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
OR13C5	138799	hgsc.bcm.edu	37	9	107360769	107360769	+	Frame_Shift_Del	DEL	T	T	-	rs11314210	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	44	156	.	0.303	.	T|0.620;-|0.380	0.380	strong	.	OR13C5	60	.	NM_001004482	exon1	c.927delC	p.H309fs	.	.	PASS	Pindel,Atlas-Indel
IGSF3	3321	hgsc.bcm.edu	37	1	117122288	117122289	+	In_Frame_Ins	INS	-	-	TCCTCC	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	30	112	0	0.285714	0	.	.	none	IGSF3_ENST00000369483,caecum,carcinoma,0,2	IGSF3	294	2	NM_001542	exon11	c.3120_3121insGGAGGA	p.D1040delinsEED	.	.	PASS	Atlas-Indel
EPSTI1	94240	hgsc.bcm.edu	37	13	43462434	43462435	+	Frame_Shift_Ins	INS	-	-	TCAGG	rs61389340	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	63	172	.	0.307	.	-|0.890;TCAGG|0.110	0.110	strong	EPSTI1,NS,carcinoma,0,1	EPSTI1	47	1	NM_001002264	exon13	c.1185_1186insCCTGA	p.E395fs	.	.	PASS	Pindel,Atlas-Indel
OR2B11	127623	hgsc.bcm.edu	37	1	247615262	247615262	+	Frame_Shift_Del	DEL	A	A	-	rs35305980	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	26	99	.	0.271	.	A|0.570;-|0.430	0.430	strong	.	OR2B11	102	.	NM_001004492	exon1	c.24delC	p.F8fs	.	.	PASS	Pindel,Atlas-Indel
CRIPAK	285464	hgsc.bcm.edu	37	4	1388504	1388505	+	Frame_Shift_Del	DEL	CG	CG	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	14	151	0	0.0769231	0	.	.	none	.	CRIPAK	185	.	NM_175918	exon1	c.204_205del	p.68_69del	.	.	PASS	Atlas-Indel
TP53TG5	27296	hgsc.bcm.edu	37	20	44004156	44004158	+	In_Frame_Del	DEL	ATT	ATT	-	rs10546815	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	20	65	.	0.364	.	ATT|0.574;-|0.426	0.426	strong	.	TP53TG5	36	.	NM_014477	exon4	c.290_292del	p.97_98del	.	.	PASS	Pindel,Atlas-Indel
ANP32E	81611	hgsc.bcm.edu	37	1	150199040	150199045	+	In_Frame_Del	DEL	TCCTCT	TCCTCT	-	rs68136184	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TCCTCT	TCCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	45	118	.	0.421	.	TCCTCT|0.685;-|0.315	0.315	strong	.	ANP32E	28	.	NM_030920	exon5	c.577_582del	p.193_194del	.	.	PASS	Pindel,Atlas-Indel
ATG2B	55102	hgsc.bcm.edu	37	14	96790337	96790338	+	Splice_Site	INS	-	-	A	rs34296665	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	10	24	.	0.370	.	-|0.648;A|0.352	0.352	strong	.	ATG2B	169	.	NM_018036	exon17	c.2438-2->T	.	.	.	PASS	Pindel,Atlas-Indel
CDR1	1038	hgsc.bcm.edu	37	X	139866424	139866441	+	In_Frame_Del	DEL	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	104	251	0	0.533333	0	.	.	none	.	CDR1	58	.	NM_004065	exon1	c.92_109del	p.31_37del	.	.	PASS	Atlas-Indel
SLC22A1	6580	hgsc.bcm.edu	37	6	160560898	160560905	+	In_Frame_Del	DEL	TGGTAAGT	TGGTAAGT	-	rs113569197	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGGTAAGT	TGGTAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	17	52	.	0.739	.	TGGTAAGT|0.311;-|0.689	0.689	strong	.	SLC22A1	69	.	NM_153187	exon7	c.1274_1276del	p.425_426del	.	.	PASS	Pindel,Atlas-Indel
KIAA0040	9674	hgsc.bcm.edu	37	1	175129946	175129946	+	Frame_Shift_Del	DEL	C	C	-	rs60195884	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	14	110	0	0.145833	0	-|1.000	.	weak	.	KIAA0040	2	.	NM_001162893	exon5	c.205delA	p.K69fs	.	.	PASS	Atlas-Indel
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361452	+	Frame_Shift_Del	DEL	GC	GC	-	rs35762823	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	455	70	600	0	0.153846	0	GC|0.500;-|0.500	0.500	strong	.	OR13C5	60	.	NM_001004482	exon1	c.244_245del	p.82_82del	.	.	PASS	Atlas-Indel
GNRH2	2797	hgsc.bcm.edu	37	20	3026345	3026346	+	Frame_Shift_Ins	INS	-	-	GCCCC	rs16996832	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	23	63	.	0.299	.	-|0.814;GCCCC|0.186	0.186	strong	.	GNRH2	15	.	NM_001501	exon4	c.326_327insGCCCC	p.E109fs	.	.	PASS	Pindel,Atlas-Indel
HERC4	26091	hgsc.bcm.edu	37	10	69785435	69785436	+	Splice_Site	INS	-	-	A	rs3834396	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	20	71	.	0.299	.	-|0.798;A|0.202	0.202	strong	.	HERC4	78	.	NM_022079	exon9	c.778-2->T	.	.	.	PASS	Pindel,Atlas-Indel
VEZF1	7716	hgsc.bcm.edu	37	17	56056604	56056605	+	In_Frame_Ins	INS	-	-	TGC	rs369163670		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	25	185	0	0.146199	0	.	.	weak	VEZF1,colon,carcinoma,0,2	VEZF1	50	2	NM_007146	exon5	c.1047_1048insGCA	p.Q349delinsQQ	.	.	PASS	Atlas-Indel
FOXD4L4	349334	hgsc.bcm.edu	37	9	42719280	42719280	+	Frame_Shift_Del	DEL	C	C	-	rs59364037		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	286	55	208	0	0.192308	0	.	.	weak	.	FOXD4L4	5	.	NM_199244	exon1	c.1214delG	p.C405fs	.	.	PASS	Atlas-Indel
MIR509-1	574514	hgsc.bcm.edu	37	X	146340339	146340339	+	RNA	DEL	T	T	-	rs36092315	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	52	395	.	0.495	.	T|0.937;-|0.063	0.063	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
GNLY	10578	hgsc.bcm.edu	37	2	85922121	85922122	+	Splice_Site	INS	-	-	A	rs113717357	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	11	50	0	0.407407	0	-|0.808;A|0.192	0.192	strong	.	GNLY	29	.	NM_012483	exon2	c.7+2->A	.	.	.	PASS	Atlas-Indel
NINL	22981	hgsc.bcm.edu	37	20	25457050	25457055	+	In_Frame_Del	DEL	CTCCCA	CTCCCA	-	rs68078266	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTCCCA	CTCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	16	73	.	0.219	.	CTCCCA|0.450;-|0.550	0.550	strong	.	NINL	148	.	NM_025176	exon17	c.2873_2878del	p.958_960del	.	.	PASS	Pindel,Atlas-Indel
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176769	70176769	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	339	58	206	.	0.171	.	.	.	weak	.	FOXD4L5	27	.	NM_001126334	exon1	c.1216delT	p.W406fs	.	.	PASS	Pindel,Atlas-Indel
PCDHGA8	9708	hgsc.bcm.edu	37	5	140772899	140772899	+	Frame_Shift_Del	DEL	C	C	-	rs3214276	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	77	111	.	0.653	.	C|0.882;-|0.118	0.118	strong	.	PCDHGA8	146	.	NM_014004	exon1	c.518delG	p.S173fs	.	.	PASS	Pindel,Atlas-Indel
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803308	43803309	+	Splice_Site	INS	-	-	TA	rs56283966	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	15	45	.	0.234	.	-|0.840;TA|0.160	0.160	strong	TMPRSS3,NS,carcinoma,0,2	TMPRSS3	40	2	NM_024022	exon9	c.617-1->TA	.	.	.	PASS	Pindel,Atlas-Indel
FAM83G	644815	hgsc.bcm.edu	37	17	18874685	18874686	+	In_Frame_Ins	INS	-	-	GGT	rs3071666	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	33	66	.	0.611	.	-|0.250;GGT|0.750	0.750	strong	.	FAM83G	51	.	NM_001039999	exon6	c.2459_2460insACC	p.R820delinsHR	.	.	PASS	Pindel,Atlas-Indel
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970760	45970774	+	In_Frame_Del	DEL	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	-	rs67692969	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	15	155	.	0.153	.	CTTGCAGCAGACAGG|0.758;-|0.242	0.242	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.569_583del	p.190_195del	.	.	PASS	Pindel,Atlas-Indel
MLL2	8085	hgsc.bcm.edu	37	12	49444214	49444214	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	47	214	.	0.244	.	.	.	none	.	MLL2	1173	.	NM_003482	exon11	c.3158delC	p.S1053fs	.	.	PASS	Pindel,Atlas-Indel
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184747	+	In_Frame_Ins	INS	-	-	TCT	rs34966908	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	18	48	.	0.340	.	-|0.500;TCT|0.500	0.500	strong	.	FERD3L	63	.	NM_152898	exon1	c.240_241insAGA	p.E80delinsEE	.	.	PASS	Pindel,Atlas-Indel
RBMX	27316	hgsc.bcm.edu	37	X	135960146	135960147	+	Frame_Shift_Ins	INS	-	-	AA	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	280	60	225	0	0.214286	0	.	.	none	.	RBMX	149	.	NM_002139	exon4	c.316_317insTT	p.P106fs	.	.	PASS	Atlas-Indel
EPB41L4A	64097	hgsc.bcm.edu	37	5	111500816	111500817	+	Splice_Site	INS	-	-	TAAAA	rs145708081	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	38	130	0	0.339286	0	-|0.025;TAAAA|0.975	0.975	strong	.	EPB41L4A	130	.	NM_022140	exon24	c.1933-1->TTTTA	.	.	.	PASS	Atlas-Indel
DDX12P	440081	hgsc.bcm.edu	37	12	9590651	9590652	+	RNA	INS	-	-	CTGAGTAAC	rs376958229	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	238	54	281	.	0.227	.	.	.	weak	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
MST1	4485	hgsc.bcm.edu	37	3	49722525	49722525	+	Splice_Site	DEL	A	A	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	11	164	0	0.0728477	0	.	.	none	.	MST1	84	.	NM_020998	exon15	c.1545-2T>-	.	.	.	PASS	Atlas-Indel
HTR3E	285242	hgsc.bcm.edu	37	3	183818222	183818222	+	Frame_Shift_Del	DEL	G	G	-	rs5855015	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	32	92	.	0.302	.	G|0.951;-|0.049	0.049	strong	.	HTR3E	65	.	NM_001256614	exon1	c.61delA	p.R21fs	.	.	PASS	Pindel,Atlas-Indel
CFTR	1080	hgsc.bcm.edu	37	7	117144306	117144307	+	Splice_Site	INS	-	-	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	20	88	.	0.230	.	.	.	none	.	CFTR	171	.	NM_000492	exon2	c.54-1->C	.	.	.	PASS	Pindel,Atlas-Indel
MGAM	8972	hgsc.bcm.edu	37	7	141708306	141708329	+	Frame_Shift_Del	DEL	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	40	154	0	0.296296	0	.	.	none	.	MGAM	767	.	NM_004668	exon3	c.128_150del	p.43_50del	.	.	PASS	Atlas-Indel
DSPP	1834	hgsc.bcm.edu	37	4	88536317	88536319	+	In_Frame_Del	DEL	AGC	AGC	-	rs143008261	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	34	216	.	0.154	.	AGC|0.917;-|0.083	0.083	strong	.	DSPP	174	.	NM_014208	exon5	c.2502_2504del	p.834_835del	.	.	PASS	Pindel,Atlas-Indel
CYP3A5	1577	hgsc.bcm.edu	37	7	99273810	99273811	+	Frame_Shift_Ins	INS	-	-	C	rs200579169	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	38	92	.	0.299	.	-|0.994;C|0.006	0.006	strong	.	CYP3A5	46	.	NM_001190484	exon2	c.93_94insG	p.G31fs	.	.	PASS	Pindel,Atlas-Indel
GPRIN1	114787	hgsc.bcm.edu	37	5	176026136	176026146	+	Frame_Shift_Del	DEL	CCTCCTTCCTC	CCTCCTTCCTC	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTCCTTCCTC	CCTCCTTCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	19	163	0	0.153226	0	.	.	none	.	GPRIN1	77	.	NM_052899	exon2	c.691_701del	p.231_234del	.	.	PASS	Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	In_Frame_Ins	INS	-	-	CTC	rs145742571	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	62	168	.	0.508	.	.	.	strong	.	KIAA1751	92	.	NM_001080484	exon11	c.1213_1214insGAG	p.K405delinsEK	.	.	PASS	Pindel,Atlas-Indel
OR13C2	392376	hgsc.bcm.edu	37	9	107367665	107367666	+	Frame_Shift_Del	DEL	GC	GC	-	rs143760725	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	566	100	568	.	0.177	.	.	.	strong	.	OR13C2	46	.	NM_001004481	exon1	c.244_245del	p.82_82del	.	.	PASS	Pindel,Atlas-Indel
SLC39A14	23516	hgsc.bcm.edu	37	8	22262229	22262234	+	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs111662782	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCTGCT	GCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	59	106	.	0.711	.	GCTGCT|0.701;-|0.299	0.299	strong	.	SLC39A14	59	.	NM_001135154	exon2	c.5_10del	p.2_4del	.	.	PASS	Pindel,Atlas-Indel
RBM12	10137	hgsc.bcm.edu	37	20	34240740	34240741	+	In_Frame_Ins	INS	-	-	GGGCCG	rs201181145	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	12	63	.	0.218	.	-|0.961;GGGCCG|0.039	0.039	strong	RBM12,rectum,carcinoma,0,1	RBM12	93	1	NM_001198840	exon2	c.2505_2506insCGGCCC	p.P835delinsPGP	.	.	PASS	Pindel,Atlas-Indel
SLC3A1	6519	hgsc.bcm.edu	37	2	44528268	44528268	+	Splice_Site	DEL	T	T	-	rs61179824	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	31	89	.	0.344	.	T|0.888;-|0.112	0.112	strong	.	SLC3A1	62	.	NM_000341	exon6	c.1136+1T>-	.	.	.	PASS	Pindel,Atlas-Indel
LCE4A	199834	hgsc.bcm.edu	37	1	152681680	152681681	+	In_Frame_Ins	INS	-	-	AGCTCTGGGGGCTGCTGT	rs6143428	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	62	195	.	0.459	.	.	.	strong	LCE4A,rectum,carcinoma,+1,3	LCE4A	37	3	NM_178356	exon1	c.129_130insAGCTCTGGGGGCTGCTGT	p.S43delinsSSSGGCC	.	.	PASS	Pindel,Atlas-Indel
ZNF408	79797	hgsc.bcm.edu	37	11	46724717	46724728	+	In_Frame_Del	DEL	AGTGGTGACAGA	AGTGGTGACAGA	-	rs148055528	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGTGGTGACAGA	AGTGGTGACAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	23	143	.	0.295	.	AGTGGTGACAGA|0.755;-|0.245	0.245	strong	.	ZNF408	70	.	NM_024741	exon4	c.575_586del	p.192_196del	.	.	PASS	Pindel,Atlas-Indel
TMEM87B	84910	hgsc.bcm.edu	37	2	112832536	112832538	+	In_Frame_Del	DEL	AAT	AAT	-	rs71385858	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	71	261	.	0.320	.	AAT|0.722;-|0.278	0.278	strong	.	TMEM87B	52	.	NM_032824	exon5	c.497_499del	p.166_167del	.	.	PASS	Pindel,Atlas-Indel
OR13C2	392376	hgsc.bcm.edu	37	9	107367393	107367396	+	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs143198170	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GTTA	GTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	376	130	366	0	0.345745	0	.	.	strong	.	OR13C2	46	.	NM_001004481	exon1	c.514_517del	p.172_173del	.	.	PASS	Atlas-Indel
GFM2	84340	hgsc.bcm.edu	37	5	74021847	74021852	+	In_Frame_Del	DEL	ACTCAA	ACTCAA	-	rs5868753	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ACTCAA	ACTCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	32	113	.	0.294	.	ACTCAA|0.643;-|0.357	0.357	strong	.	GFM2	38	.	NM_032380	exon18	c.1827_1832del	p.609_611del	.	.	PASS	Pindel,Atlas-Indel
HAVCR1	26762	hgsc.bcm.edu	37	5	156479568	156479569	+	In_Frame_Ins	INS	-	-	GTT	rs139041445	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	572	100	383	.	0.175	.	.	.	strong	.	HAVCR1	84	.	NM_001099414	exon4	c.477_478insAAC	p.T159delinsTT	.	.	PASS	Pindel,Atlas-Indel
AGAP6	414189	hgsc.bcm.edu	37	10	51768675	51768676	+	Frame_Shift_Del	DEL	AA	AA	-	rs113234838		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	14	110	.	0.156	.	AA|0.500;-|0.500	0.500	weak	.	AGAP6	53	.	NM_001077665	exon8	c.789_790del	p.263_264del	.	.	PASS	Pindel,Atlas-Indel
CRIPAK	285464	hgsc.bcm.edu	37	4	1388375	1388376	+	Frame_Shift_Ins	INS	-	-	CA	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	14	161	0	0.0804598	0	.	.	none	.	CRIPAK	185	.	NM_175918	exon1	c.76_77insCA	p.S26fs	.	.	PASS	Atlas-Indel
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964409	37964429	+	In_Frame_Del	DEL	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	-	rs200195385	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	63	188	0	0.36	0	CAGCGCCTGCTGCAAACCCCT|0.610;-|0.390	0.390	strong	.	CDC42EP1	53	.	NM_152243	exon3	c.757_777del	p.253_259del	.	.	PASS	Atlas-Indel
RBBP6	5930	hgsc.bcm.edu	37	16	24583713	24583718	+	In_Frame_Del	DEL	AAAGAG	AAAGAG	-	rs148143334	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAAGAG	AAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	13	37	0	0.40625	0	AAAGAG|0.968;-|0.032	0.032	strong	.	RBBP6	158	.	NM_006910	exon18	c.5325_5330del	p.1775_1777del	.	.	PASS	Atlas-Indel
MLL2	8085	hgsc.bcm.edu	37	12	49422949	49422950	+	Frame_Shift_Ins	INS	-	-	CA	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	29	71	.	0.309	.	.	.	none	.	MLL2	1173	.	NM_003482	exon44	c.14146_14147insTG	p.G4716fs	.	.	PASS	Pindel,Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1887112	1887112	+	Frame_Shift_Del	DEL	C	C	-	rs3838975	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	69	101	0	0.811765	0	C|0.783;-|0.217	0.217	strong	.	KIAA1751	92	.	NM_001080484	exon18	c.2195delC	p.A732fs	.	.	PASS	Atlas-Indel
NUCB2	4925	hgsc.bcm.edu	37	11	17352478	17352480	+	In_Frame_Del	DEL	ACA	ACA	-	rs3842269	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	28	154	.	0.220	.	ACA|0.718;-|0.282	0.282	strong	.	NUCB2	31	.	NM_005013	exon13	c.1202_1204del	p.401_402del	.	.	PASS	Pindel,Atlas-Indel
CRIPAK	285464	hgsc.bcm.edu	37	4	1388622	1388623	+	Frame_Shift_Ins	INS	-	-	CA	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	38	121	0	0.290076	0	.	.	none	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.323_324insCA	p.L108fs	.	.	PASS	Atlas-Indel
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586676	+	Frame_Shift_Del	DEL	TTTTA	TTTTA	-	rs201063949	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTTTA	TTTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	32	136	0	0.248062	0	TTTTA|0.983;-|0.017	0.017	strong	.	NUDT17	25	.	NM_001012758	exon8	c.901_905del	p.301_302del	.	.	PASS	Atlas-Indel
SYT14	255928	hgsc.bcm.edu	37	1	210267894	210267896	+	In_Frame_Del	DEL	GAA	GAA	-	rs144713062	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	46	165	.	0.348	.	GAA|0.912;-|0.088	0.088	strong	.	SYT14	89	.	NM_001146264	exon6	c.804_806del	p.268_269del	.	.	PASS	Pindel,Atlas-Indel
ARHGAP30	257106	hgsc.bcm.edu	37	1	161021121	161021122	+	In_Frame_Ins	INS	-	-	GGCCAG	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	16	41	0	0.32	0	.	.	none	.	ARHGAP30	105	.	NM_181720	exon10	c.1403_1404insCTGGCC	p.L468delinsPGL	.	.	PASS	Atlas-Indel
HCLS1	3059	hgsc.bcm.edu	37	3	121351315	121351316	+	In_Frame_Ins	INS	-	-	GGCTCAGGCTCA	rs150627065	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	21	106	.	0.160	.	-|0.731;GGCTCAGGCTCA|0.269	0.269	strong	HCLS1,caecum,carcinoma,0,1	HCLS1	78	1	NM_005335	exon12	c.1104_1105insTGAGCCTGAGCC	p.P368delinsPEPEP	.	.	PASS	Pindel,Atlas-Indel
ZNF844	284391	hgsc.bcm.edu	37	19	12187316	12187317	+	Frame_Shift_Del	DEL	CA	CA	-	rs201088213	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	14	52	0	0.368421	0	CA|0.987;-|0.013	0.013	strong	.	ZNF844	69	.	NM_001136501	exon4	c.1380_1381del	p.460_461del	.	.	PASS	Atlas-Indel
TDRD3	81550	hgsc.bcm.edu	37	13	61102576	61102578	+	In_Frame_Del	DEL	ATA	ATA	-	rs148917045	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	50	59	.	0.746	.	ATA|0.894;-|0.106	0.106	strong	TDRD3_ENST00000535286,NS,carcinoma,0,4	TDRD3	123	4	NM_001146070	exon11	c.1216_1218del	p.406_406del	.	.	PASS	Pindel,Atlas-Indel
ASXL3	80816	hgsc.bcm.edu	37	18	31323500	31323500	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	33	78	0	0.485294	0	.	.	none	ASXL3_ENST00000269197,NS,carcinoma,+2,2	ASXL3	405	2	NM_030632	exon12	c.3687delG	p.M1229fs	.	.	PASS	Atlas-Indel
KIAA0040	9674	hgsc.bcm.edu	37	1	175129948	175129955	+	Frame_Shift_Del	DEL	TCTTCTTG	TCTTCTTG	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TCTTCTTG	TCTTCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	14	110	0	0.14433	0	.	.	none	.	KIAA0040	2	.	NM_001162893	exon5	c.196_203del	p.66_68del	.	.	PASS	Atlas-Indel
TICAM1	148022	hgsc.bcm.edu	37	19	4817288	4817289	+	In_Frame_Ins	INS	-	-	AGG	rs144100421	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	73	205	.	0.358	.	.	.	strong	.	TICAM1	69	.	NM_182919	exon2	c.1102_1103insCCT	p.S368delinsPS	.	.	PASS	Pindel,Atlas-Indel
OR5B3	441608	hgsc.bcm.edu	37	11	58170793	58170793	+	Frame_Shift_Del	DEL	G	G	-	rs200799158	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	18	83	.	0.277	.	G|0.982;-|0.018	0.018	strong	.	OR5B3	65	.	NM_001005469	exon1	c.91delT	p.F31fs	.	.	PASS	Pindel,Atlas-Indel
APLF	200558	hgsc.bcm.edu	37	2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-	rs149897324	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	26	58	.	0.406	.	A|0.991;-|0.009	0.009	strong	.	APLF	69	.	NM_173545	exon10	c.1524delG	p.M508fs	.	.	PASS	Pindel,Atlas-Indel
CLCA4	22802	hgsc.bcm.edu	37	1	87045902	87045903	+	In_Frame_Ins	INS	-	-	CCTACT	rs56040873	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	30	160	.	0.216	.	.	.	weak	.	CLCA4	131	.	NM_012128	exon14	c.2634_2635insCCTACT	p.T878delinsTPT	.	.	PASS	Pindel,Atlas-Indel
BTBD10	84280	hgsc.bcm.edu	37	11	13410691	13410694	+	Splice_Site	DEL	GAAA	GAAA	-	rs3833472	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAAA	GAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	35	75	.	0.625	.	GAAA|0.908;-|0.092	0.092	strong	.	BTBD10	43	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
PI4KAP2	375133	hgsc.bcm.edu	37	22	21829514	21829517	+	RNA	DEL	TGTC	TGTC	-	rs113567369	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	456	47	380	0	0.10307	0	TGTC|0.500;-|0.500	0.500	strong	.	PI4KAP2	11	.	.	.	.	.	.	.	PASS	Atlas-Indel
A2ML1	144568	hgsc.bcm.edu	37	12	9016563	9016564	+	Frame_Shift_Del	DEL	GC	GC	-	rs144686314	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	21	95	.	0.356	.	GC|0.979;-|0.021	0.021	strong	.	A2ML1	199	.	NM_144670	exon29	c.3675_3676del	p.1225_1226del	.	.	PASS	Pindel,Atlas-Indel
HNRNPA0	10949	hgsc.bcm.edu	37	5	137088945	137088946	+	In_Frame_Ins	INS	-	-	GCT	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	22	59	.	0.242	.	.	.	none	.	HNRNPA0	17	.	NM_006805	exon1	c.811_812insAGC	p.G271delinsSG	.	.	PASS	Pindel,Atlas-Indel
RBMX	27316	hgsc.bcm.edu	37	X	135956571	135956572	+	Frame_Shift_Ins	INS	-	-	GG	rs369155856	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	35	119	0	0.21875	0	.	.	weak	.	RBMX	149	.	NM_002139	exon9	c.906_907insCC	p.P302fs	.	.	PASS	Atlas-Indel
PPFIBP2	8495	hgsc.bcm.edu	37	11	7661048	7661050	+	In_Frame_Del	DEL	CTC	CTC	-	rs143023559	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	47	111	.	0.343	.	CTC|0.944;-|0.056	0.056	strong	.	PPFIBP2	87	.	NM_003621	exon15	c.1321_1323del	p.441_441del	.	.	PASS	Pindel,Atlas-Indel
HSP90B1	7184	hgsc.bcm.edu	37	12	104341188	104341190	+	In_Frame_Del	DEL	GAA	GAA	-	rs5800607	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	54	150	.	0.321	.	GAA|0.865;-|0.135	0.135	strong	.	HSP90B1	72	.	NM_003299	exon17	c.2361_2363del	p.787_788del	.	.	PASS	Pindel,Atlas-Indel
IFNE	338376	hgsc.bcm.edu	37	9	21482125	21482126	+	RNA	INS	-	-	A	rs34814436	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	25	102	.	0.338	.	-|0.806;A|0.194	0.194	strong	.	IFNE	16	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
DMKN	93099	hgsc.bcm.edu	37	19	36002419	36002421	+	In_Frame_Del	DEL	CCA	CCA	-	rs72334573	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	35	60	0	0.57377	0	CCA|0.786;-|0.214	0.214	strong	DMKN,colon,carcinoma,-2,1	DMKN	116	1	NM_033317	exon5	c.811_813del	p.271_271del	.	.	PASS	Atlas-Indel
PHF14	9678	hgsc.bcm.edu	37	7	11091329	11091330	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	16	82	0	0.210526	0	.	.	none	.	PHF14	90	.	NM_014660	exon14	c.2403_2404insA	p.R801fs	.	.	PASS	Atlas-Indel
KIAA0586	9786	hgsc.bcm.edu	37	14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	61	154	.	0.357	.	.	.	none	.	KIAA0586	180	.	NM_001244189	exon5	c.427delA	p.R143fs	.	.	PASS	Pindel,Atlas-Indel
OR8B3	390271	hgsc.bcm.edu	37	11	124266697	124266698	+	Frame_Shift_Ins	INS	-	-	G	rs201661436	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	442	156	422	0	0.352941	0	-|0.977;G|0.023	0.023	strong	.	OR8B3	36	.	NM_001005467	exon1	c.551_552insC	p.L184fs	.	.	PASS	Atlas-Indel
HLA-B	3106	hgsc.bcm.edu	37	6	31324737	31324737	+	Splice_Site	DEL	G	G	-	rs371250843		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	13	13	.	0.394	.	.	.	weak	.	HLA-B	54	.	NM_005514	exon3	c.74-2C>-	.	.	.	PASS	Pindel,Atlas-Indel
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026134	+	Frame_Shift_Del	DEL	CAAAGACCCAGGA	CAAAGACCCAGGA	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAAAGACCCAGGA	CAAAGACCCAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	19	151	0	0.175926	0	.	.	none	.	GPRIN1	77	.	NM_052899	exon2	c.703_715del	p.235_239del	.	.	PASS	Atlas-Indel
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382373	24382374	+	In_Frame_Ins	INS	-	-	TGC	rs371342199		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	34	197	0	0.203593	0	.	.	weak	.	.	.	.	NM_001136234	exon1	c.1496_1497insTGC	p.I499delinsIA	.	.	PASS	Atlas-Indel
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816814	75816815	+	In_Frame_Ins	INS	-	-	ACA	rs144850646	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	26	76	.	0.406	.	.	.	strong	.	GLIPR1L2	54	.	NM_152436	exon4	c.715_716insACA	p.D239delinsDN	.	.	PASS	Pindel,Atlas-Indel
SLFN12L	100506736	hgsc.bcm.edu	37	17	33801989	33801990	+	Frame_Shift_Ins	INS	-	-	AAAA	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	25	86	.	0.410	.	.	.	none	.	SLFN12L	140	.	NM_001195790	exon4	c.1720_1721insTTTT	p.R574fs	.	.	PASS	Pindel,Atlas-Indel
HDGFRP2	0	hgsc.bcm.edu	37	19	4498017	4498019	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	32	78	.	0.405	.	.	.	none	.	.	.	.	NM_032631	exon11	c.1390_1392del	p.464_464del	.	.	PASS	Pindel,Atlas-Indel
CPS1	1373	hgsc.bcm.edu	37	2	211421452	211421453	+	In_Frame_Ins	INS	-	-	TCT	rs3835047	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	34	150	.	0.288	.	-|0.556;TCT|0.444	0.444	strong	.	CPS1	485	.	NM_001122633	exon2	c.13_14insTCT	p.I5delinsIF	.	.	PASS	Pindel,Atlas-Indel
BTN2A3P	54718	hgsc.bcm.edu	37	6	26422387	26422388	+	RNA	INS	-	-	CTTCCTCCTCCT	rs141260282	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	19	95	.	0.297	.	.	.	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
ASPHD1	253982	hgsc.bcm.edu	37	16	29912802	29912803	+	In_Frame_Ins	INS	-	-	GGT	rs140411458	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	18	14	.	0.462	.	-|0.756;GGT|0.244	0.244	strong	.	ASPHD1	28	.	NM_181718	exon1	c.510_511insGGT	p.Q170delinsQG	.	.	PASS	Pindel,Atlas-Indel
FKBP15	23307	hgsc.bcm.edu	37	9	115932150	115932151	+	In_Frame_Ins	INS	-	-	TTC	rs113480096	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	11	44	.	0.250	.	-|0.943;TTC|0.057	0.057	strong	.	FKBP15	128	.	NM_015258	exon26	c.2839_2840insGAA	p.K947delinsEK	.	.	PASS	Pindel,Atlas-Indel
TLX1NB	100038246	hgsc.bcm.edu	37	10	102849370	102849370	+	Frame_Shift_Del	DEL	T	T	-	rs200664029	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	33	94	.	0.340	.	T|0.996;-|0.004	0.004	strong	.	.	.	.	NM_001085398	exon3	c.294delG	p.Q98fs	.	.	PASS	Pindel,Atlas-Indel
HOXD9	3235	hgsc.bcm.edu	37	2	176988290	176988291	+	In_Frame_Ins	INS	-	-	GCA	rs56007470	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	13	24	.	0.394	.	-|0.685;GCA|0.315	0.315	strong	.	HOXD9	49	.	NM_014213	exon1	c.794_795insGCA	p.P265delinsPQ	.	.	PASS	Pindel,Atlas-Indel
TBP	6908	hgsc.bcm.edu	37	6	170871038	170871040	+	In_Frame_Del	DEL	CAA	CAA	-	rs71815788	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	36	62	0	0.818182	0	.	.	strong	TBP,caecum,carcinoma,0,1	TBP	58	1	NM_003194	exon3	c.213_215del	p.71_72del	.	.	PASS	Atlas-Indel
E2F4	1874	hgsc.bcm.edu	37	16	67229794	67229811	+	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAG	-	rs112970553	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	26	77	.	0.299	.	-|1.000;|0.000	1.000	alt	.	E2F4	25	.	NM_001950	exon7	c.917_934del	p.306_312del	.	.	PASS	Pindel,Atlas-Indel
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427685	70427685	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	293	45	208	.	0.154	.	.	.	weak	.	FOXD4L4	5	.	NM_199244	exon1	c.1216delT	p.W406fs	.	.	PASS	Pindel,Atlas-Indel
MICA	100507436	hgsc.bcm.edu	37	6	31380158	31380161	+	Frame_Shift_Del	DEL	GCTG	GCTG	-	rs138201170	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCTG	GCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	39	176	.	0.322	.	.	.	strong	.	MICA	21	.	NM_001177519	exon5	c.948_951del	p.316_317del	.	.	PASS	Pindel,Atlas-Indel
CHRNA7	1139	hgsc.bcm.edu	37	15	32449875	32449876	+	Frame_Shift_Del	DEL	TG	TG	-	rs374603734		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1120	202	830	0	0.180357	0	.	.	weak	.	CHRNA7	57	.	NM_001190455	exon6	c.583_584del	p.195_195del	.	.	PASS	Atlas-Indel
PRSS48	345062	hgsc.bcm.edu	37	4	152201018	152201019	+	Frame_Shift_Ins	INS	-	-	CAGGT	rs148861921	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	32	147	.	0.308	.	.	.	strong	.	PRSS48	91	.	NM_183375	exon2	c.123_124insCAGGT	p.W41fs	.	.	PASS	Pindel,Atlas-Indel
NR1H2	7376	hgsc.bcm.edu	37	19	50881820	50881821	+	In_Frame_Ins	INS	-	-	AAC	rs55652650	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	23	59	.	0.291	.	-|0.132;AAC|0.868	0.868	strong	.	NR1H2	47	.	NM_007121	exon6	c.514_515insAAC	p.K172delinsKQ	.	.	PASS	Pindel,Atlas-Indel
HAVCR1	26762	hgsc.bcm.edu	37	5	156479444	156479446	+	In_Frame_Del	DEL	TTG	TTG	-	rs45439103	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	361	126	325	.	0.349	.	TTG|0.766;-|0.234	0.234	strong	HAVCR1,NS,carcinoma,-1,1	HAVCR1	84	1	NM_001099414	exon4	c.600_602del	p.200_201del	.	.	PASS	Pindel,Atlas-Indel
KIAA1751	85452	hgsc.bcm.edu	37	1	1887092	1887092	+	Frame_Shift_Del	DEL	G	G	-	rs139735565	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	65	96	0	0.844156	0	G|0.777;-|0.223	0.223	strong	.	KIAA1751	92	.	NM_001080484	exon18	c.2215delG	p.G739fs	.	.	PASS	Atlas-Indel
ZNF816	125893	hgsc.bcm.edu	37	19	53454475	53454476	+	In_Frame_Ins	INS	-	-	ACT	rs33949217	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	24	122	.	0.235	.	ACT|1.000;|0.000	1.000	weak	.	ZNF816	73	.	NM_001202457	exon4	c.553_554insAGT	p.G185delinsSG	.	.	PASS	Pindel,Atlas-Indel
CELA1	1990	hgsc.bcm.edu	37	12	51723598	51723599	+	Frame_Shift_Ins	INS	-	-	G	rs17860363	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	20	74	.	0.417	.	-|0.851;G|0.149	0.149	strong	.	CELA1	39	.	NM_001971	exon7	c.629_630insC	p.L210fs	.	.	PASS	Pindel,Atlas-Indel
GNAI2	2771	hgsc.bcm.edu	37	3	50294456	50294458	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	18	160	0	0.103448	0	.	.	none	.	GNAI2	42	.	NM_002070	exon7	c.810_812del	p.270_271del	.	.	PASS	Atlas-Indel
PTCHD3	374308	hgsc.bcm.edu	37	10	27702256	27702257	+	Frame_Shift_Ins	INS	-	-	C	rs112067123	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	62	94	.	0.614	.	-|0.732;C|0.268	0.268	strong	.	PTCHD3	140	.	NM_001034842	exon1	c.924_925insG	p.G308fs	.	.	PASS	Pindel,Atlas-Indel
C14orf177	283598	hgsc.bcm.edu	37	14	99182527	99182535	+	Frame_Shift_Del	DEL	GGATGCATC	GGATGCATC	-	rs139827156	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GGATGCATC	GGATGCATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	18	53	.	0.346	.	GGATGCATC|0.963;-|0.037	0.037	strong	.	C14orf177	37	.	NM_182560	wholegene	.	.	.	.	PASS	Pindel,Atlas-Indel
KIAA1841	84542	hgsc.bcm.edu	37	2	61361326	61361326	+	Frame_Shift_Del	DEL	G	G	-	rs142269591	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	45	142	.	0.324	.	G|0.962;-|0.038	0.038	strong	.	KIAA1841	95	.	NM_032506	exon21	c.2082delT	p.S694fs	.	.	PASS	Pindel,Atlas-Indel
IRF8	3394	hgsc.bcm.edu	37	16	85954879	85954879	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	10	39	0	0.277778	0	.	.	none	IRF8,NS,lymphoid_neoplasm,0,1	IRF8	65	1	NM_002163	exon9	c.1271delT	p.I424fs	.	.	PASS	Atlas-Indel
SIRPA	140885	hgsc.bcm.edu	37	20	1896052	1896054	+	In_Frame_Del	DEL	CGA	CGA	-	rs139878822	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	30	393	0	0.134529	0	.	.	strong	SIRPA,NS,carcinoma,-1,1	SIRPA	83	1	NM_001040022	exon3	c.386_388del	p.129_130del	.	.	PASS	Atlas-Indel
MN1	4330	hgsc.bcm.edu	37	22	28194933	28194934	+	In_Frame_Ins	INS	-	-	TGC	rs75719175		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	20	45	0	0.327869	0	.	.	weak	MN1,caecum,carcinoma,0,2	MN1	122	2	NM_002430	exon1	c.1599_1600insGCA	p.Q533delinsQQ	.	.	PASS	Atlas-Indel
TRIOBP	11078	hgsc.bcm.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs67890459	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	83	167	.	0.568	.	-|0.368;CAA|0.632	0.368	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.1191_1193del	p.397_398del	.	.	PASS	Pindel,Atlas-Indel
OR8B2	26595	hgsc.bcm.edu	37	11	124252689	124252690	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	481	47	416	0	0.0977131	0	.	.	none	.	OR8B2	42	.	NM_001005468	exon1	c.551_552insC	p.L184fs	.	.	PASS	Atlas-Indel
GOLIM4	27333	hgsc.bcm.edu	37	3	167742354	167742356	+	In_Frame_Del	DEL	TCC	TCC	-	rs144680891	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	54	155	.	0.300	.	.	.	strong	.	GOLIM4	71	.	NM_014498	exon14	c.1819_1821del	p.607_607del	.	.	PASS	Pindel,Atlas-Indel
ZFPM1	161882	hgsc.bcm.edu	37	16	88594540	88594542	+	In_Frame_Del	DEL	GAA	GAA	-	rs10606433	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	30	70	.	0.698	.	GAA|0.940;-|0.060	0.060	strong	.	ZFPM1	32	.	NM_153813	exon6	c.605_607del	p.202_203del	.	.	PASS	Pindel,Atlas-Indel
INHBE	83729	hgsc.bcm.edu	37	12	57850304	57850319	+	Frame_Shift_Del	DEL	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	20	105	.	0.274	.	.	.	none	.	INHBE	38	.	NM_031479	exon2	c.725_740del	p.242_247del	.	.	PASS	Pindel,Atlas-Indel
RNU6-71	100873774	hgsc.bcm.edu	37	6	56510983	56510983	+	RNA	DEL	A	A	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	11	41	.	0.297	.	.	.	none	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
PSORS1C2	170680	hgsc.bcm.edu	37	6	31105858	31105858	+	Frame_Shift_Del	DEL	G	G	-	rs79153019	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	21	63	.	0.382	.	G|0.946;-|0.054	0.054	strong	.	PSORS1C2	11	.	NM_014069	exon2	c.282delT	p.P94fs	.	.	PASS	Pindel,Atlas-Indel
BPNT1	10380	hgsc.bcm.edu	37	1	220231181	220231181	+	RNA	DEL	T	T	-	rs34887640	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	58	133	.	0.569	.	T|0.776;-|0.224	0.224	strong	.	BPNT1	29	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
MIR550A1	693133	hgsc.bcm.edu	37	7	30329454	30329456	+	RNA	DEL	TGT	TGT	-	rs373052300		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	23	129	.	0.160	.	.	.	weak	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
RP1L1	94137	hgsc.bcm.edu	37	8	10467629	10467630	+	In_Frame_Ins	INS	-	-	TTC	rs146656804	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	23	208	0	0.163121	0	.	.	strong	.	RP1L1	453	.	NM_178857	exon4	c.3979_3980insGAA	p.T1327delinsET	.	.	PASS	Atlas-Indel
NUDT17	200035	hgsc.bcm.edu	37	1	145586679	145586679	+	Frame_Shift_Del	DEL	C	C	-	rs199513201	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	32	137	0	0.251969	0	C|0.983;-|0.017	0.017	strong	.	NUDT17	25	.	NM_001012758	exon8	c.898delT	p.C300fs	.	.	PASS	Atlas-Indel
SAA2	6289	hgsc.bcm.edu	37	11	18267597	18267598	+	Splice_Site	INS	-	-	GGAAA	rs202167679	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	314	39	235	0	0.124204	0	-|0.929;GGAAA|0.071	0.071	strong	.	SAA2	22	.	NM_001127380	exon4	c.92-2->TTTCC	.	.	.	PASS	Atlas-Indel
NUP54	53371	hgsc.bcm.edu	37	4	77065318	77065319	+	In_Frame_Ins	INS	-	-	TGT	rs36024409	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	38	138	.	0.325	.	-|0.827;TGT|0.173	0.173	strong	NUP54,NS,carcinoma,0,1	NUP54	48	1	NM_017426	exon3	c.279_280insACA	p.Q93delinsQQ	.	.	PASS	Pindel,Atlas-Indel
PNPLA7	375775	hgsc.bcm.edu	37	9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T	rs372921391		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	22	49	.	0.328	.	.	.	weak	.	PNPLA7	124	.	NM_001098537	exon1	c.23_24insA	p.S8fs	.	.	PASS	Pindel,Atlas-Indel
OR9K2	441639	hgsc.bcm.edu	37	12	55523587	55523587	+	Frame_Shift_Del	DEL	T	T	-	rs58036029	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	36	124	.	0.321	.	T|0.711;-|0.289	0.289	strong	.	OR9K2	63	.	NM_001005243	exon1	c.34delA	p.I12fs	.	.	PASS	Pindel,Atlas-Indel
OR7G3	390883	hgsc.bcm.edu	37	19	9236698	9236699	+	Frame_Shift_Ins	INS	-	-	ATGGT	rs111867493	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	50	137	.	0.394	.	-|0.601;ATGGT|0.399	0.399	strong	.	OR7G3	41	.	NM_001001958	exon1	c.929_930insACCAT	p.S310fs	.	.	PASS	Pindel,Atlas-Indel
FAM22F	54754	hgsc.bcm.edu	37	9	97080945	97080947	+	In_Frame_Del	DEL	AGA	AGA	-	rs150455117	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	423	142	469	0	0.335697	0	.	.	strong	.	FAM22F	72	.	NM_017561	exon7	c.2072_2074del	p.691_692del	.	.	PASS	Atlas-Indel
IRF8	3394	hgsc.bcm.edu	37	16	85954881	85954886	+	In_Frame_Del	DEL	CCGTCT	CCGTCT	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCGTCT	CCGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	10	38	0	0.263158	0	.	.	none	.	IRF8	65	.	NM_002163	exon9	c.1273_1278del	p.425_426del	.	.	PASS	Atlas-Indel
LINC00482	284185	hgsc.bcm.edu	37	17	79279019	79279020	+	RNA	INS	-	-	C	rs3215153	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	18	42	.	0.333	.	-|0.924;C|0.076	0.076	strong	.	.	.	.	.	.	.	.	.	.	PASS	Pindel,Atlas-Indel
SNAPC4	6621	hgsc.bcm.edu	37	9	139277995	139277997	+	In_Frame_Del	DEL	GCT	GCT	-	rs147271628	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	10	50	.	0.244	.	.	.	strong	.	SNAPC4	82	.	NM_003086	exon15	c.1625_1627del	p.542_543del	.	.	PASS	Pindel,Atlas-Indel
SLC38A10	124565	hgsc.bcm.edu	37	17	79219501	79219503	+	In_Frame_Del	DEL	ATG	ATG	-	rs10569617	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	61	137	.	0.310	.	ATG|0.576;-|0.424	0.424	strong	.	SLC38A10	133	.	NM_001037984	exon16	c.3214_3216del	p.1072_1072del	.	.	PASS	Pindel,Atlas-Indel
CCDC63	160762	hgsc.bcm.edu	37	12	111342460	111342460	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	52	107	.	0.317	.	.	.	none	.	CCDC63	89	.	NM_152591	exon11	c.1410delA	p.E470fs	.	.	PASS	Pindel,Atlas-Indel
IRF8	3394	hgsc.bcm.edu	37	16	85954879	85954886	+	Frame_Shift_Del	DEL	CACCGTCT	CACCGTCT	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CACCGTCT	CACCGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	10	40	.	0.270	.	.	.	none	IRF8,NS,lymphoid_neoplasm,0,1	IRF8	65	1	NM_002163	exon9	c.1271_1278del	p.424_426del	.	.	PASS	Pindel
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789313	117789327	+	In_Frame_Del	DEL	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	-	rs201746372	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	18	125	.	0.165	.	GGGCTGGAGATGCCT|0.257;-|0.743	0.743	strong	TMPRSS13_ENST00000445164,NS,NS,0,3	TMPRSS13	75	3	NM_001206790	exon2	c.249_263del	p.83_88del	.	.	PASS	Pindel
MUC4	4585	hgsc.bcm.edu	37	3	195506713	195506760	+	In_Frame_Del	DEL	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	23	17	.	0.258	.	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.11692_11739del	p.3898_3913del	.	.	PASS	Pindel
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106501	31106501	+	Frame_Shift_Del	DEL	C	C	-	rs138474986	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	76	92	.	0.539	.	.	.	strong	.	PSORS1C1	11	.	NM_014068	exon5	c.111delT	p.R37fs	.	.	PASS	Pindel
GPRIN1	114787	hgsc.bcm.edu	37	5	176026115	176026138	+	In_Frame_Del	DEL	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	36	159	.	0.288	.	.	.	none	.	GPRIN1	77	.	NM_052899	exon2	c.699_722del	p.233_241del	.	.	PASS	Pindel
KIAA0040	9674	hgsc.bcm.edu	37	1	175129925	175129933	+	In_Frame_Del	DEL	CTTCTTCTT	CTTCTTCTT	-	rs150137790	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTTCTTCTT	CTTCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	21	121	.	0.210	.	.	.	strong	.	KIAA0040	2	.	NM_001162893	exon5	c.218_226del	p.73_76del	.	.	PASS	Pindel
ARHGEF35	445328	hgsc.bcm.edu	37	7	143885448	143885449	+	Frame_Shift_Ins	INS	-	-	CTCCACGCTGGGCCTCCTCAGC	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	311	54	40	.	0.174	.	.	.	none	.	ARHGEF35	11	.	NM_001003702	exon2	c.29_30insGCTGAGGAGGCCCAGCGTGGAG	p.A10_S11delinsGX	.	.	PASS	Pindel
KRT1	3848	hgsc.bcm.edu	37	12	53069223	53069243	+	In_Frame_Del	DEL	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	11	7	.	0.611	.	.	.	none	.	KRT1	110	.	NM_006121	exon9	c.1670_1690del	p.557_564del	.	.	PASS	Pindel
SELPLG	6404	hgsc.bcm.edu	37	12	109017651	109017680	+	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	36	182	.	0.216	.	.	.	none	.	SELPLG	138	.	NM_001206609	exon2	c.453_482del	p.151_161del	.	.	PASS	Pindel
NFKB1	4790	hgsc.bcm.edu	37	4	103534740	103534741	+	Splice_Site	INS	-	-	A	rs148268461	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	18	97	.	0.234	.	-|0.899;A|0.101	0.101	strong	.	NFKB1	78	.	NM_001165412	exon23	c.2746+2->A	.	.	.	PASS	Pindel
RBM43	375287	hgsc.bcm.edu	37	2	152108088	152108088	+	Frame_Shift_Del	DEL	T	T	-	rs142934811	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	12	83	.	0.154	.	.	.	strong	.	RBM43	35	.	NM_198557	exon4	c.407delT	p.I136fs	.	.	PASS	Pindel
SKA3	221150	hgsc.bcm.edu	37	13	21729952	21729953	+	Splice_Site	INS	-	-	AA	rs11446085	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	11	39	.	0.204	.	-|0.500;A|0.500	.	strong	.	SKA3	76	.	NM_145061	exon9	c.1120-2->TT	.	.	.	PASS	Pindel
MICA	100507436	hgsc.bcm.edu	37	6	31380099	31380161	+	Frame_Shift_Del	DEL	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	31	191	.	0.214	.	.	.	none	.	MICA	21	.	NM_001177519	exon5	c.893_951del	p.298_317del	.	.	PASS	Pindel
VWDE	221806	hgsc.bcm.edu	37	7	12391268	12391269	+	Frame_Shift_Ins	INS	-	-	A	rs11454536	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	35	137	.	0.248	.	-|0.844;A|0.156	0.156	strong	.	VWDE	123	.	NM_001135924	exon19	c.3817_3818insT	p.K1273_E1274delinsX	.	.	PASS	Pindel
CCRL1	51554	hgsc.bcm.edu	37	3	132320802	132320803	+	RNA	INS	-	-	A	rs201720609	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	30	130	.	0.256	.	.	.	weak	.	CCRL1	30	.	.	.	.	.	.	.	PASS	Pindel
ASXL3	80816	hgsc.bcm.edu	37	18	31323501	31323501	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	25	76	.	0.368	.	.	.	none	.	ASXL3	405	.	NM_030632	exon12	c.3688delC	p.L1230fs	.	.	PASS	Pindel
NOTCH4	4855	hgsc.bcm.edu	37	6	32191659	32191661	+	In_Frame_Del	DEL	AGC	AGC	-	rs150280230	bycluster;by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	12	48	.	0.150	.	.	.	alt	.	NOTCH4	201	.	NM_004557	exon1	c.46_48del	p.16_16del	.	.	PASS	Pindel
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471753	39471767	+	In_Frame_Del	DEL	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	18	30	.	0.340	.	.	.	none	.	KRTAP17-1	14	.	NM_031964	exon1	c.137_151del	p.46_51del	.	.	PASS	Pindel
TNRC6B	23112	hgsc.bcm.edu	37	22	40697177	40697179	+	In_Frame_Del	DEL	GCA	GCA	-	rs10617561	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	14	39	.	0.264	.	GCA|0.779;-|0.221	0.221	strong	.	TNRC6B	195	.	NM_001162501	exon15	c.3959_3961del	p.1320_1321del	.	.	PASS	Pindel
UBXN11	91544	hgsc.bcm.edu	37	1	26608883	26608884	+	In_Frame_Ins	INS	-	-	CCGGGACCGGGACAGGGACTGGGG	rs140364749	bycluster;by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	11	39	.	0.208	.	.	.	alt	UBXN11,NS,carcinoma,-2,2	UBXN11	54	2	NM_183008	exon16	c.1470_1471insCCCCAGTCCCTGTCCCGGTCCCGG	p.G490delinsGPSPCPGPG	.	.	PASS	Pindel
ODF1	4956	hgsc.bcm.edu	37	8	103573011	103573037	+	In_Frame_Del	DEL	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	36	109	.	0.324	.	.	.	none	.	ODF1	55	.	NM_024410	exon2	c.651_677del	p.217_226del	.	.	PASS	Pindel
DNAH5	1767	hgsc.bcm.edu	37	5	13868104	13868104	+	Splice_Site	DEL	A	A	-	rs35398031	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	21	83	.	0.304	.	A|0.250;-|0.750	0.750	strong	.	DNAH5	868	.	NM_001369	exon26	c.3835-2T>-	.	.	.	PASS	Pindel
CTSA	5476	hgsc.bcm.edu	37	20	44520238	44520240	+	In_Frame_Del	DEL	CTG	CTG	-	rs3080212	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	16	12	.	0.615	.	CTG|0.332;-|0.668	0.668	strong	.	CTSA	52	.	NM_000308	exon2	c.84_86del	p.28_29del	.	.	PASS	Pindel
SAMD11	148398	hgsc.bcm.edu	37	1	874779	874826	+	In_Frame_Del	DEL	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	38	183	.	0.447	.	.	.	none	.	SAMD11	34	.	NM_152486	exon7	c.644_691del	p.215_231del	.	.	PASS	Pindel
SPATA3	130560	hgsc.bcm.edu	37	2	231861033	231861059	+	In_Frame_Del	DEL	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	-	rs72362780	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	32	82	.	0.372	.	.	.	strong	.	SPATA3	52	.	NM_139073	exon1	c.84_110del	p.28_37del	.	.	PASS	Pindel
WDR60	55112	hgsc.bcm.edu	37	7	158664075	158664077	+	In_Frame_Del	DEL	GAA	GAA	-	rs145233696	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	28	54	.	0.700	.	GAA|0.880;-|0.120	0.120	strong	.	WDR60	94	.	NM_018051	exon3	c.311_313del	p.104_105del	.	.	PASS	Pindel
RIMBP3	85376	hgsc.bcm.edu	37	22	20460113	20460115	+	In_Frame_Del	DEL	CCG	CCG	-	rs77846076	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	28	114	.	1.000	.	.	.	alt	.	RIMBP3	42	.	NM_015672	exon1	c.1188_1190del	p.396_397del	.	.	PASS	Pindel
KIAA1751	85452	hgsc.bcm.edu	37	1	1887092	1887112	+	In_Frame_Del	DEL	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	-	rs139735565	bycluster;by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	33	98	.	0.398	.	-|0.223;G|0.777	0.223	alt	.	KIAA1751	92	.	NM_001080484	exon18	c.2195_2215del	p.732_739del	.	.	PASS	Pindel
COL6A3	1293	hgsc.bcm.edu	37	2	238244864	238244866	+	In_Frame_Del	DEL	GCA	GCA	-	rs35879189	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	39	60	.	0.672	.	GCA|0.935;-|0.065	0.065	strong	.	COL6A3	608	.	NM_004369	exon40	c.8878_8880del	p.2960_2960del	.	.	PASS	Pindel
TRAK1	22906	hgsc.bcm.edu	37	3	42251578	42251580	+	In_Frame_Del	DEL	GGA	GGA	-	rs10634555	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	28	69	.	0.318	.	.	.	strong	TRAK1,caecum,carcinoma,0,1	TRAK1	188	1	NM_001265608	exon14	c.2063_2065del	p.688_689del	.	.	PASS	Pindel
TMEM255B	348013	hgsc.bcm.edu	37	13	114503876	114503957	+	Frame_Shift_Del	DEL	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	19	121	.	0.244	.	.	.	none	.	.	.	.	NM_182614	exon6	c.499_509del	p.167_170del	.	.	PASS	Pindel
KBTBD12	166348	hgsc.bcm.edu	37	3	127646660	127646661	+	Frame_Shift_Ins	INS	-	-	AGAA	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	46	183	.	0.305	.	.	.	none	KBTBD12,NS,malignant_melanoma,+1,2	KBTBD12	41	2	NM_207335	exon2	c.1124_1125insAGAA	p.R375fs	.	.	PASS	Pindel
C22orf43	51233	hgsc.bcm.edu	37	22	23964283	23964285	+	In_Frame_Del	DEL	CAT	CAT	-	rs10564183	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	14	59	.	0.298	.	.	.	weak	.	C22orf43	18	.	NM_016449	exon4	c.378_380del	p.126_127del	.	.	PASS	Pindel
SYNGR1	9145	hgsc.bcm.edu	37	22	39777822	39777823	+	In_Frame_Ins	INS	-	-	CAA	rs149306472	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	52	119	.	0.406	.	.	.	strong	.	SYNGR1	19	.	NM_004711	exon4	c.605_606insCAA	p.P202delinsPN	.	.	PASS	Pindel
DEFB132	400830	hgsc.bcm.edu	37	20	238436	238441	+	In_Frame_Del	DEL	TGGTCT	TGGTCT	-	rs66489228	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGGTCT	TGGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	24	50	.	0.750	.	TGGTCT|0.380;-|0.620	0.620	strong	.	DEFB132	17	.	NM_207469	exon1	c.16_21del	p.6_7del	.	.	PASS	Pindel
C14orf23	387978	hgsc.bcm.edu	37	14	29261309	29261310	+	RNA	INS	-	-	AAC	rs56025822	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	21	116	.	0.186	.	AAC|1.000	.	strong	.	C14orf23	5	.	.	.	.	.	.	.	PASS	Pindel
LUZP4	51213	hgsc.bcm.edu	37	X	114541251	114541252	+	In_Frame_Ins	INS	-	-	CACTCAGAGAGATCTCGTGGC	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	216	56	220	.	0.259	.	.	.	none	.	LUZP4	51	.	NM_016383	exon4	c.824_825insCACTCAGAGAGATCTCGTGGC	p.V275delinsVTQRDLVA	.	.	PASS	Pindel
PRKCSH	5589	hgsc.bcm.edu	37	19	11558341	11558343	+	In_Frame_Del	DEL	GAG	GAG	-	rs3217229	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	25	108	.	0.189	.	GAG|0.500;-|0.500	0.500	strong	.	PRKCSH	55	.	NM_001001329	exon11	c.936_938del	p.312_313del	.	.	PASS	Pindel
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-	rs201063949	by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	27	137	.	0.203	.	-|0.017;TTTTA|0.983	0.017	alt	.	NUDT17	25	.	NM_001012758	exon8	c.898_905del	p.300_302del	.	.	PASS	Pindel
CELA1	1990	hgsc.bcm.edu	37	12	51740388	51740416	+	In_Frame_Del	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs372974824	byfrequency;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	15	142	.	0.163	.	-|0.574;CACCAGGAAGCG|0.426	0.574	alt	.	CELA1	39	.	NM_001971	exon1	c.8_16del	p.3_6del	.	.	PASS	Pindel
NCOA3	8202	hgsc.bcm.edu	37	20	46279815	46279823	+	In_Frame_Del	DEL	GCAGCAGCA	GCAGCAGCA	-	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	14	88	.	0.171	.	.	.	none	.	NCOA3	156	.	NM_181659	exon20	c.3740_3748del	p.1247_1250del	.	.	PASS	Pindel
HOXB1	3211	hgsc.bcm.edu	37	17	46608184	46608185	+	In_Frame_Ins	INS	-	-	GGGCGCTGT	rs145570960	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	11	46	.	0.282	.	.	.	strong	.	HOXB1	67	.	NM_002144	exon1	c.83_84insACAGCGCCC	p.P28delinsHSAP	.	.	PASS	Pindel
ATN1	1822	hgsc.bcm.edu	37	12	7045892	7045912	+	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAGCAG	-	rs377147612	bycluster;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	30	101	.	0.236	.	.	.	alt	ATN1,NS,carcinoma,0,3	ATN1	95	3	NM_001007026	exon5	c.1461_1481del	p.487_494del	.	.	PASS	Pindel
OR52B4	143496	hgsc.bcm.edu	37	11	4389405	4389405	+	Frame_Shift_Del	DEL	G	G	-	rs11310407	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	43	113	.	0.374	.	G|0.671;-|0.329	0.329	strong	.	OR52B4	56	.	NM_001005161	exon1	c.122delT	p.L41fs	.	.	PASS	Pindel
POC1B	282809	hgsc.bcm.edu	37	12	89866055	89866064	+	Splice_Site	DEL	AGAAAGAAGA	AGAAAGAAGA	-	rs59139895	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGAAAGAAGA	AGAAAGAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	11	59	.	0.297	.	-|1.000;|0.000	1.000	strong	.	POC1B	41	.	.	.	.	.	.	.	PASS	Pindel
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535833	+	In_Frame_Ins	INS	-	-	TAGCAGTGACAGCAGCAG	rs200486992	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	36	168	.	0.186	.	.	.	alt	.	DSPP	174	.	NM_014208	exon5	c.2018_2019insTAGCAGTGACAGCAGCAG	p.D673delinsDSSDSSS	.	.	PASS	Pindel
RNH1	6050	hgsc.bcm.edu	37	11	502130	502144	+	In_Frame_Del	DEL	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	-	rs71462090	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	12	48	.	0.250	.	CTGGATGTCCAGGCT|0.938;-|0.062	0.062	strong	.	RNH1	24	.	NM_203386	exon3	c.20_34del	p.7_12del	.	.	PASS	Pindel
C17orf82	388407	hgsc.bcm.edu	37	17	59489893	59489893	+	Missense_Mutation	SNP	T	T	C	rs9907379	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	6	6	1	1	1	1	T|0.261;C|0.739	0.739	strong	C17orf82_ENST00000335108,NS,carcinoma,0,2	C17orf82	16	2	NM_203425	exon1	c.T557C	p.L186P	AACTCCTCACAGG	.	scavenged	Atlas-SNP
ENPP2	5168	hgsc.bcm.edu	37	8	120575184	120575184	+	Silent	SNP	G	G	A	rs1058913	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	64	113	0	0.512	0	G|0.859;A|0.141	0.141	strong	.	ENPP2	254	.	NM_006209	exon25	c.C2490T	p.F830F	CTGAGTGAAATCC	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140564088	140564088	+	Missense_Mutation	SNP	C	C	T	rs79316113		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	9	12	0	0.5625	0	.	.	weak	.	PCDHB16	159	.	NM_020957	exon1	c.C1954T	p.R652C	CCTCCGCGCTCGG	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783712	5783712	+	Silent	SNP	C	C	T	rs2446211	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	12	25	0	0.333333	0	C|0.689;T|0.311	0.311	strong	PRR22_ENST00000419421,NS,carcinoma,0,2	PRR22	25	2	NM_001134316	exon3	c.G546A	p.P182P	TGGCAGCGGGGCC	.	PASS	Atlas-SNP
LCE2D	353141	hgsc.bcm.edu	37	1	152636843	152636843	+	Missense_Mutation	SNP	A	A	T	rs9793541	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	76	92	1	1	0.0108696	A|0.803;T|0.197	0.197	strong	LCE2D,NS,carcinoma,-1,1	LCE2D	26	1	NM_178430	exon2	c.A262T	p.S88C	CACCAGAGCCCCG	.	scavenged	Atlas-SNP
CERS6	253782	hgsc.bcm.edu	37	2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	rs4496303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	36	55	0	0.439024	0	A|0.008;G|0.990;T|0.002	0.008	strong	.	.	.	.	NM_001256126	exon1	c.G16A	p.A6T	ATCTTAGCCTGGT	.	PASS	Atlas-SNP
SERPINC1	462	hgsc.bcm.edu	37	1	173878862	173878862	+	Silent	SNP	T	T	C	rs5877	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	103	115	0	1	0	T|0.474;C|0.526	0.526	strong	.	SERPINC1	57	.	NM_000488	exon5	c.A981G	p.V327V	CTTCTCTACCTTG	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384986	16384986	+	Silent	SNP	G	G	T	rs28496958	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	9	9	0	0.529412	0	G|0.704;T|0.296	0.296	strong	FAM131C,colon,carcinoma,0,1	FAM131C	21	1	NM_182623	exon7	c.C789A	p.L263L	GGAGGGGAGGGAG	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912406	45912406	+	Missense_Mutation	SNP	G	G	A	rs2336219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	26	60	0	0.5	0	G|0.767;A|0.233	0.233	strong	.	CD3EAP	27	.	NM_012099	exon3	c.G1180A	p.D394N	CAGCAAGATGCCA	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56463410	56463410	+	Missense_Mutation	SNP	T	T	C	rs4712138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	72	146	0	0.461538	0	C|0.341;N|0.000	0.341	strong	.	DST	1427	.	NM_015548	exon27	c.A3923G	p.Q1308R	TCTTCCTGTGACA	.	PASS	Atlas-SNP
CPZ	8532	hgsc.bcm.edu	37	4	8621172	8621172	+	Missense_Mutation	SNP	G	G	A	rs61734020	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	89	142	0	0.526627	0	G|0.977;A|0.023	0.023	strong	.	CPZ	95	.	NM_001014447	exon11	c.G1787A	p.R596Q	GGCTGCGGAGGAC	.	PASS	Atlas-SNP
ATP2B2	491	hgsc.bcm.edu	37	3	10420087	10420087	+	Silent	SNP	T	T	C	rs751122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	10	23	0	0.344828	0	T|0.596;C|0.404	0.404	strong	.	ATP2B2	304	.	NM_001001331	exon10	c.A1050G	p.Q350Q	GTCCTGTTGTTTG	.	PASS	Atlas-SNP
OR6B3	150681	hgsc.bcm.edu	37	2	240984833	240984833	+	Silent	SNP	C	C	G	rs13389099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	298	295	264	2	0.989933	0.00757576	C|0.751;G|0.249	0.249	strong	.	OR6B3	37	.	NM_173351	exon1	c.G657C	p.A219A	GATGTGCGCATAT	.	PASS	Atlas-SNP
MBD1	4152	hgsc.bcm.edu	37	18	47801800	47801800	+	Silent	SNP	G	G	A	rs140690	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	25	37	0	1	0	G|0.782;A|0.218	0.218	strong	MBD1_ENST00000457839,NS,carcinoma,0,1	MBD1	228	1	NM_001204137	exon9	c.C807T	p.R269R	ACGCAGGCGGTGA	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039075	239039075	+	Missense_Mutation	SNP	G	G	T	rs13006204	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	26	35	0	0.530612	0	G|0.611;T|0.389	0.389	strong	.	ESPNL	63	.	NM_194312	exon9	c.G1720T	p.A574S	GAGCCCGCAGGGT	.	PASS	Atlas-SNP
TDRD5	163589	hgsc.bcm.edu	37	1	179631242	179631242	+	Missense_Mutation	SNP	G	G	A	rs35448215	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	20	30	0	0.571429	0	G|0.839;A|0.161	0.161	strong	TDRD5,NS,carcinoma,0,1	TDRD5	149	1	NM_001199085	exon15	c.G2326A	p.E776K	TAGGATGAGATCC	.	PASS	Atlas-SNP
DIS3L	115752	hgsc.bcm.edu	37	15	66618342	66618342	+	Missense_Mutation	SNP	A	A	G	rs3803412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	40	91	0	0.366972	0	A|0.760;G|0.240	0.240	strong	.	DIS3L	175	.	NM_001143688	exon12	c.A1841G	p.D614G	ACTTGGATGAGAA	.	PASS	Atlas-SNP
COL3A1	1281	hgsc.bcm.edu	37	2	189862097	189862097	+	Silent	SNP	G	G	A	rs7579903	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	76	87	0	1	0	G|0.844;A|0.156	0.156	strong	.	COL3A1	292	.	NM_000090	exon26	c.G1851A	p.Q617Q	ACCTCAGGGACCC	.	PASS	Atlas-SNP
C12orf49	79794	hgsc.bcm.edu	37	12	117160976	117160976	+	Missense_Mutation	SNP	T	T	C	rs10507274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	47	73	0	0.489583	0	T|0.954;C|0.046	0.046	strong	.	C12orf49	17	.	NM_024738	exon2	c.A164G	p.Q55R	ATGGGCTGATTAT	.	PASS	Atlas-SNP
TRIML1	339976	hgsc.bcm.edu	37	4	189060803	189060803	+	Missense_Mutation	SNP	T	T	A	rs62618670	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	127	232	0	0.535865	0	T|0.993;A|0.007	0.007	strong	.	TRIML1	126	.	NM_178556	exon1	c.T91A	p.C31S	ACCGAGTGTGGGC	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	37	3	47043622	47043622	+	Silent	SNP	G	G	A	rs2305635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	75	74	0	0.974026	0	G|0.685;A|0.315	0.315	strong	.	NBEAL2	267	.	NM_015175	exon31	c.G4995A	p.V1665V	GCTGGTGCCACTG	.	PASS	Atlas-SNP
C10orf90	118611	hgsc.bcm.edu	37	10	128192985	128192985	+	Missense_Mutation	SNP	C	C	T	rs11245007	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	116	117	0	1	0	C|0.557;T|0.443	0.443	strong	.	C10orf90	121	.	NM_001004298	exon3	c.G784A	p.D262N	TTGAATCTGGACA	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942961	12942961	+	Missense_Mutation	SNP	A	A	C	rs4625290	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	370	15	296	0	0.0405405	0	A|0.894;C|0.106	0.106	strong	.	PRAMEF4	62	.	NM_001009611	exon2	c.T255G	p.D85E	CAGCCCATCGAGC	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225270409	225270409	+	Missense_Mutation	SNP	A	A	T	rs3128655	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	141	129	0	0.992958	0	A|0.283;T|0.717	0.717	strong	.	DNAH14	300	.	NM_001373	exon20	c.A3295T	p.N1099Y	GATAAAAACTGTA	.	PASS	Atlas-SNP
TUBB6	84617	hgsc.bcm.edu	37	18	12308793	12308793	+	Silent	SNP	G	G	C	rs11267036	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	44	44	0	0.52381	0	G|0.887;C|0.113	0.113	strong	.	TUBB6	35	.	NM_032525	exon2	c.G165C	p.S55S	GTCATCGTGTGAG	.	PASS	Atlas-SNP
MED16	10025	hgsc.bcm.edu	37	19	871222	871222	+	Silent	SNP	G	G	A	rs8100258	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	37	35	0	0.660714	0	G|0.860;A|0.140	0.140	strong	.	MED16	61	.	NM_005481	exon13	c.C2130T	p.D710D	CGCCTCGTCCGGC	.	PASS	Atlas-SNP
RALGAPB	57148	hgsc.bcm.edu	37	20	37168469	37168469	+	Silent	SNP	G	G	T	rs6070521	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	46	71	0	0.541176	0	G|0.954;T|0.046	0.046	strong	.	RALGAPB	134	.	NM_020336	exon17	c.G2430T	p.V810V	TTCTGTGTGCACC	.	PASS	Atlas-SNP
ANKS1B	56899	hgsc.bcm.edu	37	12	99640557	99640557	+	Silent	SNP	T	T	C	rs1552759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	85	0	1	0	T|0.381;C|0.619	0.619	strong	.	ANKS1B	180	.	NM_152788	exon13	c.A1842G	p.P614P	ACAGGCTGGAGAG	.	PASS	Atlas-SNP
GPR111	222611	hgsc.bcm.edu	37	6	47646748	47646748	+	Missense_Mutation	SNP	T	T	C	rs13212023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	89	200	0	0.481081	0	T|0.874;C|0.126	0.126	strong	.	GPR111	123	.	NM_153839	exon5	c.T145C	p.S49P	GACTACTCCCAGT	.	PASS	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	37	8	27255128	27255128	+	Silent	SNP	T	T	C	rs1045510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	46	115	0	0.547619	0	T|0.642;C|0.358	0.358	strong	.	PTK2B	304	.	NM_173174	exon7	c.T27C	p.S9S	CCTGAGTCGAGTA	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2054066	2054066	+	Silent	SNP	A	A	G	rs17684416	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	116	102	1	1	0.00980392	A|0.843;G|0.157	0.157	strong	.	MYOM2	251	.	NM_003970	exon22	c.A2769G	p.Q923Q	TGAACAAGGCAAC	.	PASS	Atlas-SNP
DNAH12	201625	hgsc.bcm.edu	37	3	57335876	57335876	+	Missense_Mutation	SNP	C	C	T	rs4060726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	66	112	1	0.431373	0.00892857	C|0.352;T|0.648	0.648	strong	DNAH12,colon,carcinoma,0,1	DNAH12	182	1	NM_178504	exon55	c.G8677A	p.G2893S	AGCTACCGGAGAG	.	scavenged	Atlas-SNP
TFIP11	24144	hgsc.bcm.edu	37	22	26897989	26897989	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	3	200	0	0.0162162	0	.	.	none	TFIP11,caecum,carcinoma,-1,1	TFIP11	72	1	NM_001008697	exon9	c.G678A	p.R226R	GTCTTTCCTCCAC	.	scavenged	Atlas-SNP
SLC39A13	91252	hgsc.bcm.edu	37	11	47431703	47431703	+	Missense_Mutation	SNP	A	A	G	rs61897432	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	57	124	0	0.478992	0	A|0.882;G|0.118	0.118	strong	.	SLC39A13	18	.	NM_152264	exon2	c.A58G	p.T20A	TTCCTCACTGCCC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6578004	6578004	+	Silent	SNP	G	G	A	rs11600179	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	103	97	0	0.962617	0	G|0.842;A|0.158	0.158	strong	.	DNHD1	198	.	NM_144666	exon25	c.G7479A	p.T2493T	GCAGACGCTGCAG	.	PASS	Atlas-SNP
CCDC86	79080	hgsc.bcm.edu	37	11	60609972	60609972	+	Silent	SNP	A	A	G	rs2074422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	88	166	0	0.505747	0	A|0.807;G|0.193	0.193	strong	.	CCDC86	24	.	NM_024098	exon1	c.A375G	p.P125P	GGCACCAAAGTGT	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186761	12186761	+	Missense_Mutation	SNP	A	A	G	rs7259845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	50	0	0.478873	0	A|0.715;G|0.285	0.285	strong	.	ZNF844	69	.	NM_001136501	exon4	c.A826G	p.T276A	ACTCACACTGGAG	.	PASS	Atlas-SNP
PPIB	5479	hgsc.bcm.edu	37	15	64455123	64455123	+	Silent	SNP	G	G	T	rs4904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	61	126	0	0.414966	0	G|0.969;T|0.031	0.031	strong	.	PPIB	20	.	NM_000942	exon1	c.C63A	p.S21S	GAAGACGGACCCC	.	PASS	Atlas-SNP
TM6SF2	53345	hgsc.bcm.edu	37	19	19379549	19379549	+	Missense_Mutation	SNP	C	C	T	rs58542926	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	31	59	0	0.378049	0	C|0.939;T|0.061	0.061	strong	.	TM6SF2	39	.	NM_001001524	exon6	c.G499A	p.E167K	TGATCTCGGAGCT	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56204768	56204768	+	Missense_Mutation	SNP	G	G	A	rs3809974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	65	112	0	0.467626	0	G|0.949;A|0.051	0.051	strong	.	ALPK2	487	.	NM_052947	exon5	c.C2651T	p.S884L	ATGACTGAGTTGC	.	PASS	Atlas-SNP
LMAN1	3998	hgsc.bcm.edu	37	18	57026450	57026450	+	Silent	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	51	80	0	0.443478	0	.	.	none	.	LMAN1	57	.	NM_005570	exon1	c.C27G	p.L9L	GGCCCGGAGACCC	.	PASS	Atlas-SNP
BAIAP2	10458	hgsc.bcm.edu	37	17	79009061	79009061	+	Silent	SNP	C	C	T	rs8068528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	33	27	0	0.452055	0	C|0.889;T|0.111	0.111	strong	BAIAP2_ENST00000321300,NS,carcinoma,0,2	BAIAP2	74	2	NM_001144888	exon1	c.C7T	p.L3L	ATGTCTCTGTCTC	.	PASS	Atlas-SNP
TUBA8	51807	hgsc.bcm.edu	37	22	18609128	18609128	+	Missense_Mutation	SNP	C	C	T	rs2234331	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	42	103	0	0.396226	0	C|0.993;T|0.007	0.007	strong	.	TUBA8	36	.	NM_018943	exon4	c.C383T	p.A128V	CAGATGCTTGCTC	.	PASS	Atlas-SNP
POC1B	282809	hgsc.bcm.edu	37	12	89865394	89865394	+	Missense_Mutation	SNP	G	G	C	rs145981936	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	34	96	0	0.336634	0	G|0.999;C|0.001	0.001	strong	.	POC1B	41	.	NM_172240	exon6	c.C673G	p.Q225E	TACCTTGGTAATG	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19751274	19751274	+	Silent	SNP	G	G	A	rs143115179	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	16	219	0	0.0733945	0	G|0.992;A|0.008	0.008	strong	.	TUBA3C	166	.	NM_006001	exon4	c.C849T	p.H283H	CTGCTCGTGGTAG	.	PASS	Atlas-SNP
HABP2	3026	hgsc.bcm.edu	37	10	115341846	115341846	+	Silent	SNP	G	G	A	rs2245058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	10	24	0	0.526316	0	G|0.599;A|0.401	0.401	strong	.	HABP2	52	.	NM_004132	exon9	c.G1050A	p.A350A	TGGGGCGCTGATC	.	PASS	Atlas-SNP
KLHL30	377007	hgsc.bcm.edu	37	2	239049540	239049540	+	Missense_Mutation	SNP	G	G	A	rs2241985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	43	61	0	0.505882	0	G|0.618;A|0.382	0.382	strong	.	KLHL30	79	.	NM_198582	exon2	c.G145A	p.G49S	CACCGCGGCCTCC	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84229580	84229580	+	Silent	SNP	C	C	T	rs2303239	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	10	29	0	0.357143	0	C|0.720;T|0.280	0.280	strong	.	ADAD2	46	.	NM_139174	exon8	c.C1458T	p.A486A	CTGGGCCGTGCTG	.	PASS	Atlas-SNP
IGDCC4	57722	hgsc.bcm.edu	37	15	65703625	65703625	+	Missense_Mutation	SNP	C	C	G	rs34355056	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	43	106	0	0.505882	0	C|0.845;G|0.155	0.155	strong	.	IGDCC4	95	.	NM_020962	exon2	c.G154C	p.A52P	CTGCAGCCTGCTC	.	PASS	Atlas-SNP
TPR	7175	hgsc.bcm.edu	37	1	186301447	186301447	+	Silent	SNP	T	T	C	rs7526540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	34	92	0	0.485714	0	T|0.958;C|0.042	0.042	strong	.	TPR	441	.	NM_003292	exon38	c.A5484G	p.P1828P	ACGCTTTGGCAAA	.	PASS	Atlas-SNP
TNFRSF4	7293	hgsc.bcm.edu	37	1	1147422	1147422	+	Silent	SNP	C	C	T	rs17568	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	133	116	0	0.985185	0	C|0.674;T|0.326	0.326	strong	.	TNFRSF4	12	.	NM_003327	exon5	c.G534A	p.E178E	CTGGGTCTCCTGG	.	PASS	Atlas-SNP
OR2W1	26692	hgsc.bcm.edu	37	6	29012116	29012116	+	Silent	SNP	G	G	A	rs7341218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	105	217	0	0.495283	0	G|0.748;A|0.252	0.252	strong	.	OR2W1	36	.	NM_030903	exon1	c.C837T	p.T279T	GATGACGGTGTAA	.	PASS	Atlas-SNP
CKAP2	26586	hgsc.bcm.edu	37	13	53039547	53039547	+	Missense_Mutation	SNP	C	C	T	rs143514154	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	78	222	0	0.428571	0	C|0.994;T|0.006	0.006	strong	.	CKAP2	51	.	NM_001098525	exon6	c.C1426T	p.P476S	ACAAGTCCTATTG	.	PASS	Atlas-SNP
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41811706	41811706	+	Silent	SNP	C	C	T	rs372346124		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	62	91	0	0.484375	0	.	.	weak	.	HNRNPUL1	73	.	NM_007040	exon14	c.C2388T	p.P796P	GGCCCCCTATACC	.	PASS	Atlas-SNP
SLC27A5	10998	hgsc.bcm.edu	37	19	59023166	59023166	+	Missense_Mutation	SNP	G	G	A	rs34415062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	47	34	0	0.559524	0	G|0.817;A|0.183	0.183	strong	.	SLC27A5	58	.	NM_012254	exon1	c.C157T	p.R53W	AGGGCCGTGCTAA	.	PASS	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64216854	64216854	+	Missense_Mutation	SNP	A	A	G	rs52797880	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	57	86	0	0.542857	0	A|0.927;G|0.073	0.073	strong	.	APOH	45	.	NM_000042	exon5	c.T422C	p.I141T	GGGCAGATGATGG	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51359503	51359503	+	Silent	SNP	A	A	G	rs1135766	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	64	92	1	0.556522	0.0108696	A|0.599;C|0.019	.	strong	KLK3_ENST00000360617,colon,carcinoma,0,2	KLK3	76	2	NM_001030050	exon2	c.A54G	p.A18A	TGCTGCACCCCTC	.	scavenged	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170103336	170103336	+	Silent	SNP	T	T	C	rs831043	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	117	183	0	0.524664	0	T|0.456;C|0.544	0.544	strong	.	LRP2	751	.	NM_004525	exon21	c.A3069G	p.T1023T	CTGCTCTGTGGGT	.	PASS	Atlas-SNP
IL17REL	400935	hgsc.bcm.edu	37	22	50435480	50435480	+	Missense_Mutation	SNP	A	A	G	rs5771069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	345	340	343	2	0.985507	0.0058309	A|0.431;G|0.569	0.569	strong	.	IL17REL	21	.	NM_001001694	exon14	c.T998C	p.L333P	GGCAAAAGCAGGG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90371202	90371202	+	Silent	SNP	G	G	A	rs9444701	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	119	229	1	0.991667	0.00436681	G|0.286;A|0.714	0.714	strong	.	MDN1	478	.	NM_014611	exon88	c.C14661T	p.L4887L	ACTGTCGAGGTTC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	145015976	145015976	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	30	174	0	0.140187	0	.	.	none	.	PDE4DIP	817	.	NM_022359	exon3	c.G325A	p.V109M	ACTGCACTGGAGG	.	PASS	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	37	2	113940839	113940839	+	Missense_Mutation	SNP	G	G	C	rs4849167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	153	148	0	1	0	G|0.507;C|0.493	0.493	strong	.	PSD4	74	.	NM_012455	exon2	c.G806C	p.G269A	CCTGGGGGGCTTC	.	PASS	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	619322	619322	+	Silent	SNP	C	C	T	rs61732115	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	22	60	0	0.44	0	C|0.986;T|0.014	0.014	strong	.	CDHR5	77	.	NM_031264	exon12	c.G1362A	p.Q454Q	GGGCTCCTGTTCG	.	PASS	Atlas-SNP
YWHAB	7529	hgsc.bcm.edu	37	20	43530234	43530234	+	Silent	SNP	A	A	C	rs4931	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	58	130	0	0.471545	0	A|0.659;C|0.340;G|0.000;T|0.000	0.340	strong	.	YWHAB	24	.	NM_003404	exon3	c.A60C	p.R20R	TGAGCGATATGAT	.	PASS	Atlas-SNP
IL12RB1	3594	hgsc.bcm.edu	37	19	18188408	18188408	+	Missense_Mutation	SNP	C	C	T	rs11575926	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	66	111	0	0.492537	0	C|0.900;T|0.100	0.100	strong	.	IL12RB1	92	.	NM_153701	exon5	c.G467A	p.R156H	TCCATACGCAGCT	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186148	12186148	+	Silent	SNP	T	T	C	rs10424893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	19	35	0	0.655172	0	T|0.725;C|0.275	0.275	strong	ZNF844,NS,NS,+2,1	ZNF844	69	1	NM_001136501	exon4	c.T213C	p.V71V	GAGAGTTGATGAA	.	PASS	Atlas-SNP
RFX7	64864	hgsc.bcm.edu	37	15	56387859	56387859	+	Silent	SNP	T	T	C	rs3803459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	88	207	0	0.511628	0	T|0.799;C|0.201	0.201	strong	.	RFX7	170	.	NM_022841	exon9	c.A2067G	p.K689K	GCCTTGTTTCTGC	.	PASS	Atlas-SNP
UNC5B	219699	hgsc.bcm.edu	37	10	73051388	73051388	+	Silent	SNP	T	T	C	rs3740460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	23	67	0	0.396552	0	T|0.845;C|0.155	0.155	strong	.	UNC5B	123	.	NM_170744	exon10	c.T1494C	p.D498D	GGCAGATGGGGCT	.	PASS	Atlas-SNP
SPECC1	92521	hgsc.bcm.edu	37	17	20107773	20107773	+	Silent	SNP	T	T	C	rs2703805	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	62	123	0	0.529915	0	T|0.550;C|0.450	0.450	strong	.	SPECC1	100	.	NM_001033553	exon4	c.T411C	p.S137S	AACTTCTTCCAAC	.	PASS	Atlas-SNP
SPAG11A	653423	hgsc.bcm.edu	37	8	7718187	7718187	+	Missense_Mutation	SNP	T	T	G	rs3177011	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	51	120	0	0.87931	0	T|0.650;G|0.350	0.350	strong	.	SPAG11A	6	.	NM_001081552	exon3	c.T234G	p.I78M	GGGAATTAGAAAT	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38344895	38344895	+	Missense_Mutation	SNP	G	G	A	rs12256916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	34	54	0	0.548387	0	G|0.970;A|0.030	0.030	strong	.	ZNF33A	103	.	NM_006954	exon5	c.G1843A	p.G615R	GAATGTGGAAAAG	.	PASS	Atlas-SNP
ZSCAN32	54925	hgsc.bcm.edu	37	16	3434699	3434699	+	Missense_Mutation	SNP	A	A	G	rs27230	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	107	200	0	0.521951	0	A|0.885;G|0.115	0.115	strong	.	.	.	.	NM_017810	exon5	c.T358C	p.Y120H	CCTCATAAAAGAT	.	PASS	Atlas-SNP
SYCE3	644186	hgsc.bcm.edu	37	22	50989742	50989742	+	Missense_Mutation	SNP	C	C	T	rs55829948	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	70	124	0	0.510949	0	C|0.995;T|0.005	0.005	strong	.	SYCE3	10	.	NM_001123225	exon3	c.G199A	p.V67I	AGTTGACGAAGGC	.	PASS	Atlas-SNP
ATR	545	hgsc.bcm.edu	37	3	142277575	142277575	+	Silent	SNP	A	A	T	rs2227930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	190	101	181	2	0.531579	0.0110497	A|0.359;T|0.641	0.641	strong	ATR,NS,carcinoma,0,1	ATR	285	1	NM_001184	exon8	c.T1776A	p.G592G	GAGCATACCACAT	.	scavenged	Atlas-SNP
EIF2A	83939	hgsc.bcm.edu	37	3	150285520	150285520	+	Silent	SNP	T	T	C	rs2293151	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	103	175	0	0.5	0	T|0.885;C|0.115	0.115	strong	.	EIF2A	59	.	NM_032025	exon7	c.T516C	p.D172D	TAATGATTTTGTA	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38370537	38370537	+	Missense_Mutation	SNP	T	T	C	rs1465567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	41	60	0	0.594203	0	T|0.741;C|0.259	0.259	strong	EGFLAM,NS,carcinoma,0,1	EGFLAM	302	1	NM_001205301	exon6	c.T685C	p.W229R	CGCAGCTGGCCCA	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86702241	86702241	+	Missense_Mutation	SNP	C	C	T	rs79814209	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	42	102	0	0.488372	0	C|0.980;T|0.020	0.020	strong	.	AGBL1	151	.	NM_152336	exon4	c.C334T	p.R112C	CGAAAGCGCACCC	.	PASS	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294127	124294127	+	Missense_Mutation	SNP	A	A	G	rs370187249		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	46	99	0	0.522727	0	.	.	weak	OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	NM_001005196	exon1	c.T641C	p.V214A	GAGATGACGATGC	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	37	16	81888152	81888152	+	Silent	SNP	A	A	G	rs1143686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	53	123	0	0.469027	0	A|0.791;G|0.209	0.209	strong	.	PLCG2	276	.	NM_002661	exon3	c.A297G	p.L99L	CATCCTATATGGC	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113542098	113542098	+	Silent	SNP	A	A	G	rs12423570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	84	168	0	0.446809	0	A|0.911;G|0.089	0.089	strong	.	RASAL1	89	.	NM_001193520	exon18	c.T1839C	p.C613C	GGAGTGACACATC	.	PASS	Atlas-SNP
CDH20	28316	hgsc.bcm.edu	37	18	59174759	59174759	+	Missense_Mutation	SNP	C	C	A	rs1943330	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	73	79	0	1	0	C|0.911;A|0.089	0.089	strong	CDH20,right_upper_lobe,carcinoma,-1,1	CDH20	117	1	NM_031891	exon5	c.C983A	p.P328H	CAGATCCCAATTT	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592312	1592312	+	Missense_Mutation	SNP	T	T	C	rs72484087	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	21	220	0	0.913043	0	T|0.465;C|0.535	0.535	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.A124G	p.I42V	CTGATATGGACTT	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56146357	56146357	+	Silent	SNP	G	G	A	rs11546	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	55	135	0	0.44	0	G|0.923;A|0.077	0.077	strong	.	KTN1	147	.	NM_001079521	exon43	c.G4023A	p.A1341A	TCAGGCGGTAAAC	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74360209	74360209	+	Silent	SNP	G	G	C	rs3739783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	21	66	0	0.381818	0	G|0.890;C|0.110	0.110	strong	TMEM2,NS,carcinoma,0,1	TMEM2	112	1	NM_001135820	exon4	c.C759G	p.P253P	CCCAAAGGGCAAG	.	PASS	Atlas-SNP
FTSJ3	117246	hgsc.bcm.edu	37	17	61898928	61898928	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	26	55	0	0.634146	0	.	.	none	FTSJ3,NS,carcinoma,0,1	FTSJ3	63	1	NM_017647	exon16	c.C1672T	p.R558W	TCCGCCGGTTCTC	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38379446	38379446	+	Missense_Mutation	SNP	C	C	T	rs6508750	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	494	493	444	0	0.997976	0	C|0.387;T|0.613	0.613	strong	.	WDR87	191	.	NM_031951	exon6	c.G4748A	p.R1583Q	TCAGCTCGGGCTC	.	PASS	Atlas-SNP
MED16	10025	hgsc.bcm.edu	37	19	872089	872089	+	Silent	SNP	A	A	G	rs72984031	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	47	87	0	0.489583	0	A|0.775;G|0.225	0.225	strong	.	MED16	61	.	NM_005481	exon12	c.T1935C	p.F645F	CCGCAGAAAGCTG	.	PASS	Atlas-SNP
PPP2R5A	5525	hgsc.bcm.edu	37	1	212459615	212459615	+	Missense_Mutation	SNP	C	C	G	rs75232123	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	16	19	0	0.5	0	C|0.980;G|0.020	0.020	strong	.	PPP2R5A	48	.	NM_006243	exon1	c.C163G	p.P55A	CTGCACCCGCTGC	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783713	5783713	+	Missense_Mutation	SNP	G	G	A	rs141874203	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	21	25	0	0.583333	0	G|0.984;A|0.016	0.016	strong	PRR22_ENST00000419421,NS,carcinoma,+1,2	PRR22	25	2	NM_001134316	exon3	c.C545T	p.P182L	GGCAGCGGGGCCG	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123847473	123847473	+	Missense_Mutation	SNP	A	A	G	rs55944888	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	42	73	0	0.608696	0	A|0.862;G|0.138	0.138	strong	.	OR10S1	78	.	NM_001004474	exon1	c.T926C	p.V309A	TGCTTCACCTCCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910622	29910622	+	Silent	SNP	C	C	T	rs199501996	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	19	113	0	0.180952	0	C|0.998;T|0.002	0.002	strong	HLA-A,NS,carcinoma,0,4	HLA-A	89	4	NM_001242758	exon2	c.C162T	p.D54D	GGACGACACGCAG	.	PASS	Atlas-SNP
CASP8AP2	9994	hgsc.bcm.edu	37	6	90565242	90565242	+	Silent	SNP	A	A	G	rs369328	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	45	68	0	0.882353	0	G|0.396;N|0.000	0.396	strong	.	CASP8AP2	108	.	NM_001137667	exon5	c.A279G	p.K93K	GAAAAAATTTAAA	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33469181	33469181	+	Silent	SNP	A	A	G	rs1048804	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	207	251	1	0.985714	0.00398406	A|0.634;G|0.366	0.366	strong	NRP1,NS,carcinoma,0,1	NRP1	126	1	NM_003873	exon17	c.T2595C	p.S865S	CAGGGCACTCATG	.	PASS	Atlas-SNP
KCNS1	3787	hgsc.bcm.edu	37	20	43727155	43727155	+	Silent	SNP	C	C	T	rs13043825	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	8	6	0	0.470588	0	C|0.838;T|0.162	0.162	strong	.	KCNS1	30	.	NM_002251	exon4	c.G258A	p.E86E	CGCCTGCTCCTCC	.	PASS	Atlas-SNP
SPPL2C	162540	hgsc.bcm.edu	37	17	43922640	43922640	+	Missense_Mutation	SNP	G	G	A	rs17763658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	88	70	0	1	0	G|0.922;A|0.078	0.078	strong	.	.	.	.	NM_175882	exon1	c.G368A	p.R123Q	TGAGCCGGGTCAG	.	PASS	Atlas-SNP
HIST1H4D	8360	hgsc.bcm.edu	37	6	26189010	26189010	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	71	163	0	0.467105	0	.	.	none	HIST1H4D,colon,carcinoma,0,1	HIST1H4D	28	1	NM_003539	exon1	c.T295G	p.Y99D	AGCCATAAAGAGT	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55142739	55142739	+	Silent	SNP	A	A	C	rs1985501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	68	115	0	0.53125	0	A|0.588;C|0.412	0.412	strong	.	LILRB1	140	.	NM_001081637	exon3	c.A52C	p.R18R	GGCCCCAGGACCC	.	PASS	Atlas-SNP
BTN1A1	696	hgsc.bcm.edu	37	6	26505403	26505403	+	Silent	SNP	C	C	A	rs3736782	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	72	95	0	1	0	C|0.487;A|0.513	0.513	strong	.	BTN1A1	68	.	NM_001732	exon3	c.C678A	p.G226G	TCTTGGCCAGGAG	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36274153	36274153	+	Missense_Mutation	SNP	C	C	T	rs12197079	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	44	86	0	0.453608	0	C|0.747;N|0.000	.	strong	.	PNPLA1	92	.	NM_001145717	exon7	c.C1469T	p.T490M	ATGTAACGTAAGT	.	PASS	Atlas-SNP
AK7	122481	hgsc.bcm.edu	37	14	96871104	96871104	+	Missense_Mutation	SNP	G	G	A	rs2275554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	38	103	0	0.452381	0	G|0.770;A|0.230	0.230	strong	.	AK7	69	.	NM_152327	exon3	c.G305A	p.R102Q	TCTCTCGAGAAGA	.	PASS	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32754232	32754232	+	Silent	SNP	C	C	T	rs57606003	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	278	149	241	1	0.535971	0.00414938	C|0.923;T|0.077	0.077	strong	.	RFPL3	91	.	NM_001098535	exon1	c.C174T	p.T58T	ATGCACCGTCTGC	.	PASS	Atlas-SNP
OR6Q1	219952	hgsc.bcm.edu	37	11	57799371	57799371	+	Missense_Mutation	SNP	G	G	C	rs1374570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	34	77	0	0.596491	0	G|0.500;C|0.500	0.500	strong	OR6Q1,NS,carcinoma,-1,1	OR6Q1	58	1	NM_001005186	exon1	c.G947C	p.G316A	GGAAGGGACAGTG	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553856	140553856	+	Silent	SNP	G	G	A	rs2907330	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	174	136	1	1	0.00735294	G|0.395;A|0.605	0.605	strong	.	PCDHB7	231	.	NM_018940	exon1	c.G1440A	p.S480S	AGACTCGGGCACC	.	PASS	Atlas-SNP
C2orf80	389073	hgsc.bcm.edu	37	2	209036712	209036712	+	Missense_Mutation	SNP	T	T	C	rs10804166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	94	197	1	0.559524	0.00507614	T|0.134;C|0.866	0.866	strong	.	C2orf80	19	.	NM_001099334	exon7	c.A454G	p.S152G	GCTTACTCTGTTT	.	PASS	Atlas-SNP
IL37	27178	hgsc.bcm.edu	37	2	113676381	113676381	+	Missense_Mutation	SNP	G	G	A	rs2723192	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	38	79	0	0.493506	0	G|0.903;A|0.097	0.097	strong	.	IL37	56	.	NM_014439	exon5	c.G652A	p.D218N	GTCAGCGATTAGG	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	37	5	74037386	74037386	+	Missense_Mutation	SNP	T	T	A	rs16872235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	283	145	236	0	0.512367	0	T|0.878;A|0.122	0.122	strong	.	GFM2	38	.	NM_032380	exon11	c.A898T	p.S300C	TCTCACTAAATTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513365	195513365	+	Missense_Mutation	SNP	G	G	A	rs62282501	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	346	121	416	0	0.349711	0	G|0.863;A|0.137	0.137	strong	.	MUC4	1505	.	NM_018406	exon2	c.C5086T	p.R1696C	GAAGACGGGTGGT	.	PASS	Atlas-SNP
RGPD8	727851	hgsc.bcm.edu	37	2	113127773	113127773	+	Silent	SNP	A	A	G	rs186330915	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	568	264	621	0	0.464789	0	A|0.999;G|0.001	0.001	strong	RGPD8_ENST00000302558,NS,carcinoma,-2,18	RGPD8	81	18	NM_001164463	exon23	c.T5280C	p.P1760P	ACGGGAAGGATTT	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386176	7386176	+	Silent	SNP	G	G	C	rs76776066	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	358	23	278	0	0.0642458	0	.	.	alt	POLR2A_ENST00000412468,NS,haematopoietic_neoplasm,0,1	.	.	1	NM_001102614	exon2	c.G873C	p.V291V	GGTGGTGGTGGCC	.	scavenged	Atlas-SNP
