SNP	T	T	C	rs3181784	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	57	139	1	0.483051	0.00719424	T|0.657;C|0.343	0.343	strong	ACPP_ENST00000351273,NS,carcinoma,0,4	ACPP	118	4	NM_001099	exon10	c.T993C	p.Y331Y	GTACTATCGGAAT	.	scavenged	Atlas-SNP
UBR5	51366	hgsc.bcm.edu	37	8	103307434	103307434	+	Silent	SNP	G	G	A	rs34739767	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	47	150	0	0.235	0	G|0.972;A|0.028	0.028	strong	.	UBR5	285	.	NM_015902	exon31	c.C4056T	p.D1352D	GTACGGGTCTTTA	.	PASS	Atlas-SNP
OR51F2	119694	hgsc.bcm.edu	37	11	4842866	4842866	+	Missense_Mutation	SNP	A	A	G	rs35003053	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	85	195	1	0.534591	0.00512821	A|0.890;G|0.110	0.110	strong	OR51F2,NS,carcinoma,+1,1	OR51F2	72	1	NM_001004753	exon1	c.A251G	p.D84G	CCACAGACCTGAG	.	PASS	Atlas-SNP
CCDC30	728621	hgsc.bcm.edu	37	1	43042703	43042703	+	Silent	SNP	C	C	T	rs12049046	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	17	172	0	0.197674	0	C|0.778;T|0.222	0.222	strong	.	CCDC30	78	.	NM_001080850	exon7	c.C868T	p.L290L	ATTGAACTAAAGC	.	PASS	Atlas-SNP
DAPK1	1612	hgsc.bcm.edu	37	9	90283514	90283514	+	Silent	SNP	C	C	T	rs3750538	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	45	73	0	0.592105	0	C|0.938;T|0.062	0.062	strong	.	DAPK1	329	.	NM_004938	exon19	c.C1926T	p.D642D	ACAGGACGGAAAG	.	PASS	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66648199	66648199	+	Silent	SNP	G	G	A	rs7776775	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	70	142	0	0.569106	0	.	.	weak	.	TYW1	71	.	NM_018264	exon14	c.G1785A	p.G595G	CCTGGGGAATCCT	.	PASS	Atlas-SNP
ZNF93	81931	hgsc.bcm.edu	37	19	20044041	20044041	+	Missense_Mutation	SNP	G	G	T	rs12151060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	101	209	0	0.517949	0	G|0.821;T|0.179	0.179	strong	.	ZNF93	81	.	NM_031218	exon4	c.G277T	p.D93Y	ATAAAAGATTCTT	.	PASS	Atlas-SNP
PRDM2	7799	hgsc.bcm.edu	37	1	14109114	14109114	+	Silent	SNP	A	A	G	rs1203651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	17	78	0	0.346939	0	A|0.657;G|0.343	0.343	strong	.	PRDM2	147	.	NM_015866	exon8	c.A4824G	p.S1608S	AACATCACGGAGC	.	PASS	Atlas-SNP
FRMD1	79981	hgsc.bcm.edu	37	6	168463624	168463624	+	Missense_Mutation	SNP	G	G	A	rs902393	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	69	146	0	0.526718	0	G|0.932;A|0.068	0.068	strong	.	FRMD1	52	.	NM_024919	exon7	c.C820T	p.R274C	TGGGACGACCTTC	.	PASS	Atlas-SNP
SERPINA6	866	hgsc.bcm.edu	37	14	94772504	94772504	+	Silent	SNP	G	G	A	rs1042394	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160	106	112	0	0.6625	0	G|0.775;A|0.225	0.225	strong	.	SERPINA6	102	.	NM_001756	exon4	c.C936T	p.L312L	ATCTCCGAGGTCA	.	PASS	Atlas-SNP
POLR2D	5433	hgsc.bcm.edu	37	2	128610648	128610648	+	Silent	SNP	T	T	C	rs10210695	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148	59	141	0	0.398649	0	T|0.848;C|0.152	0.152	strong	.	POLR2D	13	.	NM_004805	exon2	c.A105G	p.S35S	AACTTCTGAATTT	.	PASS	Atlas-SNP
GDI1	2664	hgsc.bcm.edu	37	X	153667176	153667176	+	Silent	SNP	T	T	C	rs4834	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	78	207	0	0.951219	0	0|0.001;C|0.314	0.314	strong	.	GDI1	36	.	NM_001493	exon3	c.T219C	p.N73N	CTGGAATGTTGAC	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	rs34551253	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	10	6	15	0	0.6	0	C|0.983;T|0.017	0.017	strong	.	TRPM5	86	.	NM_014555	exon9	c.G1366A	p.A456T	GCCCCGCGGGTGG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6568213	6568213	+	Missense_Mutation	SNP	T	T	C	rs58186801	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	25	54	0	0.510204	0	T|0.825;C|0.175	0.175	strong	.	DNHD1	198	.	NM_144666	exon21	c.T6044C	p.M2015T	CAGCCATGGAGGA	.	PASS	Atlas-SNP
MRGPRF	116535	hgsc.bcm.edu	37	11	68773089	68773089	+	Missense_Mutation	SNP	C	C	T	rs151254404	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	56	122	0	0.474576	0	C|1.000;T|0.000	0.000	weak	.	MRGPRF	22	.	NM_001098515	exon3	c.G689A	p.R230Q	TGGCGCCGTCGGG	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746416	143746416	+	Silent	SNP	A	A	G	rs754957	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	62	115	0	0.430556	0	A|0.478;G|0.522	0.522	strong	.	.	.	.	NM_003724	exon2	c.T1062C	p.H354H	GCGGGCATGGGGG	.	PASS	Atlas-SNP
CCDC159	126075	hgsc.bcm.edu	37	19	11465311	11465311	+	Silent	SNP	C	C	T	rs374274390		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	59	133	0	0.475806	0	.	.	weak	.	CCDC159	35	.	NM_001080503	exon10	c.C828T	p.S276S	TGACTCCGACTGT	.	PASS	Atlas-SNP
C1QTNF7	114905	hgsc.bcm.edu	37	4	15443951	15443951	+	Missense_Mutation	SNP	C	C	T	rs201630756	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	2	144	0	0.0133333	0	C|1.000;T|0.000	0.000	strong	C1QTNF7,NS,carcinoma,-1,1	C1QTNF7	36	1	NM_001135170	exon3	c.C419T	p.P140L	GGGACCCGGGGCT	.	scavenged	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68682402	68682402	+	Missense_Mutation	SNP	A	A	G	rs10896380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	68	187	2	0.447368	0.0106952	A|0.824;G|0.176	0.176	strong	IGHMBP2,NS,carcinoma,-1,2	IGHMBP2	83	2	NM_002180	exon6	c.A823G	p.I275V	GAGTCCATTCAGC	.	scavenged	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	21151913	21151913	+	Missense_Mutation	SNP	G	G	T	rs72780891	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217	90	239	1	0.414747	0.0041841	G|0.825;T|0.175	0.175	strong	DNAH3_ENST00000261383,colon,carcinoma,0,2	DNAH3	1142	2	NM_017539	exon5	c.C640A	p.Q214K	CCTGCTGTAACAT	.	scavenged	Atlas-SNP
AFAP1L2	84632	hgsc.bcm.edu	37	10	116091629	116091629	+	Missense_Mutation	SNP	T	T	C	rs117043677	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	74	127	0	0.536232	0	T|0.995;C|0.005	0.005	strong	.	AFAP1L2	90	.	NM_032550	exon4	c.A248G	p.N83S	TCCCCATTGGGTA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677630	100677630	+	Missense_Mutation	SNP	C	C	T	rs78990442	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	639	350	197	0	0.547731	0	C|0.935;T|0.065	0.065	strong	.	MUC17	804	.	NM_001040105	exon3	c.C2933T	p.P978L	CGACTCCTAGTGA	.	PASS	Atlas-SNP
NPSR1	387129	hgsc.bcm.edu	37	7	34818113	34818113	+	Missense_Mutation	SNP	A	A	T	rs324981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128	82	121	0	0.640625	0	A|0.515;T|0.485	0.485	strong	.	NPSR1	134	.	NM_207172	exon3	c.A320T	p.N107I	ATATTAATTGGCG	.	PASS	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29779936	29779936	+	Silent	SNP	G	G	A	rs45519332	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	28	64	0	0.444444	0	G|0.928;A|0.072	0.072	strong	.	SVIL	226	.	NM_021738	exon22	c.C4032T	p.S1344S	GGCCACGGAAGAC	.	PASS	Atlas-SNP
CST1	1469	hgsc.bcm.edu	37	20	23728528	23728528	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	6	216	0	0.027907	0	.	.	none	CST1,NS,carcinoma,0,2	CST1	37	2	NM_001898	exon3	c.G351A	p.L117L	AGAGCACAACTGT	.	scavenged	Atlas-SNP
ATP11B	23200	hgsc.bcm.edu	37	3	182614493	182614493	+	Silent	SNP	T	T	C	rs4859142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243	98	223	0	0.403292	0	T|0.842;C|0.158	0.158	strong	.	ATP11B	115	.	NM_014616	exon26	c.T2988C	p.F996F	GATGTTTGGAAAC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134682855	134682855	+	Silent	SNP	C	C	T	rs7908950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	20	64	0	0.425532	0	C|0.713;T|0.287	0.287	strong	.	TTC40	100	.	NM_001200049	exon33	c.G4533A	p.E1511E	CTTCAGCTCGGAG	.	PASS	Atlas-SNP
FAM83G	644815	hgsc.bcm.edu	37	17	18874965	18874965	+	Missense_Mutation	SNP	C	C	T	rs138715863	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	4	102	1	0.039604	0.00980392	C|0.995;T|0.005	0.005	strong	FAM83G,right_upper_lobe,carcinoma,0,1	FAM83G	51	1	NM_001039999	exon6	c.G2179A	p.V727I	TCTGGACGCTGTC	.	scavenged	Atlas-SNP
PPIG	9360	hgsc.bcm.edu	37	2	170493863	170493863	+	Missense_Mutation	SNP	A	A	G	rs8207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	48	139	0	0.444444	0	A|0.765;G|0.235	0.235	strong	.	PPIG	100	.	NM_004792	exon14	c.A2095G	p.N699D	CAGGACAATGAAT	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1877480	1877480	+	Missense_Mutation	SNP	T	T	G	rs17683288	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	160	218	0	0.601504	0	T|0.954;G|0.046	0.046	strong	ARHGEF10_ENST00000398564,NS,carcinoma,0,2	ARHGEF10	255	2	NM_014629	exon25	c.T2950G	p.S984A	CAAGGCTCCAAGA	.	PASS	Atlas-SNP
AGXT	189	hgsc.bcm.edu	37	2	241808314	241808314	+	Missense_Mutation	SNP	C	C	T	rs34116584	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	305	299	309	3	0.980328	0.00970874	A|0.000;C|0.871;T|0.129	0.129	strong	AGXT,NS,carcinoma,+1,1	AGXT	50	1	NM_000030	exon1	c.C32T	p.P11L	CCCCCCCCAAGGC	.	scavenged	Atlas-SNP
CLDN22	53842	hgsc.bcm.edu	37	4	184240981	184240981	+	Missense_Mutation	SNP	C	C	T	rs144080557	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	157	366	3	0.726852	0.00819672	C|0.992;T|0.008	0.008	strong	CLDN22,NS,carcinoma,+2,1	CLDN22	20	1	NM_001111319	exon1	c.G391A	p.V131I	CTGTGACTCCCGA	.	scavenged	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133795708	133795708	+	Missense_Mutation	SNP	C	C	T	rs202174159	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	2	111	0	0.0136986	0	.	.	weak	IGSF9B_ENST00000321016,NS,carcinoma,0,2	IGSF9B	290	2	NM_014987	exon14	c.G1960A	p.A654T	GCTCTGCGACACG	.	scavenged	Atlas-SNP
TRIM39-RPP21	202658	hgsc.bcm.edu	37	6	30314567	30314567	+	Missense_Mutation	SNP	C	C	A	rs974963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124	57	139	1	0.459677	0.00719424	C|0.718;A|0.282	0.282	strong	RPP21,NS,carcinoma,-1,1	.	.	1	NM_001199119	exon10	c.C1492A	p.Q498K	CAGACTCAGGGTT	.	scavenged	Atlas-SNP
CKAP4	10970	hgsc.bcm.edu	37	12	106633569	106633569	+	Missense_Mutation	SNP	C	C	T	rs3088113	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	37	49	0	0.606557	0	T|0.218;G|0.001;C|0.780	0.218	strong	CKAP4,NS,carcinoma,+1,1	CKAP4	49	1	NM_006825	exon2	c.G1042A	p.A348T	GCAGGGCGAGCCG	.	PASS	Atlas-SNP
MOK	5891	hgsc.bcm.edu	37	14	102695693	102695693	+	Missense_Mutation	SNP	T	T	C	rs2236493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	37	102	0	0.316239	0	T|0.713;C|0.287	0.287	strong	RAGE,NS,carcinoma,0,1	.	.	1	NM_014226	exon12	c.A1193G	p.Q398R	TCCTTCTGCGGAT	.	PASS	Atlas-SNP
TGFBR3	7049	hgsc.bcm.edu	37	1	92185657	92185657	+	Silent	SNP	C	C	T	rs1805112	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	40	95	0	0.677966	0	C|0.620;T|0.380	0.380	strong	TGFBR3,bladder,carcinoma,-1,1	TGFBR3	103	1	NM_003243	exon9	c.G1206A	p.P402P	AGGAAACGGAAGG	.	PASS	Atlas-SNP
PSMF1	9491	hgsc.bcm.edu	37	20	1108122	1108122	+	Silent	SNP	C	C	T	rs6514113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135	61	156	0	0.451852	0	C|0.885;T|0.115	0.115	strong	.	PSMF1	27	.	NM_006814	exon3	c.C336T	p.I112I	TTATATCGATGCA	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161518214	161518214	+	Missense_Mutation	SNP	T	T	C	rs2290834	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	626	133	398	0	0.21246	0	.	.	weak	FCGR3A,NS,carcinoma,+2,2	FCGR3A	38	2	NM_000569	exon3	c.A424G	p.I142V	CACCGATATGGAC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678693	100678693	+	Silent	SNP	T	T	C	rs78176991	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264	39	200	0	0.147727	0	T|0.994;C|0.006	0.006	strong	.	MUC17	804	.	NM_001040105	exon3	c.T3996C	p.Y1332Y	AACTTATAGTGAA	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186671256	186671256	+	Silent	SNP	T	T	C	rs17826498	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	46	101	0	0.547619	0	T|0.985;C|0.015	0.015	strong	.	FSIP2	251	.	NM_173651	exon17	c.T17490C	p.N5830N	CAAAAATATCTCT	.	PASS	Atlas-SNP
NLRP12	91662	hgsc.bcm.edu	37	19	54327313	54327313	+	Missense_Mutation	SNP	C	C	A	rs34436714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	50	133	0	0.373134	0	C|0.741;A|0.259	0.259	strong	.	NLRP12	236	.	NM_144687	exon1	c.A116T	p.K39M	CCTTCTCCCAGCT	.	PASS	Atlas-SNP
DENND1B	163486	hgsc.bcm.edu	37	1	197480927	197480927	+	Silent	SNP	C	C	T	rs12142127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	385	219	324	0	0.568831	0	C|0.754;T|0.246	0.246	strong	.	DENND1B	108	.	NM_001195215	exon22	c.G1746A	p.Q582Q	CTTCCCCTGATCT	.	PASS	Atlas-SNP
CEP164	22897	hgsc.bcm.edu	37	11	117222691	117222691	+	Missense_Mutation	SNP	C	C	A	rs143659874	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	38	35	0	0.77551	0	C|0.998;A|0.002	0.002	strong	.	CEP164	121	.	NM_001271933	exon4	c.C380A	p.P127H	ACCCCCCCAAAAG	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77328990	77328990	+	Missense_Mutation	SNP	C	C	A	rs12935394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	88	101	0	0.765217	0	C|0.893;A|0.107	0.107	strong	.	ADAMTS18	270	.	NM_199355	exon19	c.G2836T	p.A946S	CACAGGCCTTGCT	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118166385	118166385	+	Missense_Mutation	SNP	G	G	A	rs145471785	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	39	113	0	0.735849	0	G|0.995;A|0.005	0.005	strong	.	FAM46C	25	.	NM_017709	exon2	c.G895A	p.E299K	GCTGAAGAAGAGA	.	PASS	Atlas-SNP
GLO1	2739	hgsc.bcm.edu	37	6	38650588	38650588	+	Silent	SNP	T	T	A	rs1130534	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	117	101	1	1	0.00990099	T|0.811;A|0.189	0.189	strong	.	GLO1	12	.	NM_006708	exon4	c.A372T	p.G124G	ACCGAATCCTCGA	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36681953	36681953	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	3	151	0	0.0188679	0	.	.	none	MYH9,NS,carcinoma,+1,1	MYH9	225	1	NM_002473	exon36	c.G5108A	p.R1703Q	TCATCCCGCTCCT	.	scavenged	Atlas-SNP
DAAM2	23500	hgsc.bcm.edu	37	6	39851818	39851818	+	Silent	SNP	G	G	A	rs3003929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109	108	147	0	0.990826	0	G|0.407;A|0.593	0.593	strong	.	DAAM2	101	.	NM_015345	exon15	c.G1926A	p.K642K	TGAAAAGATGTTT	.	PASS	Atlas-SNP
