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
SFPQ	6421	hgsc.bcm.edu	37	1	35658418	35658432	+	In_Frame_Del	DEL	GGTGGCTGCTGCGGT	GGTGGCTGCTGCGGT	-	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	GGTGGCTGCTGCGGT	GGTGGCTGCTGCGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	29	13	27	0	0.448276	0	.	.	none	.	SFPQ	51	.	NM_005066	exon1	c.220_234del	p.74_78del	.	.	PASS	Atlas-Indel
B2M	567	hgsc.bcm.edu	37	15	45007689	45007690	+	Frame_Shift_Del	DEL	TA	TA	-	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	76	35	94	.	0.461	.	.	.	none	B2M,NS,lymphoid_neoplasm,+2,1	B2M	99	1	NM_004048	exon2	c.135_136del	p.45_46del	.	.	PASS	Pindel,Atlas-Indel
CIITA	4261	hgsc.bcm.edu	37	16	11001270	11001271	+	Frame_Shift_Del	DEL	TA	TA	-	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	97	19	71	0	0.195876	0	.	.	none	.	CIITA	92	.	NM_000246	exon11	c.1920_1921del	p.640_641del	.	.	PASS	Atlas-Indel
KIAA0947	23379	hgsc.bcm.edu	37	5	5461621	5461621	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	30	173	.	0.190	.	.	.	none	KIAA0947_ENST00000296564,NS,carcinoma,-1,2	KIAA0947	301	2	NM_015325	exon13	c.2173delT	p.Y725fs	.	.	PASS	Pindel,Atlas-Indel
PRDM1	639	hgsc.bcm.edu	37	6	106552891	106552892	+	Frame_Shift_Ins	INS	-	-	GT	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	78	19	152	.	0.244	.	.	.	none	PRDM1,colon,carcinoma,0,1	PRDM1	195	1	NM_001198	exon5	c.856_857insGT	p.R286fs	.	.	PASS	Pindel,Atlas-Indel
DGKB	1607	hgsc.bcm.edu	37	7	14775822	14775822	+	Splice_Site	DEL	G	G	-	rs139628753	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	199	146	197	0	0.733668	0	G|0.405;-|0.595	0.595	strong	.	DGKB	166	.	NM_004080	exon5	c.169-2C>-	.	.	.	PASS	Atlas-Indel
SDF2	6388	hgsc.bcm.edu	37	17	26976184	26976185	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	21	84	.	0.236	.	.	.	none	.	SDF2	17	.	NM_006923	exon3	c.459_460del	p.153_154del	.	.	PASS	Pindel
NRXN2	9379	hgsc.bcm.edu	37	11	64457918	64457919	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	54	12	46	.	0.222	.	.	.	none	NRXN2,colon,carcinoma,+1,1	NRXN2	247	1	NM_015080	exon5	c.809_810insG	p.A270fs	.	.	PASS	Pindel
FRMPD2	143162	hgsc.bcm.edu	37	10	49409419	49409420	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	125	28	121	.	0.224	.	.	.	none	.	FRMPD2	157	.	NM_001018071	exon15	c.1806_1807insA	p.K602fs	.	.	PASS	Pindel
PEAR1	375033	hgsc.bcm.edu	37	1	156877797	156877797	+	Silent	SNP	C	C	A	rs77235035	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	227	8	126	0	0.0352423	0	C|0.810;A|0.190	0.190	strong	PEAR1,NS,carcinoma,0,2	PEAR1	118	2	NM_001080471	exon8	c.C856A	p.R286R	TGTGACCGATTCA	.	scavenged	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244194	11244194	+	Missense_Mutation	SNP	T	T	C	rs71443637	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	27	10	21	0	0.37037	0	T|0.599;C|0.401	0.401	strong	TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	NM_176884	exon1	c.A635G	p.H212R	TTACCATGGAGCT	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17083872	17083872	+	Missense_Mutation	SNP	G	G	A	rs61635893	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	698	15	719	3	0.02149	0.00417246	.	.	weak	Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001271733	exon15	c.C1925T	p.P642L	GCAAGTGGGCCCC	.	scavenged	Atlas-SNP
HYLS1	219844	hgsc.bcm.edu	37	11	125769354	125769354	+	Missense_Mutation	SNP	T	T	C	rs667782	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	5	100	0	0.0431034	0	T|0.719;C|0.281	0.281	strong	.	HYLS1	25	.	NM_001134793	exon3	c.T91C	p.C31R	CACATCTGTGCAG	.	PASS	Atlas-SNP
ALS2CR8	79800	hgsc.bcm.edu	37	2	203846817	203846817	+	Missense_Mutation	SNP	A	A	T	rs72932557	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	82	4	139	0	0.0487805	0	A|0.910;T|0.090	0.090	strong	ALS2CR8,rectum,carcinoma,-1,1	ALS2CR8	56	1	NM_024744	exon16	c.A1712T	p.Y571F	CAAGGTACACCTC	.	PASS	Atlas-SNP
TPPP	11076	hgsc.bcm.edu	37	5	678087	678087	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	248	11	225	4	0.0443548	0.0177778	.	.	none	TPPP,NS,carcinoma,0,1	TPPP	24	1	NM_007030	exon2	c.G89A	p.R30K	GACAGCCTCTTGG	.	scavenged	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159399348	159399348	+	Missense_Mutation	SNP	A	A	G	rs768994	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	3	70	0	0.0337079	0	A|0.862;G|0.138	0.138	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon7	c.T1316C	p.M439T	TCATTCATTAGCC	.	scavenged	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	37	14	59797397	59797397	+	Silent	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	166	53	194	0	0.319277	0	.	.	none	.	DAAM1	95	.	NM_001270520	exon13	c.G1551A	p.E517E	CCATGAGCTCAGC	.	PASS	Atlas-SNP
FAM135A	57579	hgsc.bcm.edu	37	6	71238105	71238105	+	Missense_Mutation	SNP	A	A	G	rs2747701	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	198	9	179	0	0.0454545	0	A|0.647;G|0.353	0.353	strong	.	FAM135A	181	.	NM_001162529	exon14	c.A3725G	p.D1242G	AAGAGGATGGTTC	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939782	12939782	+	Silent	SNP	A	A	G	rs4579765		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	25	7	20	3	0.28	0.15	.	.	weak	PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	1	NM_001009611	exon4	c.T1020C	p.L340L	AGGCACAAGACTG	.	scavenged	Atlas-SNP
KCTD10	83892	hgsc.bcm.edu	37	12	109889615	109889615	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	71	24	47	0	0.338028	0	.	.	none	KCTD10,NS,carcinoma,0,1	KCTD10	24	1	NM_031954	exon7	c.G727C	p.E243Q	GAAACTCCACCTG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79030212	79030212	+	Missense_Mutation	SNP	C	C	T	rs16877147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	190	4	199	0	0.0210526	0	C|0.851;T|0.149	0.149	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon2	c.C5624T	p.A1875V	AGCCTGCGGATGT	.	scavenged	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69967897	69967897	+	Silent	SNP	T	T	C	rs2270841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	85	6	73	0	0.0705882	0	T|0.194;C|0.806	0.806	strong	WWP2,NS,carcinoma,0,1	WWP2	88	1	NM_001270454	exon17	c.T1707C	p.H569H	GTCTCATGAGGTG	.	PASS	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159398633	159398633	+	Silent	SNP	T	T	C	rs3756988	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	6	77	0	0.0821918	0	T|0.844;C|0.156	0.156	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon8	c.A1620G	p.E540E	TAAGAGTTCTCTC	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3168816	3168816	+	Silent	SNP	G	G	A	rs2230167	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	122	5	116	0	0.0409836	0	T|0.125;G|0.436;C|0.285;A|0.154	0.154	strong	.	MYOM1	192	.	NM_003803	exon9	c.C1338T	p.N446N	CTCACCGTTTCTG	.	PASS	Atlas-SNP
NBN	4683	hgsc.bcm.edu	37	8	90990479	90990479	+	Missense_Mutation	SNP	C	C	G	rs1805794	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	219	9	231	0	0.0410959	0	C|0.681;G|0.319	0.319	strong	.	NBN	86	.	NM_002485	exon5	c.G553C	p.E185Q	TGGACTCAACTGC	.	PASS	Atlas-SNP
TRPC1	7220	hgsc.bcm.edu	37	3	142523349	142523349	+	Silent	SNP	G	G	A	rs3821647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	229	6	207	0	0.0262009	0	G|0.806;A|0.194	0.194	strong	TRPC1,NS,carcinoma,0,1	TRPC1	82	1	NM_001251845	exon12	c.G2031A	p.T677T	ATGTACGTTACCT	.	scavenged	Atlas-SNP
PLK4	10733	hgsc.bcm.edu	37	4	128814492	128814492	+	Silent	SNP	G	G	A	rs56250604	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	480	22	463	0	0.0458333	0	G|0.962;A|0.038	0.038	strong	.	PLK4	65	.	NM_014264	exon11	c.G2241A	p.G747G	GACAGGGAAGTCT	.	PASS	Atlas-SNP
ZNF35	7584	hgsc.bcm.edu	37	3	44692564	44692564	+	Missense_Mutation	SNP	C	C	G	rs2272044	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	197	10	211	0	0.0507614	0	C|0.756;G|0.244	0.244	strong	.	ZNF35	34	.	NM_003420	exon2	c.C5G	p.T2S	AGATGACTGCAGA	.	PASS	Atlas-SNP
AQP12B	653437	hgsc.bcm.edu	37	2	241622187	241622187	+	Missense_Mutation	SNP	C	C	T	rs4081909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	151	14	158	0	0.0927152	0	C|0.829;T|0.171	0.171	strong	.	AQP12B	33	.	NM_001102467	exon1	c.G68A	p.R23Q	GAGGCCCGCCTGG	.	PASS	Atlas-SNP
MARCH10	162333	hgsc.bcm.edu	37	17	60821880	60821880	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	52	14	65	0	0.269231	0	.	.	none	.	MARCH10	102	.	NM_001100875	exon5	c.C392A	p.A131E	ATTGGTGCTTGGT	.	PASS	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158630643	158630643	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	67	2	71	1	0.0298507	0.0140845	.	.	none	RNF145,NS,carcinoma,+1,2	RNF145	110	2	NM_001199380	exon2	c.A73G	p.K25E	TTTTCTTTTTTTT	.	scavenged	Atlas-SNP
FBLN1	2192	hgsc.bcm.edu	37	22	45937241	45937241	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	83	28	76	0	0.337349	0	.	.	none	.	FBLN1	143	.	NM_006487	exon9	c.C1055T	p.T352M	AGGGAACGCGCTG	.	PASS	Atlas-SNP
ZNF502	91392	hgsc.bcm.edu	37	3	44762830	44762830	+	Missense_Mutation	SNP	A	A	G	rs56084453	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	202	10	184	0	0.049505	0	A|0.848;G|0.152	0.152	strong	ZNF502,NS,carcinoma,-1,1	ZNF502	58	1	NM_001134440	exon4	c.A521G	p.Q174R	AACATCAGAGAAC	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	229	11	241	2	0.0480349	0.00829876	C|0.873;T|0.127	0.127	strong	TAF1L,NS,carcinoma,-1,1	TAF1L	382	1	NM_153809	exon1	c.G4209A	p.T1403T	TGACAGCGTCACC	.	scavenged	Atlas-SNP
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs76491286		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	266	12	269	1	0.0451128	0.00371747	.	.	weak	ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	NM_005435	exon2	c.C1040T	p.T347I	GTCAAACCTTTTT	.	scavenged	Atlas-SNP
EP300	2033	hgsc.bcm.edu	37	22	41551039	41551039	+	Silent	SNP	T	T	A	rs20552	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	117	5	87	0	0.042735	0	T|0.375;A|0.625	0.625	strong	.	EP300	367	.	NM_001429	exon17	c.T3183A	p.T1061T	GCCAACTTTGGAG	.	PASS	Atlas-SNP
PLEKHA3	65977	hgsc.bcm.edu	37	2	179358665	179358665	+	Silent	SNP	A	A	G	rs41461050	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	194	3	243	0	0.0154639	0	A|1.000;|0.000	.	weak	PLEKHA3,NS,carcinoma,+1,1	PLEKHA3	25	1	NM_019091	exon4	c.A399G	p.T133T	TCATACAATACAG	.	scavenged	Atlas-SNP
ARID1A	8289	hgsc.bcm.edu	37	1	27102083	27102083	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	43	17	44	0	0.395349	0	.	.	none	ARID1A,bladder,carcinoma,0,1	ARID1A	842	1	NM_006015	exon19	c.G5009A	p.W1670X	AGGCATGGCGGGT	.	PASS	Atlas-SNP
NNT	23530	hgsc.bcm.edu	37	5	43613046	43613046	+	Missense_Mutation	SNP	A	A	G	rs35201656	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	221	5	172	1	0.0226244	0.00581395	A|0.964;G|0.036	0.036	strong	NNT,NS,carcinoma,0,1	NNT	92	1	NM_182977	exon3	c.A188G	p.K63R	TCCCCAAAGAGAT	.	scavenged	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24171051	24171051	+	Silent	SNP	C	C	T	rs6996616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	182	8	197	0	0.043956	0	C|0.809;T|0.191	0.191	strong	.	ADAM28	100	.	NM_014265	exon6	c.C534T	p.H178H	GGCCCACGATTTG	.	PASS	Atlas-SNP
MAP9	79884	hgsc.bcm.edu	37	4	156274377	156274377	+	Missense_Mutation	SNP	T	T	C	rs1058992	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	68	4	87	0	0.0588235	0	T|0.652;C|0.348	0.348	strong	MAP9,NS,carcinoma,0,1	MAP9	79	1	NM_001039580	exon11	c.A1496G	p.K499R	GTTTTCTTCTTGT	.	PASS	Atlas-SNP
DND1	373863	hgsc.bcm.edu	37	5	140050894	140050894	+	Missense_Mutation	SNP	G	G	C	rs201638404	byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	313	13	313	7	0.0415335	0.0223642	G|0.979;C|0.021	0.021	strong	DND1,NS,carcinoma,-1,1	DND1	15	1	NM_194249	exon4	c.C1046G	p.T349S	ACCATGGTACCTG	.	scavenged	Atlas-SNP
ANP32C	23520	hgsc.bcm.edu	37	4	165118819	165118819	+	Silent	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	102	34	95	0	0.333333	0	.	.	none	ANP32C,NS,carcinoma,0,1	ANP32C	59	1	NM_012403	exon1	c.G45A	p.A15A	AGAGGGCGCCCTG	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194964	18194964	+	Missense_Mutation	SNP	A	A	G	rs1869788	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	128	8	85	0	0.0625	0	A|0.673;G|0.327	0.327	strong	.	MRGPRX4	68	.	NM_054032	exon1	c.A161G	p.Y54C	TGGGCTACCGCAT	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102567207	102567207	+	Missense_Mutation	SNP	T	T	A	rs1276286	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	220	10	170	0	0.0454545	0	T|0.600;A|0.400	0.400	strong	MMP27,NS,carcinoma,0,1	MMP27	84	1	NM_022122	exon6	c.A797T	p.E266V	GCAGGTTCCTTAG	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609094	32609094	+	Silent	SNP	C	C	T	rs1129737	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	7	119	0	0.0603448	0	C|0.706;T|0.294	0.294	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.C90T	p.H30H	TGACCACGTTGCC	.	PASS	Atlas-SNP
NLRP9	338321	hgsc.bcm.edu	37	19	56249530	56249530	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	166	46	130	0	0.277108	0	.	.	none	.	NLRP9	163	.	NM_176820	exon1	c.G211T	p.V71L	GTGTTACCTCCCA	.	PASS	Atlas-SNP
MEF2A	4205	hgsc.bcm.edu	37	15	100246936	100246936	+	Silent	SNP	T	T	C	rs325408	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	94	4	71	0	0.0425532	0	T|0.332;C|0.668	0.668	strong	.	MEF2A	138	.	NM_005587	exon9	c.T867C	p.N289N	ACAGAATACCCAG	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23527724	23527724	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	195	8	237	3	0.0410256	0.0126582	.	.	none	PRDM9,trunk,malignant_melanoma,0,2	PRDM9	344	2	NM_020227	exon11	c.A2527G	p.N843D	TTTCGCAATAAGT	.	scavenged	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53993764	53993764	+	Missense_Mutation	SNP	A	A	T	rs12609217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	303	6	286	0	0.019802	0	A|0.945;T|0.055	0.055	strong	ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	NM_001004301	exon4	c.A278T	p.D93V	ATAAAGATATTCA	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	754	29	677	21	0.0384615	0.0310192	.	.	none	MUC6_ENST00000421673,NS,carcinoma,+2,2	MUC6	408	2	NM_005961	exon31	c.A5950G	p.M1984V	CAGTCATAGGACC	.	scavenged	Atlas-SNP
ESRP1	54845	hgsc.bcm.edu	37	8	95680229	95680229	+	Silent	SNP	C	C	T	rs1549466	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	138	4	120	1	0.0289855	0.00833333	C|0.648;T|0.352	0.352	strong	ESRP1_ENST00000433389,NS,carcinoma,+2,2	ESRP1	148	2	NM_001122827	exon10	c.C984T	p.V328V	CATTGTCCGCATG	.	scavenged	Atlas-SNP
SLC2A8	29988	hgsc.bcm.edu	37	9	130164993	130164993	+	Silent	SNP	C	C	T	rs1138739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	74	4	79	0	0.0540541	0	C|0.827;T|0.173	0.173	strong	.	SLC2A8	27	.	NM_014580	exon5	c.C684T	p.S228S	GGGCTCCGAGCAG	.	PASS	Atlas-SNP
CLEC18C	283971	hgsc.bcm.edu	37	16	70211218	70211218	+	Silent	SNP	G	G	A	rs149087931	byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	426	10	412	2	0.0234742	0.00485437	G|0.925;A|0.075	0.075	strong	CLEC18C,NS,carcinoma,0,1	CLEC18C	15	1	NM_173619	exon3	c.G291A	p.A97A	CCTGGCGTCCGGC	.	scavenged	Atlas-SNP
LIFR	3977	hgsc.bcm.edu	37	5	38496637	38496637	+	Missense_Mutation	SNP	C	C	T	rs3729740	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	152	7	179	0	0.0460526	0	C|0.969;T|0.031	0.031	strong	LIFR,NS,NS,0,1	LIFR	348	1	NM_002310	exon13	c.G1732A	p.D578N	CCTCATCTGATGA	.	PASS	Atlas-SNP
SATB2	23314	hgsc.bcm.edu	37	2	200173610	200173610	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	119	47	140	0	0.394958	0	.	.	none	.	SATB2	134	.	NM_015265	exon11	c.T1613C	p.L538P	GTACAGAGGTTTT	.	PASS	Atlas-SNP
NOTCH4	4855	hgsc.bcm.edu	37	6	32188823	32188823	+	Missense_Mutation	SNP	G	G	A	rs8192585	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	51	4	60	0	0.0784314	0	G|0.969;A|0.031	0.031	strong	.	NOTCH4	201	.	NM_004557	exon4	c.C731T	p.S244L	CCATTCGAACAGC	.	PASS	Atlas-SNP
DNASE2B	58511	hgsc.bcm.edu	37	1	84864256	84864256	+	Missense_Mutation	SNP	G	G	C	rs3738573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	76	3	59	0	0.0394737	0	G|0.694;C|0.306	0.306	strong	DNASE2B_ENST00000370665,NS,carcinoma,0,1	DNASE2B	40	1	NM_021233	exon1	c.G9C	p.Q3H	GAAACAGAAAATG	.	scavenged	Atlas-SNP
MTHFD1L	25902	hgsc.bcm.edu	37	6	151336739	151336739	+	Silent	SNP	C	C	G	rs509474	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	172	7	167	0	0.0406977	0	C|0.428;G|0.572	0.572	strong	.	MTHFD1L	75	.	NM_001242767	exon24	c.C2499G	p.S833S	CTGGTCCGTTGGT	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3162056	3162056	+	Silent	SNP	C	C	T	rs363099	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	144	6	138	0	0.0416667	0	T|0.148;G|0.337	0.148	strong	HTT,NS,carcinoma,0,1	HTT	221	1	NM_002111	exon29	c.C3801T	p.L1267L	GTTTCTCCGCTCA	.	PASS	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43519362	43519362	+	Silent	SNP	C	C	T	rs11083680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	191	11	188	0	0.0575916	0	C|0.424;T|0.576	0.576	strong	PSG11,right_lower_lobe,carcinoma,-2,1	PSG11	57	1	NM_002785	exon4	c.G870A	p.Q290Q	AGTAATCTGAGGG	.	PASS	Atlas-SNP
CCDC102B	79839	hgsc.bcm.edu	37	18	66513615	66513615	+	Missense_Mutation	SNP	A	A	G	rs2187094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	307	10	431	1	0.0325733	0.00232019	A|0.674;G|0.326	0.326	strong	CCDC102B,NS,carcinoma,0,2	CCDC102B	92	2	NM_001093729	exon6	c.A893G	p.K298R	AGTGGAAGTATGA	.	scavenged	Atlas-SNP
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	6	76	1	0.0674157	0.0131579	.	.	none	CBX3,colon,adenoma,0,1	CBX3	25	1	NM_007276	exon3	c.25-2A>T	.	TATTTTAGCAAAA	.	scavenged	Atlas-SNP
DPH3	285381	hgsc.bcm.edu	37	3	16305674	16305674	+	Silent	SNP	C	C	G	rs14080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	171	5	158	0	0.0292398	0	C|0.590;G|0.410	0.410	strong	DPH3,NS,adenoma,0,1	DPH3	7	1	NM_206831	exon2	c.G171C	p.V57V	ATAAATCACTTTT	.	scavenged	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196509522	196509522	+	Missense_Mutation	SNP	C	C	G	rs67093638	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	234	5	236	2	0.0213675	0.00847458	C|0.986;G|0.014	0.014	strong	PAK2_ENST00000327134,NS,carcinoma,0,4	PAK2	113	4	NM_002577	exon2	c.C5G	p.S2C	TCATGTCTGATAA	.	scavenged	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110763875	110763875	+	Missense_Mutation	SNP	A	A	G	rs723685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	63	6	70	0	0.0952381	0	A|0.905;G|0.095	0.095	strong	.	SLC22A16	81	.	NM_033125	exon4	c.T755C	p.V252A	GTTCCAACTGCAA	.	PASS	Atlas-SNP
ZBTB22	9278	hgsc.bcm.edu	37	6	33283766	33283766	+	Missense_Mutation	SNP	T	T	C	rs3130100	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	92	5	84	0	0.0543478	0	T|0.467;C|0.533	0.533	strong	.	ZBTB22	48	.	NM_001145338	exon2	c.A928G	p.T310A	GGGGTGTTGGCGC	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	37	5	79950708	79950708	+	Silent	SNP	T	T	C	rs2405875	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	29	22	11	0	0.758621	0	T|0.781;C|0.219	0.219	strong	.	MSH3	129	.	NM_002439	exon1	c.T162C	p.A54A	AGCGGCTGCAGCG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511142	195511142	+	Missense_Mutation	SNP	T	T	C	rs430037	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	92	7	64	1	0.076087	0.015625	T|0.781;C|0.219	0.219	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A7309G	p.N2437D	AAACGTTGGTGAC	.	scavenged	Atlas-SNP
OR51A2	401667	hgsc.bcm.edu	37	11	4976291	4976291	+	Missense_Mutation	SNP	G	G	A	rs55889636	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	516	5	525	0	0.00968992	0	G|0.661;A|0.339	0.339	strong	OR51A2,NS,carcinoma,0,1	OR51A2	40	1	NM_001004748	exon1	c.C653T	p.S218F	GTGTAAGACACAG	.	scavenged	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89866043	89866043	+	Missense_Mutation	SNP	T	T	C	rs7190823	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	108	4	90	0	0.037037	0	T|0.408;C|0.592	0.592	strong	FANCA,colon,carcinoma,+1,1	FANCA	99	1	NM_000135	exon9	c.A796G	p.T266A	CAACCGTGACCTG	.	scavenged	Atlas-SNP
TNRC6C	57690	hgsc.bcm.edu	37	17	76063864	76063864	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	81	4	91	0	0.0493827	0	.	.	none	.	TNRC6C	173	.	NM_018996	exon6	c.G2638A	p.G880S	GGCTGGGGCAGTG	.	PASS	Atlas-SNP
ZNF614	80110	hgsc.bcm.edu	37	19	52519608	52519608	+	Missense_Mutation	SNP	C	C	T	rs8104890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	4	100	0	0.0449438	0	C|0.666;T|0.334	0.334	strong	.	ZNF614	58	.	NM_025040	exon5	c.G1243A	p.V415I	GTATAACGAGAGT	.	PASS	Atlas-SNP
FAM76A	199870	hgsc.bcm.edu	37	1	28060574	28060574	+	Silent	SNP	A	A	G	rs6670793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	222	9	219	0	0.0405405	0	A|0.789;G|0.211	0.211	strong	.	FAM76A	11	.	NM_001143912	exon5	c.A336G	p.A112A	AATTGCAGCATTT	.	PASS	Atlas-SNP
PTAFR	5724	hgsc.bcm.edu	37	1	28476862	28476862	+	Missense_Mutation	SNP	G	G	T	rs5938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	110	4	103	0	0.0363636	0	G|0.968;T|0.030	0.030	strong	PTAFR,NS,carcinoma,0,1	PTAFR	30	1	NM_001164723	exon3	c.C671A	p.A224D	ACTTCAGCGTTGC	.	scavenged	Atlas-SNP
DOK3	79930	hgsc.bcm.edu	37	5	176936819	176936819	+	Missense_Mutation	SNP	C	C	G	rs3749728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	161	9	93	0	0.0559006	0	C|0.892;G|0.108	0.108	strong	.	DOK3	41	.	NM_024872	exon1	c.G35C	p.R12P	TGGGCACGCGCGT	.	PASS	Atlas-SNP
NOSTRIN	115677	hgsc.bcm.edu	37	2	169681151	169681151	+	Silent	SNP	C	C	T	rs3732031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	548	6	584	1	0.0109489	0.00171233	C|0.900;T|0.100	0.100	strong	NOSTRIN_ENST00000444448,NS,carcinoma,0,2	NOSTRIN	68	2	NM_001039724	exon3	c.C121T	p.L41L	GCAAACCTGGAAA	.	scavenged	Atlas-SNP
SMARCAD1	56916	hgsc.bcm.edu	37	4	95186055	95186055	+	Silent	SNP	A	A	G	rs2306802	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	400	10	442	3	0.025	0.00678733	A|0.691;G|0.309	0.309	strong	SMARCAD1,NS,carcinoma,0,1	SMARCAD1	97	1	NM_001128429	exon10	c.A1479G	p.Q493Q	AAACCAAAGGTAA	.	scavenged	Atlas-SNP
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974315	22974315	+	Missense_Mutation	SNP	A	A	C	rs61736405	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	11	128	8	0.102804	0.0625	A|0.013;C|0.987	0.987	weak	TNFRSF10C,trunk,malignant_melanoma,0,1	TNFRSF10C	30	1	NM_003841	exon5	c.A551C	p.N184T	CAATGAACACCAG	.	scavenged	Atlas-SNP
OR4M2	390538	hgsc.bcm.edu	37	15	22368855	22368855	+	Missense_Mutation	SNP	T	T	C	rs75967710	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	214	13	266	0	0.0607477	0	T|0.967;C|0.033	0.033	strong	.	OR4M2	140	.	NM_001004719	exon1	c.T280C	p.F94L	ATTTCTTTTGATG	.	PASS	Atlas-SNP
CHRNA7	1139	hgsc.bcm.edu	37	15	32450704	32450704	+	Silent	SNP	G	G	A	rs201822909	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	395	56	483	52	0.141772	0.10766	G|0.705;A|0.295	0.295	strong	CHRNA7_ENST00000437966,caecum,carcinoma,0,11	CHRNA7	57	11	NM_001190455	exon7	c.G777A	p.T259T	CAGGACGCTCTAC	.	scavenged	Atlas-SNP
