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
PARP9	83666	hgsc.bcm.edu	37	3	122247338	122247343	+	In_Frame_Del	DEL	GCCTGC	GCCTGC	-	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	GCCTGC	GCCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	115	26	149	0	0.226087	0	.	.	none	.	PARP9	72	.	NM_001146102	exon11	c.2434_2439del	p.812_813del	.	.	PASS	Atlas-Indel
AR	367	hgsc.bcm.edu	37	X	66765228	66765242	+	In_Frame_Del	DEL	AGAGACTAGCCCCAG	AGAGACTAGCCCCAG	-	rs3032358	alternate_allele	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	AGAGACTAGCCCCAG	AGAGACTAGCCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	105	23	77	0	0.219048	0	.	.	alt	.	AR	249	.	NM_000044	exon1	c.239_253del	p.80_85del	.	.	PASS	Atlas-Indel
PARP9	83666	hgsc.bcm.edu	37	3	122247346	122247346	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	120	28	144	0	0.233333	0	.	.	none	.	PARP9	72	.	NM_001146102	exon11	c.2431delA	p.M811fs	.	.	PASS	Atlas-Indel
PASD1	139135	hgsc.bcm.edu	37	X	150817142	150817144	+	In_Frame_Del	DEL	GCT	GCT	-	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	111	10	102	0	0.0900901	0	.	.	none	.	PASD1	286	.	NM_173493	exon9	c.684_686del	p.228_229del	.	.	PASS	Atlas-Indel
DLG5	9231	hgsc.bcm.edu	37	10	79565519	79565520	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	17	17	0	.	1.000	.	.	.	none	.	DLG5	154	.	NM_004747	exon27	c.5068_5069insT	p.R1690fs	.	.	PASS	Pindel,Atlas-Indel
ANKRD23	200539	hgsc.bcm.edu	37	2	97507820	97507821	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	20	20	0	.	1.000	.	.	.	none	.	ANKRD23	28	.	NM_144994	exon3	c.277_278insC	p.R93fs	.	.	PASS	Pindel,Atlas-Indel
PARP9	83666	hgsc.bcm.edu	37	3	122247336	122247347	+	In_Frame_Del	DEL	TAGCCTGCATGC	TAGCCTGCATGC	-	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	TAGCCTGCATGC	TAGCCTGCATGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	26	26	0	.	1.000	.	.	.	none	.	PARP9	72	.	NM_001146102	exon11	c.2430_2441del	p.810_814del	.	.	PASS	Pindel
HADHB	3032	hgsc.bcm.edu	37	2	26477125	26477126	+	In_Frame_Ins	INS	-	-	ACT	rs147970487	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	15	15	0	.	1.000	.	.	.	strong	HADHB,colon,carcinoma,0,1	HADHB	50	1	NM_000183	exon2	c.3_4insACT	p.M1delinsMT	.	.	PASS	Pindel
TMBIM4	51643	hgsc.bcm.edu	37	12	66531936	66531937	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	12	12	0	.	1.000	.	.	.	none	.	TMBIM4	47	.	NM_016056	exon7	c.521_522insT	p.Y174fs	.	.	PASS	Pindel
PIBF1	10464	hgsc.bcm.edu	37	13	73409508	73409509	+	Splice_Site	INS	-	-	AA	rs200683940	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	23	23	0	0	1.000	0	.	.	weak	.	PIBF1	65	.	NM_006346	exon9	c.1223+2->AA	.	.	.	PASS	Pindel
CCDC144B	284047	hgsc.bcm.edu	37	17	18498497	18498498	+	RNA	INS	-	-	A	rs59933375	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	87	87	0	0	1.000	0	.	.	weak	.	CCDC144B	106	.	.	.	.	.	.	.	PASS	Pindel
NCAM1	4684	hgsc.bcm.edu	37	11	112832309	112832340	+	Frame_Shift_Del	DEL	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	-	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	CATCCCTCCCAGCCAGCAGATTACAATGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	35	35	0	0	1.000	0	.	.	none	.	NCAM1	372	.	NM_001242607	wholegene	.	.	.	.	PASS	Pindel
PIDD	55367	hgsc.bcm.edu	37	11	804212	804212	+	Silent	SNP	C	C	A	rs7104785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	105	6	142	0	0.0571429	0	C|0.567;A|0.433	0.433	strong	.	PIDD	76	.	NM_145887	exon2	c.G177T	p.L59L	CAGCTGCAGAGGC	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878625	190878625	+	Missense_Mutation	SNP	A	A	G	rs373840195		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	548	5	522	6	0.00912409	0.0114943	.	.	weak	FRG1,NS,carcinoma,0,3	FRG1	76	3	NM_004477	exon6	c.A505G	p.S169G	GCAAAAAGTAAAA	.	scavenged	Atlas-SNP
MRPL35	51318	hgsc.bcm.edu	37	2	86433240	86433240	+	Missense_Mutation	SNP	C	C	T	rs10901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	414	8	352	2	0.0193237	0.00568182	T|0.269;G|0.143	0.269	strong	MRPL35,NS,adenoma,0,2	MRPL35	23	2	NM_016622	exon2	c.C55T	p.P19S	CTACGGCCCCTGA	.	scavenged	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	37	17	80085633	80085633	+	Missense_Mutation	SNP	A	A	G	rs11077969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	67	4	62	0	0.0597015	0	A|0.582;G|0.418	0.418	strong	CCDC57_ENST00000389641,NS,carcinoma,0,4	CCDC57	102	4	NM_198082	exon16	c.T2498C	p.M833T	CTCCACATGTCCT	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612745	53612745	+	Missense_Mutation	SNP	T	T	C	rs1133327	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	128	6	141	0	0.046875	0	T|0.490;C|0.510	0.510	strong	.	ZNF415	68	.	NM_018355	exon4	c.A553G	p.I185V	TTTTGATGGTAGA	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72135014	72135014	+	Silent	SNP	T	T	C	rs1050363	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	277	10	234	0	0.0361011	0	T|0.421;C|0.579	0.579	strong	DHX38,NS,carcinoma,0,1	DHX38	91	1	NM_014003	exon10	c.T1308C	p.A436A	GGATGCTACTTCT	.	scavenged	Atlas-SNP
KLHL38	340359	hgsc.bcm.edu	37	8	124664792	124664792	+	Silent	SNP	C	C	T	rs7387544	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	69	6	85	1	0.0869565	0.0117647	C|0.264;T|0.736	0.736	strong	KLHL38,NS,carcinoma,-1,1	KLHL38	81	1	NM_001081675	exon1	c.G375A	p.S125S	CAAGTACGAGGAG	.	scavenged	Atlas-SNP
B3GALTL	145173	hgsc.bcm.edu	37	13	31891810	31891810	+	Missense_Mutation	SNP	C	C	T	rs144117014		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	39	14	63	0	0.358974	0	C|1.000;T|0.000	0.000	weak	.	B3GALTL	48	.	NM_194318	exon13	c.C1172T	p.T391M	ACATCACGGGAGG	.	PASS	Atlas-SNP
MFSD6	54842	hgsc.bcm.edu	37	2	191300917	191300917	+	Silent	SNP	A	A	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	188	84	168	0	0.446809	0	.	.	none	.	MFSD6	58	.	NM_017694	exon3	c.A162C	p.I54I	GGAAATAGACTGG	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553994	140553994	+	Silent	SNP	G	G	T	rs374392843		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	205	7	220	1	0.0341463	0.00454545	.	.	weak	PCDHB7,NS,carcinoma,0,4	PCDHB7	231	4	NM_018940	exon1	c.G1578T	p.A526A	GCAGGCGTTCGAG	.	scavenged	Atlas-SNP
C7orf63	79846	hgsc.bcm.edu	37	7	89938680	89938680	+	Missense_Mutation	SNP	C	C	T	rs1134956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	457	9	316	1	0.0196937	0.00316456	C|0.596;N|0.000;T|0.404	0.404	strong	C7orf63_ENST00000389297,NS,carcinoma,+1,2	C7orf63	158	2	NM_001039706	exon22	c.C2654T	p.T885M	ACACAACGGTAAG	.	scavenged	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161139857	161139857	+	Silent	SNP	A	A	G	rs13231	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	73	6	75	0	0.0821918	0	A|0.787;G|0.213	0.213	strong	.	PLG	150	.	NM_000301	exon9	c.A1083G	p.Q361Q	GGAACAATTGGCT	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1252441	1252441	+	Missense_Mutation	SNP	T	T	C	rs4984636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	58	3	47	0	0.0517241	0	T|0.874;C|0.126	0.126	strong	CACNA1H_ENST00000358590,rectum,carcinoma,0,2	CACNA1H	317	2	NM_021098	exon9	c.T1991C	p.V664A	ATGTGGTCGGGGA	.	scavenged	Atlas-SNP
MYOM3	127294	hgsc.bcm.edu	37	1	24421474	24421474	+	Missense_Mutation	SNP	G	G	A	rs6678540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	104	7	147	0	0.0673077	0	G|0.633;A|0.367	0.367	strong	.	MYOM3	131	.	NM_152372	exon9	c.C797T	p.T266M	CCAAACGTCGATC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515078	195515078	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	85	4	103	2	0.0470588	0.0194175	.	.	none	MUC4_ENST00000463781,bladder,carcinoma,+1,5	MUC4	1505	5	NM_018406	exon2	c.G3373A	p.D1125N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12885059	12885059	+	Missense_Mutation	SNP	C	C	G	rs199623827	byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	204	6	264	3	0.0294118	0.0113636	C|0.973;G|0.027	0.027	strong	PRAMEF11,NS,carcinoma,0,5	PRAMEF11	72	5	NM_001146344	exon4	c.G1052C	p.C351S	GCCATGCAGATGG	.	scavenged	Atlas-SNP
DHRS3	9249	hgsc.bcm.edu	37	1	12640650	12640650	+	Silent	SNP	C	C	T	rs11540058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	133	9	154	0	0.0676692	0	C|0.868;T|0.132	0.132	strong	.	DHRS3	18	.	NM_004753	exon2	c.G240A	p.T80T	CTCCTCCGTCGTC	.	PASS	Atlas-SNP
GABRG1	2565	hgsc.bcm.edu	37	4	46086060	46086060	+	Silent	SNP	T	T	C	rs976156	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	569	11	567	2	0.0193322	0.00352734	T|0.435;C|0.565	0.565	strong	GABRG1,NS,carcinoma,0,1	GABRG1	172	1	NM_173536	exon3	c.A264G	p.T88T	AATTACTGTGGGC	.	scavenged	Atlas-SNP
ZNF227	7770	hgsc.bcm.edu	37	19	44739399	44739399	+	Silent	SNP	T	T	C	rs2279072	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	99	7	132	0	0.0707071	0	T|0.393;C|0.607	0.607	strong	.	ZNF227	62	.	NM_182490	exon6	c.T816C	p.H272H	TGTTCATACAGGA	.	PASS	Atlas-SNP
DUOX1	53905	hgsc.bcm.edu	37	15	45444518	45444518	+	Silent	SNP	A	A	G	rs1706804	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	58	4	57	0	0.0689655	0	A|0.405;G|0.595	0.595	strong	DUOX1,NS,carcinoma,0,1	DUOX1	125	1	NM_017434	exon26	c.A3228G	p.T1076T	CATCACAGACACC	.	PASS	Atlas-SNP
SMYD1	150572	hgsc.bcm.edu	37	2	88387391	88387391	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	142	48	148	0	0.338028	0	.	.	none	.	SMYD1	95	.	NM_198274	exon3	c.C325T	p.R109C	GCGGCGCGCATCA	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31116210	31116210	+	Silent	SNP	G	G	A	rs130071	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	125	6	131	0	0.048	0	G|0.746;A|0.254	0.254	strong	.	CCHCR1	68	.	NM_001105564	exon10	c.C1552T	p.L518L	GCCTCAGCTGCTC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557461	32557461	+	Missense_Mutation	SNP	A	A	G	rs35053532	bycluster;byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	125	5	115	1	0.04	0.00869565	A|0.986;G|0.013	0.013	strong	HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.T59C	p.M20T	AGCACCATCAGTG	.	scavenged	Atlas-SNP
ANXA10	11199	hgsc.bcm.edu	37	4	169083694	169083694	+	Missense_Mutation	SNP	A	A	C	rs6836994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	161	8	168	0	0.0496894	0	A|0.419;C|0.580	0.580	strong	ANXA10,NS,carcinoma,0,1	ANXA10	44	1	NM_007193	exon4	c.A211C	p.M71L	GGGGATATGAGGG	.	PASS	Atlas-SNP
PIK3C2A	5286	hgsc.bcm.edu	37	11	17191019	17191019	+	Silent	SNP	A	A	G	rs214936	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	162	7	169	0	0.0432099	0	A|0.601;G|0.399	0.399	strong	.	PIK3C2A	148	.	NM_002645	exon1	c.T270C	p.I90I	TACATCAATATCT	.	PASS	Atlas-SNP
COL11A1	1301	hgsc.bcm.edu	37	1	103379918	103379918	+	Missense_Mutation	SNP	G	G	A	rs3753841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	314	17	376	0	0.0541401	0	G|0.517;A|0.483	0.483	strong	.	COL11A1	972	.	NM_080629	exon52	c.C4004T	p.P1335L	GGGCCAGGTTCCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506569	195506569	+	Missense_Mutation	SNP	A	A	G	rs201891747	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	21	9	30	18	0.428571	0.6	.	.	weak	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.T11882C	p.V3961A	GTGGATACTGAGG	.	scavenged	Atlas-SNP
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28327371	28327371	+	Missense_Mutation	SNP	G	G	C	rs733743	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	93	5	130	0	0.0537634	0	G|0.892;C|0.108	0.108	strong	.	ZKSCAN3	50	.	NM_024493	exon2	c.G8C	p.R3T	TGGCTAGAGAATT	.	PASS	Atlas-SNP
IFT43	112752	hgsc.bcm.edu	37	14	76543004	76543004	+	Missense_Mutation	SNP	G	G	A	rs17783366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	92	5	112	0	0.0543478	0	G|0.774;A|0.226	0.226	strong	.	IFT43	63	.	NM_052873	exon4	c.G280A	p.D94N	CACAGAGATTTGG	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301206	65301206	+	Silent	SNP	T	T	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	94	5	132	0	0.0531915	0	.	.	none	.	EYS	527	.	NM_001142800	exon26	c.A4554C	p.T1518T	GGCTTTTGTACTG	.	PASS	Atlas-SNP
CFHR1	3078	hgsc.bcm.edu	37	1	196801078	196801078	+	Silent	SNP	A	A	T	rs61743621	byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	280	7	335	1	0.025	0.00298507	A|0.604;T|0.396	0.396	strong	CFHR1,right_upper_lobe,carcinoma,+1,1	CFHR1	47	1	NM_002113	exon6	c.A942T	p.R314R	ATTGCGAACAACA	.	scavenged	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	37	2	241685586	241685586	+	Silent	SNP	G	G	A	rs73102625	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	95	5	107	0	0.0526316	0	G|0.951;A|0.049	0.049	strong	.	KIF1A	152	.	NM_001244008	exon30	c.C3072T	p.S1024S	AGACTCGGACTGG	.	PASS	Atlas-SNP
CPNE8	144402	hgsc.bcm.edu	37	12	39087609	39087609	+	Silent	SNP	G	G	A	rs3759139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	164	7	161	0	0.0426829	0	G|0.695;A|0.305	0.305	strong	CPNE8,NS,carcinoma,0,1	CPNE8	66	1	NM_153634	exon15	c.C993T	p.Y331Y	ATTCATGTAGTGG	.	PASS	Atlas-SNP
SOCS3	9021	hgsc.bcm.edu	37	17	76354835	76354835	+	Silent	SNP	C	C	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	64	34	79	0	0.53125	0	.	.	none	.	SOCS3	16	.	NM_003955	exon2	c.G342T	p.V114V	GCGGGGCACGGGC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241256	3241256	+	Missense_Mutation	SNP	T	T	C	rs5983119	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	131	6	82	0	0.0458015	0	0|0.003;C|0.749	0.749	strong	.	MXRA5	815	.	NM_015419	exon5	c.A2470G	p.I824V	GAGAAATAGCAGG	.	PASS	Atlas-SNP
ITGAE	3682	hgsc.bcm.edu	37	17	3657175	3657175	+	Missense_Mutation	SNP	T	T	C	rs220479	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	51	4	59	0	0.0784314	0	T|0.196;C|0.804	0.804	strong	.	ITGAE	96	.	NM_002208	exon13	c.A1429G	p.I477V	CCGCGATGTAGGA	.	PASS	Atlas-SNP
ZCWPW2	152098	hgsc.bcm.edu	37	3	28476649	28476649	+	Silent	SNP	T	T	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	363	129	364	1	0.355372	0.00274725	.	.	none	.	ZCWPW2	49	.	NM_001040432	exon3	c.T381G	p.T127T	TGTAACTTATGAC	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124352028	124352028	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	15	14	25	0	0.933333	0	.	.	none	.	DMBT1	677	.	NM_007329	exon20	c.A2417G	p.E806G	GACACGAGTCCTA	.	PASS	Atlas-SNP
ZNF74	7625	hgsc.bcm.edu	37	22	20761063	20761063	+	Silent	SNP	G	G	A	rs2228236	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	78	6	98	0	0.0769231	0	G|0.859;A|0.141	0.141	strong	.	ZNF74	54	.	NM_003426	exon5	c.G1740A	p.E580E	CAGCGAGGGGAAG	.	PASS	Atlas-SNP
PLA2G15	23659	hgsc.bcm.edu	37	16	68293320	68293320	+	Silent	SNP	T	T	C	rs3743739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	64	3	53	0	0.046875	0	T|0.778;C|0.222	0.222	strong	PLA2G15,NS,carcinoma,0,1	PLA2G15	30	1	NM_012320	exon6	c.T999C	p.G333G	CTATGGTACTGGC	.	scavenged	Atlas-SNP
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929392	2929392	+	Silent	SNP	G	G	A	rs55904912	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	297	6	361	0	0.020202	0	G|0.579;A|0.421	0.421	strong	RAP1GAP2_ENST00000254695,NS,carcinoma,0,2	RAP1GAP2	90	2	NM_015085	exon20	c.G1842A	p.P614P	CTCTCCGGAAATC	.	scavenged	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34071525	34071525	+	Missense_Mutation	SNP	C	C	T	rs1874045	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	103	7	86	2	0.0679612	0.0232558	C|0.479;T|0.521	0.521	strong	CSMD2,brain,glioma,0,1	CSMD2	946	1	NM_052896	exon42	c.G6287A	p.R2096K	TTGGTTCTTTCCA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515077	195515077	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	84	4	101	2	0.047619	0.019802	.	.	none	MUC4_ENST00000463781,bladder,carcinoma,0,5	MUC4	1505	5	NM_018406	exon2	c.A3374G	p.D1125G	GAAGTGTCGGTGA	.	scavenged	Atlas-SNP
MFF	56947	hgsc.bcm.edu	37	2	228197238	228197238	+	Silent	SNP	G	G	A	rs11557342	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	382	5	378	1	0.013089	0.0026455	G|0.922;A|0.078	0.078	strong	MFF,NS,carcinoma,0,1	MFF	48	1	NM_020194	exon5	c.G363A	p.T121T	ACTTACGCTGAGT	.	scavenged	Atlas-SNP
DSCAM	1826	hgsc.bcm.edu	37	21	41414420	41414420	+	Missense_Mutation	SNP	G	G	A	rs200410460	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	81	31	67	0	0.382716	0	.	.	weak	.	DSCAM	347	.	NM_001271534	exon32	c.C5564T	p.T1855M	CTGTCCGTGTACT	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117797597	117797597	+	Silent	SNP	T	T	C	rs12347433	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	69	3	83	0	0.0434783	0	T|0.813;C|0.187	0.187	strong	TNC,NS,carcinoma,0,1	TNC	282	1	NM_002160	exon22	c.A5673G	p.R1891R	CAAGTCTCTTGGA	.	scavenged	Atlas-SNP
