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
TLL2	7093	hgsc.bcm.edu	37	10	98170201	98170201	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	77	13	63	0	0.168831	0	.	.	none	TLL2,NS,malignant_melanoma,-2,1	TLL2	122	1	NM_012465	exon9	c.1080delA	p.G360fs	.	.	PASS	Atlas-Indel
UBE2Q2	92912	hgsc.bcm.edu	37	15	76161328	76161330	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	194	38	142	0	0.195876	0	.	.	none	.	UBE2Q2	26	.	NM_173469	exon4	c.423_425del	p.141_142del	.	.	PASS	Atlas-Indel
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816842	75816843	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	88	11	67	0	0.125	0	.	.	none	.	GLIPR1L2	54	.	NM_152436	exon4	c.743_744insT	p.S248fs	.	.	PASS	Atlas-Indel
IGLL5	100423062	hgsc.bcm.edu	37	22	23237676	23237677	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	171	28	151	0	0.163743	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon3	c.447_448insT	p.A149fs	.	.	PASS	Atlas-Indel
ALG9	79796	hgsc.bcm.edu	37	11	111742146	111742146	+	Frame_Shift_Del	DEL	G	G	-	rs10708475	bycluster;by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	13	12	5	.	0.923	.	G|0.006;-|0.994	0.994	strong	.	ALG9	77	.	NM_024740	exon2	c.61delG	p.A21fs	.	.	PASS	Pindel
FAS	355	hgsc.bcm.edu	37	10	90773975	90773975	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	66	15	49	0	0.227273	0	.	.	none	.	FAS	47	.	NM_000043	exon9	c.T776C	p.I259T	CCAAAATAGATGA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016770	1016770	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	447	11	430	3	0.0246085	0.00697674	.	.	none	MUC6_ENST00000421673,extremity,malignant_melanoma,0,1	MUC6	408	1	NM_005961	exon31	c.C6031T	p.P2011S	AGAAAGGTGGAAC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507077	195507077	+	Missense_Mutation	SNP	G	G	A	rs76343663	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	129	14	129	8	0.108527	0.0620155	G|0.991;A|0.009	0.009	strong	MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	NM_018406	exon2	c.C11374T	p.P3792S	GAAGAGGGGTGGT	.	scavenged	Atlas-SNP
CCRL1	51554	hgsc.bcm.edu	37	3	132319910	132319910	+	Silent	SNP	A	A	G	rs3911405	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	506	20	355	10	0.0395257	0.028169	A|0.500;G|0.500	0.500	weak	CCRL1,NS,carcinoma,0,1	CCRL1	30	1	NM_178445	exon1	c.A669G	p.T223T	TATCACAGCAAGG	.	scavenged	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196651835	196651835	+	Missense_Mutation	SNP	G	G	A	rs200008102	by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	198	29	200	0	0.146465	0	G|1.000;A|0.000	0.000	strong	.	DNAH7	512	.	NM_018897	exon58	c.C10777T	p.R3593W	ATTTCCGTCTTTC	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11990882	11990882	+	Missense_Mutation	SNP	C	C	T	rs9720235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	10	9	3	0	0.9	0	C|0.499;T|0.501	0.501	strong	.	.	.	.	NM_001256869	exon1	c.G637A	p.V213I	CTGAAACGCCGTG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47754488	47754488	+	Missense_Mutation	SNP	A	A	G	rs111737555	bycluster;byfrequency;alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	92	9	64	3	0.0978261	0.046875	A|0.999;T|0.001	.	alt	PCNT,NS,carcinoma,0,1	PCNT	283	1	NM_006031	exon3	c.A445G	p.S149G	ACAGTCAGTGACC	.	scavenged	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T	rs111727691	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	189	28	170	0	0.148148	0	G|0.500;T|0.500	0.500	weak	.	ZNF814	93	.	NM_001144989	exon3	c.C968A	p.P323H	TCATAAGGTCTTT	.	PASS	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	37	2	26534617	26534617	+	Missense_Mutation	SNP	C	C	T	rs201936475	bycluster;by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	41	12	31	0	0.292683	0	C|1.000;T|0.000	0.000	strong	GPR113_ENST00000311519,NS,malignant_melanoma,0,5	GPR113	134	5	NM_001145168	exon11	c.G1979A	p.R660Q	AGTTTTCGCAGCA	.	PASS	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240794	39240794	+	Silent	SNP	C	C	A	rs9894106	by2hit2allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	9	6	22	0	0.666667	0	.	.	weak	KRTAP4-7,NS,carcinoma,0,3	KRTAP4-7	49	3	NM_033061	exon1	c.C336A	p.P112P	CCGCCCCAGCTGC	.	scavenged	Atlas-SNP