SMARCA4	6597	hgsc.bcm.edu	37	19	11170839	11170839	+	Silent	SNP	T	T	C	rs7275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52	50	143	0	0.961538	0	T|0.776;C|0.224	0.224	strong	SMARCA4_ENST00000358026,caecum,carcinoma,0,2	SMARCA4	502	2	NM_001128849	exon35	c.T4983C	p.D1661D	TGACGATGACAGT	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102745	22102745	+	Missense_Mutation	SNP	C	C	A	rs41314525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316	200	253	0	0.632911	0	C|0.782;A|0.218	0.218	strong	.	OR10G2	35	.	NM_001005466	exon1	c.G254T	p.R85L	ATAAGCCGAGGAA	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158528233	158528233	+	Silent	SNP	A	A	G	rs3816462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	46	110	0	0.69697	0	A|0.703;G|0.297	0.297	strong	.	ESYT2	70	.	NM_020728	exon20	c.T2547C	p.S849S	GCCGCCACTGTTC	.	PASS	Atlas-SNP
CATSPER4	378807	hgsc.bcm.edu	37	1	26527863	26527863	+	Silent	SNP	C	C	T	rs17163674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	32	176	0	0.283186	0	C|0.906;T|0.094	0.094	strong	.	CATSPER4	59	.	NM_198137	exon9	c.C1218T	p.R406R	GGTGCGCGCAATC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145011204	145011204	+	Silent	SNP	A	A	G	rs6993938	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205	123	176	1	0.6	0.00568182	A|0.729;C|0.001;G|0.270	0.270	strong	PLEC_ENST00000436759,NS,carcinoma,-2,8	PLEC	1144	8	NM_201380	exon5	c.T789C	p.A263A	GCCGTCAGCGATG	.	PASS	Atlas-SNP
PIK3C2G	5288	hgsc.bcm.edu	37	12	18656225	18656225	+	Silent	SNP	G	G	A	rs11044142	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	49	119	0	0.515789	0	G|0.842;A|0.158	0.158	strong	.	PIK3C2G	315	.	NM_004570	exon22	c.G2904A	p.Q968Q	GGTGCAGATGGTA	.	PASS	Atlas-SNP
THTPA	79178	hgsc.bcm.edu	37	14	24026046	24026046	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158	93	126	0	0.588608	0	.	.	none	.	THTPA	11	.	NM_001256321	exon2	c.G80A	p.G27D	TGGGGGGCACCCT	.	PASS	Atlas-SNP
CCDC110	256309	hgsc.bcm.edu	37	4	186382206	186382206	+	Silent	SNP	A	A	G	rs11132309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	16	143	0	0.166667	0	A|0.557;G|0.443	0.443	strong	.	CCDC110	78	.	NM_152775	exon5	c.T345C	p.D115D	TACCAAATCCTTT	.	PASS	Atlas-SNP
OCA2	4948	hgsc.bcm.edu	37	15	28230318	28230318	+	Missense_Mutation	SNP	C	C	T	rs1800407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	11	88	0	0.215686	0	C|0.952;T|0.048	0.048	strong	.	OCA2	173	.	NM_000275	exon13	c.G1256A	p.R419Q	CGTCCCCGGGAGA	.	PASS	Atlas-SNP
ZFP106	64397	hgsc.bcm.edu	37	15	42720288	42720288	+	Silent	SNP	G	G	C	rs11544099	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	59	66	0	1	0	G|0.904;C|0.096	0.096	strong	ZFP106,NS,carcinoma,0,1	ZFP106	117	1	NM_022473	exon12	c.C4857G	p.L1619L	GAGGCAGAGGACC	.	PASS	Atlas-SNP
LIPF	8513	hgsc.bcm.edu	37	10	90438207	90438207	+	Silent	SNP	A	A	G	rs1228187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	73	189	1	0.646018	0.00529101	A|0.799;G|0.201	0.201	strong	.	LIPF	62	.	NM_001198829	exon11	c.A996G	p.Q332Q	GTCCCAACCTCCC	.	PASS	Atlas-SNP
MAP2K3	5606	hgsc.bcm.edu	37	17	21207844	21207844	+	Silent	SNP	C	C	T	rs2230436	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	374	85	380	0	0.227273	0	C|0.592;T|0.408	0.408	strong	.	MAP2K3	135	.	NM_145109	exon8	c.C675T	p.A225A	GGATGCCGGCTGC	.	PASS	Atlas-SNP
SLC30A5	64924	hgsc.bcm.edu	37	5	68419054	68419054	+	Silent	SNP	A	A	T	rs164572	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	83	60	0	1	0	A|0.607;T|0.393	0.393	strong	.	SLC30A5	54	.	NM_022902	exon14	c.A1800T	p.T600T	AGATACACTTGGC	.	PASS	Atlas-SNP
FLNB	2317	hgsc.bcm.edu	37	3	58118555	58118555	+	Missense_Mutation	SNP	G	G	A	rs12632456	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	103	136	1	0.990385	0.00735294	G|0.538;A|0.462	0.462	strong	.	FLNB	430	.	NM_001164317	exon27	c.G4504A	p.V1502M	GTGAACGTGGTGG	.	PASS	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	37	6	168377261	168377261	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	329	34	315	0	0.103343	0	.	.	none	.	.	.	.	NM_001129895	exon1	c.A72G	p.Q24Q	AGTGTGTTGGGAG	.	PASS	Atlas-SNP
SLC26A8	116369	hgsc.bcm.edu	37	6	35967772	35967772	+	Missense_Mutation	SNP	T	T	C	rs17713154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	29	64	1	0.460317	0.015625	T|0.887;C|0.113	0.113	strong	SLC26A8,colon,carcinoma,+2,1	SLC26A8	95	1	NM_052961	exon4	c.A442G	p.I148V	CACCAATGGACAT	.	scavenged	Atlas-SNP
GSPT1	2935	hgsc.bcm.edu	37	16	11969724	11969724	+	Silent	SNP	G	G	C	rs33657	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	263	137	250	1	0.520913	0.004	G|0.405;C|0.595	0.595	strong	.	GSPT1	71	.	NM_002094	exon14	c.C1755G	p.V585V	TTGTTTGACAAAA	.	PASS	Atlas-SNP
ZNF229	7772	hgsc.bcm.edu	37	19	44932972	44932972	+	Missense_Mutation	SNP	C	C	T	rs1434579	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	124	245	0	0.551111	0	C|0.728;T|0.272	0.272	strong	ZNF229,NS,carcinoma,+1,1	ZNF229	123	1	NM_014518	exon6	c.G1984A	p.G662R	CCTTTCCGCACTC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10464885	10464885	+	Silent	SNP	T	T	C	rs56382513	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	87	79	2	0.756522	0.0253165	T|0.404;C|0.596	0.596	strong	RP1L1,NS,carcinoma,0,2	RP1L1	453	2	NM_178857	exon4	c.A6723G	p.S2241S	TCCTTCTGACTCT	.	scavenged	Atlas-SNP
TULP1	7287	hgsc.bcm.edu	37	6	35477032	35477032	+	Missense_Mutation	SNP	A	A	G	rs2064317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	44	142	0	0.411215	0	A|0.642;G|0.358	0.358	strong	TULP1,NS,carcinoma,0,1	TULP1	51	1	NM_003322	exon8	c.T776C	p.I259T	TTCTTTATCACCG	.	PASS	Atlas-SNP
IPO5	3843	hgsc.bcm.edu	37	13	98645253	98645253	+	Silent	SNP	A	A	G	rs626716	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84	38	85	0	0.452381	0	A|0.901;G|0.099	0.099	strong	.	IPO5	90	.	NM_002271	exon10	c.A831G	p.L277L	AACTCTACAGCTA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152283862	152283862	+	Missense_Mutation	SNP	G	G	C	rs58001094	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	379	125	279	2	0.329815	0.00716846	G|0.640;C|0.360	0.360	strong	FLG,brain,glioma,0,1	FLG	900	1	NM_002016	exon3	c.C3500G	p.A1167G	GGGTGTGCACGAA	.	scavenged	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90397132	90397132	+	Missense_Mutation	SNP	G	G	C	rs34766278	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	38	89	0	0.469136	0	G|0.889;C|0.111	0.111	strong	.	MDN1	478	.	NM_014611	exon68	c.C11381G	p.A3794G	GACAAAGCTCGAC	.	PASS	Atlas-SNP
LIN9	286826	hgsc.bcm.edu	37	1	226474035	226474035	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99	5	79	0	0.050505	0	.	.	none	.	LIN9	57	.	NM_173083	exon6	c.A571G	p.R191G	TTTACCTCCGTGG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160673526	160673526	+	Missense_Mutation	SNP	A	A	G	rs2059696	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	51	79	0	0.525773	0	A|0.775;G|0.225	0.225	strong	LY75,NS,carcinoma,0,1	LY75	151	1	NM_002349	exon30	c.T4171C	p.Y1391H	TATTATATTCTTC	.	PASS	Atlas-SNP
XCL2	6846	hgsc.bcm.edu	37	1	168511284	168511284	+	Silent	SNP	T	T	C	rs4282797	bycluster;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	307	45	370	0	0.14658	0	T|0.709;C|0.291	0.291	strong	XCL2,colon,carcinoma,-2,1	XCL2	18	1	NM_003175	exon2	c.A123G	p.P41P	GCTAACTGGCAGT	.	PASS	Atlas-SNP
GDF3	9573	hgsc.bcm.edu	37	12	7842932	7842932	+	Missense_Mutation	SNP	C	C	T	rs12819884	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	177	2	140	0	0.0112994	0	C|0.752;T|0.248	0.248	strong	GDF3,NS,adenoma,0,2	GDF3	68	2	NM_020634	exon2	c.G637A	p.G213R	TCACCCCTGAGTC	.	scavenged	Atlas-SNP
PPRC1	23082	hgsc.bcm.edu	37	10	103906612	103906612	+	Missense_Mutation	SNP	G	G	A	rs118161359	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	39	87	0	0.8125	0	G|0.982;A|0.018	0.018	strong	.	PPRC1	151	.	NM_015062	exon9	c.G3863A	p.R1288Q	CTAGTCGAGTCCA	.	PASS	Atlas-SNP
FRMPD2	143162	hgsc.bcm.edu	37	10	49383976	49383976	+	Missense_Mutation	SNP	T	T	C	rs76009671		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	265	46	303	1	0.173585	0.00330033	T|0.500;C|0.500	0.500	weak	FRMPD2,NS,carcinoma,0,1	FRMPD2	157	1	NM_001018071	exon23	c.A2902G	p.I968V	TGTTAATGCCACC	.	scavenged	Atlas-SNP
CAMKK2	10645	hgsc.bcm.edu	37	12	121712077	121712077	+	Missense_Mutation	SNP	T	T	A	rs3817190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	29	73	1	0.604167	0.0136986	T|0.543;A|0.457	0.457	strong	CAMKK2_ENST00000392473,NS,carcinoma,0,2	CAMKK2	87	2	NM_153500	exon2	c.A253T	p.T85S	CGGAGGTGTCAAG	.	scavenged	Atlas-SNP
REV3L	5980	hgsc.bcm.edu	37	6	111696091	111696091	+	Missense_Mutation	SNP	T	T	C	rs458017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	53	110	0	0.53	0	T|0.948;C|0.052	0.052	strong	.	REV3L	386	.	NM_002912	exon13	c.A3467G	p.Y1156C	TTCTTATATACAT	.	PASS	Atlas-SNP
LARS	51520	hgsc.bcm.edu	37	5	145499996	145499996	+	Missense_Mutation	SNP	C	C	T	rs10988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	126	165	0	0.992126	0	C|0.802;N|0.000	.	strong	LARS,NS,carcinoma,0,1	LARS	100	1	NM_020117	exon31	c.G3263A	p.R1088K	CCTTGCCTGATTT	.	PASS	Atlas-SNP
KRT84	3890	hgsc.bcm.edu	37	12	52778947	52778947	+	Silent	SNP	A	A	G	rs1791631	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	63	130	0	0.533898	0	A|0.685;G|0.315	0.315	strong	.	KRT84	61	.	NM_033045	exon1	c.T423C	p.T141T	GTTCACAGTCACA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507398	195507398	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	61	118	16	0.423611	0.135593	.	.	none	MUC4_ENST00000463781,NS,lymphoid_neoplasm,+1,1	MUC4	1505	1	NM_018406	exon2	c.G11053A	p.D3685N	AAGTGTCCGTGAC	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179545859	179545859	+	Missense_Mutation	SNP	C	C	T	rs36051007	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55	25	64	0	0.454545	0	C|0.821;T|0.179	0.179	strong	.	TTN	18412	.	NM_001267550	exon138	c.G33287A	p.R11096H	GAAATACGTATTT	.	PASS	Atlas-SNP
MFSD1	64747	hgsc.bcm.edu	37	3	158520011	158520011	+	Missense_Mutation	SNP	C	C	T	rs28364680	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	32	23	49	0	0.71875	0	C|0.842;T|0.158	0.158	strong	.	MFSD1	88	.	NM_022736	exon1	c.C217T	p.P73S	GGTGCCCCGGCCG	.	PASS	Atlas-SNP
C4orf21	55345	hgsc.bcm.edu	37	4	113482146	113482146	+	Missense_Mutation	SNP	G	G	A	rs17605622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	25	187	0	0.245098	0	G|0.939;A|0.061	0.061	strong	.	C4orf21	223	.	NM_018392	exon19	c.C4703T	p.S1568L	GTTGGCGAAGACC	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	37	12	6935995	6935995	+	Missense_Mutation	SNP	G	G	A	rs138578985	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97	57	76	1	0.587629	0.0131579	G|1.000;A|0.000	0.000	weak	GPR162,bladder,carcinoma,0,1	GPR162	55	1	NM_019858	exon5	c.G1393A	p.E465K	GAGGACGAGGAGG	.	scavenged	Atlas-SNP
FCGR2C	9103	hgsc.bcm.edu	37	1	161565381	161565381	+	Splice_Site	SNP	A	A	G	rs76277413	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	346	195	204	1	0.563584	0.00490196	A|0.922;G|0.078	0.078	strong	.	FCGR2C	2	.	NM_201563	exon6	c.798+1A>G	.	TTTGAGATGAGTA	.	PASS	Atlas-SNP
JAG2	3714	hgsc.bcm.edu	37	14	105609335	105609335	+	Silent	SNP	A	A	G	rs10149229	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14	10	14	0	0.714286	0	A|0.286;G|0.714	0.714	strong	.	JAG2	69	.	NM_002226	exon26	c.T3414C	p.I1138I	CCGCTCAATGGGG	.	PASS	Atlas-SNP
CATSPER1	117144	hgsc.bcm.edu	37	11	65787666	65787666	+	Silent	SNP	G	G	A	rs3829937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	62	142	0	0.473282	0	G|0.834;A|0.166	0.166	strong	.	CATSPER1	101	.	NM_053054	exon9	c.C2070T	p.A690A	CCGGGCGGCCCTC	.	PASS	Atlas-SNP
IL2	3558	hgsc.bcm.edu	37	4	123377482	123377482	+	Silent	SNP	C	C	A	rs2069763	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	89	204	0	0.988889	0	C|0.718;A|0.282	0.282	strong	.	IL2	23	.	NM_000586	exon1	c.G114T	p.L38L	ATCCAGCAGTAAA	.	PASS	Atlas-SNP
CACNG3	10368	hgsc.bcm.edu	37	16	24373047	24373047	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	2	141	0	0.0145985	0	.	.	none	CACNG3,NS,carcinoma,-1,1	CACNG3	112	1	NM_006539	exon4	c.C811T	p.P271S	CGGGACCCCTCAA	.	scavenged	Atlas-SNP
UBR5	51366	hgsc.bcm.edu	37	8	103307971	103307971	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	3	163	0	0.0112782	0	.	.	none	UBR5,NS,carcinoma,-1,1	UBR5	285	1	NM_015902	exon29	c.G3705A	p.W1235X	TTTCTCCCAACAA	.	scavenged	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14842557	14842557	+	Missense_Mutation	SNP	T	T	C	rs1353223	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	22	71	0	0.392857	0	T|0.917;C|0.083	0.083	strong	.	FREM1	261	.	NM_144966	exon10	c.A1495G	p.I499V	CAAATATCCGGAA	.	PASS	Atlas-SNP
TECPR1	25851	hgsc.bcm.edu	37	7	97873994	97873994	+	Silent	SNP	G	G	A	rs1874344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	53	59	1	0.576087	0.0169492	G|0.696;A|0.304	0.304	strong	TECPR1,NS,carcinoma,0,2	TECPR1	77	2	NM_015395	exon5	c.C420T	p.Y140Y	GATGGCGTACGTC	.	scavenged	Atlas-SNP
HIVEP3	59269	hgsc.bcm.edu	37	1	41978959	41978959	+	Missense_Mutation	SNP	C	C	T	rs144265546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266	194	398	1	0.729323	0.00251256	C|1.000;T|0.000	0.000	weak	HIVEP3,NS,carcinoma,-1,1	HIVEP3	235	1	NM_024503	exon8	c.G5933A	p.R1978H	GGTGGACGGCTGC	.	PASS	Atlas-SNP
KRTAP21-3	100288323	hgsc.bcm.edu	37	21	32090908	32090908	+	Missense_Mutation	SNP	C	C	T	rs2833031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209	83	186	0	0.397129	0	C|0.760;T|0.240	0.240	strong	.	KRTAP21-3	5	.	NM_001164435	exon1	c.G170A	p.C57Y	CAATGGCATTTCT	.	PASS	Atlas-SNP
YTHDC2	64848	hgsc.bcm.edu	37	5	112868693	112868693	+	Silent	SNP	C	C	A	rs6594732	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	48	86	0	0.475248	0	C|0.678;A|0.322	0.322	strong	.	YTHDC2	118	.	NM_022828	exon5	c.C793A	p.R265R	GAGAGACGGGAAA	.	PASS	Atlas-SNP
EPG5	57724	hgsc.bcm.edu	37	18	43508856	43508856	+	Missense_Mutation	SNP	C	C	G	rs3744999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	19	47	0	0.487179	0	C|0.927;G|0.073	0.073	strong	EPG5,NS,carcinoma,0,1	EPG5	199	1	NM_020964	exon13	c.G2532C	p.E844D	AATGGTCTCTTGA	.	PASS	Atlas-SNP
