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
SGK1	6446	hgsc.bcm.edu	37	6	134494703	134494703	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	68	13	56	0	0.191176	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,6	SGK1	387	6	NM_001143676	exon6	c.516delA	p.P172fs	.	.	PASS	Atlas-Indel
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493762	77493767	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs200317113	by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	25	10	18	0	0.4	0	TGCTGC|0.190;-|0.810	0.810	strong	.	IRF2BPL	40	.	NM_024496	exon1	c.370_375del	p.124_125del	.	.	PASS	Atlas-Indel
TOP2B	7155	hgsc.bcm.edu	37	3	25674218	25674218	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	261	42	204	.	0.161	.	.	.	none	.	TOP2B	98	.	NM_001068	exon9	c.1080delG	p.K360fs	.	.	PASS	Pindel,Atlas-Indel
ITPKB	3707	hgsc.bcm.edu	37	1	226836447	226836447	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	169	32	171	.	0.189	.	.	.	none	.	ITPKB	158	.	NM_002221	exon3	c.1959delC	p.N653fs	.	.	PASS	Pindel,Atlas-Indel
BNC2	54796	hgsc.bcm.edu	37	9	16436374	16436375	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	96	17	99	.	0.177	.	.	.	none	.	BNC2	166	.	NM_017637	exon6	c.1818_1819insC	p.P606fs	.	.	PASS	Pindel,Atlas-Indel
C10orf68	79741	hgsc.bcm.edu	37	10	33018277	33018277	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	107	16	99	.	0.150	.	.	.	none	.	C10orf68	75	.	NM_024688	exon10	c.717delC	p.I239fs	.	.	PASS	Pindel,Atlas-Indel
TET2	54790	hgsc.bcm.edu	37	4	106196908	106196908	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110	18	91	0	0.163636	0	.	.	none	.	TET2	1762	.	NM_001127208	exon11	c.5240delC	p.P1747fs	.	.	PASS	Atlas-Indel
NF1	4763	hgsc.bcm.edu	37	17	29661926	29661927	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	145	24	125	.	0.166	.	.	.	none	.	NF1	1586	.	NM_001042492	exon40	c.5883_5884insC	p.K1961fs	.	.	PASS	Pindel,Atlas-Indel
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789313	117789327	+	In_Frame_Del	DEL	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	-	rs201746372	by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	111	25	88	0	0.225225	0	GGGCTGGAGATGCCT|0.257;-|0.743	0.743	strong	TMPRSS13_ENST00000445164,NS,NS,0,3	TMPRSS13	75	3	NM_001206789	exon2	c.249_263del	p.83_88del	.	.	PASS	Atlas-Indel
ABCB1	5243	hgsc.bcm.edu	37	7	87195445	87195445	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	198	33	144	.	0.167	.	.	.	none	.	ABCB1	263	.	NM_000927	exon8	c.644delC	p.T215fs	.	.	PASS	Pindel,Atlas-Indel
GLI2	2736	hgsc.bcm.edu	37	2	121708820	121708820	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	221	36	241	.	0.163	.	.	.	none	.	GLI2	187	.	NM_005270	exon3	c.255delG	p.G85fs	.	.	PASS	Pindel,Atlas-Indel
EGFL6	25975	hgsc.bcm.edu	37	X	13636081	13636082	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79	22	74	.	0.278	.	.	.	none	.	EGFL6	111	.	NM_001167890	exon8	c.1011_1012insA	p.E337fs	.	.	PASS	Pindel,Atlas-Indel
REST	5978	hgsc.bcm.edu	37	4	57777675	57777676	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	89	14	97	.	0.157	.	.	.	none	.	REST	104	.	NM_001193508	exon2	c.871_872insA	p.Y291_V292delinsX	.	.	PASS	Pindel,Atlas-Indel
GRIA2	2891	hgsc.bcm.edu	37	4	158254497	158254497	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	68	11	49	0	0.161765	0	.	.	none	.	GRIA2	358	.	NM_001083619	exon8	c.1146delG	p.G382fs	.	.	PASS	Atlas-Indel
C22orf43	51233	hgsc.bcm.edu	37	22	23956338	23956340	+	In_Frame_Del	DEL	TCT	TCT	-	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	306	52	236	.	0.170	.	.	.	none	.	C22orf43	18	.	NM_016449	exon9	c.604_606del	p.202_202del	.	.	PASS	Pindel,Atlas-Indel
CNKSR1	10256	hgsc.bcm.edu	37	1	26510311	26510311	+	Frame_Shift_Del	DEL	C	C	-	rs201305445	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	59	12	49	.	0.203	.	C|0.980;-|0.020	0.020	strong	.	CNKSR1	66	.	NM_006314	exon9	c.844delA	p.T282fs	.	.	PASS	Pindel
TCEB3CL2	100506888	hgsc.bcm.edu	37	18	44543098	44543099	+	Frame_Shift_Ins	INS	-	-	GC	rs373334809		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	621	95	623	.	0.153	.	.	.	weak	.	.	.	.	NM_001242907	exon1	c.1274_1275insGC	p.Q425fs	.	.	PASS	Pindel
ASPM	259266	hgsc.bcm.edu	37	1	197070009	197070009	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	157	33	115	0	0.210191	0	.	.	none	ASPM,right_upper_lobe,carcinoma,0,1	ASPM	444	1	NM_018136	exon18	c.G8372T	p.G2791V	ATAACACCTTCAC	.	PASS	Atlas-SNP
UNC80	285175	hgsc.bcm.edu	37	2	210783352	210783352	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	167	39	141	0	0.233533	0	.	.	none	.	UNC80	280	.	NM_032504	exon32	c.G5110A	p.G1704R	TGCAGCGGGAGTG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418119	105418119	+	Missense_Mutation	SNP	G	G	C	rs201187390		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	9	9	4	4	1	1	.	.	weak	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.C3669G	p.H1223Q	GCCAGCGTGGACC	.	scavenged	Atlas-SNP
RAB8A	4218	hgsc.bcm.edu	37	19	16222712	16222712	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	102	13	41	0	0.127451	0	.	.	none	.	RAB8A	19	.	NM_005370	exon1	c.A1C	p.M1L	TGTAATATGGCGA	.	PASS	Atlas-SNP
VGLL3	389136	hgsc.bcm.edu	37	3	87018229	87018229	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	58	14	32	0	0.241379	0	.	.	none	.	VGLL3	62	.	NM_016206	exon3	c.T448G	p.F150V	TCCAAAAGGAAGT	.	PASS	Atlas-SNP
SFTPD	6441	hgsc.bcm.edu	37	10	81702261	81702261	+	Splice_Site	SNP	C	C	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	61	8	63	0	0.131148	0	.	.	none	.	SFTPD	43	.	NM_003019	exon5	c.317-1G>T	.	GAGGTCCTGAGCA	.	PASS	Atlas-SNP
ZFC3H1	196441	hgsc.bcm.edu	37	12	72022729	72022729	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	87	36	70	0	0.413793	0	.	.	none	.	ZFC3H1	172	.	NM_144982	exon20	c.T3915C	p.D1305D	TTCCTCATCACTA	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82329986	82329986	+	Silent	SNP	T	T	C	rs192169537	bycluster;by1000genomes;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	127	22	135	0	0.173228	0	T|1.000;A|0.000	.	alt	.	SH2D4B	44	.	NM_207372	exon2	c.T261C	p.P87P	AGGCCCTGGTGAC	.	PASS	Atlas-SNP
ADAMTS10	81794	hgsc.bcm.edu	37	19	8651562	8651562	+	Silent	SNP	A	A	G	rs4476282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73	5	66	0	0.0684932	0	A|0.790;G|0.210	0.210	strong	ADAMTS10,NS,carcinoma,0,2	ADAMTS10	132	2	NM_030957	exon20	c.T2283C	p.P761P	GGTCCCAGGCAGC	.	PASS	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58208119	58208119	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	94	12	90	0	0.12766	0	.	.	none	.	PCDH17	304	.	NM_001040429	exon1	c.A1439G	p.Q480R	TGCTTCAGGTGCA	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	37	17	10399321	10399321	+	Silent	SNP	G	G	T	rs145122906	alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	180	5	170	1	0.0277778	0.00588235	.	.	alt	MYH1,nipple,malignant_melanoma,0,1	MYH1	403	1	NM_005963	exon35	c.C5115A	p.I1705I	TTCTGCGATTTTC	.	scavenged	Atlas-SNP
SFTPD	6441	hgsc.bcm.edu	37	10	81702260	81702260	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	61	8	62	0	0.131148	0	.	.	none	.	SFTPD	43	.	NM_003019	exon4	c.G317A	p.G106E	GGAGGTCCTGAGC	.	PASS	Atlas-SNP
CD300LB	124599	hgsc.bcm.edu	37	17	72522004	72522004	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	280	64	248	0	0.228571	0	.	.	none	CD300LB,lower_third,carcinoma,0,1	CD300LB	38	1	NM_174892	exon2	c.C364T	p.R122C	ACGTGCGGTCTTT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	477	6	377	1	0.0125786	0.00265252	T|0.872;G|0.128	0.128	strong	FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.A6462C	p.Q2154H	TTGCTCTTGGTGG	.	scavenged	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121747495	121747495	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79	19	86	0	0.240506	0	.	.	none	.	GLI2	187	.	NM_005270	exon13	c.G4005C	p.E1335D	CCAGGAGGGCTAC	.	PASS	Atlas-SNP
GBP3	2635	hgsc.bcm.edu	37	1	89476655	89476655	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	333	64	339	0	0.192192	0	.	.	none	.	GBP3	53	.	NM_018284	exon8	c.T1294C	p.C432R	AGAGACAATAGCC	.	PASS	Atlas-SNP
ZG16	653808	hgsc.bcm.edu	37	16	29791721	29791721	+	Missense_Mutation	SNP	G	G	C	rs235638	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	7	7	0	0	1	.	G|0.120;C|0.880	0.880	strong	.	ZG16	14	.	NM_152338	exon4	c.G485C	p.S162T	ACCCCAGTAGCTG	.	PASS	Atlas-SNP
SLIT1	6585	hgsc.bcm.edu	37	10	98802756	98802756	+	Missense_Mutation	SNP	C	C	T	rs144930720	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	119	3	155	2	0.0252101	0.0129032	C|1.000;T|0.000	0.000	strong	SLIT1,NS,lymphoid_neoplasm,0,1	SLIT1	154	1	NM_003061	exon20	c.G2066A	p.R689H	ATCTTGCGCTTCC	.	scavenged	Atlas-SNP
ANKLE1	126549	hgsc.bcm.edu	37	19	17393015	17393015	+	Missense_Mutation	SNP	C	C	T	rs1864116	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	4	0	0	1	.	C|0.362;T|0.638	0.638	strong	.	ANKLE1	27	.	NM_152363	exon2	c.C212T	p.A71V	CCAACGCTCGGTA	.	PASS	Atlas-SNP
ZNF181	339318	hgsc.bcm.edu	37	19	35232469	35232469	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	122	19	137	0	0.155738	0	.	.	none	.	ZNF181	65	.	NM_001029997	exon4	c.C1183T	p.H395Y	ACTCGACATCAAA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970774	45970774	+	Missense_Mutation	SNP	G	G	A	rs76536096	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	119	12	94	0	0.10084	0	G|0.917;A|0.083	0.083	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.C568T	p.P190S	AGACAGGCTTGCA	.	PASS	Atlas-SNP
NFASC	23114	hgsc.bcm.edu	37	1	204943936	204943936	+	Missense_Mutation	SNP	C	C	T	rs149731085	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	116	30	131	0	0.258621	0	C|1.000;T|0.000	0.000	strong	.	NFASC	396	.	NM_015090	exon14	c.C1576T	p.R526C	CAAGTCCGCCTGG	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42851153	42851153	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	88	4	102	0	0.0454545	0	.	.	none	.	TMPRSS2	148	.	NM_001135099	exon7	c.T740A	p.M247K	AGTTTCATAAAGC	.	PASS	Atlas-SNP
GABRA4	2557	hgsc.bcm.edu	37	4	46995366	46995366	+	Missense_Mutation	SNP	G	G	T	rs2229940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	220	5	218	2	0.0227273	0.00917431	G|0.672;T|0.328	0.328	strong	GABRA4,NS,carcinoma,0,1	GABRA4	129	1	NM_000809	exon1	c.C76A	p.L26M	CCGCCAGGCACAG	.	scavenged	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549632	31549632	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	82	13	99	0	0.158537	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.C167T	p.T56M	GTCTCCGTTACCT	.	PASS	Atlas-SNP
ATP5J2-PTCD1	100526740	hgsc.bcm.edu	37	7	99017681	99017681	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	130	3	134	0	0.0230769	0	.	.	none	PTCD1,colon,carcinoma,+1,1	.	.	1	NM_001198879	exon9	c.C2159A	p.P720Q	GGGTGCGGGGTTT	.	scavenged	Atlas-SNP
GNAT3	346562	hgsc.bcm.edu	37	7	80117974	80117974	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	143	26	113	0	0.181818	0	.	.	none	.	GNAT3	65	.	NM_001102386	exon3	c.T180G	p.G60G	ACTGTAACCATTC	.	PASS	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	37	4	30723952	30723952	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	64	6	78	0	0.09375	0	.	.	none	.	PCDH7	215	.	NM_032457	exon1	c.A908C	p.D303A	TGAACGACAACAG	.	PASS	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	37	7	100648117	100648117	+	Missense_Mutation	SNP	C	C	G	rs11766125	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	11	4	4	1	0.363636	0.25	C|0.499;G|0.501	0.501	strong	MUC12,NS,carcinoma,0,1	MUC12	140	1	NM_001164462	exon2	c.C14273G	p.T4758R	GCATGACAAGCTC	.	scavenged	Atlas-SNP
GLYR1	84656	hgsc.bcm.edu	37	16	4882161	4882161	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	255	43	257	0	0.168627	0	.	.	none	.	GLYR1	49	.	NM_032569	exon5	c.G356A	p.R119K	TTTGGCCTACTTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513521	195513521	+	Missense_Mutation	SNP	C	C	G	rs111334497	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	1145	14	1183	11	0.0122271	0.00929839	C|0.995;G|0.005	0.005	strong	MUC4_ENST00000463781,NS,carcinoma,+2,1	MUC4	1505	1	NM_018406	exon2	c.G4930C	p.G1644R	CGTGACCTGTGGA	.	scavenged	Atlas-SNP