KRTAP11-1	337880	hgsc.bcm.edu	37	21	32253665	32253665	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	74	27	45	0	0.364865	0	.	.	none	KRTAP11-1,NS,carcinoma,+1,1	KRTAP11-1	46	1	NM_175858	exon1	c.G179T	p.C60F	TCACAGCAGGTCT	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25230091	25230091	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	64	9	53	0	0.140625	0	.	.	none	.	DOCK5	167	.	NM_024940	exon35	c.C3541T	p.R1181W	CATTGCCGGAAAC	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885567	+	Silent	SNP	A	A	C	rs75808076	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	42	8	31	0	0.190476	0	.	.	weak	NEFH,rectum,carcinoma,0,1	NEFH	178	1	NM_021076	exon4	c.A1938C	p.A646A	GGAAGCAAAGTCC	.	scavenged	Atlas-SNP
GPR50	9248	hgsc.bcm.edu	37	X	150348455	150348455	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	152	27	147	0	0.177632	0	.	.	none	.	GPR50	195	.	NM_004224	exon2	c.C400T	p.L134F	CACAGCCTCCAGT	.	PASS	Atlas-SNP
C1QTNF2	114898	hgsc.bcm.edu	37	5	159781844	159781844	+	Nonsense_Mutation	SNP	G	G	A	rs144600396	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	68	10	61	0	0.147059	0	G|1.000;A|0.000	0.000	strong	.	C1QTNF2	33	.	NM_031908	exon2	c.C310T	p.R104X	CCATTCGTCCCAT	.	PASS	Atlas-SNP
FZD10	11211	hgsc.bcm.edu	37	12	130649024	130649024	+	Missense_Mutation	SNP	G	G	C	rs369465643	alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	40	7	37	0	0.175	0	.	.	alt	.	FZD10	95	.	NM_007197	exon1	c.G1537C	p.V513L	CTGCTGGTGGTGG	.	PASS	Atlas-SNP
BBS1	582	hgsc.bcm.edu	37	11	66299440	66299440	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	46	10	62	0	0.217391	0	.	.	none	.	BBS1	58	.	NM_024649	exon17	c.G1714A	p.G572S	CGAGAAGGCCAAA	.	PASS	Atlas-SNP
RSBN1L	222194	hgsc.bcm.edu	37	7	77378893	77378893	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	87	16	98	0	0.183908	0	.	.	none	.	RSBN1L	74	.	NM_198467	exon3	c.G856A	p.D286N	CTAACTGATGTTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511237	195511237	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	233	15	203	8	0.0643777	0.0394089	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	NM_018406	exon2	c.A7214G	p.D2405G	GAAGTGTCGGTGA	.	scavenged	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525639	248525639	+	Missense_Mutation	SNP	A	A	T	rs76878172	alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	454	437	419	410	0.962555	0.97852	.	.	alt	OR2T4,brain,glioma,0,1	OR2T4	126	1	NM_001004696	exon1	c.A757T	p.I253F	TTACTCATCCTCC	.	scavenged	Atlas-SNP
MRPL19	9801	hgsc.bcm.edu	37	2	75879766	75879766	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	229	32	266	0	0.139738	0	.	.	none	.	MRPL19	21	.	NM_014763	exon4	c.A458T	p.N153I	TTAGGAATGTTAT	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542891	14542891	+	Silent	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	275	28	298	0	0.101818	0	.	.	none	POTEC,NS,carcinoma,0,1	POTEC	129	1	NM_001137671	exon1	c.C255T	p.D85D	GTCATGGTCTCCA	.	PASS	Atlas-SNP
PAPPA	5069	hgsc.bcm.edu	37	9	119097144	119097144	+	Silent	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	53	11	42	0	0.207547	0	.	.	none	.	PAPPA	243	.	NM_002581	exon13	c.C3402T	p.L1134L	AGGCCTCCATGTC	.	PASS	Atlas-SNP
LIMD1	8994	hgsc.bcm.edu	37	3	45636379	45636379	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	73	8	50	0	0.109589	0	.	.	none	.	LIMD1	34	.	NM_014240	exon1	c.A8T	p.K3M	TGGATAAGTATGA	.	PASS	Atlas-SNP
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835042	27835042	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	151	27	120	0	0.178808	0	.	.	none	.	HIST1H1B	54	.	NM_005322	exon1	c.G266A	p.S89N	ACCAAGCTCTTGA	.	PASS	Atlas-SNP
OR52L1	338751	hgsc.bcm.edu	37	11	6007398	6007398	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	77	13	58	0	0.168831	0	.	.	none	.	OR52L1	100	.	NM_001005173	exon1	c.G763A	p.A255T	TAAACGCCTTAAG	.	PASS	Atlas-SNP
FAM117A	81558	hgsc.bcm.edu	37	17	47799869	47799869	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	63	9	59	0	0.142857	0	.	.	none	.	FAM117A	45	.	NM_030802	exon3	c.C454T	p.R152X	CTTTTCGGTGGTC	.	PASS	Atlas-SNP