ZNF146	7705	hgsc.bcm.edu	37	19	36727365	36727365	+	Missense_Mutation	SNP	G	G	A	rs2070132	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	41	71	0	0.5	0	G|0.622;A|0.378	0.378	strong	.	ZNF146	32	.	NM_001099638	exon3	c.G23A	p.R8K	AGCAGAGAATTTA	.	PASS	Atlas-SNP
MAK16	84549	hgsc.bcm.edu	37	8	33356074	33356074	+	Missense_Mutation	SNP	A	A	G	rs6468171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	69	142	0	0.543307	0	A|0.389;G|0.611	0.611	strong	.	MAK16	25	.	NM_032509	exon10	c.A830G	p.Q277R	CACTGCAGAGAAA	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079889	31079889	+	Missense_Mutation	SNP	C	C	G	rs1265053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	114	131	0	1	0	C|0.471;G|0.529	0.529	strong	.	C6orf15	29	.	NM_014070	exon2	c.G247C	p.A83P	CTGATGCAGGCAC	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12542653	12542653	+	Missense_Mutation	SNP	T	T	G	rs4239550	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	97	215	0	0.487437	0	G|0.323;T|0.677	0.323	strong	.	ZNF443	63	.	NM_005815	exon4	c.A333C	p.K111N	CATGACTTTTTCT	.	PASS	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	37	5	138861078	138861078	+	Missense_Mutation	SNP	C	C	T	rs11554776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	47	113	0	0.348148	0	C|0.867;T|0.133	0.133	strong	TMEM173,NS,carcinoma,0,1	TMEM173	19	1	NM_198282	exon3	c.G212A	p.R71H	ATGTGGCGCAGCT	.	PASS	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	37	8	27255263	27255263	+	Silent	SNP	A	A	G	rs1045512	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	60	136	0	0.428571	0	A|0.641;G|0.359	0.359	strong	PTK2B_ENST00000544172,NS,carcinoma,0,1	PTK2B	304	1	NM_173174	exon7	c.A162G	p.K54K	TGGGAAAAACTTC	.	PASS	Atlas-SNP
TTC24	164118	hgsc.bcm.edu	37	1	156551848	156551848	+	Missense_Mutation	SNP	A	A	G	rs6682716	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	116	64	0	1	0	A|0.624;G|0.376	0.376	strong	TTC24,NS,carcinoma,0,1	TTC24	46	1	NM_001105669	exon2	c.A692G	p.E231G	GCACTGAGAGGCG	.	PASS	Atlas-SNP
ANKIB1	54467	hgsc.bcm.edu	37	7	92027064	92027064	+	Missense_Mutation	SNP	G	G	T	rs200132000	bycluster;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	33	59	0	0.52381	0	.	.	alt	ANKIB1,NS,carcinoma,0,1	ANKIB1	92	1	NM_019004	exon19	c.G2423T	p.R808L	GCAGCCGCAGGCC	.	PASS	Atlas-SNP
PHKB	5257	hgsc.bcm.edu	37	16	47533770	47533770	+	Silent	SNP	C	C	T	rs139431568	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	55	163	0	0.407407	0	C|0.999;T|0.001	0.001	strong	PHKB_ENST00000323584,colon,carcinoma,0,3	PHKB	298	3	NM_000293	exon3	c.C270T	p.C90C	ATACTGCGCTGCT	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160464289	160464289	+	Silent	SNP	G	G	A	rs894817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	28	80	0	0.777778	0	G|0.650;A|0.350	0.350	strong	.	IGF2R	251	.	NM_000876	exon12	c.G1590A	p.G530G	ACGAGGGTGTCCC	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15723833	15723833	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	4	60	0	0.0540541	0	.	.	none	.	FHAD1	78	.	NM_052929	exon31	c.G4163A	p.R1388K	AAGAAAGAGAGAT	.	PASS	Atlas-SNP
PROC	5624	hgsc.bcm.edu	37	2	128184770	128184770	+	Silent	SNP	T	T	C	rs5937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	23	31	0	0.560976	0	T|0.718;C|0.282	0.282	strong	.	PROC	31	.	NM_000312	exon8	c.T768C	p.D256D	CATGGATGAGTCC	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23775454	23775454	+	Missense_Mutation	SNP	G	G	A	rs10264952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	55	52	0	0.982143	0	G|0.873;A|0.127	0.127	strong	.	STK31	175	.	NM_031414	exon7	c.G781A	p.E261K	TTAAGTGAGAAAA	.	PASS	Atlas-SNP
IL12RB1	3594	hgsc.bcm.edu	37	19	18180413	18180413	+	Missense_Mutation	SNP	C	C	G	rs401502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	31	56	0	0.424658	0	C|0.703;G|0.297	0.297	strong	.	IL12RB1	92	.	NM_005535	exon10	c.G1132C	p.G378R	GGCCCCCGTCCTG	.	PASS	Atlas-SNP
SCCPDH	51097	hgsc.bcm.edu	37	1	246930564	246930564	+	Missense_Mutation	SNP	G	G	C	rs7779	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	79	168	0	0.478788	0	G|0.954;C|0.046	0.046	strong	.	SCCPDH	37	.	NM_016002	exon12	c.G1252C	p.G418R	AAACACGGTATTG	.	PASS	Atlas-SNP
GM2A	2760	hgsc.bcm.edu	37	5	150646888	150646888	+	Missense_Mutation	SNP	T	T	C	rs61740602	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	98	174	0	0.478049	0	T|0.934;C|0.066	0.066	strong	GM2A,colon,carcinoma,0,2	GM2A	24	2	NM_000405	exon4	c.T458C	p.V153A	AATTCGTTGTGCC	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16278869	16278869	+	Silent	SNP	G	G	C	rs8058696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	121	118	0	0.991803	0	G|0.598;C|0.402	0.402	strong	.	ABCC6	110	.	NM_001171	exon15	c.C1890G	p.T630T	GTGTATGGTGATG	.	PASS	Atlas-SNP
SAMM50	25813	hgsc.bcm.edu	37	22	44372632	44372632	+	Silent	SNP	C	C	T	rs17850259		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	59	120	0	0.578431	0	.	.	weak	SAMM50,NS,carcinoma,0,1	SAMM50	30	1	NM_015380	exon9	c.C780T	p.H260H	TCAGCACGCCATG	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52844246	52844246	+	Silent	SNP	A	A	G	rs3194290		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	386	64	281	2	0.165803	0.00711744	.	.	weak	KRT6B,NS,carcinoma,0,1	KRT6B	90	1	NM_005555	exon2	c.T699C	p.G233G	CAGACGACCCCGT	.	scavenged	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983374	97983374	+	Silent	SNP	A	A	G	rs4857358	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	494	251	473	0	0.508097	0	A|0.785;G|0.215	0.215	strong	.	OR5H6	89	.	NM_001005479	exon1	c.A246G	p.L82L	GAGTTTAGCCTTT	.	PASS	Atlas-SNP
GPR157	80045	hgsc.bcm.edu	37	1	9165669	9165669	+	Missense_Mutation	SNP	G	G	A	rs12075362	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	183	185	0	0.958115	0	G|0.949;A|0.051	0.051	strong	.	GPR157	14	.	NM_024980	exon3	c.C668T	p.A223V	TTGTCCGCCATGG	.	PASS	Atlas-SNP
IGFBP1	3484	hgsc.bcm.edu	37	7	45932669	45932669	+	Missense_Mutation	SNP	A	A	G	rs4619	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	29	24	0	1	0	A|0.602;G|0.397	0.397	strong	.	IGFBP1	19	.	NM_000596	exon4	c.A759G	p.I253M	CCAGATATATTTT	.	PASS	Atlas-SNP
TBC1D20	128637	hgsc.bcm.edu	37	20	428553	428553	+	Missense_Mutation	SNP	T	T	C	rs36088178	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	49	78	0	0.644737	0	T|0.953;C|0.047	0.047	strong	.	TBC1D20	34	.	NM_144628	exon2	c.A236G	p.N79S	GGGTCATTGGCAT	.	PASS	Atlas-SNP
PRDM6	93166	hgsc.bcm.edu	37	5	122435627	122435627	+	Missense_Mutation	SNP	G	G	A	rs1008058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	76	132	0	0.41989	0	G|0.784;A|0.216	0.216	strong	.	PRDM6	26	.	NM_001136239	exon3	c.G871A	p.A291T	GCAGGCGCCGTGA	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36493598	36493598	+	Silent	SNP	A	A	G	rs9894059	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	47	46	0	1	0	A|0.762;G|0.238	0.238	strong	.	GPR179	170	.	NM_001004334	exon3	c.T909C	p.V303V	CAGGGGAACACAC	.	PASS	Atlas-SNP
STARD6	147323	hgsc.bcm.edu	37	18	51855721	51855721	+	Missense_Mutation	SNP	C	C	T	rs2917782	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	16	59	0	0.275862	0	C|0.931;T|0.069	0.069	strong	.	STARD6	19	.	NM_139171	exon5	c.G475A	p.E159K	ACTCTTCCATTGG	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6541225	6541225	+	Missense_Mutation	SNP	C	C	G	rs11603869	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	43	88	0	0.518072	0	C|0.836;G|0.164	0.164	strong	.	DNHD1	198	.	NM_173589	exon8	c.C1678G	p.Q560E	TCATCACAGCTGG	.	PASS	Atlas-SNP
ZNF98	148198	hgsc.bcm.edu	37	19	22585674	22585674	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	23	43	0	0.45098	0	.	.	none	ZNF98_ENST00000357774,NS,carcinoma,0,2	ZNF98	230	2	NM_001098626	exon3	c.C170T	p.S57F	GGCTTAGAGGCAG	.	PASS	Atlas-SNP
TMPRSS2	7113	hgsc.bcm.edu	37	21	42866296	42866296	+	Silent	SNP	T	T	C	rs3787950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	42	87	0	0.518519	0	C|0.135;N|0.001	0.135	strong	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	NM_001135099	exon3	c.A336G	p.T112T	GCACACTGTCCCG	.	PASS	Atlas-SNP
ATG4B	23192	hgsc.bcm.edu	37	2	242610738	242610738	+	Silent	SNP	T	T	C	rs11538896	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	44	107	0	0.4	0	T|0.776;C|0.224	0.224	strong	.	ATG4B	35	.	NM_178326	exon12	c.T1026C	p.L342L	TCTGCTTGGAGGT	.	PASS	Atlas-SNP
TRPC4	7223	hgsc.bcm.edu	37	13	38211046	38211046	+	Silent	SNP	T	T	C	rs731860	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	59	118	0	0.464567	0	T|0.959;C|0.041	0.041	strong	.	TRPC4	389	.	NM_003306	exon11	c.A2943G	p.R981R	TCACAATCTTGTG	.	PASS	Atlas-SNP
CAST	831	hgsc.bcm.edu	37	5	96031569	96031569	+	Silent	SNP	A	A	G	rs9667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	165	165	0	1	0	A|0.818;G|0.182	0.182	strong	.	CAST	58	.	NM_001042440	exon3	c.A168G	p.Q56Q	CAGTCAATCCTCC	.	PASS	Atlas-SNP
TFAM	7019	hgsc.bcm.edu	37	10	60145342	60145342	+	Missense_Mutation	SNP	G	G	C	rs1937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	50	97	0	0.485437	0	G|0.919;C|0.081	0.081	strong	.	TFAM	52	.	NM_003201	exon1	c.G35C	p.S12T	TGCTGAGTGCCCT	.	PASS	Atlas-SNP
RPLP0	6175	hgsc.bcm.edu	37	12	120636498	120636498	+	Silent	SNP	G	G	A	rs138718343		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	86	153	0	0.427861	0	G|1.000;A|0.000	0.000	weak	.	RPLP0	27	.	NM_053275	exon6	c.C510T	p.S170S	GGCTTCGCTGGCT	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895889	1895889	+	Missense_Mutation	SNP	G	G	C	rs72620874	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	20	282	0	0.122699	0	G|0.689;C|0.311	0.311	strong	SIRPA,right_upper_lobe,carcinoma,+1,3	SIRPA	83	3	NM_001040022	exon3	c.G224C	p.G75A	GACCAGGCCGGGA	.	PASS	Atlas-SNP
SLC7A7	9056	hgsc.bcm.edu	37	14	23282449	23282449	+	Silent	SNP	C	C	T	rs1805059	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	115	94	0	1	0	C|0.412;T|0.588	0.588	strong	.	SLC7A7	36	.	NM_001126105	exon3	c.G159A	p.S53S	GATGCCCGAGCCG	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48703752	48703752	+	Silent	SNP	T	T	C	rs739925	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	119	123	1	0.97541	0.00813008	T|0.603;G|0.006	.	strong	.	CACNA1G	659	.	NM_018896	exon38	c.T6774C	p.P2258P	CCGGCCTACGTCC	.	PASS	Atlas-SNP
DNAAF1	123872	hgsc.bcm.edu	37	16	84209816	84209816	+	Missense_Mutation	SNP	T	T	C	rs2288022	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	128	108	1	0.992248	0.00925926	A|0.000;C|0.285;T|0.715	0.285	strong	.	DNAAF1	81	.	NM_178452	exon11	c.T1976C	p.L659P	GCCAGCTACTGAT	.	PASS	Atlas-SNP
MROH9	80133	hgsc.bcm.edu	37	1	170959088	170959088	+	Silent	SNP	C	C	T	rs28634500	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	75	173	0	0.517241	0	C|0.791;T|0.209	0.209	strong	.	.	.	.	NM_025063	exon11	c.C972T	p.C324C	GACATGCACTTCA	.	PASS	Atlas-SNP
ADD2	119	hgsc.bcm.edu	37	2	70900403	70900403	+	Silent	SNP	G	G	A	rs4984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	45	66	0	0.608108	0	G|0.855;A|0.145	0.145	strong	.	ADD2	261	.	NM_017488	exon15	c.C1797T	p.S599S	GGCAACGCTGAAG	.	PASS	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102495998	102495998	+	Missense_Mutation	SNP	T	T	G	rs2245803	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	59	54	0	1	0	T|0.342;G|0.658	0.658	strong	.	MMP20	52	.	NM_004771	exon1	c.A53C	p.K18T	GAAAACTTCAAAG	.	PASS	Atlas-SNP
CLEC10A	10462	hgsc.bcm.edu	37	17	6980105	6980105	+	Missense_Mutation	SNP	G	G	A	rs35318160	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	63	86	0	0.508065	0	G|0.978;A|0.022	0.022	strong	.	CLEC10A	40	.	NM_182906	exon5	c.C299T	p.T100M	GCTATCGTTTCTT	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	134145885	134145885	+	Silent	SNP	G	G	A	rs111563366	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	52	122	0	0.342105	0	G|0.500;A|0.500	0.500	weak	.	TG	416	.	NM_003235	exon47	c.G8169A	p.S2723S	CATCTCGTCTCTG	.	PASS	Atlas-SNP
RDH13	112724	hgsc.bcm.edu	37	19	55559715	55559715	+	Silent	SNP	G	G	A	rs2305543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	55	78	0	0.544554	0	G|0.701;A|0.299	0.299	strong	.	RDH13	43	.	NM_001145971	exon5	c.C640T	p.L214L	GGCTCAGCTCCTT	.	PASS	Atlas-SNP
CDRT15	146822	hgsc.bcm.edu	37	17	14139888	14139888	+	Splice_Site	SNP	C	C	T	rs11650811	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	240	25	188	0	0.104167	0	C|0.917;T|0.083	0.083	strong	CDRT15,NS,carcinoma,0,1	CDRT15	20	1	NM_001007530	exon2	c.262+1G>A	.	ACCTCACCAAGTG	.	scavenged	Atlas-SNP
WDR65	149465	hgsc.bcm.edu	37	1	43675539	43675539	+	Silent	SNP	G	G	A	rs148341430	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	58	117	0	0.495726	0	G|0.999;A|0.001	0.001	strong	.	WDR65	76	.	NM_152498	exon11	c.G1881A	p.L627L	GCCTCTGCAGAAG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910538	29910538	+	Silent	SNP	C	C	T	rs1136657	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	13	40	0	0.565217	0	C|0.821;T|0.179	0.179	strong	HLA-A,caecum,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon2	c.C78T	p.S26S	AGGCTCCCACTCC	.	PASS	Atlas-SNP
NSUN5	55695	hgsc.bcm.edu	37	7	72717933	72717933	+	Silent	SNP	C	C	T	rs61750968	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	98	168	0	0.541436	0	C|0.714;T|0.286	0.286	strong	NSUN5_ENST00000438747,NS,carcinoma,0,2	NSUN5	47	2	NM_148956	exon8	c.G1035A	p.A345A	AGTGAGCGCGTGG	.	PASS	Atlas-SNP
PTPN22	26191	hgsc.bcm.edu	37	1	114394689	114394689	+	Missense_Mutation	SNP	C	C	T	rs33996649	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	32	71	0	0.507937	0	C|0.985;T|0.015	0.015	strong	.	PTPN22	90	.	NM_015967	exon10	c.G788A	p.R263Q	ATTTCCCGGATCA	.	PASS	Atlas-SNP
C12orf43	64897	hgsc.bcm.edu	37	12	121442241	121442241	+	Silent	SNP	C	C	T	rs73214128	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	76	95	0	0.608	0	C|0.960;T|0.040	0.040	strong	.	C12orf43	30	.	NM_022895	exon6	c.G504A	p.A168A	GTCGGACGCCGAC	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1887245	1887245	+	Silent	SNP	G	G	A	rs28575980	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	68	84	0	0.918919	0	G|0.777;A|0.223	0.223	strong	KIAA1751,NS,carcinoma,0,1	KIAA1751	92	1	NM_001080484	exon18	c.C2061T	p.A687A	GGTGGCGGCTTTG	.	PASS	Atlas-SNP
TRIP11	9321	hgsc.bcm.edu	37	14	92441066	92441066	+	Missense_Mutation	SNP	C	C	T	rs1051340	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	82	176	0	0.455556	0	C|0.709;T|0.291	0.291	strong	.	TRIP11	184	.	NM_004239	exon19	c.G5479A	p.G1827S	TAACACCGCCCTG	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112379289	112379289	+	Silent	SNP	G	G	A	rs2227948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	25	50	0	0.471698	0	G|0.493;A|0.507	0.507	strong	.	MCC	234	.	NM_001085377	exon17	c.C2694T	p.A898A	GAGTTCGGCTAGG	.	PASS	Atlas-SNP
KLB	152831	hgsc.bcm.edu	37	4	39450229	39450229	+	Missense_Mutation	SNP	C	C	A	rs4975017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	70	73	0	0.985915	0	C|0.717;A|0.282	0.282	strong	.	KLB	95	.	NM_175737	exon5	c.C3058A	p.Q1020K	CAAAGGCAGAAGA	.	PASS	Atlas-SNP
TNFRSF8	943	hgsc.bcm.edu	37	1	12164437	12164437	+	Silent	SNP	C	C	T	rs2230622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	104	129	0	0.881356	0	C|0.611;A|0.050	.	strong	.	TNFRSF8	70	.	NM_001243	exon4	c.C270T	p.D90D	CTTAGACGACCTC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55341575	55341575	+	Missense_Mutation	SNP	G	G	C	rs1130513	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	43	44	0	0.605634	0	G|0.828;C|0.172	0.172	strong	.	KIR3DL1	174	.	NM_013289	exon9	c.G1180C	p.E394Q	GACCCTGAGGAGG	.	PASS	Atlas-SNP
PNN	5411	hgsc.bcm.edu	37	14	39644498	39644498	+	Silent	SNP	G	G	A	rs1061583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	60	71	0	0.967742	0	G|0.804;A|0.196	0.196	strong	PNN,right_upper_lobe,carcinoma,+2,1	PNN	67	1	NM_002687	exon1	c.G15A	p.V5V	CGCCGTGAGAACT	.	PASS	Atlas-SNP
SSFA2	6744	hgsc.bcm.edu	37	2	182766660	182766660	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	4	74	0	0.036036	0	.	.	none	SSFA2,NS,carcinoma,0,1	SSFA2	130	1	NM_001130445	exon8	c.C880T	p.R294C	GCAAATCGTTTAA	.	scavenged	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20443872	20443872	+	Silent	SNP	C	C	G	rs78523266		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	64	195	0	0.359551	0	.	.	weak	OR4K15,NS,carcinoma,+1,1	OR4K15	82	1	NM_001005486	exon1	c.C195G	p.G65G	GTTGGGCAACTTT	.	scavenged	Atlas-SNP
MADD	8567	hgsc.bcm.edu	37	11	47306628	47306628	+	Missense_Mutation	SNP	G	G	A	rs3736101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	21	79	0	0.428571	0	G|0.922;A|0.078	0.078	strong	.	MADD	172	.	NM_130470	exon13	c.G2294A	p.R765Q	TGCGCCGGCGAAT	.	PASS	Atlas-SNP
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821576	100821576	+	Missense_Mutation	SNP	G	G	A	rs7496668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	18	33	0	0.529412	0	G|0.589;A|0.411	0.411	strong	ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	NM_139057	exon4	c.C647T	p.S216L	TCCCGCGAAGGCC	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324516	31324516	+	Missense_Mutation	SNP	C	C	A	rs1131215	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	82	13	13	1	1	C|0.415;A|0.585	0.585	strong	HLA-B,colon,carcinoma,0,1	HLA-B	54	1	NM_005514	exon2	c.G292T	p.D98Y	CTCGGTCAGTCTG	.	scavenged	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	37	5	138857925	138857925	+	Missense_Mutation	SNP	C	C	G	rs78233829	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	55	115	0	0.466102	0	C|0.807;G|0.193	0.193	strong	.	TMEM173	19	.	NM_198282	exon6	c.G689C	p.G230A	TGGTCACCGGTCT	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89448530	89448530	+	Missense_Mutation	SNP	C	C	A	rs144696297	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	55	103	0	0.544554	0	C|0.999;A|0.001	0.001	strong	.	EPHA3	501	.	NM_005233	exon7	c.C1494A	p.S498R	CAGTAGCCTCAAG	.	PASS	Atlas-SNP
ABCC3	8714	hgsc.bcm.edu	37	17	48768486	48768486	+	Silent	SNP	A	A	G	rs1051640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	75	105	0	0.551471	0	A|0.876;G|0.124	0.124	strong	.	ABCC3	138	.	NM_003786	exon31	c.A4509G	p.E1503E	AGCTGAATTTGAT	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124044859	124044859	+	Silent	SNP	C	C	T	rs16835275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	86	134	0	0.450262	0	C|0.992;T|0.008	0.008	strong	KALRN_ENST00000360013,NS,malignant_melanoma,+1,2	KALRN	556	2	NM_003947	exon7	c.C1119T	p.S373S	CATGTCCGTGGCT	.	PASS	Atlas-SNP
CCDC39	339829	hgsc.bcm.edu	37	3	180365956	180365956	+	Silent	SNP	G	G	A	rs6769457	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	39	114	0	0.47561	0	G|0.678;A|0.322	0.322	strong	.	CCDC39	242	.	NM_181426	exon10	c.C1359T	p.S453S	TACCTGGCTGTAC	.	PASS	Atlas-SNP
TTC18	118491	hgsc.bcm.edu	37	10	75037999	75037999	+	Missense_Mutation	SNP	C	C	A	rs12256262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	251	120	224	1	0.478088	0.00446429	C|0.973;A|0.027	0.027	strong	.	TTC18	106	.	NM_145170	exon21	c.G2546T	p.W849L	GGATCCCAAGTTT	.	PASS	Atlas-SNP
ZNF584	201514	hgsc.bcm.edu	37	19	58929136	58929136	+	Silent	SNP	G	G	A	rs3764534	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	35	97	1	0.333333	0.0103093	G|0.453;A|0.547	0.547	strong	ZNF584,caecum,carcinoma,0,1	ZNF584	31	1	NM_173548	exon4	c.G1251A	p.K417K	TGGGAAGGTCGTT	.	scavenged	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371259	58371259	+	Silent	SNP	A	A	G	rs75951435	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	356	75	219	0	0.210674	0	A|0.963;G|0.037	0.037	strong	ZNF587,NS,carcinoma,0,1	ZNF587	53	1	NM_032828	exon3	c.A1479G	p.E493E	GTATGAATGCAGT	.	PASS	Atlas-SNP
ZNF516	9658	hgsc.bcm.edu	37	18	74154296	74154296	+	Missense_Mutation	SNP	C	C	T	rs12961584	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	26	22	0	0.666667	0	C|0.667;T|0.333	0.333	strong	.	ZNF516	102	.	NM_014643	exon3	c.G715A	p.G239S	GCTTGCCGTTCTC	.	PASS	Atlas-SNP
CD22	933	hgsc.bcm.edu	37	19	35832468	35832468	+	Missense_Mutation	SNP	T	T	C	rs369129095		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	23	43	0	0.575	0	.	.	weak	.	CD22	129	.	NM_001185100	exon8	c.T1730C	p.I577T	ACTCCATAGGACA	.	PASS	Atlas-SNP
C6orf222	389384	hgsc.bcm.edu	37	6	36287312	36287312	+	Missense_Mutation	SNP	G	G	C	rs743852	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	56	66	0	1	0	G|0.540;C|0.460	0.460	strong	.	C6orf222	72	.	NM_001010903	exon11	c.C1744G	p.L582V	TGCGCAGGGTGGC	.	PASS	Atlas-SNP
CLIC5	53405	hgsc.bcm.edu	37	6	46047458	46047458	+	Silent	SNP	C	C	T	rs3734207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	54	126	0	0.412214	0	C|0.815;T|0.185	0.185	strong	.	CLIC5	48	.	NM_001114086	exon1	c.G522A	p.E174E	GTAAATCTCAGGG	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305956	39305956	+	Missense_Mutation	SNP	G	G	A	rs1497383	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	69	146	0	0.485915	0	G|0.556;A|0.444	0.444	strong	.	KRTAP4-5	34	.	NM_033188	exon1	c.C64T	p.R22C	TGGGGCGGCAGCA	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26732987	26732987	+	Silent	SNP	G	G	A	rs2230376	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	20	49	0	0.425532	0	G|0.794;A|0.206	0.206	strong	.	ITPR2	270	.	NM_002223	exon33	c.C4482T	p.P1494P	TGAAAAGGGAGAA	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296600	39296600	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	4	76	0	0.0493827	0	.	.	none	KRTAP4-6,NS,carcinoma,0,2	KRTAP4-6	46	2	NM_030976	exon1	c.G140A	p.R47K	TGGGGTCTGCAGC	.	scavenged	Atlas-SNP
CD82	3732	hgsc.bcm.edu	37	11	44636839	44636839	+	Silent	SNP	C	C	T	rs883752	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	100	167	0	0.543478	0	C|0.739;N|0.000	.	strong	.	CD82	27	.	NM_002231	exon7	c.C354T	p.G118G	GATGGGCGGCATC	.	PASS	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	37	10	81927059	81927059	+	Missense_Mutation	SNP	C	C	T	rs2229554	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	21	51	0	0.617647	0	T|0.035;G|0.159	0.035	strong	.	ANXA11	32	.	NM_145868	exon6	c.G572A	p.R191Q	GTGCCTCGGCTTC	.	PASS	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	37	10	64927823	64927823	+	Missense_Mutation	SNP	C	C	G	rs1935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	110	133	0	1	0	C|0.570;G|0.430	0.430	strong	JMJD1C_ENST00000399262,NS,carcinoma,0,2	JMJD1C	347	2	NM_032776	exon26	c.G7605C	p.E2535D	CATATCCTCTACT	.	PASS	Atlas-SNP
OR2L2	26246	hgsc.bcm.edu	37	1	248202344	248202344	+	Missense_Mutation	SNP	G	G	C	rs6658141	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	74	181	0	0.440476	0	G|0.650;C|0.350	0.350	strong	.	OR2L2	115	.	NM_001004686	exon1	c.G775C	p.V259L	ACCTATGTACGTC	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887394	9887394	+	Silent	SNP	C	C	T	rs2240910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	38	91	0	0.567164	0	C|0.531;T|0.469	0.469	strong	TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.C918T	p.A306A	GGAAGCCATCCAG	.	PASS	Atlas-SNP
DENND3	22898	hgsc.bcm.edu	37	8	142200467	142200467	+	Silent	SNP	G	G	A	rs1045303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	65	98	0	0.546219	0	A|0.299;C|0.000;G|0.700	0.299	strong	.	DENND3	127	.	NM_014957	exon20	c.G3090A	p.P1030P	GCTGCCGCGAGGT	.	PASS	Atlas-SNP
ATP10B	23120	hgsc.bcm.edu	37	5	159992751	159992751	+	Silent	SNP	A	A	G	rs4921150	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	58	114	3	0.483333	0.0263158	A|0.867;G|0.133	0.133	strong	ATP10B,colon,carcinoma,0,1	ATP10B	201	1	NM_025153	exon26	c.T4095C	p.T1365T	GTGGTGAGTTGGT	.	scavenged	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26697480	26697480	+	Silent	SNP	C	C	T	rs80356573	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	52	119	0	0.481481	0	C|0.983;T|0.017	0.017	strong	OTOF_ENST00000402415,NS,carcinoma,0,3	OTOF	524	3	NM_194248	exon26	c.G3189A	p.A1063A	GCAGTACGCCTCG	.	PASS	Atlas-SNP
TATDN3	128387	hgsc.bcm.edu	37	1	212985592	212985592	+	Silent	SNP	G	G	A	rs78095001	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	59	178	0	0.427536	0	G|0.975;A|0.025	0.025	strong	.	TATDN3	23	.	NM_001146169	exon9	c.G624A	p.K208K	TAAGAAGCAGAAA	.	PASS	Atlas-SNP
KRT27	342574	hgsc.bcm.edu	37	17	38938591	38938591	+	Missense_Mutation	SNP	C	C	G	rs2469826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	76	68	1	0.974359	0.0147059	C|0.685;G|0.315	0.315	strong	KRT27,NS,carcinoma,0,1	KRT27	41	1	NM_181537	exon1	c.G155C	p.S52T	GATGAGCTGCCCC	.	scavenged	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31322911	31322911	+	Missense_Mutation	SNP	C	C	T	rs1051488	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	170	157	0	0.988372	0	T|0.451;G|0.000;C|0.549	0.451	strong	HLA-B,NS,carcinoma,0,7	HLA-B	54	7	NM_005514	exon5	c.G985A	p.A329T	TCACAGCAGCGAC	.	PASS	Atlas-SNP
ESRP2	80004	hgsc.bcm.edu	37	16	68269820	68269820	+	Silent	SNP	C	C	T	rs150603076	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	18	24	0	0.529412	0	C|0.997;T|0.003	0.003	strong	.	ESRP2	118	.	NM_024939	exon1	c.G129A	p.R43R	CAGGTCCCGTCCC	.	PASS	Atlas-SNP
FCRL1	115350	hgsc.bcm.edu	37	1	157768000	157768000	+	Silent	SNP	G	G	C	rs3811024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	54	103	0	0.586957	0	G|0.747;C|0.253	0.253	strong	.	FCRL1	164	.	NM_001159398	exon8	c.C1065G	p.T355T	GAGGTAGGTGAAC	.	PASS	Atlas-SNP
ZNF347	84671	hgsc.bcm.edu	37	19	53644443	53644443	+	Silent	SNP	G	G	A	rs1661935	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	37	80	0	0.366337	0	G|0.924;A|0.076	0.076	strong	.	ZNF347	87	.	NM_001172675	exon5	c.C1641T	p.C547C	TTTGCCGCACTCA	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	37	2	242350466	242350466	+	Silent	SNP	A	A	G	rs2240479	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	52	118	0	0.422764	0	A|0.904;G|0.096	0.096	strong	.	FARP2	92	.	NM_014808	exon6	c.A429G	p.Q143Q	CTTGCAACTTAAG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228486404	228486404	+	Missense_Mutation	SNP	C	C	T	rs56021350	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	7	24	0	0.4375	0	C|0.825;T|0.175	0.175	strong	OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon49	c.C13196T	p.T4399M	CGGCCACGCTCAC	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121615103	121615103	+	Missense_Mutation	SNP	G	G	A	rs1718119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	136	128	0	0.992701	0	G|0.628;N|0.001	.	strong	P2RX7,NS,carcinoma,0,1	P2RX7	53	1	NM_002562	exon11	c.G1042A	p.A348T	CAGGCCGCTGTGT	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	37	6	151670172	151670172	+	Missense_Mutation	SNP	A	A	C	rs3734799	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	17	45	0	0.944444	0	A|0.400;C|0.600	0.600	strong	.	AKAP12	170	.	NM_005100	exon4	c.A646C	p.K216Q	GACCACAAGGACC	.	PASS	Atlas-SNP
KRT82	3888	hgsc.bcm.edu	37	12	52788928	52788928	+	Missense_Mutation	SNP	G	G	A	rs2658658	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	57	101	0	0.518182	0	G|0.611;A|0.389	0.389	strong	.	KRT82	45	.	NM_033033	exon9	c.C1373T	p.T458M	ACAGGCGTGCTGA	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50555686	50555686	+	Missense_Mutation	SNP	A	A	C	rs760749	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	65	122	0	0.485075	0	A|0.868;C|0.132	0.132	strong	.	MOV10L1	238	.	NM_018995	exon9	c.A1360C	p.I454L	TCACTAATTGCTG	.	PASS	Atlas-SNP
CDH19	28513	hgsc.bcm.edu	37	18	64176365	64176365	+	Silent	SNP	G	G	T	rs1055335	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	201	224	0	0.966346	0	G|0.731;T|0.269	0.269	strong	.	CDH19	141	.	NM_021153	exon11	c.C1695A	p.T565T	GGTAAGGGTGTTT	.	PASS	Atlas-SNP
NEFL	4747	hgsc.bcm.edu	37	8	24813798	24813798	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	3	105	0	0.0168539	0	.	.	none	NEFL,colon,carcinoma,0,1	NEFL	47	1	NM_006158	exon1	c.G232A	p.A78T	TGATGGCGGCTAC	.	scavenged	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53662624	53662624	+	Missense_Mutation	SNP	C	C	A	rs6580942	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	18	37	0	0.4	0	C|0.192;A|0.808	0.808	strong	.	ESPL1	158	.	NM_012291	exon2	c.C74A	p.A25D	TGCCCGCCTTGAA	.	PASS	Atlas-SNP
DNTTIP2	30836	hgsc.bcm.edu	37	1	94343023	94343023	+	Silent	SNP	A	A	G	rs2391322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	109	95	0	0.981982	0	A|0.587;G|0.413	0.413	strong	.	DNTTIP2	59	.	NM_014597	exon2	c.T468C	p.P156P	TTCTGTAGGAAGC	.	PASS	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156917340	156917340	+	Missense_Mutation	SNP	A	A	C	rs10067096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	110	85	0	0.990991	0	A|0.827;C|0.173	0.173	strong	.	ADAM19	216	.	NM_033274	exon19	c.T2218G	p.S740A	GCTTGGAAGGGAG	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77057501	77057501	+	Silent	SNP	A	A	G	rs11558468	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	57	115	0	0.445312	0	A|0.865;G|0.135	0.135	strong	.	NUP54	48	.	NM_017426	exon4	c.T360C	p.T120T	ACTCGCAGTATTT	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34724786	34724786	+	Silent	SNP	G	G	A	rs72617336	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	235	115	248	0	0.489362	0	G|0.580;A|0.420	0.420	strong	.	FAM205A	45	.	NM_001141917	exon4	c.C2451T	p.P817P	TTCCACGGGACTA	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107677984	107677984	+	Missense_Mutation	SNP	G	G	A	rs1627354	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	108	240	0	0.507042	0	G|0.784;A|0.216	0.216	strong	.	LAMB4	253	.	NM_007356	exon30	c.C4528T	p.H1510Y	GTAGGTGAATGTC	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78519519	78519519	+	Silent	SNP	T	T	C	rs61750765	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	51	70	0	0.51	0	T|0.903;C|0.097	0.097	strong	.	RPTOR	122	.	NM_001163034	exon1	c.T90C	p.F30F	GGCTTTTATGAAA	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790482	4790482	+	Silent	SNP	T	T	C	rs12792898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	71	165	0	0.533835	0	T|0.909;C|0.091	0.091	strong	OR51F1,NS,carcinoma,-2,1	OR51F1	60	1	NM_001004752	exon1	c.A666G	p.L222L	AATAATTAAGATA	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134735672	134735672	+	Silent	SNP	A	A	G	rs7915371	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	61	163	0	0.426573	0	A|0.515;G|0.485	0.485	strong	.	TTC40	100	.	NM_001200049	exon13	c.T1542C	p.N514N	GCCTGCATTCACC	.	PASS	Atlas-SNP
UPF2	26019	hgsc.bcm.edu	37	10	12043790	12043790	+	Silent	SNP	T	T	G	rs11595168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	43	137	0	0.387387	0	T|0.947;G|0.053	0.053	strong	.	UPF2	111	.	NM_080599	exon6	c.A1539C	p.S513S	GGGACTTGATACC	.	PASS	Atlas-SNP
CDK5R2	8941	hgsc.bcm.edu	37	2	219824731	219824731	+	Silent	SNP	G	G	C	rs78141300	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	13	3	0	0.565217	0	G|0.972;C|0.028	0.028	strong	.	CDK5R2	17	.	NM_003936	exon1	c.G189C	p.A63A	CTCGGCGCTCACC	.	PASS	Atlas-SNP
PRTN3	5657	hgsc.bcm.edu	37	19	844020	844020	+	Missense_Mutation	SNP	G	G	A	rs351111	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	95	88	0	1	0	G|0.546;A|0.454	0.454	strong	.	PRTN3	9	.	NM_002777	exon3	c.G355A	p.V119I	AACGACGTTCTCC	.	PASS	Atlas-SNP
RGS6	9628	hgsc.bcm.edu	37	14	72945012	72945012	+	Silent	SNP	T	T	C	rs2302143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	44	108	0	0.488889	0	T|0.889;C|0.111	0.111	strong	RGS6_ENST00000553525,NS,carcinoma,-2,2	RGS6	92	2	NM_001204424	exon12	c.T829C	p.L277L	CATTGTTTGAAAA	.	PASS	Atlas-SNP
RASSF5	83593	hgsc.bcm.edu	37	1	206680983	206680983	+	Silent	SNP	A	A	C	rs2095124	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	13	13	0	0	1	.	A|0.080;C|0.920	0.920	strong	RASSF5,caecum,carcinoma,0,1	RASSF5	54	1	NM_182663	exon1	c.A48C	p.L16L	GCTACTATTGGAC	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102595492	102595492	+	Missense_Mutation	SNP	G	G	A	rs3765620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	78	189	0	0.461538	0	G|0.357;A|0.643	0.643	strong	.	MMP8	68	.	NM_002424	exon1	c.C95T	p.T32I	TGAACAGTTTTTG	.	PASS	Atlas-SNP
DSG3	1830	hgsc.bcm.edu	37	18	29049138	29049138	+	Missense_Mutation	SNP	C	C	T	rs61730311	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	41	80	0	0.460674	0	C|0.993;T|0.007	0.007	strong	.	DSG3	172	.	NM_001944	exon12	c.C1723T	p.R575W	AACAATCGGTGTG	.	PASS	Atlas-SNP
SLC38A6	145389	hgsc.bcm.edu	37	14	61448049	61448049	+	Silent	SNP	C	C	G	rs17097938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	37	63	0	0.480519	0	C|0.968;G|0.032	0.032	strong	.	SLC38A6	87	.	NM_153811	exon1	c.C54G	p.V18V	CTCTGTCCAGCAG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31382882	31382882	+	Missense_Mutation	SNP	C	C	A	rs9266825	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	119	157	1	0.983471	0.00636943	C|0.666;A|0.334	0.334	strong	.	MICA	21	.	NM_000247	exon7	c.C1118A	p.A373D	TGTCAGCTCTTGG	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36583651	36583651	+	Silent	SNP	G	G	A	rs61494900	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	94	141	0	0.531073	0	G|0.864;A|0.136	0.136	strong	.	WDR62	102	.	NM_173636	exon19	c.G2271A	p.L757L	CTTGCTGGAGATT	.	PASS	Atlas-SNP
HERC1	8925	hgsc.bcm.edu	37	15	63967170	63967170	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	243	106	275	0	0.436214	0	.	.	none	.	HERC1	624	.	NM_003922	exon38	c.T7217C	p.M2406T	TTGCCCATGTCTT	.	PASS	Atlas-SNP
LRRC8E	80131	hgsc.bcm.edu	37	19	7963949	7963949	+	Missense_Mutation	SNP	A	A	G	rs2042919	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	80	0	0.43662	0	A|0.759;G|0.241	0.241	strong	.	LRRC8E	67	.	NM_001268284	exon4	c.A542G	p.E181G	CCACCGAACGGGC	.	PASS	Atlas-SNP
STK11	6794	hgsc.bcm.edu	37	19	1207176	1207176	+	Silent	SNP	C	C	A	rs56354945	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	69	132	0	0.518797	0	C|0.980;A|0.020	0.020	strong	STK11,brain,glioma,0,2	STK11	410	2	NM_000455	exon1	c.C264A	p.I88I	AAGGATCCCCAAC	.	PASS	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207872595	207872595	+	Missense_Mutation	SNP	A	A	G	rs12729569	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	459	230	426	0	0.501089	0	A|0.831;G|0.169	0.169	strong	.	CR1L	97	.	NM_175710	exon8	c.A1204G	p.N402D	CTTTGGAATAGCA	.	PASS	Atlas-SNP
MAP3K6	9064	hgsc.bcm.edu	37	1	27682530	27682530	+	Missense_Mutation	SNP	C	C	G	rs17162549	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	173	215	0	0.920213	0	C|0.919;G|0.081	0.081	strong	.	MAP3K6	134	.	NM_004672	exon27	c.G3698C	p.G1233A	ATGGTGCCTGAAT	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	31	84	0	0.407895	0	G|0.888;A|0.112	0.112	strong	.	UTP20	222	.	NM_014503	exon10	c.G1143A	p.P381P	CTTGCCGGAGACC	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21792811	21792811	+	Silent	SNP	G	G	A	rs9322965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	84	94	0	1	0	G|0.856;A|0.144	0.144	strong	.	RPGRIP1	213	.	NM_020366	exon14	c.G1797A	p.P599P	CCGACCGTTGTCG	.	PASS	Atlas-SNP
ZMYM5	9205	hgsc.bcm.edu	37	13	20411701	20411701	+	Missense_Mutation	SNP	C	C	T	rs7988277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	48	111	0	0.484848	0	C|0.887;T|0.113	0.113	strong	.	ZMYM5	73	.	NM_001039650	exon6	c.G1133A	p.R378H	AGAACACGTGCAT	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	37	2	33488419	33488419	+	Silent	SNP	G	G	A	rs12468099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	100	86	0	1	0	G|0.797;A|0.203	0.203	strong	.	LTBP1	317	.	NM_206943	exon15	c.G2577A	p.T859T	TTCTACGTCTAGT	.	PASS	Atlas-SNP
CENPM	79019	hgsc.bcm.edu	37	22	42336172	42336172	+	Nonsense_Mutation	SNP	G	G	A	rs5758511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	56	100	0	0.513761	0	G|0.752;A|0.248	0.248	strong	.	CENPM	8	.	NM_001110215	exon1	c.C7T	p.R3X	ACACTCGGCCCAT	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90455084	90455084	+	Silent	SNP	A	A	G	rs9359861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	70	137	0	1	0	A|0.100;G|0.900	0.900	strong	.	MDN1	478	.	NM_014611	exon29	c.T4086C	p.H1362H	CACGATATGGCCA	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171154959	171154959	+	Missense_Mutation	SNP	A	A	G	rs2020870	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	62	113	0	0.496	0	A|0.919;G|0.081	0.081	strong	.	FMO2	66	.	NM_001460	exon2	c.A107G	p.D36G	CTGAAGATATTGG	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186281400	186281400	+	Missense_Mutation	SNP	C	C	T	rs12134934	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	51	100	0	0.459459	0	C|0.958;T|0.042	0.042	strong	.	PRG4	259	.	NM_005807	exon11	c.C3887T	p.T1296M	GAGAAACGACACA	.	PASS	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	37	2	211456639	211456639	+	Silent	SNP	C	C	T	rs2229589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	28	89	0	0.405797	0	C|0.408;T|0.592	0.592	strong	.	CPS1	485	.	NM_001122633	exon11	c.C1050T	p.T350T	CAACACCCTCCCT	.	PASS	Atlas-SNP
OR12D2	26529	hgsc.bcm.edu	37	6	29364685	29364685	+	Missense_Mutation	SNP	G	G	T	rs36210740	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	302	137	285	1	0.453642	0.00350877	A|0.001;G|0.994;T|0.005	0.005	strong	.	OR12D2	42	.	NM_013936	exon1	c.G209T	p.C70F	ATATCTGTTACTC	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	16877110	16877110	+	Missense_Mutation	SNP	G	G	A	rs1801230	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	55	112	0	0.398551	0	G|0.982;A|0.018	0.018	strong	.	CUBN	515	.	NM_001081	exon64	c.C10265T	p.T3422I	GTAACGGTGCAAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512242	195512242	+	Missense_Mutation	SNP	G	G	A	rs75928106		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	29	234	0	0.164773	0	G|0.500;A|0.500	0.500	weak	.	MUC4	1505	.	NM_018406	exon2	c.C6209T	p.P2070L	GAGGAAGGGTTAG	.	PASS	Atlas-SNP
ABCG8	64241	hgsc.bcm.edu	37	2	44078913	44078913	+	Silent	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	38	104	0	0.361905	0	.	.	none	.	ABCG8	98	.	NM_022437	exon4	c.C513A	p.A171A	CATTGCCCAGATG	.	PASS	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	37	3	73453325	73453325	+	Silent	SNP	C	C	T	rs2291463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	126	132	0	0.976744	0	C|0.427;T|0.573	0.573	strong	.	PDZRN3	196	.	NM_015009	exon4	c.G1140A	p.V380V	ATCCAGCACGGGT	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39135205	39135205	+	Silent	SNP	A	A	G	rs8064910	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	60	123	0	0.491803	0	A|0.340;G|0.660	0.660	strong	KRT40,NS,carcinoma,0,1	KRT40	27	1	NM_182497	exon8	c.T1047C	p.C349C	GATCAGACACTGA	.	PASS	Atlas-SNP
LRRCC1	85444	hgsc.bcm.edu	37	8	86057707	86057707	+	Silent	SNP	A	A	G	rs62525428	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	236	112	172	0	0.474576	0	A|0.926;G|0.074	0.074	strong	.	LRRCC1	212	.	NM_033402	exon19	c.A3060G	p.Q1020Q	TAAGCAACTTGCT	.	PASS	Atlas-SNP
TOPBP1	11073	hgsc.bcm.edu	37	3	133368362	133368362	+	Missense_Mutation	SNP	T	T	G	rs3192149	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	124	157	0	0.992	0	T|0.283;G|0.717	0.717	strong	.	TOPBP1	218	.	NM_007027	exon10	c.A1369C	p.K457Q	CAGGCTTATGTGA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150948016	150948016	+	Silent	SNP	C	C	T	rs3734062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	107	245	0	0.442149	0	C|0.944;T|0.056	0.056	strong	.	FAT2	465	.	NM_001447	exon1	c.G477A	p.E159E	CATGTCCTCAGAG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104627	168104627	+	Missense_Mutation	SNP	G	G	A	rs61750760	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	91	181	0	0.466667	0	G|0.842;A|0.158	0.158	strong	XIRP2,NS,carcinoma,+1,1	XIRP2	914	1	NM_152381	exon9	c.G6725A	p.R2242Q	AAAAGCGGGAGAC	.	PASS	Atlas-SNP
GABBR1	2550	hgsc.bcm.edu	37	6	29576393	29576393	+	Silent	SNP	A	A	G	rs29230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	40	101	0	0.4	0	A|0.820;G|0.180	0.180	strong	GABBR1,NS,carcinoma,0,1	GABBR1	95	1	NM_001470	exon16	c.T1977C	p.F659F	GAAAGGAAACTGG	.	PASS	Atlas-SNP
CLIP4	79745	hgsc.bcm.edu	37	2	29366646	29366646	+	Silent	SNP	C	C	T	rs35024908	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	88	156	0	0.44898	0	C|0.949;T|0.051	0.051	strong	CLIP4,NS,carcinoma,+2,1	CLIP4	69	1	NM_024692	exon7	c.C720T	p.A240A	TGACGCCGCAGCC	.	PASS	Atlas-SNP
CCBL2	56267	hgsc.bcm.edu	37	1	89426902	89426902	+	Silent	SNP	G	G	A	rs3738055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	31	74	0	0.516667	0	G|0.584;A|0.416	0.416	strong	CCBL2_ENST00000370491,NS,carcinoma,0,1	CCBL2	138	1	NM_001008661	exon8	c.C735T	p.S245S	CTCATCGCTGATG	.	PASS	Atlas-SNP
TBX4	9496	hgsc.bcm.edu	37	17	59557600	59557600	+	Missense_Mutation	SNP	C	C	T	rs3744438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	43	122	0	0.421569	0	C|0.789;T|0.211	0.211	strong	TBX4,mouth,carcinoma,-1,1	TBX4	69	1	NM_018488	exon7	c.C941T	p.A314V	AGCTCGCGGAGCC	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	37	2	203157538	203157538	+	Silent	SNP	A	A	G	rs16839032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	62	117	0	0.521008	0	A|0.989;G|0.011	0.011	strong	NOP58,NS,carcinoma,0,1	NOP58	41	1	NM_015934	exon9	c.A819G	p.E273E	CTATGAATATCTA	.	PASS	Atlas-SNP
N4BP1	9683	hgsc.bcm.edu	37	16	48595110	48595110	+	Missense_Mutation	SNP	T	T	C	rs371090316		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	64	145	0	0.542373	0	.	.	weak	.	N4BP1	121	.	NM_153029	exon2	c.A1444G	p.I482V	TACAAATGTAGTT	.	PASS	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3299749	3299749	+	Silent	SNP	G	G	A	rs224213	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	67	108	0	0.531746	0	G|0.373;A|0.627	0.627	strong	.	MEFV	170	.	NM_000243	exon3	c.C942T	p.R314R	GTGGCAGCGGGGA	.	PASS	Atlas-SNP
IMPACT	55364	hgsc.bcm.edu	37	18	22008842	22008842	+	Missense_Mutation	SNP	C	C	T	rs187130387	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	38	76	0	0.475	0	C|0.999;T|0.001	0.001	strong	IMPACT,pharynx,carcinoma,-2,1	IMPACT	37	1	NM_018439	exon3	c.C175T	p.P59S	ATGCTGCCGAATG	.	PASS	Atlas-SNP
LRRC18	474354	hgsc.bcm.edu	37	10	50121760	50121760	+	Silent	SNP	G	G	A	rs41283291	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	66	133	0	0.511628	0	G|0.863;A|0.137	0.137	strong	.	LRRC18	52	.	NM_001006939	exon1	c.C441T	p.H147H	TACCTCGTGGAGC	.	PASS	Atlas-SNP
KIF24	347240	hgsc.bcm.edu	37	9	34256539	34256539	+	Silent	SNP	A	A	G	rs36025573	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	55	114	0	0.486726	0	A|0.960;G|0.040	0.040	strong	.	KIF24	64	.	NM_194313	exon11	c.T3066C	p.T1022T	TTTCACAGTGCTG	.	PASS	Atlas-SNP
DCAF13	25879	hgsc.bcm.edu	37	8	104432545	104432545	+	Missense_Mutation	SNP	A	A	G	rs3134253	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	69	128	0	0.511111	0	A|0.768;G|0.232	0.232	strong	.	DCAF13	66	.	NM_015420	exon2	c.A580G	p.I194V	GAATATATAAGAG	.	PASS	Atlas-SNP
C7orf62	219557	hgsc.bcm.edu	37	7	88424115	88424115	+	Missense_Mutation	SNP	C	C	G	rs2373396	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	300	141	295	0	0.47	0	C|0.824;G|0.176	0.176	strong	.	C7orf62	63	.	NM_152706	exon2	c.G142C	p.D48H	TCCTATCAAGAAG	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	228362	228362	+	Silent	SNP	T	T	C	rs2115272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	61	116	0	0.462121	0	T|0.754;C|0.246	0.246	strong	.	SDHA	80	.	NM_004168	exon6	c.T684C	p.N228N	GGAGAATGGGGAG	.	PASS	Atlas-SNP
FMR1	2332	hgsc.bcm.edu	37	X	146993715	146993715	+	Silent	SNP	G	G	T	rs111485627	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	113	94	0	0.991228	0	C|0.000;G|0.987;T|0.013	0.013	strong	.	FMR1	93	.	NM_002024	exon1	c.G18T	p.V6V	GGTGGTGGAAGTG	.	PASS	Atlas-SNP
MAN2B2	23324	hgsc.bcm.edu	37	4	6610889	6610889	+	Missense_Mutation	SNP	G	G	A	rs61733402	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	51	116	0	0.447368	0	G|0.936;A|0.064	0.064	strong	.	MAN2B2	80	.	NM_015274	exon12	c.G1870A	p.G624R	GTCAACGGGGATG	.	PASS	Atlas-SNP
DZANK1	55184	hgsc.bcm.edu	37	20	18395988	18395988	+	Missense_Mutation	SNP	C	C	T	rs6035037	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	68	86	0	1	0	C|0.764;T|0.236	0.236	strong	DZANK1,NS,carcinoma,0,2	DZANK1	65	2	NM_001099407	exon11	c.G1060A	p.G354S	ACCAGCCGCAGAA	.	PASS	Atlas-SNP
SART3	9733	hgsc.bcm.edu	37	12	108954862	108954862	+	Missense_Mutation	SNP	G	G	C	rs2072579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	51	70	0	0.51	0	G|0.800;C|0.200	0.200	strong	.	SART3	64	.	NM_014706	exon1	c.C69G	p.D23E	CTCTCCGTCAGCC	.	PASS	Atlas-SNP
NPNT	255743	hgsc.bcm.edu	37	4	106861730	106861730	+	Missense_Mutation	SNP	A	A	G	rs4340795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	125	101	0	1	0	A|0.136;G|0.864	0.864	strong	.	NPNT	69	.	NM_001184691	exon8	c.A790G	p.I264V	TATAACATACGTG	.	PASS	Atlas-SNP
CD33	945	hgsc.bcm.edu	37	19	51728477	51728477	+	Missense_Mutation	SNP	C	C	T	rs12459419	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	31	74	0	0.596154	0	C|0.765;T|0.235	0.235	strong	.	CD33	55	.	NM_001772	exon2	c.C41T	p.A14V	CAGGGGCCCTGGC	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	242004866	242004866	+	Silent	SNP	A	A	G	rs2286321	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	48	108	0	0.466019	0	A|0.630;G|0.370	0.370	strong	.	SNED1	76	.	NM_001080437	exon21	c.A2865G	p.T955T	CCGCACAGACTTT	.	PASS	Atlas-SNP
LANCL3	347404	hgsc.bcm.edu	37	X	37527659	37527659	+	Missense_Mutation	SNP	T	T	C	rs28503960	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	112	91	0	1	0	T|0.847;C|0.153	0.153	strong	.	LANCL3	42	.	NM_198511	exon5	c.T1142C	p.L381P	ATCTGCTGTATAC	.	PASS	Atlas-SNP
DSTYK	25778	hgsc.bcm.edu	37	1	205129319	205129319	+	Silent	SNP	G	G	A	rs1062715	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	132	248	1	0.517647	0.00403226	G|0.705;A|0.295	0.295	strong	.	DSTYK	87	.	NM_199462	exon8	c.C2028T	p.F676F	ACAAGGGAAGTGT	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78437182	78437182	+	Silent	SNP	G	G	A	rs689369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	85	206	0	0.454545	0	G|0.814;A|0.186	0.186	strong	.	.	.	.	NM_001098816	exon23	c.C3492T	p.D1164D	GGACGCGTCAATT	.	PASS	Atlas-SNP
LRRC23	10233	hgsc.bcm.edu	37	12	7023123	7023123	+	Missense_Mutation	SNP	A	A	G	rs710415	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	39	87	0	0.393939	0	A|0.551;G|0.449	0.449	strong	.	LRRC23	46	.	NM_006992	exon7	c.A827G	p.E276G	ACAGAGAACAGAG	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444012	20444012	+	Missense_Mutation	SNP	A	A	T	rs3861512	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	76	158	0	0.422222	0	A|0.772;T|0.228	0.228	strong	OR4K15,colon,carcinoma,0,2	OR4K15	82	2	NM_001005486	exon1	c.A335T	p.E112V	TGGTTGAGCGCAA	.	PASS	Atlas-SNP
TMEM79	84283	hgsc.bcm.edu	37	1	156255560	156255560	+	Silent	SNP	G	G	A	rs140033065	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	39	81	0	0.557143	0	G|0.997;A|0.003	0.003	strong	.	TMEM79	43	.	NM_032323	exon2	c.G543A	p.P181P	GAGGCCGCCTGGC	.	PASS	Atlas-SNP
EGFLAM	133584	hgsc.bcm.edu	37	5	38409147	38409147	+	Silent	SNP	C	C	T	rs16903964	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	53	105	0	0.504762	0	C|0.949;T|0.051	0.051	strong	.	EGFLAM	302	.	NM_001205301	exon10	c.C1290T	p.N430N	GGAGAACGAACAC	.	PASS	Atlas-SNP
CSTF2T	23283	hgsc.bcm.edu	37	10	53458167	53458167	+	Silent	SNP	C	C	T	rs3824686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	36	78	0	0.590164	0	C|0.920;T|0.080	0.080	strong	.	CSTF2T	64	.	NM_015235	exon1	c.G1143A	p.R381R	CCCTCCCCTCATC	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113400593	113400593	+	Missense_Mutation	SNP	C	C	T	rs200778728	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	57	111	0	0.478992	0	.	.	weak	OAS3,NS,carcinoma,-1,1	OAS3	63	1	NM_006187	exon9	c.C1970T	p.T657M	TCCGGACGGTGCT	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057720	46057720	+	Missense_Mutation	SNP	A	A	C	rs4818949	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	75	136	0	0.46875	0	A|0.711;C|0.289	0.289	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.A386C	p.Q129P	GCCAGCAGTCTAG	.	PASS	Atlas-SNP
KIF1B	23095	hgsc.bcm.edu	37	1	10435324	10435324	+	Silent	SNP	C	C	A	rs11121552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	9	138	0	0.075	0	C|0.759;A|0.241	0.241	strong	KIF1B,NS,carcinoma,0,1	KIF1B	242	1	NM_015074	exon46	c.C5163A	p.T1721T	AAACACCTTTGCT	.	PASS	Atlas-SNP
C11orf21	29125	hgsc.bcm.edu	37	11	2320884	2320884	+	Silent	SNP	A	A	G	rs1501466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	80	166	0	0.5	0	A|0.799;G|0.201	0.201	strong	C11orf21,NS,carcinoma,-2,1	C11orf21	11	1	NM_001142946	exon4	c.T339C	p.G113G	AAGGGCACCATGG	.	PASS	Atlas-SNP
EIF2S3	1968	hgsc.bcm.edu	37	X	24075862	24075862	+	Missense_Mutation	SNP	A	A	G	rs16997659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	58	53	0	1	0	A|0.888;0|0.013	.	strong	.	EIF2S3	31	.	NM_001415	exon4	c.A374G	p.K125R	ACTTCAAATTAGT	.	PASS	Atlas-SNP
SETX	23064	hgsc.bcm.edu	37	9	135139901	135139901	+	Missense_Mutation	SNP	T	T	C	rs1056899	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	37	57	0	0.560606	0	T|0.505;C|0.495	0.495	strong	.	SETX	234	.	NM_015046	exon26	c.A7759G	p.I2587V	GCTGTATATGGCT	.	PASS	Atlas-SNP
RASSF7	8045	hgsc.bcm.edu	37	11	562219	562219	+	Missense_Mutation	SNP	C	C	G	rs2242183	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	41	96	0	0.471264	0	C|0.930;G|0.070	0.070	strong	.	RASSF7	22	.	NM_001143994	exon3	c.C265G	p.P89A	ACAGGGCCCAGCC	.	PASS	Atlas-SNP
ZNF30	90075	hgsc.bcm.edu	37	19	35422808	35422808	+	Missense_Mutation	SNP	C	C	T	rs10422961	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	90	84	0	0.978261	0	C|0.700;T|0.300	0.300	strong	ZNF30,colon,carcinoma,0,1	ZNF30	44	1	NM_001099438	exon3	c.C71T	p.S24F	CCTTCTCCCAGCA	.	PASS	Atlas-SNP
PTCRA	171558	hgsc.bcm.edu	37	6	42891022	42891022	+	Missense_Mutation	SNP	G	G	A	rs9471966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	82	84	0	0.453039	0	G|0.729;A|0.271	0.271	strong	.	PTCRA	24	.	NM_138296	exon2	c.G316A	p.V106I	CCTTTGGTCTGCC	.	PASS	Atlas-SNP
VEPH1	79674	hgsc.bcm.edu	37	3	157081324	157081324	+	Missense_Mutation	SNP	A	A	G	rs11918974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	84	172	0	0.48	0	A|0.767;G|0.233	0.233	strong	VEPH1,colon,carcinoma,0,2	VEPH1	129	2	NM_001167911	exon9	c.T1564C	p.S522P	TTTCTGACAAATT	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296521	39296521	+	Silent	SNP	G	G	A	rs201084737	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	24	58	0	0.444444	0	G|0.996;A|0.004	0.004	strong	.	KRTAP4-6	46	.	NM_030976	exon1	c.C219T	p.T73T	GCAGCAGGTGGTC	.	PASS	Atlas-SNP
SLC12A7	10723	hgsc.bcm.edu	37	5	1063998	1063998	+	Silent	SNP	G	G	A	rs7722287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	130	207	0	0.522088	0	G|0.675;A|0.325	0.325	strong	SLC12A7,NS,carcinoma,0,1	SLC12A7	97	1	NM_006598	exon20	c.C2700T	p.Y900Y	CAAGTGGTACAAG	.	PASS	Atlas-SNP
RAB3D	9545	hgsc.bcm.edu	37	19	11436221	11436221	+	Silent	SNP	A	A	G	rs12981706	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	16	32	0	0.457143	0	A|0.939;G|0.061;T|0.000	0.061	strong	.	RAB3D	24	.	NM_004283	exon5	c.T513C	p.N171N	CTTCACATTGATG	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3656645	3656645	+	Missense_Mutation	SNP	A	A	G	rs147826749	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	90	197	0	0.483871	0	A|0.997;G|0.003	0.003	strong	.	SLX4	173	.	NM_032444	exon3	c.T590C	p.V197A	CTTGGCACTGCTG	.	PASS	Atlas-SNP
ZNF333	84449	hgsc.bcm.edu	37	19	14829345	14829345	+	Silent	SNP	C	C	T	rs147332855	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	43	78	0	0.530864	0	C|0.999;T|0.001	0.001	strong	.	ZNF333	76	.	NM_032433	exon12	c.C1206T	p.A402A	GCAAGCCTTCAAA	.	PASS	Atlas-SNP
CRNN	49860	hgsc.bcm.edu	37	1	152383373	152383373	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	44	60	0	0.5	0	.	.	none	.	CRNN	78	.	NM_016190	exon3	c.A185T	p.D62V	TCTTCATCCAGCA	.	PASS	Atlas-SNP
GTPBP5	26164	hgsc.bcm.edu	37	20	60768497	60768497	+	Silent	SNP	C	C	T	rs2236527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	98	214	1	0.4689	0.0046729	C|0.827;T|0.173	0.173	strong	.	GTPBP5	43	.	NM_015666	exon2	c.C21T	p.F7F	GTGTTTCTCAGCA	.	PASS	Atlas-SNP
HYI	81888	hgsc.bcm.edu	37	1	43917888	43917888	+	Silent	SNP	C	C	G	rs41270373	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	51	87	0	0.542553	0	C|0.981;G|0.019	0.019	strong	.	HYI	23	.	NM_001243526	exon4	c.G489C	p.G163G	CAAAACCCCAGCT	.	PASS	Atlas-SNP
C2orf74	339804	hgsc.bcm.edu	37	2	61389737	61389737	+	Missense_Mutation	SNP	T	T	G	rs1729674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	70	143	0	0.514706	0	T|0.583;G|0.417	0.417	strong	.	C2orf74	22	.	NM_001143959	exon1	c.T109G	p.Y37D	TTTTTATATAAAT	.	PASS	Atlas-SNP
C6orf223	221416	hgsc.bcm.edu	37	6	43970602	43970602	+	Silent	SNP	G	G	C	rs117880737	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	13	9	8	0	0.692308	0	G|0.957;C|0.043	0.043	strong	.	C6orf223	14	.	NM_153246	exon4	c.G468C	p.P156P	GAGCCCGGGACAG	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26458872	26458872	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	6	103	0	0.0540541	0	.	.	none	.	BTN2A1	118	.	NM_001197234	exon2	c.C8T	p.S3L	TGGAATCAGCTGC	.	PASS	Atlas-SNP
DGCR14	8220	hgsc.bcm.edu	37	22	19132061	19132061	+	Silent	SNP	C	C	T	rs2298274	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	81	96	0	0.623077	0	C|0.926;T|0.074	0.074	strong	.	DGCR14	43	.	NM_022719	exon1	c.G93A	p.A31A	GCTCGTCGCAGCC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168099796	168099796	+	Missense_Mutation	SNP	T	T	C	rs16853306	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	248	111	287	0	0.447581	0	T|0.774;C|0.226	0.226	strong	.	XIRP2	914	.	NM_152381	exon9	c.T1894C	p.Y632H	GGGGCTTATTCTT	.	PASS	Atlas-SNP
LGALS12	85329	hgsc.bcm.edu	37	11	63277334	63277334	+	Missense_Mutation	SNP	A	A	G	rs117587231	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	70	172	0	0.404624	0	A|0.992;G|0.008	0.008	strong	.	LGALS12	35	.	NM_001142535	exon4	c.A526G	p.I176V	GGTGACATCCTGG	.	PASS	Atlas-SNP
TET3	200424	hgsc.bcm.edu	37	2	74274329	74274329	+	Missense_Mutation	SNP	C	C	T	rs61741171	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	38	104	0	0.44186	0	C|0.963;T|0.037	0.037	strong	.	TET3	101	.	NM_144993	exon1	c.C880T	p.P294S	GCAACTCCTAGAA	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	rs35901514	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	18	49	0	0.36	0	T|0.993;C|0.007	0.007	strong	.	COL15A1	211	.	NM_001855	exon24	c.T2551C	p.F851L	CCTGGCTTTCCAG	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3613207	3613207	+	Silent	SNP	G	G	T	rs9940099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	15	9	0	0.652174	0	A|0.074;G|0.926	.	strong	.	NLRC3	103	.	NM_178844	exon5	c.C1731A	p.T577T	CAGCTCGGTGTGC	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	37	1	152733301	152733301	+	Missense_Mutation	SNP	T	T	A	rs4329520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	176	163	1	0.99435	0.00613497	T|0.489;A|0.511	0.511	strong	.	KPRP	152	.	NM_001025231	exon2	c.T1237A	p.C413S	GAACCATGCATAA	.	PASS	Atlas-SNP
SNAP29	9342	hgsc.bcm.edu	37	22	21213416	21213416	+	Silent	SNP	A	A	G	rs1061064	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	91	41	0	1	0	A|0.600;G|0.400	0.400	strong	SNAP29,NS,carcinoma,0,1	SNAP29	22	1	NM_004782	exon1	c.A18G	p.K6K	CCCTAAAAGCTAC	.	PASS	Atlas-SNP
SLC12A4	6560	hgsc.bcm.edu	37	16	67997920	67997920	+	Missense_Mutation	SNP	T	T	C	rs3785100	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	44	53	0	0.517647	0	T|0.841;C|0.159	0.159	strong	.	SLC12A4	81	.	NM_001145963	exon1	c.A11G	p.E4G	GCACCTTCGGCTG	.	PASS	Atlas-SNP
MPPE1	65258	hgsc.bcm.edu	37	18	11893554	11893554	+	Silent	SNP	C	C	G	rs34932177	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	51	77	0	0.6	0	C|0.939;G|0.061	0.061	strong	.	MPPE1	21	.	NM_001242904	exon3	c.G303C	p.A101A	CTGGAACGCTCTC	.	PASS	Atlas-SNP
APOL3	80833	hgsc.bcm.edu	37	22	36537893	36537893	+	Silent	SNP	A	A	G	rs3827346	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	47	103	0	0.443396	0	A|0.793;G|0.207	0.207	strong	.	APOL3	60	.	NM_145640	exon3	c.T564C	p.N188N	CACCACATTGGAG	.	PASS	Atlas-SNP
MFGE8	4240	hgsc.bcm.edu	37	15	89450587	89450587	+	Missense_Mutation	SNP	G	G	T	rs1878326	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	76	164	0	0.436782	0	G|0.336;T|0.658	0.658	strong	MFGE8,NS,carcinoma,0,2	MFGE8	60	2	NM_001114614	exon3	c.C226A	p.L76M	TCTCCAGGCCCAG	.	PASS	Atlas-SNP
C20orf194	25943	hgsc.bcm.edu	37	20	3356878	3356878	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	90	154	0	0.456853	0	.	.	none	.	C20orf194	83	.	NM_001009984	exon4	c.C355T	p.P119S	CATAAGGTAAGAG	.	PASS	Atlas-SNP
EPHB1	2047	hgsc.bcm.edu	37	3	134670524	134670524	+	Silent	SNP	C	C	T	rs7644369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	191	201	0	1	0	C|0.559;T|0.441	0.441	strong	.	EPHB1	519	.	NM_004441	exon3	c.C435T	p.S145S	TGAGAGCTTCTCC	.	PASS	Atlas-SNP
GYG1	2992	hgsc.bcm.edu	37	3	148727133	148727133	+	Silent	SNP	G	G	A	rs4938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	90	0	1	0	G|0.703;A|0.297	0.297	strong	.	GYG1	29	.	NM_004130	exon5	c.G552A	p.P184P	CCTGCCGTTTATT	.	PASS	Atlas-SNP
MRPL45	84311	hgsc.bcm.edu	37	17	36474601	36474601	+	Silent	SNP	A	A	G	rs59939216	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	100	178	0	0.507614	0	A|0.873;G|0.127	0.127	strong	.	MRPL45	27	.	NM_032351	exon5	c.A477G	p.R159R	TGACCGACTTCAT	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17469049	17469049	+	Nonsense_Mutation	SNP	C	C	A	rs28502153	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	42	67	0	0.494118	0	C|0.664;A|0.336	0.336	strong	.	GAB4	95	.	NM_001037814	exon3	c.G487T	p.G163X	TGTTTCCCAGGAA	.	PASS	Atlas-SNP
ATP9A	10079	hgsc.bcm.edu	37	20	50235577	50235577	+	Silent	SNP	G	G	A	rs2295004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	34	80	0	0.447368	0	G|0.904;A|0.096	0.096	strong	.	ATP9A	135	.	NM_006045	exon20	c.C2121T	p.T707T	GCGGTTGGTCACC	.	PASS	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	37	1	223567803	223567803	+	Missense_Mutation	SNP	G	G	A	rs10907376	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	106	80	0	0.990654	0	G|0.814;A|0.186	0.186	strong	C1orf65,NS,carcinoma,0,4	C1orf65	71	4	NM_152610	exon1	c.G986A	p.G329D	AGCGCGGCCTGCG	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362669	32362669	+	Silent	SNP	T	T	G	rs41449245	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	44	139	0	0.40367	0	T|0.859;G|0.141	0.141	strong	.	BTNL2	50	.	NM_019602	exon6	c.A1212C	p.S404S	GGAAGATGATGGT	.	PASS	Atlas-SNP
FRMD1	79981	hgsc.bcm.edu	37	6	168479568	168479568	+	Silent	SNP	G	G	A	rs78152017	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	4	30	0	0.166667	0	G|0.913;A|0.087	0.087	strong	.	FRMD1	52	.	NM_024919	exon1	c.C207T	p.A69A	CCCCACGGCCAGC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6569896	6569896	+	Missense_Mutation	SNP	G	G	A	rs11606889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	57	61	0	1	0	G|0.887;A|0.113	0.113	strong	.	DNHD1	198	.	NM_144666	exon24	c.G7120A	p.V2374M	TATGTGGTGGACC	.	PASS	Atlas-SNP
OTUD4	54726	hgsc.bcm.edu	37	4	146062553	146062553	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	2	181	0	0.0103093	0	.	.	none	OTUD4,NS,carcinoma,-2,1	OTUD4	120	1	NM_001102653	exon19	c.G1866A	p.Q622Q	CCCAGTCTGACAC	.	scavenged	Atlas-SNP
SGOL2	151246	hgsc.bcm.edu	37	2	201437334	201437334	+	Silent	SNP	T	T	C	rs12052989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	154	176	0	0.993548	0	T|0.238;C|0.762	0.762	strong	.	SGOL2	126	.	NM_001160046	exon7	c.T2265C	p.P755P	CATCCCTGGAAAC	.	PASS	Atlas-SNP
ITGB1	3688	hgsc.bcm.edu	37	10	33214802	33214802	+	Silent	SNP	A	A	G	rs2298141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	46	89	0	0.516854	0	A|0.852;G|0.148	0.148	strong	.	ITGB1	156	.	NM_002211	exon6	c.T783C	p.C261C	TACTCCACAAACT	.	PASS	Atlas-SNP
OR4C11	219429	hgsc.bcm.edu	37	11	55371381	55371381	+	Nonsense_Mutation	SNP	G	G	A	rs75423534	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	54	127	0	1	0	G|0.926;A|0.074	0.074	strong	OR4C11,rectum,carcinoma,0,1	OR4C11	73	1	NM_001004700	exon1	c.C469T	p.Q157X	TAATCTGAGCTGT	.	PASS	Atlas-SNP
ATP13A3	79572	hgsc.bcm.edu	37	3	194157937	194157937	+	Silent	SNP	G	G	A	rs369809078		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	41	95	0	0.493976	0	.	.	weak	.	ATP13A3	94	.	NM_024524	exon19	c.C2007T	p.V669V	AAAATCGACAGGA	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21232804	21232804	+	Silent	SNP	G	G	A	rs1041968	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	143	183	1	0.979452	0.00546448	G|0.640;A|0.360	0.360	strong	APOB,NS,malignant_melanoma,-2,1	APOB	761	1	NM_000384	exon26	c.C6936T	p.D2312D	AAGAATGTCATTT	.	PASS	Atlas-SNP
STRIP2	57464	hgsc.bcm.edu	37	7	129093179	129093179	+	Missense_Mutation	SNP	T	T	C	rs201255678		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	46	77	0	0.418182	0	T|0.999;C|0.001	0.001	weak	.	.	.	.	NM_020704	exon5	c.T521C	p.M174T	TCCACATGGAAAT	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	37	3	47036756	47036756	+	Missense_Mutation	SNP	C	C	G	rs11720139	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	62	74	1	0.984127	0.0135135	C|0.687;G|0.313	0.313	strong	NBEAL2_ENST00000450053,NS,carcinoma,0,4	NBEAL2	267	4	NM_015175	exon13	c.C1531G	p.R511G	GAGGCCCGCTGCC	.	scavenged	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125590478	125590478	+	Silent	SNP	T	T	C	rs1874748	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	267	128	278	1	0.479401	0.00359712	T|0.820;C|0.180	0.180	strong	.	ANKRD50	136	.	NM_020337	exon4	c.A3954G	p.P1318P	TTTAGGTGGTGCA	.	PASS	Atlas-SNP
ELMO3	79767	hgsc.bcm.edu	37	16	67234134	67234134	+	Missense_Mutation	SNP	A	A	G	rs8058861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	39	105	0	0.458824	0	A|0.847;G|0.153	0.153	strong	.	ELMO3	41	.	NM_024712	exon5	c.A442G	p.N148D	CAGAGTAACAGTC	.	PASS	Atlas-SNP
COPG1	22820	hgsc.bcm.edu	37	3	128971751	128971751	+	Silent	SNP	C	C	T	rs73202214	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	66	120	0	0.519685	0	C|0.998;T|0.002	0.002	strong	.	.	.	.	NM_016128	exon5	c.C276T	p.I92I	GACCATCAAGGAG	.	PASS	Atlas-SNP
POPDC2	64091	hgsc.bcm.edu	37	3	119378977	119378977	+	Silent	SNP	G	G	A	rs2873788	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	45	103	0	0.517241	0	G|0.887;A|0.113	0.113	strong	POPDC2,NS,carcinoma,-1,1	POPDC2	36	1	NM_022135	exon1	c.C294T	p.R98R	ACGCAGGCGGTAT	.	PASS	Atlas-SNP
RFX7	64864	hgsc.bcm.edu	37	15	56388033	56388033	+	Silent	SNP	T	T	C	rs12439907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	19	34	0	0.452381	0	T|0.747;C|0.253	0.253	strong	.	RFX7	170	.	NM_022841	exon9	c.A1893G	p.L631L	GAAAGTTAAGTTC	.	PASS	Atlas-SNP
BCLAF1	9774	hgsc.bcm.edu	37	6	136589448	136589448	+	Missense_Mutation	SNP	C	C	A	rs78267720	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	30	160	0	0.275229	0	C|0.811;A|0.190	0.190	strong	BCLAF1_ENST00000531224,bladder,carcinoma,-1,1	BCLAF1	203	1	NM_014739	exon10	c.G2249T	p.R750L	GAAGATCGAGAAT	.	PASS	Atlas-SNP
GALNTL6	442117	hgsc.bcm.edu	37	4	172735851	172735851	+	Silent	SNP	G	G	A	rs111570068	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	42	93	0	0.446809	0	G|0.991;A|0.009	0.009	strong	GALNTL6,NS,carcinoma,0,1	GALNTL6	102	1	NM_001034845	exon2	c.G120A	p.A40A	GTCAGCGGAGCCC	.	PASS	Atlas-SNP
CRMP1	1400	hgsc.bcm.edu	37	4	5841350	5841350	+	Silent	SNP	A	A	G	rs16837723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	24	54	0	0.387097	0	A|0.731;G|0.269	0.269	strong	.	CRMP1	118	.	NM_001014809	exon9	c.T1209C	p.H403H	CCAGTAATGGGTG	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	37	19	17367354	17367354	+	Silent	SNP	G	G	A	rs141680124	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	40	70	0	0.506329	0	G|0.992;A|0.008	0.008	strong	.	USHBP1	85	.	NM_031941	exon9	c.C1396T	p.L466L	TCCCCAGAATGGC	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605271	32605271	+	Silent	SNP	C	C	T	rs1047993	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	23	116	0	0.227723	0	C|0.717;T|0.283	0.283	strong	.	HLA-DQA1	52	.	NM_002122	exon1	c.C36T	p.L12L	GGCCCTCGCTCTG	.	PASS	Atlas-SNP
ZDHHC8	29801	hgsc.bcm.edu	37	22	20131115	20131115	+	Silent	SNP	C	C	T	rs9605069	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	20	9	0	0.588235	0	C|0.905;T|0.095	0.095	strong	.	ZDHHC8	77	.	NM_001185024	exon10	c.C1962T	p.N654N	CAGCAACGCCCCG	.	PASS	Atlas-SNP
C6	729	hgsc.bcm.edu	37	5	41161898	41161898	+	Missense_Mutation	SNP	C	C	T	rs142896559	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	74	131	0	0.540146	0	C|0.996;T|0.004	0.004	strong	.	C6	197	.	NM_001115131	exon10	c.G1355A	p.G452E	GCTGCTCCATATT	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130952038	130952038	+	Missense_Mutation	SNP	G	G	A	rs13000721	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	69	277	0	0.303965	0	G|0.676;A|0.324	0.324	strong	TUBA3E,NS,carcinoma,0,8	TUBA3E	73	8	NM_207312	exon4	c.C377T	p.A126V	AGATCCGCCTGAG	.	scavenged	Atlas-SNP
ANKRD27	84079	hgsc.bcm.edu	37	19	33098632	33098632	+	Missense_Mutation	SNP	G	G	C	rs2302970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	62	72	0	1	0	G|0.651;C|0.349	0.349	strong	.	ANKRD27	86	.	NM_032139	exon23	c.C2282G	p.P761R	AGGAGGGGGATGA	.	PASS	Atlas-SNP
ISLR	3671	hgsc.bcm.edu	37	15	74467856	74467856	+	Silent	SNP	G	G	A	rs1052622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	28	59	1	0.538462	0.0169492	G|0.400;A|0.600	0.600	strong	ISLR,NS,carcinoma,0,1	ISLR	49	1	NM_201526	exon2	c.G657A	p.T219T	GGGTACGCCGCTG	.	scavenged	Atlas-SNP
PLIN5	440503	hgsc.bcm.edu	37	19	4525046	4525046	+	Missense_Mutation	SNP	A	A	G	rs1610090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	124	134	0	0.976378	0	A|0.154;G|0.846	0.846	strong	.	PLIN5	27	.	NM_001013706	exon7	c.T763C	p.C255R	CAGGGCAGGCCGG	.	PASS	Atlas-SNP
IQUB	154865	hgsc.bcm.edu	37	7	123152157	123152157	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	293	139	299	0	0.474403	0	.	.	none	.	IQUB	117	.	NM_178827	exon2	c.G238C	p.E80Q	CCTCTTCCATGAG	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33628138	33628138	+	Missense_Mutation	SNP	T	T	G	rs9536314	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	37	89	0	0.440476	0	T|0.846;G|0.154	0.154	strong	.	KL	106	.	NM_004795	exon2	c.T1054G	p.F352V	CCTGATTTTACTG	.	PASS	Atlas-SNP
ABTB2	25841	hgsc.bcm.edu	37	11	34378381	34378381	+	Missense_Mutation	SNP	G	G	C	rs1925368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	46	69	0	0.541176	0	G|0.844;C|0.156	0.156	strong	.	ABTB2	101	.	NM_145804	exon1	c.C750G	p.H250Q	AGGGCTGTGGCTG	.	PASS	Atlas-SNP
TOX3	27324	hgsc.bcm.edu	37	16	52473263	52473263	+	Silent	SNP	A	A	G	rs9925256	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	41	114	0	0.383178	0	A|0.542;G|0.458	0.458	strong	TOX3,NS,carcinoma,0,1	TOX3	121	1	NM_001080430	exon7	c.T1605C	p.P535P	GGCGACAGGGGAG	.	PASS	Atlas-SNP
PRAM1	84106	hgsc.bcm.edu	37	19	8564474	8564474	+	Missense_Mutation	SNP	G	G	T	rs4239541	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	22	61	0	0.37931	0	G|0.653;T|0.347	0.347	strong	.	PRAM1	53	.	NM_032152	exon2	c.C218A	p.P73Q	TCAGGCGGCGGGG	.	PASS	Atlas-SNP
KCNV1	27012	hgsc.bcm.edu	37	8	110986480	110986480	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	7	8	0	0.5	0	.	.	none	.	KCNV1	101	.	NM_014379	exon1	c.C138T	p.G46G	GCTGCCGCCCACG	.	PASS	Atlas-SNP
CAMKK2	10645	hgsc.bcm.edu	37	12	121712077	121712077	+	Missense_Mutation	SNP	T	T	A	rs3817190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	24	29	0	0.55814	0	T|0.543;A|0.457	0.457	strong	CAMKK2_ENST00000392473,NS,carcinoma,0,2	CAMKK2	87	2	NM_153500	exon2	c.A253T	p.T85S	CGGAGGTGTCAAG	.	PASS	Atlas-SNP
TAS2R8	50836	hgsc.bcm.edu	37	12	10959031	10959031	+	Silent	SNP	C	C	T	rs1548803	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	146	155	0	0.993197	0	C|0.498;T|0.502	0.502	strong	.	TAS2R8	42	.	NM_023918	exon1	c.G549A	p.L183L	GAGAGTCAAGGGT	.	PASS	Atlas-SNP
RSPH9	221421	hgsc.bcm.edu	37	6	43638636	43638636	+	Missense_Mutation	SNP	G	G	A	rs16896629	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	78	139	1	0.553191	0.00719424	G|0.908;A|0.092	0.092	strong	RSPH9,NS,NS,-2,1	RSPH9	60	1	NM_001193341	exon6	c.G833A	p.R278H	GGCTACGTCTACG	.	scavenged	Atlas-SNP
ZNF474	133923	hgsc.bcm.edu	37	5	121488506	121488506	+	Missense_Mutation	SNP	C	C	G	rs35262183	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	34	63	0	0.465753	0	C|0.753;G|0.247	0.247	strong	.	ZNF474	43	.	NM_207317	exon2	c.C821G	p.S274C	CACAGTCCAGCCA	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	33941759	33941759	+	Missense_Mutation	SNP	T	T	C	rs307658	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	66	137	0	0.381503	0	T|0.617;C|0.383	0.383	strong	UBAP2,NS,carcinoma,0,1	UBAP2	82	1	NM_018449	exon16	c.A1817G	p.N606S	GCAGAATTCAGTG	.	PASS	Atlas-SNP
TFB2M	64216	hgsc.bcm.edu	37	1	246707858	246707858	+	Silent	SNP	A	A	G	rs3129568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	67	108	0	0.59292	0	A|0.783;G|0.217	0.217	strong	.	TFB2M	46	.	NM_022366	exon7	c.T984C	p.F328F	CCTCCCAAAACAG	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30882781	30882781	+	Silent	SNP	G	G	T	rs1264301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	24	54	0	0.470588	0	G|0.731;T|0.269	0.269	strong	.	VARS2	60	.	NM_001167734	exon2	c.G258T	p.A86A	GCAGGCGACTCTG	.	PASS	Atlas-SNP
KLHL30	377007	hgsc.bcm.edu	37	2	239050033	239050033	+	Missense_Mutation	SNP	C	C	T	rs12692216	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	13	10	1	0	0.769231	0	C|0.280;T|0.720	0.720	strong	.	KLHL30	79	.	NM_198582	exon2	c.C638T	p.A213V	GGGCCGCCCACCT	.	PASS	Atlas-SNP
OXNAD1	92106	hgsc.bcm.edu	37	3	16327909	16327909	+	Missense_Mutation	SNP	C	C	T	rs6777976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	232	109	189	0	0.469828	0	C|0.824;T|0.176	0.176	strong	OXNAD1,NS,carcinoma,-1,1	OXNAD1	31	1	NM_138381	exon5	c.C244T	p.R82C	AGCCTCCGCTTGC	.	PASS	Atlas-SNP
CCPG1	9236	hgsc.bcm.edu	37	15	55664110	55664110	+	Missense_Mutation	SNP	G	G	C	rs117236526	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	68	127	0	0.417178	0	G|0.947;C|0.053	0.053	strong	.	CCPG1	74	.	NM_020739	exon6	c.C587G	p.A196G	TGTTCAGCAACTA	.	PASS	Atlas-SNP
TYW3	127253	hgsc.bcm.edu	37	1	75214441	75214441	+	Missense_Mutation	SNP	A	A	G	rs1133891	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	236	109	212	0	0.461864	0	A|0.763;G|0.237	0.237	strong	.	TYW3	36	.	NM_138467	exon4	c.A361G	p.M121V	CATTCCATGGCAA	.	PASS	Atlas-SNP
OR2AE1	81392	hgsc.bcm.edu	37	7	99474438	99474438	+	Silent	SNP	A	A	G	rs139077767	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	49	100	0	0.457944	0	A|0.994;G|0.006	0.006	strong	.	OR2AE1	32	.	NM_001005276	exon1	c.T219C	p.H73H	GGAGACATGCATC	.	PASS	Atlas-SNP
MT1E	4493	hgsc.bcm.edu	37	16	56660841	56660841	+	Silent	SNP	C	C	T	rs72818418	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	32	56	0	0.542373	0	C|0.877;T|0.123	0.123	strong	.	MT1E	7	.	NM_175617	exon3	c.C144T	p.C48C	GGGCTGCGTCTGC	.	PASS	Atlas-SNP
ARMC10	83787	hgsc.bcm.edu	37	7	102738862	102738862	+	Silent	SNP	T	T	C	rs76777924		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	587	198	386	0	0.337308	0	.	.	weak	.	ARMC10	25	.	NM_031905	exon7	c.T894C	p.A298A	TTTAGCTGTGCAG	.	PASS	Atlas-SNP
SOX21	11166	hgsc.bcm.edu	37	13	95364046	95364046	+	Silent	SNP	C	C	G	rs1060474	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	43	81	0	0.457447	0	C|0.605;G|0.395	0.395	strong	.	SOX21	21	.	NM_007084	exon1	c.G258C	p.L86L	CTTGAGCAGCGTC	.	PASS	Atlas-SNP
POLR1E	64425	hgsc.bcm.edu	37	9	37498215	37498215	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	46	110	0	0.474227	0	.	.	none	.	POLR1E	28	.	NM_022490	exon9	c.C880T	p.R294W	GTTAAGCGGAAAA	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6634817	6634817	+	Silent	SNP	C	C	T	rs71579347	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	51	116	0	0.586207	0	C|0.999;T|0.001	0.001	strong	.	NCAPD2	99	.	NM_014865	exon18	c.C2283T	p.T761T	GGCCACCGAGAAG	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	649505	649505	+	Missense_Mutation	SNP	T	T	A	rs4968104	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	36	65	0	0.571429	0	T|0.816;A|0.184	0.184	strong	GEMIN4_ENST00000319004,NS,carcinoma,0,4	GEMIN4	116	4	NM_015721	exon2	c.A1778T	p.E593V	CCCTGCTCTTCCA	.	PASS	Atlas-SNP
ANXA10	11199	hgsc.bcm.edu	37	4	169083757	169083757	+	Silent	SNP	C	C	T	rs114905136	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	112	230	0	0.468619	0	C|0.990;T|0.010	0.010	strong	.	ANXA10	44	.	NM_007193	exon4	c.C274T	p.L92L	CCACCACTGTATG	.	PASS	Atlas-SNP
SH2D4A	63898	hgsc.bcm.edu	37	8	19192332	19192332	+	Silent	SNP	G	G	T	rs56005620	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	26	81	0	0.38806	0	G|0.718;T|0.282	0.282	strong	SH2D4A,NS,carcinoma,+1,3	SH2D4A	49	3	NM_022071	exon4	c.G477T	p.S159S	AGGATCGAGGCCA	.	PASS	Atlas-SNP
PRKCZ	5590	hgsc.bcm.edu	37	1	2105427	2105427	+	Silent	SNP	C	C	T	rs142352833	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	89	134	0	0.908163	0	C|0.999;T|0.001	0.001	strong	.	PRKCZ	84	.	NM_002744	exon14	c.C1377T	p.D459D	CCCGGACATGAAC	.	PASS	Atlas-SNP
KIAA2026	158358	hgsc.bcm.edu	37	9	6007500	6007500	+	Silent	SNP	G	G	A	rs1061767	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	30	54	0	0.461538	0	G|0.786;A|0.214	0.214	strong	.	KIAA2026	231	.	NM_001017969	exon1	c.C288T	p.G96G	GGTGAGGCCCCGG	.	PASS	Atlas-SNP
GRID2	2895	hgsc.bcm.edu	37	4	93511396	93511396	+	Missense_Mutation	SNP	C	C	T	rs34144324	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	60	146	0	0.582524	0	C|0.961;T|0.039	0.039	strong	GRID2,NS,carcinoma,0,1	GRID2	233	1	NM_001510	exon2	c.C203T	p.T68M	CAGTGACGTTTGT	.	PASS	Atlas-SNP
OR4K2	390431	hgsc.bcm.edu	37	14	20345346	20345346	+	Missense_Mutation	SNP	A	A	T	rs12883767	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	12	13	0	0.631579	0	A|0.666;T|0.334	0.334	strong	.	OR4K2	97	.	NM_001005501	exon1	c.A920T	p.N307I	TTCTAAATTTTAA	.	PASS	Atlas-SNP
OR6C68	403284	hgsc.bcm.edu	37	12	55886489	55886489	+	Missense_Mutation	SNP	T	T	A	rs7304753	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	67	134	0	0.489051	0	T|0.768;A|0.232	0.232	strong	.	OR6C68	36	.	NM_001005519	exon1	c.T328A	p.F110I	ACTGAATTTTTTC	.	PASS	Atlas-SNP
SLC2A9	56606	hgsc.bcm.edu	37	4	9922167	9922167	+	Missense_Mutation	SNP	C	C	T	rs16890979	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	87	167	0	0.56129	0	C|0.737;T|0.263	0.263	strong	.	SLC2A9	158	.	NM_020041	exon7	c.G844A	p.V282I	GGGAAACGTCTGC	.	PASS	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	37	1	111957311	111957311	+	Missense_Mutation	SNP	G	G	C	rs10067	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	71	164	1	0.518248	0.00609756	G|0.785;C|0.214	0.214	strong	OVGP1_ENST00000369728,NS,carcinoma,-1,3	OVGP1	177	3	NM_002557	exon11	c.C1812G	p.H604Q	CCTGGGGTGAGTG	.	scavenged	Atlas-SNP
SDC4	6385	hgsc.bcm.edu	37	20	43976991	43976991	+	Missense_Mutation	SNP	A	A	G	rs2228384	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	20	30	0	0.444444	0	A|0.686;G|0.314	0.314	strong	SDC4,NS,carcinoma,0,1	SDC4	16	1	NM_002999	exon1	c.T34C	p.F12L	CGAAGAACAGCAG	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231222655	231222655	+	Silent	SNP	G	G	T	rs10498250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	47	108	0	0.439252	0	G|0.883;T|0.117	0.117	strong	SP140L_ENST00000415673,NS,carcinoma,+2,2	SP140L	68	2	NM_138402	exon3	c.G243T	p.R81R	CGATCGGGAACTC	.	PASS	Atlas-SNP
ZNF705G	100131980	hgsc.bcm.edu	37	8	7215694	7215694	+	Missense_Mutation	SNP	A	A	G	rs9693671	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	282	126	174	0	0.446809	0	A|0.500;G|0.500	0.500	strong	.	ZNF705G	24	.	NM_001164457	exon5	c.T707C	p.V236A	ATAAAGACTTTCC	.	PASS	Atlas-SNP
SACM1L	22908	hgsc.bcm.edu	37	3	45779136	45779136	+	Missense_Mutation	SNP	A	A	T	rs1468542	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	59	107	0	0.561905	0	A|0.405;T|0.595	0.595	strong	SACM1L,NS,carcinoma,0,1	SACM1L	38	1	NM_014016	exon15	c.A1301T	p.Y434F	AGATTTACAAAAA	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240981668	240981668	+	Silent	SNP	C	C	A	rs199598022	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	6	5	0	0.857143	0	C|0.678;A|0.322	0.322	strong	PRR21,caecum,carcinoma,0,2	PRR21	53	2	NM_001080835	exon1	c.G732T	p.T244T	AAGGGCCGTGGGT	.	scavenged	Atlas-SNP
SIRPD	128646	hgsc.bcm.edu	37	20	1538249	1538249	+	Silent	SNP	C	C	T	rs2250055	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	80	65	0	1	0	C|0.856;T|0.144	0.144	strong	.	SIRPD	34	.	NM_178460	exon1	c.G51A	p.L17L	CAGATACAGCAGT	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170092395	170092395	+	Silent	SNP	A	A	G	rs2229267	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	36	58	0	0.455696	0	T|0.095;G|0.314	0.314	strong	.	LRP2	751	.	NM_004525	exon29	c.T4875C	p.C1625C	ATAATCACAAAAG	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890026	7890026	+	Missense_Mutation	SNP	A	A	G	rs199947375	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	15	134	4	0.174419	0.0298507	.	.	weak	PER3,NS,carcinoma,0,4	PER3	95	4	NM_016831	exon18	c.A2992G	p.K998E	CCCATGAAGAATC	.	scavenged	Atlas-SNP
TMEM45B	120224	hgsc.bcm.edu	37	11	129722553	129722553	+	Missense_Mutation	SNP	C	C	T	rs558813	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	84	194	1	0.459016	0.00515464	C|0.754;T|0.246	0.246	strong	TMEM45B,NS,carcinoma,0,1	TMEM45B	25	1	NM_138788	exon2	c.C176T	p.T59I	CCGTCACTGGTAA	.	scavenged	Atlas-SNP
UBE4A	9354	hgsc.bcm.edu	37	11	118242324	118242324	+	Silent	SNP	A	A	G	rs145949976	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	48	79	0	0.6	0	A|0.999;G|0.001	0.001	strong	.	UBE4A	97	.	NM_004788	exon5	c.A504G	p.A168A	AGATGCAGGAGAG	.	PASS	Atlas-SNP
KLRG1	10219	hgsc.bcm.edu	37	12	9142297	9142297	+	Silent	SNP	T	T	C	rs1805723	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	72	68	0	1	0	T|0.639;C|0.361	0.361	strong	.	KLRG1	16	.	NM_005810	exon1	c.T66C	p.Y22Y	TGACTATGGACCA	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17264920	17264920	+	Missense_Mutation	SNP	C	C	T	rs4463721	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	498	227	249	0	0.455823	0	C|0.713;T|0.287	0.287	strong	CROCC,NS,carcinoma,0,3	CROCC	185	3	NM_014675	exon11	c.C1316T	p.A439V	AGCAGGCGGCCCT	.	PASS	Atlas-SNP
AKNAD1	254268	hgsc.bcm.edu	37	1	109369915	109369915	+	Missense_Mutation	SNP	G	G	T	rs7551421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	46	142	0	0.464646	0	G|0.440;N|0.001	.	strong	AKNAD1,NS,carcinoma,-2,2	AKNAD1	83	2	NM_152763	exon11	c.C1848A	p.N616K	CTCCACGTTTTGC	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420162	58420162	+	Missense_Mutation	SNP	T	T	C	rs61735221	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	135	246	0	0.992647	0	T|0.053;C|0.947	0.947	strong	.	ZNF417	44	.	NM_152475	exon3	c.A1484G	p.N495S	CATTCATTGCATT	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52556890	52556890	+	Missense_Mutation	SNP	A	A	G	rs4434138	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	84	216	1	0.466667	0.00462963	A|0.608;G|0.392	0.392	strong	.	STAB1	178	.	NM_015136	exon62	c.A6844G	p.I2282V	GTGGGCATAGTCA	.	PASS	Atlas-SNP
ADAP1	11033	hgsc.bcm.edu	37	7	940181	940181	+	Missense_Mutation	SNP	C	C	T	rs10256887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	155	162	1	0.974843	0.00617284	C|0.114;T|0.886	0.886	strong	.	ADAP1	23	.	NM_006869	exon7	c.G721A	p.G241S	CGTCGCCGGCCCC	.	PASS	Atlas-SNP
ANKRD2	26287	hgsc.bcm.edu	37	10	99332488	99332488	+	Silent	SNP	A	A	C	rs12221474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	92	189	0	0.476684	0	A|0.721;C|0.279	0.279	strong	.	ANKRD2	27	.	NM_001129981	exon1	c.A24C	p.A8A	CTGGGCAGGGGTG	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50339962	50339962	+	Missense_Mutation	SNP	A	A	T	rs75297145	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	16	44	0	0.410256	0	A|0.908;T|0.092	0.092	strong	.	FAM170B	20	.	NM_001164484	exon2	c.T548A	p.L183Q	CACTCCAGCAGGT	.	PASS	Atlas-SNP