OR4M2	390538	hgsc.bcm.edu	37	15	22369132	22369132	+	Missense_Mutation	SNP	G	G	A	rs112370472	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	323	8	322	1	0.0247678	0.00310559	G|0.973;A|0.027	0.027	strong	OR4M2,NS,carcinoma,-1,2	OR4M2	140	2	NM_001004719	exon1	c.G557A	p.R186Q	TTGTCCGGATTGC	.	scavenged	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152515683	152515683	+	Missense_Mutation	SNP	G	G	A	rs75807392	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	190	10	185	0	0.0526316	0	G|0.913;A|0.087	0.087	strong	.	NEB	1697	.	NM_004543	exon47	c.C5971T	p.H1991Y	AGAGATGCTAGGA	.	PASS	Atlas-SNP
CWF19L1	55280	hgsc.bcm.edu	37	10	102006625	102006625	+	Missense_Mutation	SNP	G	G	A	rs7073610	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	149	8	129	0	0.0536913	0	G|0.930;A|0.070	0.070	strong	.	CWF19L1	39	.	NM_018294	exon8	c.C776T	p.P259L	ACATCCGGAGGCT	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954963	30954963	+	Silent	SNP	G	G	A	rs55956203	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	6	89	3	0.0517241	0.0337079	G|0.932;A|0.068	0.068	strong	MUC21,NS,carcinoma,0,1	MUC21	98	1	NM_001010909	exon2	c.G1011A	p.T337T	CAGCACGACCTCC	.	scavenged	Atlas-SNP
KDM3A	55818	hgsc.bcm.edu	37	2	86697367	86697367	+	Silent	SNP	C	C	T	rs189936092	by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	276	6	258	0	0.0217391	0	C|0.996;T|0.004	0.004	strong	KDM3A,NS,carcinoma,0,2	KDM3A	179	2	NM_001146688	exon11	c.C1560T	p.L520L	TAAACTCAAAAAG	.	scavenged	Atlas-SNP
TWF1	5756	hgsc.bcm.edu	37	12	44196125	44196125	+	Silent	SNP	T	T	C	rs112006889	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	330	8	369	0	0.0242424	0	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
MUC5B	727897	hgsc.bcm.edu	37	11	1269835	1269835	+	Missense_Mutation	SNP	G	G	A	rs2943521	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	337	15	262	0	0.0445104	0	G|0.614;A|0.386	0.386	strong	.	MUC5B	473	.	NM_002458	exon31	c.G11725A	p.V3909I	TCCTCCGTCCCGG	.	PASS	Atlas-SNP
HS1BP3	64342	hgsc.bcm.edu	37	2	20824559	20824559	+	Silent	SNP	C	C	T	rs2305457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	67	6	84	0	0.0895522	0	C|0.772;T|0.228	0.228	strong	.	HS1BP3	33	.	NM_022460	exon5	c.G717A	p.E239E	GAGCCCCTCATCA	.	PASS	Atlas-SNP
NOTCH2	4853	hgsc.bcm.edu	37	1	120539668	120539668	+	Missense_Mutation	SNP	T	T	A	rs200464440	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	250	7	257	4	0.028	0.0155642	.	.	weak	NOTCH2_ENST00000369342,NS,carcinoma,0,2	NOTCH2	348	2	NM_001200001	exon4	c.A703T	p.T235S	GACAGGTGCCTCC	.	scavenged	Atlas-SNP
KLHL5	51088	hgsc.bcm.edu	37	4	39116911	39116911	+	Silent	SNP	T	T	C	rs3733276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	195	10	174	0	0.0512821	0	T|0.472;C|0.528	0.528	strong	.	KLHL5	75	.	NM_015990	exon10	c.T2172C	p.T724T	TAATACTGTGGAG	.	PASS	Atlas-SNP
OR13F1	138805	hgsc.bcm.edu	37	9	107266626	107266626	+	Missense_Mutation	SNP	T	T	C	rs79836745	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	124	6	117	0	0.0483871	0	T|0.991;C|0.009	0.009	strong	.	OR13F1	75	.	NM_001004485	exon1	c.T83C	p.F28S	TCATATTTGCGGT	.	PASS	Atlas-SNP
ZNF286B	729288	hgsc.bcm.edu	37	17	18565350	18565350	+	Missense_Mutation	SNP	G	G	C	rs9912644	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	317	8	354	0	0.0252366	0	G|0.648;C|0.352	0.352	strong	ZNF286B,NS,carcinoma,0,1	ZNF286B	75	1	NM_001145045	exon5	c.C1469G	p.T490S	TCTCCGGTATGAG	.	scavenged	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37234302	37234302	+	Silent	SNP	A	A	G	rs74842279	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	217	7	208	0	0.0322581	0	A|0.988;G|0.012	0.012	strong	HEATR5B,NS,carcinoma,0,1	HEATR5B	185	1	NM_019024	exon29	c.T4668C	p.S1556S	TAAACCAGATATT	.	scavenged	Atlas-SNP
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735617	140735617	+	Missense_Mutation	SNP	G	G	T	rs142728816	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	69	4	62	0	0.057971	0	G|0.994;T|0.006	0.006	strong	.	PCDHGA4	150	.	NM_018917	exon1	c.G850T	p.V284L	CGGAAAGTAAGAG	.	PASS	Atlas-SNP
BANK1	55024	hgsc.bcm.edu	37	4	102816467	102816467	+	Missense_Mutation	SNP	C	C	G	rs62321738	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	421	8	476	1	0.0190024	0.00210084	C|0.929;G|0.071	0.071	strong	BANK1,NS,lymphoid_neoplasm,0,1	BANK1	95	1	NM_017935	exon6	c.C909G	p.S303R	GAATAGCATTGAA	.	scavenged	Atlas-SNP
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675610	61675610	+	Silent	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	46	11	42	0	0.23913	0	.	.	none	.	RAB3IL1	39	.	NM_001271686	exon2	c.C321T	p.D107D	CAACACGTCCAGC	.	PASS	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	37	2	211540507	211540507	+	Missense_Mutation	SNP	C	C	A	rs1047891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	191	8	215	0	0.0418848	0	C|0.699;A|0.301	0.301	strong	.	CPS1	485	.	NM_001122633	exon37	c.C4235A	p.T1412N	CTGCCACCCCAGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515411	195515411	+	Missense_Mutation	SNP	G	G	T	rs55803325	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	67	5	53	0	0.0746269	0	G|0.993;T|0.007	0.007	strong	.	MUC4	1505	.	NM_018406	exon2	c.C3040A	p.P1014T	AGGAAGGGCTGGT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1246941	1246941	+	Missense_Mutation	SNP	A	A	G	rs2672785	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	248	4	183	0	0.016129	0	A|0.673;G|0.327	0.327	strong	MUC5B,NS,malignant_melanoma,-1,4	MUC5B	473	4	NM_002458	exon2	c.A101G	p.E34G	GCTGGGAGAATGC	.	scavenged	Atlas-SNP
ZNF100	163227	hgsc.bcm.edu	37	19	21948514	21948514	+	Silent	SNP	C	C	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	15	78	0	0.205479	0	.	.	none	.	ZNF100	62	.	NM_173531	exon2	c.G78T	p.V26V	AGACTGCACCAGA	.	PASS	Atlas-SNP
TTC16	158248	hgsc.bcm.edu	37	9	130480025	130480025	+	Missense_Mutation	SNP	C	C	T	rs117963786	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	62	5	64	0	0.0806452	0	C|0.996;T|0.004	0.004	strong	.	TTC16	55	.	NM_144965	exon4	c.C400T	p.R134C	CTGGAGCGCCTCA	.	PASS	Atlas-SNP
SYT8	90019	hgsc.bcm.edu	37	11	1858262	1858262	+	Missense_Mutation	SNP	C	C	T	rs484955	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	125	6	89	0	0.048	0	C|0.863;T|0.137	0.137	strong	SYT8,colon,carcinoma,0,1	SYT8	29	1	NM_138567	exon8	c.C908T	p.T303M	AGGGCACGGCGGC	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85401419	85401419	+	Silent	SNP	T	T	C	rs167379	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	157	3	113	1	0.0191083	0.00884956	T|0.150;C|0.850	0.850	strong	ALPK3_ENST00000258888,NS,carcinoma,0,2	ALPK3	289	2	NM_020778	exon6	c.T4056C	p.G1352G	GACAGGTCTCCCG	.	scavenged	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32032743	32032743	+	Silent	SNP	G	G	A	rs204883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	96	6	95	0	0.0625	0	G|0.569;A|0.431	0.431	strong	.	TNXB	553	.	NM_019105	exon19	c.C6696T	p.D2232D	CTGCCCGTCCCCA	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40138676	40138676	+	Missense_Mutation	SNP	A	A	G	rs2271395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	470	19	419	0	0.0404255	0	A|0.918;G|0.082	0.082	strong	.	N4BP2	166	.	NM_018177	exon14	c.A4759G	p.T1587A	TCTCATACTGGCC	.	PASS	Atlas-SNP
NUDT6	11162	hgsc.bcm.edu	37	4	123814308	123814308	+	Missense_Mutation	SNP	C	C	T	rs1048201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	77	5	59	0	0.0649351	0	C|0.825;T|0.175	0.175	strong	NUDT6_ENST00000304430,NS,carcinoma,0,3	NUDT6	50	3	NM_007083	exon5	c.G626A	p.R209Q	TGTTGCCGAATAC	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21606429	21606429	+	Missense_Mutation	SNP	G	G	T	rs4621113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	123	5	137	0	0.0406504	0	G|0.458;T|0.542	0.542	strong	.	ZNF493	178	.	NM_001076678	exon4	c.G968T	p.C323F	ATAAATGTGAAGA	.	PASS	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975052	44975052	+	Missense_Mutation	SNP	A	A	G	rs3825630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	133	7	144	0	0.0526316	0	A|0.796;G|0.204	0.204	strong	FSCB,NS,carcinoma,0,1	FSCB	173	1	NM_032135	exon1	c.T1139C	p.L380P	CCAAGAAGCTCTA	.	PASS	Atlas-SNP
C19orf21	126353	hgsc.bcm.edu	37	19	757399	757399	+	Silent	SNP	A	A	C	rs3746172	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	96	5	93	0	0.0520833	0	A|0.819;C|0.181	0.181	strong	C19orf21,NS,carcinoma,+2,1	C19orf21	56	1	NM_173481	exon2	c.A453C	p.A151A	CCAGGCAGTCAGG	.	PASS	Atlas-SNP
IKBIP	121457	hgsc.bcm.edu	37	12	99007623	99007623	+	Missense_Mutation	SNP	C	C	T	rs1048906	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	134	6	164	0	0.0447761	0	C|0.625;T|0.374	0.374	strong	.	IKBIP	46	.	NM_201612	exon3	c.G793A	p.G265S	TGTCACCTTCTAA	.	PASS	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	37	11	61505168	61505168	+	Silent	SNP	G	G	A	rs198444	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	105	4	84	0	0.0380952	0	G|0.536;A|0.464	0.464	strong	DAGLA,NS,carcinoma,+1,1	DAGLA	109	1	NM_006133	exon15	c.G1524A	p.A508A	GGATGCGATGGAG	.	scavenged	Atlas-SNP
WNT9A	7483	hgsc.bcm.edu	37	1	228109471	228109471	+	Silent	SNP	C	C	T	rs8192633	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	44	20	68	0	0.454545	0	C|0.985;T|0.015	0.015	strong	.	WNT9A	39	.	NM_003395	exon4	c.G846A	p.P282P	GGGCAGCGGGTCG	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43652442	43652442	+	Missense_Mutation	SNP	G	G	C	rs11210805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	52	5	60	0	0.0961538	0	G|0.929;C|0.071	0.071	strong	.	WDR65	76	.	NM_152498	exon6	c.G1034C	p.C345S	GCCTGTGCTTCAG	.	PASS	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651615	1651615	+	Missense_Mutation	SNP	A	A	G	rs74396270	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	45	7	33	3	0.155556	0.0909091	.	.	weak	KRTAP5-5,NS,carcinoma,0,3	KRTAP5-5	86	3	NM_001001480	exon1	c.A545G	p.Y182C	AGCCTTACTGCTG	.	scavenged	Atlas-SNP
G6PC3	92579	hgsc.bcm.edu	37	17	42152103	42152103	+	Silent	SNP	G	G	A	rs3815076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	43	6	46	0	0.139535	0	G|0.834;A|0.166	0.166	strong	.	G6PC3	26	.	NM_138387	exon3	c.G381A	p.T127T	AATGACGGCCCTG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179640650	179640650	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	135	4	148	0	0.0296296	0	.	.	none	TTN_ENST00000360870,NS,carcinoma,+2,6	TTN	18412	6	NM_001267550	exon28	c.A5941G	p.R1981G	CAGCCCTTTTCAA	.	scavenged	Atlas-SNP
ZNF318	24149	hgsc.bcm.edu	37	6	43305520	43305520	+	Silent	SNP	C	C	T	rs35650765	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	194	5	155	0	0.0257732	0	C|0.970;T|0.030	0.030	strong	ZNF318,colon,carcinoma,0,1	ZNF318	175	1	NM_014345	exon10	c.G6216A	p.P2072P	ATCTAACGGAAAC	.	scavenged	Atlas-SNP
IL1F10	84639	hgsc.bcm.edu	37	2	113831945	113831945	+	Silent	SNP	T	T	C	rs3811058	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	170	9	146	0	0.0529412	0	T|0.891;C|0.109	0.109	strong	.	IL1F10	19	.	NM_173161	exon3	c.T72C	p.D24D	AAGAGATGGCCAG	.	PASS	Atlas-SNP
DOK7	285489	hgsc.bcm.edu	37	4	3494898	3494898	+	Silent	SNP	C	C	T	rs6850908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	92	5	89	0	0.0543478	0	C|0.794;T|0.206	0.206	strong	DOK7,NS,carcinoma,0,1	DOK7	44	1	NM_173660	exon7	c.C1185T	p.Y395Y	CGAGTACCAGGTG	.	PASS	Atlas-SNP
C6orf170	221322	hgsc.bcm.edu	37	6	121602795	121602795	+	Silent	SNP	C	C	T	rs79788801	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	217	8	303	1	0.0368664	0.00330033	C|0.954;T|0.046	0.046	strong	C6orf170,NS,carcinoma,0,1	C6orf170	146	1	NM_152730	exon14	c.G1503A	p.L501L	TATCCACAGAACT	.	scavenged	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64210757	64210757	+	Missense_Mutation	SNP	C	C	A	rs4581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	140	6	150	0	0.0428571	0	C|0.581;A|0.419	0.419	strong	.	APOH	45	.	NM_000042	exon7	c.G796T	p.V266L	CAGGTACTTTACA	.	PASS	Atlas-SNP
DPP6	1804	hgsc.bcm.edu	37	7	154681050	154681050	+	Silent	SNP	C	C	T	rs1129300	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	70	5	121	1	0.0714286	0.00826446	C|0.837;G|0.000;T|0.163	0.163	strong	DPP6,NS,carcinoma,0,1	DPP6	383	1	NM_130797	exon24	c.C2373T	p.A791A	CACTGCCGATGGT	.	scavenged	Atlas-SNP
ANKUB1	389161	hgsc.bcm.edu	37	3	149479301	149479301	+	Silent	SNP	C	C	T	rs954714	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	95	5	100	0	0.0526316	0	C|0.444;T|0.556	0.556	strong	ANKUB1,NS,carcinoma,0,1	ANKUB1	27	1	NM_001144960	exon6	c.G1605A	p.A535A	TTCACACGCTGTC	.	PASS	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11420904	11420904	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	40	8	27	5	0.2	0.185185	.	.	none	PRB3_ENST00000538488,colon,carcinoma,0,2	PRB3	84	2	NM_006249	exon3	c.A279G	p.P93P	ACGAGGTGGGGGA	.	scavenged	Atlas-SNP
VWDE	221806	hgsc.bcm.edu	37	7	12395813	12395813	+	Silent	SNP	T	T	C	rs2119141	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	169	9	158	0	0.0532544	0	T|0.258;C|0.742	0.742	strong	.	VWDE	123	.	NM_001135924	exon18	c.A3669G	p.Q1223Q	GTTGGATTGGCAC	.	PASS	Atlas-SNP
NEIL3	55247	hgsc.bcm.edu	37	4	178274835	178274835	+	Missense_Mutation	SNP	A	A	C	rs13112390	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	259	7	350	3	0.027027	0.00857143	A|0.289;C|0.711	0.711	strong	NEIL3_ENST00000264596,colon,carcinoma,0,2	NEIL3	89	2	NM_018248	exon8	c.A1413C	p.Q471H	AGCCCAATACTCA	.	scavenged	Atlas-SNP
LACTB	114294	hgsc.bcm.edu	37	15	63433785	63433785	+	Silent	SNP	G	G	A	rs4775629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	142	4	162	0	0.028169	0	G|0.904;A|0.096	0.096	strong	LACTB,NS,carcinoma,0,1	LACTB	29	1	NM_032857	exon6	c.G1425A	p.S475S	TGGTTCGTGTAGA	.	scavenged	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537078	88537078	+	Silent	SNP	T	T	C	rs373805744	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	57	24	21	6	0.421053	0.285714	.	.	weak	DSPP,colon,carcinoma,0,1	DSPP	174	1	NM_014208	exon5	c.T3264C	p.S1088S	TAGCAGTGACAGC	.	scavenged	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113192655	113192655	+	Missense_Mutation	SNP	T	T	G	rs2986671	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	174	4	193	0	0.0229885	0	T|0.723;G|0.277	0.277	strong	SVEP1,NS,carcinoma,-1,3	SVEP1	326	3	NM_153366	exon33	c.A5429C	p.E1810A	GTGACTTCGGCAC	.	scavenged	Atlas-SNP
KANSL3	55683	hgsc.bcm.edu	37	2	97271090	97271090	+	Missense_Mutation	SNP	G	G	A	rs35715176	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	173	7	174	0	0.0404624	0	G|0.949;A|0.051	0.051	strong	.	.	.	.	NM_001115016	exon15	c.C1900T	p.P634S	CACAAGGCCCTCC	.	PASS	Atlas-SNP
ENDOD1	23052	hgsc.bcm.edu	37	11	94862577	94862577	+	Missense_Mutation	SNP	G	G	T	rs3740861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	204	8	145	0	0.0392157	0	G|0.794;T|0.206	0.206	strong	ENDOD1,NS,carcinoma,-1,1	ENDOD1	26	1	NM_015036	exon2	c.G1337T	p.G446V	CCATGGGCGCTAT	.	scavenged	Atlas-SNP
ZNF276	92822	hgsc.bcm.edu	37	16	89789898	89789898	+	Missense_Mutation	SNP	T	T	C	rs6500437	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	156	5	131	0	0.0320513	0	T|0.562;C|0.438	0.438	strong	ZNF276_ENST00000443381,colon,carcinoma,0,2	ZNF276	70	2	NM_001113525	exon4	c.T787C	p.W263R	TGGCCATGGGACA	.	scavenged	Atlas-SNP
TMEM232	642987	hgsc.bcm.edu	37	5	109973902	109973902	+	Silent	SNP	T	T	G	rs1422495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	245	10	303	0	0.0408163	0	T|0.910;G|0.090	0.090	strong	.	TMEM232	57	.	NM_001039763	exon5	c.A498C	p.A166A	TACCTTTGCTAGC	.	PASS	Atlas-SNP
CADPS	8618	hgsc.bcm.edu	37	3	62647994	62647994	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	36	18	31	0	0.5	0	.	.	none	.	CADPS	387	.	NM_003716	exon4	c.G964T	p.A322S	CCCTGGCTATTTG	.	PASS	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	37	1	232539219	232539219	+	Missense_Mutation	SNP	C	C	T	rs2275303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	42	4	56	0	0.0952381	0	C|0.855;T|0.145	0.145	strong	.	SIPA1L2	218	.	NM_020808	exon19	c.G4915A	p.G1639S	CTTTGCCACTGCC	.	PASS	Atlas-SNP
KLHL6	89857	hgsc.bcm.edu	37	3	183209942	183209942	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	151	52	140	0	0.344371	0	.	.	none	.	KLHL6	100	.	NM_130446	exon7	c.G1639A	p.E547K	CCCGCTCGTGGCT	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11648332	11648332	+	Silent	SNP	C	C	T	rs3744578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	123	5	134	0	0.0406504	0	C|0.256;T|0.744	0.744	strong	.	DNAH9	695	.	NM_001372	exon31	c.C6330T	p.N2110N	CCCCAACTTCGAA	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50678317	50678317	+	Missense_Mutation	SNP	C	C	G	rs4253211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	162	5	174	0	0.0308642	0	C|0.930;G|0.070	0.070	strong	ERCC6,NS,carcinoma,0,1	ERCC6	162	1	NM_000124	exon18	c.A3689C	p.K1230T	TGGTAACGCCTTT	.	scavenged	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31602967	31602967	+	Missense_Mutation	SNP	G	G	A	rs1046089	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	4	64	0	0.0625	0	G|0.611;A|0.389	0.389	strong	.	PRRC2A	152	.	NM_004638	exon22	c.G5219A	p.R1740H	CACAGCGTACAGA	.	PASS	Atlas-SNP
OR1S2	219958	hgsc.bcm.edu	37	11	57971203	57971203	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	183	5	148	1	0.0273224	0.00675676	.	.	none	OR1S2,NS,carcinoma,0,3	OR1S2	119	3	NM_001004459	exon1	c.G451C	p.A151P	ACCTGGCCCGCAT	.	scavenged	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118166096	118166096	+	Silent	SNP	C	C	T	rs2884587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	117	5	123	0	0.042735	0	C|0.874;T|0.126	0.126	strong	.	FAM46C	25	.	NM_017709	exon2	c.C606T	p.I202I	TCCCATCTCTGAG	.	PASS	Atlas-SNP
DLGAP1	9229	hgsc.bcm.edu	37	18	3814275	3814275	+	Splice_Site	SNP	T	T	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	95	23	90	0	0.242105	0	.	.	none	.	DLGAP1	201	.	NM_004746	exon6	c.958-2A>T	.	GGAACCTATTCAG	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187542755	187542755	+	Missense_Mutation	SNP	T	T	C	rs28489116	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	150	7	194	0	0.0466667	0	T|0.794;C|0.206	0.206	strong	FAT1,NS,carcinoma,0,2	FAT1	500	2	NM_005245	exon10	c.A4985G	p.N1662S	GAGGCGTTGTCAG	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	16948390	16948390	+	Missense_Mutation	SNP	G	G	C	rs3740168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	133	6	133	1	0.0451128	0.0075188	G|0.974;C|0.026	0.026	strong	CUBN,right_upper_lobe,carcinoma,-1,1	CUBN	515	1	NM_001081	exon50	c.C7724G	p.P2575R	GTATTTGGAAGAG	.	scavenged	Atlas-SNP
OR4D1	26689	hgsc.bcm.edu	37	17	56233034	56233034	+	Missense_Mutation	SNP	C	C	A	rs7218964	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	86	4	98	1	0.0465116	0.0102041	C|0.768;A|0.232	0.232	strong	OR4D1,NS,carcinoma,0,1	OR4D1	48	1	NM_012374	exon1	c.C520A	p.L174I	AATATCCTAGATA	.	scavenged	Atlas-SNP
MFN2	9927	hgsc.bcm.edu	37	1	12065841	12065841	+	Silent	SNP	C	C	T	rs1042837	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	108	4	90	0	0.037037	0	C|0.946;T|0.054	0.054	strong	MFN2,scalp,carcinoma,+1,1	MFN2	83	1	NM_014874	exon15	c.C1569T	p.S523S	CTTCTCCCTCAAC	.	scavenged	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627883	170627883	+	Missense_Mutation	SNP	T	T	G	rs143059540	bycluster;byfrequency;alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	157	11	179	4	0.0700637	0.0223464	T|1.000;C|0.000	.	alt	FAM120B,NS,carcinoma,0,2	FAM120B	108	2	NM_032448	exon2	c.T1405G	p.S469A	CCTGAATCCAGGC	.	scavenged	Atlas-SNP
EXOC7	23265	hgsc.bcm.edu	37	17	74080183	74080183	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	25	70	0	0.342466	0	.	.	none	.	EXOC7	47	.	NM_001145297	exon19	c.A2009G	p.Q670R	GCCTTCTGGATTT	.	PASS	Atlas-SNP
PRDM1	639	hgsc.bcm.edu	37	6	106555025	106555025	+	Silent	SNP	G	G	A	rs1010273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	62	4	108	0	0.0645161	0	G|0.910;A|0.090	0.090	strong	.	PRDM1	195	.	NM_001198	exon7	c.G2142A	p.P714P	GGCCCCGGCGCCT	.	PASS	Atlas-SNP
SLCO2A1	6578	hgsc.bcm.edu	37	3	133698349	133698349	+	Silent	SNP	C	C	T	rs10935090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	91	4	83	0	0.043956	0	C|0.815;T|0.185	0.185	strong	.	SLCO2A1	72	.	NM_005630	exon2	c.G210A	p.S70S	GAGACCCGATGAA	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66430870	66430870	+	Silent	SNP	G	G	A	rs61754218	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	4	113	0	0.047619	0	A|0.049;C|0.000;G|0.950	0.049	strong	.	LRIG1	138	.	NM_015541	exon19	c.C3099T	p.S1033S	CTCTGTGGAGTCC	.	PASS	Atlas-SNP
C6orf47	57827	hgsc.bcm.edu	37	6	31627449	31627449	+	Missense_Mutation	SNP	C	C	G	rs2242655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	5	49	0	0.0561798	0	C|0.866;G|0.134	0.134	strong	.	C6orf47	15	.	NM_021184	exon1	c.G276C	p.K92N	GTCCCACTTGAGG	.	PASS	Atlas-SNP
ZNF286B	729288	hgsc.bcm.edu	37	17	18565423	18565423	+	Missense_Mutation	SNP	G	G	A	rs9912852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	254	6	261	1	0.023622	0.00383142	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
ANKS1A	23294	hgsc.bcm.edu	37	6	34857324	34857324	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	8	4	4	0	0.5	0	.	.	none	ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	NM_015245	exon1	c.G145A	p.G49S	AGCGGCGGCGGCG	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52863038	52863038	+	Silent	SNP	G	G	A	rs410562	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	136	8	96	0	0.0588235	0	G|0.731;A|0.269	0.269	strong	.	KRT6C	55	.	NM_173086	exon9	c.C1503T	p.S501S	GACACCGCTGGCA	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29416481	29416481	+	Missense_Mutation	SNP	T	T	C	rs1881420	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	180	3	207	1	0.0166667	0.00483092	T|0.684;G|0.005	.	strong	ALK,NS,carcinoma,0,1	ALK	533	1	NM_004304	exon29	c.A4472G	p.K1491R	TGGACCTTGTGCA	.	scavenged	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51772895	51772895	+	Silent	SNP	G	G	T	rs78376092	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	137	3	136	0	0.0218978	0	G|0.987;T|0.013	0.013	strong	DMXL2,NS,carcinoma,-1,1	DMXL2	262	1	NM_001174116	exon24	c.C6408A	p.A2136A	TCGTTTGGCCTGC	.	scavenged	Atlas-SNP
ZNF502	91392	hgsc.bcm.edu	37	3	44763037	44763037	+	Missense_Mutation	SNP	A	A	C	rs7640654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	83	5	77	0	0.060241	0	A|0.537;C|0.463	0.463	strong	.	ZNF502	58	.	NM_001134440	exon4	c.A728C	p.E243A	GCAATGAATGTGG	.	PASS	Atlas-SNP
OR52D1	390066	hgsc.bcm.edu	37	11	5510809	5510809	+	Silent	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	260	7	228	0	0.0269231	0	.	.	none	OR52D1,NS,carcinoma,0,1	OR52D1	66	1	NM_001005163	exon1	c.C873T	p.L291L	TGTACTCAATCCT	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	275	5	214	0	0.0181818	0	C|0.846;T|0.154	0.154	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.C9954T	p.A3318A	CACAGCCACCCCC	.	scavenged	Atlas-SNP