NRG3	10718	hgsc.bcm.edu	37	10	84498369	84498369	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	213	40	191	0	0.187793	0	.	.	none	.	NRG3	301	.	NM_001165972	exon3	c.A990G	p.Q330Q	TGATCAATTTCTG	.	PASS	Atlas-SNP
SEL1L3	23231	hgsc.bcm.edu	37	4	25783964	25783964	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	175	45	184	1	0.257143	0.00543478	.	.	none	SEL1L3,NS,carcinoma,+1,2	SEL1L3	62	2	NM_015187	exon15	c.A2357T	p.Y786F	AACCAGTACTTTG	.	scavenged	Atlas-SNP
ARHGAP31	57514	hgsc.bcm.edu	37	3	119109676	119109676	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	85	3	94	0	0.0352941	0	.	.	none	ARHGAP31,NS,carcinoma,-2,1	ARHGAP31	175	1	NM_020754	exon7	c.C727A	p.L243M	CTCTCCCTGCCCA	.	scavenged	Atlas-SNP
SOCS3	9021	hgsc.bcm.edu	37	17	76354959	76354959	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	84	20	62	0	0.238095	0	.	.	none	.	SOCS3	16	.	NM_003955	exon2	c.G218A	p.S73N	TCCGAGCTGTCGC	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82816658	82816658	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	84	22	63	0	0.261905	0	.	.	none	.	VCAN	498	.	NM_004385	exon7	c.A2533C	p.S845R	ATCCCAAGTTTCA	.	PASS	Atlas-SNP
HDDC2	51020	hgsc.bcm.edu	37	6	125621684	125621684	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	186	40	193	0	0.215054	0	.	.	none	.	HDDC2	21	.	NM_016063	exon2	c.G206A	p.R69Q	GCTTACCGGTCTT	.	PASS	Atlas-SNP
MPZL1	9019	hgsc.bcm.edu	37	1	167741720	167741720	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	186	30	160	0	0.16129	0	.	.	none	.	MPZL1	25	.	NM_024569	exon3	c.A467G	p.E156G	TCGTAGAAAAAGG	.	PASS	Atlas-SNP
NOX4	50507	hgsc.bcm.edu	37	11	89182653	89182653	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	120	28	140	0	0.233333	0	.	.	none	.	NOX4	101	.	NM_001143836	exon4	c.A304G	p.R102G	ATGTTCTGCTTTT	.	PASS	Atlas-SNP
KIF16B	55614	hgsc.bcm.edu	37	20	16348090	16348090	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	188	25	175	0	0.132979	0	.	.	none	.	KIF16B	305	.	NM_001199866	exon23	c.C3880T	p.P1294S	CCGGAGGAGGTAT	.	PASS	Atlas-SNP
KBTBD6	89890	hgsc.bcm.edu	37	13	41705897	41705897	+	Missense_Mutation	SNP	G	G	C	rs150633583	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	395	4	320	1	0.0101266	0.003125	G|0.998;C|0.002	0.002	strong	KBTBD6,trunk,malignant_melanoma,0,2	KBTBD6	83	2	NM_152903	exon1	c.C751G	p.P251A	CTTTGGGAGCAGC	.	scavenged	Atlas-SNP
EPS8L1	54869	hgsc.bcm.edu	37	19	55598724	55598724	+	Missense_Mutation	SNP	A	A	G	rs1054940	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	3	7	1	0.75	0.142857	A|0.559;G|0.441	0.441	strong	EPS8L1_ENST00000245618,NS,carcinoma,0,2	EPS8L1	122	2	NM_133180	exon19	c.A2006G	p.K669R	TGCAGAAGGAGGA	.	scavenged	Atlas-SNP
DUSP5	1847	hgsc.bcm.edu	37	10	112266771	112266771	+	Silent	SNP	C	C	T	rs1889567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	271	4	235	1	0.0147601	0.00425532	C|0.692;T|0.308	0.308	strong	DUSP5_ENST00000369583,NS,carcinoma,0,1	DUSP5	62	1	NM_004419	exon3	c.C607T	p.L203L	GCCAACCTGCACA	.	scavenged	Atlas-SNP
ZSWIM8	23053	hgsc.bcm.edu	37	10	75558867	75558867	+	Silent	SNP	G	G	A	rs2271271	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	230	6	225	2	0.026087	0.00888889	G|0.465;A|0.535	0.535	strong	KIAA0913_ENST00000398706,NS,carcinoma,0,1	.	.	1	NM_015037	exon21	c.G4284A	p.L1428L	CTGGCTGTATGAG	.	scavenged	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86920904	86920904	+	Silent	SNP	A	A	G	rs2390057	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	126	2	132	1	0.015873	0.00757576	A|0.686;G|0.314	0.314	strong	CLCA2,NS,carcinoma,0,1	CLCA2	102	1	NM_006536	exon14	c.A2526G	p.Q842Q	ACCCCAAATTTCC	.	scavenged	Atlas-SNP
CHTF18	63922	hgsc.bcm.edu	37	16	847932	847932	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	81	7	88	0	0.0864198	0	.	.	none	.	CHTF18	52	.	NM_022092	exon22	c.C2885G	p.S962C	GTGTCTCCAACGC	.	PASS	Atlas-SNP
SLC18A1	6570	hgsc.bcm.edu	37	8	20031913	20031913	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	139	24	144	0	0.172662	0	.	.	none	SLC18A1,NS,carcinoma,-1,1	SLC18A1	68	1	NM_001142324	exon6	c.G590A	p.R197Q	AGGGTTCGGGCCA	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134076494	134076494	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	284	63	259	0	0.221831	0	.	.	none	.	NCAPD3	141	.	NM_015261	exon8	c.G1016A	p.S339N	CTTCACCTGATAA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970772	45970772	+	Silent	SNP	A	A	G	rs76021731	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	120	14	96	0	0.116667	0	A|0.908;G|0.092	0.092	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.T570C	p.P190P	GCAGACAGGCTTG	.	PASS	Atlas-SNP
DPY19L2	283417	hgsc.bcm.edu	37	12	63954304	63954304	+	Silent	SNP	T	T	C	rs1054891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	222	3	216	2	0.0135135	0.00925926	T|0.532;C|0.468	0.468	strong	DPY19L2,colon,carcinoma,0,1	DPY19L2	97	1	NM_173812	exon22	c.A2265G	p.L755L	AACCTTTAATACT	.	scavenged	Atlas-SNP
DPY19L1	23333	hgsc.bcm.edu	37	7	35009120	35009120	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	439	12	458	9	0.0273349	0.0196507	.	.	none	DPY19L1,NS,carcinoma,0,2	DPY19L1	56	2	NM_015283	exon9	c.C720T	p.S240S	AATCAAGCTTCCT	.	scavenged	Atlas-SNP
C9orf169	375791	hgsc.bcm.edu	37	9	140120215	140120215	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	56	13	69	0	0.232143	0	.	.	none	.	C9orf169	6	.	NM_199001	exon2	c.G142A	p.G48R	CCAGTGGGGCCCT	.	PASS	Atlas-SNP
AMICA1	120425	hgsc.bcm.edu	37	11	118085545	118085545	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	46	7	37	0	0.152174	0	.	.	none	.	AMICA1	49	.	NM_001098526	exon2	c.T37C	p.L13L	CCAGTAACACTGG	.	PASS	Atlas-SNP
BCAR1	9564	hgsc.bcm.edu	37	16	75276775	75276775	+	Missense_Mutation	SNP	G	G	A	rs1035539	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	12	9	6	1	0.75	0.166667	G|0.447;A|0.553	0.553	strong	BCAR1_ENST00000418647,rectum,carcinoma,0,6	BCAR1	184	6	NM_001170714	exon3	c.C364T	p.P122S	GGCCGGGGCCAGG	.	scavenged	Atlas-SNP
MAN2A1	4124	hgsc.bcm.edu	37	5	109202627	109202627	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	552	7	547	2	0.0126812	0.00365631	.	.	none	MAN2A1,NS,NS,0,1	MAN2A1	136	1	NM_002372	exon22	c.C3363T	p.P1121P	ACCTCCCGGCACT	.	scavenged	Atlas-SNP
FLG2	388698	hgsc.bcm.edu	37	1	152328295	152328295	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	185	10	177	0	0.0540541	0	.	.	none	.	FLG2	431	.	NM_001014342	exon3	c.G1967C	p.G656A	TATTGGCCAAAGC	.	PASS	Atlas-SNP
SLC19A1	6573	hgsc.bcm.edu	37	21	46935613	46935613	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	86	4	90	0	0.0465116	0	.	.	none	.	SLC19A1	53	.	NM_194255	exon6	c.C1735T	p.Q579X	GACACTGCAAACC	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76132841	76132841	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	219	51	203	0	0.232877	0	.	.	none	.	DTX2	64	.	NM_001102594	exon9	c.G1488A	p.S496S	GATGTCGCTCCCC	.	PASS	Atlas-SNP
GBP3	2635	hgsc.bcm.edu	37	1	89476646	89476646	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	341	73	321	0	0.214076	0	.	.	none	.	GBP3	53	.	NM_018284	exon8	c.A1303G	p.I435V	TCTGAATAAAGAG	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	37	21	28306970	28306970	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	218	4	184	0	0.0183486	0	.	.	none	ADAMTS5,NS,carcinoma,+1,1	ADAMTS5	184	1	NM_007038	exon4	c.G1504A	p.G502R	CAGGCCCGAATGT	.	scavenged	Atlas-SNP
CDH3	1001	hgsc.bcm.edu	37	16	68719113	68719113	+	Missense_Mutation	SNP	G	G	A	rs34494880	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	94	4	104	0	0.0425532	0	G|0.953;A|0.047	0.047	strong	.	CDH3	68	.	NM_001793	exon11	c.G1430A	p.R477H	GCTACCGCATCCT	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	37	7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	148	22	107	0	0.148649	0	.	.	none	MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	NM_012301	exon2	c.T340G	p.L114V	ATCGTAAGTTGAG	.	PASS	Atlas-SNP
NLGN1	22871	hgsc.bcm.edu	37	3	173322630	173322630	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	64	11	56	0	0.171875	0	.	.	none	NLGN1,NS,carcinoma,+1,1	NLGN1	209	1	NM_014932	exon3	c.T242C	p.L81P	AATTTCTTGGGGT	.	PASS	Atlas-SNP
MAP3K12	7786	hgsc.bcm.edu	37	12	53880795	53880795	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	147	39	149	0	0.265306	0	.	.	none	.	MAP3K12	160	.	NM_001193511	exon2	c.C381T	p.C127C	GCGCAGGCAGCCA	.	PASS	Atlas-SNP
OR8J1	219477	hgsc.bcm.edu	37	11	56128081	56128081	+	Missense_Mutation	SNP	A	A	G	rs10896290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	266	4	223	0	0.0150376	0	A|0.712;G|0.288	0.288	strong	OR8J1,head_neck,carcinoma,0,1	OR8J1	87	1	NM_001005205	exon1	c.A359G	p.Y120C	TGGCCTATGACCG	.	scavenged	Atlas-SNP
ENPEP	2028	hgsc.bcm.edu	37	4	111397599	111397599	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	212	31	184	0	0.146226	0	.	.	none	.	ENPEP	149	.	NM_001977	exon1	c.A29C	p.K10T	GCTCTAAGAGATA	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58577327	58577327	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	83	3	64	0	0.0361446	0	.	.	none	CNOT1_ENST00000441024,caecum,carcinoma,0,1	CNOT1	359	1	NM_206999	exon31	c.T4618G	p.F1540V	AAAAAAAACACAC	.	scavenged	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45214528	45214528	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	54	4	44	3	0.0740741	0.0681818	.	.	none	CDC27_ENST00000531206,colon,carcinoma,0,2	CDC27	337	2	NM_001114091	exon14	c.T1921A	p.Y641N	CATTATAATGTCT	.	scavenged	Atlas-SNP
OR2T2	401992	hgsc.bcm.edu	37	1	248616749	248616749	+	Silent	SNP	C	C	G	rs1770044	byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	480	6	373	0	0.0125	0	C|0.500;G|0.500	0.500	strong	OR2T2,NS,carcinoma,0,1	OR2T2	73	1	NM_001004136	exon1	c.C651G	p.V217V	CTCTGTCTCCTAC	.	scavenged	Atlas-SNP
BIRC8	112401	hgsc.bcm.edu	37	19	53793122	53793122	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110	17	116	0	0.154545	0	.	.	none	.	BIRC8	54	.	NM_033341	exon1	c.C506A	p.S169X	TGCAATGAAGTCT	.	PASS	Atlas-SNP
OSCAR	126014	hgsc.bcm.edu	37	19	54599222	54599222	+	Silent	SNP	G	G	T	rs61742144	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	9	2	0	0	0.222222	.	G|0.886;T|0.114	0.114	strong	OSCAR_ENST00000356532,NS,carcinoma,0,2	OSCAR	22	2	NM_130771	exon5	c.C582A	p.P194P	GGTGCCGGGGGCG	.	scavenged	Atlas-SNP
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626759	43626759	+	Missense_Mutation	SNP	G	G	A	rs71489755		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	3	3	0	0	1	.	A|1.000;|0.000	1.000	weak	FAM75A6,NS,carcinoma,+1,2	.	.	2	NM_001145196	exon4	c.C1928T	p.T643M	GTGGACGTGGAGG	.	scavenged	Atlas-SNP
PROX1	5629	hgsc.bcm.edu	37	1	214171399	214171399	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	65	18	49	0	0.276923	0	.	.	none	.	PROX1	124	.	NM_001270616	exon2	c.A1521C	p.K507N	TGGAAAAGACAGA	.	PASS	Atlas-SNP
CEP89	84902	hgsc.bcm.edu	37	19	33444556	33444556	+	Missense_Mutation	SNP	T	T	C	rs73579706	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	89	5	79	2	0.0561798	0.0253165	T|0.500;C|0.500	0.500	strong	CEP89,NS,carcinoma,+1,1	CEP89	82	1	NM_032816	exon4	c.A457G	p.S153G	CATCACTGTGGCC	.	scavenged	Atlas-SNP
SRSF1	6426	hgsc.bcm.edu	37	17	56083867	56083867	+	Nonsense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	174	42	149	0	0.241379	0	.	.	none	.	SRSF1	41	.	NM_006924	exon2	c.T216G	p.Y72X	GCGACCATACACC	.	PASS	Atlas-SNP
LTB	4050	hgsc.bcm.edu	37	6	31549636	31549636	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79	11	100	0	0.139241	0	.	.	none	.	LTB	19	.	NM_002341	exon2	c.G163C	p.V55L	CCGTTACCTGGTT	.	PASS	Atlas-SNP
NMBR	4829	hgsc.bcm.edu	37	6	142399929	142399929	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	176	37	145	0	0.210227	0	.	.	none	NMBR,NS,carcinoma,-2,1	NMBR	62	1	NM_002511	exon2	c.A534G	p.E178E	CACCGCTTCGGGA	.	PASS	Atlas-SNP
LOXL3	84695	hgsc.bcm.edu	37	2	74761669	74761669	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	114	6	153	0	0.0526316	0	.	.	none	.	LOXL3	73	.	NM_032603	exon10	c.C1812T	p.H604H	GCACTCGTGCCAC	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52478202	52478202	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	63	7	64	0	0.111111	0	.	.	none	.	TOX3	121	.	NM_001080430	exon6	c.A973G	p.S325G	CGAGGCTGGCCCT	.	PASS	Atlas-SNP