CASQ2	845	hgsc.bcm.edu	37	1	116310967	116310967	+	Missense_Mutation	SNP	T	T	C	rs4074536	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	100	4	138	0	0.04	0	T|0.631;C|0.369	0.369	strong	CASQ2,colon,carcinoma,0,1	CASQ2	54	1	NM_001232	exon1	c.A196G	p.T66A	TTTGCGTGACCTT	.	PASS	Atlas-SNP
ZNF782	158431	hgsc.bcm.edu	37	9	99581542	99581542	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	79	22	67	0	0.278481	0	.	.	none	.	ZNF782	64	.	NM_001001662	exon6	c.A763G	p.K255E	TTGATTTATCATA	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39161456	39161456	+	Missense_Mutation	SNP	G	G	A	rs1274972	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	198	9	245	0	0.0454545	0	G|0.555;A|0.445	0.445	strong	.	TTC21A	96	.	NM_145755	exon8	c.G869A	p.R290K	AGACAAGGGAACC	.	PASS	Atlas-SNP
DCAF4	26094	hgsc.bcm.edu	37	14	73404752	73404752	+	Missense_Mutation	SNP	G	G	C	rs2302588	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	24	4	36	0	0.166667	0	G|0.900;C|0.100	0.100	strong	.	DCAF4	40	.	NM_001163508	exon2	c.G66C	p.W22C	CCCTTGGTTCAGA	.	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-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	410	13	265	1	0.0317073	0.00377358	C|0.675;N|0.000	.	strong	PION,colon,carcinoma,+1,4	PION	74	4	NM_017439	exon13	c.G914A	p.G305E	ATTTGTCCCCAAG	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416167	105416167	+	Missense_Mutation	SNP	G	G	T	rs200366012	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	69	7	90	7	0.101449	0.0777778	G|0.999;T|0.001	0.001	strong	AHNAK2_ENST00000333244,NS,carcinoma,+1,1	AHNAK2	719	1	NM_138420	exon7	c.C5621A	p.P1874Q	GGGAGCGGAATGC	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9047271	9047271	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	81	31	76	0	0.382716	0	.	.	none	.	MUC16	4315	.	NM_024690	exon5	c.C34360T	p.P11454S	CACCAGGGGAGAC	.	PASS	Atlas-SNP
ZNF705A	440077	hgsc.bcm.edu	37	12	8329652	8329652	+	Missense_Mutation	SNP	A	A	G	rs10743251	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	358	7	292	1	0.0195531	0.00342466	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
VPS13D	55187	hgsc.bcm.edu	37	1	12387807	12387807	+	Missense_Mutation	SNP	C	C	T	rs143572864	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	120	51	127	0	0.425	0	C|1.000;T|0.000	0.000	weak	VPS13D,NS,carcinoma,+1,1	VPS13D	316	1	NM_015378	exon36	c.C8093T	p.A2698V	TGGCAGCGCCATT	.	PASS	Atlas-SNP
SERPINE2	5270	hgsc.bcm.edu	37	2	224862842	224862842	+	Silent	SNP	A	A	G	rs12457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	115	6	98	0	0.0521739	0	A|0.718;G|0.282	0.282	strong	.	SERPINE2	103	.	NM_001136530	exon3	c.T513C	p.N171N	GGTTTCATTTTTA	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	37	19	43234049	43234049	+	Missense_Mutation	SNP	A	A	T	rs28698193	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	53	5	54	0	0.0943396	0	A|0.879;T|0.121	0.121	strong	.	PSG3	82	.	NM_021016	exon4	c.T869A	p.I290N	TTTTCAATGGGTC	.	PASS	Atlas-SNP
APOBEC1	339	hgsc.bcm.edu	37	12	7805236	7805236	+	Missense_Mutation	SNP	C	C	G	rs2302515	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	161	4	123	1	0.0248447	0.00813008	C|0.248;G|0.752	0.752	strong	APOBEC1,NS,carcinoma,-1,1	APOBEC1	43	1	NM_001644	exon3	c.G240C	p.M80I	GCAGCTCATGGAT	.	scavenged	Atlas-SNP
ZNF705A	440077	hgsc.bcm.edu	37	12	8329700	8329700	+	Missense_Mutation	SNP	A	A	C	rs10743253	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	378	5	282	1	0.0132275	0.0035461	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
FMO1	2326	hgsc.bcm.edu	37	1	171252287	171252287	+	Silent	SNP	A	A	G	rs1126692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	452	6	520	1	0.0132743	0.00192308	A|0.769;C|0.000;G|0.231	0.231	strong	FMO1,left_upper_lobe,carcinoma,+2,1	FMO1	79	1	NM_002021	exon8	c.A1188G	p.V396V	AGGTGTAAATAAG	.	scavenged	Atlas-SNP
CYP1B1	1545	hgsc.bcm.edu	37	2	38298139	38298139	+	Missense_Mutation	SNP	T	T	C	rs1800440	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	160	6	154	0	0.0375	0	T|0.882;C|0.118	0.118	strong	CYP1B1,colon,carcinoma,0,3	CYP1B1	39	3	NM_000104	exon3	c.A1358G	p.N453S	TCCTTGTTGATGA	.	scavenged	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145301793	145301793	+	Silent	SNP	A	A	G	rs75332562	bycluster;byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	22	6	22	3	0.272727	0.136364	A|0.602;G|0.398	0.398	strong	NBPF10_ENST00000369338,caecum,carcinoma,0,2	NBPF10	221	2	NM_001039703	exon7	c.A1062G	p.A354A	GCTTGCAGAGCAG	.	scavenged	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186277277	186277277	+	Missense_Mutation	SNP	G	G	A	rs113308576		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	109	9	136	4	0.0825688	0.0294118	G|0.500;A|0.500	0.500	weak	PRG4,NS,carcinoma,0,2	PRG4	259	2	NM_005807	exon7	c.G2426A	p.G809E	CCAAGGGGCCCAC	.	scavenged	Atlas-SNP
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31132339	31132339	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	41	27	49	0	0.658537	0	.	.	none	.	ADCYAP1R1	78	.	NM_001118	exon13	c.A1036G	p.S346G	GAGTCCAGCATCT	.	PASS	Atlas-SNP
CAMK2G	818	hgsc.bcm.edu	37	10	75632760	75632760	+	Silent	SNP	C	C	T	rs2675671	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	128	6	119	1	0.046875	0.00840336	C|0.601;T|0.399	0.399	strong	CAMK2G_ENST00000322680,colon,carcinoma,0,2	CAMK2G	79	2	NM_172170	exon2	c.G147A	p.K49K	AGACAACTTCTTG	.	scavenged	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16248757	16248757	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	93	33	98	0	0.354839	0	.	.	none	.	ABCC6	110	.	NM_001171	exon28	c.G4014A	p.L1338L	GGAGCGCAGTGTG	.	PASS	Atlas-SNP
DNTTIP2	30836	hgsc.bcm.edu	37	1	94343023	94343023	+	Silent	SNP	A	A	G	rs2391322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	85	4	93	0	0.0470588	0	A|0.587;G|0.413	0.413	strong	.	DNTTIP2	59	.	NM_014597	exon2	c.T468C	p.P156P	TTCTGTAGGAAGC	.	PASS	Atlas-SNP
FOXD4	2298	hgsc.bcm.edu	37	9	117998	117998	+	Missense_Mutation	SNP	G	G	T	rs66612967	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	406	64	374	28	0.157635	0.0748663	G|0.977;T|0.023	0.023	strong	FOXD4_ENST00000382500,NS,carcinoma,0,3	FOXD4	75	3	NM_207305	exon1	c.C122A	p.A41E	CTCGCCGCCTCCT	.	scavenged	Atlas-SNP
MLLT3	4300	hgsc.bcm.edu	37	9	20414343	20414343	+	Silent	SNP	A	A	G	rs372894655		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	50	8	37	1	0.16	0.027027	.	.	weak	MLLT3,bladder,carcinoma,0,25	MLLT3	125	25	NM_004529	exon5	c.T501C	p.S167S	GCTGCTACTGCTG	.	scavenged	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169551682	169551682	+	Silent	SNP	T	T	C	rs6028	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	587	11	575	0	0.0187394	0	C|0.214;N|0.000	0.214	strong	F5,NS,carcinoma,0,1	F5	301	1	NM_000130	exon2	c.A237G	p.Q79Q	GGTAGATTGTGGT	.	scavenged	Atlas-SNP
RNF175	285533	hgsc.bcm.edu	37	4	154644537	154644537	+	Missense_Mutation	SNP	T	T	C	rs10517577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	102	8	113	0	0.0784314	0	T|0.917;C|0.083	0.083	strong	.	RNF175	40	.	NM_173662	exon5	c.A475G	p.M159V	TAAACATGATCGC	.	PASS	Atlas-SNP
P2RY1	5028	hgsc.bcm.edu	37	3	152554357	152554357	+	Silent	SNP	A	A	G	rs701265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	110	7	133	0	0.0636364	0	A|0.653;G|0.347	0.347	strong	.	P2RY1	49	.	NM_002563	exon1	c.A786G	p.V262V	CCTGGTAATCATT	.	PASS	Atlas-SNP
MOCS3	27304	hgsc.bcm.edu	37	20	49575721	49575721	+	Silent	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	52	17	59	0	0.326923	0	.	.	none	.	MOCS3	44	.	NM_014484	exon1	c.T342C	p.Y114Y	GGACTATGACGTG	.	PASS	Atlas-SNP
PARL	55486	hgsc.bcm.edu	37	3	183558402	183558402	+	Missense_Mutation	SNP	C	C	G	rs3732581	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	726	31	808	0	0.0426997	0	C|0.516;G|0.484	0.484	strong	PARL,NS,carcinoma,0,1	PARL	32	1	NM_018622	exon7	c.G784C	p.V262L	TACCCACGTAACT	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47545823	47545823	+	Silent	SNP	G	G	A	rs13052956	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	121	5	183	0	0.0413223	0	G|0.578;A|0.422	0.422	strong	.	COL6A2	351	.	NM_058175	exon26	c.G2094A	p.A698A	GATTGCGGGCGGC	.	PASS	Atlas-SNP
CYP26C1	340665	hgsc.bcm.edu	37	10	94824263	94824263	+	Silent	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	97	5	129	0	0.0515464	0	.	.	none	.	CYP26C1	25	.	NM_183374	exon4	c.G831T	p.L277L	GGAGCTGGGCCAT	.	PASS	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	37	9	33797962	33797962	+	Silent	SNP	A	A	G	rs374178684	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	133	5	157	5	0.037594	0.0318471	.	.	weak	PRSS3_ENST00000361005,NS,neuroblastoma,0,3	PRSS3	79	3	NM_007343	exon3	c.A507G	p.K169K	GATCAAACTCTCC	.	scavenged	Atlas-SNP
NUSAP1	51203	hgsc.bcm.edu	37	15	41634587	41634587	+	Missense_Mutation	SNP	A	A	G	rs7178634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	157	2	149	0	0.0127389	0	A|0.684;G|0.316	0.316	strong	NUSAP1,NS,carcinoma,0,2	NUSAP1	32	2	NM_018454	exon2	c.A97G	p.T33A	CAGGCAACCAAGT	.	scavenged	Atlas-SNP
PIGN	23556	hgsc.bcm.edu	37	18	59810563	59810563	+	Silent	SNP	A	A	G	rs34227891	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	446	5	369	0	0.0112108	0	A|0.789;G|0.211	0.211	strong	PIGN,NS,carcinoma,0,1	PIGN	62	1	NM_176787	exon11	c.T939C	p.N313N	CTTCCAATTCTCC	.	scavenged	Atlas-SNP
TTC14	151613	hgsc.bcm.edu	37	3	180326574	180326574	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	328	6	406	0	0.0182927	0	.	.	none	TTC14,colon,carcinoma,+1,1	TTC14	112	1	NM_133462	exon11	c.G1376A	p.R459H	AGTTGCGTAAGCT	.	scavenged	Atlas-SNP
CHD1L	9557	hgsc.bcm.edu	37	1	146736092	146736092	+	Silent	SNP	C	C	T	rs4950315	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	132	6	157	0	0.0454545	0	C|0.864;T|0.136	0.136	strong	.	CHD1L	72	.	NM_004284	exon7	c.C588T	p.V196V	AGTAGTCTTCAGT	.	PASS	Atlas-SNP
ME3	10873	hgsc.bcm.edu	37	11	86198437	86198437	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	92	58	82	0	0.630435	0	.	.	none	.	ME3	70	.	NM_006680	exon7	c.G751A	p.V251M	CGTGCACGCGCTG	.	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-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	89	5	88	0	0.0561798	0	G|0.601;C|0.399	0.399	strong	.	ZNF469	121	.	NM_001127464	exon2	c.G10888C	p.E3630Q	GTGTCTGAGGGGG	.	PASS	Atlas-SNP
FGD4	121512	hgsc.bcm.edu	37	12	32735236	32735236	+	Silent	SNP	C	C	T	rs904582	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	116	5	84	0	0.0431034	0	C|0.515;T|0.485	0.485	strong	.	FGD4	86	.	NM_139241	exon4	c.C435T	p.D145D	AACAGACAGCTGT	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68045935	68045935	+	Silent	SNP	G	G	A	rs6573781	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	42	6	65	0	0.142857	0	G|0.332;A|0.668	0.668	strong	.	PLEKHH1	118	.	NM_020715	exon21	c.G2934A	p.S978S	GCCATCGCGCATG	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3228411	3228411	+	Silent	SNP	G	G	A	rs78062277	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	124	7	90	0	0.0564516	0	A|1.000;|0.000	1.000	weak	.	MXRA5	815	.	NM_015419	exon7	c.C7833T	p.A2611A	GGCCCCGGCGTCC	.	PASS	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	37	19	41009982	41009982	+	Silent	SNP	C	C	T	rs71358911	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	171	7	195	0	0.0409357	0	C|0.938;T|0.062	0.062	strong	.	SPTBN4	213	.	NM_020971	exon12	c.C1608T	p.A536A	CCTTGCCCTGCAG	.	PASS	Atlas-SNP
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43659419	43659419	+	Missense_Mutation	SNP	G	G	T	rs79064394	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	126	6	162	1	0.047619	0.00617284	.	.	weak	CSGALNACT2,NS,carcinoma,0,5	CSGALNACT2	67	5	NM_018590	exon5	c.G1086T	p.L362F	GGTCTTGATGTTT	.	scavenged	Atlas-SNP
ITIH5	80760	hgsc.bcm.edu	37	10	7605146	7605146	+	Missense_Mutation	SNP	T	T	C	rs137874246	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	96	5	118	0	0.0520833	0	T|0.996;C|0.004	0.004	strong	.	ITIH5	343	.	NM_030569	exon14	c.A2729G	p.N910S	GCGGCATTGTTCC	.	PASS	Atlas-SNP
TMEM177	80775	hgsc.bcm.edu	37	2	120438515	120438515	+	Missense_Mutation	SNP	G	G	C	rs11684353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	71	5	106	0	0.0704225	0	C|0.155;G|0.845;T|0.000	0.155	strong	.	TMEM177	26	.	NM_030577	exon2	c.G86C	p.G29A	TGTTTGGAGTTCC	.	PASS	Atlas-SNP
TMA16	55319	hgsc.bcm.edu	37	4	164435265	164435265	+	Missense_Mutation	SNP	A	A	C	rs2304802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	55	3	65	0	0.0545455	0	C|0.418;N|0.000	0.418	strong	C4orf43,NS,carcinoma,0,2	.	.	2	NM_018352	exon4	c.A194C	p.Q65P	ATCCCCAAAAAAA	.	scavenged	Atlas-SNP
OR14C36	127066	hgsc.bcm.edu	37	1	248512749	248512749	+	Missense_Mutation	SNP	G	G	A	rs28377739	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	99	4	94	0	0.040404	0	G|0.502;A|0.498	0.498	strong	OR14C36,NS,adenoma,0,1	OR14C36	113	1	NM_001001918	exon1	c.G673A	p.G225R	GTGCTCGGGTTTC	.	PASS	Atlas-SNP
HCAR3	8843	hgsc.bcm.edu	37	12	123200768	123200768	+	Missense_Mutation	SNP	T	T	G	rs1798192	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	83	6	98	2	0.0722892	0.0204082	T|0.481;G|0.519	0.519	strong	HCAR3_ENST00000528880,NS,carcinoma,0,1	HCAR3	49	1	NM_006018	exon1	c.A517C	p.T173P	TTGCAGTGCCATT	.	scavenged	Atlas-SNP
CDH7	1005	hgsc.bcm.edu	37	18	63511176	63511176	+	Silent	SNP	T	T	C	rs2306675	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	183	6	155	1	0.0327869	0.00645161	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	.	scavenged	Atlas-SNP
CDH12	1010	hgsc.bcm.edu	37	5	21752050	21752050	+	Silent	SNP	A	A	G	rs6451992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	211	9	174	2	0.042654	0.0114943	A|0.382;G|0.618	0.618	strong	CDH12,NS,carcinoma,0,1	CDH12	238	1	NM_004061	exon15	c.T2181C	p.D727D	AGTTGGATCCACA	.	scavenged	Atlas-SNP
KCNH1	3756	hgsc.bcm.edu	37	1	211256200	211256200	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	43	18	49	0	0.418605	0	.	.	none	KCNH1,NS,carcinoma,0,1	KCNH1	199	1	NM_172362	exon5	c.C480A	p.S160R	CCTGCTGCTTGTC	.	PASS	Atlas-SNP
FAM21A	387680	hgsc.bcm.edu	37	10	51853633	51853633	+	Missense_Mutation	SNP	C	C	T	rs199520696	bycluster;byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	705	153	683	133	0.217021	0.194729	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
CDH9	1007	hgsc.bcm.edu	37	5	26988328	26988328	+	Missense_Mutation	SNP	G	G	A	rs2288466	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	177	9	152	0	0.0508475	0	G|0.501;A|0.499	0.499	strong	CDH9,NS,carcinoma,+1,1	CDH9	305	1	NM_016279	exon2	c.C113T	p.A38V	AGACCCGCTATCT	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32631196	32631196	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	301	6	265	0	0.0199336	0	.	.	none	TAF1L,NS,carcinoma,0,1	TAF1L	382	1	NM_153809	exon1	c.G4382A	p.R1461Q	TCTTCCCGAGATG	.	scavenged	Atlas-SNP
C16orf46	123775	hgsc.bcm.edu	37	16	81095091	81095091	+	Missense_Mutation	SNP	A	A	G	rs7198494	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	96	5	68	0	0.0520833	0	A|0.792;G|0.208	0.208	strong	.	C16orf46	57	.	NM_001100873	exon3	c.T863C	p.I288T	AGGGATATCTGGG	.	PASS	Atlas-SNP
SEMA3D	223117	hgsc.bcm.edu	37	7	84628989	84628989	+	Missense_Mutation	SNP	T	T	G	rs7800072	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	131	5	126	1	0.0381679	0.00793651	T|0.671;G|0.329	0.329	strong	SEMA3D,rectum,carcinoma,0,1	SEMA3D	177	1	NM_152754	exon17	c.A2101C	p.K701Q	TGACCTTCCCCTC	.	scavenged	Atlas-SNP
KCTD20	222658	hgsc.bcm.edu	37	6	36442765	36442765	+	Silent	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	144	4	148	0	0.0277778	0	.	.	none	KCTD20,NS,carcinoma,+1,1	KCTD20	37	1	NM_173562	exon3	c.G360T	p.T120T	AGTGACGCTTCTT	.	scavenged	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52709883	52709883	+	Silent	SNP	T	T	C	rs2248473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	52	2	47	1	0.0384615	0.0212766	T|0.629;C|0.371	0.371	strong	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon7	c.A1056G	p.E352E	CGCAGCTTCCAGC	.	scavenged	Atlas-SNP
MS4A6A	64231	hgsc.bcm.edu	37	11	59945745	59945745	+	Silent	SNP	T	T	C	rs12453	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	199	3	120	0	0.0150754	0	T|0.688;C|0.312	0.312	strong	MS4A6A_ENST00000529054,NS,carcinoma,0,3	MS4A6A	85	3	NM_001247999	exon5	c.A411G	p.L137L	CTTGGTTAACCTT	.	scavenged	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134646988	134646988	+	Missense_Mutation	SNP	C	C	T	rs4880433	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	119	6	201	0	0.0504202	0	C|0.686;T|0.314	0.314	strong	.	TTC40	100	.	NM_001200049	exon50	c.G6991A	p.A2331T	TGTCTGCGACCAG	.	PASS	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	37	8	100133706	100133706	+	Nonsense_Mutation	SNP	T	T	G	rs7460625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	121	7	102	0	0.0578512	0	T|0.294;G|0.706	0.706	strong	.	VPS13B	811	.	NM_181661	exon8	c.T1239G	p.Y413X	TCTCTATCAACTT	.	PASS	Atlas-SNP