HIST1H2BK	85236	hgsc.bcm.edu	37	6	27114569	27114569	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	91	7	108	5	0.0769231	0.0462963	.	.	none	HIST1H2BK_ENST00000396891,NS,carcinoma,-2,2	HIST1H2BK	68	2	NM_080593	exon1	c.A9G	p.E3E	CGCTGGTTCCGGC	.	scavenged	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3227419	3227419	+	Silent	SNP	A	A	G	rs362273	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	170	5	173	1	0.0294118	0.00578035	A|0.737;G|0.263	0.263	strong	HTT,caecum,carcinoma,0,1	HTT	221	1	NM_002111	exon57	c.A7797G	p.L2599L	GCTGCTACAGATC	.	scavenged	Atlas-SNP
TTC18	118491	hgsc.bcm.edu	37	10	75056863	75056863	+	Silent	SNP	A	A	C	rs6480692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	110	3	112	0	0.0272727	0	A|0.870;C|0.130	0.130	strong	TTC18,NS,carcinoma,-2,2	TTC18	106	2	NM_145170	exon16	c.T1791G	p.L597L	TGTCTGAAGTTCC	.	scavenged	Atlas-SNP
TCN2	6948	hgsc.bcm.edu	37	22	31011610	31011610	+	Missense_Mutation	SNP	G	G	C	rs1801198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	65	4	54	0	0.0615385	0	G|0.390;C|0.610	0.610	strong	.	TCN2	44	.	NM_000355	exon6	c.G776C	p.R259P	CCATGCGTGGGGC	.	PASS	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41386136	41386136	+	Missense_Mutation	SNP	A	A	C	rs4142867	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	152	3	172	1	0.0197368	0.00581395	A|0.502;C|0.498	0.498	strong	CYP2A7,NS,carcinoma,0,1	CYP2A7	71	1	NM_000764	exon4	c.T507G	p.D169E	GGTGGGATCGATA	.	scavenged	Atlas-SNP
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	88	5	82	0	0.0568182	0	C|0.449;T|0.551	0.551	strong	OSBPL7,colon,carcinoma,-1,1	OSBPL7	65	1	NM_145798	exon23	c.G2430A	p.T810T	GCTATCCGTCTGC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225534348	225534348	+	Missense_Mutation	SNP	G	G	A	rs7535953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	144	6	198	0	0.0416667	0	G|0.499;A|0.501	0.501	strong	.	DNAH14	300	.	NM_001373	exon69	c.G11009A	p.R3670K	AGTCTAGACTTAC	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100846936	100846936	+	Silent	SNP	A	A	G	rs654593	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	94	7	91	0	0.0744681	0	A|0.462;G|0.538	0.538	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.A2004G	p.P668P	AACCCCATCATCT	.	PASS	Atlas-SNP
ZNF423	23090	hgsc.bcm.edu	37	16	49672444	49672444	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	21	53	0	0.328125	0	.	.	none	ZNF423_ENST00000262383,NS,carcinoma,0,1	ZNF423	463	1	NM_015069	exon4	c.G619A	p.D207N	GGTGGTCGCTGCG	.	PASS	Atlas-SNP
NDUFAF5	79133	hgsc.bcm.edu	37	20	13779113	13779113	+	Silent	SNP	T	T	C	rs2273317	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	172	6	166	0	0.0348837	0	T|0.983;C|0.017	0.017	strong	C20orf7,NS,carcinoma,0,1	.	.	1	NM_024120	exon6	c.T486C	p.H162H	TTTGCATTGGGTG	.	scavenged	Atlas-SNP
ACOT11	26027	hgsc.bcm.edu	37	1	55064980	55064980	+	Missense_Mutation	SNP	G	G	A	rs2304303	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	182	5	181	0	0.0274725	0	G|0.956;A|0.044	0.044	strong	ACOT11_ENST00000371316,caecum,carcinoma,0,2	ACOT11	105	2	NM_147161	exon8	c.G776A	p.R259H	TCTGCCGTGCCCA	.	scavenged	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159398700	159398700	+	Missense_Mutation	SNP	C	C	T	rs3756987	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	92	7	92	0	0.076087	0	C|0.842;T|0.158	0.158	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon8	c.G1553A	p.G518D	AGGTAGCCTCCAT	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285497	16285497	+	Silent	SNP	A	A	G	rs706149		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	196	4	198	2	0.0204082	0.010101	G|1.000;|0.000	1.000	weak	UBB,bladder,carcinoma,0,6	UBB	30	6	NM_018955	exon2	c.A276G	p.E92E	CCTGGAAGTGGAG	.	scavenged	Atlas-SNP
EXT2	2132	hgsc.bcm.edu	37	11	44129290	44129290	+	Silent	SNP	C	C	A	rs4755228	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	97	4	84	0	0.0412371	0	C|0.958;A|0.042	0.042	strong	.	EXT2	129	.	NM_000401	exon2	c.C127A	p.R43R	AATATCCGGGGTC	.	PASS	Atlas-SNP
PIGG	54872	hgsc.bcm.edu	37	4	520853	520853	+	Missense_Mutation	SNP	G	G	A	rs13114026	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	13	98	0	0.121495	0	G|0.827;A|0.173	0.173	strong	.	PIGG	86	.	NM_001127178	exon10	c.G2095A	p.V699I	CTCTCTGTCCTGG	.	PASS	Atlas-SNP
EAF2	55840	hgsc.bcm.edu	37	3	121563355	121563355	+	Silent	SNP	T	T	C	rs9884018	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	219	8	233	0	0.0365297	0	T|0.799;C|0.201	0.201	strong	EAF2,NS,carcinoma,0,1	EAF2	26	1	NM_018456	exon2	c.T162C	p.G54G	GGTTGGTGAAGGT	.	scavenged	Atlas-SNP
DNAAF2	55172	hgsc.bcm.edu	37	14	50100683	50100683	+	Silent	SNP	C	C	G	rs2985686	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	11	11	0	0	1	.	C|0.432;G|0.568	0.568	strong	.	DNAAF2	47	.	NM_018139	exon1	c.G1185C	p.A395A	GTCCTCCGCGCGA	.	PASS	Atlas-SNP
CYP11B2	1585	hgsc.bcm.edu	37	8	143994041	143994041	+	Missense_Mutation	SNP	C	C	T	rs4545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	168	3	153	1	0.0178571	0.00653595	C|0.914;T|0.086	0.086	strong	CYP11B2,NS,carcinoma,+2,1	CYP11B2	107	1	NM_000498	exon8	c.G1303A	p.G435S	TCCTGCCGGAGCC	.	scavenged	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26164413	26164413	+	Missense_Mutation	SNP	C	C	T	rs13058434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	7	91	0	0.0786517	0	C|0.867;T|0.133	0.133	strong	.	MYO18B	322	.	NM_032608	exon4	c.C530T	p.P177L	CCCCCCCTTGCAA	.	PASS	Atlas-SNP
CORO7	79585	hgsc.bcm.edu	37	16	4445327	4445327	+	Missense_Mutation	SNP	C	C	T	rs3747579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	5	102	1	0.0595238	0.00980392	C|0.451;T|0.549	0.549	strong	CORO7,NS,carcinoma,0,1	CORO7	73	1	NM_024535	exon7	c.G578A	p.R193Q	AAGATCCGCAGCT	.	scavenged	Atlas-SNP
FRMD4A	55691	hgsc.bcm.edu	37	10	13702500	13702500	+	Missense_Mutation	SNP	G	G	A	rs145701309	alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	149	6	126	1	0.0402685	0.00793651	G|1.000;T|0.000	.	alt	FRMD4A,NS,carcinoma,+1,1	FRMD4A	108	1	NM_018027	exon20	c.C1714T	p.L572F	GAGGGAGTCCCTT	.	scavenged	Atlas-SNP
MAP3K5	4217	hgsc.bcm.edu	37	6	136944063	136944063	+	Silent	SNP	A	A	G	rs3765258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	60	5	79	0	0.0833333	0	A|0.870;G|0.130	0.130	strong	.	MAP3K5	136	.	NM_005923	exon15	c.T2073C	p.Y691Y	TATCCCATAAGTG	.	PASS	Atlas-SNP
PPP1R7	5510	hgsc.bcm.edu	37	2	242097275	242097275	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	36	102	0	0.367347	0	.	.	none	.	PPP1R7	35	.	NM_002712	exon3	c.G235A	p.E79K	GATGCAGAGGTAA	.	PASS	Atlas-SNP
PNPLA7	375775	hgsc.bcm.edu	37	9	140356422	140356422	+	Silent	SNP	G	G	C	rs28452008	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	78	5	52	0	0.0641026	0	G|0.620;C|0.380	0.380	strong	PNPLA7,NS,carcinoma,0,1	PNPLA7	124	1	NM_001098537	exon32	c.C3717G	p.L1239L	GTCGCGGAGCATC	.	PASS	Atlas-SNP
TRPC1	7220	hgsc.bcm.edu	37	3	142503605	142503605	+	Silent	SNP	G	G	A	rs7621642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	135	3	158	0	0.0222222	0	G|0.616;A|0.384	0.384	strong	TRPC1,NS,carcinoma,0,1	TRPC1	82	1	NM_001251845	exon7	c.G1020A	p.S340S	GATGTCGGGTTAC	.	scavenged	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489745	32489745	+	Missense_Mutation	SNP	C	C	G	rs41548618	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	5	5	0	0	1	.	C|0.807;G|0.193	0.193	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.G307C	p.A103P	CCACCGCGGCGCG	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	37	5	79950715	79950715	+	Missense_Mutation	SNP	G	G	C	rs144776112	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	27	15	9	0	0.555556	0	G|0.835;C|0.165	0.165	strong	MSH3_ENST00000265081,NS,carcinoma,0,1	MSH3	129	1	NM_002439	exon1	c.G169C	p.A57P	GCAGCGGCCGCAG	.	PASS	Atlas-SNP
APBB1	322	hgsc.bcm.edu	37	11	6422229	6422229	+	Silent	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	179	2	142	0	0.0111732	0	.	.	none	APBB1,NS,carcinoma,-2,1	APBB1	73	1	NM_001164	exon11	c.T1662C	p.A554A	AGGTTTAGCAACA	.	scavenged	Atlas-SNP
TDRD5	163589	hgsc.bcm.edu	37	1	179562740	179562740	+	Missense_Mutation	SNP	G	G	C	rs61310274	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	260	6	192	1	0.0230769	0.00520833	G|0.693;C|0.307	0.307	strong	TDRD5,NS,neuroblastoma,+1,1	TDRD5	149	1	NM_173533	exon3	c.G378C	p.R126S	AGGAAGGGTTGCC	.	scavenged	Atlas-SNP
ANAPC1	64682	hgsc.bcm.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	T	C	rs12466309	bycluster;byfrequency;byhapmap	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	822	25	892	7	0.0304136	0.00784753	T|0.500;C|0.500	0.500	strong	ANAPC1,NS,carcinoma,0,9	ANAPC1	116	9	NM_022662	exon14	c.A1609G	p.T537A	TTGGAGTACTAAC	.	scavenged	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147488367	147488367	+	Silent	SNP	C	C	T	rs2303071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	497	17	584	0	0.0342052	0	C|0.416;T|0.584	0.584	strong	SPINK5_ENST00000359874,NS,carcinoma,0,3	SPINK5	245	3	NM_001127699	exon18	c.C1659T	p.V553V	GAAAGTCGAGGCT	.	scavenged	Atlas-SNP
VWA2	340706	hgsc.bcm.edu	37	10	116014769	116014769	+	Missense_Mutation	SNP	A	A	T	rs75028145	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	106	4	108	0	0.0377358	0	A|0.994;T|0.006	0.006	strong	VWA2,NS,carcinoma,0,1	VWA2	64	1	NM_001272046	exon4	c.A223T	p.I75F	TTTGCCATCACAG	.	scavenged	Atlas-SNP
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	103	5	90	0	0.0485437	0	G|0.422;N|0.000	0.422	strong	.	ATG16L1	83	.	NM_030803	exon9	c.A898G	p.T300A	GTGGATACTCATC	.	PASS	Atlas-SNP
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	Silent	SNP	A	A	G	rs1065178	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	115	5	90	0	0.0434783	0	A|0.622;G|0.378	0.378	strong	.	.	.	.	NM_001206650	exon2	c.T132C	p.I44I	GGTTAAAATCACA	.	PASS	Atlas-SNP
SGTA	6449	hgsc.bcm.edu	37	19	2767594	2767594	+	Missense_Mutation	SNP	G	G	T	rs367983019	alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	82	4	99	0	0.0487805	0	.	.	alt	.	SGTA	19	.	NM_003021	exon3	c.C191A	p.A64E	GCAGCCGCTTCAA	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117113653	117113653	+	Silent	SNP	T	T	C	rs615199	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	79	5	144	0	0.0632911	0	C|0.301;N|0.000	0.301	strong	GPRC6A,NS,carcinoma,0,1	GPRC6A	152	1	NM_148963	exon6	c.A2433G	p.P811P	CACAGCTGGTACA	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124274474	124274474	+	Missense_Mutation	SNP	A	A	G	rs10846559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	118	10	127	0	0.0847458	0	A|0.235;G|0.765	0.765	strong	.	DNAH10	888	.	NM_207437	exon11	c.A1438G	p.I480V	GGACAGATTTTGG	.	PASS	Atlas-SNP
OR6B1	135946	hgsc.bcm.edu	37	7	143701884	143701884	+	Silent	SNP	C	C	T	rs728275	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	4	57	0	0.0547945	0	C|0.586;T|0.414	0.414	strong	.	OR6B1	60	.	NM_001005281	exon1	c.C795T	p.A265A	CCATGCCTTCAAC	.	PASS	Atlas-SNP
ABCC5	10057	hgsc.bcm.edu	37	3	183699516	183699516	+	Silent	SNP	T	T	C	rs7636910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	193	9	179	1	0.0466321	0.00558659	T|0.657;C|0.343	0.343	strong	ABCC5,NS,carcinoma,0,1	ABCC5	142	1	NM_005688	exon8	c.A1146G	p.Q382Q	CTCACTTTGAACA	.	scavenged	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25222165	25222165	+	Missense_Mutation	SNP	A	A	G	rs2271111	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	187	6	212	0	0.0320856	0	A|0.749;G|0.251	0.251	strong	DOCK5,NS,carcinoma,0,1	DOCK5	167	1	NM_024940	exon30	c.A3068G	p.Q1023R	TAAATCAGTTTGC	.	scavenged	Atlas-SNP
WDR60	55112	hgsc.bcm.edu	37	7	158672619	158672619	+	Missense_Mutation	SNP	A	A	G	rs2788478	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	252	14	253	0	0.0555556	0	A|0.435;G|0.565	0.565	strong	.	WDR60	94	.	NM_018051	exon5	c.A818G	p.Q273R	GGCACCAAAGCAA	.	PASS	Atlas-SNP
SLC16A4	9122	hgsc.bcm.edu	37	1	110924353	110924353	+	Silent	SNP	G	G	A	rs3738750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	448	8	441	1	0.0178571	0.00226757	G|0.839;A|0.161	0.161	strong	SLC16A4,NS,carcinoma,0,2	SLC16A4	47	2	NM_004696	exon4	c.C285T	p.F95F	AACAACGAAAGCC	.	scavenged	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	95791613	95791613	+	Silent	SNP	T	T	C	rs17109671	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	169	4	195	0	0.0236686	0	T|0.609;C|0.391	0.391	strong	PLCE1_ENST00000260766,colon,carcinoma,0,2	PLCE1	543	2	NM_016341	exon2	c.T810C	p.C270C	CTCTTGTGAGAAG	.	scavenged	Atlas-SNP
ACTR8	93973	hgsc.bcm.edu	37	3	53905308	53905308	+	Silent	SNP	T	T	C	rs1046677	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	136	5	155	1	0.0367647	0.00645161	T|0.410;C|0.590	0.590	strong	ACTR8_ENST00000231909,NS,carcinoma,-2,2	ACTR8	56	2	NM_022899	exon11	c.A1518G	p.G506G	GGCTTTTCCTTCA	.	scavenged	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031622	32031622	+	Missense_Mutation	SNP	T	T	C	rs13087612	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	346	4	345	1	0.0115607	0.00289855	T|0.621;C|0.379	0.379	strong	ZNF860_ENST00000360311,NS,carcinoma,0,2	ZNF860	96	2	NM_001137674	exon2	c.T1051C	p.F351L	AAGGCTTTCAGGC	.	scavenged	Atlas-SNP
CFH	3075	hgsc.bcm.edu	37	1	196695742	196695742	+	Silent	SNP	A	A	G	rs3753396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	570	6	441	1	0.0105263	0.00226757	A|0.777;G|0.223	0.223	strong	CFH,NS,carcinoma,+2,3	CFH	251	3	NM_000186	exon13	c.A2016G	p.Q672Q	AATTCAATGTGTT	.	scavenged	Atlas-SNP
IFNA21	3452	hgsc.bcm.edu	37	9	21166246	21166246	+	Silent	SNP	G	G	A	rs139462830		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	241	4	244	0	0.0165975	0	G|1.000;A|0.000	0.000	weak	IFNA21,colon,carcinoma,0,1	IFNA21	25	1	NM_002175	exon1	c.C366T	p.C122C	TATCACGCAGGCT	.	scavenged	Atlas-SNP
PHC2	1912	hgsc.bcm.edu	37	1	33820033	33820033	+	Silent	SNP	C	C	T	rs16835408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	76	6	74	0	0.0789474	0	C|0.900;T|0.100	0.100	strong	.	PHC2	78	.	NM_198040	exon8	c.G1524A	p.T508T	AGGGCTCGTGGGT	.	PASS	Atlas-SNP
CD3D	915	hgsc.bcm.edu	37	11	118211113	118211113	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	102	25	108	0	0.245098	0	.	.	none	.	CD3D	21	.	NM_000732	exon2	c.C251T	p.S84F	ACGGTAGATTCTT	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115377290	115377290	+	Missense_Mutation	SNP	T	T	C	rs77678145	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	75	4	82	0	0.0533333	0	A|0.000;C|0.068;T|0.932	0.068	strong	.	NRAP	208	.	NM_001261463	exon26	c.A2897G	p.D966G	AAAGCATCTGGAT	.	PASS	Atlas-SNP
OR6M1	390261	hgsc.bcm.edu	37	11	123676690	123676690	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	97	36	71	0	0.371134	0	.	.	none	.	OR6M1	60	.	NM_001005325	exon1	c.C368A	p.A123D	CAGATAGCCATGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510156	195510156	+	Missense_Mutation	SNP	G	G	C	rs201141296	byfrequency;alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	45	5	43	4	0.111111	0.0930233	G|0.996;A|0.004	.	alt	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.C8295G	p.H2765Q	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
PEX26	55670	hgsc.bcm.edu	37	22	18562701	18562701	+	Missense_Mutation	SNP	C	C	T	rs62641228	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	187	4	244	0	0.0213904	0	C|1.000;T|0.000	0.000	weak	PEX26,NS,carcinoma,0,1	PEX26	27	1	NM_001127649	exon2	c.C292T	p.R98W	ATGGATCGGTGGC	.	scavenged	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32134926	32134926	+	Missense_Mutation	SNP	G	G	A	rs3207618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	237	10	190	0	0.0421941	0	G|0.936;A|0.064	0.064	strong	.	.	.	.	NM_018169	exon4	c.G1037A	p.S346N	CCAACAGCAAACA	.	PASS	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72413423	72413423	+	Missense_Mutation	SNP	C	C	T	rs75799836		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	266	4	282	0	0.0150376	0	C|0.500;T|0.500	0.500	weak	POM121,rectum,carcinoma,0,1	POM121	131	1	NM_172020	exon11	c.C2096T	p.P699L	CATATCCGGGAGC	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1267562	1267562	+	Missense_Mutation	SNP	C	C	T	rs61737593	byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	230	11	217	2	0.0478261	0.00921659	C|0.929;T|0.071	0.071	strong	MUC5AC,NS,carcinoma,-1,1	MUC5B	473	1	NM_002458	exon31	c.C9452T	p.T3151M	GCCCCACGGCCAC	.	scavenged	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9237435	9237435	+	Silent	SNP	A	A	G	rs10407484	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	115	4	110	0	0.0347826	0	A|0.566;G|0.434	0.434	strong	OR7G3,NS,carcinoma,0,1	OR7G3	41	1	NM_001001958	exon1	c.T192C	p.S64S	CAGGATAGAGAGG	.	scavenged	Atlas-SNP
FAM126A	84668	hgsc.bcm.edu	37	7	23015831	23015831	+	Silent	SNP	T	T	C	rs3735231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	3	89	0	0.0357143	0	T|0.643;C|0.357	0.357	strong	FAM126A,NS,carcinoma,-1,1	FAM126A	53	1	NM_032581	exon7	c.A624G	p.S208S	TTACCTTGAACAA	.	scavenged	Atlas-SNP
ZNF839	55778	hgsc.bcm.edu	37	14	102792822	102792822	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	2	77	0	0.0238095	0	.	.	none	ZNF839,NS,carcinoma,+2,1	ZNF839	41	1	NM_018335	exon2	c.T789C	p.D263D	TAAAGATTATAAG	.	scavenged	Atlas-SNP
SPACA7	122258	hgsc.bcm.edu	37	13	113053470	113053470	+	Missense_Mutation	SNP	T	T	A	rs10816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	152	5	156	0	0.0328947	0	T|0.343;A|0.657	0.657	strong	SPACA7,NS,adenoma,0,1	SPACA7	36	1	NM_145248	exon4	c.T332A	p.V111D	TTGAGGTCAAAAT	.	scavenged	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11149769	11149769	+	Missense_Mutation	SNP	T	T	C	rs10845281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	184	9	205	0	0.048913	0	T|0.675;C|0.325	0.325	strong	.	TAS2R20	17	.	NM_176889	exon1	c.A706G	p.I236V	GTAATATGAGGAA	.	PASS	Atlas-SNP
DEFB127	140850	hgsc.bcm.edu	37	20	139456	139456	+	Missense_Mutation	SNP	G	G	A	rs12624954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	290	12	279	0	0.0413793	0	G|0.719;A|0.281	0.281	strong	DEFB127,NS,carcinoma,-1,1	DEFB127	15	1	NM_139074	exon2	c.G91A	p.G31R	GTACAAGGACATT	.	PASS	Atlas-SNP
WDR49	151790	hgsc.bcm.edu	37	3	167320010	167320010	+	Missense_Mutation	SNP	T	T	C	rs75218075	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	257	11	281	0	0.0428016	0	T|0.965;C|0.035	0.035	strong	.	WDR49	188	.	NM_178824	exon3	c.A157G	p.K53E	CTGGTTTAGAGAC	.	PASS	Atlas-SNP
BTBD16	118663	hgsc.bcm.edu	37	10	124096035	124096035	+	Silent	SNP	T	T	C	rs3817281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	80	5	86	0	0.0625	0	T|0.613;C|0.387	0.387	strong	.	BTBD16	44	.	NM_144587	exon15	c.T1290C	p.S430S	GGAATCTCCCTCT	.	PASS	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124293857	124293857	+	Missense_Mutation	SNP	A	A	C	rs79770470	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	172	4	123	0	0.0232558	0	A|0.995;C|0.005	0.005	strong	OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	NM_001005196	exon1	c.T911G	p.L304R	CTCTTCAGGGTTT	.	scavenged	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74897816	74897816	+	Silent	SNP	C	C	T	rs2271905	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	251	10	232	0	0.0398406	0	C|0.809;T|0.191	0.191	strong	ECD,NS,carcinoma,0,1	ECD	50	1	NM_001135752	exon13	c.G1533A	p.E511E	TGGAGCCTCAGAA	.	scavenged	Atlas-SNP
CACNG4	27092	hgsc.bcm.edu	37	17	65026886	65026886	+	Silent	SNP	C	C	T	rs11649752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	93	4	102	0	0.0430108	0	C|0.921;T|0.079	0.079	strong	.	CACNG4	44	.	NM_014405	exon4	c.C750T	p.T250T	GTCCACCGAGGCC	.	PASS	Atlas-SNP
ADD1	118	hgsc.bcm.edu	37	4	2916762	2916762	+	Missense_Mutation	SNP	C	C	G	rs4963	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	103	6	95	0	0.0582524	0	C|0.773;G|0.227;N|0.000	0.227	strong	.	ADD1	56	.	NM_176801	exon13	c.C1850G	p.S617C	AGGGCTCTGAAGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511959	195511959	+	Silent	SNP	G	G	A	rs369770584	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	57	3	65	1	0.0526316	0.0153846	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C6492T	p.T2164T	AGTGTCGGTGACA	.	scavenged	Atlas-SNP
C3orf35	339883	hgsc.bcm.edu	37	3	37476379	37476379	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	248	88	265	0	0.354839	0	.	.	none	.	C3orf35	21	.	NM_178339	exon6	c.C271T	p.P91S	TCAATCCCAGCTG	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878551	190878551	+	Splice_Site	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	211	4	237	2	0.0189573	0.00843882	.	.	none	FRG1,NS,malignant_melanoma,0,1	FRG1	76	1	NM_004477	exon6	c.433-2A>G	.	TCACTTAGGGGAA	.	scavenged	Atlas-SNP
GPRIN2	9721	hgsc.bcm.edu	37	10	46999601	46999601	+	Missense_Mutation	SNP	G	G	A	rs9422022	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	60	8	67	0	0.133333	0	G|0.638;A|0.362	0.362	strong	GPRIN2,caecum,adenoma,0,1	GPRIN2	94	1	NM_014696	exon3	c.G721A	p.V241M	AGGGAGGTGAGGG	.	PASS	Atlas-SNP
CENPC1	1060	hgsc.bcm.edu	37	4	68380215	68380215	+	Missense_Mutation	SNP	G	G	A	rs11250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	154	8	181	0	0.0519481	0	G|0.299;A|0.701	0.701	strong	.	CENPC1	66	.	NM_001812	exon8	c.C1021T	p.L341F	CTTGAAGGAGTGC	.	PASS	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117114223	117114223	+	Silent	SNP	T	T	A	rs6924002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	126	11	224	0	0.0873016	0	T|0.683;A|0.317	0.317	strong	.	GPRC6A	152	.	NM_148963	exon6	c.A1863T	p.T621T	AACAGGTGTGTTC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721042	54721042	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	167	5	128	0	0.0299401	0	.	.	none	LILRB3,NS,carcinoma,0,1	LILRB3	67	1	NM_001081450	exon13	c.A1819G	p.K607E	TTGCCTTCCGTCT	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1087972	1087972	+	Silent	SNP	C	C	T	rs10902088	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	140	10	119	0	0.0714286	0	C|0.712;T|0.288	0.288	strong	.	MUC2	614	.	NM_002457	exon25	c.C3447T	p.N1149N	CATCAACGGCATC	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147481430	147481430	+	Silent	SNP	A	A	G	rs6896303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	115	4	136	0	0.0347826	0	A|0.545;G|0.455	0.455	strong	SPINK5,NS,carcinoma,0,1	SPINK5	245	1	NM_001127699	exon15	c.A1389G	p.G463G	AGATGGAAAAATG	.	scavenged	Atlas-SNP
ZNF234	10780	hgsc.bcm.edu	37	19	44652954	44652954	+	Missense_Mutation	SNP	G	G	A	rs2293587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	191	8	223	0	0.0418848	0	G|0.660;A|0.340	0.340	strong	.	ZNF234	132	.	NM_006630	exon4	c.G46A	p.V16I	GCTGTGGTCTTCA	.	PASS	Atlas-SNP
PLEKHH2	130271	hgsc.bcm.edu	37	2	43953574	43953574	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	190	8	167	0	0.0421053	0	.	.	none	.	PLEKHH2	156	.	NM_172069	exon17	c.G2705A	p.G902E	TAATTGGATCCAA	.	PASS	Atlas-SNP
PRB4	5545	hgsc.bcm.edu	37	12	11461738	11461738	+	Missense_Mutation	SNP	G	G	C	rs79562958	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	47	3	29	2	0.0638298	0.0689655	C|1.000;|0.000	1.000	weak	PRB4,NS,carcinoma,0,1	PRB4	59	1	NM_001261399	exon3	c.C179G	p.P60R	GGGGGTGGTCCTT	.	scavenged	Atlas-SNP
