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
FZD2	2535	hgsc.bcm.edu	37	17	42636477	42636477	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90.0	19.0	96.0	0.0	0.211	.	.	.	none	.	FZD2	81	.	NM_001466	exon1	c.1420delA	p.T474fs	.	.	PASS	Pindel,Atlas-Indel
C20orf202	400831	hgsc.bcm.edu	37	20	1187535	1187536	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107.0	37.0	135.0	0.0	0.346	.	.	.	none	.	C20orf202	12	.	NM_001009612	exon2	c.157_158del	p.53_53del	.	.	PASS	Pindel,Atlas-Indel
PGGT1B	5229	hgsc.bcm.edu	37	5	114557642	114557643	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	423.0	73.0	475.0	0.0	0.173	.	.	.	none	.	PGGT1B	26	.	NM_005023	exon7	c.722_723insT	p.S241fs	.	.	PASS	Pindel,Atlas-Indel
SULT2B1	6820	hgsc.bcm.edu	37	19	49102605	49102610	+	In_Frame_Del	DEL	CCAGCC	CCAGCC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCAGCC	CCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203.0	38.0	244.0	0.0	0.187	.	.	.	none	.	SULT2B1	72	.	NM_177973	exon7	c.1039_1044del	p.347_348del	.	.	PASS	Pindel,Atlas-Indel
DLEC1	9940	hgsc.bcm.edu	37	3	38162039	38162042	+	Frame_Shift_Del	DEL	GAGA	GAGA	-	rs140494598	bycluster;by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGA	GAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	301.0	66.0	322.0	0.0	0.219	.	.	.	alt	.	DLEC1	278	.	NM_007335	exon34	c.4804_4807del	p.1602_1603del	.	.	PASS	Pindel,Atlas-Indel
MEF2B	100271849	hgsc.bcm.edu	37	19	19257101	19257102	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33.0	11.0	21.0	0.0	0.333333	0	.	.	none	.	MEF2B	41	.	NM_001145785	exon8	c.862_863insC	p.A288fs	.	.	PASS	Atlas-Indel
GGA3	23163	hgsc.bcm.edu	37	17	73234805	73234806	+	Frame_Shift_Ins	INS	-	-	TCTG	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205.0	45.0	203.0	0.0	0.220	.	.	.	none	GGA3,NS,carcinoma,0,1	GGA3	54	1	NM_138619	exon16	c.1989_1990insCAGA	p.E663fs	.	.	PASS	Pindel,Atlas-Indel
CACNA1A	773	hgsc.bcm.edu	37	19	13395957	13395959	+	In_Frame_Del	DEL	TCC	TCC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	172.0	45.0	170.0	0.0	0.262	.	.	.	none	.	CACNA1A	715	.	NM_001127221	exon21	c.3619_3621del	p.1207_1207del	.	.	PASS	Pindel,Atlas-Indel
CCL27	10850	hgsc.bcm.edu	37	9	34661945	34661945	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107.0	32.0	122.0	0.0	0.299	.	.	.	none	.	CCL27	6	.	NM_006664	exon3	c.336delC	p.G112fs	.	.	PASS	Pindel,Atlas-Indel
C1orf141	400757	hgsc.bcm.edu	37	1	67558870	67558874	+	Frame_Shift_Del	DEL	TCATT	TCATT	-	rs200104842	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCATT	TCATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125.0	14.0	267.0	0.0	0.112	0	TCATT|0.994;-|0.006	0.006	strong	.	C1orf141	58	.	NM_001276351	exon8	c.1018_1022del	p.340_341del	.	.	PASS	Atlas-Indel
EIF3A	8661	hgsc.bcm.edu	37	10	120819176	120819187	+	In_Frame_Del	DEL	AAGGAACCAAAG	AAGGAACCAAAG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AAGGAACCAAAG	AAGGAACCAAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176.0	25.0	215.0	0.0	0.142045	0	.	.	none	.	EIF3A	142	.	NM_003750	exon10	c.1371_1382del	p.457_461del	.	.	PASS	Atlas-Indel
CHD8	57680	hgsc.bcm.edu	37	14	21862616	21862616	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156.0	30.0	121.0	0.0	0.192	.	.	.	none	.	CHD8	339	.	NM_001170629	exon30	c.5420delA	p.Y1807fs	.	.	PASS	Pindel,Atlas-Indel
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084471	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	441.0	69.0	726.0	0.0	0.156463	0	.	.	none	OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	NM_001005522	exon1	c.151_152insG	p.H51fs	.	.	PASS	Atlas-Indel
SPAG16	79582	hgsc.bcm.edu	37	2	215013915	215013915	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179.0	55.0	307.0	0.0	0.307	.	.	.	none	.	SPAG16	134	.	NM_024532	exon15	c.1644delC	p.D548fs	.	.	PASS	Pindel,Atlas-Indel
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586693	79586695	+	In_Frame_Del	DEL	GTG	GTG	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39.0	22.0	57.0	0.0	0.564	.	.	.	none	.	ANKRD34C	29	.	NM_001146341	exon2	c.1066_1068del	p.356_356del	.	.	PASS	Pindel,Atlas-Indel
SF3A2	8175	hgsc.bcm.edu	37	19	2248152	2248153	+	In_Frame_Ins	INS	-	-	GGAGTCCACCCTCCAGCCCCC	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	16.0	10.0	28.0	0.0	0.625	.	.	.	none	SF3A2,colon,carcinoma,0,1	SF3A2	22	1	NM_007165	exon9	c.1002_1003insGGAGTCCACCCTCCAGCCCCC	p.P334delinsPGVHPPAP	.	.	PASS	Pindel
KIAA0754	643314	hgsc.bcm.edu	37	1	39879397	39879435	+	In_Frame_Del	DEL	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	-	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	19.0	197.0	0.0	0.292	.	.	.	none	.	KIAA0754	93	.	NM_015038	exon1	c.3459_3497del	p.1153_1166del	.	.	PASS	Pindel
DST	667	hgsc.bcm.edu	37	6	56457044	56457044	+	Missense_Mutation	SNP	T	T	C	rs186813964	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131.0	64.0	197.0	0.0	0.48855	0	T|0.998;C|0.002	0.002	strong	DST_ENST00000370769,NS,lymphoid_neoplasm,0,2	DST	1427	2	NM_015548	exon30	c.A4970G	p.K1657R	AAGTGTTTGCTCG	.	PASS	Atlas-SNP
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773812	140773812	+	Missense_Mutation	SNP	G	G	A	rs144796076	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182.0	78.0	166.0	0.0	0.428571	0	G|0.996;A|0.004	0.004	strong	.	PCDHGA8	146	.	NM_014004	exon1	c.G1432A	p.D478N	GCACACGACCCCG	.	PASS	Atlas-SNP
GBE1	2632	hgsc.bcm.edu	37	3	81720086	81720086	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104.0	35.0	95.0	0.0	0.336538	0	.	.	none	GBE1_ENST00000429644,colon,carcinoma,0,1	GBE1	111	1	NM_000158	exon3	c.C332T	p.S111L	GGGTACGAAAATG	.	PASS	Atlas-SNP
SRCAP	10847	hgsc.bcm.edu	37	16	30732558	30732558	+	Missense_Mutation	SNP	C	C	A	rs149248373	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127.0	60.0	124.0	0.0	0.472441	0	C|0.996;A|0.004	0.004	strong	.	SRCAP	298	.	NM_006662	exon21	c.C3302A	p.T1101K	CTCCCACGCCAAC	.	PASS	Atlas-SNP
ELP2	55250	hgsc.bcm.edu	37	18	33709898	33709898	+	Missense_Mutation	SNP	T	T	A	rs370904237	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93.0	39.0	125.0	0.0	0.419355	0	.	.	alt	.	ELP2	70	.	NM_001242879	exon1	c.T2A	p.M1K	GCGACATGGTGGC	.	PASS	Atlas-SNP
CEP41	95681	hgsc.bcm.edu	37	7	130051013	130051013	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71.0	54.0	128.0	0.0	0.760563	0	.	.	none	TSGA14,NS,carcinoma,+1,1	.	.	1	NM_018718	exon5	c.T227C	p.L76P	TCAGAGAGGGAAG	.	PASS	Atlas-SNP
LRRC4B	94030	hgsc.bcm.edu	37	19	51051935	51051935	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	33.0	19.0	38.0	0.0	0.575758	0	.	.	none	.	LRRC4B	89	.	NM_001080457	exon2	c.C161T	p.A54V	GAGGTGGCCGGCG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28919763	28919763	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138.0	52.0	166.0	0.0	0.376812	0	.	.	none	DSG1,NS,carcinoma,-2,1	DSG1	176	1	NM_001942	exon11	c.A1462C	p.N488H	TTTGGTAATGACG	.	PASS	Atlas-SNP
PRDM5	11107	hgsc.bcm.edu	37	4	121737704	121737704	+	Missense_Mutation	SNP	G	G	A	rs190835070	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78.0	24.0	99.0	1.0	0.307692	0.010101	G|1.000;A|0.000	0.000	strong	PRDM5,NS,carcinoma,+1,1	PRDM5	76	1	NM_018699	exon7	c.C769T	p.R257W	CCCCCCGGCAAGT	.	scavenged	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	rs142972518	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251.0	97.0	209.0	0.0	0.386454	0	G|0.986;C|0.014	0.014	strong	.	PKHD1L1	522	.	NM_177531	exon29	c.G3434C	p.G1145A	ATGTAGGGGGTGA	.	PASS	Atlas-SNP
NLRP10	338322	hgsc.bcm.edu	37	11	7981822	7981822	+	Missense_Mutation	SNP	A	A	G	rs143403695	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53.0	34.0	63.0	0.0	0.641509	0	A|0.999;G|0.001	0.001	strong	.	NLRP10	146	.	NM_176821	exon2	c.T1337C	p.F446S	CTCAGGAAAGCGG	.	PASS	Atlas-SNP
HTR2A	3356	hgsc.bcm.edu	37	13	47469939	47469939	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81.0	42.0	84.0	0.0	0.518519	0	.	.	none	.	HTR2A	98	.	NM_000621	exon2	c.G103A	p.G35R	CTTCTCCGGAGTT	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160697271	160697271	+	Missense_Mutation	SNP	G	G	A	rs147904044	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132.0	61.0	125.0	0.0	0.462121	0	G|0.996;A|0.004	0.004	strong	.	LY75	151	.	NM_002349	exon25	c.C3476T	p.S1159F	AAGGAAGAGTTGT	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7189437	7189437	+	Missense_Mutation	SNP	G	G	A	rs201588284	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59.0	31.0	40.0	0.0	0.525424	0	G|0.999;A|0.001	0.001	strong	RREB1_ENST00000379938,NS,carcinoma,-2,2	RREB1	242	2	NM_001003700	exon6	c.G307A	p.G103R	ATCTGCGGAAAGT	.	PASS	Atlas-SNP
ZNF622	90441	hgsc.bcm.edu	37	5	16465442	16465442	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143.0	66.0	147.0	0.0	0.461538	0	.	.	none	ZNF622,NS,carcinoma,-2,1	ZNF622	49	1	NM_033414	exon1	c.A333G	p.E111E	GTTCTTTTCATTC	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152712440	152712440	+	Missense_Mutation	SNP	G	G	T	rs117480635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117.0	55.0	104.0	0.0	0.470085	0	G|0.998;T|0.002	0.002	strong	.	SYNE1	3227	.	NM_033071	exon52	c.C7997A	p.T2666N	TCCAGGGTGTCTT	.	PASS	Atlas-SNP
TMEM199	147007	hgsc.bcm.edu	37	17	26684707	26684707	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41.0	16.0	49.0	0.0	0.390244	0	.	.	none	.	TMEM199	15	.	NM_152464	exon1	c.T14A	p.L5X	CCTCTTTGCTTGC	.	PASS	Atlas-SNP
CASP8	841	hgsc.bcm.edu	37	2	202137432	202137432	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107.0	71.0	139.0	0.0	0.663551	0	.	.	none	.	CASP8	272	.	NM_001080125	exon4	c.A660G	p.K220K	CCTGAAAAGAGTC	.	PASS	Atlas-SNP
LURAP1L	286343	hgsc.bcm.edu	37	9	12775855	12775855	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17.0	7.0	15.0	0.0	0.411765	0	.	.	none	.	.	.	.	NM_203403	exon1	c.T141C	p.G47G	GAGCGGTGGTGGT	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7080048	7080048	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246.0	116.0	315.0	0.0	0.471545	0	.	.	none	.	LAMA1	458	.	NM_005559	exon3	c.A271G	p.N91D	ACCAGTTATTGGT	.	PASS	Atlas-SNP
ALOX12B	242	hgsc.bcm.edu	37	17	7989492	7989492	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266.0	130.0	275.0	0.0	0.488722	0	.	.	none	.	ALOX12B	61	.	NM_001139	exon2	c.T194C	p.I65T	ATGATGATGAGCT	.	PASS	Atlas-SNP
GTF2A1	2957	hgsc.bcm.edu	37	14	81686832	81686832	+	Splice_Site	SNP	C	C	G	rs201410281	by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74.0	21.0	32.0	0.0	0.283784	0	C|1.000;T|0.000	.	alt	.	GTF2A1	34	.	NM_015859	exon2	c.30+1G>C	.	TCCTTACCACGGT	.	PASS	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100961704	100961704	+	Missense_Mutation	SNP	C	C	T	rs34769888	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135.0	64.0	144.0	0.0	0.474074	0	C|0.994;T|0.006	0.006	strong	.	TBC1D2	70	.	NM_001267571	exon13	c.G2746A	p.E916K	AGCCCTCGGACAC	.	PASS	Atlas-SNP
VWA5B1	127731	hgsc.bcm.edu	37	1	20650001	20650001	+	Silent	SNP	C	C	T	rs146423282	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	47.0	8.0	37.0	0.0	0.170213	0	C|0.995;T|0.005	0.005	strong	.	VWA5B1	44	.	NM_001039500	exon8	c.C1119T	p.S373S	CATGAGCGGGATC	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43575982	43575982	+	Silent	SNP	C	C	T	rs150568950	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	234.0	108.0	249.0	1.0	0.461538	0.00401606	C|0.998;T|0.002	0.002	strong	PSG2,NS,carcinoma,-1,1	PSG2	84	1	NM_031246	exon4	c.G834A	p.K278K	CTGAAACTTCCCA	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129046371	129046371	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186.0	85.0	193.0	0.0	0.456989	0	.	.	none	.	DOCK1	188	.	NM_001380	exon28	c.G2884A	p.V962I	GATGTGGTAGTAA	.	PASS	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	37	3	126741041	126741041	+	Silent	SNP	C	C	T	rs150052583	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150.0	67.0	206.0	0.0	0.446667	0	C|0.992;T|0.008	0.008	strong	PLXNA1,colon,carcinoma,+2,1	PLXNA1	185	1	NM_032242	exon21	c.C4152T	p.R1384R	CATGCGCGACCGC	.	PASS	Atlas-SNP
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441478	39441478	+	Missense_Mutation	SNP	C	C	A	rs138934952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	425.0	197.0	455.0	0.0	0.463529	0	C|0.998;A|0.002	0.002	strong	.	APOBEC3F	37	.	NM_145298	exon4	c.C497A	p.P166Q	GTCAGCCATTCAT	.	PASS	Atlas-SNP
PHPT1	29085	hgsc.bcm.edu	37	9	139744524	139744524	+	Silent	SNP	C	C	T	rs8666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176.0	82.0	167.0	0.0	0.465909	0	C|0.972;T|0.028	0.028	strong	.	PHPT1	14	.	NM_001135861	exon2	c.C220T	p.L74L	GAGTGTCTGGGCG	.	PASS	Atlas-SNP
IPO9	55705	hgsc.bcm.edu	37	1	201798367	201798367	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60.0	19.0	44.0	0.0	0.316667	0	.	.	none	.	IPO9	98	.	NM_018085	exon1	c.C30T	p.A10A	TGCGGCCTCCGGG	.	PASS	Atlas-SNP
DYNC1H1	1778	hgsc.bcm.edu	37	14	102508056	102508056	+	Missense_Mutation	SNP	C	C	A	rs10129889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143.0	48.0	131.0	0.0	0.335664	0	C|0.882;A|0.118	0.118	strong	.	DYNC1H1	395	.	NM_001376	exon65	c.C12087A	p.H4029Q	GACCCACATTGTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105413649	105413649	+	Silent	SNP	A	A	G	rs201545349	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281.0	13.0	239.0	2.0	0.0462633	0.0083682	A|0.998;G|0.002	0.002	weak	AHNAK2_ENST00000333244,NS,carcinoma,-2,1	AHNAK2	719	1	NM_138420	exon7	c.T8139C	p.D2713D	TTTCACATCCACC	.	scavenged	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427452	427452	+	Missense_Mutation	SNP	C	C	T	rs146645376	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166.0	76.0	124.0	0.0	0.457831	0	C|0.998;T|0.002	0.002	strong	.	TMEM8A	49	.	NM_021259	exon3	c.G433A	p.V145I	GGGAAACGTTGAC	.	PASS	Atlas-SNP
BRD1	23774	hgsc.bcm.edu	37	22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	rs35331092	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100.0	59.0	110.0	0.0	0.59	0	C|0.936;T|0.064	0.064	strong	.	BRD1	144	.	NM_014577	exon6	c.G2188A	p.A730T	TCATAGCGCAGGT	.	PASS	Atlas-SNP
CTRC	11330	hgsc.bcm.edu	37	1	15772212	15772212	+	Missense_Mutation	SNP	C	C	T	rs121909293	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37.0	10.0	63.0	0.0	0.27027	0	C|0.997;T|0.003	0.003	strong	.	CTRC	28	.	NM_007272	exon7	c.C760T	p.R254W	TACACCCGGGTGT	.	PASS	Atlas-SNP
PIK3C2A	5286	hgsc.bcm.edu	37	11	17158120	17158120	+	Missense_Mutation	SNP	C	C	T	rs61733866	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	39.0	104.0	0.0	0.506494	0	C|0.992;T|0.008	0.008	strong	.	PIK3C2A	148	.	NM_002645	exon8	c.G1757A	p.S586N	AAAGCACTACAGA	.	PASS	Atlas-SNP
AMDHD2	51005	hgsc.bcm.edu	37	16	2577943	2577943	+	Missense_Mutation	SNP	A	A	C	rs182580356	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18.0	10.0	39.0	0.0	0.555556	0	A|0.999;C|0.001	0.001	strong	.	AMDHD2	33	.	NM_001145815	exon5	c.A585C	p.E195D	CCACGAAGTGATC	.	PASS	Atlas-SNP
NOLC1	9221	hgsc.bcm.edu	37	10	103919738	103919738	+	Silent	SNP	G	G	A	rs143372447	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	16.0	53.0	0.0	0.219178	0	G|0.998;A|0.002	0.002	strong	.	NOLC1	61	.	NM_004741	exon8	c.G945A	p.K315K	GGAGAAGCAGCAG	.	PASS	Atlas-SNP
MAP3K4	4216	hgsc.bcm.edu	37	6	161508880	161508880	+	Missense_Mutation	SNP	A	A	C	rs35533223	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116.0	60.0	101.0	0.0	0.517241	0	A|0.976;C|0.024	0.024	strong	.	MAP3K4	364	.	NM_006724	exon10	c.A2717C	p.H906P	CCAAGCACGGTGA	.	PASS	Atlas-SNP
SLFN12	55106	hgsc.bcm.edu	37	17	33749758	33749758	+	Missense_Mutation	SNP	A	A	G	rs138003670	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117.0	53.0	146.0	0.0	0.452991	0	A|0.998;G|0.002	0.002	strong	.	SLFN12	56	.	NM_018042	exon2	c.T290C	p.M97T	TTCTGCATGAAGT	.	PASS	Atlas-SNP
ELK3	2004	hgsc.bcm.edu	37	12	96641452	96641452	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19.0	9.0	24.0	0.0	0.473684	0	.	.	none	.	ELK3	36	.	NM_005230	exon3	c.C942T	p.I314I	CTCCATCGCCCTC	.	PASS	Atlas-SNP
TRIM56	81844	hgsc.bcm.edu	37	7	100730707	100730707	+	Silent	SNP	T	T	C	rs372702476		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67.0	20.0	60.0	0.0	0.298507	0	.	.	weak	.	TRIM56	123	.	NM_030961	exon3	c.T114C	p.H38H	CCTGCATACCTAC	.	PASS	Atlas-SNP
POLR3D	661	hgsc.bcm.edu	37	8	22107986	22107986	+	Silent	SNP	A	A	G	rs75142930	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	186.0	53.0	124.0	0.0	0.284946	0	A|0.958;G|0.042	0.042	strong	POLR3D,NS,adenoma,0,2	POLR3D	26	2	NM_001722	exon9	c.A1152G	p.V384V	ACTTGTATGTTCC	.	PASS	Atlas-SNP
MAPK8IP1	9479	hgsc.bcm.edu	37	11	45924057	45924057	+	Missense_Mutation	SNP	C	C	T	rs117665789	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72.0	37.0	114.0	0.0	0.513889	0	C|0.993;T|0.007	0.007	strong	.	MAPK8IP1	51	.	NM_005456	exon5	c.C739T	p.P247S	ATGGCACCTCCGG	.	PASS	Atlas-SNP
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	rs150395462	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100.0	54.0	77.0	0.0	0.54	0	G|0.996;C|0.004	0.004	strong	.	ZKSCAN5	63	.	NM_145102	exon7	c.G2392C	p.E798Q	ACTGGTGAGAAAC	.	PASS	Atlas-SNP
RFTN1	23180	hgsc.bcm.edu	37	3	16419238	16419238	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135.0	37.0	101.0	0.0	0.274074	0	.	.	none	.	RFTN1	79	.	NM_015150	exon5	c.G813C	p.E271D	GAGTGGCTCTTCA	.	PASS	Atlas-SNP
FURIN	5045	hgsc.bcm.edu	37	15	91424029	91424029	+	Silent	SNP	C	C	T	rs142489043	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143.0	30.0	195.0	0.0	0.20979	0	C|0.997;T|0.003	0.003	strong	.	FURIN	85	.	NM_002569	exon14	c.C1665T	p.S555S	CACCAGCGAAGCC	.	PASS	Atlas-SNP
ZNF217	7764	hgsc.bcm.edu	37	20	52192595	52192595	+	Missense_Mutation	SNP	C	C	T	rs61748378	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157.0	82.0	197.0	1.0	0.522293	0.00507614	C|0.976;T|0.024	0.024	strong	.	ZNF217	227	.	NM_006526	exon3	c.G2708A	p.R903Q	GCACTCCGATTAC	.	PASS	Atlas-SNP
CEP250	11190	hgsc.bcm.edu	37	20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	rs56259282	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	40.0	19.0	43.0	0.0	0.475	0	G|0.993;A|0.007	0.007	strong	.	CEP250	141	.	NM_007186	exon30	c.G5879A	p.R1960Q	CTGCCCGGGCCCG	.	PASS	Atlas-SNP
FERMT1	55612	hgsc.bcm.edu	37	20	6078246	6078246	+	Silent	SNP	C	C	T	rs149893089	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	157.0	74.0	159.0	0.0	0.471338	0	C|0.999;T|0.001	0.001	strong	.	FERMT1	106	.	NM_017671	exon7	c.G882A	p.E294E	GGCTTGCTCATAG	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68053807	68053807	+	Missense_Mutation	SNP	T	T	G	rs118013098	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	255.0	159.0	199.0	0.0	0.623529	0	T|0.997;G|0.003	0.003	strong	.	PLEKHH1	118	.	NM_020715	exon29	c.T3950G	p.F1317C	CTACCTTCATCAT	.	PASS	Atlas-SNP
OR51I1	390063	hgsc.bcm.edu	37	11	5461861	5461861	+	Missense_Mutation	SNP	C	C	G	rs76233016	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125.0	75.0	149.0	0.0	0.6	0	C|0.994;G|0.006	0.006	strong	.	OR51I1	66	.	NM_001005288	exon1	c.G884C	p.S295T	TTCACACTGTAGA	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86790936	86790936	+	Silent	SNP	C	C	T	rs371409529	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105.0	80.0	135.0	0.0	0.761905	0	.	.	alt	AGBL1,bladder,carcinoma,0,1	AGBL1	151	1	NM_152336	exon6	c.C423T	p.Y141Y	AGGCTACGTCACC	.	PASS	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32193185	32193185	+	Missense_Mutation	SNP	G	G	A	rs41263977	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78.0	58.0	108.0	0.0	0.74359	0	G|0.994;A|0.006	0.006	strong	.	BAI2	128	.	NM_001703	exon33	c.C4594T	p.R1532C	TGGGGCGCTCCCC	.	PASS	Atlas-SNP
SCN7A	6332	hgsc.bcm.edu	37	2	167319011	167319011	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112.0	59.0	137.0	0.0	0.526786	0	.	.	none	.	SCN7A	410	.	NM_002976	exon9	c.A971T	p.K324I	CCAGCTTTTACAC	.	PASS	Atlas-SNP
CLVS1	157807	hgsc.bcm.edu	37	8	62370916	62370916	+	Silent	SNP	T	T	G	rs72657068	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24.0	8.0	47.0	0.0	0.333333	0	T|0.998;G|0.002	0.002	strong	.	CLVS1	74	.	NM_173519	exon5	c.T792G	p.P264P	ACACCCTGAATTT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680490	100680490	+	Missense_Mutation	SNP	A	A	G	rs199605653		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200.0	17.0	152.0	0.0	0.085	0	A|0.999;G|0.001	0.001	weak	.	MUC17	804	.	NM_001040105	exon3	c.A5793G	p.I1931M	AAGTATACCTGTC	.	PASS	Atlas-SNP
IKBKAP	8518	hgsc.bcm.edu	37	9	111665215	111665215	+	Silent	SNP	A	A	C	rs35054425	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118.0	50.0	133.0	0.0	0.423729	0	A|0.990;C|0.010	0.010	strong	.	IKBKAP	122	.	NM_003640	exon16	c.T1758G	p.P586P	CAGAGAAGGTGAC	.	PASS	Atlas-SNP
CSDE1	7812	hgsc.bcm.edu	37	1	115269685	115269685	+	Silent	SNP	A	A	G	rs150190370	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84.0	5.0	181.0	0.0	0.0595238	0	A|0.997;G|0.003	0.003	strong	.	CSDE1	145	.	NM_001242891	exon14	c.T1521C	p.Y507Y	GTCATCATAAGCA	.	PASS	Atlas-SNP
AQP12A	375318	hgsc.bcm.edu	37	2	241631499	241631499	+	Silent	SNP	G	G	A	rs200769008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110.0	49.0	191.0	0.0	0.445455	0	G|0.998;A|0.002	0.002	weak	AQP12A,NS,carcinoma,+1,1	AQP12A	32	1	NM_198998	exon2	c.G132A	p.T44T	GAGGACGCTGGTC	.	PASS	Atlas-SNP
IL21R	50615	hgsc.bcm.edu	37	16	27460436	27460436	+	Silent	SNP	C	C	T	rs3093408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105.0	55.0	131.0	0.0	0.52381	0	C|0.999;T|0.001	0.001	strong	.	IL21R	95	.	NM_181079	exon10	c.C1515T	p.A505A	CCTGGCCGGCCTG	.	PASS	Atlas-SNP
PHF17	79960	hgsc.bcm.edu	37	4	129792873	129792873	+	Missense_Mutation	SNP	A	A	G	rs6855813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96.0	21.0	128.0	0.0	0.21875	0	A|0.972;G|0.028	0.028	strong	.	PHF17	63	.	NM_199320	exon11	c.A1985G	p.N662S	GAGACAATCGTTT	.	PASS	Atlas-SNP
GBP4	115361	hgsc.bcm.edu	37	1	89655787	89655787	+	Silent	SNP	T	T	C	rs41305862	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166.0	158.0	306.0	0.0	0.951807	0	T|0.977;C|0.023	0.023	strong	.	GBP4	89	.	NM_052941	exon7	c.A1131G	p.E377E	AATGGCTTCCCTC	.	PASS	Atlas-SNP
TDP1	55775	hgsc.bcm.edu	37	14	90458308	90458308	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	15.0	80.0	0.0	0.168539	0	.	.	none	.	TDP1	47	.	NM_018319	exon13	c.T1414C	p.W472R	CAGAATTGGCTGC	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2819196	2819196	+	Silent	SNP	G	G	C	rs150110237	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	22.0	83.0	0.0	0.285714	0	G|0.998;C|0.002	0.002	strong	.	SRRM2	263	.	NM_016333	exon12	c.G7932C	p.S2644S	CTCCTCGTCGTCT	.	PASS	Atlas-SNP
ZNF433	163059	hgsc.bcm.edu	37	19	12126128	12126128	+	Silent	SNP	C	C	T	rs79356451	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153.0	84.0	163.0	1.0	0.54902	0.00613497	C|0.999;T|0.001	0.001	strong	ZNF433,colon,carcinoma,-1,2	ZNF433	49	2	NM_001080411	exon4	c.G1554A	p.S518S	GGAGCTCGAACAG	.	scavenged	Atlas-SNP
WDR41	55255	hgsc.bcm.edu	37	5	76728996	76728996	+	Silent	SNP	T	T	C	rs72769029	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	221.0	219.0	218.0	2.0	0.99095	0.00917431	T|0.979;C|0.021	0.021	strong	.	WDR41	29	.	NM_018268	exon13	c.A1344G	p.K448K	CTCTAATTTTTGA	.	PASS	Atlas-SNP
ZNF235	9310	hgsc.bcm.edu	37	19	44793278	44793278	+	Missense_Mutation	SNP	A	A	G	rs141976678	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121.0	62.0	133.0	0.0	0.512397	0	A|0.999;G|0.001	0.001	strong	.	ZNF235	60	.	NM_004234	exon5	c.T310C	p.S104P	AGCATGAAAGCTC	.	PASS	Atlas-SNP
CDKL3	51265	hgsc.bcm.edu	37	5	133655067	133655067	+	Silent	SNP	C	C	T	rs373913998		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42.0	21.0	23.0	0.0	0.5	0	.	.	weak	.	CDKL3	76	.	NM_001113575	exon6	c.G774A	p.L258L	TGCCAACAATCCA	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139263158	139263158	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137.0	74.0	122.0	0.0	0.540146	0	.	.	none	.	FAM135B	423	.	NM_015912	exon6	c.C468A	p.F156L	ATAGTCGAACATG	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	108011971	108011971	+	Silent	SNP	G	G	A	rs56296886	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64.0	28.0	82.0	0.0	0.4375	0	G|0.996;A|0.004	0.004	strong	.	BTBD11	122	.	NM_001018072	exon10	c.G2268A	p.K756K	AGAGAAGGAGAAG	.	PASS	Atlas-SNP
DBX2	440097	hgsc.bcm.edu	37	12	45444426	45444426	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68.0	21.0	84.0	0.0	0.308824	0	.	.	none	.	DBX2	45	.	NM_001004329	exon1	c.C285T	p.A95A	CGCCCCGGCGGGG	.	PASS	Atlas-SNP
ZDHHC20	253832	hgsc.bcm.edu	37	13	21976996	21976996	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51.0	32.0	41.0	0.0	0.627451	0	.	.	none	.	ZDHHC20	36	.	NM_153251	exon5	c.A380G	p.Y127C	TCACAATATCTGA	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113363466	113363466	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	20.0	80.0	0.0	0.224719	0	.	.	none	.	CSMD3	2325	.	NM_198123	exon40	c.C6263T	p.S2088F	ATGTGAGAGTGAC	.	PASS	Atlas-SNP
ASTN2	23245	hgsc.bcm.edu	37	9	119770495	119770495	+	Silent	SNP	G	G	A	rs61736198	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225.0	101.0	189.0	0.0	0.448889	0	G|0.994;A|0.006	0.006	strong	.	ASTN2	307	.	NM_014010	exon6	c.C1314T	p.S438S	CCAGTCGGAGATG	.	PASS	Atlas-SNP
CYP27C1	339761	hgsc.bcm.edu	37	2	127956964	127956964	+	Silent	SNP	G	G	A	rs149542135	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141.0	72.0	175.0	0.0	0.510638	0	G|0.999;A|0.001	0.001	strong	.	CYP27C1	52	.	NM_001001665	exon4	c.C540T	p.A180A	GACGCCGGCCAGC	.	PASS	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	37	1	152083806	152083806	+	Silent	SNP	C	C	T	rs200947543	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206.0	127.0	136.0	0.0	0.616505	0	C|0.993;T|0.007	0.007	strong	.	TCHH	275	.	NM_007113	exon3	c.G1887A	p.R629R	CTGGCGCCTCTCT	.	PASS	Atlas-SNP