HEATR5A	25938	hgsc.bcm.edu	37	14	31856407	31856407	+	Missense_Mutation	SNP	C	C	T	rs73259359	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	91	156	0	0.511236	0	C|0.977;T|0.023	0.023	strong	.	HEATR5A	181	.	NM_015473	exon8	c.G1108A	p.G370S	GACCACCTATAGT	.	PASS	Atlas-SNP
AVPI1	60370	hgsc.bcm.edu	37	10	99439541	99439541	+	Missense_Mutation	SNP	G	G	C	rs2275047	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	91	163	0	0.522988	0	G|0.524;C|0.476	0.476	strong	AVPI1,NS,carcinoma,0,2	AVPI1	16	2	NM_021732	exon2	c.C122G	p.A41G	AACAGGGCTTGGA	.	PASS	Atlas-SNP
LMTK3	114783	hgsc.bcm.edu	37	19	49001600	49001600	+	Missense_Mutation	SNP	A	A	G	rs61745738	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	41	72	0	0.577465	0	A|0.922;G|0.078	0.078	strong	.	LMTK3	125	.	NM_001080434	exon12	c.T2813C	p.V938A	CCCAGGACTGTCG	.	PASS	Atlas-SNP
TRPC1	7220	hgsc.bcm.edu	37	3	142523349	142523349	+	Silent	SNP	G	G	A	rs3821647	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	99	198	0	0.510309	0	G|0.806;A|0.194	0.194	strong	TRPC1,NS,carcinoma,0,1	TRPC1	82	1	NM_001251845	exon12	c.G2031A	p.T677T	ATGTACGTTACCT	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433444	169433444	+	Silent	SNP	C	C	T	rs72695199	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	51	91	0	0.476636	0	C|0.907;T|0.093	0.093	strong	.	PALLD	179	.	NM_001166108	exon2	c.C789T	p.S263S	CCACAGCGCCCTC	.	PASS	Atlas-SNP
SLC26A1	10861	hgsc.bcm.edu	37	4	983809	983809	+	Silent	SNP	C	C	T	rs4690221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	27	59	0	0.465517	0	C|0.606;T|0.394	0.394	strong	SLC26A1,NS,carcinoma,0,2	SLC26A1	44	2	NM_022042	exon3	c.G918A	p.S306S	GAAGTGCGACACG	.	PASS	Atlas-SNP
USP34	9736	hgsc.bcm.edu	37	2	61415492	61415492	+	Silent	SNP	A	A	G	rs14170	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	44	102	0	0.55	0	A|0.525;G|0.475	0.475	strong	.	USP34	334	.	NM_014709	exon80	c.T10386C	p.A3462A	TTCCTCAGCTAGG	.	PASS	Atlas-SNP
SKIDA1	387640	hgsc.bcm.edu	37	10	21804487	21804487	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	2	142	0	0.0162602	0	.	.	none	C10orf140_ENST00000449193,rectum,carcinoma,-2,2	.	.	2	NM_207371	exon4	c.G2265A	p.Q755Q	AAGGCCCTGACTT	.	scavenged	Atlas-SNP
MRPS27	23107	hgsc.bcm.edu	37	5	71524163	71524163	+	Silent	SNP	A	A	T	rs10942927	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	25	71	0	0.342466	0	A|0.768;T|0.232	0.232	strong	.	MRPS27	23	.	NM_015084	exon8	c.T624A	p.L208L	AAGCAAAAGGGAT	.	PASS	Atlas-SNP
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377242	49377242	+	Missense_Mutation	SNP	G	G	C	rs557806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	35	101	0	0.486111	0	G|0.699;C|0.301	0.301	strong	.	PPP1R15A	48	.	NM_014330	exon2	c.G752C	p.R251P	CCCCCCGATCTTC	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058090	79058090	+	Missense_Mutation	SNP	A	A	G	rs2929158	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	13	78	3	0.147727	0.0384615	A|0.897;G|0.103	0.103	strong	ADAMTS7,rectum,carcinoma,0,1	ADAMTS7	142	1	NM_014272	exon19	c.T4163C	p.V1388A	TCAGGGACTCTGT	.	scavenged	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140580931	140580931	+	Missense_Mutation	SNP	C	C	G	rs799834	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	274	273	209	0	0.99635	0	C|0.497;G|0.503	0.503	strong	PCDHB11,NS,carcinoma,+2,1	PCDHB11	162	1	NM_018931	exon1	c.C1584G	p.D528E	TTTCGACTTCCGC	.	PASS	Atlas-SNP
FOLH1	2346	hgsc.bcm.edu	37	11	49204779	49204779	+	Missense_Mutation	SNP	C	C	T	rs116795343	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	6	156	0	0.0335196	0	C|0.974;T|0.026	0.026	strong	FOLH1,NS,carcinoma,-1,2	FOLH1	141	2	NM_004476	exon7	c.G842A	p.R281H	ATTCCACGCCTAT	.	scavenged	Atlas-SNP
PTGIS	5740	hgsc.bcm.edu	37	20	48129706	48129706	+	Silent	SNP	G	G	T	rs5629	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	52	39	0	0.981132	0	G|0.782;T|0.218	0.218	strong	PTGIS,colon,carcinoma,+1,2	PTGIS	60	2	NM_000961	exon8	c.C1117A	p.R373R	ATTCTCGCCCGTC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3238733	3238733	+	Missense_Mutation	SNP	G	G	A	rs1974522	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	80	90	0	0.987654	0	0|0.015;A|0.441;C|0.000;G|0.544;N|0.000	0.441	strong	.	MXRA5	815	.	NM_015419	exon5	c.C4993T	p.P1665S	ATCTTGGAGTTGT	.	PASS	Atlas-SNP
NLRP14	338323	hgsc.bcm.edu	37	11	7064560	7064560	+	Missense_Mutation	SNP	A	A	T	rs200574634	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	73	171	0	0.536765	0	A|1.000;T|0.000	0.000	strong	.	NLRP14	187	.	NM_176822	exon4	c.A1303T	p.I435L	AAAGGAATATGGA	.	PASS	Atlas-SNP
HIST1H4F	8361	hgsc.bcm.edu	37	6	26240752	26240752	+	Silent	SNP	C	C	T	rs16891477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	44	97	0	0.483516	0	C|0.952;T|0.048	0.048	strong	.	HIST1H4F	9	.	NM_003540	exon1	c.C99T	p.P33P	GAAGCCCGCCATC	.	PASS	Atlas-SNP
PON3	5446	hgsc.bcm.edu	37	7	95001555	95001555	+	Silent	SNP	C	C	T	rs1053275	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	199	225	0	0.995	0	C|0.417;T|0.583	0.583	strong	.	PON3	59	.	NM_000940	exon4	c.G297A	p.A99A	TTCTAGCGCTTGT	.	PASS	Atlas-SNP
SLC45A3	85414	hgsc.bcm.edu	37	1	205633713	205633713	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	3	149	0	0.0159574	0	.	.	none	SLC45A3,right_lower_lobe,carcinoma,-1,1	SLC45A3	54	1	NM_033102	exon2	c.A72G	p.L24L	AAAGGTTAGCAGG	.	scavenged	Atlas-SNP
TBL2	26608	hgsc.bcm.edu	37	7	72985148	72985148	+	Missense_Mutation	SNP	C	C	T	rs35607697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	42	60	0	0.575342	0	C|0.966;T|0.034	0.034	strong	.	TBL2	47	.	NM_012453	exon7	c.G1033A	p.V345I	CCAAGACCTGGGC	.	PASS	Atlas-SNP
KRTAP9-4	85280	hgsc.bcm.edu	37	17	39406409	39406409	+	Missense_Mutation	SNP	C	C	A	rs2191379	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	344	172	320	0	0.5	0	C|0.336;A|0.664	0.664	strong	.	KRTAP9-4	30	.	NM_033191	exon1	c.C437A	p.S146Y	GTGTGTCCAGCTG	.	PASS	Atlas-SNP
CEP135	9662	hgsc.bcm.edu	37	4	56883987	56883987	+	Silent	SNP	C	C	G	rs35143702	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	51	118	0	0.398438	0	C|0.978;G|0.022	0.022	strong	CEP135,NS,carcinoma,0,1	CEP135	115	1	NM_025009	exon22	c.C2976G	p.T992T	TATGACCCAGCAA	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194081392	194081392	+	Silent	SNP	G	G	A	rs923936	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	65	150	0	0.53719	0	G|0.832;A|0.168	0.168	strong	.	LRRC15	137	.	NM_001135057	exon3	c.C399T	p.L133L	AGACTCGAGGCTG	.	PASS	Atlas-SNP
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32833766	32833766	+	Missense_Mutation	SNP	A	A	C	rs61731888	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	42	79	0	0.525	0	A|0.975;C|0.025	0.025	strong	.	ZSCAN30	34	.	NM_001166012	exon5	c.T1133G	p.I378S	GTGTGGATTCTCC	.	PASS	Atlas-SNP
LEPREL1	55214	hgsc.bcm.edu	37	3	189713205	189713205	+	Silent	SNP	T	T	C	rs9821880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	29	61	0	0.483333	0	C|0.302;N|0.001	0.302	strong	.	LEPREL1	95	.	NM_018192	exon2	c.A507G	p.E169E	AGCTGCTTCCACT	.	PASS	Atlas-SNP
EHMT2	10919	hgsc.bcm.edu	37	6	31864547	31864547	+	Missense_Mutation	SNP	G	G	T	rs7887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	43	92	0	0.380531	0	G|0.694;T|0.306	0.306	strong	.	EHMT2	45	.	NM_025256	exon3	c.C164A	p.T55N	TCGGGGGTGGCCT	.	PASS	Atlas-SNP
C8B	732	hgsc.bcm.edu	37	1	57422511	57422511	+	Missense_Mutation	SNP	C	C	T	rs12067507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	32	94	0	0.367816	0	C|0.944;T|0.056	0.056	strong	C8B,caecum,carcinoma,0,1	C8B	107	1	NM_000066	exon3	c.G322A	p.E108K	AGTCTTCGACTTC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45122324	45122324	+	Missense_Mutation	SNP	C	C	A	rs3735493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	40	79	0	0.506329	0	C|0.891;A|0.109	0.109	strong	.	NACAD	44	.	NM_001146334	exon2	c.G3455T	p.C1152F	TCTGGGCAGGAGT	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58757668	58757668	+	Silent	SNP	A	A	C	rs14221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	171	172	0	0.994186	0	A|0.293;C|0.707;G|0.000	0.707	strong	.	GOT2	42	.	NM_002080	exon2	c.T228G	p.V76V	AGGCAGAACGTAA	.	PASS	Atlas-SNP
OXCT2	64064	hgsc.bcm.edu	37	1	40236145	40236145	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	2	98	0	0.0175439	0	.	.	none	OXCT2,colon,carcinoma,-2,1	OXCT2	12	1	NM_022120	exon1	c.T783C	p.V261V	GTTAGGAACGTGG	.	scavenged	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214814571	214814571	+	Silent	SNP	C	C	T	rs3795521	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	33	114	0	0.388235	0	C|0.681;T|0.319	0.319	strong	CENPF,NS,carcinoma,0,2	CENPF	321	2	NM_016343	exon12	c.C2890T	p.L964L	ATTTCTCTAAATA	.	PASS	Atlas-SNP
CXorf22	170063	hgsc.bcm.edu	37	X	35969297	35969297	+	Missense_Mutation	SNP	G	G	A	rs2336029	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	99	154	0	0.99	0	0|0.015;A|0.136	0.136	strong	.	CXorf22	272	.	NM_152632	exon5	c.G706A	p.V236M	GCTCATGTGGTTG	.	PASS	Atlas-SNP
HKDC1	80201	hgsc.bcm.edu	37	10	71026510	71026510	+	Missense_Mutation	SNP	C	C	A	rs906219	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	52	67	0	0.58427	0	C|0.688;A|0.312	0.312	strong	.	HKDC1	98	.	NM_025130	exon18	c.C2751A	p.N917K	GGAGAACTAGGAA	.	PASS	Atlas-SNP
GTPBP10	85865	hgsc.bcm.edu	37	7	89984409	89984409	+	Missense_Mutation	SNP	A	A	G	rs42664	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	190	239	1	0.994764	0.0041841	A|0.499;G|0.501	0.501	strong	.	GTPBP10	31	.	NM_033107	exon4	c.A329G	p.N110S	AACTCAATAAAGA	.	PASS	Atlas-SNP
MORN4	118812	hgsc.bcm.edu	37	10	99376092	99376092	+	Silent	SNP	T	T	C	rs3814555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	21	67	2	0.428571	0.0298507	T|0.703;C|0.297	0.297	strong	MORN4_ENST00000307450,NS,carcinoma,0,4	MORN4	24	4	NM_001098831	exon5	c.A369G	p.R123R	CTCACGTCGCAGC	.	scavenged	Atlas-SNP
MAGEB3	4114	hgsc.bcm.edu	37	X	30254361	30254361	+	Missense_Mutation	SNP	G	G	A	rs2071308	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	58	73	0	1	0	G|0.569;A|0.431	0.431	strong	.	MAGEB3	54	.	NM_002365	exon5	c.G320A	p.R107H	AGTCTCGCACAGA	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60909316	60909316	+	Missense_Mutation	SNP	C	C	T	rs6062223	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	88	112	0	0.488889	0	C|0.902;T|0.098	0.098	strong	.	LAMA5	268	.	NM_005560	exon22	c.G2665A	p.V889M	AGCGCACGGCGTG	.	PASS	Atlas-SNP
RPP38	10557	hgsc.bcm.edu	37	10	15145855	15145855	+	Missense_Mutation	SNP	C	C	G	rs15772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	20	51	0	0.37037	0	C|0.612;G|0.388	0.388	strong	.	RPP38	26	.	NM_001265601	exon2	c.C542G	p.A181G	CCTTGGCGTTCAA	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10474042	10474042	+	Missense_Mutation	SNP	T	T	G	rs4388421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	33	79	0	0.417722	0	T|0.771;G|0.229	0.229	strong	RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	NM_178857	exon3	c.A665C	p.H222P	GCCTCATGCCCGG	.	PASS	Atlas-SNP
LILRB4	11006	hgsc.bcm.edu	37	19	55179145	55179145	+	Missense_Mutation	SNP	A	A	T	rs61738946	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	347	12	240	0	0.0345821	0	A|0.990;T|0.010	0.010	strong	LILRB4,NS,carcinoma,+2,1	LILRB4	86	1	NM_006847	exon11	c.A1101T	p.R367S	CTCCAGACCTAGG	.	scavenged	Atlas-SNP
DCAF12	25853	hgsc.bcm.edu	37	9	34107505	34107505	+	Missense_Mutation	SNP	C	C	T	rs11557154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	70	117	0	0.542636	0	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	.	PASS	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50752150	50752150	+	Missense_Mutation	SNP	C	C	T	rs68178377	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	42	32	0	0.583333	0	C|0.747;T|0.253	0.253	strong	.	.	.	.	NM_001001794	exon15	c.G1207A	p.V403M	TCTGCACGCCCTG	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117403235	117403235	+	Missense_Mutation	SNP	G	G	T	rs3741280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	27	93	0	0.421875	0	G|0.640;T|0.360	0.360	strong	DSCAML1,NS,carcinoma,0,1	DSCAML1	286	1	NM_020693	exon4	c.C694A	p.H232N	ACCTGTGTTCTGG	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56202231	56202231	+	Missense_Mutation	SNP	T	T	C	rs17065127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	120	194	0	0.560748	0	T|0.948;C|0.052	0.052	strong	.	ALPK2	487	.	NM_052947	exon5	c.A5188G	p.K1730E	AAATTTTCTTCTT	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536380	1536380	+	Missense_Mutation	SNP	G	G	T	rs2667672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	84	0	0.435644	0	G|0.655;T|0.345	0.345	strong	.	PTX4	46	.	NM_001013658	exon3	c.C982A	p.L328M	GCAGCAGGGAGTC	.	PASS	Atlas-SNP
HDAC7	51564	hgsc.bcm.edu	37	12	48177906	48177906	+	Silent	SNP	C	C	T	rs7306788	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	57	118	0	0.537736	0	C|0.879;G|0.000;T|0.121	0.121	strong	.	HDAC7	71	.	NM_015401	exon25	c.G2886A	p.V962V	TGCGGTCACTGCC	.	PASS	Atlas-SNP
NARFL	64428	hgsc.bcm.edu	37	16	781633	781633	+	Silent	SNP	G	G	A	rs3829492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	16	31	0	0.421053	0	G|0.714;A|0.286	0.286	strong	NARFL,NS,adenoma,0,1	NARFL	31	1	NM_022493	exon9	c.C966T	p.H322H	GAACACGTGCTCC	.	PASS	Atlas-SNP
MAP4K1	11184	hgsc.bcm.edu	37	19	39092142	39092142	+	Silent	SNP	C	C	T	rs35423612	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	26	33	0	0.472727	0	C|0.990;T|0.010	0.010	strong	.	MAP4K1	165	.	NM_007181	exon20	c.G1470A	p.L490L	ATTGAACAACTTT	.	PASS	Atlas-SNP
CENPE	1062	hgsc.bcm.edu	37	4	104062223	104062223	+	Silent	SNP	C	C	T	rs1381658	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	30	81	0	0.394737	0	C|0.861;T|0.139	0.139	strong	.	CENPE	253	.	NM_001813	exon36	c.G5502A	p.T1834T	TTTTAACGTAATA	.	PASS	Atlas-SNP
TLE3	7090	hgsc.bcm.edu	37	15	70347482	70347482	+	Missense_Mutation	SNP	G	G	A	rs200508723	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	56	94	0	0.513761	0	G|0.999;A|0.001	0.001	weak	.	TLE3	104	.	NM_005078	exon15	c.C1493T	p.T498M	TGCCTCGTGGGGT	.	PASS	Atlas-SNP
EPB41	2035	hgsc.bcm.edu	37	1	29379679	29379679	+	Missense_Mutation	SNP	G	G	A	rs138888144	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	228	260	1	0.942149	0.00384615	G|0.995;A|0.005	0.005	strong	EPB41_ENST00000343067,NS,carcinoma,+1,2	EPB41	118	2	NM_001166006	exon12	c.G1700A	p.G567D	CTCAGGGTCAGGT	.	PASS	Atlas-SNP
LANCL3	347404	hgsc.bcm.edu	37	X	37518806	37518806	+	Silent	SNP	C	C	T	rs12009345	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	46	62	0	1	0	C|0.681;0|0.003	.	strong	.	LANCL3	42	.	NM_001170331	exon3	c.C789T	p.S263S	GCAGAGCGTGGAC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134738232	134738232	+	Silent	SNP	A	A	G	rs4075501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	23	63	0	0.365079	0	A|0.499;G|0.501	0.501	strong	.	TTC40	100	.	NM_001200049	exon11	c.T1224C	p.A408A	AACGCCAGCCAGG	.	PASS	Atlas-SNP
AP1S3	130340	hgsc.bcm.edu	37	2	224642579	224642579	+	Missense_Mutation	SNP	A	A	C	rs116107386	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	31	67	0	0.424658	0	A|0.993;C|0.007	0.007	strong	.	AP1S3	10	.	NM_001039569	exon2	c.T11G	p.F4C	AATATGAAATGTA	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51361757	51361757	+	Missense_Mutation	SNP	T	T	C	rs17632542	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	51	69	0	0.62963	0	T|0.952;C|0.048	0.048	strong	.	KLK3	76	.	NM_001030047	exon4	c.T536C	p.I179T	ATGTTATTTCCAA	.	PASS	Atlas-SNP
CSTF2T	23283	hgsc.bcm.edu	37	10	53458998	53458998	+	Silent	SNP	A	A	G	rs2292828	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	49	98	0	0.453704	0	A|0.710;C|0.003;G|0.282;T|0.006	0.282	strong	CSTF2T,NS,carcinoma,0,1	CSTF2T	64	1	NM_015235	exon1	c.T312C	p.L104L	AGGCCCAAGGCTC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47831618	47831618	+	Silent	SNP	C	C	T	rs16979162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	26	50	0	0.40625	0	C|0.812;T|0.188	0.188	strong	.	PCNT	283	.	NM_006031	exon28	c.C5631T	p.I1877I	AGAAATCGACGCT	.	PASS	Atlas-SNP
SSX2IP	117178	hgsc.bcm.edu	37	1	85113229	85113229	+	Missense_Mutation	SNP	A	A	G	rs1057746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	187	208	0	1	0	A|0.476;G|0.524	0.524	strong	.	SSX2IP	53	.	NM_001166417	exon15	c.T1732C	p.C578R	TTGTACATTCTCC	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79634813	79634813	+	Silent	SNP	T	T	C	rs11546632	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	15	31	0	0.576923	0	T|0.868;C|0.132	0.132	strong	.	CCDC137	27	.	NM_199287	exon2	c.T189C	p.I63I	GGAGATTCCTTTC	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23811795	23811795	+	Missense_Mutation	SNP	T	T	G	rs10263079	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	115	113	0	0.991379	0	T|0.843;G|0.157	0.157	strong	.	STK31	175	.	NM_031414	exon15	c.T1863G	p.N621K	TTTAAATAAGAGT	.	PASS	Atlas-SNP
IRS2	8660	hgsc.bcm.edu	37	13	110435914	110435914	+	Silent	SNP	G	G	A	rs12853546	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	28	8	0	1	0	G|0.788;A|0.212	0.212	strong	IRS2,NS,carcinoma,0,1	IRS2	44	1	NM_003749	exon1	c.C2487T	p.P829P	CCCCACGGGGGAG	.	PASS	Atlas-SNP
FUT10	84750	hgsc.bcm.edu	37	8	33318913	33318913	+	Missense_Mutation	SNP	C	C	T	rs77009471	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	42	56	0	0.724138	0	C|0.980;T|0.020	0.020	strong	.	FUT10	62	.	NM_032664	exon2	c.G58A	p.V20I	GAAAGACGGTGGC	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95826485	95826485	+	Missense_Mutation	SNP	T	T	C	rs61749253	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	286	171	307	0	0.597902	0	T|0.990;C|0.010	0.010	strong	.	MAML2	94	.	NM_032427	exon2	c.A710G	p.Q237R	GGTGCTTGGCTCA	.	PASS	Atlas-SNP
CEP68	23177	hgsc.bcm.edu	37	2	65299330	65299330	+	Missense_Mutation	SNP	T	T	A	rs141499084	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	39	97	0	0.506494	0	T|0.987;A|0.013	0.013	strong	.	CEP68	69	.	NM_015147	exon3	c.T1100A	p.F367Y	TGCCATTTTCTGG	.	PASS	Atlas-SNP
KNG1	3827	hgsc.bcm.edu	37	3	186435370	186435370	+	Silent	SNP	G	G	A	rs1050274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	32	86	0	0.484848	0	G|0.637;A|0.363	0.363	strong	KNG1_ENST00000265023,NS,adenoma,0,2	KNG1	129	2	NM_000893	exon1	c.G39A	p.L13L	CAGGCTGCTACTA	.	PASS	Atlas-SNP
SPRR1A	6698	hgsc.bcm.edu	37	1	152957832	152957832	+	Missense_Mutation	SNP	C	C	A	rs1611762	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	51	121	0	0.41129	0	C|0.457;A|0.543	0.543	strong	.	SPRR1A	17	.	NM_001199828	exon2	c.C126A	p.H42Q	CTGCCACCCCAAG	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017674	109017674	+	Missense_Mutation	SNP	A	A	G	rs201851784	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	35	178	2	0.238095	0.011236	A|0.896;G|0.104	0.104	strong	SELPLG_ENST00000550948,NS,carcinoma,0,7	SELPLG	138	7	NM_001206609	exon2	c.T458C	p.V153A	GTGGGCACTGGTT	.	scavenged	Atlas-SNP
CEP97	79598	hgsc.bcm.edu	37	3	101477214	101477214	+	Silent	SNP	C	C	A	rs368609945		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	21	54	0	0.323077	0	.	.	weak	.	CEP97	122	.	NM_024548	exon9	c.C1764A	p.I588I	CGAAATCCGGCTA	.	PASS	Atlas-SNP
EML1	2009	hgsc.bcm.edu	37	14	100331876	100331876	+	Silent	SNP	T	T	C	rs11160553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	57	89	0	0.522936	0	T|0.760;C|0.240	0.240	strong	.	EML1	97	.	NM_001008707	exon3	c.T276C	p.P92P	CCTGCCTTTAAGA	.	PASS	Atlas-SNP
CCDC38	120935	hgsc.bcm.edu	37	12	96260947	96260947	+	Silent	SNP	A	A	G	rs7960706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	62	167	0	0.389937	0	A|0.677;G|0.323	0.323	strong	.	CCDC38	45	.	NM_182496	exon16	c.T1599C	p.F533F	TGAATGAAAGACA	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149529970	149529970	+	Silent	SNP	G	G	T	rs55976638	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	48	112	0	0.551724	0	G|0.938;T|0.062	0.062	strong	.	.	.	.	NM_198455	exon109	c.G15384T	p.L5128L	GGTGCTGCCGGTC	.	PASS	Atlas-SNP
SPATA6	54558	hgsc.bcm.edu	37	1	48825355	48825355	+	Missense_Mutation	SNP	G	G	A	rs1338314	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	27	74	0	0.5	0	G|0.975;A|0.025	0.025	strong	.	SPATA6	45	.	NM_019073	exon10	c.C997T	p.R333W	AATGCCGGGGCTT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38120343	38120343	+	Missense_Mutation	SNP	A	A	G	rs71317067	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	444	14	411	11	0.0315315	0.026764	A|0.500;G|0.500	0.500	weak	TRIOBP_ENST00000344404,NS,carcinoma,0,5	TRIOBP	262	5	NM_001039141	exon7	c.A1780G	p.T594A	AGAGCTACACGAG	.	scavenged	Atlas-SNP
NOM1	64434	hgsc.bcm.edu	37	7	156761818	156761818	+	Missense_Mutation	SNP	G	G	A	rs2302445	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	80	103	0	1	0	G|0.508;A|0.492	0.492	strong	.	NOM1	73	.	NM_138400	exon10	c.G2336A	p.R779H	GAGTCCGTTTTTT	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17263290	17263290	+	Missense_Mutation	SNP	G	G	A	rs57442576	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	8	50	0	0.0551724	0	G|0.924;A|0.076	0.076	strong	.	CROCC	185	.	NM_014675	exon9	c.G1115A	p.R372Q	AGCTGCGGGACAA	.	PASS	Atlas-SNP
TRAPPC11	60684	hgsc.bcm.edu	37	4	184614874	184614874	+	Silent	SNP	C	C	T	rs4862234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	71	85	0	0.986111	0	C|0.756;T|0.244	0.244	strong	.	.	.	.	NM_021942	exon21	c.C2370T	p.T790T	GCTCACCGCTGGC	.	PASS	Atlas-SNP
SNX2	6643	hgsc.bcm.edu	37	5	122165317	122165317	+	Silent	SNP	C	C	T	rs13662	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	82	180	0	0.476744	0	C|0.964;T|0.036	0.036	strong	.	SNX2	42	.	NM_003100	exon15	c.C1534T	p.L512L	GCATTCCTACCTG	.	PASS	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346468	140346468	+	Silent	SNP	T	T	A	rs155364	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	27	33	0	0.482143	0	T|0.409;A|0.591	0.591	strong	PCDHAC2,NS,carcinoma,0,1	PCDHAC2	142	1	NM_031883	exon1	c.T117A	p.P39P	TGGCCCTGCGGCC	.	PASS	Atlas-SNP
PRPF18	8559	hgsc.bcm.edu	37	10	13653653	13653653	+	Silent	SNP	A	A	G	rs1135102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	60	42	0	1	0	A|0.659;G|0.341	0.341	strong	.	PRPF18	32	.	NM_003675	exon6	c.A549G	p.K183K	TCATAAAGACATG	.	PASS	Atlas-SNP
C6orf222	389384	hgsc.bcm.edu	37	6	36294864	36294864	+	Silent	SNP	A	A	G	rs41270098	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	40	92	0	0.384615	0	A|0.926;G|0.074	0.074	strong	.	C6orf222	72	.	NM_001010903	exon4	c.T735C	p.A245A	AATGATAGCATCC	.	PASS	Atlas-SNP
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	37	91	0	0.430233	0	C|0.772;T|0.228	0.228	strong	.	ZNF17	49	.	NM_006959	exon3	c.C693T	p.S231S	CAACTCCGACCTT	.	PASS	Atlas-SNP
TMEM132A	54972	hgsc.bcm.edu	37	11	60704213	60704213	+	Missense_Mutation	SNP	C	C	T	rs2469887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	73	53	0	1	0	C|0.570;T|0.430	0.430	strong	.	TMEM132A	135	.	NM_017870	exon11	c.C2909T	p.A970V	CATTTGCGCCAGC	.	PASS	Atlas-SNP
SP110	3431	hgsc.bcm.edu	37	2	231042276	231042276	+	Missense_Mutation	SNP	A	A	G	rs1135791	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	351	171	317	1	0.487179	0.00315457	A|0.640;G|0.360	0.360	strong	.	SP110	105	.	NM_001185015	exon15	c.T1586C	p.M529T	AGGGTCATTCCTT	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107360826	107360826	+	Missense_Mutation	SNP	A	A	G	rs1851725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	67	203	0	0.435065	0	A|0.634;G|0.366	0.366	strong	.	OR13C5	60	.	NM_001004482	exon1	c.T869C	p.M290T	TTCATCATGGGAG	.	PASS	Atlas-SNP
MRPS10	55173	hgsc.bcm.edu	37	6	42185564	42185564	+	Silent	SNP	A	A	C	rs9471809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	20	45	0	0.384615	0	A|0.679;C|0.321	0.321	strong	.	MRPS10	9	.	NM_018141	exon1	c.T24G	p.G8G	CACAGCACCGAAC	.	PASS	Atlas-SNP
ATL2	64225	hgsc.bcm.edu	37	2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	rs34873284	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	43	93	0	0.409524	0	T|0.967;C|0.033	0.033	strong	.	ATL2	49	.	NM_001135673	exon8	c.A815G	p.N272S	TGTTGATTTTGTT	.	PASS	Atlas-SNP
MAP4	4134	hgsc.bcm.edu	37	3	48040283	48040283	+	Missense_Mutation	SNP	C	C	T	rs11711953	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	84	145	0	0.509091	0	C|0.948;T|0.052	0.052	strong	.	MAP4	176	.	NM_001134364	exon2	c.G68A	p.R23Q	AAGTCCCGCTTTA	.	PASS	Atlas-SNP
BAG6	7917	hgsc.bcm.edu	37	6	31606977	31606977	+	Silent	SNP	C	C	T	rs34745996	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	34	67	0	0.485714	0	C|0.997;T|0.003	0.003	strong	.	BAG6	73	.	NM_004639	exon25	c.G3330A	p.L1110L	TTCCTGCAGTCGT	.	PASS	Atlas-SNP
TPCN2	219931	hgsc.bcm.edu	37	11	68840160	68840160	+	Missense_Mutation	SNP	A	A	G	rs3750965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	58	126	0	0.483333	0	A|0.718;G|0.282	0.282	strong	TPCN2,colon,carcinoma,0,1	TPCN2	63	1	NM_139075	exon12	c.A1127G	p.K376R	CCCACAAACAGGC	.	PASS	Atlas-SNP
ANKRD13C	81573	hgsc.bcm.edu	37	1	70820008	70820008	+	Silent	SNP	C	C	T	rs61782675	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	52	39	0	0.981132	0	C|0.928;T|0.072	0.072	strong	.	ANKRD13C	36	.	NM_030816	exon1	c.G84A	p.E28E	CGCTTCCTCATCC	.	PASS	Atlas-SNP
GPR78	27201	hgsc.bcm.edu	37	4	8589023	8589023	+	Missense_Mutation	SNP	G	G	A	rs9685931	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	122	189	0	0.552036	0	G|0.871;A|0.129	0.129	strong	GPR78,NS,carcinoma,0,3	GPR78	58	3	NM_080819	exon3	c.G1025A	p.R342H	CCCCGCGCCCAGC	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912750	45912750	+	Silent	SNP	G	G	A	rs118178942	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	16	25	0	0.470588	0	G|0.990;A|0.010	0.010	strong	.	CD3EAP	27	.	NM_012099	exon3	c.G1524A	p.Q508Q	GCAGCAGCCTGTG	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56105908	56105908	+	Silent	SNP	C	C	T	rs80214241	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	78	184	0	0.448276	0	C|0.991;T|0.009	0.009	strong	.	KTN1	147	.	NM_004986	exon13	c.C1791T	p.S597S	GACCTCCGCTTCA	.	PASS	Atlas-SNP
PLA2G4A	5321	hgsc.bcm.edu	37	1	186946869	186946869	+	Missense_Mutation	SNP	A	A	G	rs28395831	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	97	248	0	0.442922	0	A|0.992;G|0.008	0.008	strong	.	PLA2G4A	125	.	NM_024420	exon16	c.A1909G	p.I637V	CCAACCATCATCC	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783634	5783634	+	Silent	SNP	T	T	C	rs2446210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	54	88	0	0.477876	0	T|0.612;C|0.388	0.388	strong	.	PRR22	25	.	NM_001134316	exon3	c.A624G	p.P208P	GGCGTCTGGGGGC	.	PASS	Atlas-SNP
FOXK2	3607	hgsc.bcm.edu	37	17	80545021	80545021	+	Silent	SNP	G	G	A	rs139592674		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	69	126	0	0.552	0	G|1.000;A|0.000	0.000	weak	.	FOXK2	46	.	NM_004514	exon8	c.G1659A	p.P553P	CACCCCGGTCCAG	.	PASS	Atlas-SNP
CLASP2	23122	hgsc.bcm.edu	37	3	33728610	33728610	+	Missense_Mutation	SNP	A	A	G	rs61738888	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	61	169	0	0.438849	0	A|0.934;G|0.066	0.066	strong	.	CLASP2	138	.	NM_015097	exon5	c.T488C	p.L163P	ATGACTAGTGGCT	.	PASS	Atlas-SNP
NXPE4	54827	hgsc.bcm.edu	37	11	114441943	114441943	+	Missense_Mutation	SNP	G	G	A	rs10891705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	179	204	0	0.983516	0	G|0.639;A|0.361	0.361	strong	.	.	.	.	NM_001077639	exon6	c.C1352T	p.A451V	TTGAGGGCCCTTC	.	PASS	Atlas-SNP
MRGPRE	116534	hgsc.bcm.edu	37	11	3249829	3249829	+	Silent	SNP	G	G	A	rs11026040	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	41	46	0	0.561644	0	A|0.172;G|0.828	0.172	strong	.	MRGPRE	35	.	NM_001039165	exon2	c.C201T	p.C67C	ATCCGCGCAGGCC	.	PASS	Atlas-SNP
SLC1A5	6510	hgsc.bcm.edu	37	19	47278859	47278859	+	Missense_Mutation	SNP	C	C	G	rs3027961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	71	144	0	0.5	0	C|0.796;G|0.204	0.204	strong	.	SLC1A5	31	.	NM_005628	exon8	c.G1534C	p.V512L	TGGGGACTGGCAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072221	9072221	+	Silent	SNP	G	G	A	rs66498329	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	42	110	1	0.506024	0.00909091	G|0.787;A|0.213	0.213	strong	MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	NM_024690	exon3	c.C15225T	p.G5075G	CACTAGGCCAGAG	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911092	29911092	+	Missense_Mutation	SNP	G	G	T	rs1136702	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	43	137	0	0.425743	0	G|0.749;T|0.251	0.251	strong	.	HLA-A	89	.	NM_001242758	exon3	c.G391T	p.G131W	TCGGACGGGCGCT	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89430506	89430506	+	Silent	SNP	C	C	T	rs3743395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	71	114	0	0.47651	0	C|0.770;T|0.230	0.230	strong	.	HAPLN3	43	.	NM_178232	exon2	c.G24A	p.P8P	GAGCAACGGGACC	.	PASS	Atlas-SNP
PLOD1	5351	hgsc.bcm.edu	37	1	12024235	12024235	+	Silent	SNP	C	C	T	rs1130529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	59	40	0	0.983333	0	C|0.687;N|0.001	.	strong	.	PLOD1	75	.	NM_000302	exon12	c.C1206T	p.N402N	CAGGAACGTCATT	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26702508	26702508	+	Silent	SNP	G	G	A	rs72853741	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	57	109	0	0.548077	0	G|0.970;A|0.030	0.030	strong	.	OTOF	524	.	NM_194248	exon17	c.C1926T	p.N642N	AACTTCGTTCCCA	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116967405	116967405	+	Silent	SNP	G	G	T	rs13290696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	22	39	0	0.415094	0	G|0.932;T|0.068	0.068	strong	.	COL27A1	200	.	NM_032888	exon8	c.G2148T	p.P716P	TGGACCGGCAGGG	.	PASS	Atlas-SNP
LRPAP1	4043	hgsc.bcm.edu	37	4	3534042	3534042	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	60	65	0	0.461538	0	.	.	none	.	LRPAP1	29	.	NM_002337	exon1	c.G98T	p.G33V	TACTTGCCGCCGT	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388508	1388508	+	Missense_Mutation	SNP	T	T	C	rs55703801	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	20	152	3	0.108108	0.0197368	.	.	weak	CRIPAK,rectum,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.T209C	p.V70A	CACGTGTCCATGT	.	scavenged	Atlas-SNP
PTX3	5806	hgsc.bcm.edu	37	3	157155314	157155314	+	Missense_Mutation	SNP	C	C	A	rs3816527	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	24	41	0	0.533333	0	C|0.346;A|0.654	0.654	strong	.	PTX3	27	.	NM_002852	exon2	c.C143A	p.A48D	CGTGCGCCTGCGG	.	PASS	Atlas-SNP
ABCC5	10057	hgsc.bcm.edu	37	3	183696402	183696402	+	Silent	SNP	A	A	G	rs1132776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	21	61	0	0.403846	0	A|0.339;G|0.661	0.661	strong	.	ABCC5	142	.	NM_005688	exon9	c.T1185C	p.A395A	GTACCCAGCTTTT	.	PASS	Atlas-SNP
C10orf120	399814	hgsc.bcm.edu	37	10	124457480	124457480	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	55	132	0	0.443548	0	.	.	none	.	C10orf120	55	.	NM_001010912	exon3	c.T777C	p.H259H	ATTTCCATGGTAT	.	PASS	Atlas-SNP
CPA5	93979	hgsc.bcm.edu	37	7	129986338	129986338	+	Silent	SNP	C	C	T	rs6973851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	9	27	0	0.346154	0	C|0.418;T|0.582	0.582	strong	.	CPA5	61	.	NM_080385	exon3	c.C12T	p.T4T	GGGCACCCCTGGA	.	PASS	Atlas-SNP
AVPR2	554	hgsc.bcm.edu	37	X	153171993	153171993	+	Silent	SNP	A	A	G	rs5201	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	95	105	0	1	0	A|0.412;0|0.001	.	strong	.	AVPR2	43	.	NM_000054	exon3	c.A927G	p.L309L	TGTGCTACTCATG	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	37	22	18310439	18310439	+	Missense_Mutation	SNP	G	G	A	rs61744286	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	21	50	0	0.388889	0	G|0.917;A|0.083	0.083	strong	.	MICAL3	53	.	NM_015241	exon22	c.C3164T	p.A1055V	GCCGGCGCCATCC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629129	32629129	+	Missense_Mutation	SNP	T	T	C	rs1130432	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	46	42	0	0.901961	0	T|0.827;C|0.173	0.173	strong	.	HLA-DQB1	15	.	NM_002123	exon4	c.A767G	p.Q256R	CCTTTCTGACTCC	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19751657	19751657	+	Silent	SNP	G	G	T	rs9507566	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	362	189	323	0	0.522099	0	G|0.957;T|0.043	0.043	strong	TUBA3C,NS,carcinoma,+1,1	TUBA3C	166	1	NM_006001	exon4	c.C466A	p.R156R	AGAGCCGCTCCAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506579	195506579	+	Missense_Mutation	SNP	T	T	C	rs71291866	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	7	34	2	0.111111	0.0588235	CGTC|0.500;TGTT|0.500	.	alt	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.A11872G	p.T3958A	AGGAAGTGTCGGT	.	scavenged	Atlas-SNP
ASXL2	55252	hgsc.bcm.edu	37	2	25991689	25991689	+	Missense_Mutation	SNP	T	T	C	rs147191545	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	52	137	0	0.429752	0	T|0.998;C|0.002	0.002	strong	.	ASXL2	217	.	NM_018263	exon6	c.A553G	p.S185G	ATATGCTTGGCCT	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32968840	32968840	+	Missense_Mutation	SNP	G	G	A	rs80359194		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	40	73	0	0.597015	0	.	.	weak	.	BRCA2	812	.	NM_000059	exon25	c.G9271A	p.V3091I	CCTTTCGTCTATT	.	PASS	Atlas-SNP
LUZP4	51213	hgsc.bcm.edu	37	X	114541277	114541277	+	Missense_Mutation	SNP	G	G	C	rs141415241		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	41	180	0	0.199029	0	.	.	weak	.	LUZP4	51	.	NM_016383	exon4	c.G850C	p.E284Q	GCCACTGAGAGAG	.	PASS	Atlas-SNP
RTTN	25914	hgsc.bcm.edu	37	18	67802449	67802449	+	Silent	SNP	T	T	C	rs35139926	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	82	140	0	0.573427	0	T|0.986;C|0.014	0.014	strong	.	RTTN	184	.	NM_173630	exon22	c.A2856G	p.L952L	ATCAAATAATAGA	.	PASS	Atlas-SNP
ZNF781	163115	hgsc.bcm.edu	37	19	38160742	38160742	+	Missense_Mutation	SNP	T	T	C	rs149500211	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	29	46	0	0.659091	0	T|0.999;C|0.001	0.001	strong	.	ZNF781	66	.	NM_152605	exon4	c.A308G	p.H103R	ATAAGATGTGCAC	.	PASS	Atlas-SNP
TBPL2	387332	hgsc.bcm.edu	37	14	55907172	55907172	+	Missense_Mutation	SNP	C	C	G	rs8019270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	67	0	0.43662	0	C|0.350;G|0.650	0.650	strong	TBPL2,NS,carcinoma,0,2	TBPL2	27	2	NM_199047	exon1	c.G92C	p.R31P	ATGGACCGTAATC	.	PASS	Atlas-SNP
STX17	55014	hgsc.bcm.edu	37	9	102677589	102677589	+	Missense_Mutation	SNP	T	T	C	rs41305451	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	36	50	0	0.507042	0	T|0.945;C|0.055	0.055	strong	.	STX17	17	.	NM_017919	exon2	c.T68C	p.I23T	TTAAGATAGTAAT	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169432673	169432673	+	Silent	SNP	C	C	T	rs61051061	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	17	61	0	0.472222	0	C|0.791;T|0.209	0.209	strong	.	PALLD	179	.	NM_001166108	exon2	c.C18T	p.S6S	CTCCTCCCATGAG	.	PASS	Atlas-SNP
ALOX5	240	hgsc.bcm.edu	37	10	45869748	45869748	+	Silent	SNP	C	C	T	rs4987105	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	25	30	0	0.5	0	C|0.852;T|0.148	0.148	strong	.	ALOX5	88	.	NM_000698	exon1	c.C21T	p.T7T	GGTCACCGTGGCC	.	PASS	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	37	1	184764824	184764824	+	Missense_Mutation	SNP	C	C	T	rs35704242	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	42	85	0	0.545455	0	C|0.954;T|0.046	0.046	strong	.	FAM129A	98	.	NM_052966	exon14	c.G2074A	p.D692N	CTTCATCCTCAAG	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147475386	147475386	+	Missense_Mutation	SNP	A	A	G	rs6892205	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	285	283	294	1	0.992982	0.00340136	A|0.517;G|0.483	0.483	strong	.	SPINK5	245	.	NM_001127699	exon10	c.A800G	p.Q267R	GCAAGCAGCGTTT	.	PASS	Atlas-SNP
EHMT1	79813	hgsc.bcm.edu	37	9	140638416	140638416	+	Silent	SNP	G	G	A	rs1129767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	14	42	0	0.4	0	G|0.862;A|0.138	0.138	strong	EHMT1_ENST00000460843,colon,carcinoma,+1,2	EHMT1	196	2	NM_001145527	exon6	c.G1044A	p.S348S	GGACTCGGATGAG	.	PASS	Atlas-SNP
WDR5B	54554	hgsc.bcm.edu	37	3	122133830	122133830	+	Silent	SNP	T	T	G	rs3749213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	58	137	0	0.426471	0	T|0.790;G|0.210	0.210	strong	.	WDR5B	36	.	NM_019069	exon1	c.A546C	p.I182I	TGACACTATCAAG	.	PASS	Atlas-SNP
OPLAH	26873	hgsc.bcm.edu	37	8	145108191	145108191	+	Missense_Mutation	SNP	T	T	C	rs200702041	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	63	124	0	0.414474	0	T|0.996;C|0.004	0.004	weak	.	OPLAH	78	.	NM_017570	exon20	c.A2792G	p.Q931R	CCCTTCTGGTTGG	.	PASS	Atlas-SNP
ACVR1	90	hgsc.bcm.edu	37	2	158636910	158636910	+	Silent	SNP	G	G	A	rs2227861	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	87	112	0	0.956044	0	G|0.366;A|0.634	0.634	strong	.	ACVR1	52	.	NM_001105	exon4	c.C270T	p.A90A	CTCCACGGCTTGG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48314279	48314279	+	Silent	SNP	G	G	A	rs6955212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	52	115	0	0.509804	0	G|0.816;A|0.184	0.184	strong	ABCA13_ENST00000435803,NS,carcinoma,+1,2	ABCA13	1192	2	NM_152701	exon17	c.G5016A	p.K1672K	TAAGAAGGCAGAC	.	PASS	Atlas-SNP
KIAA0020	9933	hgsc.bcm.edu	37	9	2804393	2804393	+	Silent	SNP	A	A	G	rs12171	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	95	165	0	0.477387	0	A|0.909;G|0.091	0.091	strong	.	KIAA0020	56	.	NM_014878	exon18	c.T1885C	p.L629L	TTTCCAATGTAGG	.	PASS	Atlas-SNP
OR51A7	119687	hgsc.bcm.edu	37	11	4928841	4928841	+	Missense_Mutation	SNP	T	T	C	rs7108225	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	73	189	1	0.496599	0.00529101	T|0.918;C|0.082	0.082	strong	OR51A7,colon,carcinoma,0,4	OR51A7	86	4	NM_001004749	exon1	c.T242C	p.M81T	CTACCATGTTGAG	.	scavenged	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627761	170627761	+	Missense_Mutation	SNP	A	A	G	rs6900199	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	6	104	0	0.1	0	A|0.862;G|0.138	0.138	strong	.	FAM120B	108	.	NM_032448	exon2	c.A1283G	p.Y428C	CCATGTATACAGA	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7184518	7184518	+	Silent	SNP	G	G	A	rs891087	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	47	83	0	0.522222	0	A|0.117;C|0.000;G|0.883;T|0.000	0.117	strong	.	INSR	265	.	NM_000208	exon3	c.C783T	p.D261D	CCTGCCGTCCAGG	.	PASS	Atlas-SNP
NASP	4678	hgsc.bcm.edu	37	1	46073697	46073697	+	Missense_Mutation	SNP	C	C	A	rs200497808	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	351	15	322	6	0.042735	0.0186335	C|0.985;A|0.015	0.015	strong	NASP,NS,carcinoma,0,3	NASP	77	3	NM_002482	exon6	c.C1114A	p.P372T	GAGGCTCCAGTTC	.	scavenged	Atlas-SNP
PZP	5858	hgsc.bcm.edu	37	12	9303296	9303296	+	Missense_Mutation	SNP	A	A	T	rs10842971	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	39	56	0	0.52	0	A|0.782;T|0.218	0.218	strong	PZP_ENST00000381997,NS,carcinoma,0,2	PZP	422	2	NM_002864	exon34	c.T4328A	p.I1443N	ACTGGGATGTCTT	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56204644	56204644	+	Silent	SNP	T	T	G	rs12963422	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	55	74	0	0.617977	0	G|0.303;N|0.000	0.303	strong	.	ALPK2	487	.	NM_052947	exon5	c.A2775C	p.V925V	AGCATGTACTGTG	.	PASS	Atlas-SNP
CDKN1A	1026	hgsc.bcm.edu	37	6	36651971	36651971	+	Missense_Mutation	SNP	C	C	A	rs1801270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	34	56	0	0.566667	0	C|0.812;A|0.188	0.188	strong	.	CDKN1A	27	.	NM_001220778	exon2	c.C93A	p.S31R	GCTGAGCCGCGAC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3228411	3228411	+	Silent	SNP	G	G	A	rs78062277	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	211	182	0	0.946188	0	A|1.000;|0.000	1.000	weak	.	MXRA5	815	.	NM_015419	exon7	c.C7833T	p.A2611A	GGCCCCGGCGTCC	.	PASS	Atlas-SNP
C17orf107	100130311	hgsc.bcm.edu	37	17	4803711	4803711	+	Nonsense_Mutation	SNP	G	G	A	rs35400274	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	30	36	0	0.47619	0	G|0.791;A|0.209	0.209	strong	.	C17orf107	8	.	NM_001145536	exon3	c.G456A	p.W152X	AGCATGGCTATGC	.	PASS	Atlas-SNP
ENTPD3	956	hgsc.bcm.edu	37	3	40468896	40468896	+	Missense_Mutation	SNP	C	C	T	rs1047855	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	171	141	1	0.994186	0.0070922	C|0.754;T|0.246	0.246	strong	ENTPD3,NS,carcinoma,-1,1	ENTPD3	48	1	NM_001248	exon11	c.C1487T	p.A496V	TCACAGCGGCAGC	.	PASS	Atlas-SNP
OR5R1	219479	hgsc.bcm.edu	37	11	56184888	56184888	+	Missense_Mutation	SNP	G	G	A	rs998544	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	84	190	0	0.545455	0	G|0.630;N|0.000	.	strong	.	OR5R1	83	.	NM_001004744	exon1	c.C821T	p.A274V	ACAGAAGCCATCT	.	PASS	Atlas-SNP
IL15RA	3601	hgsc.bcm.edu	37	10	6008172	6008172	+	Silent	SNP	C	C	T	rs2296139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	75	130	0	0.487013	0	C|0.832;T|0.168	0.168	strong	.	IL15RA	17	.	NM_001256765	exon3	c.G477A	p.T159T	GCACTCCGTCAGG	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32598630	32598630	+	Missense_Mutation	SNP	T	T	A	rs2290213	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	46	105	0	0.46	0	A|0.150;C|0.000;T|0.850	0.150	strong	.	AVL9	66	.	NM_015060	exon10	c.T769A	p.C257S	AACCCATGTGCAG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76475574	76475574	+	Silent	SNP	C	C	A	rs78514572	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	20	34	0	0.588235	0	C|0.973;A|0.027	0.027	strong	.	DNAH17	347	.	NM_173628	exon50	c.G7893T	p.A2631A	CAGGGCCGCGGCC	.	PASS	Atlas-SNP
OR5H14	403273	hgsc.bcm.edu	37	3	97869072	97869072	+	Silent	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	106	276	0	0.464912	0	.	.	none	OR5H14,colon,carcinoma,+1,1	OR5H14	56	1	NM_001005514	exon1	c.A843C	p.I281I	TGTCATAGTTCCT	.	PASS	Atlas-SNP
PON1	5444	hgsc.bcm.edu	37	7	94940880	94940880	+	Missense_Mutation	SNP	A	A	C	rs144390653	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	29	81	0	0.557692	0	A|0.998;C|0.002	0.002	strong	PON1,NS,carcinoma,0,1	PON1	55	1	NM_000446	exon5	c.T380G	p.M127R	AGGTACATGGCAT	.	PASS	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233245026	233245026	+	Missense_Mutation	SNP	G	G	A	rs71421640		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	251	121	337	0	0.482072	0	G|0.500;A|0.500	0.500	weak	ALPP,NS,carcinoma,+1,1	ALPP	53	1	NM_001632	exon6	c.G788A	p.R263H	CGAAGCGCCAGGT	.	PASS	Atlas-SNP
MYBPC3	4607	hgsc.bcm.edu	37	11	47370041	47370041	+	Missense_Mutation	SNP	T	T	C	rs3729989	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	73	108	0	0.579365	0	T|0.916;C|0.084	0.084	strong	.	MYBPC3	102	.	NM_000256	exon6	c.A706G	p.S236G	GGTAGCTGCCAGT	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38991543	38991543	+	Silent	SNP	G	G	A	rs2071088	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	60	137	0	0.384615	0	G|0.904;A|0.096	0.096	strong	.	RYR1	708	.	NM_001042723	exon47	c.G7527A	p.V2509V	CCGTGTGTATGGC	.	PASS	Atlas-SNP
C1orf177	163747	hgsc.bcm.edu	37	1	55273580	55273580	+	Missense_Mutation	SNP	G	G	T	rs9782980	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	101	81	0	1	0	G|0.474;T|0.526	0.526	strong	.	C1orf177	36	.	NM_001110533	exon4	c.G376T	p.G126C	GGCCCCGGCTCCT	.	PASS	Atlas-SNP
DCHS1	8642	hgsc.bcm.edu	37	11	6647596	6647596	+	Missense_Mutation	SNP	C	C	T	rs142577975	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	40	50	0	0.597015	0	C|1.000;T|0.000	0.000	strong	.	DCHS1	277	.	NM_003737	exon16	c.G6380A	p.R2127H	GCTGAGCGAACTG	.	PASS	Atlas-SNP
KIF4B	285643	hgsc.bcm.edu	37	5	154395470	154395470	+	Missense_Mutation	SNP	A	A	G	rs10056252	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	216	112	202	0	0.518519	0	A|0.965;G|0.035	0.035	strong	.	KIF4B	307	.	NM_001099293	exon1	c.A2051G	p.Y684C	GGCAATATGAGCT	.	PASS	Atlas-SNP
ADAMTS2	9509	hgsc.bcm.edu	37	5	178562967	178562967	+	Silent	SNP	G	G	A	rs1972715	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	69	146	0	0.456954	0	G|0.775;A|0.225	0.225	strong	.	ADAMTS2	190	.	NM_014244	exon13	c.C2028T	p.D676D	CGTCCCGTCATGC	.	PASS	Atlas-SNP
WDHD1	11169	hgsc.bcm.edu	37	14	55408294	55408294	+	Missense_Mutation	SNP	C	C	T	rs41309252	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	82	161	0	0.460674	0	C|0.980;T|0.020	0.020	strong	.	WDHD1	82	.	NM_007086	exon26	c.G3304A	p.E1102K	GGTTCTCTTTTGC	.	PASS	Atlas-SNP
ISX	91464	hgsc.bcm.edu	37	22	35463179	35463179	+	Silent	SNP	T	T	C	rs361668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	102	116	0	0.990291	0	T|0.246;C|0.754	0.754	strong	.	ISX	62	.	NM_001008494	exon1	c.T99C	p.I33I	CTCCATTGAGGCG	.	PASS	Atlas-SNP
FPGS	2356	hgsc.bcm.edu	37	9	130569258	130569258	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	42	69	0	0.5	0	.	.	none	.	FPGS	30	.	NM_004957	exon5	c.C393T	p.P131P	CTCTCCCCACCTG	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158597507	158597507	+	Missense_Mutation	SNP	G	G	C	rs3737515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	27	53	0	0.397059	0	G|0.758;C|0.242	0.242	strong	.	SPTA1	720	.	NM_003126	exon40	c.C5572G	p.L1858V	TCATTAGCAAGCT	.	PASS	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3753769	3753769	+	Silent	SNP	C	C	T	rs3746120	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	7	24	0	0.388889	0	C|0.654;T|0.346	0.346	strong	APBA3,NS,carcinoma,0,1	APBA3	28	1	NM_004886	exon6	c.G1005A	p.A335A	GTCCTCCGCGTAG	.	PASS	Atlas-SNP
NLRP1	22861	hgsc.bcm.edu	37	17	5425077	5425077	+	Missense_Mutation	SNP	T	T	C	rs11651270	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	31	69	0	0.5	0	T|0.542;C|0.458	0.458	strong	.	NLRP1	358	.	NM_001033053	exon13	c.A3562G	p.M1188V	GGGCCATTTGGAA	.	PASS	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	37	2	15470848	15470848	+	Silent	SNP	C	C	T	rs34395824	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	125	223	0	0.553097	0	C|0.972;T|0.028	0.028	strong	.	NBAS	246	.	NM_015909	exon36	c.G4221A	p.L1407L	CCAGCGCAATAGG	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	146993445	146993445	+	Missense_Mutation	SNP	T	T	C	rs9497606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	68	117	0	0.957747	0	T|0.734;C|0.266	0.266	strong	.	ADGB	93	.	NM_024694	exon8	c.T929C	p.I310T	GCAAAATAGCAGT	.	PASS	Atlas-SNP
OR11H6	122748	hgsc.bcm.edu	37	14	20692453	20692453	+	Missense_Mutation	SNP	G	G	T	rs17211285	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	84	221	0	0.48	0	G|0.540;N|0.001	.	strong	.	OR11H6	60	.	NM_001004480	exon1	c.G585T	p.L195F	CCACTTGGTGTGT	.	PASS	Atlas-SNP
GOLGA5	9950	hgsc.bcm.edu	37	14	93263982	93263982	+	Missense_Mutation	SNP	C	C	G	rs17128572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	52	100	0	0.45614	0	C|0.926;G|0.074	0.074	strong	.	GOLGA5	84	.	NM_005113	exon2	c.C200G	p.A67G	CAGCAGCTGATAA	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215901492	215901492	+	Silent	SNP	C	C	T	rs2820718	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	75	125	0	0.490196	0	C|0.836;T|0.164	0.164	strong	.	USH2A	1168	.	NM_206933	exon61	c.G11946A	p.L3982L	ATTCAACAGAACT	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115933978	115933978	+	Silent	SNP	G	G	A	rs1128117	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	46	102	0	0.484211	0	G|0.940;A|0.060	0.060	strong	.	FKBP15	128	.	NM_015258	exon24	c.C2541T	p.A847A	CTGGAGGGCTAAA	.	PASS	Atlas-SNP
COLQ	8292	hgsc.bcm.edu	37	3	15495386	15495386	+	Silent	SNP	G	G	A	rs55866379	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	45	74	0	0.473684	0	G|0.975;A|0.025	0.025	strong	.	COLQ	82	.	NM_005677	exon16	c.C1248T	p.D416D	GTCACAGTCCTCC	.	PASS	Atlas-SNP
LEPRE1	64175	hgsc.bcm.edu	37	1	43215930	43215930	+	Missense_Mutation	SNP	C	C	T	rs11581921	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	68	114	0	0.49635	0	C|0.948;T|0.052	0.052	strong	.	LEPRE1	130	.	NM_001146289	exon11	c.G1647A	p.M549I	GGACTCCATGATG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60885978	60885978	+	Silent	SNP	G	G	T	rs201094237	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	30	11	0	0.714286	0	.	.	weak	.	LAMA5	268	.	NM_005560	exon74	c.C10261A	p.R3421R	CAGGCCGGGAGCG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5372751	5372751	+	Missense_Mutation	SNP	A	A	C	rs4910755	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	80	171	0	0.451977	0	A|0.770;C|0.230	0.230	strong	.	OR51B6	53	.	NM_001004750	exon1	c.A14C	p.K5T	TCAATAAGTCTGC	.	PASS	Atlas-SNP
ACSS1	84532	hgsc.bcm.edu	37	20	24994289	24994289	+	Missense_Mutation	SNP	C	C	T	rs6050249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	27	49	0	0.409091	0	C|0.785;T|0.215	0.215	strong	ACSS1,colon,carcinoma,0,2	ACSS1	46	2	NM_001252677	exon10	c.G1462A	p.V488M	CCTCCACGACGCT	.	PASS	Atlas-SNP
ZNF132	7691	hgsc.bcm.edu	37	19	58946203	58946203	+	Missense_Mutation	SNP	C	C	T	rs1122955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	70	126	0	0.5	0	C|0.842;T|0.158	0.158	strong	ZNF132,extremity,malignant_melanoma,-1,1	ZNF132	56	1	NM_003433	exon3	c.G608A	p.G203D	CAGCTGCCCAGGA	.	PASS	Atlas-SNP
ATOH7	220202	hgsc.bcm.edu	37	10	69991099	69991099	+	Silent	SNP	G	G	A	rs201955526	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	41	44	0	0.554054	0	G|0.999;A|0.001	0.001	weak	.	ATOH7	4	.	NM_145178	exon1	c.C336T	p.H112H	CTCACAGTGGAGA	.	PASS	Atlas-SNP
VIPR2	7434	hgsc.bcm.edu	37	7	158896517	158896517	+	Silent	SNP	G	G	A	rs2270313	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	50	121	0	0.46729	0	G|0.750;A|0.250	0.250	strong	.	VIPR2	53	.	NM_003382	exon4	c.C288T	p.D96D	CCATCCGTCACTC	.	PASS	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131195712	131195712	+	Missense_Mutation	SNP	G	G	A	rs12670788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	308	142	331	1	0.461039	0.00302115	G|0.634;A|0.366	0.366	strong	.	PODXL	53	.	NM_001018111	exon2	c.C581T	p.S194L	TGCGTCGAAGTGG	.	PASS	Atlas-SNP
SEMA6A	57556	hgsc.bcm.edu	37	5	115811273	115811273	+	Missense_Mutation	SNP	C	C	T	rs17432496	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	25	59	0	0.462963	0	C|0.976;T|0.024	0.024	strong	.	SEMA6A	93	.	NM_020796	exon16	c.G1676A	p.R559H	TTGCCACGCTCTA	.	PASS	Atlas-SNP
SLC16A4	9122	hgsc.bcm.edu	37	1	110924316	110924316	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	110	259	0	0.482456	0	.	.	none	.	SLC16A4	47	.	NM_004696	exon4	c.A322G	p.T108A	TACTTGTGGCCCA	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127228596	127228596	+	Silent	SNP	A	A	G	rs4838184	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	287	285	318	1	0.993031	0.00314465	A|0.273;G|0.727	0.727	strong	.	GPR144	33	.	NM_001161808	exon11	c.A1851G	p.T617T	CACCACAGGCTGC	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228121101	228121101	+	Missense_Mutation	SNP	G	G	T	rs55703767	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	26	43	0	0.472727	0	G|0.828;T|0.172	0.172	strong	.	COL4A3	293	.	NM_000091	exon17	c.G976T	p.D326Y	GGTGAAGATGGCA	.	PASS	Atlas-SNP
ZMYM5	9205	hgsc.bcm.edu	37	13	20425911	20425911	+	Missense_Mutation	SNP	C	C	A	rs9579717	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	62	176	0	0.410596	0	C|0.902;A|0.098	0.098	strong	.	ZMYM5	73	.	NM_001039650	exon3	c.G410T	p.C137F	ATAAAACAGGAAG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54722250	54722250	+	Missense_Mutation	SNP	T	T	C	rs1132610	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	104	244	0	0.485981	0	T|0.826;C|0.174	0.174	strong	LILRB3,colon,carcinoma,+2,1	LILRB3	67	1	NM_006864	exon11	c.A1573G	p.R525G	CCACCCTGTCCTC	.	PASS	Atlas-SNP
MCF2L	23263	hgsc.bcm.edu	37	13	113720476	113720476	+	Silent	SNP	C	C	T	rs2297192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	11	27	0	0.297297	0	C|0.846;T|0.154	0.154	strong	.	MCF2L	182	.	NM_001112732	exon8	c.C873T	p.T291T	GGCCACCGTGCAG	.	PASS	Atlas-SNP
RGR	5995	hgsc.bcm.edu	37	10	86004865	86004865	+	Silent	SNP	C	C	T	rs11200938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	44	102	0	0.463158	0	C|0.948;T|0.052	0.052	strong	RGR,right_upper_lobe,carcinoma,-2,1	RGR	42	1	NM_001012722	exon1	c.C19T	p.L7L	AGTGCCCTGCCCA	.	PASS	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	37	5	96126308	96126308	+	Silent	SNP	A	A	G	rs27529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	121	151	0	0.991803	0	A|0.393;G|0.607	0.607	strong	.	ERAP1	59	.	NM_001198541	exon9	c.T1359C	p.S453S	GTCAGCACTAAGA	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8197983	8197983	+	Silent	SNP	G	G	A	rs35202360	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	32	57	0	0.507937	0	G|0.929;A|0.071	0.071	strong	.	FBN3	300	.	NM_032447	exon13	c.C1599T	p.N533N	ACACTCGTTGTGG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47850107	47850107	+	Missense_Mutation	SNP	G	G	A	rs8131693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	55	93	0	0.495495	0	G|0.933;A|0.067	0.067	strong	.	PCNT	283	.	NM_006031	exon36	c.G7874A	p.R2625Q	TGTCCCGGTCCCT	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76883797	76883797	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	45	105	0	0.511364	0	.	.	none	.	MYO7A	164	.	NM_001127179	exon16	c.G1801A	p.A601T	CAGGGCGCCGAGA	.	PASS	Atlas-SNP
MARCH2	51257	hgsc.bcm.edu	37	19	8503345	8503345	+	Missense_Mutation	SNP	G	G	C	rs34099346	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	40	73	0	0.487805	0	G|0.900;C|0.100	0.100	strong	.	MARCH2	17	.	NM_001005415	exon5	c.G656C	p.R219P	AGATCCGGGAGGC	.	PASS	Atlas-SNP
SPRR1B	6699	hgsc.bcm.edu	37	1	153004848	153004848	+	Silent	SNP	T	T	C	rs3795381	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	99	193	0	0.492537	0	T|0.497;C|0.503	0.503	strong	.	SPRR1B	18	.	NM_003125	exon2	c.T27C	p.P9P	GCAGCCTTGCACC	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079894	31079894	+	Missense_Mutation	SNP	A	A	G	rs2233977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	54	127	0	0.482143	0	A|0.825;G|0.175	0.175	strong	C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	NM_014070	exon2	c.T242C	p.V81A	GCAGGCACGCTGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9071834	9071834	+	Silent	SNP	G	G	C	rs17000803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	47	104	0	0.427273	0	G|0.792;C|0.208	0.208	strong	MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	NM_024690	exon3	c.C15612G	p.P5204P	GTCCGTGGGAAAG	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89421405	89421405	+	Silent	SNP	G	G	A	rs7182726	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	68	146	0	0.462585	0	G|0.804;A|0.196	0.196	strong	HAPLN3,NS,carcinoma,0,1	HAPLN3	43	1	NM_178232	exon5	c.C879T	p.I293I	CTTGGCGATCGTG	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12856087	12856087	+	Missense_Mutation	SNP	C	C	T	rs141070565	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	379	13	339	0	0.0343008	0	C|0.968;T|0.032	0.032	strong	PRAMEF1,trunk,malignant_melanoma,0,4	PRAMEF1	78	4	NM_023013	exon4	c.C1367T	p.P456L	CCACCCCCTGCCC	.	scavenged	Atlas-SNP
SNX9	51429	hgsc.bcm.edu	37	6	158330765	158330765	+	Silent	SNP	G	G	A	rs3211067	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	59	130	0	0.867647	0	G|0.778;A|0.222	0.222	strong	.	SNX9	43	.	NM_016224	exon8	c.G774A	p.R258R	TCCCAGGAAAGGC	.	PASS	Atlas-SNP
RASGRF1	5923	hgsc.bcm.edu	37	15	79298523	79298523	+	Silent	SNP	G	G	A	rs894780	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	35	79	0	0.4375	0	G|0.921;T|0.000	.	strong	.	RASGRF1	168	.	NM_002891	exon15	c.C2119T	p.L707L	ACCTCAGCCACCT	.	PASS	Atlas-SNP
LPPR3	0	hgsc.bcm.edu	37	19	814452	814452	+	Silent	SNP	C	C	T	rs3746138	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	28	34	0	0.528302	0	C|0.987;T|0.013	0.013	strong	.	.	.	.	NM_024888	exon6	c.G897A	p.A299A	GATGCCCGCCCCG	.	PASS	Atlas-SNP
C1orf127	148345	hgsc.bcm.edu	37	1	11008341	11008341	+	Silent	SNP	G	G	A	rs10864483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	67	70	0	0.930556	0	G|0.844;A|0.156	0.156	strong	.	C1orf127	134	.	NM_001170754	exon12	c.C1851T	p.C617C	TCCAGAGCACGTT	.	PASS	Atlas-SNP
BTN3A1	11119	hgsc.bcm.edu	37	6	26408145	26408145	+	Missense_Mutation	SNP	T	T	A	rs144114619	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	83	157	0	0.434555	0	T|0.997;A|0.003	0.003	strong	.	BTN3A1	80	.	NM_007048	exon4	c.T680A	p.L227H	CCCTCCTCGGCCT	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27203002	27203002	+	Silent	SNP	G	G	A	rs45563539	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	118	206	1	0.561905	0.00485437	G|0.961;A|0.039	0.039	strong	.	TEK	250	.	NM_000459	exon13	c.G2094A	p.Q698Q	GTATCAGCTCAAG	.	PASS	Atlas-SNP
MFGE8	4240	hgsc.bcm.edu	37	15	89450546	89450546	+	Silent	SNP	C	C	T	rs1878327	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	74	149	0	0.4625	0	C|0.333;T|0.667	0.667	strong	MFGE8,NS,carcinoma,0,1	MFGE8	60	1	NM_001114614	exon3	c.G267A	p.S89S	CACAGACGAGGCG	.	PASS	Atlas-SNP
CCDC86	79080	hgsc.bcm.edu	37	11	60610056	60610056	+	Missense_Mutation	SNP	G	G	C	rs2074421	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	41	86	0	0.518987	0	G|0.909;C|0.091	0.091	strong	.	CCDC86	24	.	NM_024098	exon1	c.G459C	p.Q153H	GCATCAGCTACCG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392347	40392347	+	Missense_Mutation	SNP	C	C	G	rs2542318	bycluster;byfrequency;by2hit2allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	24	557	0	0.143713	0	C|0.333;G|0.667	0.667	strong	FCGBP,NS,carcinoma,0,2	FCGBP	416	2	NM_003890	exon16	c.G8157C	p.Q2719H	CTCCACCTGGCCT	.	scavenged	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379794	31379794	+	Silent	SNP	C	C	T	rs1051797	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	130	0	1	0	C|0.698;T|0.302	0.302	strong	.	MICA	21	.	NM_001177519	exon4	c.C684T	p.S228S	GGCTTCCAGCTTC	.	PASS	Atlas-SNP
BAZ1A	11177	hgsc.bcm.edu	37	14	35230980	35230980	+	Missense_Mutation	SNP	C	C	T	rs45620534	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	278	125	302	1	0.44964	0.00331126	C|0.938;T|0.062	0.062	strong	.	BAZ1A	128	.	NM_013448	exon24	c.G4226A	p.R1409K	CTTTTTCTGCATC	.	PASS	Atlas-SNP
GAD2	2572	hgsc.bcm.edu	37	10	26559571	26559571	+	Silent	SNP	G	G	C	rs1556234	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	64	136	0	0.453901	0	G|0.930;C|0.070	0.070	strong	GAD2,NS,malignant_melanoma,+2,2	GAD2	116	2	NM_000818	exon10	c.G978C	p.G326G	ACAGGGGTTTGTT	.	PASS	Atlas-SNP
CD276	80381	hgsc.bcm.edu	37	15	73995247	73995247	+	Missense_Mutation	SNP	C	C	T	rs142744437	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	120	204	0	0.526316	0	C|0.999;T|0.001	0.001	strong	.	CD276	29	.	NM_001024736	exon4	c.C553T	p.P185S	GGTGTGCCCCTGA	.	PASS	Atlas-SNP
CHRNA7	1139	hgsc.bcm.edu	37	15	32450704	32450704	+	Silent	SNP	G	G	A	rs201822909	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	839	295	700	1	0.351609	0.00142857	G|0.705;A|0.295	0.295	strong	CHRNA7_ENST00000437966,caecum,carcinoma,0,11	CHRNA7	57	11	NM_001190455	exon7	c.G777A	p.T259T	CAGGACGCTCTAC	.	scavenged	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367431	107367431	+	Missense_Mutation	SNP	A	A	T	rs61735925	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	335	108	414	0	0.322388	0	A|0.158;T|0.842	0.842	strong	.	OR13C2	46	.	NM_001004481	exon1	c.T478A	p.S160T	ACACTGATTGTAC	.	PASS	Atlas-SNP
PGM5	5239	hgsc.bcm.edu	37	9	70993153	70993153	+	Silent	SNP	G	G	A	rs150515274	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	5	204	1	0.0229358	0.00490196	G|0.970;A|0.030	0.030	strong	PGM5,colon,carcinoma,0,3	PGM5	80	3	NM_021965	exon2	c.G300A	p.S100S	CTTGTCGACACCT	.	scavenged	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46009684	46009684	+	Missense_Mutation	SNP	G	G	A	rs3733101	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	48	68	0	0.607595	0	G|0.996;A|0.004	0.004	strong	FYCO1,NS,NS,0,1	FYCO1	115	1	NM_024513	exon8	c.C1142T	p.T381M	GATGCCGTATCTG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40408532	40408532	+	Missense_Mutation	SNP	G	G	A	rs36106401	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	354	162	429	0	0.457627	0	G|0.853;A|0.147	0.147	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon8	c.C4307T	p.P1436L	CTCCCCGGCGGGC	.	PASS	Atlas-SNP
CCL24	6369	hgsc.bcm.edu	37	7	75442730	75442730	+	Missense_Mutation	SNP	T	T	G	rs2302006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	25	41	0	0.543478	0	T|0.714;G|0.286	0.286	strong	.	CCL24	11	.	NM_002991	exon2	c.A85C	p.I29L	AGGGGATGACCAC	.	PASS	Atlas-SNP
KRT35	3886	hgsc.bcm.edu	37	17	39635194	39635194	+	Silent	SNP	G	G	A	rs12936485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	63	129	0	0.496063	0	G|0.919;A|0.081	0.081	strong	.	KRT35	58	.	NM_002280	exon4	c.C765T	p.D255D	GGCAGCGTCCACC	.	PASS	Atlas-SNP
ECE2	9718	hgsc.bcm.edu	37	3	183994447	183994447	+	Missense_Mutation	SNP	C	C	T	rs13063766	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	26	62	0	0.5	0	C|0.977;T|0.023	0.023	strong	.	ECE2	303	.	NM_001100120	exon2	c.C218T	p.T73I	GGGTCACCTGCCC	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115932012	115932012	+	Missense_Mutation	SNP	G	G	T	rs57348436	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	64	108	0	0.556522	0	G|0.954;T|0.046	0.046	strong	.	FKBP15	128	.	NM_015258	exon26	c.C2977A	p.P993T	GCAACGGGACAGC	.	PASS	Atlas-SNP
NBAS	51594	hgsc.bcm.edu	37	2	15359012	15359012	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	3	180	0	0.0159574	0	.	.	none	NBAS,NS,carcinoma,-1,1	NBAS	246	1	NM_015909	exon48	c.G6317A	p.R2106H	TGAATGCGGGGCC	.	scavenged	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150554553	150554553	+	Missense_Mutation	SNP	C	C	T	rs1049742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	33	67	0	0.485294	0	C|0.946;T|0.054	0.054	strong	.	ABP1	92	.	NM_001091	exon2	c.C995T	p.S332F	CCTCCTCCGGGCT	.	PASS	Atlas-SNP
HRCT1	646962	hgsc.bcm.edu	37	9	35906471	35906471	+	Missense_Mutation	SNP	C	C	T	rs76452347	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	43	48	0	0.605634	0	C|0.836;G|0.000;T|0.164	0.164	strong	HRCT1,NS,carcinoma,0,2	HRCT1	14	2	NM_001039792	exon1	c.C187T	p.R63W	TTCCGGCGGCGGG	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	37	6	151674326	151674326	+	Missense_Mutation	SNP	A	A	C	rs3823310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	35	71	0	0.76087	0	A|0.477;C|0.523	0.523	strong	.	AKAP12	170	.	NM_005100	exon4	c.A4800C	p.E1600D	AGAGGAACCTCAG	.	PASS	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41862801	41862801	+	Splice_Site	SNP	G	G	T	rs200684350	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	8	77	0	0.0930233	0	G|0.985;T|0.015	0.015	strong	TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	NM_006293	exon12	c.1484-1G>T	.	CCCACAGTGGACA	.	scavenged	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33517515	33517515	+	Missense_Mutation	SNP	C	C	T	rs28626308	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	11	31	0	0.37931	0	C|0.935;T|0.065	0.065	strong	RHPN2,NS,carcinoma,-1,1	RHPN2	107	1	NM_033103	exon3	c.G209A	p.R70Q	TGCTCCCGCACCT	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427820	427820	+	Silent	SNP	C	C	T	rs12922073	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	47	87	0	0.5	0	A|0.000;C|0.470;G|0.000;T|0.530	0.530	strong	.	TMEM8A	49	.	NM_021259	exon2	c.G150A	p.S50S	GGCCTGCGAGAAG	.	PASS	Atlas-SNP
SEZ6L	23544	hgsc.bcm.edu	37	22	26692953	26692953	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	4	104	0	0.04	0	.	.	none	.	SEZ6L	174	.	NM_001184777	exon4	c.G1069A	p.G357R	GTGGAGGGGCAGG	.	PASS	Atlas-SNP
DOPEY2	9980	hgsc.bcm.edu	37	21	37661405	37661405	+	Missense_Mutation	SNP	G	G	A	rs3827183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	69	156	0	0.522727	0	G|0.873;A|0.127	0.127	strong	DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	NM_005128	exon35	c.G6416A	p.G2139E	CAGTGGGGGAGAT	.	PASS	Atlas-SNP
DDX58	23586	hgsc.bcm.edu	37	9	32526146	32526146	+	Missense_Mutation	SNP	G	G	A	rs10813831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	55	82	0	0.509259	0	G|0.788;A|0.212	0.212	strong	.	DDX58	82	.	NM_014314	exon1	c.C19T	p.R7C	GGCTGCGTCGCTG	.	PASS	Atlas-SNP
CPN2	1370	hgsc.bcm.edu	37	3	194061907	194061907	+	Nonsense_Mutation	SNP	G	G	A	rs4974539	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	107	100	0	1	0	G|0.680;A|0.320	0.320	strong	.	CPN2	56	.	NM_001080513	exon2	c.C1525T	p.Q509X	CCTGCTGAGGAGA	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52321686	52321686	+	Missense_Mutation	SNP	C	C	T	rs11985241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	16	24	0	0.444444	0	C|0.853;T|0.147	0.147	strong	.	PXDNL	414	.	NM_144651	exon17	c.G2498A	p.S833N	ACGGAGCTGCACG	.	PASS	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	37	3	37368755	37368755	+	Missense_Mutation	SNP	T	T	A	rs62241896	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	60	112	0	0.545455	0	T|0.705;A|0.295	0.295	strong	.	GOLGA4	173	.	NM_001172713	exon15	c.T5444A	p.M1815K	AAAGTATGATAGG	.	PASS	Atlas-SNP
TCP10L	140290	hgsc.bcm.edu	37	21	33951068	33951068	+	Missense_Mutation	SNP	T	T	C	rs9622	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	326	139	266	1	0.42638	0.0037594	T|0.791;C|0.209	0.209	strong	.	TCP10L	24	.	NM_144659	exon4	c.A434G	p.H145R	TTCTTGTGGCCAG	.	PASS	Atlas-SNP
ACPP	55	hgsc.bcm.edu	37	3	132068831	132068831	+	Silent	SNP	C	C	T	rs2228402	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	58	118	0	0.449612	0	C|0.529;T|0.471	0.471	strong	.	ACPP	118	.	NM_001099	exon8	c.C849T	p.L283L	AAAACTCATCATG	.	PASS	Atlas-SNP
ZGLP1	100125288	hgsc.bcm.edu	37	19	10419130	10419130	+	Silent	SNP	C	C	T	rs281417	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	47	52	0	1	0	C|0.758;T|0.242	0.242	strong	ZGLP1_ENST00000403903,NS,lymphoid_neoplasm,0,2	ZGLP1	18	2	NM_001103167	exon1	c.G228A	p.P76P	CAGGACCGGGGTG	.	PASS	Atlas-SNP
SPINT3	10816	hgsc.bcm.edu	37	20	44141331	44141331	+	Missense_Mutation	SNP	A	A	G	rs6032259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	39	108	0	0.364486	0	A|0.558;G|0.442	0.442	strong	.	SPINT3	12	.	NM_006652	exon2	c.T230C	p.L77S	TTCCTCAAAAAGT	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276909	71276909	+	Silent	SNP	G	G	A	rs12289712	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	14	106	1	0.147368	0.00943396	A|0.153;G|0.847	0.153	strong	KRTAP5-10,rectum,carcinoma,0,3	KRTAP5-10	37	3	NM_001012710	exon1	c.G276A	p.G92G	CAAGGGGGGCTGT	.	scavenged	Atlas-SNP
C19orf55	148137	hgsc.bcm.edu	37	19	36255965	36255965	+	Silent	SNP	C	C	G	rs7252936	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	43	92	0	0.447917	0	C|0.915;G|0.085	0.085	strong	.	C19orf55	39	.	NM_001039887	exon7	c.C657G	p.L219L	CTCCCTCAGCCCC	.	PASS	Atlas-SNP
ZZZ3	26009	hgsc.bcm.edu	37	1	78098403	78098403	+	Missense_Mutation	SNP	T	T	C	rs34535037	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	79	172	0	0.50641	0	T|0.984;C|0.016	0.016	strong	.	ZZZ3	80	.	NM_015534	exon5	c.A637G	p.I213V	AGTTTATAACAGC	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190878589	190878589	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	295	13	275	4	0.0440678	0.0145455	.	.	none	FRG1,NS,carcinoma,0,1	FRG1	76	1	NM_004477	exon6	c.A469G	p.I157V	TGCTTTATTAGAT	.	scavenged	Atlas-SNP
CHRNE	1145	hgsc.bcm.edu	37	17	4804902	4804902	+	Silent	SNP	G	G	A	rs33970119	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	20	39	0	0.487805	0	G|0.958;A|0.042	0.042	strong	.	CHRNE	25	.	NM_000080	exon6	c.C519T	p.A173A	CTCTTCGGCATTG	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612720	53612720	+	Missense_Mutation	SNP	T	T	C	rs1560099	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	70	132	0	0.48951	0	T|0.843;C|0.157	0.157	strong	.	ZNF415	68	.	NM_018355	exon4	c.A578G	p.Y193C	GTCCCATATTTAT	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27374180	27374180	+	Missense_Mutation	SNP	T	T	C	rs1805015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	26	79	0	0.4	0	T|0.773;C|0.227	0.227	strong	IL4R,colon,carcinoma,0,1	IL4R	70	1	NM_000418	exon11	c.T1507C	p.S503P	AGCAACTCCCTGA	.	PASS	Atlas-SNP
RNF31	55072	hgsc.bcm.edu	37	14	24620821	24620821	+	Missense_Mutation	SNP	A	A	T	rs149481717	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	23	47	0	0.547619	0	A|0.998;T|0.002	0.002	strong	.	RNF31	95	.	NM_017999	exon10	c.A1865T	p.Q622L	TCCGCCAGCGCCT	.	PASS	Atlas-SNP
FUT5	2527	hgsc.bcm.edu	37	19	5867191	5867191	+	Silent	SNP	G	G	A	rs61744948	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	60	127	0	0.434783	0	G|0.912;A|0.088	0.088	strong	.	FUT5	29	.	NM_002034	exon2	c.C546T	p.Y182Y	CCAGCCGTAGGGC	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33767943	33767943	+	Missense_Mutation	SNP	C	C	T	rs138317636	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	40	76	0	0.487805	0	C|1.000;T|0.000	0.000	strong	.	SLFN13	79	.	NM_144682	exon6	c.G2365A	p.V789M	AGGTCACTATTTG	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51361315	51361315	+	Silent	SNP	C	C	T	rs12946	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	29	53	0	0.446154	0	C|0.890;T|0.110	0.110	strong	.	KLK3	76	.	NM_001030047	exon3	c.C237T	p.S79S	GCACAGCCTGTTT	.	PASS	Atlas-SNP
AGAP6	414189	hgsc.bcm.edu	37	10	51769799	51769799	+	Silent	SNP	C	C	T	rs61848275	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	44	128	0	0.263473	0	C|0.500;T|0.500	0.500	weak	AGAP6,NS,carcinoma,0,1	AGAP6	53	1	NM_001077665	exon8	c.C1914T	p.V638V	TGTGGTCCTGGCG	.	scavenged	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7166388	7166388	+	Silent	SNP	G	G	A	rs2229429	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	20	56	0	0.512821	0	T|0.000;G|0.746;C|0.000;A|0.254	0.254	strong	.	INSR	265	.	NM_000208	exon8	c.C1638T	p.D546D	CTGCCCGTCGAAC	.	PASS	Atlas-SNP
GPC4	2239	hgsc.bcm.edu	37	X	132438872	132438872	+	Missense_Mutation	SNP	C	C	A	rs1129980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	50	54	0	1	0	C|0.574;A|0.426	0.426	strong	.	GPC4	58	.	NM_001448	exon7	c.G1173T	p.E391D	CAGTTTCTCCTTG	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28459092	28459092	+	Silent	SNP	G	G	A	rs187225254	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	12	219	0	0.0618557	0	G|0.993;A|0.007	0.007	strong	.	HERC2	501	.	NM_004667	exon42	c.C6582T	p.D2194D	CTCGGAGTCGGGG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79447763	79447763	+	Missense_Mutation	SNP	T	T	C	rs34670941	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	106	234	0	0.46696	0	T|0.854;C|0.146	0.146	strong	.	FRAS1	779	.	NM_025074	exon70	c.T10877C	p.V3626A	CATGGGTTGACCC	.	PASS	Atlas-SNP
MYBPC3	4607	hgsc.bcm.edu	37	11	47369443	47369443	+	Silent	SNP	G	G	A	rs11570058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	39	93	0	0.428571	0	G|0.937;A|0.063	0.063	strong	.	MYBPC3	102	.	NM_000256	exon7	c.C786T	p.T262T	GTCTCCGGTGCCC	.	PASS	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9237435	9237435	+	Silent	SNP	A	A	G	rs10407484	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	57	118	0	0.428571	0	A|0.566;G|0.434	0.434	strong	OR7G3,NS,carcinoma,0,1	OR7G3	41	1	NM_001001958	exon1	c.T192C	p.S64S	CAGGATAGAGAGG	.	PASS	Atlas-SNP
ALPI	248	hgsc.bcm.edu	37	2	233321641	233321641	+	Silent	SNP	C	C	T	rs61732032	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	108	202	1	0.446281	0.00495049	C|0.912;T|0.088	0.088	strong	ALPI,NS,carcinoma,0,1	ALPI	64	1	NM_001631	exon4	c.C333T	p.S111S	AGACAGCGCAGCC	.	scavenged	Atlas-SNP
CPED1	79974	hgsc.bcm.edu	37	7	120876835	120876835	+	Missense_Mutation	SNP	A	A	G	rs35793694	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	48	93	0	0.539326	0	A|0.939;G|0.061	0.061	strong	.	.	.	.	NM_001105533	exon16	c.A2123G	p.E708G	ACATTGAAGCCAT	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29161202	29161202	+	Missense_Mutation	SNP	A	A	T	rs9910051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	55	111	0	0.478261	0	A|0.786;N|0.000	.	strong	.	ATAD5	150	.	NM_024857	exon2	c.A103T	p.T35S	ACATCTACCTGCA	.	PASS	Atlas-SNP
TMEM123	114908	hgsc.bcm.edu	37	11	102272884	102272884	+	Missense_Mutation	SNP	C	C	T	rs2155587	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	131	247	0	0.53252	0	C|0.929;T|0.071	0.071	strong	.	TMEM123	16	.	NM_052932	exon3	c.G211A	p.V71M	GTTTCACAGTACT	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109374952	109374952	+	Silent	SNP	A	A	G	rs826549	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	91	225	0	0.417431	0	A|0.745;G|0.255	0.255	strong	RANBP2_ENST00000283195,NS,carcinoma,0,1	RANBP2	488	1	NM_006267	exon18	c.A2550G	p.S850S	AGACTCAGTGCCT	.	scavenged	Atlas-SNP
MANSC1	54682	hgsc.bcm.edu	37	12	12496086	12496086	+	Missense_Mutation	SNP	C	C	T	rs3741798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	53	108	0	0.452991	0	C|0.898;T|0.102	0.102	strong	.	MANSC1	38	.	NM_018050	exon2	c.G163A	p.V55I	TATATACGGGCTC	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4827859	4827859	+	Missense_Mutation	SNP	G	G	A	rs77890266	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	68	136	0	0.441558	0	G|0.986;A|0.014	0.014	strong	.	.	.	.	NM_014855	exon12	c.G1529A	p.R510Q	CCTTCCGGGACCC	.	PASS	Atlas-SNP
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68344696	68344696	+	Missense_Mutation	SNP	C	C	T	rs3803650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	212	127	0	0.990654	0	C|0.334;T|0.666	0.666	strong	SLC7A6OS,NS,carcinoma,0,1	SLC7A6OS	22	1	NM_032178	exon1	c.G134A	p.G45D	TCCAAACCCTCCG	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209823354	209823354	+	Silent	SNP	G	G	A	rs2228339	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	28	75	0	0.388889	0	G|0.739;A|0.261	0.261	strong	LAMB3,NS,carcinoma,0,1	LAMB3	136	1	NM_000228	exon3	c.C138T	p.T46T	TCCACAGGTAGAT	.	PASS	Atlas-SNP
TMX4	56255	hgsc.bcm.edu	37	20	7980390	7980390	+	Silent	SNP	C	C	T	rs1012891	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	25	60	0	0.462963	0	C|0.691;T|0.308	0.308	strong	.	TMX4	39	.	NM_021156	exon4	c.G456A	p.P152P	AGAAGCCGGGGAT	.	PASS	Atlas-SNP
NUDT5	11164	hgsc.bcm.edu	37	10	12209752	12209752	+	Silent	SNP	T	T	C	rs6686	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	42	66	0	0.617647	0	T|0.523;C|0.477	0.477	strong	.	NUDT5	10	.	NM_014142	exon10	c.A609G	p.A203A	TTTCAGTGCTAGA	.	PASS	Atlas-SNP
CS	1431	hgsc.bcm.edu	37	12	56669799	56669799	+	Silent	SNP	G	G	A	rs61738833	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	104	163	0	0.483721	0	G|0.991;A|0.009	0.009	strong	.	CS	44	.	NM_004077	exon7	c.C769T	p.L257L	GGTACAGGCGCGT	.	PASS	Atlas-SNP
SLC31A2	1318	hgsc.bcm.edu	37	9	115925104	115925104	+	Silent	SNP	C	C	T	rs3810906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	121	204	1	0.510549	0.00490196	C|0.696;T|0.304	0.304	strong	SLC31A2,NS,carcinoma,0,1	SLC31A2	11	1	NM_001860	exon4	c.C339T	p.A113A	GCTGGCCGTAATG	.	PASS	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124154697	124154697	+	Splice_Site	SNP	G	G	T	rs10101626	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	58	88	0	0.522523	0	G|0.784;T|0.216	0.216	strong	.	WDR67	97	.	NM_145647	exon19	c.2835+1G>T	.	AAGAAGGTAAAAA	.	PASS	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9236886	9236886	+	Silent	SNP	A	A	G	rs10424352	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	49	131	1	0.365672	0.00763359	A|0.585;G|0.415	0.415	strong	OR7G3,NS,adenocarcinoma,-1,1	OR7G3	41	1	NM_001001958	exon1	c.T741C	p.V247V	GGAAACAACGATT	.	scavenged	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	37	4	3449652	3449652	+	Missense_Mutation	SNP	G	G	A	rs16844401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	70	132	0	0.466667	0	G|0.935;A|0.065	0.065	strong	.	HGFAC	69	.	NM_001528	exon12	c.G1526A	p.R509H	GGGACCGCTGTGC	.	PASS	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90338863	90338863	+	Silent	SNP	C	C	T	rs9353687	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	44	60	0	0.977778	0	C|0.815;T|0.185	0.185	strong	.	ANKRD6	51	.	NM_001242809	exon15	c.C1518T	p.C506C	CTGGTGCATGTTA	.	PASS	Atlas-SNP
ZNF354A	6940	hgsc.bcm.edu	37	5	178140090	178140090	+	Silent	SNP	C	C	T	rs1132336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	50	94	1	0.510204	0.0106383	C|0.762;T|0.238	0.238	strong	ZNF354A,NS,carcinoma,0,1	ZNF354A	74	1	NM_005649	exon5	c.G789A	p.T263T	AGTATGCGTTATT	.	scavenged	Atlas-SNP
INTS3	65123	hgsc.bcm.edu	37	1	153737498	153737498	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	31	86	0	0.295238	0	.	.	none	.	INTS3	83	.	NM_023015	exon20	c.G2049T	p.Q683H	GAAGCAGCCCAAG	.	PASS	Atlas-SNP
GPR61	83873	hgsc.bcm.edu	37	1	110086451	110086451	+	Silent	SNP	G	G	A	rs17575798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	22	54	0	0.415094	0	G|0.805;A|0.195	0.195	strong	.	GPR61	60	.	NM_031936	exon2	c.G807A	p.S269S	CAGCTCGGGGGCC	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8770822	8770822	+	Nonsense_Mutation	SNP	C	C	T	rs2294597	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	42	108	0	0.396226	0	C|0.774;T|0.226	0.226	strong	.	PLCB1	394	.	NM_182734	exon31	c.G3337T	p.G1113X	TTATAGCTAGAAG	.	PASS	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	37	14	59789727	59789727	+	Silent	SNP	G	G	A	rs8022614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	124	177	0	1	0	G|0.684;A|0.316	0.316	strong	.	DAAM1	95	.	NM_001270520	exon6	c.G558A	p.K186K	TATAAAGGCGTTA	.	PASS	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	37	21	33370900	33370900	+	Silent	SNP	T	T	C	rs9305483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	31	72	0	0.430556	0	T|0.382;C|0.618	0.618	strong	.	HUNK	74	.	NM_014586	exon11	c.T1548C	p.S516S	TTCTTCTTCCATG	.	PASS	Atlas-SNP
EMR2	30817	hgsc.bcm.edu	37	19	14875388	14875388	+	Missense_Mutation	SNP	G	G	A	rs35612307	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	50	108	0	0.462963	0	G|0.765;A|0.235	0.235	strong	.	EMR2	99	.	NM_001271052	exon10	c.C941T	p.A314V	CCAGGGGCCTCCA	.	PASS	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44418077	44418077	+	Missense_Mutation	SNP	C	C	T	rs407731	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	89	118	1	0.988889	0.00847458	C|0.480;T|0.520	0.520	strong	.	ZNF45	51	.	NM_003425	exon10	c.G1511A	p.R504K	CCACACCTCTCGC	.	PASS	Atlas-SNP
OR4C16	219428	hgsc.bcm.edu	37	11	55339652	55339652	+	Nonsense_Mutation	SNP	C	C	T	rs1459101	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	75	164	0	0.531915	0	C|0.759;T|0.241	0.241	strong	OR4C16,NS,carcinoma,-2,1	OR4C16	104	1	NM_001004701	exon1	c.C49T	p.Q17X	TTGACACAGGATC	.	PASS	Atlas-SNP
NOC3L	64318	hgsc.bcm.edu	37	10	96098373	96098373	+	Missense_Mutation	SNP	C	C	T	rs17517578	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	91	185	0	0.486631	0	C|0.868;T|0.132	0.132	strong	.	NOC3L	67	.	NM_022451	exon18	c.G2083A	p.A695T	GCAGAGCATGCAG	.	PASS	Atlas-SNP
RNF8	9025	hgsc.bcm.edu	37	6	37349033	37349033	+	Silent	SNP	G	G	A	rs2284922	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	51	107	0	0.447368	0	G|0.535;A|0.465	0.465	strong	RNF8,NS,carcinoma,+1,1	RNF8	78	1	NM_003958	exon7	c.G1344A	p.T448T	CAAAACGTACTCT	.	PASS	Atlas-SNP
RNASEH1	246243	hgsc.bcm.edu	37	2	3597974	3597974	+	Silent	SNP	T	T	C	rs10186193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	20	60	0	0.487805	0	T|0.579;C|0.421	0.421	strong	.	RNASEH1	27	.	NM_002936	exon4	c.A498G	p.P166P	ATGGCCTGGCCCC	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215848641	215848641	+	Silent	SNP	T	T	C	rs2797235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	154	188	1	1	0.00531915	T|0.265;C|0.735	0.735	strong	USH2A,NS,carcinoma,0,1	USH2A	1168	1	NM_206933	exon63	c.A12612G	p.T4204T	CTGGATTGTCTGA	.	PASS	Atlas-SNP