TOX2	84969	hgsc.bcm.edu	37	20	42694462	42694462	+	Silent	SNP	G	G	A	rs148482710	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	132	3	118	0	0.0227273	0	G|0.999;A|0.001	0.001	strong	TOX2_ENST00000348077,right_lower_lobe,carcinoma,0,2	TOX2	158	2	NM_001098797	exon7	c.G1071A	p.T357T	CCTGACGCCGTCG	.	scavenged	Atlas-SNP
AP1M2	10053	hgsc.bcm.edu	37	19	10692000	10692000	+	Silent	SNP	T	T	C	rs1045361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	151	6	124	0	0.0397351	0	T|0.749;C|0.251	0.251	strong	AP1M2,colon,carcinoma,0,1	AP1M2	35	1	NM_005498	exon6	c.A615G	p.S205S	CATTCCTGACAGA	.	scavenged	Atlas-SNP
COL24A1	255631	hgsc.bcm.edu	37	1	86512536	86512536	+	Missense_Mutation	SNP	C	C	T	rs60891279	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	397	10	446	1	0.0251889	0.00224215	C|0.832;T|0.168	0.168	strong	COL24A1,NS,carcinoma,-1,1	COL24A1	202	1	NM_152890	exon12	c.G1922A	p.R641H	TTTCCACGGATCC	.	scavenged	Atlas-SNP
PDZRN4	29951	hgsc.bcm.edu	37	12	41946463	41946463	+	Silent	SNP	C	C	T	rs74569207	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	58	4	67	0	0.0689655	0	C|0.991;T|0.009	0.009	strong	.	PDZRN4	346	.	NM_001164595	exon6	c.C1209T	p.V403V	GGAGGTCGAGTTG	.	PASS	Atlas-SNP
MEGF10	84466	hgsc.bcm.edu	37	5	126674869	126674869	+	Silent	SNP	G	G	A	rs12654455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	4	115	0	0.0408163	0	G|0.975;A|0.025	0.025	strong	.	MEGF10	152	.	NM_032446	exon4	c.G174A	p.T58T	CTACACGAGCTGC	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32906729	32906729	+	Missense_Mutation	SNP	A	A	C	rs144848	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	80	4	105	0	0.05	0	T|0.005;G|0.003	.	strong	BRCA2_ENST00000544455,NS,carcinoma,0,1	BRCA2	812	1	NM_000059	exon10	c.A1114C	p.N372H	GTAGCAAATCAGA	.	PASS	Atlas-SNP
PIK3C3	5289	hgsc.bcm.edu	37	18	39617703	39617703	+	Silent	SNP	C	C	A	rs143493401	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	4	145	0	0.0373832	0	C|0.994;A|0.006	0.006	strong	PIK3C3,lower_third,carcinoma,+1,1	PIK3C3	138	1	NM_002647	exon17	c.C1887A	p.G629G	TGGAGGCAAATAT	.	scavenged	Atlas-SNP
TYW1	55253	hgsc.bcm.edu	37	7	66479413	66479413	+	Silent	SNP	T	T	C	rs3748104		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	275	4	301	0	0.0145455	0	.	.	weak	TYW1,NS,carcinoma,0,1	TYW1	71	1	NM_018264	exon5	c.T435C	p.T145T	ACCAACTGAAAGT	.	scavenged	Atlas-SNP
KCNH2	3757	hgsc.bcm.edu	37	7	150648789	150648789	+	Silent	SNP	T	T	C	rs1805121	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	96	5	113	0	0.0520833	0	T|0.477;C|0.523	0.523	strong	KCNH2_ENST00000430723,NS,carcinoma,0,2	KCNH2	157	2	NM_000238	exon7	c.A1692G	p.L564L	GCAGGCTAGCCAG	.	PASS	Atlas-SNP
FOLH1	2346	hgsc.bcm.edu	37	11	49204779	49204779	+	Missense_Mutation	SNP	C	C	T	rs116795343	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	300	7	240	2	0.0233333	0.00833333	C|0.974;T|0.026	0.026	strong	FOLH1,NS,carcinoma,-1,2	FOLH1	141	2	NM_004476	exon7	c.G842A	p.R281H	ATTCCACGCCTAT	.	scavenged	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079894	31079894	+	Missense_Mutation	SNP	A	A	G	rs2233977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	90	4	85	1	0.0444444	0.0117647	A|0.825;G|0.175	0.175	strong	C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	NM_014070	exon2	c.T242C	p.V81A	GCAGGCACGCTGA	.	scavenged	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46330809	46330809	+	Silent	SNP	G	G	A	rs35490979	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	106	5	114	0	0.0471698	0	G|0.931;A|0.069	0.069	strong	.	SYMPK	104	.	NM_004819	exon16	c.C2140T	p.L714L	CATGCAGGTACTG	.	PASS	Atlas-SNP
GPR152	390212	hgsc.bcm.edu	37	11	67220015	67220015	+	Missense_Mutation	SNP	C	C	T	rs79423227	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	139	6	101	0	0.0431655	0	C|0.975;T|0.025	0.025	strong	.	GPR152	41	.	NM_206997	exon1	c.G181A	p.G61R	CAGCTCCATGCCG	.	PASS	Atlas-SNP
GDE1	51573	hgsc.bcm.edu	37	16	19516398	19516398	+	Missense_Mutation	SNP	C	C	T	rs2072086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	165	4	172	0	0.0242424	0	C|0.996;T|0.004	0.004	strong	GDE1,caecum,carcinoma,-1,2	GDE1	31	2	NM_016641	exon5	c.G653A	p.R218Q	ACATCCCGATCTG	.	scavenged	Atlas-SNP
ACSM2A	123876	hgsc.bcm.edu	37	16	20494408	20494408	+	Missense_Mutation	SNP	C	C	T	rs1133607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	117	6	117	1	0.0512821	0.00854701	C|0.880;T|0.120	0.120	strong	ACSM2A,NS,carcinoma,+1,1	ACSM2A	120	1	NM_001010845	exon14	c.C1538T	p.S513L	TGGCCTCGCAGTT	.	scavenged	Atlas-SNP
SLC45A2	51151	hgsc.bcm.edu	37	5	33963870	33963870	+	Missense_Mutation	SNP	C	C	T	rs26722	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	113	6	137	0	0.0530973	0	C|0.910;T|0.090	0.090	strong	.	SLC45A2	100	.	NM_016180	exon3	c.G814A	p.E272K	CTTTCTCGATAGA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385184	16385184	+	Silent	SNP	G	G	A	rs75273615	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	434	7	380	2	0.016129	0.00526316	G|0.740;A|0.260	0.260	strong	FAM131C,NS,haematopoietic_neoplasm,0,1	FAM131C	21	1	NM_182623	exon7	c.C591T	p.S197S	GGGAAGGCTGTCC	.	scavenged	Atlas-SNP
SH3BP4	23677	hgsc.bcm.edu	37	2	235951819	235951819	+	Silent	SNP	A	A	G	rs3795962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	176	10	199	0	0.0568182	0	G|0.647;N|0.001	0.647	strong	SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	NM_014521	exon4	c.A2406G	p.L802L	CGTCCTAGAAAAG	.	PASS	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234327	45234327	+	Missense_Mutation	SNP	C	C	T	rs7350889	bycluster;byhapmap	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	78	5	73	1	0.0641026	0.0136986	C|1.000;|0.000	.	weak	CDC27_ENST00000531206,NS,adenoma,0,4	CDC27	337	4	NM_001114091	exon7	c.G794A	p.G265D	CTTCGACCAGTTT	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179604859	179604859	+	Missense_Mutation	SNP	C	C	A	rs367656813		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	109	29	107	0	0.266055	0	.	.	weak	.	TTN	18412	.	NM_001267550	exon48	c.G13101T	p.K4367N	CACTTTCTTTATT	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12887686	12887686	+	Silent	SNP	T	T	C	rs59802947	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	16	4	9	0	0.25	0	T|0.986;C|0.014	0.014	strong	PRAMEF11,NS,carcinoma,0,1	PRAMEF11	72	1	NM_001146344	exon3	c.A171G	p.R57R	TTTCCATCTCCTG	.	scavenged	Atlas-SNP
CNTN6	27255	hgsc.bcm.edu	37	3	1414127	1414127	+	Missense_Mutation	SNP	A	A	G	rs145045076	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	93	4	115	0	0.0430108	0	A|0.994;G|0.006	0.006	strong	CNTN6,NS,lymphoid_neoplasm,0,1	CNTN6	245	1	NM_014461	exon13	c.A1637G	p.K546R	TAAAAAAAGGAGT	.	PASS	Atlas-SNP
KIAA0196	9897	hgsc.bcm.edu	37	8	126069044	126069044	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	23	70	0	0.315068	0	.	.	none	KIAA0196,NS,malignant_melanoma,0,1	KIAA0196	90	1	NM_014846	exon16	c.C1891T	p.P631S	TTTCTGGGATGAT	.	PASS	Atlas-SNP
KIF20B	9585	hgsc.bcm.edu	37	10	91470834	91470834	+	Silent	SNP	A	A	C	rs1048057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	205	6	247	0	0.0292683	0	A|0.632;C|0.368	0.368	strong	KIF20B,NS,carcinoma,0,1	KIF20B	191	1	NM_016195	exon6	c.A607C	p.R203R	TACTTAAGGTTAT	.	scavenged	Atlas-SNP
SAMD9L	219285	hgsc.bcm.edu	37	7	92762681	92762681	+	Silent	SNP	A	A	G	rs1029357	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	114	4	131	1	0.0350877	0.00763359	A|0.774;G|0.226	0.226	strong	SAMD9L,NS,carcinoma,0,1	SAMD9L	227	1	NM_152703	exon5	c.T2604C	p.A868A	ACCAAAAGCTCTT	.	scavenged	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	37	21	43221555	43221555	+	Silent	SNP	G	G	A	rs2236694	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	121	8	106	1	0.0661157	0.00943396	G|0.915;A|0.085	0.085	strong	PRDM15,NS,carcinoma,0,1	PRDM15	110	1	NM_022115	exon31	c.C4369T	p.L1457L	TCCCCAGGGGCGT	.	scavenged	Atlas-SNP
ANKRD11	29123	hgsc.bcm.edu	37	16	89348038	89348038	+	Missense_Mutation	SNP	G	G	C	rs113527563	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	75	2	71	0	0.0266667	0	G|0.966;C|0.034	0.034	strong	ANKRD11,NS,carcinoma,0,1	ANKRD11	195	1	NM_001256183	exon9	c.C4912G	p.P1638A	TAGCAGGAATGTC	.	scavenged	Atlas-SNP
NDUFB1	4707	hgsc.bcm.edu	37	14	92588002	92588002	+	Silent	SNP	T	T	G	rs3818263	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	170	6	148	1	0.0352941	0.00675676	T|0.520;G|0.480	0.480	strong	NDUFB1,rectum,carcinoma,0,1	NDUFB1	5	1	NM_004545	exon1	c.A120C	p.V40V	AGCGCCTACAGCG	.	scavenged	Atlas-SNP
LRRC3B	116135	hgsc.bcm.edu	37	3	26751493	26751493	+	Silent	SNP	A	A	T	rs35497952	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	8	160	0	0.0689655	0	A|0.898;T|0.102	0.102	strong	.	LRRC3B	51	.	NM_052953	exon2	c.A330T	p.G110G	CAAAGGAGTAGCT	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115410234	115410234	+	Missense_Mutation	SNP	T	T	C	rs2185913	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	129	5	115	0	0.0387597	0	T|0.781;C|0.219	0.219	strong	NRAP,NS,carcinoma,0,1	NRAP	208	1	NM_001261463	exon8	c.A746G	p.Y249C	ATCTGATAGGCGG	.	scavenged	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Silent	SNP	C	C	T	rs371465078	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	141	7	138	6	0.0496454	0.0434783	.	.	weak	SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	NM_001135844	exon2	c.G243A	p.Q81Q	TTCTTTCTGATTG	.	scavenged	Atlas-SNP
PRAMEF10	343071	hgsc.bcm.edu	37	1	12954852	12954852	+	Missense_Mutation	SNP	T	T	C	rs2797709	bycluster;by2hit2allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	27	6	29	4	0.222222	0.137931	T|0.500;C|0.500	0.500	weak	PRAMEF10,NS,NS,0,1	PRAMEF10	35	1	NM_001039361	exon3	c.A431G	p.H144R	GGCTGGTGCTCTC	.	scavenged	Atlas-SNP
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815522	23815522	+	Silent	SNP	C	C	T	rs3755863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	152	7	160	0	0.0460526	0	C|0.640;T|0.360	0.360	strong	PPARGC1A,colon,carcinoma,0,1	PPARGC1A	129	1	NM_013261	exon8	c.G1584A	p.T528T	GGATTGCGTGCCA	.	PASS	Atlas-SNP
SNPH	9751	hgsc.bcm.edu	37	20	1285933	1285933	+	Silent	SNP	G	G	A	rs3795139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	57	6	45	0	0.105263	0	G|0.650;A|0.350	0.350	strong	.	SNPH	89	.	NM_014723	exon6	c.G720A	p.G240G	GGATGGGGCAGAC	.	PASS	Atlas-SNP
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	232	15	214	5	0.0646552	0.0233645	.	.	alt	ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	NM_001012753	exon2	c.G81C	p.S27S	TATTTCGCAGAGG	.	scavenged	Atlas-SNP
IPO5	3843	hgsc.bcm.edu	37	13	98670828	98670828	+	Silent	SNP	C	C	T	rs140767528	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	192	4	213	1	0.0208333	0.00469484	C|0.997;T|0.003	0.003	strong	IPO5,colon,carcinoma,0,1	IPO5	90	1	NM_002271	exon26	c.C2760T	p.Y920Y	TAAATACGCAGAA	.	scavenged	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	104831794	104831794	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	22	114	1	0.261905	0.00877193	.	.	none	RIMS2_ENST00000507740,colon,carcinoma,+1,1	RIMS2	1357	1	NM_014677	exon1	c.T59G	p.V20G	ATGGGGTTTTTTC	.	scavenged	Atlas-SNP
CARD6	84674	hgsc.bcm.edu	37	5	40853048	40853048	+	Silent	SNP	C	C	T	rs16870407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	130	5	161	0	0.0384615	0	C|0.892;G|0.000;T|0.108	0.108	strong	CARD6,caecum,carcinoma,+1,1	CARD6	141	1	NM_032587	exon3	c.C1614T	p.S538S	AGAAAGCTTTTGG	.	scavenged	Atlas-SNP
LMBRD1	55788	hgsc.bcm.edu	37	6	70409081	70409081	+	Missense_Mutation	SNP	A	A	G	rs185334169	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	7	105	0	0.0654206	0	A|0.997;G|0.003	0.003	strong	.	LMBRD1	61	.	NM_018368	exon13	c.T1192C	p.Y398H	TTTTATATAACTG	.	PASS	Atlas-SNP
CHMP2B	25978	hgsc.bcm.edu	37	3	87276699	87276699	+	Silent	SNP	C	C	T	rs2279720	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	144	8	157	0	0.0555556	0	C|0.889;T|0.111	0.111	strong	CHMP2B,NS,carcinoma,0,1	CHMP2B	28	1	NM_014043	exon1	c.C27T	p.T9T	GAAAACCGTGGAT	.	PASS	Atlas-SNP
UBQLN1	29979	hgsc.bcm.edu	37	9	86278817	86278817	+	Silent	SNP	C	C	A	rs7866234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	121	11	108	0	0.0909091	0	C|0.700;A|0.300	0.300	strong	.	UBQLN1	49	.	NM_013438	exon10	c.G1590T	p.L530L	AGCCTGCAGCATC	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107360922	107360922	+	Missense_Mutation	SNP	A	A	G	rs1851724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	191	5	189	0	0.026178	0	A|0.421;G|0.579	0.579	strong	OR13C5,NS,lymphoid_neoplasm,0,1	OR13C5	60	1	NM_001004482	exon1	c.T773C	p.M258T	ATGTACATGAGGA	.	scavenged	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79031372	79031372	+	Missense_Mutation	SNP	G	G	C	rs6859595	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	215	9	229	0	0.0418605	0	G|0.737;C|0.263	0.263	strong	.	CMYA5	643	.	NM_153610	exon2	c.G6784C	p.V2262L	CAAAACGTTAAAG	.	PASS	Atlas-SNP
CCDC178	374864	hgsc.bcm.edu	37	18	30804758	30804758	+	Missense_Mutation	SNP	A	A	C	rs457896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	91	2	85	0	0.021978	0	A|0.836;C|0.164	0.164	strong	C18orf34_ENST00000383096,colon,carcinoma,0,2	.	.	2	NM_001105528	exon16	c.T1799G	p.L600R	TTGTCGAGACTTC	.	scavenged	Atlas-SNP
C4A	720	hgsc.bcm.edu	37	6	31963559	31963559	+	Silent	SNP	A	A	G	rs2258218	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	579	9	515	6	0.015544	0.0116505	A|0.500;G|0.500	0.500	strong	C4B,right_upper_lobe,carcinoma,0,2	C4A	15	2	NM_007293	exon25	c.G3218G	p.G1073G	CACGGGACAGCAG	.	scavenged	Atlas-SNP
EEF1A2	1917	hgsc.bcm.edu	37	20	62126299	62126299	+	Silent	SNP	C	C	T	rs2274860	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	115	7	92	0	0.0608696	0	C|0.872;T|0.128	0.128	strong	.	EEF1A2	60	.	NM_001958	exon4	c.G480A	p.P160P	GTAGGCCGGCTCT	.	PASS	Atlas-SNP
KDM3A	55818	hgsc.bcm.edu	37	2	86697366	86697366	+	Missense_Mutation	SNP	T	T	A	rs186664065	by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	278	6	259	1	0.0215827	0.003861	T|0.996;A|0.004	0.004	strong	KDM3A,NS,carcinoma,0,1	KDM3A	179	1	NM_001146688	exon11	c.T1559A	p.L520H	CTAAACTCAAAAA	.	scavenged	Atlas-SNP
CCP110	9738	hgsc.bcm.edu	37	16	19547747	19547747	+	Missense_Mutation	SNP	C	C	G	rs226891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	65	4	49	0	0.0615385	0	C|0.098;G|0.902	0.902	strong	CCP110,NS,carcinoma,0,1	CCP110	57	1	NM_001199022	exon4	c.C756G	p.I252M	TAGTATCAACAGA	.	scavenged	Atlas-SNP
SERPINB5	5268	hgsc.bcm.edu	37	18	61160320	61160320	+	Missense_Mutation	SNP	G	G	C	rs2289520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	75	4	86	0	0.0533333	0	G|0.748;C|0.252	0.252	strong	.	SERPINB5	35	.	NM_002639	exon5	c.G559C	p.V187L	TTCAGAGTCAACA	.	PASS	Atlas-SNP
ARHGAP12	94134	hgsc.bcm.edu	37	10	32141460	32141460	+	Silent	SNP	T	T	C	rs2799021	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	238	11	254	0	0.0462185	0	T|0.798;C|0.202	0.202	strong	.	ARHGAP12	79	.	NM_001270696	exon6	c.A1155G	p.E385E	TTCCCATTCTGAC	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52710309	52710309	+	Silent	SNP	G	G	A	rs75619735		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	6	85	0	0.0674157	0	.	.	weak	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon6	c.C984T	p.N328N	CAGCTCGTTGATC	.	PASS	Atlas-SNP
SALL3	27164	hgsc.bcm.edu	37	18	76753768	76753768	+	Missense_Mutation	SNP	C	C	G	rs2447437	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	6	3	4	1	0.5	0.25	C|0.211;G|0.789	0.789	strong	SALL3,NS,carcinoma,0,1	SALL3	162	1	NM_171999	exon2	c.C1777G	p.L593V	CCGCCCCTCACTA	.	scavenged	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86940622	86940622	+	Silent	SNP	T	T	C	rs4362360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	4	122	0	0.047619	0	T|0.292;C|0.708	0.708	strong	.	AGBL1	151	.	NM_152336	exon17	c.T2262C	p.T754T	GATCACTGCTCGA	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	5	109	0	0.0416667	0	G|0.552;A|0.448	0.448	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.G2137A	p.V713I	GGAGACGTTTCCC	.	PASS	Atlas-SNP
PMP2	5375	hgsc.bcm.edu	37	8	82357112	82357112	+	Silent	SNP	T	T	C	rs2229015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	110	8	137	0	0.0727273	0	T|0.706;C|0.294	0.294	strong	.	PMP2	21	.	NM_002677	exon2	c.A186G	p.E62E	GGAGATTTCTGTA	.	PASS	Atlas-SNP
RFT1	91869	hgsc.bcm.edu	37	3	53125922	53125922	+	Silent	SNP	T	T	C	rs11242	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	129	6	142	0	0.0465116	0	T|0.505;C|0.495	0.495	strong	RFT1,colon,carcinoma,-1,1	RFT1	34	1	NM_052859	exon13	c.A1623G	p.T541T	AAGTCATGTCATT	.	PASS	Atlas-SNP
SLC7A13	157724	hgsc.bcm.edu	37	8	87229739	87229739	+	Missense_Mutation	SNP	C	C	T	rs4419794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	332	12	322	1	0.0361446	0.00310559	C|0.856;T|0.144	0.144	strong	SLC7A13,NS,carcinoma,+1,1	SLC7A13	97	1	NM_138817	exon3	c.G1139A	p.R380K	CTCCGCCTTAGTA	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179454394	179454394	+	Silent	SNP	A	A	G	rs1560221	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	138	7	131	0	0.0507246	0	A|0.558;G|0.442	0.442	strong	.	TTN	18412	.	NM_001267550	exon304	c.T62058C	p.Y20686Y	CTTTAGATAGACA	.	PASS	Atlas-SNP
PRKG2	5593	hgsc.bcm.edu	37	4	82031675	82031675	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	4	119	0	0.0408163	0	.	.	none	.	PRKG2	195	.	NM_006259	exon14	c.C1867A	p.L623I	TGTTGAGAATGAC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016849	1016849	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	771	30	679	21	0.0389105	0.0309278	.	.	none	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G5952C	p.M1984I	TGCAGTCATAGGA	.	scavenged	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	37	2	133554288	133554288	+	Silent	SNP	A	A	G	rs1868076	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	81	7	108	0	0.0864198	0	A|0.307;G|0.693	0.693	strong	.	NCKAP5	322	.	NM_207481	exon12	c.T822C	p.R274R	CAAGAGACGTGAG	.	PASS	Atlas-SNP
EPCAM	4072	hgsc.bcm.edu	37	2	47601106	47601106	+	Missense_Mutation	SNP	T	T	C	rs1126497	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	126	7	99	0	0.0555556	0	T|0.385;C|0.615	0.615	strong	.	EPCAM	27	.	NM_002354	exon3	c.T344C	p.M115T	CCTCCATGTGCTG	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	37	15	39910404	39910404	+	Missense_Mutation	SNP	G	G	A	rs12908846	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	157	7	146	0	0.044586	0	G|0.862;A|0.138	0.138	strong	.	FSIP1	53	.	NM_152597	exon11	c.C1231T	p.L411F	CCAGAAGACACTT	.	PASS	Atlas-SNP
NPR3	4883	hgsc.bcm.edu	37	5	32712111	32712111	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	95	2	84	0	0.0210526	0	.	.	none	NPR3,NS,carcinoma,-2,1	NPR3	65	1	NM_000908	exon1	c.G229T	p.E77X	GCCATCGAGTATG	.	scavenged	Atlas-SNP
ENPP4	22875	hgsc.bcm.edu	37	6	46108916	46108916	+	Silent	SNP	C	C	G	rs9472696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	160	7	157	0	0.04375	0	C|0.901;G|0.099	0.099	strong	.	ENPP4	44	.	NM_014936	exon3	c.C954G	p.A318A	GGTTGCCGATGAA	.	PASS	Atlas-SNP
HECTD4	283450	hgsc.bcm.edu	37	12	112654162	112654162	+	Missense_Mutation	SNP	C	C	T	rs372438469		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	131	3	126	0	0.0229008	0	.	.	weak	C12orf51_ENST00000377560,colon,carcinoma,0,2	.	.	2	NM_001109662	exon48	c.G6997A	p.V2333M	AGTGCACGGCTCG	.	scavenged	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216420482	216420482	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	154	33	143	0	0.214286	0	.	.	none	.	USH2A	1168	.	NM_007123	exon13	c.C2254A	p.H752N	AGCCATGGAGGTT	.	PASS	Atlas-SNP
MAGED2	10916	hgsc.bcm.edu	37	X	54838077	54838077	+	Silent	SNP	C	C	T	rs2071932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	217	10	247	0	0.046083	0	C|0.586;0|0.015	.	strong	.	MAGED2	74	.	NM_201222	exon6	c.C981T	p.S327S	CTATTCCTTGGAG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160737621	160737621	+	Silent	SNP	C	C	T	rs11675155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	4	113	0	0.0408163	0	C|0.818;T|0.182	0.182	strong	LY75,NS,carcinoma,0,1	LY75	151	1	NM_002349	exon8	c.G1377A	p.T459T	GTTGGGCGTCTTA	.	PASS	Atlas-SNP
STARD13	90627	hgsc.bcm.edu	37	13	33703656	33703656	+	Silent	SNP	T	T	C	rs495680	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	4	59	0	0.0625	0	T|0.463;C|0.537	0.537	strong	.	STARD13	100	.	NM_178006	exon5	c.A1158G	p.E386E	GTGAAATTCATGC	.	PASS	Atlas-SNP
C12orf40	283461	hgsc.bcm.edu	37	12	40085906	40085906	+	Missense_Mutation	SNP	A	A	T	rs73270414	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	536	14	492	3	0.0261194	0.00609756	A|0.858;T|0.142	0.142	strong	C12orf40,fourth_ventricle,glioma,0,1	C12orf40	118	1	NM_001031748	exon11	c.A1403T	p.K468M	CTACTAAGAAAAT	.	scavenged	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22144318	22144318	+	Missense_Mutation	SNP	C	C	T	rs1105929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	71	5	65	0	0.0704225	0	C|0.477;T|0.523	0.523	strong	.	VWA3A	115	.	NM_173615	exon20	c.C1970T	p.T657I	ACACCACACCCCC	.	PASS	Atlas-SNP
FARS2	10667	hgsc.bcm.edu	37	6	5431340	5431340	+	Missense_Mutation	SNP	A	A	G	rs11243011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	151	8	161	1	0.0529801	0.00621118	A|0.822;G|0.178	0.178	strong	FARS2,NS,carcinoma,0,1	FARS2	33	1	NM_006567	exon4	c.A839G	p.N280S	AGATCAACTTTCA	.	scavenged	Atlas-SNP
SP3	6670	hgsc.bcm.edu	37	2	174820750	174820750	+	Missense_Mutation	SNP	T	T	C	rs1047640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	7	171	0	0.0443038	0	T|0.878;C|0.122	0.122	strong	SP3,NS,carcinoma,0,1	SP3	82	1	NM_003111	exon4	c.A490G	p.T164A	ACACTGTACCATT	.	PASS	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3301721	3301721	+	Silent	SNP	C	C	T	rs2282198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	88	4	49	0	0.0454545	0	C|0.713;T|0.287	0.287	strong	.	PRDM16	147	.	NM_022114	exon4	c.C444T	p.S148S	GATCTCCGAAGAC	.	PASS	Atlas-SNP
OR5D18	219438	hgsc.bcm.edu	37	11	55587457	55587457	+	Missense_Mutation	SNP	G	G	A	rs11231180	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	131	3	110	0	0.0229008	0	G|0.974;A|0.026	0.026	strong	OR5D18,NS,carcinoma,0,1	OR5D18	121	1	NM_001001952	exon1	c.G352A	p.V118M	TTAGCTGTGATGG	.	scavenged	Atlas-SNP
PNRC1	10957	hgsc.bcm.edu	37	6	89793894	89793894	+	Silent	SNP	G	G	C	rs1130809	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	174	7	263	0	0.0402299	0	G|0.746;C|0.254	0.254	strong	.	PNRC1	17	.	NM_006813	exon2	c.G963C	p.T321T	AAAAACGCTCCTC	.	PASS	Atlas-SNP
SERPINA9	327657	hgsc.bcm.edu	37	14	94936107	94936107	+	Missense_Mutation	SNP	G	G	A	rs4905204	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	5	139	0	0.0316456	0	G|0.934;A|0.066	0.066	strong	SERPINA9_ENST00000337425,NS,carcinoma,0,2	SERPINA9	105	2	NM_175739	exon2	c.C125T	p.A42V	GCATTGGCCGGGG	.	scavenged	Atlas-SNP
PTGFRN	5738	hgsc.bcm.edu	37	1	117491909	117491909	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	58	18	66	0	0.310345	0	.	.	none	.	PTGFRN	91	.	NM_020440	exon4	c.C928T	p.R310W	GACGTCCGGCCCG	.	PASS	Atlas-SNP