MTNR1A	4543	hgsc.bcm.edu	37	4	187455329	187455329	+	Silent	SNP	G	G	A	rs8192549	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	13.0	83.0	0.0	0.2	0	G|0.977;A|0.023	0.023	strong	.	MTNR1A	46	.	NM_005958	exon2	c.C567T	p.I189I	CACGGCGATGGTG	.	PASS	Atlas-SNP
HMG20A	10363	hgsc.bcm.edu	37	15	77750802	77750802	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63.0	5.0	88.0	0.0	0.0793651	0	.	.	none	.	HMG20A	48	.	NM_018200	exon3	c.A53G	p.D18G	ATGAAGACGGTTC	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241.0	117.0	230.0	1.0	0.485477	0.00434783	G|0.860;A|0.140	0.140	strong	HNF1A,brain,glioma,0,4	HNF1A	302	4	NM_000545	exon8	c.G1545A	p.T515T	CCACACGGGCCTG	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100803982	100803982	+	Silent	SNP	C	C	T	rs79213484	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211.0	56.0	126.0	0.0	0.265403	0	C|0.983;T|0.017	0.017	strong	.	ARHGAP42	32	.	NM_152432	exon7	c.C693T	p.N231N	GTTCAACTTGCAG	.	PASS	Atlas-SNP
COL21A1	81578	hgsc.bcm.edu	37	6	56035495	56035495	+	Silent	SNP	G	G	A	rs41271846	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113.0	53.0	118.0	0.0	0.469027	0	G|0.997;A|0.003	0.003	strong	.	COL21A1	201	.	NM_030820	exon5	c.C978T	p.S326S	AATTACGCTGGTT	.	PASS	Atlas-SNP
PTPN23	25930	hgsc.bcm.edu	37	3	47453659	47453659	+	Silent	SNP	G	G	T	rs147959396	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	259.0	140.0	175.0	0.0	0.540541	0	G|0.997;T|0.003	0.003	strong	.	PTPN23	85	.	NM_015466	exon22	c.G4149T	p.P1383P	GCGGCCGCTGCAC	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72358722	72358722	+	Missense_Mutation	SNP	T	T	C	rs28933375	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	59.0	124.0	0.0	0.766234	0	T|0.994;C|0.006	0.006	strong	.	PRF1	64	.	NM_001083116	exon3	c.A755G	p.N252S	ACCTCGTTGTCCG	.	PASS	Atlas-SNP
PCDHA12	56137	hgsc.bcm.edu	37	5	140256920	140256920	+	Silent	SNP	G	G	C	rs115718636	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298.0	150.0	368.0	1.0	0.503356	0.00271739	G|0.959;C|0.041	0.041	strong	PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	NM_018903	exon1	c.G1863C	p.P621P	CATCCCGTTCCAC	.	PASS	Atlas-SNP
C15orf41	84529	hgsc.bcm.edu	37	15	36989578	36989578	+	Silent	SNP	C	C	T	rs117638434	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110.0	84.0	196.0	0.0	0.763636	0	C|0.992;T|0.008	0.008	strong	.	C15orf41	24	.	NM_001130010	exon8	c.C531T	p.N177N	GAAAAACCTGTCC	.	PASS	Atlas-SNP
DDX20	11218	hgsc.bcm.edu	37	1	112309230	112309230	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87.0	4.0	132.0	0.0	0.045977	0	.	.	none	.	DDX20	50	.	NM_007204	exon11	c.C2184T	p.S728S	GGCTAGCCAGAGA	.	PASS	Atlas-SNP
RBM48	84060	hgsc.bcm.edu	37	7	92158154	92158154	+	Silent	SNP	G	G	A	rs117787377	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266.0	167.0	172.0	0.0	0.62782	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_032120	exon1	c.G27A	p.G9G	GCTAGGGAGTTTA	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89424765	89424765	+	Missense_Mutation	SNP	C	C	T	rs140982817	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70.0	21.0	112.0	0.0	0.3	0	C|0.998;T|0.002	0.002	strong	HAPLN3,caecum,carcinoma,0,1	HAPLN3	43	1	NM_178232	exon3	c.G316A	p.G106R	TCAGCCCGATGGC	.	PASS	Atlas-SNP
IFNA21	3452	hgsc.bcm.edu	37	9	21166423	21166423	+	Silent	SNP	C	C	T	rs1053884	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	232.0	121.0	243.0	0.0	0.521552	0	C|0.996;T|0.004	0.004	strong	.	IFNA21	25	.	NM_002175	exon1	c.G189A	p.Q63Q	CTCCTCCTGGGGG	.	PASS	Atlas-SNP
CAPN3	825	hgsc.bcm.edu	37	15	42702836	42702836	+	Silent	SNP	C	C	T	rs147774793	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	20.0	116.0	0.0	0.224719	0	C|0.999;T|0.001	0.001	strong	.	CAPN3	172	.	NM_000070	exon21	c.C2235T	p.Y745Y	CAGCTACGAGATG	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	37	15	101567971	101567971	+	Silent	SNP	C	C	T	rs41535348	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129.0	31.0	183.0	0.0	0.24031	0	C|0.995;T|0.005	0.005	strong	.	LRRK1	310	.	NM_024652	exon19	c.C2655T	p.N885N	CGACAACGACATC	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13409407	13409407	+	Missense_Mutation	SNP	C	C	T	rs16024	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122.0	58.0	141.0	0.0	0.47541	0	C|0.997;T|0.003	0.003	strong	.	CACNA1A	715	.	NM_001127221	exon19	c.G3043A	p.E1015K	CCCCCTCGTACGT	.	PASS	Atlas-SNP
PARP14	54625	hgsc.bcm.edu	37	3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	rs7632072	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72.0	32.0	104.0	0.0	0.444444	0	A|0.950;G|0.050	0.050	strong	.	PARP14	242	.	NM_017554	exon6	c.A1891G	p.T631A	CCAAACACTGTAA	.	PASS	Atlas-SNP
THEM6	51337	hgsc.bcm.edu	37	8	143816828	143816828	+	Missense_Mutation	SNP	G	G	A	rs11540544	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139.0	66.0	99.0	0.0	0.47482	0	G|0.992;A|0.008	0.008	strong	.	.	.	.	NM_016647	exon2	c.G598A	p.G200R	GAGAGTGGGCTCA	.	PASS	Atlas-SNP
EYA3	2140	hgsc.bcm.edu	37	1	28304899	28304899	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	155.0	40.0	253.0	0.0	0.258065	0	.	.	none	.	EYA3	38	.	NM_001990	exon17	c.A1627G	p.I543V	CTGCAATTTCTTC	.	PASS	Atlas-SNP
GATAD2A	54815	hgsc.bcm.edu	37	19	19612027	19612027	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	226.0	108.0	228.0	1.0	0.477876	0.00438596	.	.	none	GATAD2A_ENST00000360315,colon,carcinoma,+2,2	GATAD2A	81	2	NM_017660	exon9	c.C1302T	p.G434G	GAGCGGCGCCATC	.	PASS	Atlas-SNP
PTPN4	5775	hgsc.bcm.edu	37	2	120734589	120734589	+	Silent	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133.0	51.0	119.0	0.0	0.383459	0	.	.	none	PTPN4,NS,carcinoma,+2,1	PTPN4	89	1	NM_002830	exon27	c.T2724A	p.I908I	AGCTATTTTGAAA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1269655	1269655	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	341.0	98.0	219.0	0.0	0.28739	0	.	.	none	.	MUC5B	473	.	NM_002458	exon31	c.T11545G	p.S3849A	ACCGGCTCTGTGG	.	PASS	Atlas-SNP
MED12	9968	hgsc.bcm.edu	37	X	70351982	70351982	+	Silent	SNP	A	A	C	rs376058351		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	213.0	207.0	429.0	0.0	0.971831	0	.	.	weak	.	MED12	984	.	NM_005120	exon30	c.A4179C	p.S1393S	ACAGTCAGCAGAG	.	PASS	Atlas-SNP
C1orf43	25912	hgsc.bcm.edu	37	1	154184993	154184993	+	Missense_Mutation	SNP	G	G	A	rs144385115	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156.0	84.0	168.0	0.0	0.538462	0	G|0.994;A|0.006	0.006	strong	.	C1orf43	36	.	NM_001098616	exon5	c.C448T	p.R150C	CTTTGCGTACACC	.	PASS	Atlas-SNP
HTR3B	9177	hgsc.bcm.edu	37	11	113803108	113803108	+	Missense_Mutation	SNP	A	A	C	rs72466469	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	345.0	220.0	245.0	1.0	0.637681	0.00408163	A|0.996;C|0.004	0.004	strong	.	HTR3B	50	.	NM_006028	exon5	c.A466C	p.S156R	GCGTGCAGTTTAG	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83998922	83998922	+	Silent	SNP	G	G	A	rs146347192		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	28.0	4.0	35.0	0.0	0.142857	0	G|1.000;A|0.000	0.000	weak	OSGIN1,NS,carcinoma,+2,1	OSGIN1	33	1	NM_182981	exon6	c.G744A	p.T248T	AGGCACGTTCGAC	.	scavenged	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63.0	11.0	133.0	0.0	0.174603	0	A|0.976;G|0.024	0.024	strong	PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	NM_031500	exon1	c.A1584G	p.L528L	GGAGCTAGAGCTG	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160735174	160735174	+	Missense_Mutation	SNP	C	C	T	rs147820690	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	220.0	125.0	209.0	0.0	0.568182	0	C|0.998;T|0.002	0.002	strong	.	LY75	151	.	NM_002349	exon10	c.G1574A	p.G525E	TTTGTTCCAAAAG	.	PASS	Atlas-SNP
CCDC66	285331	hgsc.bcm.edu	37	3	56628033	56628033	+	Nonsense_Mutation	SNP	C	C	T	rs150364083	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125.0	51.0	163.0	0.0	0.408	0	C|0.996;T|0.004	0.004	strong	.	CCDC66	145	.	NM_001141947	exon10	c.C1381T	p.R461X	AGACGACGACAAA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129909929	129909929	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67.0	28.0	85.0	0.0	0.41791	0	.	.	none	.	MKI67	363	.	NM_002417	exon11	c.A2240C	p.D747A	TTAAAGTCCATTT	.	PASS	Atlas-SNP
SRSF1	6426	hgsc.bcm.edu	37	17	56083705	56083705	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174.0	56.0	197.0	0.0	0.321839	0	.	.	none	.	SRSF1	41	.	NM_006924	exon2	c.T378C	p.S126S	CTCACCAGAGACA	.	PASS	Atlas-SNP
COQ9	57017	hgsc.bcm.edu	37	16	57490480	57490480	+	Missense_Mutation	SNP	A	A	C	rs191446011	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175.0	24.0	163.0	0.0	0.137143	0	A|1.000;C|0.000	0.000	strong	.	COQ9	30	.	NM_020312	exon4	c.A443C	p.H148P	TACTGCATTTTGT	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33688855	33688855	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114.0	71.0	92.0	0.0	0.622807	0	.	.	none	.	URB1	176	.	NM_014825	exon38	c.C6556T	p.R2186W	CTGCCCGGCCCTG	.	PASS	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48745035	48745035	+	Silent	SNP	A	A	C	rs11568601	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100.0	45.0	80.0	0.0	0.45	0	A|0.984;C|0.016	0.016	strong	.	ABCC3	138	.	NM_003786	exon12	c.A1552C	p.R518R	GGCATCAGGCAGG	.	PASS	Atlas-SNP
CDC23	8697	hgsc.bcm.edu	37	5	137533901	137533901	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93.0	48.0	80.0	0.0	0.516129	0	.	.	none	.	CDC23	46	.	NM_004661	exon9	c.G999A	p.T333T	ACAGCACGTTTCT	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23544515	23544515	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111.0	37.0	115.0	0.0	0.333333	0	.	.	none	ZNF91_ENST00000300619,NS,lymphoid_neoplasm,-1,2	ZNF91	349	2	NM_003430	exon4	c.T1266A	p.T422T	ATGTATAGTAAGA	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23862710	23862710	+	Silent	SNP	C	C	T	rs145274612	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	422.0	277.0	306.0	1.0	0.656398	0.00326797	C|0.992;T|0.008	0.008	strong	.	MYH6	274	.	NM_002471	exon23	c.G2946A	p.E982E	CATCTCCTCTGTT	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	37	8	24333985	24333985	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103.0	37.0	69.0	0.0	0.359223	0	.	.	none	ADAM7,NS,carcinoma,-1,4	ADAM7	165	4	NM_003817	exon8	c.C673T	p.R225X	AGGAACCGAATTT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23904298	23904298	+	Missense_Mutation	SNP	T	T	G	rs34382952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124.0	50.0	85.0	0.0	0.403226	0	T|0.997;G|0.003	0.003	strong	.	SACS	871	.	NM_014363	exon10	c.A13717C	p.N4573H	TAAAATTTTCAAG	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2434799	2434799	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	392.0	126.0	388.0	1.0	0.321429	0.00257732	.	.	none	.	TRPM5	86	.	NM_014555	exon13	c.G1910T	p.W637L	CCCCACCAGATCC	.	PASS	Atlas-SNP
IKZF1	10320	hgsc.bcm.edu	37	7	50459542	50459542	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80.0	4.0	83.0	0.0	0.05	0	.	.	none	.	IKZF1	613	.	NM_006060	exon7	c.T831C	p.S277S	GAGCTCTATGCCT	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72998296	72998296	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159.0	50.0	199.0	0.0	0.314465	0	.	.	none	.	TSHZ1	104	.	NM_005786	exon2	c.T799C	p.C267R	ATGTACTGTGGAC	.	PASS	Atlas-SNP
IMPAD1	54928	hgsc.bcm.edu	37	8	57906042	57906042	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	8.0	6.0	11.0	0.0	0.75	0	.	.	none	.	IMPAD1	27	.	NM_017813	exon1	c.C103T	p.R35C	TGAAGCGGCCGGC	.	PASS	Atlas-SNP
HECTD2	143279	hgsc.bcm.edu	37	10	93221018	93221018	+	Missense_Mutation	SNP	G	G	A	rs61754655	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101.0	76.0	176.0	0.0	0.752475	0	G|0.997;A|0.003	0.003	strong	.	HECTD2	60	.	NM_173497	exon4	c.G415A	p.V139I	GAAGATGTAGAAA	.	PASS	Atlas-SNP
CEP72	55722	hgsc.bcm.edu	37	5	637637	637637	+	Missense_Mutation	SNP	A	A	G	rs62000999	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193.0	91.0	221.0	0.0	0.471503	0	A|0.989;G|0.011	0.011	strong	.	CEP72	53	.	NM_018140	exon7	c.A910G	p.M304V	GACTCCATGGATA	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102593273	102593273	+	Silent	SNP	T	T	G	rs12803000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	579.0	141.0	343.0	0.0	0.243523	0	T|0.966;G|0.034	0.034	strong	MMP8,face,malignant_melanoma,-2,1	MMP8	68	1	NM_002424	exon2	c.A234C	p.P78P	CTCATTTGGCTTC	.	PASS	Atlas-SNP
HOXD10	3236	hgsc.bcm.edu	37	2	176983923	176983923	+	Silent	SNP	G	G	C	rs33913965	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159.0	77.0	128.0	0.0	0.484277	0	G|0.984;C|0.016	0.016	strong	.	HOXD10	65	.	NM_002148	exon2	c.G987C	p.R329R	GAACCGGATCCGA	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93433289	93433289	+	Silent	SNP	A	A	G	rs374656563		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	236.0	142.0	137.0	0.0	0.601695	0	.	.	weak	.	KIAA1731	173	.	NM_033395	exon15	c.A5211G	p.T1737T	ACAAACAGCATTG	.	PASS	Atlas-SNP
NOP9	161424	hgsc.bcm.edu	37	14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	rs147123517	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	281.0	94.0	156.0	0.0	0.33452	0	C|0.996;T|0.004	0.004	strong	.	.	.	.	NM_174913	exon6	c.C1237T	p.R413C	GCCTGTCGCAGAG	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187088399	187088399	+	Missense_Mutation	SNP	G	G	T	rs111681837	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	165.0	48.0	276.0	0.0	0.290909	0	G|0.995;T|0.005	0.005	strong	.	FAM149A	52	.	NM_001006655	exon12	c.G1358T	p.G453V	GGACAGGTCAAAG	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31769293	31769293	+	Missense_Mutation	SNP	T	T	C	rs143453460	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199.0	108.0	209.0	1.0	0.542714	0.00478469	T|0.991;C|0.009	0.009	strong	TSHZ3_ENST00000240587,NS,carcinoma,+1,2	TSHZ3	549	2	NM_020856	exon2	c.A1406G	p.E469G	TTGACCTCCACAT	.	PASS	Atlas-SNP
TCP1	6950	hgsc.bcm.edu	37	6	160201577	160201577	+	Missense_Mutation	SNP	G	G	C	rs148556538	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	196.0	101.0	209.0	1.0	0.515306	0.00478469	G|0.999;C|0.001	0.001	strong	.	TCP1	37	.	NM_030752	exon9	c.C995G	p.A332G	AAATTGGCCAGGG	.	PASS	Atlas-SNP
CCBL1	883	hgsc.bcm.edu	37	9	131600394	131600394	+	Missense_Mutation	SNP	A	A	G	rs371451324		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197.0	99.0	234.0	1.0	0.502538	0.0042735	.	.	weak	.	CCBL1	36	.	NM_001122671	exon5	c.T374C	p.F125S	CAGTCAAAAAAGG	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848826	54848826	+	Missense_Mutation	SNP	C	C	T	rs145556773	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175.0	95.0	205.0	0.0	0.542857	0	C|0.997;T|0.003	0.003	strong	.	LILRA4	91	.	NM_012276	exon5	c.G797A	p.R266H	CCAGGGCGCTGGG	.	PASS	Atlas-SNP
C15orf52	388115	hgsc.bcm.edu	37	15	40629995	40629995	+	Missense_Mutation	SNP	G	G	A	rs149438052	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48.0	18.0	93.0	0.0	0.375	0	A|0.001;G|0.999	0.001	strong	.	C15orf52	47	.	NM_207380	exon6	c.C745T	p.R249C	CGAGGCGGGCTAG	.	PASS	Atlas-SNP
TRAP1	10131	hgsc.bcm.edu	37	16	3724365	3724365	+	Missense_Mutation	SNP	C	C	T	rs145715008	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163.0	90.0	138.0	0.0	0.552147	0	C|0.999;T|0.001	0.001	strong	TRAP1,colon,carcinoma,-1,1	TRAP1	53	1	NM_016292	exon9	c.G1019A	p.R340H	ATGCTGCGGATGT	.	PASS	Atlas-SNP
USP43	124739	hgsc.bcm.edu	37	17	9580092	9580092	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256.0	28.0	264.0	0.0	0.109375	0	.	.	none	.	USP43	65	.	NM_001267576	exon5	c.C863G	p.S288C	TCCCCTCTAAGAG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169294859	169294859	+	Silent	SNP	C	C	T	rs13133439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210.0	51.0	373.0	0.0	0.242857	0	C|0.979;T|0.021	0.021	strong	DDX60L,NS,carcinoma,-2,1	DDX60L	116	1	NM_001012967	exon35	c.G4734A	p.G1578G	TGTGTTCCCCGAA	.	PASS	Atlas-SNP
LGALS16	148003	hgsc.bcm.edu	37	19	40151098	40151098	+	Missense_Mutation	SNP	A	A	C	rs181925874	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29.0	9.0	23.0	0.0	0.310345	0	A|1.000;C|0.000	0.000	strong	.	LGALS16	6	.	NM_001190441	exon4	c.A367C	p.M123L	GTGAAGATGATTC	.	PASS	Atlas-SNP
LPHN1	22859	hgsc.bcm.edu	37	19	14288369	14288369	+	Silent	SNP	C	C	T	rs146417164	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119.0	62.0	140.0	0.0	0.521008	0	C|0.992;T|0.008	0.008	strong	.	LPHN1	107	.	NM_001008701	exon3	c.G258A	p.P86P	GGCGTCCGGCAGG	.	PASS	Atlas-SNP
KCNU1	157855	hgsc.bcm.edu	37	8	36788597	36788597	+	Missense_Mutation	SNP	G	G	C	rs190224798	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	218.0	61.0	156.0	0.0	0.279817	0	G|1.000;C|0.000	0.000	strong	.	KCNU1	359	.	NM_001031836	exon25	c.G2865C	p.L955F	GCTCTTGTCTGGA	.	PASS	Atlas-SNP
ASPHD1	253982	hgsc.bcm.edu	37	16	29917177	29917177	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99.0	56.0	111.0	0.0	0.565657	0	.	.	none	.	ASPHD1	28	.	NM_181718	exon3	c.G1132A	p.E378K	GGGGCTGAGCGCC	.	PASS	Atlas-SNP
CPED1	79974	hgsc.bcm.edu	37	7	120737809	120737809	+	Missense_Mutation	SNP	C	C	T	rs144805034	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	73.0	171.0	0.0	0.820225	0	C|0.996;T|0.004	0.004	strong	.	.	.	.	NM_001105533	exon5	c.C673T	p.P225S	TTAAAGCCGAGTA	.	PASS	Atlas-SNP
VSIG1	340547	hgsc.bcm.edu	37	X	107320447	107320447	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71.0	4.0	127.0	0.0	0.056338	0	.	.	none	.	VSIG1	126	.	NM_001170553	exon8	c.C1108T	p.P370S	CCTGCCCCAGGAT	.	PASS	Atlas-SNP
OR5AS1	219447	hgsc.bcm.edu	37	11	55798278	55798278	+	Silent	SNP	C	C	T	rs148523609	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	295.0	136.0	335.0	1.0	0.461017	0.00298507	C|0.993;T|0.007	0.007	strong	.	OR5AS1	121	.	NM_001001921	exon1	c.C384T	p.N128N	CTGCAACCCACTG	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2816519	2816519	+	Missense_Mutation	SNP	G	G	A	rs138447860	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99.0	48.0	87.0	0.0	0.484848	0	G|0.997;A|0.003	0.003	strong	.	SRRM2	263	.	NM_016333	exon11	c.G5990A	p.R1997H	GATCTCGCACATC	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	145006143	145006143	+	Missense_Mutation	SNP	T	T	C	rs189137260	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	154.0	83.0	114.0	0.0	0.538961	0	T|0.995;C|0.005	0.005	strong	.	PLEC	1144	.	NM_201380	exon18	c.A2551G	p.I851V	CCTCGATACAGCA	.	PASS	Atlas-SNP
KIAA1683	80726	hgsc.bcm.edu	37	19	18377981	18377981	+	Silent	SNP	C	C	G	rs61740692	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194.0	94.0	208.0	0.0	0.484536	0	C|0.984;G|0.016	0.016	strong	.	KIAA1683	190	.	NM_001145304	exon3	c.G369C	p.L123L	GGAAATCAGCTTC	.	PASS	Atlas-SNP
YPEL3	83719	hgsc.bcm.edu	37	16	30106716	30106716	+	Missense_Mutation	SNP	C	C	A	rs184524218	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37.0	24.0	44.0	0.0	0.648649	0	C|0.995;A|0.005	0.005	strong	.	YPEL3	5	.	NM_031477	exon1	c.G88T	p.V30L	GCCCCACGCGGGG	.	PASS	Atlas-SNP
VPS13C	54832	hgsc.bcm.edu	37	15	62253954	62253954	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109.0	8.0	168.0	0.0	0.0733945	0	.	.	none	.	VPS13C	506	.	NM_020821	exon35	c.C3742A	p.P1248T	TAACCGGTGCTTT	.	PASS	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157009	26157009	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109.0	35.0	103.0	0.0	0.321101	0	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.C391T	p.P131S	AAGAAGCCAGCAG	.	PASS	Atlas-SNP
XKR8	55113	hgsc.bcm.edu	37	1	28290155	28290155	+	Silent	SNP	G	G	A	rs142513353	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	128.0	16.0	201.0	0.0	0.125	0	G|0.997;A|0.003	0.003	strong	.	XKR8	15	.	NM_018053	exon2	c.G441A	p.T147T	GCTCACGCTGGTG	.	PASS	Atlas-SNP
CD1B	910	hgsc.bcm.edu	37	1	158299358	158299358	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	396.0	231.0	325.0	0.0	0.583333	0	.	.	none	CD1B,colon,carcinoma,+1,1	CD1B	78	1	NM_001764	exon4	c.T688C	p.Y230H	TTGGGTAGAATCC	.	PASS	Atlas-SNP
SLC39A13	91252	hgsc.bcm.edu	37	11	47431764	47431764	+	Missense_Mutation	SNP	G	G	A	rs35741412	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98.0	54.0	131.0	0.0	0.55102	0	G|0.984;A|0.016	0.016	strong	.	SLC39A13	18	.	NM_152264	exon2	c.G119A	p.R40Q	GGAGCCGGGGGAC	.	PASS	Atlas-SNP
KLC4	89953	hgsc.bcm.edu	37	6	43039340	43039340	+	Missense_Mutation	SNP	C	C	T	rs41274918	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251.0	134.0	280.0	2.0	0.533865	0.00714286	C|0.999;T|0.001	0.001	strong	KLC4,colon,carcinoma,0,1	KLC4	89	1	NM_201523	exon10	c.C1345T	p.R449W	GAGGAGCGGGAGG	.	scavenged	Atlas-SNP
BAI2	576	hgsc.bcm.edu	37	1	32196453	32196453	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39.0	4.0	85.0	0.0	0.102564	0	.	.	none	BAI2,colon,carcinoma,0,1	BAI2	128	1	NM_001703	exon29	c.G4328A	p.R1443Q	ATGGTCCGGCTGC	.	PASS	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	37	5	149265875	149265875	+	Silent	SNP	G	G	A	rs61733360	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163.0	79.0	159.0	0.0	0.484663	0	G|0.969;A|0.031	0.031	strong	PDE6A,NS,carcinoma,0,1	PDE6A	98	1	NM_000440	exon14	c.C1791T	p.F597F	ATGGCAGAAAGCA	.	PASS	Atlas-SNP
HNRNPL	3191	hgsc.bcm.edu	37	19	39331198	39331198	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90.0	30.0	94.0	0.0	0.333333	0	.	.	none	.	HNRNPL	67	.	NM_001533	exon7	c.T882A	p.G294G	AGGGTCACCTGTG	.	PASS	Atlas-SNP
ATXN2	6311	hgsc.bcm.edu	37	12	111907956	111907956	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174.0	54.0	183.0	0.0	0.310345	0	.	.	none	.	ATXN2	99	.	NM_002973	exon20	c.C3272G	p.S1091X	GTTGCTGAAGAAG	.	PASS	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132241682	132241682	+	Missense_Mutation	SNP	C	C	T	rs145242123	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125.0	70.0	138.0	0.0	0.56	0	C|0.998;T|0.002	0.002	strong	.	DNAJC13	253	.	NM_015268	exon49	c.C5684T	p.T1895M	GAATTACGTTAAT	.	PASS	Atlas-SNP
FLT3	2322	hgsc.bcm.edu	37	13	28623525	28623525	+	Silent	SNP	G	G	A	rs146983744	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133.0	74.0	145.0	0.0	0.556391	0	G|0.999;A|0.001	0.001	strong	.	FLT3	15525	.	NM_004119	exon8	c.C1032T	p.I344I	ACCTACGATGGTA	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	37	18	21123523	21123523	+	Missense_Mutation	SNP	C	C	T	rs375047023		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15.0	9.0	21.0	0.0	0.6	0	.	.	weak	.	NPC1	114	.	NM_000271	exon14	c.G2141A	p.R714H	TGAAGACGTTCAT	.	PASS	Atlas-SNP
PIP5K1C	23396	hgsc.bcm.edu	37	19	3633473	3633473	+	Missense_Mutation	SNP	C	C	T	rs35014191	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95.0	53.0	111.0	0.0	0.557895	0	C|0.992;T|0.008	0.008	strong	PIP5K1C_ENST00000335312,NS,carcinoma,+1,1	PIP5K1C	63	1	NM_012398	exon17	c.G1966A	p.A656T	CCTGGGCGCTATA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100677355	100677355	+	Silent	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	302.0	23.0	162.0	0.0	0.0761589	0	.	.	none	.	MUC17	804	.	NM_001040105	exon3	c.A2658C	p.S886S	CCTTTCAACAACT	.	PASS	Atlas-SNP
PNKP	11284	hgsc.bcm.edu	37	19	50364914	50364914	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24.0	4.0	25.0	0.0	0.166667	0	.	.	none	.	PNKP	71	.	NM_007254	exon15	c.G1337A	p.R446H	AAGCAGCGGCAGG	.	PASS	Atlas-SNP
CHAT	1103	hgsc.bcm.edu	37	10	50854637	50854637	+	Missense_Mutation	SNP	G	G	A	rs8178991	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104.0	104.0	141.0	0.0	1	0	G|0.986;A|0.014	0.014	strong	.	CHAT	162	.	NM_020549	exon8	c.G1198A	p.D400N	CTCAGCGACACCC	.	PASS	Atlas-SNP
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	rs77807247	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141.0	47.0	111.0	0.0	0.333333	0	C|0.969;T|0.031	0.031	strong	.	KRTAP19-6	16	.	NM_181612	exon1	c.G134A	p.R45H	GATGGGCGGCAGC	.	PASS	Atlas-SNP
KPNB1	3837	hgsc.bcm.edu	37	17	45734285	45734285	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111.0	46.0	146.0	0.0	0.414414	0	.	.	none	.	KPNB1	58	.	NM_002265	exon4	c.C342C	p.H114H	TGTGGCTGGTATT	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	37	3	113376113	113376113	+	Silent	SNP	C	C	T	rs62265537		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69.0	3.0	106.0	0.0	0.0434783	0	.	.	weak	KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	NM_001009899	exon7	c.G4416A	p.Q1472Q	CTGTTGCTGCTGC	.	scavenged	Atlas-SNP
CREBBP	1387	hgsc.bcm.edu	37	16	3808872	3808872	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141.0	44.0	136.0	0.0	0.312057	0	.	.	none	.	CREBBP	546	.	NM_004380	exon17	c.C3352T	p.Q1118X	GGAGCTGGGGATC	.	PASS	Atlas-SNP
FMO4	2329	hgsc.bcm.edu	37	1	171303626	171303626	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170.0	51.0	133.0	0.0	0.3	0	.	.	none	FMO4,caecum,carcinoma,0,1	FMO4	64	1	NM_002022	exon8	c.G904A	p.V302M	ACCAGCGTGATTG	.	PASS	Atlas-SNP
C14orf37	145407	hgsc.bcm.edu	37	14	58605734	58605734	+	Missense_Mutation	SNP	T	T	C	rs61741497	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212.0	140.0	153.0	1.0	0.660377	0.00653595	T|0.995;C|0.005	0.005	strong	.	C14orf37	87	.	NM_001001872	exon2	c.A343G	p.T115A	ACTCAGTAGGTGT	.	PASS	Atlas-SNP
CEACAM20	125931	hgsc.bcm.edu	37	19	45024535	45024535	+	Missense_Mutation	SNP	T	T	C	rs200961907	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86.0	43.0	70.0	0.0	0.5	0	T|0.996;C|0.004	0.004	weak	.	CEACAM20	31	.	NM_001102600	exon5	c.A1003G	p.S335G	GCTCACTCCGGGC	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24424346	24424346	+	Silent	SNP	G	G	A	rs4981491		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	432.0	92.0	324.0	0.0	0.212963	0	.	.	weak	.	DHRS4	22	.	NM_021004	exon2	c.G231A	p.Q77Q	GCTGCAGGGGGAG	.	PASS	Atlas-SNP
RFX2	5990	hgsc.bcm.edu	37	19	6013057	6013057	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56.0	25.0	42.0	0.0	0.446429	0	.	.	none	.	RFX2	60	.	NM_000635	exon8	c.G839A	p.R280Q	TGCAGCCGGTTCA	.	PASS	Atlas-SNP