HS3ST5	222537	hgsc.bcm.edu	37	6	114378722	114378722	+	Missense_Mutation	SNP	A	A	T	rs17793043	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199	105	247	0	0.527638	0	A|0.994;T|0.006	0.006	strong	.	HS3ST5	80	.	NM_153612	exon2	c.T740A	p.I247N	TGCTCAATTGGAA	.	PASS	Atlas-SNP
TRIM4	89122	hgsc.bcm.edu	37	7	99489868	99489868	+	Missense_Mutation	SNP	G	G	C	rs33998596	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	21	42	0	0.5	0	G|0.943;C|0.057	0.057	strong	.	TRIM4	33	.	NM_033017	exon7	c.C1421G	p.S474C	ACAGAAGAACAAG	.	PASS	Atlas-SNP
OR2C3	81472	hgsc.bcm.edu	37	1	247695427	247695427	+	Missense_Mutation	SNP	C	C	G	rs34220133	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	57	106	0	0.390411	0	C|0.891;G|0.109	0.109	strong	OR2C3,NS,carcinoma,0,1	OR2C3	92	1	NM_198074	exon2	c.G387C	p.R129S	GAGTGGCCTGCAG	.	PASS	Atlas-SNP
ZNF155	7711	hgsc.bcm.edu	37	19	44496070	44496070	+	Silent	SNP	A	A	G	rs431509	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	139	154	0	1	0	A|0.624;G|0.376	0.376	strong	.	ZNF155	30	.	NM_001260488	exon5	c.A252G	p.Q84Q	AACCCAAAGAGAA	.	PASS	Atlas-SNP
DHRS4L1	728635	hgsc.bcm.edu	37	14	24517936	24517936	+	Missense_Mutation	SNP	G	G	T	rs201609317	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1915	480	1054	1	0.250653	0.000948767	.	.	weak	.	.	.	.	NM_001082488	exon8	c.G591T	p.K197N	CAACAAGACCTTG	.	PASS	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187697883	187697883	+	Missense_Mutation	SNP	A	A	G	rs10164815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	283	128	312	1	0.452297	0.00320513	A|0.809;G|0.191	0.191	strong	ZSWIM2,NS,carcinoma,-1,1	ZSWIM2	119	1	NM_182521	exon7	c.T905C	p.I302T	TCTTCAATCTCAT	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56088780	56088780	+	Silent	SNP	G	G	A	rs75497420	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	275	23	144	0	0.0836364	0	G|0.957;A|0.044	0.044	strong	.	PSPH	23	.	NM_004577	exon4	c.C126T	p.D42D	CACCGCGTCCTCA	.	PASS	Atlas-SNP
PINX1	54984	hgsc.bcm.edu	37	8	10689212	10689212	+	Silent	SNP	C	C	T	rs12375394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	63	127	0	0.368421	0	C|0.884;T|0.116	0.116	strong	.	PINX1	38	.	NM_017884	exon4	c.G264A	p.L88L	TTCGGCCAGAAGC	.	PASS	Atlas-SNP
MTMR14	64419	hgsc.bcm.edu	37	3	9711141	9711141	+	Missense_Mutation	SNP	T	T	A	rs189614064	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	310	138	345	1	0.445161	0.00289855	T|0.998;A|0.002	0.002	strong	.	MTMR14	43	.	NM_022485	exon5	c.T519A	p.D173E	GGCAGATGTGGAG	.	PASS	Atlas-SNP
PLA2G4C	8605	hgsc.bcm.edu	37	19	48598823	48598823	+	Missense_Mutation	SNP	A	A	G	rs156631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	49	109	0	0.49	0	T|0.003;G|0.559	0.559	strong	.	PLA2G4C	76	.	NM_001159322	exon7	c.T637C	p.S213P	GTGCAGAGAAGCC	.	PASS	Atlas-SNP
SFTPC	6440	hgsc.bcm.edu	37	8	22021517	22021517	+	Missense_Mutation	SNP	G	G	A	rs1124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	293	290	279	0	0.989761	0	G|0.748;A|0.252	0.252	strong	.	SFTPC	19	.	NM_003018	exon5	c.G557A	p.S186N	CCGTGAGCACCCT	.	PASS	Atlas-SNP
DNAJB1	3337	hgsc.bcm.edu	37	19	14629138	14629138	+	Silent	SNP	C	C	T	rs141518218	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	20	61	0	0.555556	0	C|0.995;T|0.005	0.005	strong	.	DNAJB1	38	.	NM_006145	exon1	c.G24A	p.T8T	GCCCAACGTCTGG	.	PASS	Atlas-SNP
TOP2A	7153	hgsc.bcm.edu	37	17	38546274	38546274	+	Silent	SNP	A	A	C	rs17680289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	87	198	0	0.524096	0	A|0.988;C|0.012	0.012	strong	.	TOP2A	124	.	NM_001067	exon34	c.T4410G	p.T1470T	ATCAGAAGTGGAT	.	PASS	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs78337605	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298	34	283	0	0.114094	0	C|0.500;T|0.500	0.500	strong	.	CYP2A6	69	.	NM_000762	exon7	c.G1039A	p.A347T	TCTTGGCCCGGTC	.	PASS	Atlas-SNP
IBTK	25998	hgsc.bcm.edu	37	6	82900811	82900811	+	Missense_Mutation	SNP	G	G	A	rs9449444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	47	89	0	0.435185	0	G|0.756;A|0.244	0.244	strong	.	IBTK	128	.	NM_015525	exon25	c.C3554T	p.A1185V	TTGGGGGCTTTTG	.	PASS	Atlas-SNP
LIPK	643414	hgsc.bcm.edu	37	10	90512306	90512306	+	Missense_Mutation	SNP	G	G	C	rs1214464	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	36	118	0	0.923077	0	G|0.809;C|0.191	0.191	strong	.	LIPK	50	.	NM_001080518	exon9	c.G993C	p.M331I	TAAGATGGAAGTT	.	PASS	Atlas-SNP
KCNMB1	3779	hgsc.bcm.edu	37	5	169810796	169810796	+	Missense_Mutation	SNP	C	C	T	rs11739136	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	56	113	0	0.495575	0	C|0.910;T|0.090	0.090	strong	.	KCNMB1	38	.	NM_004137	exon3	c.T193A	p.S65T	TCAGCTCCTCCTG	.	PASS	Atlas-SNP
MAP7D1	55700	hgsc.bcm.edu	37	1	36642420	36642420	+	Silent	SNP	T	T	C	rs475591	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	11	8	54	0	0.727273	0	T|0.240;C|0.760	0.760	strong	.	MAP7D1	62	.	NM_018067	exon8	c.T1356C	p.S452S	CCTCTCTGCCAGC	.	PASS	Atlas-SNP
MYCBPAP	84073	hgsc.bcm.edu	37	17	48606537	48606537	+	Missense_Mutation	SNP	C	C	G	rs1133818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	61	49	0	1	0	C|0.198;G|0.802	0.802	strong	.	MYCBPAP	135	.	NM_032133	exon18	c.C2841G	p.S947R	CCAGAGCCTGCAC	.	PASS	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41827757	41827757	+	Missense_Mutation	SNP	T	T	A	rs2297382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	52	129	0	0.776119	0	T|0.855;A|0.145	0.145	strong	.	RPAP1	111	.	NM_015540	exon5	c.A494T	p.K165M	GGGCCCTTGGCTT	.	PASS	Atlas-SNP
GALNT6	11226	hgsc.bcm.edu	37	12	51771040	51771040	+	Silent	SNP	T	T	C	rs2277379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	129	307	0	0.52439	0	T|0.930;C|0.070	0.070	strong	.	GALNT6	63	.	NM_007210	exon4	c.A603G	p.L201L	GGTGTGTAGGACG	.	PASS	Atlas-SNP
MBTPS1	8720	hgsc.bcm.edu	37	16	84115393	84115393	+	Silent	SNP	G	G	A	rs12933523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	10	70	0	0.128205	0	G|0.869;A|0.131	0.131	strong	.	MBTPS1	85	.	NM_003791	exon11	c.C1407T	p.L469L	GGCTCTGAGCAGA	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140552774	140552774	+	Missense_Mutation	SNP	G	G	A	rs17286891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	25	50	0	0.431034	0	G|0.934;A|0.066	0.066	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G358A	p.E120K	CGTGCTGAACTAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280471	152280471	+	Missense_Mutation	SNP	C	C	G	rs78179835	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	974	246	615	0	0.252567	0	.	.	weak	.	FLG	900	.	NM_002016	exon3	c.G6891C	p.E2297D	GGAGCTCTCTGCA	.	PASS	Atlas-SNP
IRAK1BP1	134728	hgsc.bcm.edu	37	6	79577412	79577412	+	Missense_Mutation	SNP	C	C	G	rs41269339	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62	28	60	0	0.451613	0	C|0.975;G|0.025	0.025	strong	.	IRAK1BP1	18	.	NM_001010844	exon1	c.C119G	p.P40R	GCCACCCCCTCTC	.	PASS	Atlas-SNP
MAP3K10	4294	hgsc.bcm.edu	37	19	40711892	40711892	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126	2	149	0	0.015873	0	.	.	none	MAP3K10,right_upper_lobe,carcinoma,+1,1	MAP3K10	70	1	NM_002446	exon5	c.G1263A	p.R421R	GCGGCGGCGGGAG	.	scavenged	Atlas-SNP
NFATC4	4776	hgsc.bcm.edu	37	14	24843620	24843620	+	Silent	SNP	T	T	C	rs2295298	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	189	153	0	0.989529	0	T|0.629;C|0.371	0.371	strong	.	NFATC4	115	.	NM_001198967	exon7	c.T2010C	p.T670T	ACTGACTGGCTCC	.	PASS	Atlas-SNP
TCP11L1	55346	hgsc.bcm.edu	37	11	33094059	33094059	+	Missense_Mutation	SNP	C	C	T	rs118146715	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	71	162	0	0.455128	0	C|0.986;T|0.014	0.014	strong	.	TCP11L1	40	.	NM_001145541	exon10	c.C1367T	p.S456L	TTGCCTCGGGTCA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911063	29911063	+	Missense_Mutation	SNP	T	T	G	rs199474485	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	38	151	0	0.361905	0	G|0.303;T|0.697	0.303	strong	.	HLA-A	89	.	NM_001242758	exon3	c.T362G	p.I121R	TCCAGATAATGTA	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46929467	46929467	+	Silent	SNP	G	G	A	rs1050351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	11	7	8	0	0.636364	0	G|0.516;A|0.484	0.484	strong	.	COL18A1	129	.	NM_030582	exon39	c.G3978A	p.A1326A	GCCGGCGCGACCC	.	PASS	Atlas-SNP
ITGB6	3694	hgsc.bcm.edu	37	2	160968628	160968628	+	Silent	SNP	A	A	G	rs16844790	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	283	136	340	0	0.480565	0	A|0.805;G|0.195	0.195	strong	.	ITGB6	68	.	NM_000888	exon13	c.T2064C	p.N688N	CCCCTCATTATCT	.	PASS	Atlas-SNP
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692277	31692277	+	Missense_Mutation	SNP	G	G	T	rs3804007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245	141	207	0	0.57551	0	G|0.909;T|0.091	0.091	strong	.	KRTAP26-1	58	.	NM_203405	exon1	c.C77A	p.S26Y	TCGATGGAGGTGA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678918	100678918	+	Silent	SNP	G	G	A	rs200627718	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	6	138	1	0.0304569	0.00724638	G|0.998;A|0.002	0.002	strong	MUC17,colon,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G4221A	p.P1407P	CACGCCGGTAGTC	.	scavenged	Atlas-SNP
CYP2S1	29785	hgsc.bcm.edu	37	19	41712275	41712275	+	Missense_Mutation	SNP	C	C	T	rs34971233	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	49	122	0	0.510417	0	C|0.979;T|0.021	0.021	strong	.	CYP2S1	47	.	NM_030622	exon9	c.C1397T	p.P466L	AGAGCCCGTGCCC	.	PASS	Atlas-SNP
GRIN2D	2906	hgsc.bcm.edu	37	19	48945044	48945044	+	Silent	SNP	C	C	T	rs144676582	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	48	120	0	0.470588	0	C|0.998;T|0.002	0.002	strong	.	GRIN2D	76	.	NM_000836	exon11	c.C2271T	p.I757I	CTTCATCTACGAT	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104449098	104449098	+	Missense_Mutation	SNP	C	C	T	rs10989591	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95	43	101	0	0.452632	0	C|0.652;T|0.348	0.348	strong	.	GRIN3A	186	.	NM_133445	exon2	c.G1084A	p.V362M	CCTCCACATTCTG	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24772967	24772967	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	237	3	152	0	0.0126582	0	.	.	none	C14orf21,colon,carcinoma,0,1	.	.	1	NM_174913	exon7	c.G1314A	p.R438R	ATCCCGGCAAGTG	.	scavenged	Atlas-SNP
CYP24A1	1591	hgsc.bcm.edu	37	20	52790027	52790027	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	13	80	0	0.333333	0	.	.	none	.	CYP24A1	75	.	NM_000782	exon1	c.C92T	p.T31M	TACGCCGTAGATG	.	PASS	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159398764	159398764	+	Silent	SNP	G	G	A	rs12191022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140	60	140	0	0.428571	0	G|0.871;A|0.129	0.129	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon8	c.C1489T	p.L497L	CCTCCAGTGACTC	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22574357	22574357	+	Missense_Mutation	SNP	C	C	G	rs78240139		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	824	146	865	0	0.177184	0	C|0.500;G|0.500	0.500	weak	ZNF98_ENST00000357774,NS,carcinoma,0,4	ZNF98	230	4	NM_001098626	exon4	c.G1680C	p.K560N	GGAAATCTTTGCA	.	scavenged	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848144	54848144	+	Missense_Mutation	SNP	T	T	A	rs74869671	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179	18	233	0	0.100559	0	T|0.995;A|0.005	0.005	strong	.	LILRA4	91	.	NM_012276	exon6	c.A1223T	p.H408L	CTGGGGTGAGACA	.	PASS	Atlas-SNP
XIRP1	165904	hgsc.bcm.edu	37	3	39227495	39227495	+	Missense_Mutation	SNP	C	C	T	rs142860074	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	77	113	0	0.527397	0	C|0.999;T|0.001	0.001	strong	XIRP1,colon,carcinoma,0,1	XIRP1	173	1	NM_194293	exon2	c.G3442A	p.V1148M	TCCTCACGGGATG	.	PASS	Atlas-SNP
TSEN34	79042	hgsc.bcm.edu	37	19	54696027	54696027	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236	4	252	0	0.0169492	0	.	.	none	TSEN34,NS,carcinoma,-1,1	TSEN34	17	1	NM_024075	exon4	c.T548C	p.L183P	CTGCTCTCCTTGT	.	scavenged	Atlas-SNP
DENND4C	55667	hgsc.bcm.edu	37	9	19341045	19341045	+	Silent	SNP	A	A	G	rs928128	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	119	204	0	0.495833	0	A|0.760;G|0.240	0.240	strong	DENND4C,colon,carcinoma,0,1	DENND4C	120	1	NM_017925	exon20	c.A2790G	p.A930A	TGATGCAGAAATT	.	PASS	Atlas-SNP
TPO	7173	hgsc.bcm.edu	37	2	1520676	1520676	+	Missense_Mutation	SNP	T	T	C	rs1126799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74	39	82	0	0.527027	0	A|0.003;C|0.612	0.612	strong	TPO,NS,carcinoma,0,1	TPO	224	1	NM_001206744	exon15	c.T2540C	p.V847A	CTCGGGTGACTTG	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1509123	1509123	+	Silent	SNP	G	G	A	rs12923538	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248	142	242	2	0.572581	0.00826446	G|0.854;A|0.146	0.146	strong	CLCN7,colon,carcinoma,-1,1	CLCN7	53	1	NM_001287	exon7	c.C660T	p.H220H	CACCACGTGGGGG	.	scavenged	Atlas-SNP
MC1R	4157	hgsc.bcm.edu	37	16	89986608	89986608	+	Silent	SNP	A	A	G	rs2228478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	33	262	0	0.147321	0	A|0.821;G|0.179	0.179	strong	.	MC1R	20	.	NM_002386	exon1	c.A942G	p.T314T	GCTGACATGCTCC	.	PASS	Atlas-SNP
DCAF11	80344	hgsc.bcm.edu	37	14	24587639	24587639	+	Missense_Mutation	SNP	G	G	A	rs3825584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	216	138	154	0	0.638889	0	G|0.685;A|0.315	0.315	strong	.	.	.	.	NM_025230	exon7	c.G620A	p.R207H	GTTTCCGTAAATT	.	PASS	Atlas-SNP
GALNTL5	168391	hgsc.bcm.edu	37	7	151680175	151680175	+	Missense_Mutation	SNP	C	C	T	rs35682935	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78	19	121	1	0.24359	0.00826446	C|0.888;T|0.112	0.112	strong	GALNTL5,colon,carcinoma,+1,1	GALNTL5	87	1	NM_145292	exon4	c.C473T	p.T158M	GTGTCACGAACCT	.	scavenged	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75970070	75970070	+	Missense_Mutation	SNP	C	C	T	rs8023621	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107	104	172	1	0.971963	0.00581395	C|0.707;T|0.293	0.293	strong	.	CSPG4	175	.	NM_001897	exon9	c.G5108A	p.R1703H	CTGGGGCGCTGGG	.	PASS	Atlas-SNP