MST1R	4486	hgsc.bcm.edu	37	3	49940010	49940010	+	Missense_Mutation	SNP	C	C	T	rs367549694		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	112	18	90	0	0.160714	0	.	.	weak	.	MST1R	205	.	NM_001244937	exon1	c.G1033A	p.V345I	ATAGTACTTCCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506990	195506990	+	Missense_Mutation	SNP	C	C	G	rs200783894	byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	112	11	78	3	0.0982143	0.0384615	C|0.746;G|0.253	0.253	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G11461C	p.D3821H	TGGTGTCACCTGT	.	scavenged	Atlas-SNP
EPHA6	285220	hgsc.bcm.edu	37	3	96706499	96706499	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	155	28	126	0	0.180645	0	.	.	none	EPHA6_ENST00000389672,colon,carcinoma,+1,9	EPHA6	439	9	NM_001080448	exon3	c.G776A	p.R259H	GTGATCGCATCCT	.	PASS	Atlas-SNP
COL9A1	1297	hgsc.bcm.edu	37	6	70991128	70991128	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	72	12	52	0	0.166667	0	.	.	none	COL9A1_ENST00000320755,NS,carcinoma,+1,2	COL9A1	228	2	NM_001851	exon8	c.G841T	p.G281C	GGGGGCCCGGAGG	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77767750	77767750	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	41	8	37	0	0.195122	0	.	.	none	ZFHX4,caecum,carcinoma,0,2	ZFHX4	878	2	NM_024721	exon10	c.C8593A	p.L2865I	AAATTTCTCTTTT	.	PASS	Atlas-SNP
TMEM70	54968	hgsc.bcm.edu	37	8	74893545	74893545	+	Silent	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	180	19	125	0	0.105556	0	.	.	none	.	TMEM70	12	.	NM_017866	exon3	c.C472T	p.L158L	CCAGTGCTGCTTC	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	46	23	35	0	0.5	0	.	.	none	SPRR3,colon,carcinoma,0,3	SPRR3	45	3	NM_001097589	exon2	c.C219T	p.G73G	GCCAGGCTGTACC	.	PASS	Atlas-SNP
SSTR2	6752	hgsc.bcm.edu	37	17	71166537	71166537	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	49	12	48	0	0.244898	0	.	.	none	.	SSTR2	27	.	NM_001050	exon2	c.T1079C	p.L360P	GGACCCTCCTCAA	.	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385799	58385799	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	161	24	152	1	0.149068	0.00657895	.	.	none	ZNF814,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,2	ZNF814	93	2	NM_001144989	exon3	c.G959A	p.G320E	CTTTTCCCAGTGT	.	scavenged	Atlas-SNP
POGK	57645	hgsc.bcm.edu	37	1	166818482	166818482	+	Silent	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	95	9	75	0	0.0947368	0	.	.	none	.	POGK	54	.	NM_017542	exon5	c.G666A	p.K222K	TGCCAAGCAGTTT	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55533908	55533908	+	Missense_Mutation	SNP	C	C	T	rs147116231	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	62	14	42	0	0.225806	0	C|0.998;A|0.002	.	alt	.	RP1	429	.	NM_006269	exon2	c.C382T	p.L128F	CCCTGGCTCAGCA	.	PASS	Atlas-SNP
PPP4C	5531	hgsc.bcm.edu	37	16	30093814	30093814	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	60	8	41	0	0.133333	0	.	.	none	.	PPP4C	25	.	NM_002720	exon4	c.G160A	p.D54N	TGCGGCGACATCC	.	PASS	Atlas-SNP
AGA	175	hgsc.bcm.edu	37	4	178355570	178355570	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	213	18	259	0	0.084507	0	.	.	none	.	AGA	39	.	NM_000027	exon7	c.G772A	p.G258R	CATTCCCAGTGGC	.	PASS	Atlas-SNP
OR5H15	403274	hgsc.bcm.edu	37	3	97887970	97887970	+	Missense_Mutation	SNP	C	C	T	rs72933946	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	543	8	392	2	0.014733	0.00510204	C|0.965;A|0.035	.	alt	OR5H15,NS,carcinoma,-2,1	OR5H15	70	1	NM_001005515	exon1	c.C427T	p.R143W	TGCATCCGGCTAT	.	scavenged	Atlas-SNP
MID2	11043	hgsc.bcm.edu	37	X	107147248	107147248	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	240	39	194	0	0.1625	0	.	.	none	.	MID2	122	.	NM_012216	exon4	c.A877G	p.I293V	GAGATCATCCAGC	.	PASS	Atlas-SNP
SETD8	387893	hgsc.bcm.edu	37	12	123892235	123892235	+	Silent	SNP	G	G	A	rs61955128	bycluster;by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	61	5	41	0	0.0819672	0	G|0.999;A|0.001	0.001	strong	SETD8,NS,neuroblastoma,0,1	SETD8	35	1	NM_020382	exon8	c.G1044A	p.P348P	CCACCCGTGGCTG	.	scavenged	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385869	58385869	+	Nonsense_Mutation	SNP	C	C	A	rs199684163		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	79	23	57	2	0.291139	0.0350877	.	.	weak	ZNF814,NS,carcinoma,0,1	ZNF814	93	1	NM_001144989	exon3	c.G889T	p.E297X	CACATTCATGTTT	.	scavenged	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25007202	25007202	+	Missense_Mutation	SNP	A	A	G	rs2330838	by2hit2allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	221	6	223	1	0.0271493	0.00448431	A|1.000;|0.000	.	weak	GGT1,NS,other,0,1	GGT1	68	1	NM_013430	exon5	c.A154G	p.K52E	TGCTCGAAGATTG	.	scavenged	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385867	58385867	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	79	11	58	1	0.139241	0.0172414	.	.	none	ZNF814,NS,carcinoma,-2,1	ZNF814	93	1	NM_001144989	exon3	c.A891T	p.E297D	TCCACATTCATGT	.	scavenged	Atlas-SNP