VN1R2	317701	hgsc.bcm.edu	37	19	53761857	53761857	+	Missense_Mutation	SNP	G	G	T	rs112986288	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55.0	22.0	65.0	0.0	0.4	0	G|0.994;T|0.006	0.006	strong	.	VN1R2	71	.	NM_173856	exon1	c.G229T	p.V77F	TCTCTTGTCTCTG	.	PASS	Atlas-SNP
MAN2A2	4122	hgsc.bcm.edu	37	15	91452566	91452566	+	Silent	SNP	G	G	A	rs148266546	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62.0	6.0	101.0	0.0	0.0967742	0	G|1.000;A|0.000	0.000	strong	.	MAN2A2	99	.	NM_006122	exon8	c.G1206A	p.L402L	AGCCCTGCTTCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509722	195509722	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	520.0	83.0	327.0	0.0	0.159615	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.C8729A	p.T2910N	GGCGTGGTGTCAC	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242396209	242396209	+	Missense_Mutation	SNP	C	C	A	rs145630778	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	258.0	120.0	266.0	1.0	0.465116	0.0037594	C|1.000;A|0.000	0.000	strong	.	FARP2	92	.	NM_014808	exon14	c.C1459A	p.P487T	AAGAGCCCCCTGA	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50944294	50944294	+	Missense_Mutation	SNP	C	C	T	rs374005339		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203.0	12.0	178.0	0.0	0.0591133	0	.	.	weak	.	MYBPC2	103	.	NM_004533	exon8	c.C730T	p.R244W	CTGAAGCGGCTGA	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121742307	121742307	+	Silent	SNP	C	C	T	rs13008360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84.0	47.0	126.0	1.0	0.559524	0.00793651	C|0.984;T|0.016	0.016	strong	GLI2,NS,carcinoma,0,1	GLI2	187	1	NM_005270	exon11	c.C1944T	p.T648T	CAAGACCGAGAGC	.	scavenged	Atlas-SNP
HOXB8	3218	hgsc.bcm.edu	37	17	46690777	46690777	+	Silent	SNP	A	A	G	rs45441492	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182.0	180.0	221.0	1.0	0.989011	0.00452489	A|0.924;G|0.076	0.076	strong	.	HOXB8	26	.	NM_024016	exon2	c.T519C	p.R173R	CCGCTTACGAGTC	.	PASS	Atlas-SNP
PARD3	56288	hgsc.bcm.edu	37	10	34630575	34630575	+	Silent	SNP	T	T	A	rs141191270	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88.0	69.0	118.0	0.0	0.784091	0	T|0.999;A|0.001	0.001	strong	.	PARD3	131	.	NM_001184787	exon16	c.A2397T	p.A799A	ACTGATTGCAGCC	.	PASS	Atlas-SNP
SWSAP1	126074	hgsc.bcm.edu	37	19	11486354	11486354	+	Missense_Mutation	SNP	C	C	A	rs146815699	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66.0	25.0	70.0	0.0	0.378788	0	C|0.997;A|0.003	0.003	strong	.	.	.	.	NM_175871	exon2	c.C352A	p.L118I	GCCTTACTTCTAG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37153871	37153871	+	Missense_Mutation	SNP	G	G	T	rs77014998	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90.0	34.0	122.0	0.0	0.377778	0	G|0.992;T|0.008	0.008	strong	.	C5orf42	422	.	NM_023073	exon41	c.C8182A	p.P2728T	TTTCAGGCTTGGG	.	PASS	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	37	8	100874154	100874154	+	Missense_Mutation	SNP	G	G	A	rs149318176	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83.0	28.0	61.0	0.0	0.337349	0	G|0.998;A|0.002	0.002	strong	.	VPS13B	811	.	NM_017890	exon58	c.G11270A	p.R3757Q	TGTCCCGGCTGGG	.	PASS	Atlas-SNP
ALG6	29929	hgsc.bcm.edu	37	1	63902524	63902524	+	Missense_Mutation	SNP	C	C	G	rs41285372	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180.0	135.0	275.0	0.0	0.75	0	C|0.987;G|0.013	0.013	strong	.	ALG6	33	.	NM_013339	exon15	c.C1357G	p.L453V	GTGCTTCTGACGT	.	PASS	Atlas-SNP
IFNA1	3439	hgsc.bcm.edu	37	9	21440916	21440916	+	Missense_Mutation	SNP	C	C	T	rs2230050	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	634.0	176.0	714.0	0.0	0.277603	0	C|0.946;T|0.054	0.054	strong	IFNA1,NS,carcinoma,-1,1	IFNA1	21	1	NM_024013	exon1	c.C410T	p.A137V	TGAATGCGGACTC	.	scavenged	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	37	16	1555505	1555505	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131.0	61.0	102.0	0.0	0.465649	0	.	.	none	.	TELO2	44	.	NM_016111	exon16	c.C1937T	p.P646L	GCCTGCCAGAGGC	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102595579	102595579	+	Missense_Mutation	SNP	G	G	C	rs17099450	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	335.0	80.0	200.0	0.0	0.238806	0	G|0.946;C|0.054	0.054	strong	.	MMP8	68	.	NM_002424	exon1	c.C8G	p.S3C	TTCAGGGAGAACA	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55268916	55268916	+	Silent	SNP	C	C	T	rs2293347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	252.0	85.0	206.0	0.0	0.337302	0	C|0.894;T|0.106	0.106	strong	.	EGFR	20426	.	NM_005228	exon25	c.C2982T	p.D994D	TACAGACTCCAAC	.	PASS	Atlas-SNP
SSUH2	51066	hgsc.bcm.edu	37	3	8675447	8675447	+	Missense_Mutation	SNP	C	C	T	rs112366230	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182.0	96.0	157.0	0.0	0.527473	0	C|0.986;T|0.014	0.014	strong	.	.	.	.	NM_001256748	exon4	c.G244A	p.A82T	GGAGGGCTTCCCG	.	PASS	Atlas-SNP
CABIN1	23523	hgsc.bcm.edu	37	22	24567795	24567795	+	Missense_Mutation	SNP	C	C	T	rs145513360	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160.0	94.0	141.0	0.0	0.5875	0	C|0.999;T|0.001	0.001	strong	.	CABIN1	153	.	NM_001199281	exon34	c.C5872T	p.R1958W	GTCCAGCGGCCCA	.	PASS	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45003746	45003746	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75.0	38.0	113.0	0.0	0.506667	0	.	.	none	B2M,caecum,carcinoma,-1,17	B2M	99	17	NM_004048	exon1	c.T2G	p.M1R	CCGAGATGTCTCG	.	PASS	Atlas-SNP
PPP1R42	286187	hgsc.bcm.edu	37	8	67926717	67926717	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	60.0	127.0	0.0	0.821918	0	.	.	none	.	PPP1R42	2	.	NM_001013626	exon3	c.A240G	p.Q80Q	ATTGTTTTGTAGG	.	PASS	Atlas-SNP
PLXNC1	10154	hgsc.bcm.edu	37	12	94631496	94631496	+	Silent	SNP	C	C	T	rs2230755	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54.0	12.0	82.0	0.0	0.222222	0	C|0.929;T|0.071	0.071	strong	.	PLXNC1	135	.	NM_005761	exon10	c.C2037T	p.N679N	AAGCAACGTGATA	.	PASS	Atlas-SNP
PCDP1	0	hgsc.bcm.edu	37	2	120383248	120383248	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113.0	36.0	134.0	0.0	0.318584	0	.	.	none	.	.	.	.	NM_001271049	exon15	c.A1500G	p.K500K	AGCAAAACAATCG	.	PASS	Atlas-SNP
TSPAN32	10077	hgsc.bcm.edu	37	11	2325427	2325427	+	Missense_Mutation	SNP	T	T	C	rs61744929	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36.0	14.0	36.0	0.0	0.388889	0	T|0.992;C|0.008	0.008	strong	.	TSPAN32	19	.	NM_139022	exon3	c.T272C	p.M91T	GCCTCATGGCAGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682156	100682156	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268.0	13.0	214.0	0.0	0.0485075	0	.	.	none	MUC17,bladder,carcinoma,-2,2	MUC17	804	2	NM_001040105	exon3	c.A7459G	p.M2487V	ACACCTATGACCA	.	scavenged	Atlas-SNP
ZNF697	90874	hgsc.bcm.edu	37	1	120166528	120166528	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162.0	40.0	158.0	0.0	0.246914	0	.	.	none	.	ZNF697	26	.	NM_001080470	exon3	c.T438C	p.H146H	GGAGAGATGTCGC	.	PASS	Atlas-SNP
TFG	10342	hgsc.bcm.edu	37	3	100455433	100455433	+	Silent	SNP	T	T	G	rs12562	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256.0	132.0	244.0	0.0	0.515625	0	T|0.993;G|0.007	0.007	strong	.	TFG	42	.	NM_006070	exon6	c.T594G	p.A198A	CAGTGCTCCTGCA	.	PASS	Atlas-SNP
FMO4	2329	hgsc.bcm.edu	37	1	171303810	171303810	+	Missense_Mutation	SNP	C	C	T	rs144578261	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156.0	63.0	111.0	1.0	0.403846	0.00900901	C|1.000;T|0.000	0.000	weak	FMO4,NS,NS,-1,1	FMO4	64	1	NM_002022	exon8	c.C1088T	p.A363V	AGAGAGCGACATT	.	scavenged	Atlas-SNP
PSG11	5680	hgsc.bcm.edu	37	19	43528921	43528921	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	359.0	27.0	310.0	0.0	0.0752089	0	.	.	none	PSG11,NS,carcinoma,+2,1	PSG11	57	1	NM_002785	exon2	c.G352C	p.G118R	AGGATCCTGCGTC	.	scavenged	Atlas-SNP
MUT	4594	hgsc.bcm.edu	37	6	49425446	49425446	+	Silent	SNP	T	T	C	rs138085432	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117.0	46.0	69.0	0.0	0.393162	0	T|0.991;C|0.009	0.009	strong	.	MUT	70	.	NM_000255	exon3	c.A711G	p.P237P	CATGGATGGTTCT	.	PASS	Atlas-SNP
SSH1	54434	hgsc.bcm.edu	37	12	109198832	109198832	+	Silent	SNP	G	G	A	rs140151008	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132.0	63.0	132.0	0.0	0.477273	0	G|0.996;A|0.004	0.004	strong	.	SSH1	144	.	NM_001161331	exon9	c.C987T	p.L329L	TCTTACGAGATAA	.	PASS	Atlas-SNP
USP25	29761	hgsc.bcm.edu	37	21	17181168	17181168	+	Nonsense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80.0	15.0	55.0	0.0	0.1875	0	.	.	none	.	USP25	156	.	NM_013396	exon8	c.T821G	p.L274X	ATTGGTTAGAAGA	.	PASS	Atlas-SNP
KRT77	374454	hgsc.bcm.edu	37	12	53090181	53090181	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56.0	27.0	51.0	1.0	0.482143	0.0196078	.	.	none	KRT77,NS,carcinoma,0,1	KRT77	58	1	NM_175078	exon3	c.C792T	p.S264S	ATTCTCGCTGCCA	.	scavenged	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100971024	100971024	+	Silent	SNP	G	G	A	rs148143158	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	245.0	121.0	243.0	0.0	0.493878	0	G|0.996;A|0.004	0.004	strong	TBC1D2_ENST00000375063,NS,carcinoma,0,2	TBC1D2	70	2	NM_001267571	exon9	c.C2076T	p.P692P	CTTGTCGGGGAAG	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78369573	78369573	+	Missense_Mutation	SNP	C	C	T	rs75922333	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105.0	47.0	106.0	0.0	0.447619	0	C|0.990;T|0.010	0.010	strong	.	.	.	.	NM_001098816	exon34	c.G7840A	p.V2614M	TATCCACCCCATC	.	PASS	Atlas-SNP
SF3A2	8175	hgsc.bcm.edu	37	19	2248185	2248185	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15.0	10.0	24.0	0.0	0.666667	0	.	.	none	SF3A2,colon,carcinoma,0,1	SF3A2	22	1	NM_007165	exon9	c.A1035T	p.P345P	TCACCCACCAGCC	.	scavenged	Atlas-SNP
TET2	54790	hgsc.bcm.edu	37	4	106196819	106196819	+	Missense_Mutation	SNP	G	G	T	rs142312318	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200.0	95.0	263.0	0.0	0.475	0	G|0.999;T|0.001	0.001	strong	TET2,NS,lymphoid_neoplasm,0,8	TET2	1762	8	NM_001127208	exon11	c.G5152T	p.V1718L	CATCATGTAGGGA	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	37	11	108106435	108106435	+	Missense_Mutation	SNP	A	A	G	rs148590073	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212.0	64.0	135.0	0.0	0.301887	0	A|0.997;G|0.003	0.003	strong	.	ATM	1657	.	NM_000051	exon5	c.A370G	p.I124V	AATTATATCATGG	.	PASS	Atlas-SNP
SIK3	23387	hgsc.bcm.edu	37	11	116719841	116719841	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	461.0	306.0	326.0	1.0	0.663774	0.00306748	.	.	none	.	SIK3	112	.	NM_025164	exon21	c.G3496A	p.A1166T	CATAAGCATCGTC	.	PASS	Atlas-SNP
NETO1	81832	hgsc.bcm.edu	37	18	70526301	70526301	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	150.0	51.0	144.0	0.0	0.34	0	.	.	none	.	NETO1	178	.	NM_001201465	exon4	c.A229G	p.R77G	ACTGTCTTGGAGC	.	PASS	Atlas-SNP
APBA2	321	hgsc.bcm.edu	37	15	29368269	29368269	+	Silent	SNP	G	G	A	rs149285403	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95.0	76.0	138.0	0.0	0.8	0	G|0.999;A|0.001	0.001	strong	.	APBA2	132	.	NM_005503	exon5	c.G1044A	p.V348V	GAAGGTGGCATCA	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21607296	21607296	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71.0	4.0	70.0	0.0	0.056338	0	.	.	none	ZNF493_ENST00000392288,NS,carcinoma,0,4	ZNF493	178	4	NM_001076678	exon4	c.G1835A	p.R612Q	TTAACCGATCTTC	.	scavenged	Atlas-SNP
FAM160A1	729830	hgsc.bcm.edu	37	4	152577473	152577473	+	Nonsense_Mutation	SNP	C	C	T	rs367582779		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181.0	122.0	278.0	1.0	0.674033	0.00359712	.	.	weak	.	FAM160A1	60	.	NM_001109977	exon12	c.C2641T	p.Q881X	ATTACTCAGCTAG	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238280553	238280553	+	Silent	SNP	G	G	A	rs35114079	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	28.0	127.0	0.0	0.363636	0	G|0.994;A|0.006	0.006	strong	.	COL6A3	608	.	NM_004369	exon9	c.C4107T	p.I1369I	CCTGGCGATCGTG	.	PASS	Atlas-SNP
FAM98A	25940	hgsc.bcm.edu	37	2	33820635	33820635	+	Silent	SNP	C	C	T	rs72785999	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171.0	94.0	133.0	0.0	0.549708	0	C|0.995;T|0.005	0.005	strong	.	FAM98A	42	.	NM_015475	exon2	c.G123A	p.E41E	GGTAAACTCGGGG	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72360197	72360197	+	Silent	SNP	T	T	C	rs116554195	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126.0	92.0	235.0	0.0	0.730159	0	T|0.987;C|0.013	0.013	strong	.	PRF1	64	.	NM_001083116	exon2	c.A462G	p.A154A	GTTGGCTGCCTGT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093481	1093481	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69.0	20.0	72.0	0.0	0.289855	0	.	.	none	.	MUC2	614	.	NM_002457	exon30	c.C5300T	p.T1767M	CAACCACGGTACT	.	PASS	Atlas-SNP
TRIP6	7205	hgsc.bcm.edu	37	7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	rs2437100	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	105.0	73.0	71.0	0.0	0.695238	0	G|0.985;A|0.015	0.015	strong	.	TRIP6	45	.	NM_003302	exon3	c.G332A	p.R111Q	GGGGTCGGGGTCA	.	PASS	Atlas-SNP
GNB5	10681	hgsc.bcm.edu	37	15	52446260	52446260	+	Silent	SNP	C	C	T	rs35581121	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26.0	6.0	51.0	0.0	0.230769	0	C|0.973;T|0.027	0.027	strong	.	GNB5	28	.	NM_016194	exon4	c.G252A	p.A84A	CCGCTCCGCCACC	.	PASS	Atlas-SNP
GBP7	388646	hgsc.bcm.edu	37	1	89613280	89613280	+	Silent	SNP	G	G	A	rs115454072	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159.0	158.0	300.0	0.0	0.993711	0	G|0.976;A|0.024	0.024	strong	.	GBP7	57	.	NM_207398	exon8	c.C1335T	p.D445D	TGTATAGTCCTGT	.	PASS	Atlas-SNP
ACSL1	2180	hgsc.bcm.edu	37	4	185724503	185724503	+	Missense_Mutation	SNP	C	C	T	rs114493597	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93.0	64.0	126.0	0.0	0.688172	0	C|0.998;T|0.002	0.002	strong	.	ACSL1	77	.	NM_001995	exon2	c.G166A	p.D56N	AGAGGTCGCATGG	.	PASS	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879340	39879340	+	Missense_Mutation	SNP	G	G	C	rs141110458	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61.0	37.0	140.0	0.0	0.606557	0	G|0.990;C|0.010	0.010	strong	.	KIAA0754	93	.	NM_015038	exon1	c.G3403C	p.A1135P	CCAGCTGCTGCAG	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46496910	46496910	+	Silent	SNP	G	G	A	rs145526650	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161.0	80.0	196.0	0.0	0.496894	0	G|0.998;A|0.002	0.002	strong	LTF,NS,carcinoma,0,1	LTF	98	1	NM_002343	exon5	c.C522T	p.A174A	ACAGCTGGCTGAG	.	PASS	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	37	4	184192231	184192231	+	Splice_Site	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68.0	3.0	144.0	0.0	0.0441176	0	.	.	none	WWC2,NS,carcinoma,0,1	WWC2	78	1	NM_024949	exon16	c.2401-2A>G	.	TTACATAGGCTGG	.	scavenged	Atlas-SNP
TCEB3B	51224	hgsc.bcm.edu	37	18	44560337	44560337	+	Silent	SNP	G	G	T	rs3744864	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122.0	53.0	119.0	0.0	0.434426	0	G|0.992;T|0.008	0.008	strong	TCEB3B,NS,carcinoma,-1,1	TCEB3B	141	1	NM_016427	exon1	c.C1299A	p.V433V	TTCCTGGACAGGA	.	PASS	Atlas-SNP
ETV3L	440695	hgsc.bcm.edu	37	1	157069134	157069134	+	Missense_Mutation	SNP	G	G	A	rs61730132	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	231.0	94.0	150.0	0.0	0.406926	0	G|0.994;A|0.006	0.006	strong	.	ETV3L	73	.	NM_001004341	exon2	c.C95T	p.S32L	GGGGACGACTCGG	.	PASS	Atlas-SNP
ARID4A	5926	hgsc.bcm.edu	37	14	58831995	58831995	+	Missense_Mutation	SNP	A	A	G	rs377087834		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99.0	42.0	84.0	0.0	0.424242	0	.	.	weak	.	ARID4A	222	.	NM_002892	exon20	c.A3188G	p.Q1063R	TTGTACAAGAGAG	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187078745	187078745	+	Missense_Mutation	SNP	A	A	G	rs113168248	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38.0	5.0	41.0	0.0	0.131579	0	A|0.995;G|0.005	0.005	strong	.	FAM149A	52	.	NM_001006655	exon7	c.A601G	p.K201E	ACATTGAAAGTGG	.	PASS	Atlas-SNP
PAK7	57144	hgsc.bcm.edu	37	20	9523244	9523244	+	Missense_Mutation	SNP	C	C	T	rs150828790	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	189.0	96.0	159.0	0.0	0.507937	0	C|0.999;T|0.001	0.001	strong	.	PAK7	194	.	NM_177990	exon9	c.G1993A	p.D665N	GTAGGTCCTTCAC	.	PASS	Atlas-SNP
KLHL34	257240	hgsc.bcm.edu	37	X	21675125	21675125	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87.0	83.0	203.0	0.0	0.954023	0	.	.	none	.	KLHL34	76	.	NM_153270	exon1	c.C782T	p.T261M	GAGGGCGTCGTGT	.	PASS	Atlas-SNP
KCNK16	83795	hgsc.bcm.edu	37	6	39284148	39284148	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	46.0	89.0	0.0	0.516854	0	.	.	none	.	KCNK16	59	.	NM_001135106	exon5	c.G732A	p.L244L	CCACGCCAGGCCC	.	PASS	Atlas-SNP
C6orf70	55780	hgsc.bcm.edu	37	6	170169688	170169688	+	Missense_Mutation	SNP	A	A	G	rs61738268	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61.0	25.0	77.0	0.0	0.409836	0	A|0.991;G|0.009	0.009	strong	.	C6orf70	63	.	NM_018341	exon12	c.A1112G	p.H371R	GAGATCATTTAAG	.	PASS	Atlas-SNP
CSRP2BP	57325	hgsc.bcm.edu	37	20	18168099	18168099	+	Missense_Mutation	SNP	G	G	A	rs376874386		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	29.0	66.0	0.0	0.446154	0	.	.	weak	.	CSRP2BP	80	.	NM_020536	exon10	c.G2345A	p.R782H	TCCGGCGCTGATG	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848145	54848145	+	Missense_Mutation	SNP	G	G	A	rs75547479	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182.0	19.0	235.0	0.0	0.104396	0	A|0.005;G|0.995	0.005	strong	.	LILRA4	91	.	NM_012276	exon6	c.C1222T	p.H408Y	TGGGGTGAGACAG	.	PASS	Atlas-SNP
GPR151	134391	hgsc.bcm.edu	37	5	145894882	145894882	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	113.0	32.0	94.0	0.0	0.283186	0	.	.	none	.	GPR151	35	.	NM_194251	exon1	c.C795T	p.P265P	CCATTCGGGGAGC	.	PASS	Atlas-SNP
PLCL2	23228	hgsc.bcm.edu	37	3	17053613	17053613	+	Silent	SNP	C	C	T	rs61751588	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51.0	22.0	70.0	0.0	0.431373	0	C|0.987;T|0.013	0.013	strong	.	PLCL2	145	.	NM_015184	exon2	c.C2397T	p.P799P	CCAGCCCCCTATA	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216248820	216248820	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71.0	19.0	114.0	0.0	0.267606	0	.	.	none	.	FN1	521	.	NM_212482	exon30	c.C4817A	p.T1606N	GTGATGGTATAAT	.	PASS	Atlas-SNP
U2AF2	11338	hgsc.bcm.edu	37	19	56181019	56181019	+	Silent	SNP	C	C	T	rs147666260	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162.0	81.0	151.0	0.0	0.5	0	C|0.994;T|0.006	0.006	strong	.	U2AF2	62	.	NM_007279	exon11	c.C1254T	p.P418P	GATCCCCCGGCCT	.	PASS	Atlas-SNP
VEGFC	7424	hgsc.bcm.edu	37	4	177713326	177713326	+	Missense_Mutation	SNP	T	T	A	rs55728985	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15.0	4.0	25.0	0.0	0.266667	0	T|0.996;A|0.004	0.004	strong	VEGFC,NS,carcinoma,-1,1	VEGFC	94	1	NM_005429	exon1	c.A140T	p.E47V	GTGGCCTCGCCCG	.	PASS	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43638436	43638436	+	Silent	SNP	G	G	T	rs6695238	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69.0	53.0	175.0	0.0	0.768116	0	G|0.920;T|0.080	0.080	strong	.	WDR65	76	.	NM_152498	exon2	c.G12T	p.V4V	AGCCGTGGTAGCT	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242373714	242373714	+	Missense_Mutation	SNP	C	C	T	rs372818608		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90.0	4.0	121.0	0.0	0.0444444	0	.	.	weak	.	FARP2	92	.	NM_014808	exon10	c.C1009T	p.R337W	TTCAGCCGGGGCT	.	PASS	Atlas-SNP
ZNF732	654254	hgsc.bcm.edu	37	4	289877	289877	+	Missense_Mutation	SNP	G	G	T	rs62619793	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	291.0	138.0	326.0	1.0	0.474227	0.00306748	G|0.958;T|0.042	0.042	strong	.	ZNF732	117	.	NM_001137608	exon1	c.C68A	p.A23D	TGCTGGGCAGGGT	.	PASS	Atlas-SNP
EXPH5	23086	hgsc.bcm.edu	37	11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	rs10890850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	211.0	60.0	152.0	0.0	0.28436	0	T|0.967;A|0.033	0.033	strong	.	EXPH5	193	.	NM_015065	exon6	c.A2674T	p.N892Y	AAGAATTCTTTGA	.	PASS	Atlas-SNP
KIAA1731	85459	hgsc.bcm.edu	37	11	93430474	93430474	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229.0	79.0	117.0	0.0	0.344978	0	.	.	none	.	KIAA1731	173	.	NM_033395	exon15	c.C2396G	p.P799R	CTCTGCCTGTTAA	.	PASS	Atlas-SNP
COPB1	1315	hgsc.bcm.edu	37	11	14515829	14515829	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124.0	55.0	112.0	0.0	0.443548	0	.	.	none	.	COPB1	81	.	NM_001144062	exon3	c.A248G	p.E83G	ACAATTTCCCAAA	.	PASS	Atlas-SNP
ZNF281	23528	hgsc.bcm.edu	37	1	200378495	200378495	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38.0	26.0	43.0	0.0	0.684211	0	.	.	none	.	ZNF281	74	.	NM_012482	exon2	c.G339A	p.S113S	CCTCTGCGAGGGG	.	PASS	Atlas-SNP
C17orf62	79415	hgsc.bcm.edu	37	17	80404555	80404555	+	Missense_Mutation	SNP	G	G	A	rs72857481	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	31.0	66.0	0.0	0.424658	0	G|0.989;A|0.011	0.011	strong	.	C17orf62	23	.	NM_001193657	exon5	c.C145T	p.L49F	AGAAGAGCTTCCA	.	PASS	Atlas-SNP
RIMS4	140730	hgsc.bcm.edu	37	20	43386414	43386414	+	Splice_Site	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80.0	26.0	81.0	0.0	0.325	0	.	.	none	.	RIMS4	47	.	NM_001205317	exon5	c.353-2A>T	.	ATCCCCTGGAAGA	.	PASS	Atlas-SNP
LARP4B	23185	hgsc.bcm.edu	37	10	909711	909711	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70.0	10.0	112.0	0.0	0.142857	0	.	.	none	.	LARP4B	110	.	NM_015155	exon5	c.T402C	p.Y134Y	AGAGTCATATTCT	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	304670	304670	+	Missense_Mutation	SNP	C	C	T	rs146490788	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58.0	30.0	67.0	0.0	0.517241	0	C|0.999;T|0.001	0.001	strong	.	DOCK8	401	.	NM_203447	exon5	c.C494T	p.S165L	TTGAGTCGGAAAC	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891009	44891009	+	Silent	SNP	C	C	T	rs139913772	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200.0	84.0	236.0	0.0	0.42	0	C|0.999;T|0.001	0.001	strong	ZNF285,NS,carcinoma,0,2	ZNF285	86	2	NM_152354	exon4	c.G1398A	p.A466A	GCTATACGCAAAA	.	PASS	Atlas-SNP
AP3B2	8120	hgsc.bcm.edu	37	15	83378366	83378366	+	Silent	SNP	G	G	A	rs200226421	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	12.0	10.0	10.0	0.0	0.833333	0	.	.	weak	.	AP3B2	103	.	NM_004644	exon1	c.C93T	p.I31I	GGAGAAGATGCCG	.	PASS	Atlas-SNP
PRSS41	360226	hgsc.bcm.edu	37	16	2849372	2849372	+	Missense_Mutation	SNP	C	C	A	rs201777593		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112.0	54.0	128.0	0.0	0.482143	0	.	.	weak	.	.	.	.	NM_001135086	exon3	c.C382A	p.R128S	AGCAGTCGTTACA	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26.0	26.0	60.0	0.0	1	0	G|0.754;C|0.246	0.246	strong	HNF1A,brain,glioma,0,1	HNF1A	302	1	NM_000545	exon4	c.G864C	p.G288G	CAGCGGGCCCCCC	.	PASS	Atlas-SNP
DCST1	149095	hgsc.bcm.edu	37	1	155019698	155019698	+	Missense_Mutation	SNP	G	G	A	rs200041699	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	253.0	144.0	184.0	0.0	0.56917	0	G|0.999;A|0.001	0.001	weak	.	DCST1	69	.	NM_152494	exon14	c.G1522A	p.G508R	AAGGTCGGGGGAG	.	PASS	Atlas-SNP
DIDO1	11083	hgsc.bcm.edu	37	20	61528044	61528044	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109.0	53.0	91.0	0.0	0.486239	0	.	.	none	.	DIDO1	321	.	NM_080797	exon7	c.C1893T	p.S631S	AGCAGCGGAGCCA	.	PASS	Atlas-SNP
RBM17	84991	hgsc.bcm.edu	37	10	6139078	6139078	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118.0	5.0	174.0	0.0	0.0423729	0	.	.	none	.	RBM17	45	.	NM_001145547	exon2	c.A50G	p.E17G	AAACAGAAGGCTG	.	PASS	Atlas-SNP
ZNF33B	7582	hgsc.bcm.edu	37	10	43089370	43089370	+	Missense_Mutation	SNP	T	T	A	rs71505625	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	132.0	23.0	215.0	0.0	0.174242	0	T|0.998;A|0.002	0.002	strong	.	ZNF33B	78	.	NM_006955	exon5	c.A1028T	p.H343L	GTGAGATGTGACT	.	PASS	Atlas-SNP
STXBP2	6813	hgsc.bcm.edu	37	19	7712050	7712050	+	Silent	SNP	C	C	T	rs146425381	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	50.0	15.0	57.0	0.0	0.3	0	C|0.999;T|0.001	0.001	strong	.	STXBP2	63	.	NM_001272034	exon17	c.C1488T	p.D496D	CCAGGACGCCGTG	.	PASS	Atlas-SNP
SLITRK3	22865	hgsc.bcm.edu	37	3	164906800	164906800	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87.0	15.0	111.0	0.0	0.172414	0	.	.	none	.	SLITRK3	263	.	NM_014926	exon2	c.C1819A	p.L607M	CTTCCAGCTCAAT	.	PASS	Atlas-SNP
KLHL17	339451	hgsc.bcm.edu	37	1	899824	899824	+	Silent	SNP	C	C	T	rs201807567	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48.0	38.0	88.0	0.0	0.791667	0	C|0.996;T|0.004	0.004	strong	.	KLHL17	31	.	NM_198317	exon11	c.C1614T	p.N538N	GGGCAACGACGGC	.	PASS	Atlas-SNP
EP300	2033	hgsc.bcm.edu	37	22	41546158	41546158	+	Missense_Mutation	SNP	C	C	A	rs148884710	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58.0	33.0	59.0	0.0	0.568965	0	C|0.995;A|0.005	0.005	strong	EP300,NS,lymphoid_neoplasm,0,1	EP300	367	1	NM_001429	exon14	c.C2773A	p.P925T	TCTGTTCCTACCC	.	PASS	Atlas-SNP
SLAIN1	122060	hgsc.bcm.edu	37	13	78320801	78320801	+	Missense_Mutation	SNP	C	C	G	rs144139933	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181.0	95.0	181.0	0.0	0.524862	0	C|0.999;G|0.001	0.001	strong	.	SLAIN1	43	.	NM_001242868	exon4	c.C1069G	p.P357A	CCACCACCTCAGC	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126241565	126241565	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93.0	54.0	154.0	0.0	0.580645	0	.	.	none	FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	2	NM_024582	exon1	c.C3999T	p.L1333L	TGAACTCGTGTCC	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8229140	8229140	+	Missense_Mutation	SNP	G	G	T	rs141562329	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93.0	40.0	97.0	0.0	0.430108	0	G|0.999;T|0.001	0.001	strong	.	SH3TC1	105	.	NM_018986	exon12	c.G1719T	p.R573S	CAGGAGGCTCAAG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	rs147173571		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	753.0	89.0	206.0	0.0	0.118194	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.T3335C	p.L1112P	CCAGGCTGGTGGT	.	PASS	Atlas-SNP
LAMC1	3915	hgsc.bcm.edu	37	1	183091040	183091040	+	Missense_Mutation	SNP	G	G	A	rs147401305	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146.0	88.0	103.0	1.0	0.60274	0.00970874	G|0.999;A|0.001	0.001	strong	LAMC1,NS,carcinoma,0,1	LAMC1	176	1	NM_002293	exon12	c.G2173A	p.A725T	CTTTGCGCCTGCA	.	scavenged	Atlas-SNP