ASMTL	8623	hgsc.bcm.edu	37	X	1537953	1537953	+	Missense_Mutation	SNP	C	C	T	rs11553052	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	6	124	0	0.0517241	0	C|0.858;T|0.142	0.142	strong	.	ASMTL	56	.	NM_004192	exon10	c.G1300A	p.G434S	TCATGCCGTGCAT	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954729	30954729	+	Missense_Mutation	SNP	G	G	C	rs111834205	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	126	5	109	0	0.0396825	0	G|0.938;C|0.062	0.062	strong	MUC21,bladder,carcinoma,0,1	MUC21	98	1	NM_001010909	exon2	c.G777C	p.E259D	CTCTGAGTCCAGC	.	scavenged	Atlas-SNP
CDH26	60437	hgsc.bcm.edu	37	20	58587641	58587641	+	Silent	SNP	C	C	T	rs375717739		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	78	24	84	0	0.307692	0	.	.	weak	.	CDH26	229	.	NM_177980	exon18	c.C2355T	p.S785S	CTACAGCGAGGAA	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248084440	248084440	+	Missense_Mutation	SNP	T	T	G	rs111379878	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	597	7	479	4	0.0117253	0.00835073	T|0.988;G|0.012	0.012	strong	OR2T8,NS,other,0,1	OR2T8	67	1	NM_001005522	exon1	c.T121G	p.S41A	GGCAATTCCCTCA	.	scavenged	Atlas-SNP
PRDM5	11107	hgsc.bcm.edu	37	4	121738049	121738049	+	Silent	SNP	T	T	C	rs343192	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	306	11	353	0	0.0359477	0	T|0.707;C|0.293	0.293	strong	PRDM5,NS,carcinoma,-2,1	PRDM5	76	1	NM_018699	exon6	c.A681G	p.L227L	CTCCTTTAGACTG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511131	195511131	+	Silent	SNP	C	C	T	rs71321826	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	7	59	0	0.0786517	0	C|0.500;T|0.500	0.500	weak	.	MUC4	1505	.	NM_018406	exon2	c.G7320A	p.S2440S	GGATGCCGAGGAA	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69970329	69970329	+	Silent	SNP	A	A	G	rs1983016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	4	136	2	0.0344828	0.0147059	A|0.193;G|0.807	0.807	strong	WWP2,NS,carcinoma,0,2	WWP2	88	2	NM_001270454	exon19	c.A2091G	p.T697T	GGTCACAGAGGAG	.	scavenged	Atlas-SNP
ATP6V1A	523	hgsc.bcm.edu	37	3	113517215	113517215	+	Silent	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	201	7	225	2	0.0348259	0.00888889	.	.	none	ATP6V1A,NS,carcinoma,0,2	ATP6V1A	71	2	NM_001690	exon12	c.C1416T	p.F472F	AGAGTTCGTTCCT	.	scavenged	Atlas-SNP
SMPDL3A	10924	hgsc.bcm.edu	37	6	123126138	123126138	+	Silent	SNP	T	T	C	rs61741159	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	5	133	0	0.078125	0	T|0.981;C|0.019	0.019	strong	.	SMPDL3A	31	.	NM_006714	exon6	c.T823C	p.L275L	GAGAAATTGATAG	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	168810874	168810874	+	Silent	SNP	C	C	T	rs17466625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	87	6	84	0	0.0689655	0	C|0.871;T|0.129	0.129	strong	.	MECOM	216	.	NM_004991	exon14	c.G3036A	p.S1012S	ATGAGGCGACGAT	.	PASS	Atlas-SNP
SLC24A5	283652	hgsc.bcm.edu	37	15	48426484	48426484	+	Missense_Mutation	SNP	A	A	G	rs1426654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	141	8	146	0	0.0567376	0	A|0.618;G|0.382	0.382	strong	.	SLC24A5	64	.	NM_205850	exon3	c.A331G	p.T111A	GCAGGCACAACTT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721049	54721049	+	Silent	SNP	A	A	G	rs60566950	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	174	5	137	1	0.0287356	0.00729927	A|0.980;G|0.020	0.020	strong	LILRB3,NS,carcinoma,0,1	LILRB3	67	1	NM_001081450	exon13	c.T1812C	p.L604L	CCGTCTAAGGGTC	.	scavenged	Atlas-SNP
PALM2-AKAP2	445815	hgsc.bcm.edu	37	9	112900785	112900785	+	Silent	SNP	A	A	G	rs3739456	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	48	5	41	0	0.104167	0	A|0.728;G|0.272	0.272	strong	PALM2-AKAP2,NS,carcinoma,0,2	PALM2-AKAP2	117	2	NM_007203	exon8	c.A2961G	p.S987S	CCCATCACTGCCC	.	PASS	Atlas-SNP
ZNF566	84924	hgsc.bcm.edu	37	19	36940698	36940698	+	Silent	SNP	A	A	G	rs10410711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	179	9	174	0	0.0502793	0	A|0.947;G|0.053	0.053	strong	.	ZNF566	40	.	NM_001145343	exon5	c.T441C	p.H147H	ATCTTCATGAGTG	.	PASS	Atlas-SNP
SHISA2	387914	hgsc.bcm.edu	37	13	26620777	26620777	+	Silent	SNP	G	G	A	rs77556088	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	90	4	86	0	0.0444444	0	G|0.962;A|0.038	0.038	strong	SHISA2,NS,carcinoma,0,3	SHISA2	43	3	NM_001007538	exon2	c.C762T	p.H254H	AGAGTCGTGCTGC	.	PASS	Atlas-SNP
ARHGEF5	7984	hgsc.bcm.edu	37	7	144062632	144062632	+	Nonsense_Mutation	SNP	C	C	G	rs202036368		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	174	41	127	30	0.235632	0.23622	.	.	weak	ARHGEF5,NS,carcinoma,0,1	ARHGEF5	73	1	NM_005435	exon2	c.C2870G	p.S957X	GGGTCTCAGAACA	.	scavenged	Atlas-SNP
ZNF627	199692	hgsc.bcm.edu	37	19	11725413	11725413	+	Silent	SNP	G	G	A	rs12151212	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	6	120	0	0.0560748	0	G|0.865;A|0.135	0.135	strong	ZNF627,NS,carcinoma,0,1	ZNF627	43	1	NM_145295	exon2	c.G75A	p.Q25Q	TTCCCAGAAGAAT	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17108135	17108135	+	Missense_Mutation	SNP	C	C	T	rs3745340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	175	9	167	0	0.0514286	0	C|0.647;T|0.353	0.353	strong	.	CPAMD8	192	.	NM_015692	exon11	c.G1022A	p.R341Q	AAGTCCCGGGAGC	.	PASS	Atlas-SNP
DYNC1LI2	1783	hgsc.bcm.edu	37	16	66783159	66783159	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	88	4	100	0	0.0454545	0	.	.	none	.	DYNC1LI2	37	.	NM_006141	exon3	c.G239A	p.G80D	TTTTTGCCATGCT	.	PASS	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22383189	22383189	+	Silent	SNP	G	G	A	rs1820851	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	85	6	99	0	0.0705882	0	G|0.536;A|0.464	0.464	strong	OR4N4,NS,carcinoma,0,2	OR4N4	108	2	NM_001005241	exon1	c.G717A	p.T239T	GTCCACGTGCACC	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733227	52733227	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	243	5	234	4	0.0205761	0.017094	.	.	none	PCMTD1,trunk,malignant_melanoma,0,3	PCMTD1	73	3	NM_052937	exon6	c.G758A	p.R253H	AGTGTGCGTCGAA	.	scavenged	Atlas-SNP
VN1R2	317701	hgsc.bcm.edu	37	19	53761881	53761881	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	114	35	109	0	0.307018	0	.	.	none	.	VN1R2	71	.	NM_173856	exon1	c.A253C	p.T85P	AAACCCACCAAAC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113169631	113169631	+	Missense_Mutation	SNP	G	G	A	rs7030192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	115	5	114	0	0.0434783	0	A|0.380;G|0.620	0.380	strong	.	SVEP1	326	.	NM_153366	exon38	c.C8249T	p.A2750V	GAGCCTGCTAGAA	.	PASS	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107456763	107456763	+	Missense_Mutation	SNP	T	T	C	rs10991359	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	105	4	86	0	0.0380952	0	T|0.800;C|0.200	0.200	strong	OR13D1,NS,carcinoma,0,1	OR13D1	42	1	NM_001004484	exon1	c.T61C	p.F21L	GTCCTTTTCTATA	.	scavenged	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145642002	145642002	+	Missense_Mutation	SNP	C	C	T	rs2280838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	88	6	82	0	0.0681818	0	C|0.520;T|0.480	0.480	strong	.	SLC39A4	54	.	NM_130849	exon1	c.G172A	p.A58T	CGTTGGCGCAGTG	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	199	4	217	0	0.0201005	0	G|0.784;C|0.216	0.216	strong	STRC_ENST00000450892,colon,carcinoma,0,1	STRC	58	1	NM_153700	exon26	c.C4878G	p.L1626L	GCACTGGAGATGC	.	scavenged	Atlas-SNP
UGT2B7	7364	hgsc.bcm.edu	37	4	69962449	69962449	+	Missense_Mutation	SNP	G	G	T	rs12233719	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	169	7	170	0	0.0414201	0	A|0.000;G|0.986;T|0.013	0.013	strong	.	UGT2B7	79	.	NM_001074	exon1	c.G211T	p.A71S	TCATCCGCTCTTA	.	PASS	Atlas-SNP
TLR1	7096	hgsc.bcm.edu	37	4	38798935	38798935	+	Silent	SNP	C	C	T	rs5743614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	198	8	163	1	0.040404	0.00613497	C|0.575;T|0.425	0.425	strong	TLR1,NS,carcinoma,-1,1	TLR1	70	1	NM_003263	exon4	c.G1518A	p.S506S	ATCAGCCGATGGG	.	scavenged	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42522613	42522613	+	Missense_Mutation	SNP	G	G	C	rs1135840	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	126	3	132	0	0.0238095	0	G|0.600;C|0.400	0.400	strong	CYP2D6_ENST00000360608,brain,glioma,0,2	CYP2D6	104	2	NM_000106	exon9	c.C1457G	p.T486S	GATGGGGTCACCA	.	scavenged	Atlas-SNP
RNF111	54778	hgsc.bcm.edu	37	15	59347929	59347929	+	Silent	SNP	C	C	A	rs1446239	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	211	12	226	0	0.056872	0	C|0.554;A|0.446	0.446	strong	RNF111_ENST00000434298,rectum,carcinoma,0,4	RNF111	179	4	NM_017610	exon4	c.C1056A	p.S352S	GGGTTCCAGTTCT	.	PASS	Atlas-SNP
TDRD9	122402	hgsc.bcm.edu	37	14	104452640	104452640	+	Silent	SNP	G	G	A	rs10143389	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	185	7	168	2	0.0378378	0.0119048	G|0.674;A|0.326	0.326	strong	TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	NM_153046	exon8	c.G1098A	p.L366L	TGACTTGGATATG	.	scavenged	Atlas-SNP
OR1A2	26189	hgsc.bcm.edu	37	17	3101691	3101691	+	Missense_Mutation	SNP	G	G	T	rs12150427	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	101	8	113	0	0.0792079	0	G|0.697;N|0.000	.	strong	OR1A2,NS,carcinoma,0,1	OR1A2	52	1	NM_012352	exon1	c.G879T	p.W293C	AAATTGGGATATG	.	PASS	Atlas-SNP
CACNA2D3	55799	hgsc.bcm.edu	37	3	54880461	54880461	+	Silent	SNP	A	A	G	rs3773603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	122	5	139	0	0.0409836	0	A|0.825;G|0.175	0.175	strong	.	CACNA2D3	159	.	NM_018398	exon17	c.A1593G	p.G531G	TAATGGATATATC	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102563739	102563739	+	Silent	SNP	C	C	T	rs1276289	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	125	6	82	0	0.048	0	C|0.594;T|0.406	0.406	strong	MMP27,NS,carcinoma,0,1	MMP27	84	1	NM_022122	exon9	c.G1227A	p.G409G	CGGGAACCCTTTG	.	PASS	Atlas-SNP
PANK1	53354	hgsc.bcm.edu	37	10	91371689	91371689	+	Silent	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	83	2	79	0	0.0240964	0	.	.	none	PANK1,NS,carcinoma,+1,1	PANK1	35	1	NM_148977	exon2	c.C820A	p.R274R	ACTTCCGGATGCT	.	scavenged	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361452	107361452	+	Silent	SNP	C	C	G	rs75081605		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	608	9	677	5	0.0148026	0.00738552	.	.	weak	OR13C5,NS,carcinoma,-2,1	OR13C5	60	1	NM_001004482	exon1	c.G243C	p.T81T	CACTAGCGTGGAG	.	scavenged	Atlas-SNP
CREBBP	1387	hgsc.bcm.edu	37	16	3789597	3789597	+	Missense_Mutation	SNP	C	C	A	rs200616542	alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	76	45	74	1	0.592105	0.0135135	.	.	alt	CREBBP,NS,lymphoid_neoplasm,0,1	CREBBP	546	1	NM_004380	exon25	c.G4262T	p.C1421F	GGGGGGCAATCAG	.	scavenged	Atlas-SNP
FCRLA	84824	hgsc.bcm.edu	37	1	161681780	161681780	+	Missense_Mutation	SNP	A	A	G	rs2275603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	189	8	119	0	0.042328	0	A|0.595;G|0.405	0.405	strong	.	FCRLA	101	.	NM_001184866	exon5	c.A625G	p.S209G	GCAGGAAGCCCCA	.	PASS	Atlas-SNP
FOXD4	2298	hgsc.bcm.edu	37	9	117998	117998	+	Missense_Mutation	SNP	G	G	T	rs66612967	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	371	29	328	14	0.0781671	0.0426829	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
NOX4	50507	hgsc.bcm.edu	37	11	89060002	89060002	+	Silent	SNP	G	G	A	rs28517716	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	222	5	217	2	0.0225225	0.00921659	G|0.912;A|0.088	0.088	strong	NOX4,NS,carcinoma,-1,1	NOX4	101	1	NM_016931	exon18	c.C1659T	p.S553S	AGTCTTGGATAGT	.	scavenged	Atlas-SNP
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	187	8	184	0	0.0427807	0	A|0.634;G|0.366	0.366	strong	.	ZNF879	41	.	NM_001136116	exon5	c.A334G	p.T112A	GATGGCACATTTG	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32010272	32010272	+	Missense_Mutation	SNP	T	T	A	rs76250508	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	306	4	273	0	0.0130719	0	T|0.754;A|0.246	0.246	strong	TNXB_ENST00000375247,colon,carcinoma,0,3	TNXB	553	3	NM_019105	exon40	c.A12164T	p.N4055I	AACACGTTCAGGG	.	scavenged	Atlas-SNP
OR3A3	8392	hgsc.bcm.edu	37	17	3324810	3324810	+	Missense_Mutation	SNP	A	A	G	rs227787	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	4	80	0	0.0547945	0	G|0.262;N|0.001	0.262	strong	.	OR3A3	20	.	NM_012373	exon1	c.A949G	p.K317E	GTGGGGAAGCGAT	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17831419	17831419	+	Silent	SNP	G	G	A	rs2277080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	140	8	190	0	0.0571429	0	G|0.777;A|0.223	0.223	strong	.	KIF13A	276	.	NM_001105567	exon13	c.C1314T	p.S438S	GATACCGGACATC	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	37	1	229772932	229772932	+	Missense_Mutation	SNP	A	A	G	rs3811474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	100	8	127	0	0.08	0	A|0.836;G|0.164	0.164	strong	.	URB2	152	.	NM_014777	exon4	c.A2572G	p.K858E	TTTGCAAAAGCTG	.	PASS	Atlas-SNP
BHLHB9	80823	hgsc.bcm.edu	37	X	102004884	102004884	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	154	38	179	0	0.246753	0	.	.	none	.	BHLHB9	60	.	NM_001142530	exon2	c.G961T	p.D321Y	TATATGGATTCTG	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9998493	9998493	+	Silent	SNP	A	A	G	rs13113918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	196	9	193	0	0.0459184	0	A|0.196;G|0.804	0.804	strong	.	SLC2A9	158	.	NM_020041	exon3	c.T322C	p.L108L	AGAGCAAAGTCAG	.	PASS	Atlas-SNP
XAF1	54739	hgsc.bcm.edu	37	17	6663895	6663895	+	Silent	SNP	C	C	G	rs2271231	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	203	7	221	1	0.0344828	0.00452489	C|0.550;G|0.450	0.450	strong	XAF1,colon,carcinoma,+2,1	XAF1	16	1	NM_017523	exon4	c.C396G	p.R132R	CTGTCGCAGTGAA	.	scavenged	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244166	11244166	+	Silent	SNP	G	G	C	rs35720106	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	31	14	20	0	0.451613	0	G|0.614;C|0.386	0.386	strong	TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	NM_176884	exon1	c.C663G	p.T221T	GACCTTGGTGCTG	.	PASS	Atlas-SNP
ADAM23	8745	hgsc.bcm.edu	37	2	207425911	207425911	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	139	6	199	0	0.0431655	0	.	.	none	ADAM23_ENST00000374416,NS,carcinoma,0,2	ADAM23	239	2	NM_003812	exon12	c.G1229A	p.R410H	GTTCTCGCACAAG	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50584201	50584201	+	Silent	SNP	A	A	C	rs2272838	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	3	48	0	0.046875	0	A|0.774;C|0.226	0.226	strong	MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	NM_018995	exon19	c.A2589C	p.T863T	CACCACATGCAGC	.	scavenged	Atlas-SNP
FAM208B	54906	hgsc.bcm.edu	37	10	5781969	5781969	+	Silent	SNP	A	A	T	rs2797486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	92	4	92	0	0.0434783	0	A|0.163;T|0.837	0.837	strong	C10orf18,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	.	.	1	NM_017782	exon13	c.A1836T	p.T612T	CTTAACAGTTAGC	.	PASS	Atlas-SNP
CCDC132	55610	hgsc.bcm.edu	37	7	92887682	92887682	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	281	61	255	0	0.217082	0	.	.	none	.	CCDC132	136	.	NM_024553	exon8	c.T554C	p.V185A	CAGATGTACGGTT	.	PASS	Atlas-SNP
CRB2	286204	hgsc.bcm.edu	37	9	126133497	126133497	+	Silent	SNP	C	C	T	rs13290763	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	91	4	77	0	0.043956	0	C|0.763;T|0.237	0.237	strong	.	CRB2	86	.	NM_173689	exon8	c.C2076T	p.S692S	TGACTCCGCAGCT	.	PASS	Atlas-SNP
ASAH1	427	hgsc.bcm.edu	37	8	17942220	17942220	+	Missense_Mutation	SNP	T	T	C	rs3213606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	83	4	79	0	0.0481928	0	T|0.991;C|0.009	0.009	strong	ASAH1_ENST00000381733,NS,carcinoma,0,1	ASAH1	71	1	NM_001127505	exon1	c.A91G	p.I31V	CCAGAATTGAGGC	.	PASS	Atlas-SNP
MSX1	4487	hgsc.bcm.edu	37	4	4861745	4861745	+	Missense_Mutation	SNP	C	C	G	rs36059701	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	10	8	5	1	0.8	0.2	C|0.868;G|0.132	0.132	strong	MSX1,NS,carcinoma,0,1	MSX1	19	1	NM_002448	exon1	c.C119G	p.A40G	CCACGGCAGCCGC	.	scavenged	Atlas-SNP
DNAJC6	9829	hgsc.bcm.edu	37	1	65860687	65860687	+	Silent	SNP	A	A	C	rs4582839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	119	6	126	0	0.0504202	0	A|0.300;C|0.700	0.700	strong	.	DNAJC6	104	.	NM_001256864	exon13	c.A2010C	p.P670P	CCAGCCAACAAGA	.	PASS	Atlas-SNP
F8	2157	hgsc.bcm.edu	37	X	154158201	154158201	+	Silent	SNP	T	T	G	rs1800292	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	119	5	121	0	0.0420168	0	T|0.888;0|0.022	.	strong	.	F8	646	.	NM_000132	exon14	c.A3864C	p.S1288S	TTTTTTTGAGAAA	.	PASS	Atlas-SNP
FUT10	84750	hgsc.bcm.edu	37	8	33246538	33246538	+	Silent	SNP	A	A	G	rs16880849	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	139	2	166	0	0.0143885	0	A|0.769;G|0.231	0.231	strong	FUT10,NS,carcinoma,0,1	FUT10	62	1	NM_032664	exon4	c.T1155C	p.D385D	AAATGCATCGATG	.	scavenged	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	37	17	15960883	15960883	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	4	193	0	0.0253165	0	.	.	none	NCOR1,NS,carcinoma,0,1	NCOR1	240	1	NM_006311	exon40	c.C6337A	p.Q2113K	GTCTTTGATGATG	.	scavenged	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9312951	9312951	+	Missense_Mutation	SNP	G	G	A	rs57006764	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	7	90	0	0.0603448	0	G|0.805;A|0.195	0.195	strong	PZP_ENST00000381997,NS,carcinoma,+1,2	PZP	422	2	NM_002864	exon24	c.C3008T	p.T1003M	TCCTGCGTCAGCT	.	PASS	Atlas-SNP
SPATA31A6	389730	hgsc.bcm.edu	37	9	43628679	43628679	+	Missense_Mutation	SNP	G	G	A	rs2491538	bycluster;byfrequency;bysubmitter	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	462	5	556	0	0.0108225	0	G|0.996;A|0.004	0.004	strong	FAM75A6,right_upper_lobe,carcinoma,0,2	.	.	2	NM_001145196	exon3	c.C263T	p.P88L	CCTCTCGGGCACT	.	scavenged	Atlas-SNP
FUT6	2528	hgsc.bcm.edu	37	19	5832209	5832209	+	Missense_Mutation	SNP	G	G	A	rs778805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	106	4	90	0	0.0377358	0	G|0.555;A|0.445	0.445	strong	FUT6,NS,carcinoma,+1,1	FUT6	30	1	NM_000150	exon3	c.C370T	p.P124S	GCCTCGGGGAGCG	.	scavenged	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195452951	195452951	+	Missense_Mutation	SNP	G	G	C	rs2688542	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	321	12	313	1	0.0373832	0.00319489	G|0.379;C|0.621	0.621	strong	MUC20,NS,carcinoma,0,1	MUC20	84	1	NM_152673	exon3	c.G964C	p.D322H	GCACCTGATGCCA	.	scavenged	Atlas-SNP
SYT6	148281	hgsc.bcm.edu	37	1	114680540	114680540	+	Silent	SNP	C	C	T	rs201787036	alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	71	6	68	0	0.084507	0	.	.	alt	SYT6,NS,carcinoma,0,1	SYT6	66	1	NM_205848	exon3	c.G393A	p.S131S	ATCCACCGACTTC	.	PASS	Atlas-SNP
CWF19L1	55280	hgsc.bcm.edu	37	10	102016044	102016044	+	Missense_Mutation	SNP	C	C	T	rs2270962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	153	7	152	1	0.0457516	0.00657895	C|0.775;T|0.225	0.225	strong	CWF19L1,NS,carcinoma,0,1	CWF19L1	39	1	NM_018294	exon5	c.G479A	p.C160Y	CCCACACACTTGG	.	scavenged	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114377885	114377885	+	Silent	SNP	G	G	C	rs2290790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	90	4	67	0	0.0444444	0	G|0.761;C|0.239	0.239	strong	.	RBM19	117	.	NM_001146699	exon15	c.C1818G	p.T606T	GCCGAAGGTCTCC	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72503344	72503344	+	Silent	SNP	G	G	A	rs10999502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	134	7	111	1	0.0522388	0.00900901	G|0.768;A|0.232	0.232	strong	ADAMTS14,NS,adenoma,0,1	ADAMTS14	148	1	NM_139155	exon13	c.G1974A	p.T658T	GGACACGGGGGAC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510786	195510786	+	Silent	SNP	T	T	G	rs2948677	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	130	6	118	5	0.0461538	0.0423729	T|0.500;G|0.500	0.500	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A7665C	p.T2555T	GTGACCTGTGGAT	.	scavenged	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110778128	110778128	+	Missense_Mutation	SNP	T	T	C	rs714368	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	88	4	106	0	0.0454545	0	T|0.701;C|0.299	0.299	strong	.	SLC22A16	81	.	NM_033125	exon2	c.A146G	p.H49R	ACATGATGAGGGG	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	619021	619021	+	Silent	SNP	G	G	C	rs14155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	131	4	98	0	0.0305344	0	G|0.442;C|0.558	0.558	strong	POLRMT,colon,carcinoma,0,2	POLRMT	91	2	NM_005035	exon15	c.C3243G	p.P1081P	GCGATAGGGCTGG	.	scavenged	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627869	170627869	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	160	14	170	8	0.0875	0.0470588	.	.	none	FAM120B,NS,carcinoma,+1,1	FAM120B	108	1	NM_032448	exon2	c.A1391G	p.Y464C	CCATGTATACAGG	.	scavenged	Atlas-SNP
ARHGEF2	9181	hgsc.bcm.edu	37	1	155920171	155920171	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	72	16	65	0	0.222222	0	.	.	none	.	ARHGEF2	81	.	NM_001162383	exon21	c.C2806T	p.R936W	GCAGCCGCTCTTC	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890024	7890024	+	Missense_Mutation	SNP	T	T	G	rs201662971	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	63	4	47	0	0.0634921	0	.	.	weak	PER3,NS,carcinoma,0,3	PER3	95	3	NM_016831	exon18	c.T2990G	p.M997R	CTCCCATGAAGAA	.	scavenged	Atlas-SNP
MAGEB16	139604	hgsc.bcm.edu	37	X	35821127	35821127	+	Nonsense_Mutation	SNP	C	C	T	rs4829392	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	320	13	357	0	0.040625	0	C|0.356;0|0.042	.	strong	.	MAGEB16	64	.	NM_001099921	exon2	c.C814T	p.R272X	CCTGCACGATATG	.	PASS	Atlas-SNP
DDR1	780	hgsc.bcm.edu	37	6	30864829	30864829	+	Silent	SNP	T	T	C	rs1049623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	7	142	0	0.0443038	0	T|0.539;C|0.461	0.461	strong	DDR1_ENST00000376575,NS,adenoma,0,3	DDR1	213	3	NM_013994	exon13	c.T1908C	p.V636V	TCTGGTTAGTCTT	.	PASS	Atlas-SNP
LRRC47	57470	hgsc.bcm.edu	37	1	3703710	3703710	+	Silent	SNP	G	G	A	rs2253143	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	66	5	74	0	0.0757576	0	G|0.949;A|0.051	0.051	strong	.	LRRC47	42	.	NM_020710	exon2	c.C780T	p.V260V	GCCTCCGACGCGC	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102587062	102587062	+	Silent	SNP	G	G	A	rs3740938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	242	8	232	0	0.0330578	0	G|0.920;A|0.080	0.080	strong	MMP8,colon,carcinoma,0,5	MMP8	68	5	NM_002424	exon6	c.C873T	p.L291L	TCCACGGAGTGTG	.	scavenged	Atlas-SNP
LAMA3	3909	hgsc.bcm.edu	37	18	21394444	21394444	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	139	52	152	0	0.374101	0	.	.	none	.	LAMA3	397	.	NM_001127717	exon15	c.A1866C	p.K622N	GGACAAAGAAAAC	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141759688	141759688	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	169	4	169	5	0.0236686	0.0295858	.	.	none	MGAM_ENST00000549489,NS,carcinoma,0,5	MGAM	767	5	NM_004668	exon33	c.T3981C	p.P1327P	ACAGCCTTATCCT	.	scavenged	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31473872	31473872	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	26	10	17	0	0.384615	0	.	.	none	ARMC5_ENST00000457010,NS,carcinoma,+1,2	ARMC5	94	2	NM_024742	exon3	c.G1004A	p.R335Q	AGCGCCGGGATCC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9012826	9012826	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	135	5	134	1	0.037037	0.00746269	.	.	none	MUC16_ENST00000397910,NS,lymphoid_neoplasm,0,2	MUC16	4315	2	NM_024690	exon34	c.A38618G	p.H12873R	GGGTGATGCATGT	.	scavenged	Atlas-SNP