WDYHV1	55093	hgsc.bcm.edu	37	8	124448804	124448804	+	Missense_Mutation	SNP	T	T	A	rs6470147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	196	193	0	0.994924	0	T|0.626;A|0.374	0.374	strong	WDYHV1,NS,carcinoma,0,1	WDYHV1	30	1	NM_018024	exon4	c.T346A	p.F116I	GATGCCTTTAAGT	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373104	5373104	+	Missense_Mutation	SNP	A	A	G	rs5006889	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	60	239	0	0.35503	0	A|0.761;G|0.239	0.239	strong	.	OR51B6	53	.	NM_001004750	exon1	c.A367G	p.T123A	TTCATTACCATCC	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255503	25255503	+	Missense_Mutation	SNP	G	G	C	rs116889865	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	41	89	0	0.43617	0	G|0.999;C|0.001	0.001	strong	.	ZKSCAN2	90	.	NM_001012981	exon6	c.C1584G	p.S528R	CAATTTGCTCTTC	.	PASS	Atlas-SNP
BANF2	140836	hgsc.bcm.edu	37	20	17716416	17716416	+	Missense_Mutation	SNP	C	C	G	rs1053993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	64	83	0	0.533333	0	C|0.647;G|0.353	0.353	strong	.	BANF2	12	.	NM_001159495	exon3	c.C254G	p.T85S	AGCAGACTTCTCA	.	PASS	Atlas-SNP
CCDC70	83446	hgsc.bcm.edu	37	13	52440130	52440130	+	Missense_Mutation	SNP	A	A	G	rs1054515	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	28	55	0	0.482759	0	A|0.658;G|0.342	0.342	strong	.	CCDC70	31	.	NM_031290	exon2	c.A616G	p.I206V	GGCCACATTGCCG	.	PASS	Atlas-SNP
DCHS1	8642	hgsc.bcm.edu	37	11	6643976	6643976	+	Silent	SNP	C	C	T	rs7122587	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	22	33	0	0.478261	0	C|0.764;T|0.236	0.236	strong	.	DCHS1	277	.	NM_003737	exon21	c.G8931A	p.Q2977Q	TGCTGCCTGTGAC	.	PASS	Atlas-SNP
AP2M1	1173	hgsc.bcm.edu	37	3	183899832	183899832	+	Silent	SNP	C	C	T	rs8478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	44	115	0	0.463158	0	C|0.853;T|0.147	0.147	strong	.	AP2M1	35	.	NM_001025205	exon8	c.C954T	p.I318I	GAAGATCGAGGTG	.	PASS	Atlas-SNP
KIAA1551	55196	hgsc.bcm.edu	37	12	32134815	32134815	+	Missense_Mutation	SNP	G	G	A	rs16919122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	50	118	0	0.454545	0	G|0.878;A|0.122	0.122	strong	.	.	.	.	NM_018169	exon4	c.G926A	p.R309Q	AGAGTCGAGAAAT	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51613012	51613012	+	Silent	SNP	C	C	T	rs143737660	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	43	108	0	0.472527	0	C|0.999;T|0.001	0.001	strong	.	PKHD1	927	.	NM_170724	exon58	c.G9402A	p.K3134K	ACTTTCCTTATAG	.	PASS	Atlas-SNP
GABBR1	2550	hgsc.bcm.edu	37	6	29600104	29600104	+	Missense_Mutation	SNP	G	G	A	rs1805056	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	27	69	0	0.428571	0	G|0.962;A|0.038	0.038	strong	.	GABBR1	95	.	NM_021904	exon2	c.C59T	p.A20V	GTCTGCGCCCCGC	.	PASS	Atlas-SNP
DNAH3	55567	hgsc.bcm.edu	37	16	21078693	21078693	+	Silent	SNP	T	T	G	rs861424	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	54	82	0	0.556701	0	G|0.438;T|0.562	0.438	strong	.	DNAH3	1142	.	NM_017539	exon24	c.A3429C	p.A1143A	CTTCTCTGCCATC	.	PASS	Atlas-SNP
C11orf34	349633	hgsc.bcm.edu	37	11	112123095	112123095	+	Missense_Mutation	SNP	A	A	G	rs2564872	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	80	0	1	0	G|0.640;N|0.001	0.640	strong	.	C11orf34	6	.	NM_001145024	exon3	c.T424C	p.S142P	GAGTAGAAAGTAT	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45124286	45124286	+	Missense_Mutation	SNP	A	A	G	rs3735494	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	45	95	0	0.48913	0	A|0.677;G|0.323	0.323	strong	.	NACAD	44	.	NM_001146334	exon2	c.T1493C	p.V498A	GTAGCCACCTCCA	.	PASS	Atlas-SNP
ADRA1D	146	hgsc.bcm.edu	37	20	4228779	4228779	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	16	32	0	0.551724	0	.	.	none	.	ADRA1D	36	.	NM_000678	exon1	c.C826A	p.R276S	ACACGCGGCAGTA	.	PASS	Atlas-SNP
GNAS	2778	hgsc.bcm.edu	37	20	57429163	57429163	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	22	53	0	0.349206	0	.	.	none	.	GNAS	867	.	NM_001077490	exon1	c.C656T	p.S219L	CGCCATCGGCAGC	.	PASS	Atlas-SNP
ATF5	22809	hgsc.bcm.edu	37	19	50435921	50435921	+	Missense_Mutation	SNP	C	C	T	rs201354210	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	28	101	0	0.35	0	C|0.985;T|0.015	0.015	strong	.	ATF5	27	.	NM_012068	exon4	c.C421T	p.L141F	CCCTCCCTCCCCC	.	PASS	Atlas-SNP
HGS	9146	hgsc.bcm.edu	37	17	79662067	79662067	+	Silent	SNP	A	A	G	rs34384005	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	13	52	0	0.302326	0	A|0.915;G|0.085	0.085	strong	.	HGS	54	.	NM_004712	exon13	c.A1089G	p.E363E	TGGGGAAGGGCAC	.	PASS	Atlas-SNP
NKPD1	284353	hgsc.bcm.edu	37	19	45655647	45655647	+	Missense_Mutation	SNP	G	G	T	rs117934605	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	10	9	6	0	0.9	0	G|0.941;T|0.059	0.059	strong	.	NKPD1	46	.	NM_198478	exon4	c.C2048A	p.A683E	TCGGGCGCGCCCC	.	PASS	Atlas-SNP
SLC22A10	387775	hgsc.bcm.edu	37	11	63057925	63057925	+	Nonsense_Mutation	SNP	G	G	A	rs1790218	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	225	115	190	0	0.511111	0	G|0.538;A|0.462	0.462	strong	.	SLC22A10	79	.	NM_001039752	exon1	c.G288A	p.W96X	CCAGTGGCAGCTT	.	PASS	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1373518	1373518	+	Missense_Mutation	SNP	T	T	C	rs9905106	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	102	108	1	1	0.00925926	T|0.270;C|0.730	0.730	strong	MYO1C,NS,carcinoma,0,2	MYO1C	57	2	NM_001080779	exon24	c.A2477G	p.Q826R	ACATTCTGGGGCA	.	PASS	Atlas-SNP
OR5AS1	219447	hgsc.bcm.edu	37	11	55798259	55798259	+	Missense_Mutation	SNP	G	G	T	rs12224086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	117	222	0	0.531818	0	A|0.000;G|0.900;T|0.099	0.099	strong	OR5AS1,NS,carcinoma,+1,5	OR5AS1	121	5	NM_001001921	exon1	c.G365T	p.R122L	ATGACCGCTATGC	.	PASS	Atlas-SNP
CCDC34	91057	hgsc.bcm.edu	37	11	27362359	27362359	+	Missense_Mutation	SNP	T	T	G	rs17244028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	263	113	314	0	0.429658	0	T|0.772;G|0.228	0.228	strong	.	CCDC34	48	.	NM_030771	exon5	c.A791C	p.E264A	TGTATTTCAGCTT	.	PASS	Atlas-SNP
GP6	51206	hgsc.bcm.edu	37	19	55539049	55539049	+	Silent	SNP	C	C	T	rs5030705	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	35	88	0	0.432099	0	C|0.847;T|0.153	0.153	strong	.	GP6	55	.	NM_016363	exon4	c.G507A	p.T169T	GGTCACCGTGATG	.	PASS	Atlas-SNP
FZD6	8323	hgsc.bcm.edu	37	8	104312432	104312432	+	Missense_Mutation	SNP	A	A	G	rs827528	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	92	190	0	0.462312	0	A|0.785;G|0.215;T|0.000	0.215	strong	FZD6,colon,carcinoma,0,1	FZD6	61	1	NM_003506	exon2	c.A97G	p.M33V	AGATGTATGAAAA	.	PASS	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792171	8792171	+	Silent	SNP	T	T	C	rs11650737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	3	17	0	0.428571	0	T|0.722;C|0.278	0.278	strong	PIK3R5,NS,carcinoma,0,1	PIK3R5	79	1	NM_001142633	exon10	c.A933G	p.L311L	CTGGAGTAGCTCC	.	scavenged	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21796784	21796784	+	Missense_Mutation	SNP	G	G	C	rs3748361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	23	40	0	0.433962	0	G|0.722;C|0.277	0.277	strong	RPGRIP1,NS,carcinoma,0,1	RPGRIP1	213	1	NM_020366	exon18	c.G3097C	p.E1033Q	ACACCAGAGGTAA	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50965272	50965272	+	Silent	SNP	T	T	C	rs25668	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	74	86	0	0.986667	0	T|0.231;C|0.769	0.769	strong	.	MYBPC2	103	.	NM_004533	exon26	c.T3207C	p.C1069C	CAACTGTGCTGTC	.	PASS	Atlas-SNP
KHNYN	23351	hgsc.bcm.edu	37	14	24901433	24901433	+	Silent	SNP	C	C	T	rs17795094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	59	114	0	0.460938	0	C|0.904;T|0.096	0.096	strong	.	KHNYN	46	.	NM_015299	exon3	c.C966T	p.H322H	TGTCCACCGTGAG	.	PASS	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	37	4	184190233	184190233	+	Missense_Mutation	SNP	G	G	T	rs11941467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	60	108	0	0.545455	0	G|0.917;T|0.083	0.083	strong	.	WWC2	78	.	NM_024949	exon15	c.G2317T	p.A773S	AGAGTCGCCATTT	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	72998526	72998526	+	Silent	SNP	G	G	A	rs34095753	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	57	117	0	0.478992	0	G|0.955;A|0.045	0.045	strong	.	TSHZ1	104	.	NM_005786	exon2	c.G1029A	p.P343P	GAACCCGTACGTC	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103027234	103027234	+	Missense_Mutation	SNP	A	A	G	rs17301750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	33	75	0	0.417722	0	A|0.912;G|0.088	0.088	strong	.	DYNC2H1	246	.	NM_001377	exon26	c.A3862G	p.T1288A	AGTCGAACTATGA	.	PASS	Atlas-SNP
TIGD1	200765	hgsc.bcm.edu	37	2	233413771	233413771	+	Silent	SNP	C	C	T	rs6752614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	15	20	0	1	0	C|0.535;T|0.465	0.465	strong	TIGD1,colon,carcinoma,0,1	TIGD1	17	1	NM_145702	exon1	c.G822A	p.A274A	AAACCACGCTGTA	.	PASS	Atlas-SNP
ALS2CL	259173	hgsc.bcm.edu	37	3	46713457	46713457	+	Silent	SNP	C	C	G	rs7625303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	93	117	1	0.989362	0.00854701	C|0.780;G|0.220	0.220	strong	.	ALS2CL	78	.	NM_001190707	exon24	c.G2601C	p.T867T	CGACACCGTGCCC	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78865630	78865630	+	Silent	SNP	A	A	G	rs2289765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	21	40	0	0.488372	0	A|0.803;G|0.197	0.197	strong	.	RPTOR	122	.	NM_020761	exon18	c.A2094G	p.A698A	TCCAGCAACCACA	.	PASS	Atlas-SNP
CTU2	348180	hgsc.bcm.edu	37	16	88779032	88779032	+	Silent	SNP	G	G	C	rs2290896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	86	160	0	0.49711	0	G|0.895;C|0.105	0.105	strong	CTU2_ENST00000453996,NS,carcinoma,0,2	CTU2	66	2	NM_001012759	exon7	c.G456C	p.V152V	GAAGGTGTTCAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509939	195509939	+	Missense_Mutation	SNP	G	G	T	rs202039836		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	11	252	2	0.0662651	0.00793651	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.C8512A	p.P2838T	AGGAAGGGATGGT	.	scavenged	Atlas-SNP
CNTLN	54875	hgsc.bcm.edu	37	9	17273731	17273731	+	Missense_Mutation	SNP	A	A	G	rs3808795	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	141	149	1	0.992958	0.00671141	A|0.706;G|0.294	0.294	strong	.	CNTLN	128	.	NM_017738	exon6	c.A850G	p.T284A	TTTTAGACCTTTG	.	PASS	Atlas-SNP
POLDIP3	84271	hgsc.bcm.edu	37	22	43010821	43010821	+	Missense_Mutation	SNP	C	C	T	rs61744232	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	41	52	0	0.414141	0	C|0.995;T|0.005	0.005	strong	.	POLDIP3	58	.	NM_178136	exon1	c.G43A	p.A15T	CCGCCGCCCCGCG	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147480955	147480955	+	Missense_Mutation	SNP	A	A	G	rs2303067	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	240	301	1	0.991736	0.00332226	A|0.569;G|0.431	0.431	strong	.	SPINK5	245	.	NM_001127699	exon14	c.A1258G	p.K420E	GAAGGTAAATCAA	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263652	263652	+	Missense_Mutation	SNP	G	G	A	rs111543298	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	31	169	1	0.205298	0.00591716	G|0.162;A|0.838	0.838	strong	C17orf97_ENST00000360127,rectum,carcinoma,0,5	C17orf97	76	5	NM_001013672	exon2	c.G1018A	p.E340K	GACCCCGAGGCCC	.	scavenged	Atlas-SNP
ARHGEF25	115557	hgsc.bcm.edu	37	12	58010163	58010163	+	Missense_Mutation	SNP	A	A	G	rs1564374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	38	59	0	0.520548	0	A|0.402;G|0.598;T|0.000	0.598	strong	.	ARHGEF25	111	.	NM_001111270	exon15	c.A1634G	p.Q545R	GAATTCAGCTTGG	.	PASS	Atlas-SNP
VCX2	51480	hgsc.bcm.edu	37	X	8138170	8138170	+	Missense_Mutation	SNP	C	C	G	rs75657421	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	72	118	1	0.888889	0.00847458	C|0.367;G|0.633	0.633	strong	.	VCX2	16	.	NM_016378	exon3	c.G323C	p.S108T	ACCTCGCTCTCCT	.	PASS	Atlas-SNP
FAM209B	388799	hgsc.bcm.edu	37	20	55108538	55108538	+	Silent	SNP	C	C	T	rs141117316	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	346	74	207	0	0.213873	0	C|0.994;T|0.006	0.006	strong	.	.	.	.	NM_001013646	exon1	c.C141T	p.N47N	GCAGAACCTACCA	.	PASS	Atlas-SNP
PEX6	5190	hgsc.bcm.edu	37	6	42932202	42932202	+	Silent	SNP	C	C	T	rs1129186	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	53	101	0	0.449153	0	C|0.441;T|0.559	0.559	strong	PEX6,colon,carcinoma,0,1	PEX6	44	1	NM_000287	exon17	c.G2814A	p.E938E	ACCTGGCTCCAGC	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10071347	10071347	+	Missense_Mutation	SNP	C	C	T	rs2277969	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	20	29	0	0.408163	0	C|0.770;T|0.230	0.230	strong	.	COL5A3	243	.	NM_015719	exon66	c.G5071A	p.V1691I	GGGGGACGCTGAC	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2436201	2436201	+	Missense_Mutation	SNP	C	C	T	rs202052284	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	16	13	0	0.8	0	C|0.998;T|0.002	0.002	weak	.	TRPM5	86	.	NM_014555	exon10	c.G1556A	p.R519Q	AGGTCCCGCCAGG	.	PASS	Atlas-SNP
SLC24A4	123041	hgsc.bcm.edu	37	14	92922900	92922900	+	Silent	SNP	G	G	A	rs77671856	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	28	43	0	0.528302	0	G|0.792;A|0.208	0.208	strong	SLC24A4,colon,carcinoma,0,1	SLC24A4	112	1	NM_153646	exon12	c.G1203A	p.P401P	ACCACCGCCAGAG	.	PASS	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139701209	139701209	+	Missense_Mutation	SNP	G	G	T	rs4909444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	52	84	0	0.536082	0	G|0.699;T|0.301	0.301	strong	.	COL22A1	390	.	NM_152888	exon37	c.C2813A	p.A938D	CCGGGAGCACCCT	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124947396	124947396	+	Missense_Mutation	SNP	A	A	G	rs55752830	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	51	95	0	0.573034	0	A|0.619;G|0.381	0.381	strong	.	SLC37A2	105	.	NM_001145290	exon4	c.A286G	p.I96V	TTCCTCATCGCCT	.	PASS	Atlas-SNP
OSBPL10	114884	hgsc.bcm.edu	37	3	31789582	31789582	+	Missense_Mutation	SNP	T	T	C	rs2290532	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	31	86	0	0.462687	0	C|0.372;N|0.000	0.372	strong	.	OSBPL10	160	.	NM_017784	exon5	c.A760G	p.N254D	CAAGGTTCTTCTG	.	PASS	Atlas-SNP
SCD5	79966	hgsc.bcm.edu	37	4	83582064	83582064	+	Missense_Mutation	SNP	G	G	T	rs3733228	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	69	98	0	0.552	0	G|0.729;T|0.271	0.271	strong	.	SCD5	58	.	NM_024906	exon4	c.C736A	p.L246M	CACGCAGCATCAA	.	PASS	Atlas-SNP
TBC1D8	11138	hgsc.bcm.edu	37	2	101638828	101638828	+	Silent	SNP	C	C	T	rs34685616	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	64	139	0	0.571429	0	C|0.922;T|0.078	0.078	strong	.	TBC1D8	169	.	NM_001102426	exon16	c.G2631A	p.T877T	GATCTCCGTGTGG	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107360922	107360922	+	Missense_Mutation	SNP	A	A	G	rs1851724	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	85	218	0	0.461957	0	A|0.421;G|0.579	0.579	strong	OR13C5,NS,lymphoid_neoplasm,0,1	OR13C5	60	1	NM_001004482	exon1	c.T773C	p.M258T	ATGTACATGAGGA	.	PASS	Atlas-SNP
GCFC2	6936	hgsc.bcm.edu	37	2	75917161	75917161	+	Missense_Mutation	SNP	G	G	C	rs41286005	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	93	206	0	0.472081	0	G|0.970;C|0.030	0.030	strong	.	.	.	.	NM_003203	exon9	c.C1273G	p.Q425E	CTTCCTGATGGTT	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55524314	55524314	+	Silent	SNP	T	T	C	rs7137261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	58	105	0	0.460317	0	T|0.674;C|0.326	0.326	strong	.	OR9K2	63	.	NM_001005243	exon1	c.T762C	p.H254H	GATACATTCTACT	.	PASS	Atlas-SNP
PCDHGA10	56106	hgsc.bcm.edu	37	5	140793007	140793007	+	Missense_Mutation	SNP	A	A	G	rs4912751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	96	106	0	1	0	A|0.483;G|0.517	0.517	strong	.	PCDHGA10	114	.	NM_032090	exon1	c.A265G	p.I89V	AGCTTGATCACCG	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610436	32610436	+	Silent	SNP	T	T	C	rs1048372	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	291	288	179	0	0.989691	0	T|0.391;C|0.609	0.609	strong	.	HLA-DQA1	52	.	NM_002122	exon4	c.T663C	p.C221C	GGTCTGTGCCCTG	.	PASS	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90333599	90333599	+	Silent	SNP	A	A	G	rs17292811	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	50	116	0	1	0	A|0.116;G|0.884	0.884	strong	.	ANKRD6	51	.	NM_001242809	exon12	c.A1041G	p.A347A	GTCAGCATTTTCT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537249	88537249	+	Silent	SNP	T	T	C	rs371359066		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	14	134	7	0.10219	0.0522388	.	.	weak	DSPP,NS,carcinoma,0,5	DSPP	174	5	NM_014208	exon5	c.T3435C	p.S1145S	CAGCAGTGACAGC	.	scavenged	Atlas-SNP
IL37	27178	hgsc.bcm.edu	37	2	113674709	113674709	+	Missense_Mutation	SNP	C	C	G	rs2708943	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	36	78	0	0.461538	0	C|0.903;G|0.097	0.097	strong	.	IL37	56	.	NM_014439	exon3	c.C149G	p.P50R	TAGGTCCAAAGGT	.	PASS	Atlas-SNP
ENOX1	55068	hgsc.bcm.edu	37	13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	rs7338624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	21	80	0	0.304348	0	C|0.955;G|0.045	0.045	strong	.	ENOX1	158	.	NM_017993	exon4	c.G48C	p.E16D	AGGAAGCTCCTGG	.	PASS	Atlas-SNP
IFI44L	10964	hgsc.bcm.edu	37	1	79093818	79093818	+	Missense_Mutation	SNP	A	A	G	rs273259	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	32	83	0	0.444444	0	G|0.407;N|0.001	0.407	strong	.	IFI44L	93	.	NM_006820	exon2	c.A218G	p.H73R	ATTTACATGAAAG	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788145	3788145	+	Missense_Mutation	SNP	C	C	T	rs242018	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	54	105	0	0.568421	0	C|0.763;T|0.237	0.237	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.G460A	p.E154K	CATCTTCGCCCAT	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135956575	135956575	+	Missense_Mutation	SNP	G	G	A	rs78646793	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	29	112	0	0.208633	0	G|0.500;A|0.500	0.500	weak	.	RBMX	149	.	NM_002139	exon9	c.C902T	p.P301L	GATGGCGGGGGCC	.	PASS	Atlas-SNP
NLRP14	338323	hgsc.bcm.edu	37	11	7059981	7059981	+	Missense_Mutation	SNP	G	G	A	rs61063081	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	44	97	0	0.494382	0	G|0.835;A|0.165	0.165	strong	.	NLRP14	187	.	NM_176822	exon2	c.G164A	p.R55Q	CCAGGCGGGAGGA	.	PASS	Atlas-SNP
EEF2	1938	hgsc.bcm.edu	37	19	3982967	3982967	+	Silent	SNP	G	G	A	rs2230561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	31	69	0	0.574074	0	G|0.937;A|0.063	0.063	strong	.	EEF2	57	.	NM_001961	exon4	c.C450T	p.R150R	CTTGATGCGCTCG	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3645607	3645607	+	Missense_Mutation	SNP	A	A	G	rs77985244	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	21	43	0	0.552632	0	A|0.932;G|0.068	0.068	strong	.	SLX4	173	.	NM_032444	exon9	c.T2012C	p.L671S	CTTACCAAGGTGC	.	PASS	Atlas-SNP
CMKLR1	1240	hgsc.bcm.edu	37	12	108686008	108686008	+	Silent	SNP	C	C	G	rs1057401	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	33	71	0	0.445946	0	C|0.627;G|0.373	0.373	strong	CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	NM_001142344	exon3	c.G732C	p.V244V	TTTGCACACGATG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016825	1016825	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1138	68	953	0	0.059754	0	.	.	none	MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	NM_005961	exon31	c.C5976T	p.T1992T	GGTAGTGGTGGTC	.	PASS	Atlas-SNP
THEMIS2	9473	hgsc.bcm.edu	37	1	28209002	28209002	+	Silent	SNP	C	C	T	rs76072311	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	152	156	1	0.944099	0.00641026	C|0.976;T|0.024	0.024	strong	.	.	.	.	NM_001105556	exon4	c.C1167T	p.D389D	CAGTGACGTGGAT	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219610433	219610433	+	Silent	SNP	A	A	G	rs586194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	60	142	0	0.483871	0	A|0.446;G|0.554	0.554	strong	.	TTLL4	96	.	NM_014640	exon7	c.A1806G	p.E602E	CTGGGAACAGAGG	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43017426	43017426	+	Silent	SNP	T	T	G	rs16957091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	59	172	0	0.421429	0	T|0.565;G|0.435	0.435	strong	.	CDAN1	70	.	NM_138477	exon27	c.A3474C	p.L1158L	CTCCCGTAGCAAG	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9886275	9886275	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	34	94	0	0.472222	0	.	.	none	.	TXNDC2	168	.	NM_001098529	exon1	c.C104T	p.A35V	GTGATGCTAATGG	.	PASS	Atlas-SNP
SEBOX	645832	hgsc.bcm.edu	37	17	26691916	26691916	+	Silent	SNP	T	T	C	rs2277667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	108	0	0.435644	0	T|0.855;C|0.145	0.145	strong	.	SEBOX	20	.	NM_001080837	exon2	c.A171G	p.L57L	CTCCAGTAGCTGC	.	PASS	Atlas-SNP
SORBS1	10580	hgsc.bcm.edu	37	10	97143826	97143826	+	Missense_Mutation	SNP	T	T	C	rs35808802	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	64	113	0	0.542373	0	T|0.963;C|0.037	0.037	strong	.	SORBS1	185	.	NM_001034955	exon15	c.A1520G	p.Y507C	TCAATGTAGCTCA	.	PASS	Atlas-SNP
TAF7L	54457	hgsc.bcm.edu	37	X	100547805	100547805	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	44	52	0	0.956522	0	.	.	none	.	TAF7L	64	.	NM_024885	exon1	c.G229A	p.A77T	CTGGGGCCTGGGC	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100074446	100074446	+	Silent	SNP	C	C	T	rs3747504	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	44	77	0	0.54321	0	C|0.766;T|0.234	0.234	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon4	c.C444T	p.I148I	CACCATCGCTGCC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17085452	17085452	+	Silent	SNP	A	A	G	rs3981980		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	310	58	332	9	0.187097	0.0271084	A|1.000;|0.000	.	weak	Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001271733	exon10	c.T1239C	p.F413F	GGGAGCAAAATCG	.	scavenged	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792003	8792003	+	Silent	SNP	C	C	T	rs9915880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	21	64	0	0.362069	0	C|0.736;T|0.264	0.264	strong	.	PIK3R5	79	.	NM_001142633	exon10	c.G1101A	p.S367S	CGGCCCCGAGGCC	.	PASS	Atlas-SNP
ODF2	4957	hgsc.bcm.edu	37	9	131245130	131245130	+	Silent	SNP	G	G	A	rs139481144	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	41	57	0	0.5	0	G|0.999;A|0.001	0.001	strong	.	ODF2	227	.	NM_153435	exon10	c.G1143A	p.E381E	CAAGGAGGTGGAA	.	PASS	Atlas-SNP
GPATCH1	55094	hgsc.bcm.edu	37	19	33617583	33617583	+	Silent	SNP	C	C	T	rs6510356	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	24	38	0	0.55814	0	C|0.792;N|0.001	.	strong	.	GPATCH1	79	.	NM_018025	exon19	c.C2709T	p.S903S	CAGCAGCGACAGC	.	PASS	Atlas-SNP
ZNF385B	151126	hgsc.bcm.edu	37	2	180308028	180308028	+	Silent	SNP	C	C	T	rs2367796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	30	44	0	0.566038	0	C|0.827;T|0.173	0.173	strong	.	ZNF385B	68	.	NM_152520	exon10	c.G1365A	p.G455G	CCCATGCCCAGGC	.	PASS	Atlas-SNP
CCL8	6355	hgsc.bcm.edu	37	17	32647831	32647831	+	Missense_Mutation	SNP	A	A	C	rs1133763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	68	198	0	0.414634	0	A|0.839;C|0.161	0.161	strong	.	CCL8	12	.	NM_005623	exon3	c.A205C	p.K69Q	AAGACCAAACGGG	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46913477	46913477	+	Missense_Mutation	SNP	G	G	C	rs2230693	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	54	99	0	0.524272	0	G|0.935;C|0.065	0.065	strong	.	COL18A1	129	.	NM_030582	exon25	c.G2880C	p.Q960H	TGCCCAGAAAGGA	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940290	144940290	+	Missense_Mutation	SNP	C	C	G	rs201976887	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	240	14	205	0	0.0583333	0	.	.	weak	EPPK1,NS,carcinoma,0,5	EPPK1	199	5	NM_031308	exon1	c.G7132C	p.D2378H	TGGGGTCGGCCAG	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186026474	186026474	+	Missense_Mutation	SNP	T	T	C	rs12129650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	39	88	0	0.410526	0	C|0.538;N|0.000	0.538	strong	.	HMCN1	797	.	NM_031935	exon46	c.T7253C	p.I2418T	CTTCCATAACCTG	.	PASS	Atlas-SNP
GMPPB	29925	hgsc.bcm.edu	37	3	49760431	49760431	+	Missense_Mutation	SNP	G	G	C	rs34345884	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	251	125	274	0	0.498008	0	G|0.986;C|0.014	0.014	strong	.	GMPPB	14	.	NM_021971	exon4	c.C376G	p.H126D	CATGGTGCCGGTG	.	PASS	Atlas-SNP
FGFBP2	83888	hgsc.bcm.edu	37	4	15964485	15964485	+	Missense_Mutation	SNP	G	G	A	rs758329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	14	28	0	0.482759	0	G|0.606;A|0.394	0.394	strong	FGFBP2,colon,carcinoma,0,2	FGFBP2	22	2	NM_031950	exon1	c.C268T	p.P90S	AGTAAGGTTTGGG	.	PASS	Atlas-SNP
CCDC11	220136	hgsc.bcm.edu	37	18	47777244	47777244	+	Missense_Mutation	SNP	C	C	T	rs35193847	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	342	342	399	1	1	0.00250627	C|0.738;T|0.262	0.262	strong	.	CCDC11	59	.	NM_145020	exon5	c.G880A	p.E294K	TCCTCTCTTGTAG	.	PASS	Atlas-SNP
IER2	9592	hgsc.bcm.edu	37	19	13264398	13264398	+	Missense_Mutation	SNP	C	C	T	rs1042164	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	17	13	0	0.548387	0	C|0.921;T|0.079	0.079	strong	.	IER2	14	.	NM_004907	exon2	c.C398T	p.A133V	GGGACGCTGGACT	.	PASS	Atlas-SNP
SIRT1	23411	hgsc.bcm.edu	37	10	69666598	69666598	+	Silent	SNP	T	T	C	rs2273773	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	55	98	0	0.514019	0	T|0.910;C|0.090	0.090	strong	.	SIRT1	38	.	NM_012238	exon5	c.T994C	p.L332L	ATAGCCTTGTCAG	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26733062	26733062	+	Silent	SNP	T	T	C	rs2230375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	58	57	0	1	0	T|0.774;C|0.226	0.226	strong	.	ITPR2	270	.	NM_002223	exon33	c.A4407G	p.K1469K	TGCATGTTTCCTG	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46875586	46875586	+	Missense_Mutation	SNP	C	C	G	rs61749002	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	66	111	0	0.455172	0	C|0.976;G|0.024	0.024	strong	.	COL18A1	129	.	NM_030582	exon1	c.C142G	p.P48A	CCTGAGCCCCAGG	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45120248	45120248	+	Silent	SNP	G	G	A	rs1132130	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	97	181	0	0.480198	0	G|0.875;C|0.000;A|0.124	0.124	strong	.	NACAD	44	.	NM_001146334	exon7	c.C4665T	p.N1555N	GATGGCGTTGACG	.	PASS	Atlas-SNP
C9orf123	90871	hgsc.bcm.edu	37	9	7799653	7799653	+	Missense_Mutation	SNP	G	G	T	rs1127430	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	25	42	0	0.471698	0	G|0.647;T|0.353	0.353	strong	.	C9orf123	7	.	NM_033428	exon1	c.C82A	p.P28T	CTGGGGGCGCAGG	.	PASS	Atlas-SNP
CPEB3	22849	hgsc.bcm.edu	37	10	93999850	93999850	+	Silent	SNP	A	A	G	rs3824734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	22	9	0	1	0	A|0.307;G|0.693	0.693	strong	.	CPEB3	43	.	NM_014912	exon2	c.T258C	p.P86P	CTGAGGAGGCTGA	.	PASS	Atlas-SNP
LRG1	116844	hgsc.bcm.edu	37	19	4538599	4538599	+	Missense_Mutation	SNP	G	G	A	rs966384	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	15	31	0	0.483871	0	G|0.705;A|0.295	0.295	strong	.	LRG1	25	.	NM_052972	exon2	c.C397T	p.P133S	GGCCCGGGGGCAG	.	PASS	Atlas-SNP
C14orf166B	145497	hgsc.bcm.edu	37	14	77297656	77297656	+	Missense_Mutation	SNP	G	G	A	rs142627436	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	51	88	0	0.451327	0	G|0.995;A|0.005	0.005	strong	.	C14orf166B	52	.	NM_194287	exon3	c.G328A	p.V110M	TCCTACGTGAACC	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444607	20444607	+	Missense_Mutation	SNP	C	C	G	rs10135467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	99	172	0	0.538043	0	C|0.770;G|0.230	0.230	strong	.	OR4K15	82	.	NM_001005486	exon1	c.C930G	p.I310M	TGTAATCTACACG	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186857	12186857	+	Missense_Mutation	SNP	G	G	C	rs6511763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	37	84	0	0.4625	0	G|0.739;C|0.261	0.261	strong	.	ZNF844	69	.	NM_001136501	exon4	c.G922C	p.A308P	GAGAAGGCTTATG	.	PASS	Atlas-SNP
ZNF215	7762	hgsc.bcm.edu	37	11	6977109	6977109	+	Missense_Mutation	SNP	T	T	C	rs149189074	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	51	74	0	0.472222	0	T|0.996;C|0.004	0.004	strong	.	ZNF215	72	.	NM_013250	exon7	c.T901C	p.F301L	GAAGATTTTGAAT	.	PASS	Atlas-SNP
RAD54B	25788	hgsc.bcm.edu	37	8	95399378	95399378	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	81	190	0	0.45	0	.	.	none	.	RAD54B	88	.	NM_012415	exon11	c.T1819C	p.C607R	AGCTACATTCCTT	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201016296	201016296	+	Missense_Mutation	SNP	G	G	A	rs3850625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	66	104	0	0.481752	0	G|0.919;A|0.081	0.081	strong	.	CACNA1S	249	.	NM_000069	exon38	c.C4615T	p.R1539C	CTTGGCGTTTCAT	.	PASS	Atlas-SNP
TMEM132C	92293	hgsc.bcm.edu	37	12	129153986	129153986	+	Missense_Mutation	SNP	G	G	A	rs4272850	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	127	141	0	1	0	G|0.692;A|0.308	0.308	strong	.	TMEM132C	142	.	NM_001136103	exon5	c.G1330A	p.V444I	ACCGCCGTACTCA	.	PASS	Atlas-SNP
DCAF6	55827	hgsc.bcm.edu	37	1	168014204	168014204	+	Missense_Mutation	SNP	T	T	A	rs41271647	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	358	175	368	0	0.488827	0	T|0.933;A|0.067	0.067	strong	.	DCAF6	99	.	NM_001198956	exon16	c.T1997A	p.L666H	TCAATCTTGATCG	.	PASS	Atlas-SNP
ZFP2	80108	hgsc.bcm.edu	37	5	178359136	178359136	+	Silent	SNP	A	A	G	rs961030	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	28	65	1	0.5	0.0153846	A|0.718;G|0.282	0.282	strong	ZFP2,NS,carcinoma,+2,1	ZFP2	70	1	NM_030613	exon5	c.A822G	p.Q274Q	TAGTCAATGTGGA	.	scavenged	Atlas-SNP
ZBTB2	57621	hgsc.bcm.edu	37	6	151686905	151686905	+	Silent	SNP	C	C	T	rs11155787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	106	225	1	0.898305	0.00444444	C|0.495;T|0.505	0.505	strong	.	ZBTB2	30	.	NM_020861	exon3	c.G1296A	p.E432E	CCCTTCCTCAAAT	.	PASS	Atlas-SNP
GPRIN2	9721	hgsc.bcm.edu	37	10	46998904	46998904	+	Silent	SNP	G	G	A	rs140651048	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	32	239	0	0.228571	0	G|0.999;A|0.001	0.001	strong	.	GPRIN2	94	.	NM_014696	exon3	c.G24A	p.P8P	CGAGCCGGGTCCC	.	PASS	Atlas-SNP
ZNF594	84622	hgsc.bcm.edu	37	17	5087040	5087040	+	Missense_Mutation	SNP	A	A	G	rs9908414	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	30	77	0	0.352941	0	A|0.710;G|0.290	0.290	strong	ZNF594,caecum,carcinoma,0,1	ZNF594	89	1	NM_032530	exon2	c.T512C	p.I171T	TGTATAATAAGAT	.	PASS	Atlas-SNP
PDCD6IP	10015	hgsc.bcm.edu	37	3	33879770	33879770	+	Missense_Mutation	SNP	G	G	A	rs3203777	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	72	193	0	0.5	0	G|0.682;A|0.317	0.317	strong	PDCD6IP,NS,carcinoma,0,1	PDCD6IP	62	1	NM_001162429	exon9	c.G1147A	p.V383I	GATTTGGTTAACA	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43095101	43095101	+	Missense_Mutation	SNP	A	A	G	rs536119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	37	148	0	0.345794	0	A|0.413;G|0.587	0.587	strong	.	FAM198A	23	.	NM_001129908	exon3	c.A1379G	p.Q460R	AATGCCAGAACCC	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123970722	123970722	+	Missense_Mutation	SNP	T	T	A	rs2295876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	47	85	0	0.522222	0	A|0.085;C|0.000;T|0.915	0.085	strong	.	TACC2	271	.	NM_206862	exon9	c.T6782A	p.L2261H	AAGGGCTCTCCGT	.	PASS	Atlas-SNP
NRG1	3084	hgsc.bcm.edu	37	8	32611970	32611970	+	Missense_Mutation	SNP	G	G	T	rs74942016	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	76	146	0	0.452381	0	G|0.968;T|0.032	0.032	strong	.	NRG1	260	.	NM_013956	exon9	c.G796T	p.V266L	ATGTGTGTGGTGG	.	PASS	Atlas-SNP
ENTPD1	953	hgsc.bcm.edu	37	10	97599537	97599537	+	Silent	SNP	G	G	C	rs61731067	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	73	123	0	0.536765	0	G|0.945;C|0.055	0.055	strong	.	ENTPD1	44	.	NM_001164178	exon3	c.G270C	p.V90V	CGTGGTGCATCAA	.	PASS	Atlas-SNP
PCDHB12	56124	hgsc.bcm.edu	37	5	140590766	140590766	+	Missense_Mutation	SNP	A	A	G	rs2910006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	40	94	0	0.5	0	A|0.559;G|0.441	0.441	strong	PCDHB12,tonsil,carcinoma,0,1	PCDHB12	179	1	NM_018932	exon1	c.A2287G	p.K763E	TCAAATAAGTTCA	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179640255	179640255	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	3	184	0	0.0179641	0	.	.	none	TTN_ENST00000360870,NS,adenocarcinoma,-2,6	TTN	18412	6	NM_001267550	exon28	c.C6336T	p.Y2112Y	ATTTTTGTACCAT	.	scavenged	Atlas-SNP
KIF3C	3797	hgsc.bcm.edu	37	2	26204640	26204640	+	Silent	SNP	G	G	A	rs6721440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	37	48	0	0.544118	0	G|0.496;A|0.504	0.504	strong	.	KIF3C	79	.	NM_002254	exon1	c.C147T	p.A49A	CGGGGCGGCGCGG	.	PASS	Atlas-SNP
DGCR8	54487	hgsc.bcm.edu	37	22	20074006	20074006	+	Missense_Mutation	SNP	A	A	G	rs35987994	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	34	55	0	0.472222	0	A|0.958;G|0.042	0.042	strong	.	DGCR8	53	.	NM_001190326	exon2	c.A520G	p.I174V	GTAGGCATAGGGG	.	PASS	Atlas-SNP
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	70	186	0	0.460526	0	A|0.732;G|0.268	0.268	strong	NEB,NS,carcinoma,0,1	NEB	1697	1	NM_001271208	exon116	c.T18294C	p.Y6098Y	GTTAGGATAGTTT	.	PASS	Atlas-SNP
SLC12A8	84561	hgsc.bcm.edu	37	3	124802888	124802888	+	Missense_Mutation	SNP	C	C	T	rs2981482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	124	124	1	1	0.00806452	C|0.403;T|0.597	0.597	strong	.	SLC12A8	81	.	NM_024628	exon14	c.G1991A	p.R664Q	GGGGACCGCAAGC	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147486677	147486677	+	Silent	SNP	C	C	A	rs880687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	134	146	0	0.992593	0	C|0.571;A|0.429	0.429	strong	SPINK5,NS,carcinoma,0,1	SPINK5	245	1	NM_001127699	exon17	c.C1557A	p.G519G	CCGTGGCCCAGAT	.	PASS	Atlas-SNP
LTA	4049	hgsc.bcm.edu	37	6	31540784	31540784	+	Missense_Mutation	SNP	C	C	A	rs1041981	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	44	58	0	0.517647	0	C|0.603;A|0.397	0.397	strong	.	LTA	18	.	NM_001159740	exon3	c.C179A	p.T60N	ACAGCACCCTCAA	.	PASS	Atlas-SNP
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	52	93	0	0.460177	0	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	.	PASS	Atlas-SNP
NIPBL	25836	hgsc.bcm.edu	37	5	36985303	36985303	+	Missense_Mutation	SNP	A	A	G	rs3822471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	80	140	0	0.551724	0	A|0.879;G|0.121	0.121	strong	NIPBL_ENST00000448238,NS,carcinoma,-1,2	NIPBL	513	2	NM_015384	exon10	c.A2021G	p.N674S	AACAAAATGAAAA	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14991439	14991439	+	Silent	SNP	T	T	G	rs34590588	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	45	70	0	0.523256	0	T|0.950;G|0.050	0.050	strong	.	OR7A17	37	.	NM_030901	exon1	c.A729C	p.S243S	GAGGTGTGATGCA	.	PASS	Atlas-SNP
MB21D2	151963	hgsc.bcm.edu	37	3	192516931	192516931	+	Silent	SNP	A	A	C	rs35594076	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	85	150	0	0.574324	0	A|0.991;C|0.009	0.009	strong	.	MB21D2	75	.	NM_178496	exon2	c.T720G	p.S240S	TTTGAAAGATACC	.	PASS	Atlas-SNP
ZNF585A	199704	hgsc.bcm.edu	37	19	37642922	37642922	+	Missense_Mutation	SNP	C	C	T	rs79071992	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	241	91	209	0	0.377593	0	C|0.454;T|0.546	0.546	strong	.	ZNF585A	117	.	NM_199126	exon6	c.G1714A	p.V572I	TGTGAACTGGCTG	.	PASS	Atlas-SNP
ANXA2R	389289	hgsc.bcm.edu	37	5	43039793	43039793	+	Missense_Mutation	SNP	T	T	C	rs1054428	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	56	106	0	0.482759	0	T|0.756;C|0.244	0.244	strong	.	.	.	.	NM_001014279	exon1	c.A356G	p.Q119R	AGCTGCTGGAGCC	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	37	6	151670690	151670690	+	Silent	SNP	G	G	A	rs35341741	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	7	106	0	0.0933333	0	G|0.924;A|0.076	0.076	strong	.	AKAP12	170	.	NM_005100	exon4	c.G1164A	p.S388S	TGGCTCGCAGGGA	.	PASS	Atlas-SNP
TRPM7	54822	hgsc.bcm.edu	37	15	50867082	50867082	+	Silent	SNP	G	G	A	rs473357	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	35	85	0	0.4375	0	G|0.417;A|0.583	0.583	strong	.	TRPM7	145	.	NM_017672	exon34	c.C4986T	p.Y1662Y	TTCTTTGTAAATA	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	37	3	113379865	113379865	+	Missense_Mutation	SNP	G	G	C	rs9866806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	71	84	1	1	0.0119048	G|0.747;C|0.253	0.253	strong	KIAA2018,NS,carcinoma,+1,1	KIAA2018	180	1	NM_001009899	exon7	c.C664G	p.P222A	GAACAGGCTGGTT	.	scavenged	Atlas-SNP
SPRY3	10251	hgsc.bcm.edu	37	X	155004280	155004280	+	Silent	SNP	A	A	G	rs306888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	58	154	0	0.36478	0	A|0.771;G|0.229	0.229	strong	.	SPRY3	52	.	NM_005840	exon2	c.A747G	p.Q249Q	GTGCCAACAGGGC	.	PASS	Atlas-SNP
LRRCC1	85444	hgsc.bcm.edu	37	8	86021994	86021994	+	Missense_Mutation	SNP	G	G	A	rs62525422	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	70	160	0	0.463576	0	G|0.925;A|0.075	0.075	strong	.	LRRCC1	212	.	NM_033402	exon2	c.G269A	p.C90Y	AACTGTGCACATT	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	37	6	43172529	43172529	+	Silent	SNP	G	G	A	rs45496798	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	52	113	0	0.429752	0	G|0.990;A|0.010	0.010	strong	CUL9,NS,adenoma,0,1	CUL9	248	1	NM_015089	exon22	c.G4383A	p.S1461S	GCCTTCGCCAGTG	.	PASS	Atlas-SNP
METTL22	79091	hgsc.bcm.edu	37	16	8722629	8722629	+	Missense_Mutation	SNP	G	G	C	rs2270286	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	76	142	0	0.535211	0	G|0.810;C|0.190	0.190	strong	.	METTL22	23	.	NM_024109	exon3	c.G176C	p.W59S	ACTCTTGGACAGA	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50532812	50532812	+	Missense_Mutation	SNP	A	A	G	rs11101093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	97	180	0	0.489899	0	A|0.908;G|0.092	0.092	strong	.	C10orf71	179	.	NM_001135196	exon3	c.A2222G	p.D741G	CATTTGATGATCA	.	PASS	Atlas-SNP
SNX32	254122	hgsc.bcm.edu	37	11	65601560	65601560	+	Silent	SNP	G	G	C	rs17854357	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	15	45	0	0.365854	0	G|0.893;C|0.107	0.107	strong	SNX32,NS,carcinoma,0,1	SNX32	46	1	NM_152760	exon1	c.G24C	p.G8G	GGTTGGGAAGGAG	.	PASS	Atlas-SNP
LRBA	987	hgsc.bcm.edu	37	4	151719263	151719263	+	Silent	SNP	A	A	G	rs1129998	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	404	194	365	1	0.480198	0.00273973	A|0.839;G|0.161	0.161	strong	.	LRBA	253	.	NM_006726	exon34	c.T5550C	p.V1850V	TTCCACAACTGAA	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155219361	155219361	+	Silent	SNP	A	A	G	rs17031387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	88	206	0	0.453608	0	A|0.826;G|0.174	0.174	strong	DCHS2,NS,carcinoma,-2,1	DCHS2	594	1	NM_017639	exon18	c.T4740C	p.D1580D	AACTGGATCATTG	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113189954	113189954	+	Silent	SNP	T	T	G	rs41279045	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	61	128	0	0.465649	0	T|0.963;G|0.037	0.037	strong	.	SVEP1	326	.	NM_153366	exon36	c.A5892C	p.G1964G	TGGTTCTCCACAG	.	PASS	Atlas-SNP
TAS2R13	50838	hgsc.bcm.edu	37	12	11061122	11061122	+	Missense_Mutation	SNP	T	T	C	rs1015443	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	116	131	0	0.966667	0	T|0.499;C|0.501	0.501	strong	.	TAS2R13	29	.	NM_023920	exon1	c.A776G	p.N259S	ACTGTGTTCTGAT	.	PASS	Atlas-SNP
IFT122	55764	hgsc.bcm.edu	37	3	129237966	129237966	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	42	81	0	0.42	0	.	.	none	.	IFT122	117	.	NM_052985	exon29	c.G3561A	p.R1187R	TCTGCGGCTAGTG	.	PASS	Atlas-SNP
MAP3K9	4293	hgsc.bcm.edu	37	14	71267772	71267772	+	Silent	SNP	G	G	A	rs147891121	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	35	68	0	0.466667	0	G|1.000;A|0.000	0.000	strong	.	MAP3K9	109	.	NM_033141	exon2	c.C432T	p.L144L	CAAGGTGAGCTCC	.	PASS	Atlas-SNP
CPN2	1370	hgsc.bcm.edu	37	3	194063153	194063153	+	Silent	SNP	G	G	A	rs3732474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	114	87	0	0.991304	0	G|0.700;A|0.300	0.300	strong	.	CPN2	56	.	NM_001080513	exon2	c.C279T	p.F93F	CCCCCCGAAGGCA	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	rs187128776	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	27	97	0	0.375	0	T|0.985;C|0.015	0.015	strong	RADIL,brain,glioma,0,1	RADIL	110	1	NM_018059	exon11	c.A2369G	p.N790S	AGGCAGTTGGCTT	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25016911	25016911	+	Missense_Mutation	SNP	C	C	T	rs199703506	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	475	16	397	4	0.0336842	0.0100756	C|0.996;T|0.004	0.004	strong	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon9	c.C607T	p.R203W	GTGCTTCGGGAGG	.	scavenged	Atlas-SNP
C12orf43	64897	hgsc.bcm.edu	37	12	121454148	121454148	+	Missense_Mutation	SNP	C	C	T	rs11537857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	25	53	0	0.520833	0	T|0.040;C|0.960	0.040	strong	.	C12orf43	30	.	NM_022895	exon1	c.G130A	p.G44R	GCTTCCCTGCCAC	.	PASS	Atlas-SNP
FAM22G	441457	hgsc.bcm.edu	37	9	99699485	99699485	+	Missense_Mutation	SNP	G	G	C	rs7866127	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	64	110	1	0.520325	0.00909091	G|0.893;C|0.107	0.107	strong	FAM22G,NS,carcinoma,0,1	FAM22G	66	1	NM_001045477	exon5	c.G1122C	p.E374D	TGAGGAGATCCCC	.	scavenged	Atlas-SNP
PNPO	55163	hgsc.bcm.edu	37	17	46020698	46020698	+	Silent	SNP	C	C	T	rs11079804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	75	143	0	0.436047	0	C|0.855;T|0.145	0.145	strong	PNPO,NS,adenoma,0,1	PNPO	18	1	NM_018129	exon2	c.C165T	p.S55S	GACCTCCCTTGAC	.	PASS	Atlas-SNP
CHM	1121	hgsc.bcm.edu	37	X	85219021	85219021	+	Silent	SNP	T	T	C	rs10217950	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	61	63	0	0.983871	0	T|0.840;C|0.160	0.160	strong	.	CHM	57	.	NM_000390	exon5	c.A351G	p.A117A	CTGCAGTGCACCA	.	PASS	Atlas-SNP
CCDC102A	92922	hgsc.bcm.edu	37	16	57555076	57555076	+	Silent	SNP	C	C	T	rs28446687	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	50	87	0	0.581395	0	C|0.768;T|0.232	0.232	strong	.	CCDC102A	22	.	NM_033212	exon4	c.G825A	p.A275A	GCTCAACGCCAGT	.	PASS	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	37	17	73839326	73839326	+	Missense_Mutation	SNP	C	C	T	rs9904366	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	48	70	0	0.527473	0	C|0.984;T|0.016	0.016	strong	.	UNC13D	68	.	NM_199242	exon3	c.G175A	p.A59T	AGAGTGCGTCCTC	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833369	82833369	+	Missense_Mutation	SNP	A	A	G	rs309559	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	40	71	0	0.571429	0	T|0.003;G|0.491	0.491	strong	.	VCAN	498	.	NM_004385	exon8	c.A4547G	p.K1516R	CAGCCAAAAAAGG	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50406630	50406630	+	Missense_Mutation	SNP	T	T	G	rs6091375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	279	136	259	0	0.487455	0	T|0.917;G|0.083	0.083	strong	.	SALL4	168	.	NM_020436	exon2	c.A2392C	p.I798L	ACTTGATGCTTTC	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305654	48305654	+	Missense_Mutation	SNP	C	C	T	rs73036913	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	21	36	0	0.488372	0	C|0.949;T|0.051	0.051	strong	TPRX1,colon,carcinoma,0,1	TPRX1	46	1	NM_198479	exon2	c.G614A	p.G205D	ATCGGGCCTGGGA	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118229	93118229	+	Missense_Mutation	SNP	C	C	T	rs117068593	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	28	32	0	0.54902	0	C|0.886;T|0.114	0.114	strong	.	RIN3	81	.	NM_024832	exon6	c.C835T	p.R279C	CCACGCCGCCCAC	.	PASS	Atlas-SNP
DOCK6	57572	hgsc.bcm.edu	37	19	11348960	11348960	+	Missense_Mutation	SNP	G	G	A	rs12609039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	35	89	0	0.416667	0	G|0.960;A|0.040	0.040	strong	.	DOCK6	104	.	NM_020812	exon15	c.C1664T	p.P555L	CTGTGCGGGTACA	.	PASS	Atlas-SNP
CSTA	1475	hgsc.bcm.edu	37	3	122056432	122056432	+	Silent	SNP	C	C	T	rs17589	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	57	121	0	0.398601	0	C|0.552;T|0.448	0.448	strong	.	CSTA	11	.	NM_005213	exon2	c.C105T	p.Y35Y	GACTTACGGAAAA	.	PASS	Atlas-SNP
ASB17	127247	hgsc.bcm.edu	37	1	76387795	76387795	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	48	105	0	0.461538	0	.	.	none	.	ASB17	53	.	NM_080868	exon2	c.G651A	p.V217V	AGAAAGCACTCTG	.	PASS	Atlas-SNP
CYP3A5	1577	hgsc.bcm.edu	37	7	99273815	99273815	+	Missense_Mutation	SNP	G	G	A	rs28383468	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	50	88	0	0.403226	0	G|0.994;A|0.006	0.006	strong	.	CYP3A5	46	.	NM_001190484	exon2	c.C88T	p.H30Y	GTCCATGTGTACG	.	PASS	Atlas-SNP
TCN2	6948	hgsc.bcm.edu	37	22	31006860	31006860	+	Missense_Mutation	SNP	A	A	G	rs9606756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	44	83	0	0.444444	0	A|0.885;G|0.115	0.115	strong	.	TCN2	44	.	NM_001184726	exon2	c.A67G	p.I23V	TAAGAAATACCAG	.	PASS	Atlas-SNP
PRMT7	54496	hgsc.bcm.edu	37	16	68389772	68389772	+	Silent	SNP	C	C	T	rs1131933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	21	33	0	0.552632	0	C|0.488;T|0.512	0.512	strong	.	PRMT7	51	.	NM_019023	exon17	c.C1797T	p.T599T	GGGCACCGTGGAG	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11251	11251	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	12	2	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.A492G	p.L164L	CGCACTAATTTAC	.	PASS	Atlas-SNP
ANP32C	23520	hgsc.bcm.edu	37	4	165118796	165118796	+	Missense_Mutation	SNP	G	G	A	rs2288674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	78	189	0	0.47561	0	G|0.673;A|0.327	0.327	strong	.	ANP32C	59	.	NM_012403	exon1	c.C68T	p.A23V	TCCAGGGCAAGTT	.	PASS	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64023971	64023971	+	Silent	SNP	G	G	A	rs7943988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	71	153	0	0.533835	0	G|0.807;A|0.193	0.193	strong	.	PLCB3	103	.	NM_000932	exon9	c.G822A	p.L274L	CCGGCTGCTCATC	.	PASS	Atlas-SNP
DEF6	50619	hgsc.bcm.edu	37	6	35288696	35288696	+	Silent	SNP	C	C	T	rs34278260	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	21	91	0	0.5	0	C|0.970;T|0.030	0.030	strong	.	DEF6	36	.	NM_022047	exon10	c.C1617T	p.N539N	CACCAACGTGAAA	.	PASS	Atlas-SNP
H2AFX	3014	hgsc.bcm.edu	37	11	118965688	118965688	+	Silent	SNP	G	G	A	rs1064180	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	12	9	0	0.48	0	G|0.999;A|0.001	0.001	weak	.	H2AFX	8	.	NM_002105	exon1	c.C417T	p.A139A	CTGGGAGGCCTGG	.	PASS	Atlas-SNP
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246979	47246979	+	Silent	SNP	A	A	G	rs16946912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	7	34	0	0.4375	0	A|0.888;G|0.112	0.112	strong	.	B4GALNT2	67	.	NM_153446	exon11	c.A1590G	p.E530E	CTCAGAACTGGCT	.	PASS	Atlas-SNP
C1QTNF8	390664	hgsc.bcm.edu	37	16	1143496	1143496	+	Splice_Site	SNP	C	C	A	rs150337362	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	13	7	0	0.764706	0	C|0.984;A|0.016	0.016	strong	.	C1QTNF8	15	.	NM_207419	exon5	c.763+1G>T	.	CCCTCACCCGGCT	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121592689	121592689	+	Missense_Mutation	SNP	T	T	C	rs17525809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	63	97	0	0.533898	0	T|0.944;C|0.056	0.056	strong	.	P2RX7	53	.	NM_002562	exon2	c.T227C	p.V76A	AGATCGTGGAGAA	.	PASS	Atlas-SNP
ADAL	161823	hgsc.bcm.edu	37	15	43632549	43632549	+	Silent	SNP	T	T	C	rs2278857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	52	94	0	0.541667	0	T|0.487;C|0.513	0.513	strong	.	ADAL	48	.	NM_001012969	exon6	c.T342C	p.T114T	TGCTACTGGTAGA	.	PASS	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	37	4	169188780	169188780	+	Missense_Mutation	SNP	T	T	C	rs576619	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	335	139	348	1	0.414925	0.00287356	T|0.915;C|0.085	0.085	strong	.	DDX60	304	.	NM_017631	exon22	c.A2992G	p.I998V	AATGAATGTCACC	.	PASS	Atlas-SNP
TRIB3	57761	hgsc.bcm.edu	37	20	368905	368905	+	Missense_Mutation	SNP	A	A	G	rs2295490	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	25	41	0	0.555556	0	A|0.840;G|0.160	0.160	strong	.	TRIB3	50	.	NM_021158	exon2	c.A251G	p.Q84R	CCTACCAGGCCCT	.	PASS	Atlas-SNP
DZIP1	22873	hgsc.bcm.edu	37	13	96239805	96239805	+	Missense_Mutation	SNP	G	G	A	rs11070136	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	46	90	0	0.505495	0	G|0.704;A|0.296	0.296	strong	DZIP1,NS,carcinoma,0,1	DZIP1	195	1	NM_198968	exon20	c.C2206T	p.P736S	GCTTGGGAGAATC	.	PASS	Atlas-SNP
ATG16L1	55054	hgsc.bcm.edu	37	2	234171812	234171812	+	Silent	SNP	A	A	G	rs13011156	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	53	76	0	0.546392	0	A|0.957;G|0.043	0.043	strong	.	ATG16L1	83	.	NM_017974	exon3	c.A246G	p.L82L	TCAGCTACAAGAA	.	PASS	Atlas-SNP
ZBTB12	221527	hgsc.bcm.edu	37	6	31868938	31868938	+	Missense_Mutation	SNP	C	C	T	rs9394078	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	113	119	0	0.660819	0	C|0.967;T|0.033	0.033	strong	ZBTB12,NS,carcinoma,+2,1	ZBTB12	25	1	NM_181842	exon2	c.G145A	p.V49I	AGATGACCTTGTG	.	PASS	Atlas-SNP
ITGAE	3682	hgsc.bcm.edu	37	17	3654980	3654980	+	Silent	SNP	A	A	G	rs11652878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	24	64	0	0.4	0	A|0.864;G|0.136	0.136	strong	.	ITGAE	96	.	NM_002208	exon15	c.T1857C	p.N619N	GTGTCCATTGTAG	.	PASS	Atlas-SNP
C16orf55	124045	hgsc.bcm.edu	37	16	89724755	89724755	+	Missense_Mutation	SNP	C	C	T	rs13329897	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	35	62	0	0.416667	0	C|0.987;T|0.013	0.013	strong	.	C16orf55	6	.	NM_001271910	exon2	c.C137T	p.S46L	GGGAGTCGGAGAA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921277	12921277	+	Silent	SNP	A	A	G	rs3204826	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	288	9	264	2	0.03125	0.00757576	A|0.996;G|0.004	0.004	strong	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon4	c.A1068G	p.L356L	CGTGTTAGAGGGC	.	scavenged	Atlas-SNP
CPNE6	9362	hgsc.bcm.edu	37	14	24545366	24545366	+	Silent	SNP	T	T	C	rs2070342	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	124	121	0	0.992	0	T|0.579;C|0.421	0.421	strong	.	CPNE6	40	.	NM_006032	exon11	c.T933C	p.I311I	GGCCATTGACTTC	.	PASS	Atlas-SNP
CAPN13	92291	hgsc.bcm.edu	37	2	30976058	30976058	+	Silent	SNP	C	C	T	rs2926304	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	80	90	0	1	0	C|0.617;N|0.000	.	strong	CAPN13,NS,carcinoma,0,1	CAPN13	70	1	NM_144575	exon10	c.G948A	p.S316S	TTGACACGACATC	.	PASS	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	37	17	32962050	32962050	+	Missense_Mutation	SNP	C	C	T	rs75594429	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	21	50	0	0.396226	0	C|0.979;T|0.021	0.021	strong	.	TMEM132E	122	.	NM_207313	exon8	c.C1651T	p.H551Y	GTGGCACACATGG	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	131864652	131864652	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	21	64	0	0.318182	0	.	.	none	.	PLXNA4	873	.	NM_020911	exon20	c.C3668T	p.P1223L	ATCCCCGGGGAGT	.	PASS	Atlas-SNP
GIMAP7	168537	hgsc.bcm.edu	37	7	150217309	150217309	+	Missense_Mutation	SNP	C	C	T	rs3735080	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	46	80	0	0.534884	0	C|0.840;T|0.160	0.160	strong	GIMAP7,NS,carcinoma,0,1	GIMAP7	47	1	NM_153236	exon2	c.C247T	p.R83C	ATCAGCCGCTGCA	.	PASS	Atlas-SNP
WSCD1	23302	hgsc.bcm.edu	37	17	6014188	6014188	+	Silent	SNP	C	C	T	rs74858033	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	63	128	0	0.547826	0	C|0.991;T|0.009	0.009	strong	.	WSCD1	84	.	NM_015253	exon7	c.C1107T	p.H369H	ACGGCACCTCATT	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	37	10	3180298	3180298	+	Silent	SNP	C	C	T	rs10175	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	72	0	0.5	0	C|0.756;T|0.244	0.244	strong	.	PITRM1	109	.	NM_001242307	exon27	c.G3042A	p.K1014K	TGTGCTCTTCCCA	.	PASS	Atlas-SNP
PARP15	165631	hgsc.bcm.edu	37	3	122354037	122354037	+	Silent	SNP	A	A	G	rs1106346	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	72	98	0	0.533333	0	A|0.654;G|0.346	0.346	strong	.	PARP15	115	.	NM_001113523	exon11	c.A1743G	p.K581K	TGGGAAAAATGGT	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17264939	17264939	+	Silent	SNP	T	T	C	rs4558023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	508	225	244	1	0.442913	0.00409836	T|0.699;C|0.301	0.301	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon11	c.T1335C	p.D445D	AGAGGATGGAGAG	.	PASS	Atlas-SNP
ZNF566	84924	hgsc.bcm.edu	37	19	36940760	36940760	+	Silent	SNP	G	G	T	rs2967532	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	65	153	0	0.445205	0	G|0.483;T|0.517	0.517	strong	ZNF566,mouth,carcinoma,+2,1	ZNF566	40	1	NM_001145343	exon5	c.C379A	p.R127R	ACTGCCGATTACA	.	PASS	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32756744	32756744	+	Silent	SNP	A	A	G	rs2076035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	273	215	261	2	0.787546	0.00766284	A|0.497;G|0.503	0.503	strong	.	RFPL3	91	.	NM_001098535	exon2	c.A879G	p.Q293Q	TGATCAAGGTGTC	.	PASS	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201047062	201047062	+	Silent	SNP	G	G	A	rs4915476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	89	156	0	0.523529	0	G|0.776;A|0.224	0.224	strong	.	CACNA1S	249	.	NM_000069	exon11	c.C1564T	p.L522L	TGCCCAGGGGTGT	.	PASS	Atlas-SNP
CWF19L1	55280	hgsc.bcm.edu	37	10	102006681	102006681	+	Silent	SNP	C	C	T	rs17112787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	37	97	0	0.425287	0	C|0.921;T|0.079	0.079	strong	CWF19L1,NS,carcinoma,-1,2	CWF19L1	39	2	NM_018294	exon8	c.G720A	p.A240A	ACTGAACGCGTAA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9077581	9077581	+	Missense_Mutation	SNP	G	G	T	rs73011014	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	452	212	386	0	0.469027	0	G|0.809;T|0.191	0.191	strong	.	MUC16	4315	.	NM_024690	exon3	c.C9865A	p.P3289T	CAGGTGGGGATGG	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52131119	52131119	+	Missense_Mutation	SNP	A	A	G	rs2278831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	62	103	0	0.484375	0	A|0.913;G|0.087	0.087	strong	.	SIGLEC5	67	.	NM_003830	exon5	c.T965C	p.F322S	TGCAGGAAGCCCA	.	PASS	Atlas-SNP
SNX7	51375	hgsc.bcm.edu	37	1	99164434	99164434	+	Silent	SNP	G	G	A	rs6577322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	70	190	0	0.434783	0	G|0.762;A|0.238	0.238	strong	.	SNX7	76	.	NM_015976	exon6	c.G1011A	p.E337E	ACATGAGTACGTG	.	PASS	Atlas-SNP
FAM135B	51059	hgsc.bcm.edu	37	8	139149406	139149406	+	Silent	SNP	G	G	A	rs6577876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	40	114	0	0.338983	0	G|0.777;A|0.223	0.223	strong	.	FAM135B	423	.	NM_015912	exon19	c.C3999T	p.L1333L	GTCTTTGAGGGCA	.	PASS	Atlas-SNP
GLIS1	148979	hgsc.bcm.edu	37	1	54060248	54060248	+	Missense_Mutation	SNP	T	T	C	rs4307514	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	49	116	0	0.466667	0	T|0.751;C|0.249	0.249	strong	GLIS1,NS,carcinoma,0,1	GLIS1	52	1	NM_147193	exon3	c.A328G	p.T110A	CTCCCGTCAGAGG	.	PASS	Atlas-SNP
OR4A15	81328	hgsc.bcm.edu	37	11	55135435	55135435	+	Missense_Mutation	SNP	C	C	T	rs1425193	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	63	150	0	0.477273	0	C|0.778;T|0.222	0.222	strong	.	OR4A15	161	.	NM_001005275	exon1	c.C76T	p.P26S	CCAACACCTTCAG	.	PASS	Atlas-SNP
RGAG1	57529	hgsc.bcm.edu	37	X	109694685	109694685	+	Silent	SNP	T	T	A	rs2073787	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	85	101	1	1	0.00990099	T|0.511;0|0.003	.	strong	.	RGAG1	168	.	NM_020769	exon3	c.T840A	p.G280G	TGGAGGTACATCA	.	PASS	Atlas-SNP
NUP88	4927	hgsc.bcm.edu	37	17	5308377	5308377	+	Silent	SNP	C	C	T	rs2301739	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	102	170	0	0.534031	0	C|0.806;T|0.194	0.194	strong	.	NUP88	47	.	NM_002532	exon6	c.G1044A	p.T348T	ACTTACCGTGTGG	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713674	32713674	+	Silent	SNP	C	C	A	rs34357612	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	388	66	516	0	0.170103	0	C|0.886;A|0.114	0.114	strong	.	HLA-DQA2	27	.	NM_020056	exon3	c.C438A	p.T146T	CATCACCTGGCTG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465190	10465190	+	Missense_Mutation	SNP	C	C	T	rs72494282	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	65	130	0	0.460993	0	C|0.835;T|0.165	0.165	strong	.	RP1L1	453	.	NM_178857	exon4	c.G6418A	p.E2140K	GGGCCTCCCCTTC	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43818079	43818079	+	Missense_Mutation	SNP	G	G	A	rs62020612	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	22	75	0	0.338462	0	G|0.831;A|0.169	0.169	strong	MAP1A,colon,carcinoma,0,1	MAP1A	189	1	NM_002373	exon4	c.G4408A	p.A1470T	GACAAGGCCCTGG	.	PASS	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792514	8792514	+	Silent	SNP	G	G	A	rs394811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	34	72	0	0.441558	0	G|0.527;A|0.473	0.473	strong	.	PIK3R5	79	.	NM_001142633	exon9	c.C837T	p.H279H	GATGGTGTGGAGC	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121600253	121600253	+	Missense_Mutation	SNP	T	T	C	rs208294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	36	56	0	0.5625	0	T|0.429;C|0.571	0.571	strong	.	P2RX7	53	.	NM_002562	exon5	c.T463C	p.Y155H	GTAGTGTATGAAG	.	PASS	Atlas-SNP
COL14A1	7373	hgsc.bcm.edu	37	8	121357700	121357700	+	Missense_Mutation	SNP	C	C	G	rs137867605	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	73	99	0	0.58871	0	C|0.999;G|0.001	0.001	strong	.	COL14A1	292	.	NM_021110	exon45	c.C4975G	p.P1659A	GGGGAGCCTGGGA	.	PASS	Atlas-SNP
CCDC24	149473	hgsc.bcm.edu	37	1	44461822	44461822	+	Missense_Mutation	SNP	C	C	T	rs2301983	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	62	134	0	0.462687	0	C|0.956;T|0.044	0.044	strong	.	CCDC24	22	.	NM_152499	exon9	c.C914T	p.A305V	CCCAAGCCCCAGC	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79170578	79170578	+	Missense_Mutation	SNP	C	C	T	rs4613097	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	38	98	1	0.493506	0.0102041	C|0.909;T|0.091	0.091	strong	AZI1_ENST00000450824,NS,carcinoma,+2,2	AZI1	145	2	NM_014984	exon15	c.G1822A	p.A608T	TCAGCGCCTTCTC	.	scavenged	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592605	167592605	+	Missense_Mutation	SNP	T	T	G	rs200932131	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	20	100	0	0.333333	0	T|0.926;G|0.074	0.074	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.T764G	p.V255G	CCGGAGTTGCTGG	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	37	19	6467910	6467910	+	Missense_Mutation	SNP	T	T	C	rs35173535	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	78	172	0	0.47561	0	T|0.977;C|0.023	0.023	strong	.	DENND1C	93	.	NM_024898	exon23	c.A2011G	p.K671E	AGGGTTTGGGGTC	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573956	140573956	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	13	5	0	0.684211	0	.	.	none	.	PCDHB10	177	.	NM_018930	exon1	c.G1831A	p.E611K	GCCACGGAGCCCG	.	PASS	Atlas-SNP
NLRP1	22861	hgsc.bcm.edu	37	17	5442790	5442790	+	Missense_Mutation	SNP	C	C	T	rs61754791	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	25	51	0	0.373134	0	A|0.000;C|0.986;T|0.014	0.014	strong	.	NLRP1	358	.	NM_033007	exon7	c.G2815A	p.V939M	GTCGCACGCCAAC	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A	rs114397261	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	85	142	0	0.586207	0	G|0.928;A|0.072	0.072	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.G301A	p.V101M	TGCTGTGTGCCCG	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56499279	56499279	+	Missense_Mutation	SNP	G	G	C	rs306457	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	25	60	0	0.333333	0	G|0.274;C|0.726	0.726	strong	.	NLRP8	225	.	NM_176811	exon10	c.G3147C	p.X1049Y	TCCTTAGGCCGTC	.	PASS	Atlas-SNP
ARSF	416	hgsc.bcm.edu	37	X	3002687	3002687	+	Silent	SNP	A	A	G	rs5983003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	40	51	0	1	0	A|0.253;0|0.015	.	strong	.	ARSF	97	.	NM_004042	exon6	c.A810G	p.E270E	GAAGGAAGCGATT	.	PASS	Atlas-SNP
MAGEA1	4100	hgsc.bcm.edu	37	X	152482796	152482796	+	Missense_Mutation	SNP	C	C	T	rs2008144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	125	138	0	1	0	0|0.027;T|0.150	0.150	strong	.	MAGEA1	57	.	NM_004988	exon3	c.G215A	p.R72Q	CTCTGTCGAGTGA	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531091	140531091	+	Missense_Mutation	SNP	C	C	T	rs145637479	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	57	138	0	0.452381	0	C|0.997;T|0.003	0.003	strong	.	PCDHB6	161	.	NM_018939	exon1	c.C1253T	p.T418I	ACATCACTATCAC	.	PASS	Atlas-SNP
CDC45	8318	hgsc.bcm.edu	37	22	19468514	19468514	+	Silent	SNP	T	T	C	rs13447189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	49	120	0	0.422414	0	T|0.963;C|0.037	0.037	strong	.	CDC45	48	.	NM_003504	exon3	c.T150C	p.V50V	GCTGGTTCCAGTT	.	PASS	Atlas-SNP
PTPRH	5794	hgsc.bcm.edu	37	19	55693244	55693244	+	Missense_Mutation	SNP	T	T	C	rs2288419	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	105	112	0	0.972222	0	T|0.668;C|0.332	0.332	strong	.	PTPRH	139	.	NM_002842	exon20	c.A3226G	p.I1076V	GCAGGATGCACTG	.	PASS	Atlas-SNP
NLRP12	91662	hgsc.bcm.edu	37	19	54327313	54327313	+	Missense_Mutation	SNP	C	C	A	rs34436714	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	59	95	0	0.472	0	C|0.741;A|0.259	0.259	strong	.	NLRP12	236	.	NM_144687	exon1	c.A116T	p.K39M	CCTTCTCCCAGCT	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140554006	140554006	+	Silent	SNP	C	C	G	rs2907329	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	127	76	0	0.984496	0	C|0.393;G|0.607	0.607	strong	PCDHB7,colon,carcinoma,+2,1	PCDHB7	231	1	NM_018940	exon1	c.C1590G	p.R530R	GTTCCGCGTGGGC	.	PASS	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31242861	31242861	+	Silent	SNP	A	A	C	rs200751040	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	533	66	543	0	0.123827	0	A|0.977;C|0.023	0.023	strong	DDX11_ENST00000407793,bladder,carcinoma,0,10	DDX11	188	10	NM_030653	exon9	c.A922C	p.R308R	AGGAGGAGGCAGG	.	scavenged	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31238886	31238886	+	Missense_Mutation	SNP	A	A	G	rs77935220	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	313	123	171	0	0.392971	0	A|0.956;G|0.044	0.044	strong	.	HLA-C	92	.	NM_002117	exon3	c.T583C	p.Y195H	CCAGGTATCTGCG	.	PASS	Atlas-SNP
C9orf62	157927	hgsc.bcm.edu	37	9	138236031	138236031	+	Silent	SNP	A	A	G	rs914398	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	17	41	0	0.447368	0	A|0.488;G|0.512	0.512	strong	.	C9orf62	1	.	NM_173520	exon2	c.A237G	p.P79P	ACGCCCAGTCCTG	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	37	15	52611451	52611451	+	Silent	SNP	A	A	G	rs2290332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	93	161	0	0.462687	0	A|0.716;G|0.284	0.284	strong	.	MYO5A	145	.	NM_000259	exon38	c.T4965C	p.D1655D	GCCCTCATCGGCG	.	PASS	Atlas-SNP
ITGB4	3691	hgsc.bcm.edu	37	17	73729660	73729660	+	Missense_Mutation	SNP	G	G	A	rs61735297	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	23	36	0	0.433962	0	G|0.988;A|0.012	0.012	strong	ITGB4,caecum,carcinoma,0,1	ITGB4	165	1	NM_001005731	exon13	c.G1544A	p.R515H	CCGGCCGTGGGGA	.	PASS	Atlas-SNP
CRIM1	51232	hgsc.bcm.edu	37	2	36706780	36706780	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	3	133	0	0.0206897	0	.	.	none	CRIM1,NS,carcinoma,0,1	CRIM1	88	1	NM_016441	exon7	c.G1315A	p.G439R	GTCTGCGGACAGA	.	scavenged	Atlas-SNP
DGKQ	1609	hgsc.bcm.edu	37	4	961373	961373	+	Silent	SNP	G	G	A	rs1377586	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	129	103	0	1	0	G|0.561;A|0.439	0.439	strong	.	DGKQ	29	.	NM_001347	exon8	c.C951T	p.V317V	CACCGTGACGAGG	.	PASS	Atlas-SNP
INPP5F	22876	hgsc.bcm.edu	37	10	121587116	121587116	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	58	134	0	0.5	0	.	.	none	INPP5F,NS,carcinoma,0,1	INPP5F	112	1	NM_014937	exon20	c.C3223T	p.R1075X	AAGATTCGAAGTT	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227872995	227872995	+	Silent	SNP	T	T	C	rs2228555	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	67	156	0	0.401198	0	T|0.294;G|0.193	.	strong	.	COL4A4	215	.	NM_000092	exon47	c.A4548G	p.V1516V	GCTAAATACGGGA	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30762140	30762140	+	Missense_Mutation	SNP	G	G	A	rs740223	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	81	70	0	1	0	G|0.814;A|0.186	0.186	strong	.	CCDC157	86	.	NM_001017437	exon3	c.G151A	p.D51N	GACCTCGACATGG	.	PASS	Atlas-SNP
KIF24	347240	hgsc.bcm.edu	37	9	34256347	34256347	+	Silent	SNP	C	C	T	rs10814083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	31	90	0	0.382716	0	C|0.626;T|0.374	0.374	strong	.	KIF24	64	.	NM_194313	exon11	c.G3258A	p.G1086G	TGGGCCCCCTGTG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2159996	2159996	+	Silent	SNP	G	G	A	rs9935526	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	77	100	0	0.466667	0	G|0.724;A|0.276	0.276	strong	.	PKD1	184	.	NM_000296	exon15	c.C5172T	p.A1724A	GGAGGCGGCCACC	.	PASS	Atlas-SNP
MRPL50	54534	hgsc.bcm.edu	37	9	104152846	104152846	+	Missense_Mutation	SNP	G	G	A	rs8131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	66	157	1	0.471429	0.00636943	G|0.950;A|0.050	0.050	strong	MRPL50,colon,carcinoma,0,1	MRPL50	18	1	NM_019051	exon2	c.C379T	p.L127F	AATCAAGAACATC	.	scavenged	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46010077	46010077	+	Missense_Mutation	SNP	C	C	T	rs4683158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	18	47	0	0.545455	0	A|0.000;C|0.136;T|0.864	0.864	strong	FYCO1,colon,carcinoma,-1,1	FYCO1	115	1	NM_024513	exon8	c.G749A	p.R250Q	CGCTCCCGTAGCT	.	PASS	Atlas-SNP
RPL4	6124	hgsc.bcm.edu	37	15	66791920	66791920	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	33	122	0	0.370787	0	.	.	none	.	RPL4	29	.	NM_000968	exon10	c.C1109T	p.A370V	GCAACCGCCGCCT	.	PASS	Atlas-SNP
GSTA1	2938	hgsc.bcm.edu	37	6	52658962	52658962	+	Silent	SNP	T	T	C	rs1051775	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	159	148	1	0.987578	0.00675676	T|0.707;C|0.293	0.293	strong	.	GSTA1	40	.	NM_145740	exon5	c.A375G	p.K125K	TTTCTCTTTGATC	.	PASS	Atlas-SNP
HEATR6	63897	hgsc.bcm.edu	37	17	58123571	58123571	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	2	66	0	0.0210526	0	.	.	none	HEATR6,NS,neuroblastoma,-1,1	HEATR6	98	1	NM_022070	exon19	c.G2789A	p.R930Q	AGGGCCCGGACTG	.	scavenged	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51224417	51224417	+	Missense_Mutation	SNP	G	G	C	rs2236316	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	76	164	0	0.484076	0	G|0.805;C|0.195	0.195	strong	.	NIN	475	.	NM_020921	exon18	c.C3331G	p.P1111A	TAGCTGGCTCATC	.	PASS	Atlas-SNP
TRAP1	10131	hgsc.bcm.edu	37	16	3726074	3726074	+	Silent	SNP	G	G	C	rs61753377	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	29	70	0	0.47541	0	G|0.958;C|0.042	0.042	strong	TRAP1,NS,carcinoma,-2,1	TRAP1	53	1	NM_016292	exon7	c.C777G	p.S259S	GCAGTCGGATTTC	.	PASS	Atlas-SNP
PTDSS2	81490	hgsc.bcm.edu	37	11	490035	490035	+	Missense_Mutation	SNP	C	C	T	rs61742833	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	22	63	0	0.44898	0	C|0.925;T|0.075	0.075	strong	PTDSS2,caecum,carcinoma,-1,3	PTDSS2	27	3	NM_030783	exon11	c.C1268T	p.A423V	TCCTGGCGCTCAC	.	PASS	Atlas-SNP
SYT14	255928	hgsc.bcm.edu	37	1	210334081	210334081	+	Silent	SNP	T	T	C	rs17188183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	39	100	0	0.481481	0	T|0.914;C|0.086	0.086	strong	.	SYT14	89	.	NM_001146261	exon10	c.T1554C	p.Y518Y	TACATATGTTAAG	.	PASS	Atlas-SNP
KAT2A	2648	hgsc.bcm.edu	37	17	40266533	40266533	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	57	85	0	0.6	0	.	.	none	.	KAT2A	54	.	NM_021078	exon14	c.C2109T	p.I703I	CACAGGGATCTGC	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79638805	79638805	+	Missense_Mutation	SNP	C	C	T	rs11150805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	68	96	0	0.527132	0	C|0.863;T|0.137	0.137	strong	.	CCDC137	27	.	NM_199287	exon4	c.C529T	p.R177W	GTCCGACGGAAAA	.	PASS	Atlas-SNP
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679120	37679120	+	Missense_Mutation	SNP	G	G	C	rs139953443	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	65	134	0	0.511811	0	G|0.998;C|0.002	0.002	strong	.	CSNK1A1L	69	.	NM_145203	exon1	c.C274G	p.L92V	CCAGAAGGTCCAT	.	PASS	Atlas-SNP
ARHGEF15	22899	hgsc.bcm.edu	37	17	8215534	8215534	+	Silent	SNP	C	C	T	rs3744651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	318	313	255	0	0.984277	0	C|0.620;T|0.380	0.380	strong	.	ARHGEF15	97	.	NM_025014	exon2	c.C177T	p.T59T	GTGCACCCCCATC	.	PASS	Atlas-SNP
OR14A16	284532	hgsc.bcm.edu	37	1	247978135	247978135	+	Silent	SNP	C	C	A	rs12734733	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	40	132	0	0.373832	0	C|0.875;A|0.125	0.125	strong	.	OR14A16	90	.	NM_001001966	exon1	c.G897T	p.G299G	CAACATCCCCAGA	.	PASS	Atlas-SNP
RAB11FIP3	9727	hgsc.bcm.edu	37	16	570557	570557	+	Silent	SNP	T	T	C	rs11537754	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	48	106	0	0.539326	0	T|0.353;C|0.647	0.647	strong	.	RAB11FIP3	31	.	NM_014700	exon13	c.T2115C	p.S705S	CTTCTCTGAGTCC	.	PASS	Atlas-SNP
GALNT6	11226	hgsc.bcm.edu	37	12	51773201	51773201	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	2	201	0	0.0115607	0	.	.	none	GALNT6,mouth,carcinoma,+1,1	GALNT6	63	1	NM_007210	exon3	c.A365G	p.K122R	TTGCTCTTCTGAA	.	scavenged	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921333	12921333	+	Missense_Mutation	SNP	G	G	A	rs56145411	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	322	11	290	0	0.0341615	0	G|0.837;A|0.163	0.163	strong	PRAMEF2,NS,carcinoma,+1,1	PRAMEF2	85	1	NM_023014	exon4	c.G1124A	p.C375Y	TGAGCTGCTGCTC	.	scavenged	Atlas-SNP
ABI3BP	25890	hgsc.bcm.edu	37	3	100712249	100712249	+	Missense_Mutation	SNP	T	T	C	rs3732895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	43	67	0	0.477778	0	T|0.753;C|0.246	0.246	strong	.	ABI3BP	305	.	NM_015429	exon1	c.A1G	p.M1V	CTCGCATGGGGAA	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	88	151	0	0.606897	0	A|0.687;G|0.313	0.313	strong	IFT140,NS,carcinoma,0,1	IFT140	128	1	NM_014714	exon19	c.T2253C	p.P751P	CATCTGAGGGATG	.	PASS	Atlas-SNP
FGFBP2	83888	hgsc.bcm.edu	37	4	15964670	15964670	+	Missense_Mutation	SNP	C	C	T	rs35496730	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	25	92	0	0.568182	0	C|0.872;T|0.128	0.128	strong	.	FGFBP2	22	.	NM_031950	exon1	c.G83A	p.S28N	CCAGTGCTTCCTT	.	PASS	Atlas-SNP
SNAPC4	6621	hgsc.bcm.edu	37	9	139276430	139276430	+	Silent	SNP	G	G	A	rs34850728	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	71	157	0	0.486301	0	G|0.876;A|0.124	0.124	strong	.	SNAPC4	82	.	NM_003086	exon17	c.C2163T	p.H721H	GGCTCTGTGCCGT	.	PASS	Atlas-SNP
BCDIN3D	144233	hgsc.bcm.edu	37	12	50232496	50232496	+	Silent	SNP	T	T	C	rs17260403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	22	62	0	0.415094	0	T|0.938;C|0.062	0.062	strong	.	BCDIN3D	20	.	NM_181708	exon2	c.A537G	p.L179L	CTCCCATAGGCCA	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	125107207	125107207	+	Silent	SNP	C	C	T	rs6470220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	141	120	0	1	0	C|0.200;T|0.800	0.800	strong	.	FER1L6	268	.	NM_001039112	exon35	c.C4623T	p.V1541V	GGAAGTCGGGTGT	.	PASS	Atlas-SNP
SULF1	23213	hgsc.bcm.edu	37	8	70513996	70513996	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	291	4	245	0	0.0137457	0	.	.	none	SULF1,NS,malignant_melanoma,+1,1	SULF1	153	1	NM_001128205	exon10	c.C993T	p.S331S	GAAATCCATGCCA	.	scavenged	Atlas-SNP
KCNQ4	9132	hgsc.bcm.edu	37	1	41285585	41285585	+	Silent	SNP	G	G	A	rs12117176	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	155	184	1	0.939394	0.00543478	G|0.918;A|0.082	0.082	strong	.	KCNQ4	58	.	NM_004700	exon6	c.G873A	p.P291P	GACACCGCACACA	.	PASS	Atlas-SNP
MYLK3	91807	hgsc.bcm.edu	37	16	46773999	46773999	+	Missense_Mutation	SNP	C	C	A	rs28407821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	46	108	1	0.505495	0.00925926	C|0.544;A|0.456	0.456	strong	MYLK3,NS,carcinoma,0,2	MYLK3	82	2	NM_182493	exon2	c.G538T	p.V180L	ACTGCACCCCACT	.	scavenged	Atlas-SNP
TRIM66	9866	hgsc.bcm.edu	37	11	8671369	8671369	+	Silent	SNP	C	C	T	rs10840101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	35	73	0	0.454545	0	C|0.817;T|0.183	0.183	strong	.	TRIM66	45	.	NM_014818	exon3	c.G75A	p.L25L	GCTGCACAGCCAG	.	PASS	Atlas-SNP
ARHGEF7	8874	hgsc.bcm.edu	37	13	111938511	111938511	+	Silent	SNP	T	T	C	rs72653559	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	30	96	0	0.422535	0	T|0.989;C|0.011	0.011	strong	.	ARHGEF7	157	.	NM_001113511	exon18	c.T2031C	p.P677P	GAGCCCTAAGACC	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214820099	214820099	+	Missense_Mutation	SNP	A	A	G	rs3748697	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	132	118	0	0.985075	0	A|0.689;G|0.311	0.311	strong	CENPF,NS,carcinoma,0,1	CENPF	321	1	NM_016343	exon13	c.A7186G	p.N2396D	AAAGAAAATCTGA	.	PASS	Atlas-SNP
CLPSL1	340204	hgsc.bcm.edu	37	6	35748931	35748931	+	Missense_Mutation	SNP	T	T	C	rs34109614	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	69	156	0	0.43125	0	C|0.301;G|0.000;T|0.698	0.301	strong	.	.	.	.	NM_001010886	exon1	c.T44C	p.F15S	TCTTCTTCTTTCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228402508	228402508	+	Silent	SNP	C	C	T	rs2776853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	29	60	0	0.446154	0	C|0.687;T|0.313	0.313	strong	.	OBSCN	2142	.	NM_001271223	exon5	c.C1537T	p.L513L	CCTCCCCTGCAAC	.	PASS	Atlas-SNP
CD300E	342510	hgsc.bcm.edu	37	17	72613589	72613589	+	Missense_Mutation	SNP	T	T	G	rs581157	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	26	79	0	0.412698	0	T|0.531;G|0.469	0.469	strong	.	CD300E	70	.	NM_181449	exon2	c.A56C	p.K19T	GGGCCCTTCAGAG	.	PASS	Atlas-SNP
MR1	3140	hgsc.bcm.edu	37	1	181018236	181018236	+	Missense_Mutation	SNP	A	A	G	rs2236410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	286	167	248	0	0.583916	0	A|0.833;G|0.167	0.167	strong	MR1,NS,carcinoma,0,1	MR1	46	1	NM_001195035	exon3	c.A116G	p.H39R	CCATCCATGGGGT	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48287840	48287840	+	Missense_Mutation	SNP	G	G	A	rs2361519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	40	73	0	0.434783	0	G|0.802;A|0.197	0.197	strong	.	ABCA13	1192	.	NM_152701	exon14	c.G1664A	p.R555H	AGGATCGTATTTT	.	PASS	Atlas-SNP
FAM47C	442444	hgsc.bcm.edu	37	X	37028127	37028127	+	Silent	SNP	A	A	G	rs73631164	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	65	68	0	1	0	A|0.644;G|0.356	0.356	strong	.	FAM47C	267	.	NM_001013736	exon1	c.A1644G	p.P548P	CCGCCCAGAGCCT	.	PASS	Atlas-SNP
KRT7	3855	hgsc.bcm.edu	37	12	52639302	52639302	+	Missense_Mutation	SNP	G	G	C	rs2608009	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	89	95	0	0.988889	0	G|0.148;C|0.852	0.852	strong	.	KRT7	48	.	NM_005556	exon7	c.G1091C	p.G364A	AGCGGGGCAAGCA	.	PASS	Atlas-SNP
YAE1D1	57002	hgsc.bcm.edu	37	7	39610177	39610177	+	Missense_Mutation	SNP	A	A	G	rs6947660	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	47	68	0	0.552941	0	A|0.858;G|0.142	0.142	strong	.	YAE1D1	2	.	NM_020192	exon2	c.A202G	p.K68E	TATAAGAAAGGTG	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535868	88535868	+	Missense_Mutation	SNP	A	A	G	rs199719429	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	21	185	0	0.108808	0	.	.	weak	DSPP,NS,carcinoma,-1,2	DSPP	174	2	NM_014208	exon5	c.A2054G	p.N685S	GCAGCAACAGCAG	.	PASS	Atlas-SNP
PCSK9	255738	hgsc.bcm.edu	37	1	55518416	55518416	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	5	111	0	0.0285714	0	.	.	none	PCSK9,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	PCSK9	76	2	NM_174936	exon5	c.C751T	p.R251C	AGCCTGCGCGTGC	.	scavenged	Atlas-SNP
ENPP5	59084	hgsc.bcm.edu	37	6	46129345	46129345	+	Silent	SNP	G	G	A	rs2235881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	65	127	0	0.503876	0	G|0.569;T|0.002	.	strong	.	ENPP5	44	.	NM_021572	exon4	c.C1152T	p.T384T	CATGGCGGTGATA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144909956	144909956	+	Silent	SNP	G	G	A	rs638260	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	371	107	311	0	0.28841	0	A|0.001;C|0.701	0.001	strong	.	PDE4DIP	817	.	NM_001002811	exon13	c.C2721T	p.D907D	GTCCAAGTCTCCT	.	PASS	Atlas-SNP
SIGLEC14	100049587	hgsc.bcm.edu	37	19	52149165	52149165	+	Silent	SNP	G	G	A	rs71358847	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	512	209	294	1	0.408203	0.00340136	G|0.621;A|0.379	0.379	strong	.	SIGLEC14	46	.	NM_001098612	exon3	c.C570T	p.P190P	GGTCTCGGGGTCC	.	PASS	Atlas-SNP
DNTTIP2	30836	hgsc.bcm.edu	37	1	94342564	94342564	+	Missense_Mutation	SNP	C	C	A	rs3747965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	93	122	0	1	0	C|0.661;A|0.339	0.339	strong	.	DNTTIP2	59	.	NM_014597	exon2	c.G927T	p.E309D	TTTCCCCTCATCT	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36594063	36594063	+	Silent	SNP	C	C	T	rs17851502	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	64	97	0	0.598131	0	C|0.869;T|0.131	0.131	strong	.	WDR62	102	.	NM_001083961	exon29	c.C3468T	p.L1156L	GGTCCTCGCTGCA	.	PASS	Atlas-SNP
NPLOC4	55666	hgsc.bcm.edu	37	17	79580457	79580457	+	Silent	SNP	C	C	A	rs17852306	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	52	108	0	0.472727	0	C|0.916;A|0.084	0.084	strong	.	NPLOC4	27	.	NM_017921	exon4	c.G273T	p.T91T	AACTGACGTCTCC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228504591	228504591	+	Missense_Mutation	SNP	C	C	A	rs61825301	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	23	22	0	0.638889	0	C|0.841;A|0.159	0.159	strong	.	OBSCN	2142	.	NM_001271223	exon62	c.C16338A	p.H5446Q	TCACCACGCCCTA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9056989	9056989	+	Missense_Mutation	SNP	C	C	G	rs4804381	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	56	112	0	0.5	0	C|0.780;G|0.220	0.220	strong	.	MUC16	4315	.	NM_024690	exon3	c.G30457C	p.E10153Q	TGGTCTCAAAATT	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8825096	8825096	+	Silent	SNP	G	G	A	rs113084211	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	36	94	0	0.395604	0	G|0.987;A|0.013	0.013	strong	.	.	.	.	NM_015210	exon15	c.G3588A	p.P1196P	CAGCCCGCCTGCC	.	PASS	Atlas-SNP
COBLL1	22837	hgsc.bcm.edu	37	2	165551000	165551000	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	65	137	0	0.442177	0	.	.	none	.	COBLL1	122	.	NM_014900	exon12	c.C3016T	p.L1006L	TCTTCAGATTTTG	.	PASS	Atlas-SNP
TRIM3	10612	hgsc.bcm.edu	37	11	6477831	6477831	+	Silent	SNP	C	C	T	rs10606	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	22	30	0	0.52381	0	C|0.791;T|0.209	0.209	strong	TRIM3,NS,lymphoid_neoplasm,0,1	TRIM3	67	1	NM_001248006	exon6	c.G1125A	p.P375P	TGGCACCGGAAGG	.	PASS	Atlas-SNP
TIMELESS	8914	hgsc.bcm.edu	37	12	56827694	56827694	+	Silent	SNP	C	C	G	rs2279665	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	117	104	0	1	0	C|0.472;G|0.528	0.528	strong	TIMELESS,NS,carcinoma,0,1	TIMELESS	107	1	NM_003920	exon3	c.G114C	p.L38L	GCGGATCAGATCC	.	PASS	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28504258	28504258	+	Silent	SNP	A	A	G	rs9625409	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	43	104	0	0.518072	0	A|0.942;G|0.058	0.058	strong	.	TTC28	84	.	NM_001145418	exon7	c.T1575C	p.N525N	CAGGGCATTGTAG	.	PASS	Atlas-SNP
MX1	4599	hgsc.bcm.edu	37	21	42812891	42812891	+	Silent	SNP	C	C	T	rs467960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	46	98	0	0.403509	0	C|0.547;T|0.453	0.453	strong	.	MX1	58	.	NM_001144925	exon11	c.C669T	p.I223I	GGACATCGCCACC	.	PASS	Atlas-SNP
RGP1	9827	hgsc.bcm.edu	37	9	35749845	35749845	+	Silent	SNP	G	G	C	rs2236288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	60	136	0	0.535714	0	G|0.688;C|0.312	0.312	strong	.	RGP1	60	.	NM_001080496	exon2	c.G93C	p.P31P	CCTTCCGCCCACG	.	PASS	Atlas-SNP
FBXO10	26267	hgsc.bcm.edu	37	9	37537557	37537557	+	Silent	SNP	G	G	A	rs7044153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	83	0	1	0	G|0.429;A|0.571	0.571	strong	.	FBXO10	75	.	NM_012166	exon3	c.C969T	p.A323A	GCTAGAGGCTGGG	.	PASS	Atlas-SNP
FYB	2533	hgsc.bcm.edu	37	5	39124367	39124367	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	302	149	332	1	0.493377	0.00301205	.	.	none	.	FYB	354	.	NM_001243093	exon13	c.C2089T	p.P697S	GTTTAGGAGGAGC	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6683215	6683215	+	Missense_Mutation	SNP	C	C	T	rs4796555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	52	115	0	0.464286	0	C|0.730;N|0.000	.	strong	.	FBXO39	50	.	NM_153230	exon2	c.C28T	p.P10S	ATCCAGCCCCAAG	.	PASS	Atlas-SNP