RPS6KA2	6196	hgsc.bcm.edu	37	6	166862233	166862233	+	Silent	SNP	T	T	C	rs2230730	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	319	5	337	1	0.015674	0.00296736	T|0.764;C|0.236;A|0.000	0.236	strong	RPS6KA2_ENST00000503859,NS,carcinoma,-1,2	RPS6KA2	212	2	NM_001006932	exon15	c.A1335G	p.T445T	GGTGTCTGTGGCT	.	scavenged	Atlas-SNP
RPAP3	79657	hgsc.bcm.edu	37	12	48090083	48090083	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	171	5	132	0	0.0292398	0	.	.	none	RPAP3,caecum,carcinoma,-1,1	RPAP3	45	1	NM_024604	exon5	c.C521A	p.A174E	GCTGACGCTCTGT	.	scavenged	Atlas-SNP
CCDC64B	146439	hgsc.bcm.edu	37	16	3078165	3078165	+	Missense_Mutation	SNP	A	A	G	rs12448103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	3	0	0	0.75	.	A|0.823;G|0.177	0.177	strong	CCDC64B,NS,carcinoma,0,1	CCDC64B	19	1	NM_001103175	exon9	c.T1469C	p.L490P	AGGCGCAGCGAGA	.	scavenged	Atlas-SNP
KIRREL3	84623	hgsc.bcm.edu	37	11	126294687	126294687	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	122	31	144	0	0.254098	0	.	.	none	KIRREL3_ENST00000525144,NS,carcinoma,0,2	KIRREL3	183	2	NM_032531	exon17	c.C2125T	p.R709W	ACTCCCGCTCACA	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276291	186276291	+	Silent	SNP	A	A	G	rs151267614	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	45	15	46	7	0.333333	0.152174	A|0.906;G|0.094	0.094	strong	PRG4,NS,carcinoma,0,1	PRG4	259	1	NM_005807	exon7	c.A1440G	p.K480K	TCCCAAAGAGCCT	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230404	23230404	+	Missense_Mutation	SNP	A	A	G	rs115653109	byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	59	14	97	0	0.237288	0	A|0.999;G|0.001	0.001	strong	.	IGLL5	26	.	NM_001256296	exon1	c.A65G	p.E22G	AGTTGGAAGCAGC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228482059	228482059	+	Missense_Mutation	SNP	G	G	T	rs56218706	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	356	4	386	3	0.011236	0.00777202	G|0.979;A|0.021	.	alt	OBSCN_ENST00000570156,NS,carcinoma,-2,4	OBSCN	2142	4	NM_001271223	exon47	c.G12625T	p.G4209W	GATGCCGGGGAGT	.	scavenged	Atlas-SNP
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552577	102552577	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	117	30	125	0	0.25641	0	.	.	none	.	HSP90AA1	65	.	NM_001017963	exon3	c.G505C	p.E169Q	TGAGCTCTCTCAG	.	PASS	Atlas-SNP
DOCK5	80005	hgsc.bcm.edu	37	8	25198452	25198452	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	87	13	77	0	0.149425	0	.	.	none	.	DOCK5	167	.	NM_024940	exon23	c.T2387C	p.L796P	TATTTCTTGCTTT	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	37	15	24921512	24921512	+	Silent	SNP	G	G	A	rs35737140	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	62	2	46	0	0.0322581	0	G|0.997;A|0.003	0.003	strong	C15orf2,colon,carcinoma,0,5	.	.	5	NM_018958	exon1	c.G498A	p.P166P	GGATCCGGTGCAG	.	scavenged	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141356256	141356256	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	295	58	246	0	0.19661	0	.	.	none	LRP1B,NS,carcinoma,+1,3	LRP1B	1315	3	NM_018557	exon43	c.T7138C	p.S2380P	CATCTGAGAAATA	.	PASS	Atlas-SNP
USP44	84101	hgsc.bcm.edu	37	12	95926864	95926864	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	250	62	195	0	0.248	0	.	.	none	.	USP44	83	.	NM_032147	exon2	c.A1169G	p.Q390R	ATGACTTGGAACA	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386300	7386300	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	111	3	160	1	0.027027	0.00625	.	.	none	POLR2A_ENST00000412468,NS,carcinoma,-1,1	.	.	1	NM_001102614	exon2	c.G997A	p.E333K	GAGAGGGAAGGGA	.	scavenged	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186277277	186277277	+	Missense_Mutation	SNP	G	G	A	rs113308576		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	289	11	218	8	0.0380623	0.0366972	G|0.500;A|0.500	0.500	weak	PRG4,NS,carcinoma,0,2	PRG4	259	2	NM_005807	exon7	c.G2426A	p.G809E	CCAAGGGGCCCAC	.	scavenged	Atlas-SNP
DCAF12	25853	hgsc.bcm.edu	37	9	34107505	34107505	+	Missense_Mutation	SNP	C	C	T	rs11557154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	144	3	155	1	0.0208333	0.00645161	C|0.846;T|0.154	0.154	strong	DCAF12,colon,carcinoma,+1,1	DCAF12	37	1	NM_015397	exon3	c.G392A	p.R131Q	GGCTCCCGGTCTT	.	scavenged	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29885823	29885823	+	Missense_Mutation	SNP	A	A	T	rs145125701		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	231	7	189	4	0.030303	0.021164	.	.	weak	NEFH,NS,lymphoid_neoplasm,0,2	NEFH	178	2	NM_021076	exon4	c.A2194T	p.T732S	GCAAAGACCCCCG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509843	195509843	+	Missense_Mutation	SNP	C	C	T	rs200739317	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	489	29	448	16	0.0593047	0.0357143	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G8608A	p.A2870T	AGGAAGCGTCGGT	.	scavenged	Atlas-SNP
RBMXL2	27288	hgsc.bcm.edu	37	11	7111451	7111451	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	67	14	68	0	0.208955	0	.	.	none	.	RBMXL2	47	.	NM_014469	exon1	c.G1100T	p.R367L	ACAGCCGGTCAGG	.	PASS	Atlas-SNP
ENTPD5	957	hgsc.bcm.edu	37	14	74441684	74441684	+	Silent	SNP	G	G	A	rs2074932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	116	7	118	0	0.0603448	0	G|0.494;A|0.506	0.506	strong	ENTPD5,NS,carcinoma,+1,1	ENTPD5	26	1	NM_001249	exon11	c.C727T	p.L243L	ATCCCAGGTAACT	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133790483	133790483	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	151	39	113	0	0.258278	0	.	.	none	.	IGSF9B	290	.	NM_014987	exon18	c.C3137T	p.P1046L	CCGAAGGGGAATT	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887149	9887149	+	Missense_Mutation	SNP	G	G	C	rs11662946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	145	8	107	0	0.0551724	0	G|0.937;C|0.063	0.063	strong	TXNDC2_ENST00000306084,colon,carcinoma,-1,2	TXNDC2	168	2	NM_001098529	exon2	c.G673C	p.A225P	AATATTGCCAAGA	.	scavenged	Atlas-SNP
CPXCR1	53336	hgsc.bcm.edu	37	X	88008609	88008609	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	57	17	82	0	0.298246	0	.	.	none	.	CPXCR1	83	.	NM_001184771	exon3	c.A194G	p.Q65R	TTCCTCAAGCAGC	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	37	17	10409204	10409204	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	521	88	490	0	0.168906	0	.	.	none	MYH1,NS,carcinoma,+1,1	MYH1	403	1	NM_005963	exon19	c.A2099C	p.N700T	ACACCGTTACACC	.	PASS	Atlas-SNP
RSBN1	54665	hgsc.bcm.edu	37	1	114354654	114354654	+	Silent	SNP	T	T	C	rs3195954	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	7	6	2	0	0.857143	0	T|0.861;C|0.139	0.139	strong	RSBN1,colon,carcinoma,0,2	RSBN1	71	2	NM_018364	exon1	c.A381G	p.P127P	ATTCGTTGGCGGC	.	PASS	Atlas-SNP
SPATA31A3	727830	hgsc.bcm.edu	37	9	40702760	40702760	+	Missense_Mutation	SNP	T	T	G	rs192661010	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	793	8	676	6	0.0100883	0.00887574	T|0.744;G|0.256	0.256	strong	FAM75A3_ENST00000356699,NS,carcinoma,+2,2	.	.	2	NM_001083124	exon4	c.T417G	p.H139Q	CTCTCATGAGCCT	.	scavenged	Atlas-SNP
SLC22A25	387601	hgsc.bcm.edu	37	11	62997098	62997098	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	54	13	42	0	0.240741	0	.	.	none	SLC22A25,right_upper_lobe,carcinoma,-2,1	SLC22A25	87	1	NM_199352	exon1	c.A27C	p.Q9H	TCCAACTTGATCT	.	PASS	Atlas-SNP
CSHL1	1444	hgsc.bcm.edu	37	17	61987570	61987570	+	Missense_Mutation	SNP	G	G	T	rs2727307	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	684	10	696	4	0.0146199	0.00574713	G|0.670;T|0.330	0.330	strong	CSHL1_ENST00000561003,bladder,carcinoma,-2,4	CSHL1	42	4	NM_022579	exon4	c.C423A	p.D141E	GTGATAGTCATCG	.	scavenged	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825407	95825407	+	Silent	SNP	C	C	T	rs61901862	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	180	23	192	0	0.127778	0	C|0.250;T|0.750	0.750	weak	MAML2,rectum,carcinoma,0,2	MAML2	94	2	NM_032427	exon2	c.G1788A	p.Q596Q	CTGCTGCTGCTGC	.	PASS	Atlas-SNP
CDH9	1007	hgsc.bcm.edu	37	5	26890585	26890585	+	Missense_Mutation	SNP	G	G	A	rs148731332	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	163	4	170	0	0.0245399	0	G|1.000;A|0.000	0.000	strong	CDH9,colon,carcinoma,+1,1	CDH9	305	1	NM_016279	exon8	c.C1342T	p.R448W	ATTCCCGGTCAAG	.	scavenged	Atlas-SNP
SLMO2	51012	hgsc.bcm.edu	37	20	57613585	57613585	+	Missense_Mutation	SNP	G	G	C	rs80245608	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	180	2	86	0	0.0111111	0	.	.	weak	SLMO2,hand,malignant_melanoma,0,1	SLMO2	10	1	NM_001256403	exon2	c.C137G	p.S46C	TTTCCAGAGGGAT	.	scavenged	Atlas-SNP
ZNF546	339327	hgsc.bcm.edu	37	19	40504295	40504295	+	Missense_Mutation	SNP	C	C	T	rs139751800		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	103	31	107	0	0.300971	0	C|1.000;T|0.000	0.000	weak	.	ZNF546	93	.	NM_178544	exon3	c.C62T	p.P21L	TCATTCCTCTGCA	.	PASS	Atlas-SNP
ZBTB17	7709	hgsc.bcm.edu	37	1	16272337	16272337	+	Splice_Site	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	16	5	16	0	0.3125	0	.	.	none	.	ZBTB17	45	.	NM_003443	exon7	c.536-2A>T	.	TGCACCTGGGTGG	.	PASS	Atlas-SNP
GAK	2580	hgsc.bcm.edu	37	4	843695	843695	+	Silent	SNP	A	A	G	rs8093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	4	0	0	1	.	A|0.228;G|0.772	0.772	strong	.	GAK	104	.	NM_005255	exon27	c.T3819C	p.A1273A	GTGCACAGCCAGC	.	PASS	Atlas-SNP
POTEF	728378	hgsc.bcm.edu	37	2	130877892	130877892	+	Missense_Mutation	SNP	C	C	T	rs11889701	bycluster;byhapmap	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	492	32	396	19	0.0650406	0.0479798	C|0.500;T|0.500	0.500	weak	POTEF,NS,carcinoma,-1,12	POTEF	140	12	NM_001099771	exon3	c.G197A	p.R66H	CAGTGGCGGCACC	.	scavenged	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825362	95825362	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	169	7	177	3	0.0414201	0.0169492	.	.	none	MAML2,NS,carcinoma,0,4	MAML2	94	4	NM_032427	exon2	c.G1833A	p.Q611Q	TTGCTGCTGCTGC	.	scavenged	Atlas-SNP
ARHGEF18	23370	hgsc.bcm.edu	37	19	7533850	7533850	+	Missense_Mutation	SNP	A	A	G	rs9329368	bycluster;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	2	3	1	0.5	0.333333	A|0.184;G|0.816	0.816	strong	ARHGEF18_ENST00000359920,NS,carcinoma,0,2	ARHGEF18	129	2	NM_001130955	exon17	c.A3056G	p.N1019S	CCGAGAACCGGCT	.	scavenged	Atlas-SNP
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123342220	123342220	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	185	4	156	0	0.0216216	0	.	.	none	CDK5RAP2,NS,carcinoma,0,1	CDK5RAP2	157	1	NM_018249	exon1	c.C37A	p.P13T	TCCCAGGGACGGT	.	scavenged	Atlas-SNP
TEKT4	150483	hgsc.bcm.edu	37	2	95542364	95542364	+	Silent	SNP	G	G	A	rs113812263	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	82	5	65	2	0.0609756	0.0307692	G|0.972;A|0.028	0.028	strong	TEKT4,caecum,carcinoma,0,3	TEKT4	72	3	NM_144705	exon6	c.G1158A	p.A386A	AGAAGCGGAGCAG	.	scavenged	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31322910	31322910	+	Missense_Mutation	SNP	G	G	A	rs74189305	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	196	7	179	5	0.0357143	0.027933	.	.	weak	HLA-B,NS,carcinoma,-1,7	HLA-B	54	7	NM_005514	exon5	c.C986T	p.A329V	ATCACAGCAGCGA	.	scavenged	Atlas-SNP
SLC43A2	124935	hgsc.bcm.edu	37	17	1494567	1494567	+	Silent	SNP	G	G	A	rs12953268	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	9	7	4	1	0.777778	0.25	A|0.422;C|0.000;G|0.578	0.422	strong	SLC43A2,NS,carcinoma,0,1	SLC43A2	37	1	NM_152346	exon8	c.C927T	p.A309A	ACCTGCGGCATCC	.	scavenged	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121615103	121615103	+	Missense_Mutation	SNP	G	G	A	rs1718119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	194	2	172	1	0.0103093	0.00581395	G|0.628;N|0.001	.	strong	P2RX7,NS,carcinoma,0,1	P2RX7	53	1	NM_002562	exon11	c.G1042A	p.A348T	CAGGCCGCTGTGT	.	scavenged	Atlas-SNP
UNC45B	146862	hgsc.bcm.edu	37	17	33497208	33497208	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	150	23	169	0	0.153333	0	.	.	none	.	UNC45B	133	.	NM_001267052	exon12	c.C1623T	p.D541D	GCTGGACGCTGAT	.	PASS	Atlas-SNP
TTLL1	25809	hgsc.bcm.edu	37	22	43447891	43447891	+	Silent	SNP	C	C	T	rs9607998	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	210	6	176	1	0.0285714	0.00568182	C|0.971;T|0.029	0.029	strong	TTLL1,NS,carcinoma,-2,1	TTLL1	41	1	NM_012263	exon9	c.G894A	p.P298P	CATCACCGGCTGG	.	scavenged	Atlas-SNP