TPSD1	23430	hgsc.bcm.edu	37	16	1306346	1306346	+	Missense_Mutation	SNP	C	C	T	rs3865205	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	209	6	200	0	0.0287081	0	C|0.851;T|0.149	0.149	strong	TPSD1,rectum,carcinoma,0,4	TPSD1	47	4	NM_012217	exon1	c.C65T	p.P22L	CGAGCCCGGCCTA	.	scavenged	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16351310	16351310	+	Silent	SNP	T	T	C	rs118025694	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	4	57	0	0.047619	0	T|0.997;C|0.003	0.003	strong	CLCNKA,NS,carcinoma,+2,1	CLCNKA	56	1	NM_004070	exon4	c.T282C	p.L94L	GTATCTTTCCTGG	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	194	3	193	1	0.0154639	0.00518135	C|0.996;T|0.004	0.004	strong	UBB,bladder,carcinoma,0,2	UBB	30	2	NM_018955	exon2	c.C270T	p.T90T	CATCACCCTGGAA	.	scavenged	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62193445	62193445	+	Missense_Mutation	SNP	G	G	A	rs3810481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	106	6	83	0	0.0566038	0	G|0.836;A|0.164	0.164	strong	.	.	.	.	NM_001037335	exon11	c.C6509T	p.T2170M	ATGACCGTGAAAG	.	PASS	Atlas-SNP
SFT2D1	113402	hgsc.bcm.edu	37	6	166739646	166739646	+	Missense_Mutation	SNP	T	T	C	rs11551053	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	302	10	298	0	0.0331126	0	T|0.932;C|0.068	0.068	strong	SFT2D1,colon,carcinoma,+1,2	SFT2D1	12	2	NM_145169	exon5	c.A325G	p.I109V	TAAATATGAAACA	.	scavenged	Atlas-SNP
ABI3BP	25890	hgsc.bcm.edu	37	3	100617680	100617680	+	Silent	SNP	C	C	T	rs2245370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	6	107	0	0.0612245	0	C|0.280;T|0.720	0.720	strong	.	ABI3BP	305	.	NM_015429	exon4	c.G408A	p.S136S	GAAGACCGAGCTC	.	PASS	Atlas-SNP
TUBA3D	113457	hgsc.bcm.edu	37	2	132237927	132237927	+	Missense_Mutation	SNP	C	C	A	rs76585620	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	211	4	184	0	0.0189573	0	C|0.500;A|0.500	0.500	weak	TUBA3D,trunk,malignant_melanoma,0,1	TUBA3D	60	1	NM_080386	exon4	c.C661A	p.R221S	ATTGAACGTCCCA	.	scavenged	Atlas-SNP
KIR2DL3	3804	hgsc.bcm.edu	37	19	55263898	55263898	+	Missense_Mutation	SNP	G	G	A	rs78177475		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	103	6	97	1	0.0582524	0.0103093	.	.	weak	KIR2DL3,NS,carcinoma,0,2	KIR2DL3	68	2	NM_015868	exon8	c.G953A	p.R318H	TCACTCGCCCTTC	.	scavenged	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989365	60989365	+	Missense_Mutation	SNP	C	C	T	rs3810553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	52	6	50	0	0.115385	0	C|0.684;T|0.316	0.316	strong	.	.	.	.	NM_080833	exon10	c.G1042A	p.D348N	GAAGGTCCTGCAT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179444939	179444939	+	Missense_Mutation	SNP	C	C	T	rs2303838	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	199	9	187	0	0.0452261	0	C|0.677;T|0.323	0.323	strong	.	TTN	18412	.	NM_001267550	exon318	c.G67075A	p.V22359I	CATTGACAGGTGG	.	PASS	Atlas-SNP
SEMA3E	9723	hgsc.bcm.edu	37	7	83037731	83037731	+	Missense_Mutation	SNP	C	C	G	rs61729612	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	109	5	128	0	0.0458716	0	C|0.877;G|0.123	0.123	strong	.	SEMA3E	125	.	NM_012431	exon6	c.G623C	p.R208P	GCCAGTCGCCCCA	.	PASS	Atlas-SNP
TMEM45A	55076	hgsc.bcm.edu	37	3	100287764	100287764	+	Silent	SNP	T	T	C	rs28722928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	5	128	0	0.0416667	0	T|0.783;C|0.217	0.217	strong	.	TMEM45A	35	.	NM_018004	exon5	c.T687C	p.Y229Y	GCATTATGCAGTA	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	37	10	135438933	135438933	+	Silent	SNP	C	C	T	rs200793608		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	303	4	324	3	0.0132013	0.00925926	C|0.996;T|0.004	0.004	weak	FRG2B,colon,carcinoma,-1,1	FRG2B	47	1	NM_001080998	exon4	c.G507A	p.P169P	AATTGACGGTGTT	.	scavenged	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222713503	222713503	+	Silent	SNP	C	C	G	rs3748664	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	60	5	94	0	0.0833333	0	C|0.679;G|0.321	0.321	strong	HHIPL2,colon,carcinoma,0,1	HHIPL2	122	1	NM_024746	exon4	c.G1299C	p.T433T	CTGGCGCGTGATG	.	PASS	Atlas-SNP
CLASP2	23122	hgsc.bcm.edu	37	3	33552202	33552202	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	160	49	191	0	0.30625	0	.	.	none	.	CLASP2	138	.	NM_015097	exon37	c.G4192A	p.E1398K	ACTGCTCTGGACT	.	PASS	Atlas-SNP
GATA3	2625	hgsc.bcm.edu	37	10	8100789	8100789	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	13	4	13	0	0.307692	0	.	.	none	.	GATA3	182	.	NM_002051	exon3	c.G763A	p.A255T	CCCAAGGCCCGGT	.	PASS	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11420773	11420773	+	Missense_Mutation	SNP	C	C	T	rs200940772	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	41	5	40	2	0.121951	0.05	C|0.998;T|0.002	0.002	weak	PRB3,NS,carcinoma,0,2	PRB3	84	2	NM_006249	exon3	c.G410A	p.R137H	CCCGGACGAGGCG	.	scavenged	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238009	31238009	+	Silent	SNP	T	T	C	rs1131014	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	41	18	54	16	0.439024	0.296296	T|0.651;C|0.349	0.349	strong	HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	92	2	NM_002117	exon4	c.A873G	p.Q291Q	GGGCTCTTGCAGC	.	scavenged	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33385235	33385235	+	Missense_Mutation	SNP	T	T	G	rs202043723	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	49	5	37	2	0.102041	0.0540541	G|0.184;T|0.816	0.184	strong	AQP7,NS,malignant_melanoma,0,2	AQP7	58	2	NM_001170	exon8	c.A797C	p.Y266S	CCTAGATAGGCAC	.	scavenged	Atlas-SNP
TPTE2	93492	hgsc.bcm.edu	37	13	20067011	20067011	+	Missense_Mutation	SNP	A	A	C	rs76437836	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	153	7	152	1	0.0457516	0.00657895	A|0.375;C|0.625	0.625	strong	TPTE2_ENST00000400230,adrenal_gland,adrenal_cortical_adenoma,0,3	TPTE2	225	3	NM_199254	exon4	c.T98G	p.L33R	GACACCAGGGCTG	.	scavenged	Atlas-SNP
OTOA	146183	hgsc.bcm.edu	37	16	21742188	21742188	+	Silent	SNP	G	G	A	rs76494517	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	1039	20	914	4	0.0192493	0.00437637	G|0.972;A|0.028	0.028	strong	OTOA_ENST00000388957,NS,haematopoietic_neoplasm,+1,3	OTOA	144	3	NM_144672	exon20	c.G2238A	p.T746T	GACCACGAAGGAC	.	scavenged	Atlas-SNP
CCDC30	728621	hgsc.bcm.edu	37	1	43047057	43047057	+	Silent	SNP	A	A	G	rs12037518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	395	17	381	0	0.043038	0	A|0.811;G|0.189	0.189	strong	.	CCDC30	78	.	NM_001080850	exon8	c.A1092G	p.E364E	ATTAGAACATGCT	.	PASS	Atlas-SNP
NOX4	50507	hgsc.bcm.edu	37	11	89088168	89088168	+	Silent	SNP	G	G	A	rs75735530	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	415	13	341	0	0.0313253	0	G|0.942;A|0.058	0.058	strong	NOX4,right_upper_lobe,carcinoma,-1,1	NOX4	101	1	NM_001143836	exon13	c.C1179T	p.S393S	AATTTCGGAGTCT	.	scavenged	Atlas-SNP
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43659338	43659338	+	Silent	SNP	C	C	T	rs78146682	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	139	2	171	0	0.0143885	0	C|0.996;T|0.005	0.005	strong	CSGALNACT2,NS,carcinoma,0,3	CSGALNACT2	67	3	NM_018590	exon5	c.C1005T	p.T335T	TTACACCTTGGTC	.	scavenged	Atlas-SNP
CPA2	1358	hgsc.bcm.edu	37	7	129916515	129916515	+	Silent	SNP	T	T	C	rs17590	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	113	5	144	0	0.0442478	0	T|0.354;C|0.646	0.646	strong	.	CPA2	36	.	NM_001869	exon7	c.T633C	p.D211D	TCTGGATGCCCTG	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195452814	195452814	+	Missense_Mutation	SNP	C	C	T	rs199753483	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	415	31	440	29	0.0746988	0.0659091	C|0.996;T|0.005	0.005	weak	MUC20,NS,carcinoma,0,2	MUC20	84	2	NM_152673	exon3	c.C827T	p.T276M	TCCCCACGGAAGG	.	scavenged	Atlas-SNP
GPRC6A	222545	hgsc.bcm.edu	37	6	117114025	117114025	+	Silent	SNP	G	G	A	rs6901250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	8	126	0	0.0898876	0	G|0.686;A|0.314	0.314	strong	GPRC6A,NS,carcinoma,0,2	GPRC6A	152	2	NM_148963	exon6	c.C2061T	p.A687A	GCTGAAGGCTAGC	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023419	25023419	+	Silent	SNP	C	C	T	rs202087650	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	254	10	238	8	0.0393701	0.0336134	C|0.989;T|0.011	0.011	strong	GGT1,NS,carcinoma,0,2	GGT1	68	2	NM_013430	exon12	c.C1041T	p.S347S	GACCTCCGAGTTC	.	scavenged	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	37	1	20671961	20671961	+	Missense_Mutation	SNP	G	G	A	rs11582960	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	248	5	253	1	0.0201613	0.00395257	G|0.696;A|0.304	0.304	strong	VWA5B1,colon,carcinoma,0,1	VWA5B1	44	1	NM_001039500	exon17	c.G2639A	p.R880H	ACCGCCGCTACCA	.	scavenged	Atlas-SNP
RBM23	55147	hgsc.bcm.edu	37	14	23371055	23371055	+	Missense_Mutation	SNP	G	G	C	rs1127066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	130	8	118	0	0.0615385	0	G|0.760;C|0.240	0.240	strong	.	RBM23	44	.	NM_001077351	exon13	c.C1284G	p.F428L	GAGCTGGAAACAC	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	179	9	165	0	0.0502793	0	A|0.732;G|0.268	0.268	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_001271208	exon116	c.T18294C	p.Y6098Y	GTTAGGATAGTTT	.	PASS	Atlas-SNP
GPR128	84873	hgsc.bcm.edu	37	3	100368546	100368546	+	Missense_Mutation	SNP	A	A	G	rs61730367	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	100	5	84	0	0.05	0	A|0.920;G|0.080	0.080	strong	.	GPR128	126	.	NM_032787	exon11	c.A1274G	p.K425R	CTTTCAAAAAGGA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384999	16384999	+	Missense_Mutation	SNP	G	G	A	rs1807284	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	132	5	118	0	0.0378788	0	G|0.717;A|0.283	0.283	strong	FAM131C,NS,carcinoma,0,2	FAM131C	21	2	NM_182623	exon7	c.C776T	p.P259L	CCCGGGGGGTGGG	.	scavenged	Atlas-SNP
MBL2	4153	hgsc.bcm.edu	37	10	54528266	54528266	+	Silent	SNP	G	G	C	rs930507	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	58	2	53	1	0.0344828	0.0188679	G|0.238;C|0.762	0.762	strong	MBL2,colon,carcinoma,0,1	MBL2	55	1	NM_000242	exon4	c.C378G	p.L126L	GAAGGTGAGCCCT	.	scavenged	Atlas-SNP
PLD4	122618	hgsc.bcm.edu	37	14	105395204	105395204	+	Missense_Mutation	SNP	G	G	A	rs3803295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	133	6	133	0	0.0451128	0	G|0.994;A|0.006	0.006	strong	.	PLD4	46	.	NM_138790	exon4	c.G403A	p.V135M	GTCCACGTGGCTT	.	PASS	Atlas-SNP
CCDC102B	79839	hgsc.bcm.edu	37	18	66564514	66564514	+	Missense_Mutation	SNP	G	G	C	rs117721069	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	104	5	131	0	0.0480769	0	G|0.988;C|0.012	0.012	strong	.	CCDC102B	92	.	NM_001093729	exon8	c.G1112C	p.R371T	TTGAAAGAGAAAA	.	PASS	Atlas-SNP
UBC	7316	hgsc.bcm.edu	37	12	125397358	125397358	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	284	6	246	0	0.0211268	0	.	.	none	UBC,NS,carcinoma,0,2	UBC	79	2	NM_021009	exon2	c.A960G	p.E320E	CTCCACTTCGAGA	.	scavenged	Atlas-SNP
HCN2	610	hgsc.bcm.edu	37	19	603826	603826	+	Silent	SNP	C	C	T	rs56170955	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	65	5	76	0	0.0769231	0	C|0.835;T|0.165	0.165	strong	.	HCN2	36	.	NM_001194	exon2	c.C915T	p.F305F	CATCTTCCTTATC	.	PASS	Atlas-SNP
FANCA	2175	hgsc.bcm.edu	37	16	89836323	89836323	+	Missense_Mutation	SNP	C	C	T	rs7195066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	103	5	106	0	0.0485437	0	C|0.485;T|0.515	0.515	strong	FANCA,NS,carcinoma,0,1	FANCA	99	1	NM_000135	exon26	c.G2426A	p.G809D	CCAGCACCAGGTG	.	PASS	Atlas-SNP
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381826	39381826	+	Missense_Mutation	SNP	A	A	G	rs2076109	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	9	95	0	0.0918367	0	A|0.388;G|0.612	0.612	strong	.	APOBEC3B	32	.	NM_004900	exon3	c.A184G	p.K62E	TATTTCAAGCCTC	.	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-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	3	162	0	0.0189873	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
MUC2	4583	hgsc.bcm.edu	37	11	1093424	1093424	+	Missense_Mutation	SNP	C	C	G	rs111642532		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	3	67	1	0.046875	0.0149254	C|0.500;G|0.500	0.500	weak	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.C5243G	p.T1748S	CCATCACCACCAC	.	scavenged	Atlas-SNP
CST9L	128821	hgsc.bcm.edu	37	20	23546639	23546639	+	Missense_Mutation	SNP	T	T	G	rs2295564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	111	4	144	0	0.036036	0	T|0.629;G|0.371	0.371	strong	CST9L,NS,carcinoma,0,1	CST9L	25	1	NM_080610	exon2	c.A326C	p.H109P	TGGAAATGGCAGT	.	scavenged	Atlas-SNP
EMC1	23065	hgsc.bcm.edu	37	1	19565344	19565344	+	Missense_Mutation	SNP	C	C	G	rs709683	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	112	5	97	0	0.0446429	0	C|0.506;G|0.494	0.494	strong	.	.	.	.	NM_001271428	exon10	c.G1034C	p.S345T	CTGCTACTTTTCT	.	PASS	Atlas-SNP
SLITRK2	84631	hgsc.bcm.edu	37	X	144905286	144905286	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	37	133	0	0.308333	0	.	.	none	.	SLITRK2	221	.	NM_001144005	exon5	c.G1343A	p.S448N	TGCAGAGCTTGCA	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33395103	33395103	+	Silent	SNP	G	G	A	rs148012859	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	105	3	71	0	0.0285714	0	A|0.002;G|0.998;T|0.000	0.002	strong	AQP7,NS,carcinoma,0,1	AQP7	58	1	NM_001170	exon3	c.C117T	p.A39A	GAACTCGGCCAGG	.	scavenged	Atlas-SNP
SENP1	29843	hgsc.bcm.edu	37	12	48477422	48477422	+	Silent	SNP	A	A	G	rs886588	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	140	2	112	1	0.0142857	0.00892857	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
UNC5CL	222643	hgsc.bcm.edu	37	6	40998141	40998141	+	Silent	SNP	G	G	A	rs736795	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	99	5	101	0	0.050505	0	G|0.767;A|0.233	0.233	strong	.	UNC5CL	52	.	NM_173561	exon8	c.C1320T	p.C440C	CATGCCGCAAAGC	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100122291	100122291	+	Missense_Mutation	SNP	T	T	C	rs3747495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	148	5	177	0	0.0337838	0	T|0.807;C|0.193	0.193	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon26	c.T3523C	p.F1175L	CTCAGCTTCGTCC	.	scavenged	Atlas-SNP
WDR91	29062	hgsc.bcm.edu	37	7	134880931	134880931	+	Silent	SNP	C	C	T	rs2288240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	95	4	87	0	0.0421053	0	C|0.966;T|0.034	0.034	strong	.	WDR91	82	.	NM_014149	exon8	c.G1209A	p.E403E	CCCGTACTCCTCC	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79173545	79173545	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	45	4	25	0	0.0888889	0	.	.	none	.	AZI1	145	.	NM_014984	exon9	c.C997A	p.R333S	CTTGGCGTGCCTT	.	PASS	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12501907	12501907	+	Silent	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	125	7	145	3	0.056	0.0206897	.	.	none	ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	111	2	NM_001080821	exon4	c.T1305C	p.S435S	TCGAAGAGAACTG	.	scavenged	Atlas-SNP
FAM200B	285550	hgsc.bcm.edu	37	4	15689632	15689632	+	Silent	SNP	G	G	A	rs11729955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	425	9	421	1	0.0211765	0.0023753	G|0.683;A|0.317	0.317	strong	FAM200B_ENST00000422728,NS,carcinoma,0,2	FAM200B	56	2	NM_001145191	exon2	c.G1032A	p.E344E	CATGGAGGTATTG	.	scavenged	Atlas-SNP
PJA2	9867	hgsc.bcm.edu	37	5	108672946	108672946	+	Missense_Mutation	SNP	C	C	T	rs246105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	228	16	256	0	0.0701754	0	C|0.735;T|0.265	0.265	strong	.	PJA2	53	.	NM_014819	exon10	c.G2113A	p.A705T	CTTCTGCAATACT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	395	8	345	4	0.0202532	0.0115942	.	.	weak	MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G4827C	p.Q1609H	TGTGGTCTGAGGG	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179427536	179427536	+	Missense_Mutation	SNP	T	T	C	rs3829746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	119	6	126	0	0.0504202	0	T|0.555;C|0.445	0.445	strong	.	TTN	18412	.	NM_001267550	exon326	c.A83323G	p.I27775V	CTCTTATGGTCAA	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102576382	102576382	+	Missense_Mutation	SNP	G	G	A	rs12099177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	193	7	159	0	0.0362694	0	G|0.882;A|0.118	0.118	strong	MMP27,NS,carcinoma,0,1	MMP27	84	1	NM_022122	exon1	c.C64T	p.R22W	TCATCCGGACTAA	.	scavenged	Atlas-SNP
WFS1	7466	hgsc.bcm.edu	37	4	6293696	6293696	+	Silent	SNP	C	C	G	rs1801213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	199	6	211	0	0.0301508	0	C|0.294;G|0.706	0.706	strong	WFS1,NS,carcinoma,0,1	WFS1	71	1	NM_001145853	exon6	c.C684G	p.R228R	GAGGCGCATGCTG	.	scavenged	Atlas-SNP
REST	5978	hgsc.bcm.edu	37	4	57798189	57798189	+	Silent	SNP	G	G	A	rs2227901	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	174	11	181	0	0.0632184	0	G|0.791;A|0.209	0.209	strong	.	REST	104	.	NM_001193508	exon4	c.G3165A	p.A1055A	CAAAGCGGCTAAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507398	195507398	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	52	3	38	4	0.0576923	0.105263	.	.	none	MUC4_ENST00000463781,NS,lymphoid_neoplasm,+1,1	MUC4	1505	1	NM_018406	exon2	c.G11053A	p.D3685N	AAGTGTCCGTGAC	.	scavenged	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4718776	4718776	+	Silent	SNP	G	G	A	rs1132448	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	5	106	0	0.046729	0	G|0.370;A|0.630	0.630	strong	.	PLD2	138	.	NM_001243108	exon13	c.G1179A	p.E393E	GGAGGAGGGTGTC	.	PASS	Atlas-SNP
POTEM	641455	hgsc.bcm.edu	37	14	20010235	20010235	+	Missense_Mutation	SNP	A	A	G	rs8135863	bycluster;by2hit2allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	72	4	77	0	0.0555556	0	A|0.250;G|0.750	0.750	weak	POTEM_ENST00000551509,NS,carcinoma,0,4	POTEM	51	4	NM_001145442	exon5	c.T923C	p.V308A	ATGAGAACAGTTC	.	scavenged	Atlas-SNP
HAGHL	84264	hgsc.bcm.edu	37	16	778158	778158	+	Silent	SNP	C	C	G	rs1406815	bycluster;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	8	7	1	0	0.875	0	C|0.556;G|0.444	0.444	strong	.	HAGHL	18	.	NM_032304	exon3	c.C213G	p.P71P	TCGTCCCGGGCTG	.	PASS	Atlas-SNP
PAEP	5047	hgsc.bcm.edu	37	9	138456155	138456155	+	Missense_Mutation	SNP	C	C	A	rs74725576		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	301	14	287	0	0.0465116	0	.	.	weak	PAEP,NS,carcinoma,0,2	PAEP	16	2	NM_002571	exon4	c.C376A	p.Q126K	TGCCTACAGGACA	.	PASS	Atlas-SNP
WTAP	9589	hgsc.bcm.edu	37	6	160169258	160169258	+	Silent	SNP	G	G	T	rs7766006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	350	5	333	0	0.0142857	0	G|0.800;T|0.200	0.200	strong	WTAP,NS,carcinoma,+2,1	WTAP	44	1	NM_001270533	exon6	c.G309T	p.P103P	GCAGCCGAGCGTT	.	scavenged	Atlas-SNP
MIS12	79003	hgsc.bcm.edu	37	17	5392791	5392791	+	Silent	SNP	A	A	G	rs74577983	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	79	4	77	0	0.0506329	0	A|0.972;G|0.028	0.028	strong	.	MIS12	19	.	NM_001258220	exon2	c.A609G	p.K203K	ACTGAAAATATCT	.	PASS	Atlas-SNP
RNPS1	10921	hgsc.bcm.edu	37	16	2305693	2305693	+	Silent	SNP	G	G	A	rs117291307	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	167	8	140	0	0.0479042	0	G|0.993;A|0.007	0.007	strong	.	RNPS1	18	.	NM_006711	exon7	c.C711T	p.A237A	CAGCACGGCGGTG	.	PASS	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9237436	9237436	+	Missense_Mutation	SNP	G	G	A	rs61745558	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	114	4	109	2	0.0350877	0.0183486	G|0.980;A|0.020	0.020	strong	OR7G3,NS,carcinoma,+1,1	OR7G3	41	1	NM_001001958	exon1	c.C191T	p.S64F	AGGATAGAGAGGA	.	scavenged	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225454386	225454386	+	Missense_Mutation	SNP	T	T	C	rs4653415	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	87	5	147	0	0.0574713	0	T|0.980;C|0.020	0.020	strong	.	DNAH14	300	.	NM_001373	exon49	c.T7436C	p.M2479T	CAGATATGTATGG	.	PASS	Atlas-SNP
APH1B	83464	hgsc.bcm.edu	37	15	63597857	63597857	+	Missense_Mutation	SNP	T	T	G	rs1047552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	86	5	87	0	0.0581395	0	G|0.065;T|0.935	0.065	strong	APH1B,NS,carcinoma,0,1	APH1B	27	1	NM_031301	exon6	c.T651G	p.F217L	AGCATTTATAATC	.	PASS	Atlas-SNP
ITGA5	3678	hgsc.bcm.edu	37	12	54795600	54795600	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	106	42	94	0	0.396226	0	.	.	none	.	ITGA5	99	.	NM_002205	exon22	c.G2266A	p.D756N	TAGTGTCCCGGAG	.	PASS	Atlas-SNP
IKBKE	9641	hgsc.bcm.edu	37	1	206651107	206651107	+	Silent	SNP	G	G	A	rs2297545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	168	4	131	0	0.0238095	0	G|0.745;A|0.255	0.255	strong	IKBKE,NS,carcinoma,0,1	IKBKE	77	1	NM_001193322	exon8	c.G717A	p.T239T	CACCACGGAGAAG	.	scavenged	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12501852	12501852	+	Missense_Mutation	SNP	C	C	T	rs200077318		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	143	9	155	4	0.0629371	0.0258065	.	.	weak	ZNF799_ENST00000430385,head_neck,carcinoma,0,2	ZNF799	111	2	NM_001080821	exon4	c.G1360A	p.G454R	CTTTCCCACATTT	.	scavenged	Atlas-SNP
SHISA2	387914	hgsc.bcm.edu	37	13	26620978	26620978	+	Silent	SNP	G	G	T	rs74965018	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	84	5	94	0	0.0595238	0	G|0.945;T|0.055	0.055	strong	.	SHISA2	43	.	NM_001007538	exon2	c.C561A	p.S187S	GGAGCTGGAACTG	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3215158	3215158	+	Missense_Mutation	SNP	C	C	G	rs1791085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	101	6	62	0	0.0594059	0	C|0.887;G|0.113	0.113	strong	.	MYOM1	192	.	NM_003803	exon2	c.G64C	p.V22L	TGCGCACGTCCTT	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	39038962	39038962	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	122	3	113	0	0.0245902	0	.	.	none	RYR1,NS,carcinoma,0,2	RYR1	708	2	NM_000540	exon89	c.G12184T	p.D4062Y	TTCTTCGACATGT	.	scavenged	Atlas-SNP
PLGLB2	5342	hgsc.bcm.edu	37	2	87244699	87244699	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	1123	3	1219	0	0.00267142	0	.	.	none	PLGLB1,rectum,carcinoma,0,1	PLGLB2	1	1	NM_002665	exon2	c.A162G	p.E54E	GTCCTCTTCACAT	.	scavenged	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129511373	129511373	+	Silent	SNP	T	T	C	rs2306220	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	55	4	101	0	0.0727273	0	T|0.969;C|0.031	0.031	strong	.	LAMA2	481	.	NM_000426	exon11	c.T1491C	p.C497C	AGACTGTAGTCGT	.	PASS	Atlas-SNP
WRNIP1	56897	hgsc.bcm.edu	37	6	2784571	2784571	+	Silent	SNP	G	G	A	rs160703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	65	4	54	0	0.0615385	0	G|0.824;A|0.176	0.176	strong	.	WRNIP1	39	.	NM_020135	exon6	c.G1656A	p.P552P	AGACCCGTCTGCG	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48063076	48063076	+	Silent	SNP	T	T	C	rs568215	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	6	110	0	0.0560748	0	T|0.258;C|0.742	0.742	strong	.	SEMA6D	322	.	NM_153618	exon19	c.T2316C	p.P772P	TCTTCCTACTCCT	.	PASS	Atlas-SNP