SP2	6668	hgsc.bcm.edu	37	17	45994044	45994044	+	Silent	SNP	C	C	T	rs2228253	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	34	84	0	0.395349	0	C|0.479;T|0.521	0.521	strong	.	SP2	38	.	NM_003110	exon3	c.C607T	p.L203L	GTGAAGCTGACAG	.	PASS	Atlas-SNP
HSH2D	84941	hgsc.bcm.edu	37	19	16259623	16259623	+	Silent	SNP	C	C	T	rs8103852	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	49	103	0	0.466667	0	C|0.891;T|0.109	0.109	strong	.	HSH2D	16	.	NM_032855	exon4	c.C63T	p.T21T	GCACACCCAGATG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118624123	118624123	+	Silent	SNP	C	C	T	rs2298176	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87	79	150	0	0.908046	0	C|0.922;T|0.078	0.078	strong	.	SPAG17	263	.	NM_206996	exon14	c.G1905A	p.P635P	GTCCCACGGTATG	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228102723	228102723	+	Missense_Mutation	SNP	G	G	C	rs13424243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89	89	135	0	1	0	G|0.734;C|0.266	0.266	strong	.	COL4A3	293	.	NM_000091	exon2	c.G127C	p.G43R	TGTGACGGGGCCA	.	PASS	Atlas-SNP
GSDMC	56169	hgsc.bcm.edu	37	8	130760774	130760774	+	Silent	SNP	C	C	T	rs4733559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	202	112	181	0	0.554455	0	C|0.868;T|0.132	0.132	strong	.	GSDMC	71	.	NM_031415	exon14	c.G1500A	p.S500S	CAGCAACGAGAGA	.	PASS	Atlas-SNP
KIAA1462	57608	hgsc.bcm.edu	37	10	30316072	30316072	+	Missense_Mutation	SNP	C	C	G	rs3739998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	6	74	0	0.142857	0	C|0.706;G|0.294	0.294	strong	.	KIAA1462	162	.	NM_020848	exon3	c.G3005C	p.S1002T	TTCGGACTTTCCT	.	PASS	Atlas-SNP
EFR3A	23167	hgsc.bcm.edu	37	8	132982824	132982824	+	Missense_Mutation	SNP	A	A	G	rs1051221	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147	146	104	0	0.993197	0	A|0.517;C|0.002	.	strong	.	EFR3A	96	.	NM_015137	exon10	c.A1093G	p.N365D	AGTGTCAACTTAA	.	PASS	Atlas-SNP
PLSCR2	57047	hgsc.bcm.edu	37	3	146177815	146177815	+	Silent	SNP	C	C	T	rs6806535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	15	32	0	0.454545	0	C|0.496;T|0.504	0.504	strong	.	PLSCR2	68	.	NM_001199978	exon4	c.G96A	p.Q32Q	GTCAGCCTGTTTC	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33768354	33768354	+	Missense_Mutation	SNP	C	C	T	rs3744371	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	24	42	0	0.5	0	C|0.421;T|0.579	0.579	strong	.	SLFN13	79	.	NM_144682	exon6	c.G1954A	p.E652K	AAGTTTCCCGGGT	.	PASS	Atlas-SNP
ZNF502	91392	hgsc.bcm.edu	37	3	44762830	44762830	+	Missense_Mutation	SNP	A	A	G	rs56084453	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	66	166	0	0.409938	0	A|0.848;G|0.152	0.152	strong	ZNF502,NS,carcinoma,-1,1	ZNF502	58	1	NM_001134440	exon4	c.A521G	p.Q174R	AACATCAGAGAAC	.	PASS	Atlas-SNP
ZBED5	58486	hgsc.bcm.edu	37	11	10875741	10875741	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134	2	139	0	0.0149254	0	.	.	none	ZBED5_ENST00000432999,NS,carcinoma,0,2	ZBED5	50	2	NM_021211	exon3	c.G752A	p.R251Q	TTAATTCGACGTG	.	scavenged	Atlas-SNP
DCSTAMP	81501	hgsc.bcm.edu	37	8	105361354	105361354	+	Missense_Mutation	SNP	G	G	C	rs67114147	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	54	37	0	1	0	G|0.883;C|0.117	0.117	strong	.	.	.	.	NM_001257317	exon2	c.G574C	p.E192Q	AAAGGGGAAGTCC	.	PASS	Atlas-SNP
FOXD4L1	200350	hgsc.bcm.edu	37	2	114256840	114256840	+	Silent	SNP	C	C	T	rs2441583	by2hit2allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246	4	266	1	0.0162602	0.0037594	.	.	weak	FOXD4L1,colon,carcinoma,-2,1	FOXD4L1	48	1	NM_012184	exon1	c.C7T	p.L3L	ATGAACCTGCCAA	.	scavenged	Atlas-SNP
PSD3	23362	hgsc.bcm.edu	37	8	18729529	18729529	+	Missense_Mutation	SNP	C	C	G	rs78452893	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	85	193	0	0.429293	0	C|0.937;G|0.063	0.063	strong	.	PSD3	142	.	NM_015310	exon3	c.G845C	p.G282A	CATCCCCCTGGGT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016770	1016770	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1260	33	1512	15	0.0261905	0.00992064	.	.	none	MUC6_ENST00000421673,extremity,malignant_melanoma,0,1	MUC6	408	1	NM_005961	exon31	c.C6031T	p.P2011S	AGAAAGGTGGAAC	.	scavenged	Atlas-SNP
PTPN21	11099	hgsc.bcm.edu	37	14	88946343	88946343	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	4	55	0	0.0816327	0	.	.	none	.	PTPN21	113	.	NM_007039	exon13	c.G1432A	p.G478S	AGCTGCCGATGTT	.	PASS	Atlas-SNP
PLK5	126520	hgsc.bcm.edu	37	19	1535084	1535084	+	Silent	SNP	G	G	A	rs12984316	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	5	5	3	0	1	0	G|0.685;A|0.315	0.315	strong	PLK5,NS,carcinoma,0,1	PLK5	1	1	NM_001243079	exon14	c.G846A	p.P282P	AGTCCCGGCCCAA	.	PASS	Atlas-SNP
SIK1	150094	hgsc.bcm.edu	37	21	44840138	44840138	+	Silent	SNP	G	G	A	rs17004546	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	308	176	247	0	0.571429	0	G|0.970;A|0.030	0.030	strong	.	SIK1	65	.	NM_173354	exon8	c.C948T	p.G316G	GTCCACGCCCAGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682814	100682814	+	Missense_Mutation	SNP	A	A	G	rs201007776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198	15	139	2	0.0757576	0.0143885	A|0.999;G|0.001	0.001	weak	MUC17,NS,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.A8117G	p.N2706S	TGGCCAATTCTGA	.	scavenged	Atlas-SNP
NAA40	79829	hgsc.bcm.edu	37	11	63713317	63713317	+	Silent	SNP	G	G	A	rs3740637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132	59	109	0	0.44697	0	G|0.756;A|0.244	0.244	strong	.	NAA40	13	.	NM_024771	exon2	c.G12A	p.K4K	GAGAAAGTCAAGC	.	PASS	Atlas-SNP
TAS2R41	259287	hgsc.bcm.edu	37	7	143175345	143175345	+	Missense_Mutation	SNP	C	C	T	rs10278721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	57	104	0	1	0	C|0.770;T|0.230	0.230	strong	.	TAS2R41	43	.	NM_176883	exon1	c.C380T	p.P127L	GGTTCCCAGGGTG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50533463	50533463	+	Missense_Mutation	SNP	T	T	A	rs10857470	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	15	107	0	0.230769	0	T|0.906;A|0.094	0.094	strong	.	C10orf71	179	.	NM_001135196	exon3	c.T2873A	p.F958Y	GGAATTTCCCATC	.	PASS	Atlas-SNP
NBPF16	728936	hgsc.bcm.edu	37	1	148756664	148756664	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	208	51	196	21	0.245192	0.107143	.	.	none	NBPF16,NS,carcinoid-endocrine_tumour,0,1	NBPF16	7	1	NM_001102663	exon16	c.G1993T	p.G665X	CAGATGGGAGTCA	.	scavenged	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31606682	31606682	+	Silent	SNP	A	A	G	rs145596057	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166	85	165	0	0.512048	0	A|0.999;G|0.001	0.001	strong	.	XDH	191	.	NM_000379	exon10	c.T825C	p.F275F	CATAGGAAACAGC	.	PASS	Atlas-SNP
PAPOLB	56903	hgsc.bcm.edu	37	7	4900095	4900095	+	Silent	SNP	A	A	G	rs1553960	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	399	153	302	1	0.383459	0.00331126	A|0.574;G|0.426	0.426	strong	PAPOLB,NS,carcinoma,0,1	PAPOLB	93	1	NM_020144	exon1	c.T1347C	p.N449N	TTCAGAATTATCT	.	PASS	Atlas-SNP
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739865	20739865	+	Silent	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39	18	91	0	0.461538	0	.	.	none	GOLGA6L6,NS,carcinoma,+1,1	GOLGA6L6	37	1	NM_001145004	exon8	c.C1885A	p.R629R	GCTCCCGTATCTT	.	scavenged	Atlas-SNP
CCDC74A	90557	hgsc.bcm.edu	37	2	132290464	132290464	+	Missense_Mutation	SNP	G	G	A	rs13660	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	94	221	0	0.482051	0	G|0.866;A|0.134	0.134	strong	CCDC74A,NS,carcinoma,-1,3	CCDC74A	44	3	NM_138770	exon6	c.G904A	p.G302R	CTGGAAGGGAGCC	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2144176	2144176	+	Missense_Mutation	SNP	G	G	A	rs34197769	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217	120	238	0	0.552995	0	G|0.911;A|0.089	0.089	strong	.	PKD1	184	.	NM_001009944	exon35	c.C10535T	p.A3512V	TGCAGCGCCAGCG	.	PASS	Atlas-SNP
SLC28A3	64078	hgsc.bcm.edu	37	9	86900926	86900926	+	Silent	SNP	G	G	A	rs7853758	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122	54	159	0	0.442623	0	G|0.802;A|0.198	0.198	strong	.	SLC28A3	72	.	NM_001199633	exon13	c.C1381T	p.L461L	AAGACAGCAGGGC	.	PASS	Atlas-SNP
ATP5J2-PTCD1	100526740	hgsc.bcm.edu	37	7	99032517	99032517	+	Missense_Mutation	SNP	G	G	A	rs34943973	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	280	120	236	0	0.428571	0	G|0.958;A|0.042	0.042	strong	.	.	.	.	NM_001198879	exon3	c.C496T	p.R166W	CTCTCCGTTCCCC	.	PASS	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167645888	167645888	+	Silent	SNP	T	T	C	rs1363560	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	257	127	249	0	0.494163	0	T|0.589;C|0.411	0.411	strong	.	.	.	.	NM_001122679	exon23	c.T4965C	p.N1655N	CACCAATGGAGGC	.	PASS	Atlas-SNP
PLIN3	10226	hgsc.bcm.edu	37	19	4861381	4861381	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48	13	42	0	0.270833	0	.	.	none	PLIN3,NS,carcinoma,-1,1	PLIN3	36	1	NM_001164189	exon2	c.A26G	p.D9G	CTGCCATCAGCCT	.	PASS	Atlas-SNP
DIAPH3	81624	hgsc.bcm.edu	37	13	60566644	60566644	+	Missense_Mutation	SNP	T	T	C	rs36084898	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68	34	73	0	0.5	0	T|0.940;C|0.060	0.060	strong	.	DIAPH3	139	.	NM_001042517	exon10	c.A1088G	p.N363S	AATTCATTTCTGA	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19499560	19499560	+	Missense_Mutation	SNP	T	T	C	rs16862578	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76	54	143	0	0.710526	0	T|0.826;C|0.174	0.174	strong	UBR4,NS,carcinoma,0,1	UBR4	415	1	NM_020765	exon25	c.A3319G	p.T1107A	TGGTGGTACAGTC	.	PASS	Atlas-SNP
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19127347	19127347	+	Missense_Mutation	SNP	C	C	T	rs11074362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	46	93	0	0.575	0	C|0.945;T|0.055	0.055	strong	.	ITPRIPL2	40	.	NM_001034841	exon1	c.C1564T	p.P522S	CCCCCACCCCGGA	.	PASS	Atlas-SNP
ZNF750	79755	hgsc.bcm.edu	37	17	80789628	80789628	+	Missense_Mutation	SNP	T	T	C	rs8074277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197	97	214	0	0.492386	0	T|0.855;C|0.145	0.145	strong	ZNF750,NS,adenoma,0,1	ZNF750	60	1	NM_024702	exon2	c.A703G	p.M235V	GGTGCATGTAAGG	.	PASS	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860882	16860882	+	Missense_Mutation	SNP	G	G	A	rs61746179	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	42	93	0	0.461538	0	G|0.985;A|0.015	0.015	strong	.	NWD1	303	.	NM_001007525	exon6	c.G1429A	p.D477N	GTTTTGGACACCT	.	PASS	Atlas-SNP
MYBL2	4605	hgsc.bcm.edu	37	20	42343821	42343821	+	Missense_Mutation	SNP	C	C	G	rs11556379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	271	127	249	0	0.468635	0	C|0.968;G|0.032	0.032	strong	.	MYBL2	82	.	NM_002466	exon13	c.C1872G	p.I624M	AGGTATCAAAGAA	.	PASS	Atlas-SNP
C10orf25	220979	hgsc.bcm.edu	37	10	45496126	45496126	+	Missense_Mutation	SNP	G	G	A	rs41301609	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	13	106	0	0.216667	0	G|0.948;A|0.052	0.052	strong	.	C10orf25	11	.	NM_001039380	exon1	c.C182T	p.P61L	ATTTGTGGAAAGT	.	PASS	Atlas-SNP
HSPH1	10808	hgsc.bcm.edu	37	13	31729729	31729729	+	Silent	SNP	A	A	G	rs1047086	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171	78	193	0	0.45614	0	A|0.651;G|0.349	0.349	strong	.	HSPH1	65	.	NM_006644	exon3	c.T228C	p.N76N	GGGGTCATTGAAT	.	PASS	Atlas-SNP
PAX9	5083	hgsc.bcm.edu	37	14	37135752	37135752	+	Silent	SNP	C	C	T	rs12881240	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221	3	165	0	0.0135747	0	C|0.841;T|0.159	0.159	strong	PAX9,NS,carcinoma,0,1	PAX9	34	1	NM_006194	exon4	c.C717T	p.H239H	CCCGCACGCGGTG	.	scavenged	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	37	3	184550501	184550501	+	Missense_Mutation	SNP	A	A	G	rs9830734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	267	122	275	0	0.456929	0	A|0.480;G|0.520	0.520	strong	.	VPS8	109	.	NM_001009921	exon4	c.A247G	p.I83V	TCTTTTATTCTTG	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9888069	9888069	+	Silent	SNP	A	A	G	rs2240905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	136	102	1	1	0.00980392	G|0.522;N|0.000	0.522	strong	TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.A1593G	p.E531E	AAAAGAAGAAAAG	.	PASS	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	37	7	100635143	100635143	+	Silent	SNP	T	T	C	rs34337783	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4	4	0	0	1	.	T|0.890;C|0.110	0.110	strong	MUC12,NS,carcinoma,+2,1	MUC12	140	1	NM_001164462	exon2	c.T1299C	p.R433R	AGGCCGTAGTGAG	.	PASS	Atlas-SNP
HEATR1	55127	hgsc.bcm.edu	37	1	236767288	236767288	+	Silent	SNP	C	C	T	rs16834056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161	54	127	0	0.335404	0	C|0.985;T|0.015	0.015	strong	.	HEATR1	197	.	NM_018072	exon2	c.G108A	p.A36A	TGTGGCCGCTTCC	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136561367	136561367	+	Silent	SNP	G	G	A	rs2502740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	26	44	0	0.42623	0	G|0.744;A|0.256	0.256	strong	SARDH,NS,carcinoma,0,1	SARDH	112	1	NM_007101	exon14	c.C1785T	p.S595S	ATCTGCGGAGAAG	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25255338	25255338	+	Silent	SNP	C	C	T	rs2227894	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	22	32	0	0.578947	0	C|0.873;G|0.000;T|0.126	0.126	strong	PYGB,NS,carcinoma,+2,1	PYGB	84	1	NM_002862	exon5	c.C639T	p.G213G	CGACGGCGTGAAG	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732497	138732497	+	Missense_Mutation	SNP	G	G	A	rs3735007	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	8	132	0	0.112676	0	G|0.444;N|0.000	.	strong	ZC3HAV1,colon,carcinoma,+1,1	ZC3HAV1	75	1	NM_020119	exon13	c.C2552T	p.T851I	CCTTCAGTAAACT	.	PASS	Atlas-SNP
CCDC28A	25901	hgsc.bcm.edu	37	6	139094937	139094937	+	Silent	SNP	C	C	T	rs11154999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	99	206	1	0.5625	0.00485437	C|0.970;T|0.030	0.030	strong	.	CCDC28A	34	.	NM_015439	exon1	c.C126T	p.S42S	CGGGTCCCGGGAT	.	PASS	Atlas-SNP