SUCLG2	8801	hgsc.bcm.edu	37	3	67579535	67579535	+	Missense_Mutation	SNP	T	T	C	rs74675534	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	57.0	129.0	0.0	0.558824	0	T|0.993;C|0.007	0.007	strong	.	SUCLG2	95	.	NM_001177599	exon3	c.A302G	p.K101R	CCTCCTTTCAAAC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4513549	4513549	+	Silent	SNP	G	G	A	rs146566557	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	47.0	80.0	0.0	0.52809	0	G|0.998;A|0.002	0.002	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C381T	p.S127S	GACCCCGCTGGAC	.	PASS	Atlas-SNP
METTL25	84190	hgsc.bcm.edu	37	12	82792792	82792792	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31.0	11.0	48.0	0.0	0.354839	0	.	.	none	.	.	.	.	NM_032230	exon4	c.T750G	p.N250K	GCAAAATAAAGTT	.	PASS	Atlas-SNP
THBS1	7057	hgsc.bcm.edu	37	15	39880818	39880818	+	Silent	SNP	C	C	T	rs41338344	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54.0	15.0	80.0	0.0	0.277778	0	C|0.975;T|0.025	0.025	strong	.	THBS1	106	.	NM_003246	exon10	c.C1563T	p.N521N	CAACAACCCCACA	.	PASS	Atlas-SNP
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118231317	118231317	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200.0	86.0	233.0	0.0	0.43	0	.	.	none	.	PNLIPRP3	101	.	NM_001011709	exon10	c.C1098T	p.S366S	TGGAAGCGAAGTC	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	30143499	30143499	+	Silent	SNP	G	G	C	rs4358080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4.0	4.0	0.0	0.0	1	.	G|0.120;C|0.880	0.880	strong	.	ALK	533	.	NM_004304	exon1	c.C27G	p.L9L	CGGCAGGAGCCAC	.	PASS	Atlas-SNP
IL12B	3593	hgsc.bcm.edu	37	5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	rs3213096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63.0	29.0	57.0	0.0	0.460317	0	C|0.994;T|0.006	0.006	strong	.	IL12B	30	.	NM_002187	exon3	c.G97A	p.V33I	ATTCTACGACATA	.	PASS	Atlas-SNP
ZNF16	7564	hgsc.bcm.edu	37	8	146157265	146157265	+	Missense_Mutation	SNP	C	C	T	rs80044147	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159.0	48.0	137.0	0.0	0.301887	0	C|0.998;T|0.002	0.002	strong	.	ZNF16	80	.	NM_006958	exon3	c.G908A	p.S303N	TTCTGGCTGAAGG	.	PASS	Atlas-SNP
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	135.0	13.0	156.0	0.0	0.0962963	0	.	.	none	KRTAP1-1,NS,malignant_melanoma,0,1	KRTAP1-1	23	1	NM_030967	exon1	c.A346G	p.I116V	ACCTGATACGGGT	.	PASS	Atlas-SNP
ZNF345	25850	hgsc.bcm.edu	37	19	37369032	37369032	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101.0	56.0	97.0	0.0	0.554455	0	.	.	none	.	ZNF345	68	.	NM_001242476	exon4	c.G1300C	p.A434P	GGGAAGGCTTTTT	.	PASS	Atlas-SNP
PTCH2	8643	hgsc.bcm.edu	37	1	45294295	45294295	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67.0	4.0	102.0	0.0	0.0597015	0	.	.	none	.	PTCH2	96	.	NM_001166292	exon12	c.G1473A	p.M491I	CTCGCCCATGCGC	.	PASS	Atlas-SNP
BCOR	54880	hgsc.bcm.edu	37	X	39932808	39932808	+	Silent	SNP	G	G	A	rs144606152	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38.0	36.0	90.0	0.0	0.947368	0	G|0.963;A|0.037	0.037	strong	.	BCOR	351	.	NM_001123385	exon4	c.C1791T	p.H597H	GCCCACGTGCTGA	.	PASS	Atlas-SNP
ARAP2	116984	hgsc.bcm.edu	37	4	36230634	36230634	+	Missense_Mutation	SNP	G	G	A	rs141442791	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94.0	43.0	82.0	0.0	0.457447	0	G|0.998;A|0.002	0.002	strong	.	ARAP2	210	.	NM_015230	exon2	c.C475T	p.P159S	GGTGTGGTTCCTC	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55541738	55541738	+	Missense_Mutation	SNP	A	A	C	rs147009600	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100.0	15.0	184.0	0.0	0.15	0	A|0.999;C|0.001	0.001	strong	.	RP1	429	.	NM_006269	exon4	c.A5296C	p.N1766H	TGTGGCAATGCAG	.	PASS	Atlas-SNP
PPHLN1	51535	hgsc.bcm.edu	37	12	42839923	42839923	+	Missense_Mutation	SNP	G	G	A	rs201876048	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93.0	47.0	92.0	0.0	0.505376	0	.	.	weak	.	PPHLN1	101	.	NM_016488	exon12	c.G1181A	p.R394H	GGGTTCGTCGGAC	.	PASS	Atlas-SNP
GDPD5	81544	hgsc.bcm.edu	37	11	75150971	75150971	+	Silent	SNP	G	G	A	rs115438239	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117.0	62.0	115.0	0.0	0.529915	0	G|0.997;A|0.003	0.003	strong	.	GDPD5	49	.	NM_030792	exon15	c.C1509T	p.A503A	CAGGTCGGCAGTG	.	PASS	Atlas-SNP
AQPEP	0	hgsc.bcm.edu	37	5	115351066	115351066	+	Silent	SNP	T	T	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	35.0	3.0	31.0	0.0	0.0857143	0	.	.	none	FLJ90650,caecum,carcinoma,0,1	.	.	1	NM_173800	exon17	c.T2568A	p.I856I	AAAGATTCAACTT	.	scavenged	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165664562	165664562	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99.0	23.0	100.0	0.0	0.232323	0	.	.	none	.	ALDH9A1	75	.	NM_000696	exon2	c.C254T	p.A85V	TTAAAAGCAGCCT	.	PASS	Atlas-SNP
PTPRO	5800	hgsc.bcm.edu	37	12	15661564	15661564	+	Missense_Mutation	SNP	G	G	A	rs71459181	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198.0	109.0	198.0	0.0	0.550505	0	G|0.991;A|0.009	0.009	strong	.	PTPRO	148	.	NM_002848	exon7	c.G1327A	p.V443I	GTCCACGTTTTAA	.	PASS	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879435	39879435	+	Silent	SNP	C	C	A	rs112569629	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74.0	44.0	200.0	0.0	0.594595	0	C|0.995;A|0.005	0.005	weak	.	KIAA0754	93	.	NM_015038	exon1	c.C3498A	p.P1166P	CACCCCCGAGGAA	.	PASS	Atlas-SNP
PBK	55872	hgsc.bcm.edu	37	8	27685663	27685663	+	Silent	SNP	C	C	T	rs55973425	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	41.0	69.0	0.0	0.42268	0	C|0.998;T|0.002	0.002	strong	.	PBK	29	.	NM_018492	exon3	c.G111A	p.K37K	GCCAAGCTTCTGC	.	PASS	Atlas-SNP
ATP9A	10079	hgsc.bcm.edu	37	20	50346491	50346491	+	Missense_Mutation	SNP	C	C	A	rs142435125	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	57.0	27.0	46.0	0.0	0.473684	0	C|0.997;A|0.003	0.003	strong	.	ATP9A	135	.	NM_006045	exon2	c.G95T	p.G32V	CCTCCACCGCAGC	.	PASS	Atlas-SNP
COX5B	1329	hgsc.bcm.edu	37	2	98264478	98264478	+	Silent	SNP	C	C	T	rs142899936		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151.0	58.0	182.0	0.0	0.384106	0	C|1.000;T|0.000	0.000	weak	.	COX5B	9	.	NM_001862	exon4	c.C297T	p.S99S	TACCAGCGTCGTC	.	PASS	Atlas-SNP
CBX5	23468	hgsc.bcm.edu	37	12	54639963	54639963	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159.0	73.0	191.0	0.0	0.459119	0	.	.	none	.	CBX5	24	.	NM_012117	exon4	c.C361T	p.L121L	GTTCCAGTCCTCT	.	PASS	Atlas-SNP
ZNF679	168417	hgsc.bcm.edu	37	7	63727212	63727212	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	43.0	33.0	46.0	0.0	0.767442	0	.	.	none	.	ZNF679	80	.	NM_153363	exon5	c.A1201T	p.M401L	AAGAGTATGCATA	.	PASS	Atlas-SNP
PION	54103	hgsc.bcm.edu	37	7	76984961	76984961	+	Missense_Mutation	SNP	T	T	C	rs375426636		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163.0	106.0	112.0	0.0	0.650307	0	.	.	weak	.	PION	74	.	NM_017439	exon15	c.A1031G	p.Y344C	ACATAATAGTCTA	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130282383	130282383	+	Missense_Mutation	SNP	C	C	A	rs114511272	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	207.0	91.0	232.0	1.0	0.439614	0.00431034	C|0.992;A|0.008	0.008	strong	COL6A6_ENST00000358511,colon,carcinoma,-1,3	COL6A6	497	3	NM_001102608	exon2	c.C536A	p.T179K	TGGCCACGTCTCA	.	PASS	Atlas-SNP
CCDC169	728591	hgsc.bcm.edu	37	13	36871782	36871782	+	Silent	SNP	G	G	T	rs201215750	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60.0	26.0	61.0	0.0	0.433333	0	G|0.993;T|0.007	0.007	strong	.	CCDC169	20	.	NM_001144981	exon1	c.C75A	p.V25V	CTTGCGGACTTCT	.	PASS	Atlas-SNP
GCN1L1	10985	hgsc.bcm.edu	37	12	120602208	120602208	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94.0	4.0	107.0	0.0	0.0425532	0	.	.	none	.	GCN1L1	207	.	NM_006836	exon18	c.T1780C	p.S594P	CAAGAGAGGACAG	.	PASS	Atlas-SNP
ZNF668	79759	hgsc.bcm.edu	37	16	31072912	31072912	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20.0	9.0	20.0	0.0	0.45	0	.	.	none	.	ZNF668	121	.	NM_001172669	exon4	c.C1406T	p.P469L	GCTGCCGGGGCGG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11017141	11017141	+	Silent	SNP	G	G	A	rs75810903	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	52.0	29.0	40.0	0.0	0.557692	0	G|0.996;A|0.004	0.004	strong	.	C1orf127	134	.	NM_001170754	exon8	c.C717T	p.L239L	TGGCAGGAGCTCA	.	PASS	Atlas-SNP
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797919	31797919	+	Silent	SNP	G	G	A	rs73356706	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171.0	61.0	108.0	0.0	0.356725	0	G|0.975;A|0.025	0.025	strong	.	KRTAP13-3	47	.	NM_181622	exon1	c.C312T	p.S104S	GCTATTGGATCCA	.	PASS	Atlas-SNP
RTEL1	51750	hgsc.bcm.edu	37	20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	rs190887884	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	34.0	13.0	53.0	0.0	0.382353	0	G|0.994;A|0.006	0.006	strong	.	RTEL1	114	.	NM_032957	exon27	c.G2618A	p.G873D	GCCCTGGCGAGGA	.	PASS	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879410	39879410	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58.0	9.0	206.0	0.0	0.155172	0	.	.	none	KIAA0754_ENST00000530275,NS,carcinoma,-1,2	KIAA0754	93	2	NM_015038	exon1	c.C3473T	p.S1158F	CCGCCTCCGCAGC	.	scavenged	Atlas-SNP
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774076	140774076	+	Missense_Mutation	SNP	G	G	T	rs367855808		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182.0	83.0	172.0	0.0	0.456044	0	.	.	weak	.	PCDHGA8	146	.	NM_014004	exon1	c.G1696T	p.A566S	TACCCCGCCCTCC	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133899008	133899008	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	170.0	72.0	76.0	0.0	0.423529	0	.	.	none	.	TG	416	.	NM_003235	exon9	c.C1391A	p.P464Q	CCAACCCAAAGAG	.	PASS	Atlas-SNP
MYBPC3	4607	hgsc.bcm.edu	37	11	47365164	47365164	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	4.0	89.0	0.0	0.0412371	0	.	.	none	.	MYBPC3	102	.	NM_000256	exon13	c.A1102G	p.K368E	CCAGCTTCTTCTG	.	PASS	Atlas-SNP
GANAB	23193	hgsc.bcm.edu	37	11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	rs76572368	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	228.0	92.0	205.0	0.0	0.403509	0	T|0.974;C|0.026	0.026	strong	.	GANAB	110	.	NM_198335	exon16	c.A1846G	p.M616V	GTTCCATGCCCCC	.	PASS	Atlas-SNP
SYTL5	94122	hgsc.bcm.edu	37	X	37935844	37935844	+	Silent	SNP	G	G	A	rs12558731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41.0	40.0	146.0	0.0	0.97561	0	G|0.993;A|0.007	0.007	strong	.	SYTL5	72	.	NM_001163334	exon5	c.G579A	p.S193S	CAGATCGGCAACC	.	PASS	Atlas-SNP
TXNDC16	57544	hgsc.bcm.edu	37	14	52981664	52981664	+	Missense_Mutation	SNP	G	G	C	rs117463339	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100.0	37.0	67.0	0.0	0.37	0	G|0.979;C|0.021	0.021	strong	.	TXNDC16	59	.	NM_020784	exon8	c.C539G	p.A180G	ACAAAAGCGGCTT	.	PASS	Atlas-SNP
DISC1	27185	hgsc.bcm.edu	37	1	231902975	231902975	+	Missense_Mutation	SNP	C	C	T	rs28930675	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124.0	32.0	108.0	0.0	0.258065	0	C|0.998;T|0.002	0.002	strong	.	DISC1	207	.	NM_001164537	exon6	c.C1454T	p.T485M	CCATCACGAGACG	.	PASS	Atlas-SNP
AVPR1B	553	hgsc.bcm.edu	37	1	206225260	206225260	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190.0	39.0	144.0	0.0	0.205263	0	.	.	none	.	AVPR1B	47	.	NM_000707	exon1	c.C820G	p.R274G	ATCTCACGGGCCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681920	100681920	+	Missense_Mutation	SNP	C	C	T	rs140211048	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	314.0	16.0	210.0	0.0	0.0509554	0	C|1.000;T|0.000	0.000	strong	MUC17,NS,carcinoma,-1,1	MUC17	804	1	NM_001040105	exon3	c.C7223T	p.P2408L	CCATGCCGGTGGT	.	PASS	Atlas-SNP
C20orf85	128602	hgsc.bcm.edu	37	20	56735761	56735761	+	Silent	SNP	C	C	T	rs61749694	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	80.0	36.0	90.0	0.0	0.45	0	C|0.997;T|0.003	0.003	strong	.	C20orf85	35	.	NM_178456	exon4	c.C297T	p.I99I	CTTCATCGGCTGG	.	PASS	Atlas-SNP
C1orf35	79169	hgsc.bcm.edu	37	1	228290223	228290223	+	Silent	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175.0	66.0	148.0	0.0	0.377143	0	.	.	none	.	C1orf35	17	.	NM_024319	exon4	c.C330G	p.P110P	CTCCTCGGGGTCG	.	PASS	Atlas-SNP
ZNF556	80032	hgsc.bcm.edu	37	19	2877426	2877426	+	Missense_Mutation	SNP	C	C	T	rs34849844	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	36.0	94.0	0.0	0.553846	0	C|0.987;T|0.013	0.013	strong	.	ZNF556	73	.	NM_024967	exon4	c.C470T	p.T157I	TCTTCACCCATTC	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230408	23230408	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145.0	38.0	164.0	0.0	0.262069	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.A175C	p.S59R	GGAAGCAGCCGAT	.	PASS	Atlas-SNP
ABR	29	hgsc.bcm.edu	37	17	970419	970419	+	Silent	SNP	G	G	A	rs199545490	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	40.0	66.0	1.0	0.547945	0.0151515	G|0.999;A|0.001	0.001	weak	ABR,colon,carcinoma,0,1	ABR	119	1	NM_021962	exon10	c.C1080T	p.P360P	CTCCTCGGGGGAT	.	scavenged	Atlas-SNP
KIAA0754	643314	hgsc.bcm.edu	37	1	39879405	39879405	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55.0	20.0	206.0	0.0	0.363636	0	.	.	none	.	KIAA0754	93	.	NM_015038	exon1	c.C3468T	p.S1156S	GGAATCCGCCTCC	.	PASS	Atlas-SNP
MGAT4A	11320	hgsc.bcm.edu	37	2	99271976	99271976	+	Missense_Mutation	SNP	T	T	C	rs61748145	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98.0	48.0	99.0	0.0	0.489796	0	T|0.993;C|0.007	0.007	strong	.	MGAT4A	51	.	NM_012214	exon8	c.A706G	p.T236A	GCTTTGTTCTCCA	.	PASS	Atlas-SNP
HOXA7	3204	hgsc.bcm.edu	37	7	27196116	27196116	+	Missense_Mutation	SNP	C	C	T	rs78410337	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164.0	47.0	116.0	0.0	0.286585	0	C|0.993;T|0.007	0.007	strong	.	HOXA7	34	.	NM_006896	exon1	c.G49A	p.G17R	AAGCCCCCGCCGT	.	PASS	Atlas-SNP
PARK2	5071	hgsc.bcm.edu	37	6	162864492	162864492	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129.0	35.0	118.0	0.0	0.271318	0	.	.	none	.	PARK2	96	.	NM_004562	exon2	c.C21G	p.F7L	GGAGTTGAACCTG	.	PASS	Atlas-SNP
TCF3	6929	hgsc.bcm.edu	37	19	1615393	1615393	+	Silent	SNP	C	C	T	rs143212973	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74.0	37.0	99.0	0.0	0.5	0	C|0.997;T|0.003	0.003	strong	.	TCF3	72	.	NM_003200	exon18	c.G1713A	p.E571E	CCCCAGCTCCTTA	.	PASS	Atlas-SNP
ANXA7	310	hgsc.bcm.edu	37	10	75139952	75139952	+	Missense_Mutation	SNP	C	C	T	rs10159690	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62.0	3.0	89.0	0.0	0.0483871	0	C|0.994;T|0.006	0.006	strong	ANXA7,colon,carcinoma,-1,1	ANXA7	50	1	NM_004034	exon11	c.G992A	p.R331H	TCATCACGATTTC	.	scavenged	Atlas-SNP
PBLD	64081	hgsc.bcm.edu	37	10	70066553	70066553	+	Missense_Mutation	SNP	G	G	A	rs12359690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117.0	117.0	264.0	0.0	1	0	G|0.961;A|0.039	0.039	strong	.	PBLD	53	.	NM_022129	exon2	c.C49T	p.R17C	TCCCACGAAATGC	.	PASS	Atlas-SNP
ACE	1636	hgsc.bcm.edu	37	17	61573777	61573777	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	248.0	124.0	245.0	1.0	0.5	0.00408163	.	.	none	.	ACE	187	.	NM_000789	exon23	c.C3403A	p.Q1135K	ATCATCCAGTTCC	.	PASS	Atlas-SNP
SLC6A15	55117	hgsc.bcm.edu	37	12	85257230	85257230	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	241.0	76.0	247.0	0.0	0.315353	0	.	.	none	.	SLC6A15	159	.	NM_182767	exon11	c.G1806T	p.W602C	TTCAATCCATGCG	.	PASS	Atlas-SNP
ACOT4	122970	hgsc.bcm.edu	37	14	74060476	74060476	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181.0	85.0	98.0	0.0	0.469613	0	.	.	none	.	ACOT4	25	.	NM_152331	exon2	c.C528A	p.S176R	AGCCAGCCTCCTT	.	PASS	Atlas-SNP
EXOC4	60412	hgsc.bcm.edu	37	7	133689801	133689801	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61.0	9.0	122.0	0.0	0.147541	0	.	.	none	EXOC4_ENST00000545148,NS,carcinoma,0,2	EXOC4	118	2	NM_021807	exon16	c.A2485G	p.S829G	GCCATGAGCGCCA	.	PASS	Atlas-SNP
FNDC1	84624	hgsc.bcm.edu	37	6	159667972	159667972	+	Missense_Mutation	SNP	C	C	T	rs61746218	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104.0	42.0	136.0	0.0	0.403846	0	C|0.995;T|0.005	0.005	strong	.	FNDC1	250	.	NM_032532	exon15	c.C4661T	p.T1554M	TACCTACGGAAGA	.	PASS	Atlas-SNP
PCDHGB4	8641	hgsc.bcm.edu	37	5	140768442	140768442	+	Missense_Mutation	SNP	G	G	T	rs201053346	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	33.0	64.0	0.0	0.428571	0	.	.	weak	.	PCDHGB4	125	.	NM_032098	exon1	c.G991T	p.V331L	TGCACAGTGGAGG	.	PASS	Atlas-SNP
OXNAD1	92106	hgsc.bcm.edu	37	3	16336381	16336381	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214.0	94.0	216.0	0.0	0.439252	0	.	.	none	.	OXNAD1	31	.	NM_138381	exon6	c.A309G	p.P103P	TATTCCAGGAGTC	.	PASS	Atlas-SNP
SZT2	23334	hgsc.bcm.edu	37	1	43870071	43870071	+	Silent	SNP	C	C	A	rs41312024	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83.0	68.0	147.0	0.0	0.819277	0	C|0.990;A|0.010	0.010	strong	.	SZT2	383	.	NM_015284	exon4	c.C348A	p.I116I	GGAGATCTTGTTT	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144991925	144991925	+	Missense_Mutation	SNP	G	G	A	rs189061273	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	63.0	96.0	0.0	0.617647	0	G|0.995;A|0.005	0.005	strong	PLEC_ENST00000436759,bladder,carcinoma,+2,3	PLEC	1144	3	NM_201380	exon32	c.C12475T	p.L4159F	AGATGAGCTTCCC	.	PASS	Atlas-SNP
CCDC11	220136	hgsc.bcm.edu	37	18	47788544	47788544	+	Silent	SNP	T	T	G	rs112087763	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121.0	53.0	100.0	0.0	0.438017	0	T|0.997;G|0.003	0.003	strong	.	CCDC11	59	.	NM_145020	exon2	c.A115C	p.R39R	GGATTCTTTCTAG	.	PASS	Atlas-SNP
KLHL7	55975	hgsc.bcm.edu	37	7	23212627	23212627	+	Silent	SNP	A	A	G	rs118185564	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	437.0	278.0	297.0	0.0	0.636156	0	A|0.994;G|0.006	0.006	strong	.	KLHL7	102	.	NM_001031710	exon10	c.A1440G	p.K480K	TGTAAAAGACAAG	.	PASS	Atlas-SNP
GPR133	283383	hgsc.bcm.edu	37	12	131620650	131620650	+	Missense_Mutation	SNP	C	C	T	rs61746588	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	197.0	82.0	238.0	0.0	0.416244	0	C|0.997;T|0.003	0.003	strong	.	GPR133	136	.	NM_198827	exon22	c.C2336T	p.A779V	TGCTTGCTGTCAA	.	PASS	Atlas-SNP
ZNF676	163223	hgsc.bcm.edu	37	19	22364230	22364230	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	282.0	100.0	292.0	1.0	0.35461	0.00342466	.	.	none	ZNF676,NS,carcinoma,+1,2	ZNF676	146	2	NM_001001411	exon3	c.G289T	p.G97C	TATAACCTTCTTT	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77038912	77038912	+	Missense_Mutation	SNP	A	A	T	rs144785979	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	256.0	115.0	251.0	0.0	0.449219	0	A|0.999;T|0.001	0.001	strong	.	NUP54	48	.	NM_017426	exon11	c.T1300A	p.L434M	ACATCAATTCATT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105413220	105413220	+	Silent	SNP	A	A	C	rs151173659	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249.0	167.0	205.0	1.0	0.670683	0.00487805	A|0.994;C|0.006	0.006	strong	.	AHNAK2	719	.	NM_138420	exon7	c.T8568G	p.L2856L	GGTCTTAAGATCC	.	PASS	Atlas-SNP
UBTFL1	642623	hgsc.bcm.edu	37	11	89819431	89819431	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	411.0	270.0	321.0	1.0	0.656934	0.00311526	.	.	none	.	.	.	.	NM_001143975	exon1	c.C314T	p.T105I	CCCTTACTGCTTA	.	PASS	Atlas-SNP
NAP1L3	4675	hgsc.bcm.edu	37	X	92927728	92927728	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78.0	5.0	159.0	0.0	0.0641026	0	.	.	none	.	NAP1L3	81	.	NM_004538	exon1	c.A576G	p.E192E	TTCTTCTTCCTCA	.	PASS	Atlas-SNP
BOD1L1	259282	hgsc.bcm.edu	37	4	13602793	13602793	+	Missense_Mutation	SNP	C	C	G	rs199927242	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147.0	68.0	160.0	0.0	0.462585	0	.	.	weak	.	.	.	.	NM_148894	exon10	c.G5731C	p.V1911L	CTACCACAGTACC	.	PASS	Atlas-SNP
NBPF14	25832	hgsc.bcm.edu	37	1	148004783	148004783	+	Missense_Mutation	SNP	C	C	A	rs147480284	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	412.0	393.0	529.0	2.0	0.953883	0.00378072	C|0.960;A|0.040	0.040	strong	NBPF14,NS,adenoma,0,2	NBPF14	107	2	NM_015383	exon22	c.G2531T	p.S844I	AGCATGCTGTTGA	.	scavenged	Atlas-SNP
VNN2	8875	hgsc.bcm.edu	37	6	133073844	133073844	+	Silent	SNP	C	C	T	rs33980664	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95.0	45.0	84.0	0.0	0.473684	0	C|0.976;T|0.024	0.024	strong	.	VNN2	83	.	NM_004665	exon4	c.G582A	p.P194P	CAACTCCGGCTTT	.	PASS	Atlas-SNP
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159.0	103.0	98.0	0.0	0.647799	0	A|0.817;G|0.183	0.183	strong	.	MET	412	.	NM_000245	exon7	c.A1944G	p.Q648Q	AACACAATACAGT	.	PASS	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	37	5	140262582	140262582	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141.0	49.0	133.0	0.0	0.347518	0	.	.	none	.	PCDHA13	213	.	NM_031865	exon1	c.C729G	p.Y243X	ATTTTACCAATCC	.	PASS	Atlas-SNP
ST20	400410	hgsc.bcm.edu	37	15	80191280	80191280	+	Missense_Mutation	SNP	T	T	A	rs184575290	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129.0	87.0	285.0	1.0	0.674419	0.00350877	T|0.998;A|0.002	0.002	strong	ST20,NS,carcinoma,+1,1	ST20	9	1	NM_001199757	exon3	c.A233T	p.Y78F	TAAAAGTAGAAGT	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789317	117789317	+	Silent	SNP	T	T	C	rs201369736		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268.0	13.0	118.0	0.0	0.0485075	0	.	.	weak	TMPRSS13,caecum,carcinoma,0,1	TMPRSS13	75	1	NM_001206790	exon2	c.A258G	p.P86P	CCGGGCTGGAGAT	.	PASS	Atlas-SNP
PRF1	5551	hgsc.bcm.edu	37	10	72360224	72360224	+	Silent	SNP	C	C	T	rs115281140	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119.0	87.0	226.0	2.0	0.731092	0.00884956	C|0.990;T|0.010	0.010	strong	PRF1,NS,carcinoma,-2,1	PRF1	64	1	NM_001083116	exon2	c.G435A	p.V145V	CACAGACACATGC	.	scavenged	Atlas-SNP
TRAF3	7187	hgsc.bcm.edu	37	14	103336727	103336727	+	Silent	SNP	G	G	A	rs142350527	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	93.0	37.0	82.0	0.0	0.397849	0	G|0.996;A|0.004	0.004	strong	.	TRAF3	60	.	NM_145726	exon3	c.G189A	p.P63P	CAGCCCGAAGCAG	.	PASS	Atlas-SNP
DNA2	1763	hgsc.bcm.edu	37	10	70178965	70178965	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	38.0	19.0	49.0	0.0	0.5	0	.	.	none	.	DNA2	76	.	NM_001080449	exon19	c.A2793G	p.G931G	ACTGCATCCAGCC	.	PASS	Atlas-SNP
PRPF4B	8899	hgsc.bcm.edu	37	6	4044109	4044109	+	Silent	SNP	G	G	A	rs12195092	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119.0	56.0	163.0	0.0	0.470588	0	G|0.982;A|0.018	0.018	strong	.	PRPF4B	140	.	NM_003913	exon6	c.G1713A	p.Q571Q	CCCCCAGAGCAGT	.	PASS	Atlas-SNP
TAT	6898	hgsc.bcm.edu	37	16	71602660	71602660	+	Missense_Mutation	SNP	G	G	A	rs142634310	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156.0	32.0	148.0	0.0	0.205128	0	G|0.999;A|0.001	0.001	strong	.	TAT	80	.	NM_000353	exon11	c.C1178T	p.T393M	CGCTCCGTGAACT	.	PASS	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139.0	62.0	211.0	0.0	0.446043	0	G|0.957;A|0.043	0.043	strong	.	PCDHA10	358	.	NM_031859	exon1	c.G1525A	p.V509M	GTGTCGGTGCACG	.	PASS	Atlas-SNP
GAD2	2572	hgsc.bcm.edu	37	10	26575277	26575277	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56.0	15.0	84.0	0.0	0.267857	0	.	.	none	.	GAD2	116	.	NM_000818	exon13	c.T1240C	p.L414L	TAGGGATTGATGC	.	PASS	Atlas-SNP
ZNF300	91975	hgsc.bcm.edu	37	5	150275835	150275835	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	26.0	126.0	0.0	0.254902	0	.	.	none	.	ZNF300	69	.	NM_001172831	exon7	c.G1014T	p.E338D	AGGTTTCTCCCCA	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28459393	28459393	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53.0	45.0	82.0	0.0	0.849057	0	.	.	none	.	HERC2	501	.	NM_004667	exon41	c.G6384A	p.V2128V	CGGGCGCACCCTG	.	PASS	Atlas-SNP
SPNS2	124976	hgsc.bcm.edu	37	17	4434031	4434031	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205.0	103.0	201.0	0.0	0.502439	0	.	.	none	SPNS2,colon,carcinoma,+1,1	SPNS2	24	1	NM_001124758	exon4	c.G678A	p.T226T	GAACACGCGTACG	.	PASS	Atlas-SNP
CCDC108	255101	hgsc.bcm.edu	37	2	219890814	219890814	+	Missense_Mutation	SNP	C	C	T	rs114017706	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	164.0	47.0	230.0	0.0	0.286585	0	C|0.989;T|0.011	0.011	strong	CCDC108,right_upper_lobe,carcinoma,+1,1	CCDC108	208	1	NM_194302	exon14	c.G2279A	p.R760Q	CGTGCCCGCACCG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124351974	124351974	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78.0	26.0	90.0	0.0	0.333333	0	.	.	none	.	DMBT1	677	.	NM_007329	exon20	c.T2363G	p.F788C	CCCGGTTTGGCCA	.	PASS	Atlas-SNP
PKM	5315	hgsc.bcm.edu	37	15	72501072	72501072	+	Silent	SNP	C	C	T	rs11558376	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85.0	64.0	140.0	1.0	0.752941	0.00714286	C|0.999;T|0.001	0.001	strong	PKM2,NS,neuroblastoma,-1,2	PKM	25	2	NM_001206796	exon7	c.G948A	p.A316A	GAATGACGCAAAC	.	PASS	Atlas-SNP
KIAA1324	57535	hgsc.bcm.edu	37	1	109714593	109714593	+	Silent	SNP	C	C	T	rs112023388	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	160.0	122.0	267.0	0.0	0.7625	0	C|0.999;T|0.001	0.001	strong	.	KIAA1324	77	.	NM_020775	exon4	c.C573T	p.F191F	TAACTTCGAATAC	.	PASS	Atlas-SNP
SLC35F1	222553	hgsc.bcm.edu	37	6	118588185	118588185	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	379.0	117.0	366.0	2.0	0.308707	0.00546448	.	.	none	SLC35F1,bladder,carcinoma,-2,2	SLC35F1	65	2	NM_001029858	exon4	c.G505A	p.V169M	CCAGTCGTGATTT	.	scavenged	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	37	17	80059690	80059690	+	Silent	SNP	G	G	A	rs61735692	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101.0	49.0	121.0	0.0	0.485149	0	G|0.975;A|0.025	0.025	strong	.	CCDC57	102	.	NM_198082	exon17	c.C2616T	p.G872G	GGCAATGCCTGCC	.	PASS	Atlas-SNP
XRCC3	7517	hgsc.bcm.edu	37	14	104174950	104174950	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144.0	46.0	83.0	0.0	0.319444	0	.	.	none	.	XRCC3	16	.	NM_005432	exon5	c.C102A	p.D34E	CTTCAAGTCTGGT	.	PASS	Atlas-SNP