DSG3	1830	hgsc.bcm.edu	37	18	29039873	29039873	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	90	12	60	2	0.133333	0.0333333	.	.	none	DSG3,colon,carcinoma,0,1	DSG3	172	1	NM_001944	exon6	c.G583T	p.A195S	AAAATTGCCTTCA	.	scavenged	Atlas-SNP
P4HA3	283208	hgsc.bcm.edu	37	11	73997431	73997431	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	112	28	81	0	0.25	0	.	.	none	.	P4HA3	43	.	NM_182904	exon6	c.G775A	p.D259N	TATTATCTGGGCC	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2152129	2152129	+	Silent	SNP	A	A	G	rs79276175		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	39	10	34	5	0.25641	0.147059	A|0.500;G|0.500	0.500	weak	PKD1,NS,carcinoma,0,1	PKD1	184	1	NM_000296	exon26	c.T9330C	p.P3110P	ACAGAAAGGGATG	.	scavenged	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29885564	29885564	+	Silent	SNP	A	A	G	rs202065964	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	40	6	31	0	0.15	0	.	.	weak	NEFH,rectum,carcinoma,0,1	NEFH	178	1	NM_021076	exon4	c.A1935G	p.E645E	GGAGGAAGCAAAG	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	252	7	257	6	0.0277778	0.0233463	.	.	weak	MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G4827C	p.Q1609H	TGTGGTCTGAGGG	.	scavenged	Atlas-SNP
PTCHD2	57540	hgsc.bcm.edu	37	1	11595630	11595630	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	48	5	44	0	0.104167	0	.	.	none	PTCHD2,NS,carcinoma,-2,1	PTCHD2	193	1	NM_020780	exon20	c.G3745A	p.V1249M	TCCTCCGTGGATT	.	PASS	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72413896	72413896	+	Missense_Mutation	SNP	A	A	G	rs71554689		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	156	5	155	1	0.0320513	0.00645161	A|0.500;G|0.500	0.500	weak	POM121_ENST00000395270,NS,carcinoma,0,8	POM121	131	8	NM_172020	exon11	c.A2569G	p.T857A	TCCAGCACCACCA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508070	195508070	+	Missense_Mutation	SNP	C	C	T	rs374027103		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	166	18	118	7	0.108434	0.059322	.	.	weak	MUC4_ENST00000463781,caecum,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G10381A	p.D3461N	AAGTGTCGGTGAC	.	scavenged	Atlas-SNP
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679015	37679015	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	165	27	134	0	0.163636	0	.	.	none	.	CSNK1A1L	69	.	NM_145203	exon1	c.G379A	p.V127M	TATGCACGTATTC	.	PASS	Atlas-SNP
AHRR	57491	hgsc.bcm.edu	37	5	427978	427978	+	Silent	SNP	G	G	A	rs371473301		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	93	22	72	0	0.236559	0	.	.	weak	.	AHRR	67	.	NM_020731	exon9	c.G831A	p.P277P	GGCGCCGTCAGGA	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17085791	17085791	+	Missense_Mutation	SNP	G	G	A	rs2297532	bycluster;byhapmap;by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	96	11	88	3	0.114583	0.0340909	G|0.943;A|0.057	0.057	strong	Q13209_HUMAN,NS,carcinoma,0,4	.	.	4	NM_001271733	exon8	c.C1030T	p.R344C	TACAACGCCGGAT	.	scavenged	Atlas-SNP
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56736100	56736100	+	Missense_Mutation	SNP	T	T	C	rs200493184		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	390	13	319	6	0.0333333	0.0188088	.	.	weak	ZSCAN5A,trunk,malignant_melanoma,0,2	ZSCAN5A	118	2	NM_024303	exon2	c.A316G	p.M106V	CGTTCATCATGAC	.	scavenged	Atlas-SNP
NMBR	4829	hgsc.bcm.edu	37	6	142400028	142400028	+	Silent	SNP	G	G	T	rs147371910	alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	88	21	63	0	0.238636	0	G|1.000;A|0.000	.	alt	.	NMBR	62	.	NM_002511	exon2	c.C435A	p.I145I	GTTAACGATGGCT	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46860090	46860090	+	Missense_Mutation	SNP	C	C	T	rs200980049	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	58	8	45	0	0.137931	0	.	.	weak	CELSR1,NS,carcinoma,+2,1	CELSR1	242	1	NM_014246	exon2	c.G3697A	p.A1233T	GCACGGCGGCCAC	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975739	152975739	+	Silent	SNP	T	T	A	rs17851565	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	46	12	47	0	0.26087	0	A|0.010;C|0.001;T|0.988	0.010	strong	SPRR3,colon,carcinoma,0,4	SPRR3	45	4	NM_001097589	exon2	c.T243A	p.G81G	GCCAGGTTGTACC	.	PASS	Atlas-SNP