AGAP1	116987	hgsc.bcm.edu	37	2	236715883	236715883	+	Missense_Mutation	SNP	T	T	C	rs202230563	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	57	5	38	0	0.0877193	0	T|0.998;C|0.002	0.002	strong	.	AGAP1	95	.	NM_014914	exon9	c.T958C	p.S320P	TTGCAGTCTCGGA	.	PASS	Atlas-SNP
CEPT1	10390	hgsc.bcm.edu	37	1	111724864	111724864	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137	36	137	0	0.262774	0	.	.	none	.	CEPT1	25	.	NM_006090	exon6	c.G770A	p.G257E	TAGCAGGGACCAT	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970771	45970771	+	Missense_Mutation	SNP	C	C	T	rs200215960	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	125	12	100	0	0.096	0	C|0.956;T|0.044	0.044	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G571A	p.V191I	AGCAGACAGGCTT	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	128807004	128807004	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	107	14	141	0	0.130841	0	.	.	none	.	DOCK1	188	.	NM_001380	exon11	c.G994A	p.V332I	ATGGATGTAACAG	.	PASS	Atlas-SNP
TARDBP	23435	hgsc.bcm.edu	37	1	11073808	11073808	+	Silent	SNP	C	C	T	rs72870030	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	148	2	108	1	0.0135135	0.00925926	C|0.999;T|0.001	0.001	strong	TARDBP,caecum,carcinoma,0,1	TARDBP	31	1	NM_007375	exon2	c.C24T	p.T8T	GGTAACCGAAGAT	.	scavenged	Atlas-SNP
ARHGAP44	9912	hgsc.bcm.edu	37	17	12859254	12859254	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	210	38	236	0	0.180952	0	.	.	none	.	ARHGAP44	55	.	NM_014859	exon14	c.G1207A	p.A403T	AATATGGCAATTG	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145296403	145296403	+	Silent	SNP	C	C	T	rs4996269	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	162	4	146	1	0.0246914	0.00684932	T|0.001;G|0.956	0.001	strong	NBPF10,NS,carcinoma,0,1	NBPF10	221	1	NM_001039703	exon3	c.C325T	p.L109L	ACCCAGCTAAGGG	.	scavenged	Atlas-SNP
RNF216	54476	hgsc.bcm.edu	37	7	5662542	5662542	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	51	8	47	0	0.156863	0	.	.	none	.	RNF216	71	.	NM_207111	exon17	c.G2721A	p.L907L	GTGCTCCAGGGGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507064	195507064	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	307	13	296	5	0.0423453	0.0168919	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C11387G	p.T3796S	GTGTCGGTGACAG	.	scavenged	Atlas-SNP
OR5AP2	338675	hgsc.bcm.edu	37	11	56409697	56409697	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	102	15	82	0	0.147059	0	.	.	none	.	OR5AP2	69	.	NM_001002925	exon1	c.T219G	p.S73S	TACAAAAGAGAGG	.	PASS	Atlas-SNP
GNL2	29889	hgsc.bcm.edu	37	1	38032563	38032563	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	133	27	142	0	0.203008	0	.	.	none	.	GNL2	58	.	NM_013285	exon16	c.C2089T	p.R697C	AGTAGCGCACACC	.	PASS	Atlas-SNP
DNAJB1	3337	hgsc.bcm.edu	37	19	14627500	14627500	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	165	3	160	0	0.0181818	0	.	.	none	DNAJB1,NS,carcinoma,0,1	DNAJB1	38	1	NM_006145	exon2	c.A570G	p.L190L	GGGGTTTAGCCGC	.	scavenged	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51909826	51909826	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	122	3	125	0	0.0245902	0	.	.	none	PKHD1_ENST00000340994,scalp,malignant_melanoma,0,2	PKHD1	927	2	NM_170724	exon25	c.G2653T	p.G885C	CTCCACCATCATA	.	scavenged	Atlas-SNP
DDX42	11325	hgsc.bcm.edu	37	17	61895140	61895140	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	215	44	208	0	0.204651	0	.	.	none	.	DDX42	86	.	NM_203499	exon18	c.T2199C	p.S733S	GACTAGTGCAGGG	.	PASS	Atlas-SNP
TBC1D14	57533	hgsc.bcm.edu	37	4	7008366	7008366	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	125	26	98	0	0.208	0	.	.	none	.	TBC1D14	110	.	NM_001113361	exon9	c.T1359C	p.G453G	TGCTGGTTTTTCA	.	PASS	Atlas-SNP
OR2T2	401992	hgsc.bcm.edu	37	1	248616764	248616764	+	Silent	SNP	C	C	T	rs77869864	byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	509	28	409	8	0.0550098	0.0195599	C|0.500;T|0.500	0.500	strong	OR2T2,NS,carcinoma,0,1	OR2T2	73	1	NM_001004136	exon1	c.C666T	p.I222I	GCACATCCTCCTG	.	scavenged	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494704	134494704	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	50	5	51	0	0.1	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,6	SGK1	387	6	NM_001143676	exon6	c.C514G	p.P172A	GACTTGGCTAGAA	.	PASS	Atlas-SNP
PLOD2	5352	hgsc.bcm.edu	37	3	145841964	145841964	+	Silent	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	97	16	85	0	0.164948	0	.	.	none	PLOD2,colon,carcinoma,-2,5	PLOD2	81	5	NM_182943	exon2	c.A162C	p.R54R	CATAAATCGATGG	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124103697	124103697	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	279	52	277	0	0.18638	0	.	.	none	KALRN_ENST00000360013,NS,carcinoma,+1,4	KALRN	556	4	NM_003947	exon11	c.G1770A	p.T590T	GAATACGTACACC	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	388	4	313	2	0.0103093	0.00638978	C|0.996;T|0.004	0.004	strong	UBB,bladder,carcinoma,0,2	UBB	30	2	NM_018955	exon2	c.C270T	p.T90T	CATCACCCTGGAA	.	scavenged	Atlas-SNP
RHOA	387	hgsc.bcm.edu	37	3	49413009	49413009	+	Missense_Mutation	SNP	C	C	T	rs11552758		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	171	51	233	0	0.298246	0	.	.	weak	RHOA,NS,lymphoid_neoplasm,0,7	RHOA	46	7	NM_001664	exon2	c.G14A	p.R5Q	TTCTTCCGGATGG	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216221971	216221971	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	175	50	167	0	0.285714	0	.	.	none	.	USH2A	1168	.	NM_206933	exon31	c.T6068C	p.L2023P	AAGGGTAGCAAGC	.	PASS	Atlas-SNP
PDE2A	5138	hgsc.bcm.edu	37	11	72301503	72301503	+	Missense_Mutation	SNP	G	G	A	rs341047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	3	3	2	2	1	1	G|0.921;A|0.079	0.079	strong	PDE2A,colon,carcinoma,0,2	PDE2A	156	2	NM_002599	exon8	c.C671T	p.T224I	CGGTCGGTGTACG	.	scavenged	Atlas-SNP
CLPTM1	1209	hgsc.bcm.edu	37	19	45495643	45495643	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	134	4	136	1	0.0298507	0.00735294	.	.	none	CLPTM1_ENST00000347493,colon,carcinoma,0,2	CLPTM1	109	2	NM_001294	exon13	c.G1708A	p.G570S	CGGATCGGCTGCC	.	scavenged	Atlas-SNP
CD274	29126	hgsc.bcm.edu	37	9	5457196	5457196	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	130	20	93	0	0.153846	0	.	.	none	CD274,spleen,lymphoid_neoplasm,-1,1	CD274	26	1	NM_014143	exon3	c.G170A	p.W57X	TCTATTGGGAAAT	.	PASS	Atlas-SNP
TNFRSF18	8784	hgsc.bcm.edu	37	1	1139804	1139804	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	123	4	128	0	0.0325203	0	.	.	none	TNFRSF18_ENST00000379268,NS,carcinoma,0,2	TNFRSF18	13	2	NM_148902	exon3	c.G373T	p.E125X	GGCCTTCGTGGCC	.	scavenged	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285497	16285497	+	Silent	SNP	A	A	G	rs706149		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	400	12	332	2	0.03	0.0060241	G|1.000;|0.000	1.000	weak	UBB,bladder,carcinoma,0,6	UBB	30	6	NM_018955	exon2	c.A276G	p.E92E	CCTGGAAGTGGAG	.	scavenged	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98231221	98231221	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	119	4	122	0	0.0336134	0	.	.	none	PTCH1_ENST00000430669,colon,carcinoma,+1,18	PTCH1	1850	18	NM_000264	exon14	c.C2062A	p.Q688K	CGGGCTGCACAGA	.	scavenged	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855752	12855752	+	Silent	SNP	G	G	A	rs80197258	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	581	13	533	5	0.0223752	0.00938086	G|0.997;A|0.003	0.003	strong	PRAMEF1,NS,carcinoma,0,2	PRAMEF1	78	2	NM_023013	exon4	c.G1032A	p.L344L	TCTGCTGGAGAAA	.	scavenged	Atlas-SNP
MTNR1A	4543	hgsc.bcm.edu	37	4	187455075	187455075	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137	14	131	0	0.10219	0	.	.	none	.	MTNR1A	46	.	NM_005958	exon2	c.A821G	p.E274G	AGCCACTCTGGGA	.	PASS	Atlas-SNP
MANSC1	54682	hgsc.bcm.edu	37	12	12483713	12483713	+	Silent	SNP	A	A	G	rs4763282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	165	3	148	1	0.0181818	0.00675676	A|0.380;G|0.620	0.620	strong	MANSC1,NS,carcinoma,0,1	MANSC1	38	1	NM_018050	exon4	c.T544C	p.L182L	TCTCCAAGTGATC	.	scavenged	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	101	26	104	0	0.257426	0	.	.	none	SPRR3,colon,carcinoma,0,3	SPRR3	45	3	NM_001097589	exon2	c.C219T	p.G73G	GCCAGGCTGTACC	.	PASS	Atlas-SNP
C1orf87	127795	hgsc.bcm.edu	37	1	60491072	60491072	+	Splice_Site	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79	20	77	0	0.253165	0	.	.	none	.	C1orf87	55	.	NM_152377	exon9	c.1127+1G>C	.	GACTTACTTTATT	.	PASS	Atlas-SNP
POTEG	404785	hgsc.bcm.edu	37	14	19553680	19553680	+	Silent	SNP	C	C	T	rs28578761		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	754	16	777	15	0.0212202	0.019305	.	.	weak	POTEG,bladder,carcinoma,0,1	POTEG	118	1	NM_001005356	exon1	c.C264T	p.D88D	CGACGACTCTGCT	.	scavenged	Atlas-SNP
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775641	27775641	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	286	71	272	0	0.248252	0	.	.	none	.	HIST1H2BL	48	.	NM_003519	exon1	c.C44T	p.S15F	TTCTTGGAGCCCT	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144941419	144941419	+	Silent	SNP	C	C	T	rs12681478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	108	4	103	1	0.037037	0.00970874	C|0.740;T|0.260	0.260	strong	EPPK1,NS,carcinoma,0,1	EPPK1	199	1	NM_031308	exon1	c.G6003A	p.A2001A	TGCCTCCGCCTTC	.	scavenged	Atlas-SNP
ABR	29	hgsc.bcm.edu	37	17	970326	970326	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	76	21	110	0	0.276316	0	.	.	none	.	ABR	119	.	NM_021962	exon10	c.C1173T	p.I391I	CTTCTGGATTTCA	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17316782	17316782	+	Missense_Mutation	SNP	T	T	C	rs7248508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	4	6	1	1	0.166667	T|0.406;C|0.594	0.594	strong	MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	NM_001130065	exon32	c.T5078C	p.V1693A	CAGGCGTTGAGCC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512262	195512262	+	Silent	SNP	C	C	G	rs79929234		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	554	64	471	56	0.115523	0.118896	C|0.500;G|0.500	0.500	weak	MUC4_ENST00000463781,rectum,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G6189C	p.T2063T	AAGAGGCGTGGTG	.	scavenged	Atlas-SNP
CTTNBP2	83992	hgsc.bcm.edu	37	7	117368154	117368154	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	177	33	182	0	0.186441	0	.	.	none	.	CTTNBP2	200	.	NM_033427	exon17	c.A4044G	p.Q1348Q	TGTCACTTGGGCA	.	PASS	Atlas-SNP
SEC62	7095	hgsc.bcm.edu	37	3	169684611	169684611	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	173	33	214	0	0.190751	0	.	.	none	.	SEC62	27	.	NM_003262	exon1	c.A1G	p.M1V	GCCAACATGGCGG	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907275	12907275	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	313	4	238	1	0.0127796	0.00420168	.	.	none	HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	68	1	NM_001013631	exon2	c.C868G	p.Q290E	CATCCTGGCCATT	.	scavenged	Atlas-SNP
ZNF471	57573	hgsc.bcm.edu	37	19	57036891	57036891	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	61	7	64	0	0.114754	0	.	.	none	.	ZNF471	99	.	NM_020813	exon5	c.A1455C	p.K485N	TGAAAAACCCTAT	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228173618	228173618	+	Missense_Mutation	SNP	C	C	A	rs200818438	bycluster;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	105	33	103	0	0.314286	0	.	.	alt	.	COL4A3	293	.	NM_000091	exon49	c.C4466A	p.T1489N	TAGGAACTCTTGG	.	PASS	Atlas-SNP
SPATA31E1	286234	hgsc.bcm.edu	37	9	90499849	90499849	+	Silent	SNP	C	C	T	rs148586576	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71	8	86	0	0.112676	0	C|1.000;T|0.000	0.000	weak	C9orf79,colon,carcinoma,0,1	.	.	1	NM_178828	exon4	c.C447T	p.G149G	CGCTGGCGAAGGC	.	PASS	Atlas-SNP
PDCL3	79031	hgsc.bcm.edu	37	2	101188050	101188050	+	Splice_Site	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	29	7	45	0	0.241379	0	.	.	none	PDCL3,NS,carcinoma,0,1	PDCL3	27	1	NM_024065	exon5	c.369-2A>G	.	TTTTATAGAATTC	.	PASS	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27765242	27765242	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	124	26	112	0	0.209677	0	.	.	none	.	GABRG3	115	.	NM_033223	exon7	c.A837C	p.K279N	CAAAAAAGATGCT	.	PASS	Atlas-SNP