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017397	26017397	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251.0	125.0	292.0	1.0	0.498008	0.00342466	.	.	none	.	HIST1H1A	25	.	NM_005325	exon1	c.G564C	p.K188N	TACAGCCTTAGCT	.	PASS	Atlas-SNP
CDK12	51755	hgsc.bcm.edu	37	17	37627387	37627387	+	Silent	SNP	A	A	G	rs56158954	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59.0	33.0	68.0	0.0	0.559322	0	A|0.987;G|0.013	0.013	strong	CDK12,NS,carcinoma,0,1	CDK12	161	1	NM_016507	exon2	c.A1302G	p.S434S	CAGTTCAGTAGAG	.	PASS	Atlas-SNP
CRYBB3	1417	hgsc.bcm.edu	37	22	25603052	25603052	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127.0	51.0	150.0	0.0	0.401575	0	.	.	none	.	CRYBB3	13	.	NM_004076	exon6	c.T509G	p.V170G	GGCGCCAGTACGT	.	PASS	Atlas-SNP
CCDC129	223075	hgsc.bcm.edu	37	7	31682829	31682829	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91.0	26.0	68.0	0.0	0.285714	0	.	.	none	.	CCDC129	127	.	NM_001257968	exon11	c.G1923C	p.E641D	CTCTGAGGCCCCA	.	PASS	Atlas-SNP
HS6ST1	9394	hgsc.bcm.edu	37	2	129025800	129025800	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96.0	5.0	140.0	0.0	0.0520833	0	.	.	none	.	HS6ST1	31	.	NM_004807	exon2	c.A1172G	p.D391G	TCGGCATCCTCCC	.	PASS	Atlas-SNP
NPAT	4863	hgsc.bcm.edu	37	11	108044204	108044204	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	386.0	99.0	207.0	0.0	0.256477	0	.	.	none	.	NPAT	124	.	NM_002519	exon13	c.G1507C	p.D503H	GCTGATCAGGCTG	.	PASS	Atlas-SNP
ADCK1	57143	hgsc.bcm.edu	37	14	78399654	78399654	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268.0	122.0	217.0	0.0	0.455224	0	.	.	none	.	ADCK1	81	.	NM_020421	exon11	c.C1492T	p.L498F	CATGAGCTCATCC	.	PASS	Atlas-SNP
NPAS3	64067	hgsc.bcm.edu	37	14	34247747	34247747	+	Silent	SNP	C	C	T	rs147070037	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166.0	108.0	133.0	0.0	0.650602	0	C|0.999;T|0.001	0.001	strong	.	NPAS3	266	.	NM_001164749	exon9	c.C1122T	p.D374D	TGAAGACGTGGAG	.	PASS	Atlas-SNP
GPR108	56927	hgsc.bcm.edu	37	19	6733582	6733582	+	Missense_Mutation	SNP	G	G	A	rs201134279	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129.0	129.0	159.0	1.0	1	0.00628931	G|0.995;A|0.005	0.005	strong	.	GPR108	35	.	NM_001080452	exon8	c.C722T	p.T241M	CTCACCGTGATGT	.	PASS	Atlas-SNP
NFKBIB	4793	hgsc.bcm.edu	37	19	39399416	39399416	+	Missense_Mutation	SNP	C	C	T	rs17886215	bycluster;byfrequency;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127.0	58.0	109.0	0.0	0.456693	0	C|0.998;T|0.002	0.002	strong	.	NFKBIB	23	.	NM_002503	exon6	c.C1015T	p.R339W	CAAACCCGGCTGC	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33014876	33014876	+	Silent	SNP	C	C	T	rs375820695		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123.0	51.0	89.0	0.0	0.414634	0	.	.	weak	.	AKAP6	308	.	NM_004274	exon4	c.C1017T	p.P339P	TCAACCCTCCTCT	.	PASS	Atlas-SNP
CACNA1B	774	hgsc.bcm.edu	37	9	140773613	140773613	+	Splice_Site	SNP	T	T	A	rs201604190		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	68.0	10.0	59.0	2.0	0.147059	0.0338983	.	.	weak	CACNA1B,colon,carcinoma,0,8	CACNA1B	266	8	NM_001243812	exon2	c.390+2T>A	.	GGCTGGTGAGTGC	.	scavenged	Atlas-SNP
COG3	83548	hgsc.bcm.edu	37	13	46104849	46104849	+	Silent	SNP	C	C	T	rs62637564	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122.0	61.0	106.0	0.0	0.5	0	C|0.964;T|0.036	0.036	strong	.	COG3	52	.	NM_031431	exon22	c.C2391T	p.H797H	GTTCCACGCTCTG	.	PASS	Atlas-SNP
HDAC9	9734	hgsc.bcm.edu	37	7	18687542	18687542	+	Silent	SNP	A	A	T	rs35614472	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88.0	34.0	90.0	0.0	0.386364	0	A|0.992;T|0.008	0.008	strong	.	HDAC9	560	.	NM_178425	exon9	c.A1170T	p.P390P	AAAGCCACCCAAC	.	PASS	Atlas-SNP
ALKBH8	91801	hgsc.bcm.edu	37	11	107375703	107375703	+	Missense_Mutation	SNP	C	C	T	rs139390837	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133.0	36.0	91.0	0.0	0.270677	0	C|0.998;T|0.002	0.002	strong	.	ALKBH8	88	.	NM_138775	exon12	c.G1676A	p.R559H	TTAATGCGGGGGA	.	PASS	Atlas-SNP
CPT2	1376	hgsc.bcm.edu	37	1	53668099	53668099	+	Missense_Mutation	SNP	C	C	T	rs74315294	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123.0	78.0	162.0	0.0	0.634146	0	C|0.999;T|0.001	0.001	strong	CPT2,right_upper_lobe,carcinoma,0,1	CPT2	34	1	NM_000098	exon3	c.C338T	p.S113L	ACATTTCGGGTAG	.	PASS	Atlas-SNP
RFWD3	55159	hgsc.bcm.edu	37	16	74664698	74664698	+	Silent	SNP	A	A	G	rs78796563	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87.0	16.0	91.0	0.0	0.183908	0	A|0.981;G|0.019	0.019	strong	RFWD3,NS,carcinoma,0,1	RFWD3	49	1	NM_018124	exon10	c.T1735C	p.L579L	CTACTAACTCCTG	.	PASS	Atlas-SNP
SCRIB	23513	hgsc.bcm.edu	37	8	144885669	144885669	+	Missense_Mutation	SNP	G	G	C	rs138257744	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	15.0	9.0	21.0	0.0	0.6	0	G|0.999;C|0.001	0.001	strong	.	SCRIB	192	.	NM_015356	exon24	c.C3487G	p.Q1163E	GGCTCTGCTGGTT	.	PASS	Atlas-SNP
FPR3	2359	hgsc.bcm.edu	37	19	52327479	52327479	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243.0	97.0	258.0	0.0	0.399177	0	.	.	none	.	FPR3	66	.	NM_002030	exon2	c.A478T	p.N160Y	TTACCAAATTTCA	.	PASS	Atlas-SNP
MLKL	197259	hgsc.bcm.edu	37	16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	rs144526386	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122.0	25.0	126.0	0.0	0.204918	0	C|0.986;A|0.014	0.014	strong	.	MLKL	51	.	NM_001142497	exon4	c.G605T	p.G202V	GCTGAGCCAGTCT	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733127	52733127	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	518.0	28.0	400.0	0.0	0.0540541	0	.	.	none	.	PCMTD1	73	.	NM_052937	exon6	c.C858T	p.N286N	GTAAGTGTTAATT	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	37	6	75836079	75836079	+	Missense_Mutation	SNP	A	A	G	rs200450866	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84.0	40.0	100.0	0.0	0.47619	0	.	.	weak	.	COL12A1	385	.	NM_004370	exon39	c.T6448C	p.Y2150H	GCTTATATACTAT	.	PASS	Atlas-SNP
FBXW5	54461	hgsc.bcm.edu	37	9	139836694	139836694	+	Silent	SNP	C	C	T	rs34391108	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7.0	6.0	40.0	0.0	0.857143	0	C|0.975;T|0.025	0.025	strong	.	FBXW5	36	.	NM_018998	exon6	c.G900A	p.E300E	CAAGCCCTCCTTG	.	PASS	Atlas-SNP
SLC1A6	6511	hgsc.bcm.edu	37	19	15083555	15083555	+	Silent	SNP	G	G	A	rs115001292	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110.0	57.0	133.0	0.0	0.518182	0	G|0.993;A|0.007	0.007	strong	.	SLC1A6	111	.	NM_001272087	exon4	c.C168T	p.N56N	GAAGGCGTTTCGG	.	PASS	Atlas-SNP
MLLT6	4302	hgsc.bcm.edu	37	17	36868976	36868976	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123.0	34.0	107.0	0.0	0.276423	0	.	.	none	.	MLLT6	80	.	NM_005937	exon8	c.G753A	p.K251K	GCAGAAGCACAAG	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130.0	31.0	82.0	0.0	0.238462	0	G|0.965;A|0.035	0.035	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.G730A	p.A244T	CAGGCCGCCACGC	.	PASS	Atlas-SNP
GAK	2580	hgsc.bcm.edu	37	4	843536	843536	+	Silent	SNP	G	G	A	rs55904229	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	268.0	132.0	279.0	0.0	0.492537	0	G|0.997;A|0.003	0.003	strong	.	GAK	104	.	NM_005255	exon28	c.C3861T	p.H1287H	CTTGGCGTGCTGC	.	PASS	Atlas-SNP
SDK2	54549	hgsc.bcm.edu	37	17	71344769	71344769	+	Missense_Mutation	SNP	G	G	A	rs199591952	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67.0	34.0	88.0	0.0	0.507463	0	A|0.000;G|1.000	0.000	strong	.	SDK2	219	.	NM_001144952	exon44	c.C6134T	p.T2045M	TTCTCCGTCAGGC	.	PASS	Atlas-SNP
PRPF4	9128	hgsc.bcm.edu	37	9	116045007	116045007	+	Missense_Mutation	SNP	A	A	C	rs148684386	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127.0	61.0	162.0	0.0	0.480315	0	A|0.999;C|0.001	0.001	strong	.	PRPF4	56	.	NM_004697	exon4	c.A477C	p.K159N	GTCCAAAGAAGAG	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125873796	125873796	+	Splice_Site	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	5.0	60.0	0.0	0.0515464	0	.	.	none	.	CDON	137	.	NM_001243597	exon11	c.2026+1G>A	.	CACTCACCTTTGC	.	PASS	Atlas-SNP
ZNF560	147741	hgsc.bcm.edu	37	19	9579809	9579809	+	Missense_Mutation	SNP	C	C	A	rs61737643	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	194.0	85.0	251.0	0.0	0.438144	0	C|0.997;A|0.003	0.003	strong	.	ZNF560	162	.	NM_152476	exon9	c.G584T	p.C195F	TTTAAACAAAAAT	.	PASS	Atlas-SNP
ALDH4A1	8659	hgsc.bcm.edu	37	1	19212007	19212007	+	Missense_Mutation	SNP	G	G	A	rs139640415	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	44.0	32.0	98.0	0.0	0.727273	0	G|0.999;A|0.001	0.001	strong	ALDH4A1_ENST00000375341,NS,carcinoma,+1,2	ALDH4A1	72	2	NM_003748	exon5	c.C413T	p.P138L	CTGCGCGGCCCAC	.	PASS	Atlas-SNP
DDX54	79039	hgsc.bcm.edu	37	12	113596866	113596866	+	Missense_Mutation	SNP	G	G	A	rs1048889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86.0	36.0	117.0	0.0	0.418605	0	G|0.963;A|0.037	0.037	strong	.	DDX54	73	.	NM_001111322	exon20	c.C2465T	p.P822L	AGTTCCGGGCGGA	.	PASS	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	37	8	17824674	17824674	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134.0	82.0	144.0	0.0	0.61194	0	.	.	none	PCM1,colon,carcinoma,0,1	PCM1	120	1	NM_006197	exon21	c.C3407T	p.A1136V	CATTTGCACCAGG	.	PASS	Atlas-SNP
HSD3B1	3283	hgsc.bcm.edu	37	1	120056849	120056849	+	Silent	SNP	C	C	T	rs141977722	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175.0	65.0	128.0	0.0	0.371429	0	C|0.998;T|0.002	0.002	strong	.	HSD3B1	53	.	NM_000862	exon4	c.C703T	p.L235L	CACATTCTGGCCT	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15519029	15519029	+	Silent	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	272.0	32.0	295.0	0.0	0.117647	0	.	.	none	.	CDRT1	83	.	NM_006382	exon2	c.T600G	p.T200T	GTGCTGAGTTTTG	.	PASS	Atlas-SNP
CLEC16A	23274	hgsc.bcm.edu	37	16	11272330	11272330	+	Missense_Mutation	SNP	G	G	A	rs72650689	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	96.0	44.0	106.0	0.0	0.458333	0	A|0.006;G|0.994	0.006	strong	.	CLEC16A	101	.	NM_015226	exon23	c.G2945A	p.S982N	CCCCCAGCCTCGT	.	PASS	Atlas-SNP
HEATR6	63897	hgsc.bcm.edu	37	17	58153586	58153586	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	24.0	12.0	15.0	0.0	0.5	0	.	.	none	.	HEATR6	98	.	NM_022070	exon2	c.C232G	p.L78V	CAAGAAGAGCACT	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103395769	103395769	+	Silent	SNP	G	G	C	rs117896704	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203.0	103.0	241.0	0.0	0.507389	0	G|0.986;C|0.014	0.014	strong	.	.	.	.	NM_001146197	exon4	c.C7278G	p.T2426T	CAGTTTGGTTTTT	.	PASS	Atlas-SNP
SEMA3C	10512	hgsc.bcm.edu	37	7	80380645	80380645	+	Silent	SNP	G	G	T	rs138526129		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251.0	151.0	210.0	0.0	0.601594	0	G|1.000;T|0.000	0.000	weak	.	SEMA3C	106	.	NM_006379	exon16	c.C1651A	p.R551R	GTCTTCGGCTCCT	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71851969	71851969	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148.0	68.0	155.0	0.0	0.459459	0	.	.	none	.	TJP2	120	.	NM_001170416	exon14	c.T2189C	p.L730P	AGAACCTGAGGAA	.	PASS	Atlas-SNP
CIDEB	27141	hgsc.bcm.edu	37	14	24775287	24775287	+	Silent	SNP	G	G	A	rs139893717	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	83.0	53.0	53.0	0.0	0.638554	0	G|0.995;A|0.005	0.005	strong	.	CIDEB	17	.	NM_014430	exon6	c.C393T	p.I131I	TCGGGCGATGTCC	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33635910	33635910	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18.0	11.0	17.0	0.0	0.611111	0	.	.	none	.	KL	106	.	NM_004795	exon4	c.T2694C	p.A898A	CGAAGCTCTCAAA	.	PASS	Atlas-SNP
ANKS3	124401	hgsc.bcm.edu	37	16	4776685	4776685	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	5.0	91.0	0.0	0.0490196	0	.	.	none	.	ANKS3	44	.	NM_133450	exon5	c.G466A	p.D156N	CACTGTCCAAGAG	.	PASS	Atlas-SNP
NDUFA13	51079	hgsc.bcm.edu	37	19	19627083	19627083	+	Silent	SNP	G	G	C	rs11552886	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243.0	112.0	262.0	2.0	0.460905	0.00763359	.	.	alt	NDUFA13,NS,carcinoma,0,1	NDUFA13	17	1	NM_015965	exon1	c.G36C	p.P12P	GCCTCCGCCGGGG	.	scavenged	Atlas-SNP
FRMPD4	9758	hgsc.bcm.edu	37	X	12720127	12720127	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39.0	39.0	101.0	0.0	1	0	.	.	none	.	FRMPD4	214	.	NM_014728	exon10	c.C1068T	p.I356I	ATACATCGAGTAA	.	PASS	Atlas-SNP
TSNAX	7257	hgsc.bcm.edu	37	1	231665038	231665038	+	Silent	SNP	C	C	T	rs138421350	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190.0	67.0	143.0	0.0	0.352632	0	C|0.999;T|0.001	0.001	strong	.	TSNAX	14	.	NM_005999	exon2	c.C54T	p.F18F	CAATTTCCCACAT	.	PASS	Atlas-SNP
CLTCL1	8218	hgsc.bcm.edu	37	22	19175133	19175133	+	Silent	SNP	C	C	A	rs187075533	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	215.0	108.0	278.0	0.0	0.502326	0	C|0.999;A|0.001	0.001	strong	.	CLTCL1	115	.	NM_007098	exon29	c.G4542T	p.L1514L	CTTGTACAGATAG	.	PASS	Atlas-SNP
KRTAP6-1	337966	hgsc.bcm.edu	37	21	31986163	31986163	+	Missense_Mutation	SNP	C	C	T	rs138494765	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	383.0	158.0	267.0	0.0	0.412533	0	C|1.000;T|0.000	0.000	weak	.	KRTAP6-1	21	.	NM_181602	exon1	c.G61A	p.G21R	GGCCTCCATAGCC	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103292201	103292201	+	Missense_Mutation	SNP	G	G	A	rs78008536	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163.0	71.0	102.0	0.0	0.435583	0	G|0.990;A|0.010	0.010	strong	.	RELN	593	.	NM_173054	exon15	c.C1799T	p.S600F	GACCAGGAGCGCC	.	PASS	Atlas-SNP
OR8K5	219453	hgsc.bcm.edu	37	11	55927584	55927584	+	Missense_Mutation	SNP	A	A	T	rs141612231	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	193.0	99.0	177.0	0.0	0.512953	0	A|0.998;T|0.002	0.002	strong	.	OR8K5	82	.	NM_001004058	exon1	c.T210A	p.D70E	ACCAAGATCAACA	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71347333	71347333	+	Missense_Mutation	SNP	C	C	T	rs72655156	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	409.0	185.0	398.0	1.0	0.452323	0.00251256	C|0.985;T|0.015	0.015	strong	.	MUC7	91	.	NM_001145007	exon4	c.C872T	p.T291I	CAACTACACCAGC	.	PASS	Atlas-SNP
NOL8	55035	hgsc.bcm.edu	37	9	95076771	95076771	+	Silent	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	90.0	24.0	98.0	0.0	0.266667	0	.	.	none	.	NOL8	118	.	NM_017948	exon7	c.T2136G	p.S712S	TGAATCAGACCGC	.	PASS	Atlas-SNP
ANKAR	150709	hgsc.bcm.edu	37	2	190569908	190569908	+	Missense_Mutation	SNP	G	G	A	rs116660656	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	235.0	110.0	306.0	0.0	0.468085	0	G|0.983;A|0.017	0.017	strong	.	ANKAR	184	.	NM_144708	exon8	c.G1868A	p.C623Y	CTCTCTGTAGGAA	.	PASS	Atlas-SNP
GLIS3	169792	hgsc.bcm.edu	37	9	4286248	4286248	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145.0	55.0	149.0	0.0	0.37931	0	.	.	none	.	GLIS3	152	.	NM_001042413	exon2	c.C178A	p.L60I	TCTTGAGATGGAG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76488794	76488794	+	Silent	SNP	G	G	A	rs76641546	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	129.0	68.0	137.0	0.0	0.527132	0	G|0.994;A|0.006	0.006	strong	.	DNAH17	347	.	NM_173628	exon42	c.C6462T	p.A2154A	GTCCACGGCGACC	.	PASS	Atlas-SNP
RASL12	51285	hgsc.bcm.edu	37	15	65357558	65357558	+	Silent	SNP	A	A	G	rs36045000	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101.0	18.0	144.0	0.0	0.178218	0	A|0.987;G|0.013	0.013	strong	.	RASL12	32	.	NM_016563	exon2	c.T157C	p.L53L	TACCCAAGTTGGG	.	PASS	Atlas-SNP
ZNF345	25850	hgsc.bcm.edu	37	19	37368535	37368535	+	Missense_Mutation	SNP	G	G	C	rs112729744	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131.0	70.0	123.0	0.0	0.534351	0	G|0.993;C|0.007	0.007	strong	.	ZNF345	68	.	NM_001242476	exon4	c.G803C	p.S268T	CCTTTAGTTTTGG	.	PASS	Atlas-SNP
CDH1	999	hgsc.bcm.edu	37	16	68855966	68855966	+	Missense_Mutation	SNP	G	G	A	rs35187787	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	161.0	21.0	171.0	0.0	0.130435	0	A|0.003;G|0.997	0.003	strong	CDH1,NS,carcinoma,0,4	CDH1	535	4	NM_004360	exon12	c.G1774A	p.A592T	GACAACGCCCCCA	.	PASS	Atlas-SNP
TYK2	7297	hgsc.bcm.edu	37	19	10463118	10463118	+	Missense_Mutation	SNP	G	G	C	rs34536443	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	260.0	160.0	213.0	1.0	0.615385	0.00469484	G|0.975;C|0.025	0.025	strong	.	TYK2	126	.	NM_003331	exon23	c.C3310G	p.P1104A	TGGGGGGGCTCTG	.	PASS	Atlas-SNP
VPS53	55275	hgsc.bcm.edu	37	17	534812	534812	+	Missense_Mutation	SNP	G	G	A	rs138639431	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109.0	47.0	98.0	0.0	0.431193	0	G|1.000;A|0.000	0.000	strong	.	VPS53	109	.	NM_001128159	exon8	c.C665T	p.A222V	GGAAACGCTTCTT	.	PASS	Atlas-SNP
SLC16A8	23539	hgsc.bcm.edu	37	22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	rs75640043	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46.0	44.0	94.0	0.0	0.956522	0	G|0.951;A|0.049	0.049	strong	SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	NM_013356	exon4	c.C770T	p.A257V	GTGACGGCGTACA	.	PASS	Atlas-SNP
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77510008	77510008	+	Silent	SNP	C	C	A	rs35763299	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	19.0	111.0	0.0	0.292308	0	T|0.009;C|0.980;A|0.010	0.010	strong	.	ST6GALNAC5	59	.	NM_030965	exon3	c.C381A	p.P127P	CGCCCCCACACGC	.	PASS	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21607253	21607253	+	Missense_Mutation	SNP	A	A	G	rs150159158		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	11.0	75.0	0.0	0.169231	0	.	.	weak	.	ZNF493	178	.	NM_001076678	exon4	c.A1792G	p.K598E	ACTGATAAGAAAC	.	PASS	Atlas-SNP
SIGLEC15	284266	hgsc.bcm.edu	37	18	43422149	43422149	+	Silent	SNP	G	G	A	rs143689799	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115.0	61.0	131.0	0.0	0.530435	0	G|0.997;A|0.003	0.003	strong	.	SIGLEC15	10	.	NM_213602	exon6	c.G984A	p.P328P	CTCACCGTGAGGA	.	PASS	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98244242	98244242	+	Silent	SNP	T	T	C	rs1805154	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95.0	45.0	106.0	0.0	0.473684	0	T|0.976;C|0.024	0.024	strong	.	PTCH1	1850	.	NM_000264	exon5	c.A735G	p.T245T	GTATGCTGTCCCA	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1729958	1729958	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95.0	59.0	67.0	0.0	0.621053	0	.	.	none	.	TACC3	69	.	NM_006342	exon4	c.G829T	p.A277S	TGCCCTGCGGGTG	.	PASS	Atlas-SNP
LTA4H	4048	hgsc.bcm.edu	37	12	96408716	96408716	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185.0	8.0	148.0	0.0	0.0432432	0	.	.	none	.	LTA4H	38	.	NM_000895	exon12	c.A1121G	p.D374G	TCAGGGTCTATAT	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	37	4	183721088	183721088	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101.0	5.0	198.0	0.0	0.049505	0	.	.	none	.	.	.	.	NM_001080477	exon27	c.C7684T	p.L2562L	GGCACGCTGCGGT	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90500067	90500067	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130.0	6.0	114.0	0.0	0.0461538	0	.	.	none	.	MDN1	478	.	NM_014611	exon6	c.G909A	p.V303V	AACCAGCACATAA	.	PASS	Atlas-SNP
ITIH2	3698	hgsc.bcm.edu	37	10	7759736	7759736	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	122.0	86.0	154.0	0.0	0.704918	0	.	.	none	.	ITIH2	144	.	NM_002216	exon6	c.G615A	p.L205L	ACGGCTGGCCAAA	.	PASS	Atlas-SNP
DDX54	79039	hgsc.bcm.edu	37	12	113600940	113600940	+	Missense_Mutation	SNP	C	C	T	rs11564	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103.0	45.0	101.0	0.0	0.436893	0	C|0.954;T|0.046	0.046	strong	.	DDX54	73	.	NM_024072	exon16	c.G2078A	p.R693Q	CACCCCCGCTCGC	.	PASS	Atlas-SNP
C14orf79	122616	hgsc.bcm.edu	37	14	105457923	105457923	+	Missense_Mutation	SNP	T	T	A	rs61745867	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	159.0	69.0	116.0	0.0	0.433962	0	T|0.990;A|0.010	0.010	strong	.	C14orf79	13	.	NM_174891	exon3	c.T665A	p.F222Y	AGAACTTCTTTCT	.	PASS	Atlas-SNP
TRIP6	7205	hgsc.bcm.edu	37	7	100465747	100465747	+	Missense_Mutation	SNP	G	G	T	rs139351872	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	212.0	71.0	180.0	0.0	0.334906	0	C|0.000;G|0.999;T|0.001	0.001	strong	.	TRIP6	45	.	NM_003302	exon3	c.G255T	p.R85S	AGACAGGGGGGGC	.	PASS	Atlas-SNP
CPSF1	29894	hgsc.bcm.edu	37	8	145624559	145624559	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	153.0	36.0	103.0	0.0	0.235294	0	.	.	none	.	CPSF1	92	.	NM_013291	exon15	c.G1426A	p.A476T	CATTGGCACAGGG	.	PASS	Atlas-SNP
UBE4A	9354	hgsc.bcm.edu	37	11	118253436	118253436	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	110.0	76.0	85.0	0.0	0.690909	0	.	.	none	.	UBE4A	97	.	NM_004788	exon13	c.T2163C	p.Y721Y	TCAGTATGCACCC	.	PASS	Atlas-SNP
SLC22A16	85413	hgsc.bcm.edu	37	6	110763935	110763935	+	Missense_Mutation	SNP	T	T	C	rs41288594	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	107.0	52.0	91.0	0.0	0.485981	0	T|0.985;C|0.015	0.015	strong	.	SLC22A16	81	.	NM_033125	exon4	c.A695G	p.E232G	ATGAATTCCATCA	.	PASS	Atlas-SNP
RPE65	6121	hgsc.bcm.edu	37	1	68914353	68914353	+	Silent	SNP	A	A	G	rs62642581	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	25.0	158.0	0.0	0.257732	0	A|1.000;G|0.000	0.000	strong	.	RPE65	87	.	NM_000329	exon2	c.T48C	p.F16F	AGTTTCAAACAGT	.	PASS	Atlas-SNP
EXOC1	55763	hgsc.bcm.edu	37	4	56737278	56737278	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158.0	77.0	198.0	0.0	0.487342	0	.	.	none	.	EXOC1	103	.	NM_018261	exon7	c.C843G	p.D281E	CATGGACTTGGCC	.	PASS	Atlas-SNP
PLEKHO2	80301	hgsc.bcm.edu	37	15	65158047	65158047	+	Missense_Mutation	SNP	G	G	A	rs77456635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	17.0	13.0	24.0	0.0	0.764706	0	G|0.982;A|0.018	0.018	strong	.	PLEKHO2	50	.	NM_025201	exon6	c.G1433A	p.R478Q	AGAAGCGGAAGGA	.	PASS	Atlas-SNP
EFEMP1	2202	hgsc.bcm.edu	37	2	56144930	56144930	+	Silent	SNP	T	T	C	rs14282	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101.0	48.0	97.0	0.0	0.475248	0	T|0.979;C|0.021	0.021	strong	.	EFEMP1	81	.	NM_001039349	exon4	c.A387G	p.E129E	CTGCATTTCAGGG	.	PASS	Atlas-SNP
TTLL6	284076	hgsc.bcm.edu	37	17	46877017	46877017	+	Silent	SNP	C	C	T	rs201225285	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148.0	63.0	189.0	0.0	0.425676	0	C|0.996;T|0.004	0.004	strong	.	TTLL6	113	.	NM_001130918	exon6	c.G717A	p.V239V	TTCTTTCACTGTC	.	PASS	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	37	19	41356246	41356246	+	Missense_Mutation	SNP	C	C	T	rs28399435	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	330.0	166.0	341.0	1.0	0.50303	0.00293255	C|0.975;T|0.025	0.025	strong	.	CYP2A6	69	.	NM_000762	exon1	c.G86A	p.S29N	CCCTTGCTCTTCC	.	PASS	Atlas-SNP
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350044	65350044	+	Silent	SNP	A	A	G	rs35278406	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94.0	33.0	97.0	0.0	0.351064	0	A|0.974;G|0.026	0.026	strong	.	ERBB2IP	120	.	NM_001253699	exon21	c.A2898G	p.Q966Q	CCCACAATCTGCA	.	PASS	Atlas-SNP
OR9G9	504191	hgsc.bcm.edu	37	11	56468225	56468225	+	Missense_Mutation	SNP	G	G	A	rs148651508	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298.0	76.0	289.0	2.0	0.255034	0.00692042	G|1.000;A|0.000	0.000	weak	OR9G1,NS,carcinoma,0,1	.	.	1	NM_001013358	exon1	c.G362A	p.R121H	ATGACCGCTACGT	.	scavenged	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789327	117789327	+	Missense_Mutation	SNP	T	T	C	rs61900346	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266.0	25.0	108.0	1.0	0.093985	0.00925926	T|0.814;C|0.186	0.186	strong	TMPRSS13_ENST00000445164,NS,carcinoma,0,4	TMPRSS13	75	4	NM_001206790	exon2	c.A248G	p.Q83R	GATGCCTGGGCTG	.	scavenged	Atlas-SNP
PLAT	5327	hgsc.bcm.edu	37	8	42044965	42044965	+	Missense_Mutation	SNP	G	G	A	rs2020921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	60.0	35.0	37.0	0.0	0.583333	0	G|0.987;A|0.013	0.013	strong	PLAT,NS,carcinoma,+1,1	PLAT	62	1	NM_000930	exon6	c.C490T	p.R164W	GCCTCCGCCCGCT	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154388363	154388363	+	Missense_Mutation	SNP	C	C	T	rs78441178	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	137.0	93.0	218.0	0.0	0.678832	0	.	.	weak	.	KIAA0922	214	.	NM_001131007	exon2	c.C125T	p.A42V	CTGCAGCGATTGA	.	PASS	Atlas-SNP
PRX	57716	hgsc.bcm.edu	37	19	40909695	40909695	+	Silent	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116.0	56.0	159.0	0.0	0.482759	0	.	.	none	.	PRX	151	.	NM_181882	exon5	c.A102C	p.V34V	GCCCGCTACGTTG	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40574434	40574434	+	Missense_Mutation	SNP	T	T	C	rs144295288	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	151.0	55.0	115.0	0.0	0.364238	0	T|0.997;C|0.003	0.003	strong	.	BRWD1	325	.	NM_018963	exon38	c.A4402G	p.I1468V	GAATTATTTTTGT	.	PASS	Atlas-SNP
PVR	5817	hgsc.bcm.edu	37	19	45153113	45153113	+	Missense_Mutation	SNP	G	G	C	rs35959395	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133.0	60.0	155.0	0.0	0.451128	0	G|0.999;C|0.001	0.001	strong	.	PVR	23	.	NM_001135769	exon3	c.G460C	p.V154L	CAGAAGGTCCAGC	.	PASS	Atlas-SNP
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802629	31802629	+	Silent	SNP	C	C	T	rs73356729	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	240.0	79.0	181.0	0.0	0.329167	0	C|0.963;T|0.037	0.037	strong	.	KRTAP13-4	46	.	NM_181600	exon1	c.C36T	p.S12S	CTCCTCCCGCTCC	.	PASS	Atlas-SNP
RTTN	25914	hgsc.bcm.edu	37	18	67755252	67755252	+	Missense_Mutation	SNP	C	C	G	rs376382612		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59.0	26.0	70.0	0.0	0.440678	0	.	.	weak	.	RTTN	184	.	NM_173630	exon31	c.G4275C	p.Q1425H	TTCTGACTGGTCC	.	PASS	Atlas-SNP
MSI2	124540	hgsc.bcm.edu	37	17	55752389	55752389	+	Missense_Mutation	SNP	G	G	A	rs116924898	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120.0	57.0	142.0	0.0	0.475	0	A|0.007;C|0.000;G|0.992	0.007	strong	.	MSI2	52	.	NM_138962	exon12	c.G847A	p.A283T	CCTGTCGCCGATC	.	PASS	Atlas-SNP
GBP1	2633	hgsc.bcm.edu	37	1	89523911	89523911	+	Missense_Mutation	SNP	C	C	T	rs75161612	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27.0	27.0	55.0	0.0	1	0	C|0.981;T|0.019	0.019	strong	.	GBP1	68	.	NM_002053	exon6	c.G638A	p.S213N	TTTTGACTGGTAC	.	PASS	Atlas-SNP