SH3TC2	79628	hgsc.bcm.edu	37	5	148408101	148408101	+	Silent	SNP	A	A	G	rs1432793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	42	74	0	0.506024	0	A|0.535;G|0.465	0.465	strong	SH3TC2_ENST00000394358,NS,carcinoma,0,2	SH3TC2	178	2	NM_024577	exon11	c.T1194C	p.G398G	CTTGAAACCTTCA	.	PASS	Atlas-SNP
LHCGR	3973	hgsc.bcm.edu	37	2	48921375	48921375	+	Missense_Mutation	SNP	T	T	C	rs2293275	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224	110	258	0	0.491071	0	T|0.446;C|0.554	0.554	strong	.	LHCGR	154	.	NM_000233	exon10	c.A935G	p.N312S	TTGTTATTCACTT	.	PASS	Atlas-SNP
ASIC2	40	hgsc.bcm.edu	37	17	31618732	31618732	+	Silent	SNP	A	A	G	rs9893935	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	39	110	2	0.386139	0.0181818	A|0.468;G|0.532	0.532	strong	ACCN1,NS,carcinoma,0,2	.	.	2	NM_183377	exon1	c.T402C	p.T134T	GCACACAGTGACG	.	scavenged	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26164700	26164700	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53	31	60	0	0.584906	0	.	.	none	.	MYO18B	322	.	NM_032608	exon4	c.C817T	p.P273S	CAAGGGCCCGGCG	.	PASS	Atlas-SNP
PIK3R4	30849	hgsc.bcm.edu	37	3	130449222	130449222	+	Silent	SNP	A	A	G	rs2170990	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	43	81	0	0.488636	0	A|0.812;G|0.188	0.188	strong	.	PIK3R4	145	.	NM_014602	exon5	c.T1515C	p.L505L	CATATTAAGATTT	.	PASS	Atlas-SNP
UBXN6	80700	hgsc.bcm.edu	37	19	4454000	4454000	+	Silent	SNP	G	G	A	rs11909	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	31	65	0	0.476923	0	G|0.653;A|0.347	0.347	strong	.	UBXN6	27	.	NM_025241	exon2	c.C174T	p.A58A	TAGGGCGGCAGCG	.	PASS	Atlas-SNP
ZNF512B	57473	hgsc.bcm.edu	37	20	62591460	62591460	+	Silent	SNP	G	G	A	rs45570933	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	37	82	0	0.402174	0	G|0.955;A|0.045	0.045	strong	.	ZNF512B	72	.	NM_020713	exon17	c.C2460T	p.P820P	GTGTTTGGGAGGT	.	PASS	Atlas-SNP
CSTL1	128817	hgsc.bcm.edu	37	20	23424613	23424613	+	Missense_Mutation	SNP	T	T	C	rs3746736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154	73	134	0	0.474026	0	C|0.629;N|0.000	0.629	strong	.	CSTL1	30	.	NM_138283	exon3	c.T262C	p.W88R	ATTGGCTGGACCA	.	PASS	Atlas-SNP
OVCH2	341277	hgsc.bcm.edu	37	11	7727872	7727872	+	Missense_Mutation	SNP	T	T	C	rs12289558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	47	96	1	0.580247	0.0104167	T|0.837;C|0.163	0.163	strong	OVCH2,colon,carcinoma,0,1	OVCH2	47	1	NM_198185	exon1	c.A70G	p.T24A	AAAGAGTTGCAGA	.	scavenged	Atlas-SNP
ZNF302	55900	hgsc.bcm.edu	37	19	35173717	35173717	+	Missense_Mutation	SNP	T	T	A	rs199664059	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	300	87	222	0	0.29	0	T|0.954;A|0.046	0.046	strong	ZNF302,NS,carcinoma,0,3	ZNF302	27	3	NM_018443	exon3	c.T45A	p.H15Q	CTCTCATGAAGAG	.	scavenged	Atlas-SNP
ZCCHC14	23174	hgsc.bcm.edu	37	16	87445270	87445270	+	Silent	SNP	T	T	C	rs3748399	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61	54	87	2	0.885246	0.0229885	T|0.901;C|0.099	0.099	strong	ZCCHC14,rectum,carcinoma,-2,1	ZCCHC14	87	1	NM_015144	exon12	c.A2646G	p.T882T	CCCTGCTGTCCCT	.	scavenged	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	37	3	172061988	172061988	+	Silent	SNP	C	C	T	rs200807692	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	90	216	0	0.505618	0	C|1.000;T|0.000	0.000	strong	.	FNDC3B	118	.	NM_001135095	exon19	c.C2190T	p.V730V	CACCGTCGGCAAC	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53856761	53856761	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	12	155	0	0.0685714	0	.	.	none	ZNF845,NS,carcinoma,0,1	ZNF845	101	1	NM_138374	exon4	c.T2833C	p.C945R	TACAAGTGTAATG	.	PASS	Atlas-SNP
USP35	57558	hgsc.bcm.edu	37	11	77920964	77920964	+	Missense_Mutation	SNP	C	C	T	rs118006862	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	37	95	0	0.451219	0	C|0.991;T|0.009	0.009	strong	.	USP35	179	.	NM_020798	exon10	c.C2063T	p.T688M	AGAGAACGGAGAA	.	PASS	Atlas-SNP
AOAH	313	hgsc.bcm.edu	37	7	36763672	36763672	+	Missense_Mutation	SNP	C	C	T	rs2228410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80	31	49	0	0.3875	0	C|0.697;T|0.303	0.303	strong	.	AOAH	79	.	NM_001177507	exon1	c.G82A	p.D28N	GGTCATCGTTGGC	.	PASS	Atlas-SNP
SLAIN2	57606	hgsc.bcm.edu	37	4	48424058	48424058	+	Silent	SNP	C	C	T	rs17609614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	33	77	0	0.515625	0	C|0.968;T|0.032	0.032	strong	.	SLAIN2	31	.	NM_020846	exon8	c.C1710T	p.S570S	TGGTAGCATGAAA	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113148346	113148346	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	2	85	0	0.0190476	0	.	.	none	SVEP1,NS,carcinoma,+1,1	SVEP1	326	1	NM_153366	exon43	c.T10069C	p.C3357R	CAGGGCATGGATT	.	scavenged	Atlas-SNP
MSH2	4436	hgsc.bcm.edu	37	2	47630528	47630528	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111	62	171	0	0.558559	0	.	.	none	.	MSH2	198	.	NM_000251	exon1	c.C198T	p.Y66Y	CAAGTACATGGGG	.	PASS	Atlas-SNP
DHX57	90957	hgsc.bcm.edu	37	2	39042718	39042718	+	Missense_Mutation	SNP	T	T	G	rs150735204	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	61	112	0	0.495935	0	T|0.996;G|0.004	0.004	strong	DHX57,NS,carcinoma,0,1	DHX57	127	1	NM_198963	exon20	c.A3551C	p.E1184A	TCAATTTCCCTTG	.	PASS	Atlas-SNP
DPF3	8110	hgsc.bcm.edu	37	14	73137882	73137882	+	Missense_Mutation	SNP	G	G	A	rs202093453	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	91	86	0	0.654676	0	.	.	weak	.	DPF3	117	.	NM_012074	exon9	c.C1036T	p.R346W	AACCCCGGCCACT	.	PASS	Atlas-SNP
BRICD5	283870	hgsc.bcm.edu	37	16	2260567	2260567	+	Missense_Mutation	SNP	C	C	T	rs26857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	54	121	1	0.586957	0.00826446	C|0.523;T|0.477	0.477	strong	C16orf79,NS,lymphoid_neoplasm,0,1	.	.	1	NM_182563	exon2	c.G136A	p.V46I	CCACAACCCCCAC	.	scavenged	Atlas-SNP
ACSL1	2180	hgsc.bcm.edu	37	4	185687863	185687863	+	Silent	SNP	A	A	G	rs11727009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	46	112	0	0.779661	0	A|0.768;G|0.232	0.232	strong	.	ACSL1	77	.	NM_001995	exon13	c.T1176C	p.F392F	GGAGGCAAAGTCC	.	PASS	Atlas-SNP
SNX29	92017	hgsc.bcm.edu	37	16	12162969	12162969	+	Silent	SNP	A	A	G	rs1641843	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	56	96	0	0.466667	0	A|0.468;G|0.532	0.532	strong	SNX29_ENST00000306030,NS,carcinoma,0,1	SNX29	60	1	NM_032167	exon10	c.A1299G	p.P433P	TCTCCCAGATCCT	.	PASS	Atlas-SNP
NFATC2	4773	hgsc.bcm.edu	37	20	50140627	50140627	+	Silent	SNP	G	G	C	rs3746420	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77	46	95	0	0.597403	0	G|0.939;C|0.061	0.061	strong	.	NFATC2	112	.	NM_012340	exon2	c.C153G	p.V51V	GCTGGCGACCTTA	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12885289	12885289	+	Silent	SNP	G	G	T	rs78694969		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19	3	87	0	0.157895	0	T|1.000;|0.000	1.000	weak	PRAMEF11,NS,carcinoma,0,7	PRAMEF11	72	7	NM_001146344	exon4	c.C822A	p.L274L	CTGGGAGAGATGC	.	scavenged	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31476458	31476458	+	Missense_Mutation	SNP	C	C	T	rs11150624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	69	124	0	0.453947	0	C|0.636;T|0.364	0.364	strong	ARMC5_ENST00000457010,brain,glioma,0,1	ARMC5	94	1	NM_024742	exon4	c.C2114T	p.A705V	GCCCCGCGCCCAG	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169819835	169819835	+	Silent	SNP	A	A	G	rs113676921	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70	47	119	0	0.671429	0	A|0.996;G|0.004	0.004	strong	.	PALLD	179	.	NM_001166108	exon14	c.A2442G	p.T814T	TTTCACATGTAGA	.	PASS	Atlas-SNP
TAS2R46	259292	hgsc.bcm.edu	37	12	11213994	11213994	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	286	4	247	3	0.013986	0.0121457	.	.	none	TAS2R46,lower_third,carcinoma,0,1	TAS2R46	43	1	NM_176887	exon1	c.G900A	p.W300X	TTTCACCCAGTAC	.	scavenged	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39872804	39872804	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	191	4	168	0	0.0209424	0	.	.	none	IDO2_ENST00000502986,NS,malignant_melanoma,-1,4	IDO2	78	4	NM_194294	exon11	c.T946C	p.S316P	CCTCCTTCCCATA	.	scavenged	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848121	54848121	+	Missense_Mutation	SNP	C	C	T	rs141881690	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144	13	191	0	0.0902778	0	C|0.999;T|0.001	0.001	weak	.	LILRA4	91	.	NM_012276	exon6	c.G1246A	p.V416M	AGACCACGAGCTC	.	PASS	Atlas-SNP
AQPEP	0	hgsc.bcm.edu	37	5	115298898	115298898	+	Missense_Mutation	SNP	C	C	T	rs145336539	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	56	131	0	0.427481	0	C|0.997;T|0.003	0.003	strong	.	.	.	.	NM_173800	exon1	c.C584T	p.P195L	GTGAGCCCCTGAA	.	PASS	Atlas-SNP
EDN1	1906	hgsc.bcm.edu	37	6	12296255	12296255	+	Missense_Mutation	SNP	G	G	T	rs5370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	51	108	1	0.472222	0.00925926	G|0.787;T|0.213	0.213	strong	EDN1,NS,carcinoma,0,1	EDN1	23	1	NM_001955	exon5	c.G594T	p.K198N	AGGCAAGCCCTCC	.	scavenged	Atlas-SNP
CHRNA9	55584	hgsc.bcm.edu	37	4	40337908	40337908	+	Silent	SNP	T	T	C	rs10022491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228	112	225	0	0.491228	0	T|0.360;C|0.640	0.640	strong	.	CHRNA9	53	.	NM_017581	exon2	c.T129C	p.S43S	TTATTCTAATGCT	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129902281	129902281	+	Missense_Mutation	SNP	G	G	A	rs1063535	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	63	147	0	0.456522	0	G|0.522;A|0.478	0.478	strong	.	MKI67	363	.	NM_002417	exon13	c.C7823T	p.P2608L	TTCCTGGGACGTG	.	PASS	Atlas-SNP
MOB3A	126308	hgsc.bcm.edu	37	19	2078176	2078176	+	Silent	SNP	C	C	T	rs35452475	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	267	267	302	1	1	0.00331126	C|0.956;T|0.044	0.044	strong	MOBKL2A,caecum,carcinoma,-1,1	.	.	1	NM_130807	exon3	c.G384A	p.A128A	GATCTGCGCCTCG	.	PASS	Atlas-SNP
SLITRK5	26050	hgsc.bcm.edu	37	13	88328488	88328488	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	2	98	0	0.0217391	0	.	.	none	SLITRK5,NS,carcinoma,+1,2	SLITRK5	192	2	NM_015567	exon2	c.A845G	p.E282G	AGCAGGAACTTTG	.	scavenged	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367350	142367350	+	Missense_Mutation	SNP	C	C	T	rs201039593	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20	20	20	0	1	0	.	.	weak	.	GPR20	43	.	NM_005293	exon2	c.G674A	p.R225Q	CCCGGCCGCGACA	.	PASS	Atlas-SNP
OAF	220323	hgsc.bcm.edu	37	11	120099791	120099791	+	Silent	SNP	C	C	T	rs2465654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	270	198	142	0	0.733333	0	C|0.869;T|0.131	0.131	strong	.	OAF	12	.	NM_178507	exon4	c.C762T	p.F254F	CAGCTTCGACTTC	.	PASS	Atlas-SNP
SPHK2	56848	hgsc.bcm.edu	37	19	49132634	49132634	+	Silent	SNP	G	G	A	rs3745733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	26	56	0	0.590909	0	G|0.907;A|0.093	0.093	strong	SPHK2,NS,carcinoma,0,1	SPHK2	62	1	NM_020126	exon7	c.G1569A	p.L523L	TCCGCTGGGCACC	.	PASS	Atlas-SNP
MRGPRD	116512	hgsc.bcm.edu	37	11	68747529	68747529	+	Silent	SNP	C	C	T	rs138573323	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	37	48	0	0.451219	0	C|0.989;T|0.011	0.011	strong	.	MRGPRD	53	.	NM_198923	exon1	c.G927A	p.G309G	CGTCTCCCCACCT	.	PASS	Atlas-SNP
KIF24	347240	hgsc.bcm.edu	37	9	34256347	34256347	+	Silent	SNP	C	C	T	rs10814083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105	52	106	0	0.495238	0	C|0.626;T|0.374	0.374	strong	.	KIF24	64	.	NM_194313	exon11	c.G3258A	p.G1086G	TGGGCCCCCTGTG	.	PASS	Atlas-SNP
PTPRU	10076	hgsc.bcm.edu	37	1	29630455	29630455	+	Silent	SNP	C	C	T	rs2295061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213	61	360	0	0.286385	0	C|0.746;T|0.254	0.254	strong	.	PTPRU	374	.	NM_005704	exon17	c.C2595T	p.Y865Y	CCCATACCACACG	.	PASS	Atlas-SNP
EML5	161436	hgsc.bcm.edu	37	14	89151392	89151392	+	Silent	SNP	C	C	A	rs17204164	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	61	158	0	0.305	0	C|0.962;A|0.038	0.038	strong	.	EML5	141	.	NM_183387	exon20	c.G2949T	p.V983V	TTTATCCACTTCT	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4874420	4874420	+	Missense_Mutation	SNP	G	G	C	rs2292498	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	38	83	0	0.327586	0	G|0.754;C|0.246	0.246	strong	.	RADIL	110	.	NM_018059	exon4	c.C1234G	p.H412D	CCAGGTGGGGCTC	.	PASS	Atlas-SNP
BEND3	57673	hgsc.bcm.edu	37	6	107391213	107391213	+	Silent	SNP	C	C	T	rs3814072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	73	89	0	0.574803	0	C|0.925;T|0.075	0.075	strong	.	BEND3	70	.	NM_001080450	exon5	c.G1182A	p.T394T	GTCCTGCGTGTCC	.	PASS	Atlas-SNP
OGDHL	55753	hgsc.bcm.edu	37	10	50959965	50959965	+	Silent	SNP	C	C	T	rs7090775	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	73	184	0	0.793478	0	C|0.960;T|0.040	0.040	strong	.	OGDHL	149	.	NM_018245	exon6	c.G657A	p.Q219Q	GATCCACTGGCAC	.	PASS	Atlas-SNP
MTA1	9112	hgsc.bcm.edu	37	14	105930406	105930406	+	Missense_Mutation	SNP	G	G	A	rs4983413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	154	266	1	0.641667	0.0037594	G|0.782;A|0.218	0.218	strong	MTA1,NS,carcinoma,0,1	MTA1	61	1	NM_004689	exon13	c.G1114A	p.V372I	AACAACGTCAAGG	.	PASS	Atlas-SNP
CASP12	100506742	hgsc.bcm.edu	37	11	104768098	104768098	+	Silent	SNP	T	T	C	rs555367	bycluster;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4	4	0	0	1	.	T|0.010;C|0.990	0.990	strong	.	CASP12	4	.	NM_001191016	exon2	c.A105G	p.V35V	ATTTAATACATTA	.	PASS	Atlas-SNP
OR10V1	390201	hgsc.bcm.edu	37	11	59480759	59480759	+	Missense_Mutation	SNP	C	C	T	rs141649641	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	52	102	0	0.553191	0	C|0.998;T|0.002	0.002	strong	.	OR10V1	40	.	NM_001005324	exon1	c.G560A	p.R187H	GCCAGGCGCATGA	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	rs11556285	bycluster;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1415	159	1032	1	0.112367	0.000968992	G|0.998;T|0.002	0.002	weak	.	DHRS4	22	.	NM_021004	exon6	c.G582T	p.K194N	GACCAAGACCCTG	.	PASS	Atlas-SNP
VEGFB	7423	hgsc.bcm.edu	37	11	64004692	64004692	+	Silent	SNP	C	C	T	rs12366035	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58	58	105	0	1	0	C|0.792;T|0.208	0.208	strong	VEGFB,NS,carcinoma,0,1	VEGFB	18	1	NM_003377	exon5	c.C408T	p.D136D	GCCAGACAGGTGA	.	PASS	Atlas-SNP