ZNF729	100287226	hgsc.bcm.edu	37	19	22496574	22496574	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71	16	68	0	0.225352	0	.	.	none	.	ZNF729	78	.	NM_001242680	exon4	c.A355G	p.N119D	CATAAGAATTTAC	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190876224	190876224	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	444	5	387	0	0.0112613	0	.	.	none	FRG1,NS,carcinoma,0,1	FRG1	76	1	NM_004477	exon5	c.T350G	p.L117R	AATATCTTGGTAT	.	scavenged	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495169	134495169	+	Missense_Mutation	SNP	G	G	C	rs141028225		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110	22	109	0	0.2	0	G|1.000;C|0.000	0.000	weak	.	SGK1	387	.	NM_001143676	exon5	c.C487G	p.L163V	TCATAAGCTCAGG	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs56451138		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	290	8	223	8	0.0275862	0.0358744	C|0.750;T|0.250	0.250	weak	OR10G2,NS,carcinoma,0,1	OR10G2	35	1	NM_001005466	exon1	c.G706A	p.A236T	CATCAGCGGTGCG	.	scavenged	Atlas-SNP
INSC	387755	hgsc.bcm.edu	37	11	15267551	15267551	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	214	40	199	0	0.186916	0	.	.	none	.	INSC	104	.	NM_001031853	exon13	c.T1705G	p.L569V	TCCTTCTTACTCT	.	PASS	Atlas-SNP
RABGEF1	27342	hgsc.bcm.edu	37	7	66270294	66270294	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	200	2	200	0	0.01	0	.	.	none	RABGEF1,NS,carcinoma,-1,1	RABGEF1	56	1	NM_014504	exon8	c.C988T	p.R330C	CCCCCACGCCTTC	.	scavenged	Atlas-SNP
SLIT2	9353	hgsc.bcm.edu	37	4	20619095	20619095	+	Silent	SNP	G	G	A	rs61746361	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	261	54	330	0	0.206897	0	G|0.996;A|0.004	0.004	strong	.	SLIT2	290	.	NM_004787	exon36	c.G4170A	p.A1390A	CAATGCGTTCTCC	.	PASS	Atlas-SNP
ZNF57	126295	hgsc.bcm.edu	37	19	2917857	2917857	+	Missense_Mutation	SNP	C	C	T	rs148390269	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	221	5	243	3	0.0226244	0.0123457	C|0.999;T|0.001	0.001	weak	ZNF57,NS,carcinoma,0,1	ZNF57	57	1	NM_173480	exon4	c.C1238T	p.T413M	TGAGGACGCACAC	.	scavenged	Atlas-SNP
NASP	4678	hgsc.bcm.edu	37	1	46073299	46073299	+	Missense_Mutation	SNP	C	C	T	rs140271488	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	113	4	108	1	0.0353982	0.00925926	C|0.998;T|0.002	0.002	weak	NASP,NS,carcinoma,0,1	NASP	77	1	NM_002482	exon6	c.C716T	p.A239V	CAGATGCTGAGGA	.	scavenged	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32754250	32754250	+	Silent	SNP	C	C	T	rs376474772		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	321	10	326	3	0.0311526	0.00920245	.	.	weak	RFPL3_ENST00000249007,NS,carcinoma,+2,2	RFPL3	91	2	NM_001098535	exon1	c.C192T	p.I64I	GTGCATCAATTCG	.	scavenged	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11188922	11188922	+	Missense_Mutation	SNP	T	T	C	rs76944947	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	305	11	220	4	0.0360656	0.0181818	T|0.754;C|0.246	0.246	strong	AMAC1L2,colon,carcinoma,0,2	.	.	2	NM_054028	exon1	c.T307C	p.W103R	CGAGGCTGGGCCT	.	scavenged	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377187	49377187	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	81	3	70	0	0.037037	0	.	.	none	PPP1R15A,caecum,carcinoma,0,1	PPP1R15A	48	1	NM_014330	exon2	c.G697T	p.E233X	GCCACGGAGGATA	.	scavenged	Atlas-SNP
CHRM3	1131	hgsc.bcm.edu	37	1	240071117	240071117	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	349	58	377	1	0.166189	0.00265252	.	.	none	CHRM3,NS,carcinoma,0,1	CHRM3	118	1	NM_000740	exon5	c.G366T	p.M122I	TTCAATGAATCTG	.	scavenged	Atlas-SNP
PRPH2	5961	hgsc.bcm.edu	37	6	42690015	42690015	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	133	38	116	0	0.285714	0	.	.	none	.	PRPH2	47	.	NM_000322	exon1	c.C58A	p.L20I	GCCAGAGCCCTTG	.	PASS	Atlas-SNP
PBX2	5089	hgsc.bcm.edu	37	6	32155509	32155509	+	Missense_Mutation	SNP	T	T	A	rs202223627		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	212	14	223	2	0.0660377	0.00896861	T|0.999;A|0.001	0.001	weak	PBX2,NS,carcinoma,0,4	PBX2	29	4	NM_002586	exon5	c.A785T	p.Y262F	TAGAAATACTCAT	.	scavenged	Atlas-SNP
BPIFB3	359710	hgsc.bcm.edu	37	20	31656632	31656632	+	Missense_Mutation	SNP	C	C	G	rs6057717	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	79	2	90	0	0.0253165	0	C|0.625;G|0.375	0.375	strong	C20orf185,NS,carcinoma,0,1	.	.	1	NM_182658	exon10	c.C1002G	p.H334Q	CCTGCACCAGCAA	.	scavenged	Atlas-SNP
OR8D4	338662	hgsc.bcm.edu	37	11	123777861	123777861	+	Silent	SNP	T	T	C	rs61748875	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	253	7	201	1	0.027668	0.00497512	T|0.815;C|0.185	0.185	strong	OR8D4,NS,carcinoma,0,1	OR8D4	62	1	NM_001005197	exon1	c.T723C	p.C241C	CACCTGTAGCTCC	.	scavenged	Atlas-SNP
SRA1	10011	hgsc.bcm.edu	37	5	139931629	139931629	+	Missense_Mutation	SNP	C	C	G	rs368142622	alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	184	69	213	74	0.375	0.347418	.	.	alt	SRA1,NS,carcinoma,+1,2	SRA1	24	2	NM_001035235	exon3	c.G328C	p.V110L	CCATCACAGCCTC	.	scavenged	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883856	152883856	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	96	21	77	0	0.21875	0	.	.	none	.	IVL	100	.	NM_005547	exon2	c.G1583A	p.G528E	AGGAGGGGCAGCT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38120006	38120006	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	206	7	227	5	0.0339806	0.0220264	.	.	none	TRIOBP_ENST00000344404,NS,carcinoma,0,5	TRIOBP	262	5	NM_001039141	exon7	c.T1443C	p.C481C	ATCCTGTGCCCAG	.	scavenged	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23117736	23117736	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	249	40	201	0	0.160643	0	.	.	none	.	USP31	122	.	NM_020718	exon3	c.T844G	p.F282V	CTTGAAAGAGTTC	.	PASS	Atlas-SNP
OR52I2	143502	hgsc.bcm.edu	37	11	4608396	4608396	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	572	149	503	1	0.26049	0.00198807	.	.	none	.	OR52I2	50	.	NM_001005170	exon1	c.A354C	p.G118G	CTCAGGAGACAGC	.	PASS	Atlas-SNP
WHSC1	7468	hgsc.bcm.edu	37	4	1957912	1957912	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	18	6	18	0	0.333333	0	.	.	none	.	WHSC1	180	.	NM_133335	exon15	c.A2878C	p.N960H	TTCAAAAACGGTA	.	PASS	Atlas-SNP
TIAM1	7074	hgsc.bcm.edu	37	21	32554842	32554842	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	95	25	111	0	0.263158	0	.	.	none	.	TIAM1	522	.	NM_003253	exon16	c.C2783A	p.P928H	AGCTCGGGGTAGG	.	PASS	Atlas-SNP
IRF5	3663	hgsc.bcm.edu	37	7	128587374	128587374	+	Missense_Mutation	SNP	G	G	A	rs113806178	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	45	16	12	0	0.355556	0	G|0.714;A|0.286	0.286	strong	IRF5,NS,haematopoietic_neoplasm,0,2	IRF5	40	2	NM_001098629	exon6	c.G572A	p.R191Q	CTCTGCGGCCGCC	.	PASS	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45003745	45003745	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	169	49	140	1	0.289941	0.00714286	.	.	none	B2M,caecum,carcinoma,-2,17	B2M	99	17	NM_004048	exon1	c.A1G	p.M1V	GCCGAGATGTCTC	.	scavenged	Atlas-SNP
LAMP5	24141	hgsc.bcm.edu	37	20	9498795	9498795	+	Missense_Mutation	SNP	C	C	T	rs137866690		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	303	72	272	0	0.237624	0	C|1.000;T|0.000	0.000	weak	.	.	.	.	NM_012261	exon5	c.C584T	p.P195L	GTGATCCGCAGAA	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285542	16285542	+	Silent	SNP	G	G	A	rs17052364	byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	492	6	440	3	0.0121951	0.00681818	G|0.540;A|0.460	0.460	strong	UBB,NS,carcinoma,0,1	UBB	30	1	NM_018955	exon2	c.G321A	p.Q107Q	GATCCAGGATAAA	.	scavenged	Atlas-SNP
CRYZ	1429	hgsc.bcm.edu	37	1	75184932	75184932	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	231	4	185	0	0.017316	0	.	.	none	CRYZ,colon,carcinoma,-1,1	CRYZ	28	1	NM_001130043	exon4	c.G389A	p.G130D	GGAATGCCGATGG	.	scavenged	Atlas-SNP
SYT16	83851	hgsc.bcm.edu	37	14	62536400	62536400	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	227	50	212	0	0.220264	0	.	.	none	.	SYT16	144	.	NM_031914	exon2	c.C603T	p.S201S	GATTTCCGTGTCC	.	PASS	Atlas-SNP
HIPK1	204851	hgsc.bcm.edu	37	1	114495495	114495495	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	144	27	165	0	0.1875	0	.	.	none	.	HIPK1	195	.	NM_198268	exon3	c.C1184G	p.A395G	CTGGTGCTTCAGA	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79399181	79399181	+	Silent	SNP	C	C	T	rs371145937		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	322	80	274	0	0.248447	0	.	.	weak	.	FRAS1	779	.	NM_025074	exon55	c.C8064T	p.S2688S	CGAGAGCGCTGGT	.	PASS	Atlas-SNP
C10orf129	142827	hgsc.bcm.edu	37	10	96971738	96971738	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	514	26	478	29	0.0505837	0.0606695	.	.	none	C10orf129_ENST00000341686,extremity,malignant_melanoma,0,2	C10orf129	52	2	NM_207321	exon6	c.G859T	p.A287S	CAAGGAGCCTGTG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505819	195505819	+	Missense_Mutation	SNP	A	A	T	rs425588	alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	405	5	407	3	0.0123457	0.00737101	.	.	alt	MUC4_ENST00000463781,trunk,malignant_melanoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T12632A	p.V4211D	TCGGTGACAGGAA	.	scavenged	Atlas-SNP
RFC5	5985	hgsc.bcm.edu	37	12	118458748	118458748	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	83	19	84	0	0.228916	0	.	.	none	.	RFC5	35	.	NM_007370	exon4	c.G305A	p.R102Q	TCATTCGAGGACC	.	PASS	Atlas-SNP
LTA4H	4048	hgsc.bcm.edu	37	12	96409429	96409429	+	Nonsense_Mutation	SNP	C	C	A	rs138184255	bycluster;byfrequency;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73	4	61	0	0.0547945	0	C|0.999;T|0.001	.	alt	.	LTA4H	38	.	NM_000895	exon11	c.G991T	p.G331X	ATCGTCCGCAAAT	.	PASS	Atlas-SNP
PIWIL1	9271	hgsc.bcm.edu	37	12	130855827	130855827	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	202	39	187	0	0.193069	0	.	.	none	.	PIWIL1	157	.	NM_004764	exon20	c.C2428T	p.R810C	ATACAGCGCTTGA	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52584787	52584787	+	Silent	SNP	T	T	C	rs2251219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	101	5	140	0	0.049505	0	T|0.654;C|0.346	0.346	strong	.	PBRM1	1252	.	NM_018313	exon28	c.A4335G	p.P1445P	TCCACCTGGTGCT	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975739	152975739	+	Silent	SNP	T	T	A	rs17851565	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	90	7	119	1	0.0777778	0.00840336	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	.	scavenged	Atlas-SNP
CDH20	28316	hgsc.bcm.edu	37	18	59195219	59195219	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	179	28	180	0	0.156425	0	.	.	none	.	CDH20	117	.	NM_031891	exon6	c.A1037G	p.K346R	AAAGCAAGAAAAG	.	PASS	Atlas-SNP
AOX1	316	hgsc.bcm.edu	37	2	201478599	201478599	+	Silent	SNP	G	G	T	rs200716526	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	124	3	106	0	0.0241935	0	G|1.000;T|0.000	0.000	strong	AOX1,NS,carcinoma,+1,3	AOX1	152	3	NM_001159	exon15	c.G1521T	p.A507A	CTCGGCGCCAGGT	.	scavenged	Atlas-SNP
BRAF	673	hgsc.bcm.edu	37	7	140453134	140453134	+	Missense_Mutation	SNP	T	T	C	rs121913364	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	115	19	87	0	0.165217	0	.	.	weak	BRAF,NS,malignant_melanoma,0,81	BRAF	36346	81	NM_004333	exon15	c.A1801G	p.K601E	GAGATTTCACTGT	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427516	427516	+	Silent	SNP	T	T	C	rs11649031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	37	15	22	1	0.405405	0.0454545	T|0.429;C|0.571	0.571	strong	TMEM8A,colon,carcinoma,0,2	TMEM8A	49	2	NM_021259	exon3	c.A369G	p.V123V	GGGCTGTACCGCG	.	scavenged	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117122285	117122285	+	Missense_Mutation	SNP	G	G	C	rs114915440	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	117	8	104	3	0.0683761	0.0288462	.	.	weak	IGSF3_ENST00000369483,NS,carcinoma,0,4	IGSF3	294	4	NM_001542	exon11	c.C3123G	p.D1041E	GTCGTCGTCGTCC	.	scavenged	Atlas-SNP