TRPV3	162514	hgsc.bcm.edu	37	17	3436080	3436080	+	Silent	SNP	C	C	T	rs395357	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	105	6	131	0	0.0571429	0	C|0.601;T|0.399	0.399	strong	.	TRPV3	85	.	NM_001258205	exon8	c.G936A	p.T312T	ATTCTGCGTCTTG	.	PASS	Atlas-SNP
OR52N5	390075	hgsc.bcm.edu	37	11	5799468	5799468	+	Missense_Mutation	SNP	C	C	T	rs12360738	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	77	5	42	0	0.0649351	0	C|0.824;T|0.176	0.176	strong	.	OR52N5	58	.	NM_001001922	exon1	c.G397A	p.V133I	TGGCTACATAGCG	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24432839	24432839	+	Silent	SNP	A	A	G	rs2303296	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	85	7	87	0	0.0823529	0	A|0.824;G|0.176	0.176	strong	.	ITSN2	224	.	NM_006277	exon35	c.T4321C	p.L1441L	TGTATAATTTCCC	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17697102	17697102	+	Silent	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	38	6	63	3	0.157895	0.047619	.	.	none	RAI1,colon,carcinoma,0,3	RAI1	121	3	NM_030665	exon3	c.G840A	p.Q280Q	GCAGCAGCAGCAG	.	scavenged	Atlas-SNP
SPATA16	83893	hgsc.bcm.edu	37	3	172835125	172835125	+	Missense_Mutation	SNP	T	T	C	rs1515442	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	108	3	103	0	0.0277778	0	T|0.604;C|0.396	0.396	strong	SPATA16,NS,carcinoma,+2,1	SPATA16	111	1	NM_031955	exon2	c.A397G	p.M133V	CACCCATTTCATC	.	scavenged	Atlas-SNP
GPR156	165829	hgsc.bcm.edu	37	3	119892302	119892302	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	109	36	119	0	0.330275	0	.	.	none	GPR156,rectum,carcinoma,0,1	GPR156	85	1	NM_153002	exon8	c.G949T	p.A317S	CAAATGCCTTCCA	.	PASS	Atlas-SNP
SETD2	29072	hgsc.bcm.edu	37	3	47125385	47125385	+	Missense_Mutation	SNP	G	G	A	rs4082155	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	148	7	152	2	0.0472973	0.0131579	G|0.524;A|0.476	0.476	strong	SETD2_ENST00000409792,NS,carcinoma,0,2	SETD2	721	2	NM_014159	exon12	c.C5885T	p.P1962L	TCTTTGGGCTCTA	.	scavenged	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145293535	145293535	+	Missense_Mutation	SNP	C	C	G	rs55936365		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	55	7	53	4	0.127273	0.0754717	.	.	weak	NBPF10,NS,carcinoma,0,2	NBPF10	221	2	NM_001039703	exon1	c.C130G	p.L44V	TGTTTTCTAACTC	.	scavenged	Atlas-SNP
CSNK2B	1460	hgsc.bcm.edu	37	6	31637636	31637636	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	23	11	38	0	0.478261	0	.	.	none	.	CSNK2B	15	.	NM_001320	exon7	c.C581T	p.P194L	TCCATCCGATGGC	.	PASS	Atlas-SNP
OR8J1	219477	hgsc.bcm.edu	37	11	56127971	56127971	+	Missense_Mutation	SNP	T	T	G	rs62001034	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	162	8	187	0	0.0493827	0	T|0.986;G|0.014	0.014	strong	.	OR8J1	87	.	NM_001005205	exon1	c.T249G	p.I83M	GCTGATTAACTTT	.	PASS	Atlas-SNP
BBS12	166379	hgsc.bcm.edu	37	4	123664881	123664881	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	91	5	94	0	0.0549451	0	.	.	none	.	BBS12	63	.	NM_001178007	exon3	c.G1834T	p.E612X	TCATCAGAATTTG	.	PASS	Atlas-SNP
SPZ1	84654	hgsc.bcm.edu	37	5	79616573	79616573	+	Missense_Mutation	SNP	C	C	A	rs184214819	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	372	8	386	4	0.0215054	0.0103627	C|0.995;A|0.005	0.005	strong	SPZ1,NS,carcinoma,0,1	SPZ1	60	1	NM_032567	exon1	c.C539A	p.A180D	GTTTAGCCCCAGA	.	scavenged	Atlas-SNP
C10orf90	118611	hgsc.bcm.edu	37	10	128193433	128193433	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	98	39	115	0	0.397959	0	.	.	none	C10orf90,NS,carcinoma,-1,1	C10orf90	121	1	NM_001004298	exon3	c.G336A	p.P112P	ATCTGACGGTGCC	.	PASS	Atlas-SNP
KMO	8564	hgsc.bcm.edu	37	1	241755414	241755414	+	Missense_Mutation	SNP	G	G	A	rs55662927	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	84	4	82	0	0.047619	0	G|0.998;A|0.002	0.002	strong	.	KMO	69	.	NM_003679	exon15	c.G1420A	p.V474M	AAGGCCGTGGACT	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21232804	21232804	+	Silent	SNP	G	G	A	rs1041968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	170	14	151	1	0.0823529	0.00662252	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	.	scavenged	Atlas-SNP
GOLGA6A	342096	hgsc.bcm.edu	37	15	74363379	74363379	+	Splice_Site	SNP	C	C	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	927	10	1210	2	0.0107875	0.00165289	.	.	none	GOLGA6A,NS,lymphoid_neoplasm,0,2	GOLGA6A	28	2	NM_001038640	exon19	c.1955-1G>T	.	AAAAAACTTCGGA	.	scavenged	Atlas-SNP
ACADL	33	hgsc.bcm.edu	37	2	211060050	211060050	+	Missense_Mutation	SNP	T	T	G	rs2286963	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	101	5	81	0	0.049505	0	G|0.250;N|0.000	0.250	strong	.	ACADL	38	.	NM_001608	exon9	c.A997C	p.K333Q	CTAATTTATGTTG	.	PASS	Atlas-SNP
RGL4	266747	hgsc.bcm.edu	37	22	24038847	24038847	+	Missense_Mutation	SNP	T	T	C	rs1007298	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	156	6	210	0	0.0384615	0	T|0.235;C|0.765	0.765	strong	RGL4,brain,glioma,0,1	RGL4	29	1	NM_153615	exon7	c.T1133C	p.V378A	AGAGAGTCCAGAT	.	scavenged	Atlas-SNP
MVK	4598	hgsc.bcm.edu	37	12	110019233	110019233	+	Silent	SNP	G	G	A	rs34368092	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	75	6	87	0	0.08	0	G|0.950;A|0.050	0.050	strong	MVK,colon,carcinoma,+1,1	MVK	42	1	NM_000431	exon5	c.G405A	p.S135S	GTGGTCGGAGCTG	.	PASS	Atlas-SNP
CTAGE5	4253	hgsc.bcm.edu	37	14	39818145	39818145	+	Missense_Mutation	SNP	G	G	A	rs1060878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	219	14	235	0	0.0639269	0	G|0.654;A|0.346	0.346	strong	.	CTAGE5	75	.	NM_001247989	exon23	c.G2227A	p.G743R	CCACCAGGGGATT	.	PASS	Atlas-SNP
CACNA2D1	781	hgsc.bcm.edu	37	7	81601100	81601100	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	330	70	259	0	0.212121	0	.	.	none	.	CACNA2D1	191	.	NM_000722	exon26	c.A2134G	p.K712E	TATTTTTCTGCTT	.	PASS	Atlas-SNP
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000624	52000624	+	Missense_Mutation	SNP	T	T	G	rs3752135	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	109	4	107	0	0.0366972	0	T|0.148;G|0.852	0.852	strong	SIGLEC12,rectum,carcinoma,-1,1	SIGLEC12	243	1	NM_053003	exon6	c.A1481C	p.Y494S	CAGAAGTACAGGA	.	scavenged	Atlas-SNP
GBA	2629	hgsc.bcm.edu	37	1	155207245	155207245	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	160	49	221	0	0.30625	0	.	.	none	GBA,NS,carcinoma,+1,1	GBA	46	1	NM_001005742	exon8	c.C886T	p.R296X	AGTCTCGCTGATG	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44943104	44943104	+	Missense_Mutation	SNP	G	G	C	rs937838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	120	4	181	0	0.0333333	0	G|0.924;C|0.076	0.076	strong	TGM4,NS,carcinoma,0,1	TGM4	82	1	NM_003241	exon7	c.G746C	p.S249T	CAGGCAGTGCCCC	.	scavenged	Atlas-SNP
PDILT	204474	hgsc.bcm.edu	37	16	20376755	20376755	+	Silent	SNP	T	T	C	rs8054266	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	111	5	70	0	0.045045	0	T|0.448;C|0.552	0.552	strong	.	PDILT	120	.	NM_174924	exon9	c.A1224G	p.V408V	CACAAATACGTCC	.	PASS	Atlas-SNP
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31132340	31132340	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	40	27	48	0	0.675	0	.	.	none	.	ADCYAP1R1	78	.	NM_001118	exon13	c.G1037C	p.S346T	AGTCCAGCATCTA	.	PASS	Atlas-SNP
PIP5K1A	8394	hgsc.bcm.edu	37	1	151215011	151215011	+	Silent	SNP	A	A	G	rs61729862	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	135	4	155	0	0.0296296	0	A|0.975;G|0.025	0.025	strong	PIP5K1A,NS,carcinoma,0,1	PIP5K1A	61	1	NM_001135638	exon14	c.A1608G	p.L536L	ACCTCTAGTTGGA	.	scavenged	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104082349	104082349	+	Silent	SNP	C	C	T	rs2251634	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	220	10	185	0	0.0454545	0	T|0.446;G|0.001	0.446	strong	.	CENPE	253	.	NM_001813	exon20	c.G2025A	p.Q675Q	CTCCAACTGGCTT	.	PASS	Atlas-SNP
GRAMD1A	57655	hgsc.bcm.edu	37	19	35510102	35510102	+	Silent	SNP	G	G	C	rs2290646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	83	4	115	0	0.0481928	0	G|0.623;C|0.377	0.377	strong	.	GRAMD1A	39	.	NM_020895	exon12	c.G1221C	p.T407T	CGTGACGCTGAGC	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3887876	3887876	+	Silent	SNP	T	T	C	rs2120609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	67	5	64	0	0.0746269	0	T|0.432;C|0.568	0.568	strong	.	LRRN1	82	.	NM_020873	exon2	c.T1551C	p.N517N	GGTTAATGGGACC	.	PASS	Atlas-SNP
C22orf42	150297	hgsc.bcm.edu	37	22	32547000	32547000	+	Missense_Mutation	SNP	A	A	G	rs201521774		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	398	4	434	3	0.0100503	0.00691244	.	.	weak	C22orf42,NS,carcinoma,0,1	C22orf42	37	1	NM_001010859	exon6	c.T472C	p.S158P	CCTCAGATATTTC	.	scavenged	Atlas-SNP
TAS2R1	50834	hgsc.bcm.edu	37	5	9629529	9629529	+	Missense_Mutation	SNP	G	G	A	rs2234233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	110	3	90	1	0.0272727	0.0111111	G|0.878;A|0.122	0.122	strong	TAS2R1,NS,carcinoma,0,1	TAS2R1	84	1	NM_019599	exon1	c.C616T	p.R206W	TTTGCCGGGTGTG	.	scavenged	Atlas-SNP
THRAP3	9967	hgsc.bcm.edu	37	1	36752152	36752152	+	Silent	SNP	C	C	T	rs2242428	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	135	5	167	1	0.037037	0.00598802	C|0.710;T|0.290	0.290	strong	THRAP3,NS,carcinoma,+1,2	THRAP3	93	2	NM_005119	exon4	c.C321T	p.Y107Y	AAACTACCGCTCA	.	scavenged	Atlas-SNP
PTCH2	8643	hgsc.bcm.edu	37	1	45292173	45292173	+	Missense_Mutation	SNP	G	G	A	rs11573590	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	107	6	139	0	0.0560748	0	G|0.962;A|0.038	0.038	strong	PTCH2,NS,carcinoma,0,1	PTCH2	96	1	NM_003738	exon18	c.C2963T	p.T988M	CCAGCCGTCCAGG	.	PASS	Atlas-SNP
ZNF584	201514	hgsc.bcm.edu	37	19	58928299	58928299	+	Silent	SNP	A	A	T	rs11668757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	97	5	105	0	0.0515464	0	A|0.846;T|0.154	0.154	strong	.	ZNF584	31	.	NM_173548	exon4	c.A414T	p.A138A	TGGGGCAGCTTTC	.	PASS	Atlas-SNP
TNPO2	30000	hgsc.bcm.edu	37	19	12822220	12822220	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	90	2	76	0	0.0222222	0	.	.	none	TNPO2_ENST00000425528,NS,carcinoma,0,3	TNPO2	108	3	NM_013433	exon11	c.G1007T	p.R336L	TGGAAGCGTGGCT	.	scavenged	Atlas-SNP
BCL11B	64919	hgsc.bcm.edu	37	14	99642463	99642463	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	43	14	35	0	0.325581	0	.	.	none	.	BCL11B	108	.	NM_138576	exon4	c.T710C	p.L237P	TGCTGCAGCAGGA	.	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-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	117	3	102	0	0.025641	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	.	scavenged	Atlas-SNP
FOLH1	2346	hgsc.bcm.edu	37	11	49208267	49208267	+	Missense_Mutation	SNP	G	G	A	rs75940285	bycluster;byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	261	6	279	0	0.0229885	0	G|0.877;A|0.123	0.123	strong	FOLH1,NS,carcinoma,+1,2	FOLH1	141	2	NM_004476	exon5	c.C568T	p.R190W	TGTCCCGTTCCAA	.	scavenged	Atlas-SNP
SVIL	6840	hgsc.bcm.edu	37	10	29840164	29840164	+	Silent	SNP	A	A	G	rs3740002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	42	4	35	0	0.0952381	0	A|0.744;G|0.256	0.256	strong	.	SVIL	226	.	NM_003174	exon8	c.T189C	p.S63S	AGAATCAGAAGTT	.	PASS	Atlas-SNP
SUPT16H	11198	hgsc.bcm.edu	37	14	21831419	21831419	+	Silent	SNP	C	C	T	rs61746713	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	90	3	96	0	0.0333333	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	.	scavenged	Atlas-SNP
SENP1	29843	hgsc.bcm.edu	37	12	48477422	48477422	+	Silent	SNP	A	A	G	rs886588	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	142	3	127	0	0.0211268	0	A|0.817;G|0.183	0.183	strong	SENP1,NS,carcinoma,0,1	SENP1	44	1	NM_001267594	exon6	c.T504C	p.L168L	GCTCAAAAGACTT	.	scavenged	Atlas-SNP
ZNF503	84858	hgsc.bcm.edu	37	10	77161102	77161102	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	18	9	31	0	0.5	0	.	.	none	.	ZNF503	25	.	NM_032772	exon1	c.G76A	p.G26S	CACCGCCGCCTCC	.	PASS	Atlas-SNP
SLC22A23	63027	hgsc.bcm.edu	37	6	3284179	3284179	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	83	37	96	1	0.445783	0.0104167	.	.	none	SLC22A23_ENST00000406686,NS,carcinoma,-1,2	SLC22A23	89	2	NM_015482	exon9	c.C1610T	p.S537F	GCGATGGAAAATT	.	scavenged	Atlas-SNP
ADAMTS13	11093	hgsc.bcm.edu	37	9	136287582	136287582	+	Missense_Mutation	SNP	C	C	T	rs34024143	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	29	3	33	1	0.103448	0.030303	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
SLC35G6	643664	hgsc.bcm.edu	37	17	7386176	7386176	+	Silent	SNP	G	G	C	rs76776066	alternate_allele	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	80	9	116	1	0.1125	0.00862069	.	.	alt	POLR2A_ENST00000412468,NS,haematopoietic_neoplasm,0,1	.	.	1	NM_001102614	exon2	c.G873C	p.V291V	GGTGGTGGTGGCC	.	scavenged	Atlas-SNP
SERPINB6	5269	hgsc.bcm.edu	37	6	2959513	2959513	+	Silent	SNP	C	C	T	rs2236277	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	100	6	102	0	0.06	0	C|0.691;A|0.002	.	strong	SERPINB6,NS,carcinoma,0,1	SERPINB6	31	1	NM_001271823	exon2	c.G111A	p.T37T	ACCCAGCGTTTTC	.	PASS	Atlas-SNP
SARDH	1757	hgsc.bcm.edu	37	9	136577806	136577806	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	24	11	34	0	0.458333	0	.	.	none	.	SARDH	112	.	NM_007101	exon10	c.G1263A	p.G421G	CTCCTGCCCACAG	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186148	12186148	+	Silent	SNP	T	T	C	rs10424893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	72	4	67	0	0.0555556	0	T|0.725;C|0.275	0.275	strong	ZNF844,NS,NS,+2,1	ZNF844	69	1	NM_001136501	exon4	c.T213C	p.V71V	GAGAGTTGATGAA	.	PASS	Atlas-SNP
CCDC88B	283234	hgsc.bcm.edu	37	11	64124515	64124515	+	Silent	SNP	T	T	C	rs612448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	169	5	141	1	0.0295858	0.0070922	T|0.706;C|0.294	0.294	strong	CCDC88B_ENST00000359902,NS,carcinoma,-1,1	CCDC88B	89	1	NM_032251	exon27	c.T4380C	p.P1460P	AGGCCCTGAGGTA	.	scavenged	Atlas-SNP
PRR23C	389152	hgsc.bcm.edu	37	3	138762875	138762875	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	94	39	111	0	0.414894	0	.	.	none	.	PRR23C	31	.	NM_001134657	exon1	c.G588A	p.G196G	ACAGGGCCCTCGG	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9998440	9998440	+	Silent	SNP	C	C	T	rs10939650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	186	7	226	1	0.0376344	0.00442478	C|0.307;T|0.693	0.693	strong	SLC2A9,NS,carcinoma,0,1	SLC2A9	158	1	NM_020041	exon3	c.G375A	p.T125T	AATTAACGTCCCC	.	scavenged	Atlas-SNP
EPHA2	1969	hgsc.bcm.edu	37	1	16451767	16451767	+	Silent	SNP	G	G	A	rs3754334	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	122	10	157	0	0.0819672	0	G|0.777;A|0.223	0.223	strong	.	EPHA2	102	.	NM_004431	exon17	c.C2874T	p.I958I	GTAGGCGATGCGC	.	PASS	Atlas-SNP
PALMD	54873	hgsc.bcm.edu	37	1	100159608	100159608	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	562	6	512	0	0.0106762	0	.	.	none	PALMD,colon,carcinoma,-1,1	PALMD	64	1	NM_017734	exon8	c.A1646G	p.K549R	GAAAAAAGGTGAT	.	scavenged	Atlas-SNP
LHX8	431707	hgsc.bcm.edu	37	1	75622616	75622616	+	Silent	SNP	C	C	T	rs941032	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	85	4	102	0	0.0470588	0	C|0.598;N|0.000	.	strong	.	LHX8	73	.	NM_001001933	exon9	c.C849T	p.H283H	GAAACACGTCAGT	.	PASS	Atlas-SNP
PKP4	8502	hgsc.bcm.edu	37	2	159389762	159389762	+	Silent	SNP	C	C	T	rs35112233	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	89	7	102	0	0.0786517	0	C|0.953;T|0.047	0.047	strong	.	PKP4	133	.	NM_001005476	exon2	c.C66T	p.A22A	AGCTGCCTCCACT	.	PASS	Atlas-SNP
OR11L1	391189	hgsc.bcm.edu	37	1	248004296	248004296	+	Silent	SNP	A	A	G	rs6681483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	144	3	165	0	0.0208333	0	A|0.825;G|0.175	0.175	strong	OR11L1,right_lower_lobe,carcinoma,-2,1	OR11L1	108	1	NM_001001959	exon1	c.T903C	p.V301V	CTTTCTAACAGCT	.	scavenged	Atlas-SNP
ZNF705A	440077	hgsc.bcm.edu	37	12	8329676	8329676	+	Missense_Mutation	SNP	C	C	T	rs10743252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	335	4	284	0	0.0119403	0	C|0.481;T|0.519	0.519	strong	ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	NM_001004328	exon5	c.C400T	p.R134C	ACTCAGCGTTTGT	.	scavenged	Atlas-SNP
RFPL2	10739	hgsc.bcm.edu	37	22	32587027	32587027	+	Missense_Mutation	SNP	G	G	C	rs71326515		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	179	8	252	0	0.0446927	0	C|1.000;|0.000	1.000	weak	.	RFPL2	81	.	NM_001098527	exon5	c.C869G	p.T290S	ACCGTGGTGGCAG	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169127097	169127097	+	Silent	SNP	C	C	A	rs2112703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	49	4	73	0	0.0816327	0	C|0.852;A|0.148	0.148	strong	.	DOCK2	389	.	NM_004946	exon13	c.C1212A	p.T404T	CAGGACCACCGTG	.	PASS	Atlas-SNP