PCDHB1	29930	hgsc.bcm.edu	37	5	140431538	140431538	+	Silent	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	96	18	90	0	0.1875	0	.	.	none	.	PCDHB1	148	.	NM_013340	exon1	c.C483T	p.D161D	TCTGGACGTGGGC	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71836110	71836110	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	59	9	56	0	0.152542	0	.	.	none	.	TJP2	120	.	NM_001170416	exon5	c.G743A	p.R248H	GCAGCCGTGGCCG	.	PASS	Atlas-SNP
PATE4	399968	hgsc.bcm.edu	37	11	125708273	125708273	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	52	9	45	0	0.173077	0	.	.	none	.	PATE4	10	.	NM_001144874	exon3	c.T248C	p.L83P	GAGGCCTGTTGAG	.	PASS	Atlas-SNP
KIAA1644	85352	hgsc.bcm.edu	37	22	44681413	44681413	+	Missense_Mutation	SNP	G	G	A	rs372785890		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	81	11	90	0	0.135802	0	.	.	weak	.	KIAA1644	39	.	NM_001099294	exon4	c.C494T	p.P165L	GGCTGCGGCTGTG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525060	248525060	+	Missense_Mutation	SNP	T	T	A	rs28491677	bycluster;byfrequency;by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	489	9	479	4	0.0184049	0.00835073	T|0.787;A|0.213	0.213	strong	OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	NM_001004696	exon1	c.T178A	p.C60S	CTACTTTGTGTGG	.	scavenged	Atlas-SNP
ADAMTS19	171019	hgsc.bcm.edu	37	5	128863470	128863470	+	Silent	SNP	G	G	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	399	18	369	0	0.0451128	0	.	.	none	ADAMTS19,NS,carcinoma,+2,1	ADAMTS19	216	1	NM_133638	exon5	c.G1098C	p.L366L	GAGTCTGAGTGTG	.	PASS	Atlas-SNP
ABCF1	23	hgsc.bcm.edu	37	6	30553108	30553108	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	109	24	100	0	0.220183	0	.	.	none	.	ABCF1	61	.	NM_001025091	exon15	c.T1463A	p.I488N	CTGTCATCTGGCT	.	PASS	Atlas-SNP
POTEG	404785	hgsc.bcm.edu	37	14	19571357	19571357	+	Missense_Mutation	SNP	T	T	C	rs2845206	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	95	24	99	30	0.252632	0.30303	T|0.500;C|0.500	0.500	strong	POTEG,NS,carcinoma,0,3	POTEG	118	3	NM_001005356	exon7	c.T1136C	p.L379S	AAGACTTAAAGCT	.	scavenged	Atlas-SNP
PLCL2	23228	hgsc.bcm.edu	37	3	17051505	17051505	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	107	11	49	0	0.102804	0	.	.	none	.	PLCL2	145	.	NM_015184	exon2	c.G289A	p.G97R	ATATATGGAGAGA	.	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385798	58385798	+	Silent	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	163	24	152	0	0.147239	0	.	.	none	ZNF814,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	ZNF814	93	2	NM_001144989	exon3	c.G960A	p.G320G	TCTTTTCCCAGTG	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	37	13	25671795	25671795	+	Missense_Mutation	SNP	C	C	T	rs113416318	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	69	6	45	0	0.0869565	0	C|0.988;T|0.012	0.012	strong	PABPC3,rectum,carcinoma,0,1	PABPC3	129	1	NM_030979	exon1	c.C1459T	p.R487C	GGTCCACGTCCTG	.	scavenged	Atlas-SNP
CEP85	64793	hgsc.bcm.edu	37	1	26584680	26584680	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	85	17	73	0	0.2	0	.	.	none	.	CEP85	61	.	NM_022778	exon6	c.G1084A	p.E362K	GAGAGCGAACTGC	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23908091	23908091	+	Silent	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	107	20	89	0	0.186916	0	.	.	none	.	SACS	871	.	NM_014363	exon10	c.C9924T	p.H3308H	TGCAATGTGCATA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151932991	151932991	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	145	8	129	5	0.0551724	0.0387597	.	.	none	MLL3_ENST00000355193,NS,malignant_melanoma,+2,4	MLL3	1564	4	NM_170606	exon16	c.C2680T	p.R894W	GTCTCCGCTTTCC	.	scavenged	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65388334	65388334	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	66	12	50	0	0.181818	0	.	.	none	.	PCNXL3	140	.	NM_032223	exon10	c.C2132T	p.S711L	TCCACTCGGCTGA	.	PASS	Atlas-SNP