FAT3	120114	hgsc.bcm.edu	37	11	92577819	92577819	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	451	80	399	0	0.177384	0	.	.	none	FAT3_ENST00000409404,colon,carcinoma,0,6	FAT3	1822	6	NM_001008781	exon18	c.C11286T	p.H3762H	TTCCCACGCGCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515244	195515244	+	Silent	SNP	G	G	A	rs368817935		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	401	9	412	3	0.0224439	0.00728155	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C3207T	p.H1069H	GGTGACGTGACCT	.	scavenged	Atlas-SNP
OR56B4	196335	hgsc.bcm.edu	37	11	6129720	6129720	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	153	3	154	0	0.0196078	0	.	.	none	OR56B4,bladder,carcinoma,0,1	OR56B4	50	1	NM_001005181	exon1	c.G712T	p.E238X	TCAGCAGAAGCAA	.	scavenged	Atlas-SNP
ASUN	55726	hgsc.bcm.edu	37	12	27070328	27070328	+	Silent	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	168	40	117	0	0.238095	0	.	.	none	.	.	.	.	NM_018164	exon10	c.A1026C	p.V342V	ACTATTTACATCT	.	PASS	Atlas-SNP
WDR18	57418	hgsc.bcm.edu	37	19	984533	984533	+	Silent	SNP	T	T	C	rs2301810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	4	9	0	1	0	T|0.552;C|0.448	0.448	strong	.	WDR18	20	.	NM_024100	exon1	c.T180C	p.N60N	CAAGAATTACATC	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139164570	139164570	+	Silent	SNP	C	C	T	rs3750307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	151	2	137	1	0.013245	0.00729927	C|0.791;N|0.000	.	strong	LOC51059,caecum,carcinoma,0,2	FAM135B	423	2	NM_015912	exon13	c.G2148A	p.P716P	AACAAACGGGTGC	.	scavenged	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	296	4	238	1	0.0135135	0.00420168	.	.	none	TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	NM_001039141	exon7	c.A1339G	p.T447A	AGAGCTACACGAG	.	scavenged	Atlas-SNP
SCUBE1	80274	hgsc.bcm.edu	37	22	43600118	43600118	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	192	46	212	0	0.239583	0	.	.	none	.	SCUBE1	105	.	NM_173050	exon22	c.C2852T	p.A951V	GGATGCGCCAGCA	.	PASS	Atlas-SNP
SLX4IP	128710	hgsc.bcm.edu	37	20	10603706	10603706	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71	11	77	0	0.15493	0	.	.	none	.	.	.	.	NM_001009608	exon8	c.G906A	p.A302A	CTCTGCGGAAGAC	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17265560	17265560	+	Missense_Mutation	SNP	C	C	T	rs9435793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	6	6	3	1	1	0.333333	C|0.643;T|0.357	0.357	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon12	c.C1531T	p.P511S	CGAGGCCCCTCCC	.	scavenged	Atlas-SNP
UBA6	55236	hgsc.bcm.edu	37	4	68514904	68514904	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	197	55	205	0	0.279188	0	.	.	none	.	UBA6	98	.	NM_018227	exon14	c.A1130G	p.H377R	AGCCAATGCACAA	.	PASS	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3328358	3328358	+	Missense_Mutation	SNP	T	T	C	rs870124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	10	6	4	0	0.6	0	T|0.095;G|0.001	.	strong	.	PRDM16	147	.	NM_022114	exon9	c.T1597C	p.S533P	CCCACATCGCTGC	.	PASS	Atlas-SNP
TROAP	10024	hgsc.bcm.edu	37	12	49724403	49724403	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	150	5	164	0	0.0333333	0	.	.	none	TROAP,bladder,carcinoma,0,3	TROAP	80	3	NM_005480	exon13	c.A1775G	p.Y592C	AGTCCTACTGTAG	.	scavenged	Atlas-SNP
IL3	3562	hgsc.bcm.edu	37	5	131396478	131396478	+	Missense_Mutation	SNP	C	C	T	rs40401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	207	5	189	1	0.0241546	0.00529101	C|0.616;N|0.000	.	strong	IL3,NS,carcinoma,0,1	IL3	28	1	NM_000588	exon1	c.C79T	p.P27S	ACAACGCCCTTGA	.	scavenged	Atlas-SNP
FGGY	55277	hgsc.bcm.edu	37	1	60223665	60223665	+	Splice_Site	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73	9	80	0	0.123288	0	.	.	none	.	FGGY	99	.	NM_001113411	exon16	c.1646+1G>T	.	TAAAAAGTAAGTG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130128909	130128909	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	78	16	65	0	0.205128	0	.	.	none	.	COL6A5	205	.	NM_153264	exon19	c.A4599T	p.Q1533H	AGAACAAGGAAGA	.	PASS	Atlas-SNP
CHST9	83539	hgsc.bcm.edu	37	18	24496569	24496569	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	209	47	148	1	0.22488	0.00675676	.	.	none	CHST9_ENST00000284224,NS,carcinoma,0,2	CHST9	114	2	NM_031422	exon6	c.A986G	p.K329R	TTGAACTTGACTC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195475799	195475799	+	Silent	SNP	C	C	T	rs3205933	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	65	3	51	0	0.0461538	0	C|0.917;T|0.083	0.083	strong	MUC4_ENST00000463781,rectum,carcinoma,0,3	MUC4	1505	3	NM_018406	exon24	c.G16008A	p.Q5336Q	CAGGTGCTGGCAC	.	scavenged	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017316	1017316	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	1796	82	1645	57	0.045657	0.0346505	.	.	none	MUC6_ENST00000421673,right_upper_lobe,carcinoma,+1,2	MUC6	408	2	NM_005961	exon31	c.C5485A	p.P1829T	GTGATGGGGTTGG	.	scavenged	Atlas-SNP
OR4E2	26686	hgsc.bcm.edu	37	14	22134018	22134018	+	Missense_Mutation	SNP	C	C	T	rs61732411	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	326	7	307	2	0.0214724	0.00651466	C|0.830;T|0.170	0.170	strong	OR4E2,NS,carcinoma,-1,1	OR4E2	44	1	NM_001001912	exon1	c.C722T	p.S241L	CCTGCTCGGCCCA	.	scavenged	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150922050	150922050	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	185	3	171	0	0.0162162	0	.	.	none	FAT2,NS,carcinoma,+2,1	FAT2	465	1	NM_001447	exon9	c.C8638A	p.H2880N	GTCCGTGGTCATA	.	scavenged	Atlas-SNP
DDX25	29118	hgsc.bcm.edu	37	11	125775114	125775114	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	146	3	142	0	0.0205479	0	.	.	none	DDX25_ENST00000263576,caecum,carcinoma,+1,1	DDX25	65	1	NM_013264	exon2	c.A71G	p.N24S	TTTCAAACCTCAG	.	scavenged	Atlas-SNP
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157012	26157012	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73	15	103	0	0.205479	0	.	.	none	.	HIST1H1E	69	.	NM_005321	exon1	c.G394A	p.A132T	AAGCCAGCAGGAG	.	PASS	Atlas-SNP
AGO4	192670	hgsc.bcm.edu	37	1	36307020	36307020	+	Missense_Mutation	SNP	G	G	T	rs146736735	bycluster;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	281	5	205	0	0.0177936	0	G|1.000;A|0.000	.	alt	EIF2C4,NS,carcinoma,+1,1	.	.	1	NM_017629	exon14	c.G1979T	p.R660L	CCACACGCTTCAA	.	scavenged	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2794937	2794937	+	Missense_Mutation	SNP	C	C	T	rs201777030		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	194	11	195	9	0.056701	0.0461538	.	.	weak	Q6YL47_HUMAN,trunk,malignant_melanoma,0,3	CACNA1C	1023	3	NM_199460	exon47	c.C5858T	p.T1953M	AACTGACGCTCCC	.	scavenged	Atlas-SNP
PDHA2	5161	hgsc.bcm.edu	37	4	96761615	96761615	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	436	7	336	0	0.016055	0	.	.	none	PDHA2,NS,carcinoma,0,1	PDHA2	118	1	NM_005390	exon1	c.G314A	p.G105D	AGGCCGGCATAAA	.	scavenged	Atlas-SNP
DRD5	1816	hgsc.bcm.edu	37	4	9783982	9783982	+	Missense_Mutation	SNP	G	G	A	rs2227849	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	127	15	137	5	0.11811	0.0364963	G|0.916;A|0.084	0.084	strong	DRD5,NS,carcinoma,0,2	DRD5	119	2	NM_000798	exon1	c.G329A	p.G110E	CCTTTGGAGCGTT	.	scavenged	Atlas-SNP
CSHL1	1444	hgsc.bcm.edu	37	17	61987576	61987576	+	Silent	SNP	G	G	A	rs2246207	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	658	8	687	6	0.0121581	0.00873362	G|0.566;A|0.434	0.434	strong	CSHL1_ENST00000561003,NS,adenoma,0,2	CSHL1	42	2	NM_022579	exon4	c.C417T	p.S139S	GTCATCGCTGTCC	.	scavenged	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	37	14	74971792	74971792	+	Silent	SNP	C	C	T	rs61738017	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	49	22	38	0	0.44898	0	C|0.979;T|0.021	0.021	strong	LTBP2,colon,carcinoma,-1,1	LTBP2	158	1	NM_000428	exon29	c.G4263A	p.A1421A	GCAGGGCGCATGG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6978290	6978290	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	255	3	195	1	0.0117647	0.00512821	.	.	none	LAMA1,colon,carcinoma,+1,1	LAMA1	458	1	NM_005559	exon43	c.T6095C	p.L2032P	TGGCTCAGCCCCG	.	scavenged	Atlas-SNP
PGM1	5236	hgsc.bcm.edu	37	1	64104389	64104389	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	302	18	368	0	0.0596026	0	.	.	none	.	PGM1	75	.	NM_001172818	exon7	c.G1116A	p.E372E	GTATGAGACCCCA	.	PASS	Atlas-SNP
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743235	22743235	+	Silent	SNP	A	A	G	rs371649333	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	54	4	59	2	0.0740741	0.0338983	.	.	weak	GOLGA6L1,NS,carcinoma,0,5	GOLGA6L1	20	5	NM_001001413	exon8	c.A1620G	p.R540R	GATACGAGAGCAG	.	scavenged	Atlas-SNP
RGPD8	727851	hgsc.bcm.edu	37	2	113147238	113147238	+	Missense_Mutation	SNP	A	A	G	rs3960708		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	57	6	47	3	0.105263	0.0638298	.	.	weak	RGPD8_ENST00000302558,NS,carcinoma,0,2	RGPD8	81	2	NM_001164463	exon20	c.T3284C	p.L1095P	ATTCTTAGTTTGC	.	scavenged	Atlas-SNP
EPB41L5	57669	hgsc.bcm.edu	37	2	120799656	120799656	+	Silent	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	241	36	219	0	0.149378	0	.	.	none	.	EPB41L5	98	.	NM_020909	exon3	c.T255G	p.G85G	TTTTGGTCTGAGA	.	PASS	Atlas-SNP
OR2T33	391195	hgsc.bcm.edu	37	1	248436963	248436963	+	Silent	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	940	37	769	28	0.0393617	0.0364109	.	.	none	OR2T33,NS,carcinoma,0,1	OR2T33	133	1	NM_001004695	exon1	c.C154A	p.R52R	GGAGCCGGTGGTC	.	scavenged	Atlas-SNP
BIRC6	57448	hgsc.bcm.edu	37	2	32724813	32724813	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	286	65	210	2	0.227273	0.00952381	.	.	none	BIRC6_ENST00000421745,NS,carcinoma,-1,4	BIRC6	838	4	NM_016252	exon46	c.C8668T	p.R2890X	GGTGCTCGAGCAT	.	scavenged	Atlas-SNP
TRPC3	7222	hgsc.bcm.edu	37	4	122846198	122846198	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	212	11	205	0	0.0518868	0	.	.	none	.	TRPC3	201	.	NM_001130698	exon3	c.T1151G	p.L384R	ATGGCAAGTTTGA	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	54025345	54025345	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	67	14	89	0	0.208955	0	.	.	none	.	WDR72	177	.	NM_182758	exon2	c.T2G	p.M1R	GTCCTCATTTTGG	.	PASS	Atlas-SNP
SPG11	80208	hgsc.bcm.edu	37	15	44943757	44943757	+	Missense_Mutation	SNP	A	A	G	rs3759871	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	166	3	157	0	0.0180723	0	A|0.523;G|0.477	0.477	strong	SPG11,NS,carcinoma,0,1	SPG11	207	1	NM_025137	exon6	c.T1388C	p.F463S	AGGGAAAAACACT	.	scavenged	Atlas-SNP
MAN2B1	4125	hgsc.bcm.edu	37	19	12772090	12772090	+	Missense_Mutation	SNP	C	C	T	rs1133330	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	345	5	285	1	0.0144928	0.00350877	C|0.675;T|0.325	0.325	strong	MAN2B1,NS,meningioma,0,1	MAN2B1	91	1	NM_001173498	exon7	c.G1010A	p.R337Q	ACCAGCCGGATGA	.	scavenged	Atlas-SNP
HSD3B7	80270	hgsc.bcm.edu	37	16	30997460	30997460	+	Missense_Mutation	SNP	C	C	T	rs371576756		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	355	74	318	0	0.208451	0	.	.	weak	.	HSD3B7	33	.	NM_025193	exon3	c.C257T	p.T86M	TCCACACGGCTGG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230315	23230315	+	Silent	SNP	C	C	T	rs148489860	by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	68	20	45	0	0.294118	0	C|1.000;T|0.000	0.000	strong	.	IGLL5	26	.	NM_001178126	exon1	c.C82T	p.L28L	CTGCTGCTGCTGG	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96055063	96055063	+	Silent	SNP	C	C	T	rs41278286	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	98	2	94	1	0.0204082	0.0106383	C|0.672;T|0.328	0.328	strong	WNK2_ENST00000297954,colon,carcinoma,+2,4	WNK2	277	4	NM_006648	exon22	c.C5316T	p.D1772D	ACCCGACGTCTAC	.	scavenged	Atlas-SNP
GALNT8	26290	hgsc.bcm.edu	37	12	4873163	4873163	+	Missense_Mutation	SNP	G	G	T	rs1468556	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	329	6	306	1	0.0182371	0.00326797	G|0.627;T|0.373	0.373	strong	GALNT8,NS,adenoma,0,1	GALNT8	89	1	NM_017417	exon9	c.G1543T	p.V515F	GGACCCGTTCCAG	.	scavenged	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43837052	43837052	+	Missense_Mutation	SNP	C	C	A	rs199672858	by1000genomes;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	158	5	200	1	0.0316456	0.005	C|1.000;T|0.000	.	alt	SEMG1,bladder,carcinoma,0,3	SEMG1	71	3	NM_003007	exon2	c.C1114A	p.R372S	TCCCAACGCAGTA	.	scavenged	Atlas-SNP