CKM	1158	hgsc.bcm.edu	37	19	45815163	45815163	+	Missense_Mutation	SNP	G	G	A	rs17357122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152.0	58.0	189.0	0.0	0.381579	0	G|0.995;A|0.005	0.005	strong	.	CKM	40	.	NM_001824	exon5	c.C497T	p.T166M	TCGCCCGTCAGGC	.	PASS	Atlas-SNP
APOD	347	hgsc.bcm.edu	37	3	195306289	195306289	+	Missense_Mutation	SNP	A	A	G	rs5952	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53.0	24.0	50.0	0.0	0.45283	0	A|0.996;G|0.004	0.004	strong	.	APOD	28	.	NM_001647	exon2	c.T44C	p.F15S	GCACCGAAGAGGC	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38345455	38345455	+	Silent	SNP	A	A	G	rs12242343	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66.0	17.0	102.0	0.0	0.257576	0	A|0.968;G|0.032	0.032	strong	.	ZNF33A	103	.	NM_006954	exon5	c.A2403G	p.G801G	CTGTGGAGAAAGC	.	PASS	Atlas-SNP
FAM118A	55007	hgsc.bcm.edu	37	22	45719125	45719125	+	Silent	SNP	C	C	T	rs138980075	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	175.0	83.0	165.0	0.0	0.474286	0	C|0.997;T|0.003	0.003	strong	.	FAM118A	32	.	NM_017911	exon3	c.C117T	p.S39S	CGTCAGCGCAGCA	.	PASS	Atlas-SNP
LRRIQ1	84125	hgsc.bcm.edu	37	12	85450426	85450426	+	Missense_Mutation	SNP	G	G	A	rs74720621	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99.0	46.0	118.0	0.0	0.464646	0	G|0.992;A|0.008	0.008	strong	.	LRRIQ1	512	.	NM_001079910	exon8	c.G1855A	p.E619K	ACATCAGAAAATT	.	PASS	Atlas-SNP
OSMR	9180	hgsc.bcm.edu	37	5	38904082	38904082	+	Missense_Mutation	SNP	T	T	C	rs35117676	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	365.0	171.0	387.0	1.0	0.468493	0.00258398	T|0.991;C|0.009	0.009	strong	.	OSMR	133	.	NM_003999	exon8	c.T1090C	p.Y364H	TTCACATATTTGT	.	PASS	Atlas-SNP
PIKFYVE	200576	hgsc.bcm.edu	37	2	209168942	209168942	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59.0	42.0	93.0	0.0	0.711864	0	.	.	none	.	PIKFYVE	223	.	NM_015040	exon11	c.C1368T	p.N456N	AGTGAACTCCGTG	.	PASS	Atlas-SNP
CNOT4	4850	hgsc.bcm.edu	37	7	135098310	135098310	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	133.0	72.0	242.0	0.0	0.541353	0	.	.	none	.	CNOT4	146	.	NM_001190850	exon6	c.G614A	p.C205Y	TTTGGACACTGCA	.	PASS	Atlas-SNP
LAMC1	3915	hgsc.bcm.edu	37	1	183079729	183079729	+	Missense_Mutation	SNP	C	C	T	rs142614579	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203.0	122.0	162.0	0.0	0.600985	0	C|0.999;T|0.001	0.001	strong	.	LAMC1	176	.	NM_002293	exon4	c.C961T	p.P321S	TGTCTTCCTTTCT	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	37	15	52635394	52635394	+	Missense_Mutation	SNP	T	T	A	rs61731219	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	56.0	48.0	152.0	0.0	0.857143	0	T|0.955;A|0.045	0.045	strong	.	MYO5A	145	.	NM_000259	exon31	c.A3960T	p.R1320S	AGATGATCTTCCA	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681917	100681917	+	Missense_Mutation	SNP	T	T	G	rs111633703	bycluster;byfrequency;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	326.0	16.0	217.0	0.0	0.0490798	0	T|0.996;C|0.004	.	alt	.	MUC17	804	.	NM_001040105	exon3	c.T7220G	p.M2407R	GCACCATGCCGGT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093344	1093344	+	Silent	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	7.0	88.0	0.0	0.0909091	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.G5163T	p.P1721P	AACCCCGACACCC	.	PASS	Atlas-SNP
DMKN	93099	hgsc.bcm.edu	37	19	36002421	36002421	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72.0	6.0	35.0	0.0	0.0833333	0	.	.	none	DMKN,colon,carcinoma,0,1	DMKN	116	1	NM_001126058	exon5	c.T810C	p.G270G	GCTGCCACCACTG	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24426581	24426581	+	Missense_Mutation	SNP	G	G	A	rs140804905	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	32.0	82.0	0.0	0.415584	0	G|0.999;A|0.001	0.001	strong	.	ITSN2	224	.	NM_006277	exon40	c.C5008T	p.R1670C	GTCGGCGGGTCAT	.	PASS	Atlas-SNP
CCND1	595	hgsc.bcm.edu	37	11	69457987	69457987	+	Silent	SNP	C	C	T	rs371689281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42.0	18.0	47.0	0.0	0.428571	0	.	.	weak	.	CCND1	107	.	NM_053056	exon2	c.C387T	p.D129D	CACCGACAACTCC	.	PASS	Atlas-SNP
LEPRE1	64175	hgsc.bcm.edu	37	1	43212926	43212926	+	Missense_Mutation	SNP	G	G	A	rs67014447	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45.0	11.0	65.0	0.0	0.244444	0	G|0.936;A|0.064	0.064	strong	.	LEPRE1	130	.	NM_001146289	exon14	c.C2072T	p.A691V	TCACCCGCTCGAG	.	PASS	Atlas-SNP
MED12L	116931	hgsc.bcm.edu	37	3	151150568	151150568	+	Silent	SNP	G	G	A	rs142871635	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166.0	90.0	173.0	0.0	0.542169	0	G|0.997;A|0.003	0.003	strong	.	MED12L	271	.	NM_053002	exon43	c.G6414A	p.P2138P	GACTCCGTATGGG	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133253180	133253180	+	Missense_Mutation	SNP	A	A	T	rs139075637	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	167.0	91.0	223.0	0.0	0.54491	0	A|0.999;T|0.001	0.001	strong	.	POLE	416	.	NM_006231	exon9	c.T861A	p.D287E	CTCAGCATCAGGA	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225393787	225393787	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103.0	34.0	79.0	0.0	0.330097	0	.	.	none	.	DNAH14	300	.	NM_001373	exon39	c.T6026G	p.I2009R	AGAGAATAGCTTT	.	PASS	Atlas-SNP
UTP6	55813	hgsc.bcm.edu	37	17	30200750	30200750	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51.0	4.0	69.0	0.0	0.0784314	0	.	.	none	.	UTP6	46	.	NM_018428	exon15	c.C1328T	p.S443F	GCCCAGGAAATCC	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196529917	196529917	+	Silent	SNP	A	A	G	rs183020057	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	214.0	10.0	180.0	0.0	0.046729	0	A|1.000;G|0.000	0.000	strong	.	PAK2	113	.	NM_002577	exon4	c.A318G	p.L106L	ATTACTACAGACC	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92257991	92257991	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	200.0	123.0	134.0	0.0	0.615	0	.	.	none	.	FAT3	1822	.	NM_001008781	exon2	c.C3484A	p.P1162T	AACTCTCCAAAGG	.	PASS	Atlas-SNP
SCAMP5	192683	hgsc.bcm.edu	37	15	75308976	75308976	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67.0	33.0	118.0	0.0	0.492537	0	.	.	none	.	SCAMP5	34	.	NM_001178111	exon5	c.C179T	p.A60V	GTCTCGCGTGGCT	.	PASS	Atlas-SNP
DRG2	1819	hgsc.bcm.edu	37	17	18003919	18003919	+	Missense_Mutation	SNP	G	G	A	rs143296623	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	51.0	83.0	0.0	0.5	0	G|0.996;A|0.004	0.004	strong	.	DRG2	27	.	NM_001388	exon7	c.G577A	p.V193I	TCGACAGTCACGC	.	PASS	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2577809	2577809	+	Missense_Mutation	SNP	G	G	A	rs375916445		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	72.0	53.0	65.0	0.0	0.736111	0	.	.	weak	.	BRAT1	57	.	NM_152743	exon14	c.C2360T	p.T787M	GCCAGCGTGCTCC	.	PASS	Atlas-SNP
CUL4A	8451	hgsc.bcm.edu	37	13	113909008	113909008	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104.0	53.0	98.0	0.0	0.509615	0	.	.	none	.	CUL4A	50	.	NM_001008895	exon17	c.G1754A	p.G585E	TCCAGGGGAAGAA	.	PASS	Atlas-SNP
FAM178A	55719	hgsc.bcm.edu	37	10	102716222	102716222	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98.0	4.0	127.0	0.0	0.0408163	0	.	.	none	.	FAM178A	9	.	NM_001136123	exon18	c.A3345G	p.L1115L	TGTGCTACTCTGT	.	PASS	Atlas-SNP
CAMKMT	79823	hgsc.bcm.edu	37	2	44942450	44942450	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106.0	45.0	99.0	0.0	0.424528	0	.	.	none	.	CAMKMT	20	.	NM_024766	exon7	c.A581G	p.N194S	CAAGGAATCAGAA	.	PASS	Atlas-SNP
ADAMTS6	11174	hgsc.bcm.edu	37	5	64756136	64756136	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114.0	8.0	113.0	0.0	0.0701754	0	.	.	none	.	ADAMTS6	174	.	NM_197941	exon4	c.G492A	p.E164E	AAAATACTCTTCA	.	PASS	Atlas-SNP
SAMD4A	23034	hgsc.bcm.edu	37	14	55226987	55226987	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	46.0	32.0	45.0	0.0	0.695652	0	.	.	none	.	SAMD4A	68	.	NM_015589	exon6	c.C1285T	p.R429C	GCTCGCCGCCGGG	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123846252	123846252	+	Missense_Mutation	SNP	G	G	A	rs201709460	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119.0	51.0	106.0	0.0	0.428571	0	G|0.999;A|0.001	0.001	strong	.	TACC2	271	.	NM_206862	exon4	c.G4237A	p.A1413T	CACATCGCCAAGA	.	PASS	Atlas-SNP
RBM6	10180	hgsc.bcm.edu	37	3	50005855	50005855	+	Missense_Mutation	SNP	G	G	A	rs143972186	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205.0	106.0	219.0	1.0	0.517073	0.00456621	G|0.997;A|0.003	0.003	strong	.	RBM6	85	.	NM_005777	exon3	c.G997A	p.E333K	AAGGGAGAATTTG	.	PASS	Atlas-SNP
ZNF215	7762	hgsc.bcm.edu	37	11	6962879	6962879	+	Missense_Mutation	SNP	C	C	T	rs141940336	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	87.0	40.0	83.0	0.0	0.45977	0	C|1.000;T|0.000	0.000	strong	.	ZNF215	72	.	NM_013250	exon4	c.C478T	p.P160S	GGCAAACCACAGG	.	PASS	Atlas-SNP
SYNGR4	23546	hgsc.bcm.edu	37	19	48879375	48879375	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147.0	38.0	147.0	0.0	0.258503	0	.	.	none	SYNGR4,NS,carcinoma,-2,3	SYNGR4	31	3	NM_012451	exon5	c.C505T	p.R169X	GACCTCCGAAATG	.	PASS	Atlas-SNP
PRKAA1	5562	hgsc.bcm.edu	37	5	40765280	40765280	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	306.0	131.0	277.0	0.0	0.428105	0	.	.	none	.	PRKAA1	27	.	NM_206907	exon8	c.T927C	p.Y309Y	TGAACTATATGAT	.	PASS	Atlas-SNP
PHF17	79960	hgsc.bcm.edu	37	4	129792787	129792787	+	Silent	SNP	A	A	G	rs6850940	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86.0	22.0	117.0	0.0	0.255814	0	A|0.972;G|0.028	0.028	strong	.	PHF17	63	.	NM_199320	exon11	c.A1899G	p.L633L	GGGTTTAGAAAAG	.	PASS	Atlas-SNP
OR4A5	81318	hgsc.bcm.edu	37	11	51411918	51411918	+	Missense_Mutation	SNP	C	C	T	rs150995059	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	148.0	72.0	143.0	0.0	0.486486	0	C|0.993;T|0.007	0.007	strong	.	OR4A5	116	.	NM_001005272	exon1	c.G478A	p.V160M	TGTACACAACAAT	.	PASS	Atlas-SNP
HIP1	3092	hgsc.bcm.edu	37	7	75171262	75171262	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	317.0	72.0	256.0	0.0	0.227129	0	.	.	none	HIP1,NS,carcinoma,-2,1	HIP1	91	1	NM_005338	exon29	c.C2928T	p.I976I	GCGTTTGATCTGT	.	PASS	Atlas-SNP
FAM171A1	221061	hgsc.bcm.edu	37	10	15256368	15256368	+	Missense_Mutation	SNP	C	C	T	rs143772901	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58.0	21.0	94.0	0.0	0.362069	0	C|1.000;T|0.000	0.000	weak	.	FAM171A1	252	.	NM_001010924	exon8	c.G1219A	p.E407K	CCCCTTCGCCGCC	.	PASS	Atlas-SNP
FRMPD1	22844	hgsc.bcm.edu	37	9	37733752	37733752	+	Missense_Mutation	SNP	G	G	A	rs140800271	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126.0	64.0	109.0	0.0	0.507937	0	G|0.997;A|0.003	0.003	strong	.	FRMPD1	237	.	NM_014907	exon12	c.G1148A	p.R383H	AGCTACGTTTAAA	.	PASS	Atlas-SNP
ARID4B	51742	hgsc.bcm.edu	37	1	235383742	235383742	+	Missense_Mutation	SNP	C	C	G	rs148132837	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	487.0	158.0	405.0	0.0	0.324435	0	C|0.999;G|0.001	0.001	strong	.	ARID4B	142	.	NM_016374	exon15	c.G1282C	p.V428L	CCTTAACTTTTAT	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	37	11	119050906	119050906	+	Missense_Mutation	SNP	G	G	A	rs45450295	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	428.0	99.0	234.0	0.0	0.231308	0	G|0.988;A|0.012	0.012	strong	.	NLRX1	128	.	NM_024618	exon7	c.G2176A	p.A726T	AGGCATGCCCTGG	.	PASS	Atlas-SNP
KIAA0319L	79932	hgsc.bcm.edu	37	1	35972375	35972375	+	Silent	SNP	A	A	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	103.0	29.0	161.0	0.0	0.281553	0	.	.	none	.	KIAA0319L	156	.	NM_024874	exon3	c.T504A	p.A168A	GAGTGCAGCTCTG	.	PASS	Atlas-SNP
MMP19	4327	hgsc.bcm.edu	37	12	56236136	56236136	+	Splice_Site	SNP	C	C	T	rs145293054	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230.0	117.0	227.0	1.0	0.508696	0.00440529	C|0.999;T|0.001	0.001	strong	.	MMP19	61	.	NM_002429	exon3	c.173+1G>A	.	TTCTCACCTCAGA	.	PASS	Atlas-SNP
MAD2L1BP	9587	hgsc.bcm.edu	37	6	43608220	43608220	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	101.0	30.0	100.0	0.0	0.29703	0	.	.	none	.	MAD2L1BP	12	.	NM_001003690	exon4	c.G871A	p.D291N	TGGGAAGACTACA	.	PASS	Atlas-SNP
ORC4	5000	hgsc.bcm.edu	37	2	148730367	148730367	+	Missense_Mutation	SNP	G	G	C	rs2307397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206.0	122.0	223.0	0.0	0.592233	0	G|0.964;C|0.036	0.036	strong	.	ORC4	40	.	NM_002552	exon4	c.C166G	p.L56V	CATGGAGAGCAGT	.	PASS	Atlas-SNP
EPHA4	2043	hgsc.bcm.edu	37	2	222301160	222301160	+	Silent	SNP	G	G	T	rs56159060		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71.0	16.0	106.0	0.0	0.225352	0	.	.	weak	.	EPHA4	263	.	NM_004438	exon13	c.C2305A	p.R769R	GCACTCGGGACAT	.	PASS	Atlas-SNP
C11orf35	256329	hgsc.bcm.edu	37	11	556584	556584	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	45.0	28.0	67.0	0.0	0.622222	0	.	.	none	.	C11orf35	22	.	NM_173573	exon9	c.C981T	p.L327L	TTTCTGGAGATCT	.	PASS	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92568149	92568149	+	Missense_Mutation	SNP	A	A	G	rs75651194	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	183.0	50.0	118.0	0.0	0.273224	0	A|0.991;G|0.009	0.009	strong	.	FAT3	1822	.	NM_001008781	exon14	c.A9985G	p.I3329V	GTCAACATCAACC	.	PASS	Atlas-SNP
ZNF33B	7582	hgsc.bcm.edu	37	10	43089278	43089278	+	Missense_Mutation	SNP	T	T	C	rs71505624	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174.0	33.0	200.0	0.0	0.189655	0	T|0.998;C|0.002	0.002	strong	.	ZNF33B	78	.	NM_006955	exon5	c.A1120G	p.K374E	GATGTTTAGTGAG	.	PASS	Atlas-SNP
BTN2A2	10385	hgsc.bcm.edu	37	6	26384092	26384092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	125.0	6.0	125.0	0.0	0.048	0	.	.	none	BTN2A2_ENST00000432533,bladder,carcinoma,-1,2	BTN2A2	87	2	NM_181531	exon2	c.C43T	p.L15F	GCCTCCCTCCTCC	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100681345	100681345	+	Missense_Mutation	SNP	T	T	G	rs142097516	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	249.0	23.0	177.0	0.0	0.0923695	0	.	.	weak	.	MUC17	804	.	NM_001040105	exon3	c.T6648G	p.S2216R	TCCTAGTGAAGGA	.	PASS	Atlas-SNP
RRM1	6240	hgsc.bcm.edu	37	11	4154851	4154851	+	Missense_Mutation	SNP	T	T	C	rs145770432	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112.0	40.0	118.0	0.0	0.357143	0	T|0.999;C|0.001	0.001	strong	.	RRM1	31	.	NM_001033	exon17	c.T1964C	p.M655T	AAGAGATGAAAAA	.	PASS	Atlas-SNP
PAPD7	11044	hgsc.bcm.edu	37	5	6753013	6753013	+	Silent	SNP	C	C	T	rs28381429	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210.0	89.0	219.0	0.0	0.42381	0	C|0.979;T|0.021	0.021	strong	.	PAPD7	69	.	NM_001171805	exon12	c.C1297T	p.L433L	CCGACCCTAGGGG	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218682757	218682757	+	Missense_Mutation	SNP	G	G	A	rs140104262	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39.0	37.0	73.0	0.0	0.948718	0	G|0.999;A|0.001	0.001	strong	TNS1,NS,carcinoma,+1,1	TNS1	251	1	NM_022648	exon24	c.C3986T	p.P1329L	TCCTCCGGGGTAG	.	PASS	Atlas-SNP
MAP3K10	4294	hgsc.bcm.edu	37	19	40712040	40712040	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144.0	80.0	168.0	0.0	0.555556	0	.	.	none	.	MAP3K10	70	.	NM_002446	exon5	c.G1411A	p.G471S	GAAGGCGGCAGCC	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411619	105411619	+	Missense_Mutation	SNP	T	T	C	rs200461684	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246.0	96.0	156.0	0.0	0.390244	0	T|0.999;C|0.001	0.001	weak	.	AHNAK2	719	.	NM_138420	exon7	c.A10169G	p.H3390R	GGCAGGTGCCCTT	.	PASS	Atlas-SNP
ND1	10625	hgsc.bcm.edu	37	MT	4153	4153	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	12.0	8.0	5.0	0.0	0.666667	0	.	.	none	.	.	.	.	ENST00000361390	exon1	c.G847A	p.D283N	CGCTACGACCAAC	.	PASS	Atlas-SNP
RBM6	10180	hgsc.bcm.edu	37	3	50005373	50005373	+	Missense_Mutation	SNP	C	C	T	rs142246877	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	49.0	112.0	0.0	0.480392	0	C|0.997;T|0.003	0.003	strong	.	RBM6	85	.	NM_005777	exon3	c.C515T	p.P172L	CTCCTCCATCTGA	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	147038089	147038089	+	Missense_Mutation	SNP	G	G	T	rs61748896	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	78.0	42.0	117.0	0.0	0.538462	0	G|0.941;T|0.059	0.059	strong	.	ADGB	93	.	NM_024694	exon15	c.G1812T	p.E604D	AAGAGAGATAGTC	.	PASS	Atlas-SNP
CLGN	1047	hgsc.bcm.edu	37	4	141313500	141313500	+	Silent	SNP	G	G	A	rs34492995	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	163.0	117.0	223.0	0.0	0.717791	0	G|0.992;A|0.008	0.008	strong	.	CLGN	76	.	NM_001130675	exon14	c.C1524T	p.T508T	TATGTCGGTTTTT	.	PASS	Atlas-SNP
HIVEP1	3096	hgsc.bcm.edu	37	6	12164308	12164308	+	Missense_Mutation	SNP	G	G	A	rs181056704	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	117.0	58.0	120.0	0.0	0.495726	0	G|0.999;A|0.001	0.001	strong	.	HIVEP1	242	.	NM_002114	exon9	c.G7771A	p.A2591T	GCCAGCGCAAACC	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	182.0	92.0	188.0	0.0	0.505495	0	A|0.976;G|0.024	0.024	strong	.	ADGB	93	.	NM_024694	exon8	c.A876G	p.K292K	CCTGAAAGAAATA	.	PASS	Atlas-SNP
MYH9	4627	hgsc.bcm.edu	37	22	36689434	36689434	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100.0	4.0	75.0	0.0	0.04	0	.	.	none	.	MYH9	225	.	NM_002473	exon30	c.G4036A	p.E1346K	CCTCCTCCAGCTG	.	PASS	Atlas-SNP
FAM32A	26017	hgsc.bcm.edu	37	19	16301759	16301759	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131.0	53.0	127.0	0.0	0.40458	0	.	.	none	FAM32A,NS,carcinoma,0,1	FAM32A	6	1	NM_014077	exon4	c.C332T	p.T111M	GCTGGACGAAGTA	.	PASS	Atlas-SNP
TUBB1	81027	hgsc.bcm.edu	37	20	57598808	57598808	+	Missense_Mutation	SNP	G	G	A	rs41303899	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124.0	59.0	113.0	0.0	0.475806	0	G|0.999;A|0.001	0.001	strong	TUBB1,mucosal,malignant_melanoma,+1,1	TUBB1	42	1	NM_030773	exon4	c.G326A	p.G109E	CGGAGGGAGCCGA	.	PASS	Atlas-SNP
CNNM2	54805	hgsc.bcm.edu	37	10	104678801	104678801	+	Silent	SNP	C	C	T	rs117691462	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75.0	62.0	134.0	0.0	0.826667	0	C|0.996;T|0.004	0.004	strong	.	CNNM2	119	.	NM_199076	exon1	c.C564T	p.S188S	CAAGTCCTATTAC	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23091371	23091371	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264.0	15.0	248.0	0.0	0.0568182	0	.	.	none	.	USP31	122	.	NM_020718	exon13	c.C2072T	p.P691L	CTCCACGGGGACC	.	PASS	Atlas-SNP
SLC26A9	115019	hgsc.bcm.edu	37	1	205884508	205884508	+	Missense_Mutation	SNP	C	C	T	rs147005854	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	254.0	88.0	180.0	0.0	0.346457	0	C|0.999;T|0.001	0.001	strong	.	SLC26A9	176	.	NM_134325	exon21	c.G2353A	p.A785T	TCTCTGCGTGAAA	.	PASS	Atlas-SNP
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43630156	43630156	+	Silent	SNP	A	A	C	rs11559311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	119.0	87.0	148.0	0.0	0.731092	0	A|0.912;C|0.088	0.088	strong	.	EBNA1BP2	37	.	NM_001159936	exon10	c.T1044G	p.P348P	TTTTCCAGGTCTC	.	PASS	Atlas-SNP
PIAS1	8554	hgsc.bcm.edu	37	15	68479959	68479959	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	171.0	16.0	272.0	0.0	0.0935673	0	.	.	none	PIAS1,NS,carcinoma,-1,1	PIAS1	42	1	NM_016166	exon14	c.T1742C	p.F581S	GGTTTTTCCCGTA	.	PASS	Atlas-SNP
KLC1	3831	hgsc.bcm.edu	37	14	104143806	104143806	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126.0	35.0	98.0	0.0	0.277778	0	.	.	none	.	KLC1	54	.	NM_182923	exon12	c.C1434T	p.G478G	TCAAGGCAAATTT	.	PASS	Atlas-SNP
RBM44	375316	hgsc.bcm.edu	37	2	238742968	238742968	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	262.0	128.0	297.0	1.0	0.48855	0.003367	.	.	none	.	RBM44	167	.	NM_001080504	exon15	c.G3083A	p.G1028D	ATAAAGGTTTTCT	.	PASS	Atlas-SNP
SFN	2810	hgsc.bcm.edu	37	1	27190196	27190196	+	Missense_Mutation	SNP	A	A	T	rs77755255	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	37.0	6.0	59.0	0.0	0.162162	0	.	.	weak	.	SFN	20	.	NM_006142	exon1	c.A493T	p.T165S	CCGCCCACCAACC	.	PASS	Atlas-SNP
SPRY4	81848	hgsc.bcm.edu	37	5	141693948	141693948	+	Silent	SNP	G	G	A	rs145360326	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	229.0	108.0	251.0	0.0	0.471616	0	G|0.999;A|0.001	0.001	strong	SPRY4,rectum,carcinoma,0,2	SPRY4	31	2	NM_030964	exon3	c.C795T	p.S265S	CACCACGGAGAGA	.	PASS	Atlas-SNP
MEF2A	4205	hgsc.bcm.edu	37	15	100250918	100250918	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	71.0	139.0	0.0	0.731959	0	.	.	none	.	MEF2A	138	.	NM_005587	exon10	c.G1071A	p.S357S	GGTGTCGGCCTGG	.	PASS	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92734358	92734358	+	Silent	SNP	G	G	A	rs200454238	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198.0	68.0	128.0	0.0	0.343434	0	G|0.999;A|0.001	0.001	weak	.	SAMD9	239	.	NM_001193307	exon2	c.C1053T	p.D351D	CGTAATGTCCTTA	.	PASS	Atlas-SNP
RHBDF2	79651	hgsc.bcm.edu	37	17	74473329	74473329	+	Missense_Mutation	SNP	C	C	T	rs140433374	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138.0	74.0	158.0	0.0	0.536232	0	C|0.999;T|0.001	0.001	strong	.	RHBDF2	57	.	NM_024599	exon8	c.G940A	p.A314T	AGCTGGCAGAGAG	.	PASS	Atlas-SNP
MTHFSD	64779	hgsc.bcm.edu	37	16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	rs34005514	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	142.0	113.0	130.0	0.0	0.795775	0	G|0.968;C|0.032	0.032	strong	.	MTHFSD	52	.	NM_001159377	exon3	c.C133G	p.L45V	AAGCCAGATAAGA	.	PASS	Atlas-SNP
LPAR2	9170	hgsc.bcm.edu	37	19	19737992	19737992	+	Silent	SNP	G	G	A	rs150741448	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	75.0	35.0	66.0	0.0	0.466667	0	G|0.997;A|0.003	0.003	strong	.	LPAR2	28	.	NM_004720	exon2	c.C102T	p.V34V	CACCACGACCACA	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	rs117833529	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69.0	35.0	59.0	0.0	0.507246	0	C|0.976;T|0.024	0.024	strong	.	LRRC16B	120	.	NM_138360	exon33	c.C3184T	p.R1062W	CGGCCCCGGAGCT	.	PASS	Atlas-SNP
PCDHA12	56137	hgsc.bcm.edu	37	5	140256807	140256807	+	Missense_Mutation	SNP	T	T	A	rs199811254	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	224.0	117.0	295.0	0.0	0.522321	0	T|0.999;A|0.001	0.001	strong	PCDHA12,NS,carcinoma,-1,2	PCDHA12	196	2	NM_018903	exon1	c.T1750A	p.S584T	CCGCGGTCGGTGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682117	100682117	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238.0	15.0	187.0	0.0	0.0630252	0	.	.	none	MUC17,right_upper_lobe,carcinoma,-2,1	MUC17	804	1	NM_001040105	exon3	c.G7420A	p.G2474S	GAGGCTGGCACCC	.	scavenged	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	rs191412861	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	217.0	73.0	149.0	0.0	0.336406	0	A|0.997;C|0.003	0.003	strong	.	PKHD1L1	522	.	NM_177531	exon67	c.A10792C	p.S3598R	ATCATGAGTTACA	.	PASS	Atlas-SNP
PADI2	11240	hgsc.bcm.edu	37	1	17410253	17410253	+	Nonsense_Mutation	SNP	G	G	A	rs142403504	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121.0	35.0	219.0	0.0	0.289256	0	G|0.998;A|0.002	0.002	strong	.	PADI2	72	.	NM_007365	exon9	c.C1018T	p.Q340X	GGTACTGGAAGCA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115158	168115158	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85.0	37.0	88.0	0.0	0.435294	0	.	.	none	.	XIRP2	914	.	NM_001199143	exon11	c.A2201C	p.K734T	ATCATAAAGAAAA	.	PASS	Atlas-SNP
DMPK	1760	hgsc.bcm.edu	37	19	46273740	46273740	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95.0	45.0	157.0	0.0	0.473684	0	.	.	none	.	DMPK	74	.	NM_001081562	exon15	c.A1877G	p.X626W	CAGTTCTAGGGTT	.	PASS	Atlas-SNP
CACNA2D1	781	hgsc.bcm.edu	37	7	81635083	81635083	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	475.0	107.0	380.0	0.0	0.225263	0	.	.	none	.	CACNA2D1	191	.	NM_000722	exon17	c.A1513G	p.T505A	TTACTGTAAAACG	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3248333	3248333	+	Silent	SNP	T	T	C	rs372395776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	176.0	171.0	397.0	2.0	0.971591	0.00503778	.	.	weak	.	MXRA5	815	.	NM_015419	exon4	c.A435G	p.Q145Q	GAAAGCTTGAGGG	.	PASS	Atlas-SNP
PDE8A	5151	hgsc.bcm.edu	37	15	85610349	85610349	+	Silent	SNP	C	C	T	rs35666574	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	62.0	105.0	0.0	0.849315	0	C|0.976;T|0.024	0.024	strong	.	PDE8A	50	.	NM_173454	exon3	c.C348T	p.V116V	GGCTGTCCTTGCC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678988	100678988	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	205.0	12.0	120.0	0.0	0.0585366	0	.	.	none	MUC17,NS,carcinoma,0,2	MUC17	804	2	NM_001040105	exon3	c.G4291A	p.A1431T	ACTTCTGCTGAAG	.	scavenged	Atlas-SNP
MTX3	345778	hgsc.bcm.edu	37	5	79286042	79286042	+	Missense_Mutation	SNP	T	T	A	rs371364933		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	349.0	162.0	380.0	0.0	0.464183	0	.	.	weak	.	MTX3	29	.	NM_001010891	exon3	c.A169T	p.T57S	CAGTTGTCAAAAT	.	PASS	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	841238	841238	+	Silent	SNP	G	G	A	rs151271197	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	79.0	41.0	76.0	0.0	0.518987	0	G|0.995;A|0.005	0.005	strong	.	CHTF18	52	.	NM_022092	exon8	c.G972A	p.K324K	CCGGAAGCCCAGG	.	PASS	Atlas-SNP
TREML4	285852	hgsc.bcm.edu	37	6	41196169	41196169	+	Missense_Mutation	SNP	G	G	T	rs112680060	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85.0	46.0	75.0	0.0	0.541176	0	G|0.995;T|0.005	0.005	strong	.	TREML4	25	.	NM_198153	exon1	c.G4T	p.A2S	GGAATGGCCTGGG	.	PASS	Atlas-SNP
SPACA3	124912	hgsc.bcm.edu	37	17	31322691	31322691	+	Missense_Mutation	SNP	A	A	G	rs28963	bycluster;byfrequency;bysubmitter;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203.0	101.0	245.0	0.0	0.497537	0	A|0.998;G|0.002	0.002	strong	.	SPACA3	35	.	NM_173847	exon2	c.A299G	p.H100R	TGCTACATGACTT	.	PASS	Atlas-SNP
CHST13	166012	hgsc.bcm.edu	37	3	126260995	126260995	+	Silent	SNP	C	C	T	rs7614066	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18.0	11.0	16.0	0.0	0.611111	0	C|0.956;T|0.044	0.044	strong	.	CHST13	21	.	NM_152889	exon3	c.C600T	p.Y200Y	GCGCTACGGTGCA	.	PASS	Atlas-SNP
TRIO	7204	hgsc.bcm.edu	37	5	14304588	14304588	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168.0	81.0	151.0	0.0	0.482143	0	.	.	none	.	TRIO	305	.	NM_007118	exon8	c.T1387G	p.S463A	GTGGATTCATGGT	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81232294	81232294	+	Missense_Mutation	SNP	T	T	C	rs61734110	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109.0	88.0	122.0	0.0	0.807339	0	T|0.956;C|0.044	0.044	strong	.	PKD1L2	361	.	NM_001076780	exon7	c.A1516G	p.I506V	GGCAAATCCCAAA	.	PASS	Atlas-SNP