FNBP1	23048	hgsc.bcm.edu	37	9	132687349	132687349	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236	4	204	0	0.0169492	0	.	.	none	FNBP1_ENST00000372416,colon,carcinoma,0,1	FNBP1	51	1	NM_015033	exon9	c.C877T	p.R293C	CAGTGCGCTTCAT	.	scavenged	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65	12	136	0	0.184615	0	.	.	none	.	PCDHA4	419	.	NM_031500	exon1	c.G1581A	p.E527E	CGAGGAGCTAGAG	.	PASS	Atlas-SNP
GPAA1	8733	hgsc.bcm.edu	37	8	145138063	145138063	+	Silent	SNP	G	G	A	rs138412600	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	76	177	0	0.337778	0	G|0.993;A|0.007	0.007	strong	.	GPAA1	40	.	NM_003801	exon2	c.G111A	p.L37L	GTTCTTGGCGCTG	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	37	6	158516882	158516882	+	Missense_Mutation	SNP	C	C	T	rs137935231	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59	30	60	0	0.508475	0	C|0.997;T|0.003	0.003	strong	.	SYNJ2	111	.	NM_003898	exon27	c.C3977T	p.P1326L	AGGCGCCGCCTCT	.	PASS	Atlas-SNP
COBLL1	22837	hgsc.bcm.edu	37	2	165551184	165551184	+	Silent	SNP	C	C	T	rs76695941	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113	59	114	1	0.522124	0.00877193	C|0.970;T|0.030	0.030	strong	COBLL1,caecum,carcinoma,-1,1	COBLL1	122	1	NM_014900	exon12	c.G2832A	p.R944R	CATATCCCTTTCT	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513521	195513521	+	Missense_Mutation	SNP	C	C	G	rs111334497	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1101	21	833	5	0.0190736	0.0060024	C|0.995;G|0.005	0.005	strong	MUC4_ENST00000463781,NS,carcinoma,+2,1	MUC4	1505	1	NM_018406	exon2	c.G4930C	p.G1644R	CGTGACCTGTGGA	.	scavenged	Atlas-SNP
RRM1	6240	hgsc.bcm.edu	37	11	4159457	4159457	+	Silent	SNP	A	A	G	rs9937	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	119	98	0	0.991667	0	A|0.587;G|0.413	0.413	strong	.	RRM1	31	.	NM_001033	exon19	c.A2223G	p.T741T	AAGGACAAGACCA	.	PASS	Atlas-SNP
VEZT	55591	hgsc.bcm.edu	37	12	95660182	95660182	+	Missense_Mutation	SNP	A	A	G	rs17855933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	139	266	0	0.712821	0	A|0.925;G|0.075	0.075	strong	.	VEZT	106	.	NM_017599	exon5	c.A484G	p.T162A	CTTCCCACTTGGT	.	PASS	Atlas-SNP
CASP9	842	hgsc.bcm.edu	37	1	15844615	15844615	+	Silent	SNP	A	A	G	rs1132312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	88	132	1	0.956522	0.00757576	G|0.589;A|0.411	0.589	strong	CASP9,NS,carcinoma,0,1	CASP9	40	1	NM_001229	exon2	c.T408C	p.F136F	ATCACCAAATCCT	.	PASS	Atlas-SNP
EPS15	2060	hgsc.bcm.edu	37	1	51912760	51912760	+	Silent	SNP	T	T	G	rs34704431	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	26	60	0	0.742857	0	T|0.955;G|0.045	0.045	strong	EPS15,NS,carcinoma,-2,1	EPS15	72	1	NM_001981	exon10	c.A669C	p.A223A	TTTTTCTGCAGGG	.	PASS	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	37	10	81917486	81917486	+	Missense_Mutation	SNP	T	T	C	rs1802932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	39	121	0	0.609375	0	T|0.992;C|0.008	0.008	strong	.	ANXA11	32	.	NM_145868	exon15	c.A1369G	p.I457V	CCATGATGCGAAT	.	PASS	Atlas-SNP
C16orf96	342346	hgsc.bcm.edu	37	16	4625274	4625274	+	Missense_Mutation	SNP	A	A	G	rs1256768	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	17	49	0	0.515152	0	A|0.856;G|0.144	0.144	strong	.	C16orf96	28	.	NM_001145011	exon5	c.A793G	p.I265V	CGTGCCATCCAGG	.	PASS	Atlas-SNP
CCR2	729230	hgsc.bcm.edu	37	3	46399208	46399208	+	Missense_Mutation	SNP	G	G	A	rs1799864	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	310	135	354	1	0.435484	0.00282486	G|0.844;A|0.156	0.156	strong	CCR2_ENST00000445132,colon,carcinoma,-2,2	CCR2	103	2	NM_001123041	exon2	c.G190A	p.V64I	CTGGTCGTCCTCA	.	PASS	Atlas-SNP
PTPRO	5800	hgsc.bcm.edu	37	12	15669737	15669737	+	Silent	SNP	T	T	C	rs1050646	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	84	212	0	0.48	0	T|0.853;C|0.147	0.147	strong	.	PTPRO	148	.	NM_002848	exon9	c.T1626C	p.G542G	TTTGGGTCCTACG	.	PASS	Atlas-SNP
NUP205	23165	hgsc.bcm.edu	37	7	135329690	135329690	+	Silent	SNP	T	T	C	rs12540688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	91	174	0	0.716535	0	T|0.778;C|0.222	0.222	strong	NUP205,NS,carcinoma,0,1	NUP205	198	1	NM_015135	exon40	c.T5607C	p.A1869A	CACTGCTCAGAAA	.	PASS	Atlas-SNP
KIAA1456	57604	hgsc.bcm.edu	37	8	12879198	12879198	+	Missense_Mutation	SNP	A	A	T	rs34995506	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	98	76	0	1	0	A|0.832;T|0.168	0.168	strong	.	KIAA1456	20	.	NM_020844	exon5	c.A1010T	p.H337L	GAGACCATCAAGG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373309	5373309	+	Missense_Mutation	SNP	C	C	A	rs115333544	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215	93	237	1	0.432558	0.00421941	C|0.937;A|0.063	0.063	strong	.	OR51B6	53	.	NM_001004750	exon1	c.C572A	p.T191N	ACATCACCTTCAA	.	PASS	Atlas-SNP
TYROBP	7305	hgsc.bcm.edu	37	19	36398454	36398454	+	Silent	SNP	G	G	C	rs111477177	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	46	133	2	0.425926	0.0150376	A|0.000;C|0.024;G|0.976	0.024	strong	TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	NM_198125	exon3	c.C123G	p.G41G	CAGCACGCCCGGG	.	scavenged	Atlas-SNP
REXO1	57455	hgsc.bcm.edu	37	19	1827927	1827927	+	Silent	SNP	T	T	G	rs144940979	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138	71	128	0	0.514493	0	T|0.999;G|0.001	0.001	strong	.	REXO1	55	.	NM_020695	exon2	c.A861C	p.S287S	TGAGTCTGAGAAC	.	PASS	Atlas-SNP
USP29	57663	hgsc.bcm.edu	37	19	57642782	57642782	+	Nonsense_Mutation	SNP	C	C	A	rs9973206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123	123	118	0	1	0	C|0.100;A|0.900	0.900	strong	.	USP29	186	.	NM_020903	exon4	c.C2739A	p.Y913X	GGAATACGAAGGT	.	PASS	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	37	21	43913112	43913112	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251	62	148	0	0.247012	0	.	.	none	RSPH1,NS,carcinoma,0,1	RSPH1	36	1	NM_080860	exon2	c.C132T	p.Y44Y	CCCTTCGTAGGTG	.	PASS	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693155	187693155	+	Missense_Mutation	SNP	A	A	T	rs10195758	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100	54	89	0	0.54	0	A|0.819;T|0.181	0.181	strong	.	ZSWIM2	119	.	NM_182521	exon9	c.T1458A	p.D486E	TTTATAATCATAG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2166542	2166542	+	Silent	SNP	G	G	A	rs367983387		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	34	62	0	0.566667	0	.	.	weak	.	PKD1	184	.	NM_000296	exon8	c.C1710T	p.H570H	GGGCTCGTGCGGG	.	PASS	Atlas-SNP
MTHFR	4524	hgsc.bcm.edu	37	1	11855269	11855269	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66	10	93	0	0.151515	0	.	.	none	.	MTHFR	65	.	NM_005957	exon6	c.G917A	p.C306Y	TCCTGGCACAGGC	.	PASS	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71577132	71577132	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159	2	159	0	0.0125786	0	.	.	none	ZNF638,rectum,carcinoma,0,4	ZNF638	179	4	NM_014497	exon2	c.C1048T	p.R350W	CAAGAGCGGATCC	.	scavenged	Atlas-SNP
ZNF99	7652	hgsc.bcm.edu	37	19	22941071	22941071	+	Missense_Mutation	SNP	T	T	C	rs144632185	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90	49	95	1	0.544444	0.0105263	T|0.913;C|0.087	0.087	strong	ZNF99,NS,carcinoma,0,1	ZNF99	273	1	NM_001080409	exon4	c.A1640G	p.N547S	GAATTGTTAAAAG	.	scavenged	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78261805	78261805	+	Silent	SNP	A	A	G	rs7215243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36	15	65	0	0.416667	0	A|0.731;G|0.269	0.269	strong	RNF213_ENST00000456466,NS,carcinoma,0,3	RNF213	766	3	NM_001256071	exon4	c.A453G	p.P151P	GCCCCCAGGCACA	.	PASS	Atlas-SNP
MTRR	4552	hgsc.bcm.edu	37	5	7878192	7878192	+	Silent	SNP	T	T	C	rs161870	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94	94	107	0	1	0	T|0.784;C|0.216	0.216	strong	.	MTRR	74	.	NM_024010	exon5	c.T618C	p.L206L	AGACCTTGTGAAG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90499502	90499502	+	Silent	SNP	G	G	A	rs1036853	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	115	114	0	0.991379	0	G|0.905;A|0.095	0.095	strong	.	MDN1	478	.	NM_014611	exon7	c.C1227T	p.D409D	TACCACGTCTAAG	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160468278	160468278	+	Silent	SNP	A	A	G	rs998075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	54	117	1	0.947368	0.00854701	A|0.458;G|0.542	0.542	strong	.	IGF2R	251	.	NM_000876	exon16	c.A2139G	p.T713T	CGGCACACCCTAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678568	100678568	+	Missense_Mutation	SNP	A	A	T	rs75492258	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259	87	131	0	0.335907	0	A|0.934;T|0.066	0.066	strong	MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	NM_001040105	exon3	c.A3871T	p.T1291S	CTGGTGACCAGTC	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141707868	141707868	+	Silent	SNP	G	G	T	rs6748626	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	101	197	0	0.505	0	G|0.770;T|0.230	0.230	strong	.	LRP1B	1315	.	NM_018557	exon20	c.C3072A	p.A1024A	ATCACAGGCCCAG	.	PASS	Atlas-SNP
SON	6651	hgsc.bcm.edu	37	21	34926043	34926043	+	Missense_Mutation	SNP	G	G	A	rs61743204	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	21	61	0	0.328125	0	G|0.884;A|0.116	0.116	strong	.	SON	343	.	NM_032195	exon3	c.G4506A	p.M1502I	TGGCATGCAGGAG	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	37	7	138602916	138602916	+	Missense_Mutation	SNP	G	G	C	rs2718131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	32	85	0	0.969697	0	G|0.756;C|0.244	0.244	strong	.	KIAA1549	314	.	NM_020910	exon2	c.C1456G	p.P486A	TGGAGGGGAAAAG	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362639	32362639	+	Silent	SNP	G	G	A	rs41535850	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	76	136	0	0.487179	0	G|0.859;A|0.141	0.141	strong	.	BTNL2	50	.	NM_019602	exon6	c.C1242T	p.H414H	CAGCCCGTGGCTG	.	PASS	Atlas-SNP
ZNF532	55205	hgsc.bcm.edu	37	18	56648756	56648756	+	Silent	SNP	C	C	T	rs61733373	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235	111	242	0	0.47234	0	C|0.910;T|0.090	0.090	strong	.	ZNF532	108	.	NM_018181	exon10	c.C3318T	p.H1106H	GAAGCACGTCCAG	.	PASS	Atlas-SNP
FAM194A	131831	hgsc.bcm.edu	37	3	150421419	150421419	+	Silent	SNP	G	G	A	rs17281287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101	40	106	0	0.39604	0	G|0.601;A|0.399	0.399	strong	FAM194A,NS,adenoma,0,1	FAM194A	91	1	NM_152394	exon1	c.C267T	p.D89D	GAAGTCGTCGTCG	.	PASS	Atlas-SNP
NPW	283869	hgsc.bcm.edu	37	16	2070200	2070200	+	Missense_Mutation	SNP	G	G	C	rs11248906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7	6	48	0	0.857143	0	G|0.881;C|0.119	0.119	strong	.	NPW	4	.	NM_001099456	exon1	c.G298C	p.E100Q	CTGTGGGAGACGC	.	PASS	Atlas-SNP
PTPN6	5777	hgsc.bcm.edu	37	12	7067226	7067226	+	Missense_Mutation	SNP	G	G	A	rs62621988	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22	11	41	0	0.5	0	G|0.999;A|0.001	0.001	strong	.	PTPN6	42	.	NM_080548	exon11	c.G1357A	p.V453M	ATCATCGTGCACT	.	PASS	Atlas-SNP
H6PD	9563	hgsc.bcm.edu	37	1	9323910	9323910	+	Missense_Mutation	SNP	G	G	A	rs6688832	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47	12	90	0	0.255319	0	G|0.662;A|0.338	0.338	strong	.	H6PD	71	.	NM_004285	exon5	c.G1358A	p.R453Q	CTGTGCGGGAGCG	.	PASS	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	37	7	76916819	76916819	+	Silent	SNP	G	G	A	rs3763402	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	336	334	214	0	0.994048	0	G|0.769;A|0.231	0.231	strong	.	CCDC146	87	.	NM_020879	exon17	c.G2340A	p.Q780Q	TGAGCAGGTCTCC	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53856776	53856776	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	7	145	0	0.0448718	0	.	.	none	.	ZNF845	101	.	NM_138374	exon4	c.A2848G	p.K950E	TGTGGCAAGGTTT	.	PASS	Atlas-SNP
CDH24	64403	hgsc.bcm.edu	37	14	23523353	23523353	+	Silent	SNP	G	G	T	rs139832060	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51	34	35	0	0.666667	0	G|0.997;T|0.003	0.003	strong	.	CDH24	129	.	NM_022478	exon6	c.C969A	p.R323R	AACCTTGCGGACA	.	PASS	Atlas-SNP
PLAC8L1	153770	hgsc.bcm.edu	37	5	145483844	145483844	+	Missense_Mutation	SNP	A	A	T	rs12187913	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	221	251	2	0.991031	0.00796813	A|0.797;T|0.203	0.203	strong	PLAC8L1,NS,carcinoma,0,1	PLAC8L1	17	1	NM_001029869	exon1	c.T31A	p.C11S	CAGGACACCTGAA	.	PASS	Atlas-SNP
OR11H12	440153	hgsc.bcm.edu	37	14	19378322	19378322	+	Missense_Mutation	SNP	G	G	A	rs201485834		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1329	22	1144	1	0.0165538	0.000874126	.	.	weak	OR11H12,NS,malignant_melanoma,+1,1	OR11H12	58	1	NM_001013354	exon1	c.G729A	p.M243I	GGGTATGCCTTCA	.	scavenged	Atlas-SNP
HGS	9146	hgsc.bcm.edu	37	17	79660570	79660570	+	Missense_Mutation	SNP	C	C	T	rs150616739	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223	117	264	1	0.524664	0.00378788	C|1.000;T|0.000	0.000	weak	.	HGS	54	.	NM_004712	exon9	c.C700T	p.P234S	GAGCTGCCCCCCG	.	PASS	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77707422	77707422	+	Missense_Mutation	SNP	G	G	A	rs145931726	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	3	132	0	0.025	0	G|1.000;A|0.000	0.000	strong	ENPP7,NS,carcinoma,0,1	ENPP7	63	1	NM_178543	exon2	c.G370A	p.V124M	GGCAGCGTGCCCA	.	scavenged	Atlas-SNP
KRT81	3887	hgsc.bcm.edu	37	12	52681056	52681056	+	Silent	SNP	C	C	T	rs4761856	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119	66	153	0	0.554622	0	C|0.673;T|0.327	0.327	strong	.	KRT81	46	.	NM_002281	exon7	c.G1077A	p.A359A	GAGGGCCGCCTCA	.	PASS	Atlas-SNP