NYNRIN	57523	hgsc.bcm.edu	37	14	24878537	24878537	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	102	13	110	0	0.127451	0	.	.	none	.	NYNRIN	120	.	NM_025081	exon4	c.G1537A	p.A513T	GGACCCGCTCCAG	.	PASS	Atlas-SNP
POU2AF1	5450	hgsc.bcm.edu	37	11	111249896	111249896	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	366	82	313	0	0.224044	0	.	.	none	.	POU2AF1	23	.	NM_006235	exon1	c.T7C	p.W3R	TTTGCCAGAGCAT	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	37	13	23907902	23907902	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	96	20	90	0	0.208333	0	.	.	none	SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	NM_014363	exon10	c.T10113G	p.T3371T	TGTTGAAGTTTGG	.	PASS	Atlas-SNP
ST7L	54879	hgsc.bcm.edu	37	1	113153627	113153627	+	Splice_Site	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	92	20	85	0	0.217391	0	.	.	none	.	ST7L	31	.	NM_138728	exon4	c.289-2A>G	.	AATATCTATGACA	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	217	3	217	1	0.0138249	0.00460829	G|0.511;C|0.489	0.489	strong	KEAP1,NS,carcinoma,0,1	KEAP1	182	1	NM_012289	exon4	c.C1413G	p.L471L	ATAAAGGAGACGA	.	scavenged	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124340397	124340397	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	784	158	726	2	0.201531	0.00275482	.	.	none	DMBT1_ENST00000368915,NS,carcinoma,-1,13	DMBT1	677	13	NM_007329	exon11	c.C1019T	p.P340L	CCCGGCCGACACC	.	scavenged	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230318	23230318	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	62	18	39	0	0.290323	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C85G	p.L29V	CTGCTGCTGGGTC	.	PASS	Atlas-SNP
NECAP1	25977	hgsc.bcm.edu	37	12	8245311	8245311	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	138	40	104	0	0.289855	0	.	.	none	.	NECAP1	21	.	NM_015509	exon5	c.A423G	p.Q141Q	ATCTCAAGAAATG	.	PASS	Atlas-SNP
PI4KA	5297	hgsc.bcm.edu	37	22	21167787	21167787	+	Silent	SNP	G	G	A	rs165854	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	117	3	110	0	0.025641	0	G|0.526;A|0.474	0.474	strong	PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	NM_058004	exon8	c.C864T	p.C288C	GGGCAAGCAGGAG	.	scavenged	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	37	5	89948249	89948249	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	153	31	168	0	0.202614	0	.	.	none	.	GPR98	605	.	NM_032119	exon19	c.A3503T	p.E1168V	GGCAGGAGTTCTA	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230283	23230283	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	142	38	107	0	0.267606	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.G50A	p.G17D	AGCTGGGCCCTGG	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386301	7386301	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	107	3	155	0	0.0280374	0	.	.	none	POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	NM_001102614	exon2	c.A998C	p.E333A	AGAGGGAAGGGAA	.	scavenged	Atlas-SNP
RABEP2	79874	hgsc.bcm.edu	37	16	28935738	28935738	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	81	10	73	0	0.123457	0	.	.	none	.	RABEP2	48	.	NM_024816	exon2	c.A260G	p.Q87R	ATGGCCTGCAGCG	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186276981	186276981	+	Silent	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	118	5	123	0	0.0423729	0	.	.	none	PRG4,NS,carcinoma,0,6	PRG4	259	6	NM_005807	exon7	c.A2130G	p.K710K	CCCTAAAGGGACT	.	scavenged	Atlas-SNP
RERE	473	hgsc.bcm.edu	37	1	8421203	8421203	+	Silent	SNP	T	T	C	rs13596	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	4	0	0	1	.	T|0.214;C|0.786	0.786	strong	RERE,NS,carcinoma,0,4	RERE	129	4	NM_012102	exon19	c.A2364G	p.P788P	AGCCTGTGGCTGG	.	PASS	Atlas-SNP
SCN1A	6323	hgsc.bcm.edu	37	2	166847770	166847770	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	55	16	45	0	0.290909	0	.	.	none	SCN1A_ENST00000303395,NS,carcinoma,-1,2	SCN1A	641	2	NM_001165963	exon26	c.A6015C	p.K2005N	TTTGGCTTTTTCA	.	PASS	Atlas-SNP
DUSP2	1844	hgsc.bcm.edu	37	2	96809580	96809580	+	Silent	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	201	3	178	0	0.0149254	0	.	.	none	DUSP2,NS,NS,-2,2	DUSP2	20	2	NM_004418	exon4	c.C927A	p.T309T	CACCTGGGTCTCA	.	scavenged	Atlas-SNP
DYRK2	8445	hgsc.bcm.edu	37	12	68051819	68051819	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	285	3	238	0	0.0105263	0	.	.	none	DYRK2,colon,carcinoma,-1,2	DYRK2	63	2	NM_006482	exon3	c.C1132T	p.R378C	CATCAGCGTGTCT	.	scavenged	Atlas-SNP
PCDHA7	56141	hgsc.bcm.edu	37	5	140215022	140215022	+	Missense_Mutation	SNP	C	C	A	rs150063888	alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	577	9	490	4	0.0155979	0.00816326	.	.	alt	PCDHA7,shoulder,malignant_melanoma,0,1	PCDHA7	367	1	NM_031852	exon1	c.C1054A	p.L352I	TTGACTCTCACTT	.	scavenged	Atlas-SNP
WASF3	10810	hgsc.bcm.edu	37	13	27239258	27239258	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	110	34	79	0	0.309091	0	.	.	none	.	WASF3	68	.	NM_006646	exon4	c.T227C	p.L76P	ATCGCCTTGCTGT	.	PASS	Atlas-SNP
ATG2B	55102	hgsc.bcm.edu	37	14	96771961	96771961	+	Silent	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	51	18	65	0	0.352941	0	.	.	none	.	ATG2B	169	.	NM_018036	exon31	c.A4698T	p.G1566G	GACTATTCCAAAA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385042	16385042	+	Missense_Mutation	SNP	G	G	A	rs77667563	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	5	2	3	1	0.4	0.333333	G|0.646;A|0.354	0.354	strong	FAM131C,NS,other,0,1	FAM131C	21	1	NM_182623	exon7	c.C733T	p.R245W	GCCGCCGCCGATG	.	scavenged	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39262561	39262561	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	132	28	109	0	0.212121	0	.	.	none	.	FREM2	385	.	NM_207361	exon1	c.T1080C	p.T360T	CCTTACTTCTCCA	.	PASS	Atlas-SNP
CPNE6	9362	hgsc.bcm.edu	37	14	24544773	24544773	+	Silent	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	191	32	162	0	0.167539	0	.	.	none	CPNE6,mouth,carcinoma,+1,1	CPNE6	40	1	NM_006032	exon9	c.A837C	p.S279S	GAGCTCAGGGACG	.	PASS	Atlas-SNP
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	272	3	346	2	0.0110294	0.00578035	G|0.784;C|0.216	0.216	strong	STRC_ENST00000450892,colon,carcinoma,0,1	STRC	58	1	NM_153700	exon26	c.C4878G	p.L1626L	GCACTGGAGATGC	.	scavenged	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318698	21318698	+	Missense_Mutation	SNP	C	C	T	rs1657738	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	6	5	11	1	0.833333	0.0909091	C|0.500;T|0.500	0.500	strong	KCNJ12,NS,carcinoma,0,1	.	.	1	NM_001194958	exon3	c.C44T	p.S15L	TGTCATCGGAGGA	.	scavenged	Atlas-SNP
ZNF454	285676	hgsc.bcm.edu	37	5	178392474	178392474	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	49	5	63	0	0.102041	0	.	.	none	.	ZNF454	99	.	NM_001178089	exon5	c.G1069A	p.E357K	CCCTTTGAATGTA	.	PASS	Atlas-SNP
BRD1	23774	hgsc.bcm.edu	37	22	50170766	50170766	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	161	4	136	0	0.0248447	0	.	.	none	BRD1_ENST00000342989,NS,carcinoma,+1,2	BRD1	144	2	NM_014577	exon9	c.C2644T	p.R882X	GCCGTCGCACAAG	.	scavenged	Atlas-SNP
ZNF727	442319	hgsc.bcm.edu	37	7	63538777	63538777	+	Silent	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	90	3	83	0	0.0333333	0	.	.	none	ZNF727,NS,carcinoma,0,1	ZNF727	35	1	NM_001159522	exon4	c.G1350A	p.K450K	AGAGAAGCCCTAC	.	scavenged	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887155	9887155	+	Missense_Mutation	SNP	A	A	G	rs200725516	by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137	9	109	0	0.0656934	0	A|1.000;G|0.000	0.000	strong	TXNDC2_ENST00000306084,NS,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.A679G	p.T227A	GCCAAGACCTCAG	.	PASS	Atlas-SNP
MMP15	4324	hgsc.bcm.edu	37	16	58079165	58079165	+	Missense_Mutation	SNP	G	G	A	rs3743563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	13	6	7	1	0.461538	0.142857	G|0.829;A|0.171	0.171	strong	MMP15,hand,carcinoma,0,3	MMP15	58	3	NM_002428	exon10	c.G1825A	p.G609R	AAGGACGGGGGCA	.	scavenged	Atlas-SNP
IL7R	3575	hgsc.bcm.edu	37	5	35861068	35861068	+	Missense_Mutation	SNP	T	T	C	rs1494558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	412	6	321	2	0.0145631	0.00623053	T|0.349;C|0.651	0.651	strong	IL7R,NS,carcinoma,0,1	IL7R	200	1	NM_002185	exon2	c.T197C	p.I66T	TCAACATCACCAA	.	scavenged	Atlas-SNP
OR4C3	256144	hgsc.bcm.edu	37	11	48347041	48347041	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	361	26	347	0	0.0720222	0	.	.	none	.	OR4C3	75	.	NM_001004702	exon1	c.T549C	p.V183V	ATTGGTTCAGCTC	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825383	95825383	+	Silent	SNP	C	C	T	rs113349418	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	154	24	122	2	0.155844	0.0163934	C|0.500;T|0.500	0.500	weak	MAML2,rectum,carcinoma,0,1	MAML2	94	1	NM_032427	exon2	c.G1812A	p.Q604Q	CTGCTGCTGCTGC	.	scavenged	Atlas-SNP
PDLIM1	9124	hgsc.bcm.edu	37	10	96998439	96998439	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	225	46	248	0	0.204444	0	.	.	none	.	PDLIM1	33	.	NM_020992	exon6	c.A689G	p.D230G	TTGGGATCCCCTG	.	PASS	Atlas-SNP
PRDM6	93166	hgsc.bcm.edu	37	5	122425832	122425832	+	Silent	SNP	G	G	T	rs13182369	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	4	1	1	1	1	G|0.741;T|0.259	0.259	strong	PRDM6,NS,NS,0,1	PRDM6	26	1	NM_001136239	exon2	c.G123T	p.A41A	CGCCGCGGGTCTC	.	scavenged	Atlas-SNP
TSPAN19	144448	hgsc.bcm.edu	37	12	85421763	85421763	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	119	22	108	0	0.184874	0	.	.	none	TSPAN19_ENST00000532498,NS,carcinoma,+2,2	TSPAN19	23	2	NM_001100917	exon4	c.T178G	p.L60V	CAATCAAAATTTG	.	PASS	Atlas-SNP
PENK	5179	hgsc.bcm.edu	37	8	57354094	57354094	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	116	20	104	0	0.172414	0	.	.	none	PENK,NS,carcinoma,0,1	PENK	59	1	NM_001135690	exon4	c.G541A	p.E181K	TCACTTCTTCCTC	.	PASS	Atlas-SNP
ZNF629	23361	hgsc.bcm.edu	37	16	30795076	30795076	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	20	7	16	0	0.35	0	.	.	none	ZNF629,colon,carcinoma,-1,1	ZNF629	44	1	NM_001080417	exon3	c.G573A	p.S191S	CAGGTGCGAGCTC	.	PASS	Atlas-SNP
LRP11	84918	hgsc.bcm.edu	37	6	150174287	150174287	+	Missense_Mutation	SNP	G	G	T	rs150922217	bycluster;byfrequency;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	123	2	121	0	0.0162602	0	G|1.000;A|0.000	.	alt	LRP11,NS,carcinoma,0,2	LRP11	27	2	NM_032832	exon2	c.C623A	p.A208E	GGAGGCGCATCCT	.	scavenged	Atlas-SNP
ADAM29	11086	hgsc.bcm.edu	37	4	175898913	175898913	+	Missense_Mutation	SNP	C	C	T	rs142711835		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	144	7	118	8	0.0486111	0.0677966	.	.	weak	ADAM29,rectum,carcinoma,0,22	ADAM29	262	22	NM_001130703	exon4	c.C2237T	p.T746M	CTGTGACGCCTTC	.	scavenged	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31250830	31250830	+	Missense_Mutation	SNP	C	C	G	rs2911826	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	404	25	395	17	0.0618812	0.043038	.	.	weak	DDX11,extremity,malignant_melanoma,0,1	DDX11	188	1	NM_030653	exon18	c.C1774G	p.Q592E	CTCAGTCAGAGCA	.	scavenged	Atlas-SNP
KCND2	3751	hgsc.bcm.edu	37	7	120373050	120373050	+	Silent	SNP	G	G	T	rs139984469	byfrequency;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	347	5	328	0	0.0144092	0	G|1.000;A|0.000	.	alt	KCND2,NS,carcinoma,+1,2	KCND2	194	2	NM_012281	exon2	c.G1209T	p.P403P	TGTTCCGGTGATT	.	scavenged	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14859353	14859353	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	130	25	125	0	0.192308	0	.	.	none	.	FREM1	261	.	NM_144966	exon5	c.G459A	p.A153A	ATCAATCGCTTGG	.	PASS	Atlas-SNP
LYN	4067	hgsc.bcm.edu	37	8	56910951	56910951	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	287	73	227	0	0.254355	0	.	.	none	.	LYN	54	.	NM_002350	exon11	c.G1097A	p.R366Q	TTCACCGGGACCT	.	PASS	Atlas-SNP
QPCTL	54814	hgsc.bcm.edu	37	19	46206262	46206262	+	Silent	SNP	G	G	A	rs17850756	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	383	7	427	3	0.0182768	0.00702576	G|0.727;A|0.273	0.273	strong	QPCTL,NS,carcinoma,0,1	QPCTL	24	1	NM_017659	exon7	c.G1104A	p.L368L	CAACTTGTGCCGC	.	scavenged	Atlas-SNP