RHPN1	114822	hgsc.bcm.edu	37	8	144462841	144462841	+	Silent	SNP	G	G	A	rs117282246	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	210.0	95.0	233.0	0.0	0.452381	0	G|0.994;A|0.006	0.006	strong	.	RHPN1	76	.	NM_052924	exon11	c.G1299A	p.V433V	CGAGGTGGACCTG	.	PASS	Atlas-SNP
KAT2A	2648	hgsc.bcm.edu	37	17	40265751	40265751	+	Silent	SNP	C	C	T	rs147642400	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54.0	15.0	35.0	0.0	0.277778	0	C|0.998;T|0.002	0.002	strong	.	KAT2A	54	.	NM_021078	exon18	c.G2430A	p.P810P	GCTGTCCGGGGGG	.	PASS	Atlas-SNP
CSF3R	1441	hgsc.bcm.edu	37	1	36937106	36937106	+	Missense_Mutation	SNP	C	C	T	rs3918019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	50.0	105.0	0.0	0.684932	0	C|0.996;T|0.004	0.004	strong	.	CSF3R	157	.	NM_156039	exon10	c.G1213A	p.E405K	CCACCTCCTGGGC	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76918411	76918411	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118.0	72.0	112.0	0.0	0.610169	0	.	.	none	.	MYO7A	164	.	NM_000260	exon42	c.A5820G	p.S1940S	GTCCTCAGAGGGA	.	PASS	Atlas-SNP
HEATR6	63897	hgsc.bcm.edu	37	17	58156228	58156228	+	Silent	SNP	C	C	T	rs116476597	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88.0	52.0	93.0	0.0	0.590909	0	C|0.996;T|0.004	0.004	strong	.	HEATR6	98	.	NM_022070	exon1	c.G48A	p.R16R	TGCCTCCCGCGGC	.	PASS	Atlas-SNP
PALD1	27143	hgsc.bcm.edu	37	10	72291172	72291172	+	Missense_Mutation	SNP	G	G	A	rs61737673	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	54.0	13.0	92.0	0.0	0.240741	0	G|0.979;A|0.021	0.021	strong	.	.	.	.	NM_014431	exon5	c.G595A	p.V199I	CCCGGGGTCCGGG	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982119	75982119	+	Silent	SNP	G	G	T	rs199778089	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88.0	15.0	134.0	0.0	0.170455	0	G|0.997;T|0.003	0.003	strong	CSPG4,NS,neuroblastoma,0,1	CSPG4	175	1	NM_001897	exon3	c.C1287A	p.T429T	CAGCTGGGTGAAA	.	PASS	Atlas-SNP
DLEC1	9940	hgsc.bcm.edu	37	3	38125704	38125704	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178.0	89.0	159.0	0.0	0.5	0	.	.	none	.	DLEC1	278	.	NM_007337	exon7	c.C1229T	p.P410L	TCCTCCCGCCTTC	.	PASS	Atlas-SNP
CDH19	28513	hgsc.bcm.edu	37	18	64172434	64172434	+	Missense_Mutation	SNP	C	C	G	rs55874520	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	201.0	97.0	239.0	0.0	0.482587	0	C|0.983;G|0.017	0.017	strong	.	CDH19	141	.	NM_021153	exon12	c.G1934C	p.G645A	CCACCCCCTTCAT	.	PASS	Atlas-SNP
GTF3C4	9329	hgsc.bcm.edu	37	9	135546021	135546021	+	Silent	SNP	G	G	A	rs146201597	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	9.0	8.0	13.0	0.0	0.888889	0	G|0.986;A|0.014	0.014	strong	.	GTF3C4	53	.	NM_012204	exon1	c.G36A	p.A12A	GCCCGCGGACGAC	.	PASS	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136029138	136029138	+	Silent	SNP	G	G	A	rs35902535	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140.0	68.0	122.0	0.0	0.485714	0	G|0.944;A|0.056	0.056	strong	.	GBGT1	25	.	NM_021996	exon7	c.C870T	p.G290G	CATGATGCCATTG	.	PASS	Atlas-SNP
GLRA1	2741	hgsc.bcm.edu	37	5	151208500	151208500	+	Silent	SNP	C	C	T	rs75463357	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71.0	35.0	66.0	0.0	0.492958	0	C|0.983;T|0.017	0.017	strong	.	GLRA1	61	.	NM_000171	exon8	c.G1041A	p.R347R	CCGCTTCCTCCTG	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	37	17	8396176	8396176	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91.0	4.0	125.0	0.0	0.043956	0	.	.	none	.	MYH10	148	.	NM_001256012	exon33	c.A4376G	p.E1459G	TCCAGCTCCTGCT	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84926756	84926756	+	Silent	SNP	G	G	A	rs74514752	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	85.0	38.0	94.0	0.0	0.447059	0	G|0.994;A|0.006	0.006	strong	.	DNAH6	194	.	NM_001370	exon48	c.G7716A	p.L2572L	GAAGCTGCACATT	.	PASS	Atlas-SNP
VWCE	220001	hgsc.bcm.edu	37	11	61053895	61053895	+	Silent	SNP	G	G	A	rs146572904	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64.0	26.0	56.0	0.0	0.40625	0	G|0.998;A|0.002	0.002	strong	.	VWCE	84	.	NM_152718	exon5	c.C432T	p.D144D	ACATTCGTCAATG	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137734084	137734084	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	144.0	68.0	156.0	0.0	0.472222	0	.	.	none	.	COL5A1	323	.	NM_000093	exon66	c.A5452G	p.N1818D	ATGTTCAATGACT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489754	32489754	+	Missense_Mutation	SNP	T	T	C	rs41551116	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	29.0	27.0	2.0	0.0	0.931035	0	T|0.952;C|0.047	0.047	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.A298G	p.R100G	CGCGCCTGTCTTC	.	PASS	Atlas-SNP
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349037	65349037	+	Silent	SNP	G	G	A	rs74684453	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	209.0	92.0	195.0	0.0	0.440191	0	G|0.989;A|0.011	0.011	strong	.	EHBP1L1	64	.	NM_001099409	exon9	c.G894A	p.T298T	GGACACGGCCCCC	.	PASS	Atlas-SNP
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519637	113519637	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	181.0	53.0	188.0	0.0	0.292818	0	.	.	none	.	PPP1R3A	317	.	NM_002711	exon4	c.G1510C	p.G504R	AAGATCCTTCTTC	.	PASS	Atlas-SNP
TOP2A	7153	hgsc.bcm.edu	37	17	38564363	38564363	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	58.0	27.0	43.0	0.0	0.465517	0	.	.	none	.	TOP2A	124	.	NM_001067	exon12	c.C1356T	p.S452S	CTCAGTGGAGTTT	.	PASS	Atlas-SNP
C20orf112	140688	hgsc.bcm.edu	37	20	31044059	31044059	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152.0	71.0	181.0	0.0	0.467105	0	.	.	none	.	C20orf112	39	.	NM_001256798	exon6	c.C981T	p.A327A	CTCGGCGGCCGTG	.	PASS	Atlas-SNP
ISM2	145501	hgsc.bcm.edu	37	14	77942316	77942316	+	Silent	SNP	G	G	A	rs3742732	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	14.0	7.0	12.0	0.0	0.5	0	G|0.930;A|0.070	0.070	strong	.	ISM2	68	.	NM_199296	exon7	c.C1338T	p.D446D	GTGCTCGTCCTGT	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68606192	68606192	+	Missense_Mutation	SNP	C	C	T	rs368307734		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	100.0	78.0	158.0	0.0	0.78	0	.	.	weak	.	ITGA11	110	.	NM_001004439	exon23	c.G2807A	p.R936Q	CTGTCCCGCTCAT	.	PASS	Atlas-SNP
HDHD3	81932	hgsc.bcm.edu	37	9	116136262	116136262	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145.0	75.0	116.0	0.0	0.517241	0	.	.	none	.	HDHD3	10	.	NM_031219	exon2	c.C373T	p.R125C	GTGTGCGGCACTC	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978210	45978210	+	Missense_Mutation	SNP	G	G	C	rs200250794	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199.0	118.0	165.0	0.0	0.592965	0	G|0.999;C|0.001	0.001	weak	.	KRTAP10-3	17	.	NM_198696	exon1	c.C389G	p.S130C	GCCCCAGAGCAGA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149489540	149489540	+	Missense_Mutation	SNP	G	G	A	rs199795943	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	7.0	5.0	27.0	0.0	0.714286	0	G|0.998;A|0.002	0.002	weak	.	.	.	.	NM_198455	exon37	c.G5693A	p.R1898Q	GGCCCCGACGCTG	.	PASS	Atlas-SNP
CCDC9	26093	hgsc.bcm.edu	37	19	47774358	47774358	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145.0	72.0	150.0	0.0	0.496552	0	.	.	none	.	CCDC9	37	.	NM_015603	exon11	c.G1105C	p.E369Q	CGCTGGGAGACAA	.	PASS	Atlas-SNP
RPS24	6229	hgsc.bcm.edu	37	10	79814612	79814612	+	Silent	SNP	T	T	C	rs2257155	bycluster;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94.0	67.0	169.0	0.0	0.712766	0	T|1.000;|0.000	.	weak	.	RPS24	23	.	NM_001142285	exon5	c.T714C	p.G238G	GGACGGTGACTTG	.	PASS	Atlas-SNP
KHSRP	8570	hgsc.bcm.edu	37	19	6415735	6415735	+	Silent	SNP	A	A	G	rs145698454	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31.0	10.0	48.0	0.0	0.322581	0	A|0.994;G|0.006	0.006	strong	KHSRP,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	KHSRP	51	1	NM_003685	exon17	c.T1698C	p.A566A	CGCTGCAGCTGCT	.	PASS	Atlas-SNP
DUSP19	142679	hgsc.bcm.edu	37	2	183951796	183951796	+	Missense_Mutation	SNP	G	G	A	rs368865344		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48.0	17.0	57.0	0.0	0.354167	0	.	.	weak	.	DUSP19	41	.	NM_080876	exon3	c.G302A	p.G101E	CATATGGAGTTGA	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38345409	38345409	+	Missense_Mutation	SNP	A	A	G	rs71491230	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	95.0	24.0	162.0	0.0	0.252632	0	A|0.998;G|0.002	0.002	strong	ZNF33A,NS,carcinoma,0,1	ZNF33A	103	1	NM_006954	exon5	c.A2357G	p.Q786R	ATTTCCAGCCACA	.	PASS	Atlas-SNP
SF3B4	10262	hgsc.bcm.edu	37	1	149895866	149895866	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120.0	31.0	101.0	0.0	0.258333	0	.	.	none	.	SF3B4	37	.	NM_005850	exon5	c.C954T	p.G318G	TCCTAAGCCATGA	.	PASS	Atlas-SNP
ZNF85	7639	hgsc.bcm.edu	37	19	21133078	21133078	+	Missense_Mutation	SNP	A	A	G	rs142868740	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98.0	46.0	99.0	0.0	0.469388	0	A|0.999;G|0.001	0.001	strong	.	ZNF85	72	.	NM_001256171	exon5	c.A1848G	p.I616M	TAAGATAATTCAT	.	PASS	Atlas-SNP
TJP1	7082	hgsc.bcm.edu	37	15	30026582	30026582	+	Missense_Mutation	SNP	T	T	C	rs2229517	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61.0	43.0	135.0	0.0	0.704918	0	T|0.991;C|0.009	0.009	strong	.	TJP1	140	.	NM_175610	exon12	c.A1412G	p.N471S	ACGTTGTTTACCT	.	PASS	Atlas-SNP
SFN	2810	hgsc.bcm.edu	37	1	27190149	27190149	+	Missense_Mutation	SNP	C	C	T	rs78707984	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	41.0	11.0	48.0	0.0	0.268293	0	.	.	weak	.	SFN	20	.	NM_006142	exon1	c.C446T	p.S149L	CCCGGTCAGCCTA	.	PASS	Atlas-SNP
PRDM4	11108	hgsc.bcm.edu	37	12	108140191	108140191	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	109.0	46.0	122.0	0.0	0.422018	0	.	.	none	PRDM4,bladder,carcinoma,-1,1	PRDM4	64	1	NM_012406	exon6	c.G1137A	p.L379L	GTCACACAGAGTA	.	PASS	Atlas-SNP
SCAF1	58506	hgsc.bcm.edu	37	19	50154607	50154607	+	Missense_Mutation	SNP	C	C	T	rs146455893	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	19.0	16.0	20.0	0.0	0.842105	0	A|0.000;C|0.999;T|0.001	0.001	strong	.	SCAF1	78	.	NM_021228	exon7	c.C961T	p.R321C	AGCCCCCGCCCGG	.	PASS	Atlas-SNP
CLDN19	149461	hgsc.bcm.edu	37	1	43201614	43201614	+	Missense_Mutation	SNP	C	C	T	rs9660973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	134.0	45.0	216.0	0.0	0.335821	0	C|0.945;T|0.055	0.055	strong	.	CLDN19	21	.	NM_001185117	exon3	c.G476A	p.R159Q	TGGCTCCGGGCAT	.	PASS	Atlas-SNP
TPCN1	53373	hgsc.bcm.edu	37	12	113733830	113733830	+	Silent	SNP	C	C	T	rs61943642	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	121.0	60.0	158.0	0.0	0.495868	0	C|0.958;T|0.042	0.042	strong	.	TPCN1	109	.	NM_001143819	exon29	c.C2616T	p.P872P	AGCCCCCGCCGCC	.	PASS	Atlas-SNP
SAE1	10055	hgsc.bcm.edu	37	19	47700542	47700542	+	Silent	SNP	T	T	C	rs117605411	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	190.0	74.0	238.0	0.0	0.389474	0	T|0.997;C|0.003	0.003	strong	.	SAE1	50	.	NM_005500	exon7	c.T786C	p.Y262Y	TACATATGAGGAA	.	PASS	Atlas-SNP
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493809	77493809	+	Silent	SNP	C	C	T	rs61991638	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	13.0	4.0	15.0	0.0	0.307692	0	C|0.978;T|0.022	0.022	strong	.	IRF2BPL	40	.	NM_024496	exon1	c.G327A	p.Q109Q	CTGCTGCTGCTGT	.	PASS	Atlas-SNP
PEX5	5830	hgsc.bcm.edu	37	12	7343153	7343153	+	Silent	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	61.0	6.0	49.0	2.0	0.0983607	0.0408163	.	.	none	PEX5_ENST00000434354,colon,carcinoma,0,3	PEX5	63	3	NM_001131023	exon2	c.A180G	p.A60A	AGGTGCAGCCTCT	.	scavenged	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48226458	48226458	+	Silent	SNP	C	C	T	rs144318062		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	141.0	116.0	148.0	0.0	0.822695	0	C|1.000;T|0.000	0.000	weak	.	ABCC11	177	.	NM_033151	exon19	c.G2679A	p.T893T	CAGGGCCGTGGAT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149485557	149485557	+	Silent	SNP	C	C	T	rs73168056	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	86.0	15.0	117.0	0.0	0.174419	0	C|0.986;T|0.014	0.014	strong	.	.	.	.	NM_198455	exon27	c.C3963T	p.H1321H	GCTGCACGGTGTG	.	PASS	Atlas-SNP
CGRRF1	10668	hgsc.bcm.edu	37	14	55005083	55005083	+	Silent	SNP	C	C	T	rs202061859	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98.0	32.0	87.0	0.0	0.326531	0	C|0.999;T|0.001	0.001	weak	.	CGRRF1	30	.	NM_006568	exon6	c.C981T	p.D327D	TAAAGACAAACCG	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149519742	149519742	+	Missense_Mutation	SNP	G	G	A	rs201102091	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48.0	11.0	118.0	0.0	0.229167	0	.	.	weak	.	.	.	.	NM_198455	exon91	c.G13232A	p.R4411Q	ACTTCCGGCCTTG	.	PASS	Atlas-SNP
MAP2K1	5604	hgsc.bcm.edu	37	15	66727483	66727483	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	54.0	141.0	0.0	0.556701	0	.	.	none	MAP2K1,NS,lymphoid_neoplasm,0,5	MAP2K1	115	5	NM_002755	exon2	c.G199A	p.D67N	GATGACGACTTTG	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	37	16	2329071	2329071	+	Missense_Mutation	SNP	G	G	A	rs146709251	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	143.0	67.0	134.0	0.0	0.468531	0	G|0.997;A|0.003	0.003	strong	.	ABCA3	176	.	NM_001089	exon29	c.C4420T	p.R1474W	TCTCCCGGCCTGT	.	PASS	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11421004	11421004	+	Missense_Mutation	SNP	C	C	T	rs71455364	bycluster;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	27.0	108.0	0.0	0.369863	0	C|0.500;G|0.500	.	alt	.	PRB3	84	.	NM_006249	exon3	c.G179A	p.R60Q	GGGGGTCGTCCTT	.	PASS	Atlas-SNP
YAP1	10413	hgsc.bcm.edu	37	11	102094424	102094424	+	Silent	SNP	C	C	T	rs61749258	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	316.0	209.0	156.0	1.0	0.661392	0.00641026	C|0.995;T|0.005	0.005	strong	.	YAP1	45	.	NM_001130145	exon7	c.C1104T	p.P368P	TTCTCCCGGGATG	.	PASS	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	rs35898523	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	23.0	7.0	24.0	0.0	0.304348	0	G|0.941;T|0.059	0.059	strong	GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	NM_021996	exon7	c.C363A	p.Y121X	ATGAGTGTACCTA	.	PASS	Atlas-SNP
WRAP73	49856	hgsc.bcm.edu	37	1	3551828	3551828	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118.0	48.0	157.0	0.0	0.40678	0	.	.	none	WRAP73,NS,carcinoma,+1,1	WRAP73	43	1	NM_017818	exon7	c.C634T	p.R212W	ACAACCGGCCATC	.	PASS	Atlas-SNP
PCM1	5108	hgsc.bcm.edu	37	8	17847418	17847418	+	Silent	SNP	A	A	G	rs145539051	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	45.0	79.0	0.0	0.463918	0	A|0.991;G|0.009	0.009	strong	.	PCM1	120	.	NM_006197	exon27	c.A4461G	p.Q1487Q	TGAGCAAAATGAT	.	PASS	Atlas-SNP
CBS	875	hgsc.bcm.edu	37	21	44483101	44483101	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120.0	27.0	106.0	0.0	0.225	0	.	.	none	.	CBS	85	.	NM_000071	exon10	c.A916G	p.I306V	AGCCGATCCCTTC	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	37	7	24789386	24789386	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	114.0	29.0	113.0	0.0	0.254386	0	.	.	none	.	DFNA5	51	.	NM_001127453	exon2	c.C8T	p.A3V	GCTTTGGCAAACA	.	PASS	Atlas-SNP
DHX15	1665	hgsc.bcm.edu	37	4	24550580	24550580	+	Silent	SNP	G	G	A	rs33972724	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92.0	39.0	102.0	0.0	0.423913	0	G|0.991;A|0.009	0.009	strong	.	DHX15	69	.	NM_001358	exon6	c.C1146T	p.D382D	TTTAATGTCACCA	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30868352	30868352	+	Silent	SNP	C	C	T	rs201645679	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98.0	48.0	80.0	0.0	0.489796	0	C|0.999;T|0.001	0.001	weak	.	FAM188B	62	.	NM_032222	exon6	c.C1131T	p.L377L	GCGGCTCGGTAGG	.	PASS	Atlas-SNP
IKBKB	3551	hgsc.bcm.edu	37	8	42174380	42174380	+	Silent	SNP	G	G	A	rs56230731	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	115.0	37.0	106.0	0.0	0.321739	0	G|0.991;A|0.009	0.009	strong	.	IKBKB	88	.	NM_001556	exon11	c.G1083A	p.L361L	GGCGTTGATCCCC	.	PASS	Atlas-SNP
PARP3	10039	hgsc.bcm.edu	37	3	51981769	51981769	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	57.0	103.0	0.0	0.587629	0	.	.	none	.	PARP3	90	.	NM_001003931	exon10	c.G1311A	p.K437K	CATGAAGTGTGGG	.	PASS	Atlas-SNP
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	140.0	64.0	141.0	0.0	0.457143	0	G|0.968;A|0.032	0.032	strong	.	SCYL1	76	.	NM_020680	exon4	c.G600A	p.K200K	AGAGAAGTGGTGG	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680463	100680463	+	Missense_Mutation	SNP	G	G	T	rs368849364	alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	204.0	19.0	157.0	0.0	0.0931373	0	.	.	alt	.	MUC17	804	.	NM_001040105	exon3	c.G5766T	p.R1922S	TCCTAGGGAAGGA	.	PASS	Atlas-SNP
PANX2	56666	hgsc.bcm.edu	37	22	50617671	50617671	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	127.0	44.0	146.0	0.0	0.346457	0	.	.	none	.	PANX2	69	.	NM_052839	exon3	c.G1999A	p.E667K	TTCGACGAGCCGA	.	PASS	Atlas-SNP
TGM4	7047	hgsc.bcm.edu	37	3	44948563	44948563	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	230.0	117.0	270.0	0.0	0.508696	0	.	.	none	.	TGM4	82	.	NM_003241	exon10	c.A1198G	p.M400V	GTGAAGATGGTGA	.	PASS	Atlas-SNP
HNRNPA1	3178	hgsc.bcm.edu	37	12	54676630	54676630	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104.0	38.0	125.0	0.0	0.365385	0	.	.	none	.	HNRNPA1	72	.	NM_002136	exon7	c.G723A	p.G241G	CAGTGGGGATGGC	.	PASS	Atlas-SNP
TMEM45A	55076	hgsc.bcm.edu	37	3	100274090	100274090	+	Missense_Mutation	SNP	C	C	A	rs200878698	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156.0	68.0	195.0	0.0	0.435897	0	.	.	weak	TMEM45A,NS,carcinoma,+1,1	TMEM45A	35	1	NM_018004	exon2	c.C35A	p.T12N	CTGGAACCTTCTT	.	PASS	Atlas-SNP
HENMT1	113802	hgsc.bcm.edu	37	1	109200108	109200108	+	Missense_Mutation	SNP	C	C	T	rs36100901	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	69.0	53.0	111.0	0.0	0.768116	0	C|0.984;T|0.016	0.016	strong	.	HENMT1	38	.	NM_144584	exon3	c.G115A	p.V39I	TTTTAACGAACTG	.	PASS	Atlas-SNP
XKR9	389668	hgsc.bcm.edu	37	8	71646201	71646201	+	Missense_Mutation	SNP	C	C	T	rs61734026	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	461.0	266.0	365.0	0.0	0.577007	0	C|0.990;T|0.010	0.010	strong	.	XKR9	43	.	NM_001011720	exon5	c.C664T	p.L222F	GTTGTACTTCTAC	.	PASS	Atlas-SNP
C9orf172	389813	hgsc.bcm.edu	37	9	139740436	139740436	+	Missense_Mutation	SNP	G	G	A	rs375030600		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	63.0	37.0	81.0	0.0	0.587302	0	.	.	weak	.	C9orf172	23	.	NM_001080482	exon1	c.G1570A	p.G524S	GGCCTGGGCCGCA	.	PASS	Atlas-SNP
MBD1	4152	hgsc.bcm.edu	37	18	47796399	47796399	+	Missense_Mutation	SNP	A	A	C	rs183864846	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	5.0	4.0	5.0	0.0	0.8	0	A|0.993;C|0.007	0.007	strong	MBD1_ENST00000339998,NS,carcinoma,-1,1	MBD1	228	1	NM_001204142	exon14	c.T1635G	p.I545M	CAAATAAATTTCA	.	scavenged	Atlas-SNP
FAM134A	79137	hgsc.bcm.edu	37	2	220046155	220046155	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74.0	18.0	82.0	0.0	0.243243	0	.	.	none	FAM134A,colon,carcinoma,0,1	FAM134A	34	1	NM_024293	exon7	c.C849T	p.S283S	TGAAAGCGAGGCA	.	PASS	Atlas-SNP
MEP1B	4225	hgsc.bcm.edu	37	18	29782953	29782953	+	Missense_Mutation	SNP	A	A	G	rs71361372	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39.0	24.0	37.0	0.0	0.615385	0	A|0.992;G|0.008	0.008	strong	.	MEP1B	54	.	NM_005925	exon6	c.A348G	p.I116M	CTATATATCAGTG	.	PASS	Atlas-SNP
LEPRE1	64175	hgsc.bcm.edu	37	1	43223489	43223489	+	Missense_Mutation	SNP	C	C	T	rs6700677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	98.0	20.0	170.0	0.0	0.204082	0	C|0.940;T|0.060	0.060	strong	LEPRE1_ENST00000296388,colon,carcinoma,0,8	LEPRE1	130	8	NM_001146289	exon5	c.G1045A	p.G349R	CTTCTCCAAGCAT	.	PASS	Atlas-SNP
PTH1R	5745	hgsc.bcm.edu	37	3	46939456	46939456	+	Splice_Site	SNP	G	G	C	rs201472450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	147.0	49.0	123.0	0.0	0.333333	0	.	.	weak	.	PTH1R	49	.	NM_000316	exon6	c.424+1G>C	.	ACAAAGGTGAGGC	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789345	117789345	+	Missense_Mutation	SNP	G	G	C	rs61900347	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	243.0	27.0	144.0	0.0	0.111111	0	G|0.899;C|0.101	0.101	strong	TMPRSS13_ENST00000445164,NS,carcinoma,0,2	TMPRSS13	75	2	NM_001206790	exon2	c.C230G	p.A77G	GCCTGGGCTGGAG	.	PASS	Atlas-SNP
PAX8	7849	hgsc.bcm.edu	37	2	113976146	113976146	+	Silent	SNP	T	T	C	rs368201100		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70.0	32.0	54.0	0.0	0.457143	0	.	.	weak	.	PAX8	42	.	NM_003466	exon12	c.A1317G	p.A439A	GGGCGGTGCACTC	.	PASS	Atlas-SNP
AKR1B15	441282	hgsc.bcm.edu	37	7	134261174	134261174	+	Missense_Mutation	SNP	A	A	G	rs2458502	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	77.0	17.0	91.0	0.0	0.220779	0	A|0.998;G|0.002	0.002	strong	.	AKR1B15	105	.	NM_001080538	exon9	c.A817G	p.T273A	AAAACCACAGCCC	.	PASS	Atlas-SNP
CCDC178	374864	hgsc.bcm.edu	37	18	30928852	30928852	+	Splice_Site	SNP	A	A	G	rs140419270	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62.0	24.0	77.0	0.0	0.387097	0	A|0.997;G|0.003	0.003	strong	.	.	.	.	NM_001105528	exon8	c.457+2T>C	.	AACTTTACCTCTC	.	PASS	Atlas-SNP
PAGE5	90737	hgsc.bcm.edu	37	X	55247817	55247817	+	Missense_Mutation	SNP	T	T	C	rs61745114	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	278.0	272.0	622.0	0.0	0.978417	0	T|0.994;C|0.006	0.006	strong	.	PAGE5	20	.	NM_130467	exon2	c.T62C	p.M21T	GAGATATGAGTGA	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489753	32489753	+	Missense_Mutation	SNP	C	C	T	rs41544215	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	27.0	25.0	2.0	0.0	0.925926	0	T|0.078;C|0.922	0.078	strong	.	HLA-DRB5	31	.	NM_002125	exon2	c.G299A	p.R100K	GCGCGCCTGTCTT	.	PASS	Atlas-SNP
QPCTL	54814	hgsc.bcm.edu	37	19	46202131	46202131	+	Missense_Mutation	SNP	C	C	T	rs145016874	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92.0	45.0	113.0	0.0	0.48913	0	C|0.999;T|0.001	0.001	strong	.	QPCTL	24	.	NM_017659	exon5	c.C859T	p.R287C	ACGGTCCGCTGGT	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42526775	42526775	+	Missense_Mutation	SNP	C	C	T	rs72552268	byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	289.0	154.0	308.0	1.0	0.532872	0.00324675	C|0.996;T|0.004	0.004	strong	.	CYP2D6	104	.	NM_000106	exon1	c.G19A	p.V7M	GGGGCACCAGTGC	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3267108	3267108	+	Silent	SNP	A	A	G	rs190257069	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	38.0	90.0	0.0	0.372549	0	A|0.999;G|0.001	0.001	strong	.	CSMD1	1469	.	NM_033225	exon13	c.T1581C	p.C527C	ATCCCCACACCCT	.	PASS	Atlas-SNP
KIAA0895	23366	hgsc.bcm.edu	37	7	36366404	36366404	+	Missense_Mutation	SNP	C	C	T	rs191576648	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	246.0	100.0	171.0	0.0	0.406504	0	C|1.000;T|0.000	0.000	strong	.	KIAA0895	89	.	NM_001100425	exon7	c.G1528A	p.E510K	TCAGTTCATTCAC	.	PASS	Atlas-SNP
OSGIN1	29948	hgsc.bcm.edu	37	16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	rs62640905	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53.0	43.0	76.0	0.0	0.811321	0	T|0.985;C|0.015	0.015	strong	.	OSGIN1	33	.	NM_182981	exon6	c.T1370C	p.V457A	GGTTTGTGCAGGG	.	PASS	Atlas-SNP
GAB3	139716	hgsc.bcm.edu	37	X	153925443	153925443	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	74.0	4.0	158.0	0.0	0.0540541	0	.	.	none	.	GAB3	73	.	NM_001081573	exon7	c.A1391G	p.E464G	GCATGTTCCCGGA	.	PASS	Atlas-SNP
NDST3	9348	hgsc.bcm.edu	37	4	118975189	118975189	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123.0	60.0	224.0	1.0	0.487805	0.00446429	.	.	none	.	NDST3	107	.	NM_004784	exon2	c.G124T	p.E42X	GAAAATGAACTCT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	rs112900956	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	40.0	89.0	0.0	0.615385	0	G|0.994;A|0.006	0.006	strong	MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	NM_001130065	exon22	c.G3838A	p.G1280S	CCATGTGGCAGCC	.	PASS	Atlas-SNP
POU4F2	5458	hgsc.bcm.edu	37	4	147561804	147561804	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	55.0	3.0	74.0	0.0	0.0545455	0	.	.	none	POU4F2,caecum,carcinoma,+1,1	POU4F2	83	1	NM_004575	exon2	c.C1074T	p.R358R	GAAGCGCTCGCTC	.	scavenged	Atlas-SNP
ZNF493	284443	hgsc.bcm.edu	37	19	21607252	21607252	+	Missense_Mutation	SNP	T	T	A	rs142288436		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66.0	11.0	77.0	0.0	0.166667	0	.	.	weak	.	ZNF493	178	.	NM_001076678	exon4	c.T1791A	p.D597E	TACTGATAAGAAA	.	PASS	Atlas-SNP
USP40	55230	hgsc.bcm.edu	37	2	234429744	234429744	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	67.0	6.0	60.0	0.0	0.0895522	0	.	.	none	USP40_ENST00000450966,caecum,carcinoma,+2,2	USP40	174	2	NM_018218	exon16	c.G2251A	p.E751K	ATTTCTCTTCCTT	.	scavenged	Atlas-SNP
CCR2	729230	hgsc.bcm.edu	37	3	46399226	46399226	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	353.0	141.0	380.0	1.0	0.399433	0.00263158	.	.	none	.	CCR2	103	.	NM_001123041	exon2	c.T208G	p.C70G	ATAAACTGCAAAA	.	PASS	Atlas-SNP
AHCTF1	25909	hgsc.bcm.edu	37	1	247051714	247051714	+	Silent	SNP	A	A	G	rs144599339	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	565.0	328.0	477.0	1.0	0.580531	0.00209644	A|0.997;G|0.003	0.003	strong	.	AHCTF1	187	.	NM_015446	exon18	c.T2277C	p.Y759Y	AGGAGGATATTTT	.	PASS	Atlas-SNP
TMEM52B	120939	hgsc.bcm.edu	37	12	10332198	10332198	+	Missense_Mutation	SNP	G	G	T	rs140071448	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118.0	54.0	163.0	0.0	0.457627	0	G|1.000;T|0.000	0.000	strong	.	.	.	.	NM_153022	exon1	c.G9T	p.W3C	GTCGTGGCGGCCT	.	PASS	Atlas-SNP
NAV2	89797	hgsc.bcm.edu	37	11	19735325	19735325	+	Silent	SNP	C	C	A	rs11828836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	21.0	9.0	38.0	0.0	0.428571	0	C|0.975;A|0.025	0.025	strong	.	NAV2	255	.	NM_145117	exon1	c.C84A	p.P28P	CGTGCCCCCGGCC	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561313	32561313	+	Nonsense_Mutation	SNP	C	C	T	rs201986816	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126.0	7.0	116.0	0.0	0.0555556	0	C|0.998;T|0.002	0.002	strong	.	ARHGAP5	166	.	NM_001173	exon2	c.C1438T	p.R480X	CATCAGCGAGAAA	.	PASS	Atlas-SNP