SEC31B	25956	hgsc.bcm.edu	37	10	102265847	102265847	+	Missense_Mutation	SNP	A	A	C	rs2295774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	83	190	1	0.715517	0.00526316	A|0.836;C|0.164	0.164	strong	SEC31B,colon,carcinoma,0,1	SEC31B	84	1	NM_015490	exon9	c.T994G	p.S332A	TCACAGAGTACAA	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51192659	51192659	+	Silent	SNP	G	G	A	rs1983764	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	337	337	259	1	1	0.003861	G|0.744;A|0.256	0.256	strong	.	NIN	475	.	NM_182946	exon30	c.C6204T	p.P2068P	ATGACCGGGTAGG	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91660861	91660861	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91	6	87	0	0.0659341	0	.	.	none	.	AKAP9	788	.	NM_005751	exon16	c.T4281C	p.N1427N	AACAAATATCGTT	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50407255	50407255	+	Silent	SNP	G	G	A	rs201329321	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	50	136	0	0.297619	0	G|1.000;A|0.000	0.000	strong	.	SALL4	168	.	NM_020436	exon2	c.C1767T	p.T589T	CTCCCCGGTGTGG	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152283236	152283236	+	Missense_Mutation	SNP	T	T	C	rs11581433	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	67	150	0	0.34359	0	T|0.807;C|0.193	0.193	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.A4126G	p.R1376G	CTTGTCTGTGCCC	.	PASS	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72412427	72412427	+	Missense_Mutation	SNP	G	G	A	rs2429277		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	455	34	360	15	0.0747253	0.0416667	.	.	weak	POM121,NS,malignant_melanoma,0,2	POM121	131	2	NM_172020	exon11	c.G1100A	p.S367N	CACCCAGCCTCCT	.	scavenged	Atlas-SNP
PRSS53	339105	hgsc.bcm.edu	37	16	31096164	31096164	+	Missense_Mutation	SNP	G	G	C	rs7199949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	337	171	401	4	0.507418	0.00997506	G|0.648;C|0.352	0.352	strong	PRSS53,NS,carcinoma,0,2	PRSS53	29	2	NM_001039503	exon8	c.C1216G	p.P406A	GGTCAGGATAGGG	.	scavenged	Atlas-SNP
DCD	117159	hgsc.bcm.edu	37	12	55038536	55038536	+	Silent	SNP	G	G	A	rs139716642		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	120	214	0	0.504202	0	G|1.000;A|0.000	0.000	weak	.	DCD	20	.	NM_053283	exon5	c.C294T	p.A98A	ATGGACGGCTCCT	.	PASS	Atlas-SNP
ZNF404	342908	hgsc.bcm.edu	37	19	44377972	44377972	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240	3	248	0	0.0125	0	.	.	none	ZNF404,NS,carcinoma,+2,1	ZNF404	46	1	NM_001033719	exon2	c.G385A	p.E129K	TACACTCATATGA	.	scavenged	Atlas-SNP
GPD1L	23171	hgsc.bcm.edu	37	3	32181761	32181761	+	Silent	SNP	C	C	T	rs9835387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	70	125	0	0.432099	0	C|0.828;T|0.172	0.172	strong	.	GPD1L	25	.	NM_015141	exon4	c.C408T	p.D136D	TTCTGACATCATC	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29473982	29473982	+	Silent	SNP	G	G	A	rs56017149		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	2	77	0	0.0204082	0	.	.	weak	ALK,colon,carcinoma,0,1	ALK	533	1	NM_004304	exon12	c.C2193T	p.T731T	GGTGTCGGTGGCT	.	scavenged	Atlas-SNP
CNTLN	54875	hgsc.bcm.edu	37	9	17135322	17135322	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49	12	76	0	0.244898	0	.	.	none	.	CNTLN	128	.	NM_017738	exon1	c.A259G	p.R87G	GGGTCCAGACGGC	.	PASS	Atlas-SNP
KIF27	55582	hgsc.bcm.edu	37	9	86504005	86504005	+	Missense_Mutation	SNP	C	C	T	rs13289566	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137	69	159	0	0.50365	0	C|0.798;T|0.202	0.202	strong	.	KIF27	103	.	NM_017576	exon7	c.G1973A	p.G658E	CTAGTTCCAGATT	.	PASS	Atlas-SNP
MAN2A1	4124	hgsc.bcm.edu	37	5	109110591	109110591	+	Silent	SNP	G	G	A	rs61735369	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115	61	122	0	0.530435	0	G|0.920;A|0.080	0.080	strong	.	MAN2A1	136	.	NM_002372	exon8	c.G1299A	p.T433T	ATACACGGAATGG	.	PASS	Atlas-SNP
PHACTR2	9749	hgsc.bcm.edu	37	6	144081768	144081768	+	Silent	SNP	C	C	A	rs2073215	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44	16	44	0	0.363636	0	C|0.800;A|0.200	0.200	strong	.	PHACTR2	99	.	NM_001100164	exon5	c.C685A	p.R229R	ACGACCCGAGAGG	.	PASS	Atlas-SNP
PI4KA	5297	hgsc.bcm.edu	37	22	21065645	21065645	+	Silent	SNP	A	A	G	rs444310	bycluster;by2hit2allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	412	22	776	6	0.0533981	0.00773196	A|1.000;|0.000	.	weak	PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	NM_058004	exon51	c.T5907C	p.G1969G	GATATGACCCTTC	.	scavenged	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049939	69049939	+	Missense_Mutation	SNP	G	G	T	rs4241344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	28	46	0	0.518519	0	G|0.789;T|0.211	0.211	strong	.	ARHGAP25	175	.	NM_001007231	exon10	c.G1668T	p.R556S	GCAGAGGATGGTC	.	PASS	Atlas-SNP
NUP93	9688	hgsc.bcm.edu	37	16	56873495	56873495	+	Silent	SNP	C	C	T	rs1138295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	254	201	301	1	0.791339	0.00332226	C|0.811;T|0.189	0.189	strong	.	NUP93	75	.	NM_014669	exon20	c.C2199T	p.A733A	GGCTGCCTTCAGA	.	PASS	Atlas-SNP
IFNGR1	3459	hgsc.bcm.edu	37	6	137540423	137540423	+	Silent	SNP	C	C	T	rs17181471	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131	52	179	0	0.396947	0	C|0.995;T|0.005	0.005	strong	.	IFNGR1	46	.	NM_000416	exon1	c.G42A	p.V14V	CCTGCTCACACCC	.	PASS	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170176146	170176146	+	Missense_Mutation	SNP	G	G	A	rs41265401	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143	54	107	0	0.377622	0	G|0.925;A|0.075	0.075	strong	.	C6orf70	63	.	NM_018341	exon15	c.G1505A	p.R502H	TGGATCGTCTTCC	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786230	75786230	+	Silent	SNP	C	C	T	rs2118755	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57	26	75	0	0.45614	0	C|0.620;T|0.380	0.380	strong	ZNF717,NS,carcinoma,0,1	ZNF717	160	1	NM_001128223	exon5	c.G2544A	p.R848R	AGTTTTCCTACAT	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9071916	9071916	+	Missense_Mutation	SNP	G	G	A	rs35346115	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163	78	209	0	0.478528	0	G|0.980;A|0.020	0.020	strong	.	MUC16	4315	.	NM_024690	exon3	c.C15530T	p.T5177I	TTTGTAGTCTCAG	.	PASS	Atlas-SNP
BMPR2	659	hgsc.bcm.edu	37	2	203421199	203421199	+	Silent	SNP	G	G	A	rs1061157	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35	30	69	0	0.857143	0	G|0.907;A|0.093	0.093	strong	.	BMPR2	142	.	NM_001204	exon12	c.G2811A	p.R937R	ACAGAGGCCTAAT	.	PASS	Atlas-SNP
RBM6	10180	hgsc.bcm.edu	37	3	50114515	50114515	+	Silent	SNP	C	C	T	rs7061	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118	51	134	0	0.432203	0	C|0.329;T|0.671	0.671	strong	.	RBM6	85	.	NM_005777	exon21	c.C3321T	p.Y1107Y	GACTTACCGAGAT	.	PASS	Atlas-SNP
SFXN1	94081	hgsc.bcm.edu	37	5	174936038	174936038	+	Silent	SNP	A	A	G	rs35420613	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151	67	155	0	0.443709	0	A|0.947;G|0.053	0.053	strong	.	SFXN1	23	.	NM_022754	exon3	c.A168G	p.Q56Q	TAGGCAAGGAATT	.	PASS	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159407446	159407446	+	Missense_Mutation	SNP	C	C	T	rs34582178	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217	106	212	0	0.488479	0	C|0.861;T|0.139	0.139	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon3	c.G638A	p.R213Q	TCAGGCCGTCCGA	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151166422	151166422	+	Silent	SNP	C	C	T	rs6798252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63	26	67	0	0.412698	0	C|0.276;N|0.000	.	strong	.	IGSF10	279	.	NM_178822	exon4	c.G1347A	p.Q449Q	CTGGATCTGTAAT	.	PASS	Atlas-SNP
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31104520	31104520	+	Missense_Mutation	SNP	A	A	G	rs144472289	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139	69	85	0	0.496403	0	A|0.997;G|0.003	0.003	strong	.	ADCYAP1R1	78	.	NM_001118	exon3	c.A125G	p.N42S	GGGCCAATGAGCT	.	PASS	Atlas-SNP
TOX4	9878	hgsc.bcm.edu	37	14	21960969	21960969	+	Silent	SNP	G	G	A	rs7617	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225	223	191	0	0.991111	0	G|0.511;A|0.489	0.489	strong	.	TOX4	50	.	NM_014828	exon7	c.G1194A	p.R398R	CTCCCGGGGGCTC	.	PASS	Atlas-SNP
PSG8	440533	hgsc.bcm.edu	37	19	43269705	43269705	+	Missense_Mutation	SNP	G	G	A	rs7245423	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33	13	53	0	0.393939	0	G|0.635;A|0.365	0.365	strong	.	PSG8	101	.	NM_001130168	exon1	c.C29T	p.T10I	CGCTGTGTGCAGG	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64	11	133	0	0.171875	0	C|0.999;G|0.001	0.001	weak	PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	NM_031500	exon1	c.C1582G	p.L528V	GAGGAGCTAGAGC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179462494	179462494	+	Silent	SNP	A	A	G	rs35833641	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146	65	177	0	0.445205	0	A|0.821;G|0.179	0.179	strong	.	TTN	18412	.	NM_001267550	exon294	c.T57315C	p.H19105H	TCCAGCATGGACA	.	PASS	Atlas-SNP
PKNOX2	63876	hgsc.bcm.edu	37	11	125280737	125280737	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	3	110	0	0.0153846	0	.	.	none	PKNOX2,caecum,carcinoma,-1,1	PKNOX2	60	1	NM_022062	exon9	c.A781C	p.I261L	CAAGCAATCCCCC	.	scavenged	Atlas-SNP
SFRP2	6423	hgsc.bcm.edu	37	4	154709854	154709854	+	Missense_Mutation	SNP	G	G	A	rs4643790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	78	113	0	0.951219	0	G|0.806;A|0.194	0.194	strong	SFRP2,NS,carcinoma,-1,1	SFRP2	45	1	NM_003013	exon1	c.C134T	p.A45V	AGGTTGGCAGGGA	.	PASS	Atlas-SNP
CAMK2B	816	hgsc.bcm.edu	37	7	44282928	44282928	+	Silent	SNP	G	G	A	rs17172630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141	41	125	0	0.29078	0	G|0.945;A|0.055	0.055	strong	CAMK2B,NS,carcinoma,0,1	CAMK2B	56	1	NM_172081	exon8	c.C522T	p.F174F	GCCAGCGAAACCT	.	PASS	Atlas-SNP
TWF1	5756	hgsc.bcm.edu	37	12	44191625	44191625	+	Silent	SNP	G	G	A	rs12829856	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54	19	55	0	0.351852	0	G|0.896;A|0.104	0.104	strong	.	TWF1	37	.	NM_001242397	exon7	c.C516T	p.D172D	ACCCACGTCAGTC	.	PASS	Atlas-SNP
CRTAP	10491	hgsc.bcm.edu	37	3	33174156	33174156	+	Silent	SNP	T	T	G	rs1135127	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168	84	175	0	0.5	0	T|0.645;G|0.355	0.355	strong	CRTAP,NS,carcinoma,0,1	CRTAP	16	1	NM_006371	exon5	c.T1032G	p.T344T	GGACACTTGGGGC	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134108546	134108546	+	Missense_Mutation	SNP	T	T	C	rs2069569	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	118	174	0	0.614583	0	C|0.598;N|0.002	0.598	strong	.	TG	416	.	NM_003235	exon43	c.T7501C	p.W2501R	TCTTTATGGGTAG	.	PASS	Atlas-SNP
EVC2	132884	hgsc.bcm.edu	37	4	5642274	5642274	+	Silent	SNP	T	T	C	rs13131655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	192	74	211	0	0.385417	0	T|0.716;C|0.284	0.284	strong	.	EVC2	202	.	NM_147127	exon10	c.A1437G	p.E479E	TTCTGCTTCCTCC	.	PASS	Atlas-SNP
ABI3BP	25890	hgsc.bcm.edu	37	3	100617680	100617680	+	Silent	SNP	C	C	T	rs2245370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88	34	109	0	0.386364	0	C|0.280;T|0.720	0.720	strong	.	ABI3BP	305	.	NM_015429	exon4	c.G408A	p.S136S	GAAGACCGAGCTC	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66432381	66432381	+	Missense_Mutation	SNP	T	T	C	rs16956504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	78	132	0	0.8125	0	T|0.940;C|0.060	0.060	strong	.	CDH5	111	.	NM_001795	exon10	c.T1508C	p.I503T	CCGCAATAGACAA	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82363404	82363404	+	Missense_Mutation	SNP	A	A	G	rs7075840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	20	129	0	0.204082	0	A|0.661;G|0.339	0.339	strong	SH2D4B,NS,carcinoma,0,1	SH2D4B	44	1	NM_207372	exon5	c.A713G	p.H238R	ACCGACACCACTC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168103925	168103925	+	Missense_Mutation	SNP	A	A	G	rs7607246	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	195	100	188	0	0.512821	0	A|0.837;G|0.163	0.163	strong	.	XIRP2	914	.	NM_152381	exon9	c.A6023G	p.N2008S	ATGGCAATTTAGT	.	PASS	Atlas-SNP
PCDHA1	56147	hgsc.bcm.edu	37	5	140167463	140167463	+	Silent	SNP	C	C	T	rs3733710	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56	25	119	0	0.446429	0	C|0.485;T|0.515	0.515	strong	PCDHA1_ENST00000504120,NS,carcinoma,0,2	PCDHA1	387	2	NM_031411	exon1	c.C1588T	p.L530L	CTGGAGCTGCTGC	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197408085	197408085	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	75	172	0	0.480769	0	.	.	none	.	KIAA0226	136	.	NM_014687	exon16	c.T2345G	p.I782S	ATCTTAATGAGCA	.	PASS	Atlas-SNP
ASB6	140459	hgsc.bcm.edu	37	9	132401753	132401753	+	Silent	SNP	G	G	A	rs144137235	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81	34	82	0	0.419753	0	G|0.999;A|0.001	0.001	strong	.	ASB6	31	.	NM_017873	exon3	c.C330T	p.A110A	CAGGACGGCGATG	.	PASS	Atlas-SNP
ZFP28	140612	hgsc.bcm.edu	37	19	57066013	57066013	+	Missense_Mutation	SNP	C	C	T	rs10409531	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150	69	178	1	0.46	0.00561798	C|0.594;T|0.406	0.406	strong	ZFP28,NS,carcinoma,0,1	ZFP28	99	1	NM_020828	exon8	c.C1859T	p.A620V	AATGTGCGGAGTG	.	scavenged	Atlas-SNP
COQ7	10229	hgsc.bcm.edu	37	16	19085298	19085298	+	Missense_Mutation	SNP	C	C	T	rs11074359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178	90	194	0	0.505618	0	C|0.434;T|0.566	0.566	strong	.	COQ7	16	.	NM_016138	exon3	c.C308T	p.T103M	TGGTTACGTTCAG	.	PASS	Atlas-SNP
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116	57	112	0	0.491379	0	G|0.899;A|0.101	0.101	strong	.	BRD1	144	.	NM_014577	exon1	c.C579T	p.F193F	CTTCTCGAAGCGG	.	PASS	Atlas-SNP
MNDA	4332	hgsc.bcm.edu	37	1	158817521	158817521	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120	5	77	0	0.0416667	0	.	.	none	MNDA,colon,carcinoma,0,2	MNDA	147	2	NM_002432	exon6	c.A991G	p.S331G	CAGAAAAGCGTAC	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88789687	88789687	+	Missense_Mutation	SNP	C	C	T	rs188337046	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	27	47	0	0.870968	0	C|0.983;T|0.017	0.017	strong	.	PIEZO1	79	.	NM_001142864	exon32	c.G4385A	p.R1462Q	TGCTGCCGCCGCC	.	PASS	Atlas-SNP
LPIN3	64900	hgsc.bcm.edu	37	20	39986549	39986549	+	Silent	SNP	G	G	A	rs41277020	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	76	121	0	0.558824	0	G|0.997;A|0.003	0.003	strong	LPIN3,NS,carcinoma,+1,1	LPIN3	69	1	NM_022896	exon17	c.G2067A	p.S689S	CTGCTCGGCGCGG	.	PASS	Atlas-SNP