SEC61G	23480	hgsc.bcm.edu	37	7	54823513	54823513	+	Silent	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	80	9	51	0	0.1125	0	.	.	none	.	SEC61G	10	.	NM_001012456	exon3	c.C156T	p.F52F	CACAAAGAAGCCA	.	PASS	Atlas-SNP
OR4A15	81328	hgsc.bcm.edu	37	11	55135959	55135959	+	Silent	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	314	49	315	0	0.156051	0	.	.	none	.	OR4A15	161	.	NM_001005275	exon1	c.T600C	p.N200N	ACCCAATGTCATT	.	PASS	Atlas-SNP
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56736102	56736102	+	Missense_Mutation	SNP	A	A	T	rs201600248		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	395	12	322	5	0.0303797	0.015528	.	.	weak	ZSCAN5A,trunk,malignant_melanoma,0,2	ZSCAN5A	118	2	NM_024303	exon2	c.T314A	p.M105K	TTCATCATGACTA	.	scavenged	Atlas-SNP
CDK5RAP3	80279	hgsc.bcm.edu	37	17	46053334	46053334	+	Silent	SNP	A	A	G	rs202125432	byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	41	7	30	0	0.170732	0	A|0.949;G|0.051	0.051	strong	CDK5RAP3,NS,carcinoma,0,2	CDK5RAP3	38	2	NM_176096	exon8	c.A753G	p.E251E	GGTGGAACGACCC	.	scavenged	Atlas-SNP
CARD17	440068	hgsc.bcm.edu	37	11	104970112	104970112	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	34	8	43	0	0.235294	0	.	.	none	.	CARD17	15	.	NM_001007232	exon3	c.C311T	p.S104F	ATTTGAGAATCTT	.	PASS	Atlas-SNP
OR5L1	219437	hgsc.bcm.edu	37	11	55579056	55579056	+	Silent	SNP	G	G	A	rs147224918		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	155	28	136	1	0.180645	0.00735294	G|1.000;A|0.000	0.000	weak	OR5L1,colon,carcinoma,+2,2	OR5L1	145	2	NM_001004738	exon1	c.G114A	p.T38T	AGTCACGTTGTTA	.	scavenged	Atlas-SNP
VMA21	203547	hgsc.bcm.edu	37	X	150573426	150573426	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	146	35	134	0	0.239726	0	.	.	none	.	VMA21	17	.	NM_001017980	exon3	c.G202A	p.A68T	TTTTACGCTGCTA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151970877	151970877	+	Missense_Mutation	SNP	G	G	A	rs138627563	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	257	9	251	3	0.0350195	0.0119522	.	.	weak	MLL3_ENST00000355193,NS,carcinoma,+1,6	MLL3	1564	6	NM_170606	exon7	c.C925T	p.P309S	CACAAGGATAATG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511447	195511447	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	100	6	71	0	0.06	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C7004T	p.T2335M	AGAGGCGTGGTGT	.	scavenged	Atlas-SNP
PIP5K1A	8394	hgsc.bcm.edu	37	1	151206713	151206713	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	218	70	193	0	0.321101	0	.	.	none	.	PIP5K1A	61	.	NM_001135638	exon8	c.A680G	p.Y227C	AATTCTATGGACT	.	PASS	Atlas-SNP
SHANK1	50944	hgsc.bcm.edu	37	19	51165532	51165532	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	68	15	81	0	0.220588	0	.	.	none	.	SHANK1	210	.	NM_016148	exon23	c.C6176T	p.P2059L	ATCCCCGGGTGTG	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43382402	43382402	+	Silent	SNP	G	G	A	rs17423717	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	112	5	118	1	0.0446429	0.00847458	G|0.996;A|0.004	0.004	strong	PSG1_ENST00000312439,NS,carcinoma,-1,4	PSG1	196	4	NM_001184826	exon2	c.C93T	p.P31P	AGTGGTGGGCAGG	.	scavenged	Atlas-SNP
GYPA	2993	hgsc.bcm.edu	37	4	145041720	145041720	+	Missense_Mutation	SNP	A	A	G	rs7682260	bycluster;byfrequency;by2hit2allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	72	70	50	49	0.972222	0.98	A|0.519;G|0.481	0.481	strong	GYPA,NS,carcinoma,0,1	GYPA	27	1	NM_002099	exon2	c.T59C	p.L20S	GTACTTAATGCTG	.	scavenged	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196530022	196530022	+	Silent	SNP	C	C	T	rs115224945	bycluster;byfrequency;by1000genomes	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	68	5	32	1	0.0735294	0.03125	C|0.986;T|0.015	0.015	strong	PAK2_ENST00000327134,rectum,carcinoma,0,2	PAK2	113	2	NM_002577	exon4	c.C423T	p.S141S	TCTGAGCTTTACT	.	scavenged	Atlas-SNP
SPOCD1	90853	hgsc.bcm.edu	37	1	32258931	32258931	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	150	28	124	0	0.186667	0	.	.	none	.	SPOCD1	109	.	NM_144569	exon13	c.G2633A	p.R878Q	CGGAACCGCTTGA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	433	57	405	53	0.13164	0.130864	C|0.500;T|0.500	0.500	weak	MUC6,NS,carcinoma,-1,1	MUC6	408	1	NM_005961	exon31	c.G5733A	p.T1911T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	37	19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T	rs113623532	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	179	25	161	0	0.139665	0	C|0.500;T|0.500	0.500	weak	.	ZNF814	93	.	NM_001144989	exon3	c.G965A	p.R322K	TAAGGTCTTTTCC	.	PASS	Atlas-SNP