NBN	4683	hgsc.bcm.edu	37	8	90958422	90958422	+	Silent	SNP	T	T	C	rs1061302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	115	8	130	0	0.0695652	0	T|0.690;C|0.310	0.310	strong	.	NBN	86	.	NM_002485	exon13	c.A2016G	p.P672P	GCCAGATGGATTT	.	PASS	Atlas-SNP
GALNTL5	168391	hgsc.bcm.edu	37	7	151668119	151668119	+	Missense_Mutation	SNP	G	G	A	rs181262306	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	291	4	261	2	0.0137457	0.00766284	G|0.998;A|0.002	0.002	strong	GALNTL5,scalp,carcinoma,0,2	GALNTL5	87	2	NM_145292	exon3	c.G337A	p.E113K	GGCATCGAAAGAG	.	scavenged	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56204489	56204489	+	Missense_Mutation	SNP	C	C	G	rs3809975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	118	6	109	0	0.0508475	0	C|0.962;G|0.038	0.038	strong	.	ALPK2	487	.	NM_052947	exon5	c.G2930C	p.S977T	CTATAACTGGCTG	.	PASS	Atlas-SNP
UNC13C	440279	hgsc.bcm.edu	37	15	54847677	54847677	+	Silent	SNP	C	C	T	rs11639005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	95	7	115	0	0.0736842	0	C|0.625;T|0.375	0.375	strong	.	UNC13C	674	.	NM_001080534	exon27	c.C5925T	p.C1975C	ACAATGCGCTATA	.	PASS	Atlas-SNP
ZNF354A	6940	hgsc.bcm.edu	37	5	178154018	178154018	+	Missense_Mutation	SNP	T	T	C	rs146060491		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	5	134	0	0.046729	0	T|1.000;C|0.000	0.000	weak	ZNF354A,NS,carcinoma,+1,1	ZNF354A	74	1	NM_005649	exon3	c.A142G	p.R48G	GGTTCCTATAGTT	.	PASS	Atlas-SNP
OR7A10	390892	hgsc.bcm.edu	37	19	14951929	14951929	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	92	30	112	0	0.326087	0	.	.	none	OR7A10,NS,carcinoma,-1,1	OR7A10	33	1	NM_001005190	exon1	c.C761A	p.T254K	AAGCATGTACCAT	.	PASS	Atlas-SNP
MAP3K5	4217	hgsc.bcm.edu	37	6	136977568	136977568	+	Silent	SNP	T	T	C	rs2076260	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	63	5	95	0	0.0793651	0	T|0.613;C|0.387	0.387	strong	MAP3K5,NS,carcinoma,0,1	MAP3K5	136	1	NM_005923	exon10	c.A1557G	p.L519L	ATATATTAAAATT	.	PASS	Atlas-SNP
FAM22A	728118	hgsc.bcm.edu	37	10	88992641	88992641	+	Missense_Mutation	SNP	G	G	A	rs71252699	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	97	8	100	0	0.0824742	0	G|0.250;A|0.750	0.750	strong	FAM22D,colon,carcinoma,-2,2	FAM22A	20	2	NM_001099338	exon5	c.G1633A	p.G545S	GAAGAGGGCGAAG	.	scavenged	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	37	5	9052036	9052036	+	Missense_Mutation	SNP	C	C	T	rs139882587	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	137	44	163	0	0.321168	0	C|1.000;T|0.000	0.000	strong	SEMA5A,colon,carcinoma,+2,1	SEMA5A	236	1	NM_003966	exon20	c.G2794A	p.G932R	TGTTCCCGGAGCA	.	PASS	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	37	9	33797828	33797828	+	Missense_Mutation	SNP	C	C	T	rs143209949	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	5	82	2	0.0684932	0.0243902	C|0.999;T|0.001	0.001	strong	PRSS3_ENST00000361005,NS,carcinoma,-1,2	PRSS3	79	2	NM_007343	exon3	c.C373T	p.R125C	ATCAGCCGCATCC	.	scavenged	Atlas-SNP
TBC1D1	23216	hgsc.bcm.edu	37	4	38016395	38016395	+	Missense_Mutation	SNP	T	T	G	rs10501	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	85	4	81	0	0.0470588	0	T|0.448;G|0.552	0.552	strong	TBC1D1,NS,carcinoma,0,1	TBC1D1	94	1	NM_015173	exon3	c.T683G	p.V228G	AGCCTGTGCGCAG	.	PASS	Atlas-SNP
KLRC2	3822	hgsc.bcm.edu	37	12	10588444	10588444	+	Missense_Mutation	SNP	G	G	C	rs34194304		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	213	17	242	13	0.0798122	0.053719	.	.	weak	KLRC2,NS,carcinoma,+1,1	KLRC2	29	1	NM_002260	exon1	c.C142G	p.P48A	GGGAAGGATTTTG	.	scavenged	Atlas-SNP
MAN1B1	11253	hgsc.bcm.edu	37	9	139981546	139981546	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	48	12	43	0	0.25	0	.	.	none	.	MAN1B1	40	.	NM_016219	exon1	c.C95T	p.A32V	CCGTCGCCACCAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509170	195509170	+	Missense_Mutation	SNP	A	A	G	rs202189117	byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	53	5	45	4	0.0943396	0.0888889	A|0.994;G|0.006	0.006	strong	MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	NM_018406	exon2	c.T9281C	p.L3094P	GAGGAAAGGCTGG	.	scavenged	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769276	43769276	+	Silent	SNP	T	T	C	rs10880473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	104	5	167	0	0.0480769	0	T|0.747;C|0.253	0.253	strong	ADAMTS20_ENST00000389420,neck,malignant_melanoma,-2,1	ADAMTS20	635	1	NM_025003	exon36	c.A5352G	p.R1784R	TTCCCTTCTACTC	.	PASS	Atlas-SNP
ARHGAP12	94134	hgsc.bcm.edu	37	10	32128611	32128611	+	Missense_Mutation	SNP	A	A	G	rs2808096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	68	4	101	0	0.0588235	0	G|0.199;N|0.000	0.199	strong	.	ARHGAP12	79	.	NM_001270695	exon8	c.T1325C	p.F442S	TCAGGAAAGCAGG	.	PASS	Atlas-SNP
EIF2AK4	440275	hgsc.bcm.edu	37	15	40259848	40259848	+	Missense_Mutation	SNP	A	A	C	rs2291627	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	124	8	88	0	0.0645161	0	C|0.219;N|0.000	0.219	strong	.	EIF2AK4	107	.	NM_001013703	exon9	c.A1321C	p.I441L	GTCAAGATTACGG	.	PASS	Atlas-SNP
KIF20B	9585	hgsc.bcm.edu	37	10	91503660	91503660	+	Silent	SNP	A	A	G	rs1126480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	498	10	501	0	0.0200803	0	A|0.701;G|0.299	0.299	strong	KIF20B_ENST00000416354,adrenal_gland,adrenal_cortical_adenoma,0,2	KIF20B	191	2	NM_016195	exon22	c.A3891G	p.K1297K	TATGAAACAGCGA	.	scavenged	Atlas-SNP
HS3ST2	9956	hgsc.bcm.edu	37	16	22826243	22826243	+	Silent	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	66	21	47	0	0.318182	0	.	.	none	.	HS3ST2	59	.	NM_006043	exon1	c.C312T	p.S104S	CCACTCCGGCTCA	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274172	39274172	+	Silent	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	3	68	1	0.046875	0.0147059	.	.	none	KRTAP4-11,NS,carcinoma,-2,2	KRTAP4-11	94	2	NM_033059	exon1	c.C396A	p.P132P	GCAGGTGGGCTGG	.	scavenged	Atlas-SNP
NPEPPS	9520	hgsc.bcm.edu	37	17	45669359	45669359	+	Missense_Mutation	SNP	T	T	G	rs76398682	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	387	4	428	0	0.0103359	0	T|1.000;|0.000	.	weak	NPEPPS,mouth,carcinoma,0,1	NPEPPS	59	1	NM_006310	exon11	c.T1298G	p.F433C	AGATATTTGATGC	.	scavenged	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225528183	225528183	+	Missense_Mutation	SNP	C	C	A	rs3856145	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	253	12	351	0	0.0474308	0	C|0.498;A|0.500	0.500	strong	.	DNAH14	300	.	NM_001373	exon67	c.C10179A	p.D3393E	AATAGACAACCCC	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3215156	3215156	+	Silent	SNP	C	C	G	rs1662316	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	100	7	60	0	0.07	0	C|0.891;G|0.109	0.109	strong	.	MYOM1	192	.	NM_003803	exon2	c.G66C	p.V22V	GCTGCGCACGTCC	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152527608	152527608	+	Missense_Mutation	SNP	C	C	T	rs34577613	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	149	8	116	0	0.0536913	0	C|0.705;T|0.295	0.295	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_004543	exon38	c.G4435A	p.V1479I	ACTTGACGGTATC	.	PASS	Atlas-SNP
FBXO18	84893	hgsc.bcm.edu	37	10	5960434	5960434	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	4	41	0	0.0625	0	.	.	none	.	FBXO18	108	.	NM_032807	exon14	c.T2246C	p.L749P	TCTATCTCACGCA	.	PASS	Atlas-SNP
CLEC18A	348174	hgsc.bcm.edu	37	16	69988292	69988292	+	Missense_Mutation	SNP	C	C	T	rs2549089		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	288	4	275	0	0.0138889	0	.	.	weak	CLEC18A,NS,malignant_melanoma,0,2	CLEC18A	9	2	NM_001271197	exon4	c.C272T	p.T91I	GTGGAACCCCAAC	.	scavenged	Atlas-SNP
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434254	42434254	+	Silent	SNP	G	G	A	rs655427	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	95	6	68	0	0.0631579	0	G|0.540;N|0.000	.	strong	.	PLA2G4F	75	.	NM_213600	exon20	c.C2478T	p.N826N	CTCCACGTTGTTC	.	PASS	Atlas-SNP
ADPRH	141	hgsc.bcm.edu	37	3	119305379	119305379	+	Silent	SNP	T	T	A	rs25676	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	68	6	54	0	0.0882353	0	T|0.650;A|0.350	0.350	strong	.	ADPRH	33	.	NM_001125	exon4	c.T546A	p.A182A	CTATGCTGTGAAT	.	PASS	Atlas-SNP
SH3RF2	153769	hgsc.bcm.edu	37	5	145393364	145393364	+	Missense_Mutation	SNP	C	C	T	rs758037	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	6	127	0	0.05	0	C|0.411;T|0.589	0.589	strong	.	SH3RF2	58	.	NM_152550	exon5	c.C799T	p.R267C	TCATCCCGCACAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510133	195510133	+	Missense_Mutation	SNP	T	T	C	rs371587475		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	65	5	54	3	0.0769231	0.0555556	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.A8318G	p.N2773S	GAAGTGTTGGTGA	.	scavenged	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3075746	3075746	+	Silent	SNP	G	G	A	rs1143657	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	90	4	90	1	0.0444444	0.0111111	G|0.810;A|0.190	0.190	strong	MYOM1,NS,carcinoma,0,2	MYOM1	192	2	NM_003803	exon35	c.C4662T	p.A1554A	AGCATAGGCCTCA	.	scavenged	Atlas-SNP
UGT2B11	10720	hgsc.bcm.edu	37	4	70070366	70070366	+	Silent	SNP	A	A	T	rs72551395		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	161	11	182	0	0.068323	0	.	.	weak	.	UGT2B11	92	.	NM_001073	exon5	c.T1092A	p.G364G	TGGATGACCTAGG	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	33941759	33941759	+	Missense_Mutation	SNP	T	T	C	rs307658	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	107	4	141	0	0.0373832	0	T|0.617;C|0.383	0.383	strong	UBAP2,NS,carcinoma,0,1	UBAP2	82	1	NM_018449	exon16	c.A1817G	p.N606S	GCAGAATTCAGTG	.	scavenged	Atlas-SNP
DNAH8	1769	hgsc.bcm.edu	37	6	38781866	38781866	+	Silent	SNP	C	C	G	rs1678690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	257	6	276	1	0.0233463	0.00362319	C|0.558;G|0.442	0.442	strong	DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	NM_001206927	exon25	c.C3294G	p.S1098S	TATTTCCTTTATA	.	scavenged	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152328051	152328051	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	191	6	147	0	0.0314136	0	.	.	none	FLG2,NS,carcinoma,-1,1	FLG2	431	1	NM_001014342	exon3	c.A2211G	p.S737S	TGAGCCTGATCCA	.	scavenged	Atlas-SNP
SHISA2	387914	hgsc.bcm.edu	37	13	26620924	26620924	+	Silent	SNP	G	G	A	rs77010561	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	94	5	83	0	0.0531915	0	G|0.962;A|0.038	0.038	strong	.	SHISA2	43	.	NM_001007538	exon2	c.C615T	p.N205N	GCAACAGTTGGTC	.	PASS	Atlas-SNP
ZNF658	26149	hgsc.bcm.edu	37	9	40773337	40773337	+	Silent	SNP	C	C	T	rs78487056	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	176	4	216	0	0.0227273	0	C|0.824;T|0.176	0.176	strong	ZNF658,NS,carcinoma,0,1	ZNF658	100	1	NM_033160	exon5	c.G1938A	p.K646K	ATGTGCCTTGAGA	.	scavenged	Atlas-SNP
SETD6	79918	hgsc.bcm.edu	37	16	58550484	58550484	+	Silent	SNP	G	G	A	rs3743567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	5	62	0	0.0561798	0	G|0.896;A|0.104	0.104	strong	.	SETD6	27	.	NM_001160305	exon4	c.G579A	p.L193L	CGTGCTGCCCTTC	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592120	1592120	+	Missense_Mutation	SNP	G	G	T	rs1135201	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	134	6	139	5	0.0447761	0.0359712	G|0.744;T|0.256	0.256	strong	SIRPB1_ENST00000279477,NS,carcinoma,0,1	SIRPB1	83	1	NM_001135844	exon2	c.C316A	p.R106S	TGATGCGGATGGA	.	scavenged	Atlas-SNP
USP32	84669	hgsc.bcm.edu	37	17	58275693	58275693	+	Missense_Mutation	SNP	G	G	T	rs202121527	by1000genomes;alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	243	3	234	0	0.0123457	0	G|1.000;A|0.000	.	alt	USP32,rectum,carcinoma,0,3	USP32	128	3	NM_032582	exon27	c.C3362A	p.A1121E	CAAACCGCATCAT	.	scavenged	Atlas-SNP
ANKRD11	29123	hgsc.bcm.edu	37	16	89352567	89352567	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	53	19	38	0	0.358491	0	.	.	none	.	ANKRD11	195	.	NM_001256183	exon8	c.G772A	p.G258R	GGTTCCCTCCGTA	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276981	186276981	+	Silent	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	139	3	78	0	0.0215827	0	.	.	none	PRG4,NS,carcinoma,0,6	PRG4	259	6	NM_005807	exon7	c.A2130G	p.K710K	CCCTAAAGGGACT	.	scavenged	Atlas-SNP
C7orf63	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	263	8	269	0	0.0304183	0	C|0.602;T|0.398	0.398	strong	C7orf63_ENST00000389297,colon,carcinoma,+2,2	C7orf63	158	2	NM_001039706	exon11	c.C1116T	p.N372N	ATTCAACGTAATT	.	scavenged	Atlas-SNP
FBXO30	84085	hgsc.bcm.edu	37	6	146125793	146125793	+	Missense_Mutation	SNP	A	A	T	rs3811102	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	114	6	152	0	0.0526316	0	A|0.672;T|0.328	0.328	strong	.	FBXO30	56	.	NM_032145	exon2	c.T1749A	p.H583Q	CCTCAAATGGCGG	.	PASS	Atlas-SNP
TYR	7299	hgsc.bcm.edu	37	11	88911368	88911368	+	Missense_Mutation	SNP	G	G	A	rs149684917		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	24	63	0	0.375	0	G|1.000;A|0.000	0.000	weak	.	TYR	130	.	NM_000372	exon1	c.G247A	p.V83I	CCTTCCGTCTTTT	.	PASS	Atlas-SNP
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876355	74876355	+	Missense_Mutation	SNP	G	G	C	rs61734850	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	4	89	0	0.0408163	0	G|0.868;C|0.132	0.132	strong	.	SYNDIG1L	24	.	NM_001105579	exon2	c.C93G	p.S31R	GGACCAGCTGGGT	.	PASS	Atlas-SNP
MARVELD3	91862	hgsc.bcm.edu	37	16	71660310	71660310	+	Missense_Mutation	SNP	G	G	A	rs4788821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	200	11	176	0	0.055	0	G|0.561;A|0.439	0.439	strong	.	MARVELD3	63	.	NM_001017967	exon1	c.G178A	p.E60K	GACCCGGAGAGAG	.	PASS	Atlas-SNP
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	207	13	176	0	0.0628019	0	C|0.686;T|0.314	0.314	strong	.	DDX47	37	.	NM_201224	exon2	c.C150T	p.I50I	CAAGATCCAGATT	.	PASS	Atlas-SNP
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257354	114257354	+	Missense_Mutation	SNP	A	A	G	rs202243377		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	76	12	65	4	0.157895	0.0615385	A|0.999;G|0.001	0.001	weak	FOXD4L1,NS,carcinoma,0,1	FOXD4L1	48	1	NM_012184	exon1	c.A521G	p.H174R	CGGGCCACCCAGG	.	scavenged	Atlas-SNP
ZC2HC1C	79696	hgsc.bcm.edu	37	14	75537381	75537381	+	Silent	SNP	C	C	T	rs11546525	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	108	8	104	0	0.0740741	0	C|0.608;T|0.392	0.392	strong	FAM164C,colon,carcinoma,0,3	.	.	3	NM_024643	exon2	c.C105T	p.Y35Y	CTCTTACGAACAA	.	PASS	Atlas-SNP
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	282	11	321	2	0.0390071	0.00623053	A|0.634;C|0.366	0.366	strong	ZNF879,NS,carcinoma,0,2	ZNF879	41	2	NM_001136116	exon5	c.A477C	p.E159D	TGTTGAATTTGGG	.	scavenged	Atlas-SNP
CCDC176	80127	hgsc.bcm.edu	37	14	74514674	74514674	+	Missense_Mutation	SNP	A	A	T	rs3784038	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	236	14	258	0	0.059322	0	A|0.410;T|0.590	0.590	strong	.	.	.	.	NM_025057	exon7	c.A689T	p.D230V	AGAATGATTATCT	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25264786	25264786	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	87	25	114	0	0.287356	0	.	.	none	.	PYGB	84	.	NM_002862	exon14	c.T1667C	p.V556A	ACAAGGTGAAGAT	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	37	17	27448927	27448927	+	Missense_Mutation	SNP	C	C	T	rs201811476	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	49	17	58	0	0.346939	0	C|0.999;T|0.001	0.001	strong	.	MYO18A	217	.	NM_078471	exon4	c.G1136A	p.R379H	TTCACACGCACCT	.	PASS	Atlas-SNP
HRH3	11255	hgsc.bcm.edu	37	20	60791422	60791422	+	Silent	SNP	C	C	T	rs3787430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	69	5	55	0	0.0724638	0	C|0.833;T|0.167	0.167	strong	.	HRH3	25	.	NM_007232	exon3	c.G978A	p.P326P	CGCCGACGGCTTG	.	PASS	Atlas-SNP
TAS2R43	259289	hgsc.bcm.edu	37	12	11244725	11244725	+	Missense_Mutation	SNP	C	C	G	rs68157013	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	27	18	10	0	0.666667	0	C|0.597;G|0.403	0.403	strong	TAS2R46_ENST00000422992,NS,carcinoma,0,4	TAS2R43	19	4	NM_176884	exon1	c.G104C	p.W35S	TTGAACCACTCAA	.	PASS	Atlas-SNP
IKBKB	3551	hgsc.bcm.edu	37	8	42176069	42176069	+	Splice_Site	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	132	39	95	0	0.295455	0	.	.	none	.	IKBKB	88	.	NM_001242778	exon12	c.1064-1G>T	.	TCTCCAGTTCAAG	.	PASS	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2039776	2039776	+	Silent	SNP	A	A	G	rs13296987	byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	86	7	87	0	0.0813954	0	A|0.750;G|0.250	0.250	strong	SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	NM_139045	exon4	c.A666G	p.Q222Q	GCAGCAACAGCAG	.	PASS	Atlas-SNP
NPLOC4	55666	hgsc.bcm.edu	37	17	79580457	79580457	+	Silent	SNP	C	C	A	rs17852306	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	96	7	81	0	0.0729167	0	C|0.916;A|0.084	0.084	strong	.	NPLOC4	27	.	NM_017921	exon4	c.G273T	p.T91T	AACTGACGTCTCC	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107620867	107620867	+	Missense_Mutation	SNP	C	C	T	rs2230806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	110	5	113	0	0.0454545	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
OR4M2	390538	hgsc.bcm.edu	37	15	22369426	22369426	+	Missense_Mutation	SNP	G	G	A	rs4087943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	330	7	339	2	0.0212121	0.0058997	G|0.493;A|0.507	0.507	strong	OR4M2,colon,carcinoma,0,1	OR4M2	140	1	NM_001004719	exon1	c.G851A	p.R284H	CTTTACGTAATCC	.	scavenged	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66717784	66717784	+	Silent	SNP	T	T	A	rs35536133	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	7	100	0	0.0583333	0	T|0.913;A|0.087	0.087	strong	.	HELB	90	.	NM_033647	exon10	c.T2319A	p.V773V	ACTTGTTTTTGGA	.	PASS	Atlas-SNP
DNAJC9	23234	hgsc.bcm.edu	37	10	75006804	75006804	+	Silent	SNP	A	A	G	rs35302968	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	117	7	99	0	0.0598291	0	A|0.827;G|0.173	0.173	strong	.	DNAJC9	19	.	NM_015190	exon1	c.T144C	p.G48G	GCCCTCACCCACC	.	PASS	Atlas-SNP
GIGYF2	26058	hgsc.bcm.edu	37	2	233659553	233659553	+	Missense_Mutation	SNP	C	C	A	rs2289912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	132	8	156	0	0.0606061	0	C|0.950;A|0.050	0.050	strong	GIGYF2,NS,carcinoma,0,1	GIGYF2	288	1	NM_001103147	exon15	c.C1441A	p.P481T	CCTAGTCCTACTC	.	PASS	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	37	11	4945196	4945196	+	Missense_Mutation	SNP	T	T	G	rs1378739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	96	5	91	0	0.0520833	0	T|0.355;G|0.645	0.645	strong	.	OR51G1	74	.	NM_001005237	exon1	c.A374C	p.Y125S	GCCACGTAGCGGT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489749	32489749	+	Silent	SNP	G	G	C	rs1064594	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	5	5	0	0	1	.	G|0.339;C|0.661	0.661	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.C303G	p.R101R	CGCGGCGCGCCTG	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238443226	238443226	+	Missense_Mutation	SNP	A	A	G	rs2292884	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	7	111	0	0.0583333	0	A|0.644;G|0.356	0.356	strong	.	MLPH	41	.	NM_024101	exon9	c.A1040G	p.H347R	ATAAGCATATTTC	.	PASS	Atlas-SNP
ATP8A2	51761	hgsc.bcm.edu	37	13	26043182	26043182	+	Silent	SNP	A	A	C	rs7317185	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	81	4	74	0	0.0493827	0	A|0.790;C|0.210	0.210	strong	ATP8A2,colon,carcinoma,0,1	ATP8A2	181	1	NM_016529	exon2	c.A144C	p.G48G	TGTTGGAGACCAG	.	scavenged	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285542	16285542	+	Silent	SNP	G	G	A	rs17052364	byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	245	4	238	1	0.0163265	0.00420168	G|0.540;A|0.460	0.460	strong	UBB,NS,carcinoma,0,1	UBB	30	1	NM_018955	exon2	c.G321A	p.Q107Q	GATCCAGGATAAA	.	scavenged	Atlas-SNP
TTC18	118491	hgsc.bcm.edu	37	10	75035257	75035257	+	Missense_Mutation	SNP	T	T	C	rs4294502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	138	7	123	0	0.0507246	0	T|0.811;C|0.189	0.189	strong	TTC18,NS,carcinoma,0,1	TTC18	106	1	NM_145170	exon23	c.A2830G	p.N944D	CAAAGTTCTTCTT	.	PASS	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	37	20	47246077	47246077	+	Missense_Mutation	SNP	C	C	G	rs3936192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	111	5	103	0	0.045045	0	C|0.908;G|0.092	0.092	strong	.	PREX1	441	.	NM_020820	exon37	c.G4676C	p.S1559T	CCCACACTCCCAG	.	PASS	Atlas-SNP
VPS41	27072	hgsc.bcm.edu	37	7	38796570	38796570	+	Silent	SNP	G	G	A	rs2240350	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	109	5	102	0	0.0458716	0	G|0.643;A|0.357	0.357	strong	.	VPS41	102	.	NM_014396	exon19	c.C1563T	p.D521D	GTTCTTGTCATAG	.	PASS	Atlas-SNP
CENPC1	1060	hgsc.bcm.edu	37	4	68384008	68384008	+	Silent	SNP	C	C	T	rs355510	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	155	7	189	0	0.0451613	0	C|0.352;T|0.648	0.648	strong	.	CENPC1	66	.	NM_001812	exon7	c.G696A	p.S232S	TCCTTCCGATGTT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093008	1093008	+	Silent	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	60	6	46	5	0.1	0.108696	.	.	none	MUC2_ENST00000441003,colon,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.C4827T	p.I1609I	ACCCATCACCACC	.	scavenged	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49723141	49723141	+	Silent	SNP	A	A	G	rs144982232	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	130	6	123	0	0.0461538	0	A|0.989;G|0.011	0.011	strong	.	MST1	84	.	NM_020998	exon11	c.T1275C	p.H425H	TTGTGCATGCGGT	.	PASS	Atlas-SNP
SMC1B	27127	hgsc.bcm.edu	37	22	45767391	45767391	+	Missense_Mutation	SNP	C	C	T	rs9614653	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	6	176	1	0.0379747	0.00568182	C|0.845;T|0.155	0.155	strong	SMC1B_ENST00000357450,rectum,carcinoma,-1,3	SMC1B	215	3	NM_148674	exon14	c.G2273A	p.R758Q	CGTTGTCGTTCCT	.	scavenged	Atlas-SNP
SP1	6667	hgsc.bcm.edu	37	12	53776587	53776587	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	117	6	106	0	0.0512821	0	.	.	none	.	SP1	57	.	NM_138473	exon3	c.A856G	p.I286V	GTCACGATCAGCA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384986	16384986	+	Silent	SNP	G	G	T	rs28496958	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	124	5	106	0	0.0403226	0	G|0.704;T|0.296	0.296	strong	FAM131C,colon,carcinoma,0,1	FAM131C	21	1	NM_182623	exon7	c.C789A	p.L263L	GGAGGGGAGGGAG	.	PASS	Atlas-SNP