GPR1	2825	hgsc.bcm.edu	37	2	207041933	207041933	+	Silent	SNP	T	T	C	rs3755227	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	27	67	0	0.421875	0	T|0.899;C|0.101	0.101	strong	.	GPR1	38	.	NM_001098199	exon3	c.A39G	p.E13E	ATAGTTTTCAAAT	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389005	1389005	+	Missense_Mutation	SNP	T	T	C	rs71614970	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	7	61	1	0.111111	0.0163934	C|1.000;|0.000	1.000	weak	CRIPAK,rectum,NS,0,1	CRIPAK	185	1	NM_175918	exon1	c.T706C	p.C236R	TGCCGATGCGGAG	.	scavenged	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40389657	40389657	+	Missense_Mutation	SNP	T	T	G	rs3746010	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	330	44	834	0	0.133333	0	T|0.250;G|0.750	0.750	weak	FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	NM_003890	exon18	c.A8525C	p.N2842T	CCTTTGTTGACGC	.	scavenged	Atlas-SNP
ZNF236	7776	hgsc.bcm.edu	37	18	74672703	74672703	+	Missense_Mutation	SNP	A	A	G	rs183845634	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	31	44	0	0.455882	0	A|0.999;G|0.001	0.001	strong	.	ZNF236	325	.	NM_007345	exon30	c.A5305G	p.M1769V	GTGCACATGAAGA	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367704	107367704	+	Missense_Mutation	SNP	A	A	T	rs57169158	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	665	48	641	0	0.0721804	0	A|0.222;T|0.778	0.778	strong	OR13C2,NS,carcinoma,0,1	OR13C2	46	1	NM_001004481	exon1	c.T205A	p.L69M	TGTCCAAGAAGGA	.	scavenged	Atlas-SNP
FAF1	11124	hgsc.bcm.edu	37	1	51121198	51121198	+	Silent	SNP	T	T	C	rs11205753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	30	61	0	0.526316	0	T|0.918;C|0.082	0.082	strong	.	FAF1	64	.	NM_007051	exon8	c.A660G	p.V220V	TCTCTTTACCTAT	.	PASS	Atlas-SNP
ZSWIM2	151112	hgsc.bcm.edu	37	2	187698751	187698751	+	Silent	SNP	G	G	A	rs7559533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	26	53	0	0.490566	0	G|0.784;A|0.216	0.216	strong	ZSWIM2,NS,carcinoma,-1,1	ZSWIM2	119	1	NM_182521	exon6	c.C750T	p.T250T	GCATTCGGTACAC	.	PASS	Atlas-SNP
DNAAF1	123872	hgsc.bcm.edu	37	16	84209864	84209864	+	Missense_Mutation	SNP	G	G	C	rs2288023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	104	95	0	0.990476	0	G|0.706;C|0.294	0.294	strong	DNAAF1,rectum,carcinoma,0,1	DNAAF1	81	1	NM_178452	exon11	c.G2024C	p.S675T	CTTCCAGTGGAGA	.	PASS	Atlas-SNP
ABCA5	23461	hgsc.bcm.edu	37	17	67267317	67267317	+	Missense_Mutation	SNP	T	T	C	rs557491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	41	92	0	0.460674	0	T|0.519;C|0.481	0.481	strong	.	ABCA5	162	.	NM_018672	exon20	c.A2878G	p.M960V	AATGCATCACATT	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165648709	165648709	+	Silent	SNP	C	C	T	rs1143661	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	93	120	0	0.570552	0	C|0.910;T|0.090	0.090	strong	.	ALDH9A1	75	.	NM_000696	exon6	c.G900A	p.A300A	CATCAGCGCCCCC	.	PASS	Atlas-SNP
CHRNA3	1136	hgsc.bcm.edu	37	15	78911181	78911181	+	Silent	SNP	T	T	C	rs8040868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	85	73	0	1	0	T|0.616;C|0.384	0.384	strong	.	CHRNA3	56	.	NM_000743	exon2	c.A159G	p.V53V	GTTGGCTACAGGC	.	PASS	Atlas-SNP
C10orf120	399814	hgsc.bcm.edu	37	10	124459139	124459139	+	Silent	SNP	T	T	C	rs11813597	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	58	116	0	0.504348	0	C|0.427;N|0.000	0.427	strong	C10orf120,NS,carcinoma,0,1	C10orf120	55	1	NM_001010912	exon1	c.A168G	p.S56S	CAACGGTGAAGCA	.	PASS	Atlas-SNP
OR2H2	7932	hgsc.bcm.edu	37	6	29555864	29555864	+	Missense_Mutation	SNP	C	C	T	rs1233387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	120	219	0	0.547945	0	C|0.722;T|0.278	0.278	strong	OR2H2,NS,carcinoma,0,1	OR2H2	29	1	NM_007160	exon1	c.C143T	p.A48V	TGTCTGCGCTGGA	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130107442	130107442	+	Silent	SNP	C	C	T	rs138213174	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	17	44	0	0.326923	0	C|0.990;T|0.010	0.010	strong	.	COL6A5	205	.	NM_153264	exon6	c.C1881T	p.A627A	GAAGGCCGACATC	.	PASS	Atlas-SNP
CCDC147	159686	hgsc.bcm.edu	37	10	106159180	106159180	+	Silent	SNP	A	A	G	rs61732098	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	58	99	0	0.568627	0	A|0.982;G|0.018	0.018	strong	.	CCDC147	137	.	NM_001008723	exon12	c.A1737G	p.E579E	GCAAGAAGCTGAA	.	PASS	Atlas-SNP
PCDHGA11	56105	hgsc.bcm.edu	37	5	140803241	140803241	+	Missense_Mutation	SNP	C	C	A	rs57195665	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	89	133	0	1	0	C|0.900;A|0.100	0.100	strong	.	PCDHGA11	128	.	NM_032091	exon1	c.C2447A	p.S816Y	TTATTTCTCTGCC	.	PASS	Atlas-SNP
NIPA2	81614	hgsc.bcm.edu	37	15	23021238	23021238	+	Silent	SNP	C	C	T	rs7170838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	43	100	0	0.413462	0	C|0.792;T|0.208	0.208	strong	NIPA2,NS,adenoma,0,1	NIPA2	49	1	NM_001184889	exon6	c.G99A	p.K33K	GAGGCCCTTTTTT	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29161503	29161503	+	Missense_Mutation	SNP	A	A	G	rs11080134	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	13	36	0	0.342105	0	A|0.786;G|0.214	0.214	strong	.	ATAD5	150	.	NM_024857	exon2	c.A404G	p.E135G	CAATTGAAATTAG	.	PASS	Atlas-SNP
MAP4	4134	hgsc.bcm.edu	37	3	47958037	47958037	+	Missense_Mutation	SNP	G	G	T	rs1060407	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	87	173	0	0.416268	0	G|0.754;T|0.246	0.246	strong	.	MAP4	176	.	NM_001134364	exon7	c.C1280A	p.S427Y	TCTGTGGATGATA	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30918400	30918400	+	Missense_Mutation	SNP	A	A	G	rs2844699	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	61	116	0	0.512605	0	A|0.768;G|0.232	0.232	strong	DPCR1_ENST00000462446,NS,carcinoma,0,1	DPCR1	99	1	NM_080870	exon2	c.A2159G	p.E720G	CAGCAGAGCCTAC	.	PASS	Atlas-SNP
VIT	5212	hgsc.bcm.edu	37	2	37041480	37041480	+	Silent	SNP	G	G	A	rs17441812	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	23	66	0	0.403509	0	G|0.956;A|0.044	0.044	strong	.	VIT	138	.	NM_053276	exon16	c.G2058A	p.E686E	TACAGAGTTCAAC	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	12633	12633	+	Silent	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	11	11	3	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.C297A	p.S99S	ATGGTCCATCATA	.	PASS	Atlas-SNP
GRIN2B	2904	hgsc.bcm.edu	37	12	13724742	13724742	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	7	144	0	0.0429448	0	.	.	none	.	GRIN2B	303	.	NM_000834	exon10	c.A2167G	p.T723A	ACCCTGTTTTCAG	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32029431	32029431	+	Missense_Mutation	SNP	G	G	A	rs12524664	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	48	90	0	0.428571	0	G|0.894;A|0.106	0.106	strong	TNXB_ENST00000375247,NS,carcinoma,+1,2	TNXB	553	2	NM_019105	exon21	c.C7235T	p.P2412L	AGGAGCGGCTCCT	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2203167	2203167	+	Missense_Mutation	SNP	T	T	G	rs216195	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	55	119	0	0.419847	0	T|0.655;G|0.345	0.345	strong	.	SMG6	97	.	NM_017575	exon2	c.A880C	p.K294Q	CTTGCTTCTTCAG	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	107	76	0	1	0	T|0.432;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.T4179C	p.T1393T	CAGGACTGTGGAA	.	PASS	Atlas-SNP
ZNF48	197407	hgsc.bcm.edu	37	16	30409241	30409241	+	Missense_Mutation	SNP	A	A	G	rs34843513	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	19	30	0	0.487179	0	A|0.973;G|0.027	0.027	strong	.	ZNF48	34	.	NM_001214906	exon3	c.A670G	p.I224V	TGTGGCATATGTG	.	PASS	Atlas-SNP
CAV3	859	hgsc.bcm.edu	37	3	8787220	8787220	+	Silent	SNP	T	T	C	rs13087941	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	23	57	0	0.5	0	T|0.791;C|0.209	0.209	strong	CAV3,NS,carcinoma,0,1	CAV3	20	1	NM_033337	exon2	c.T123C	p.F41F	GGATTTTGAAGAC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388429	1388429	+	Missense_Mutation	SNP	G	G	A	rs79298048	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	72	145	1	0.426035	0.00689655	G|0.725;A|0.275	0.275	strong	CRIPAK,colon,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.G130A	p.A44T	GTGCCCGCCTGCT	.	scavenged	Atlas-SNP
PRSS58	136541	hgsc.bcm.edu	37	7	141957504	141957504	+	Silent	SNP	A	A	G	rs7786497	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	146	126	0	1	0	A|0.764;G|0.236	0.236	strong	.	PRSS58	41	.	NM_001001317	exon2	c.T24C	p.A8A	CAAGAGAGCCCAG	.	PASS	Atlas-SNP
TBCD	6904	hgsc.bcm.edu	37	17	80710097	80710097	+	Missense_Mutation	SNP	G	G	T	rs11550062	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	13	1	0	0.684211	0	G|0.918;T|0.082	0.082	strong	TBCD_ENST00000355528,rectum,carcinoma,-2,1	TBCD	94	1	NM_005993	exon1	c.G28T	p.G10C	GCCGCGGGCGGCC	.	PASS	Atlas-SNP
TMEM175	84286	hgsc.bcm.edu	37	4	944210	944210	+	Missense_Mutation	SNP	A	A	C	rs34884217	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	113	223	0	0.476793	0	A|0.930;C|0.070	0.070	strong	.	TMEM175	44	.	NM_032326	exon4	c.A194C	p.Q65P	TCCAGCAGTTCGA	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74003805	74003805	+	Silent	SNP	G	G	A	rs7342882	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	48	88	0	0.5	0	G|0.804;A|0.196	0.196	strong	.	EVPL	155	.	NM_001988	exon22	c.C5481T	p.I1827I	CCCGGCGATAGGG	.	PASS	Atlas-SNP
ISYNA1	51477	hgsc.bcm.edu	37	19	18546678	18546678	+	Silent	SNP	T	T	C	rs2303697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	70	100	0	0.564516	0	T|0.535;C|0.465	0.465	strong	.	ISYNA1	31	.	NM_016368	exon8	c.A1029G	p.L343L	CGCCGATAGGTTC	.	PASS	Atlas-SNP
USP10	9100	hgsc.bcm.edu	37	16	84778694	84778694	+	Missense_Mutation	SNP	T	T	C	rs2326391	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	52	151	0	0.371429	0	T|0.774;C|0.226	0.226	strong	.	USP10	51	.	NM_001272075	exon5	c.T619C	p.S207P	CCCCCGTCAGTTA	.	PASS	Atlas-SNP
MRPL12	6182	hgsc.bcm.edu	37	17	79671714	79671714	+	Missense_Mutation	SNP	T	T	C	rs11546280	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	56	143	0	0.388889	0	T|0.923;C|0.077	0.077	strong	.	MRPL12	12	.	NM_002949	exon3	c.T313C	p.S105P	GTGATGTCTGGGG	.	PASS	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22382821	22382821	+	Missense_Mutation	SNP	G	G	C	rs75595142		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	356	104	363	0	0.292135	0	.	.	weak	.	OR4N4	108	.	NM_001005241	exon1	c.G349C	p.V117L	CTTGTTGTGATGG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50533776	50533776	+	Silent	SNP	C	C	G	rs10857471	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	31	76	0	0.418919	0	C|0.643;G|0.357	0.357	strong	.	C10orf71	179	.	NM_001135196	exon3	c.C3186G	p.P1062P	CTCCCCCGGGGAG	.	PASS	Atlas-SNP
FAM124B	79843	hgsc.bcm.edu	37	2	225244352	225244352	+	Missense_Mutation	SNP	G	G	A	rs61732371	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	108	0	1	0	G|0.965;A|0.035	0.035	strong	.	FAM124B	71	.	NM_001122779	exon2	c.C1306T	p.L436F	GAAGGAGACATTC	.	PASS	Atlas-SNP
SEPT4	5414	hgsc.bcm.edu	37	17	56598991	56598991	+	Missense_Mutation	SNP	T	T	A	rs17741424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	47	134	0	0.345588	0	T|0.923;A|0.077	0.077	strong	SEPT4,lymph_node,lymphoid_neoplasm,0,1	SEPT4	48	1	NM_001256782	exon9	c.A977T	p.E326V	AAATGCTCAATCT	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68678962	68678962	+	Missense_Mutation	SNP	T	T	C	rs560096	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	132	127	0	1	0	A|0.001;C|0.675	0.675	strong	.	IGHMBP2	83	.	NM_002180	exon5	c.T602C	p.L201S	CGGTTTTATTTGC	.	PASS	Atlas-SNP
C17orf96	100170841	hgsc.bcm.edu	37	17	36830727	36830727	+	Missense_Mutation	SNP	G	G	A	rs76756126	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	7	2	0	0.777778	0	G|0.953;A|0.047	0.047	strong	.	.	.	.	NM_001130677	exon1	c.C22T	p.P8S	GGCGGGGCGCAGG	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3656680	3656680	+	Silent	SNP	G	G	A	rs74640850	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	74	160	0	0.513889	0	G|0.954;A|0.046	0.046	strong	SLX4,colon,carcinoma,-2,1	SLX4	173	1	NM_032444	exon3	c.C555T	p.D185D	CTGGGAGTCGCTG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016630	1016630	+	Silent	SNP	G	G	A	rs369775657		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	446	27	429	0	0.0605381	0	.	.	weak	.	MUC6	408	.	NM_005961	exon31	c.C6171T	p.S2057S	GTGGGTGGACCCT	.	PASS	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	37	18	56203837	56203837	+	Silent	SNP	G	G	A	rs17065139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	53	65	0	0.546392	0	G|0.949;A|0.051	0.051	strong	.	ALPK2	487	.	NM_052947	exon5	c.C3582T	p.S1194S	CACCACGGAGACC	.	PASS	Atlas-SNP
LRPAP1	4043	hgsc.bcm.edu	37	4	3519762	3519762	+	Silent	SNP	A	A	G	rs13325	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	17	53	0	0.472222	0	A|0.853;G|0.147	0.147	strong	.	LRPAP1	29	.	NM_002337	exon5	c.T750C	p.A250A	CTCACCAGCCTCA	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27212856	27212856	+	Silent	SNP	C	C	T	rs45505400	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	46	102	0	0.541176	0	C|0.993;T|0.007	0.007	strong	.	TEK	250	.	NM_000459	exon17	c.C2838T	p.A946A	CGCTGCCGACGTG	.	PASS	Atlas-SNP
GNRH2	2797	hgsc.bcm.edu	37	20	3025107	3025107	+	Missense_Mutation	SNP	C	C	T	rs6051545	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	69	113	0	0.594828	0	C|0.815;T|0.185	0.185	strong	.	GNRH2	15	.	NM_001501	exon2	c.C47T	p.A16V	TGACTGCCCACCT	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324647	31324647	+	Missense_Mutation	SNP	T	T	C	rs9266183	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	33	0	1	0	T|0.965;C|0.035	0.035	strong	.	HLA-B	54	.	NM_005514	exon2	c.A161G	p.D54G	TGGGTGTCGTCCA	.	PASS	Atlas-SNP
ACADSB	36	hgsc.bcm.edu	37	10	124800853	124800853	+	Silent	SNP	C	C	T	rs1140591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	48	99	0	0.421053	0	A|0.000;C|0.783;G|0.000;T|0.217	0.217	strong	.	ACADSB	45	.	NM_001609	exon5	c.C639T	p.H213H	TGAGCACGCAGGG	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52133292	52133292	+	Missense_Mutation	SNP	A	A	G	rs1973019	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1021	502	785	3	0.491675	0.00382166	A|0.500;G|0.500	0.500	strong	SIGLEC5,NS,carcinoid-endocrine_tumour,0,1	SIGLEC5	67	1	NM_003830	exon2	c.T215C	p.V72A	GCCACAACCTCAG	.	scavenged	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77709339	77709339	+	Silent	SNP	C	C	G	rs11657217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	93	73	0	1	0	C|0.672;G|0.328	0.328	strong	.	ENPP7	63	.	NM_178543	exon3	c.C897G	p.A299A	CGATGCCCTCAAG	.	PASS	Atlas-SNP
ZNF286A	57335	hgsc.bcm.edu	37	17	15620481	15620481	+	Silent	SNP	C	C	T	rs74608540		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	41	218	0	0.253086	0	C|0.250;T|0.750	0.750	weak	ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	NM_020652	exon6	c.C1443T	p.L481L	AGCTCTCATTCAA	.	PASS	Atlas-SNP
ZNF749	388567	hgsc.bcm.edu	37	19	57955244	57955244	+	Missense_Mutation	SNP	A	A	G	rs12986235	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	71	101	0	0.986111	0	A|0.771;G|0.229	0.229	strong	.	ZNF749	75	.	NM_001023561	exon3	c.A728G	p.Q243R	AATATCAGCAAAA	.	PASS	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113222036	113222036	+	Silent	SNP	G	G	A	rs11537650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	53	85	0	0.504762	0	T|0.051;G|0.602;C|0.139;A|0.208	0.208	strong	.	SPICE1	130	.	NM_144718	exon3	c.C138T	p.P46P	ATCTTCGGGAGTT	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276681	71276681	+	Silent	SNP	T	T	C	rs113879786	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	39	180	0	0.282609	0	T|0.717;C|0.283	0.283	strong	.	KRTAP5-10	37	.	NM_001012710	exon1	c.T48C	p.G16G	TGGGGGTTGTGGC	.	PASS	Atlas-SNP
IFIH1	64135	hgsc.bcm.edu	37	2	163124051	163124051	+	Missense_Mutation	SNP	C	C	T	rs1990760	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	52	119	0	0.485981	0	C|0.588;T|0.412	0.412	strong	.	IFIH1	102	.	NM_022168	exon15	c.G2836A	p.A946T	GCAGTGCTTTGTT	.	PASS	Atlas-SNP
MSH5	4439	hgsc.bcm.edu	37	6	31729359	31729359	+	Silent	SNP	A	A	G	rs707938	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	24	65	0	0.45283	0	A|0.573;G|0.427	0.427	strong	.	MSH5	108	.	NM_025259	exon22	c.A2202G	p.Q734Q	GCTACAACTGCTG	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	125076589	125076589	+	Missense_Mutation	SNP	T	T	G	rs7012186	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	140	138	0	1	0	T|0.207;G|0.793	0.793	strong	.	FER1L6	268	.	NM_001039112	exon26	c.T3330G	p.D1110E	TTCAGATATTTCA	.	PASS	Atlas-SNP
ZNF189	7743	hgsc.bcm.edu	37	9	104170227	104170227	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	40	57	0	0.512821	0	.	.	none	.	ZNF189	79	.	NM_003452	exon3	c.T177G	p.D59E	CAGAGATAAGGAT	.	PASS	Atlas-SNP
LGI3	203190	hgsc.bcm.edu	37	8	22006123	22006123	+	Silent	SNP	G	G	A	rs201271501	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	34	55	0	0.5	0	G|1.000;A|0.000	0.000	strong	.	LGI3	44	.	NM_139278	exon8	c.C1197T	p.P399P	GATGACGGGTGCC	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194081635	194081635	+	Silent	SNP	T	T	C	rs923935	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	30	49	0	0.555556	0	T|0.795;C|0.205	0.205	strong	.	LRRC15	137	.	NM_001135057	exon3	c.A156G	p.A52A	GGGCACTGCCACA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971023	45971023	+	Missense_Mutation	SNP	G	G	T	rs478967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	74	156	0	0.493333	0	G|0.811;T|0.189	0.189	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.C319A	p.P107T	ACACAGGCTTGCA	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143452	55143452	+	Missense_Mutation	SNP	T	T	C	rs1061680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	70	153	0	0.522388	0	T|0.567;C|0.433	0.433	strong	LILRB1,NS,carcinoma,-1,1	LILRB1	140	1	NM_001081637	exon5	c.T425C	p.I142T	ATGTAATCCTCCA	.	PASS	Atlas-SNP
RASSF7	8045	hgsc.bcm.edu	37	11	562437	562437	+	Silent	SNP	G	G	A	rs11246189	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	53	77	0	0.495327	0	G|0.827;A|0.173	0.173	strong	.	RASSF7	22	.	NM_001143994	exon3	c.G483A	p.R161R	GCTCAGGGTGCAG	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	125072426	125072426	+	Silent	SNP	T	T	C	rs4483140	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	68	55	0	0.971429	0	T|0.177;C|0.823	0.823	strong	.	FER1L6	268	.	NM_001039112	exon23	c.T2880C	p.P960P	GGTTCCTCCTTCT	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11650958	11650958	+	Missense_Mutation	SNP	G	G	A	rs61743635	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	62	95	0	0.508197	0	G|0.922;A|0.078	0.078	strong	.	DNAH9	695	.	NM_001372	exon32	c.G6485A	p.R2162K	TGCTGAGGTCCTT	.	PASS	Atlas-SNP
DCPS	28960	hgsc.bcm.edu	37	11	126174164	126174164	+	Silent	SNP	C	C	T	rs695029	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	43	82	0	0.505882	0	C|0.772;T|0.228	0.228	strong	DCPS,NS,carcinoma,+2,1	DCPS	33	1	NM_014026	exon1	c.C189T	p.F63F	CATTTTCCTACAC	.	PASS	Atlas-SNP
SLK	9748	hgsc.bcm.edu	37	10	105762933	105762933	+	Missense_Mutation	SNP	G	G	A	rs7071400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	94	0	0.435644	0	G|0.982;A|0.018	0.018	strong	.	SLK	107	.	NM_014720	exon9	c.G1997A	p.G666E	CTTTAGGAAGTGA	.	PASS	Atlas-SNP
SMOC1	64093	hgsc.bcm.edu	37	14	70418881	70418881	+	Silent	SNP	G	G	A	rs3742909	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	42	104	0	0.477273	0	G|0.784;A|0.216	0.216	strong	.	SMOC1	61	.	NM_001034852	exon2	c.G126A	p.Q42Q	CCCACAGTGCAAC	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119545	19119545	+	Silent	SNP	C	C	T	rs45604134	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	48	95	0	0.527473	0	C|0.846;T|0.154	0.154	strong	.	TSSK2	29	.	NM_053006	exon1	c.C633T	p.C211C	GGTCTGCGGCTCC	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62019103	62019103	+	Silent	SNP	G	G	T	rs56342400	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	87	138	0	0.491525	0	A|0.000;C|0.000;G|0.831;T|0.168	0.168	strong	SCN4A,NS,carcinoma,0,1	SCN4A	205	1	NM_000334	exon24	c.C4539A	p.I1513I	ATCATCGATGCCC	.	PASS	Atlas-SNP
SOGA2	23255	hgsc.bcm.edu	37	18	8819246	8819246	+	Missense_Mutation	SNP	C	C	T	rs55676538	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	23	36	0	0.46	0	C|0.985;T|0.015	0.015	strong	.	.	.	.	NM_015210	exon13	c.C3145T	p.R1049C	AGGAACCGCCTCC	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361451	+	Silent	SNP	G	G	A	rs80227456		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	461	76	607	0	0.164859	0	.	.	weak	.	OR13C5	60	.	NM_001004482	exon1	c.C244T	p.L82L	TCACTAGCGTGGA	.	PASS	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038659	22038659	+	Missense_Mutation	SNP	T	T	C	rs17792778	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	130	126	0	1	0	T|0.310;C|0.690	0.690	strong	OR10G3,colon,carcinoma,0,2	OR10G3	40	2	NM_001005465	exon1	c.A217G	p.S73G	AGATGCTCATATC	.	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-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	31	37	0	1	0	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	.	PASS	Atlas-SNP
SLIT2	9353	hgsc.bcm.edu	37	4	20535275	20535275	+	Missense_Mutation	SNP	C	C	T	rs201411609	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	433	6	412	0	0.0138568	0	C|1.000;T|0.000	0.000	strong	SLIT2,right_lower_lobe,carcinoma,-1,1	SLIT2	290	1	NM_004787	exon18	c.C1769T	p.T590M	TTCTTACGAGTAA	.	scavenged	Atlas-SNP
CD48	962	hgsc.bcm.edu	37	1	160650938	160650938	+	Missense_Mutation	SNP	C	C	T	rs6667145	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	17	69	0	0.361702	0	C|0.927;T|0.073	0.073	strong	.	CD48	31	.	NM_001256030	exon3	c.G706A	p.E236K	TTTGTTCAAAACA	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107084739	107084739	+	Silent	SNP	A	A	G	rs6718521	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	214	270	0	0.934498	0	A|0.626;G|0.374	0.374	strong	.	RGPD3	316	.	NM_001144013	exon1	c.T6C	p.S2S	GCTGCAACTCATC	.	PASS	Atlas-SNP
CASK	8573	hgsc.bcm.edu	37	X	41604809	41604809	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	126	70	0	0.992126	0	.	.	none	.	CASK	93	.	NM_001126054	exon4	c.C324T	p.D108D	ACCAGCGTCAGCT	.	PASS	Atlas-SNP
NMU	10874	hgsc.bcm.edu	37	4	56475338	56475338	+	Silent	SNP	G	G	A	rs3805383	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	46	82	0	0.474227	0	G|0.795;A|0.205	0.205	strong	.	NMU	17	.	NM_006681	exon4	c.C228T	p.N76N	CAGTGCGTTGGAT	.	PASS	Atlas-SNP
ISM1	140862	hgsc.bcm.edu	37	20	13251325	13251325	+	Missense_Mutation	SNP	C	C	T	rs76665689	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	47	90	0	0.505376	0	C|0.997;T|0.003	0.003	strong	.	ISM1	41	.	NM_080826	exon2	c.C313T	p.L105F	TTTCTCCTTGATC	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3656625	3656625	+	Missense_Mutation	SNP	G	G	A	rs79842542	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	103	218	0	0.497585	0	G|0.937;A|0.063	0.063	strong	SLX4,NS,carcinoma,+1,2	SLX4	173	2	NM_032444	exon3	c.C610T	p.R204C	CTGTGCGGGGTTT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506446	195506446	+	Missense_Mutation	SNP	G	G	T	rs62282468	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	34	27	0	0.62963	0	G|0.899;T|0.101	0.101	strong	.	MUC4	1505	.	NM_018406	exon2	c.C12005A	p.P4002H	GTGACAGGAAGAG	.	PASS	Atlas-SNP
RNF169	254225	hgsc.bcm.edu	37	11	74546905	74546905	+	Silent	SNP	G	G	A	rs1125609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	41	90	0	0.539474	0	G|0.788;A|0.212	0.212	strong	RNF169,colon,carcinoma,0,1	RNF169	36	1	NM_001098638	exon6	c.G1257A	p.Q419Q	CCTGCAGAAGCAG	.	PASS	Atlas-SNP
WNT10B	7480	hgsc.bcm.edu	37	12	49359989	49359989	+	Silent	SNP	G	G	A	rs1051886	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	72	71	0	1	0	G|0.679;A|0.321	0.321	strong	.	WNT10B	41	.	NM_003394	exon5	c.C1059T	p.H353H	CACGTTGTGCCCA	.	PASS	Atlas-SNP
OR7A5	26659	hgsc.bcm.edu	37	19	14938248	14938248	+	Missense_Mutation	SNP	T	T	A	rs112284734	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	9	88	0	0.0825688	0	T|0.993;A|0.007	0.007	strong	OR7A5,rectum,carcinoma,0,1	OR7A5	43	1	NM_017506	exon1	c.A806T	p.H269L	CTTGAGTGTGAGT	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	14767	14767	+	Silent	SNP	T	T	C	rs3135031	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	49	26	0	0.98	0	T|0.826;C|0.174	0.174	strong	.	.	.	.	ENST00000361789	exon1	c.T21C	p.T7T	CAAAACTAACCCC	.	PASS	Atlas-SNP
NOS3	4846	hgsc.bcm.edu	37	7	150704250	150704250	+	Silent	SNP	C	C	G	rs2566514	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	39	72	0	0.393939	0	C|0.648;G|0.352	0.352	strong	NOS3,NS,carcinoma,+2,1	NOS3	131	1	NM_000603	exon17	c.C1998G	p.A666A	TCGTGCCGTGGAC	.	PASS	Atlas-SNP
ASTL	431705	hgsc.bcm.edu	37	2	96798440	96798440	+	Missense_Mutation	SNP	C	C	T	rs61735195	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	58	97	0	0.54717	0	C|0.991;T|0.009	0.009	strong	.	ASTL	59	.	NM_001002036	exon6	c.G476A	p.R159H	CCACTGCGCCCCA	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1268485	1268485	+	Silent	SNP	C	C	T	rs2738891	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	14	32	0	0.518519	0	C|0.936;T|0.064	0.064	strong	.	CACNA1H	317	.	NM_021098	exon33	c.C5721T	p.G1907G	TCCGGGCGCCAGG	.	PASS	Atlas-SNP
ANKS1B	56899	hgsc.bcm.edu	37	12	99640428	99640428	+	Silent	SNP	T	T	C	rs3751323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	96	208	0	0.513369	0	T|0.481;C|0.519	0.519	strong	.	ANKS1B	180	.	NM_152788	exon13	c.A1971G	p.S657S	AGGTTCTGAGTTA	.	PASS	Atlas-SNP
JPH3	57338	hgsc.bcm.edu	37	16	87678165	87678165	+	Silent	SNP	G	G	A	rs3751725	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	50	48	0	0.961538	0	G|0.816;A|0.184	0.184	strong	.	JPH3	95	.	NM_020655	exon2	c.G684A	p.S228S	CAAGTCGGAGTCC	.	PASS	Atlas-SNP
MT1E	4493	hgsc.bcm.edu	37	16	56660816	56660816	+	Missense_Mutation	SNP	G	G	A	rs72818417	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	26	53	0	0.5	0	G|0.948;A|0.052	0.052	strong	.	MT1E	7	.	NM_175617	exon3	c.G119A	p.G40D	CCGTGGGCTGTGC	.	PASS	Atlas-SNP
SLC2A1	6513	hgsc.bcm.edu	37	1	43408966	43408966	+	Silent	SNP	G	G	A	rs1385129	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	37	76	0	0.411111	0	G|0.781;A|0.219	0.219	strong	.	SLC2A1	36	.	NM_006516	exon2	c.C45T	p.A15A	TCCCACGGCCAGC	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216363590	216363590	+	Silent	SNP	C	C	T	rs56013136	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	42	115	0	0.488372	0	C|0.987;T|0.013	0.013	strong	.	USH2A	1168	.	NM_007123	exon20	c.G4371A	p.S1457S	TGCTCCCGAAGCA	.	PASS	Atlas-SNP
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773388	140773388	+	Silent	SNP	G	G	T	rs2240700	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	236	310	0	0.995781	0	G|0.805;T|0.195	0.195	strong	PCDHGA8,caecum,carcinoma,+1,3	PCDHGA8	146	3	NM_014004	exon1	c.G1008T	p.S336S	CATTTCGGTGGAA	.	PASS	Atlas-SNP
BIVM-ERCC5	0	hgsc.bcm.edu	37	13	103504517	103504517	+	Silent	SNP	T	T	C	rs1047768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	62	144	0	0.516667	0	T|0.449;C|0.551	0.551	strong	.	.	.	.	NM_001204425	exon10	c.T1500C	p.H500H	TCGCCATGGGAAC	.	PASS	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	37	1	222721288	222721288	+	Silent	SNP	C	C	T	rs4846382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	80	128	0	0.503145	0	C|0.444;T|0.556	0.556	strong	.	HHIPL2	122	.	NM_024746	exon1	c.G99A	p.L33L	CTGGCCCAACAAG	.	PASS	Atlas-SNP
TBX4	9496	hgsc.bcm.edu	37	17	59560685	59560685	+	Silent	SNP	C	C	T	rs2270150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	55	130	0	0.518868	0	C|0.880;T|0.120	0.120	strong	.	TBX4	69	.	NM_018488	exon8	c.C1446T	p.V482V	TCAGGTCCGAGAG	.	PASS	Atlas-SNP
NACA2	342538	hgsc.bcm.edu	37	17	59668352	59668352	+	Missense_Mutation	SNP	C	C	T	rs17531723	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	96	194	0	0.468293	0	C|0.884;T|0.116	0.116	strong	NACA2,NS,carcinoma,0,1	NACA2	33	1	NM_199290	exon1	c.G190A	p.V64I	TACCGACTGGTTC	.	PASS	Atlas-SNP
CIZ1	25792	hgsc.bcm.edu	37	9	130938661	130938661	+	Missense_Mutation	SNP	C	C	T	rs11549266	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	40	70	0	0.519481	0	C|0.908;T|0.092	0.092	strong	CIZ1,colon,carcinoma,+1,2	CIZ1	75	2	NM_001257975	exon11	c.G2002A	p.V668M	GGGGCACGGGCAG	.	PASS	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31349642	31349642	+	Silent	SNP	C	C	T	rs41269521	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	9	55	0	0.109756	0	C|0.972;G|0.000;T|0.028	0.028	strong	.	SDC3	45	.	NM_014654	exon3	c.G627A	p.R209R	AAGCCTCCGTACG	.	PASS	Atlas-SNP
CMTM2	146225	hgsc.bcm.edu	37	16	66614008	66614008	+	Missense_Mutation	SNP	T	T	C	rs2290182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	447	221	399	0	0.494407	0	T|0.810;C|0.190	0.190	strong	.	CMTM2	33	.	NM_144673	exon2	c.T365C	p.I122T	TGGAGATATCCTT	.	PASS	Atlas-SNP
CREB3L3	84699	hgsc.bcm.edu	37	19	4154910	4154910	+	Silent	SNP	C	C	T	rs35474881	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	57	79	0	0.467213	0	C|0.881;T|0.119	0.119	strong	CREB3L3,NS,carcinoma,+1,2	CREB3L3	53	2	NM_001271997	exon2	c.C42T	p.A14A	TGCTGCCTGCTCC	.	PASS	Atlas-SNP
RDH12	145226	hgsc.bcm.edu	37	14	68193731	68193731	+	Missense_Mutation	SNP	G	G	A	rs17852293	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	50	73	0	0.574713	0	G|0.882;A|0.118	0.118	strong	RDH12,brain,glioma,0,1	RDH12	43	1	NM_152443	exon7	c.G482A	p.R161Q	TGGAGCGGCTAAA	.	PASS	Atlas-SNP
SLC12A2	6558	hgsc.bcm.edu	37	5	127469859	127469859	+	Silent	SNP	A	A	G	rs2228112	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	64	138	0	0.441379	0	A|0.627;C|0.000;G|0.373;T|0.000	0.373	strong	.	SLC12A2	119	.	NM_001046	exon6	c.A1191G	p.E397E	CTAGGAACATTCC	.	PASS	Atlas-SNP
FUCA2	2519	hgsc.bcm.edu	37	6	143816859	143816859	+	Silent	SNP	C	C	T	rs8161	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	64	116	0	1	0	C|0.585;T|0.415	0.415	strong	FUCA2,NS,carcinoma,0,1	FUCA2	28	1	NM_032020	exon7	c.G1389A	p.L463L	ATTAGTCAGGGCT	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7231843	7231843	+	Missense_Mutation	SNP	G	G	A	rs9379084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	34	62	0	0.548387	0	G|0.896;A|0.104	0.104	strong	.	RREB1	242	.	NM_001003700	exon10	c.G3511A	p.D1171N	GGGGTGGACCTGG	.	PASS	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92537354	92537354	+	Missense_Mutation	SNP	C	C	G	rs12895357	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	28	59	2	0.622222	0.0338983	C|0.783;G|0.217	0.217	strong	ATXN3,NS,carcinoma,0,2	ATXN3	46	2	NM_004993	exon10	c.G916C	p.G306R	GGTCCCCCTGCTG	.	scavenged	Atlas-SNP
HMOX2	3163	hgsc.bcm.edu	37	16	4558064	4558064	+	Silent	SNP	G	G	A	rs2404579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	51	93	0	0.53125	0	G|0.996;A|0.004	0.004	strong	.	HMOX2	22	.	NM_001127205	exon4	c.G555A	p.Q185Q	GACCCAGTTCTAC	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113565933	113565933	+	Missense_Mutation	SNP	G	G	A	rs34598602	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	19	31	0	0.452381	0	G|0.957;A|0.043	0.043	strong	.	RASAL1	89	.	NM_004658	exon4	c.C173T	p.T58M	TGCACCGTGTACT	.	PASS	Atlas-SNP
C5orf45	51149	hgsc.bcm.edu	37	5	179285752	179285752	+	Silent	SNP	G	G	A	rs10060182	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	28	24	0	0.608696	0	G|0.579;A|0.421	0.421	strong	C5orf45,colon,carcinoma,0,1	C5orf45	23	1	NM_016175	exon1	c.C45T	p.C15C	GAGGCGGCAGCTG	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	37	16	81971403	81971403	+	Silent	SNP	T	T	C	rs1071644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	40	76	0	0.493827	0	C|0.387;N|0.000	0.387	strong	.	PLCG2	276	.	NM_002661	exon28	c.T3093C	p.N1031N	TCTCAATGGGCGC	.	PASS	Atlas-SNP
CDHR2	54825	hgsc.bcm.edu	37	5	176017455	176017455	+	Missense_Mutation	SNP	C	C	T	rs2291442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	50	134	0	0.438596	0	C|0.719;T|0.281	0.281	strong	CDHR2,colon,carcinoma,0,1	CDHR2	152	1	NM_017675	exon27	c.C3383T	p.T1128M	CGCTGACGCAGCT	.	PASS	Atlas-SNP
GPC4	2239	hgsc.bcm.edu	37	X	132437337	132437337	+	Missense_Mutation	SNP	G	G	A	rs1048369	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	65	64	0	1	0	G|0.566;0|0.012	.	strong	.	GPC4	58	.	NM_001448	exon8	c.C1325T	p.A442V	TGGTTGGCTAATC	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100105735	100105735	+	Silent	SNP	T	T	C	rs1947717	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	49	108	0	0.576471	0	T|0.445;C|0.555	0.555	strong	.	.	.	.	NM_020893	exon19	c.T2520C	p.C840C	GCATTGTAGGAAG	.	PASS	Atlas-SNP
PSPC1	55269	hgsc.bcm.edu	37	13	20279879	20279879	+	Missense_Mutation	SNP	T	T	C	rs200516102	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	697	84	603	9	0.120517	0.0149254	T|0.998;C|0.002	0.002	strong	PSPC1,NS,haematopoietic_neoplasm,0,1	PSPC1	61	1	NM_001042414	exon9	c.A1309G	p.M437V	GACCCATTGGTGG	.	scavenged	Atlas-SNP
ANGPT2	285	hgsc.bcm.edu	37	8	6371303	6371303	+	Silent	SNP	A	A	G	rs17063434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	71	111	0	0.529851	0	A|0.942;G|0.058	0.058	strong	.	ANGPT2	126	.	NM_001147	exon7	c.T1095C	p.N365N	TTGCTGATTAGTC	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151171542	151171542	+	Silent	SNP	A	A	G	rs7621591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	79	82	0	1	0	A|0.195;G|0.805	0.805	strong	.	IGSF10	279	.	NM_178822	exon3	c.T345C	p.N115N	GACTTTATTATAG	.	PASS	Atlas-SNP
PIEZO1	9780	hgsc.bcm.edu	37	16	88782079	88782079	+	Silent	SNP	G	G	A	rs1061228	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	40	84	0	0.533333	0	T|0.000;G|0.884;C|0.000;A|0.115	0.115	strong	.	PIEZO1	79	.	NM_001142864	exon51	c.C7500T	p.Y2500Y	CTTGGCGTACAAC	.	PASS	Atlas-SNP
DOCK11	139818	hgsc.bcm.edu	37	X	117700141	117700141	+	Silent	SNP	A	A	G	rs2286977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	104	114	0	0.981132	0	0|0.012;G|0.317	0.317	strong	.	DOCK11	185	.	NM_144658	exon8	c.A867G	p.A289A	AACAGCACAAGGT	.	PASS	Atlas-SNP
DDX18	8886	hgsc.bcm.edu	37	2	118575215	118575215	+	Missense_Mutation	SNP	C	C	G	rs1052637	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	66	154	0	0.407407	0	C|0.601;G|0.399	0.399	strong	.	DDX18	79	.	NM_006773	exon2	c.C281G	p.T94S	TATTAACCAATGG	.	PASS	Atlas-SNP
CCDC34	91057	hgsc.bcm.edu	37	11	27379026	27379026	+	Missense_Mutation	SNP	C	C	T	rs138159804	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	72	187	0	0.476821	0	C|1.000;T|0.000	0.000	weak	.	CCDC34	48	.	NM_030771	exon2	c.G422A	p.R141H	GTCAGGCGGCTTT	.	PASS	Atlas-SNP
SDC4	6385	hgsc.bcm.edu	37	20	43964514	43964514	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	24	27	0	0.461538	0	.	.	none	.	SDC4	16	.	NM_002999	exon2	c.G107A	p.R36Q	AAGTATCGGCCTT	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	26	34	0	0.666667	0	A|0.830;C|0.170	0.170	strong	ATXN1,colon,carcinoma,0,3	ATXN1	117	3	NM_001128164	exon7	c.T633G	p.H211Q	CTGCTGATGCTGA	.	PASS	Atlas-SNP
VAMP8	8673	hgsc.bcm.edu	37	2	85806266	85806266	+	Silent	SNP	C	C	T	rs3731828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	11	48	0	0.275	0	C|0.698;T|0.302	0.302	strong	VAMP8,NS,carcinoma,0,1	VAMP8	10	1	NM_003761	exon2	c.C138T	p.N46N	CCGCAACAAGACA	.	PASS	Atlas-SNP
ZNF442	79973	hgsc.bcm.edu	37	19	12463856	12463856	+	Missense_Mutation	SNP	T	T	C	rs73921445	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	38	71	0	0.436782	0	T|0.986;C|0.014	0.014	strong	.	ZNF442	102	.	NM_030824	exon4	c.A151G	p.K51E	GACTCTTCTGTGA	.	PASS	Atlas-SNP
HSPB7	27129	hgsc.bcm.edu	37	1	16342237	16342237	+	Silent	SNP	A	A	G	rs1739840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	31	45	0	1	0	A|0.376;G|0.624	0.624	strong	.	HSPB7	17	.	NM_014424	exon3	c.T351C	p.T117T	CATGACAGTGCCG	.	PASS	Atlas-SNP
SLC16A6	9120	hgsc.bcm.edu	37	17	66267691	66267691	+	Missense_Mutation	SNP	A	A	T	rs7222013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	74	175	0	0.474359	0	A|0.636;T|0.364	0.364	strong	.	SLC16A6	56	.	NM_001174166	exon6	c.T610A	p.F204I	TGATAAAGATGGG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228505204	228505204	+	Missense_Mutation	SNP	G	G	A	rs4653942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	75	185	0	0.457317	0	G|0.671;A|0.329	0.329	strong	.	OBSCN	2142	.	NM_001271223	exon63	c.G16472A	p.R5491H	TGGCTCGCAGCAG	.	PASS	Atlas-SNP
TRAPPC10	7109	hgsc.bcm.edu	37	21	45479055	45479055	+	Silent	SNP	C	C	T	rs2838475	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	24	58	0	0.358209	0	C|0.929;T|0.071	0.071	strong	.	TRAPPC10	109	.	NM_003274	exon6	c.C750T	p.D250D	ACTGGACGCCCTC	.	PASS	Atlas-SNP
TMEM133	83935	hgsc.bcm.edu	37	11	100863319	100863319	+	Missense_Mutation	SNP	A	A	C	rs61995873	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	69	104	0	0.575	0	A|0.949;C|0.051	0.051	strong	.	TMEM133	9	.	NM_032021	exon1	c.A280C	p.N94H	GGTCTCAATTTCC	.	PASS	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41383137	41383137	+	Silent	SNP	C	C	T	rs148915421	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	94	199	0	0.441315	0	C|0.978;T|0.022	0.022	strong	CYP2A7,NS,carcinoma,-1,1	CYP2A7	71	1	NM_000764	exon7	c.G1119A	p.R373R	TTTAACCCTGCGG	.	PASS	Atlas-SNP
NEIL1	79661	hgsc.bcm.edu	37	15	75641682	75641682	+	Splice_Site	SNP	T	T	C	rs5745908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	15	23	0	0.483871	0	T|0.993;C|0.007	0.007	strong	.	NEIL1	36	.	NM_024608	exon2	c.434+2T>C	.	TTCAGGTAGGGCC	.	PASS	Atlas-SNP
PLA2G4F	255189	hgsc.bcm.edu	37	15	42439376	42439376	+	Silent	SNP	G	G	A	rs4923929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	8	30	0	0.470588	0	G|0.534;A|0.466	0.466	strong	PLA2G4F,NS,carcinoma,0,1	PLA2G4F	75	1	NM_213600	exon13	c.C1365T	p.S455S	GGACACGCTGTGG	.	PASS	Atlas-SNP
SNAPC2	6618	hgsc.bcm.edu	37	19	7986638	7986638	+	Missense_Mutation	SNP	C	C	G	rs475002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	41	69	0	0.5	0	C|0.546;G|0.454	0.454	strong	.	SNAPC2	20	.	NM_003083	exon3	c.C352G	p.L118V	GAAGCCCTGGCAG	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197427557	197427557	+	Silent	SNP	A	A	G	rs28394098	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	71	151	0	0.464052	0	A|0.885;G|0.115	0.115	strong	.	KIAA0226	136	.	NM_014687	exon7	c.T1188C	p.T396T	GGTGACAGTGAGT	.	PASS	Atlas-SNP
RHOBTB3	22836	hgsc.bcm.edu	37	5	95084131	95084131	+	Silent	SNP	G	G	A	rs34896	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	98	107	0	1	0	A|0.416;C|0.001	0.416	strong	.	RHOBTB3	43	.	NM_014899	exon4	c.G510A	p.A170A	AGGAGCGACCTAT	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608877	26608877	+	Silent	SNP	G	G	A	rs1134582	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	39	33	4	0.795918	0.121212	G|0.870;A|0.130	0.130	strong	UBXN11,NS,carcinoma,0,2	UBXN11	54	2	NM_183008	exon16	c.C1476T	p.G492G	ACTGGGGCCGGGA	.	scavenged	Atlas-SNP
OR52E6	390078	hgsc.bcm.edu	37	11	5862416	5862416	+	Missense_Mutation	SNP	C	C	T	rs61735020	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	60	125	0	0.487805	0	C|0.984;T|0.016	0.016	strong	.	OR52E6	70	.	NM_001005167	exon1	c.G712A	p.A238T	TGAGAGCTTTGAG	.	PASS	Atlas-SNP
ZNF132	7691	hgsc.bcm.edu	37	19	58946056	58946056	+	Missense_Mutation	SNP	G	G	A	rs1465789	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	39	82	0	0.333333	0	G|0.464;A|0.536	0.536	strong	.	ZNF132	56	.	NM_003433	exon3	c.C755T	p.P252L	TGGTTGGGGAGAG	.	PASS	Atlas-SNP
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23059324	23059324	+	Missense_Mutation	SNP	C	C	G	rs20575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	42	78	0	0.461538	0	C|0.521;G|0.478	0.478	strong	.	TNFRSF10A	40	.	NM_003844	exon4	c.G626C	p.R209T	CACCCTCTGCTGC	.	PASS	Atlas-SNP
TKTL1	8277	hgsc.bcm.edu	37	X	153537783	153537783	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	53	56	0	1	0	.	.	none	.	TKTL1	61	.	NM_012253	exon3	c.C339T	p.F113F	GTACTTCGACAGG	.	PASS	Atlas-SNP
ABCA12	26154	hgsc.bcm.edu	37	2	215865575	215865575	+	Silent	SNP	T	T	C	rs10498030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	125	278	0	0.545852	0	T|0.804;C|0.196	0.196	strong	.	ABCA12	368	.	NM_173076	exon22	c.A3033G	p.P1011P	GTGTGATGGAGAA	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305602	48305602	+	Silent	SNP	C	C	T	rs147608412	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	18	32	0	0.367347	0	C|0.943;T|0.057	0.057	strong	TPRX1,NS,carcinoma,-1,1	TPRX1	46	1	NM_198479	exon2	c.G666A	p.P222P	TGGGATCGGGCCT	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	116931099	116931099	+	Missense_Mutation	SNP	G	G	A	rs2241671	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	54	113	0	0.514286	0	G|0.596;A|0.404	0.404	strong	COL27A1,NS,carcinoma,0,1	COL27A1	200	1	NM_032888	exon3	c.G1264A	p.A422T	CGTCCCGCAGAGA	.	PASS	Atlas-SNP
FURIN	5045	hgsc.bcm.edu	37	15	91419548	91419548	+	Missense_Mutation	SNP	C	C	T	rs148110342	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	37	78	0	0.445783	0	C|0.998;T|0.002	0.002	strong	FURIN,NS,carcinoma,-1,1	FURIN	85	1	NM_002569	exon3	c.C241T	p.R81C	CCTCACCGCCCGC	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	37	18	21120444	21120444	+	Missense_Mutation	SNP	T	T	C	rs1805082	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	30	46	0	0.566038	0	T|0.533;C|0.467	0.467	strong	.	NPC1	114	.	NM_000271	exon17	c.A2572G	p.I858V	ATCCAATATCTAC	.	PASS	Atlas-SNP
CCDC79	283847	hgsc.bcm.edu	37	16	66792714	66792714	+	Missense_Mutation	SNP	T	T	C	rs363156	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	61	0	1	0	T|0.651;C|0.349	0.349	strong	.	CCDC79	32	.	NM_001136505	exon18	c.A1958G	p.Q653R	AGTCGTTGTCTTC	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103082558	103082558	+	Silent	SNP	A	A	G	rs17394217	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	41	60	0	0.488095	0	A|0.913;G|0.087	0.087	strong	.	DYNC2H1	246	.	NM_001377	exon54	c.A8580G	p.E2860E	CCATGAATCTTGT	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121880520	121880520	+	Silent	SNP	G	G	A	rs3751131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	62	46	0	0.568807	0	G|0.651;A|0.349	0.349	strong	KDM2B_ENST00000377071,colon,carcinoma,-2,2	KDM2B	218	2	NM_032590	exon19	c.C2724T	p.D908D	GGAGTGGTCGCTC	.	PASS	Atlas-SNP
KRT8	3856	hgsc.bcm.edu	37	12	53298775	53298775	+	Silent	SNP	A	A	T	rs137898974	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	16	27	0	0.533333	0	A|0.935;T|0.065	0.065	strong	.	KRT8	41	.	NM_001256282	exon2	c.T75A	p.P25P	AGAGGCAGGAGTG	.	PASS	Atlas-SNP
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052981	33052981	+	Missense_Mutation	SNP	C	C	A	rs14362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	107	178	0	0.488584	0	C|0.874;A|0.126	0.126	strong	.	HLA-DPB1	28	.	NM_002121	exon3	c.C619A	p.L207M	ACCAGCCTGGATA	.	PASS	Atlas-SNP
DHODH	1723	hgsc.bcm.edu	37	16	72055078	72055078	+	Silent	SNP	G	G	A	rs148523165	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	45	68	0	0.548781	0	G|0.996;A|0.004	0.004	strong	.	DHODH	33	.	NM_001361	exon5	c.G573A	p.A191A	CGCCGCGGAGGAC	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026138	176026138	+	Missense_Mutation	SNP	T	T	A	rs201635586	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	25	165	0	0.235849	0	T|0.795;A|0.205	0.205	strong	.	GPRIN1	77	.	NM_052899	exon2	c.A698T	p.E233V	GGATCCTCCTTCC	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1729660	1729660	+	Silent	SNP	C	C	T	rs1063742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	78	167	0	0.490566	0	C|0.805;T|0.195	0.195	strong	TACC3,NS,carcinoma,0,1	TACC3	69	1	NM_006342	exon4	c.C531T	p.S177S	TGGCAGCCCTGAG	.	PASS	Atlas-SNP
INPP5E	56623	hgsc.bcm.edu	37	9	139324737	139324737	+	Silent	SNP	C	C	A	rs33982662	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	30	38	0	0.535714	0	C|0.796;A|0.204	0.204	strong	.	INPP5E	18	.	NM_019892	exon9	c.G1794T	p.G598G	GTCTCGCCCCGGC	.	PASS	Atlas-SNP
ASTN2	23245	hgsc.bcm.edu	37	9	119448979	119448979	+	Missense_Mutation	SNP	C	C	T	rs10983304	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	22	55	0	0.468085	0	C|0.979;T|0.021	0.021	strong	.	ASTN2	307	.	NM_198186	exon1	c.G106A	p.E36K	TACCTTCAGTCTG	.	PASS	Atlas-SNP
C22orf26	55267	hgsc.bcm.edu	37	22	46447714	46447714	+	Missense_Mutation	SNP	T	T	C	rs59929908	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	23	56	0	0.469388	0	T|0.897;C|0.103	0.103	strong	.	C22orf26	1	.	NM_018280	exon2	c.A410G	p.Q137R	CATACCTGTAATT	.	PASS	Atlas-SNP
PCDH12	51294	hgsc.bcm.edu	37	5	141335498	141335498	+	Missense_Mutation	SNP	C	C	T	rs164515	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	39	92	0	0.493671	0	C|0.796;T|0.204	0.204	strong	PCDH12,colon,carcinoma,+1,1	PCDH12	133	1	NM_016580	exon1	c.G1919A	p.S640N	TTTCCACTGCGGA	.	PASS	Atlas-SNP
PDSS1	23590	hgsc.bcm.edu	37	10	27035396	27035396	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	31	82	0	0.418919	0	.	.	none	.	PDSS1	36	.	NM_014317	exon12	c.T1242A	p.D414E	AAGAGATAAATGA	.	PASS	Atlas-SNP
SHARPIN	81858	hgsc.bcm.edu	37	8	145154257	145154257	+	Missense_Mutation	SNP	C	C	G	rs11541804	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	43	86	0	0.452632	0	C|0.939;G|0.061	0.061	strong	.	SHARPIN	16	.	NM_030974	exon6	c.G845C	p.S282T	GCAAGGCTGCGCT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790396	4790396	+	Missense_Mutation	SNP	G	G	A	rs17324609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	57	130	0	0.401408	0	G|0.915;A|0.085	0.085	strong	.	OR51F1	60	.	NM_001004752	exon1	c.C752T	p.A251V	AAGAAAGCAACTG	.	PASS	Atlas-SNP
JPH3	57338	hgsc.bcm.edu	37	16	87678144	87678144	+	Silent	SNP	T	T	C	rs918368	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	61	54	0	0.968254	0	T|0.400;C|0.600	0.600	strong	.	JPH3	95	.	NM_020655	exon2	c.T663C	p.S221S	GCTGAGTGGGCTG	.	PASS	Atlas-SNP
MMP3	4314	hgsc.bcm.edu	37	11	102713620	102713620	+	Missense_Mutation	SNP	T	T	C	rs679620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	28	67	0	0.466667	0	T|0.428;C|0.572	0.572	strong	MMP3,NS,carcinoma,0,1	MMP3	60	1	NM_002422	exon2	c.A133G	p.K45E	CTTTTTTGAGGTC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910402	29910402	+	Silent	SNP	G	G	A	rs1136656	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	38	113	0	0.520548	0	G|0.870;A|0.130	0.130	strong	.	HLA-A	89	.	NM_001242758	exon1	c.G72A	p.A24A	CTGGGCGGGTGAG	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11521428	11521428	+	Silent	SNP	A	A	G	rs61996277	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	94	224	0	0.479592	0	A|0.946;G|0.054	0.054	strong	.	THSD7A	219	.	NM_015204	exon7	c.T2004C	p.Y668Y	ACCCGCATAGGCC	.	PASS	Atlas-SNP
FAM170B	170370	hgsc.bcm.edu	37	10	50339754	50339754	+	Missense_Mutation	SNP	G	G	T	rs73302786	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	50	125	0	0.434783	0	G|0.844;T|0.156	0.156	strong	.	FAM170B	20	.	NM_001164484	exon2	c.C756A	p.D252E	CTGTTGGTCATGT	.	PASS	Atlas-SNP
FZD5	7855	hgsc.bcm.edu	37	2	208632817	208632817	+	Missense_Mutation	SNP	G	G	A	rs35994626	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	17	57	0	0.53125	0	G|0.953;A|0.047	0.047	strong	.	FZD5	22	.	NM_003468	exon2	c.C647T	p.P216L	CAGTTGGGCACCT	.	PASS	Atlas-SNP
C19orf40	91442	hgsc.bcm.edu	37	19	33467413	33467413	+	Missense_Mutation	SNP	C	C	T	rs2304103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	53	99	0	0.486239	0	C|0.939;T|0.061	0.061	strong	.	C19orf40	21	.	NM_152266	exon5	c.C473T	p.S158L	AGCCTTCGCTCCT	.	PASS	Atlas-SNP
CES4A	283848	hgsc.bcm.edu	37	16	67037054	67037054	+	Missense_Mutation	SNP	A	A	C	rs61744399	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	76	123	0	0.580153	0	A|0.791;C|0.209	0.209	strong	.	CES4A	24	.	NM_173815	exon6	c.A772C	p.S258R	ATCACTAGTAACC	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608849	26608849	+	Missense_Mutation	SNP	T	T	A	rs199707978		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	16	25	0	0.4	0	.	.	weak	.	UBXN11	54	.	NM_183008	exon16	c.A1504T	p.S502C	CGGGACTGGGGCC	.	PASS	Atlas-SNP
DLG5	9231	hgsc.bcm.edu	37	10	79566632	79566632	+	Silent	SNP	G	G	A	rs1058198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	87	102	0	0.988636	0	G|0.688;A|0.312	0.312	strong	.	DLG5	154	.	NM_004747	exon26	c.C4851T	p.D1617D	GATGTCGTCCTTC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40405999	40405999	+	Missense_Mutation	SNP	C	C	A	rs7248839	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	475	89	696	0	0.187368	0	C|0.897;A|0.103	0.103	strong	FCGBP,mouth,carcinoma,+1,1	FCGBP	416	1	NM_003890	exon10	c.G4847T	p.G1616V	ACCATGCCTTTAC	.	scavenged	Atlas-SNP
PEX13	5194	hgsc.bcm.edu	37	2	61258816	61258816	+	Missense_Mutation	SNP	G	G	A	rs147707348	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	70	157	0	0.530303	0	G|0.998;A|0.002	0.002	strong	.	PEX13	27	.	NM_002618	exon2	c.G355A	p.V119I	AGATTTGTTCAGC	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039637	239039637	+	Missense_Mutation	SNP	T	T	C	rs4663845	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	13	16	0	0.464286	0	T|0.151;C|0.849	0.849	strong	.	ESPNL	63	.	NM_194312	exon9	c.T2282C	p.V761A	AGACAGTGGCCTG	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115370254	115370254	+	Silent	SNP	A	A	G	rs12243176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	69	113	0	0.552	0	A|0.547;G|0.453	0.453	strong	.	NRAP	208	.	NM_001261463	exon31	c.T3567C	p.I1189I	CCCTTCAATCTCT	.	PASS	Atlas-SNP
GAD1	2571	hgsc.bcm.edu	37	2	171678625	171678625	+	Silent	SNP	T	T	C	rs769404	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	42	27	1	1	0.037037	T|0.654;C|0.346	0.346	strong	GAD1,colon,carcinoma,0,1	GAD1	79	1	NM_000817	exon3	c.T111C	p.H37H	GGCCCATGGATGC	.	scavenged	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50754466	50754466	+	Silent	SNP	C	C	T	rs62241230	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	62	130	0	0.476923	0	C|0.691;T|0.309	0.309	strong	.	.	.	.	NM_001001794	exon8	c.G690A	p.Q230Q	GTCAAACTGCTTC	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48053229	48053229	+	Silent	SNP	C	C	A	rs501916	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	97	220	1	0.468599	0.00454545	C|0.567;A|0.433	0.433	strong	.	SEMA6D	322	.	NM_153617	exon4	c.C276A	p.P92P	AATACCCAACAAG	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384998	16384998	+	Silent	SNP	G	G	C	rs1807285	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	8	6	0	0.571429	0	G|0.706;C|0.294	0.294	strong	FAM131C,NS,carcinoma,-1,2	FAM131C	21	2	NM_182623	exon7	c.C777G	p.P259P	GCCCGGGGGGTGG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911207	29911207	+	Missense_Mutation	SNP	G	G	A	rs1059520	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	85	197	0	0.472222	0	A|0.308;G|0.692	0.308	strong	.	HLA-A	89	.	NM_001242758	exon3	c.G506A	p.R169H	CCAAGCGCAAGTG	.	PASS	Atlas-SNP
FIGLA	344018	hgsc.bcm.edu	37	2	71012604	71012604	+	Silent	SNP	G	G	A	rs7566541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	56	174	0	0.414815	0	G|0.225;A|0.774	0.774	strong	.	FIGLA	23	.	NM_001004311	exon3	c.C552T	p.H184H	ACAAGCGTGTGCT	.	PASS	Atlas-SNP
CXorf22	170063	hgsc.bcm.edu	37	X	36007614	36007614	+	Missense_Mutation	SNP	T	T	G	rs6629027	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	76	0	1	0	0|0.015;G|0.213	0.213	strong	.	CXorf22	272	.	NM_152632	exon16	c.T2892G	p.F964L	TGAATTTGTTGGG	.	PASS	Atlas-SNP
LRRC69	100130742	hgsc.bcm.edu	37	8	92213022	92213022	+	Splice_Site	SNP	T	T	A	rs72666050	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	105	224	1	0.488372	0.00446429	T|0.991;A|0.009	0.009	strong	.	LRRC69	24	.	NM_001129890	exon7	c.933+2T>A	.	CAAAGGTAAATGA	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385184	16385184	+	Silent	SNP	G	G	A	rs75273615	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	383	186	346	0	0.48564	0	G|0.740;A|0.260	0.260	strong	FAM131C,NS,haematopoietic_neoplasm,0,1	FAM131C	21	1	NM_182623	exon7	c.C591T	p.S197S	GGGAAGGCTGTCC	.	PASS	Atlas-SNP
TELO2	9894	hgsc.bcm.edu	37	16	1545448	1545448	+	Missense_Mutation	SNP	A	A	G	rs2235624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	19	47	0	0.395833	0	A|0.531;G|0.469	0.469	strong	.	TELO2	44	.	NM_016111	exon3	c.A437G	p.Q146R	AGACGCAGCCCGG	.	PASS	Atlas-SNP
PASD1	139135	hgsc.bcm.edu	37	X	150791512	150791512	+	Silent	SNP	C	C	T	rs5924978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	112	142	0	0.982456	0	C|0.879;0|0.003	.	strong	.	PASD1	286	.	NM_173493	exon7	c.C522T	p.C174C	TGTTTGCATTCTC	.	PASS	Atlas-SNP
CRMP1	1400	hgsc.bcm.edu	37	4	5837708	5837708	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	77	175	0	0.420765	0	.	.	none	CRMP1,NS,carcinoma,-1,2	CRMP1	118	2	NM_001014809	exon11	c.G1557A	p.S519S	GGCATCCGAGCCC	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21770730	21770730	+	Missense_Mutation	SNP	A	A	G	rs6571751	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	80	88	0	0.987654	0	A|0.546;G|0.454	0.454	strong	.	RPGRIP1	213	.	NM_020366	exon4	c.A574G	p.K192E	GCCAGTAAACCCA	.	PASS	Atlas-SNP
SETMAR	6419	hgsc.bcm.edu	37	3	4354697	4354697	+	Missense_Mutation	SNP	G	G	A	rs6801634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	67	127	0	0.489051	0	G|0.871;A|0.129	0.129	strong	.	SETMAR	30	.	NM_001243723	exon2	c.G272A	p.R91H	GTCTCCGCCATGG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	55	161	1	0.366667	0.00621118	C|0.803;T|0.197	0.197	strong	FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	2	NM_025074	exon66	c.C10377T	p.T3459T	TGTAACCGCTGAC	.	scavenged	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25007202	25007202	+	Missense_Mutation	SNP	A	A	G	rs2330838	by2hit2allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	304	98	398	0	0.322368	0	A|1.000;|0.000	.	weak	GGT1,NS,other,0,1	GGT1	68	1	NM_013430	exon5	c.A154G	p.K52E	TGCTCGAAGATTG	.	scavenged	Atlas-SNP
RGS18	64407	hgsc.bcm.edu	37	1	192153626	192153626	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	4	194	0	0.0183486	0	.	.	none	RGS18,NS,carcinoma,-1,1	RGS18	54	1	NM_130782	exon5	c.G650A	p.R217H	GATCACGCTCATT	.	scavenged	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	142567910	142567910	+	Missense_Mutation	SNP	T	T	C	rs12990449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	241	115	254	0	0.477178	0	C|0.208;N|0.000	0.208	strong	.	LRP1B	1315	.	NM_018557	exon2	c.A143G	p.Q48R	CAGCTCTGGGAGA	.	PASS	Atlas-SNP
GADL1	339896	hgsc.bcm.edu	37	3	30819751	30819751	+	Missense_Mutation	SNP	C	C	T	rs143542109	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	259	117	235	0	0.451737	0	C|0.995;T|0.005	0.005	strong	.	GADL1	91	.	NM_207359	exon14	c.G1312A	p.A438T	TATTGGCATATTC	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1614097	1614097	+	Silent	SNP	A	A	G	rs8048410	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	89	136	0	0.511494	0	A|0.566;G|0.434	0.434	strong	.	IFT140	128	.	NM_014714	exon17	c.T1968C	p.S656S	GGGCTCACTCTGG	.	PASS	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132218623	132218623	+	Missense_Mutation	SNP	G	G	T	rs3762672	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	49	87	0	0.597561	0	G|0.315;T|0.685	0.685	strong	.	DNAJC13	253	.	NM_015268	exon38	c.G4387T	p.A1463S	ACTCGTGCTAGTA	.	PASS	Atlas-SNP
TNIP1	10318	hgsc.bcm.edu	37	5	150410219	150410219	+	Missense_Mutation	SNP	C	C	A	rs2233311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	44	69	0	0.60274	0	G|0.000;C|0.890;A|0.109	0.109	strong	.	TNIP1	51	.	NM_001252393	exon18	c.G1892T	p.R631I	GGCAATCTGAGAT	.	PASS	Atlas-SNP
IFIT2	3433	hgsc.bcm.edu	37	10	91066769	91066769	+	Missense_Mutation	SNP	C	C	A	rs1727	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	34	87	0	0.472222	0	C|0.132;A|0.868	0.868	strong	.	IFIT2	39	.	NM_001547	exon2	c.C1056A	p.D352E	TGAAGACGCAGAG	.	PASS	Atlas-SNP
AMPD3	272	hgsc.bcm.edu	37	11	10521749	10521749	+	Silent	SNP	C	C	T	rs114718879	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	82	156	0	0.503067	0	C|0.983;T|0.017	0.017	strong	.	AMPD3	68	.	NM_000480	exon11	c.C1701T	p.Y567Y	CTACTACCTGTAC	.	PASS	Atlas-SNP
VWA8	23078	hgsc.bcm.edu	37	13	42404710	42404710	+	Missense_Mutation	SNP	C	C	T	rs41288297	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	24	52	0	0.510638	0	C|0.947;T|0.053	0.053	strong	.	.	.	.	NM_015058	exon14	c.G1655A	p.R552H	TTTAAACGCATAT	.	PASS	Atlas-SNP
ABRA	137735	hgsc.bcm.edu	37	8	107782395	107782395	+	Silent	SNP	G	G	A	rs11996466	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	28	54	0	0.509091	0	G|0.575;A|0.425	0.425	strong	ABRA,rectum,carcinoma,-1,1	ABRA	57	1	NM_139166	exon1	c.C24T	p.S8S	CTCCCCGCTTTCC	.	PASS	Atlas-SNP
ATP10B	23120	hgsc.bcm.edu	37	5	159992655	159992655	+	Silent	SNP	T	T	C	rs3812005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	58	131	0	0.464	0	T|0.662;C|0.338	0.338	strong	.	ATP10B	201	.	NM_025153	exon26	c.A4191G	p.V1397V	GTGGAGTACTGAC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241256	3241256	+	Missense_Mutation	SNP	T	T	C	rs5983119	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	67	82	0	1	0	0|0.003;C|0.749	0.749	strong	.	MXRA5	815	.	NM_015419	exon5	c.A2470G	p.I824V	GAGAAATAGCAGG	.	PASS	Atlas-SNP
MRPL45	84311	hgsc.bcm.edu	37	17	36478450	36478450	+	Missense_Mutation	SNP	G	G	T	rs34749623	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	22	55	0	0.392857	0	G|0.956;T|0.044	0.044	strong	.	MRPL45	27	.	NM_032351	exon8	c.G893T	p.G298V	CACAAGGAGAGGC	.	PASS	Atlas-SNP
TMEM43	79188	hgsc.bcm.edu	37	3	14174427	14174427	+	Missense_Mutation	SNP	A	A	T	rs4685076	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	146	152	0	0.986486	0	A|0.701;T|0.299	0.299	strong	.	TMEM43	33	.	NM_024334	exon6	c.A504T	p.K168N	CCACAAAAACCCC	.	PASS	Atlas-SNP
PLK1	5347	hgsc.bcm.edu	37	16	23701313	23701313	+	Missense_Mutation	SNP	C	C	T	rs34359215	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	18	51	0	0.36	0	.	.	weak	.	PLK1	67	.	NM_005030	exon10	c.C1741T	p.R581C	CGGCTCCGCTACG	.	PASS	Atlas-SNP
SNX15	29907	hgsc.bcm.edu	37	11	64799998	64799998	+	Silent	SNP	T	T	C	rs534236	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	20	57	0	0.37037	0	T|0.524;C|0.476	0.476	strong	.	SNX15	35	.	NM_147777	exon3	c.T231C	p.P77P	GTTCCCTGCTTTC	.	PASS	Atlas-SNP
TMPRSS15	5651	hgsc.bcm.edu	37	21	19713821	19713821	+	Silent	SNP	C	C	T	rs2824751	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	54	119	0	0.509434	0	C|0.811;T|0.189	0.189	strong	TMPRSS15,NS,carcinoma,-1,1	TMPRSS15	189	1	NM_002772	exon13	c.G1473A	p.A491A	ATCCAACGCAATA	.	PASS	Atlas-SNP
ISX	91464	hgsc.bcm.edu	37	22	35463162	35463162	+	Missense_Mutation	SNP	A	A	G	rs361863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	103	113	0	0.980952	0	A|0.242;G|0.758	0.758	strong	.	ISX	62	.	NM_001008494	exon1	c.A82G	p.S28G	AAGCTGAGCCTGT	.	PASS	Atlas-SNP
RDH13	112724	hgsc.bcm.edu	37	19	55559740	55559740	+	Silent	SNP	G	G	A	rs1059211	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	61	95	0	0.495935	0	G|0.867;A|0.133	0.133	strong	.	RDH13	43	.	NM_001145971	exon5	c.C615T	p.L205L	GATGGCGAGCTTG	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536323	1536323	+	Silent	SNP	A	A	G	rs2667671	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	27	65	0	0.457627	0	A|0.662;G|0.338	0.338	strong	PTX4,NS,carcinoma,0,1	PTX4	46	1	NM_001013658	exon3	c.T1039C	p.L347L	GCTGCAAGGGCAG	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7890024	7890024	+	Missense_Mutation	SNP	T	T	G	rs201662971	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	12	138	5	0.141176	0.0362319	.	.	weak	PER3,NS,carcinoma,0,3	PER3	95	3	NM_016831	exon18	c.T2990G	p.M997R	CTCCCATGAAGAA	.	scavenged	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47917087	47917087	+	Silent	SNP	C	C	T	rs72601626	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	42	93	0	0.407767	0	C|0.942;T|0.058	0.058	strong	.	PKD1L1	328	.	NM_138295	exon22	c.G3663A	p.P1221P	ACGTACCGGTTTT	.	PASS	Atlas-SNP
P2RX4	5025	hgsc.bcm.edu	37	12	121660787	121660787	+	Silent	SNP	T	T	C	rs25643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	74	112	1	0.510345	0.00892857	C|0.421;N|0.000;T|0.579	0.421	strong	P2RX4,NS,carcinoma,0,1	P2RX4	27	1	NM_001256796	exon6	c.T513C	p.S171S	CGGGTCTGTCAAG	.	scavenged	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113176122	113176122	+	Silent	SNP	G	G	A	rs7637618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	63	71	0	0.520661	0	G|0.662;A|0.338	0.338	strong	.	SPICE1	130	.	NM_144718	exon13	c.C1518T	p.P506P	TTTAACGGGCAAC	.	PASS	Atlas-SNP
NBN	4683	hgsc.bcm.edu	37	8	90967711	90967711	+	Silent	SNP	A	A	G	rs709816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	73	150	0	0.496599	0	A|0.459;G|0.541	0.541	strong	.	NBN	86	.	NM_002485	exon10	c.T1197C	p.D399D	GGGTGCATCTTGT	.	PASS	Atlas-SNP
GPC1	2817	hgsc.bcm.edu	37	2	241405485	241405485	+	Silent	SNP	C	C	T	rs2228330	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	79	131	0	0.487654	0	C|0.832;T|0.168	0.168	strong	.	GPC1	32	.	NM_002081	exon9	c.C1455T	p.G485G	CGACGGCAGCGGC	.	PASS	Atlas-SNP
YIPF2	78992	hgsc.bcm.edu	37	19	11036415	11036415	+	Missense_Mutation	SNP	C	C	T	rs148361413	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	49	58	0	0.590361	0	C|1.000;T|0.000	0.000	strong	.	YIPF2	13	.	NM_024029	exon5	c.G314A	p.R105Q	CCAGGCCGGGGCA	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9888069	9888069	+	Silent	SNP	A	A	G	rs2240905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	61	106	0	0.539823	0	G|0.522;N|0.000	0.522	strong	TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.A1593G	p.E531E	AAAAGAAGAAAAG	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169461547	169461547	+	Silent	SNP	C	C	T	rs3763048	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	30	46	0	0.555556	0	C|0.536;T|0.464	0.464	strong	DOCK2,caecum,carcinoma,+1,2	DOCK2	389	2	NM_004946	exon35	c.C3612T	p.T1204T	CTGCACCGTGAAC	.	PASS	Atlas-SNP
MRPL50	54534	hgsc.bcm.edu	37	9	104152790	104152790	+	Silent	SNP	G	G	C	rs8394		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	43	125	0	0.394495	0	G|0.013;C|0.987	0.987	weak	.	MRPL50	18	.	NM_019051	exon2	c.C435G	p.A145A	ATTACTGGCACTG	.	PASS	Atlas-SNP
KRT15	3866	hgsc.bcm.edu	37	17	39671724	39671724	+	Missense_Mutation	SNP	T	T	C	rs2305556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	14	46	0	0.451613	0	T|0.806;C|0.194	0.194	strong	.	KRT15	60	.	NM_002275	exon6	c.A1247G	p.K416R	GCCTACTTGGCAT	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100792335	100792335	+	Silent	SNP	G	G	A	rs75746929	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	29	85	0	0.426471	0	G|0.910;A|0.090	0.090	strong	.	ARHGAP42	32	.	NM_152432	exon6	c.G597A	p.P199P	TGAACCGGTAAGT	.	PASS	Atlas-SNP
NOTCH2	4853	hgsc.bcm.edu	37	1	120458924	120458924	+	Silent	SNP	G	G	A	rs3795666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	79	185	0	0.481707	0	G|0.952;A|0.048	0.048	strong	.	NOTCH2	348	.	NM_024408	exon34	c.C6421T	p.L2141L	CAGACAGTTGGAC	.	PASS	Atlas-SNP
GEMIN4	50628	hgsc.bcm.edu	37	17	648157	648157	+	Silent	SNP	G	G	A	rs1045481	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	47	56	0	0.552941	0	G|0.829;A|0.172	0.172	strong	.	GEMIN4	116	.	NM_015721	exon2	c.C3126T	p.I1042I	AGGGCCGATGCCC	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112997554	112997554	+	Silent	SNP	A	A	G	rs775228	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	93	78	0	1	0	A|0.404;G|0.596	0.596	strong	.	BOC	139	.	NM_033254	exon11	c.A1737G	p.K579K	CAGCAAAGAGCAG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910700	29910700	+	Silent	SNP	G	G	T	rs1059452	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	39	143	0	0.378641	0	G|0.769;T|0.231	0.231	strong	.	HLA-A	89	.	NM_001242758	exon2	c.G240T	p.G80G	GGAGGGGCCGGAG	.	PASS	Atlas-SNP
OCEL1	79629	hgsc.bcm.edu	37	19	17337557	17337557	+	Missense_Mutation	SNP	G	G	T	rs10425488	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	4	3	0	0.8	0	G|0.934;T|0.066	0.066	strong	.	OCEL1	20	.	NM_024578	exon2	c.G125T	p.R42L	GGACCCGCCCATC	.	PASS	Atlas-SNP
WNK1	65125	hgsc.bcm.edu	37	12	994014	994014	+	Silent	SNP	C	C	T	rs10849577	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	245	104	212	0	0.42449	0	C|0.885;T|0.115	0.115	strong	.	WNK1	403	.	NM_001184985	exon19	c.C4824T	p.T1608T	CCCAACCACAGCA	.	PASS	Atlas-SNP
SLC4A10	57282	hgsc.bcm.edu	37	2	162696414	162696414	+	Silent	SNP	C	C	T	rs2084543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	51	88	0	0.53125	0	C|0.922;T|0.078	0.078	strong	.	SLC4A10	309	.	NM_001178016	exon5	c.C426T	p.D142D	TGAGGACGCTGAG	.	PASS	Atlas-SNP
C16orf70	80262	hgsc.bcm.edu	37	16	67173922	67173922	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	3	180	1	0.016129	0.00555556	.	.	none	C16orf70,NS,carcinoma,-1,1	C16orf70	38	1	NM_025187	exon9	c.C697T	p.R233W	AAGATGCGGGTAT	.	scavenged	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573439	140573439	+	Silent	SNP	G	G	C	rs610836	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	121	145	0	0.991803	0	G|0.551;C|0.449	0.449	strong	.	PCDHB10	177	.	NM_018930	exon1	c.G1314C	p.T438T	CATAACGGTCCTG	.	PASS	Atlas-SNP
C6orf57	135154	hgsc.bcm.edu	37	6	71289188	71289188	+	Nonsense_Mutation	SNP	C	C	T	rs61735710	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	7	94	0	0.2	0	C|0.994;T|0.006	0.006	strong	.	C6orf57	13	.	NM_145267	exon2	c.C136T	p.Q46X	GTCAAACAGTCCC	.	PASS	Atlas-SNP
SLC38A10	124565	hgsc.bcm.edu	37	17	79220016	79220016	+	Silent	SNP	T	T	C	rs61740863	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	26	55	0	0.490566	0	A|0.000;C|0.089;G|0.000;T|0.910	0.089	strong	.	SLC38A10	133	.	NM_001037984	exon16	c.A2700G	p.A900A	AGTGGCTGCCACC	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	15452	15452	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	8	8	4	0	1	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.C706A	p.L236I	CTCTTCCTTCTCT	.	PASS	Atlas-SNP
GALNT15	117248	hgsc.bcm.edu	37	3	16268986	16268986	+	Silent	SNP	C	C	A	rs14576	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	37	74	0	0.521127	0	C|0.670;A|0.330	0.330	strong	.	.	.	.	NM_054110	exon10	c.C1899A	p.I633I	CCAGATCAATGCT	.	PASS	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	37	19	53854397	53854397	+	Missense_Mutation	SNP	G	G	C	rs10415799	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	73	155	0	0.434524	0	G|0.643;C|0.357	0.357	strong	ZNF845,NS,carcinoma,0,6	ZNF845	101	6	NM_138374	exon4	c.G469C	p.E157Q	CAGACCGAAGGGA	.	PASS	Atlas-SNP
MMAA	166785	hgsc.bcm.edu	37	4	146572227	146572227	+	Silent	SNP	G	G	A	rs11721553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	134	115	0	1	0	G|0.927;A|0.073	0.073	strong	.	MMAA	46	.	NM_172250	exon5	c.G747A	p.S249S	TCAGTCGGAGTTT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228505739	228505739	+	Missense_Mutation	SNP	G	G	A	rs3795801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	97	163	0	0.5	0	G|0.828;A|0.172	0.172	strong	.	OBSCN	2142	.	NM_001271223	exon64	c.G16867A	p.G5623S	CAGCCCGGTGGGC	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60899182	60899182	+	Missense_Mutation	SNP	C	C	T	rs11698080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	57	49	0	0.581633	0	C|0.759;T|0.241	0.241	strong	LAMA5,caecum,carcinoma,0,1	LAMA5	268	1	NM_005560	exon43	c.G5722A	p.A1908T	AGGGGGCGCTGGG	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157931119	157931119	+	Silent	SNP	A	A	G	rs1130500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	43	122	0	0.447917	0	A|0.625;G|0.375	0.375	strong	.	PTPRN2	243	.	NM_130843	exon7	c.T999C	p.A333A	CAGCTCAGCCATG	.	PASS	Atlas-SNP
PMPCA	23203	hgsc.bcm.edu	37	9	139311471	139311471	+	Silent	SNP	C	C	T	rs3812581	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	44	100	0	0.423077	0	C|0.785;T|0.215	0.215	strong	.	PMPCA	29	.	NM_015160	exon7	c.C702T	p.N234N	GATCAACCGAGAG	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324602	31324602	+	Missense_Mutation	SNP	T	T	G	rs41562914	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	78	14	0	1	0	T|0.638;G|0.265;C|0.001;A|0.096	0.265	strong	.	HLA-B	54	.	NM_005514	exon2	c.A206C	p.E69A	GGCTCCTCTCTCG	.	PASS	Atlas-SNP
TMTC4	84899	hgsc.bcm.edu	37	13	101287404	101287404	+	Silent	SNP	G	G	A	rs2297943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	42	88	0	0.362069	0	G|0.737;A|0.263	0.263	strong	.	TMTC4	103	.	NM_032813	exon11	c.C1248T	p.P416P	ACTCGCGGGGAGA	.	PASS	Atlas-SNP
FLRT2	23768	hgsc.bcm.edu	37	14	86089032	86089032	+	Missense_Mutation	SNP	A	A	G	rs137990800	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	42	79	0	0.518519	0	A|0.999;G|0.001	0.001	strong	.	FLRT2	168	.	NM_013231	exon2	c.A1174G	p.S392G	AACCCTAGCAGAA	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596546	48596546	+	Missense_Mutation	SNP	C	C	T	rs75531856	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	63	108	0	0.520661	0	C|0.935;T|0.065	0.065	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.G530A	p.S177N	AAGAAGCTTTCTA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537243	88537243	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	7	124	1	0.0542636	0.00806452	.	.	none	DSPP,NS,carcinoma,0,6	DSPP	174	6	NM_014208	exon5	c.C3429A	p.D1143E	CAGTGACAGCAGT	.	scavenged	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238249717	238249717	+	Silent	SNP	G	G	A	rs34558385	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	202	190	1	0.95283	0.00526316	G|0.929;A|0.071	0.071	strong	.	COL6A3	608	.	NM_004369	exon38	c.C7842T	p.S2614S	CACATCGCTCCCT	.	PASS	Atlas-SNP
TLL1	7092	hgsc.bcm.edu	37	4	166929102	166929102	+	Silent	SNP	G	G	A	rs17590218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	32	79	0	0.385542	0	G|0.953;A|0.047	0.047	strong	TLL1,NS,carcinoma,0,2	TLL1	194	2	NM_001204760	exon7	c.G819A	p.E273E	TCAAGAGTACAAT	.	PASS	Atlas-SNP
HAUS6	54801	hgsc.bcm.edu	37	9	19058483	19058483	+	Missense_Mutation	SNP	C	C	A	rs4977493	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	80	186	0	0.365297	0	C|1.000;|0.000	.	weak	.	HAUS6	66	.	NM_017645	exon16	c.G2282T	p.S761I	ATTCCACTTGATA	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	644337	644337	+	Missense_Mutation	SNP	G	G	A	rs2075033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	31	37	0	0.96875	0	G|0.885;A|0.115	0.115	strong	.	B4GALNT3	64	.	NM_173593	exon2	c.G175A	p.G59S	GGGTACGGCAGCT	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38993547	38993547	+	Silent	SNP	C	C	T	rs2229142	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	18	29	0	0.428571	0	C|0.834;T|0.166	0.166	strong	RYR1,NS,carcinoma,0,1	RYR1	708	1	NM_001042723	exon49	c.C7863T	p.H2621H	GCAGCACCTGTTG	.	PASS	Atlas-SNP
CREBBP	1387	hgsc.bcm.edu	37	16	3788618	3788618	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	22	54	0	0.415094	0	.	.	none	CREBBP,rectum,carcinoma,0,21	CREBBP	546	21	NM_004380	exon26	c.C4336T	p.R1446C	CTGTGCGGAGGCA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90448092	90448092	+	Missense_Mutation	SNP	C	C	T	rs4140446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	97	219	0	0.979798	0	C|0.154;T|0.846	0.846	strong	.	MDN1	478	.	NM_014611	exon33	c.G4676A	p.S1559N	TTATGACTGATGA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82834630	82834630	+	Silent	SNP	T	T	C	rs309557	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	43	73	0	0.5	0	T|0.507;C|0.493	0.493	strong	.	VCAN	498	.	NM_004385	exon8	c.T5808C	p.G1936G	CAGTGGTGACTTT	.	PASS	Atlas-SNP
CLHC1	130162	hgsc.bcm.edu	37	2	55436934	55436934	+	Missense_Mutation	SNP	G	G	A	rs9677948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	41	71	0	0.594203	0	G|0.762;A|0.238	0.238	strong	.	.	.	.	NM_152385	exon6	c.C533T	p.A178V	GTGAGAGCATCTA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150886882	150886882	+	Missense_Mutation	SNP	G	G	A	rs1105168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	98	174	0	0.494949	0	G|0.304;A|0.696	0.696	strong	.	FAT2	465	.	NM_001447	exon22	c.C12350T	p.P4117L	GGTTCCGGTTGGT	.	PASS	Atlas-SNP
SNRNP70	6625	hgsc.bcm.edu	37	19	49611319	49611319	+	Silent	SNP	C	C	T	rs1058882	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	6	5	0	0	0.833333	.	C|0.830;T|0.170	0.170	strong	SNRNP70,NS,carcinoma,0,1	SNRNP70	30	1	NM_003089	exon10	c.C933T	p.G311G	GCGTGGCGGCGGT	.	PASS	Atlas-SNP
SLC39A14	23516	hgsc.bcm.edu	37	8	22262379	22262379	+	Silent	SNP	C	C	T	rs33999442	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	91	93	0	0.98913	0	C|0.817;G|0.000;T|0.183	0.183	strong	.	SLC39A14	59	.	NM_001135153	exon2	c.C156T	p.G52G	GTATGGCGAGGGT	.	PASS	Atlas-SNP
PDZD7	79955	hgsc.bcm.edu	37	10	102782113	102782113	+	Missense_Mutation	SNP	A	A	T	rs118098246	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	62	118	0	0.442857	0	A|0.996;T|0.004	0.004	strong	.	PDZD7	101	.	NM_001195263	exon5	c.T572A	p.V191E	TTCTCCACTACCA	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	62960101	62960101	+	Silent	SNP	A	A	G	rs10889335	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	69	153	0	0.482517	0	A|0.670;G|0.330	0.330	strong	.	DOCK7	184	.	NM_001271999	exon40	c.T5035C	p.L1679L	AGGTCAATCGCAG	.	PASS	Atlas-SNP
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626759	43626759	+	Missense_Mutation	SNP	G	G	A	rs71489755		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	7	45	2	1	0.0444444	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
DNAH9	1770	hgsc.bcm.edu	37	17	11833365	11833365	+	Silent	SNP	G	G	A	rs1859887	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	88	126	0	0.55	0	G|0.743;A|0.257	0.257	strong	.	DNAH9	695	.	NM_001372	exon63	c.G12060A	p.T4020T	CCCCACGGGCATG	.	PASS	Atlas-SNP
NLRP1	22861	hgsc.bcm.edu	37	17	5485367	5485367	+	Missense_Mutation	SNP	A	A	T	rs12150220	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	42	88	1	0.538462	0.0113636	A|0.737;T|0.263	0.263	strong	NLRP1,NS,carcinoma,0,1	NLRP1	358	1	NM_033007	exon3	c.T464A	p.L155H	TAGAGGAGTGAGG	.	scavenged	Atlas-SNP
ID1	3397	hgsc.bcm.edu	37	20	30193538	30193538	+	Silent	SNP	A	A	G	rs15817	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	58	98	0	0.456693	0	A|0.677;G|0.323	0.323	strong	.	ID1	12	.	NM_002165	exon1	c.A348G	p.G116G	AGTTGGAACCCCC	.	PASS	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	37	6	33653486	33653486	+	Missense_Mutation	SNP	G	G	A	rs12528378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	87	146	0	0.491525	0	G|0.935;A|0.065	0.065	strong	.	ITPR3	409	.	NM_002224	exon41	c.G5549A	p.R1850Q	TGCGCCGGGGGCA	.	PASS	Atlas-SNP
C11orf24	53838	hgsc.bcm.edu	37	11	68030173	68030173	+	Missense_Mutation	SNP	C	C	A	rs3802746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	105	167	0	0.527638	0	T|0.000;C|0.709;A|0.291	0.291	strong	.	C11orf24	35	.	NM_022338	exon4	c.G290T	p.G97V	GCTGCACCTCCTG	.	PASS	Atlas-SNP
LRWD1	222229	hgsc.bcm.edu	37	7	102112980	102112980	+	Silent	SNP	G	G	A	rs3800987	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	22	10	0	1	0	G|0.476;A|0.524	0.524	strong	LRWD1,NS,carcinoma,0,1	LRWD1	41	1	NM_152892	exon13	c.G1614A	p.T538T	GTCCACGGTGGCA	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13865980	13865980	+	Silent	SNP	T	T	C	rs7703349	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	30	101	0	0.4	0	T|0.533;C|0.467	0.467	strong	DNAH5,NS,carcinoma,0,1	DNAH5	868	1	NM_001369	exon27	c.A4152G	p.T1384T	AGTATATGTGATG	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15498181	15498181	+	Silent	SNP	A	A	G	rs12601532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	52	163	0	0.371429	0	A|0.715;G|0.285	0.285	strong	.	CDRT1	83	.	NM_006382	exon10	c.T1728C	p.A576A	TTTCACAGCTCCC	.	PASS	Atlas-SNP
FAM71F2	346653	hgsc.bcm.edu	37	7	128312463	128312463	+	Missense_Mutation	SNP	C	C	G	rs74343948	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	30	53	0	0.5	0	C|0.884;G|0.116	0.116	strong	.	FAM71F2	19	.	NM_001012454	exon1	c.C12G	p.I4M	TAAAATCAGGGGC	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16384999	16384999	+	Missense_Mutation	SNP	G	G	A	rs1807284	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	9	6	0	0.6	0	G|0.717;A|0.283	0.283	strong	FAM131C,NS,carcinoma,0,2	FAM131C	21	2	NM_182623	exon7	c.C776T	p.P259L	CCCGGGGGGTGGG	.	PASS	Atlas-SNP
RASL12	51285	hgsc.bcm.edu	37	15	65347405	65347405	+	Silent	SNP	G	G	A	rs2232762	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	38	59	0	0.575758	0	G|0.606;A|0.394	0.394	strong	.	RASL12	32	.	NM_016563	exon5	c.C633T	p.T211T	CCGCGCGGTGAGC	.	PASS	Atlas-SNP
FAM174A	345757	hgsc.bcm.edu	37	5	99897866	99897866	+	Silent	SNP	G	G	A	rs6874840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	99	191	0	0.456221	0	G|0.774;A|0.226	0.226	strong	.	FAM174A	13	.	NM_198507	exon2	c.G543A	p.T181T	CAACACGTTGTTT	.	PASS	Atlas-SNP
ZACN	353174	hgsc.bcm.edu	37	17	74076415	74076415	+	Missense_Mutation	SNP	G	G	A	rs2257020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	45	102	0	0.494505	0	G|0.403;A|0.597	0.597	strong	.	ZACN	29	.	NM_180990	exon5	c.G454A	p.A152T	GCCCTCGCCACGG	.	PASS	Atlas-SNP
USP20	10868	hgsc.bcm.edu	37	9	132637712	132637712	+	Silent	SNP	G	G	A	rs735115	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	61	104	0	0.491935	0	G|0.730;A|0.270	0.270	strong	.	USP20	186	.	NM_001008563	exon20	c.G2172A	p.A724A	CTTCGCGGAGCCA	.	PASS	Atlas-SNP
CD1D	912	hgsc.bcm.edu	37	1	158151892	158151892	+	Silent	SNP	T	T	C	rs140563679	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	107	201	0	0.490826	0	T|0.999;C|0.001	0.001	strong	.	CD1D	60	.	NM_001766	exon4	c.T399C	p.H133H	CTTCCATGTAGCA	.	PASS	Atlas-SNP
GALP	85569	hgsc.bcm.edu	37	19	56693620	56693620	+	Missense_Mutation	SNP	C	C	G	rs3745833	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	17	59	0	0.369565	0	C|0.667;G|0.332	0.332	strong	.	GALP	13	.	NM_033106	exon4	c.C216G	p.I72M	GGCCATCGGTGAG	.	PASS	Atlas-SNP
EXOC3L1	283849	hgsc.bcm.edu	37	16	67222676	67222676	+	Silent	SNP	G	G	A	rs13334403	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	72	124	0	0.510638	0	G|0.920;A|0.080	0.080	strong	LOC283849,NS,carcinoma,-1,2	EXOC3L1	52	2	NM_178516	exon4	c.C375T	p.A125A	GTGCTGGGCAACC	.	PASS	Atlas-SNP
PHC1	1911	hgsc.bcm.edu	37	12	9074259	9074259	+	Silent	SNP	C	C	T	rs76479220		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	224	213	195	0	0.950893	0	.	.	weak	.	PHC1	67	.	NM_004426	exon5	c.C369T	p.P123P	CTCTCCCAGTGCT	.	PASS	Atlas-SNP
SBF2	81846	hgsc.bcm.edu	37	11	10019879	10019879	+	Silent	SNP	G	G	A	rs16907355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	58	59	0	1	0	G|0.942;A|0.058	0.058	strong	.	SBF2	146	.	NM_030962	exon9	c.C909T	p.P303P	ACATTCGGGAATT	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512629	4512629	+	Missense_Mutation	SNP	C	C	T	rs146679364	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	48	178	1	0.979592	0.00561798	C|0.949;T|0.051	0.051	strong	PLIN4,NS,carcinoma,0,1	PLIN4	191	1	NM_001080400	exon3	c.G1301A	p.R434K	GTTCCTCTGGCCA	.	PASS	Atlas-SNP
TMEM187	8269	hgsc.bcm.edu	37	X	153247722	153247722	+	Missense_Mutation	SNP	C	C	T	rs2266890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	76	88	0	1	0	C|0.761;T|0.239	0.239	strong	.	TMEM187	21	.	NM_003492	exon2	c.C209T	p.S70L	GGCTGTCGTGGCT	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	45	88	1	0.416667	0.0113636	T|0.799;C|0.201	0.201	strong	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	NM_001163213	exon7	c.T882C	p.N294N	GGTGAATGGCAGC	.	scavenged	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79025157	79025157	+	Missense_Mutation	SNP	A	A	G	rs10942901	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	74	172	0	0.477419	0	A|0.832;G|0.162	0.162	strong	.	CMYA5	643	.	NM_153610	exon2	c.A569G	p.D190G	TTTATGATAAAGC	.	PASS	Atlas-SNP