RNF207	388591	hgsc.bcm.edu	37	1	6279370	6279370	+	Missense_Mutation	SNP	G	G	C	rs846111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	337	6	445	0	0.0178042	0	G|0.803;C|0.197	0.197	strong	RNF207,caecum,carcinoma,0,2	RNF207	45	2	NM_207396	exon18	c.G1808C	p.G603A	CGAACGGCCTCTC	.	scavenged	Atlas-SNP
TMA16	55319	hgsc.bcm.edu	37	4	164440581	164440581	+	Missense_Mutation	SNP	T	T	C	rs1561736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	455	17	441	0	0.0373626	0	T|0.582;C|0.418	0.418	strong	C4orf43,NS,carcinoma,0,1	.	.	1	NM_018352	exon7	c.T527C	p.I176T	AAACTATTATAAC	.	scavenged	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82834316	82834316	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	89	34	122	0	0.382022	0	.	.	none	.	VCAN	498	.	NM_004385	exon8	c.T5494C	p.F1832L	TCTGTCTTTATGG	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135722264	135722264	+	Missense_Mutation	SNP	A	A	G	rs17197552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	211	11	218	0	0.0521327	0	A|0.779;G|0.221	0.221	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.A1924G	p.S642G	TGTAGAAGTCCTG	.	PASS	Atlas-SNP
SH3RF2	153769	hgsc.bcm.edu	37	5	145393493	145393493	+	Missense_Mutation	SNP	C	C	T	rs149514957	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	171	7	194	0	0.0409357	0	C|0.998;T|0.002	0.002	strong	.	SH3RF2	58	.	NM_152550	exon5	c.C928T	p.R310W	CTCAACCGGATGG	.	PASS	Atlas-SNP
TLR2	7097	hgsc.bcm.edu	37	4	154625039	154625039	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	109	41	99	0	0.376147	0	.	.	none	TLR2,NS,lymphoid_neoplasm,0,3	TLR2	84	3	NM_003264	exon3	c.A980T	p.D327V	TTTATGATCTGAG	.	PASS	Atlas-SNP
L1TD1	54596	hgsc.bcm.edu	37	1	62676612	62676612	+	Silent	SNP	A	A	G	rs66958136	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	399	14	395	0	0.0350877	0	A|0.804;G|0.196	0.196	strong	L1TD1,NS,carcinoma,0,2	L1TD1	114	2	NM_001164835	exon5	c.A2166G	p.K722K	AATTAAAGAAATA	.	scavenged	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	37	5	483564	483564	+	Silent	SNP	A	A	G	rs56098739	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	176	5	174	0	0.0284091	0	A|0.839;G|0.161	0.161	strong	SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	NM_004174	exon6	c.T966C	p.Y322Y	CTTCACATACTTC	.	scavenged	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71015329	71015329	+	Missense_Mutation	SNP	G	G	T	rs78763837	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	170	6	151	1	0.0352941	0.00662252	.	.	weak	LOC652153,NS,haematopoietic_neoplasm,0,2	HYDIN	788	2	NM_001270974	exon29	c.C4475A	p.P1492H	ATTTGGGGAAAGA	.	scavenged	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38994910	38994910	+	Silent	SNP	G	G	A	rs2229144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	86	2	110	0	0.0232558	0	G|0.657;A|0.343	0.343	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon50	c.G7977A	p.T2659T	ACCCACGGGCTGG	.	scavenged	Atlas-SNP
RABL5	64792	hgsc.bcm.edu	37	7	100958542	100958542	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	99	36	90	0	0.363636	0	.	.	none	.	RABL5	15	.	NM_022777	exon5	c.A431C	p.K144T	ACCAGCTTCAGCT	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247021085	247021085	+	Silent	SNP	G	G	C	rs41308162	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	263	6	300	0	0.0228137	0	G|0.826;C|0.174	0.174	strong	AHCTF1,NS,carcinoma,0,1	AHCTF1	187	1	NM_015446	exon30	c.C4191G	p.L1397L	AACTAAGAGATCC	.	scavenged	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104102563	104102563	+	Silent	SNP	T	T	C	rs17217250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	549	20	592	3	0.0364299	0.00506757	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
LPPR1	0	hgsc.bcm.edu	37	9	104079734	104079734	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	134	41	108	0	0.30597	0	.	.	none	.	.	.	.	NM_207299	exon7	c.G901T	p.A301S	CTAATGGCTTTCC	.	PASS	Atlas-SNP
KRTAP9-4	85280	hgsc.bcm.edu	37	17	39406409	39406409	+	Missense_Mutation	SNP	C	C	A	rs2191379	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	242	12	246	0	0.0495868	0	C|0.336;A|0.664	0.664	strong	.	KRTAP9-4	30	.	NM_033191	exon1	c.C437A	p.S146Y	GTGTGTCCAGCTG	.	PASS	Atlas-SNP
STEAP2	261729	hgsc.bcm.edu	37	7	89856644	89856644	+	Silent	SNP	C	C	T	rs2016903	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	197	5	180	0	0.0253807	0	C|0.869;T|0.131	0.131	strong	STEAP2_ENST00000394626,NS,adenoma,0,2	STEAP2	78	2	NM_001244946	exon4	c.C852T	p.Y284Y	TTATTACGGCACC	.	scavenged	Atlas-SNP
SPNS3	201305	hgsc.bcm.edu	37	17	4351560	4351560	+	Silent	SNP	G	G	A	rs12450838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	77	6	79	0	0.0779221	0	G|0.750;A|0.250	0.250	strong	.	SPNS3	52	.	NM_182538	exon6	c.G732A	p.R244R	CTTCAGGAGCAGC	.	PASS	Atlas-SNP
ANKRD27	84079	hgsc.bcm.edu	37	19	33098632	33098632	+	Missense_Mutation	SNP	G	G	C	rs2302970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	127	6	104	0	0.0472441	0	G|0.651;C|0.349	0.349	strong	.	ANKRD27	86	.	NM_032139	exon23	c.C2282G	p.P761R	AGGAGGGGGATGA	.	PASS	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	37	3	172046861	172046861	+	Silent	SNP	T	T	C	rs2270568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	178	8	187	1	0.0449438	0.00534759	T|0.483;C|0.517	0.517	strong	FNDC3B,NS,carcinoma,0,1	FNDC3B	118	1	NM_001135095	exon12	c.T1374C	p.G458G	CATTGGTACCAGG	.	scavenged	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31116246	31116246	+	Missense_Mutation	SNP	G	G	A	rs130068	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	99	7	107	0	0.0707071	0	G|0.568;A|0.432	0.432	strong	.	CCHCR1	68	.	NM_001105564	exon10	c.C1516T	p.R506W	GCCACCGACGCCT	.	PASS	Atlas-SNP
GEMIN5	25929	hgsc.bcm.edu	37	5	154300940	154300940	+	Silent	SNP	A	A	C	rs348739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	91	3	84	1	0.032967	0.0119048	A|0.188;C|0.812	0.812	strong	GEMIN5,colon,carcinoma,-2,1	GEMIN5	120	1	NM_015465	exon10	c.T1425G	p.T475T	GGCTAAAGTATAT	.	scavenged	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	98893437	98893437	+	Silent	SNP	A	A	G	rs783960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	296	5	330	0	0.0168919	0	A|0.578;G|0.422	0.422	strong	C4orf37,NS,carcinoma,0,2	.	.	2	NM_174952	exon7	c.T927C	p.D309D	CTGATAATCAGCA	.	scavenged	Atlas-SNP
L1TD1	54596	hgsc.bcm.edu	37	1	62675619	62675619	+	Silent	SNP	C	C	T	rs4625314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	185	9	280	2	0.0486486	0.00714286	C|0.605;T|0.395	0.395	strong	L1TD1,NS,carcinoma,0,1	L1TD1	114	1	NM_001164835	exon5	c.C1173T	p.A391A	AGAGGCCTCAGGG	.	scavenged	Atlas-SNP
AATK	9625	hgsc.bcm.edu	37	17	79098602	79098602	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	92	5	146	0	0.0543478	0	.	.	none	.	AATK	102	.	NM_001080395	exon9	c.G887A	p.W296X	GCGATCCAGCGCA	.	PASS	Atlas-SNP
ZDBF2	57683	hgsc.bcm.edu	37	2	207172627	207172627	+	Silent	SNP	A	A	G	rs7582864	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	208	5	237	0	0.0240385	0	A|0.540;G|0.460	0.460	strong	ZDBF2_ENST00000374423,NS,carcinoma,0,2	ZDBF2	531	2	NM_020923	exon5	c.A3375G	p.Q1125Q	TGTCCAATCTGTG	.	scavenged	Atlas-SNP
ZNF248	57209	hgsc.bcm.edu	37	10	38120720	38120720	+	Silent	SNP	C	C	T	rs1779132	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	80	4	76	0	0.05	0	C|0.937;T|0.063	0.063	strong	.	ZNF248	61	.	NM_001267597	exon6	c.G1563A	p.K521K	ATTACACTTATAT	.	PASS	Atlas-SNP
RPAP1	26015	hgsc.bcm.edu	37	15	41826971	41826971	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	43	15	58	0	0.348837	0	.	.	none	.	RPAP1	111	.	NM_015540	exon6	c.T704C	p.L235P	GCCTGCAGTCTTG	.	PASS	Atlas-SNP
OPA1	4976	hgsc.bcm.edu	37	3	193334991	193334991	+	Missense_Mutation	SNP	G	G	A	rs7624750	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	459	10	410	0	0.0217865	0	G|0.517;A|0.483	0.483	strong	OPA1,NS,carcinoma,0,1	OPA1	79	1	NM_130836	exon4	c.G473A	p.S158N	TTCCTAGTTCAGA	.	scavenged	Atlas-SNP
IFI44L	10964	hgsc.bcm.edu	37	1	79093818	79093818	+	Missense_Mutation	SNP	A	A	G	rs273259	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	105	6	118	0	0.0571429	0	G|0.407;N|0.001	0.407	strong	.	IFI44L	93	.	NM_006820	exon2	c.A218G	p.H73R	ATTTACATGAAAG	.	PASS	Atlas-SNP
SPATA4	132851	hgsc.bcm.edu	37	4	177113836	177113836	+	Silent	SNP	C	C	T	rs6832177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	212	3	175	0	0.0141509	0	C|0.701;T|0.299	0.299	strong	SPATA4,NS,carcinoma,-1,1	SPATA4	44	1	NM_144644	exon4	c.G630A	p.A210A	GAACTCCGCTTTA	.	scavenged	Atlas-SNP
FBXO34	55030	hgsc.bcm.edu	37	14	55818517	55818517	+	Missense_Mutation	SNP	T	T	A	rs1045002	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	176	6	173	0	0.0340909	0	A|0.366;N|0.000	0.366	strong	FBXO34,NS,carcinoma,0,1	FBXO34	61	1	NM_017943	exon2	c.T1409A	p.I470N	CTTCCATTTTAAA	.	scavenged	Atlas-SNP
ZSCAN20	7579	hgsc.bcm.edu	37	1	33960062	33960062	+	Silent	SNP	A	A	G	rs9943259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	175	6	215	0	0.0342857	0	A|0.230;G|0.770	0.770	strong	ZSCAN20,NS,carcinoma,+2,2	ZSCAN20	107	2	NM_145238	exon8	c.A2118G	p.A706A	CCTTGCAGAGAAA	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152499143	152499143	+	Missense_Mutation	SNP	C	C	T	rs35974308	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	134	7	122	0	0.0522388	0	C|0.981;T|0.019	0.019	strong	.	NEB	1697	.	NM_004543	exon60	c.G8318A	p.R2773Q	TCTACCCGCATGT	.	PASS	Atlas-SNP
TLR2	7097	hgsc.bcm.edu	37	4	154624656	154624656	+	Silent	SNP	T	T	C	rs3804099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	126	9	141	0	0.0714286	0	T|0.532;C|0.468	0.468	strong	.	TLR2	84	.	NM_003264	exon3	c.T597C	p.N199N	TCAGAATGTAAGT	.	PASS	Atlas-SNP
SNAPC1	6617	hgsc.bcm.edu	37	14	62234030	62234030	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	176	3	182	2	0.0170455	0.010989	.	.	none	SNAPC1,colon,carcinoma,0,1	SNAPC1	32	1	NM_003082	exon3	c.G389T	p.R130L	AGCTACGACTAGA	.	scavenged	Atlas-SNP
MYC	4609	hgsc.bcm.edu	37	8	128750844	128750844	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	90	36	118	0	0.4	0	.	.	none	.	MYC	168	.	NM_002467	exon2	c.C381T	p.N127N	GGTGAACCAGAGT	.	PASS	Atlas-SNP
ZNF280A	129025	hgsc.bcm.edu	37	22	22868776	22868776	+	Silent	SNP	G	G	A	rs362173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	49	12	224	0	0.244898	0	G|0.454;A|0.546	0.546	strong	ZNF280A,NS,adenoma,0,1	ZNF280A	67	1	NM_080740	exon2	c.C1179T	p.P393P	CACGTAGGGCATT	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	121	7	117	0	0.0578512	0	G|0.712;A|0.288	0.288	strong	.	FKBP15	128	.	NM_015258	exon26	c.C3286T	p.L1096L	GGGACAGTCTTGT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487174	32487174	+	Missense_Mutation	SNP	C	C	G	rs112872773	bycluster;byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	65	2	64	0	0.0307692	0	C|0.859;G|0.120;T|0.021	0.120	strong	HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	NM_002125	exon3	c.G625C	p.V209L	TCGTCACGCTTGG	.	scavenged	Atlas-SNP
ANGPT2	285	hgsc.bcm.edu	37	8	6377433	6377433	+	Silent	SNP	C	C	T	rs1961222	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	96	7	124	0	0.0729167	0	C|0.786;T|0.214	0.214	strong	.	ANGPT2	126	.	NM_001147	exon5	c.G882A	p.T294T	GCCATTCGTGGTG	.	PASS	Atlas-SNP
SH3BP5	9467	hgsc.bcm.edu	37	3	15311325	15311325	+	Silent	SNP	A	A	G	rs1287467	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	72	10	74	0	0.138889	0	A|0.378;G|0.621	0.621	strong	.	SH3BP5	32	.	NM_004844	exon4	c.T390C	p.R130R	GGCGGCACGGAGC	.	PASS	Atlas-SNP
TLE6	79816	hgsc.bcm.edu	37	19	2989697	2989697	+	Silent	SNP	T	T	C	rs6510730	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	116	5	116	0	0.0431034	0	T|0.637;C|0.363	0.363	strong	.	TLE6	68	.	NM_001143986	exon13	c.T1158C	p.D386D	CCTGGATGCCAAC	.	PASS	Atlas-SNP
GABRD	2563	hgsc.bcm.edu	37	1	1957037	1957037	+	Silent	SNP	T	T	C	rs2229110	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	179	9	186	1	0.0502793	0.00537634	T|0.334;C|0.666	0.666	strong	GABRD,colon,carcinoma,0,2	GABRD	49	2	NM_000815	exon4	c.T330C	p.G110G	CCTGGGTCTGGAC	.	scavenged	Atlas-SNP
C5orf47	133491	hgsc.bcm.edu	37	5	173416306	173416306	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	77	29	67	0	0.376623	0	.	.	none	.	C5orf47	14	.	NM_001144954	exon1	c.C40T	p.R14C	TCGGCGCGCTTCG	.	PASS	Atlas-SNP
ATG2B	55102	hgsc.bcm.edu	37	14	96771959	96771959	+	Missense_Mutation	SNP	A	A	G	rs2289622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	96	7	99	0	0.0729167	0	A|0.056;G|0.944	0.944	strong	ATG2B,NS,carcinoma,+1,1	ATG2B	169	1	NM_018036	exon31	c.T4700C	p.I1567T	GGGACTATTCCAA	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52710309	52710309	+	Silent	SNP	G	G	A	rs75619735		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	76	2	79	0	0.0263158	0	.	.	weak	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon6	c.C984T	p.N328N	CAGCTCGTTGATC	.	scavenged	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129903802	129903802	+	Missense_Mutation	SNP	A	A	G	rs11016073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	192	4	210	0	0.0208333	0	A|0.842;G|0.158	0.158	strong	MKI67,NS,carcinoma,+1,1	MKI67	363	1	NM_002417	exon13	c.T6302C	p.I2101T	CAGGCTATTTTGG	.	scavenged	Atlas-SNP
CPB1	1360	hgsc.bcm.edu	37	3	148562310	148562310	+	Missense_Mutation	SNP	G	G	A	rs1059502	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	102	5	124	0	0.0490196	0	G|0.743;A|0.257	0.257	strong	.	CPB1	74	.	NM_001871	exon7	c.G622A	p.D208N	CTTCTCGACAAGT	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24507652	24507652	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	504	8	465	0	0.015873	0	.	.	none	ITSN2,NS,carcinoma,0,1	ITSN2	224	1	NM_147152	exon17	c.A1924G	p.N642D	AGAGGTTGTTGAG	.	scavenged	Atlas-SNP
RECQL5	9400	hgsc.bcm.edu	37	17	73654377	73654377	+	Splice_Site	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	55	18	60	0	0.327273	0	.	.	none	.	RECQL5	77	.	NM_004259	exon8	c.1149+1G>A	.	GCCTTACCTGGAG	.	PASS	Atlas-SNP
STARD7	56910	hgsc.bcm.edu	37	2	96861159	96861159	+	Missense_Mutation	SNP	C	C	G	rs2276650	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	129	5	114	0	0.0387597	0	C|0.878;G|0.122	0.122	strong	STARD7,NS,carcinoma,0,1	STARD7	49	1	NM_020151	exon2	c.G419C	p.R140P	TCCCAACGTTGCT	.	scavenged	Atlas-SNP
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43659372	43659372	+	Nonsense_Mutation	SNP	C	C	T	rs76607193	bycluster;byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	131	5	175	1	0.0381679	0.00571429	C|0.997;T|0.003	0.003	strong	CSGALNACT2,trunk,malignant_melanoma,0,1	CSGALNACT2	67	1	NM_018590	exon5	c.C1039T	p.R347X	CGTGGACGAGGAC	.	scavenged	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279884	46279884	+	Silent	SNP	A	A	G	rs112355546		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	61	4	68	0	0.0655738	0	A|0.500;G|0.500	0.500	weak	.	NCOA3	156	.	NM_181659	exon20	c.A3810G	p.Q1270Q	ACAGCAACAGCAG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144941419	144941419	+	Silent	SNP	C	C	T	rs12681478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	60	5	94	2	0.0833333	0.0212766	C|0.740;T|0.260	0.260	strong	EPPK1,NS,carcinoma,0,1	EPPK1	199	1	NM_031308	exon1	c.G6003A	p.A2001A	TGCCTCCGCCTTC	.	scavenged	Atlas-SNP
DNAJB11	51726	hgsc.bcm.edu	37	3	186301703	186301703	+	Missense_Mutation	SNP	A	A	G	rs8147	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	127	6	98	0	0.0472441	0	A|0.723;G|0.277	0.277	strong	.	DNAJB11	42	.	NM_016306	exon8	c.A790G	p.I264V	GTGACAATCTCAT	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51637536	51637536	+	Missense_Mutation	SNP	G	G	T	rs142522748	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	64	4	78	0	0.0625	0	G|0.991;T|0.009	0.009	strong	.	PKHD1	927	.	NM_170724	exon55	c.C8606A	p.T2869K	AGATGTGTCCAGG	.	PASS	Atlas-SNP
USP15	9958	hgsc.bcm.edu	37	12	62785663	62785663	+	Silent	SNP	T	T	C	rs11174457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	591	6	447	1	0.0101523	0.00223714	T|0.933;C|0.067	0.067	strong	USP15,NS,carcinoma,0,1	USP15	105	1	NM_001252078	exon17	c.T2301C	p.A767A	TGCTGCTGAGGTA	.	scavenged	Atlas-SNP
HTR5A	3361	hgsc.bcm.edu	37	7	154862621	154862621	+	Silent	SNP	T	T	A	rs6320	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	18	11	10	1	0.611111	0.1	T|0.726;A|0.274	0.274	strong	HTR5A,NS,carcinoma,+1,2	HTR5A	114	2	NM_024012	exon1	c.T12A	p.P4P	TTTACCTGTGAAC	.	scavenged	Atlas-SNP