SORCS1	114815	hgsc.bcm.edu	37	10	108380213	108380213	+	Silent	SNP	G	G	A	rs4917481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	60	6	62	0	0.1	0	G|0.707;A|0.293	0.293	strong	.	SORCS1	534	.	NM_001206572	exon20	c.C2769T	p.Y923Y	CCACACGTAAGTG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130114190	130114190	+	Silent	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	123	5	152	0	0.0406504	0	.	.	none	.	COL6A5	205	.	NM_153264	exon8	c.C3450T	p.L1150L	ACATCTCCTGCCA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384998	16384998	+	Silent	SNP	G	G	C	rs1807285	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	129	5	117	0	0.0387597	0	G|0.706;C|0.294	0.294	strong	FAM131C,NS,carcinoma,-1,2	FAM131C	21	2	NM_182623	exon7	c.C777G	p.P259P	GCCCGGGGGGTGG	.	scavenged	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125590478	125590478	+	Silent	SNP	T	T	C	rs1874748	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	132	7	150	0	0.0530303	0	T|0.820;C|0.180	0.180	strong	.	ANKRD50	136	.	NM_020337	exon4	c.A3954G	p.P1318P	TTTAGGTGGTGCA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951949	130951949	+	Missense_Mutation	SNP	G	G	A	rs76125467	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	327	12	335	0	0.0366972	0	G|0.500;A|0.500	0.500	weak	TUBA3E,NS,carcinoma,+2,1	TUBA3E	73	1	NM_207312	exon4	c.C466T	p.R156W	AGAGCCGCTCCAT	.	scavenged	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110777962	110777962	+	Silent	SNP	A	A	G	rs6907567	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	70	4	102	0	0.0571429	0	A|0.716;G|0.284	0.284	strong	.	SLC22A16	81	.	NM_033125	exon2	c.T312C	p.N104N	CCTCTTATTCCTG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79029749	79029749	+	Missense_Mutation	SNP	A	A	G	rs1428225	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	104	10	108	0	0.0961538	0	A|0.752;G|0.248	0.248	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon2	c.A5161G	p.I1721V	AAGATCATCAGCC	.	PASS	Atlas-SNP
RCAN3	11123	hgsc.bcm.edu	37	1	24861704	24861704	+	Missense_Mutation	SNP	G	G	A	rs196432	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	154	5	130	2	0.0324675	0.0153846	G|0.515;A|0.485	0.485	strong	RCAN3,colon,carcinoma,0,1	RCAN3	22	1	NM_001251982	exon3	c.G491A	p.R164Q	CCAGACGAGGCGC	.	scavenged	Atlas-SNP
DMXL2	23312	hgsc.bcm.edu	37	15	51795172	51795172	+	Silent	SNP	G	G	A	rs12592889	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	198	10	170	1	0.050505	0.00588235	G|0.548;A|0.452	0.452	strong	DMXL2,NS,carcinoma,0,1	DMXL2	262	1	NM_001174116	exon17	c.C2823T	p.N941N	ATCTACGTTCTTC	.	scavenged	Atlas-SNP
PTPRS	5802	hgsc.bcm.edu	37	19	5222916	5222916	+	Missense_Mutation	SNP	C	C	T	rs62113240		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	19	9	8	0	0.473684	0	.	.	weak	.	PTPRS	169	.	NM_002850	exon18	c.G2887A	p.V963I	ATTTGACGATGGC	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19447843	19447843	+	Silent	SNP	C	C	G	rs1044010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	317	12	307	2	0.0378549	0.00651466	C|0.417;G|0.583	0.583	strong	UBR4,colon,carcinoma,0,1	UBR4	415	1	NM_020765	exon68	c.G9981C	p.L3327L	GCCGCACAGAGCA	.	scavenged	Atlas-SNP
C16orf62	57020	hgsc.bcm.edu	37	16	19680546	19680546	+	Silent	SNP	T	T	C	rs957676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	76	5	100	0	0.0657895	0	T|0.656;C|0.344	0.344	strong	.	C16orf62	164	.	NM_020314	exon27	c.T2553C	p.D851D	TATTGATGGGAAG	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26462790	26462790	+	Silent	SNP	G	G	A	rs3740232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	162	2	138	0	0.0123457	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
CCDC86	79080	hgsc.bcm.edu	37	11	60610065	60610065	+	Silent	SNP	G	G	A	rs2074420	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	104	5	90	0	0.0480769	0	G|0.725;A|0.275	0.275	strong	CCDC86,NS,carcinoma,0,1	CCDC86	24	1	NM_024098	exon1	c.G468A	p.P156P	ACCGCCGGTCCCA	.	PASS	Atlas-SNP
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	210	9	187	0	0.0428571	0	G|0.691;T|0.309	0.309	strong	.	DNAJC25	20	.	NM_001015882	exon3	c.G702T	p.G234G	AAAGGGGGGCTAT	.	PASS	Atlas-SNP
JAG2	3714	hgsc.bcm.edu	37	14	105615648	105615648	+	Missense_Mutation	SNP	C	C	T	rs9972231	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	97	3	81	0	0.0309278	0	C|0.899;T|0.101	0.101	strong	JAG2,scalp,carcinoma,0,3	JAG2	69	3	NM_002226	exon13	c.G1612A	p.D538N	AAAGGTCGACATC	.	scavenged	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15733454	15733454	+	Silent	SNP	A	A	C	rs1058212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	160	4	146	0	0.025	0	A|0.883;C|0.117	0.117	strong	BST1,colon,carcinoma,0,3	BST1	30	3	NM_004334	exon9	c.A943C	p.R315R	GCTTCCAGGACTC	.	scavenged	Atlas-SNP
ELL2	22936	hgsc.bcm.edu	37	5	95236415	95236415	+	Silent	SNP	G	G	A	rs17085249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	179	6	178	0	0.0335196	0	G|0.697;A|0.303	0.303	strong	ELL2,NS,carcinoma,0,1	ELL2	63	1	NM_012081	exon7	c.C936T	p.D312D	TACAGCGTCTCTA	.	scavenged	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848741	54848741	+	Silent	SNP	T	T	C	rs12985462	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	153	6	157	1	0.0392157	0.00636943	T|0.855;C|0.145	0.145	strong	LILRA4,NS,carcinoma,0,1	LILRA4	91	1	NM_012276	exon5	c.A882G	p.R294R	GTAGCATCTGTAC	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093296	1093296	+	Silent	SNP	T	T	C	rs56068864		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	65	15	43	11	0.230769	0.255814	.	.	weak	MUC2_ENST00000441003,rectum,carcinoma,+1,2	MUC2	614	2	NM_002457	exon30	c.T5115C	p.T1705T	CACCACTACGGTG	.	scavenged	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101831995	101831995	+	Missense_Mutation	SNP	G	G	A	rs10519	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	137	3	112	1	0.0218978	0.00892857	G|0.860;A|0.140	0.140	strong	COL15A1,colon,carcinoma,0,1	COL15A1	211	1	NM_001855	exon42	c.G3994A	p.V1332I	CATGGCGTCCGCC	.	scavenged	Atlas-SNP
PPP1R26	9858	hgsc.bcm.edu	37	9	138376649	138376649	+	Missense_Mutation	SNP	T	T	C	rs3748192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	66	4	77	0	0.0606061	0	T|0.723;C|0.277	0.277	strong	KIAA0649,NS,carcinoma,0,1	.	.	1	NM_014811	exon4	c.T293C	p.V98A	TGGCTGTCTGTGG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239613	31239613	+	Missense_Mutation	SNP	C	C	T	rs2308538	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	6	76	3	0.05	0.0394737	T|0.155;C|0.845	0.155	strong	HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	NM_002117	exon2	c.G106A	p.V36M	GGGACACGGCGGT	.	scavenged	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22383066	22383066	+	Silent	SNP	A	A	G	rs67576397	alternate_allele	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	132	4	168	0	0.030303	0	ATG|0.500;CTA|0.500	.	alt	OR4N4,colon,carcinoma,+2,1	OR4N4	108	1	NM_001005241	exon1	c.A594G	p.L198L	GCTTCTAATGGTC	.	scavenged	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43519270	43519270	+	Missense_Mutation	SNP	A	A	G	rs111493043	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	148	5	176	0	0.0337838	0	A|0.982;G|0.018	0.018	strong	PSG11,NS,carcinoma,0,1	PSG11	57	1	NM_002785	exon4	c.T962C	p.I321T	TTACCAATGACTC	.	scavenged	Atlas-SNP
CTAGE4	100128553	hgsc.bcm.edu	37	7	143882697	143882697	+	Missense_Mutation	SNP	A	A	G	rs77624986	byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	112	8	112	1	0.0714286	0.00892857	A|0.500;G|0.500	0.500	strong	CTAGE4,right_upper_lobe,carcinoma,-2,1	CTAGE4	10	1	NM_198495	exon1	c.A2101G	p.I701V	GCTCCAATCAGCG	.	scavenged	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3628212	3628212	+	Missense_Mutation	SNP	T	T	C	rs220461	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	50	4	42	0	0.08	0	T|0.769;C|0.230	0.230	strong	.	GSG2	48	.	NM_031965	exon1	c.T983C	p.I328T	GGGGAATAGACAG	.	PASS	Atlas-SNP
INTU	27152	hgsc.bcm.edu	37	4	128628100	128628100	+	Missense_Mutation	SNP	A	A	C	rs35858752	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	110	5	114	0	0.0454545	0	A|0.963;C|0.037	0.037	strong	.	INTU	92	.	NM_015693	exon12	c.A2247C	p.L749F	TGGTTTAGAAGAA	.	PASS	Atlas-SNP
UFL1	23376	hgsc.bcm.edu	37	6	96999725	96999725	+	Silent	SNP	C	C	T	rs1127175	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	352	10	523	3	0.0284091	0.00573614	C|0.662;T|0.338	0.338	strong	KIAA0776,NS,carcinoma,0,2	.	.	2	NM_015323	exon17	c.C1911T	p.D637D	AGAAGACTTTATT	.	scavenged	Atlas-SNP
NAPEPLD	222236	hgsc.bcm.edu	37	7	102760511	102760511	+	Missense_Mutation	SNP	A	A	C	rs12540583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	116	5	108	0	0.0431034	0	A|0.876;C|0.124	0.124	strong	.	NAPEPLD	49	.	NM_001122838	exon3	c.T454G	p.S152A	CACGAGAGCTAAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506007	195506007	+	Silent	SNP	G	G	A	rs71635085		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	31	6	32	4	0.193548	0.125	G|1.000;|0.000	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C12444T	p.T4148T	AGGGATGGTGACA	.	scavenged	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553994	140553994	+	Silent	SNP	G	G	T	rs374392843		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	233	6	218	3	0.0257511	0.0137615	.	.	weak	PCDHB7,NS,carcinoma,0,4	PCDHB7	231	4	NM_018940	exon1	c.G1578T	p.A526A	GCAGGCGTTCGAG	.	scavenged	Atlas-SNP
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	253	8	201	0	0.0316206	0	G|0.996;A|0.004	0.004	strong	OR2M5,NS,carcinoma,0,2	OR2M5	117	2	NM_001004690	exon1	c.G571A	p.D191N	TGCAATGACACAT	.	scavenged	Atlas-SNP
BCL10	8915	hgsc.bcm.edu	37	1	85736460	85736460	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	154	71	106	0	0.461039	0	.	.	none	.	BCL10	39	.	NM_003921	exon2	c.A187C	p.K63Q	CCCTTTTTCTACT	.	PASS	Atlas-SNP
ZNF418	147686	hgsc.bcm.edu	37	19	58439306	58439306	+	Silent	SNP	G	G	A	rs7253514	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	179	8	164	0	0.0446927	0	G|0.704;A|0.296	0.296	strong	.	ZNF418	76	.	NM_133460	exon4	c.C243T	p.A81A	AGAGTGGGCCTTC	.	PASS	Atlas-SNP
LAP3	51056	hgsc.bcm.edu	37	4	17586703	17586703	+	Silent	SNP	T	T	C	rs3733576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	99	7	125	0	0.0707071	0	T|0.266;C|0.734	0.734	strong	.	LAP3	50	.	NM_015907	exon6	c.T648C	p.A216A	ATTTGCTGAAATT	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73466709	73466709	+	Silent	SNP	T	T	C	rs10823829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	8	99	0	0.0666667	0	T|0.793;C|0.207	0.207	strong	.	CDH23	365	.	NM_022124	exon25	c.T3009C	p.S1003S	TGTGTCTGTGTCC	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	20071386	20071386	+	Missense_Mutation	SNP	C	C	G	rs76731633	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	96	4	89	0	0.0416667	0	C|0.998;G|0.002	0.002	strong	.	NAV2	255	.	NM_001244963	exon17	c.C4444G	p.L1482V	AGCCCTCTCTCTT	.	PASS	Atlas-SNP
PM20D2	135293	hgsc.bcm.edu	37	6	89868128	89868128	+	Missense_Mutation	SNP	A	A	G	rs10944433	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	219	8	313	2	0.0365297	0.00638978	A|0.990;G|0.010	0.010	strong	PM20D2,NS,carcinoma,-1,1	PM20D2	30	1	NM_001010853	exon5	c.A997G	p.K333E	GGAAGAAAGCTAG	.	scavenged	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17764996	17764996	+	Missense_Mutation	SNP	C	C	T	rs184686655	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	86	28	97	0	0.325581	0	C|1.000;T|0.000	0.000	strong	.	KIF13A	276	.	NM_022113	exon39	c.G4763A	p.R1588H	GGGCTACGGGACA	.	PASS	Atlas-SNP
NR4A3	8013	hgsc.bcm.edu	37	9	102595685	102595685	+	Silent	SNP	C	C	T	rs10988904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	171	7	182	0	0.0409357	0	C|0.649;T|0.351	0.351	strong	.	NR4A3	80	.	NM_173200	exon6	c.C1236T	p.A412A	GAATGCCCTTGTC	.	PASS	Atlas-SNP
SLC15A2	6565	hgsc.bcm.edu	37	3	121647286	121647286	+	Missense_Mutation	SNP	C	C	T	rs1143671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	56	6	66	0	0.107143	0	C|0.523;T|0.477	0.477	strong	.	SLC15A2	92	.	NM_021082	exon15	c.C1225T	p.P409S	GCCCAGCCAGGTC	.	PASS	Atlas-SNP
PLCH1	23007	hgsc.bcm.edu	37	3	155218568	155218568	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	63	7	64	0	0.111111	0	.	.	none	.	PLCH1	406	.	NM_001130960	exon13	c.C1684T	p.R562W	TAGACCGTGATTT	.	PASS	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	98	6	157	0	0.0612245	0	A|0.692;G|0.308	0.308	strong	.	HBS1L	75	.	NM_006620	exon17	c.T1977C	p.F659F	CTCTTTAAAGTCT	.	PASS	Atlas-SNP
PROSER1	80209	hgsc.bcm.edu	37	13	39603498	39603498	+	Silent	SNP	G	G	A	rs61737582	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	275	9	307	0	0.0327273	0	G|0.921;A|0.079	0.079	strong	C13orf23,NS,carcinoma,-2,1	.	.	1	NM_025138	exon4	c.C195T	p.V65V	TGGCTGGACAGCC	.	scavenged	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168107491	168107491	+	Missense_Mutation	SNP	A	A	G	rs3749004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	130	6	174	0	0.0461538	0	A|0.817;G|0.183	0.183	strong	.	XIRP2	914	.	NM_152381	exon9	c.A9589G	p.I3197V	GGGGCCATCCCAT	.	PASS	Atlas-SNP
C8orf48	157773	hgsc.bcm.edu	37	8	13424866	13424866	+	Silent	SNP	G	G	C	rs75484711	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	158	9	183	0	0.056962	0	G|0.960;C|0.040	0.040	strong	.	C8orf48	18	.	NM_001007090	exon1	c.G366C	p.L122L	TGCCCTGCAGTCT	.	PASS	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	37	2	133542014	133542014	+	Silent	SNP	T	T	C	rs12616282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	106	5	136	0	0.0471698	0	T|0.335;C|0.665	0.665	strong	.	NCKAP5	322	.	NM_207363	exon14	c.A2370G	p.A790A	CATGGGTGCCGAA	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276961	186276961	+	Missense_Mutation	SNP	A	A	C	rs145338869	bycluster;byfrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	113	6	67	0	0.0530973	0	A|0.996;C|0.004	0.004	strong	PRG4,NS,malignant_melanoma,0,1	PRG4	259	1	NM_005807	exon7	c.A2110C	p.T704P	AAGGAGACTGCTC	.	PASS	Atlas-SNP
SETD1B	23067	hgsc.bcm.edu	37	12	122247634	122247634	+	Silent	SNP	C	C	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	55	17	44	0	0.309091	0	.	.	none	.	SETD1B	105	.	NM_015048	exon5	c.C783T	p.C261C	CAGCTGCCGCCTG	.	PASS	Atlas-SNP
RAB11FIP2	22841	hgsc.bcm.edu	37	10	119774598	119774598	+	Missense_Mutation	SNP	T	T	A	rs58533443	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	122	7	110	0	0.057377	0	T|0.967;A|0.033	0.033	strong	.	RAB11FIP2	39	.	NM_014904	exon4	c.A1289T	p.N430I	TCTTCATTGCTTG	.	PASS	Atlas-SNP
TGFBR2	7048	hgsc.bcm.edu	37	3	30713842	30713842	+	Silent	SNP	C	C	T	rs2228048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	136	6	127	0	0.0441176	0	C|0.947;T|0.053	0.053	strong	.	TGFBR2	139	.	NM_001024847	exon5	c.C1242T	p.N414N	GAAGAACGACCTA	.	PASS	Atlas-SNP
PPARA	5465	hgsc.bcm.edu	37	22	46615880	46615880	+	Missense_Mutation	SNP	T	T	C	rs1800234	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	64	4	44	0	0.0625	0	T|0.989;C|0.011	0.011	strong	.	PPARA	36	.	NM_001001928	exon6	c.T680C	p.V227A	CCCGGGTCATCCT	.	PASS	Atlas-SNP
LRCH3	84859	hgsc.bcm.edu	37	3	197597044	197597044	+	Silent	SNP	C	C	T	rs77281724	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	79	4	69	0	0.0506329	0	C|0.887;T|0.113	0.113	strong	.	LRCH3	96	.	NM_032773	exon18	c.C1887T	p.P629P	TTCACCCCTTCCT	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186857	12186857	+	Missense_Mutation	SNP	G	G	C	rs6511763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	147	6	121	0	0.0408163	0	G|0.739;C|0.261	0.261	strong	.	ZNF844	69	.	NM_001136501	exon4	c.G922C	p.A308P	GAGAAGGCTTATG	.	PASS	Atlas-SNP
RGS22	26166	hgsc.bcm.edu	37	8	101011612	101011612	+	Missense_Mutation	SNP	G	G	A	rs3133711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	92	4	102	0	0.0434783	0	G|0.964;A|0.036	0.036	strong	.	RGS22	319	.	NM_015668	exon19	c.C2827T	p.H943Y	GCTCATGAAGAAT	.	PASS	Atlas-SNP
FAM162B	221303	hgsc.bcm.edu	37	6	117086652	117086652	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	13	7	23	0	0.538462	0	.	.	none	.	FAM162B	19	.	NM_001085480	exon1	c.C88T	p.R30W	CGGGCCGTCGCGT	.	PASS	Atlas-SNP
SOCS6	9306	hgsc.bcm.edu	37	18	67992810	67992810	+	Silent	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	113	3	115	1	0.0265487	0.00869565	.	.	none	SOCS6,NS,carcinoma,+2,1	SOCS6	54	1	NM_004232	exon2	c.G906T	p.A302A	GAGAGCGGGTCAC	.	scavenged	Atlas-SNP
XAF1	54739	hgsc.bcm.edu	37	17	6663894	6663894	+	Missense_Mutation	SNP	G	G	A	rs2271232	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	202	7	218	2	0.0346535	0.00917431	G|0.925;A|0.075	0.075	strong	XAF1,colon,carcinoma,+1,1	XAF1	16	1	NM_017523	exon4	c.G395A	p.R132H	TCTGTCGCAGTGA	.	scavenged	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158630642	158630642	+	Missense_Mutation	SNP	T	T	C	rs202186112		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	74	4	77	1	0.0540541	0.012987	.	.	weak	RNF145,NS,carcinoma,0,2	RNF145	110	2	NM_001199380	exon2	c.A74G	p.K25R	TTTTTCTTTTTTT	.	scavenged	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11149711	11149711	+	Missense_Mutation	SNP	C	C	A	rs10845279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	225	8	241	0	0.0355556	0	C|0.671;A|0.329	0.329	strong	TAS2R20,colon,carcinoma,0,1	TAS2R20	17	1	NM_176889	exon1	c.G764T	p.R255L	TTTGGTCGCATCT	.	scavenged	Atlas-SNP
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711241	140711241	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	183	26	162	0	0.142077	0	.	.	none	.	PCDHGA1	397	.	NM_018912	exon1	c.A990C	p.K330N	GGCTAAAGTTAAG	.	PASS	Atlas-SNP
TAPT1	202018	hgsc.bcm.edu	37	4	16188159	16188159	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	404	5	399	2	0.0123762	0.00501253	.	.	none	TAPT1,NS,carcinoma,0,2	TAPT1	31	2	NM_153365	exon7	c.C915A	p.S305R	CATACCGCTATTT	.	scavenged	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5778597	5778597	+	Silent	SNP	C	C	G	rs2305926	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	148	9	145	0	0.0608108	0	C|0.978;G|0.022	0.022	strong	TMEM146,NS,carcinoma,0,1	.	.	1	NM_152784	exon22	c.C2307G	p.V769V	GACGGTCTGCCAG	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56552307	56552307	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	58	6	62	0	0.103448	0	.	.	none	.	NLRP5	217	.	NM_153447	exon11	c.A2806C	p.T936P	GGCATCACAGCCA	.	PASS	Atlas-SNP
IQSEC2	23096	hgsc.bcm.edu	37	X	53280102	53280102	+	Silent	SNP	C	C	T	rs200411197	by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	120	7	148	0	0.0583333	0	C|1.000;T|0.000	0.000	strong	.	IQSEC2	195	.	NM_001111125	exon5	c.G1656A	p.P552P	AACTGGCGGGAGA	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14747412	14747412	+	Silent	SNP	A	A	G	rs4741426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	133	7	112	0	0.0526316	0	A|0.848;G|0.152	0.152	strong	.	FREM1	261	.	NM_144966	exon34	c.T5859C	p.V1953V	CAAGGAAACTATC	.	PASS	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57325083	57325083	+	Missense_Mutation	SNP	C	C	T	rs34051133	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	125	11	102	0	0.088	0	C|0.872;T|0.128	0.128	strong	ZIM2_ENST00000326441,colon,carcinoma,-1,4	PEG3	414	4	NM_001146184	exon9	c.G4727A	p.R1576H	GACAGGCGGTCAT	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186672897	186672897	+	Silent	SNP	A	A	G	rs4666690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	415	10	433	0	0.0240964	0	A|0.658;G|0.342	0.342	strong	FSIP2_ENST00000343098,caecum,carcinoma,+2,2	FSIP2	251	2	NM_173651	exon17	c.A19131G	p.L6377L	CTTTTTAATGGTG	.	scavenged	Atlas-SNP
CFHR4	10877	hgsc.bcm.edu	37	1	196884258	196884258	+	Silent	SNP	A	A	T	rs379049		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	890	13	733	2	0.0146067	0.00272851	.	.	weak	CFHR4_ENST00000367416,right_lower_lobe,carcinoma,+1,2	CFHR4	141	2	NM_001201550	exon9	c.A1530T	p.P510P	ACCACCAAGATGC	.	scavenged	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55655597	55655597	+	Silent	SNP	A	A	G	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	580	27	599	41	0.0465517	0.0684474	.	.	none	SPRYD5_ENST00000327733,NS,carcinoma,+2,2	.	.	2	NM_032681	exon4	c.A597G	p.E199E	CTTGGAAAGGCTG	.	scavenged	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179579822	179579822	+	Silent	SNP	T	T	A	rs2562836	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	115	9	127	0	0.0782609	0	T|0.630;N|0.001	.	strong	.	TTN	18412	.	NM_001267550	exon90	c.A26091T	p.L8697L	ACTGGTTAGGAAG	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103474041	103474041	+	Missense_Mutation	SNP	G	G	C	rs79471015	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	110	7	107	0	0.0636364	0	G|0.993;C|0.007	0.007	strong	.	RELN	593	.	NM_173054	exon3	c.C416G	p.T139S	AGGTTGGTTGTGG	.	PASS	Atlas-SNP
RASSF8	11228	hgsc.bcm.edu	37	12	26218197	26218197	+	Silent	SNP	G	G	A	rs79553120	bycluster;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	269	8	258	0	0.0297398	0	G|0.992;A|0.008	0.008	strong	RASSF8_ENST00000541490,right_lower_lobe,carcinoma,+2,4	RASSF8	56	4	NM_007211	exon4	c.G870A	p.E290E	GGAAGAGGTTAAA	.	scavenged	Atlas-SNP
FRMD6	122786	hgsc.bcm.edu	37	14	52156605	52156605	+	Silent	SNP	T	T	C	novel		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	246	7	246	3	0.0284553	0.0121951	.	.	none	FRMD6,NS,carcinoma,+1,2	FRMD6	100	2	NM_001267046	exon2	c.T51C	p.S17S	CCGCAGTGTGTGC	.	scavenged	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23929842	23929842	+	Silent	SNP	T	T	C	rs41315020	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	175	6	170	0	0.0342857	0	T|0.956;C|0.044	0.044	strong	SACS,NS,carcinoma,0,1	SACS	871	1	NM_014363	exon8	c.A909G	p.A303A	TGTGTCTGCATCT	.	scavenged	Atlas-SNP
ST6GAL2	84620	hgsc.bcm.edu	37	2	107459974	107459974	+	Missense_Mutation	SNP	C	C	T	rs3796110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	112	7	91	0	0.0625	0	C|0.893;T|0.107	0.107	strong	ST6GAL2,NS,carcinoma,+1,1	ST6GAL2	159	1	NM_032528	exon2	c.G460A	p.G154R	GCTCCCCGGGGGA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506005	195506005	+	Missense_Mutation	SNP	A	A	C	rs202017381	bycluster	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	30	7	33	7	0.233333	0.212121	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.T12446G	p.I4149S	GAAGGGATGGTGA	.	scavenged	Atlas-SNP
RSPH3	83861	hgsc.bcm.edu	37	6	159407446	159407446	+	Missense_Mutation	SNP	C	C	T	rs34582178	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	73	4	82	0	0.0547945	0	C|0.861;T|0.139	0.139	strong	RSPH3,NS,carcinoma,0,1	RSPH3	48	1	NM_031924	exon3	c.G638A	p.R213Q	TCAGGCCGTCCGA	.	PASS	Atlas-SNP
KLHL6	89857	hgsc.bcm.edu	37	3	183226186	183226186	+	Silent	SNP	C	C	T	rs61447052	bycluster;byfrequency;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	90	6	94	1	0.0666667	0.0106383	C|0.963;T|0.037	0.037	strong	KLHL6,NS,carcinoma,0,1	KLHL6	100	1	NM_130446	exon3	c.G570A	p.K190K	CTGCTTCTTTAGA	.	scavenged	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	90151589	90151589	+	Missense_Mutation	SNP	G	G	A	rs2247870	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	122	5	144	0	0.0409836	0	G|0.534;A|0.466	0.466	strong	GPR98,NS,carcinoma,0,1	GPR98	605	1	NM_032119	exon82	c.G17626A	p.V5876I	AAAGTGGTTGAGG	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52548818	52548818	+	Silent	SNP	C	C	T	rs740903	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	52	4	59	0	0.0769231	0	C|0.890;T|0.110	0.110	strong	.	STAB1	178	.	NM_015136	exon35	c.C3780T	p.C1260C	TCGCTGCCTGCAT	.	PASS	Atlas-SNP
PPARGC1B	133522	hgsc.bcm.edu	37	5	149212510	149212510	+	Missense_Mutation	SNP	C	C	A	rs11959820	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	89	6	97	0	0.0674157	0	C|0.912;A|0.087	0.087	strong	PPARGC1B,NS,carcinoma,0,1	PPARGC1B	74	1	NM_133263	exon5	c.C874A	p.R292S	CTCATACGCTACA	.	PASS	Atlas-SNP