C9orf123	90871	hgsc.bcm.edu	37	9	7799606	7799606	+	Silent	SNP	C	C	A	rs14059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	38	58	0	0.487179	0	C|0.639;A|0.361	0.361	strong	.	C9orf123	7	.	NM_033428	exon1	c.G129T	p.L43L	CTTCAACAGGCGG	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626718	140626718	+	Silent	SNP	G	G	T	rs141887199	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	312	138	241	0	0.442308	0	G|0.997;T|0.003	0.003	strong	.	PCDHB15	138	.	NM_018935	exon1	c.G1572T	p.L524L	GGCCCTGCAGGCT	.	PASS	Atlas-SNP
HFM1	164045	hgsc.bcm.edu	37	1	91809036	91809036	+	Silent	SNP	T	T	C	rs148872247	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	113	211	0	0.45935	0	T|0.999;C|0.001	0.001	strong	.	HFM1	188	.	NM_001017975	exon20	c.A2286G	p.S762S	CAGGGATGATAAA	.	PASS	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51097216	51097216	+	Missense_Mutation	SNP	G	G	A	rs17656599	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	52	108	0	0.536082	0	G|0.919;A|0.081	0.081	strong	.	COBL	167	.	NM_015198	exon10	c.C1577T	p.P526L	TCCTGTGGGCAGT	.	PASS	Atlas-SNP
MAP3K19	80122	hgsc.bcm.edu	37	2	135745392	135745392	+	Silent	SNP	G	G	A	rs11888766	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	23	46	0	0.46	0	G|0.781;A|0.219	0.219	strong	.	.	.	.	NM_025052	exon7	c.C1050T	p.D350D	ATGGCAGTCAATA	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102745	22102745	+	Missense_Mutation	SNP	C	C	A	rs41314525	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	224	223	246	0	0.995536	0	C|0.782;A|0.218	0.218	strong	.	OR10G2	35	.	NM_001005466	exon1	c.G254T	p.R85L	ATAAGCCGAGGAA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092827	1092827	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	3	78	0	0.0365854	0	.	.	none	MUC2_ENST00000441003,NS,malignant_melanoma,0,2	MUC2	614	2	NM_002457	exon30	c.C4646A	p.T1549N	CCCCAACCCCAAC	.	scavenged	Atlas-SNP
DIS3L2	129563	hgsc.bcm.edu	37	2	233201328	233201328	+	Silent	SNP	A	A	G	rs3811578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	22	50	0	0.468085	0	A|0.797;G|0.203	0.203	strong	.	DIS3L2	77	.	NM_152383	exon21	c.A2646G	p.S882S	GGACTCAAGCACC	.	PASS	Atlas-SNP
PDLIM4	8572	hgsc.bcm.edu	37	5	131607020	131607020	+	Silent	SNP	G	G	A	rs147858379	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	9	33	0	0.321429	0	G|0.989;A|0.011	0.011	strong	.	PDLIM4	22	.	NM_003687	exon5	c.G531A	p.P177P	CCTCCCGCGGAGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195474159	195474159	+	Missense_Mutation	SNP	G	G	A	rs62284986	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	62	231	0	0.298077	0	G|0.849;A|0.151	0.151	strong	.	MUC4	1505	.	NM_018406	exon25	c.C16127T	p.A5376V	CCCAGGGCCCCAA	.	PASS	Atlas-SNP
NR4A2	4929	hgsc.bcm.edu	37	2	157184995	157184995	+	Silent	SNP	G	G	A	rs201103933		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	102	207	0	0.474419	0	G|0.999;A|0.001	0.001	weak	.	NR4A2	82	.	NM_006186	exon4	c.C915T	p.C305C	CACTGGGCAGTTT	.	PASS	Atlas-SNP
SCN3A	6328	hgsc.bcm.edu	37	2	165996107	165996107	+	Silent	SNP	T	T	A	rs1946892	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	96	0	1	0	A|0.544;N|0.000	0.544	strong	.	SCN3A	544	.	NM_006922	exon14	c.A2031T	p.T677T	CGTTTCTGTGGTG	.	PASS	Atlas-SNP
TESPA1	9840	hgsc.bcm.edu	37	12	55356258	55356258	+	Missense_Mutation	SNP	C	C	T	rs61733025	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	51	99	0	0.579545	0	C|0.976;T|0.024	0.024	strong	KIAA0748_ENST00000449076,colon,carcinoma,0,3	.	.	3	NM_001098815	exon9	c.G1424A	p.R475Q	AAAGACCGACGCA	.	PASS	Atlas-SNP
CSHL1	1444	hgsc.bcm.edu	37	17	61987576	61987576	+	Silent	SNP	G	G	A	rs2246207	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	313	311	449	1	0.99361	0.00222717	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	.	PASS	Atlas-SNP
BCMO1	53630	hgsc.bcm.edu	37	16	81314496	81314496	+	Missense_Mutation	SNP	C	C	T	rs7501331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	43	66	0	0.488636	0	C|0.837;T|0.163	0.163	strong	.	BCMO1	53	.	NM_017429	exon8	c.C1136T	p.A379V	AAGTGGCATCTAC	.	PASS	Atlas-SNP
ENTPD6	955	hgsc.bcm.edu	37	20	25187213	25187213	+	Missense_Mutation	SNP	G	G	A	rs2076559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	44	107	0	0.411215	0	G|0.702;A|0.298	0.298	strong	.	ENTPD6	57	.	NM_001247	exon2	c.G41A	p.S14N	AAACGAGCTACAT	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125591687	125591687	+	Silent	SNP	A	A	G	rs3733471	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	118	263	0	0.553991	0	A|0.742;G|0.258	0.258	strong	.	ANKRD50	136	.	NM_020337	exon4	c.T2745C	p.N915N	CAGTGCATTTCTT	.	PASS	Atlas-SNP
VWA5A	4013	hgsc.bcm.edu	37	11	124006993	124006993	+	Missense_Mutation	SNP	G	G	A	rs2276053	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	41	84	0	0.518987	0	G|0.883;A|0.117	0.117	strong	.	VWA5A	102	.	NM_014622	exon12	c.G1517A	p.R506K	CCGGGAGGATGCC	.	PASS	Atlas-SNP
C4orf36	132989	hgsc.bcm.edu	37	4	87809020	87809020	+	Missense_Mutation	SNP	C	C	G	rs72613147	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	114	0	1	0	C|0.864;G|0.136	0.136	strong	C4orf36,NS,carcinoma,0,1	C4orf36	10	1	NM_144645	exon4	c.G247C	p.V83L	GCTTCACTTCATA	.	PASS	Atlas-SNP
KLHL36	79786	hgsc.bcm.edu	37	16	84691044	84691044	+	Silent	SNP	C	C	T	rs3751762	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	22	14	0	0.956522	0	C|0.757;T|0.243	0.243	strong	KLHL36,NS,carcinoma,0,1	KLHL36	51	1	NM_024731	exon3	c.C631T	p.L211L	GACCTCCTGCAGG	.	PASS	Atlas-SNP
ATP5J2-PTCD1	100526740	hgsc.bcm.edu	37	7	99032559	99032559	+	Missense_Mutation	SNP	G	G	A	rs150504114	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	76	144	0	0.554745	0	G|0.991;A|0.009	0.009	strong	.	.	.	.	NM_001198879	exon3	c.C454T	p.R152C	ATTTGCGGAATAG	.	PASS	Atlas-SNP
LZIC	84328	hgsc.bcm.edu	37	1	9992024	9992024	+	Missense_Mutation	SNP	C	C	G	rs146375448	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	7	68	0	0.0673077	0	C|0.999;G|0.001	0.001	strong	LZIC,NS,carcinoma,+1,1	LZIC	11	1	NM_032368	exon6	c.G439C	p.A147P	CATCTGCAGTCAG	.	PASS	Atlas-SNP
ZNF568	374900	hgsc.bcm.edu	37	19	37441111	37441111	+	Silent	SNP	C	C	T	rs571294	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	16	39	0	0.533333	0	C|0.422;T|0.578	0.578	strong	.	ZNF568	106	.	NM_198539	exon7	c.C1056T	p.H352H	TGAGCACGAGAAA	.	PASS	Atlas-SNP
FAM83D	81610	hgsc.bcm.edu	37	20	37570725	37570725	+	Silent	SNP	C	C	T	rs3752293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	138	155	0	1	0	C|0.607;T|0.393	0.393	strong	.	FAM83D	60	.	NM_030919	exon2	c.C697T	p.L233L	CAATTTCTGGATA	.	PASS	Atlas-SNP
GBE1	2632	hgsc.bcm.edu	37	3	81720076	81720076	+	Silent	SNP	G	G	A	rs13320194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	49	95	0	0.445455	0	G|0.910;A|0.090	0.090	strong	GBE1_ENST00000429644,NS,carcinoma,0,1	GBE1	111	1	NM_000158	exon3	c.C342T	p.Y114Y	TTTTTTGTATGGG	.	PASS	Atlas-SNP
HIPK4	147746	hgsc.bcm.edu	37	19	40886993	40886993	+	Missense_Mutation	SNP	C	C	T	rs11670988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	29	44	0	0.446154	0	C|0.921;T|0.079	0.079	strong	HIPK4_ENST00000291823,larynx,carcinoma,-1,1	HIPK4	100	1	NM_144685	exon3	c.G905A	p.R302Q	GTTAGCCGACTGG	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52558008	52558008	+	Missense_Mutation	SNP	T	T	C	rs13303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	39	86	0	0.458824	0	T|0.423;C|0.577	0.577	strong	.	STAB1	178	.	NM_015136	exon67	c.T7517C	p.M2506T	AGCCCATGGGCTT	.	PASS	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161137779	161137779	+	Silent	SNP	T	T	C	rs14224	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	31	59	0	1	0	T|0.540;C|0.460	0.460	strong	.	PLG	150	.	NM_000301	exon7	c.T771C	p.C257C	ACTTTGTGACATC	.	PASS	Atlas-SNP
OR5I1	10798	hgsc.bcm.edu	37	11	55703011	55703011	+	Missense_Mutation	SNP	G	G	A	rs61995929	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	38	111	1	0.487179	0.00900901	G|0.964;A|0.036	0.036	strong	OR5I1,NS,carcinoma,+1,1	OR5I1	110	1	NM_006637	exon1	c.C866T	p.P289L	ATCAACGGATTCA	.	scavenged	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5037241	5037241	+	Silent	SNP	G	G	A	rs117611547		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	5	55	3	0.0925926	0.0545455	.	.	weak	USP6_ENST00000250066,NS,carcinoma,0,3	USP6	213	3	NM_004505	exon7	c.G444A	p.V148V	GGACGTGAGGACG	.	scavenged	Atlas-SNP
NEK5	341676	hgsc.bcm.edu	37	13	52676275	52676275	+	Missense_Mutation	SNP	T	T	G	rs34756139	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	34	94	0	0.507463	0	T|0.912;G|0.088	0.088	strong	NEK5,NS,carcinoma,0,1	NEK5	189	1	NM_199289	exon10	c.A763C	p.K255Q	GCCTTTTCAAAAT	.	PASS	Atlas-SNP
FANCE	2178	hgsc.bcm.edu	37	6	35430686	35430686	+	Missense_Mutation	SNP	G	G	A	rs9462088	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	30	90	0	0.441176	0	G|0.843;A|0.157	0.157	strong	.	FANCE	45	.	NM_021922	exon9	c.G1504A	p.A502T	TATCAGGCTAACG	.	PASS	Atlas-SNP
C5orf42	65250	hgsc.bcm.edu	37	5	37196028	37196028	+	Missense_Mutation	SNP	C	C	T	rs72736758	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	86	253	0	0.4	0	C|0.972;T|0.028	0.028	strong	.	C5orf42	422	.	NM_023073	exon21	c.G3743A	p.G1248D	GCGATACCTCCTT	.	PASS	Atlas-SNP
DNAAF1	123872	hgsc.bcm.edu	37	16	84209634	84209634	+	Silent	SNP	C	C	G	rs2288019	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	103	91	0	0.980952	0	C|0.475;G|0.525	0.525	strong	DNAAF1,NS,carcinoma,0,1	DNAAF1	81	1	NM_178452	exon11	c.C1794G	p.L598L	AAACCTCCCCACA	.	PASS	Atlas-SNP
ALCAM	214	hgsc.bcm.edu	37	3	105264176	105264176	+	Missense_Mutation	SNP	G	G	T	rs34926152	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	77	161	0	0.527397	0	G|0.968;T|0.032	0.032	strong	ALCAM,colon,carcinoma,+1,1	ALCAM	71	1	NM_001627	exon9	c.G1101T	p.M367I	ATGGATGAAAGTA	.	PASS	Atlas-SNP
SLC12A4	6560	hgsc.bcm.edu	37	16	67979423	67979423	+	Silent	SNP	G	G	T	rs17851876	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	45	120	0	0.39823	0	G|0.959;T|0.041	0.041	strong	.	SLC12A4	81	.	NM_001145962	exon21	c.C2887A	p.R963R	CCAGCCGCAGGGC	.	PASS	Atlas-SNP
ADORA3	140	hgsc.bcm.edu	37	1	112043139	112043139	+	Silent	SNP	G	G	A	rs2789537	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	60	82	0	0.550459	0	G|0.981;A|0.019	0.019	strong	.	ADORA3	104	.	NM_000677	exon2	c.C390T	p.A130A	GCCCAGGGCCAGC	.	PASS	Atlas-SNP
TMEM176B	28959	hgsc.bcm.edu	37	7	150490238	150490238	+	Missense_Mutation	SNP	G	G	A	rs17256042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	87	174	0	0.465241	0	G|0.964;A|0.036	0.036	strong	TMEM176B,NS,carcinoma,+1,2	TMEM176B	36	2	NM_014020	exon5	c.C538T	p.R180W	TTCGCCGCATCCA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2161087	2161087	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	64	66	0	0.52459	0	.	.	none	.	PKD1	184	.	NM_000296	exon15	c.C4081G	p.L1361V	TGGACAGCACCAG	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155410650	155410650	+	Missense_Mutation	SNP	T	T	C	rs72731014	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	59	110	0	0.551402	0	T|0.834;C|0.166	0.166	strong	.	DCHS2	594	.	NM_001142552	exon1	c.A1858G	p.T620A	CTAGAGTCCGGAT	.	PASS	Atlas-SNP
COL17A1	1308	hgsc.bcm.edu	37	10	105836066	105836066	+	Silent	SNP	C	C	T	rs61731085	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	70	132	0	0.492958	0	C|0.988;T|0.012	0.012	strong	.	COL17A1	149	.	NM_000494	exon5	c.G324A	p.A108A	TTCATACGCATGG	.	PASS	Atlas-SNP
RASGRF1	5923	hgsc.bcm.edu	37	15	79296172	79296172	+	Silent	SNP	G	G	A	rs1562008	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	65	0	0.43662	0	G|0.849;A|0.151	0.151	strong	.	RASGRF1	168	.	NM_002891	exon16	c.C2469T	p.P823P	GTCTTCGGGCTTC	.	PASS	Atlas-SNP
MRGPRF	116535	hgsc.bcm.edu	37	11	68773403	68773403	+	Silent	SNP	G	G	A	rs11544722	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	19	31	0	0.38	0	G|0.763;A|0.237	0.237	strong	.	MRGPRF	22	.	NM_001098515	exon3	c.C375T	p.C125C	GAACATGCAGAGC	.	PASS	Atlas-SNP
PLEKHB1	58473	hgsc.bcm.edu	37	11	73371842	73371842	+	Silent	SNP	C	C	G	rs147173613	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	48	69	0	0.466019	0	C|0.993;G|0.007	0.007	strong	.	PLEKHB1	16	.	NM_021200	exon7	c.C540G	p.P180P	GGTGCCCCCCAAT	.	PASS	Atlas-SNP
FAM83A	84985	hgsc.bcm.edu	37	8	124206324	124206324	+	Missense_Mutation	SNP	G	G	A	rs7813708	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	64	100	0	0.566372	0	G|0.835;A|0.165	0.165	strong	.	FAM83A	64	.	NM_032899	exon3	c.G709A	p.A237T	AAATTCGCTGGCC	.	PASS	Atlas-SNP
CCDC15	80071	hgsc.bcm.edu	37	11	124861377	124861377	+	Silent	SNP	A	A	G	rs61752520	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	37	90	0	0.440476	0	A|0.976;G|0.024	0.024	strong	.	CCDC15	134	.	NM_025004	exon9	c.A1929G	p.P643P	GGAGCCATACTCT	.	PASS	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55873334	55873334	+	Silent	SNP	A	A	G	rs11227212	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	65	189	0	0.541667	0	A|0.902;G|0.098	0.098	strong	OR8H2,NS,carcinoma,0,1	OR8H2	117	1	NM_001005200	exon1	c.A816G	p.Q272Q	AGATCAAGTGGCT	.	PASS	Atlas-SNP
APOA4	337	hgsc.bcm.edu	37	11	116691634	116691634	+	Missense_Mutation	SNP	C	C	A	rs5110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	73	133	0	0.521429	0	C|0.956;A|0.044	0.044	strong	APOA4,rectum,carcinoma,0,1	APOA4	51	1	NM_000482	exon3	c.G1140T	p.Q380H	CTCCTGCTGCTGT	.	PASS	Atlas-SNP
DPYD	1806	hgsc.bcm.edu	37	1	97770920	97770920	+	Missense_Mutation	SNP	C	C	T	rs1801160	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	49	107	0	0.453704	0	C|0.955;T|0.045	0.045	strong	.	DPYD	219	.	NM_000110	exon18	c.G2194A	p.V732I	CTGTAACGCCATT	.	PASS	Atlas-SNP
FOXI1	2299	hgsc.bcm.edu	37	5	169535450	169535450	+	Silent	SNP	G	G	C	rs56128152	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	83	133	2	0.509202	0.0150376	G|0.989;C|0.011	0.011	strong	FOXI1,NS,carcinoma,0,1	FOXI1	70	1	NM_012188	exon2	c.G972C	p.P324P	CTCCCCGCTCACC	.	scavenged	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1732978	1732978	+	Missense_Mutation	SNP	G	G	A	rs17680881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	54	98	0	0.534653	0	G|0.805;A|0.195	0.195	strong	.	TACC3	69	.	NM_006342	exon6	c.G1541A	p.G514E	AGCAGGGGCAGCC	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4876100	4876100	+	Silent	SNP	G	G	A	rs138811640	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	17	8	0	0.894737	0	G|0.987;A|0.013	0.013	strong	RADIL,brain,glioma,0,2	RADIL	110	2	NM_018059	exon3	c.C672T	p.N224N	CAGGGCGTTCACT	.	PASS	Atlas-SNP
GGH	8836	hgsc.bcm.edu	37	8	63951312	63951312	+	Missense_Mutation	SNP	A	A	G	rs1800909	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	13	1	0	0.65	0	A|0.769;G|0.231	0.231	strong	.	GGH	32	.	NM_003878	exon1	c.T16C	p.C6R	GCAGGCAGCCCGG	.	PASS	Atlas-SNP
DYTN	391475	hgsc.bcm.edu	37	2	207527840	207527840	+	Missense_Mutation	SNP	G	G	T	rs2115591	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	267	122	313	0	0.456929	0	G|0.615;N|0.000	.	strong	.	DYTN	168	.	NM_001093730	exon11	c.C1420A	p.Q474K	CTTTCTGTGGCAT	.	PASS	Atlas-SNP
NUB1	51667	hgsc.bcm.edu	37	7	151064064	151064064	+	Silent	SNP	C	C	T	rs386956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	121	106	0	1	0	C|0.538;T|0.462	0.462	strong	NUB1,caecum,carcinoma,0,1	NUB1	31	1	NM_016118	exon9	c.C912T	p.Y304Y	TAACTACGCCGTC	.	PASS	Atlas-SNP
TRAP1	10131	hgsc.bcm.edu	37	16	3726075	3726075	+	Missense_Mutation	SNP	G	G	A	rs61753378	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	28	70	0	0.459016	0	A|0.042;C|0.000;G|0.957	0.042	strong	TRAP1,NS,carcinoma,-1,1	TRAP1	53	1	NM_016292	exon7	c.C776T	p.S259F	CAGTCGGATTTCA	.	PASS	Atlas-SNP
C1orf168	199920	hgsc.bcm.edu	37	1	57257817	57257817	+	Silent	SNP	T	T	C	rs2298130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	80	142	0	0.597015	0	T|0.778;C|0.222	0.222	strong	.	C1orf168	102	.	NM_001004303	exon2	c.A669G	p.K223K	CCAGCTTTTTCTG	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86891073	86891073	+	Missense_Mutation	SNP	G	G	A	rs11580625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	75	168	0	0.46875	0	G|0.969;A|0.031	0.031	strong	.	CLCA2	102	.	NM_006536	exon2	c.G238A	p.V80I	AGAAGAGTATTTT	.	PASS	Atlas-SNP
GPR125	166647	hgsc.bcm.edu	37	4	22390719	22390719	+	Silent	SNP	G	G	A	rs143611399	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	59	98	0	0.584158	0	G|0.999;A|0.001	0.001	strong	.	GPR125	118	.	NM_145290	exon18	c.C2715T	p.N905N	GGGTGCGTTTGGC	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140581510	140581510	+	Silent	SNP	G	G	T	rs638054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	36	63	0	0.391304	0	G|0.802;T|0.198	0.198	strong	.	PCDHB11	162	.	NM_018931	exon1	c.G2163T	p.S721S	GGCCTCGGTGGGA	.	PASS	Atlas-SNP
BRDT	676	hgsc.bcm.edu	37	1	92442695	92442695	+	Missense_Mutation	SNP	A	A	C	rs1156281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	59	114	0	0.504274	0	A|0.865;C|0.135	0.135	strong	.	BRDT	133	.	NM_001242806	exon6	c.A726C	p.K242N	AGAAAAATCAGTG	.	PASS	Atlas-SNP
SEC31A	22872	hgsc.bcm.edu	37	4	83795806	83795806	+	Silent	SNP	T	T	C	rs10025654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	53	91	0	0.546392	0	T|0.602;C|0.398	0.398	strong	.	SEC31A	227	.	NM_001077206	exon6	c.A597G	p.R199R	ATTTTTTCTAAGA	.	PASS	Atlas-SNP
VAV3	10451	hgsc.bcm.edu	37	1	108307727	108307727	+	Missense_Mutation	SNP	T	T	A	rs7528153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	122	163	0	0.976	0	T|0.379;A|0.621	0.621	strong	.	VAV3	176	.	NM_006113	exon9	c.A892T	p.T298S	CTTTTGTCTTAGA	.	PASS	Atlas-SNP
PLAUR	5329	hgsc.bcm.edu	37	19	44153100	44153100	+	Missense_Mutation	SNP	A	A	G	rs4760	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	50	121	0	0.462963	0	A|0.908;G|0.092	0.092	strong	.	PLAUR	71	.	NM_002659	exon7	c.T950C	p.L317P	ATGGTGAGGCTGA	.	PASS	Atlas-SNP
TBC1D9	23158	hgsc.bcm.edu	37	4	141598126	141598126	+	Silent	SNP	C	C	T	rs2303911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	47	100	0	0.439252	0	C|0.866;G|0.000;T|0.133	0.133	strong	.	TBC1D9	198	.	NM_015130	exon6	c.G981A	p.Q327Q	AAACATCTGCCCC	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33880003	33880003	+	Silent	SNP	C	C	G	rs28498569	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	50	67	0	0.581395	0	C|0.765;G|0.235	0.235	strong	.	SLFN14	43	.	NM_001129820	exon3	c.G1650C	p.V550V	GGAGACCACCACC	.	PASS	Atlas-SNP
FAM207A	85395	hgsc.bcm.edu	37	21	46387078	46387078	+	Missense_Mutation	SNP	G	G	T	rs2294168	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	24	13	0	0.631579	0	G|0.887;T|0.113	0.113	strong	C21orf70,NS,carcinoma,-1,1	.	.	1	NM_058190	exon4	c.G482T	p.S161I	CTGGCAGCCGGCG	.	PASS	Atlas-SNP
KDM6A	7403	hgsc.bcm.edu	37	X	44938563	44938563	+	Silent	SNP	G	G	A	rs20539	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	246	208	1	0.987952	0.00480769	0|0.018;A|0.156	0.156	strong	.	KDM6A	274	.	NM_021140	exon20	c.G3111A	p.Q1037Q	TGCACAGTACCAG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509354	195509354	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	8	163	0	0.0776699	0	.	.	none	MUC4_ENST00000463781,uveal_tract,malignant_melanoma,0,4	MUC4	1505	4	NM_018406	exon2	c.G9097A	p.A3033T	TGGATGCTGAGGA	.	scavenged	Atlas-SNP
PBDC1	51260	hgsc.bcm.edu	37	X	75394784	75394784	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	99	97	0	1	0	.	.	none	.	.	.	.	NM_016500	exon3	c.G156T	p.K52N	TTACAAGGTGAGT	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52708565	52708565	+	Silent	SNP	A	A	G	rs2857670	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	159	176	1	0.987578	0.00568182	A|0.272;G|0.728	0.728	strong	.	KRT83	64	.	NM_002282	exon9	c.T1332C	p.D444D	GCAGAGATCCCCG	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33482821	33482821	+	Missense_Mutation	SNP	G	G	A	rs79314177	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	113	173	0	0.553922	0	G|0.974;A|0.026	0.026	strong	.	RHPN2	107	.	NM_033103	exon13	c.C1552T	p.R518C	TGAAGCGGATGCT	.	PASS	Atlas-SNP
TGIF1	7050	hgsc.bcm.edu	37	18	3457606	3457606	+	Missense_Mutation	SNP	C	C	T	rs4468717	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	73	158	0	0.434524	0	C|0.945;T|0.055	0.055	strong	.	TGIF1	41	.	NM_170695	exon3	c.C874T	p.P292S	TCATCCCCGGGAT	.	PASS	Atlas-SNP
COMT	1312	hgsc.bcm.edu	37	22	19951207	19951207	+	Silent	SNP	C	C	G	rs4818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	45	76	0	0.483871	0	C|0.677;G|0.323	0.323	strong	.	COMT	10	.	NM_000754	exon4	c.C408G	p.L136L	GAGGCTCATCACC	.	PASS	Atlas-SNP
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	334	9	382	4	0.0269461	0.0104712	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
ESYT2	57488	hgsc.bcm.edu	37	7	158536267	158536267	+	Missense_Mutation	SNP	T	T	C	rs2305473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	48	133	0	0.417391	0	T|0.712;C|0.288	0.288	strong	.	ESYT2	70	.	NM_020728	exon16	c.A1828G	p.S610G	AGTTACTGAGCTG	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79455733	79455733	+	Silent	SNP	C	C	T	rs4975139	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	93	117	0	1	0	C|0.484;T|0.516	0.516	strong	.	FRAS1	779	.	NM_025074	exon71	c.C11056T	p.L3686L	ATGTCACTAGCAG	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	37	3	113377361	113377361	+	Silent	SNP	A	A	G	rs9813630	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	123	125	0	0.968504	0	A|0.657;G|0.343	0.343	strong	.	KIAA2018	180	.	NM_001009899	exon7	c.T3168C	p.N1056N	ATCATCATTGTTC	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57180563	57180563	+	Missense_Mutation	SNP	G	G	C	rs59615456	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	11	18	0	0.354839	0	G|0.738;C|0.262	0.262	strong	.	KIAA1211	178	.	NM_020722	exon8	c.G895C	p.G299R	GCGCCAGGTTGGG	.	PASS	Atlas-SNP
C6orf211	79624	hgsc.bcm.edu	37	6	151789868	151789868	+	Missense_Mutation	SNP	G	G	A	rs35972078	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	56	118	0	0.982456	0	G|0.904;A|0.096	0.096	strong	C6orf211,NS,carcinoma,0,1	C6orf211	30	1	NM_024573	exon5	c.G949A	p.A317T	TGTGGGGCTGACT	.	PASS	Atlas-SNP
ZNF404	342908	hgsc.bcm.edu	37	19	44377669	44377669	+	Missense_Mutation	SNP	G	G	A	rs12977303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	114	88	0	0.991304	0	G|0.588;A|0.412	0.412	strong	.	ZNF404	46	.	NM_001033719	exon2	c.C688T	p.H230Y	TCTGATGTTCTGT	.	PASS	Atlas-SNP
POC5	134359	hgsc.bcm.edu	37	5	75003678	75003678	+	Missense_Mutation	SNP	T	T	C	rs2307111	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	208	187	0	0.981132	0	T|0.429;C|0.571	0.571	strong	.	POC5	82	.	NM_001099271	exon3	c.A107G	p.H36R	GCATAATGAAGCA	.	PASS	Atlas-SNP
LAMC3	10319	hgsc.bcm.edu	37	9	133963008	133963008	+	Missense_Mutation	SNP	G	G	A	rs4740412	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	35	56	0	0.472973	0	G|0.817;A|0.183	0.183	strong	LAMC3,NS,carcinoma,-1,1	LAMC3	167	1	NM_006059	exon26	c.G4376A	p.R1459Q	CTGAGCGGGTACG	.	PASS	Atlas-SNP
LPCAT2	54947	hgsc.bcm.edu	37	16	55562466	55562466	+	Missense_Mutation	SNP	G	G	A	rs837550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	282	124	270	0	0.439716	0	G|0.457;A|0.543	0.543	strong	.	LPCAT2	35	.	NM_017839	exon3	c.G489A	p.M163I	TTCTATGGTATCT	.	PASS	Atlas-SNP
ST14	6768	hgsc.bcm.edu	37	11	130068491	130068491	+	Silent	SNP	G	G	C	rs11827924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	96	132	0	0.502618	0	G|0.868;C|0.132	0.132	strong	ST14,NS,malignant_melanoma,+1,1	ST14	82	1	NM_021978	exon14	c.G1659C	p.G553G	GGACGGGTCCGAC	.	PASS	Atlas-SNP
MMRN1	22915	hgsc.bcm.edu	37	4	90857518	90857518	+	Missense_Mutation	SNP	T	T	A	rs200343754	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	52	116	0	0.468468	0	T|0.999;A|0.001	0.001	weak	.	MMRN1	174	.	NM_007351	exon6	c.T2687A	p.L896Q	TTCAACTGCAAGT	.	PASS	Atlas-SNP
USP13	8975	hgsc.bcm.edu	37	3	179371154	179371154	+	Silent	SNP	C	C	T	rs2276803	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	107	71	0	0.990741	0	C|0.795;T|0.205	0.205	strong	.	USP13	117	.	NM_003940	exon1	c.C141T	p.N47N	CAAGAACGAGTGC	.	PASS	Atlas-SNP
SIRT4	23409	hgsc.bcm.edu	37	12	120741382	120741382	+	Silent	SNP	G	G	A	rs61748115	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	33	44	0	0.702128	0	G|0.947;A|0.053	0.053	strong	SIRT4,NS,adenoma,0,1	SIRT4	29	1	NM_012240	exon2	c.G18A	p.A6A	CTTTGCGTTGACT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9084183	9084183	+	Silent	SNP	G	G	A	rs1609460	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	128	219	0	0.584475	0	G|0.573;A|0.427	0.427	strong	.	MUC16	4315	.	NM_024690	exon1	c.C7632T	p.P2544P	GAGATGGGGAGTG	.	PASS	Atlas-SNP
PCDH17	27253	hgsc.bcm.edu	37	13	58207711	58207711	+	Missense_Mutation	SNP	G	G	T	rs41292834	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	21	22	0	0.677419	0	G|0.993;T|0.007	0.007	strong	.	PCDH17	304	.	NM_001040429	exon1	c.G1031T	p.R344L	TCGACCGCAACGA	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55485899	55485899	+	Silent	SNP	G	G	A	rs2217659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	31	63	0	0.492063	0	G|0.829;A|0.171	0.171	strong	.	NLRP2	161	.	NM_001174082	exon3	c.G312A	p.K104K	AAGGAAGCCTCTA	.	PASS	Atlas-SNP
PON3	5446	hgsc.bcm.edu	37	7	95025600	95025600	+	Silent	SNP	G	G	A	rs13226149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	45	67	0	0.473684	0	G|0.723;A|0.277	0.277	strong	.	PON3	59	.	NM_000940	exon1	c.C63T	p.F21F	CGCCAGGAACATC	.	PASS	Atlas-SNP
SH3BGR	6450	hgsc.bcm.edu	37	21	40823902	40823902	+	Missense_Mutation	SNP	C	C	G	rs11575939	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	62	96	0	0.596154	0	C|0.802;G|0.198	0.198	strong	.	SH3BGR	29	.	NM_007341	exon1	c.C69G	p.D23E	AGTGGACCCCTGG	.	PASS	Atlas-SNP
SLC15A3	51296	hgsc.bcm.edu	37	11	60718792	60718792	+	Missense_Mutation	SNP	C	C	T	rs150370599	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	9	2	0	0.6	0	C|0.968;T|0.032	0.032	strong	.	SLC15A3	34	.	NM_016582	exon1	c.G232A	p.V78I	GGAATACCAGCGC	.	PASS	Atlas-SNP
HFM1	164045	hgsc.bcm.edu	37	1	91816313	91816313	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	53	65	0	0.490741	0	.	.	none	.	HFM1	188	.	NM_001017975	exon18	c.A2188G	p.K730E	GATTTTTCAAGGC	.	PASS	Atlas-SNP
KIAA0040	9674	hgsc.bcm.edu	37	1	175129933	175129933	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	6	118	0	0.0625	0	.	.	none	KIAA0040,colon,carcinoma,0,1	KIAA0040	2	1	NM_001162895	exon3	c.A217G	p.K73E	TCTTCTTCTTCTT	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	37	11	108163487	108163487	+	Silent	SNP	C	C	T	rs1800889	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	67	164	0	0.455782	0	C|0.972;T|0.028	0.028	strong	.	ATM	1657	.	NM_000051	exon30	c.C4578T	p.P1526P	TATACCCCTTGTG	.	PASS	Atlas-SNP
NAT6	24142	hgsc.bcm.edu	37	3	50334592	50334592	+	Silent	SNP	G	G	A	rs374560438		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	74	112	0	0.564885	0	.	.	weak	.	NAT6	14	.	NM_012191	exon2	c.C369T	p.F123F	GAGGGGGAAGGCA	.	PASS	Atlas-SNP
SLFNL1	200172	hgsc.bcm.edu	37	1	41482917	41482917	+	Missense_Mutation	SNP	A	A	G	rs147062455	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	48	44	0	0.941176	0	A|0.998;G|0.002	0.002	strong	.	SLFNL1	37	.	NM_001168247	exon5	c.T1090C	p.W364R	TGCACCACTCCTG	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81592802	81592802	+	Silent	SNP	A	A	G	rs11073001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	85	116	1	0.988372	0.00862069	A|0.697;G|0.303	0.303	strong	.	IL16	254	.	NM_001172128	exon14	c.A3135G	p.T1045T	GGACACAGGGTTC	.	PASS	Atlas-SNP
CPED1	79974	hgsc.bcm.edu	37	7	120901695	120901695	+	Missense_Mutation	SNP	G	G	A	rs10953934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	114	210	1	0.522936	0.0047619	G|0.648;A|0.352	0.352	strong	.	.	.	.	NM_001105533	exon18	c.G2320A	p.D774N	GGTGTCGATGTCC	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23809303	23809303	+	Silent	SNP	A	A	G	rs55860134	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	59	87	0	0.551402	0	A|0.989;G|0.011	0.011	strong	.	STK31	175	.	NM_031414	exon13	c.A1641G	p.A547A	AGACGCAATGGAT	.	PASS	Atlas-SNP
WDYHV1	55093	hgsc.bcm.edu	37	8	124448736	124448736	+	Missense_Mutation	SNP	A	A	G	rs7014678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	248	210	1	0.995984	0.0047619	A|0.626;G|0.374	0.374	strong	WDYHV1,NS,carcinoma,0,1	WDYHV1	30	1	NM_018024	exon4	c.A278G	p.N93S	GACAGAACTTCAT	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50957397	50957397	+	Missense_Mutation	SNP	G	G	A	rs25665	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	95	151	0	0.555556	0	G|0.772;A|0.227	0.227	strong	.	MYBPC2	103	.	NM_004533	exon17	c.G1870A	p.V624I	AACCCCGTCGGCG	.	PASS	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	37	13	67800935	67800935	+	Silent	SNP	G	G	A	rs9571740	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	139	197	0	0.992857	0	G|0.559;A|0.441	0.441	strong	.	PCDH9	252	.	NM_203487	exon2	c.C1638T	p.D546D	CCCATTGTCCCTG	.	PASS	Atlas-SNP
MSH6	2956	hgsc.bcm.edu	37	2	48027375	48027375	+	Silent	SNP	T	T	C	rs2020913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	47	108	0	0.465347	0	T|0.980;C|0.020	0.020	strong	.	MSH6	341	.	NM_000179	exon4	c.T2253C	p.N751N	AACAAATGGTTCT	.	PASS	Atlas-SNP
FUT8	2530	hgsc.bcm.edu	37	14	66082793	66082793	+	Missense_Mutation	SNP	A	A	C	rs2229678	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	55	119	0	0.486726	0	A|0.990;C|0.010	0.010	strong	.	FUT8	101	.	NM_178155	exon4	c.A301C	p.K101Q	AATTACAAGAAAC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388631	1388631	+	Missense_Mutation	SNP	C	C	G	rs200849975	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	31	122	0	0.238462	0	C|0.935;G|0.065	0.065	strong	CRIPAK,rectum,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.C332G	p.P111R	CGTGCCCATGTGG	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82785304	82785304	+	Missense_Mutation	SNP	G	G	A	rs61738783	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	238	134	235	1	0.563025	0.00425532	G|0.989;A|0.011	0.011	strong	Q9Y6V0-3,NS,carcinoma,+1,5	PCLO	1506	5	NM_014510	exon2	c.C653T	p.P218L	GGAATCGGCTTGG	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595106	140595106	+	Missense_Mutation	SNP	C	C	G	rs2910329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	67	172	0	0.507576	0	C|0.532;G|0.468	0.468	strong	.	PCDHB13	142	.	NM_018933	exon1	c.C1411G	p.R471G	CACATCCGCAGCG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40408821	40408821	+	Missense_Mutation	SNP	C	C	G	rs45613437	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	69	148	0	0.530769	0	.	.	weak	FCGBP,caecum,carcinoma,0,2	FCGBP	416	2	NM_003890	exon8	c.G4018C	p.V1340L	GCACCACGGGCAG	.	PASS	Atlas-SNP
LRRC56	115399	hgsc.bcm.edu	37	11	554047	554047	+	Missense_Mutation	SNP	G	G	A	rs12793222	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	65	99	0	0.585586	0	G|0.781;A|0.219	0.219	strong	.	LRRC56	23	.	NM_198075	exon14	c.G1400A	p.R467Q	CCCCGCGGTGGTC	.	PASS	Atlas-SNP
DDI1	414301	hgsc.bcm.edu	37	11	103908735	103908735	+	Silent	SNP	G	G	A	rs1052313	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	98	172	0	0.563218	0	G|0.625;A|0.374	0.374	strong	.	DDI1	222	.	NM_001001711	exon1	c.G1185A	p.E395E	AAAAGAGCATTAA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9069792	9069792	+	Missense_Mutation	SNP	G	G	A	rs1862458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	64	145	0	0.460432	0	G|0.798;A|0.202	0.202	strong	.	MUC16	4315	.	NM_024690	exon3	c.C17654T	p.S5885F	TCCCAGGAAGCTG	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	37	10	61832131	61832131	+	Silent	SNP	A	A	G	rs11815168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	67	121	0	0.577586	0	A|0.995;G|0.005	0.005	strong	.	ANK3	703	.	NM_020987	exon37	c.T8508C	p.H2836H	GGTTATATGACAT	.	PASS	Atlas-SNP
GIT1	28964	hgsc.bcm.edu	37	17	27901903	27901903	+	Silent	SNP	T	T	C	rs11548560	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	16	38	0	0.516129	0	T|0.987;C|0.013	0.013	strong	.	GIT1	84	.	NM_001085454	exon21	c.A2130G	p.S710S	CCGCAGTGAGCTC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629809	32629809	+	Missense_Mutation	SNP	C	C	T	rs701564	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	49	100	0	0.4375	0	T|0.225;C|0.775	0.225	strong	HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	NM_002123	exon3	c.G596A	p.R199H	TCTCCACGCTGGG	.	PASS	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22382655	22382655	+	Missense_Mutation	SNP	A	A	C	rs535034	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	456	107	498	0	0.234649	0	A|0.776;C|0.224	0.224	strong	.	OR4N4	108	.	NM_001005241	exon1	c.A183C	p.L61F	CTATTTATTTCTG	.	PASS	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55653164	55653164	+	Missense_Mutation	SNP	G	G	A	rs10897403	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	59	160	0	0.453846	0	G|0.613;A|0.387	0.387	strong	.	.	.	.	NM_032681	exon2	c.G260A	p.S87N	TCCTTAGCTCTGA	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133208979	133208979	+	Silent	SNP	T	T	C	rs5745022	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	77	160	0	0.447674	0	T|0.339;C|0.661	0.661	strong	.	POLE	416	.	NM_006231	exon45	c.A6252G	p.S2084S	CATCTCTGAGAGC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634303	32634303	+	Silent	SNP	G	G	A	rs1049061	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	19	4	0	0.703704	0	G|0.848;A|0.152	0.152	strong	.	HLA-DQB1	15	.	NM_002123	exon1	c.C82T	p.L28L	CCAGTAGGGAGCT	.	PASS	Atlas-SNP
TOP1MT	116447	hgsc.bcm.edu	37	8	144406705	144406705	+	Missense_Mutation	SNP	C	C	T	rs11544484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	103	86	0	0.980952	0	C|0.689;T|0.311	0.311	strong	.	TOP1MT	63	.	NM_052963	exon6	c.G766A	p.V256I	TCTGAACGCTCTC	.	PASS	Atlas-SNP
ZNF704	619279	hgsc.bcm.edu	37	8	81733727	81733727	+	Missense_Mutation	SNP	C	C	A	rs3907424	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	80	158	0	0.40404	0	C|0.783;A|0.217	0.217	strong	.	ZNF704	32	.	NM_001033723	exon2	c.G103T	p.A35S	TGTCTGCTGTTTT	.	PASS	Atlas-SNP
FOXQ1	94234	hgsc.bcm.edu	37	6	1313470	1313470	+	Silent	SNP	C	C	T	rs4435985	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	58	95	0	0.446154	0	C|0.811;T|0.189	0.189	strong	FOXQ1,NS,carcinoma,0,1	FOXQ1	8	1	NM_033260	exon1	c.C531T	p.F177F	CTGCTTCGTCAAG	.	PASS	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177929940	177929940	+	Silent	SNP	G	G	A	rs7413442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	107	196	0	0.540404	0	G|0.727;A|0.273	0.273	strong	.	SEC16B	92	.	NM_033127	exon7	c.C922T	p.L308L	TGTGCAGTTCAAC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9086819	9086819	+	Silent	SNP	G	G	A	rs1823056	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	82	141	0	0.543046	0	G|0.811;A|0.189	0.189	strong	.	MUC16	4315	.	NM_024690	exon1	c.C4996T	p.L1666L	TTTCCAGTGCCAT	.	PASS	Atlas-SNP
ALDH7A1	501	hgsc.bcm.edu	37	5	125887715	125887715	+	Missense_Mutation	SNP	T	T	G	rs12514417	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	23	28	0	0.522727	0	T|0.916;G|0.084	0.084	strong	.	ALDH7A1	57	.	NM_001182	exon14	c.A1315C	p.K439Q	TTACCTTGAATTT	.	PASS	Atlas-SNP
SASH1	23328	hgsc.bcm.edu	37	6	148854984	148854984	+	Silent	SNP	G	G	A	rs2294787	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	52	83	0	0.981132	0	G|0.931;A|0.069	0.069	strong	.	SASH1	123	.	NM_015278	exon15	c.G1812A	p.T604T	CGGCACGTTCAAG	.	PASS	Atlas-SNP
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	87	144	0	0.537037	0	G|0.422;N|0.000	0.422	strong	.	ATG16L1	83	.	NM_030803	exon9	c.A898G	p.T300A	GTGGATACTCATC	.	PASS	Atlas-SNP
PAIP2B	400961	hgsc.bcm.edu	37	2	71429687	71429687	+	Silent	SNP	C	C	G	rs13001756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	289	138	220	1	0.477509	0.00454545	C|0.934;G|0.066	0.066	strong	.	PAIP2B	7	.	NM_020459	exon2	c.G33C	p.P11P	TACACTCGGTGAT	.	PASS	Atlas-SNP
ZDHHC19	131540	hgsc.bcm.edu	37	3	195938177	195938177	+	Silent	SNP	A	A	G	rs1522394	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	85	0	0.478873	0	A|0.742;G|0.258	0.258	strong	.	ZDHHC19	25	.	NM_001039617	exon1	c.T10C	p.L4L	CCGTTAAGAGTGT	.	PASS	Atlas-SNP
RPA1	6117	hgsc.bcm.edu	37	17	1782957	1782957	+	Silent	SNP	C	C	T	rs2230930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	30	73	0	0.32967	0	C|0.802;N|0.000	.	strong	.	RPA1	48	.	NM_002945	exon11	c.C1056T	p.S352S	CACATCCGGGAAG	.	PASS	Atlas-SNP
SHPRH	257218	hgsc.bcm.edu	37	6	146234644	146234644	+	Silent	SNP	G	G	A	rs9497426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	30	64	0	1	0	G|0.174;A|0.826	0.826	strong	.	SHPRH	169	.	NM_173082	exon24	c.C4308T	p.C1436C	GATTGGGCAAGGT	.	PASS	Atlas-SNP
MRAP2	112609	hgsc.bcm.edu	37	6	84799185	84799185	+	Silent	SNP	C	C	T	rs2875382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	8	76	0	0.153846	0	C|0.654;T|0.346	0.346	strong	MRAP2,NS,carcinoma,0,1	MRAP2	40	1	NM_138409	exon4	c.C603T	p.H201H	CTCACACAAAGAC	.	PASS	Atlas-SNP
MAN2B1	4125	hgsc.bcm.edu	37	19	12768948	12768948	+	Missense_Mutation	SNP	T	T	C	rs35836657	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	39	62	0	0.4875	0	T|0.924;C|0.076	0.076	strong	MAN2B1,NS,carcinoma,0,1	MAN2B1	91	1	NM_000528	exon10	c.A1238G	p.N413S	AGCTGGTTGCACA	.	PASS	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30339234	30339234	+	Missense_Mutation	SNP	T	T	C	rs61735768	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	33	95	0	0.434211	0	T|0.880;C|0.120	0.120	strong	LTN1,NS,carcinoma,0,1	LTN1	141	1	NM_015565	exon10	c.A1717G	p.S573G	ATGAGCTCTTCGG	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1421531	1421531	+	Silent	SNP	C	C	A	rs819976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	201	200	0	0.952607	0	C|0.587;A|0.413	0.413	strong	.	ATAD3B	68	.	NM_031921	exon10	c.C1005A	p.T335T	AGCAACCAGGAAC	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	37	10	126715436	126715436	+	Missense_Mutation	SNP	C	C	T	rs3781411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	66	136	0	0.404908	0	C|0.882;T|0.118	0.118	strong	.	CTBP2	100	.	NM_022802	exon1	c.G893A	p.R298Q	TCCGCCCGCAGAA	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6579354	6579354	+	Silent	SNP	G	G	C	rs16915382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	55	96	0	0.5	0	G|0.805;C|0.195	0.195	strong	.	DNHD1	198	.	NM_144666	exon25	c.G8829C	p.L2943L	GGCTCTGTTGGTA	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50940778	50940778	+	Missense_Mutation	SNP	C	C	T	rs61731791	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	41	80	0	0.41	0	C|0.969;T|0.031	0.031	strong	MYBPC2_ENST00000357701,colon,carcinoma,0,1	MYBPC2	103	1	NM_004533	exon6	c.C512T	p.T171M	AGCGTACGTAAGT	.	PASS	Atlas-SNP
RING1	6015	hgsc.bcm.edu	37	6	33177782	33177782	+	Silent	SNP	C	C	T	rs61736933	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	56	107	0	0.513761	0	C|0.991;T|0.009	0.009	strong	RING1,NS,carcinoma,+1,1	RING1	40	1	NM_002931	exon4	c.C330T	p.I110I	TAAGATCTATCCT	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541542	12541542	+	Missense_Mutation	SNP	C	C	T	rs74181783	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	31	77	0	0.407895	0	TACGTT|0.500;CAAGTG|0.500	.	alt	.	ZNF443	63	.	NM_005815	exon4	c.G1444A	p.G482R	CTTTCCCAAGTTT	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26310506	26310506	+	Silent	SNP	C	C	T	rs34067308	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	48	89	0	0.5	0	C|0.933;T|0.067	0.067	strong	.	MYO3A	371	.	NM_017433	exon8	c.C660T	p.A220A	CACGGCCATTGAG	.	PASS	Atlas-SNP
PI16	221476	hgsc.bcm.edu	37	6	36926952	36926952	+	Missense_Mutation	SNP	A	A	G	rs113848006	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	54	96	0	0.504673	0	A|0.982;G|0.018	0.018	strong	.	PI16	50	.	NM_001199159	exon3	c.A203G	p.K68R	TCGCCAAGGCCTA	.	PASS	Atlas-SNP
DCDC2	51473	hgsc.bcm.edu	37	6	24357796	24357796	+	Silent	SNP	G	G	A	rs33943110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	37	46	0	0.544118	0	G|0.955;A|0.045	0.045	strong	.	DCDC2	53	.	NM_001195610	exon2	c.C183T	p.A61A	CCTGACGGCCCCA	.	PASS	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	37	8	100443885	100443885	+	Missense_Mutation	SNP	C	C	T	rs61753722	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	7	17	0	0.368421	0	C|0.994;T|0.006	0.006	strong	.	VPS13B	811	.	NM_152564	exon22	c.C3203T	p.T1068I	ATCTCACACTACA	.	PASS	Atlas-SNP
ASPSCR1	79058	hgsc.bcm.edu	37	17	79941511	79941511	+	Silent	SNP	C	C	T	rs11539917	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	31	55	0	0.553571	0	C|0.988;T|0.012	0.012	strong	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	NM_001251888	exon3	c.C240T	p.P80P	GGTGCCCGCTTCC	.	PASS	Atlas-SNP
CCDC171	203238	hgsc.bcm.edu	37	9	15784560	15784560	+	Silent	SNP	A	A	G	rs55780067	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	44	99	0	0.494382	0	A|0.966;G|0.034	0.034	strong	.	.	.	.	NM_173550	exon21	c.A3135G	p.A1045A	TAATGCATTACTT	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100846936	100846936	+	Silent	SNP	A	A	G	rs654593	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	98	109	0	1	0	A|0.462;G|0.538	0.538	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.A2004G	p.P668P	AACCCCATCATCT	.	PASS	Atlas-SNP
EXD1	161829	hgsc.bcm.edu	37	15	41476209	41476209	+	Missense_Mutation	SNP	T	T	C	rs522063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	161	130	1	1	0.00769231	T|0.221;C|0.779	0.779	strong	.	EXD1	52	.	NM_152596	exon10	c.A1465G	p.T489A	CCACAGTCTTTCT	.	PASS	Atlas-SNP
DCLRE1B	64858	hgsc.bcm.edu	37	1	114448389	114448389	+	Missense_Mutation	SNP	C	C	T	rs11552449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	47	79	0	0.559524	0	C|0.806;G|0.000;T|0.194	0.194	strong	.	DCLRE1B	36	.	NM_022836	exon1	c.C181T	p.H61Y	CATCGTCACCTAC	.	PASS	Atlas-SNP
DCP2	167227	hgsc.bcm.edu	37	5	112349109	112349109	+	Silent	SNP	C	C	T	rs149633478	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	36	84	0	0.444444	0	C|0.999;T|0.001	0.001	strong	.	DCP2	34	.	NM_152624	exon11	c.C1191T	p.F397F	CAAGTTCCCCTTT	.	PASS	Atlas-SNP
GPR149	344758	hgsc.bcm.edu	37	3	154146922	154146922	+	Silent	SNP	A	A	G	rs34792862	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	21	41	0	0.333333	0	A|0.841;G|0.159	0.159	strong	.	GPR149	134	.	NM_001038705	exon1	c.T483C	p.S161S	CAGCAGACTGGCT	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50531524	50531524	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	2	69	0	0.0363636	0	.	.	none	C10orf71_ENST00000374144,NS,carcinoma,0,2	C10orf71	179	2	NM_001135196	exon3	c.C934T	p.L312L	ACCTTGCTAAGAG	.	scavenged	Atlas-SNP
TEKT3	64518	hgsc.bcm.edu	37	17	15234895	15234895	+	Missense_Mutation	SNP	C	C	T	rs7226363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	21	40	0	0.525	0	C|0.794;T|0.206	0.206	strong	.	TEKT3	64	.	NM_031898	exon3	c.G8A	p.R3H	CCTACACGTTCCA	.	PASS	Atlas-SNP
CSF3R	1441	hgsc.bcm.edu	37	1	36937878	36937878	+	Missense_Mutation	SNP	C	C	T	rs3918018	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	9	226	0	0.0456853	0	C|0.981;T|0.019	0.019	strong	.	CSF3R	157	.	NM_156039	exon8	c.G958A	p.D320N	TCCAGTCGCTCCA	.	PASS	Atlas-SNP
KITLG	4254	hgsc.bcm.edu	37	12	88900891	88900891	+	Missense_Mutation	SNP	C	C	A	rs41283112	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	14	46	0	0.482759	0	C|0.991;A|0.009	0.009	strong	.	KITLG	26	.	NM_000899	exon7	c.G628T	p.D210Y	TGGAGTCTCCAGG	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380177	107380177	+	Silent	SNP	A	A	G	rs1813819	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	384	175	413	0	0.455729	0	A|0.694;G|0.306	0.306	strong	.	OR13C9	42	.	NM_001001956	exon1	c.T309C	p.L103L	CAAGCCAAGGAAC	.	PASS	Atlas-SNP
AQP3	360	hgsc.bcm.edu	37	9	33443867	33443867	+	Silent	SNP	G	G	A	rs2228333	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	22	48	0	0.333333	0	G|0.996;A|0.004	0.004	strong	.	AQP3	18	.	NM_004925	exon2	c.C132T	p.A44A	AACCTGGGCCACG	.	PASS	Atlas-SNP
SLC25A22	79751	hgsc.bcm.edu	37	11	794790	794790	+	Silent	SNP	G	G	A	rs146402942	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	73	140	0	0.493243	0	G|0.999;A|0.001	0.001	strong	.	SLC25A22	19	.	NM_001191061	exon3	c.C132T	p.R44R	GTACACGCGCTGG	.	PASS	Atlas-SNP
DCAF4L1	285429	hgsc.bcm.edu	37	4	41984782	41984782	+	Missense_Mutation	SNP	G	G	A	rs369307123		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	86	156	0	0.419512	0	.	.	weak	.	DCAF4L1	70	.	NM_001029955	exon1	c.G973A	p.E325K	CACGAGGAAGAGG	.	PASS	Atlas-SNP
BRAT1	221927	hgsc.bcm.edu	37	7	2578246	2578246	+	Silent	SNP	C	C	T	rs2917726	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	5	1	0	0.714286	0	C|0.772;T|0.228	0.228	strong	.	BRAT1	57	.	NM_152743	exon14	c.G1923A	p.A641A	GCTCGCCGCCTGC	.	PASS	Atlas-SNP
PLS1	5357	hgsc.bcm.edu	37	3	142408606	142408606	+	Silent	SNP	G	G	A	rs6793735	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	177	169	0	0.994382	0	G|0.314;A|0.686	0.686	strong	PLS1,NS,carcinoma,0,1	PLS1	71	1	NM_001172312	exon10	c.G1128A	p.P376P	ATACCCGTGCCTG	.	PASS	Atlas-SNP
CERCAM	51148	hgsc.bcm.edu	37	9	131196704	131196704	+	Silent	SNP	G	G	A	rs7259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	61	0	1	0	G|0.673;A|0.327	0.327	strong	.	CERCAM	104	.	NM_016174	exon11	c.G1347A	p.K449K	ACGGAAGCAGGTG	.	PASS	Atlas-SNP
PRRC2B	84726	hgsc.bcm.edu	37	9	134334588	134334588	+	Missense_Mutation	SNP	A	A	G	rs34553878	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	42	93	0	0.482759	0	A|0.928;G|0.072	0.072	strong	.	PRRC2B	266	.	NM_013318	exon10	c.A1249G	p.M417V	TTGTCAATGAGCT	.	PASS	Atlas-SNP
PEBP4	157310	hgsc.bcm.edu	37	8	22570904	22570904	+	Silent	SNP	C	C	T	rs61732772	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	58	129	0	0.537037	0	C|0.986;T|0.014	0.014	strong	.	PEBP4	23	.	NM_144962	exon7	c.G663A	p.Q221Q	CTCCGCCTGGTTT	.	PASS	Atlas-SNP
TAOK2	9344	hgsc.bcm.edu	37	16	29999225	29999225	+	Missense_Mutation	SNP	G	G	A	rs11864149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	10	15	0	0.526316	0	G|0.914;A|0.086	0.086	strong	.	TAOK2	142	.	NM_016151	exon16	c.G3632A	p.R1211H	CCTCCCGCCAGCC	.	PASS	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	96006281	96006281	+	Missense_Mutation	SNP	G	G	A	rs61751498	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	46	111	0	0.438095	0	G|0.997;A|0.003	0.003	strong	.	PLCE1	543	.	NM_016341	exon8	c.G2999A	p.S1000N	TCTTCAGCGGATT	.	PASS	Atlas-SNP
SLC16A9	220963	hgsc.bcm.edu	37	10	61414011	61414011	+	Missense_Mutation	SNP	G	G	T	rs2242206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	83	186	0	0.378995	0	G|0.740;T|0.260	0.260	strong	.	SLC16A9	58	.	NM_194298	exon5	c.C773A	p.T258K	GTCACTGTGGGGT	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53682326	53682326	+	Silent	SNP	G	G	A	rs1110720	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	29	67	0	0.426471	0	G|0.402;A|0.598	0.598	strong	.	ESPL1	158	.	NM_012291	exon20	c.G4551A	p.G1517G	AGGTGGGAAGACT	.	PASS	Atlas-SNP
HABP2	3026	hgsc.bcm.edu	37	10	115334124	115334124	+	Silent	SNP	C	C	T	rs3740530	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	35	82	0	0.448718	0	C|0.467;T|0.533	0.533	strong	.	HABP2	52	.	NM_004132	exon3	c.C183T	p.H61H	TACCCACGCTGAG	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147477551	147477551	+	Missense_Mutation	SNP	C	C	T	rs34482796	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	80	66	0	1	0	C|0.530;T|0.470	0.470	strong	SPINK5_ENST00000359874,colon,carcinoma,+1,2	SPINK5	245	2	NM_001127699	exon11	c.C1004T	p.A335V	GTCAAGCCTACTT	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	37	1	222803204	222803204	+	Missense_Mutation	SNP	A	A	G	rs2936051	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	48	117	0	0.448598	0	A|0.748;G|0.252	0.252	strong	.	MIA3	167	.	NM_198551	exon4	c.A2642G	p.E881G	ACCATGAGAACAC	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96021254	96021254	+	Silent	SNP	G	G	A	rs55768771	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	100	183	0	0.5	0	G|0.993;A|0.007	0.007	strong	.	WNK2	277	.	NM_006648	exon11	c.G2424A	p.A808A	CCTGGCGGGAATC	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080983	194080983	+	Missense_Mutation	SNP	C	C	T	rs13060627	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	277	140	235	0	0.505415	0	C|0.796;T|0.204	0.204	strong	LRRC15_ENST00000439944,NS,carcinoma,0,2	LRRC15	137	2	NM_001135057	exon3	c.G808A	p.V270I	TGAAGACGCTGGG	.	PASS	Atlas-SNP
BRD3	8019	hgsc.bcm.edu	37	9	136907005	136907005	+	Silent	SNP	G	G	A	rs467387	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	99	174	0	0.515625	0	G|0.751;A|0.249	0.249	strong	.	BRD3	82	.	NM_007371	exon8	c.C1284T	p.P428P	GGCCGCGGGGGCA	.	PASS	Atlas-SNP
UAP1L1	91373	hgsc.bcm.edu	37	9	139973582	139973582	+	Silent	SNP	C	C	G	rs75127829	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	74	0	0.478873	0	C|0.965;G|0.035	0.035	strong	.	UAP1L1	46	.	NM_207309	exon4	c.C825G	p.G275G	GCAGGGCGCAGAC	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57181995	57181995	+	Missense_Mutation	SNP	C	C	T	rs3796547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	24	52	0	0.413793	0	C|0.728;T|0.272	0.272	strong	KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	NM_020722	exon8	c.C2327T	p.S776L	AGAAGTCGGAGAT	.	PASS	Atlas-SNP
DUSP13	51207	hgsc.bcm.edu	37	10	76855421	76855421	+	Silent	SNP	G	G	A	rs3740316	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	56	100	0	0.470588	0	G|0.795;A|0.205	0.205	strong	.	DUSP13	82	.	NM_001007273	exon5	c.C585T	p.I195I	CGCCTCGATGCCA	.	PASS	Atlas-SNP
ATAD3A	55210	hgsc.bcm.edu	37	1	1458150	1458150	+	Silent	SNP	T	T	C	rs1135025	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	384	346	255	1	0.901042	0.00392157	T|0.991;C|0.009	0.009	strong	.	ATAD3A	35	.	NM_018188	exon8	c.T921C	p.V307V	GGCTGTTGGGGTC	.	PASS	Atlas-SNP
TVP23C	201158	hgsc.bcm.edu	37	17	15406197	15406197	+	Missense_Mutation	SNP	A	A	T	rs12150518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	82	115	0	0.506173	0	A|0.951;T|0.049	0.049	strong	.	.	.	.	NM_145301	exon6	c.T812A	p.L271Q	GATGCCAGATGAA	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30887988	30887988	+	Silent	SNP	C	C	T	rs2249459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	48	131	0	0.436364	0	C|0.730;T|0.270	0.270	strong	.	VARS2	60	.	NM_001167734	exon13	c.C1378T	p.L460L	GACTGGCTGCAGG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379807	31379807	+	Missense_Mutation	SNP	C	C	T	rs1051798	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	62	126	1	0.984127	0.00793651	C|0.730;T|0.270	0.270	strong	.	MICA	21	.	NM_001177519	exon4	c.C697T	p.R233W	TATCCCCGGAATA	.	PASS	Atlas-SNP
MYT1	4661	hgsc.bcm.edu	37	20	62863580	62863580	+	Silent	SNP	C	C	T	rs41279352	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	56	0	0.5	0	C|0.954;T|0.046	0.046	strong	.	MYT1	152	.	NM_004535	exon19	c.C2739T	p.S913S	CAGGAGCGCATCC	.	PASS	Atlas-SNP
LCA5L	150082	hgsc.bcm.edu	37	21	40800371	40800371	+	Missense_Mutation	SNP	C	C	T	rs2837029	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	45	87	0	0.517241	0	C|0.751;T|0.249	0.249	strong	.	LCA5L	57	.	NM_152505	exon4	c.G49A	p.G17S	CCACGCCGAAGAA	.	PASS	Atlas-SNP
SMARCAD1	56916	hgsc.bcm.edu	37	4	95173928	95173928	+	Missense_Mutation	SNP	C	C	T	rs139839410	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	30	81	0	0.47619	0	C|0.992;T|0.008	0.008	strong	.	SMARCAD1	97	.	NM_001128429	exon9	c.C1051T	p.P351S	TTTAATCCAAAGA	.	PASS	Atlas-SNP
C1orf68	100129271	hgsc.bcm.edu	37	1	152692074	152692074	+	Missense_Mutation	SNP	G	G	C	rs1332500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	175	163	0	0.983146	0	G|0.655;C|0.345	0.345	strong	C1orf68,NS,carcinoma,0,1	C1orf68	19	1	NM_001024679	exon1	c.G77C	p.S26T	AGGGTAGCAATGG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9083427	9083427	+	Silent	SNP	A	A	G	rs1609453	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	43	99	0	0.40566	0	A|0.789;G|0.211	0.211	strong	.	MUC16	4315	.	NM_024690	exon1	c.T8388C	p.A2796A	AGAGCTAGCCATA	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50532588	50532588	+	Missense_Mutation	SNP	C	C	G	rs10857469	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	39	74	0	0.527027	0	C|0.906;G|0.094	0.094	strong	.	C10orf71	179	.	NM_001135196	exon3	c.C1998G	p.H666Q	GACCCACCAGCTA	.	PASS	Atlas-SNP
ADAMTS4	9507	hgsc.bcm.edu	37	1	161168189	161168189	+	Missense_Mutation	SNP	C	C	T	rs34448954	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	36	87	0	0.387097	0	C|0.946;T|0.054	0.054	strong	ADAMTS4_ENST00000367996,rectum,carcinoma,0,2	ADAMTS4	171	2	NM_005099	exon1	c.G229A	p.A77T	CAGGGGCGCCCGA	.	PASS	Atlas-SNP
PDLIM2	64236	hgsc.bcm.edu	37	8	22442661	22442661	+	Silent	SNP	A	A	G	rs2294047	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	58	143	0	0.402778	0	A|0.422;G|0.578	0.578	strong	.	PDLIM2	42	.	NM_021630	exon5	c.A1197G	p.A399A	AGAGGCAGCCATC	.	PASS	Atlas-SNP
CHAD	1101	hgsc.bcm.edu	37	17	48543154	48543154	+	Silent	SNP	G	G	A	rs2231507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	49	83	0	0.49	0	G|0.964;A|0.036	0.036	strong	CHAD,upper_leg,malignant_melanoma,-2,1	CHAD	36	1	NM_001267	exon2	c.C852T	p.P284P	GTTGGAGGGTAGC	.	PASS	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107456933	107456933	+	Silent	SNP	C	C	T	rs12347076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	90	148	0	0.502793	0	C|0.771;T|0.229	0.229	strong	.	OR13D1	42	.	NM_001004484	exon1	c.C231T	p.L77L	CCTCCTCATTATC	.	PASS	Atlas-SNP
UBOX5	22888	hgsc.bcm.edu	37	20	3090848	3090848	+	Missense_Mutation	SNP	T	T	G	rs708973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	35	66	0	0.460526	0	T|0.734;G|0.266	0.266	strong	.	UBOX5	47	.	NM_001267584	exon5	c.A1525C	p.T509P	GCAGGGTCGGCAC	.	PASS	Atlas-SNP
HNRNPH1	3187	hgsc.bcm.edu	37	5	179044053	179044053	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	367	5	348	2	0.013624	0.00574713	.	.	none	HNRPH1,NS,carcinoma,-2,3	HNRNPH1	62	3	NM_001257293	exon10	c.C1116T	p.Y372Y	GCTACCGTAAGCA	.	scavenged	Atlas-SNP
C7orf33	202865	hgsc.bcm.edu	37	7	148288135	148288135	+	Silent	SNP	C	C	T	rs111320068	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	57	89	0	0.491379	0	C|0.974;T|0.026	0.026	strong	.	C7orf33	28	.	NM_145304	exon1	c.C118T	p.L40L	CTTCGCCTGAGTG	.	PASS	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	37	21	43905887	43905887	+	Silent	SNP	C	C	T	rs2839536	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	89	103	0	0.978022	0	C|0.704;T|0.296	0.296	strong	.	RSPH1	36	.	NM_080860	exon5	c.G393A	p.A131A	CGTCTCCGCGTAT	.	PASS	Atlas-SNP
MS4A6A	64231	hgsc.bcm.edu	37	11	59945789	59945789	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	60	98	0	0.461538	0	.	.	none	.	MS4A6A	85	.	NM_001247999	exon5	c.T367C	p.F123L	TGATAAACTAAGA	.	PASS	Atlas-SNP
RETNLB	84666	hgsc.bcm.edu	37	3	108475974	108475974	+	Missense_Mutation	SNP	G	G	A	rs11708527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	36	75	0	0.521739	0	G|0.795;A|0.205	0.205	strong	RETNLB,NS,carcinoma,+1,1	RETNLB	38	1	NM_032579	exon1	c.C59T	p.P20L	CTCCCCGGGTTGA	.	PASS	Atlas-SNP
HLX	3142	hgsc.bcm.edu	37	1	221057739	221057739	+	Missense_Mutation	SNP	C	C	G	rs11578466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	81	168	0	0.473684	0	C|0.877;G|0.123	0.123	strong	.	HLX	67	.	NM_021958	exon4	c.C1160G	p.A387G	ACATGGCCCCCAG	.	PASS	Atlas-SNP
OR5D16	390144	hgsc.bcm.edu	37	11	55606302	55606302	+	Silent	SNP	G	G	T	rs6591699	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	276	276	300	2	1	0.00666667	G|0.350;T|0.650	0.650	strong	OR5D16,NS,carcinoma,+1,1	OR5D16	94	1	NM_001005496	exon1	c.G75T	p.L25L	GGAACTGCAAATT	.	scavenged	Atlas-SNP
OR13A1	79290	hgsc.bcm.edu	37	10	45799451	45799451	+	Silent	SNP	C	C	T	rs17157674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	37	59	0	0.45679	0	C|0.992;T|0.008	0.008	strong	.	OR13A1	49	.	NM_001004297	exon4	c.G420A	p.R140R	TGCGTACCGGTCA	.	PASS	Atlas-SNP
SALL3	27164	hgsc.bcm.edu	37	18	76753588	76753588	+	Missense_Mutation	SNP	A	A	G	rs7240860	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	3	3	3	1	1	0.333333	A|0.251;G|0.749	0.749	strong	SALL3,NS,carcinoma,0,1	SALL3	162	1	NM_171999	exon2	c.A1597G	p.T533A	CCGCCCACTGTCC	.	scavenged	Atlas-SNP
MMADHC	27249	hgsc.bcm.edu	37	2	150432976	150432976	+	Silent	SNP	C	C	T	rs11545261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	245	105	271	0	0.428571	0	C|0.220;T|0.780	0.780	strong	.	MMADHC	20	.	NM_015702	exon5	c.G453A	p.Q151Q	ACATGTCTGTATT	.	PASS	Atlas-SNP
TRIML2	205860	hgsc.bcm.edu	37	4	189012680	189012680	+	Silent	SNP	G	G	A	rs17881718	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	42	133	0	0.407767	0	G|0.888;A|0.112	0.112	strong	TRIML2,NS,carcinoma,0,2	TRIML2	80	2	NM_173553	exon7	c.C1011T	p.T337T	CATCTCGGTCACA	.	PASS	Atlas-SNP
PLEKHH1	57475	hgsc.bcm.edu	37	14	68022572	68022572	+	Missense_Mutation	SNP	G	G	A	rs200379117		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	263	120	256	1	0.456274	0.00390625	.	.	weak	.	PLEKHH1	118	.	NM_020715	exon3	c.G157A	p.A53T	CTGGAGGCAGAGC	.	PASS	Atlas-SNP
KPNA2	3838	hgsc.bcm.edu	37	17	66042639	66042639	+	Missense_Mutation	SNP	T	T	A	rs138669765	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	62	127	0	0.5	0	T|0.979;A|0.021	0.021	strong	.	KPNA2	55	.	NM_002266	exon11	c.T1517A	p.V506D	AAAACGTTGTACC	.	PASS	Atlas-SNP
GCFC2	6936	hgsc.bcm.edu	37	2	75923413	75923413	+	Missense_Mutation	SNP	T	T	C	rs7560262	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	66	161	2	0.485294	0.0124224	T|0.465;C|0.535	0.535	strong	C2orf3,NS,carcinoma,0,1	.	.	1	NM_003203	exon5	c.A746G	p.N249S	GATCCATTGCCAC	.	scavenged	Atlas-SNP
PRDM10	56980	hgsc.bcm.edu	37	11	129772309	129772309	+	Silent	SNP	G	G	A	rs12275633	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	115	210	0	0.537383	0	G|0.921;A|0.079	0.079	strong	.	PRDM10	120	.	NM_020228	exon22	c.C3382T	p.L1128L	GGTCCAGGGAGTC	.	PASS	Atlas-SNP
KIF20B	9585	hgsc.bcm.edu	37	10	91468925	91468925	+	Missense_Mutation	SNP	C	C	G	rs1129777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	37	107	0	0.425287	0	C|0.817;G|0.183	0.183	strong	.	KIF20B	191	.	NM_016195	exon3	c.C149G	p.A50G	TTAAGGCAAACAG	.	PASS	Atlas-SNP
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17949562	17949562	+	Silent	SNP	C	C	T	rs55693639	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	103	104	0	0.903509	0	C|0.964;T|0.036	0.036	strong	.	ARHGEF10L	219	.	NM_018125	exon12	c.C1092T	p.F364F	GTTCTTCCGCGTG	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91827264	91827264	+	Silent	SNP	C	C	T	rs2301664	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	71	102	0	0.5	0	C|0.870;T|0.130	0.130	strong	.	SV2B	98	.	NM_014848	exon12	c.C1521T	p.H507H	CGAGCACAAGTTC	.	PASS	Atlas-SNP
CDH16	1014	hgsc.bcm.edu	37	16	66948130	66948130	+	Missense_Mutation	SNP	G	G	A	rs2271023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	56	120	0	0.434109	0	A|0.053;G|0.947;T|0.000	0.053	strong	.	CDH16	91	.	NM_004062	exon7	c.C769T	p.H257Y	CCATGTGGTGCGG	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	426432	426432	+	Missense_Mutation	SNP	T	T	C	rs2071915	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	48	86	0	0.615385	0	C|0.542;N|0.001	0.542	strong	.	TMEM8A	49	.	NM_021259	exon6	c.A928G	p.I310V	GCTGGATGGTCAC	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3418391	3418391	+	Silent	SNP	C	C	T	rs4648508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	240	187	0	0.963855	0	C|0.703;T|0.297	0.297	strong	MEGF6,colon,carcinoma,0,2	MEGF6	91	2	NM_001409	exon18	c.G2283A	p.P761P	CCCCGGCGGACAC	.	PASS	Atlas-SNP
RANBP17	64901	hgsc.bcm.edu	37	5	170597190	170597190	+	Silent	SNP	G	G	A	rs36104512	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	38	150	0	0.311475	0	G|0.917;A|0.083	0.083	strong	.	RANBP17	108	.	NM_022897	exon15	c.G1767A	p.E589E	TCTAGAGACGTTC	.	PASS	Atlas-SNP
GRM7	2917	hgsc.bcm.edu	37	3	7620828	7620828	+	Silent	SNP	G	G	A	rs1485174	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	109	217	0	0.531707	0	G|0.803;A|0.197	0.197	strong	.	GRM7	223	.	NM_000844	exon8	c.G2235A	p.G745G	CAGAGGGGTTCTC	.	PASS	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74896664	74896664	+	Missense_Mutation	SNP	T	T	C	rs36152134	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	39	100	0	0.423913	0	T|0.887;C|0.113	0.113	strong	.	ECD	50	.	NM_001135752	exon14	c.A1601G	p.N534S	GACTCATTAGGCC	.	PASS	Atlas-SNP
RASSF4	83937	hgsc.bcm.edu	37	10	45478092	45478092	+	Missense_Mutation	SNP	A	A	G	rs870957	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	63	129	0	0.504	0	A|0.750;G|0.250	0.250	strong	.	RASSF4	33	.	NM_032023	exon4	c.A262G	p.R88G	ATGCCCAGACGGC	.	PASS	Atlas-SNP
ZSCAN1	284312	hgsc.bcm.edu	37	19	58549395	58549395	+	Missense_Mutation	SNP	G	G	A	rs369859464		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	12	12	0	0.5	0	.	.	weak	.	ZSCAN1	102	.	NM_182572	exon3	c.G191A	p.R64H	TGTGCCGCCAGTG	.	PASS	Atlas-SNP
FANCD2	2177	hgsc.bcm.edu	37	3	10089723	10089723	+	Silent	SNP	G	G	A	rs12330369	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	24	107	0	0.205128	0	G|0.750;A|0.250	0.250	weak	.	FANCD2	253	.	NM_001018115	exon16	c.G1401A	p.T467T	TGACACGTACTGC	.	PASS	Atlas-SNP
MICALCL	84953	hgsc.bcm.edu	37	11	12313845	12313845	+	Splice_Site	SNP	G	G	A	rs200949393	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	52	87	0	0.52	0	.	.	weak	.	MICALCL	59	.	NM_032867	exon2	c.129+1G>A	.	CCTCAGGTGAGTG	.	PASS	Atlas-SNP
FHL2	2274	hgsc.bcm.edu	37	2	105977761	105977761	+	Silent	SNP	G	G	A	rs11124029	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	41	96	0	0.525641	0	G|0.852;A|0.148	0.148	strong	.	FHL2	18	.	NM_001039492	exon7	c.C819T	p.P273P	ACAGTCGGGGCAC	.	PASS	Atlas-SNP
GRIN2D	2906	hgsc.bcm.edu	37	19	48908452	48908452	+	Silent	SNP	G	G	A	rs369747884		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	13	8	0	0.619048	0	.	.	weak	.	GRIN2D	76	.	NM_000836	exon3	c.G927A	p.S309S	GCGCTCGGCTGGC	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17086183	17086183	+	Splice_Site	SNP	T	T	G	rs61769735	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	27	207	4	0.127962	0.0193237	T|0.988;G|0.011	0.011	strong	Q13209_HUMAN,NS,carcinoma,0,6	.	.	6	NM_001271733	exon8	c.716-2A>C	.	GGACCCTTAGATG	.	scavenged	Atlas-SNP
RPRD2	23248	hgsc.bcm.edu	37	1	150445058	150445058	+	Missense_Mutation	SNP	C	C	T	rs201108869	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	76	127	0	0.575758	0	.	.	weak	.	RPRD2	189	.	NM_015203	exon11	c.C3634T	p.P1212S	GTGGGGCCATCAT	.	PASS	Atlas-SNP
PLAU	5328	hgsc.bcm.edu	37	10	75673879	75673879	+	Silent	SNP	C	C	T	rs2227568	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	18	36	0	0.486486	0	C|0.859;T|0.141	0.141	strong	.	PLAU	47	.	NM_002658	exon8	c.C822T	p.N274N	CCACAACGACATT	.	PASS	Atlas-SNP
TPST2	8459	hgsc.bcm.edu	37	22	26936766	26936766	+	Silent	SNP	G	G	A	rs58274935	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	22	32	0	0.6875	0	G|0.952;A|0.048	0.048	strong	.	TPST2	23	.	NM_001008566	exon3	c.C831T	p.V277V	CAGGGAGACACCA	.	PASS	Atlas-SNP
TNK2	10188	hgsc.bcm.edu	37	3	195595054	195595054	+	Silent	SNP	C	C	T	rs7516	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	15	43	0	0.3125	0	C|0.921;T|0.079	0.079	strong	TNK2_ENST00000381916,NS,carcinoma,0,3	TNK2	246	3	NM_001010938	exon13	c.G2304A	p.P768P	CTGGGGCGGGAGG	.	PASS	Atlas-SNP
OR5J2	282775	hgsc.bcm.edu	37	11	55944474	55944474	+	Silent	SNP	G	G	A	rs4489763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	311	140	353	2	0.450161	0.00566572	G|0.903;A|0.097	0.097	strong	OR5J2,NS,carcinoma,0,1	OR5J2	98	1	NM_001005492	exon1	c.G381A	p.V127V	CATTGTGAGTCCC	.	scavenged	Atlas-SNP
CCDC88C	440193	hgsc.bcm.edu	37	14	91773568	91773568	+	Silent	SNP	T	T	C	rs1970912	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	28	49	0	0.571429	0	C|0.517;N|0.000	0.517	strong	.	CCDC88C	192	.	NM_001080414	exon18	c.A3009G	p.L1003L	CTTCTTTAGCTAC	.	PASS	Atlas-SNP
CWC27	10283	hgsc.bcm.edu	37	5	64273018	64273018	+	Silent	SNP	G	G	A	rs1309581	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	126	251	0	0.545455	0	G|0.631;A|0.369	0.369	strong	.	CWC27	47	.	NM_005869	exon13	c.G1209A	p.T403T	TGAAACGCCTGAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910358	29910358	+	Missense_Mutation	SNP	C	C	G	rs1143146	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	144	177	0	0.979592	0	C|0.511;G|0.489	0.489	strong	.	HLA-A	89	.	NM_001242758	exon1	c.C28G	p.L10V	ACCCTCCTCCTGC	.	PASS	Atlas-SNP
GDF3	9573	hgsc.bcm.edu	37	12	7848202	7848202	+	Silent	SNP	G	G	C	rs17727707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	50	72	0	0.561798	0	G|0.951;C|0.049	0.049	strong	.	GDF3	68	.	NM_020634	exon1	c.C123G	p.P41P	CTTCTGGGGTGAA	.	PASS	Atlas-SNP
PGBD5	79605	hgsc.bcm.edu	37	1	230461079	230461079	+	Silent	SNP	G	G	A	rs2306813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	37	100	0	0.425287	0	G|0.791;N|0.000	.	strong	.	PGBD5	73	.	NM_001258311	exon6	c.C1356T	p.C452C	GTATCTGCAGATG	.	PASS	Atlas-SNP
C1orf53	388722	hgsc.bcm.edu	37	1	197874949	197874949	+	Silent	SNP	T	T	C	rs2270763	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	104	225	0	0.45614	0	T|0.659;C|0.341	0.341	strong	.	C1orf53	18	.	NM_001024594	exon2	c.T288C	p.D96D	TGTGGATCCAGCT	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539246	92539246	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	8	110	0	0.0487805	0	.	.	none	.	BTG1	30	.	NM_001731	exon1	c.C66T	p.I22I	CTTGGAGATGAAG	.	PASS	Atlas-SNP
PTPRR	5801	hgsc.bcm.edu	37	12	71139664	71139664	+	Missense_Mutation	SNP	T	T	C	rs3803036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	173	195	1	0.988571	0.00512821	T|0.322;C|0.678	0.678	strong	.	PTPRR	109	.	NM_002849	exon6	c.A941G	p.K314R	GTAGCTTTGATCT	.	PASS	Atlas-SNP
GRIN2C	2905	hgsc.bcm.edu	37	17	72838649	72838649	+	Missense_Mutation	SNP	C	C	A	rs3744215	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	72	123	0	0.45283	0	C|0.689;A|0.311	0.311	strong	GRIN2C_ENST00000293190,NS,carcinoma,0,4	GRIN2C	144	4	NM_000835	exon13	c.G3627T	p.R1209S	GGCTACCCTGCTG	.	PASS	Atlas-SNP
DCSTAMP	81501	hgsc.bcm.edu	37	8	105367121	105367121	+	Missense_Mutation	SNP	A	A	G	rs3802204	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	49	98	0	0.515789	0	A|0.886;G|0.114	0.114	strong	.	.	.	.	NM_030788	exon3	c.A1046G	p.D349G	CTCAAGATATTAT	.	PASS	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136575199	136575199	+	Silent	SNP	G	G	T	rs6719488	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	41	87	0	0.386792	0	G|0.592;T|0.408	0.408	strong	.	LCT	309	.	NM_002299	exon6	c.C1419A	p.G473G	GGCAACGCCTGGG	.	PASS	Atlas-SNP
HIST1H4B	8366	hgsc.bcm.edu	37	6	26027286	26027286	+	Silent	SNP	G	G	A	rs115249469	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	66	87	0	0.568965	0	G|0.998;A|0.002	0.002	strong	.	HIST1H4B	27	.	NM_003544	exon1	c.C195T	p.N65N	GATCACGTTCTCC	.	PASS	Atlas-SNP
CASP7	840	hgsc.bcm.edu	37	10	115457264	115457264	+	Missense_Mutation	SNP	T	T	G	rs11555408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	39	95	0	0.464286	0	T|0.889;G|0.111	0.111	strong	.	CASP7	21	.	NM_001267057	exon2	c.T236G	p.I79S	AGATGATCAGGGC	.	PASS	Atlas-SNP
ZNF568	374900	hgsc.bcm.edu	37	19	37441980	37441980	+	Missense_Mutation	SNP	A	A	G	rs1644634	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	22	43	0	0.611111	0	A|0.447;G|0.553	0.553	strong	.	ZNF568	106	.	NM_198539	exon7	c.A1925G	p.Q642R	GACACCAAGTATA	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10116508	10116508	+	Missense_Mutation	SNP	C	C	T	rs2303098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	9	32	0	0.409091	0	C|0.847;T|0.153	0.153	strong	.	COL5A3	243	.	NM_015719	exon3	c.G401A	p.R134H	AGGGGGCGGAAGG	.	PASS	Atlas-SNP
FRRS1	391059	hgsc.bcm.edu	37	1	100203648	100203648	+	Silent	SNP	C	C	T	rs7537296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	95	184	0	0.530726	0	C|0.486;T|0.514	0.514	strong	.	FRRS1	50	.	NM_001013660	exon7	c.G753A	p.Q251Q	CATCCACTGATCA	.	PASS	Atlas-SNP
PARP15	165631	hgsc.bcm.edu	37	3	122354792	122354792	+	Missense_Mutation	SNP	G	G	A	rs12489170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	58	112	0	0.471545	0	G|0.823;A|0.177	0.177	strong	.	PARP15	115	.	NM_001113523	exon12	c.G1882A	p.G628R	ACAAAGGGACGTG	.	PASS	Atlas-SNP
SUGP2	10147	hgsc.bcm.edu	37	19	19105259	19105259	+	Silent	SNP	G	G	A	rs4808897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	75	128	2	0.551471	0.015625	G|0.940;A|0.060	0.060	strong	SUGP2,NS,adenoma,0,1	SUGP2	107	1	NM_014884	exon10	c.C3165T	p.D1055D	CTGCCCGTCAGCA	.	scavenged	Atlas-SNP
INSL4	3641	hgsc.bcm.edu	37	9	5231712	5231712	+	Silent	SNP	T	T	A	rs12720	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	89	78	0	1	0	T|0.613;A|0.387	0.387	strong	INSL4,bladder,carcinoma,+2,1	INSL4	20	1	NM_002195	exon1	c.T189A	p.R63R	TGGACGTCCCAAA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512889	4512889	+	Silent	SNP	A	A	G	rs200699570	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	64	288	1	0.969697	0.00347222	A|0.986;G|0.014	0.014	strong	.	PLIN4	191	.	NM_001080400	exon3	c.T1041C	p.T347T	TAGGACAGTCTTG	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40103767	40103767	+	Missense_Mutation	SNP	G	G	T	rs17511668	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	46	67	0	0.455446	0	G|0.859;T|0.141	0.141	strong	.	N4BP2	166	.	NM_018177	exon4	c.G302T	p.S101I	CACAAAGTTTCGT	.	PASS	Atlas-SNP
NFE2L3	9603	hgsc.bcm.edu	37	7	26224668	26224668	+	Silent	SNP	C	C	T	rs61730063	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	57	135	0	0.44186	0	C|0.790;T|0.210	0.210	strong	.	NFE2L3	77	.	NM_004289	exon4	c.C1350T	p.C450C	TTATTGCACTGAC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340836	55340836	+	Missense_Mutation	SNP	A	A	G	rs45551936	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	10	22	0	0.322581	0	A|0.847;G|0.153	0.153	strong	.	KIR3DL1	174	.	NM_013289	exon7	c.A1021G	p.I341V	CTGCACATTCTGA	.	PASS	Atlas-SNP
TTLL11	158135	hgsc.bcm.edu	37	9	124855211	124855211	+	Missense_Mutation	SNP	C	C	T	rs61742319	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	14	0	0	1	.	C|0.742;T|0.258	0.258	strong	.	TTLL11	67	.	NM_001139442	exon1	c.G487A	p.A163T	CCTCAGCCGCACT	.	PASS	Atlas-SNP
DNAAF1	123872	hgsc.bcm.edu	37	16	84209738	84209738	+	Missense_Mutation	SNP	T	T	C	rs2288020	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	78	82	1	1	0.0121951	C|0.283;N|0.000	0.283	strong	DNAAF1,NS,carcinoma,0,2	DNAAF1	81	2	NM_178452	exon11	c.T1898C	p.L633S	GGGACTTGGAAAT	.	scavenged	Atlas-SNP
ASB15	142685	hgsc.bcm.edu	37	7	123277002	123277002	+	Nonsense_Mutation	SNP	T	T	A	rs140369638	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	64	82	0	0.551724	0	T|0.999;A|0.001	0.001	strong	.	ASB15	94	.	NM_080928	exon10	c.T1734A	p.Y578X	AGAGTATGATCTC	.	PASS	Atlas-SNP
POLR2D	5433	hgsc.bcm.edu	37	2	128610648	128610648	+	Silent	SNP	T	T	C	rs10210695	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	60	105	0	0.495868	0	T|0.848;C|0.152	0.152	strong	.	POLR2D	13	.	NM_004805	exon2	c.A105G	p.S35S	AACTTCTGAATTT	.	PASS	Atlas-SNP
BLM	641	hgsc.bcm.edu	37	15	91326099	91326099	+	Missense_Mutation	SNP	C	C	T	rs2227935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	70	147	0	0.492958	0	C|0.940;T|0.060	0.060	strong	.	BLM	122	.	NM_000057	exon13	c.C2603T	p.P868L	TATTACCGAAAAA	.	PASS	Atlas-SNP
ZSCAN29	146050	hgsc.bcm.edu	37	15	43653649	43653649	+	Silent	SNP	G	G	A	rs62019445	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	62	102	0	0.439716	0	G|0.943;A|0.057	0.057	strong	.	ZSCAN29	57	.	NM_152455	exon5	c.C2181T	p.I727I	TGTGTGGATTCTC	.	PASS	Atlas-SNP
KIAA1586	57691	hgsc.bcm.edu	37	6	56917520	56917520	+	Missense_Mutation	SNP	T	T	C	rs36113897	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	31	40	0	0.462687	0	T|0.952;C|0.048	0.048	strong	.	KIAA1586	59	.	NM_020931	exon4	c.T223C	p.F75L	GGTGATTTTTTGC	.	PASS	Atlas-SNP
KRT8	3856	hgsc.bcm.edu	37	12	53298769	53298769	+	Silent	SNP	A	A	G	rs1065306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	15	29	0	0.483871	0	A|0.655;G|0.345	0.345	strong	.	KRT8	41	.	NM_001256282	exon2	c.T81C	p.S27S	CATGGTAGAGGCA	.	PASS	Atlas-SNP
NAPEPLD	222236	hgsc.bcm.edu	37	7	102760511	102760511	+	Missense_Mutation	SNP	A	A	C	rs12540583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	47	118	0	0.465347	0	A|0.876;C|0.124	0.124	strong	.	NAPEPLD	49	.	NM_001122838	exon3	c.T454G	p.S152A	CACGAGAGCTAAA	.	PASS	Atlas-SNP
TRIM10	10107	hgsc.bcm.edu	37	6	30121525	30121525	+	Silent	SNP	G	G	A	rs12210298	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	65	110	0	0.448276	0	G|0.970;A|0.030	0.030	strong	.	TRIM10	65	.	NM_052828	exon8	c.C1128T	p.D376D	GCCTGAGTCCCCA	.	PASS	Atlas-SNP
PER1	5187	hgsc.bcm.edu	37	17	8053085	8053085	+	Silent	SNP	T	T	G	rs3027178	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	9	42	0	0.375	0	T|0.699;G|0.301	0.301	strong	PER1,NS,carcinoma,0,1	PER1	104	1	NM_002616	exon5	c.A639C	p.T213T	CTGAAGTGTGTAC	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135961560	135961560	+	Missense_Mutation	SNP	C	C	G	rs80321628	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	35	123	0	0.221519	0	.	.	weak	.	RBMX	149	.	NM_001164803	exon2	c.G27C	p.K9N	GAAGAGCTTTCCT	.	PASS	Atlas-SNP
NACC2	138151	hgsc.bcm.edu	37	9	138903635	138903635	+	Silent	SNP	G	G	A	rs9753	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	9	5	0	0.642857	0	G|0.844;A|0.156	0.156	strong	NACC2,NS,carcinoma,-2,1	NACC2	16	1	NM_144653	exon6	c.C1491T	p.A497A	CCGCTCGGCGTAG	.	PASS	Atlas-SNP
OR6M1	390261	hgsc.bcm.edu	37	11	123676231	123676231	+	Missense_Mutation	SNP	G	G	T	rs4936845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	63	152	0	0.463235	0	G|0.763;T|0.237	0.237	strong	OR6M1,colon,carcinoma,0,1	OR6M1	60	1	NM_001005325	exon1	c.C827A	p.T276K	ACCACTGTGATGA	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940331	144940331	+	Missense_Mutation	SNP	C	C	T	rs200585601	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	21	148	0	0.111111	0	C|0.997;T|0.003	0.003	weak	EPPK1,NS,carcinoma,0,6	EPPK1	199	6	NM_031308	exon1	c.G7091A	p.R2364Q	CCGCGCCGGTAGG	.	PASS	Atlas-SNP
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956194	18956194	+	Silent	SNP	T	T	C	rs2014931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	102	95	1	1	0.0105263	T|0.636;C|0.364	0.364	strong	MRGPRX1,caecum,carcinoma,-2,3	MRGPRX1	84	3	NM_147199	exon1	c.A138G	p.A46A	CACAACTGCGTTT	.	scavenged	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68701948	68701948	+	Silent	SNP	C	C	T	rs11228413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	94	133	0	0.516484	0	C|0.805;T|0.195	0.195	strong	IGHMBP2,colon,carcinoma,+2,3	IGHMBP2	83	3	NM_002180	exon11	c.C1554T	p.V518V	CCTCGTCAGTTTG	.	PASS	Atlas-SNP
TRIM66	9866	hgsc.bcm.edu	37	11	8662516	8662516	+	Missense_Mutation	SNP	T	T	C	rs11042023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	129	130	0	0.984733	0	T|0.470;C|0.530	0.530	strong	TRIM66,rectum,carcinoma,0,1	TRIM66	45	1	NM_014818	exon9	c.A971G	p.H324R	GAGCAGTGGGAGC	.	PASS	Atlas-SNP
ITPA	3704	hgsc.bcm.edu	37	20	3193978	3193978	+	Silent	SNP	G	G	A	rs8362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	56	122	0	0.5	0	G|0.607;A|0.393	0.393	strong	.	ITPA	16	.	NM_033453	exon3	c.G138A	p.Q46Q	GTACCAGGGGGAG	.	PASS	Atlas-SNP
CRTAP	10491	hgsc.bcm.edu	37	3	33174168	33174168	+	Silent	SNP	G	G	A	rs1135128	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	57	121	0	0.422222	0	G|0.639;A|0.361	0.361	strong	.	CRTAP	16	.	NM_006371	exon5	c.G1044A	p.S348S	CCTCTCGGATGAG	.	PASS	Atlas-SNP
RBPJ	3516	hgsc.bcm.edu	37	4	26417136	26417136	+	Silent	SNP	T	T	C	rs2270226	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	107	228	1	0.473451	0.00438596	T|0.487;C|0.513	0.513	strong	.	RBPJ	78	.	NM_005349	exon5	c.T234C	p.S78S	GGGCAGTGGATGG	.	PASS	Atlas-SNP
WSB1	26118	hgsc.bcm.edu	37	17	25639329	25639329	+	Silent	SNP	C	C	T	rs61761626	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	85	166	1	0.518293	0.0060241	C|0.994;T|0.006	0.006	strong	WSB1,NS,carcinoma,+1,1	WSB1	29	1	NM_015626	exon9	c.C1200T	p.P400P	GATGCCCACCCAA	.	scavenged	Atlas-SNP
OR6C68	403284	hgsc.bcm.edu	37	12	55887087	55887087	+	Missense_Mutation	SNP	G	G	T	rs12579181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	12	36	0	0.5	0	G|0.703;T|0.297	0.297	strong	OR6C68,NS,carcinoma,+1,1	OR6C68	36	1	NM_001005519	exon1	c.G926T	p.R309L	CATTTCGTTTAAA	.	PASS	Atlas-SNP
NXPE3	91775	hgsc.bcm.edu	37	3	101540552	101540552	+	Silent	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	63	139	0	0.508065	0	.	.	none	.	.	.	.	NM_145037	exon8	c.G1434T	p.V478V	GACCGTGGTGGTC	.	PASS	Atlas-SNP
TBC1D22B	55633	hgsc.bcm.edu	37	6	37252210	37252210	+	Silent	SNP	C	C	T	rs3818136	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	46	44	0	1	0	C|0.335;T|0.665	0.665	strong	.	TBC1D22B	37	.	NM_017772	exon6	c.C771T	p.N257N	TCGAAACGAGGAA	.	PASS	Atlas-SNP
MSX1	4487	hgsc.bcm.edu	37	4	4864582	4864582	+	Silent	SNP	G	G	T	rs369820958		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	70	100	0	0.588235	0	.	.	weak	MSX1,NS,carcinoma,+1,1	MSX1	19	1	NM_002448	exon2	c.G624T	p.S208S	CAGCTCGCTCAGC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134691496	134691496	+	Missense_Mutation	SNP	A	A	C	rs187274296	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	28	265	0	0.121212	0	A|0.993;C|0.007	0.007	strong	.	TTC40	100	.	NM_001200049	exon30	c.T4101G	p.N1367K	CCTCTCATTCTCC	.	PASS	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294377	124294377	+	Missense_Mutation	SNP	A	A	G	rs4057750	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	117	132	0	1	0	A|0.742;G|0.258	0.258	strong	OR8B4,NS,carcinoma,+1,1	OR8B4	60	1	NM_001005196	exon1	c.T391C	p.Y131H	CCATGTAGAGCAG	.	PASS	Atlas-SNP
GSTA3	2940	hgsc.bcm.edu	37	6	52767193	52767193	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	84	148	0	0.415842	0	.	.	none	.	GSTA3	21	.	NM_000847	exon4	c.A223G	p.I75V	TGGCAATGTAGTT	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086457	46086457	+	Missense_Mutation	SNP	G	G	A	rs12483730	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	265	152	211	0	0.573585	0	G|0.846;A|0.154	0.154	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.C347T	p.A116V	GGAGCCGCATACA	.	PASS	Atlas-SNP
ADCYAP1	116	hgsc.bcm.edu	37	18	909561	909561	+	Missense_Mutation	SNP	A	A	G	rs2231187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	62	99	0	0.534483	0	A|0.757;C|0.001	.	strong	ADCYAP1,NS,carcinoma,0,1	ADCYAP1	24	1	NM_001117	exon4	c.T456G	p.C152W	CAAGAAATACTTG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373334	5373334	+	Silent	SNP	A	A	G	rs5006882	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	72	209	1	0.433735	0.00478469	A|0.757;G|0.243	0.243	strong	OR51B6,NS,carcinoma,+2,1	OR51B6	53	1	NM_001004750	exon1	c.A597G	p.V199V	AGTTGTAGTTTTA	.	scavenged	Atlas-SNP
DDX58	23586	hgsc.bcm.edu	37	9	32459450	32459450	+	Silent	SNP	T	T	G	rs3205166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	63	127	0	0.492188	0	T|0.672;G|0.328	0.328	strong	.	DDX58	82	.	NM_014314	exon17	c.A2400C	p.V800V	ATCAGGTACAGGT	.	PASS	Atlas-SNP
TAS2R20	259295	hgsc.bcm.edu	37	12	11150054	11150054	+	Missense_Mutation	SNP	C	C	T	rs79420812	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	103	97	0	0.990385	0	C|0.838;T|0.162	0.162	strong	TAS2R20,NS,carcinoma,0,1	TAS2R20	17	1	NM_176889	exon1	c.G421A	p.V141I	GACAAACCAAAAA	.	PASS	Atlas-SNP
CTSH	1512	hgsc.bcm.edu	37	15	79237293	79237293	+	Missense_Mutation	SNP	C	C	T	rs2289702	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	31	37	0	0.508197	0	C|0.917;T|0.083	0.083	strong	.	CTSH	23	.	NM_004390	exon1	c.G31A	p.G11R	AGGCCCCGGCGCA	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882981	152882981	+	Silent	SNP	A	A	T	rs62637699	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	22	85	0	0.275	0	A|0.696;T|0.304	0.304	strong	IVL,colon,carcinoma,+2,2	IVL	100	2	NM_005547	exon2	c.A708T	p.P236P	GCTCCCACAGCAG	.	PASS	Atlas-SNP