ANLN	54443	hgsc.bcm.edu	37	7	36438709	36438709	+	Missense_Mutation	SNP	C	C	G	rs3735400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	324	6	228	0	0.0185185	0	C|0.882;G|0.118	0.118	strong	ANLN,NS,carcinoma,0,1	ANLN	101	1	NM_018685	exon3	c.C194G	p.S65W	AACCATCGCCATC	.	scavenged	Atlas-SNP
IFI44L	10964	hgsc.bcm.edu	37	1	79095581	79095581	+	Missense_Mutation	SNP	T	T	C	rs987495	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	127	4	121	1	0.0314961	0.00826446	T|0.785;G|0.001	.	strong	IFI44L,NS,carcinoma,-1,1	IFI44L	93	1	NM_006820	exon4	c.T704C	p.I235T	CTGATATCACCAG	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412163	105412163	+	Missense_Mutation	SNP	C	C	G	rs201181175	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	105	6	134	2	0.0571429	0.0149254	.	.	weak	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.G9625C	p.V3209L	GCTTCACGTCCAC	.	scavenged	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536466	1536466	+	Missense_Mutation	SNP	C	C	T	rs61751878	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	134	7	169	0	0.0522388	0	C|0.995;T|0.005	0.005	strong	.	PTX4	46	.	NM_001013658	exon3	c.G896A	p.R299H	GCCGTGCGGACCC	.	PASS	Atlas-SNP
MRS2	57380	hgsc.bcm.edu	37	6	24418786	24418786	+	Silent	SNP	T	T	C	rs79527965	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	123	4	123	0	0.0325203	0	T|0.887;C|0.113	0.113	strong	MRS2,NS,carcinoma,0,1	MRS2	31	1	NM_020662	exon9	c.T1087C	p.L363L	ATGAATTTGGAAT	.	scavenged	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1730215	1730215	+	Silent	SNP	C	C	G	rs798757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	143	6	165	0	0.041958	0	C|0.830;G|0.170	0.170	strong	.	TACC3	69	.	NM_006342	exon4	c.C1086G	p.G362G	GTCCGGCCTCAAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679366	100679366	+	Missense_Mutation	SNP	A	A	G	rs74209688	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	154	4	93	0	0.025974	0	A|0.784;G|0.216	0.216	strong	MUC17,NS,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.A4669G	p.T1557A	CCTACAACTGCTG	.	scavenged	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13762972	13762972	+	Silent	SNP	T	T	C	rs6554812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	120	5	101	1	0.0416667	0.00990099	T|0.714;C|0.286	0.286	strong	DNAH5,NS,carcinoma,-2,1	DNAH5	868	1	NM_001369	exon60	c.A10140G	p.E3380E	CAAAAATTCTATC	.	scavenged	Atlas-SNP
CNTN1	1272	hgsc.bcm.edu	37	12	41337435	41337435	+	Silent	SNP	C	C	T	rs1056019	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	471	11	371	2	0.0233546	0.00539084	C|0.397;T|0.603	0.603	strong	CNTN1,NS,carcinoma,0,1	CNTN1	207	1	NM_001256063	exon13	c.C1416T	p.N472N	AATCAACAACATT	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179400129	179400129	+	Missense_Mutation	SNP	C	C	T	rs192391568	by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	69	38	67	0	0.550725	0	C|1.000;T|0.000	0.000	strong	.	TTN	18412	.	NM_001267550	exon358	c.G101213A	p.R33738H	CCTACACGGAGCC	.	PASS	Atlas-SNP
SMIM5	643008	hgsc.bcm.edu	37	17	73636368	73636368	+	Silent	SNP	C	C	T	rs117954398	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	49	5	80	0	0.102041	0	C|0.994;T|0.006	0.006	strong	.	.	.	.	NM_001162995	exon2	c.C87T	p.P29P	TGAGCCCGTGGAG	.	PASS	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	37	1	154842244	154842244	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	52	21	54	2	0.403846	0.037037	.	.	none	KCNN3,NS,carcinoma,+1,3	KCNN3	141	3	NM_001204087	exon1	c.T197A	p.L66H	TGCTGAAGCTGCG	.	scavenged	Atlas-SNP
VWCE	220001	hgsc.bcm.edu	37	11	61048187	61048187	+	Silent	SNP	G	G	A	rs375996793		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	67	34	64	0	0.507463	0	.	.	weak	.	VWCE	84	.	NM_152718	exon9	c.C1233T	p.D411D	CTTCCCGTCCTAG	.	PASS	Atlas-SNP
HCAR3	8843	hgsc.bcm.edu	37	12	123200693	123200693	+	Missense_Mutation	SNP	A	A	G	rs17884481	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	103	6	118	0	0.0582524	0	A|0.479;G|0.521	0.521	strong	HCAR3_ENST00000528880,colon,carcinoma,0,3	HCAR3	49	3	NM_006018	exon1	c.T592C	p.F198L	GCAGGAAGAACTC	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48674136	48674136	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	37	13	39	0	0.351351	0	.	.	none	.	CACNA1G	659	.	NM_001256360	exon16	c.C3110T	p.P1037L	TGCTGCCGCCTCT	.	PASS	Atlas-SNP
ABHD12	26090	hgsc.bcm.edu	37	20	25288632	25288632	+	Silent	SNP	G	G	A	rs6107027	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	77	5	94	0	0.0649351	0	G|0.608;A|0.392	0.392	strong	.	ABHD12	46	.	NM_001042472	exon9	c.C837T	p.R279R	TTCTTCGCGGATA	.	PASS	Atlas-SNP
ANAPC4	29945	hgsc.bcm.edu	37	4	25408838	25408838	+	Missense_Mutation	SNP	G	G	A	rs34811474	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	313	13	252	1	0.0415335	0.00396825	G|0.858;A|0.142	0.142	strong	ANAPC4,NS,carcinoma,+1,1	ANAPC4	61	1	NM_013367	exon20	c.G1394A	p.R465Q	ATAATCGAAAAGG	.	scavenged	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3238733	3238733	+	Missense_Mutation	SNP	G	G	A	rs1974522	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	140	6	88	0	0.0428571	0	0|0.015;A|0.441;C|0.000;G|0.544;N|0.000	0.441	strong	.	MXRA5	815	.	NM_015419	exon5	c.C4993T	p.P1665S	ATCTTGGAGTTGT	.	PASS	Atlas-SNP
SPATA18	132671	hgsc.bcm.edu	37	4	52938302	52938302	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	203	78	203	0	0.384236	0	.	.	none	SPATA18_ENST00000295213,colon,carcinoma,+2,5	SPATA18	222	5	NM_145263	exon6	c.G738T	p.E246D	TGCTGAGAAAAGT	.	PASS	Atlas-SNP
SPP2	6694	hgsc.bcm.edu	37	2	234967539	234967539	+	Silent	SNP	T	T	A	rs593668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	116	6	104	0	0.0517241	0	T|0.324;A|0.676	0.676	strong	.	SPP2	35	.	NM_006944	exon3	c.T270A	p.T90T	GGAGACTACATGC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9059232	9059232	+	Missense_Mutation	SNP	T	T	C	rs12710265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	112	5	97	0	0.0446429	0	T|0.786;C|0.214	0.214	strong	.	MUC16	4315	.	NM_024690	exon3	c.A28214G	p.Q9405R	ACTGACTGTGGAA	.	PASS	Atlas-SNP
APITD1-CORT	100526739	hgsc.bcm.edu	37	1	10511544	10511544	+	Silent	SNP	C	C	T	rs628462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	189	7	239	0	0.037037	0	C|0.685;T|0.315	0.315	strong	CORT,colon,carcinoma,0,2	.	.	2	NM_198544	exon5	c.C387T	p.A129A	GGAAGCCCGGGAG	.	scavenged	Atlas-SNP
EPHA5	2044	hgsc.bcm.edu	37	4	66467586	66467586	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	110	39	102	0	0.354545	0	.	.	none	EPHA5,colon,carcinoma,0,1	EPHA5	315	1	NM_004439	exon3	c.T683C	p.V228A	TAGTATACACGCA	.	PASS	Atlas-SNP
YEATS2	55689	hgsc.bcm.edu	37	3	183476685	183476685	+	Missense_Mutation	SNP	G	G	A	rs262993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	423	7	445	0	0.0165485	0	G|0.576;A|0.424	0.424	strong	YEATS2,NS,carcinoma,-1,1	YEATS2	111	1	NM_018023	exon13	c.G1588A	p.V530I	TCTCAGGTCTCCC	.	scavenged	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907358	12907358	+	Missense_Mutation	SNP	T	T	C	rs74587302	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	55	4	56	1	0.0727273	0.0178571	.	.	weak	HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.A785G	p.Q262R	TCCCCCTGATCTT	.	scavenged	Atlas-SNP
TNFSF12	8742	hgsc.bcm.edu	37	17	7452542	7452542	+	Silent	SNP	C	C	T	rs77711855	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	9	6	4	0	0.666667	0	C|0.883;T|0.117	0.117	strong	.	TNFSF12	20	.	NM_003809	exon1	c.C72T	p.L24L	CCCGCTCGCGCTG	.	PASS	Atlas-SNP
SCUBE1	80274	hgsc.bcm.edu	37	22	43610207	43610207	+	Missense_Mutation	SNP	A	A	G	rs138993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	92	6	96	0	0.0652174	0	A|0.489;G|0.511	0.511	strong	SCUBE1,NS,carcinoma,0,1	SCUBE1	105	1	NM_173050	exon16	c.T1942C	p.S648P	TACATGACACACA	.	PASS	Atlas-SNP
HIST1H2AE	3012	hgsc.bcm.edu	37	6	26217398	26217398	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	124	52	127	0	0.419355	0	.	.	none	.	HIST1H2AE	25	.	NM_021052	exon1	c.C196G	p.L66V	TTAGAGCTAGCTG	.	PASS	Atlas-SNP
CBWD1	55871	hgsc.bcm.edu	37	9	163985	163985	+	Silent	SNP	A	A	G	rs2482169		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	605	19	550	8	0.031405	0.0145455	.	.	weak	CBWD1,NS,carcinoma,0,4	CBWD1	24	4	NM_001145356	exon5	c.T483C	p.Y161Y	ATCAAGATAAATA	.	scavenged	Atlas-SNP
SLC30A5	64924	hgsc.bcm.edu	37	5	68419054	68419054	+	Silent	SNP	A	A	T	rs164572	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	84	5	84	0	0.0595238	0	A|0.607;T|0.393	0.393	strong	.	SLC30A5	54	.	NM_022902	exon14	c.A1800T	p.T600T	AGATACACTTGGC	.	PASS	Atlas-SNP
OSBP2	23762	hgsc.bcm.edu	37	22	31091139	31091139	+	Silent	SNP	A	A	G	rs13053290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	143	5	172	3	0.034965	0.0174419	A|0.726;G|0.274	0.274	strong	OSBP2,NS,carcinoma,0,1	OSBP2	52	1	NM_030758	exon1	c.A243G	p.E81E	ATCGGAACCTGTG	.	scavenged	Atlas-SNP
FAR2	55711	hgsc.bcm.edu	37	12	29423460	29423460	+	Silent	SNP	G	G	A	rs2216854	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	259	7	191	0	0.027027	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	.	scavenged	Atlas-SNP
CELF5	60680	hgsc.bcm.edu	37	19	3224896	3224896	+	Silent	SNP	G	G	C	rs17852497	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	173	13	230	5	0.0751445	0.0217391	G|0.815;C|0.185	0.185	strong	CELF5,NS,carcinoma,0,1	CELF5	32	1	NM_021938	exon1	c.G159C	p.P53P	GATCCCGCGGCAC	.	scavenged	Atlas-SNP
ATG14	22863	hgsc.bcm.edu	37	14	55864146	55864146	+	Silent	SNP	G	G	A	rs61743178	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	116	5	138	0	0.0431034	0	G|0.966;A|0.034	0.034	strong	.	ATG14	36	.	NM_014924	exon2	c.C228T	p.I76I	CTTGTCGATAAAC	.	PASS	Atlas-SNP
PSD3	23362	hgsc.bcm.edu	37	8	18725428	18725428	+	Silent	SNP	A	A	G	rs17127370	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	82	4	89	0	0.0487805	0	A|0.898;G|0.102	0.102	strong	.	PSD3	142	.	NM_015310	exon4	c.T1390C	p.L464L	AGTATAATGTCTC	.	PASS	Atlas-SNP
ZNF280A	129025	hgsc.bcm.edu	37	22	22868773	22868773	+	Silent	SNP	G	G	A	rs361737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	49	12	232	0	0.244898	0	G|0.453;A|0.547	0.547	strong	ZNF280A,NS,adenoma,0,1	ZNF280A	67	1	NM_080740	exon2	c.C1182T	p.Y394Y	GCACACGTAGGGC	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234725	45234725	+	Silent	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	201	14	203	6	0.0696517	0.0295567	.	.	none	CDC27_ENST00000531206,NS,carcinoma,0,10	CDC27	337	10	NM_001114091	exon6	c.A501G	p.T167T	TTTAAATGTTTGG	.	scavenged	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907513	12907513	+	Silent	SNP	T	T	C	rs79873981		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	113	3	108	6	0.0265487	0.0555556	C|1.000;|0.000	1.000	weak	HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.A630G	p.K210K	CTCTTGTTTGCTC	.	scavenged	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40408532	40408532	+	Missense_Mutation	SNP	G	G	A	rs36106401	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	225	8	299	0	0.0355556	0	G|0.853;A|0.147	0.147	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon8	c.C4307T	p.P1436L	CTCCCCGGCGGGC	.	scavenged	Atlas-SNP
TIMELESS	8914	hgsc.bcm.edu	37	12	56814653	56814653	+	Missense_Mutation	SNP	G	G	A	rs2291739	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	88	5	62	0	0.0568182	0	G|0.548;A|0.452	0.452	strong	.	TIMELESS	107	.	NM_003920	exon25	c.C3053T	p.P1018L	AGGAGCGGGATAG	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38995438	38995438	+	Silent	SNP	T	T	C	rs2960340	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	71	4	66	0	0.056338	0	T|0.657;C|0.343	0.343	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon51	c.T8118C	p.I2706I	CGCCATTGCCGGG	.	scavenged	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145024578	145024578	+	Silent	SNP	G	G	A	rs190222339	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	117	7	138	0	0.0598291	0	G|0.997;A|0.003	0.003	strong	.	PLEC	1144	.	NM_201380	exon1	c.C297T	p.R99R	GCGCACGCGCTGC	.	PASS	Atlas-SNP
MEP1A	4224	hgsc.bcm.edu	37	6	46766884	46766884	+	Silent	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	135	43	139	0	0.318519	0	.	.	none	.	MEP1A	93	.	NM_005588	exon5	c.G228T	p.T76T	GTGGACGTTCCCC	.	PASS	Atlas-SNP
ERO1LB	56605	hgsc.bcm.edu	37	1	236413230	236413230	+	Missense_Mutation	SNP	T	T	A	rs2477599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	145	6	173	0	0.0413793	0	T|0.570;A|0.430	0.430	strong	.	ERO1LB	48	.	NM_019891	exon5	c.A386T	p.D129V	TCACAATCTTCTA	.	PASS	Atlas-SNP
UGT2A1	10941	hgsc.bcm.edu	37	4	70512773	70512773	+	Missense_Mutation	SNP	A	A	G	rs41292307	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	79	5	85	0	0.0632911	0	A|0.882;G|0.118	0.118	strong	.	UGT2A1	131	.	NM_001252274	exon2	c.T590C	p.L197S	TCTGATAAAACAG	.	PASS	Atlas-SNP
SIGLEC11	114132	hgsc.bcm.edu	37	19	50463670	50463670	+	Missense_Mutation	SNP	T	T	G	rs79085301	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	140	11	150	0	0.0785714	0	T|0.840;G|0.160	0.160	strong	.	SIGLEC11	70	.	NM_052884	exon3	c.A469C	p.K157Q	GCTTCTTAGTCAG	.	PASS	Atlas-SNP
CBWD3	445571	hgsc.bcm.edu	37	9	70871836	70871836	+	Splice_Site	SNP	C	C	G	rs76283403		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	964	19	987	6	0.0197095	0.00607903	C|0.500;G|0.500	0.500	weak	CBWD3,rectum,carcinoma,-1,1	CBWD3	10	1	NM_201453	exon5	c.431-1C>G	.	TTTTCACGTGCAG	.	scavenged	Atlas-SNP
LAMP3	27074	hgsc.bcm.edu	37	3	182871600	182871600	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	131	3	147	0	0.0229008	0	.	.	none	LAMP3,NS,carcinoma,0,1	LAMP3	48	1	NM_014398	exon2	c.C629A	p.T210K	GGAACCGTGGAGG	.	scavenged	Atlas-SNP
OR51E1	143503	hgsc.bcm.edu	37	11	4674575	4674575	+	Silent	SNP	G	G	A	rs3817098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	57	6	59	0	0.105263	0	G|0.615;A|0.385	0.385	strong	.	OR51E1	67	.	NM_152430	exon2	c.G819A	p.P273P	CTCTCCGCTGCCC	.	PASS	Atlas-SNP
IFIT2	3433	hgsc.bcm.edu	37	10	91066075	91066075	+	Missense_Mutation	SNP	A	A	G	rs2070845	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	93	5	60	0	0.0537634	0	A|0.781;G|0.219	0.219	strong	.	IFIT2	39	.	NM_001547	exon2	c.A362G	p.K121R	AGGTGAAACATGT	.	PASS	Atlas-SNP
NEK9	91754	hgsc.bcm.edu	37	14	75590846	75590846	+	Silent	SNP	A	A	T	rs175449	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	80	6	89	0	0.075	0	A|0.436;T|0.564	0.564	strong	.	NEK9	64	.	NM_033116	exon2	c.T300A	p.I100I	AATAACAATCTCA	.	PASS	Atlas-SNP
SLC35E1	79939	hgsc.bcm.edu	37	19	16666101	16666101	+	Silent	SNP	G	G	C	rs2287869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	86	5	88	0	0.0581395	0	G|0.568;C|0.432	0.432	strong	.	SLC35E1	48	.	NM_024881	exon5	c.C864G	p.P288P	GCTCAGGGGGCTA	.	PASS	Atlas-SNP
IFI30	10437	hgsc.bcm.edu	37	19	18285944	18285944	+	Missense_Mutation	SNP	G	G	A	rs11554159	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	96	5	125	0	0.0520833	0	G|0.789;A|0.211	0.211	strong	.	IFI30	12	.	NM_006332	exon2	c.G227A	p.R76Q	GCTGCCGAGCCTT	.	PASS	Atlas-SNP
MAGEA8	4107	hgsc.bcm.edu	37	X	149013727	149013727	+	Silent	SNP	A	A	G	rs5983916	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	121	8	86	0	0.0661157	0	A|0.130;0|0.004	.	strong	.	MAGEA8	40	.	NM_005364	exon3	c.A681G	p.A227A	GGAAGCATTGAGT	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29364951	29364951	+	Missense_Mutation	SNP	G	G	A	rs2073151	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	99	5	89	0	0.050505	0	G|0.639;A|0.361	0.361	strong	.	OR12D2	42	.	NM_013936	exon1	c.G475A	p.V159I	CACTCCGTAATGA	.	PASS	Atlas-SNP
LRRIQ3	127255	hgsc.bcm.edu	37	1	74648408	74648408	+	Missense_Mutation	SNP	C	C	T	rs17094900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	111	5	120	0	0.045045	0	C|0.956;T|0.044	0.044	strong	.	LRRIQ3	146	.	NM_001105659	exon3	c.G387A	p.M129I	ATCAAACATAGTG	.	PASS	Atlas-SNP
HSPD1	3329	hgsc.bcm.edu	37	2	198363534	198363534	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	438	7	361	0	0.0159817	0	.	.	none	HSPD1_ENST00000426480,NS,haematopoietic_neoplasm,0,3	HSPD1	68	3	NM_002156	exon2	c.G39A	p.P13P	GGACACCGGTCTC	.	scavenged	Atlas-SNP
OR4D5	219875	hgsc.bcm.edu	37	11	123811056	123811056	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	139	35	75	0	0.251799	0	.	.	none	.	OR4D5	94	.	NM_001001965	exon1	c.G733A	p.A245T	CACATTGCTGTGG	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48056958	48056958	+	Silent	SNP	C	C	T	rs3743281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	65	5	64	0	0.0769231	0	C|0.814;T|0.186	0.186	strong	.	SEMA6D	322	.	NM_153617	exon12	c.C1221T	p.A407A	CATTGCCGATGAG	.	PASS	Atlas-SNP