ZC4H2	55906	hgsc.bcm.edu	37	X	64141833	64141833	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	438	76	382	0	0.173516	0	.	.	none	.	ZC4H2	64	.	NM_018684	exon2	c.G89A	p.R30H	TTCAAACGAGCCT	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107049681	107049681	+	Missense_Mutation	SNP	T	T	C	rs369310197		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	683	9	693	5	0.0131772	0.00721501	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,6	RGPD3	316	6	NM_001144013	exon16	c.A2266G	p.N756D	TATAGTTTTCGAG	.	scavenged	Atlas-SNP
POF1B	79983	hgsc.bcm.edu	37	X	84586065	84586065	+	Silent	SNP	G	G	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	357	58	287	0	0.162465	0	.	.	none	.	POF1B	77	.	NM_024921	exon7	c.C744A	p.G248G	TTCAGGGCCATCA	.	PASS	Atlas-SNP
USP9X	8239	hgsc.bcm.edu	37	X	41075218	41075218	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	289	62	357	0	0.214533	0	.	.	none	.	USP9X	385	.	NM_001039591	exon35	c.T5398G	p.F1800V	AAGCGATTTGACT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284823	152284823	+	Missense_Mutation	SNP	A	A	G	rs74129459	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	170	5	135	4	0.0294118	0.0296296	A|0.984;T|0.016	.	alt	FLG,NS,carcinoma,0,1	FLG	900	1	NM_002016	exon3	c.T2539C	p.S847P	TGCTTGACCCCGG	.	scavenged	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954414	30954414	+	Missense_Mutation	SNP	C	C	G	rs138015704	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	28	5	28	1	0.178571	0.0357143	C|0.993;G|0.007	0.007	strong	MUC21,NS,carcinoma,0,2	MUC21	98	2	NM_001010909	exon2	c.C462G	p.D154E	CTCTGACTCCAGC	.	scavenged	Atlas-SNP
MST1	4485	hgsc.bcm.edu	37	3	49723296	49723296	+	Missense_Mutation	SNP	G	G	A	rs80308386	byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	78	3	61	1	0.0384615	0.0163934	G|0.375;A|0.625	0.625	strong	MST1,trunk,malignant_melanoma,0,3	MST1	84	3	NM_020998	exon10	c.C1247T	p.P416L	CACTGCGGCTTGT	.	scavenged	Atlas-SNP
PCDHA2	56146	hgsc.bcm.edu	37	5	140174824	140174824	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	86	13	82	0	0.151163	0	.	.	none	.	PCDHA2	404	.	NM_031495	exon1	c.G275A	p.R92Q	TCGACCGGGAGGA	.	PASS	Atlas-SNP
PCDHA10	56139	hgsc.bcm.edu	37	5	140236219	140236219	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	171	26	153	0	0.152047	0	.	.	none	.	PCDHA10	358	.	NM_031859	exon1	c.C586T	p.R196W	GTTCTGCGGAAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507817	195507817	+	Missense_Mutation	SNP	A	A	G	rs200993341	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	416	16	320	13	0.0384615	0.040625	G|0.994;T|0.006	0.994	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T10634C	p.V3545A	GTGGATACTGAGG	.	scavenged	Atlas-SNP
PRB1	5542	hgsc.bcm.edu	37	12	11506837	11506837	+	Missense_Mutation	SNP	T	T	C	rs200080540		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	347	7	287	4	0.0201729	0.0139373	.	.	weak	PRB1,NS,carcinoma,-1,6	PRB1	33	6	NM_199353	exon3	c.A200G	p.K67R	TGAGGTTTGTTGC	.	scavenged	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52252217	52252217	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	138	19	150	0	0.137681	0	.	.	none	.	PXDNL	414	.	NM_144651	exon21	c.A4113T	p.E1371D	CTGAATTTCCGCT	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27772692	27772692	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	74	8	78	0	0.108108	0	.	.	none	.	GABRG3	115	.	NM_033223	exon8	c.G979A	p.V327I	CTGTTTGTCTTCG	.	PASS	Atlas-SNP
THBD	7056	hgsc.bcm.edu	37	20	23028813	23028813	+	Silent	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	72	9	72	0	0.125	0	.	.	none	.	THBD	26	.	NM_000361	exon1	c.C1329T	p.D443D	GCACTCGTCGATG	.	PASS	Atlas-SNP
PLEKHH2	130271	hgsc.bcm.edu	37	2	43919728	43919728	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	217	41	180	0	0.18894	0	.	.	none	.	PLEKHH2	156	.	NM_172069	exon4	c.T262C	p.C88R	AATAAGTGTCAAG	.	PASS	Atlas-SNP