ALX1	8092	hgsc.bcm.edu	37	12	85674196	85674196	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	66	12	73	1	0.181818	0.0136986	.	.	none	ALX1,lower_third,carcinoma,-2,1	ALX1	61	1	NM_006982	exon1	c.T157G	p.F53V	CAGGCCTTCGGAC	.	scavenged	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	37	7	100635679	100635679	+	Missense_Mutation	SNP	C	C	G	rs10953314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	5	4	2	0	0.8	0	C|0.505;G|0.495	0.495	strong	.	MUC12	140	.	NM_001164462	exon2	c.C1835G	p.T612S	GCAGCACCAGATC	.	PASS	Atlas-SNP
PRSS3	5646	hgsc.bcm.edu	37	9	33797861	33797861	+	Missense_Mutation	SNP	A	A	G	rs151192741	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	310	11	257	11	0.0354839	0.0428016	.	.	weak	PRSS3_ENST00000361005,NS,carcinoma,-2,3	PRSS3	79	3	NM_007343	exon3	c.A406G	p.K136E	AACATCAAAGTCC	.	scavenged	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	37	3	37368928	37368928	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	71	18	75	0	0.253521	0	.	.	none	.	GOLGA4	173	.	NM_001172713	exon15	c.A5617T	p.I1873F	TGTCAGATTTTGG	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495658	134495658	+	Missense_Mutation	SNP	G	G	A	rs375777416		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	88	14	86	0	0.159091	0	.	.	weak	.	SGK1	387	.	NM_001143676	exon4	c.C428T	p.A143V	TTGCATGCATAGG	.	PASS	Atlas-SNP
PAX1	5075	hgsc.bcm.edu	37	20	21687153	21687153	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	27	8	22	0	0.296296	0	.	.	none	.	PAX1	152	.	NM_006192	exon2	c.C364T	p.R122C	CGCTTGCGCATTG	.	PASS	Atlas-SNP
TMX4	56255	hgsc.bcm.edu	37	20	8000141	8000141	+	Silent	SNP	C	C	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	40	11	14	0	0.275	0	.	.	none	.	TMX4	39	.	NM_021156	exon1	c.G120A	p.Q40Q	CATGGGCTGGACC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505810	195505810	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	390	8	389	5	0.0205128	0.0128535	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	NM_018406	exon2	c.C12641A	p.T4214N	GAGGAAGTGTCGG	.	scavenged	Atlas-SNP
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280162	39280162	+	Silent	SNP	A	A	G	rs28515113	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	16	4	12	1	0.25	0.0833333	A|0.891;G|0.109	0.109	strong	KRTAP4-12,colon,carcinoma,0,3	KRTAP4-12	32	3	NM_031854	exon1	c.T213C	p.C71C	GGTCCTACAGCAG	.	scavenged	Atlas-SNP
CHAT	1103	hgsc.bcm.edu	37	10	50824117	50824117	+	Missense_Mutation	SNP	G	G	A	rs1880676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	189	3	235	2	0.015873	0.00851064	G|0.836;A|0.164	0.164	strong	CHAT_ENST00000395562,NS,meningioma,0,1	CHAT	162	1	NM_001142933	exon2	c.G19A	p.D7N	TGCAGAGATGAAG	.	scavenged	Atlas-SNP
ROPN1B	152015	hgsc.bcm.edu	37	3	125702141	125702141	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	137	19	114	0	0.138686	0	.	.	none	.	ROPN1B	16	.	NM_001012337	exon6	c.A617G	p.N206S	CCCAAAACCCCAG	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49116555	49116555	+	Silent	SNP	A	A	G	rs368654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	6	4	4	1	0.666667	0.25	A|0.144;G|0.856	0.856	strong	FAM83E,NS,carcinoma,0,1	FAM83E	34	1	NM_017708	exon1	c.T75C	p.F25F	ATATAGAAAGCCG	.	scavenged	Atlas-SNP
ASIC1	41	hgsc.bcm.edu	37	12	50467769	50467769	+	Silent	SNP	G	G	A	rs706793	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	4	4	2	0	1	0	G|0.753;A|0.247	0.247	strong	.	.	.	.	NM_001256830	exon1	c.G402A	p.P134P	CTTCCCGGCAGTC	.	PASS	Atlas-SNP
HRH1	3269	hgsc.bcm.edu	37	3	11301217	11301217	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	134	2	142	1	0.0149254	0.00704225	.	.	none	HRH1,NS,carcinoma,-1,1	HRH1	58	1	NM_000861	exon3	c.G494T	p.W165L	TAGGCTGGAATCA	.	scavenged	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167168208	167168208	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	81	19	90	0	0.234568	0	.	.	none	SCN9A,colon,carcinoma,+1,2	SCN9A	296	2	NM_002977	exon2	c.T59C	p.L20P	AGGGCAAGAGACT	.	PASS	Atlas-SNP
SEC23B	10483	hgsc.bcm.edu	37	20	18513372	18513372	+	Missense_Mutation	SNP	C	C	T	rs17807673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	251	4	219	2	0.0159363	0.00913242	C|0.909;T|0.091	0.091	strong	SEC23B,NS,carcinoma,-1,1	SEC23B	70	1	NM_032985	exon11	c.C1298T	p.P433L	AAGGACCGTGTGT	.	scavenged	Atlas-SNP
PTPRT	11122	hgsc.bcm.edu	37	20	40709537	40709537	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	31	7	39	0	0.225806	0	.	.	none	PTPRT,upper_back,malignant_melanoma,-2,1	PTPRT	372	1	NM_133170	exon32	c.A4365T	p.E1455D	TAAATATTCCAGT	.	PASS	Atlas-SNP
KIRREL3	84623	hgsc.bcm.edu	37	11	126299148	126299148	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	108	36	158	0	0.333333	0	.	.	none	.	KIRREL3	183	.	NM_032531	exon15	c.C1732T	p.R578X	CCACTCGGATATC	.	PASS	Atlas-SNP
TARS	6897	hgsc.bcm.edu	37	5	33461355	33461355	+	Silent	SNP	G	G	A	rs2270905	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	97	4	130	1	0.0412371	0.00769231	G|0.816;A|0.184	0.184	strong	TARS,NS,carcinoma,+1,1	TARS	66	1	NM_001258438	exon14	c.G1605A	p.P535P	TCGCCCGGAAAAA	.	scavenged	Atlas-SNP
MAP2K3	5606	hgsc.bcm.edu	37	17	21206529	21206529	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	98	12	89	0	0.122449	0	.	.	none	.	MAP2K3	135	.	NM_145109	exon7	c.T551C	p.L184P	GCAAGCTGTCGGT	.	PASS	Atlas-SNP
GRK6	2870	hgsc.bcm.edu	37	5	176863212	176863212	+	Missense_Mutation	SNP	G	G	A	rs200870863		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	122	6	132	1	0.0491803	0.00757576	.	.	weak	GRK6,NS,carcinoma,0,1	GRK6	48	1	NM_002082	exon12	c.G1196A	p.R399Q	TGGAGCGGCTGGT	.	scavenged	Atlas-SNP
CDC27	996	hgsc.bcm.edu	37	17	45234327	45234327	+	Missense_Mutation	SNP	C	C	T	rs7350889	bycluster;byhapmap	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	55	6	61	1	0.109091	0.0163934	C|1.000;|0.000	.	weak	CDC27_ENST00000531206,NS,adenoma,0,4	CDC27	337	4	NM_001114091	exon7	c.G794A	p.G265D	CTTCGACCAGTTT	.	scavenged	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833506	82833506	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	73	16	51	0	0.219178	0	.	.	none	.	VCAN	498	.	NM_004385	exon8	c.T4684G	p.F1562V	ATAGCCTTTGCAA	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021817	132021817	+	Missense_Mutation	SNP	C	C	T	rs74772922		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	303	7	244	4	0.0231023	0.0163934	C|1.000;|0.000	.	weak	ENSG00000188219,NS,carcinoma,0,1	.	.	1	NM_001083538	exon15	c.C2789T	p.A930V	CCACGGCGGCCTC	.	scavenged	Atlas-SNP
ABCE1	6059	hgsc.bcm.edu	37	4	146033391	146033391	+	Silent	SNP	T	T	C	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	101	12	96	0	0.118812	0	.	.	none	.	ABCE1	47	.	NM_002940	exon9	c.T711C	p.I237I	TCATAGTTTCATG	.	PASS	Atlas-SNP
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs28583670		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	749	11	644	6	0.0146862	0.00931677	.	.	weak	ENSG00000188219,NS,carcinoma,-1,1	.	.	1	NM_001083538	exon15	c.C2656A	p.P886T	GAACTGCCTGACT	.	scavenged	Atlas-SNP
IRF5	3663	hgsc.bcm.edu	37	7	128587381	128587381	+	Silent	SNP	T	T	C	rs79724471	bycluster;byfrequency;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	25	15	8	0	0.6	0	T|0.661;C|0.339	0.339	strong	.	IRF5	40	.	NM_001098629	exon6	c.T579C	p.P193P	GCCGCCTACTCTG	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112406832	112406832	+	Nonsense_Mutation	SNP	G	G	T	rs140633829	alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	364	4	308	1	0.010989	0.00324675	G|1.000;A|0.000	.	alt	MCC_ENST00000408903,NS,carcinoma,-1,2	MCC	234	2	NM_001085377	exon12	c.C1884A	p.Y628X	GGATTCGTATTTT	.	scavenged	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32020562	32020562	+	Silent	SNP	G	G	A	rs375459891		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	41	5	58	0	0.121951	0	.	.	weak	.	TNXB	553	.	NM_019105	exon26	c.C8994T	p.G2998G	CTCCTCGCCCCTG	.	PASS	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	618683	618683	+	Missense_Mutation	SNP	T	T	C	rs200124815		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	272	12	191	3	0.0441176	0.0157068	.	.	weak	CDHR5,NS,malignant_melanoma,0,1	CDHR5	77	1	NM_021924	exon13	c.A1876G	p.T626A	GTGTGGTTGGTTG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195508959	195508959	+	Silent	SNP	A	A	T	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	359	9	361	7	0.0250696	0.0193906	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T9492A	p.G3164G	GGCCTGACCTGTG	.	scavenged	Atlas-SNP
CACNA1B	774	hgsc.bcm.edu	37	9	140773504	140773504	+	Splice_Site	SNP	A	A	C	rs77221813	bycluster	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	86	6	65	4	0.0697674	0.0615385	.	.	weak	CACNA1B,colon,carcinoma,0,1	CACNA1B	266	1	NM_001243812	exon2	c.285-2A>C	.	TCACGCACTCCAT	.	scavenged	Atlas-SNP
ZBBX	79740	hgsc.bcm.edu	37	3	167023655	167023655	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	42	9	54	0	0.214286	0	.	.	none	.	ZBBX	299	.	NM_024687	exon17	c.T1501C	p.S501P	CAAAGGAGGTGCT	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427479	427479	+	Missense_Mutation	SNP	T	T	C	rs11248931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	43	15	22	2	0.348837	0.0909091	T|0.463;C|0.537	0.537	strong	TMEM8A,colon,carcinoma,0,1	TMEM8A	49	1	NM_021259	exon3	c.A406G	p.T136A	TCGGTGTGGTGCT	.	scavenged	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	37	9	137779176	137779176	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	164	19	149	0	0.115854	0	.	.	none	.	FCN2	55	.	NM_004108	exon8	c.G857A	p.S286N	ATGGCAGCTTTGC	.	PASS	Atlas-SNP
PPFIA1	8500	hgsc.bcm.edu	37	11	70171055	70171055	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	95	22	93	0	0.231579	0	.	.	none	.	PPFIA1	114	.	NM_177423	exon4	c.G469A	p.E157K	TCCAGCGAAGTGG	.	PASS	Atlas-SNP
MAZ	4150	hgsc.bcm.edu	37	16	29821438	29821438	+	Silent	SNP	G	G	A	rs199924629	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	69	3	63	1	0.0434783	0.015873	G|0.993;A|0.007	0.007	strong	MAZ_ENST00000322945,caecum,carcinoma,0,2	MAZ	48	2	NM_002383	exon5	c.G1320A	p.A440A	GGCAGCGGCGGCA	.	scavenged	Atlas-SNP
OR10G4	390264	hgsc.bcm.edu	37	11	123887164	123887164	+	Missense_Mutation	SNP	A	A	C	rs4936881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	167	4	232	0	0.0239521	0	A|0.539;C|0.461	0.461	strong	OR10G4,NS,carcinoma,-2,2	OR10G4	77	2	NM_001004462	exon1	c.A883C	p.K295Q	GAGGTGAAGAAAG	.	scavenged	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920498	51920498	+	Silent	SNP	G	G	T	rs201146870	alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	258	3	227	0	0.0116279	0	G|0.999;A|0.001	.	alt	SIGLEC12_ENST00000439889,NS,carcinoma,0,5	SIGLEC10	112	5	NM_001171161	exon2	c.C259A	p.R87R	GGCCCCGGGTGCT	.	scavenged	Atlas-SNP
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	bycluster;byfrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	454	5	429	5	0.0110132	0.011655	G|0.996;A|0.004	0.004	strong	OR2M5,NS,carcinoma,0,2	OR2M5	117	2	NM_001004690	exon1	c.G571A	p.D191N	TGCAATGACACAT	.	scavenged	Atlas-SNP
ARHGAP29	9411	hgsc.bcm.edu	37	1	94670633	94670633	+	Missense_Mutation	SNP	T	T	G	rs201001778	by1000genomes;alternate_allele	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	140	18	133	0	0.128571	0	T|1.000;C|0.000	.	alt	.	ARHGAP29	132	.	NM_004815	exon7	c.A681C	p.E227D	CTTTTTTTCAACC	.	PASS	Atlas-SNP
ZNF592	9640	hgsc.bcm.edu	37	15	85328068	85328068	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	286	54	250	0	0.188811	0	.	.	none	.	ZNF592	95	.	NM_014630	exon4	c.G2162A	p.R721Q	AGATGCGGGACTA	.	PASS	Atlas-SNP
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	492	5	423	3	0.0101626	0.0070922	C|0.873;T|0.127	0.127	strong	TAF1L,NS,carcinoma,-1,1	TAF1L	382	1	NM_153809	exon1	c.G4209A	p.T1403T	TGACAGCGTCACC	.	scavenged	Atlas-SNP
GSDMA	284110	hgsc.bcm.edu	37	17	38122591	38122591	+	Missense_Mutation	SNP	C	C	T	rs140044904	bycluster;by1000genomes	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	278	54	298	0	0.194245	0	C|0.991;T|0.009	0.009	strong	.	GSDMA	26	.	NM_178171	exon3	c.C293T	p.T98M	CAAAGACGGTGAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507985	195507985	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	536	29	538	0	0.0541045	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.T10466C	p.L3489P	ACATGAAGAGGGG	.	PASS	Atlas-SNP