B3GNT8	374907	hgsc.bcm.edu	37	19	41932420	41932420	+	Silent	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	52	13	53	0	0.25	0	.	.	none	.	B3GNT8	20	.	NM_198540	exon3	c.C264T	p.S88S	TTCAGTGCTGTCC	.	PASS	Atlas-SNP
MURC	347273	hgsc.bcm.edu	37	9	103348634	103348634	+	Silent	SNP	G	G	A	rs2780956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	52	5	41	0	0.0961538	0	G|0.649;A|0.351	0.351	strong	.	MURC	43	.	NM_001018116	exon2	c.G996A	p.R332R	AGGAAGGGAAATC	.	PASS	Atlas-SNP
EIF5B	9669	hgsc.bcm.edu	37	2	99995517	99995517	+	Silent	SNP	C	C	T	rs11896520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	547	7	497	2	0.0127971	0.00402414	C|0.813;T|0.187	0.187	strong	EIF5B,caecum,carcinoma,0,1	EIF5B	95	1	NM_015904	exon11	c.C1878T	p.T626T	AAACACCGAAAAG	.	scavenged	Atlas-SNP
ZNF700	90592	hgsc.bcm.edu	37	19	12059467	12059467	+	Missense_Mutation	SNP	C	C	G	rs73509026	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	155	4	164	0	0.0258065	0	C|0.940;G|0.060	0.060	strong	ZNF700,NS,carcinoma,-1,1	ZNF700	81	1	NM_001271848	exon4	c.C637G	p.R213G	AGCATTCGAAGAC	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092885	1092885	+	Silent	SNP	G	G	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	40	7	69	3	0.175	0.0434783	.	.	none	MUC2_ENST00000441003,NS,carcinoma,+1,8	MUC2	614	8	NM_002457	exon30	c.G4704C	p.T1568T	CACCACGGTGACC	.	scavenged	Atlas-SNP
MLLT3	4300	hgsc.bcm.edu	37	9	20414376	20414376	+	Silent	SNP	A	A	G	rs1761445	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	48	6	31	1	0.125	0.0322581	A|0.906;G|0.094	0.094	strong	MLLT3,colon,carcinoma,0,3	MLLT3	125	3	NM_004529	exon5	c.T468C	p.S156S	GCTGCTACTGCTG	.	scavenged	Atlas-SNP
SLC13A3	64849	hgsc.bcm.edu	37	20	45204266	45204266	+	Silent	SNP	G	G	A	rs1880898	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	106	5	95	0	0.0471698	0	G|0.419;T|0.006	.	strong	.	SLC13A3	88	.	NM_022829	exon10	c.C1278T	p.P426P	GTTCCAGGGCACT	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90501448	90501448	+	Missense_Mutation	SNP	C	C	A	rs4076795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	73	6	71	0	0.0821918	0	C|0.297;N|0.002	.	strong	C9orf79,caecum,carcinoma,0,1	.	.	1	NM_178828	exon4	c.C2046A	p.D682E	TTCTGACTTTGCA	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5058808	5058808	+	Missense_Mutation	SNP	G	G	A	rs9899177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	221	4	220	0	0.0180995	0	G|0.541;A|0.459	0.459	strong	USP6_ENST00000250066,NS,carcinoma,-1,1	USP6	213	1	NM_004505	exon23	c.G2735A	p.R912Q	ATACCCGGAAGAA	.	scavenged	Atlas-SNP
LCE3D	84648	hgsc.bcm.edu	37	1	152552285	152552285	+	Missense_Mutation	SNP	C	C	A	rs61745411		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	147	4	191	0	0.0272109	0	C|0.986;A|0.014	0.014	weak	LCE3D,NS,carcinoma,0,1	LCE3D	28	1	NM_032563	exon2	c.G128T	p.G43V	CCACAGCCCCCAG	.	scavenged	Atlas-SNP
P2RX5	5026	hgsc.bcm.edu	37	17	3599205	3599205	+	Missense_Mutation	SNP	A	A	T	rs142863822	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	98	6	122	0	0.0612245	0	A|0.996;T|0.004	0.004	strong	.	P2RX5	36	.	NM_001204519	exon1	c.T95A	p.L32Q	CGGTACAGCAGGC	.	PASS	Atlas-SNP
ADAMTS3	9508	hgsc.bcm.edu	37	4	73205310	73205310	+	Silent	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	108	41	88	0	0.37963	0	.	.	none	.	ADAMTS3	164	.	NM_014243	exon5	c.C762T	p.N254N	GTAATCGTTTTCT	.	PASS	Atlas-SNP
CHIA	27159	hgsc.bcm.edu	37	1	111861841	111861841	+	Missense_Mutation	SNP	A	A	G	rs2275253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	145	5	138	0	0.0344828	0	A|0.322;G|0.678	0.678	strong	CHIA_ENST00000369740,NS,adenoma,0,2	CHIA	115	2	NM_201653	exon10	c.A1015G	p.I339V	GACAACATCAAGA	.	scavenged	Atlas-SNP
KRT13	3860	hgsc.bcm.edu	37	17	39661359	39661359	+	Silent	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	58	20	75	0	0.344828	0	.	.	none	.	KRT13	72	.	NM_002274	exon1	c.T444C	p.P148P	CCGCTCAGGGCTA	.	PASS	Atlas-SNP
CNR1	1268	hgsc.bcm.edu	37	6	88853635	88853635	+	Silent	SNP	C	C	T	rs1049353	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	38	5	70	0	0.131579	0	C|0.840;T|0.160	0.160	strong	CNR1,NS,carcinoma,-1,1	CNR1	91	1	NM_001160258	exon4	c.G1359A	p.T453T	CTTGACCGTGCTC	.	PASS	Atlas-SNP
KLHL14	57565	hgsc.bcm.edu	37	18	30257203	30257203	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	166	3	142	0	0.0180723	0	.	.	none	KLHL14,colon,carcinoma,-1,2	KLHL14	92	2	NM_020805	exon8	c.G1679A	p.R560Q	CCACTTCGACCCT	.	scavenged	Atlas-SNP
C20orf26	26074	hgsc.bcm.edu	37	20	20257958	20257958	+	Silent	SNP	C	C	T	rs2424317	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	61	4	70	0	0.0655738	0	C|0.824;T|0.176	0.176	strong	.	C20orf26	188	.	NM_015585	exon22	c.C2652T	p.S884S	GGAGAGCGCCGTG	.	PASS	Atlas-SNP
BTG2	7832	hgsc.bcm.edu	37	1	203274847	203274847	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	95	38	119	0	0.4	0	.	.	none	.	BTG2	16	.	NM_006763	exon1	c.T113G	p.F38C	AGGTCTTCAGCGG	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15668319	15668319	+	Missense_Mutation	SNP	G	G	A	rs12126178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	153	5	210	2	0.0326797	0.00952381	G|0.930;A|0.070	0.070	strong	FHAD1_ENST00000375999,NS,carcinoma,0,2	FHAD1	78	2	NM_052929	exon15	c.G1994A	p.R665Q	CTGAACGAGGAGA	.	scavenged	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	37	1	154842243	154842243	+	Silent	SNP	A	A	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	52	20	54	3	0.384615	0.0555556	.	.	none	KCNN3,NS,carcinoma,0,3	KCNN3	141	3	NM_001204087	exon1	c.T198G	p.L66L	CTGCTGAAGCTGC	.	scavenged	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	37	4	169197297	169197297	+	Missense_Mutation	SNP	C	C	T	rs550625	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	133	4	121	1	0.0300752	0.00826446	C|0.882;T|0.118	0.118	strong	DDX60_ENST00000393743,NS,carcinoma,+2,2	DDX60	304	2	NM_017631	exon15	c.G2014A	p.V672M	TCATCACCTGAAC	.	scavenged	Atlas-SNP
BRIP1	83990	hgsc.bcm.edu	37	17	59763465	59763465	+	Silent	SNP	T	T	C	rs4986765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	183	6	195	0	0.0327869	0	T|0.221;C|0.779	0.779	strong	BRIP1_ENST00000259008,NS,carcinoma,0,2	BRIP1	237	2	NM_032043	exon19	c.A2637G	p.E879E	CAAGGATTCCAGT	.	scavenged	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152640110	152640110	+	Missense_Mutation	SNP	G	G	A	rs2306914	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	90	8	107	0	0.0888889	0	G|0.962;A|0.038	0.038	strong	SYNE1_ENST00000423061,NS,carcinoma,+1,5	SYNE1	3227	5	NM_182961	exon85	c.C16277T	p.T5426M	TGGCTCGTGGCCT	.	PASS	Atlas-SNP
IQCF6	440956	hgsc.bcm.edu	37	3	51812952	51812952	+	Missense_Mutation	SNP	C	C	T	rs11130296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	75	5	72	0	0.0666667	0	C|0.837;T|0.163	0.163	strong	.	IQCF6	2	.	NM_001143833	exon2	c.G11A	p.R4Q	AACGTCCGGCGCA	.	PASS	Atlas-SNP
CMKLR1	1240	hgsc.bcm.edu	37	12	108686008	108686008	+	Silent	SNP	C	C	G	rs1057401	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	67	2	71	0	0.0298507	0	C|0.627;G|0.373	0.373	strong	CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	NM_001142344	exon3	c.G732C	p.V244V	TTTGCACACGATG	.	scavenged	Atlas-SNP
CELA3A	10136	hgsc.bcm.edu	37	1	22336308	22336308	+	Silent	SNP	G	G	A	rs12908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	184	4	214	0	0.0217391	0	G|0.745;A|0.255	0.255	strong	CELA3A,NS,carcinoma,+2,1	CELA3A	35	1	NM_005747	exon7	c.G753A	p.T251T	GCCCACGGTGTTC	.	scavenged	Atlas-SNP
ACTG1	71	hgsc.bcm.edu	37	17	79478007	79478007	+	Silent	SNP	G	G	A	rs1135989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	66	4	109	0	0.0606061	0	G|0.711;A|0.289	0.289	strong	.	ACTG1	55	.	NM_001614	exon5	c.C930T	p.A310A	CCTGTCGGCAATG	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31250830	31250830	+	Missense_Mutation	SNP	C	C	G	rs2911826	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	183	9	133	12	0.0491803	0.0902256	.	.	weak	DDX11,extremity,malignant_melanoma,0,1	DDX11	188	1	NM_030653	exon18	c.C1774G	p.Q592E	CTCAGTCAGAGCA	.	scavenged	Atlas-SNP
GUF1	60558	hgsc.bcm.edu	37	4	44682465	44682465	+	Missense_Mutation	SNP	T	T	C	rs6447368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	246	9	253	0	0.0365854	0	T|0.484;C|0.516	0.516	strong	GUF1,NS,carcinoma,0,1	GUF1	72	1	NM_021927	exon2	c.T173C	p.L58P	AAAAACTTGACAT	.	scavenged	Atlas-SNP
PLXNA3	55558	hgsc.bcm.edu	37	X	153692374	153692374	+	Missense_Mutation	SNP	G	G	A	rs150546014	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	110	5	82	0	0.0454545	0	G|0.997;A|0.003	0.003	strong	.	PLXNA3	156	.	NM_017514	exon7	c.G1628A	p.R543Q	AGGTGCGGGTCCG	.	PASS	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	37	18	14848820	14848820	+	Missense_Mutation	SNP	C	C	T	rs76917476	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	302	13	494	1	0.0430464	0.00202429	.	.	weak	ANKRD30B_ENST00000358984,NS,carcinoma,0,1	ANKRD30B	237	1	NM_001145029	exon34	c.C2930T	p.T977M	AACAAACGAAAAA	.	scavenged	Atlas-SNP
BAI3	577	hgsc.bcm.edu	37	6	70042873	70042873	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	134	41	151	0	0.30597	0	.	.	none	BAI3,NS,carcinoma,+1,2	BAI3	451	2	NM_001704	exon24	c.T3161C	p.L1054P	GAATCCTAGATAA	.	PASS	Atlas-SNP
ANKRD33	341405	hgsc.bcm.edu	37	12	52284586	52284586	+	Missense_Mutation	SNP	C	C	T	rs200291062	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	44	19	42	0	0.431818	0	.	.	weak	.	ANKRD33	33	.	NM_182608	exon5	c.C856T	p.R286W	CTAGAACGGCTGC	.	PASS	Atlas-SNP
ZNF573	126231	hgsc.bcm.edu	37	19	38229824	38229824	+	Missense_Mutation	SNP	T	T	C	rs3095726	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	62	4	66	0	0.0645161	0	T|0.180;C|0.820	0.820	strong	ZNF573,colon,carcinoma,0,1	ZNF573	63	1	NM_001172690	exon5	c.A1567G	p.M523V	GTTTCATACCAGT	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	63954304	63954304	+	Silent	SNP	T	T	C	rs1054891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	271	5	186	0	0.0184502	0	T|0.532;C|0.468	0.468	strong	DPY19L2,colon,carcinoma,0,1	DPY19L2	97	1	NM_173812	exon22	c.A2265G	p.L755L	AACCTTTAATACT	.	scavenged	Atlas-SNP
TLR3	7098	hgsc.bcm.edu	37	4	187004217	187004217	+	Silent	SNP	C	C	T	rs3775290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	198	9	178	1	0.0454545	0.00561798	C|0.727;T|0.273	0.273	strong	TLR3,caecum,carcinoma,0,1	TLR3	83	1	NM_003265	exon4	c.C1377T	p.F459F	TATTTTCGAAATC	.	scavenged	Atlas-SNP
LRP4	4038	hgsc.bcm.edu	37	11	46897446	46897446	+	Missense_Mutation	SNP	G	G	A	rs2306033	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	87	5	106	0	0.0574713	0	G|0.848;A|0.152	0.152	strong	.	LRP4	160	.	NM_002334	exon26	c.C3608T	p.A1203V	AGCACCGCGCGGT	.	PASS	Atlas-SNP
CPXM2	119587	hgsc.bcm.edu	37	10	125557598	125557598	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	100	29	99	0	0.29	0	.	.	none	.	CPXM2	120	.	NM_198148	exon6	c.G783A	p.E261E	GGGTAGCTCATTG	.	PASS	Atlas-SNP
PRDM1	639	hgsc.bcm.edu	37	6	106543518	106543518	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	61	30	123	0	0.491803	0	.	.	none	.	PRDM1	195	.	NM_001198	exon3	c.T320A	p.I107K	AATACATACCAAA	.	PASS	Atlas-SNP
TTC21A	199223	hgsc.bcm.edu	37	3	39161464	39161464	+	Missense_Mutation	SNP	G	G	A	rs1274971	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	186	9	226	0	0.0483871	0	G|0.552;A|0.448	0.448	strong	.	TTC21A	96	.	NM_145755	exon8	c.G877A	p.E293K	GAACCCGAAAATC	.	PASS	Atlas-SNP
PFN1	5216	hgsc.bcm.edu	37	17	4851557	4851557	+	Splice_Site	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	23	10	34	0	0.434783	0	.	.	none	.	PFN1	6	.	NM_005022	exon2	c.132+1G>A	.	GCAGTACCGTGAT	.	PASS	Atlas-SNP
TMEM171	134285	hgsc.bcm.edu	37	5	72419267	72419267	+	Missense_Mutation	SNP	T	T	C	rs638333	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	78	5	82	0	0.0641026	0	T|0.791;C|0.209	0.209	strong	.	TMEM171	41	.	NM_173490	exon2	c.T67C	p.F23L	CTCATCTTCTGCT	.	PASS	Atlas-SNP
CDH12	1010	hgsc.bcm.edu	37	5	21752056	21752056	+	Silent	SNP	A	A	G	rs6451993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	202	7	180	1	0.0346535	0.00555556	A|0.402;G|0.598	0.598	strong	CDH12,NS,carcinoma,0,1	CDH12	238	1	NM_004061	exon15	c.T2175C	p.D725D	ATCCACATCATTT	.	scavenged	Atlas-SNP
SHROOM1	134549	hgsc.bcm.edu	37	5	132159134	132159134	+	Silent	SNP	C	C	T	rs4705870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	66	5	68	0	0.0757576	0	C|0.888;T|0.112	0.112	strong	.	SHROOM1	35	.	NM_133456	exon6	c.G2034A	p.A678A	GGCCCACGCTTGT	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17083782	17083782	+	Missense_Mutation	SNP	A	A	C	rs200844502	byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	310	9	354	1	0.0290323	0.00282486	A|0.972;C|0.029	0.029	strong	Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	NM_001271733	exon15	c.T2015G	p.F672C	CGCGTGAAGACGG	.	scavenged	Atlas-SNP
KRT6A	3853	hgsc.bcm.edu	37	12	52885485	52885485	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	136	4	129	1	0.0294118	0.00775194	.	.	none	KRT6A,NS,haematopoietic_neoplasm,0,1	KRT6A	89	1	NM_005554	exon2	c.A576C	p.E192D	CTTTGTTTCCAGA	.	scavenged	Atlas-SNP
ZNF485	220992	hgsc.bcm.edu	37	10	44112245	44112245	+	Missense_Mutation	SNP	G	G	A	rs12354886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	105	5	108	0	0.047619	0	G|0.786;A|0.214	0.214	strong	.	ZNF485	102	.	NM_145312	exon5	c.G754A	p.A252T	GCCTTCGCTCAGA	.	PASS	Atlas-SNP
PDE4C	5143	hgsc.bcm.edu	37	19	18329240	18329240	+	Silent	SNP	T	T	C	rs1042050	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	83	5	100	0	0.060241	0	T|0.483;C|0.517	0.517	strong	PDE4C,NS,carcinoma,0,1	PDE4C	80	1	NM_000923	exon11	c.A1134G	p.E378E	GTGACCTTCCAGC	.	PASS	Atlas-SNP
AMBN	258	hgsc.bcm.edu	37	4	71468348	71468348	+	Missense_Mutation	SNP	G	G	T	rs199556863	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	381	17	303	0	0.0446194	0	.	.	weak	.	AMBN	73	.	NM_016519	exon7	c.G539T	p.G180V	TCCCAGGAGTAGA	.	PASS	Atlas-SNP
ANXA10	11199	hgsc.bcm.edu	37	4	169086441	169086441	+	Silent	SNP	A	A	G	rs4405979	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	223	6	263	0	0.0269058	0	A|0.421;G|0.579	0.579	strong	ANXA10,NS,carcinoma,0,1	ANXA10	44	1	NM_007193	exon6	c.A444G	p.S148S	GACCTCAGGACAC	.	scavenged	Atlas-SNP
B4GALNT4	338707	hgsc.bcm.edu	37	11	372700	372700	+	Silent	SNP	G	G	C	rs35475866	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	41	5	60	0	0.121951	0	G|0.714;C|0.286	0.286	strong	B4GALNT4,rectum,carcinoma,0,1	B4GALNT4	83	1	NM_178537	exon3	c.G294C	p.G98G	TGGGGGGGCTGGG	.	PASS	Atlas-SNP
AMACR	23600	hgsc.bcm.edu	37	5	34004707	34004707	+	Missense_Mutation	SNP	C	C	T	rs10941112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	324	15	345	0	0.0462963	0	C|0.655;T|0.345	0.345	strong	.	AMACR	38	.	NM_014324	exon3	c.G524A	p.G175D	CCCTTGCCAGTGC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1046827	1046827	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	23	6	23	0	0.26087	0	.	.	none	.	ABCA7	174	.	NM_019112	exon14	c.T1649C	p.L550P	GGTCGCTGCCGCT	.	PASS	Atlas-SNP
SNX13	23161	hgsc.bcm.edu	37	7	17879484	17879484	+	Silent	SNP	T	T	C	rs35507251	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	119	5	138	0	0.0420168	0	T|0.975;C|0.025	0.025	strong	.	SNX13	113	.	NM_015132	exon13	c.A1305G	p.K435K	AAGACCTTTGGTT	.	PASS	Atlas-SNP
AKR1B15	441282	hgsc.bcm.edu	37	7	134264286	134264286	+	Silent	SNP	C	C	T	rs6467538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	77	8	62	0	0.103896	0	C|0.651;T|0.349	0.349	strong	.	AKR1B15	105	.	NM_001080538	exon12	c.C1020T	p.F340F	TCCCTTCGATGCA	.	PASS	Atlas-SNP
SEMA3C	10512	hgsc.bcm.edu	37	7	80433481	80433481	+	Missense_Mutation	SNP	G	G	T	rs143347984		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	147	48	93	0	0.326531	0	G|1.000;T|0.000	0.000	weak	.	SEMA3C	106	.	NM_006379	exon8	c.C742A	p.L248M	CAGTCAGTTTTTC	.	PASS	Atlas-SNP
ZNF286B	729288	hgsc.bcm.edu	37	17	18565423	18565423	+	Missense_Mutation	SNP	G	G	A	rs9912852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	215	5	211	0	0.0232558	0	G|0.698;A|0.302	0.302	strong	ZNF286B_ENST00000545289,colon,carcinoma,+2,2	ZNF286B	75	2	NM_001145045	exon5	c.C1396T	p.P466S	TGTACGGTTTCTT	.	scavenged	Atlas-SNP