COMMD2	51122	hgsc.bcm.edu	37	3	149459413	149459413	+	Silent	SNP	C	C	T	rs11549572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	251	136	213	1	0.541833	0.00469484	C|0.755;T|0.245	0.245	strong	.	COMMD2	21	.	NM_016094	exon5	c.G495A	p.L165L	TGTCTGCAGAACT	.	PASS	Atlas-SNP
SNAPC3	6619	hgsc.bcm.edu	37	9	15459821	15459821	+	Missense_Mutation	SNP	A	A	C	rs3087653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	72	95	0	0.537313	0	A|0.956;C|0.044	0.044	strong	.	SNAPC3	28	.	NM_001039697	exon9	c.A1193C	p.E398A	TGGGGGAATTCCT	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	56000451	56000451	+	Silent	SNP	G	G	A	rs11227598	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	30	70	0	0.526316	0	G|0.901;A|0.099	0.099	strong	OR5T2,colon,carcinoma,0,2	OR5T2	107	2	NM_001004746	exon1	c.C211T	p.L71L	TTGCTAGAAACAG	.	PASS	Atlas-SNP
WNT7A	7476	hgsc.bcm.edu	37	3	13896140	13896140	+	Silent	SNP	A	A	G	rs3762719	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	23	42	0	0.575	0	A|0.795;G|0.205	0.205	strong	.	WNT7A	70	.	NM_004625	exon3	c.T459C	p.S153S	GTCGGCAGAGCAG	.	PASS	Atlas-SNP
RPN1	6184	hgsc.bcm.edu	37	3	128344786	128344786	+	Silent	SNP	G	G	A	rs1126828	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	37	70	0	0.451219	0	G|0.779;A|0.221	0.221	strong	RPN1,NS,carcinoma,0,1	RPN1	39	1	NM_002950	exon7	c.C1206T	p.D402D	AAATGTGTCCAGA	.	PASS	Atlas-SNP
GTF2H3	2967	hgsc.bcm.edu	37	12	124144395	124144395	+	Silent	SNP	A	A	G	rs1051793	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	76	159	0	0.393782	0	A|0.577;G|0.423	0.423	strong	.	GTF2H3	20	.	NM_001516	exon11	c.A738G	p.P246P	ACCCCCAGTTCAT	.	PASS	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	37	4	184203990	184203990	+	Silent	SNP	C	C	T	rs17291770	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	34	74	0	0.453333	0	C|0.961;T|0.039	0.039	strong	.	WWC2	78	.	NM_024949	exon18	c.C2814T	p.D938D	TGAAGACGGGAAC	.	PASS	Atlas-SNP
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815681	23815681	+	Silent	SNP	G	G	A	rs17574213	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	78	119	0	0.557143	0	G|0.955;A|0.045	0.045	strong	.	PPARGC1A	129	.	NM_013261	exon8	c.C1425T	p.D475D	TTCGTCGTCAAAA	.	PASS	Atlas-SNP
PIH1D1	55011	hgsc.bcm.edu	37	19	49949652	49949652	+	Missense_Mutation	SNP	G	G	A	rs7462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	94	204	0	0.449761	0	G|0.723;A|0.277	0.277	strong	.	PIH1D1	23	.	NM_017916	exon9	c.C860T	p.P287L	GGCACCGGCAGAA	.	PASS	Atlas-SNP
HK2	3099	hgsc.bcm.edu	37	2	75115108	75115108	+	Silent	SNP	A	A	G	rs10194657	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	87	133	2	0.478022	0.0150376	A|0.442;C|0.004	.	strong	HK2,NS,carcinoma,0,1	HK2	85	1	NM_000189	exon16	c.A2298G	p.L766L	TGGACTACTCTTC	.	scavenged	Atlas-SNP
STK36	27148	hgsc.bcm.edu	37	2	219555262	219555262	+	Missense_Mutation	SNP	G	G	A	rs1344642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	48	102	0	0.494845	0	G|0.530;A|0.470	0.470	strong	.	STK36	111	.	NM_015690	exon14	c.G1748A	p.R583Q	CTTTGCGGAGGGA	.	PASS	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133975283	133975283	+	Missense_Mutation	SNP	G	G	A	rs2069561	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	219	188	0	0.995455	0	G|0.642;A|0.358	0.358	strong	TG,NS,carcinoma,0,1	TG	416	1	NM_003235	exon29	c.G5512A	p.D1838N	AGAAAAGACACAG	.	PASS	Atlas-SNP
MED17	9440	hgsc.bcm.edu	37	11	93529674	93529674	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	4	55	0	0.0481928	0	.	.	none	.	MED17	37	.	NM_004268	exon7	c.C1111T	p.L371L	TATGTCCTAGAGC	.	PASS	Atlas-SNP
USP17L7	392197	hgsc.bcm.edu	37	8	11990882	11990882	+	Missense_Mutation	SNP	C	C	T	rs9720235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	6	6	5	0	1	0	C|0.499;T|0.501	0.501	strong	.	.	.	.	NM_001256869	exon1	c.G637A	p.V213I	CTGAAACGCCGTG	.	PASS	Atlas-SNP
PRSS55	203074	hgsc.bcm.edu	37	8	10383138	10383138	+	Missense_Mutation	SNP	G	G	A	rs35102108	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	53	94	0	0.552083	0	G|0.834;A|0.166	0.166	strong	.	PRSS55	67	.	NM_001197020	exon1	c.G43A	p.G15R	GTCACGGGAACTC	.	PASS	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	37	17	48628160	48628160	+	Missense_Mutation	SNP	A	A	G	rs62621401	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	55	116	0	0.416667	0	A|0.956;G|0.044	0.044	strong	.	SPATA20	59	.	NM_022827	exon11	c.A1265G	p.K422R	CGGTCAAAGAGGT	.	PASS	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102477395	102477395	+	Missense_Mutation	SNP	A	A	G	rs1784423	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	136	126	0	0.985507	0	G|0.400;N|0.000	0.400	strong	.	MMP20	52	.	NM_004771	exon6	c.T824C	p.V275A	AGGAATACTTTCC	.	PASS	Atlas-SNP
ESRP1	54845	hgsc.bcm.edu	37	8	95680229	95680229	+	Silent	SNP	C	C	T	rs1549466	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	61	118	0	0.442029	0	C|0.648;T|0.352	0.352	strong	ESRP1_ENST00000433389,NS,carcinoma,+2,2	ESRP1	148	2	NM_001122827	exon10	c.C984T	p.V328V	CATTGTCCGCATG	.	PASS	Atlas-SNP
FBXL19	54620	hgsc.bcm.edu	37	16	30936081	30936081	+	Missense_Mutation	SNP	G	G	A	rs35675346	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	16	38	0	0.4	0	G|0.772;A|0.228	0.228	strong	.	FBXL19	74	.	NM_001099784	exon1	c.G28A	p.E10K	AAGGGGGAATCTG	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11000848	11000848	+	Missense_Mutation	SNP	G	G	C	rs4774	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	20	51	0	0.425532	0	G|0.737;C|0.263	0.263	strong	CIITA_ENST00000324288,NS,carcinoma,0,1	CIITA	92	1	NM_000246	exon11	c.G1499C	p.G500A	TAGACGGCTTCGA	.	PASS	Atlas-SNP
ACSBG1	23205	hgsc.bcm.edu	37	15	78466127	78466127	+	Missense_Mutation	SNP	T	T	C	rs2304824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	49	107	0	0.422414	0	T|0.468;C|0.532	0.532	strong	.	ACSBG1	79	.	NM_015162	exon13	c.A1897G	p.M633V	ACTCCATAGCTTG	.	PASS	Atlas-SNP
SPOCD1	90853	hgsc.bcm.edu	37	1	32279629	32279629	+	Missense_Mutation	SNP	G	G	A	rs6669563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	6	70	0	0.0540541	0	G|0.624;A|0.376	0.376	strong	SPOCD1,NS,carcinoma,0,2	SPOCD1	109	2	NM_144569	exon2	c.C1306T	p.R436W	TGCCCCGGTCTTG	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78854223	78854223	+	Silent	SNP	A	A	G	rs2289759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	48	130	0	0.436364	0	A|0.768;G|0.232	0.232	strong	.	RPTOR	122	.	NM_020761	exon14	c.A1518G	p.Q506Q	GTGCCAAGCGGAC	.	PASS	Atlas-SNP
ENPP5	59084	hgsc.bcm.edu	37	6	46135984	46135984	+	Missense_Mutation	SNP	G	G	T	rs3806995	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	25	56	0	0.396825	0	G|0.573;T|0.427	0.427	strong	.	ENPP5	44	.	NM_021572	exon2	c.C16A	p.L6I	CCAAGAGAAATTT	.	PASS	Atlas-SNP
ABCG8	64241	hgsc.bcm.edu	37	2	44079606	44079606	+	Silent	SNP	G	G	A	rs9282575	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	36	54	0	0.529412	0	G|0.949;A|0.051	0.051	strong	.	ABCG8	98	.	NM_022437	exon5	c.G675A	p.V225V	TGGGGTGCAGCTC	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637046	248637046	+	Missense_Mutation	SNP	G	G	A	rs148025314	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	490	164	480	0	0.334694	0	G|0.744;A|0.256	0.256	strong	.	OR2T3	79	.	NM_001005495	exon1	c.G395A	p.C132Y	CTGTTTGCAGACC	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44143153	44143153	+	Missense_Mutation	SNP	C	C	T	rs36086089	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	23	60	0	0.45098	0	C|0.919;T|0.081	0.081	strong	.	LOXHD1	367	.	NM_144612	exon18	c.G2473A	p.V825M	CACCCACATCTCC	.	PASS	Atlas-SNP
CYP2C18	1562	hgsc.bcm.edu	37	10	96447920	96447920	+	Missense_Mutation	SNP	C	C	T	rs117111102	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	105	217	0	0.458515	0	C|0.990;T|0.010	0.010	strong	.	CYP2C18	79	.	NM_000772	exon3	c.C370T	p.R124W	GAGATCCGGCGTT	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167585654	167585654	+	Missense_Mutation	SNP	G	G	A	rs142318145	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	14	145	0	0.152174	0	G|0.982;A|0.018	0.018	strong	.	TCP10L2	41	.	NM_001145121	exon2	c.G22A	p.A8T	CTCGAGGCCAGGG	.	PASS	Atlas-SNP
PHF2	5253	hgsc.bcm.edu	37	9	96407983	96407983	+	Silent	SNP	C	C	T	rs9695734	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	37	44	0	1	0	C|0.853;T|0.147	0.147	strong	PHF2,NS,carcinoma,0,1	PHF2	113	1	NM_005392	exon4	c.C372T	p.T124T	CTTCACCGAGCCC	.	PASS	Atlas-SNP
PCDHAC1	56135	hgsc.bcm.edu	37	5	140307284	140307284	+	Silent	SNP	G	G	A	rs155361	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	39	74	0	0.423913	0	G|0.421;A|0.579	0.579	strong	.	PCDHAC1	141	.	NM_031882	exon1	c.G807A	p.Q269Q	AGTCCAGTACTCC	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151165678	151165678	+	Silent	SNP	T	T	C	rs9871952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	173	180	0	0.994253	0	T|0.213;C|0.787	0.787	strong	.	IGSF10	279	.	NM_178822	exon4	c.A2091G	p.Q697Q	ACGGAGTTGTGCA	.	PASS	Atlas-SNP
TNNT1	7138	hgsc.bcm.edu	37	19	55658387	55658387	+	Missense_Mutation	SNP	T	T	C	rs112562759	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	87	129	0	0.524096	0	T|0.942;C|0.058	0.058	strong	.	TNNT1	28	.	NM_001126132	exon3	c.A35G	p.E12G	GGCTGCTCCCTGC	.	PASS	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	37	11	61511133	61511133	+	Silent	SNP	G	G	A	rs3741251	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	10	11	0	0.833333	0	G|0.868;A|0.132	0.132	strong	.	DAGLA	109	.	NM_006133	exon20	c.G2301A	p.A767A	GCTGGCGGCGGAG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1013987	1013987	+	Missense_Mutation	SNP	G	G	A	rs10902268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	41	54	0	0.455556	0	G|0.877;A|0.123	0.123	strong	.	MUC6	408	.	NM_005961	exon32	c.C7054T	p.R2352W	GCTCCCGCACACT	.	PASS	Atlas-SNP
C3orf18	51161	hgsc.bcm.edu	37	3	50598396	50598396	+	Silent	SNP	G	G	A	rs41291736	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	74	109	0	0.528571	0	G|0.908;A|0.092	0.092	strong	.	C3orf18	12	.	NM_016210	exon5	c.C360T	p.D120D	GGCGGCGTCCCGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513126	195513126	+	Silent	SNP	G	G	A	rs62282488	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	478	120	673	1	0.251046	0.00148588	G|0.897;A|0.103	0.103	strong	.	MUC4	1505	.	NM_018406	exon2	c.C5325T	p.T1775T	AAGTGGGGTGGCG	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79169641	79169641	+	Silent	SNP	G	G	A	rs61741559	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	23	69	0	0.45098	0	G|0.907;A|0.093	0.093	strong	.	AZI1	145	.	NM_014984	exon16	c.C2010T	p.H670H	CAGCTCGTGCTGC	.	PASS	Atlas-SNP
FBXW8	26259	hgsc.bcm.edu	37	12	117402583	117402583	+	Missense_Mutation	SNP	G	G	C	rs141777878	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	47	93	0	0.566265	0	G|0.999;C|0.001	0.001	strong	.	FBXW8	53	.	NM_153348	exon5	c.G759C	p.E253D	CGAGGAGGATGAG	.	PASS	Atlas-SNP
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257296	114257296	+	Missense_Mutation	SNP	A	A	G	rs199845792	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	317	58	242	1	0.182965	0.00413223	A|0.985;G|0.015	0.015	strong	FOXD4L1,colon,carcinoma,-2,3	FOXD4L1	48	3	NM_012184	exon1	c.A463G	p.I155V	AACAGCATCCGCC	.	scavenged	Atlas-SNP
ZNF385D	79750	hgsc.bcm.edu	37	3	21552486	21552486	+	Silent	SNP	C	C	T	rs150360612		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	5	196	0	0.0285714	0	.	.	weak	ZNF385D,caecum,carcinoma,0,2	ZNF385D	93	2	NM_024697	exon4	c.G306A	p.T102T	ATGTTTCGTGCCT	.	scavenged	Atlas-SNP
WSCD1	23302	hgsc.bcm.edu	37	17	6023792	6023792	+	Silent	SNP	C	C	T	rs16955477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	45	85	0	0.542169	0	C|0.974;T|0.026	0.026	strong	.	WSCD1	84	.	NM_015253	exon9	c.C1539T	p.S513S	TGTGAGCGAGGAG	.	PASS	Atlas-SNP
SPRR4	163778	hgsc.bcm.edu	37	1	152944594	152944594	+	Silent	SNP	C	C	T	rs3170863	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	162	168	0	0.987805	0	C|0.355;T|0.645	0.645	strong	.	SPRR4	8	.	NM_173080	exon2	c.C228T	p.S76S	CAAGAGCAAACAG	.	PASS	Atlas-SNP
UBR1	197131	hgsc.bcm.edu	37	15	43299467	43299467	+	Missense_Mutation	SNP	A	A	C	rs141543407	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	37	83	0	0.536232	0	A|0.999;C|0.001	0.001	strong	.	UBR1	124	.	NM_174916	exon30	c.T3225G	p.S1075R	GTAGTCACTGACT	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592120	1592120	+	Missense_Mutation	SNP	G	G	T	rs1135201	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	18	601	0	0.818182	0	G|0.744;T|0.256	0.256	strong	SIRPB1_ENST00000279477,NS,carcinoma,0,1	SIRPB1	83	1	NM_001135844	exon2	c.C316A	p.R106S	TGATGCGGATGGA	.	scavenged	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882610	152882610	+	Missense_Mutation	SNP	A	A	G	rs2229496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	48	99	0	0.489796	0	A|0.668;G|0.332	0.332	strong	.	IVL	100	.	NM_005547	exon2	c.A337G	p.T113A	GAGAAAACACAAA	.	PASS	Atlas-SNP
XKR9	389668	hgsc.bcm.edu	37	8	71593425	71593425	+	Silent	SNP	G	G	A	rs6991329	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	252	259	0	0.988235	0	G|0.625;A|0.375	0.375	strong	.	XKR9	43	.	NM_001011720	exon3	c.G132A	p.A44A	TTTAGCGTTAAGC	.	PASS	Atlas-SNP
GRID2IP	392862	hgsc.bcm.edu	37	7	6591008	6591008	+	Silent	SNP	C	C	T	rs73059373	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	58	46	2	0.966667	0.0434783	C|0.859;T|0.141	0.141	strong	GRID2IP_ENST00000457091,NS,carcinoma,0,2	GRID2IP	82	2	NM_001145118	exon1	c.G60A	p.R20R	ACCTAGCCGGAAG	.	scavenged	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240371469	240371469	+	Silent	SNP	C	C	T	rs199920451		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	6	74	8	0.0909091	0.108108	C|0.999;T|0.001	0.001	weak	FMN2,NS,carcinoma,0,1	FMN2	451	1	NM_020066	exon5	c.C3357T	p.P1119P	CATACCCCCTCCT	.	scavenged	Atlas-SNP
FCRL4	83417	hgsc.bcm.edu	37	1	157559122	157559122	+	Missense_Mutation	SNP	C	C	T	rs11582663	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	394	202	384	0	0.51269	0	C|0.911;T|0.089	0.089	strong	.	FCRL4	95	.	NM_031282	exon3	c.G179A	p.R60Q	TAGTGCCGATGAT	.	PASS	Atlas-SNP
XRCC3	7517	hgsc.bcm.edu	37	14	104165753	104165753	+	Missense_Mutation	SNP	G	G	A	rs861539	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	60	117	0	0.521739	0	G|0.729;A|0.271	0.271	strong	XRCC3,NS,carcinoma,0,1	XRCC3	16	1	NM_005432	exon8	c.C722T	p.T241M	CGCAGCGTGGCCC	.	PASS	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20622975	20622975	+	Missense_Mutation	SNP	G	G	A	rs1443547	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	10	6	25	0	0.6	0	G|0.607;A|0.393	0.393	strong	.	SLC6A5	151	.	NM_004211	exon2	c.G304A	p.G102S	GCGCAAGGCGCGC	.	PASS	Atlas-SNP
HEPN1	641654	hgsc.bcm.edu	37	11	124789828	124789828	+	Missense_Mutation	SNP	A	A	T	rs78859654	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	96	163	1	0.477612	0.00613497	A|0.939;T|0.061	0.061	strong	HEPN1,NS,haematopoietic_neoplasm,0,1	HEPN1	11	1	NM_001037558	exon1	c.A182T	p.H61L	ACTGCCACTCCTA	.	scavenged	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141267573	141267573	+	Silent	SNP	G	G	A	rs35821928	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	85	154	0	0.559211	0	G|0.946;A|0.054	0.054	strong	.	LRP1B	1315	.	NM_018557	exon52	c.C8322T	p.C2774C	GGGCACGCAGGCA	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786230	75786230	+	Silent	SNP	C	C	T	rs2118755	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	42	48	0	0.677419	0	C|0.620;T|0.380	0.380	strong	ZNF717,NS,carcinoma,0,1	ZNF717	160	1	NM_001128223	exon5	c.G2544A	p.R848R	AGTTTTCCTACAT	.	scavenged	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38956839	38956839	+	Silent	SNP	C	C	T	rs2228070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	46	53	0	0.597403	0	C|0.798;T|0.202	0.202	strong	.	RYR1	708	.	NM_001042723	exon24	c.C2979T	p.N993N	GCACAACGTGTGG	.	PASS	Atlas-SNP
CXorf58	254158	hgsc.bcm.edu	37	X	23928489	23928489	+	Missense_Mutation	SNP	C	C	T	rs2707164	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	94	102	0	1	0	0|0.003;T|0.491	0.491	strong	.	CXorf58	53	.	NM_152761	exon2	c.C70T	p.R24C	AAAGTTCGCAGAG	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46352122	46352122	+	Silent	SNP	A	A	G	rs2303014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	72	124	0	0.493151	0	A|0.892;G|0.108	0.108	strong	SYMPK,colon,carcinoma,-2,1	SYMPK	104	1	NM_004819	exon6	c.T312C	p.I104I	CAACTCAATGTCT	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51225132	51225132	+	Silent	SNP	G	G	T	rs2073349	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	94	184	0	0.423423	0	G|0.635;T|0.365	0.365	strong	.	NIN	475	.	NM_020921	exon18	c.C2616A	p.A872A	CTCCTGGGCTTCC	.	PASS	Atlas-SNP
MS4A4A	51338	hgsc.bcm.edu	37	11	60070176	60070176	+	Missense_Mutation	SNP	A	A	G	rs6591561	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	97	166	0	0.477833	0	A|0.685;G|0.315	0.315	strong	.	MS4A4A	76	.	NM_148975	exon5	c.A532G	p.M178V	GGGACTATGTCCA	.	PASS	Atlas-SNP
AZU1	566	hgsc.bcm.edu	37	19	831865	831865	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	30	41	0	0.447761	0	.	.	none	.	AZU1	31	.	NM_001700	exon5	c.G744A	p.P248P	GGGACCGGGGCCA	.	PASS	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39871135	39871135	+	Silent	SNP	C	C	T	rs2001923	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	74	140	1	0.578125	0.00714286	C|0.932;T|0.068	0.068	strong	IDO2_ENST00000502986,trunk,malignant_melanoma,+1,1	IDO2	78	1	NM_194294	exon10	c.C810T	p.S270S	AGTTTCCCAAGAG	.	scavenged	Atlas-SNP
LPPR1	0	hgsc.bcm.edu	37	9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	rs41296085	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	99	214	1	0.478261	0.0046729	T|0.990;G|0.010	0.010	strong	.	.	.	.	NM_207299	exon2	c.T34G	p.S12A	AGTTATTCCATCA	.	PASS	Atlas-SNP
PSMD5	5711	hgsc.bcm.edu	37	9	123583192	123583192	+	Silent	SNP	A	A	G	rs1060817	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	33	67	0	0.515625	0	A|0.532;G|0.468	0.468	strong	.	PSMD5	34	.	NM_005047	exon9	c.T1182C	p.D394D	CAGTGGATCCCGA	.	PASS	Atlas-SNP
PET112	5188	hgsc.bcm.edu	37	4	152609826	152609826	+	Silent	SNP	A	A	C	rs62327344	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	74	159	0	0.445783	0	A|0.977;C|0.023	0.023	strong	PET112,NS,carcinoma,0,1	PET112	43	1	NM_004564	exon10	c.T1287G	p.T429T	CAGAAAAGTGTTG	.	PASS	Atlas-SNP
IGF2BP2	10644	hgsc.bcm.edu	37	3	185542653	185542653	+	Silent	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	81	132	0	0.433155	0	.	.	none	.	IGF2BP2	69	.	NM_001007225	exon1	c.A96T	p.G32G	GACCTGTCCCGCC	.	PASS	Atlas-SNP
HSD17B12	51144	hgsc.bcm.edu	37	11	43702530	43702530	+	Silent	SNP	A	A	G	rs56168061	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	21	43	0	0.411765	0	A|0.873;G|0.127	0.127	strong	HSD17B12,NS,carcinoma,0,1	HSD17B12	25	1	NM_016142	exon1	c.A153G	p.E51E	CGGAGAATGGGCA	.	PASS	Atlas-SNP
TBC1D14	57533	hgsc.bcm.edu	37	4	7006636	7006636	+	Missense_Mutation	SNP	G	G	C	rs11731231	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	27	62	0	0.473684	0	G|0.997;C|0.003	0.003	strong	.	TBC1D14	110	.	NM_001113361	exon8	c.G1336C	p.E446Q	GGCTCTGAAGTGG	.	PASS	Atlas-SNP
KIF15	56992	hgsc.bcm.edu	37	3	44884647	44884647	+	Missense_Mutation	SNP	C	C	A	rs3804583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	31	34	0	0.516667	0	C|0.543;A|0.457	0.457	strong	.	KIF15	103	.	NM_020242	exon30	c.C3616A	p.L1206M	CTACGCCTGGAAA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168099738	168099738	+	Silent	SNP	T	T	C	rs10497323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	258	115	260	0	0.445736	0	T|0.689;C|0.311	0.311	strong	.	XIRP2	914	.	NM_152381	exon9	c.T1836C	p.G612G	TGGTGGTGATGTG	.	PASS	Atlas-SNP
MRPL19	9801	hgsc.bcm.edu	37	2	75882399	75882399	+	Silent	SNP	G	G	A	rs17689863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	55	158	0	0.357143	0	G|0.829;A|0.171	0.171	strong	.	MRPL19	21	.	NM_014763	exon6	c.G867A	p.S289S	AGCGTCGAAAAGG	.	PASS	Atlas-SNP
CDK7	1022	hgsc.bcm.edu	37	5	68531253	68531253	+	Silent	SNP	C	C	T	rs2972388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	248	248	295	2	1	0.00677966	C|0.407;T|0.593	0.593	strong	.	CDK7	48	.	NM_001799	exon2	c.C99T	p.N33N	TAAGAACACCAAC	.	PASS	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	37	5	96124330	96124330	+	Missense_Mutation	SNP	T	T	C	rs30187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	182	168	0	0.98913	0	C|0.606;N|0.001	0.606	strong	.	ERAP1	59	.	NM_001198541	exon11	c.A1583G	p.K528R	AAACCCTTCTGCA	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16281007	16281007	+	Missense_Mutation	SNP	A	A	G	rs12931472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	62	44	0	1	0	A|0.599;G|0.400	0.400	strong	.	ABCC6	110	.	NM_001171	exon14	c.T1841C	p.V614A	TCTACGACACCAG	.	PASS	Atlas-SNP
ASMTL	8623	hgsc.bcm.edu	37	X	1537881	1537881	+	Missense_Mutation	SNP	C	C	T	rs4503285	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	56	71	0	0.543689	0	C|0.757;T|0.243	0.243	strong	.	ASMTL	56	.	NM_004192	exon10	c.G1372A	p.V458M	CTCCCACGTCGCA	.	PASS	Atlas-SNP
RAD50	10111	hgsc.bcm.edu	37	5	131924538	131924538	+	Missense_Mutation	SNP	A	A	G	rs200017020	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	95	182	0	0.545977	0	A|1.000;G|0.000	0.000	strong	.	RAD50	246	.	NM_005732	exon8	c.A1211G	p.Q404R	AGAGACAAGAAGG	.	PASS	Atlas-SNP
METTL16	79066	hgsc.bcm.edu	37	17	2323517	2323517	+	Missense_Mutation	SNP	C	C	T	rs17834783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	20	70	0	0.30303	0	C|0.956;T|0.044	0.044	strong	.	METTL16	75	.	NM_024086	exon10	c.G1436A	p.S479N	TGACAACTTTCCA	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373006	5373006	+	Missense_Mutation	SNP	T	T	C	rs7483122	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	58	168	0	0.371795	0	T|0.768;C|0.232	0.232	strong	.	OR51B6	53	.	NM_001004750	exon1	c.T269C	p.I90T	GGGAGATTGGCCA	.	PASS	Atlas-SNP
FHOD1	29109	hgsc.bcm.edu	37	16	67268008	67268008	+	Missense_Mutation	SNP	G	G	A	rs77958237	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	57	147	0	0.448819	0	G|0.958;A|0.042	0.042	strong	.	FHOD1	86	.	NM_013241	exon13	c.C1598T	p.P533L	CGGGTAGGGAGCT	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939674	12939674	+	Silent	SNP	C	C	G	rs72474510	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	4	88	0	0.0430108	0	C|0.879;G|0.121	0.121	strong	PRAMEF4,NS,carcinoma,0,2	PRAMEF4	62	2	NM_001009611	exon4	c.G1128C	p.L376L	GCGGCTCAGGGCA	.	scavenged	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361129	107361129	+	Missense_Mutation	SNP	C	C	T	rs4117966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	376	184	327	0	0.489362	0	C|0.726;T|0.274	0.274	strong	.	OR13C5	60	.	NM_001004482	exon1	c.G566A	p.C189Y	TCAGCACAGGCCA	.	PASS	Atlas-SNP
C20orf26	26074	hgsc.bcm.edu	37	20	20144772	20144772	+	Missense_Mutation	SNP	G	G	A	rs6081901	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	78	91	0	1	0	G|0.482;A|0.518	0.518	strong	.	C20orf26	188	.	NM_015585	exon11	c.G1105A	p.V369I	TCGCTCGTACTGC	.	PASS	Atlas-SNP
MUC20	200958	hgsc.bcm.edu	37	3	195453257	195453257	+	Missense_Mutation	SNP	G	G	A	rs3828406	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	48	151	0	0.309677	0	G|0.643;A|0.357	0.357	strong	.	MUC20	84	.	NM_152673	exon3	c.G1270A	p.A424T	GACATCGCAACCA	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79634774	79634774	+	Missense_Mutation	SNP	A	A	T	rs61742303	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	15	32	0	0.6	0	A|0.867;T|0.133	0.133	strong	.	CCDC137	27	.	NM_199287	exon2	c.A150T	p.K50N	GAAGAAAGTGAAC	.	PASS	Atlas-SNP
OR4C46	119749	hgsc.bcm.edu	37	11	51515912	51515912	+	Missense_Mutation	SNP	C	C	T	rs77689730	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	2	165	0	0.0136054	0	C|0.864;T|0.136	0.136	strong	OR4C46,NS,carcinoma,-2,1	OR4C46	96	1	NM_001004703	exon1	c.C631T	p.L211F	TTTGCCCTCCTGC	.	scavenged	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39620399	39620399	+	Silent	SNP	C	C	T	rs12948056	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	69	129	0	0.448052	0	C|0.683;N|0.000	.	strong	KRT32,rectum,carcinoma,0,1	KRT32	57	1	NM_002278	exon5	c.G927A	p.Q309Q	GTCTGACTGGTAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9060085	9060085	+	Missense_Mutation	SNP	C	C	T	rs4804382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	95	119	0	0.59375	0	C|0.786;T|0.214	0.214	strong	.	MUC16	4315	.	NM_024690	exon3	c.G27361A	p.A9121T	TAAGAGCGGTCAT	.	PASS	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	37	2	133540176	133540176	+	Missense_Mutation	SNP	A	A	G	rs2278752	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	29	104	0	0.333333	0	A|0.931;G|0.069	0.069	strong	.	NCKAP5	322	.	NM_207363	exon14	c.T4208C	p.V1403A	CCAAGTACAGCCA	.	PASS	Atlas-SNP
BCAS4	55653	hgsc.bcm.edu	37	20	49411698	49411698	+	Missense_Mutation	SNP	G	G	T	rs2272962	bycluster;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	8	13	0	0.421053	0	G|0.867;T|0.133	0.133	strong	.	BCAS4	41	.	NM_198799	exon1	c.G168T	p.E56D	CCCCGAGCCTGGG	.	PASS	Atlas-SNP
ATP13A2	23400	hgsc.bcm.edu	37	1	17314702	17314702	+	Silent	SNP	C	C	T	rs3738815	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	135	92	0	0.964286	0	C|0.770;T|0.230	0.230	strong	ATP13A2,NS,carcinoma,-1,1	ATP13A2	85	1	NM_022089	exon25	c.G2790A	p.S930S	GCTGAACGAAGTG	.	PASS	Atlas-SNP
CCDC146	57639	hgsc.bcm.edu	37	7	76871113	76871113	+	Silent	SNP	A	A	G	rs17230060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	277	126	246	0	0.454874	0	A|0.896;G|0.104	0.104	strong	CCDC146,NS,carcinoma,0,1	CCDC146	87	1	NM_020879	exon4	c.A345G	p.A115A	AGAAGCATTCTCC	.	PASS	Atlas-SNP
HOXD1	3231	hgsc.bcm.edu	37	2	177054769	177054769	+	Missense_Mutation	SNP	G	G	A	rs6710142	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	68	129	0	0.515152	0	G|0.768;A|0.232	0.232	strong	.	HOXD1	33	.	NM_024501	exon2	c.G886A	p.A296T	GCCACGGCCATTC	.	PASS	Atlas-SNP
PSCA	8000	hgsc.bcm.edu	37	8	143763490	143763490	+	Silent	SNP	T	T	C	rs2978982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	25	57	0	0.342466	0	T|0.576;C|0.424	0.424	strong	.	PSCA	9	.	NM_005672	exon3	c.T285C	p.A95A	GGCTGCTGCCATC	.	PASS	Atlas-SNP
GLYATL3	389396	hgsc.bcm.edu	37	6	49494241	49494241	+	Missense_Mutation	SNP	A	A	G	rs9367359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	160	162	1	0.993789	0.00617284	A|0.510;G|0.490	0.490	strong	.	GLYATL3	19	.	NM_001010904	exon6	c.A481G	p.N161D	GTTGCCAATGCGG	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101778265	101778265	+	Missense_Mutation	SNP	G	G	T	rs2297603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	37	60	0	0.474359	0	G|0.909;T|0.091	0.091	strong	COL15A1,brain,glioma,0,1	COL15A1	211	1	NM_001855	exon11	c.G1511T	p.G504V	GTCCTGGTGATGA	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135430483	135430483	+	Missense_Mutation	SNP	T	T	C	rs912002	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	75	69	0	0.974026	0	0|0.015;C|0.478	0.478	strong	.	GPR112	459	.	NM_153834	exon6	c.T4618C	p.S1540P	AAATCTTCTAAAA	.	PASS	Atlas-SNP
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	65	203	0	0.384615	0	C|0.681;T|0.319	0.319	strong	C16orf73_ENST00000412554,NS,carcinoma,-1,2	.	.	2	NM_001163560	exon10	c.G831A	p.T277T	AACATTCGTTTCT	.	PASS	Atlas-SNP
SPINK8	646424	hgsc.bcm.edu	37	3	48360992	48360992	+	Missense_Mutation	SNP	T	T	G	rs11718350	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	100	84	0	0.990099	0	T|0.820;G|0.180	0.180	strong	.	SPINK8	5	.	NM_001080525	exon3	c.A234C	p.K78N	CAGAATTTTGGAG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228465346	228465346	+	Missense_Mutation	SNP	A	A	G	rs493945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	36	75	0	0.486486	0	A|0.659;G|0.341	0.341	strong	.	OBSCN	2142	.	NM_001271223	exon29	c.A8020G	p.N2674D	ACTGACAACGTGC	.	PASS	Atlas-SNP
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	Silent	SNP	G	G	A	rs1047057	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	100	84	0	0.980392	0	G|0.609;A|0.391	0.391	strong	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	NM_001144915	exon17	c.C2107T	p.L703L	CAGCCAGTACGCA	.	PASS	Atlas-SNP
PINX1	54984	hgsc.bcm.edu	37	8	10623240	10623240	+	Missense_Mutation	SNP	T	T	C	rs17711777	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	24	83	0	0.289157	0	T|0.963;C|0.037	0.037	strong	.	PINX1	38	.	NM_017884	exon7	c.A658G	p.T220A	TACCTGTGGCCTC	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129242515	129242515	+	Silent	SNP	G	G	A	rs11371	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	65	83	0	1	0	G|0.667;A|0.333	0.333	strong	.	DOCK1	188	.	NM_001380	exon50	c.G5322A	p.R1774R	ACCAAGGGCCAAG	.	PASS	Atlas-SNP
FCN1	2219	hgsc.bcm.edu	37	9	137804360	137804360	+	Silent	SNP	A	A	G	rs2274845	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	73	0	1	0	A|0.323;G|0.677	0.677	strong	.	FCN1	62	.	NM_002003	exon7	c.T570C	p.N190N	GTTGTCATTCCCC	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	37	18	21119777	21119777	+	Silent	SNP	G	G	A	rs1140458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	49	117	0	0.471154	0	T|0.094;G|0.438;C|0.101;A|0.366	0.366	strong	NPC1,NS,carcinoma,0,1	NPC1	114	1	NM_000271	exon18	c.C2793T	p.N931N	TGACTAGTTGTCC	.	PASS	Atlas-SNP
VPS8	23355	hgsc.bcm.edu	37	3	184700426	184700426	+	Missense_Mutation	SNP	C	C	T	rs11555405	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	235	114	183	0	0.485106	0	C|0.726;T|0.274	0.274	strong	.	VPS8	109	.	NM_001009921	exon40	c.C3493T	p.H1165Y	CATCTACACTCTG	.	PASS	Atlas-SNP
ATAD3C	219293	hgsc.bcm.edu	37	1	1387764	1387764	+	Missense_Mutation	SNP	G	G	A	rs9793256	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	306	287	260	2	0.937908	0.00769231	G|0.744;A|0.256	0.256	strong	.	ATAD3C	23	.	NM_001039211	exon3	c.G172A	p.G58R	TTGTTTGGGGAAG	.	PASS	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	37	1	184764681	184764681	+	Silent	SNP	G	G	A	rs35545276	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	27	55	0	0.482143	0	G|0.954;A|0.046	0.046	strong	.	FAM129A	98	.	NM_052966	exon14	c.C2217T	p.H739H	GGGAACGTGGCTC	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139371342	139371342	+	Silent	SNP	G	G	A	rs11999525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	18	51	0	0.545455	0	G|0.849;A|0.151	0.151	strong	SEC16A_NM_014866.1,NS,carcinoma,0,2	SEC16A	249	2	NM_014866	exon3	c.C726T	p.P242P	GGCACAGGGCACC	.	PASS	Atlas-SNP
GLS2	27165	hgsc.bcm.edu	37	12	56865338	56865338	+	Missense_Mutation	SNP	A	A	G	rs2657879	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	55	81	0	0.518868	0	A|0.864;G|0.136	0.136	strong	.	GLS2	42	.	NM_013267	exon18	c.T1742C	p.L581P	TCAGAGAGTGTGT	.	PASS	Atlas-SNP
BHLHE40	8553	hgsc.bcm.edu	37	3	5024771	5024771	+	Silent	SNP	T	T	C	rs908078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	20	55	0	0.333333	0	T|0.855;C|0.145	0.145	strong	.	BHLHE40	35	.	NM_003670	exon5	c.T633C	p.G211G	CAAAGGTTCGGAA	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568789	33568789	+	Silent	SNP	T	T	G	rs10971566	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	50	88	0	0.50505	0	T|0.756;G|0.244	0.244	strong	.	ANKRD18B	46	.	NM_001244752	exon15	c.T2886G	p.L962L	AAATCTTAATAGT	.	PASS	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15733454	15733454	+	Silent	SNP	A	A	C	rs1058212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	83	149	0	0.522013	0	A|0.883;C|0.117	0.117	strong	BST1,colon,carcinoma,0,3	BST1	30	3	NM_004334	exon9	c.A943C	p.R315R	GCTTCCAGGACTC	.	PASS	Atlas-SNP
FBXO15	201456	hgsc.bcm.edu	37	18	71740743	71740743	+	Missense_Mutation	SNP	A	A	G	rs35815390	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	95	147	0	0.549133	0	A|0.951;G|0.049	0.049	strong	FBXO15_ENST00000419743,lymph_node,lymphoid_neoplasm,0,2	FBXO15	97	2	NM_001142958	exon10	c.T1486C	p.Y496H	TAAGATAAAGGAC	.	PASS	Atlas-SNP
GSTM5	2949	hgsc.bcm.edu	37	1	110257835	110257835	+	Silent	SNP	C	C	T	rs78183574	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	473	236	446	4	0.498943	0.00896861	C|0.907;T|0.093	0.093	strong	GSTM5,brain,glioma,0,2	GSTM5	89	2	NM_000851	exon7	c.C540T	p.N180N	CCTAAACTTGAAG	.	scavenged	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228407260	228407260	+	Silent	SNP	G	G	A	rs1771484	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	37	94	0	0.521127	0	G|0.718;A|0.282	0.282	strong	.	OBSCN	2142	.	NM_001271223	exon9	c.G2889A	p.E963E	CTGTGAGGCCAGG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169279364	169279364	+	Silent	SNP	C	C	T	rs11736382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	26	68	0	0.393939	0	C|0.960;T|0.040	0.040	strong	.	DDX60L	116	.	NM_001012967	exon38	c.G5055A	p.L1685L	TTGACTCAATTGT	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3235724	3235724	+	Missense_Mutation	SNP	C	C	T	rs1635242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	67	59	0	0.985294	0	C|0.319;T|0.681	0.681	strong	.	MXRA5	815	.	NM_015419	exon6	c.G5998A	p.G2000S	TGCGGCCCTCCAC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8176640	8176640	+	Missense_Mutation	SNP	C	C	T	rs12975322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	45	95	0	0.436893	0	C|0.722;T|0.278	0.278	strong	FBN3,colon,carcinoma,0,1	FBN3	300	1	NM_032447	exon31	c.G3976A	p.V1326I	GGGAGACGCATTC	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103397937	103397937	+	Missense_Mutation	SNP	T	T	G	rs9300759	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	40	99	0	0.540541	0	T|0.697;G|0.303	0.303	strong	.	.	.	.	NM_001146197	exon4	c.A5110C	p.N1704H	TGGGATTCACTAA	.	PASS	Atlas-SNP
LY75	4065	hgsc.bcm.edu	37	2	160676350	160676350	+	Missense_Mutation	SNP	T	T	C	rs17827158	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	169	188	0	1	0	T|0.915;C|0.085	0.085	strong	.	LY75	151	.	NM_002349	exon29	c.A4040G	p.K1347R	AAAAACTTCTCAT	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362639	32362639	+	Silent	SNP	G	G	A	rs41535850	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	48	126	0	0.424779	0	G|0.859;A|0.141	0.141	strong	.	BTNL2	50	.	NM_019602	exon6	c.C1242T	p.H414H	CAGCCCGTGGCTG	.	PASS	Atlas-SNP
ACSF3	197322	hgsc.bcm.edu	37	16	89199651	89199651	+	Silent	SNP	G	G	A	rs12447947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	33	77	0	0.6	0	G|0.746;A|0.254	0.254	strong	.	ACSF3	40	.	NM_174917	exon8	c.G1347A	p.L449L	CACCCTGGATGGC	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39139348	39139348	+	Silent	SNP	A	A	G	rs16968859	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	26	44	0	0.419355	0	A|0.859;G|0.141	0.141	strong	.	KRT40	27	.	NM_182497	exon4	c.T480C	p.L160L	TACAGCAAGTCTA	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30920890	30920890	+	Missense_Mutation	SNP	G	G	A	rs2240804	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	19	39	0	0.38	0	G|0.759;A|0.241	0.241	strong	.	DPCR1	99	.	NM_080870	exon3	c.G4178A	p.R1393Q	CCCCACGGTGATC	.	PASS	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13183486	13183486	+	Silent	SNP	T	T	C	rs34704118	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	41	109	0	0.450549	0	T|0.997;C|0.003	0.003	strong	MPDZ_ENST00000541718,colon,carcinoma,-2,2	MPDZ	324	2	NM_003829	exon19	c.A2580G	p.L860L	AAGAGATAAAATA	.	PASS	Atlas-SNP
MAP2K2	5605	hgsc.bcm.edu	37	19	4117528	4117528	+	Silent	SNP	G	G	A	rs8157	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	32	75	0	0.415584	0	G|0.943;A|0.057	0.057	strong	.	MAP2K2	72	.	NM_030662	exon2	c.C192T	p.V64V	TTCGCCGACCTTG	.	PASS	Atlas-SNP
DNMT3L	29947	hgsc.bcm.edu	37	21	45675997	45675997	+	Missense_Mutation	SNP	C	C	T	rs142917827	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	98	139	0	0.535519	0	C|0.999;T|0.001	0.001	strong	.	DNMT3L	33	.	NM_013369	exon7	c.G557A	p.R186K	TGTCTCCTCCACA	.	PASS	Atlas-SNP
PKP2	5318	hgsc.bcm.edu	37	12	33003762	33003762	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	3	108	0	0.0212766	0	.	.	none	PKP2,right_upper_lobe,carcinoma,-1,1	PKP2	110	1	NM_004572	exon5	c.T1316C	p.V439A	CGAGGTACCCCAT	.	scavenged	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52584787	52584787	+	Silent	SNP	T	T	C	rs2251219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	55	111	0	0.466102	0	T|0.654;C|0.346	0.346	strong	.	PBRM1	1252	.	NM_018313	exon28	c.A4335G	p.P1445P	TCCACCTGGTGCT	.	PASS	Atlas-SNP
STK16	8576	hgsc.bcm.edu	37	2	220113145	220113145	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	42	107	0	0.461538	0	.	.	none	.	STK16	22	.	NM_001008910	exon8	c.A782G	p.H261R	ACAGGCATTCTTC	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970718	45970718	+	Silent	SNP	C	C	T	rs233238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	28	113	0	0.329412	0	C|0.742;T|0.258	0.258	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.G624A	p.P208P	GCAGCACGGAGAG	.	PASS	Atlas-SNP
NUP153	9972	hgsc.bcm.edu	37	6	17629004	17629004	+	Silent	SNP	T	T	C	rs78541395	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	44	87	0	0.392857	0	T|0.996;C|0.004	0.004	strong	.	NUP153	116	.	NM_005124	exon18	c.A3426G	p.K1142K	CTCATCTTTGGTT	.	PASS	Atlas-SNP
QSER1	79832	hgsc.bcm.edu	37	11	32996805	32996805	+	Silent	SNP	C	C	T	rs11032076	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	36	82	0	0.48	0	C|0.907;T|0.093	0.093	strong	QSER1,caecum,carcinoma,0,1	QSER1	153	1	NM_001076786	exon12	c.C4983T	p.V1661V	TGCTGTCGATCCA	.	PASS	Atlas-SNP
DNPEP	23549	hgsc.bcm.edu	37	2	220250232	220250232	+	Missense_Mutation	SNP	G	G	C	rs115897075	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	55	99	0	0.390071	0	G|0.990;C|0.010	0.010	strong	.	DNPEP	40	.	NM_012100	exon8	c.C688G	p.L230V	ACATGAGGACCGA	.	PASS	Atlas-SNP
CPEB1	64506	hgsc.bcm.edu	37	15	83296073	83296073	+	Missense_Mutation	SNP	C	C	T	rs61733713	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	37	73	0	0.480519	0	C|0.989;T|0.011	0.011	strong	.	CPEB1	114	.	NM_030594	exon2	c.G61A	p.A21T	CAGGTGCTTCCTG	.	PASS	Atlas-SNP
SSC5D	284297	hgsc.bcm.edu	37	19	56030009	56030009	+	Missense_Mutation	SNP	C	C	T	rs925878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	35	66	0	0.555556	0	C|0.809;T|0.191	0.191	strong	.	SSC5D	65	.	NM_001144950	exon14	c.C4366T	p.P1456S	CTTGACCCCCTCA	.	PASS	Atlas-SNP
HINFP	25988	hgsc.bcm.edu	37	11	119005132	119005132	+	Missense_Mutation	SNP	C	C	T	rs100803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	35	43	0	0.454545	0	C|0.611;T|0.389	0.389	strong	.	HINFP	50	.	NM_015517	exon11	c.C1478T	p.A493V	CCCCAGCCCCTGA	.	PASS	Atlas-SNP
BLM	641	hgsc.bcm.edu	37	15	91354521	91354521	+	Missense_Mutation	SNP	G	G	A	rs7167216	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	20	68	0	0.289855	0	G|0.928;A|0.072	0.072	strong	.	BLM	122	.	NM_000057	exon21	c.G3961A	p.V1321I	ATACCCGTATCTT	.	PASS	Atlas-SNP
TSHZ1	10194	hgsc.bcm.edu	37	18	73000005	73000005	+	Silent	SNP	G	G	A	rs34878160	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	20	38	0	0.47619	0	G|0.972;A|0.028	0.028	strong	.	TSHZ1	104	.	NM_005786	exon2	c.G2508A	p.P836P	GTCACCGGTCCAC	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32010272	32010272	+	Missense_Mutation	SNP	T	T	A	rs76250508	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	282	127	175	0	0.450355	0	T|0.754;A|0.246	0.246	strong	TNXB_ENST00000375247,colon,carcinoma,0,3	TNXB	553	3	NM_019105	exon40	c.A12164T	p.N4055I	AACACGTTCAGGG	.	PASS	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60986019	60986019	+	Missense_Mutation	SNP	A	A	C	rs2236200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	71	114	1	0.47973	0.00877193	A|0.827;C|0.173	0.173	strong	C20orf151,NS,carcinoma,0,1	.	.	1	NM_080833	exon14	c.T1910G	p.L637R	GCTGTCAGTTTCC	.	scavenged	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38764998	38764998	+	Missense_Mutation	SNP	A	A	G	rs12632942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	59	114	0	0.495798	0	A|0.777;G|0.223	0.223	strong	.	SCN10A	359	.	NM_006514	exon18	c.T3275C	p.L1092P	GGATCTAGGCAGT	.	PASS	Atlas-SNP
PPM1N	147699	hgsc.bcm.edu	37	19	46002007	46002007	+	Missense_Mutation	SNP	C	C	T	rs140525169	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	54	47	0	0.524272	0	C|0.995;T|0.005	0.005	strong	.	PPM1N	25	.	NM_001080401	exon1	c.C277T	p.P93S	GGTCTGCCCCCGG	.	PASS	Atlas-SNP
ABCB8	11194	hgsc.bcm.edu	37	7	150733025	150733025	+	Silent	SNP	T	T	A	rs2303926	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	25	72	0	0.462963	0	T|0.697;A|0.303	0.303	strong	ABCB8,rectum,carcinoma,+1,2	ABCB8	65	2	NM_007188	exon7	c.T984A	p.R328R	TGTGCGTGCCTTC	.	PASS	Atlas-SNP
VMAC	400673	hgsc.bcm.edu	37	19	5908969	5908969	+	Missense_Mutation	SNP	G	G	A	rs10404195	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	38	60	0	0.493506	0	G|0.872;A|0.128	0.128	strong	VMAC,NS,carcinoma,0,1	VMAC	5	1	NM_001017921	exon2	c.G326A	p.R109H	TCTGCCGCCGCCG	.	PASS	Atlas-SNP
CXorf22	170063	hgsc.bcm.edu	37	X	35988996	35988996	+	Silent	SNP	T	T	C	rs6632446	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	143	153	0	0.993056	0	T|0.861;C|0.139	0.139	strong	.	CXorf22	272	.	NM_152632	exon11	c.T1926C	p.L642L	GTATCTTAAATAT	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56549510	56549510	+	Missense_Mutation	SNP	T	T	C	rs16986899	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	71	148	1	0.427711	0.00675676	T|0.731;C|0.269	0.269	strong	NLRP5,NS,carcinoma,0,1	NLRP5	217	1	NM_153447	exon10	c.T2735C	p.M912T	GAGTAATGCCTCT	.	scavenged	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512636	4512636	+	Missense_Mutation	SNP	A	A	C	rs140230284	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	37	179	1	1	0.00558659	A|0.966;C|0.034	0.034	strong	PLIN4_ENST00000301286,caecum,carcinoma,0,4	PLIN4	191	4	NM_001080400	exon3	c.T1294G	p.L432V	TGGCCAAATTCAT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912042	29912042	+	Missense_Mutation	SNP	G	G	A	rs60318678		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	24	315	0	0.16	0	A|1.000;|0.000	1.000	weak	HLA-A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	HLA-A	89	1	NM_001242758	exon4	c.G763A	p.V255M	GAGCTCGTGGAGA	.	scavenged	Atlas-SNP
CPT2	1376	hgsc.bcm.edu	37	1	53679229	53679229	+	Missense_Mutation	SNP	A	A	G	rs1799822	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	30	91	0	0.5	0	A|0.854;G|0.146	0.146	strong	.	CPT2	34	.	NM_000098	exon5	c.A1939G	p.M647V	GAAGACATGTTTG	.	PASS	Atlas-SNP
HRH4	59340	hgsc.bcm.edu	37	18	22056766	22056766	+	Missense_Mutation	SNP	C	C	T	rs11665084	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	230	112	229	0	0.486957	0	C|0.930;T|0.070	0.070	strong	.	HRH4	46	.	NM_021624	exon3	c.C413T	p.A138V	TGGTGGCCGTTTG	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33884804	33884804	+	Missense_Mutation	SNP	T	T	C	rs10512472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	143	123	0	0.993056	0	T|0.743;C|0.257	0.257	strong	.	SLFN14	43	.	NM_001129820	exon1	c.A278G	p.Q93R	TATTTCTGTGAAC	.	PASS	Atlas-SNP
SETD6	79918	hgsc.bcm.edu	37	16	58552921	58552921	+	Silent	SNP	G	G	A	rs3607	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	17	41	0	0.435897	0	G|0.344;A|0.656	0.656	strong	.	SETD6	27	.	NM_001160305	exon8	c.G1410A	p.E470E	GTTGGAGCTGACA	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46930107	46930107	+	Silent	SNP	C	C	T	rs8141744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	102	205	0	0.488038	0	C|0.794;T|0.206	0.206	strong	.	CELSR1	242	.	NM_014246	exon1	c.G2961A	p.V987V	GATGGTCACCTGG	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153218365	153218365	+	Silent	SNP	C	C	A	rs3027878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	32	0	1	0	C|0.637;A|0.363	0.363	strong	.	HCFC1	284	.	NM_005334	exon19	c.G4542T	p.L1514L	TGGCGGCAGCTGC	.	PASS	Atlas-SNP
AGFG2	3268	hgsc.bcm.edu	37	7	100160264	100160264	+	Missense_Mutation	SNP	T	T	C	rs17855473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	33	77	0	0.388235	0	T|0.797;C|0.203	0.203	strong	AGFG2,NS,carcinoma,0,1	AGFG2	44	1	NM_006076	exon8	c.T1046C	p.M349T	TCACGATGGGCGG	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33584289	33584289	+	Silent	SNP	C	C	T	rs3746438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	59	79	0	0.602041	0	C|0.542;T|0.458	0.458	strong	.	MYH7B	145	.	NM_020884	exon29	c.C3210T	p.T1070T	GCTGACCAAGGCC	.	PASS	Atlas-SNP
CLU	1191	hgsc.bcm.edu	37	8	27462481	27462481	+	Silent	SNP	A	A	G	rs7982	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	118	110	1	0.975207	0.00909091	G|0.610;C|0.000;A|0.390	0.610	strong	.	CLU	54	.	NM_001831	exon5	c.T789C	p.H263H	CGGGCTATGGAAG	.	PASS	Atlas-SNP
ELOVL4	6785	hgsc.bcm.edu	37	6	80626375	80626375	+	Missense_Mutation	SNP	T	T	C	rs3812153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	161	224	0	0.993827	0	T|0.831;C|0.169	0.169	strong	.	ELOVL4	46	.	NM_022726	exon6	c.A895G	p.M299V	CTATCATGAGTTG	.	PASS	Atlas-SNP
CLCA1	1179	hgsc.bcm.edu	37	1	86947975	86947975	+	Silent	SNP	A	A	T	rs1321694	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	153	172	0	1	0	T|0.353;N|0.000	0.353	strong	.	CLCA1	109	.	NM_001285	exon5	c.A645T	p.V215V	TAAAGTAACAGGA	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017672	109017672	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	44	179	3	0.278481	0.0167598	.	.	none	SELPLG_ENST00000550948,NS,carcinoma,0,14	SELPLG	138	14	NM_001206609	exon2	c.C460G	p.P154A	CCGTGGGCACTGG	.	scavenged	Atlas-SNP
RBM11	54033	hgsc.bcm.edu	37	21	15599466	15599466	+	Missense_Mutation	SNP	A	A	G	rs7280643	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	94	221	0	0.516484	0	A|0.907;G|0.093	0.093	strong	RBM11,NS,carcinoma,0,1	RBM11	41	1	NM_144770	exon5	c.A698G	p.H233R	GGACTCACCAACA	.	PASS	Atlas-SNP
IFI30	10437	hgsc.bcm.edu	37	19	18285944	18285944	+	Missense_Mutation	SNP	G	G	A	rs11554159	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	74	159	0	0.569231	0	G|0.789;A|0.211	0.211	strong	.	IFI30	12	.	NM_006332	exon2	c.G227A	p.R76Q	GCTGCCGAGCCTT	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079264	31079264	+	Missense_Mutation	SNP	C	C	T	rs2233984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	40	98	0	0.449438	0	C|0.921;T|0.079	0.079	strong	C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	NM_014070	exon2	c.G872A	p.G291D	TTGATACCTGGGT	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465344	10465344	+	Missense_Mutation	SNP	C	C	A	rs11778341	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	54	124	0	0.504673	0	C|0.846;A|0.154	0.154	strong	.	RP1L1	453	.	NM_178857	exon4	c.G6264T	p.Q2088H	TGCCTCCTGGGCA	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72130203	72130203	+	Silent	SNP	C	C	G	rs1050361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	54	153	0	0.394161	0	C|0.490;G|0.510	0.510	strong	DHX38,NS,carcinoma,0,1	DHX38	91	1	NM_014003	exon2	c.C147G	p.L49L	ATTACTCGGACTG	.	PASS	Atlas-SNP
NLRP1	22861	hgsc.bcm.edu	37	17	5436263	5436263	+	Missense_Mutation	SNP	C	C	T	rs2301582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	43	95	0	0.409524	0	C|0.738;T|0.262	0.262	strong	.	NLRP1	358	.	NM_001033053	exon11	c.G3187A	p.V1063M	AAGGCACGCACAA	.	PASS	Atlas-SNP
SIM1	6492	hgsc.bcm.edu	37	6	100868721	100868721	+	Missense_Mutation	SNP	G	G	A	rs3734355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	13	137	1	0.160494	0.00729927	G|0.857;A|0.143	0.143	strong	SIM1,NS,carcinoma,0,1	SIM1	173	1	NM_005068	exon9	c.C1112T	p.A371V	GATTTGGCCCCCT	.	scavenged	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129249676	129249676	+	Silent	SNP	C	C	T	rs2229604	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	15	37	0	0.46875	0	C|0.571;T|0.429	0.429	strong	.	DOCK1	188	.	NM_001380	exon52	c.C5583T	p.S1861S	GGACTCCGGGATC	.	PASS	Atlas-SNP
PDZD3	79849	hgsc.bcm.edu	37	11	119059404	119059404	+	Missense_Mutation	SNP	G	G	A	rs1815811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	75	142	0	0.559702	0	G|0.395;A|0.605	0.605	strong	.	PDZD3	42	.	NM_001168468	exon9	c.G1115A	p.R372Q	CGCCCCGGGGCAG	.	PASS	Atlas-SNP
ZNF570	148268	hgsc.bcm.edu	37	19	37975379	37975379	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	16	35	0	0.410256	0	.	.	none	.	ZNF570	58	.	NM_144694	exon5	c.G855A	p.Q285Q	CAGTCAGAATGCA	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124351954	124351954	+	Silent	SNP	G	G	A	rs4752722	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	89	81	0	0.695312	0	G|0.732;A|0.268	0.268	strong	.	DMBT1	677	.	NM_007329	exon20	c.G2343A	p.S781S	CACGTCGGCCCCA	.	PASS	Atlas-SNP
CHRDL1	91851	hgsc.bcm.edu	37	X	109931856	109931856	+	Silent	SNP	T	T	C	rs5943053	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	107	101	1	1	0.00990099	C|0.491;G|0.000;T|0.508	0.491	strong	.	CHRDL1	78	.	NM_001143981	exon9	c.A954G	p.K318K	GCAGCATTTTCCG	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72137561	72137561	+	Silent	SNP	G	G	A	rs2240243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	55	121	0	0.462185	0	G|0.533;A|0.467	0.467	strong	.	DHX38	91	.	NM_014003	exon13	c.G1698A	p.T566T	GCTGACGCAGTAC	.	PASS	Atlas-SNP
NXPE1	120400	hgsc.bcm.edu	37	11	114393652	114393652	+	Missense_Mutation	SNP	C	C	T	rs10891692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	137	141	0	1	0	C|0.645;T|0.355	0.355	strong	FAM55A,NS,adenoma,0,1	NXPE1	8	1	NM_152315	exon5	c.G631A	p.G211R	AGTCTCCCAGGAG	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52478315	52478315	+	Silent	SNP	A	A	G	rs1051069	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	89	63	1	0.988889	0.015873	A|0.354;G|0.646	0.646	strong	NID2,NS,carcinoma,-1,1	NID2	201	1	NM_007361	exon17	c.T3507C	p.A1169A	CAGACCAGCACGG	.	scavenged	Atlas-SNP
TRIM37	4591	hgsc.bcm.edu	37	17	57158552	57158552	+	Missense_Mutation	SNP	G	G	A	rs61758100	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	18	45	0	0.305085	0	G|0.994;A|0.006	0.006	strong	.	TRIM37	105	.	NM_015294	exon6	c.C398T	p.A133V	ATTTCTGCCAAAG	.	PASS	Atlas-SNP
BTN1A1	696	hgsc.bcm.edu	37	6	26509330	26509330	+	Missense_Mutation	SNP	C	C	G	rs9393728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	77	80	0	1	0	C|0.505;G|0.495	0.495	strong	.	BTN1A1	68	.	NM_001732	exon7	c.C1509G	p.D503E	GGAGGACTCTGCC	.	PASS	Atlas-SNP
TRIM59	286827	hgsc.bcm.edu	37	3	160156951	160156951	+	Silent	SNP	C	C	T	rs1141023	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	82	166	0	0.535948	0	C|0.882;T|0.118	0.118	strong	.	TRIM59	42	.	NM_173084	exon3	c.G21A	p.E7E	AGTTAACTCTTCC	.	PASS	Atlas-SNP
COL6A6	131873	hgsc.bcm.edu	37	3	130311398	130311398	+	Missense_Mutation	SNP	C	C	T	rs73868925	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	65	128	0	0.532787	0	C|0.864;T|0.136	0.136	strong	COL6A6,NS,carcinoma,0,1	COL6A6	497	1	NM_001102608	exon13	c.C4286T	p.A1429V	GAGGAGCCCCTGG	.	PASS	Atlas-SNP
TULP4	56995	hgsc.bcm.edu	37	6	158910698	158910698	+	Missense_Mutation	SNP	G	G	A	rs12206717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	13	125	0	0.149425	0	G|0.962;A|0.038	0.038	strong	.	TULP4	137	.	NM_020245	exon9	c.G1565A	p.S522N	AGCTGAGTGATGA	.	PASS	Atlas-SNP
SLC38A10	124565	hgsc.bcm.edu	37	17	79226362	79226362	+	Silent	SNP	G	G	A	rs3803767	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	34	86	0	0.425	0	G|0.930;A|0.070	0.070	strong	.	SLC38A10	133	.	NM_001037984	exon13	c.C1578T	p.H526H	GCCCGCGTGTCTG	.	PASS	Atlas-SNP
KRT7	3855	hgsc.bcm.edu	37	12	52631313	52631313	+	Missense_Mutation	SNP	A	A	G	rs6580870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	100	92	0	1	0	A|0.149;G|0.851	0.851	strong	.	KRT7	48	.	NM_005556	exon3	c.A557G	p.H186R	TTAACCACCGCAC	.	PASS	Atlas-SNP
RSAD1	55316	hgsc.bcm.edu	37	17	48557348	48557348	+	Missense_Mutation	SNP	T	T	C	rs2290861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	118	117	0	0.983333	0	T|0.339;C|0.661	0.661	strong	.	RSAD1	36	.	NM_018346	exon3	c.T377C	p.L126S	CAGACTTGGAAGT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536917	88536917	+	Missense_Mutation	SNP	G	G	A	rs199901845	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	21	140	0	0.156716	0	.	.	weak	DSPP,NS,carcinoma,-2,3	DSPP	174	3	NM_014208	exon5	c.G3103A	p.D1035N	AGCAGCGATAGCA	.	PASS	Atlas-SNP
TMPRSS6	164656	hgsc.bcm.edu	37	22	37482458	37482458	+	Missense_Mutation	SNP	C	C	A	rs201148397	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	83	151	0	0.535484	0	C|0.999;A|0.001	0.001	strong	TMPRSS6_ENST00000442782,NS,carcinoma,0,2	TMPRSS6	99	2	NM_153609	exon8	c.G865T	p.V289L	CGTACACCCTGGC	.	PASS	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	7046901	7046901	+	Missense_Mutation	SNP	C	C	G	rs1407856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	73	121	0	0.561538	0	C|0.833;G|0.167	0.167	strong	KDM4C_ENST00000381306,NS,chondrosarcoma,-2,2	KDM4C	186	2	NM_001146696	exon16	c.C2365G	p.Q789E	CTTAAGCAAACGA	.	PASS	Atlas-SNP
TGFA	7039	hgsc.bcm.edu	37	2	70677994	70677994	+	Silent	SNP	G	G	A	rs2166975	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	117	166	0	0.570732	0	G|0.782;A|0.218	0.218	strong	TGFA,NS,lymphoid_neoplasm,0,1	TGFA	14	1	NM_003236	exon6	c.C480T	p.V160V	TCTTCAGACCACT	.	PASS	Atlas-SNP
SLCO2B1	11309	hgsc.bcm.edu	37	11	74883577	74883577	+	Missense_Mutation	SNP	G	G	A	rs12422149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	75	59	0	0.986842	0	G|0.836;A|0.164	0.164	strong	.	SLCO2B1	84	.	NM_007256	exon7	c.G935A	p.R312Q	TTCGGCGAAAGGT	.	PASS	Atlas-SNP
RAET1G	353091	hgsc.bcm.edu	37	6	150239330	150239330	+	Silent	SNP	C	C	T	rs17079029	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	122	297	0	0.824324	0	C|0.785;T|0.215	0.215	strong	.	RAET1G	31	.	NM_001001788	exon4	c.G822A	p.R274R	GACTCTCCTCAGC	.	PASS	Atlas-SNP
DGCR14	8220	hgsc.bcm.edu	37	22	19122665	19122665	+	Silent	SNP	C	C	T	rs2240111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	75	125	0	0.535714	0	C|0.835;A|0.001	.	strong	.	DGCR14	43	.	NM_022719	exon9	c.G1059A	p.E353E	CAGCCGCTCCCTG	.	PASS	Atlas-SNP
ARID4A	5926	hgsc.bcm.edu	37	14	58830978	58830978	+	Missense_Mutation	SNP	A	A	G	rs2230098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	50	102	0	0.515464	0	A|0.960;G|0.040	0.040	strong	ARID4A_ENST00000355431,NS,carcinoma,0,2	ARID4A	222	2	NM_002892	exon20	c.A2171G	p.N724S	AAAAAAATGAAAA	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634369	32634369	+	Missense_Mutation	SNP	C	C	A	rs1049056	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	18	6	0	0.72	0	C|0.811;A|0.189	0.189	strong	.	HLA-DQB1	15	.	NM_002123	exon1	c.G16T	p.A6S	GCAAAGCCTTCTT	.	PASS	Atlas-SNP
C6orf223	221416	hgsc.bcm.edu	37	6	43970658	43970658	+	Missense_Mutation	SNP	T	T	A	rs115402675	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	22	36	0	0.594595	0	T|0.955;A|0.045	0.045	strong	C6orf223,NS,carcinoma,0,1	C6orf223	14	1	NM_153246	exon4	c.T524A	p.L175H	CCCTTCTTCGCGG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28913599	28913599	+	Silent	SNP	C	C	T	rs12967407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	61	140	1	0.445255	0.00714286	C|0.616;T|0.384	0.384	strong	DSG1,colon,carcinoma,+2,1	DSG1	176	1	NM_001942	exon7	c.C732T	p.G244G	AGATGGCGGGGCA	.	scavenged	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605344	84605344	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	59	137	0	0.427536	0	.	.	none	.	.	.	.	NM_001001670	exon3	c.G245A	p.W82X	CAGACTGGAAAAG	.	PASS	Atlas-SNP
GLTPD2	388323	hgsc.bcm.edu	37	17	4693054	4693054	+	Silent	SNP	G	G	A	rs12951761	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	41	51	0	1	0	G|0.443;A|0.557	0.557	strong	.	GLTPD2	15	.	NM_001014985	exon4	c.G339A	p.E113E	CCGCAGGTTCCTG	.	PASS	Atlas-SNP
SLC30A8	169026	hgsc.bcm.edu	37	8	118184783	118184783	+	Missense_Mutation	SNP	C	C	T	rs13266634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	60	76	0	0.666667	0	C|0.758;T|0.242	0.242	strong	.	SLC30A8	102	.	NM_173851	exon8	c.C973T	p.R325W	GCCAGCCGGGACA	.	PASS	Atlas-SNP
STX16	8675	hgsc.bcm.edu	37	20	57244493	57244493	+	Silent	SNP	G	G	A	rs2296524	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	30	58	0	0.46875	0	G|0.492;A|0.508	0.508	strong	.	STX16	36	.	NM_001001433	exon5	c.G540A	p.Q180Q	CGCACAGTCAGGC	.	PASS	Atlas-SNP
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766045	27766045	+	Missense_Mutation	SNP	A	A	G	rs5926895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	99	0	1	0	A|0.784;0|0.046	.	strong	.	DCAF8L2	79	.	NM_001136533	exon1	c.A1033G	p.T345A	GTCTTCACCATTG	.	PASS	Atlas-SNP
SLC41A1	254428	hgsc.bcm.edu	37	1	205767885	205767885	+	Silent	SNP	G	G	A	rs708727	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	253	253	232	0	1	0	G|0.751;A|0.249	0.249	strong	SLC41A1,colon,carcinoma,0,1	SLC41A1	46	1	NM_173854	exon6	c.C756T	p.N252N	GGCCACGTTGTCT	.	PASS	Atlas-SNP
ITIH3	3699	hgsc.bcm.edu	37	3	52833805	52833805	+	Missense_Mutation	SNP	C	C	A	rs3617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	17	47	0	0.414634	0	T|0.010;G|0.001	.	strong	ITIH3_ENST00000449956,NS,carcinoma,0,2	ITIH3	132	2	NM_002217	exon9	c.C943A	p.Q315K	GATATGCAAGAGG	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	37	17	65103373	65103373	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	315	147	306	0	0.466667	0	.	.	none	.	HELZ	160	.	NM_014877	exon31	c.A5153G	p.Q1718R	TGATTCTGTATTT	.	PASS	Atlas-SNP
C20orf201	198437	hgsc.bcm.edu	37	20	62714783	62714783	+	Silent	SNP	C	C	G	rs6010717	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	46	36	0	1	0	C|0.368;G|0.632	0.632	strong	C20orf201,NS,carcinoma,0,1	C20orf201	4	1	NM_001007125	exon2	c.G678C	p.A226A	CTCAGTCGCCGTC	.	PASS	Atlas-SNP
DHTKD1	55526	hgsc.bcm.edu	37	10	12131218	12131218	+	Silent	SNP	C	C	T	rs3740016	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	24	55	0	0.48	0	C|0.923;T|0.077	0.077	strong	DHTKD1,NS,carcinoma,0,1	DHTKD1	104	1	NM_018706	exon5	c.C951T	p.N317N	AGACAACTCAGCC	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30882634	30882634	+	Silent	SNP	C	C	T	rs1264302	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	55	99	0	0.528846	0	C|0.733;T|0.267	0.267	strong	.	VARS2	60	.	NM_001167734	exon2	c.C111T	p.A37A	TCTCGCCTCTTTT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104199	168104199	+	Silent	SNP	C	C	T	rs7581190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	68	145	0	0.523077	0	C|0.840;T|0.160	0.160	strong	.	XIRP2	914	.	NM_152381	exon9	c.C6297T	p.D2099D	ATCAGACAGGGCA	.	PASS	Atlas-SNP
NRXN3	9369	hgsc.bcm.edu	37	14	79181226	79181226	+	Silent	SNP	C	C	T	rs1004212	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	110	168	0	0.526316	0	C|0.808;T|0.192	0.192	strong	.	NRXN3	342	.	NM_004796	exon5	c.C669T	p.T223T	CCCCACCGAGCTG	.	PASS	Atlas-SNP
ZC3H3	23144	hgsc.bcm.edu	37	8	144623574	144623574	+	Missense_Mutation	SNP	T	T	C	rs2242093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	80	85	0	0.512821	0	T|0.850;C|0.150	0.150	strong	.	ZC3H3	75	.	NM_015117	exon1	c.A18G	p.I6M	CCGTAATATCTCC	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127215778	127215778	+	Missense_Mutation	SNP	C	C	T	rs67997410	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	15	6	0	1	0	C|0.271;T|0.729	0.729	strong	GPR144,rectum,carcinoma,0,1	GPR144	33	1	NM_001161808	exon4	c.C802T	p.L268F	CACGCCCTCAGCG	.	PASS	Atlas-SNP
LCORL	254251	hgsc.bcm.edu	37	4	17886146	17886146	+	Missense_Mutation	SNP	A	A	G	rs17526944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	75	145	0	0.451807	0	A|0.972;G|0.028	0.028	strong	.	LCORL	60	.	NM_001166139	exon7	c.T1006C	p.Y336H	CCTTATATGAATA	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801403	27801403	+	Missense_Mutation	SNP	C	C	G	rs1919125	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	250	106	298	1	0.424	0.0033557	C|0.375;G|0.625	0.625	strong	.	C2orf16	357	.	NM_032266	exon1	c.C1964G	p.T655S	CATGTACTCAAGT	.	PASS	Atlas-SNP
POLR3A	11128	hgsc.bcm.edu	37	10	79744042	79744042	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	34	70	0	0.441558	0	.	.	none	.	POLR3A	104	.	NM_007055	exon25	c.C3257A	p.T1086K	TGTGCTGTGATAA	.	PASS	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	37	21	43236176	43236176	+	Silent	SNP	G	G	A	rs4075967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	87	125	0	0.530488	0	G|0.802;A|0.198	0.198	strong	.	PRDM15	110	.	NM_022115	exon26	c.C3375T	p.H1125H	CAGCGCGTGCTTG	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15129970	15129970	+	Silent	SNP	A	A	G	rs7200543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	64	0	1	0	A|0.706;G|0.294	0.294	strong	.	PDXDC1	59	.	NM_015027	exon23	c.A2205G	p.L735L	GCGCCTATCCAGT	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6524072	6524072	+	Missense_Mutation	SNP	A	A	C	rs11605196	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	38	73	0	0.417582	0	A|0.862;C|0.138	0.138	strong	.	DNHD1	198	.	NM_173589	exon3	c.A836C	p.Q279P	ATAGCCAGGTGAT	.	PASS	Atlas-SNP
ZAK	0	hgsc.bcm.edu	37	2	174055646	174055646	+	Silent	SNP	T	T	C	rs35853276	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	42	84	0	0.552632	0	T|0.858;C|0.142	0.142	strong	.	ZAK	62	.	NM_133646	exon6	c.T439C	p.L147L	GGAGTATTGAAGG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1248960	1248960	+	Silent	SNP	G	G	A	rs2075855	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	39	56	0	0.464286	0	G|0.929;A|0.071	0.071	strong	MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	NM_002458	exon7	c.G723A	p.T241T	GCCCACGGAGCAG	.	PASS	Atlas-SNP
SP140	11262	hgsc.bcm.edu	37	2	231149097	231149097	+	Missense_Mutation	SNP	T	T	C	rs4972945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	101	191	0	0.490291	0	T|0.878;C|0.122	0.122	strong	.	SP140	121	.	NM_007237	exon16	c.T1535C	p.M512T	TGAGAATGAGAAG	.	PASS	Atlas-SNP
DCAF13	25879	hgsc.bcm.edu	37	8	104427359	104427359	+	Missense_Mutation	SNP	A	A	C	rs3134295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	96	79	0	0.989691	0	A|0.537;C|0.463	0.463	strong	DCAF13,NS,carcinoma,0,1	DCAF13	66	1	NM_015420	exon1	c.A141C	p.R47S	GCACAGACACTAC	.	PASS	Atlas-SNP
STAMBPL1	57559	hgsc.bcm.edu	37	10	90673024	90673024	+	Missense_Mutation	SNP	G	G	A	rs12254856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	58	140	0	0.417266	0	G|0.874;A|0.126	0.126	strong	.	STAMBPL1	63	.	NM_020799	exon6	c.G587A	p.S196N	TGCGAAGTCAGCA	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	59	187	0	0.504274	0	G|0.552;A|0.448	0.448	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.G2137A	p.V713I	GGAGACGTTTCCC	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1551485	1551485	+	Silent	SNP	C	C	T	rs2254458	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	107	106	0	0.981651	0	C|0.290;T|0.710	0.710	strong	SIRPB1,NS,carcinoma,-1,1	SIRPB1	83	1	NM_006065	exon4	c.G1050A	p.A350A	CTGGTGCGCTGAG	.	PASS	Atlas-SNP
NID1	4811	hgsc.bcm.edu	37	1	236141174	236141174	+	Missense_Mutation	SNP	T	T	C	rs3213190	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	42	126	0	0.42	0	T|0.706;C|0.293	0.293	strong	.	NID1	196	.	NM_002508	exon20	c.A3737G	p.Q1246R	CATTTCTGTTCGA	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5372856	5372856	+	Missense_Mutation	SNP	A	A	G	rs4910756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	125	243	0	0.516529	0	A|0.824;G|0.176	0.176	strong	.	OR51B6	53	.	NM_001004750	exon1	c.A119G	p.N40S	TTGGCAATGGCAC	.	PASS	Atlas-SNP
MUSK	4593	hgsc.bcm.edu	37	9	113459655	113459655	+	Silent	SNP	C	C	T	rs41279051	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	55	117	0	0.491071	0	C|0.866;T|0.134	0.134	strong	MUSK,colon,carcinoma,+1,7	MUSK	112	7	NM_001166281	exon5	c.C537T	p.N179N	TCATAACGTACAA	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49116438	49116438	+	Silent	SNP	A	A	G	rs376524	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	57	88	0	0.491379	0	A|0.708;G|0.292	0.292	strong	FAM83E,colon,carcinoma,0,1	FAM83E	34	1	NM_017708	exon1	c.T192C	p.V64V	GCCCTGAACCTCA	.	PASS	Atlas-SNP
APH1B	83464	hgsc.bcm.edu	37	15	63569902	63569902	+	Missense_Mutation	SNP	C	C	T	rs117618017	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	48	44	1	0.510638	0.0227273	C|0.915;T|0.085	0.085	strong	APH1B,NS,lymphoid_neoplasm,0,3	APH1B	27	3	NM_001145646	exon1	c.C80T	p.T27I	TCGCCACCGAGCC	.	scavenged	Atlas-SNP
CCL25	6370	hgsc.bcm.edu	37	19	8121360	8121360	+	Missense_Mutation	SNP	A	A	G	rs2032887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	23	60	0	0.410714	0	A|0.785;G|0.215	0.215	strong	.	CCL25	12	.	NM_001201359	exon4	c.A302G	p.H101R	AGCTCCACCACAA	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1629969	1629969	+	Silent	SNP	C	C	T	rs80035274	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	34	39	0	0.53125	0	C|0.833;T|0.167	0.167	strong	WDR81_ENST00000409644,NS,carcinoma,0,1	WDR81	180	1	NM_001163809	exon1	c.C1716T	p.H572H	CGCCCACACTCAC	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37232822	37232822	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	2	108	0	0.0148148	0	.	.	none	HEATR5B,NS,carcinoma,+2,1	HEATR5B	185	1	NM_019024	exon30	c.A4858G	p.T1620A	GCAAGGTATGTAA	.	scavenged	Atlas-SNP
METTL4	64863	hgsc.bcm.edu	37	18	2554915	2554915	+	Silent	SNP	G	G	A	rs61749937	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	71	201	0	0.412791	0	G|0.984;A|0.016	0.016	strong	.	METTL4	40	.	NM_022840	exon4	c.C582T	p.D194D	GCAGGCGTCAAGT	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39135207	39135207	+	Missense_Mutation	SNP	A	A	G	rs150812789	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	59	128	0	0.491667	0	A|0.787;G|0.213	0.213	strong	KRT40,NS,carcinoma,+2,1	KRT40	27	1	NM_182497	exon8	c.T1045C	p.C349R	TCAGACACTGAAT	.	PASS	Atlas-SNP
OPA1	4976	hgsc.bcm.edu	37	3	193374964	193374964	+	Silent	SNP	T	T	C	rs9851685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	44	87	0	0.488889	0	T|0.517;C|0.483	0.483	strong	.	OPA1	79	.	NM_130837	exon23	c.T2274C	p.A758A	AGAGGCTGTTAAG	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140529938	140529938	+	Missense_Mutation	SNP	G	G	A	rs141476251	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	39	83	0	0.464286	0	G|0.997;A|0.003	0.003	strong	.	PCDHB6	161	.	NM_018939	exon1	c.G100A	p.V34I	TATTCCGTATTGG	.	PASS	Atlas-SNP
NDUFS4	4724	hgsc.bcm.edu	37	5	52942197	52942197	+	Silent	SNP	A	A	G	rs31303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	123	144	0	0.991935	0	A|0.211;G|0.789	0.789	strong	.	NDUFS4	17	.	NM_002495	exon3	c.A312G	p.R104R	TACCAGAGAGCGA	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12187210	12187210	+	Silent	SNP	A	A	G	rs6511764	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	17	42	1	0.447368	0.0238095	A|0.772;G|0.228	0.228	strong	ZNF844,right_upper_lobe,carcinoma,0,2	ZNF844	69	2	NM_001136501	exon4	c.A1275G	p.V425V	CAGTGTAGTAAAG	.	scavenged	Atlas-SNP
PSD3	23362	hgsc.bcm.edu	37	8	18656805	18656805	+	Silent	SNP	G	G	A	rs2306825	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	33	49	0	0.478261	0	G|0.811;A|0.189	0.189	strong	.	PSD3	142	.	NM_015310	exon8	c.C2082T	p.H694H	ACTTACGTGGCCA	.	PASS	Atlas-SNP
PLBD1	79887	hgsc.bcm.edu	37	12	14656768	14656768	+	Missense_Mutation	SNP	G	G	C	rs1600	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	74	159	0	0.490066	0	G|0.490;C|0.510	0.510	strong	.	PLBD1	36	.	NM_024829	exon11	c.C1600G	p.P534A	CCTCTGGCATGCC	.	PASS	Atlas-SNP
CSMD2	114784	hgsc.bcm.edu	37	1	34238283	34238283	+	Missense_Mutation	SNP	T	T	C	rs474474	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	76	78	0	1	0	T|0.662;C|0.338	0.338	strong	.	CSMD2	946	.	NM_052896	exon13	c.A1613G	p.H538R	CCGTGGTGAAACC	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	236617	236617	+	Silent	SNP	G	G	T	rs200223188	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	315	4	309	4	0.0126984	0.012945	A|0.002;G|0.988;T|0.011	0.011	strong	SDHA,NS,carcinoma,0,1	SDHA	80	1	NM_004168	exon10	c.G1335T	p.S445S	TGCCTCGGTACAT	.	scavenged	Atlas-SNP
TNK2	10188	hgsc.bcm.edu	37	3	195594805	195594805	+	Silent	SNP	A	A	G	rs1056749	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	11	5	13	0	0.454545	0	A|0.886;G|0.114	0.114	strong	TNK2_ENST00000381916,NS,carcinoma,0,3	TNK2	246	3	NM_001010938	exon13	c.T2553C	p.A851A	AGGGGAAGCAGGT	.	scavenged	Atlas-SNP
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726774	32726774	+	Missense_Mutation	SNP	C	C	T	rs200716952	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	19	171	0	0.0964467	0	C|0.997;T|0.003	0.003	weak	HLA-DQB2,NS,carcinoma,0,4	HLA-DQB2	22	4	NM_001198858	exon3	c.G499A	p.A167T	CACCGGCTGTCTC	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609192	32609192	+	Missense_Mutation	SNP	A	A	G	rs1142323	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	30	21	0	0.280374	0	A|0.709;G|0.291	0.291	strong	.	HLA-DQA1	52	.	NM_002122	exon2	c.A188G	p.E63G	ACCTGGAGAGGAA	.	PASS	Atlas-SNP
TSR2	90121	hgsc.bcm.edu	37	X	54469894	54469894	+	Silent	SNP	T	T	C	rs36032873	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	93	61	0	1	0	T|0.996;C|0.004	0.004	strong	.	TSR2	15	.	NM_058163	exon3	c.T234C	p.D78D	GTTTGATACAGTT	.	PASS	Atlas-SNP
FAXDC2	10826	hgsc.bcm.edu	37	5	154203121	154203121	+	Missense_Mutation	SNP	C	C	T	rs17641488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	97	99	0	0.95098	0	C|0.950;T|0.050	0.050	strong	.	.	.	.	NM_032385	exon6	c.G398A	p.R133H	ACTGTGCGGATAG	.	PASS	Atlas-SNP
TRIM46	80128	hgsc.bcm.edu	37	1	155149718	155149718	+	Silent	SNP	G	G	A	rs3814316	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	68	108	0	0.544	0	G|0.609;A|0.391	0.391	strong	TRIM46,colon,carcinoma,0,1	TRIM46	79	1	NM_025058	exon5	c.G861A	p.T287T	GGACACGGTACAG	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	15	113	0	0.245902	0	G|0.965;A|0.035	0.035	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.G730A	p.A244T	CAGGCCGCCACGC	.	PASS	Atlas-SNP
ALKBH5	54890	hgsc.bcm.edu	37	17	18088094	18088094	+	Silent	SNP	C	C	T	rs11078411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	90	66	0	0.967742	0	C|0.787;T|0.213	0.213	strong	.	ALKBH5	24	.	NM_017758	exon1	c.C537T	p.H179H	GGAGCACCGCGTC	.	PASS	Atlas-SNP
LYPD6B	130576	hgsc.bcm.edu	37	2	150071221	150071221	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	4	148	1	0.0213904	0.00675676	.	.	none	LYPD6B,NS,carcinoma,+2,1	LYPD6B	25	1	NM_177964	exon7	c.G621A	p.L207L	ATTGCTGTGATGC	.	scavenged	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139694521	139694521	+	Missense_Mutation	SNP	T	T	G	rs4546744	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	18	20	0	0.545455	0	T|0.772;G|0.228	0.228	strong	KIAA1984,NS,carcinoma,0,1	KIAA1984	39	1	NM_001039374	exon4	c.T338G	p.L113R	TCCACCTGGTGCG	.	PASS	Atlas-SNP
ULBP1	80329	hgsc.bcm.edu	37	6	150285209	150285209	+	Silent	SNP	G	G	C	rs61742437	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	12	99	0	0.116505	0	G|0.819;C|0.181	0.181	strong	.	ULBP1	25	.	NM_025218	exon1	c.G24C	p.A8A	CCCCGCGTTCCTT	.	PASS	Atlas-SNP
TBX1	6899	hgsc.bcm.edu	37	22	19751829	19751829	+	Silent	SNP	C	C	T	rs2301558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	37	31	0	0.925	0	C|0.672;T|0.328	0.328	strong	.	TBX1	62	.	NM_080647	exon5	c.C664T	p.L222L	AACAACCTACTGG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632724	32632724	+	Missense_Mutation	SNP	C	C	T	rs1049083	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	14	0	0	0.388889	.	C|0.828;T|0.172	0.172	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.G230A	p.G77E	TACACCCCCACGT	.	PASS	Atlas-SNP
LAMC3	10319	hgsc.bcm.edu	37	9	133914570	133914570	+	Silent	SNP	G	G	A	rs2293518	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	32	65	0	0.457143	0	G|0.809;A|0.191	0.191	strong	LAMC3,NS,adenoma,0,1	LAMC3	167	1	NM_006059	exon6	c.G1218A	p.T406T	GCCCACGGTGACT	.	PASS	Atlas-SNP
TPR	7175	hgsc.bcm.edu	37	1	186291512	186291512	+	Silent	SNP	T	T	C	rs10911846	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	324	165	311	1	0.509259	0.00321543	T|0.965;C|0.035	0.035	strong	.	TPR	441	.	NM_003292	exon45	c.A6399G	p.T2133T	TGGAACTGTTCTG	.	PASS	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	37	17	48628470	48628470	+	Missense_Mutation	SNP	T	T	A	rs9913430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	36	69	1	0.507042	0.0144928	T|0.605;A|0.395	0.395	strong	SPATA20,colon,carcinoma,0,1	SPATA20	59	1	NM_022827	exon12	c.T1495A	p.S499T	CTCAATTCAGGGC	.	scavenged	Atlas-SNP
ARPC1B	10095	hgsc.bcm.edu	37	7	98985781	98985781	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	3	187	0	0.0163043	0	.	.	none	ARPC1B,NS,carcinoma,-2,1	ARPC1B	41	1	NM_005720	exon4	c.C289T	p.R97W	ATCAACCGGGCTG	.	scavenged	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5749171	5749171	+	Missense_Mutation	SNP	A	A	G	rs72983139	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	34	33	0	0.566667	0	A|0.957;G|0.043	0.043	strong	.	.	.	.	NM_152784	exon11	c.A964G	p.I322V	CTGGGCATCGTGC	.	PASS	Atlas-SNP
KLHL33	123103	hgsc.bcm.edu	37	14	20897676	20897676	+	Missense_Mutation	SNP	T	T	C	rs1953225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	22	52	0	0.4	0	T|0.747;C|0.253	0.253	strong	.	KLHL33	37	.	NM_001109997	exon3	c.A1034G	p.E345G	TTGAGCTCAGGGT	.	PASS	Atlas-SNP
KIF24	347240	hgsc.bcm.edu	37	9	34257979	34257979	+	Silent	SNP	C	C	T	rs76547823	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	75	103	1	0.528169	0.00970874	C|0.977;T|0.023	0.023	strong	KIF24,NS,carcinoma,0,2	KIF24	64	2	NM_194313	exon11	c.G1626A	p.R542R	TTTGACCCTGTAA	.	scavenged	Atlas-SNP
TOPBP1	11073	hgsc.bcm.edu	37	3	133329943	133329943	+	Silent	SNP	G	G	A	rs1444601	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	235	234	227	0	0.995745	0	G|0.298;A|0.702	0.702	strong	.	TOPBP1	218	.	NM_007027	exon25	c.C4078T	p.L1360L	CAGTCAGAACATC	.	PASS	Atlas-SNP
DPPA3	359787	hgsc.bcm.edu	37	12	7867847	7867847	+	Missense_Mutation	SNP	G	G	C	rs41449345	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	67	146	0	0.468531	0	G|0.700;C|0.300	0.300	strong	DPPA3,NS,carcinoma,0,1	DPPA3	26	1	NM_199286	exon2	c.G151C	p.E51Q	AGTAGCGAATCTG	.	PASS	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136555659	136555659	+	Missense_Mutation	SNP	T	T	C	rs2322659	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	34	48	0	0.53125	0	T|0.466;C|0.534	0.534	strong	LCT,NS,carcinoma,-1,2	LCT	309	2	NM_002299	exon13	c.A4916G	p.N1639S	ACCTCATTGTAAT	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43327793	43327793	+	Silent	SNP	C	C	T	rs3746904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	38	56	0	0.558824	0	C|0.655;T|0.345	0.345	strong	C2CD2,NS,carcinoma,0,1	C2CD2	47	1	NM_015500	exon9	c.G1119A	p.S373S	CAGCACCGAGCTG	.	PASS	Atlas-SNP
GCC1	79571	hgsc.bcm.edu	37	7	127224286	127224286	+	Silent	SNP	A	A	G	rs3735642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	69	191	0	0.425926	0	A|0.765;G|0.235	0.235	strong	.	GCC1	83	.	NM_024523	exon1	c.T951C	p.D317D	CCGGGGATCTGGC	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38151170	38151170	+	Silent	SNP	G	G	A	rs11704996	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	48	121	0	0.417391	0	G|0.950;A|0.050	0.050	strong	TRIOBP_ENST00000344404,NS,carcinoma,+2,2	TRIOBP	262	2	NM_001039141	exon14	c.G5550A	p.V1850V	CGCGGTGCAGCGC	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19447819	19447819	+	Silent	SNP	T	T	C	rs35802543	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	260	230	230	0	0.884615	0	T|0.921;C|0.079	0.079	strong	.	UBR4	415	.	NM_020765	exon68	c.A10005G	p.A3335A	TGCCAGTGCAGCG	.	PASS	Atlas-SNP
DRP2	1821	hgsc.bcm.edu	37	X	100490933	100490933	+	Missense_Mutation	SNP	G	G	C	rs7066252	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	81	73	0	1	0	0|0.014;C|0.134	0.134	strong	.	DRP2	98	.	NM_001939	exon4	c.G202C	p.V68L	GGGTCTGTTGGTG	.	PASS	Atlas-SNP
ABR	29	hgsc.bcm.edu	37	17	1028676	1028676	+	Missense_Mutation	SNP	C	C	T	rs117732533	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	38	56	0	0.535211	0	C|0.992;T|0.008	0.008	strong	.	ABR	119	.	NM_021962	exon2	c.G88A	p.D30N	CTCCGTCGTACTC	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3886919	3886919	+	Silent	SNP	C	C	T	rs3749348	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	23	68	0	0.418182	0	C|0.817;T|0.183	0.183	strong	.	LRRN1	82	.	NM_020873	exon2	c.C594T	p.I198I	CATGATCGGAGAA	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	15607	15607	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	6	6	8	0	1	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.A861G	p.K287K	TAACAAACTAGGA	.	PASS	Atlas-SNP
CBWD6	644019	hgsc.bcm.edu	37	9	69247582	69247582	+	Splice_Site	SNP	G	G	C	rs76283403		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	8	61	1	0.173913	0.0163934	G|0.500;C|0.500	0.500	weak	CBWD6,NS,neuroblastoma,0,1	CBWD6	19	1	NM_001085457	exon6	c.431-1C>G	.	CTGCACGTGAAAA	.	scavenged	Atlas-SNP
CEP70	80321	hgsc.bcm.edu	37	3	138289221	138289221	+	Missense_Mutation	SNP	C	C	T	rs1673607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	285	122	266	0	0.42807	0	C|0.378;T|0.622	0.622	strong	.	CEP70	51	.	NM_024491	exon6	c.G404A	p.S135N	GCCCTACTTAGTG	.	PASS	Atlas-SNP
PPIL2	23759	hgsc.bcm.edu	37	22	22039199	22039199	+	Silent	SNP	C	C	T	rs861833	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	30	49	0	0.47619	0	C|0.901;T|0.099	0.099	strong	PPIL2,colon,carcinoma,0,1	PPIL2	38	1	NM_014337	exon10	c.C711T	p.N237N	GCTGAACGCTGTG	.	PASS	Atlas-SNP
SLIT3	6586	hgsc.bcm.edu	37	5	168244447	168244447	+	Silent	SNP	C	C	G	rs4867964	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	57	97	0	0.475	0	C|0.847;G|0.153	0.153	strong	.	SLIT3	224	.	NM_001271946	exon8	c.G651C	p.L217L	GCAGTACAGGTGG	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194081089	194081089	+	Silent	SNP	C	C	T	rs11713861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	118	164	0	0.592965	0	C|0.792;T|0.208	0.208	strong	.	LRRC15	137	.	NM_001135057	exon3	c.G702A	p.L234L	CTGCTGCAGAGCC	.	PASS	Atlas-SNP
CLYBL	171425	hgsc.bcm.edu	37	13	100511247	100511247	+	Missense_Mutation	SNP	G	G	A	rs35680839	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	36	78	0	0.514286	0	G|0.956;A|0.044	0.044	strong	.	CLYBL	48	.	NM_206808	exon3	c.G382A	p.V128I	TCCCGGGTCCTTC	.	PASS	Atlas-SNP
SOS2	6655	hgsc.bcm.edu	37	14	50585248	50585248	+	Silent	SNP	C	C	T	rs2227276	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	81	173	0	0.529412	0	T|0.202;C|0.798	0.202	strong	.	SOS2	195	.	NM_006939	exon23	c.G3813A	p.P1271P	TCGACGCGGTACC	.	PASS	Atlas-SNP
CCDC61	729440	hgsc.bcm.edu	37	19	46518651	46518651	+	Missense_Mutation	SNP	A	A	G	rs7895	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	11	30	0	0.34375	0	A|0.897;G|0.103	0.103	strong	.	CCDC61	32	.	NM_001267723	exon7	c.A811G	p.T271A	CTGAAGACGCTGA	.	PASS	Atlas-SNP
OR51I2	390064	hgsc.bcm.edu	37	11	5475118	5475118	+	Missense_Mutation	SNP	A	A	G	rs12577167	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	259	128	241	0	0.494208	0	A|0.857;G|0.143	0.143	strong	.	OR51I2	76	.	NM_001004754	exon1	c.A400G	p.T134A	TATGCAACTGTGC	.	PASS	Atlas-SNP
SETD4	54093	hgsc.bcm.edu	37	21	37417997	37417997	+	Silent	SNP	G	G	A	rs79501672	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	69	134	0	0.5	0	G|0.989;A|0.011	0.011	strong	.	SETD4	37	.	NM_001007259	exon6	c.C609T	p.T203T	GTTGACGGTGCAC	.	PASS	Atlas-SNP
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs76491286		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1202	541	462	2	0.450083	0.004329	.	.	weak	ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	NM_005435	exon2	c.C1040T	p.T347I	GTCAAACCTTTTT	.	scavenged	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76922868	76922868	+	Silent	SNP	C	C	T	rs41298757	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	25	35	0	0.581395	0	C|0.975;T|0.025	0.025	strong	.	MYO7A	164	.	NM_000260	exon46	c.C6240T	p.S2080S	ATAGTCCATCGTC	.	PASS	Atlas-SNP