RNGTT	8732	hgsc.bcm.edu	37	6	89614521	89614521	+	Silent	SNP	G	G	A	rs139029923		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	206.0	103.0	227.0	0.0	0.5	0	G|1.000;A|0.000	0.000	weak	.	RNGTT	52	.	NM_003800	exon6	c.C597T	p.D199D	ATCTTCGTCTTCA	.	PASS	Atlas-SNP
RUFY2	55680	hgsc.bcm.edu	37	10	70143826	70143826	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	84.0	4.0	132.0	0.0	0.047619	0	.	.	none	.	RUFY2	58	.	NM_017987	exon9	c.A909G	p.K303K	CTGTGTTTTCATT	.	PASS	Atlas-SNP
CTNNA3	29119	hgsc.bcm.edu	37	10	68535222	68535222	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	6.0	175.0	0.0	0.0588235	0	.	.	none	.	CTNNA3	401	.	NM_013266	exon8	c.A1108G	p.T370A	CTCTTGTCTTCTT	.	PASS	Atlas-SNP
AGPAT4	56895	hgsc.bcm.edu	37	6	161567601	161567601	+	Silent	SNP	G	G	A	rs16892215	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	76.0	36.0	77.0	0.0	0.473684	0	G|0.975;A|0.025	0.025	strong	.	AGPAT4	50	.	NM_020133	exon7	c.C798T	p.D266D	GTCATCGTCTTCA	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121742124	121742124	+	Silent	SNP	G	G	A	rs61732852	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	180.0	83.0	206.0	0.0	0.461111	0	G|0.991;A|0.009	0.009	strong	.	GLI2	187	.	NM_005270	exon11	c.G1761A	p.T587T	GAAAACGGTCCAC	.	PASS	Atlas-SNP
BIRC3	330	hgsc.bcm.edu	37	11	102195297	102195297	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	442.0	95.0	315.0	0.0	0.214932	0	.	.	none	.	BIRC3	56	.	NM_001165	exon2	c.G57A	p.T19T	CAACACGTTTGAA	.	PASS	Atlas-SNP
GBP7	388646	hgsc.bcm.edu	37	1	89599013	89599013	+	Silent	SNP	G	G	T	rs115671591	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	274.0	272.0	473.0	0.0	0.992701	0	G|0.979;T|0.021	0.021	strong	.	GBP7	57	.	NM_207398	exon10	c.C1590A	p.L530L	CTTCTTGAGTTGA	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231226371	231226371	+	Missense_Mutation	SNP	A	A	G	rs190007801	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	4.0	103.0	0.0	0.0449438	0	A|0.999;G|0.001	0.001	strong	.	SP140L	68	.	NM_138402	exon5	c.A482G	p.E161G	GAAAAGAAAGGGA	.	PASS	Atlas-SNP
BIRC3	330	hgsc.bcm.edu	37	11	102195984	102195984	+	Silent	SNP	T	T	A	rs147757750	bycluster;by1000genomes;alternate_allele	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	106.0	20.0	66.0	0.0	0.188679	0	T|1.000;C|0.000	.	alt	BIRC3,colon,carcinoma,+2,2	BIRC3	56	2	NM_001165	exon2	c.T744A	p.S248S	AGTTTCTAATCTG	.	PASS	Atlas-SNP
NCKIPSD	51517	hgsc.bcm.edu	37	3	48717276	48717276	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123.0	67.0	166.0	0.0	0.544715	0	.	.	none	.	NCKIPSD	52	.	NM_016453	exon7	c.C1308T	p.N436N	GAACTCGTTTCTC	.	PASS	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20897065	20897065	+	Silent	SNP	G	G	A	rs368179614		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	302.0	123.0	246.0	0.0	0.407285	0	.	.	weak	.	KLHL33	37	.	NM_001109997	exon4	c.C1545T	p.P515P	CACAGCGGGCAGT	.	PASS	Atlas-SNP
PCIF1	63935	hgsc.bcm.edu	37	20	44575932	44575932	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104.0	6.0	110.0	0.0	0.0576923	0	.	.	none	.	PCIF1	51	.	NM_022104	exon16	c.T1738C	p.S580P	CCCCTGTCCTTCA	.	PASS	Atlas-SNP
SAR1B	51128	hgsc.bcm.edu	37	5	133945288	133945288	+	Silent	SNP	C	C	T	rs140899111	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145.0	56.0	138.0	0.0	0.386207	0	C|0.999;T|0.001	0.001	strong	.	SAR1B	19	.	NM_001033503	exon6	c.G321A	p.R107R	TAACAGCCTTTCG	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33697576	33697576	+	Missense_Mutation	SNP	G	G	A	rs187640762	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	88.0	34.0	67.0	0.0	0.386364	0	G|0.995;A|0.005	0.005	strong	.	URB1	176	.	NM_014825	exon31	c.C5084T	p.S1695L	AAGTGCGAGTAGT	.	PASS	Atlas-SNP
HOXB5	3215	hgsc.bcm.edu	37	17	46669730	46669730	+	Silent	SNP	G	G	T	rs36049616	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	203.0	76.0	187.0	0.0	0.374384	0	G|0.960;T|0.040	0.040	strong	.	HOXB5	20	.	NM_002147	exon2	c.C651A	p.R217R	CAGGTAGCGGTTG	.	PASS	Atlas-SNP
VWA2	340706	hgsc.bcm.edu	37	10	116045993	116045993	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	89.0	43.0	117.0	0.0	0.483146	0	.	.	none	.	VWA2	64	.	NM_001272046	exon11	c.G1293A	p.E431E	GGCAGAGCGTGGC	.	PASS	Atlas-SNP
GNB5	10681	hgsc.bcm.edu	37	15	52433397	52433397	+	Silent	SNP	C	C	T	rs17612637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94.0	24.0	186.0	0.0	0.255319	0	C|0.973;G|0.000;T|0.027	0.027	strong	.	GNB5	28	.	NM_016194	exon7	c.G567A	p.K189K	AACAGACTTCTTT	.	PASS	Atlas-SNP
RCOR1	23186	hgsc.bcm.edu	37	14	103173756	103173756	+	Silent	SNP	C	C	A	rs149418829	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	162.0	51.0	161.0	0.0	0.314815	0	C|0.990;A|0.010	0.010	strong	.	RCOR1	39	.	NM_015156	exon5	c.C567A	p.T189T	CTTTACCCCTTTC	.	PASS	Atlas-SNP
KRT1	3848	hgsc.bcm.edu	37	12	53069243	53069243	+	Missense_Mutation	SNP	T	T	C	rs77846840	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	25.0	8.0	17.0	0.0	0.32	0	T|0.500;C|0.500	0.500	weak	.	KRT1	110	.	NM_006121	exon9	c.A1669G	p.S557G	AGCTGCTACCTCC	.	PASS	Atlas-SNP
TRDMT1	1787	hgsc.bcm.edu	37	10	17243610	17243610	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	18.0	12.0	44.0	0.0	0.666667	0	.	.	none	.	TRDMT1	46	.	NM_004412	exon1	c.G24A	p.E8E	GTATAGCTCCAGC	.	PASS	Atlas-SNP
BPIFA2	140683	hgsc.bcm.edu	37	20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	rs17304572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	126.0	58.0	148.0	0.0	0.460317	0	A|0.994;G|0.006	0.006	strong	.	.	.	.	NM_080574	exon4	c.A337G	p.K113E	GATGTCAAAGCTG	.	PASS	Atlas-SNP
INF2	64423	hgsc.bcm.edu	37	14	105179184	105179184	+	Missense_Mutation	SNP	G	G	A	rs142678449	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145.0	50.0	121.0	0.0	0.344828	0	G|0.992;A|0.008	0.008	strong	.	INF2	148	.	NM_022489	exon18	c.G2630A	p.R877Q	CCTTCCGGGCACT	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82451984	82451984	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	62.0	12.0	60.0	0.0	0.193548	0	.	.	none	.	PCLO	1506	.	NM_014510	exon20	c.A14618C	p.E4873A	GATTTCTCAATGG	.	PASS	Atlas-SNP
SYT15	83849	hgsc.bcm.edu	37	10	46967514	46967514	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	145.0	15.0	141.0	0.0	0.103448	0	.	.	none	.	SYT15	165	.	NM_031912	exon4	c.A563G	p.Y188C	AGCAGGTAGAGCT	.	PASS	Atlas-SNP
CTNS	1497	hgsc.bcm.edu	37	17	3563221	3563221	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	174.0	46.0	134.0	0.0	0.264368	0	.	.	none	.	CTNS	42	.	NM_001031681	exon11	c.G922A	p.G308R	TTCACCGGGGGCA	.	PASS	Atlas-SNP
CELA1	1990	hgsc.bcm.edu	37	12	51739625	51739625	+	Missense_Mutation	SNP	C	C	T	rs74336876	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53.0	26.0	66.0	0.0	0.490566	0	C|0.995;T|0.005	0.005	strong	.	CELA1	39	.	NM_001971	exon2	c.G53A	p.R18H	ACTACGCGGGCAT	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	rs34551253	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	10.0	6.0	15.0	0.0	0.6	0	C|0.983;T|0.017	0.017	strong	.	TRPM5	86	.	NM_014555	exon9	c.G1366A	p.A456T	GCCCCGCGGGTGG	.	PASS	Atlas-SNP
MRGPRF	116535	hgsc.bcm.edu	37	11	68773089	68773089	+	Missense_Mutation	SNP	C	C	T	rs151254404	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	118.0	56.0	122.0	0.0	0.474576	0	C|1.000;T|0.000	0.000	weak	.	MRGPRF	22	.	NM_001098515	exon3	c.G689A	p.R230Q	TGGCGCCGTCGGG	.	PASS	Atlas-SNP
CCDC159	126075	hgsc.bcm.edu	37	19	11465311	11465311	+	Silent	SNP	C	C	T	rs374274390		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	124.0	59.0	133.0	0.0	0.475806	0	.	.	weak	.	CCDC159	35	.	NM_001080503	exon10	c.C828T	p.S276S	TGACTCCGACTGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100678693	100678693	+	Silent	SNP	T	T	C	rs78176991	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	264.0	39.0	200.0	0.0	0.147727	0	T|0.994;C|0.006	0.006	strong	.	MUC17	804	.	NM_001040105	exon3	c.T3996C	p.Y1332Y	AACTTATAGTGAA	.	PASS	Atlas-SNP
CEP164	22897	hgsc.bcm.edu	37	11	117222691	117222691	+	Missense_Mutation	SNP	C	C	A	rs143659874	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49.0	38.0	35.0	0.0	0.77551	0	C|0.998;A|0.002	0.002	strong	.	CEP164	121	.	NM_001271933	exon4	c.C380A	p.P127H	ACCCCCCCAAAAG	.	PASS	Atlas-SNP
FAM46C	54855	hgsc.bcm.edu	37	1	118166385	118166385	+	Missense_Mutation	SNP	G	G	A	rs145471785	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53.0	39.0	113.0	0.0	0.735849	0	G|0.995;A|0.005	0.005	strong	.	FAM46C	25	.	NM_017709	exon2	c.G895A	p.E299K	GCTGAAGAAGAGA	.	PASS	Atlas-SNP
THTPA	79178	hgsc.bcm.edu	37	14	24026046	24026046	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	158.0	93.0	126.0	0.0	0.588608	0	.	.	none	.	THTPA	11	.	NM_001256321	exon2	c.G80A	p.G27D	TGGGGGGCACCCT	.	PASS	Atlas-SNP
LIN9	286826	hgsc.bcm.edu	37	1	226474035	226474035	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	99.0	5.0	79.0	0.0	0.050505	0	.	.	none	.	LIN9	57	.	NM_173083	exon6	c.A571G	p.R191G	TTTACCTCCGTGG	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	37	12	6935995	6935995	+	Missense_Mutation	SNP	G	G	A	rs138578985	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	97.0	57.0	76.0	1.0	0.587629	0.0131579	G|1.000;A|0.000	0.000	weak	GPR162,bladder,carcinoma,0,1	GPR162	55	1	NM_019858	exon5	c.G1393A	p.E465K	GAGGACGAGGAGG	.	scavenged	Atlas-SNP
HIVEP3	59269	hgsc.bcm.edu	37	1	41978959	41978959	+	Missense_Mutation	SNP	C	C	T	rs144265546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	266.0	194.0	398.0	1.0	0.729323	0.00251256	C|1.000;T|0.000	0.000	weak	HIVEP3,NS,carcinoma,-1,1	HIVEP3	235	1	NM_024503	exon8	c.G5933A	p.R1978H	GGTGGACGGCTGC	.	PASS	Atlas-SNP
HS3ST5	222537	hgsc.bcm.edu	37	6	114378722	114378722	+	Missense_Mutation	SNP	A	A	T	rs17793043	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	199.0	105.0	247.0	0.0	0.527638	0	A|0.994;T|0.006	0.006	strong	.	HS3ST5	80	.	NM_153612	exon2	c.T740A	p.I247N	TGCTCAATTGGAA	.	PASS	Atlas-SNP
DNAJB1	3337	hgsc.bcm.edu	37	19	14629138	14629138	+	Silent	SNP	C	C	T	rs141518218	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	36.0	20.0	61.0	0.0	0.555556	0	C|0.995;T|0.005	0.005	strong	.	DNAJB1	38	.	NM_006145	exon1	c.G24A	p.T8T	GCCCAACGTCTGG	.	PASS	Atlas-SNP
TOP2A	7153	hgsc.bcm.edu	37	17	38546274	38546274	+	Silent	SNP	A	A	C	rs17680289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166.0	87.0	198.0	0.0	0.524096	0	A|0.988;C|0.012	0.012	strong	.	TOP2A	124	.	NM_001067	exon34	c.T4410G	p.T1470T	ATCAGAAGTGGAT	.	PASS	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs78337605	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	298.0	34.0	283.0	0.0	0.114094	0	C|0.500;T|0.500	0.500	strong	.	CYP2A6	69	.	NM_000762	exon7	c.G1039A	p.A347T	TCTTGGCCCGGTC	.	PASS	Atlas-SNP
GRIN2D	2906	hgsc.bcm.edu	37	19	48945044	48945044	+	Silent	SNP	C	C	T	rs144676582	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	48.0	120.0	0.0	0.470588	0	C|0.998;T|0.002	0.002	strong	.	GRIN2D	76	.	NM_000836	exon11	c.C2271T	p.I757I	CTTCATCTACGAT	.	PASS	Atlas-SNP
CYP24A1	1591	hgsc.bcm.edu	37	20	52790027	52790027	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	39.0	13.0	80.0	0.0	0.333333	0	.	.	none	.	CYP24A1	75	.	NM_000782	exon1	c.C92T	p.T31M	TACGCCGTAGATG	.	PASS	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848144	54848144	+	Missense_Mutation	SNP	T	T	A	rs74869671	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	179.0	18.0	233.0	0.0	0.100559	0	T|0.995;A|0.005	0.005	strong	.	LILRA4	91	.	NM_012276	exon6	c.A1223T	p.H408L	CTGGGGTGAGACA	.	PASS	Atlas-SNP
XIRP1	165904	hgsc.bcm.edu	37	3	39227495	39227495	+	Missense_Mutation	SNP	C	C	T	rs142860074	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	146.0	77.0	113.0	0.0	0.527397	0	C|0.999;T|0.001	0.001	strong	XIRP1,colon,carcinoma,0,1	XIRP1	173	1	NM_194293	exon2	c.G3442A	p.V1148M	TCCTCACGGGATG	.	PASS	Atlas-SNP
PTPN21	11099	hgsc.bcm.edu	37	14	88946343	88946343	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49.0	4.0	55.0	0.0	0.0816327	0	.	.	none	.	PTPN21	113	.	NM_007039	exon13	c.G1432A	p.G478S	AGCTGCCGATGTT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100682814	100682814	+	Missense_Mutation	SNP	A	A	G	rs201007776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	198.0	15.0	139.0	2.0	0.0757576	0.0143885	A|0.999;G|0.001	0.001	weak	MUC17,NS,carcinoma,0,1	MUC17	804	1	NM_001040105	exon3	c.A8117G	p.N2706S	TGGCCAATTCTGA	.	scavenged	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31606682	31606682	+	Silent	SNP	A	A	G	rs145596057	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	166.0	85.0	165.0	0.0	0.512048	0	A|0.999;G|0.001	0.001	strong	.	XDH	191	.	NM_000379	exon10	c.T825C	p.F275F	CATAGGAAACAGC	.	PASS	Atlas-SNP
PLIN3	10226	hgsc.bcm.edu	37	19	4861381	4861381	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	48.0	13.0	42.0	0.0	0.270833	0	.	.	none	PLIN3,NS,carcinoma,-1,1	PLIN3	36	1	NM_001164189	exon2	c.A26G	p.D9G	CTGCCATCAGCCT	.	PASS	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	37	7	100635143	100635143	+	Silent	SNP	T	T	C	rs34337783	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4.0	4.0	0.0	0.0	1	.	T|0.890;C|0.110	0.110	strong	MUC12,NS,carcinoma,+2,1	MUC12	140	1	NM_001164462	exon2	c.T1299C	p.R433R	AGGCCGTAGTGAG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26164700	26164700	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	53.0	31.0	60.0	0.0	0.584906	0	.	.	none	.	MYO18B	322	.	NM_032608	exon4	c.C817T	p.P273S	CAAGGGCCCGGCG	.	PASS	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	37	3	172061988	172061988	+	Silent	SNP	C	C	T	rs200807692	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	178.0	90.0	216.0	0.0	0.505618	0	C|1.000;T|0.000	0.000	strong	.	FNDC3B	118	.	NM_001135095	exon19	c.C2190T	p.V730V	CACCGTCGGCAAC	.	PASS	Atlas-SNP
MSH2	4436	hgsc.bcm.edu	37	2	47630528	47630528	+	Silent	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	111.0	62.0	171.0	0.0	0.558559	0	.	.	none	.	MSH2	198	.	NM_000251	exon1	c.C198T	p.Y66Y	CAAGTACATGGGG	.	PASS	Atlas-SNP
DHX57	90957	hgsc.bcm.edu	37	2	39042718	39042718	+	Missense_Mutation	SNP	T	T	G	rs150735204	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	123.0	61.0	112.0	0.0	0.495935	0	T|0.996;G|0.004	0.004	strong	DHX57,NS,carcinoma,0,1	DHX57	127	1	NM_198963	exon20	c.A3551C	p.E1184A	TCAATTTCCCTTG	.	PASS	Atlas-SNP
DPF3	8110	hgsc.bcm.edu	37	14	73137882	73137882	+	Missense_Mutation	SNP	G	G	A	rs202093453	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139.0	91.0	86.0	0.0	0.654676	0	.	.	weak	.	DPF3	117	.	NM_012074	exon9	c.C1036T	p.R346W	AACCCCGGCCACT	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169819835	169819835	+	Silent	SNP	A	A	G	rs113676921	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	70.0	47.0	119.0	0.0	0.671429	0	A|0.996;G|0.004	0.004	strong	.	PALLD	179	.	NM_001166108	exon14	c.A2442G	p.T814T	TTTCACATGTAGA	.	PASS	Atlas-SNP
AQPEP	0	hgsc.bcm.edu	37	5	115298898	115298898	+	Missense_Mutation	SNP	C	C	T	rs145336539	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131.0	56.0	131.0	0.0	0.427481	0	C|0.997;T|0.003	0.003	strong	.	.	.	.	NM_173800	exon1	c.C584T	p.P195L	GTGAGCCCCTGAA	.	PASS	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367350	142367350	+	Missense_Mutation	SNP	C	C	T	rs201039593	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	20.0	20.0	20.0	0.0	1	0	.	.	weak	.	GPR20	43	.	NM_005293	exon2	c.G674A	p.R225Q	CCCGGCCGCGACA	.	PASS	Atlas-SNP
OGDHL	55753	hgsc.bcm.edu	37	10	50959965	50959965	+	Silent	SNP	C	C	T	rs7090775	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	92.0	73.0	184.0	0.0	0.793478	0	C|0.960;T|0.040	0.040	strong	.	OGDHL	149	.	NM_018245	exon6	c.G657A	p.Q219Q	GATCCACTGGCAC	.	PASS	Atlas-SNP
CASP12	100506742	hgsc.bcm.edu	37	11	104768098	104768098	+	Silent	SNP	T	T	C	rs555367	bycluster;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	4.0	4.0	0.0	0.0	1	.	T|0.010;C|0.990	0.990	strong	.	CASP12	4	.	NM_001191016	exon2	c.A105G	p.V35V	ATTTAATACATTA	.	PASS	Atlas-SNP
OR10V1	390201	hgsc.bcm.edu	37	11	59480759	59480759	+	Missense_Mutation	SNP	C	C	T	rs141649641	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	94.0	52.0	102.0	0.0	0.553191	0	C|0.998;T|0.002	0.002	strong	.	OR10V1	40	.	NM_001005324	exon1	c.G560A	p.R187H	GCCAGGCGCATGA	.	PASS	Atlas-SNP
DHRS4	10901	hgsc.bcm.edu	37	14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	rs11556285	bycluster;byhapmap	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	1415.0	159.0	1032.0	1.0	0.112367	0.000968992	G|0.998;T|0.002	0.002	weak	.	DHRS4	22	.	NM_021004	exon6	c.G582T	p.K194N	GACCAAGACCCTG	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	65.0	12.0	136.0	0.0	0.184615	0	.	.	none	.	PCDHA4	419	.	NM_031500	exon1	c.G1581A	p.E527E	CGAGGAGCTAGAG	.	PASS	Atlas-SNP
GPAA1	8733	hgsc.bcm.edu	37	8	145138063	145138063	+	Silent	SNP	G	G	A	rs138412600	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	225.0	76.0	177.0	0.0	0.337778	0	G|0.993;A|0.007	0.007	strong	.	GPAA1	40	.	NM_003801	exon2	c.G111A	p.L37L	GTTCTTGGCGCTG	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	37	6	158516882	158516882	+	Missense_Mutation	SNP	C	C	T	rs137935231	bycluster;byfrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	59.0	30.0	60.0	0.0	0.508475	0	C|0.997;T|0.003	0.003	strong	.	SYNJ2	111	.	NM_003898	exon27	c.C3977T	p.P1326L	AGGCGCCGCCTCT	.	PASS	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	37	10	81917486	81917486	+	Missense_Mutation	SNP	T	T	C	rs1802932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64.0	39.0	121.0	0.0	0.609375	0	T|0.992;C|0.008	0.008	strong	.	ANXA11	32	.	NM_145868	exon15	c.A1369G	p.I457V	CCATGATGCGAAT	.	PASS	Atlas-SNP
TYROBP	7305	hgsc.bcm.edu	37	19	36398454	36398454	+	Silent	SNP	G	G	C	rs111477177	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	108.0	46.0	133.0	2.0	0.425926	0.0150376	A|0.000;C|0.024;G|0.976	0.024	strong	TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	NM_198125	exon3	c.C123G	p.G41G	CAGCACGCCCGGG	.	scavenged	Atlas-SNP
REXO1	57455	hgsc.bcm.edu	37	19	1827927	1827927	+	Silent	SNP	T	T	G	rs144940979	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	138.0	71.0	128.0	0.0	0.514493	0	T|0.999;G|0.001	0.001	strong	.	REXO1	55	.	NM_020695	exon2	c.A861C	p.S287S	TGAGTCTGAGAAC	.	PASS	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	37	21	43913112	43913112	+	Silent	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	251.0	62.0	148.0	0.0	0.247012	0	.	.	none	RSPH1,NS,carcinoma,0,1	RSPH1	36	1	NM_080860	exon2	c.C132T	p.Y44Y	CCCTTCGTAGGTG	.	PASS	Atlas-SNP
MTHFR	4524	hgsc.bcm.edu	37	1	11855269	11855269	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	66.0	10.0	93.0	0.0	0.151515	0	.	.	none	.	MTHFR	65	.	NM_005957	exon6	c.G917A	p.C306Y	TCCTGGCACAGGC	.	PASS	Atlas-SNP
PTPN6	5777	hgsc.bcm.edu	37	12	7067226	7067226	+	Missense_Mutation	SNP	G	G	A	rs62621988	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	22.0	11.0	41.0	0.0	0.5	0	G|0.999;A|0.001	0.001	strong	.	PTPN6	42	.	NM_080548	exon11	c.G1357A	p.V453M	ATCATCGTGCACT	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53856776	53856776	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156.0	7.0	145.0	0.0	0.0448718	0	.	.	none	.	ZNF845	101	.	NM_138374	exon4	c.A2848G	p.K950E	TGTGGCAAGGTTT	.	PASS	Atlas-SNP
CDH24	64403	hgsc.bcm.edu	37	14	23523353	23523353	+	Silent	SNP	G	G	T	rs139832060	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	51.0	34.0	35.0	0.0	0.666667	0	G|0.997;T|0.003	0.003	strong	.	CDH24	129	.	NM_022478	exon6	c.C969A	p.R323R	AACCTTGCGGACA	.	PASS	Atlas-SNP
HGS	9146	hgsc.bcm.edu	37	17	79660570	79660570	+	Missense_Mutation	SNP	C	C	T	rs150616739	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	223.0	117.0	264.0	1.0	0.524664	0.00378788	C|1.000;T|0.000	0.000	weak	.	HGS	54	.	NM_004712	exon9	c.C700T	p.P234S	GAGCTGCCCCCCG	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91660861	91660861	+	Silent	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	91.0	6.0	87.0	0.0	0.0659341	0	.	.	none	.	AKAP9	788	.	NM_005751	exon16	c.T4281C	p.N1427N	AACAAATATCGTT	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50407255	50407255	+	Silent	SNP	G	G	A	rs201329321	by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	168.0	50.0	136.0	0.0	0.297619	0	G|1.000;A|0.000	0.000	strong	.	SALL4	168	.	NM_020436	exon2	c.C1767T	p.T589T	CTCCCCGGTGTGG	.	PASS	Atlas-SNP
DCD	117159	hgsc.bcm.edu	37	12	55038536	55038536	+	Silent	SNP	G	G	A	rs139716642		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	238.0	120.0	214.0	0.0	0.504202	0	G|1.000;A|0.000	0.000	weak	.	DCD	20	.	NM_053283	exon5	c.C294T	p.A98A	ATGGACGGCTCCT	.	PASS	Atlas-SNP
CNTLN	54875	hgsc.bcm.edu	37	9	17135322	17135322	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	49.0	12.0	76.0	0.0	0.244898	0	.	.	none	.	CNTLN	128	.	NM_017738	exon1	c.A259G	p.R87G	GGGTCCAGACGGC	.	PASS	Atlas-SNP
IFNGR1	3459	hgsc.bcm.edu	37	6	137540423	137540423	+	Silent	SNP	C	C	T	rs17181471	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	131.0	52.0	179.0	0.0	0.396947	0	C|0.995;T|0.005	0.005	strong	.	IFNGR1	46	.	NM_000416	exon1	c.G42A	p.V14V	CCTGCTCACACCC	.	PASS	Atlas-SNP
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31104520	31104520	+	Missense_Mutation	SNP	A	A	G	rs144472289	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	139.0	69.0	85.0	0.0	0.496403	0	A|0.997;G|0.003	0.003	strong	.	ADCYAP1R1	78	.	NM_001118	exon3	c.A125G	p.N42S	GGGCCAATGAGCT	.	PASS	Atlas-SNP
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	64.0	11.0	133.0	0.0	0.171875	0	C|0.999;G|0.001	0.001	weak	PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	NM_031500	exon1	c.C1582G	p.L528V	GAGGAGCTAGAGC	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197408085	197408085	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	156.0	75.0	172.0	0.0	0.480769	0	.	.	none	.	KIAA0226	136	.	NM_014687	exon16	c.T2345G	p.I782S	ATCTTAATGAGCA	.	PASS	Atlas-SNP
ASB6	140459	hgsc.bcm.edu	37	9	132401753	132401753	+	Silent	SNP	G	G	A	rs144137235	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	81.0	34.0	82.0	0.0	0.419753	0	G|0.999;A|0.001	0.001	strong	.	ASB6	31	.	NM_017873	exon3	c.C330T	p.A110A	CAGGACGGCGATG	.	PASS	Atlas-SNP
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	116.0	57.0	112.0	0.0	0.491379	0	G|0.899;A|0.101	0.101	strong	.	BRD1	144	.	NM_014577	exon1	c.C579T	p.F193F	CTTCTCGAAGCGG	.	PASS	Atlas-SNP
MNDA	4332	hgsc.bcm.edu	37	1	158817521	158817521	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	120.0	5.0	77.0	0.0	0.0416667	0	.	.	none	MNDA,colon,carcinoma,0,2	MNDA	147	2	NM_002432	exon6	c.A991G	p.S331G	CAGAAAAGCGTAC	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88789687	88789687	+	Missense_Mutation	SNP	C	C	T	rs188337046	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	31.0	27.0	47.0	0.0	0.870968	0	C|0.983;T|0.017	0.017	strong	.	PIEZO1	79	.	NM_001142864	exon32	c.G4385A	p.R1462Q	TGCTGCCGCCGCC	.	PASS	Atlas-SNP
CACUL1	143384	hgsc.bcm.edu	37	10	120489828	120489828	+	Silent	SNP	G	G	A	rs41284412	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	104.0	54.0	137.0	0.0	0.519231	0	G|0.998;A|0.002	0.002	strong	.	.	.	.	NM_153810	exon2	c.C462T	p.D154D	GATATAGTCACCA	.	PASS	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42525089	42525089	+	Missense_Mutation	SNP	G	G	C	rs78482768	bycluster	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	102.0	52.0	119.0	0.0	0.509804	0	G|1.000;|0.000	.	weak	.	CYP2D6	104	.	NM_000106	exon3	c.C451G	p.Q151E	CCCACTGCTCCAG	.	PASS	Atlas-SNP
IRX6	79190	hgsc.bcm.edu	37	16	55362625	55362625	+	Silent	SNP	C	C	T	rs199714803		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	42.0	36.0	34.0	0.0	0.857143	0	C|0.999;T|0.001	0.001	weak	.	IRX6	66	.	NM_024335	exon5	c.C735T	p.S245S	TGCTAGCCAGGAG	.	PASS	Atlas-SNP
S100PBP	64766	hgsc.bcm.edu	37	1	33292189	33292189	+	Silent	SNP	C	C	T	rs41265867	bycluster;byfrequency;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	26.0	20.0	36.0	0.0	0.769231	0	C|0.992;T|0.008	0.008	strong	.	S100PBP	31	.	NM_001256121	exon3	c.C489T	p.D163D	TAAGGACGAGACT	.	PASS	Atlas-SNP
MYLK	4638	hgsc.bcm.edu	37	3	123419422	123419422	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	71.0	5.0	76.0	0.0	0.0704225	0	.	.	none	.	MYLK	224	.	NM_053025	exon18	c.A2893G	p.T965A	CGGGGGTCTTGGA	.	PASS	Atlas-SNP
CTC1	80169	hgsc.bcm.edu	37	17	8135446	8135446	+	Silent	SNP	G	G	A	rs3027235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	73.0	28.0	79.0	0.0	0.383562	0	G|0.964;A|0.036	0.036	strong	.	CTC1	75	.	NM_025099	exon13	c.C2160T	p.T720T	TGGGCCGGTGGGA	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	152.0	72.0	211.0	2.0	0.473684	0.00947867	T|0.799;C|0.201	0.201	strong	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	NM_001163213	exon7	c.T882C	p.N294N	GGTGAATGGCAGC	.	scavenged	Atlas-SNP
SLC44A3	126969	hgsc.bcm.edu	37	1	95322903	95322903	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	112.0	59.0	213.0	1.0	0.526786	0.00469484	.	.	none	.	SLC44A3	109	.	NM_001114106	exon10	c.T1085C	p.V362A	CCCAGGTTATGGA	.	PASS	Atlas-SNP
AMIGO2	347902	hgsc.bcm.edu	37	12	47471287	47471287	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	130.0	56.0	167.0	0.0	0.430769	0	.	.	none	AMIGO2,NS,carcinoma,-1,1	AMIGO2	50	1	NM_181847	exon2	c.C1499T	p.T500M	CCCCTCGTGGACT	.	PASS	Atlas-SNP
CLTCL1	8218	hgsc.bcm.edu	37	22	19175095	19175095	+	Missense_Mutation	SNP	A	A	C	rs182434700	bycluster;by1000genomes	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	185.0	90.0	209.0	1.0	0.486486	0.00478469	A|0.999;C|0.001	0.001	strong	.	CLTCL1	115	.	NM_007098	exon29	c.T4580G	p.L1527R	TTGCAGAGCTCCA	.	PASS	Atlas-SNP