INO80D	54891	hgsc.bcm.edu	37	2	206882530	206882530	+	Silent	SNP	G	G	C	rs41272653	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	152	9	166	0	0.0592105	0	G|0.978;C|0.022	0.022	strong	.	INO80D	134	.	NM_017759	exon8	c.C1416G	p.L472L	GTTCAAGAGGATA	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	132070054	132070054	+	Missense_Mutation	SNP	T	T	C	rs741664	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	60	5	47	0	0.0833333	0	C|0.318;N|0.000	0.318	strong	.	PLXNA4	873	.	NM_001105543	exon4	c.A1372G	p.M458V	CAGGCATCTGGAA	.	PASS	Atlas-SNP
SOX17	64321	hgsc.bcm.edu	37	8	55372347	55372347	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	18	9	32	0	0.5	0	.	.	none	.	SOX17	37	.	NM_022454	exon2	c.C1037T	p.T346M	ACGGCACGGACCC	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49751585	49751585	+	Silent	SNP	C	C	T	rs2291542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	64	4	76	0	0.0625	0	C|0.736;T|0.264	0.264	strong	RNF123,caecum,carcinoma,0,1	RNF123	100	1	NM_022064	exon31	c.C2988T	p.D996D	TGAGGACGCCAAT	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14846036	14846036	+	Missense_Mutation	SNP	C	C	G	rs2779500	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	178	3	170	1	0.0168539	0.00588235	C|0.496;G|0.504	0.504	strong	FREM1,NS,carcinoma,0,1	FREM1	261	1	NM_144966	exon9	c.G1315C	p.V439L	CGACAACCTGAAA	.	scavenged	Atlas-SNP
SCN3A	6328	hgsc.bcm.edu	37	2	165987772	165987772	+	Silent	SNP	T	T	G	rs62174900	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	278	16	191	0	0.057554	0	T|0.828;G|0.172	0.172	strong	.	SCN3A	544	.	NM_006922	exon16	c.A2547C	p.V849V	TCGCAGTACAGAC	.	PASS	Atlas-SNP
ATG14	22863	hgsc.bcm.edu	37	14	55864130	55864130	+	Silent	SNP	A	A	G	rs8003279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	128	8	148	0	0.0625	0	A|0.760;G|0.240	0.240	strong	.	ATG14	36	.	NM_014924	exon2	c.T244C	p.L82L	GGCTTAACCTTTC	.	PASS	Atlas-SNP
VEZT	55591	hgsc.bcm.edu	37	12	95660182	95660182	+	Missense_Mutation	SNP	A	A	G	rs17855933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	97	5	98	0	0.0515464	0	A|0.925;G|0.075	0.075	strong	.	VEZT	106	.	NM_017599	exon5	c.A484G	p.T162A	CTTCCCACTTGGT	.	PASS	Atlas-SNP
TPO	7173	hgsc.bcm.edu	37	2	1459995	1459995	+	Missense_Mutation	SNP	G	G	A	rs371917329		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	96	36	129	0	0.375	0	.	.	weak	TPO,NS,carcinoma,-2,1	TPO	224	1	NM_175719	exon7	c.G760A	p.G254R	GCCTTCGGGGGAG	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	76990178	76990178	+	Silent	SNP	C	C	G	rs4727366	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	165	3	133	0	0.0181818	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	.	scavenged	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1417994	1417994	+	Silent	SNP	G	G	A	rs142344235	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	308	6	363	1	0.0194805	0.00275482	G|0.999;A|0.001	0.001	strong	ATAD3B_ENST00000378741,NS,carcinoma,+1,2	ATAD3B	68	2	NM_031921	exon7	c.G750A	p.T250T	AGCCACGGTAAAC	.	scavenged	Atlas-SNP
CFHR1	3078	hgsc.bcm.edu	37	1	196801042	196801042	+	Silent	SNP	G	G	T	rs4230	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	309	12	346	0	0.038835	0	G|0.519;T|0.481	0.481	strong	CFHR1,right_upper_lobe,carcinoma,+1,2	CFHR1	47	2	NM_002113	exon6	c.G906T	p.R302R	TAAACGGGGATAT	.	scavenged	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3240343	3240343	+	Missense_Mutation	SNP	G	G	A	rs1635246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	138	6	82	0	0.0434783	0	G|0.441;A|0.559	0.559	strong	.	MXRA5	815	.	NM_015419	exon5	c.C3383T	p.A1128V	GTTGTTGCTGTTG	.	PASS	Atlas-SNP
PLEKHA8	84725	hgsc.bcm.edu	37	7	30113706	30113706	+	Silent	SNP	A	A	G	rs11977829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	180	6	140	0	0.0333333	0	A|0.748;G|0.252	0.252	strong	PLEKHA8_ENST00000449726,NS,carcinoma,0,2	PLEKHA8	68	2	NM_001197027	exon13	c.A1320G	p.T440T	TAAAACATTGCGG	.	scavenged	Atlas-SNP
MLLT3	4300	hgsc.bcm.edu	37	9	20414310	20414310	+	Silent	SNP	A	A	G	rs148318848	bycluster	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	68	7	50	3	0.102941	0.06	.	.	weak	MLLT3,caecum,carcinoma,0,1	MLLT3	125	1	NM_004529	exon5	c.T534C	p.S178S	GCTGCTACTGCTG	.	scavenged	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183752964	183752964	+	Silent	SNP	A	A	C	rs77099580	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	71	5	92	0	0.0704225	0	A|0.974;C|0.026	0.026	strong	.	HTR3D	65	.	NM_001163646	exon2	c.A238C	p.R80R	TATTCCAGGATTC	.	PASS	Atlas-SNP
HERC1	8925	hgsc.bcm.edu	37	15	63922752	63922752	+	Silent	SNP	T	T	A	rs10851731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	128	6	128	0	0.046875	0	T|0.342;A|0.658	0.658	strong	HERC1_ENST00000443617,NS,carcinoma,0,1	HERC1	624	1	NM_003922	exon69	c.A12879T	p.I4293I	ATCTTCTATGATT	.	PASS	Atlas-SNP
GRHL3	57822	hgsc.bcm.edu	37	1	24668667	24668667	+	Silent	SNP	C	C	G	rs11576645	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	120	5	126	0	0.0416667	0	C|0.832;G|0.168	0.168	strong	.	GRHL3	69	.	NM_021180	exon9	c.C1125G	p.V375V	GGGTGTCCCCCTG	.	PASS	Atlas-SNP
SLC25A26	115286	hgsc.bcm.edu	37	3	66293688	66293688	+	Silent	SNP	A	A	G	rs3772197	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	79	3	93	0	0.0379747	0	A|0.941;G|0.059	0.059	strong	SLC25A26,NS,carcinoma,0,1	SLC25A26	12	1	NM_173471	exon4	c.A252G	p.S84S	ATCTTCATATTTG	.	scavenged	Atlas-SNP
CES5A	221223	hgsc.bcm.edu	37	16	55890347	55890347	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	60	42	48	0	0.7	0	.	.	none	.	CES5A	206	.	NM_001190158	exon10	c.C1154T	p.P385L	ATCTCAGGAGCCT	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25052261	25052261	+	Silent	SNP	C	C	T	rs4770696	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	102	3	101	3	0.0294118	0.029703	C|0.494;T|0.506	0.506	strong	PARP4,mouth,carcinoma,-1,1	PARP4	142	1	NM_006437	exon13	c.G1602A	p.S534S	TGTTTGCGAAACT	.	scavenged	Atlas-SNP
IHH	3549	hgsc.bcm.edu	37	2	219920412	219920412	+	Silent	SNP	A	A	G	rs3731881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	97	10	93	0	0.103093	0	A|0.454;G|0.546	0.546	strong	.	IHH	33	.	NM_002181	exon3	c.T753C	p.P251P	CCTGTGAGGCTCG	.	PASS	Atlas-SNP
CCDC6	8030	hgsc.bcm.edu	37	10	61552774	61552774	+	Silent	SNP	C	C	T	rs1053265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	75	3	86	0	0.04	0	C|0.350;T|0.650	0.650	strong	CCDC6,caecum,carcinoma,0,2	CCDC6	44	2	NM_005436	exon9	c.G1326A	p.P442P	TGGAGGCGGAGGT	.	scavenged	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801559	185801559	+	Missense_Mutation	SNP	A	A	G	rs35676856	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	317	9	292	0	0.0283912	0	A|0.947;G|0.053	0.053	strong	ZNF804A,NS,carcinoma,+1,1	ZNF804A	322	1	NM_194250	exon4	c.A1436G	p.D479G	AGCCAGACTTAAA	.	scavenged	Atlas-SNP
SMC2	10592	hgsc.bcm.edu	37	9	106889642	106889642	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	377	5	349	0	0.0132626	0	.	.	none	SMC2L1,NS,carcinoma,0,2	SMC2	127	2	NM_006444	exon20	c.G2671T	p.A891S	ATTAAAGCTAAAT	.	scavenged	Atlas-SNP
EVPLL	645027	hgsc.bcm.edu	37	17	18291559	18291559	+	Silent	SNP	T	T	C	rs9890369	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	545	7	687	4	0.012844	0.00582242	T|0.770;C|0.230	0.230	strong	EVPLL,NS,NS,+2,1	EVPLL	10	1	NM_001145127	exon10	c.T903C	p.H301H	TCCTCATTGACTC	.	scavenged	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26462790	26462790	+	Silent	SNP	G	G	A	rs3740232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	176	3	152	0	0.0170455	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	.	scavenged	Atlas-SNP
CKAP2	26586	hgsc.bcm.edu	37	13	53047966	53047966	+	Missense_Mutation	SNP	G	G	A	rs41292820	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	182	8	184	0	0.043956	0	G|0.996;A|0.004	0.004	strong	.	CKAP2	51	.	NM_001098525	exon8	c.G1552A	p.E518K	ATAGGAGAAAATA	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159653635	159653635	+	Silent	SNP	C	C	G	rs381639	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	63	4	69	0	0.0634921	0	C|0.423;G|0.577	0.577	strong	.	FNDC1	250	.	NM_032532	exon11	c.C2091G	p.A697A	GCCGGCCCGGAGG	.	PASS	Atlas-SNP
MAT2A	4144	hgsc.bcm.edu	37	2	85769711	85769711	+	Silent	SNP	C	C	G	rs1078004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	161	5	173	0	0.0310559	0	C|0.483;G|0.517	0.517	strong	MAT2A,NS,carcinoma,0,1	MAT2A	23	1	NM_005911	exon7	c.C792G	p.R264R	TGGACGCAAAATC	.	scavenged	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862984	5862984	+	Missense_Mutation	SNP	G	G	C	rs10769272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	124	5	135	0	0.0403226	0	G|0.607;C|0.393	0.393	strong	OR52E6,NS,carcinoma,0,1	OR52E6	70	1	NM_001005167	exon1	c.C144G	p.F48L	CACAAAGAAGATA	.	PASS	Atlas-SNP
ERBB3	2065	hgsc.bcm.edu	37	12	56494991	56494991	+	Silent	SNP	G	G	A	rs2271189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	92	7	92	0	0.076087	0	G|0.703;A|0.297	0.297	strong	.	ERBB3	350	.	NM_001982	exon27	c.G3348A	p.R1116R	GTGTAGGAGCCGG	.	PASS	Atlas-SNP
OR51S1	119692	hgsc.bcm.edu	37	11	4869649	4869649	+	Missense_Mutation	SNP	G	G	A	rs12361955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	119	3	124	0	0.0252101	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	.	scavenged	Atlas-SNP
STPG2	285555	hgsc.bcm.edu	37	4	98893476	98893476	+	Silent	SNP	C	C	T	rs783959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	331	8	400	1	0.0241692	0.0025	C|0.581;T|0.419	0.419	strong	C4orf37,NS,carcinoma,0,2	.	.	2	NM_174952	exon7	c.G888A	p.S296S	CTGAACCGAGAAG	.	scavenged	Atlas-SNP
UGT2B28	54490	hgsc.bcm.edu	37	4	70160277	70160277	+	Missense_Mutation	SNP	T	T	G	rs6843900	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	130	5	106	0	0.0384615	0	T|0.630;G|0.370	0.370	strong	UGT2B28,NS,carcinoma,0,1	UGT2B28	101	1	NM_053039	exon6	c.T1340G	p.I447R	TATCAATAATTCA	.	scavenged	Atlas-SNP
DEPDC4	120863	hgsc.bcm.edu	37	12	100657658	100657658	+	Silent	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	313	4	319	1	0.0127796	0.0031348	.	.	none	DEPDC4,NS,malignant_melanoma,-2,1	DEPDC4	34	1	NM_152317	exon2	c.T171C	p.P57P	TTGAAAAGGACCA	.	scavenged	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263442	263442	+	Missense_Mutation	SNP	G	G	A	rs200834723		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	351	4	436	2	0.011396	0.00458716	.	.	weak	C17orf97,extremity,malignant_melanoma,0,1	C17orf97	76	1	NM_001013672	exon2	c.G808A	p.E270K	GACCCTGAGGCCC	.	scavenged	Atlas-SNP
QSOX1	5768	hgsc.bcm.edu	37	1	180148012	180148012	+	Missense_Mutation	SNP	G	G	C	rs17855475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	89	6	106	0	0.0674157	0	G|0.866;C|0.134	0.134	strong	.	QSOX1	79	.	NM_002826	exon5	c.G599C	p.G200A	ACCTGGGTAGAGA	.	PASS	Atlas-SNP
INTS3	65123	hgsc.bcm.edu	37	1	153719461	153719461	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	100	34	105	0	0.34	0	.	.	none	.	INTS3	83	.	NM_023015	exon4	c.G347A	p.R116H	TGAGTCGTGATGG	.	PASS	Atlas-SNP
CALU	813	hgsc.bcm.edu	37	7	128394606	128394606	+	Missense_Mutation	SNP	C	C	T	rs2307040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	336	4	193	0	0.0119048	0	C|0.785;T|0.215	0.215	strong	CALU_ENST00000542996,NS,carcinoma,0,1	CALU	42	1	NM_001199672	exon4	c.C269T	p.A90V	TAGACGCGGATAA	.	scavenged	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72412427	72412427	+	Missense_Mutation	SNP	G	G	A	rs2429277		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	415	37	362	21	0.0891566	0.0580111	.	.	weak	POM121,NS,malignant_melanoma,0,2	POM121	131	2	NM_172020	exon11	c.G1100A	p.S367N	CACCCAGCCTCCT	.	scavenged	Atlas-SNP
C2orf71	388939	hgsc.bcm.edu	37	2	29296870	29296870	+	Silent	SNP	C	C	T	rs62132765	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	183	5	174	1	0.0273224	0.00574713	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
EFEMP2	30008	hgsc.bcm.edu	37	11	65638719	65638719	+	Silent	SNP	G	G	A	rs633800	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	133	7	123	0	0.0526316	0	G|0.642;A|0.358	0.358	strong	.	EFEMP2	42	.	NM_016938	exon4	c.C276T	p.H92H	CTCGCCGTGTAGG	.	PASS	Atlas-SNP
LGMN	5641	hgsc.bcm.edu	37	14	93171022	93171022	+	Silent	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	125	8	119	0	0.064	0	.	.	none	.	LGMN	28	.	NM_005606	exon13	c.C1222T	p.L408L	TGACCAGCACGTA	.	PASS	Atlas-SNP
OPRK1	4986	hgsc.bcm.edu	37	8	54142312	54142312	+	Missense_Mutation	SNP	C	C	T	rs186551684	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	122	41	125	0	0.336066	0	C|1.000;T|0.000	0.000	strong	OPRK1,colon,carcinoma,0,1	OPRK1	90	1	NM_000912	exon4	c.G688A	p.V230I	TGAAGACGCAGAT	.	PASS	Atlas-SNP
NANOG	79923	hgsc.bcm.edu	37	12	7945559	7945559	+	Silent	SNP	T	T	C	rs4294629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	464	6	394	0	0.012931	0	T|0.548;C|0.452	0.452	strong	NANOG,NS,malignant_melanoma,+2,1	NANOG	30	1	NM_024865	exon2	c.T165C	p.P55P	TCTTCCTTCCTCC	.	scavenged	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2583328	2583328	+	Silent	SNP	C	C	T	rs61753095	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	177	5	141	1	0.0282486	0.0070922	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	.	scavenged	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161132146	161132146	+	Silent	SNP	C	C	T	rs4757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	220	10	192	0	0.0454545	0	C|0.671;T|0.329	0.329	strong	.	PLG	150	.	NM_001168338	exon4	c.C330T	p.N110N	AAAGAACTACAGA	.	PASS	Atlas-SNP
WDR43	23160	hgsc.bcm.edu	37	2	29152456	29152456	+	Silent	SNP	A	A	G	rs1140697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	318	12	283	1	0.0377358	0.00353357	A|0.564;G|0.436	0.436	strong	WDR43,NS,carcinoma,+2,1	WDR43	38	1	NM_015131	exon11	c.A1317G	p.E439E	CATTGAAGAACGT	.	scavenged	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72130815	72130815	+	Silent	SNP	C	C	A	rs1050362	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	130	5	124	0	0.0384615	0	C|0.529;A|0.471	0.471	strong	DHX38,right_upper_lobe,carcinoma,-2,2	DHX38	91	2	NM_014003	exon3	c.C418A	p.R140R	GAGCGGCGGGAAC	.	scavenged	Atlas-SNP
ARID3B	10620	hgsc.bcm.edu	37	15	74836319	74836319	+	Silent	SNP	A	A	G	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	92	9	100	5	0.0978261	0.05	.	.	none	ARID3B,right_lower_lobe,carcinoma,0,1	ARID3B	35	1	NM_006465	exon2	c.A42G	p.Q14Q	GCAACAACAGAAG	.	scavenged	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44417575	44417575	+	Silent	SNP	A	A	G	rs417699	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	63	6	59	0	0.0952381	0	A|0.474;G|0.526	0.526	strong	ZNF45,NS,carcinoma,-2,2	ZNF45	51	2	NM_003425	exon10	c.T2013C	p.F671F	TGAAGGAAAGTCC	.	PASS	Atlas-SNP
TCF3	6929	hgsc.bcm.edu	37	19	1646364	1646364	+	Silent	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	145	6	204	0	0.0413793	0	.	.	none	.	TCF3	72	.	NM_003200	exon3	c.C135T	p.F45F	ACCTCCGAACTGC	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239501	31239501	+	Missense_Mutation	SNP	G	G	T	rs1050409	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	179	4	203	0	0.0223464	0	T|0.136;G|0.864	0.136	strong	HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	NM_002117	exon2	c.C218A	p.A73E	CACGGCGCCCGCG	.	scavenged	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	48	9	70	0	0.1875	0	.	.	none	SPRR3,colon,carcinoma,0,3	SPRR3	45	3	NM_001097589	exon2	c.C219T	p.G73G	GCCAGGCTGTACC	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30765502	30765502	+	Silent	SNP	G	G	A	rs5749080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	51	5	45	0	0.0980392	0	A|0.198;C|0.000;G|0.802	0.198	strong	.	CCDC157	86	.	NM_001017437	exon4	c.G330A	p.A110A	GGCTGCGGGGCCC	.	PASS	Atlas-SNP
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709691	31709691	+	Missense_Mutation	SNP	G	G	A	rs2244485	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	131	4	160	0	0.0305344	0	G|0.654;A|0.346	0.346	strong	KRTAP27-1,NS,carcinoma,-1,1	KRTAP27-1	53	1	NM_001077711	exon1	c.C296T	p.A99V	TGGCACGCTGTCC	.	scavenged	Atlas-SNP
SALL2	6297	hgsc.bcm.edu	37	14	21991626	21991626	+	Missense_Mutation	SNP	C	C	G	rs1263810	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	54	4	53	0	0.0740741	0	C|0.711;G|0.289	0.289	strong	.	SALL2	95	.	NM_005407	exon2	c.G2236C	p.G746R	AACTCCCTGCCCC	.	PASS	Atlas-SNP
SLC38A6	145389	hgsc.bcm.edu	37	14	61550378	61550378	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	24	15	47	0	0.625	0	.	.	none	.	SLC38A6	87	.	NM_001172702	exon17	c.G1514A	p.R505H	CCAAACGTGTCCA	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141756637	141756637	+	Silent	SNP	G	G	A	rs181422456	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	69	15	58	0	0.217391	0	G|1.000;A|0.000	0.000	strong	.	MGAM	767	.	NM_004668	exon30	c.G3588A	p.T1196T	TGTGACGTTCCAG	.	PASS	Atlas-SNP