CACUL1	143384	hgsc.bcm.edu	37	10	120489828	120489828	+	Silent	SNP	G	G	A	rs41284412	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104	54	137	0	0.519231	0	G|0.998;A|0.002	0.002	strong	.	.	.	.	NM_153810	exon2	c.C462T	p.D154D	GATATAGTCACCA	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	20	53	0	0.243902	0	A|0.830;C|0.170	0.170	strong	ATXN1,colon,carcinoma,0,3	ATXN1	117	3	NM_001128164	exon7	c.T633G	p.H211Q	CTGCTGATGCTGA	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42525089	42525089	+	Missense_Mutation	SNP	G	G	C	rs78482768	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102	52	119	0	0.509804	0	G|1.000;|0.000	.	weak	.	CYP2D6	104	.	NM_000106	exon3	c.C451G	p.Q151E	CCCACTGCTCCAG	.	PASS	Atlas-SNP
TNS4	84951	hgsc.bcm.edu	37	17	38643385	38643385	+	Silent	SNP	G	G	A	rs8071312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	277	138	212	1	0.498195	0.00471698	G|0.921;A|0.079	0.079	strong	.	TNS4	72	.	NM_032865	exon4	c.C1191T	p.S397S	TTGAACGGAGTTC	.	PASS	Atlas-SNP
CNR2	1269	hgsc.bcm.edu	37	1	24201262	24201262	+	Silent	SNP	A	A	G	rs2502993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96	94	169	1	0.979167	0.00591716	A|0.359;G|0.641	0.641	strong	CNR2_ENST00000374472,NS,carcinoma,-2,3	CNR2	78	3	NM_001841	exon2	c.T846C	p.A282A	GCAGAAAGCAAAG	.	PASS	Atlas-SNP
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119964052	119964052	+	Missense_Mutation	SNP	G	G	C	rs2073618	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155	98	177	1	0.632258	0.00564972	G|0.374;C|0.626	0.626	strong	TNFRSF11B_ENST00000297350,rectum,carcinoma,0,6	TNFRSF11B	87	6	NM_002546	exon1	c.C9G	p.N3K	CAGCAAGTTGTTC	.	PASS	Atlas-SNP
IRX6	79190	hgsc.bcm.edu	37	16	55362625	55362625	+	Silent	SNP	C	C	T	rs199714803		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42	36	34	0	0.857143	0	C|0.999;T|0.001	0.001	weak	.	IRX6	66	.	NM_024335	exon5	c.C735T	p.S245S	TGCTAGCCAGGAG	.	PASS	Atlas-SNP
FZD6	8323	hgsc.bcm.edu	37	8	104337523	104337523	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256	3	215	0	0.0117188	0	.	.	none	FZD6,NS,carcinoma,-1,1	FZD6	61	1	NM_003506	exon4	c.C1189T	p.R397X	CATGTTCGACAAG	.	scavenged	Atlas-SNP
BMPR1A	657	hgsc.bcm.edu	37	10	88635779	88635779	+	Missense_Mutation	SNP	C	C	A	rs3182217	bycluster;bysubmitter;by2hit2allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162	116	301	0	0.716049	0	.	.	weak	.	BMPR1A	118	.	NM_004329	exon3	c.C4A	p.P2T	ACAATGCCTCAGC	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29364615	29364615	+	Missense_Mutation	SNP	G	G	T	rs9257834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200	198	251	0	0.99	0	G|0.636;T|0.364	0.364	strong	.	OR12D2	42	.	NM_013936	exon1	c.G139T	p.V47F	ATGATTGTCATCT	.	PASS	Atlas-SNP
DOK7	285489	hgsc.bcm.edu	37	4	3494898	3494898	+	Silent	SNP	C	C	T	rs6850908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93	45	120	0	0.483871	0	C|0.794;T|0.206	0.206	strong	DOK7,NS,carcinoma,0,1	DOK7	44	1	NM_173660	exon7	c.C1185T	p.Y395Y	CGAGTACCAGGTG	.	PASS	Atlas-SNP
CELA2B	51032	hgsc.bcm.edu	37	1	15808872	15808872	+	Missense_Mutation	SNP	G	G	A	rs3766160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165	157	242	1	0.951515	0.00413223	G|0.715;A|0.285	0.285	strong	.	CELA2B	37	.	NM_015849	exon4	c.G340A	p.D114N	AACTCCGACCAGG	.	PASS	Atlas-SNP
OGFOD1	55239	hgsc.bcm.edu	37	16	56485554	56485554	+	Silent	SNP	C	C	G	rs11076155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34	7	38	0	0.205882	0	C|0.948;G|0.052	0.052	strong	.	OGFOD1	31	.	NM_018233	exon1	c.C30G	p.G10G	GCCCGGCCCAGCC	.	PASS	Atlas-SNP
FAM47C	442444	hgsc.bcm.edu	37	X	37029254	37029254	+	Missense_Mutation	SNP	A	A	C	rs1995914	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67	65	132	0	0.970149	0	A|0.631;C|0.369	0.369	strong	.	FAM47C	267	.	NM_001013736	exon1	c.A2771C	p.N924T	TCCAGAATGCACC	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39138692	39138692	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	82	2	72	0	0.0243902	0	.	.	none	KRT40,colon,carcinoma,-1,1	KRT40	27	1	NM_182497	exon5	c.G554T	p.R185L	AGCTGGCGAAGGG	.	scavenged	Atlas-SNP
WSCD1	23302	hgsc.bcm.edu	37	17	6023792	6023792	+	Silent	SNP	C	C	T	rs16955477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86	36	109	0	0.418605	0	C|0.974;T|0.026	0.026	strong	.	WSCD1	84	.	NM_015253	exon9	c.C1539T	p.S513S	TGTGAGCGAGGAG	.	PASS	Atlas-SNP
KRT77	374454	hgsc.bcm.edu	37	12	53088484	53088484	+	Missense_Mutation	SNP	C	C	T	rs10783528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127	63	108	0	0.496063	0	C|0.676;T|0.324	0.324	strong	.	KRT77	58	.	NM_175078	exon5	c.G1006A	p.D336N	CTGCATCGATGAT	.	PASS	Atlas-SNP
NUDT5	11164	hgsc.bcm.edu	37	10	12209752	12209752	+	Silent	SNP	T	T	C	rs6686	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60	10	83	0	0.166667	0	T|0.523;C|0.477	0.477	strong	.	NUDT5	10	.	NM_014142	exon10	c.A609G	p.A203A	TTTCAGTGCTAGA	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642817	1642817	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172	14	158	0	0.0813954	0	.	.	none	KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	NM_001012709	exon1	c.T507C	p.G169G	CCCACAACCTGAG	.	PASS	Atlas-SNP
TNR	7143	hgsc.bcm.edu	37	1	175375469	175375469	+	Missense_Mutation	SNP	C	C	A	rs2239819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	365	225	301	2	0.616438	0.00664452	C|0.755;N|0.000	.	strong	TNR,NS,carcinoma,0,1	TNR	399	1	NM_003285	exon3	c.G382T	p.A128S	AACTGGCACATGG	.	scavenged	Atlas-SNP
S100PBP	64766	hgsc.bcm.edu	37	1	33292189	33292189	+	Silent	SNP	C	C	T	rs41265867	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26	20	36	0	0.769231	0	C|0.992;T|0.008	0.008	strong	.	S100PBP	31	.	NM_001256121	exon3	c.C489T	p.D163D	TAAGGACGAGACT	.	PASS	Atlas-SNP
YIF1B	90522	hgsc.bcm.edu	37	19	38798086	38798086	+	Silent	SNP	T	T	C	rs3178327	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117	67	115	0	0.57265	0	T|0.699;C|0.301	0.301	strong	YIF1B_ENST00000339413,NS,carcinoma,-2,3	YIF1B	47	3	NM_001039672	exon7	c.A771G	p.V257V	GATGGCTACGCAG	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123419422	123419422	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71	5	76	0	0.0704225	0	.	.	none	.	MYLK	224	.	NM_053025	exon18	c.A2893G	p.T965A	CGGGGGTCTTGGA	.	PASS	Atlas-SNP
CH25H	9023	hgsc.bcm.edu	37	10	90966546	90966546	+	Silent	SNP	C	C	T	rs4078488	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	19	137	0	0.206522	0	C|0.850;T|0.150	0.150	strong	CH25H,NS,carcinoma,-1,1	CH25H	19	1	NM_003956	exon1	c.G504A	p.A168A	TGCCAGCGCGAAC	.	PASS	Atlas-SNP
ZMIZ2	83637	hgsc.bcm.edu	37	7	44805814	44805814	+	Missense_Mutation	SNP	C	C	T	rs145522270	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83	48	74	0	0.578313	0	C|0.994;T|0.006	0.006	strong	.	ZMIZ2	82	.	NM_031449	exon17	c.C2294T	p.T765M	CCACCACGCCCAG	.	PASS	Atlas-SNP
MARVELD3	91862	hgsc.bcm.edu	37	16	71660404	71660404	+	Missense_Mutation	SNP	G	G	A	rs61753635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29	5	28	0	0.172414	0	G|0.784;A|0.216	0.216	strong	.	MARVELD3	63	.	NM_001017967	exon1	c.G272A	p.R91Q	CCCGCCGGGACAC	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11189402	11189402	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	350	7	260	1	0.02	0.00384615	.	.	none	AMAC1L2,NS,carcinoma,0,1	.	.	1	NM_054028	exon1	c.G787A	p.A263T	ATCCTCGCCTTGG	.	scavenged	Atlas-SNP
DDR1	780	hgsc.bcm.edu	37	6	30857072	30857072	+	Silent	SNP	G	G	C	rs2229933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	184	85	240	0	0.461957	0	G|0.733;C|0.267	0.267	strong	.	DDR1	213	.	NM_001202523	exon4	c.G336C	p.L112L	ACGACTGCACCTG	.	PASS	Atlas-SNP
EPHA8	2046	hgsc.bcm.edu	37	1	22915753	22915753	+	Missense_Mutation	SNP	T	T	C	rs606002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38	10	50	0	0.263158	0	T|0.543;C|0.457	0.457	strong	.	EPHA8	221	.	NM_001006943	exon5	c.T1369C	p.S457P	CCTGCCTCAGACC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168107491	168107491	+	Missense_Mutation	SNP	A	A	G	rs3749004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176	90	183	0	0.511364	0	A|0.817;G|0.183	0.183	strong	.	XIRP2	914	.	NM_152381	exon9	c.A9589G	p.I3197V	GGGGCCATCCCAT	.	PASS	Atlas-SNP
NUPR1L	389493	hgsc.bcm.edu	37	7	56183895	56183895	+	Missense_Mutation	SNP	C	C	A	rs190448728	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	22	57	0	0.30137	0	A|0.001;C|0.999	0.001	strong	.	.	.	.	NM_001145712	exon1	c.G113T	p.R38L	AAGTCGCGCAGGT	.	PASS	Atlas-SNP
CTC1	80169	hgsc.bcm.edu	37	17	8135446	8135446	+	Silent	SNP	G	G	A	rs3027235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73	28	79	0	0.383562	0	G|0.964;A|0.036	0.036	strong	.	CTC1	75	.	NM_025099	exon13	c.C2160T	p.T720T	TGGGCCGGTGGGA	.	PASS	Atlas-SNP
PI16	221476	hgsc.bcm.edu	37	6	36930814	36930814	+	Silent	SNP	T	T	C	rs41272198	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98	40	113	0	0.408163	0	T|0.893;C|0.107	0.107	strong	.	PI16	50	.	NM_001199159	exon6	c.T696C	p.T232T	GGGTACTCCTTCT	.	PASS	Atlas-SNP
MYEOV2	150678	hgsc.bcm.edu	37	2	241066280	241066280	+	Silent	SNP	C	C	T	rs4292120	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145	60	168	0	0.413793	0	C|0.304;T|0.696	0.696	strong	.	MYEOV2	20	.	NM_138336	exon5	c.G459A	p.E153E	TAGCGCCTCCGCC	.	PASS	Atlas-SNP
WDR26	80232	hgsc.bcm.edu	37	1	224599230	224599230	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	247	3	194	1	0.0121457	0.00515464	.	.	none	WDR26_ENST00000414423,colon,carcinoma,+2,2	WDR26	104	2	NM_025160	exon7	c.G1057A	p.E353K	AATGCTCCGTAAG	.	scavenged	Atlas-SNP
R3HCC1	203069	hgsc.bcm.edu	37	8	23148978	23148978	+	Silent	SNP	G	G	T	rs2272760	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	149	102	133	0	0.684564	0	G|0.820;T|0.180	0.180	strong	.	R3HCC1	11	.	NM_001136108	exon5	c.G396T	p.V132V	CCACGTGGTAGAG	.	PASS	Atlas-SNP
POMGNT1	55624	hgsc.bcm.edu	37	1	46658217	46658217	+	Silent	SNP	C	C	T	rs41292143	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92	28	104	0	0.304348	0	C|0.991;T|0.009	0.009	strong	.	POMGNT1	96	.	NM_017739	exon15	c.G1257A	p.L419L	GCAGTACAGGCTG	.	PASS	Atlas-SNP
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695695	45695695	+	Silent	SNP	G	G	A	rs1153849	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31	5	69	0	0.16129	0	G|0.415;A|0.585	0.585	strong	.	SPATA5L1	40	.	NM_024063	exon1	c.G1068A	p.R356R	GCGTAGGCCCGGG	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152	72	211	2	0.473684	0.00947867	T|0.799;C|0.201	0.201	strong	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	NM_001163213	exon7	c.T882C	p.N294N	GGTGAATGGCAGC	.	scavenged	Atlas-SNP
SLC44A3	126969	hgsc.bcm.edu	37	1	95322903	95322903	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112	59	213	1	0.526786	0.00469484	.	.	none	.	SLC44A3	109	.	NM_001114106	exon10	c.T1085C	p.V362A	CCCAGGTTATGGA	.	PASS	Atlas-SNP
PAICS	10606	hgsc.bcm.edu	37	4	57314905	57314905	+	Missense_Mutation	SNP	A	A	C	rs11549976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238	120	270	0	0.504202	0	A|0.968;C|0.032	0.032	strong	.	PAICS	21	.	NM_001079525	exon6	c.A624C	p.K208N	CACCAAAGAAATT	.	PASS	Atlas-SNP
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744163	31744163	+	Silent	SNP	C	C	G	rs2009546	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	219	125	140	0	0.570776	0	C|0.947;G|0.053	0.053	strong	.	KRTAP13-2	29	.	NM_181621	exon1	c.G369C	p.G123G	ACTGGACCCACAG	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118668	93118668	+	Missense_Mutation	SNP	C	C	T	rs3742717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175	113	125	0	0.645714	0	C|0.777;T|0.223	0.223	strong	RIN3,rectum,carcinoma,-1,1	RIN3	81	1	NM_024832	exon6	c.C1274T	p.T425M	AGGACACGCCCCG	.	PASS	Atlas-SNP
AMIGO2	347902	hgsc.bcm.edu	37	12	47471287	47471287	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130	56	167	0	0.430769	0	.	.	none	AMIGO2,NS,carcinoma,-1,1	AMIGO2	50	1	NM_181847	exon2	c.C1499T	p.T500M	CCCCTCGTGGACT	.	PASS	Atlas-SNP
CDH8	1006	hgsc.bcm.edu	37	16	61855012	61855012	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	242	5	243	0	0.0206612	0	.	.	none	CDH8,NS,carcinoma,0,1	CDH8	273	1	NM_001796	exon6	c.T841C	p.Y281H	AGTGATACAGGCC	.	scavenged	Atlas-SNP
CCDC33	80125	hgsc.bcm.edu	37	15	74622533	74622533	+	Missense_Mutation	SNP	A	A	G	rs2277603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156	101	284	1	0.647436	0.00352113	A|0.887;G|0.113;T|0.000	0.113	strong	.	CCDC33	160	.	NM_025055	exon12	c.A1294G	p.M432V	CAGGAGATGAACA	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171400449	171400449	+	Silent	SNP	T	T	C	rs56181206	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108	56	85	0	0.518519	0	T|0.981;C|0.019	0.019	strong	.	MYO3B	320	.	NM_138995	exon32	c.T3684C	p.P1228P	CCATCCTGCTCCA	.	PASS	Atlas-SNP
CLTCL1	8218	hgsc.bcm.edu	37	22	19175095	19175095	+	Missense_Mutation	SNP	A	A	C	rs182434700	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185	90	209	1	0.486486	0.00478469	A|0.999;C|0.001	0.001	strong	.	CLTCL1	115	.	NM_007098	exon29	c.T4580G	p.L1527R	TTGCAGAGCTCCA	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1003221	1003221	+	Missense_Mutation	SNP	C	C	A	rs35592366	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45	23	46	0	0.511111	0	C|0.904;A|0.096	0.096	strong	GRIN3B,NS,carcinoma,0,1	GRIN3B	46	1	NM_138690	exon2	c.C519A	p.D173E	GGAAGACGTCGGC	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91712698	91712698	+	Missense_Mutation	SNP	A	A	G	rs6960867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	173	173	145	0	1	0	A|0.667;G|0.333	0.333	strong	.	AKAP9	788	.	NM_005751	exon33	c.A8375G	p.N2792S	GCAGCAATCAGAC	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33718326	33718326	+	Missense_Mutation	SNP	A	A	C	rs1785934	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	136	73	127	0	0.536765	0	A|0.654;C|0.346	0.346	strong	.	ELP2	70	.	NM_001242879	exon4	c.A382C	p.T128P	TTATGTACACTGA	.	PASS	Atlas-SNP