C1orf173	127254	hgsc.bcm.edu	37	1	75038599	75038599	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	79	16	84	0	0.202532	0	.	.	none	.	C1orf173	380	.	NM_001002912	exon14	c.A2795G	p.E932G	TCAGCCTCTCCCT	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525640	248525640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	47	24	13	0	0.510638	0	.	.	none	OR2T4,brain,glioma,+1,1	OR2T4	126	1	NM_001004696	exon1	c.T758C	p.I253T	TACTCATCCTCCT	.	PASS	Atlas-SNP
FAM171B	165215	hgsc.bcm.edu	37	2	187559047	187559047	+	Silent	SNP	G	G	A	rs73979342	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	48	14	46	0	0.291667	0	G|0.500;A|0.500	0.500	weak	FAM171B,NS,carcinoma,0,1	FAM171B	146	1	NM_177454	exon1	c.G147A	p.Q49Q	GCAGCAGCAACAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515304	195515304	+	Silent	SNP	T	T	A	rs202019266		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	94	6	88	1	0.0638298	0.0113636	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.A3147T	p.A1049A	TGTGGATGCTGAG	.	scavenged	Atlas-SNP
SLC16A12	387700	hgsc.bcm.edu	37	10	91195994	91195994	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	69	12	76	0	0.173913	0	.	.	none	.	SLC16A12	40	.	NM_213606	exon7	c.C1111T	p.Q371X	GACTTTGAAGCAT	.	PASS	Atlas-SNP
PAK2	5062	hgsc.bcm.edu	37	3	196529982	196529982	+	Missense_Mutation	SNP	A	A	G	rs78043821	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	84	5	56	0	0.0595238	0	A|0.915;G|0.084	0.084	strong	PAK2_ENST00000327134,NS,lymphoid_neoplasm,0,2	PAK2	113	2	NM_002577	exon4	c.A383G	p.K128R	TCCTAAAGTTCTA	.	PASS	Atlas-SNP
LY9	4063	hgsc.bcm.edu	37	1	160794028	160794028	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	84	26	54	0	0.309524	0	.	.	none	.	LY9	115	.	NM_002348	exon9	c.C1888T	p.R630W	TCCATACGGAAAC	.	PASS	Atlas-SNP
UQCRFS1	7386	hgsc.bcm.edu	37	19	29699033	29699033	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	51	12	35	2	0.235294	0.0571429	.	.	none	UQCRFS1,NS,carcinoma,0,4	UQCRFS1	23	4	NM_006003	exon2	c.A247G	p.I83V	CCTTGATGTCTGT	.	scavenged	Atlas-SNP
CHM	1121	hgsc.bcm.edu	37	X	85119697	85119697	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	210	16	184	0	0.0761905	0	.	.	none	.	CHM	57	.	NM_000390	exon15	c.G1900T	p.A634S	AGTTAGCCTCTGG	.	PASS	Atlas-SNP
CNNM2	54805	hgsc.bcm.edu	37	10	104679785	104679785	+	Silent	SNP	A	A	G	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	167	9	133	0	0.0538922	0	.	.	none	.	CNNM2	119	.	NM_199076	exon1	c.A1548G	p.K516K	CACCAAATTTTAT	.	PASS	Atlas-SNP
HTR2A	3356	hgsc.bcm.edu	37	13	47409701	47409701	+	Silent	SNP	G	G	T	rs141413930	bycluster;byfrequency;alternate_allele	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	85	22	63	0	0.258824	0	G|0.999;A|0.001	.	alt	.	HTR2A	98	.	NM_000621	exon4	c.C687A	p.L229L	ATCGGCGAGTAAG	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30955179	30955179	+	Missense_Mutation	SNP	G	G	C	rs76175261	bycluster;byfrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	54	4	35	1	0.0740741	0.0285714	G|0.976;C|0.024	0.024	strong	MUC21,NS,carcinoma,0,1	MUC21	98	1	NM_001010909	exon2	c.G1227C	p.E409D	CTCTGAGTCCAGC	.	scavenged	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42523558	42523558	+	Missense_Mutation	SNP	T	T	C	rs202102799	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	89	4	82	1	0.0449438	0.0121951	T|0.999;C|0.001	0.001	weak	CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	NM_000106	exon7	c.A1064G	p.Y355C	GTGGTGTAGGGCA	.	scavenged	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092978	1092978	+	Silent	SNP	C	C	T	rs192998922	bycluster	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	16	6	8	0	0.375	0	.	.	weak	.	MUC2	614	.	NM_002457	exon30	c.C4797T	p.T1599T	ACCCACCGGCACA	.	PASS	Atlas-SNP
RBMXL2	27288	hgsc.bcm.edu	37	11	7111164	7111164	+	Silent	SNP	G	G	A	rs138708788		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	68	14	50	0	0.205882	0	G|1.000;A|0.000	0.000	weak	.	RBMXL2	47	.	NM_014469	exon1	c.G813A	p.G271G	CTACGGGGATCAT	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218712997	218712997	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	61	9	78	0	0.147541	0	.	.	none	.	TNS1	251	.	NM_022648	exon17	c.C1868T	p.S623L	GCTTCCGAAAAGG	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125590963	125590963	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	72	11	78	0	0.152778	0	.	.	none	.	ANKRD50	136	.	NM_020337	exon4	c.C3469T	p.P1157S	GAGTAGGCCCATT	.	PASS	Atlas-SNP