TROAP	10024	hgsc.bcm.edu	37	12	49723963	49723963	+	Silent	SNP	A	A	G	rs4243545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	183	7	189	1	0.0382514	0.00529101	A|0.789;G|0.211	0.211	strong	TROAP,NS,carcinoma,0,1	TROAP	80	1	NM_005480	exon13	c.A1335G	p.E445E	ACAGGAAGTAGAG	.	scavenged	Atlas-SNP
ZNF585A	199704	hgsc.bcm.edu	37	19	37642917	37642917	+	Silent	SNP	G	G	A	rs77675231	bycluster;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	234	15	264	0	0.0641026	0	G|0.497;A|0.503	0.503	strong	.	ZNF585A	117	.	NM_199126	exon6	c.C1719T	p.H573H	TCCTGTGTGAACT	.	PASS	Atlas-SNP
GUCA1C	9626	hgsc.bcm.edu	37	3	108639423	108639423	+	Missense_Mutation	SNP	C	C	T	rs2715687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	252	11	264	0	0.0436508	0	C|0.337;T|0.662	0.662	strong	.	GUCA1C	39	.	NM_005459	exon2	c.G214A	p.V72I	AGTCAACAAATCC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9090531	9090531	+	Silent	SNP	T	T	C	rs12976721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	78	3	110	1	0.0384615	0.00909091	T|0.772;C|0.228	0.228	strong	MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	NM_024690	exon1	c.A1284G	p.E428E	TTCTGTTTCCTTT	.	scavenged	Atlas-SNP
THBS3	7059	hgsc.bcm.edu	37	1	155172725	155172725	+	Missense_Mutation	SNP	T	T	C	rs35154152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	74	6	67	0	0.0810811	0	T|0.857;C|0.143	0.143	strong	.	THBS3	70	.	NM_007112	exon8	c.A835G	p.S279G	TGGGGCTGCAGTG	.	PASS	Atlas-SNP
RPTN	126638	hgsc.bcm.edu	37	1	152127455	152127455	+	Missense_Mutation	SNP	T	T	C	rs75957773	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	67	4	87	1	0.0597015	0.0114943	T|0.884;C|0.116	0.116	strong	RPTN,NS,carcinoma,0,1	RPTN	123	1	NM_001122965	exon3	c.A2120G	p.E707G	TGCTCTTCCTCTG	.	scavenged	Atlas-SNP
PLEK	5341	hgsc.bcm.edu	37	2	68592512	68592512	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	91	25	77	0	0.274725	0	.	.	none	.	PLEK	64	.	NM_002664	exon1	c.A29T	p.Y10F	AGGGCTACCTTGT	.	PASS	Atlas-SNP
ATR	545	hgsc.bcm.edu	37	3	142277575	142277575	+	Silent	SNP	A	A	T	rs2227930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	279	11	265	2	0.0394265	0.00754717	A|0.359;T|0.641	0.641	strong	ATR,NS,carcinoma,0,1	ATR	285	1	NM_001184	exon8	c.T1776A	p.G592G	GAGCATACCACAT	.	scavenged	Atlas-SNP
PLEKHG6	55200	hgsc.bcm.edu	37	12	6427052	6427052	+	Silent	SNP	C	C	T	rs1468603	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	124	11	125	0	0.0887097	0	C|0.580;T|0.420	0.420	strong	.	PLEKHG6	62	.	NM_001144856	exon10	c.C1047T	p.H349H	GCGACACATCAAT	.	PASS	Atlas-SNP
BCL6	604	hgsc.bcm.edu	37	3	187443314	187443314	+	Silent	SNP	G	G	A	rs61732778	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	67	3	77	0	0.0447761	0	G|0.930;A|0.070	0.070	strong	BCL6,caecum,carcinoma,0,1	BCL6	107	1	NM_001706	exon8	c.C1812T	p.C604C	GGTTTCGCATTTG	.	scavenged	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47545826	47545826	+	Silent	SNP	C	C	T	rs13046639	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	119	6	185	0	0.0504202	0	C|0.584;T|0.416	0.416	strong	.	COL6A2	351	.	NM_058175	exon26	c.C2097T	p.G699G	TGCGGGCGGCACC	.	PASS	Atlas-SNP
HOXD11	3237	hgsc.bcm.edu	37	2	176972104	176972104	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	124	34	100	0	0.274194	0	.	.	none	.	HOXD11	26	.	NM_021192	exon1	c.C21T	p.C7C	CGAGTGCGGCCAG	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77690572	77690572	+	Silent	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	80	29	74	0	0.3625	0	.	.	none	.	ZFHX4	878	.	NM_024721	exon4	c.T3222C	p.T1074T	GCAGACTGAGGGC	.	PASS	Atlas-SNP
NXPE3	91775	hgsc.bcm.edu	37	3	101540387	101540387	+	Missense_Mutation	SNP	T	T	G	rs35598292	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	96	4	116	0	0.0416667	0	T|0.974;G|0.026	0.026	strong	.	.	.	.	NM_145037	exon8	c.T1269G	p.H423Q	GCTCCATTATGTG	.	PASS	Atlas-SNP
TEKT4	150483	hgsc.bcm.edu	37	2	95542418	95542418	+	Silent	SNP	T	T	C	rs3209453	alternate_allele	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	32	6	33	1	0.1875	0.030303	.	.	alt	TEKT4,NS,neuroblastoma,0,1	TEKT4	72	1	NM_144705	exon6	c.T1212C	p.I404I	GGACATTGCCGCC	.	scavenged	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	162	6	139	0	0.037037	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	.	scavenged	Atlas-SNP
NWD1	284434	hgsc.bcm.edu	37	19	16860860	16860860	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	82	22	84	0	0.268293	0	.	.	none	NWD1_ENST00000524140,NS,neuroblastoma,+2,2	NWD1	303	2	NM_001007525	exon6	c.C1407T	p.C469C	AGCTTGCTCGGGG	.	PASS	Atlas-SNP
CHRNA3	1136	hgsc.bcm.edu	37	15	78894447	78894447	+	Silent	SNP	G	G	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	107	38	123	0	0.35514	0	.	.	none	.	CHRNA3	56	.	NM_000743	exon5	c.C537T	p.S179S	GGACCAGGAACCG	.	PASS	Atlas-SNP
TAS2R38	5726	hgsc.bcm.edu	37	7	141672705	141672705	+	Missense_Mutation	SNP	G	G	A	rs1726866	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	175	8	154	0	0.0457143	0	G|0.560;A|0.440	0.440	strong	TAS2R38,NS,carcinoma,-1,2	TAS2R38	51	2	NM_176817	exon1	c.C785T	p.A262V	AAGGCAGCACAGG	.	PASS	Atlas-SNP
PNPO	55163	hgsc.bcm.edu	37	17	46020698	46020698	+	Silent	SNP	C	C	T	rs11079804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	88	3	115	0	0.0340909	0	C|0.855;T|0.145	0.145	strong	PNPO,NS,adenoma,0,1	PNPO	18	1	NM_018129	exon2	c.C165T	p.S55S	GACCTCCCTTGAC	.	scavenged	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	37	2	241696843	241696843	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	88	6	84	0	0.0681818	0	.	.	none	.	KIF1A	152	.	NM_001244008	exon27	c.G2751T	p.E917D	CTCATCCTCCTCC	.	PASS	Atlas-SNP
DGCR2	9993	hgsc.bcm.edu	37	22	19026613	19026613	+	Missense_Mutation	SNP	A	A	G	rs2072123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	94	5	122	0	0.0531915	0	T|0.004;G|0.408	0.408	strong	.	DGCR2	45	.	NM_005137	exon10	c.T1418C	p.V473A	ACCTCCACAGGCT	.	PASS	Atlas-SNP
OPTN	10133	hgsc.bcm.edu	37	10	13152400	13152400	+	Missense_Mutation	SNP	T	T	A	rs11258194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	145	4	248	2	0.0275862	0.00806452	T|0.937;A|0.063	0.063	strong	OPTN,NS,carcinoma,-1,1	OPTN	57	1	NM_001008212	exon4	c.T293A	p.M98K	GTCTAATGGCCTT	.	scavenged	Atlas-SNP
GLT6D1	360203	hgsc.bcm.edu	37	9	138516128	138516128	+	Missense_Mutation	SNP	C	C	T	rs61739510	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	86	4	86	0	0.0465116	0	C|0.947;T|0.053	0.053	strong	.	GLT6D1	56	.	NM_182974	exon5	c.G646A	p.A216T	TGCAAGCTGCTGA	.	PASS	Atlas-SNP
PCDHGA2	56113	hgsc.bcm.edu	37	5	140720954	140720954	+	Missense_Mutation	SNP	T	T	C	rs66823521	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	225	5	276	1	0.0222222	0.00362319	T|0.910;C|0.090	0.090	strong	PCDHG_cluster,NS,carcinoma,-2,2	PCDHGA2	205	2	NM_018915	exon1	c.T2416C	p.F806L	GAAACGTTTTCTC	.	scavenged	Atlas-SNP
MYT1	4661	hgsc.bcm.edu	37	20	62839368	62839368	+	Missense_Mutation	SNP	G	G	T	rs369047925	alternate_allele	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	22	4	28	0	0.181818	0	.	.	alt	MYT1,NS,carcinoma,0,1	MYT1	152	1	NM_004535	exon7	c.G819T	p.E273D	GGAGGAGGATGAA	.	scavenged	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27374180	27374180	+	Missense_Mutation	SNP	T	T	C	rs1805015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	61	4	57	2	0.0655738	0.0350877	T|0.773;C|0.227	0.227	strong	IL4R,colon,carcinoma,0,1	IL4R	70	1	NM_000418	exon11	c.T1507C	p.S503P	AGCAACTCCCTGA	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	158	5	163	0	0.0316456	0	A|0.732;G|0.268	0.268	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_001271208	exon116	c.T18294C	p.Y6098Y	GTTAGGATAGTTT	.	scavenged	Atlas-SNP
MOCS3	27304	hgsc.bcm.edu	37	20	49575719	49575719	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	51	17	62	0	0.333333	0	.	.	none	.	MOCS3	44	.	NM_014484	exon1	c.T340A	p.Y114N	GTGGACTATGACG	.	PASS	Atlas-SNP
FAM214A	56204	hgsc.bcm.edu	37	15	52901977	52901977	+	Silent	SNP	G	G	A	rs2414166	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	54	5	51	1	0.0925926	0.0196078	G|0.561;A|0.439	0.439	strong	KIAA1370,NS,carcinoma,0,1	.	.	1	NM_019600	exon6	c.C1134T	p.A378A	ATGTTGGGCAATT	.	scavenged	Atlas-SNP
ALG10B	144245	hgsc.bcm.edu	37	12	38715000	38715000	+	Silent	SNP	A	A	G	rs35518352	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	386	4	359	1	0.0103627	0.00278552	A|0.664;G|0.336	0.336	strong	ALG10B,colon,carcinoma,0,1	ALG10B	58	1	NM_001013620	exon3	c.A1407G	p.Q469Q	CATTCAAAGGTTT	.	scavenged	Atlas-SNP
CYP4A11	1579	hgsc.bcm.edu	37	1	47395874	47395874	+	Missense_Mutation	SNP	A	A	C	rs45475502		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	134	5	158	5	0.0373134	0.0316456	.	.	weak	CYP4A11,NS,carcinoma,0,1	CYP4A11	77	1	NM_000778	exon12	c.T1473G	p.I491M	TCGTGCAATGGGG	.	scavenged	Atlas-SNP
DIEXF	27042	hgsc.bcm.edu	37	1	210004199	210004199	+	Missense_Mutation	SNP	C	C	G	rs585627	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	206	5	295	0	0.0242718	0	C|0.331;G|0.669	0.669	strong	DIEXF,colon,carcinoma,0,1	DIEXF	97	1	NM_014388	exon3	c.C199G	p.Q67E	GAACCACAACAAG	.	scavenged	Atlas-SNP
NUFIP2	57532	hgsc.bcm.edu	37	17	27613677	27613677	+	Silent	SNP	G	G	A	rs12452857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	108	7	91	0	0.0648148	0	G|0.815;A|0.185	0.185	strong	.	NUFIP2	60	.	NM_020772	exon2	c.C1335T	p.P445P	AGAGATGGGTGTT	.	PASS	Atlas-SNP
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100452832	100452832	+	Silent	SNP	C	C	T	rs11832216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	154	6	148	2	0.038961	0.0135135	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	.	scavenged	Atlas-SNP
S100A7A	338324	hgsc.bcm.edu	37	1	153391729	153391729	+	Missense_Mutation	SNP	G	G	A	rs56232841		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	289	5	277	0	0.017301	0	.	.	weak	S100A7A,rectum,carcinoma,0,2	S100A7A	24	2	NM_176823	exon3	c.G250A	p.A84T	ATAGCCGCAGACT	.	scavenged	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224294	248224294	+	Missense_Mutation	SNP	C	C	T	rs6658256	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	83	4	105	0	0.0481928	0	C|0.712;T|0.288	0.288	strong	.	OR2L3	97	.	NM_001004687	exon1	c.C311T	p.S104L	TCTTCTCGGCATT	.	PASS	Atlas-SNP
PPYR1	5540	hgsc.bcm.edu	37	10	47087299	47087299	+	Silent	SNP	G	G	C	rs140965359	byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	81	7	103	0	0.0864198	0	G|0.998;C|0.002	0.002	strong	.	PPYR1	54	.	NM_005972	exon3	c.G516C	p.L172L	CTCCCTGCCCTTC	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	37	3	113376116	113376116	+	Silent	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	28	10	36	0	0.357143	0	.	.	none	.	KIAA2018	180	.	NM_001009899	exon7	c.G4413A	p.Q1471Q	TTGCTGCTGCTGC	.	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-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	307	13	297	0	0.0423453	0	T|0.647;C|0.353	0.353	strong	.	GUCA1C	39	.	NM_005459	exon2	c.A253G	p.M85V	CTTGCATGATTAG	.	PASS	Atlas-SNP
CAMKV	79012	hgsc.bcm.edu	37	3	49898273	49898273	+	Silent	SNP	A	A	G	rs2681781	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	68	4	97	0	0.0588235	0	A|0.515;G|0.485	0.485	strong	.	CAMKV	84	.	NM_024046	exon8	c.T651C	p.N217N	AGGTGGATTGCCT	.	PASS	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5863013	5863013	+	Missense_Mutation	SNP	T	T	C	rs4362173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	135	6	157	0	0.0444444	0	T|0.606;C|0.394	0.394	strong	.	OR52E6	70	.	NM_001005167	exon1	c.A115G	p.I39V	GTGCAATAAGATA	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021860	132021860	+	Silent	SNP	T	T	C	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	121	7	121	10	0.0578512	0.0826446	.	.	none	ENSG00000188219,NS,carcinoma,+1,1	.	.	1	NM_001083538	exon15	c.T2832C	p.D944D	GCCCGATGGCCAG	.	scavenged	Atlas-SNP
UGT2B28	54490	hgsc.bcm.edu	37	4	70146804	70146804	+	Missense_Mutation	SNP	G	G	C	rs72551402		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	213	6	277	0	0.028169	0	.	.	weak	UGT2B28,NS,carcinoma,0,1	UGT2B28	101	1	NM_053039	exon1	c.G586C	p.V196L	ATACCTGTTGTTA	.	scavenged	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107049714	107049714	+	Missense_Mutation	SNP	C	C	G	rs79619029		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	1066	13	892	0	0.0121951	0	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
CXCR2	3579	hgsc.bcm.edu	37	2	219000310	219000310	+	Silent	SNP	C	C	T	rs2230054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	66	7	85	1	0.106061	0.0117647	C|0.465;T|0.535	0.535	strong	CXCR2,NS,carcinoma,0,1	CXCR2	54	1	NM_001168298	exon4	c.C786T	p.L262L	CCTGCTCTGCTGG	.	scavenged	Atlas-SNP
SIM2	6493	hgsc.bcm.edu	37	21	38117308	38117308	+	Missense_Mutation	SNP	C	C	A	rs2073601	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	81	7	93	0	0.0864198	0	C|0.777;A|0.223	0.223	strong	.	SIM2	55	.	NM_005069	exon10	c.C1447A	p.L483M	AGCACACTGCCAG	.	PASS	Atlas-SNP
STRN	6801	hgsc.bcm.edu	37	2	37152329	37152329	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	258	9	221	6	0.0348837	0.0271493	.	.	none	STRN,NS,carcinoma,0,1	STRN	71	1	NM_003162	exon2	c.G257A	p.G86E	CTTTCTCCCTGCA	.	scavenged	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41952852	41952852	+	Missense_Mutation	SNP	T	T	C	rs35263917	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	294	7	295	1	0.0238095	0.00338983	T|0.887;C|0.113	0.113	strong	ULK4_ENST00000301831,colon,carcinoma,+1,2	ULK4	150	2	NM_017886	exon11	c.A1042G	p.S348G	GAGTACTCTTAGG	.	scavenged	Atlas-SNP
MUS81	80198	hgsc.bcm.edu	37	11	65629934	65629934	+	Missense_Mutation	SNP	G	G	C	rs545500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	141	6	118	0	0.0425532	0	G|0.499;C|0.501	0.501	strong	.	MUS81	68	.	NM_025128	exon6	c.G539C	p.R180P	GTGCTCGACCCTG	.	PASS	Atlas-SNP
DENND4A	10260	hgsc.bcm.edu	37	15	66034069	66034069	+	Silent	SNP	A	A	C	rs61751117	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	97	4	74	0	0.0412371	0	A|0.979;C|0.021	0.021	strong	.	DENND4A	217	.	NM_001144823	exon5	c.T615G	p.T205T	AGATACAGTGTTC	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	37	2	128367092	128367092	+	Silent	SNP	G	G	A	rs777432	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	81	4	80	3	0.0493827	0.0375	G|0.692;A|0.308	0.308	strong	MYO7B_ENST00000428314,colon,carcinoma,0,2	MYO7B	359	2	NM_001080527	exon23	c.G2826A	p.S942S	GGAATCGAAGACC	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152527608	152527608	+	Missense_Mutation	SNP	C	C	T	rs34577613	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	137	6	145	1	0.0437956	0.00689655	C|0.705;T|0.295	0.295	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_004543	exon38	c.G4435A	p.V1479I	ACTTGACGGTATC	.	scavenged	Atlas-SNP
PARM1	25849	hgsc.bcm.edu	37	4	75938236	75938236	+	Silent	SNP	A	A	G	rs1062293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	106	3	108	0	0.0283019	0	A|0.598;G|0.402	0.402	strong	PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	NM_015393	exon2	c.A645G	p.V215V	GCCAGTACCCCAG	.	scavenged	Atlas-SNP
CD79A	973	hgsc.bcm.edu	37	19	42384803	42384803	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	51	20	78	0	0.392157	0	.	.	none	.	CD79A	25	.	NM_001783	exon4	c.G565T	p.E189X	CTTTATGAAGTGA	.	PASS	Atlas-SNP
RNF144A	9781	hgsc.bcm.edu	37	2	7164578	7164578	+	Silent	SNP	A	A	G	rs376219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	55	4	44	0	0.0727273	0	A|0.727;G|0.273	0.273	strong	.	RNF144A	38	.	NM_014746	exon7	c.A588G	p.E196E	AGACGAAGGCTGC	.	PASS	Atlas-SNP
CEACAM6	4680	hgsc.bcm.edu	37	19	42260569	42260569	+	Silent	SNP	G	G	A	rs55738855		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	146	4	152	0	0.0273973	0	.	.	weak	CEACAM6,NS,carcinoma,0,1	CEACAM6	52	1	NM_002483	exon2	c.G126A	p.P42P	CACGCCGTTCAAT	.	scavenged	Atlas-SNP
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68780427	68780427	+	Missense_Mutation	SNP	C	C	T	rs150048717	bycluster;byfrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	143	8	172	1	0.0559441	0.00581395	C|0.998;T|0.002	0.002	strong	TMPRSS11A,colon,carcinoma,0,1	TMPRSS11A	74	1	NM_182606	exon9	c.G983A	p.R328Q	GCTTCTCGGAGAT	.	scavenged	Atlas-SNP
TWF1	5756	hgsc.bcm.edu	37	12	44196125	44196125	+	Silent	SNP	T	T	C	rs112006889	bycluster;byfrequency;by1000genomes	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	412	7	305	3	0.0169903	0.00983607	T|0.973;C|0.027	0.027	strong	TWF1,NS,carcinoma,-2,1	TWF1	37	1	NM_002822	exon3	c.A246G	p.E82E	TATCCATTCATAT	.	scavenged	Atlas-SNP