C1orf68	100129271	hgsc.bcm.edu	37	1	152692472	152692472	+	Missense_Mutation	SNP	A	A	C	rs873775	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	204	221	0	0.990291	0	A|0.656;C|0.344	0.344	strong	C1orf68,NS,malignant_melanoma,-1,2	C1orf68	19	2	NM_001024679	exon1	c.A475C	p.T159P	TGTGTCACTGACC	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079643	31079643	+	Missense_Mutation	SNP	T	T	C	rs1265054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	90	89	0	0.989011	0	T|0.473;C|0.527	0.527	strong	.	C6orf15	29	.	NM_014070	exon2	c.A493G	p.K165E	AAGCCTTGGGTGA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	rs199592093	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	596	32	479	0	0.0536913	0	.	.	weak	.	MUC6	408	.	NM_005961	exon31	c.A5279C	p.E1760A	GTGACTTCAGGAT	.	PASS	Atlas-SNP
GIMAP6	474344	hgsc.bcm.edu	37	7	150325175	150325175	+	Missense_Mutation	SNP	C	C	T	rs13234724	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	21	46	0	0.411765	0	C|0.832;G|0.000;T|0.168	0.168	strong	GIMAP6,NS,carcinoma,+2,2	GIMAP6	60	2	NM_001244072	exon3	c.G721A	p.G241S	GGGAGCCGCCAGC	.	PASS	Atlas-SNP
ZNF610	162963	hgsc.bcm.edu	37	19	52856955	52856955	+	Silent	SNP	C	C	T	rs1961205	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	35	29	0	1	0	C|0.610;T|0.390	0.390	strong	ZNF610,NS,carcinoma,+1,2	ZNF610	84	2	NM_001161427	exon4	c.C84T	p.D28D	CATGGACGTGGCC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2037833	2037833	+	Silent	SNP	G	G	C	rs2294061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	48	125	0	0.40678	0	G|0.783;C|0.217	0.217	strong	.	MYOM2	251	.	NM_003970	exon15	c.G1647C	p.S549S	GTAGTCGGTGGTG	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26810777	26810777	+	Silent	SNP	T	T	C	rs2291264	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	83	160	0	0.601449	0	T|0.606;C|0.394	0.394	strong	.	ITPR2	270	.	NM_002223	exon18	c.A2055G	p.S685S	GTCATCTGAAAGG	.	PASS	Atlas-SNP
REC8	9985	hgsc.bcm.edu	37	14	24642348	24642348	+	Silent	SNP	C	C	T	rs11547058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	21	62	0	0.428571	0	C|0.862;T|0.138	0.138	strong	.	REC8	47	.	NM_001048205	exon4	c.C282T	p.H94H	CCAGCACATCTTG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608873	26608873	+	Missense_Mutation	SNP	T	T	A	rs1134583	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	35	30	1	0.777778	0.0333333	T|0.870;A|0.130	0.130	strong	UBXN11,NS,carcinoma,0,1	UBXN11	54	1	NM_183008	exon16	c.A1480T	p.S494C	CGGGACTGGGGCC	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911306	29911306	+	Missense_Mutation	SNP	C	C	T	rs9391665	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	24	182	0	0.184615	0	C|0.855;T|0.145	0.145	strong	HLA-A,NS,adenoma,0,2	HLA-A	89	2	NM_001242758	exon3	c.C605T	p.T202M	AGGAGACGCTGCA	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50667105	50667105	+	Missense_Mutation	SNP	T	T	C	rs2228529	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	143	128	0	0.986207	0	T|0.826;C|0.173	0.173	strong	ERCC6,NS,carcinoma,0,1	ERCC6	162	1	NM_000124	exon21	c.C4238G	p.P1413R	GCTTCCTGCAGGT	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46875683	46875683	+	Missense_Mutation	SNP	C	C	G	rs61739237	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	47	107	0	0.412281	0	C|0.976;G|0.024	0.024	strong	.	COL18A1	129	.	NM_030582	exon1	c.C239G	p.P80R	GCAGCCCTGAGCC	.	PASS	Atlas-SNP
CWC22	57703	hgsc.bcm.edu	37	2	180810358	180810358	+	Missense_Mutation	SNP	C	C	T	rs71425650	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	78	159	0	0.527027	0	C|0.832;T|0.168	0.168	strong	.	CWC22	62	.	NM_020943	exon20	c.G2225A	p.R742K	TGTTTCCTATCAT	.	PASS	Atlas-SNP
DHCR7	1717	hgsc.bcm.edu	37	11	71152459	71152459	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	68	155	0	0.478873	0	.	.	none	DHCR7_ENST00000355527,NS,haematopoietic_neoplasm,-1,2	DHCR7	98	2	NM_001163817	exon6	c.G440A	p.G147D	TGCAGGCCATTGA	.	PASS	Atlas-SNP
ARL16	339231	hgsc.bcm.edu	37	17	79650828	79650828	+	Missense_Mutation	SNP	T	T	G	rs8066889	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	20	24	0	0.952381	0	T|0.736;G|0.264	0.264	strong	.	ARL16	14	.	NM_001040025	exon1	c.A28C	p.S10R	CGCGGCTCAAGGC	.	PASS	Atlas-SNP
C7orf62	219557	hgsc.bcm.edu	37	7	88423881	88423881	+	Missense_Mutation	SNP	T	T	C	rs2293583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	48	120	0	0.45283	0	T|0.902;C|0.098	0.098	strong	.	C7orf62	63	.	NM_152706	exon2	c.A376G	p.I126V	GTTGAATAAAAAA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392631	40392631	+	Missense_Mutation	SNP	G	G	A	rs80068592	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	390	126	362	0	0.323077	0	G|0.772;A|0.228	0.228	strong	.	FCGBP	416	.	NM_003890	exon16	c.C7873T	p.P2625S	AGTCGGGCACCAC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329851	55329851	+	Missense_Mutation	SNP	A	A	G	rs145262243	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	20	26	0	0.571429	0	A|0.992;G|0.008	0.008	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.A152G	p.Y51C	GTCACTATCGTCA	.	PASS	Atlas-SNP
TRIM17	51127	hgsc.bcm.edu	37	1	228602459	228602459	+	Silent	SNP	G	G	A	rs142505325	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	56	115	0	0.459016	0	G|0.999;A|0.001	0.001	strong	.	TRIM17	66	.	NM_001024940	exon2	c.C315T	p.P105P	CTTGAGGGGCTCG	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79657391	79657391	+	Silent	SNP	G	G	A	rs1984195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	9	116	0	0.155172	0	G|0.542;A|0.458	0.458	strong	.	PHIP	177	.	NM_017934	exon36	c.C4155T	p.V1385V	AAGTCTGACATCT	.	PASS	Atlas-SNP
RSPH10B	222967	hgsc.bcm.edu	37	7	6005323	6005323	+	Missense_Mutation	SNP	C	C	T	rs200962894	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1317	358	962	0	0.27183	0	C|0.950;T|0.050	0.050	strong	RSPH10B,NS,carcinoma,0,2	RSPH10B	28	2	NM_173565	exon4	c.G275A	p.R92H	AGCCCACGAACCT	.	scavenged	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15713446	15713446	+	Silent	SNP	C	C	T	rs2302463	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	45	137	0	0.384615	0	C|0.946;T|0.054	0.054	strong	BST1,NS,carcinoma,0,1	BST1	30	1	NM_004334	exon4	c.C468T	p.S156S	CCAATCCTGCCCT	.	PASS	Atlas-SNP
LTBP2	4053	hgsc.bcm.edu	37	14	74992800	74992800	+	Silent	SNP	A	A	G	rs699374	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	42	90	0	0.5	0	A|0.644;G|0.356	0.356	strong	LTBP2,NS,adenoma,0,1	LTBP2	158	1	NM_000428	exon14	c.T2406C	p.T802T	TGCATGAGTGACA	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129612808	129612808	+	Silent	SNP	A	A	G	rs1027199	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	35	64	0	1	0	A|0.726;G|0.274	0.274	strong	.	LAMA2	481	.	NM_000426	exon20	c.A2799G	p.Q933Q	CAGTCAAACTGGA	.	PASS	Atlas-SNP
SLC22A10	387775	hgsc.bcm.edu	37	11	63064823	63064823	+	Silent	SNP	T	T	C	rs576641	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	90	144	0	0.529412	0	T|0.413;C|0.587	0.587	strong	.	SLC22A10	79	.	NM_001039752	exon3	c.T555C	p.I185I	TGCCATTACTGAC	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52509501	52509501	+	Silent	SNP	T	T	C	rs3818186	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	111	89	0	1	0	T|0.667;C|0.333	0.333	strong	.	NID2	201	.	NM_007361	exon6	c.A1578G	p.E526E	ATTACCTTCAGGC	.	PASS	Atlas-SNP
PEBP4	157310	hgsc.bcm.edu	37	8	22584718	22584718	+	Missense_Mutation	SNP	T	T	C	rs1129474	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	42	93	0	0.518519	0	T|0.516;C|0.484	0.484	strong	PEBP4,NS,carcinoma,0,1	PEBP4	23	1	NM_144962	exon5	c.A373G	p.K125E	TCCCTTTCTTCAG	.	PASS	Atlas-SNP
PELI1	57162	hgsc.bcm.edu	37	2	64327592	64327592	+	Silent	SNP	T	T	C	rs329497	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	48	138	0	0.448598	0	T|0.705;C|0.295	0.295	strong	.	PELI1	34	.	NM_020651	exon4	c.A243G	p.L81L	CCGAGATAAAGTA	.	PASS	Atlas-SNP
KCNK13	56659	hgsc.bcm.edu	37	14	90651079	90651079	+	Missense_Mutation	SNP	G	G	A	rs150186575	bycluster;by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	74	129	0	0.524823	0	G|0.999;T|0.001	.	alt	.	KCNK13	76	.	NM_022054	exon2	c.G959A	p.R320Q	GCGTCCGGAACCG	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56505175	56505175	+	Silent	SNP	T	T	A	rs113432929	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	69	168	0	0.442308	0	T|0.997;A|0.003	0.003	strong	.	DST	1427	.	NM_001723	exon4	c.A645T	p.S215S	CATCCCTGATGAC	.	PASS	Atlas-SNP
NPBWR2	2832	hgsc.bcm.edu	37	20	62737318	62737318	+	Silent	SNP	G	G	A	rs13036542	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	38	46	0	0.481013	0	G|0.545;A|0.455	0.455	strong	.	NPBWR2	36	.	NM_005286	exon1	c.C867T	p.P289P	GGTCTGGGGCAGG	.	PASS	Atlas-SNP
ELFN2	114794	hgsc.bcm.edu	37	22	37770066	37770066	+	Silent	SNP	G	G	T	rs8142615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	31	64	0	0.449275	0	G|0.597;T|0.403	0.403	strong	ELFN2,colon,carcinoma,0,1	ELFN2	89	1	NM_052906	exon3	c.C1509A	p.I503I	CACCTCGATATAG	.	PASS	Atlas-SNP
INSR	3643	hgsc.bcm.edu	37	19	7163154	7163154	+	Silent	SNP	G	G	A	rs2963	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	50	180	0	0.314465	0	G|0.876;A|0.124	0.124	strong	.	INSR	265	.	NM_000208	exon9	c.C1918T	p.L640L	ACTTCAGAATAAT	.	PASS	Atlas-SNP
RAD52	5893	hgsc.bcm.edu	37	12	1022569	1022569	+	Nonsense_Mutation	SNP	A	A	C	rs4987208	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	89	125	0	0.546012	0	A|0.979;C|0.021	0.021	strong	.	RAD52	27	.	NM_134424	exon12	c.T1245G	p.Y415X	TGGATCATATTTC	.	PASS	Atlas-SNP
STX2	2054	hgsc.bcm.edu	37	12	131306314	131306314	+	Missense_Mutation	SNP	C	C	G	rs17564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	55	158	0	0.486726	0	C|0.443;G|0.557	0.557	strong	.	STX2	66	.	NM_194356	exon3	c.G125C	p.S42T	TCAATACTGTTTC	.	PASS	Atlas-SNP
WDR64	128025	hgsc.bcm.edu	37	1	241901757	241901757	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	3	145	0	0.0225564	0	.	.	none	WDR64_ENST00000366552,NS,carcinoma,+2,1	WDR64	234	1	NM_144625	exon10	c.G1257A	p.M419I	CTCTATGATATAT	.	scavenged	Atlas-SNP
MAP4K1	11184	hgsc.bcm.edu	37	19	39101772	39101772	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	65	117	0	0.396341	0	.	.	none	.	MAP4K1	165	.	NM_007181	exon11	c.G729A	p.W243X	AGCCGACCTTGGG	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883680	152883680	+	Silent	SNP	A	A	G	rs7535306	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	54	113	0	0.469565	0	A|0.667;G|0.333	0.333	strong	IVL,NS,lymphoid_neoplasm,+1,1	IVL	100	1	NM_005547	exon2	c.A1407G	p.Q469Q	GAAGCAACTGGAG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549607	32549607	+	Missense_Mutation	SNP	T	T	G	rs17405219	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	24	206	0	0.258065	0	.	.	weak	.	HLA-DRB1	41	.	NM_002124	exon3	c.A379C	p.K127Q	TCACCTTAGGTTG	.	PASS	Atlas-SNP
PAX7	5081	hgsc.bcm.edu	37	1	19018405	19018405	+	Silent	SNP	G	G	A	rs2076020	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	75	81	0	0.903614	0	G|0.933;A|0.067	0.067	strong	PAX7_ENST00000420770,NS,carcinoma,+2,2	PAX7	127	2	NM_002584	exon5	c.G744A	p.E248E	CCGCGAGGAGCTG	.	PASS	Atlas-SNP
CEP89	84902	hgsc.bcm.edu	37	19	33372814	33372814	+	Missense_Mutation	SNP	G	G	A	rs34626245	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	23	36	0	0.621622	0	G|0.930;A|0.070	0.070	strong	.	CEP89	82	.	NM_032816	exon18	c.C2071T	p.R691W	GGTGCCGCATCTC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3228891	3228891	+	Silent	SNP	A	A	G	rs1635235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	117	129	0	0.991525	0	A|0.431;0|0.003	.	strong	.	MXRA5	815	.	NM_015419	exon7	c.T7353C	p.T2451T	CCGCACAGTGGTG	.	PASS	Atlas-SNP
OR4C46	119749	hgsc.bcm.edu	37	11	51516191	51516191	+	Missense_Mutation	SNP	G	G	A	rs140000110	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	16	63	0	0.307692	0	G|0.995;A|0.005	0.005	strong	.	OR4C46	96	.	NM_001004703	exon1	c.G910A	p.D304N	AGAAAGGACATTT	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84229559	84229559	+	Silent	SNP	T	T	C	rs2303238	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	30	28	0	0.967742	0	T|0.179;C|0.821	0.821	strong	ADAD2,NS,carcinoma,0,1	ADAD2	46	1	NM_139174	exon8	c.T1437C	p.S479S	AGCCAGTGACAAG	.	PASS	Atlas-SNP
TPX2	22974	hgsc.bcm.edu	37	20	30382315	30382315	+	Silent	SNP	A	A	G	rs3203770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	41	79	0	0.61194	0	A|0.722;G|0.278	0.278	strong	.	TPX2	61	.	NM_012112	exon15	c.A1797G	p.R599R	TGACAGAAGAGGT	.	PASS	Atlas-SNP
FCGR2B	2213	hgsc.bcm.edu	37	1	161642985	161642985	+	Silent	SNP	G	G	A	rs182968886	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	673	579	526	2	0.860327	0.00380228	G|0.895;A|0.105	0.105	strong	.	FCGR2B	33	.	NM_001002274	exon4	c.G612A	p.L204L	CACGCTGTACTCA	.	PASS	Atlas-SNP
AXIN2	8313	hgsc.bcm.edu	37	17	63554591	63554591	+	Missense_Mutation	SNP	G	G	A	rs2240308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	25	64	0	0.555556	0	G|0.641;A|0.359	0.359	strong	.	AXIN2	92	.	NM_004655	exon2	c.C148T	p.P50S	AGACAGGCATGGG	.	PASS	Atlas-SNP
RASEF	158158	hgsc.bcm.edu	37	9	85627408	85627408	+	Missense_Mutation	SNP	G	G	A	rs4146960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	47	87	0	0.465347	0	G|0.470;A|0.530	0.530	strong	RASEF,NS,carcinoma,+2,1	RASEF	69	1	NM_152573	exon5	c.C784T	p.R262C	TTACGCGTTTTGA	.	PASS	Atlas-SNP
CC2D2A	57545	hgsc.bcm.edu	37	4	15516389	15516389	+	Silent	SNP	C	C	T	rs2286976	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	49	124	0	0.453704	0	C|0.900;T|0.100	0.100	strong	.	CC2D2A	158	.	NM_001080522	exon10	c.C777T	p.H259H	AGATCACGTGGCT	.	PASS	Atlas-SNP
DNAH14	127602	hgsc.bcm.edu	37	1	225155191	225155191	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	37	94	0	0.411111	0	.	.	none	.	DNAH14	300	.	NM_144989	exon6	c.C557G	p.S186C	CTAAATCCCTTTA	.	PASS	Atlas-SNP
DMRT3	58524	hgsc.bcm.edu	37	9	990840	990840	+	Silent	SNP	C	C	T	rs7021244	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	51	106	0	0.536842	0	C|0.827;N|0.000	.	strong	DMRT3,NS,carcinoma,+2,2	DMRT3	83	2	NM_021240	exon2	c.C1254T	p.V418V	CAGCGTCTTCAGA	.	PASS	Atlas-SNP
SLC25A10	1468	hgsc.bcm.edu	37	17	79682051	79682051	+	Silent	SNP	C	C	T	rs3204270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	69	136	0	0.453947	0	C|0.937;G|0.000;T|0.062	0.062	strong	SLC25A10,NS,carcinoma,0,2	SLC25A10	24	2	NM_001270888	exon2	c.C162T	p.T54T	GCGTACCGACGGC	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66432717	66432717	+	Missense_Mutation	SNP	T	T	C	rs148946048	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	55	113	0	0.55	0	T|0.995;C|0.005	0.005	strong	.	LRIG1	138	.	NM_015541	exon16	c.A2597G	p.N866S	TGCCCATTGGCCT	.	PASS	Atlas-SNP
FAM3D	131177	hgsc.bcm.edu	37	3	58625875	58625875	+	Missense_Mutation	SNP	C	C	A	rs33966924	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	41	89	0	0.418367	0	C|0.868;A|0.132	0.132	strong	.	FAM3D	29	.	NM_138805	exon7	c.G352T	p.A118S	CAAATGCCTTCTG	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32598656	32598656	+	Silent	SNP	C	C	T	rs2290214	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	48	103	0	0.527473	0	C|0.781;T|0.219	0.219	strong	.	AVL9	66	.	NM_015060	exon10	c.C795T	p.S265S	TGCATCCACTGCT	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3238167	3238167	+	Silent	SNP	T	T	G	rs1635245	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	100	135	0	0.990099	0	T|0.500;G|0.500	0.500	strong	.	MXRA5	815	.	NM_015419	exon5	c.A5559C	p.P1853P	GATTTGTGGCTTT	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13754394	13754394	+	Silent	SNP	C	C	T	rs2401809	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	235	127	231	0	0.540426	0	C|0.669;T|0.331	0.331	strong	.	DNAH5	868	.	NM_001369	exon62	c.G10473A	p.T3491T	GATGAGCGTGGAA	.	PASS	Atlas-SNP
NFX1	4799	hgsc.bcm.edu	37	9	33369943	33369943	+	Silent	SNP	G	G	A	rs2230122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	60	108	0	0.6	0	G|0.943;A|0.057	0.057	strong	.	NFX1	85	.	NM_002504	exon24	c.G3330A	p.E1110E	CAAGGAGCCAATA	.	PASS	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049939	69049939	+	Missense_Mutation	SNP	G	G	T	rs4241344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	51	53	0	1	0	G|0.789;T|0.211	0.211	strong	.	ARHGAP25	175	.	NM_001007231	exon10	c.G1668T	p.R556S	GCAGAGGATGGTC	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52710715	52710715	+	Silent	SNP	G	G	A	rs2857669	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	76	184	0	0.436782	0	G|0.593;A|0.407	0.407	strong	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon5	c.C843T	p.A281A	GATCTCGGCAACG	.	PASS	Atlas-SNP
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939664	12939664	+	Missense_Mutation	SNP	A	A	T	rs78455617	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	5	100	0	0.0462963	0	A|0.881;T|0.119	0.119	strong	PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	1	NM_001009611	exon4	c.T1138A	p.F380I	GCTCAAAGCAGCG	.	scavenged	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2152129	2152129	+	Silent	SNP	A	A	G	rs79276175		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	18	178	0	0.144	0	A|0.500;G|0.500	0.500	weak	PKD1,NS,carcinoma,0,1	PKD1	184	1	NM_000296	exon26	c.T9330C	p.P3110P	ACAGAAAGGGATG	.	scavenged	Atlas-SNP
C2orf57	165100	hgsc.bcm.edu	37	2	232457857	232457857	+	Silent	SNP	T	T	C	rs17199614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	37	88	0	0.402174	0	T|0.976;C|0.024	0.024	strong	.	C2orf57	35	.	NM_152614	exon1	c.T195C	p.S65S	AACATCTGGAGAC	.	PASS	Atlas-SNP
NUP210	23225	hgsc.bcm.edu	37	3	13395475	13395475	+	Missense_Mutation	SNP	G	G	C	rs2280085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	99	202	0	0.512953	0	G|0.807;C|0.193	0.193	strong	.	NUP210	182	.	NM_024923	exon17	c.C2461G	p.P821A	GCTCAGGCTCGAT	.	PASS	Atlas-SNP
OR7D2	162998	hgsc.bcm.edu	37	19	9296664	9296664	+	Silent	SNP	T	T	C	rs56246934	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	34	72	0	0.485714	0	T|0.761;C|0.239	0.239	strong	.	OR7D2	55	.	NM_175883	exon1	c.T207C	p.V69V	CTGGGTTGACATC	.	PASS	Atlas-SNP
CYP39A1	51302	hgsc.bcm.edu	37	6	46620240	46620240	+	Missense_Mutation	SNP	C	C	T	rs61661828	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	41	76	0	0.44086	0	C|0.995;T|0.005	0.005	strong	.	CYP39A1	41	.	NM_016593	exon1	c.G80A	p.R27H	GGTCTACGCAAAT	.	PASS	Atlas-SNP
ZMIZ1	57178	hgsc.bcm.edu	37	10	81064950	81064950	+	Silent	SNP	G	G	C	rs34305410	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	40	112	0	0.493827	0	G|0.957;C|0.043	0.043	strong	.	ZMIZ1	101	.	NM_020338	exon20	c.G2316C	p.L772L	GCAGCTGAATTGC	.	PASS	Atlas-SNP
MAGEH1	28986	hgsc.bcm.edu	37	X	55479299	55479299	+	Silent	SNP	G	G	A	rs11545211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	38	31	0	1	0	0|0.003;A|0.216	0.216	strong	.	MAGEH1	37	.	NM_014061	exon1	c.G492A	p.G164G	CTGGGGGCCCCGA	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970812	45970812	+	Missense_Mutation	SNP	G	G	A	rs2329834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	69	166	0	0.570248	0	G|0.491;A|0.509	0.509	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.C530T	p.P177L	TGACACGGGGAGG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130134492	130134492	+	Missense_Mutation	SNP	T	T	C	rs16827497	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	271	271	226	1	1	0.00442478	T|0.539;C|0.461	0.461	strong	.	COL6A5	205	.	NM_153264	exon23	c.T4765C	p.S1589P	AAGGGGTCACAGG	.	PASS	Atlas-SNP
PRODH2	58510	hgsc.bcm.edu	37	19	36303664	36303664	+	Missense_Mutation	SNP	G	G	C	rs3848666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	67	104	0	0.527559	0	G|0.901;C|0.099	0.099	strong	.	PRODH2	68	.	NM_021232	exon2	c.C272G	p.P91R	CTGGAGGGGGGAC	.	PASS	Atlas-SNP
CCDC74B	91409	hgsc.bcm.edu	37	2	130897234	130897234	+	Missense_Mutation	SNP	C	C	T	rs3177472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	283	148	225	0	0.522968	0	C|0.654;T|0.346	0.346	strong	.	CCDC74B	27	.	NM_207310	exon8	c.G1037A	p.R346H	ATGGCACGCTCCG	.	PASS	Atlas-SNP
JPH3	57338	hgsc.bcm.edu	37	16	87678302	87678302	+	Missense_Mutation	SNP	C	C	T	rs144403955	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	34	46	0	0.566667	0	C|0.998;T|0.002	0.002	strong	.	JPH3	95	.	NM_020655	exon2	c.C821T	p.A274V	AGCTGGCGGTCAT	.	PASS	Atlas-SNP
FOXK2	3607	hgsc.bcm.edu	37	17	80543901	80543901	+	Silent	SNP	C	C	T	rs61737960	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	48	85	0	0.489796	0	C|0.986;T|0.014	0.014	strong	.	FOXK2	46	.	NM_004514	exon7	c.C1401T	p.V467V	ACCCGTCGTGCAG	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84229436	84229436	+	Silent	SNP	G	G	A	rs62049905	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	26	20	0	0.65	0	G|0.696;A|0.304	0.304	strong	ADAD2,NS,carcinoma,0,1	ADAD2	46	1	NM_139174	exon8	c.G1314A	p.S438S	CACCTCGGAAGGT	.	PASS	Atlas-SNP
DEFB108B	245911	hgsc.bcm.edu	37	11	71548544	71548544	+	Missense_Mutation	SNP	A	A	G	rs79483234		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	90	206	1	0.46875	0.00485437	.	.	weak	DEFB108B,arm,malignant_melanoma,0,1	DEFB108B	6	1	NM_001002035	exon2	c.A158G	p.Q53R	ATAGCCAACCCTG	.	scavenged	Atlas-SNP
HLA-DOB	3112	hgsc.bcm.edu	37	6	32783086	32783086	+	Silent	SNP	A	A	G	rs7383287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	79	115	0	0.5	0	A|0.838;G|0.162	0.162	strong	.	HLA-DOB	17	.	NM_002120	exon2	c.T96C	p.D32D	CACAAAATCTTCT	.	PASS	Atlas-SNP
FGL1	2267	hgsc.bcm.edu	37	8	17743051	17743051	+	Missense_Mutation	SNP	A	A	T	rs61745164	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	15	33	0	0.441176	0	A|0.973;T|0.027	0.027	strong	.	FGL1	31	.	NM_201553	exon3	c.T13A	p.F5I	AACTGAACACCTT	.	PASS	Atlas-SNP
DDX49	54555	hgsc.bcm.edu	37	19	19030571	19030571	+	Silent	SNP	C	C	T	rs2231992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	71	116	0	0.541985	0	C|0.958;T|0.042	0.042	strong	.	DDX49	37	.	NM_019070	exon1	c.C21T	p.L7L	GGAGCTCGGGCTG	.	PASS	Atlas-SNP
PWWP2A	114825	hgsc.bcm.edu	37	5	159520661	159520661	+	Silent	SNP	T	T	C	rs56251777	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	79	185	0	0.512987	0	T|0.946;C|0.054	0.054	strong	.	PWWP2A	64	.	NM_052927	exon2	c.A996G	p.E332E	CTTTTTTTCAGCA	.	PASS	Atlas-SNP
FSTL4	23105	hgsc.bcm.edu	37	5	132652281	132652281	+	Missense_Mutation	SNP	C	C	T	rs17683306	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	50	133	0	0.526316	0	C|0.936;T|0.064	0.064	strong	.	FSTL4	74	.	NM_015082	exon5	c.G473A	p.R158H	TGCAGACGGGTCT	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	70990054	70990054	+	Missense_Mutation	SNP	T	T	C	rs2465811	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	25	87	0	0.431034	0	C|0.325;N|0.000	0.325	strong	.	PTPRB	676	.	NM_001109754	exon5	c.A1033G	p.S345G	GCAAGCTGGTTGA	.	PASS	Atlas-SNP
ZNF320	162967	hgsc.bcm.edu	37	19	53384197	53384197	+	Silent	SNP	A	A	G	rs61745485	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	48	59	0	1	0	A|0.933;G|0.067	0.067	strong	.	ZNF320	67	.	NM_207333	exon4	c.T1182C	p.F394F	TGTACTAAAAACC	.	PASS	Atlas-SNP
CASP9	842	hgsc.bcm.edu	37	1	15832543	15832543	+	Missense_Mutation	SNP	T	T	C	rs1052576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	235	149	0	0.943775	0	T|0.410;C|0.590	0.590	strong	.	CASP9	40	.	NM_001229	exon5	c.A662G	p.Q221R	TCCTGCTGCGCCA	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79455714	79455714	+	Silent	SNP	C	C	G	rs4975070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	102	118	0	1	0	C|0.485;G|0.515	0.515	strong	.	FRAS1	779	.	NM_025074	exon71	c.C11037G	p.P3679P	GGATCCCAATACA	.	PASS	Atlas-SNP
PIM3	415116	hgsc.bcm.edu	37	22	50354819	50354819	+	Silent	SNP	C	C	A	rs11541025	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	24	0	0	1	.	C|0.669;A|0.331	0.331	strong	.	PIM3	15	.	NM_001001852	exon2	c.C132A	p.A44A	GGGCGCCGTGCTG	.	PASS	Atlas-SNP
BEST1	7439	hgsc.bcm.edu	37	11	61719387	61719387	+	Silent	SNP	T	T	C	rs1800007	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	52	101	0	0.464286	0	T|0.448;C|0.552	0.552	strong	.	BEST1	85	.	NM_004183	exon2	c.T109C	p.L37L	GAGTTCTTAATCT	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220417266	220417266	+	Missense_Mutation	SNP	C	C	T	rs59332477	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	12	5	0	0.8	0	C|0.582;T|0.418	0.418	strong	.	OBSL1	120	.	NM_015311	exon18	c.G5300A	p.R1767Q	TCCTGTCGGATGC	.	PASS	Atlas-SNP
CERS4	79603	hgsc.bcm.edu	37	19	8321946	8321946	+	Silent	SNP	T	T	C	rs36247	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	70	127	0	0.463576	0	T|0.623;C|0.376	0.376	strong	.	.	.	.	NM_024552	exon9	c.T726C	p.S242S	TTCCTCTGACTAC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6550309	6550309	+	Missense_Mutation	SNP	G	G	A	rs2344829	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	99	134	0	0.99	0	G|0.292;A|0.708	0.708	strong	.	DNHD1	198	.	NM_144666	exon12	c.G2305A	p.G769R	AAAGGCGGGTTGC	.	PASS	Atlas-SNP
SPACA7	122258	hgsc.bcm.edu	37	13	113052388	113052388	+	Silent	SNP	A	A	G	rs2296895	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	52	117	0	0.641975	0	A|0.363;G|0.637	0.637	strong	SPACA7,NS,adenoma,0,1	SPACA7	36	1	NM_145248	exon3	c.A177G	p.L59L	GATTTTAGATCTG	.	PASS	Atlas-SNP
RGL4	266747	hgsc.bcm.edu	37	22	24036563	24036563	+	Silent	SNP	G	G	A	rs2070447	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	45	106	0	0.412844	0	G|0.908;A|0.092	0.092	strong	.	RGL4	29	.	NM_153615	exon5	c.G942A	p.S314S	CTCCTCGGTGCAC	.	PASS	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170626943	170626943	+	Silent	SNP	T	T	C	rs3800266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	10	135	0	0.10989	0	T|0.857;C|0.143	0.143	strong	.	FAM120B	108	.	NM_032448	exon2	c.T465C	p.S155S	GTGTTCTTTGCAG	.	PASS	Atlas-SNP
TSC2	7249	hgsc.bcm.edu	37	16	2138269	2138269	+	Silent	SNP	T	T	C	rs1748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	31	73	0	0.360465	0	T|0.695;G|0.000;C|0.305;A|0.000	0.305	strong	.	TSC2	364	.	NM_000548	exon41	c.T5202C	p.D1734D	CACCGATATCTAC	.	PASS	Atlas-SNP
HOXB1	3211	hgsc.bcm.edu	37	17	46608030	46608030	+	Silent	SNP	G	G	A	rs12946855	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	18	30	0	0.375	0	G|0.833;A|0.167	0.167	strong	.	HOXB1	67	.	NM_002144	exon1	c.C237T	p.S79S	GGGCGCGGAGCTG	.	PASS	Atlas-SNP
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138418910	138418910	+	Silent	SNP	G	G	A	rs1026435	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	66	71	0	1	0	G|0.304;A|0.696	0.696	strong	.	ATP6V0A4	93	.	NM_130841	exon15	c.C1662T	p.F554F	GACACCGAAAACC	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121435342	121435342	+	Silent	SNP	C	C	T	rs2259820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	45	116	0	0.436893	0	C|0.718;T|0.282	0.282	strong	.	HNF1A	302	.	NM_000545	exon7	c.C1375T	p.L459L	ACCACCCTGCAGC	.	PASS	Atlas-SNP
CALCRL	10203	hgsc.bcm.edu	37	2	188245439	188245439	+	Missense_Mutation	SNP	A	A	G	rs61739909	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	96	192	0	0.551724	0	A|0.999;G|0.001	0.001	strong	.	CALCRL	73	.	NM_001271751	exon5	c.T260C	p.L87P	GGGCAGAGCTGCA	.	PASS	Atlas-SNP
SLC39A14	23516	hgsc.bcm.edu	37	8	22262321	22262321	+	Missense_Mutation	SNP	T	T	C	rs896378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	100	118	1	1	0.00847458	C|0.584;N|0.000	0.584	strong	.	SLC39A14	59	.	NM_001135153	exon2	c.T98C	p.L33P	CATCCCTGGGTGC	.	PASS	Atlas-SNP
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993884	96993884	+	Silent	SNP	A	A	G	rs1048675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	56	120	0	0.470588	0	A|0.691;C|0.000;G|0.309	0.309	strong	ITPRIPL1,NS,carcinoma,0,1	ITPRIPL1	58	1	NM_178495	exon1	c.A1539G	p.P513P	CATCCCAATCCCT	.	PASS	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	37	14	45644589	45644589	+	Missense_Mutation	SNP	G	G	T	rs1367580	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	21	47	0	0.617647	0	G|0.796;T|0.204	0.204	strong	.	FANCM	225	.	NM_020937	exon14	c.G2632T	p.V878L	GATTCTGTAGATA	.	PASS	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10447194	10447194	+	Missense_Mutation	SNP	T	T	G	rs73224493	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	52	83	0	0.536082	0	T|0.987;G|0.013	0.013	strong	.	ZNF518B	116	.	NM_053042	exon3	c.A759C	p.Q253H	CTTATTTTGAAAT	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152883608	152883608	+	Silent	SNP	G	G	A	rs7545413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	49	129	0	0.4375	0	G|0.664;A|0.336	0.336	strong	.	IVL	100	.	NM_005547	exon2	c.G1335A	p.Q445Q	GGAGCAGCAGCAG	.	PASS	Atlas-SNP
FAM46D	169966	hgsc.bcm.edu	37	X	79698593	79698593	+	Missense_Mutation	SNP	C	C	G	rs1113265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	62	77	0	1	0	C|0.503;0|0.028	.	strong	.	FAM46D	69	.	NM_001170574	exon5	c.C555G	p.D185E	GTTAGACTTCTAC	.	PASS	Atlas-SNP
FAM207A	85395	hgsc.bcm.edu	37	21	46396659	46396659	+	Missense_Mutation	SNP	G	G	C	rs3737075	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	8	31	0	0.25	0	G|0.835;C|0.165	0.165	strong	.	.	.	.	NM_058190	exon6	c.G634C	p.V212L	CCCCTGGTGGCCA	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46896312	46896312	+	Silent	SNP	G	G	T	rs2230688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	37	93	0	0.544118	0	A|0.000;C|0.000;G|0.800;T|0.199	0.199	strong	.	COL18A1	129	.	NM_030582	exon5	c.G1386T	p.T462T	CACCACGCCACCC	.	PASS	Atlas-SNP
KCNE1L	23630	hgsc.bcm.edu	37	X	108868153	108868153	+	Missense_Mutation	SNP	G	G	A	rs17003955	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	19	32	0	0.95	0	0|0.009;A|0.075	0.075	strong	.	KCNE1L	8	.	NM_012282	exon1	c.C97T	p.P33S	GACGAGGGCCAGC	.	PASS	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77704912	77704912	+	Missense_Mutation	SNP	T	T	C	rs8074547	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	77	74	0	1	0	T|0.556;C|0.444	0.444	strong	.	ENPP7	63	.	NM_178543	exon1	c.T11C	p.L4P	GAGGCCTGGCCGT	.	PASS	Atlas-SNP
KCNG4	93107	hgsc.bcm.edu	37	16	84270476	84270476	+	Missense_Mutation	SNP	G	G	A	rs11646443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	55	92	0	0.544554	0	G|0.721;A|0.279	0.279	strong	.	KCNG4	71	.	NM_172347	exon2	c.C616T	p.R206W	GCAGCCGGTTCAT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1266479	1266479	+	Missense_Mutation	SNP	G	G	T	rs202133597	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	350	16	333	6	0.0457143	0.018018	G|0.728;T|0.273	0.273	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.G8369T	p.G2790V	CCACGGGGACTTC	.	scavenged	Atlas-SNP
SHROOM2	357	hgsc.bcm.edu	37	X	9863112	9863112	+	Silent	SNP	A	A	G	rs6530341	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	44	0	1	0	A|0.805;0|0.004	.	strong	.	SHROOM2	139	.	NM_001649	exon4	c.A1164G	p.P388P	CTGCCCACAGGAG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388350	1388350	+	Silent	SNP	G	G	A	rs77782813	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	29	190	0	0.164773	0	G|0.858;A|0.142	0.142	strong	.	CRIPAK	185	.	NM_175918	exon1	c.G51A	p.T17T	TCACACGTGCCCA	.	PASS	Atlas-SNP
TUBAL3	79861	hgsc.bcm.edu	37	10	5435918	5435918	+	Silent	SNP	G	G	A	rs7097775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	59	130	0	0.42446	0	G|0.324;A|0.676	0.676	strong	TUBAL3,NS,carcinoma,0,1	TUBAL3	54	1	NM_024803	exon4	c.C903T	p.A301A	AAAGCAGGCAGTG	.	PASS	Atlas-SNP
PLEKHD1	400224	hgsc.bcm.edu	37	14	69966850	69966850	+	Silent	SNP	G	G	A	rs4902723	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	48	108	0	0.377953	0	G|0.881;A|0.119	0.119	strong	.	PLEKHD1	24	.	NM_001161498	exon2	c.G168A	p.E56E	CAAAGAGAGCTTT	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596641	48596641	+	Silent	SNP	A	A	G	rs75539159	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	71	143	0	0.420118	0	A|0.949;G|0.051	0.051	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.T435C	p.L145L	TCCCACAAGCCTG	.	PASS	Atlas-SNP
LRIG1	26018	hgsc.bcm.edu	37	3	66434643	66434643	+	Missense_Mutation	SNP	T	T	C	rs2306272	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	276	273	272	2	0.98913	0.00735294	T|0.707;C|0.293	0.293	strong	.	LRIG1	138	.	NM_015541	exon14	c.A1843G	p.M615V	GGGCCATGGTGGT	.	PASS	Atlas-SNP
ERAP2	64167	hgsc.bcm.edu	37	5	96231056	96231056	+	Missense_Mutation	SNP	T	T	G	rs34261036	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	40	75	0	0.43956	0	T|0.997;G|0.003	0.003	strong	.	ERAP2	77	.	NM_001130140	exon7	c.T1232G	p.L411R	CAGAGCTGCAATT	.	PASS	Atlas-SNP
CPS1	1373	hgsc.bcm.edu	37	2	211481257	211481257	+	Silent	SNP	C	C	G	rs2287599	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	25	71	0	0.543478	0	C|0.357;G|0.643	0.643	strong	.	CPS1	485	.	NM_001122633	exon22	c.C2697G	p.G899G	GAAAGGCCTCAAC	.	PASS	Atlas-SNP
DLG1	1739	hgsc.bcm.edu	37	3	196865242	196865242	+	Missense_Mutation	SNP	C	C	T	rs1134986	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	29	49	0	0.491525	0	C|0.882;T|0.118	0.118	strong	.	DLG1	120	.	NM_001098424	exon10	c.G833A	p.R278Q	TTTACTCGTAATA	.	PASS	Atlas-SNP
FHAD1	114827	hgsc.bcm.edu	37	1	15599025	15599025	+	Silent	SNP	G	G	A	rs75432354	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	7	48	0	0.106061	0	G|0.874;A|0.126	0.126	strong	.	FHAD1	78	.	NM_052929	exon3	c.G300A	p.P100P	ACCTCCGGTGAGT	.	PASS	Atlas-SNP
NMD3	51068	hgsc.bcm.edu	37	3	160956548	160956548	+	Silent	SNP	A	A	G	rs11539155	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	258	113	290	0	0.437984	0	A|0.972;G|0.028	0.028	strong	.	NMD3	49	.	NM_015938	exon9	c.A687G	p.Q229Q	CTCTCAAGATATC	.	PASS	Atlas-SNP
SCRIB	23513	hgsc.bcm.edu	37	8	144895018	144895018	+	Silent	SNP	C	C	T	rs75171224	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	40	32	0	0.701754	0	C|0.991;T|0.009	0.009	strong	.	SCRIB	192	.	NM_015356	exon8	c.G756A	p.Q252Q	CAGGTTCTGGGAC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs55790575		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	13	42	0	0.433333	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.C1758A	p.D586E	ACACACGTCGACC	.	PASS	Atlas-SNP
PDLIM4	8572	hgsc.bcm.edu	37	5	131607080	131607080	+	Silent	SNP	A	A	G	rs270619	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	10	35	0	0.27027	0	A|0.766;G|0.233	0.233	strong	.	PDLIM4	22	.	NM_003687	exon5	c.A591G	p.P197P	GGAGCCAGCCGAG	.	PASS	Atlas-SNP
HSPA4	3308	hgsc.bcm.edu	37	5	132387979	132387979	+	Missense_Mutation	SNP	T	T	A	rs61745470	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	27	50	0	0.5	0	T|0.985;A|0.015	0.015	strong	.	HSPA4	68	.	NM_002154	exon1	c.T37A	p.C13S	CAGAGCTGCTACG	.	PASS	Atlas-SNP
ATP5J2-PTCD1	100526740	hgsc.bcm.edu	37	7	99022873	99022873	+	Missense_Mutation	SNP	C	C	T	rs147045279	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	51	78	0	0.554348	0	C|1.000;T|0.000	0.000	strong	.	.	.	.	NM_001198879	exon7	c.G1429A	p.A477T	CCACTGCGGTGAG	.	PASS	Atlas-SNP
TMEM244	253582	hgsc.bcm.edu	37	6	130154686	130154686	+	Missense_Mutation	SNP	A	A	G	rs4629709	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	42	60	0	0.976744	0	A|0.296;G|0.704	0.704	strong	.	.	.	.	NM_001010876	exon4	c.T238C	p.F80L	CAAAAAACAATCC	.	PASS	Atlas-SNP
LASP1	3927	hgsc.bcm.edu	37	17	37070658	37070658	+	Silent	SNP	A	A	G	rs525989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	93	183	0	0.537572	0	A|0.285;G|0.715	0.715	strong	LASP1,colon,carcinoma,0,3	LASP1	24	3	NM_006148	exon5	c.A438G	p.S146S	GGATTCACAGGAC	.	PASS	Atlas-SNP
DISP2	85455	hgsc.bcm.edu	37	15	40660566	40660566	+	Silent	SNP	G	G	A	rs72733420	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	13	26	0	0.419355	0	G|0.847;A|0.153	0.153	strong	DISP2,NS,carcinoma,0,1	DISP2	86	1	NM_033510	exon8	c.G2253A	p.A751A	CGACGCGGAGTAT	.	scavenged	Atlas-SNP
LAMB2	3913	hgsc.bcm.edu	37	3	49161004	49161004	+	Silent	SNP	C	C	A	rs34967349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	70	134	0	0.48951	0	C|0.996;A|0.004	0.004	strong	.	LAMB2	156	.	NM_002292	exon25	c.G3858T	p.V1286V	ATCTTGCACATCT	.	PASS	Atlas-SNP
ATP6	0	hgsc.bcm.edu	37	MT	8697	8697	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	5	4	0	1	0	.	.	none	.	.	.	.	ENST00000361899	exon1	c.G171A	p.M57M	ACAAATGATAACC	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373562	5373562	+	Missense_Mutation	SNP	C	C	A	rs5024042	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	107	198	0	0.511962	0	C|0.767;A|0.233	0.233	strong	.	OR51B6	53	.	NM_001004750	exon1	c.C825A	p.S275R	AATGAGCTACATC	.	PASS	Atlas-SNP
THBS2	7058	hgsc.bcm.edu	37	6	169632219	169632219	+	Silent	SNP	G	G	A	rs35935937	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	6	139	0	0.0769231	0	G|0.839;C|0.000;A|0.161	0.161	strong	THBS2,NS,carcinoma,0,1	THBS2	230	1	NM_003247	exon14	c.C2007T	p.G669G	GAAGTGGCCCAGG	.	PASS	Atlas-SNP
TAS2R5	54429	hgsc.bcm.edu	37	7	141490238	141490238	+	Missense_Mutation	SNP	G	G	T	rs2227264	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	86	187	0	0.472527	0	G|0.549;N|0.000	.	strong	.	TAS2R5	33	.	NM_018980	exon1	c.G77T	p.S26I	ATGGAAGCCTGGT	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140564263	140564263	+	Missense_Mutation	SNP	C	C	T	rs61742755	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	45	66	0	0.56962	0	C|0.931;T|0.069	0.069	strong	.	PCDHB16	159	.	NM_020957	exon1	c.C2129T	p.A710V	TCGTGGCGGTGCG	.	PASS	Atlas-SNP
GCC1	79571	hgsc.bcm.edu	37	7	127222157	127222157	+	Silent	SNP	G	G	A	rs3735644	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	111	255	1	0.49115	0.00392157	G|0.799;A|0.201	0.201	strong	.	GCC1	83	.	NM_024523	exon2	c.C2239T	p.L747L	TAGTCAGTATGGC	.	PASS	Atlas-SNP
ERMP1	79956	hgsc.bcm.edu	37	9	5787439	5787439	+	Missense_Mutation	SNP	T	T	C	rs148237651	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	27	51	0	0.482143	0	T|1.000;C|0.000	0.000	weak	.	ERMP1	63	.	NM_024896	exon14	c.A2541G	p.I847M	CACTTCTATCCAG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169327191	169327191	+	Silent	SNP	C	C	T	rs3762856	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	55	124	0	0.429688	0	C|0.674;T|0.326	0.326	strong	.	DDX60L	116	.	NM_001012967	exon24	c.G3123A	p.K1041K	GACTATCTTATTC	.	PASS	Atlas-SNP
NT5C2	22978	hgsc.bcm.edu	37	10	104934709	104934709	+	Missense_Mutation	SNP	T	T	C	rs10883841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	32	67	0	0.457143	0	T|0.899;C|0.101	0.101	strong	.	NT5C2	41	.	NM_012229	exon3	c.A7G	p.T3A	AGGAGGTTGACAT	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31110786	31110786	+	Silent	SNP	T	T	A	rs12364	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	170	167	0	0.994152	0	T|0.846;A|0.154	0.154	strong	.	CCHCR1	68	.	NM_001105564	exon17	c.A2445T	p.A815A	TGCAGATGCTGAA	.	PASS	Atlas-SNP
MET	4233	hgsc.bcm.edu	37	7	116339315	116339315	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	58	139	0	0.449612	0	.	.	none	.	MET	412	.	NM_000245	exon2	c.G177A	p.E59E	ACATGAGCATCAC	.	PASS	Atlas-SNP
ZWINT	11130	hgsc.bcm.edu	37	10	58118569	58118569	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	243	117	278	0	0.481481	0	.	.	none	.	ZWINT	39	.	NM_007057	exon6	c.A620G	p.Q207R	TACCTCTGCAGCT	.	PASS	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233243981	233243981	+	Missense_Mutation	SNP	A	A	T	rs13026692	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	71	180	0	0.438272	0	A|0.675;T|0.325	0.325	strong	ALPP,NS,carcinoma,0,1	ALPP	53	1	NM_001632	exon3	c.A265T	p.I89L	CCTGAGATACCCC	.	PASS	Atlas-SNP
TTC18	118491	hgsc.bcm.edu	37	10	75056863	75056863	+	Silent	SNP	A	A	C	rs6480692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	78	140	0	0.481481	0	A|0.870;C|0.130	0.130	strong	TTC18,NS,carcinoma,-2,2	TTC18	106	2	NM_145170	exon16	c.T1791G	p.L597L	TGTCTGAAGTTCC	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113554946	113554946	+	Silent	SNP	G	G	A	rs34456143	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	25	34	0	0.490196	0	G|0.898;A|0.102	0.102	strong	.	RASAL1	89	.	NM_004658	exon9	c.C663T	p.T221T	CTGGAGGGTCTTT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	270	106	279	0	0.392593	0	C|0.846;T|0.154	0.154	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon31	c.C9954T	p.A3318A	CACAGCCACCCCC	.	PASS	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	80904844	80904844	+	Missense_Mutation	SNP	C	C	T	rs7225887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	32	70	0	0.450704	0	C|0.840;T|0.160	0.160	strong	B3GNTL1,NS,carcinoma,+2,1	B3GNTL1	40	1	NM_001009905	exon12	c.G1021A	p.A341T	CAAAGGCGCCCCC	.	PASS	Atlas-SNP
ZNF532	55205	hgsc.bcm.edu	37	18	56648756	56648756	+	Silent	SNP	C	C	T	rs61733373	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	106	152	0	0.54359	0	C|0.910;T|0.090	0.090	strong	.	ZNF532	108	.	NM_018181	exon10	c.C3318T	p.H1106H	GAAGCACGTCCAG	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176482	57176482	+	Missense_Mutation	SNP	C	C	T	rs12462469	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	36	107	0	0.409091	0	C|0.621;T|0.379	0.379	strong	.	ZNF835	106	.	NM_001005850	exon2	c.G85A	p.E29K	GGTTTTCCTGCAG	.	PASS	Atlas-SNP
DLG5	9231	hgsc.bcm.edu	37	10	79584178	79584178	+	Silent	SNP	G	G	C	rs1248629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	73	99	0	1	0	G|0.288;C|0.712	0.712	strong	.	DLG5	154	.	NM_004747	exon14	c.C2346G	p.R782R	GCAGCTGCGCAGC	.	PASS	Atlas-SNP
SEC24D	9871	hgsc.bcm.edu	37	4	119736796	119736796	+	Silent	SNP	A	A	C	rs2389688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	128	131	0	0.992248	0	T|0.108;G|0.070	.	strong	SEC24D,NS,carcinoma,0,1	SEC24D	96	1	NM_014822	exon5	c.T483G	p.P161P	AATGGAAGGCTGT	.	PASS	Atlas-SNP
PEX14	5195	hgsc.bcm.edu	37	1	10596341	10596341	+	Silent	SNP	C	C	T	rs12375	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	20	214	0	0.103627	0	C|0.770;T|0.230	0.230	strong	.	PEX14	40	.	NM_004565	exon3	c.C156T	p.F52F	AGCATTCCTAAAG	.	PASS	Atlas-SNP
NPBWR1	2831	hgsc.bcm.edu	37	8	53853160	53853160	+	Silent	SNP	T	T	C	rs75387626	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	29	68	0	0.467742	0	T|0.975;C|0.025	0.025	strong	.	NPBWR1	38	.	NM_005285	exon1	c.T693C	p.H231H	GCTGCATGCCATG	.	PASS	Atlas-SNP
MYH14	79784	hgsc.bcm.edu	37	19	50760716	50760716	+	Silent	SNP	C	C	G	rs378811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	79	0	1	0	C|0.617;G|0.383	0.383	strong	MYH14_ENST00000262269,NS,carcinoma,0,4	MYH14	261	4	NM_001145809	exon18	c.C2205G	p.R735R	TGTCCGCTGCATT	.	PASS	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	700	107	606	2	0.152857	0.00330033	C|0.972;T|0.028	0.028	strong	LILRA6,NS,carcinoma,+1,4	LILRA6	75	4	NM_024318	exon4	c.G445A	p.G149R	GATATCCCTTCTG	.	scavenged	Atlas-SNP
KIF19	124602	hgsc.bcm.edu	37	17	72346868	72346868	+	Missense_Mutation	SNP	C	C	T	rs2382644	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	62	110	0	0.504065	0	C|0.910;T|0.090	0.090	strong	.	KIF19	102	.	NM_153209	exon12	c.C1411T	p.R471W	TCCCGCCGGGCCC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388693	1388693	+	Missense_Mutation	SNP	C	C	G	rs78906219	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	24	54	1	0.363636	0.0185185	G|1.000;|0.000	1.000	weak	CRIPAK,caecum,carcinoma,0,2	CRIPAK	185	2	NM_175918	exon1	c.C394G	p.H132D	CGTGCCCATGCGG	.	scavenged	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919231	51919231	+	Silent	SNP	A	A	G	rs112584540	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	41	199	0	0.341667	0	A|0.994;G|0.006	0.006	strong	.	SIGLEC10	112	.	NM_001171157	exon5	c.T945C	p.A315A	ATCCCCAGCCTTC	.	PASS	Atlas-SNP
MCM3AP	8888	hgsc.bcm.edu	37	21	47685939	47685939	+	Silent	SNP	A	A	G	rs2839181	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	42	68	0	0.531646	0	A|0.554;G|0.446	0.446	strong	MCM3AP,NS,carcinoma,0,1	MCM3AP	146	1	NM_003906	exon11	c.T2931C	p.H977H	AGGGGTATGACGA	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	125061895	125061895	+	Silent	SNP	G	G	A	rs4870887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	88	179	0	0.419048	0	G|0.501;A|0.498	0.498	strong	FER1L6,colon,carcinoma,+2,2	FER1L6	268	2	NM_001039112	exon22	c.G2772A	p.K924K	TGTGAAGCTGGCT	.	PASS	Atlas-SNP
GPR108	56927	hgsc.bcm.edu	37	19	6737516	6737516	+	Silent	SNP	C	C	T	rs11539591	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	10	3	0	0.588235	0	C|0.900;T|0.100	0.100	strong	.	GPR108	35	.	NM_001080452	exon1	c.G72A	p.V24V	CAGCAGCACCAGA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1094690	1094690	+	Silent	SNP	C	C	T	rs10794291	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	100	103	0	1	0	C|0.311;T|0.689	0.689	strong	.	MUC2	614	.	NM_002457	exon32	c.C5766T	p.T1922T	CACGACCGGGTCA	.	PASS	Atlas-SNP
FBXW10	10517	hgsc.bcm.edu	37	17	18653145	18653145	+	Missense_Mutation	SNP	C	C	G	rs75316384	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	491	135	369	0	0.274949	0	.	.	weak	.	FBXW10	82	.	NM_001267585	exon3	c.C781G	p.L261V	GTTGACCTGGATG	.	PASS	Atlas-SNP
MFSD4	148808	hgsc.bcm.edu	37	1	205561372	205561372	+	Silent	SNP	C	C	T	rs7529077	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	73	113	0	0.459119	0	C|0.812;T|0.188	0.188	strong	.	MFSD4	46	.	NM_181644	exon7	c.C1254T	p.F418F	CACCTTCCCCAGC	.	PASS	Atlas-SNP
NPHP4	261734	hgsc.bcm.edu	37	1	5937168	5937168	+	Silent	SNP	G	G	A	rs3747992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	167	153	0	0.917582	0	G|0.536;A|0.464	0.464	strong	NPHP4,NS,carcinoma,0,2	NPHP4	119	2	NM_015102	exon20	c.C2802T	p.R934R	CGTCCCGCGCCGG	.	PASS	Atlas-SNP
LPP	4026	hgsc.bcm.edu	37	3	188478055	188478055	+	Silent	SNP	C	C	T	rs6771786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	88	167	0	0.475676	0	C|0.994;T|0.006	0.006	strong	.	LPP	72	.	NM_005578	exon8	c.C1395T	p.C465C	ATACTGCGAGCCC	.	PASS	Atlas-SNP
UQCR10	29796	hgsc.bcm.edu	37	22	30163526	30163526	+	Missense_Mutation	SNP	A	A	G	rs76013375	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	15	43	0	0.3	0	A|0.883;G|0.117	0.117	strong	.	UQCR10	10	.	NM_001003684	exon1	c.A139G	p.I47V	GACCACATCAACG	.	PASS	Atlas-SNP
VENTX	27287	hgsc.bcm.edu	37	10	135053784	135053784	+	Missense_Mutation	SNP	A	A	G	rs148086757	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	15	19	0	0.365854	0	A|0.995;G|0.005	0.005	strong	.	VENTX	24	.	NM_014468	exon3	c.A751G	p.M251V	TGTGCTATGCCAC	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2161796	2161796	+	Silent	SNP	G	G	A	rs75510884	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	30	18	0	0.517241	0	G|0.854;A|0.146	0.146	strong	PKD1,colon,carcinoma,-2,1	PKD1	184	1	NM_000296	exon15	c.C3372T	p.A1124A	CAGGGAGGCGCGC	.	PASS	Atlas-SNP
GSPT1	2935	hgsc.bcm.edu	37	16	11969985	11969985	+	Silent	SNP	C	C	T	rs369462446		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	56	121	0	0.459016	0	.	.	weak	.	GSPT1	71	.	NM_002094	exon13	c.G1650A	p.A550A	CAGCACCGCATTA	.	PASS	Atlas-SNP
CBLC	23624	hgsc.bcm.edu	37	19	45296806	45296806	+	Missense_Mutation	SNP	C	C	T	rs3208856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	27	37	0	0.490909	0	C|0.972;G|0.000;T|0.028	0.028	strong	.	CBLC	41	.	NM_012116	exon8	c.C1213T	p.H405Y	CAGTTCCACGGTC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2057298	2057298	+	Silent	SNP	C	C	T	rs2280897	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	66	122	0	0.511628	0	C|0.875;T|0.125	0.125	strong	.	MYOM2	251	.	NM_003970	exon25	c.C3156T	p.N1052N	TATTAACGACAGA	.	PASS	Atlas-SNP
DEFB127	140850	hgsc.bcm.edu	37	20	139576	139576	+	Missense_Mutation	SNP	C	C	A	rs16995685	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	92	219	0	0.497297	0	C|0.718;A|0.282	0.282	strong	.	DEFB127	15	.	NM_139074	exon2	c.C211A	p.R71S	CCACCTCGTCCAA	.	PASS	Atlas-SNP
AKAP13	11214	hgsc.bcm.edu	37	15	86123216	86123216	+	Silent	SNP	A	A	G	rs112396662	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	61	112	0	0.488	0	A|0.994;G|0.006	0.006	strong	.	AKAP13	394	.	NM_007200	exon7	c.A1917G	p.S639S	AAATTCATCTCAT	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113353052	113353052	+	Silent	SNP	C	C	T	rs17044681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	18	36	0	0.6	0	C|0.912;T|0.088	0.088	strong	.	ALPK1	125	.	NM_001102406	exon11	c.C2349T	p.S783S	TCCCTCCTGGGTT	.	PASS	Atlas-SNP
IZUMO1	284359	hgsc.bcm.edu	37	19	49244220	49244220	+	Missense_Mutation	SNP	G	G	A	rs66877153	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	67	104	0	0.609091	0	AA|0.500;CG|0.500	.	alt	.	IZUMO1	30	.	NM_182575	exon10	c.C998T	p.A333V	TCGGCCGCTCCAC	.	PASS	Atlas-SNP
TSPYL4	23270	hgsc.bcm.edu	37	6	116575116	116575116	+	Missense_Mutation	SNP	G	G	T	rs17524614	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	8	109	0	0.106667	0	G|0.876;T|0.124	0.124	strong	.	TSPYL4	18	.	NM_021648	exon1	c.C56A	p.A19D	GGAGCAGCCAGGC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28459227	28459227	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	245	22	192	1	0.0897959	0.00520833	.	.	none	HERC2,NS,carcinoma,0,1	HERC2	501	1	NM_004667	exon41	c.G6550A	p.E2184K	CCCCTTCGGAAGG	.	scavenged	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629955	32629955	+	Silent	SNP	C	C	T	rs9280019	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	23	65	0	0.234694	0	C|0.370;T|0.630	0.630	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.G450A	p.S150S	TGTCACCGAGCAG	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	241991875	241991875	+	Silent	SNP	G	G	A	rs57214830	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	32	59	0	0.492308	0	G|0.756;A|0.244	0.244	strong	.	SNED1	76	.	NM_001080437	exon15	c.G2073A	p.R691R	ACGCCGGTGCCAG	.	PASS	Atlas-SNP
WDR45B	56270	hgsc.bcm.edu	37	17	80573888	80573888	+	Silent	SNP	G	G	A	rs147083174	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	24	23	0	0.45283	0	G|0.995;A|0.005	0.005	strong	.	.	.	.	NM_019613	exon10	c.C942T	p.D314D	GCTGCCGTCTGCA	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110489620	110489620	+	Silent	SNP	A	A	T	rs1783148	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	22	56	0	0.488889	0	A|0.634;T|0.366	0.366	strong	.	PKHD1L1	522	.	NM_177531	exon53	c.A9084T	p.T3028T	AGCCACATATAAG	.	PASS	Atlas-SNP
OR11H12	440153	hgsc.bcm.edu	37	14	19378322	19378322	+	Missense_Mutation	SNP	G	G	A	rs201485834		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	632	12	566	0	0.0189873	0	.	.	weak	OR11H12,NS,malignant_melanoma,+1,1	OR11H12	58	1	NM_001013354	exon1	c.G729A	p.M243I	GGGTATGCCTTCA	.	scavenged	Atlas-SNP
HTR1A	3350	hgsc.bcm.edu	37	5	63257310	63257310	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	62	125	0	0.4	0	.	.	none	HTR1A,colon,carcinoma,-1,2	HTR1A	128	2	NM_000524	exon1	c.G237A	p.A79A	GGTGACCGCCAAA	.	PASS	Atlas-SNP
ALKBH5	54890	hgsc.bcm.edu	37	17	18111598	18111598	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	65	154	0	0.485075	0	.	.	none	ALKBH5,NS,carcinoma,+1,1	ALKBH5	24	1	NM_017758	exon4	c.G1073A	p.R358Q	ACCGGCGGAGGGG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379823	31379823	+	Missense_Mutation	SNP	C	C	G	rs1051799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	66	115	0	1	0	C|0.703;G|0.297	0.297	strong	.	MICA	21	.	NM_001177519	exon4	c.C713G	p.T238S	TACTGACCTGGCG	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124886979	124886979	+	Silent	SNP	C	C	T	rs202047482	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	70	101	0	0.57377	0	C|0.999;T|0.001	0.001	weak	.	NCOR2	475	.	NM_006312	exon16	c.G1611A	p.E537E	CTCCACCTCCGGC	.	PASS	Atlas-SNP
CH25H	9023	hgsc.bcm.edu	37	10	90966546	90966546	+	Silent	SNP	C	C	T	rs4078488	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	60	99	0	0.508475	0	C|0.850;T|0.150	0.150	strong	CH25H,NS,carcinoma,-1,1	CH25H	19	1	NM_003956	exon1	c.G504A	p.A168A	TGCCAGCGCGAAC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557488	32557488	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	9	274	2	0.0365854	0.00729927	.	.	none	HLA-DRB1,colon,carcinoma,-1,1	HLA-DRB1	41	1	NM_002124	exon1	c.G32A	p.C11Y	GTCATGCAGGAGC	.	scavenged	Atlas-SNP
ACSL5	51703	hgsc.bcm.edu	37	10	114169276	114169276	+	Missense_Mutation	SNP	A	A	G	rs3736946	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	66	113	0	0.536585	0	A|0.915;G|0.085	0.085	strong	.	ACSL5	51	.	NM_016234	exon7	c.A712G	p.M238V	ATCGCCATGGTGA	.	PASS	Atlas-SNP
ENPP4	22875	hgsc.bcm.edu	37	6	46107752	46107752	+	Missense_Mutation	SNP	C	C	G	rs7451713	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	48	134	0	0.372093	0	C|0.562;G|0.438	0.438	strong	.	ENPP4	44	.	NM_014936	exon2	c.C432G	p.H144Q	CATTCACGATACC	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51483961	51483961	+	Missense_Mutation	SNP	T	T	C	rs9381994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	74	0	1	0	T|0.458;C|0.542	0.542	strong	PKHD1,colon,carcinoma,0,2	PKHD1	927	2	NM_138694	exon67	c.A12143G	p.Q4048R	TTCTCTTGGGAAA	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1537874	1537874	+	Missense_Mutation	SNP	G	G	A	rs7202502	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	29	76	0	0.402778	0	G|0.894;A|0.106	0.106	strong	PTX4,colon,carcinoma,0,1	PTX4	46	1	NM_001013658	exon2	c.C224T	p.A75V	TCTTCCGCCAGGC	.	PASS	Atlas-SNP
EPM2A	7957	hgsc.bcm.edu	37	6	146007332	146007332	+	Silent	SNP	C	C	T	rs35230590	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	77	126	0	0.855556	0	C|0.823;T|0.177	0.177	strong	.	EPM2A	21	.	NM_005670	exon2	c.G402A	p.G134G	GGTGTGCCCAGTG	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	46	72	0	0.5	0	G|0.878;C|0.122	0.122	strong	.	UTP20	222	.	NM_014503	exon59	c.G7834C	p.E2612Q	AAGGAAGAGCTCG	.	PASS	Atlas-SNP
ZNF212	7988	hgsc.bcm.edu	37	7	148936878	148936878	+	Missense_Mutation	SNP	G	G	T	rs11548535	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	22	4	0	0.536585	0	G|0.935;T|0.065	0.065	strong	.	ZNF212	28	.	NM_012256	exon1	c.G9T	p.E3D	GGCGGAGTCGGCG	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157396697	157396697	+	Silent	SNP	G	G	A	rs17853260	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	39	120	0	0.428571	0	G|0.779;A|0.221	0.221	strong	PTPRN2,NS,carcinoma,0,1	PTPRN2	243	1	NM_002847	exon16	c.C2415T	p.P805P	TACGATGGGGCTA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911056	29911056	+	Missense_Mutation	SNP	A	A	C	rs1071743	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	49	112	0	0.628205	0	A|0.782;C|0.180;G|0.037	0.180	strong	.	HLA-A	89	.	NM_001242758	exon3	c.A355C	p.I119L	CACACCATCCAGA	.	PASS	Atlas-SNP
BFSP1	631	hgsc.bcm.edu	37	20	17479617	17479617	+	Silent	SNP	G	G	A	rs11537702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	78	179	0	0.4875	0	G|0.955;A|0.045	0.045	strong	.	BFSP1	55	.	NM_001195	exon6	c.C804T	p.N268N	CTGCTCGTTATAA	.	PASS	Atlas-SNP
FAM210B	116151	hgsc.bcm.edu	37	20	54940148	54940148	+	Silent	SNP	C	C	T	rs148836702	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	38	82	0	0.475	0	C|0.998;T|0.002	0.002	strong	.	.	.	.	NM_080821	exon2	c.C192T	p.P64P	GGACCCCAGCCAG	.	PASS	Atlas-SNP
ISM2	145501	hgsc.bcm.edu	37	14	77950699	77950699	+	Silent	SNP	G	G	A	rs141373850		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	2	126	0	0.0145985	0	G|1.000;A|0.000	0.000	weak	ISM2,colon,carcinoma,0,1	ISM2	68	1	NM_199296	exon3	c.C594T	p.H198H	GGTTGCGTGGACC	.	scavenged	Atlas-SNP
USP19	10869	hgsc.bcm.edu	37	3	49146612	49146612	+	Missense_Mutation	SNP	G	G	A	rs79965514	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	30	124	0	0.291262	0	G|0.999;A|0.001	0.001	strong	.	USP19	158	.	NM_001199160	exon27	c.C4039T	p.R1347W	AAATCCGGGAAGC	.	PASS	Atlas-SNP
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105889349	105889349	+	Silent	SNP	G	G	A	rs11676273	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	62	142	1	0.466165	0.00704225	G|0.864;A|0.135	0.135	strong	TGFBRAP1,NS,carcinoma,-2,1	TGFBRAP1	70	1	NM_004257	exon10	c.C1935T	p.L645L	TTTCTGGAGCAGC	.	scavenged	Atlas-SNP
TRIM39	56658	hgsc.bcm.edu	37	6	30297505	30297505	+	Silent	SNP	C	C	T	rs1264581	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	68	123	0	0.489209	0	C|0.951;T|0.049	0.049	strong	.	TRIM39	56	.	NM_172016	exon3	c.C411T	p.A137A	CCGGGCCCACACC	.	PASS	Atlas-SNP
FAM221B	392307	hgsc.bcm.edu	37	9	35826038	35826038	+	Missense_Mutation	SNP	T	T	C	rs13294245	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	38	84	0	0.452381	0	T|0.758;C|0.242	0.242	strong	.	FAM221B	38	.	NM_001012446	exon2	c.A121G	p.K41E	AAGGCTTCAAGAA	.	PASS	Atlas-SNP
PAPLN	89932	hgsc.bcm.edu	37	14	73716774	73716774	+	Silent	SNP	G	G	A	rs177393	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	45	107	0	0.428571	0	G|0.667;A|0.333	0.333	strong	.	PAPLN	180	.	NM_173462	exon6	c.G417A	p.T139T	TGGGACGCCCTGC	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86909582	86909582	+	Missense_Mutation	SNP	G	G	A	rs1413426	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	49	103	0	0.505155	0	G|0.904;A|0.096	0.096	strong	.	CLCA2	102	.	NM_006536	exon10	c.G1601A	p.G534D	CCAGTGGTCCTCC	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112991312	112991312	+	Silent	SNP	C	C	T	rs3814398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	66	135	0	0.423077	0	C|0.788;T|0.212	0.212	strong	.	BOC	139	.	NM_033254	exon7	c.C723T	p.I241I	CATCATCGTCACC	.	PASS	Atlas-SNP
HHLA3	11147	hgsc.bcm.edu	37	1	70820880	70820880	+	Silent	SNP	G	G	A	rs55863806	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	42	49	0	1	0	G|0.926;A|0.074	0.074	strong	.	HHLA3	11	.	NM_001036645	exon1	c.G246A	p.A82A	AAAAGCGGAGGCG	.	PASS	Atlas-SNP
APCDD1L	164284	hgsc.bcm.edu	37	20	57045765	57045765	+	Missense_Mutation	SNP	A	A	G	rs3946003	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	27	31	0	0.964286	0	A|0.555;G|0.445	0.445	strong	.	APCDD1L	48	.	NM_153360	exon2	c.T88C	p.C30R	GCAGGCAGCTGCC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113168501	113168501	+	Missense_Mutation	SNP	A	A	G	rs41278435	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	66	148	0	0.452055	0	A|0.964;G|0.036	0.036	strong	.	SVEP1	326	.	NM_153366	exon38	c.T9379C	p.S3127P	CGACAGACGGTGG	.	PASS	Atlas-SNP
CRTAP	10491	hgsc.bcm.edu	37	3	33174156	33174156	+	Silent	SNP	T	T	G	rs1135127	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	62	131	0	0.421769	0	T|0.645;G|0.355	0.355	strong	CRTAP,NS,carcinoma,0,1	CRTAP	16	1	NM_006371	exon5	c.T1032G	p.T344T	GGACACTTGGGGC	.	PASS	Atlas-SNP
TSC1	7248	hgsc.bcm.edu	37	9	135782221	135782221	+	Silent	SNP	T	T	C	rs7862221	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	91	114	0	1	0	T|0.841;C|0.159	0.159	strong	.	TSC1	167	.	NM_000368	exon14	c.A1335G	p.E445E	TGGCTCTTCTGAA	.	PASS	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207870916	207870916	+	Missense_Mutation	SNP	G	G	A	rs201832831	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	480	231	394	0	0.48125	0	G|0.999;A|0.001	0.001	strong	.	CR1L	97	.	NM_175710	exon6	c.G931A	p.G311R	TCACCCGGGCAGG	.	PASS	Atlas-SNP
BAG3	9531	hgsc.bcm.edu	37	10	121432139	121432139	+	Missense_Mutation	SNP	C	C	T	rs144585878		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	2	116	1	0.0125786	0.00862069	C|1.000;T|0.000	0.000	weak	BAG3,NS,carcinoma,-1,2	BAG3	42	2	NM_004281	exon3	c.C880T	p.R294C	CCCATCCGTGTGC	.	scavenged	Atlas-SNP
HDGFRP2	0	hgsc.bcm.edu	37	19	4493708	4493708	+	Silent	SNP	A	A	G	rs892161	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	82	103	0	0.987952	0	A|0.431;G|0.569	0.569	strong	HDGF2,NS,carcinoma,0,1	.	.	1	NM_032631	exon7	c.A687G	p.P229P	GGCGCCATCAGCC	.	PASS	Atlas-SNP
LAMB1	3912	hgsc.bcm.edu	37	7	107569517	107569517	+	Silent	SNP	A	A	G	rs1131398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	243	117	267	0	0.481481	0	A|0.547;G|0.453	0.453	strong	.	LAMB1	185	.	NM_002291	exon31	c.T4879C	p.L1627L	AAGTTAACAGGTT	.	PASS	Atlas-SNP
SPACA7	122258	hgsc.bcm.edu	37	13	113053470	113053470	+	Missense_Mutation	SNP	T	T	A	rs10816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	52	123	0	0.55914	0	T|0.343;A|0.657	0.657	strong	SPACA7,NS,adenoma,0,1	SPACA7	36	1	NM_145248	exon4	c.T332A	p.V111D	TTGAGGTCAAAAT	.	PASS	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	37	2	26536299	26536299	+	Silent	SNP	C	C	G	rs11886746	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	42	77	0	0.494118	0	C|0.631;G|0.369	0.369	strong	.	GPR113	134	.	NM_001145168	exon9	c.G1419C	p.P473P	GTGGACCGGCCCC	.	PASS	Atlas-SNP
CAPZA2	830	hgsc.bcm.edu	37	7	116528240	116528240	+	Silent	SNP	C	C	T	rs4808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	17	58	0	0.414634	0	C|0.707;T|0.293	0.293	strong	.	CAPZA2	29	.	NM_006136	exon2	c.C99T	p.F33F	GGTTTTCAATGGT	.	PASS	Atlas-SNP
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	115	212	1	0.545024	0.00471698	A|0.598;G|0.402	0.402	strong	.	KRTAP3-3	11	.	NM_033185	exon1	c.T66C	p.S22S	TTTGTCAGAGGAG	.	PASS	Atlas-SNP
PREX2	80243	hgsc.bcm.edu	37	8	68864728	68864728	+	Silent	SNP	G	G	A	rs61753697	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	58	61	0	0.491525	0	G|0.766;A|0.234	0.234	strong	PREX2_ENST00000354677,NS,carcinoma,0,2	PREX2	614	2	NM_025170	exon1	c.G99A	p.K33K	CCAGAAGACCGAG	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505159	37505159	+	Missense_Mutation	SNP	G	G	A	rs34552277	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	52	202	0	0.385185	0	G|0.768;A|0.232	0.232	strong	.	ANKRD30A	448	.	NM_052997	exon32	c.G2752A	p.A918T	GAAAGAGCAAGGG	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29449819	29449819	+	Silent	SNP	C	C	T	rs2293563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	109	135	0	1	0	C|0.816;T|0.184	0.184	strong	ALK,NS,carcinoma,0,1	ALK	533	1	NM_004304	exon18	c.G3036A	p.T1012T	CAGCACCGTCCCG	.	PASS	Atlas-SNP
GRM7	2917	hgsc.bcm.edu	37	3	7620789	7620789	+	Silent	SNP	T	T	C	rs1485175	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	266	140	255	1	0.526316	0.00392157	T|0.451;C|0.549	0.549	strong	.	GRM7	223	.	NM_000844	exon8	c.T2196C	p.Y732Y	AGACTATGATGAA	.	PASS	Atlas-SNP
GZMB	3002	hgsc.bcm.edu	37	14	25100282	25100282	+	Missense_Mutation	SNP	A	A	G	rs2236338	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	270	136	260	0	0.503704	0	A|0.729;G|0.271	0.271	strong	GZMB,NS,carcinoma,0,1	GZMB	73	1	NM_004131	exon5	c.T739C	p.Y247H	GTTAGTAGCGTTT	.	PASS	Atlas-SNP
TMEM18	129787	hgsc.bcm.edu	37	2	677295	677295	+	Silent	SNP	C	C	T	rs3210390	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	9	25	0	0.45	0	C|0.864;T|0.136	0.136	strong	.	TMEM18	22	.	NM_152834	exon1	c.G51A	p.V17V	CGTGAGCACGGCT	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10081322	10081322	+	Silent	SNP	G	G	A	rs61729461	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	31	39	0	0.449275	0	G|0.915;A|0.085	0.085	strong	COL5A3,NS,carcinoma,0,2	COL5A3	243	2	NM_015719	exon54	c.C3912T	p.G1304G	GGGGGCGCCGGGC	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141116447	141116447	+	Missense_Mutation	SNP	G	G	T	rs35546150	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	84	173	0	0.502994	0	G|0.960;T|0.040	0.040	strong	.	LRP1B	1315	.	NM_018557	exon73	c.C11200A	p.Q3734K	ACATTTGCTCCGA	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596254	48596254	+	Silent	SNP	A	A	C	rs11830378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	45	97	0	0.45	0	A|0.938;C|0.062	0.062	strong	OR10AD1,colon,carcinoma,-1,1	OR10AD1	24	1	NM_001004134	exon1	c.T822G	p.P274P	GGAGAAAGGTTTG	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193081122	193081122	+	Missense_Mutation	SNP	G	G	T	rs12637558	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	84	78	0	0.988235	0	G|0.618;T|0.382	0.382	strong	ATP13A5,NS,carcinoma,0,2	ATP13A5	171	2	NM_198505	exon3	c.C287A	p.S96Y	AGTGTGGATAAGT	.	PASS	Atlas-SNP
OR13C8	138802	hgsc.bcm.edu	37	9	107331504	107331504	+	Missense_Mutation	SNP	C	C	A	rs7026705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	38	91	0	0.469136	0	C|0.434;A|0.566	0.566	strong	.	OR13C8	77	.	NM_001004483	exon1	c.C56A	p.A19D	TTTCTGCCCACCC	.	PASS	Atlas-SNP
FMNL2	114793	hgsc.bcm.edu	37	2	153468107	153468107	+	Silent	SNP	C	C	T	rs35776654	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	24	62	0	0.4	0	C|0.918;T|0.082	0.082	strong	FMNL2,NS,carcinoma,0,1	FMNL2	75	1	NM_052905	exon11	c.C1050T	p.D350D	CCTGGACGAATAC	.	PASS	Atlas-SNP
EXOSC1	51013	hgsc.bcm.edu	37	10	99205731	99205731	+	Silent	SNP	A	A	G	rs4919098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	40	76	0	0.547945	0	A|0.888;G|0.112	0.112	strong	.	EXOSC1	8	.	NM_016046	exon1	c.T12C	p.P4P	TCTCACAGGTGGC	.	PASS	Atlas-SNP
SMCR9	140776	hgsc.bcm.edu	37	17	17326604	17326604	+	Missense_Mutation	SNP	C	C	T	rs7225976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	20	18	0	0.952381	0	C|0.662;T|0.338	0.338	strong	.	.	.	.	NM_001243312	exon3	c.C419T	p.A140V	ATGGGGCAAATGC	.	PASS	Atlas-SNP
ANP32E	81611	hgsc.bcm.edu	37	1	150199123	150199123	+	Silent	SNP	G	G	T	rs7522034	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	50	37	0	1	0	G|0.433;T|0.567	0.567	strong	ANP32E,NS,adenoma,0,1	ANP32E	28	1	NM_030920	exon5	c.C498A	p.G166G	TTCATCGCCATCT	.	PASS	Atlas-SNP
CHRNA2	1135	hgsc.bcm.edu	37	8	27328511	27328511	+	Missense_Mutation	SNP	G	G	A	rs2472553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	49	104	0	0.449541	0	G|0.819;A|0.181	0.181	strong	.	CHRNA2	48	.	NM_000742	exon2	c.C65T	p.T22I	GCTGGGGTCAGAA	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388635	1388635	+	Silent	SNP	T	T	C	rs74518227	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	30	117	1	0.227273	0.00854701	T|0.937;C|0.063	0.063	strong	CRIPAK,rectum,carcinoma,0,4	CRIPAK	185	4	NM_175918	exon1	c.T336C	p.C112C	CCCATGTGGAGTG	.	scavenged	Atlas-SNP
SFTPC	6440	hgsc.bcm.edu	37	8	22021037	22021037	+	Missense_Mutation	SNP	C	C	A	rs4715	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	60	114	0	0.504202	0	C|0.796;A|0.204	0.204	strong	.	SFTPC	19	.	NM_003018	exon4	c.C413A	p.T138N	CTCTCACTAGAAA	.	PASS	Atlas-SNP
STEAP2	261729	hgsc.bcm.edu	37	7	89856644	89856644	+	Silent	SNP	C	C	T	rs2016903	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	85	176	0	0.472222	0	C|0.869;T|0.131	0.131	strong	STEAP2_ENST00000394626,NS,adenoma,0,2	STEAP2	78	2	NM_001244946	exon4	c.C852T	p.Y284Y	TTATTACGGCACC	.	PASS	Atlas-SNP
ITPA	3704	hgsc.bcm.edu	37	20	3204084	3204084	+	Silent	SNP	G	G	A	rs9101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	23	33	0	0.425926	0	G|0.729;A|0.271	0.271	strong	ITPA,NS,carcinoma,0,1	ITPA	16	1	NM_033453	exon8	c.G561A	p.E187E	GCAGGAGTACTTT	.	PASS	Atlas-SNP
POU2F1	5451	hgsc.bcm.edu	37	1	167358837	167358837	+	Missense_Mutation	SNP	A	A	G	rs142378150	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	72	115	0	0.470588	0	A|0.997;G|0.003	0.003	strong	.	POU2F1	120	.	NM_002697	exon9	c.A826G	p.T276A	ACCCCAACACGCA	.	PASS	Atlas-SNP
GNAO1	2775	hgsc.bcm.edu	37	16	56377748	56377748	+	Silent	SNP	A	A	G	rs1799917	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	88	81	0	0.988764	0	A|0.609;G|0.391	0.391	strong	.	GNAO1	95	.	NM_138736	exon8	c.A951G	p.K317K	CCACAAAGAGATC	.	PASS	Atlas-SNP
KIAA0922	23240	hgsc.bcm.edu	37	4	154387597	154387597	+	Silent	SNP	G	G	C	rs71620317	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	10	8	5	0	0.8	0	G|0.548;C|0.452	0.452	strong	.	KIAA0922	214	.	NM_001131007	exon1	c.G48C	p.A16A	CACCGCGGCGGCC	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47584046	47584046	+	Missense_Mutation	SNP	G	G	A	rs1058793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	288	144	234	0	0.5	0	G|0.747;A|0.253	0.253	strong	.	ATP10D	168	.	NM_020453	exon21	c.G3718A	p.V1240I	TTCATCGTTCTCC	.	PASS	Atlas-SNP
OR2T29	343563	hgsc.bcm.edu	37	1	248722723	248722723	+	Nonsense_Mutation	SNP	G	G	A	rs200037558	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	468	147	599	0	0.314103	0	G|0.996;A|0.004	0.004	strong	.	OR2T29	8	.	NM_001004694	exon1	c.C70T	p.Q24X	TGGATTGTCTGAA	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26157068	26157068	+	Missense_Mutation	SNP	C	C	G	rs61734946	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	45	77	0	0.494505	0	C|0.888;G|0.112	0.112	strong	.	MYO18B	322	.	NM_032608	exon2	c.C9G	p.I3M	GGCCATCTCATCA	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27356203	27356203	+	Missense_Mutation	SNP	A	A	G	rs1805010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	89	117	0	1	0	A|0.524;G|0.476	0.476	strong	.	IL4R	70	.	NM_000418	exon5	c.A223G	p.I75V	ACGTGTATCCCTG	.	PASS	Atlas-SNP
CHRNA2	1135	hgsc.bcm.edu	37	8	27327369	27327369	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	43	79	0	0.467391	0	.	.	none	CHRNA2,caecum,carcinoma,-1,2	CHRNA2	48	2	NM_000742	exon3	c.G203A	p.R68Q	TAGCCCCGGAAGA	.	PASS	Atlas-SNP
FN3KRP	79672	hgsc.bcm.edu	37	17	80676896	80676896	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	59	94	0	0.541284	0	.	.	none	.	FN3KRP	31	.	NM_024619	exon2	c.C256T	p.L86L	AGCGTGCTGGTGA	.	PASS	Atlas-SNP
DUS1L	64118	hgsc.bcm.edu	37	17	80020812	80020812	+	Silent	SNP	C	C	T	rs11542332	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	22	45	0	0.488889	0	C|0.901;T|0.099	0.099	strong	DUS1L,colon,carcinoma,-1,1	DUS1L	25	1	NM_022156	exon5	c.G435A	p.T145T	TTTGCACGTGACA	.	PASS	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140640527	140640527	+	Missense_Mutation	SNP	G	G	A	rs61743025	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	41	68	0	0.43617	0	G|0.999;A|0.001	0.001	strong	.	MAML3	192	.	NM_018717	exon6	c.C3355T	p.P1119S	CCCCTGGCCCGCC	.	PASS	Atlas-SNP
RALGAPB	57148	hgsc.bcm.edu	37	20	37198582	37198582	+	Missense_Mutation	SNP	C	C	T	rs142678293	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	66	149	0	0.478261	0	C|0.995;T|0.005	0.005	strong	.	RALGAPB	134	.	NM_020336	exon27	c.C4006T	p.P1336S	GTTCCTCCCCTTG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130125116	130125116	+	Missense_Mutation	SNP	G	G	C	rs1497312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	92	152	0	1	0	G|0.545;C|0.455	0.455	strong	.	COL6A5	205	.	NM_153264	exon17	c.G4430C	p.C1477S	AGGGCTGTCATGG	.	PASS	Atlas-SNP
PFKM	5213	hgsc.bcm.edu	37	12	48526659	48526659	+	Silent	SNP	G	G	A	rs2228501	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	36	66	0	0.514286	0	G|0.947;A|0.053	0.053	strong	.	PFKM	117	.	NM_001166686	exon7	c.G459A	p.T153T	AGGCACGGTGATT	.	PASS	Atlas-SNP
CD5	921	hgsc.bcm.edu	37	11	60893235	60893235	+	Missense_Mutation	SNP	C	C	T	rs2229177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	25	50	0	0.403226	0	C|0.419;T|0.581	0.581	strong	CD5,colon,carcinoma,0,1	CD5	52	1	NM_014207	exon10	c.C1412T	p.A471V	AAGGGGCTCTGCA	.	PASS	Atlas-SNP
CSRP2BP	57325	hgsc.bcm.edu	37	20	18142564	18142564	+	Silent	SNP	A	A	G	rs3828013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	69	74	0	0.971831	0	A|0.896;G|0.104	0.104	strong	CSRP2BP,NS,carcinoma,0,2	CSRP2BP	80	2	NM_020536	exon5	c.A783G	p.K261K	AGAGAAAAGGTCT	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	37	21	28305212	28305212	+	Missense_Mutation	SNP	C	C	T	rs2830585	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	47	100	0	0.522222	0	C|0.872;T|0.128	0.128	strong	ADAMTS5,colon,carcinoma,-1,6	ADAMTS5	184	6	NM_007038	exon5	c.G1841A	p.R614H	CAGGAGCGGTAGA	.	PASS	Atlas-SNP
METTL21D	79609	hgsc.bcm.edu	37	14	50583083	50583083	+	Missense_Mutation	SNP	G	G	T	rs11157729	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	14	22	0	0.482759	0	G|0.812;T|0.188	0.188	strong	.	METTL21D	11	.	NM_024558	exon1	c.C188A	p.A63D	GCGTGGGCCCCGT	.	PASS	Atlas-SNP
SMCR8	140775	hgsc.bcm.edu	37	17	18219835	18219835	+	Silent	SNP	T	T	C	rs3829956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	91	102	1	1	0.00980392	T|0.772;C|0.228	0.228	strong	.	SMCR8	62	.	NM_144775	exon1	c.T732C	p.I244I	CATCATTGAACAT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38122448	38122448	+	Silent	SNP	C	C	T	rs739137	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	8	8	2	0	1	0	C|0.621;T|0.379	0.379	strong	.	TRIOBP	262	.	NM_001039141	exon7	c.C3885T	p.S1295S	CAGCAGCGGGGGC	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84218565	84218565	+	Silent	SNP	T	T	C	rs2230126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	49	83	0	0.515789	0	T|0.829;C|0.171	0.171	strong	.	TAF1C	60	.	NM_001243156	exon2	c.A30G	p.A10A	AAACAATGCAGGG	.	PASS	Atlas-SNP
PRPF19	27339	hgsc.bcm.edu	37	11	60666341	60666341	+	Silent	SNP	G	G	A	rs3763840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	215	176	0	0.977273	0	G|0.691;A|0.309	0.309	strong	.	PRPF19	62	.	NM_014502	exon12	c.C1047T	p.S349S	GCAGCCGGAGGTC	.	PASS	Atlas-SNP
PLA2G4D	283748	hgsc.bcm.edu	37	15	42373810	42373810	+	Missense_Mutation	SNP	G	G	C	rs11635685	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	122	115	0	1	0	G|0.713;C|0.287	0.287	strong	.	PLA2G4D	72	.	NM_178034	exon11	c.C824G	p.P275R	TCCTCAGGGCTGT	.	PASS	Atlas-SNP
OTUD5	55593	hgsc.bcm.edu	37	X	48783183	48783183	+	Silent	SNP	G	G	C	rs141488277	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	30	39	0	1	0	G|0.998;C|0.002	0.002	strong	.	OTUD5	66	.	NM_017602	exon6	c.C1218G	p.S406S	CAGGTAGGATTCC	.	PASS	Atlas-SNP
TEF	7008	hgsc.bcm.edu	37	22	41790179	41790179	+	Silent	SNP	G	G	A	rs17365991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	23	55	0	0.323944	0	G|0.970;A|0.030	0.030	strong	.	TEF	21	.	NM_003216	exon3	c.G555A	p.P185P	CAATCCGGACCCC	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7247344	7247344	+	Missense_Mutation	SNP	C	C	A	rs35742417	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	58	101	0	0.446154	0	C|0.843;A|0.157	0.157	strong	RREB1,NS,carcinoma,0,1	RREB1	242	1	NM_001003699	exon12	c.C4661A	p.S1554Y	CAGACTCCCCCAA	.	PASS	Atlas-SNP
B4GALT4	8702	hgsc.bcm.edu	37	3	118948716	118948716	+	Silent	SNP	G	G	A	rs4422294	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	48	94	0	0.390244	0	G|0.776;A|0.224	0.224	strong	B4GALT4,NS,carcinoma,0,1	B4GALT4	30	1	NM_212543	exon4	c.C231T	p.C77C	AGAAGGGCAGTTG	.	PASS	Atlas-SNP
CAPN13	92291	hgsc.bcm.edu	37	2	30980940	30980940	+	Missense_Mutation	SNP	C	C	T	rs508405	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	45	38	0	1	0	C|0.223;T|0.777	0.777	strong	.	CAPN13	70	.	NM_144575	exon8	c.G838A	p.A280T	ATTCGGCCTCGCC	.	PASS	Atlas-SNP
IL37	27178	hgsc.bcm.edu	37	2	113674721	113674721	+	Missense_Mutation	SNP	A	A	G	rs2723183	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	39	82	0	0.433333	0	A|0.903;G|0.097	0.097	strong	.	IL37	56	.	NM_014439	exon3	c.A161G	p.N54S	TGAAGAACTTAAA	.	PASS	Atlas-SNP
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255242	25255242	+	Missense_Mutation	SNP	T	T	A	rs8059494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	99	238	0	0.466981	0	T|0.895;A|0.105	0.105	strong	.	ZKSCAN2	90	.	NM_001012981	exon6	c.A1845T	p.E615D	TGTAGGTTCCTGG	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113146130	113146130	+	Missense_Mutation	SNP	T	T	C	rs59722850	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	102	207	0	0.490385	0	T|0.784;C|0.216	0.216	strong	.	WDR52	151	.	NM_001164496	exon3	c.A157G	p.K53E	CCCCTTTGGTAAA	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924613	70924613	+	Nonsense_Mutation	SNP	C	C	T	rs138262361	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	10	117	1	0.0763359	0.00854701	C|0.993;T|0.007	0.007	strong	ADAM21_ENST00000267499,NS,carcinoma,0,6	ADAM21	181	6	NM_003813	exon2	c.C397T	p.R133X	GGCTTTCGAGGAG	.	scavenged	Atlas-SNP
KCNG4	93107	hgsc.bcm.edu	37	16	84256410	84256410	+	Missense_Mutation	SNP	C	C	T	rs7196482	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	34	79	0	0.441558	0	C|0.810;T|0.190	0.190	strong	.	KCNG4	71	.	NM_172347	exon3	c.G973A	p.G325R	AGCTCCCGCTCGG	.	PASS	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44418343	44418343	+	Silent	SNP	C	C	T	rs406968	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	141	191	0	0.992958	0	C|0.504;T|0.496	0.496	strong	ZNF45,caecum,carcinoma,0,1	ZNF45	51	1	NM_003425	exon10	c.G1245A	p.P415P	CTGATACGGTTTC	.	PASS	Atlas-SNP
TBRG4	9238	hgsc.bcm.edu	37	7	45140914	45140914	+	Silent	SNP	C	C	T	rs1042984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	25	64	0	0.446429	0	C|0.946;T|0.054	0.054	strong	.	TBRG4	52	.	NM_001261834	exon10	c.G1770A	p.L590L	GCGACCCAGCAAG	.	PASS	Atlas-SNP
C16orf62	57020	hgsc.bcm.edu	37	16	19693627	19693627	+	Silent	SNP	C	C	T	rs117014682	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	73	148	0	0.489933	0	C|0.985;T|0.015	0.015	strong	.	C16orf62	164	.	NM_020314	exon28	c.C2709T	p.S903S	CAACAGCGATGAG	.	PASS	Atlas-SNP
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695695	45695695	+	Silent	SNP	G	G	A	rs1153849	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	37	44	0	0.552239	0	G|0.415;A|0.585	0.585	strong	.	SPATA5L1	40	.	NM_024063	exon1	c.G1068A	p.R356R	GCGTAGGCCCGGG	.	PASS	Atlas-SNP
FRS2	10818	hgsc.bcm.edu	37	12	69967862	69967862	+	Silent	SNP	G	G	A	rs547497	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	73	62	0	1	0	G|0.554;A|0.446	0.446	strong	FRS2_ENST00000299293,NS,carcinoma,0,1	FRS2	88	1	NM_001042555	exon10	c.G654A	p.A218A	GGAGGCGAGGGTT	.	PASS	Atlas-SNP
C9orf156	51531	hgsc.bcm.edu	37	9	100672338	100672338	+	Missense_Mutation	SNP	C	C	T	rs2282192	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	34	102	0	0.414634	0	C|0.504;T|0.496	0.496	strong	C9orf156,NS,meningioma,0,1	C9orf156	35	1	NM_016481	exon4	c.G970A	p.V324M	GAACCACGCTGCG	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5353344	5353344	+	Missense_Mutation	SNP	G	G	A	rs12532973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	21	12	0	0.75	0	G|0.908;A|0.092	0.092	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7178T	p.P2393L	TGCGGCGGTGCCG	.	PASS	Atlas-SNP
LCLAT1	253558	hgsc.bcm.edu	37	2	30863092	30863092	+	Silent	SNP	C	C	T	rs12467646	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	142	144	0	0.993007	0	C|0.872;T|0.128	0.128	strong	.	LCLAT1	51	.	NM_182551	exon7	c.C852T	p.H284H	CTTTCACGTCCAC	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367612	107367612	+	Silent	SNP	C	C	T	rs55706329	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	529	206	455	0	0.389414	0	C|0.652;T|0.348	0.348	strong	.	OR13C2	46	.	NM_001004481	exon1	c.G297A	p.V99V	CATCTGCACTGCA	.	PASS	Atlas-SNP
IMPG1	3617	hgsc.bcm.edu	37	6	76640803	76640803	+	Missense_Mutation	SNP	G	G	A	rs10943299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	61	132	0	0.847222	0	G|0.883;A|0.117	0.117	strong	.	IMPG1	143	.	NM_001563	exon15	c.C2110T	p.R704W	CAGTCCGTTCGTT	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113209195	113209195	+	Missense_Mutation	SNP	T	T	G	rs1889323	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	10	27	0	0.30303	0	T|0.902;G|0.098	0.098	strong	.	SVEP1	326	.	NM_153366	exon25	c.A4246C	p.K1416Q	ACCTTTTGCCTGA	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637291	248637291	+	Missense_Mutation	SNP	G	G	A	rs1770109	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	39	335	3	0.188406	0.00895522	G|0.754;A|0.246	0.246	strong	OR2T3,trunk,malignant_melanoma,0,1	OR2T3	79	1	NM_001005495	exon1	c.G640A	p.A214T	CTTCTCGCCCCCA	.	scavenged	Atlas-SNP
COX2	5743	hgsc.bcm.edu	37	MT	7853	7853	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	7	6	0	1	0	.	.	none	.	.	.	.	ENST00000361739	exon1	c.G268A	p.V90I	GACGAGGTCAACG	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10959799	10959799	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	521	9	529	5	0.0172745	0.0094518	.	.	none	TPTE_ENST00000361285,right_lower_lobe,carcinoma,+2,4	TPTE	513	4	NM_199261	exon8	c.G175A	p.V59M	CTAACACACTTTA	.	scavenged	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31323353	31323353	+	Silent	SNP	G	G	A	rs2257269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	238	163	1	0.983471	0.00613497	G|0.600;A|0.400	0.400	strong	.	HLA-B	54	.	NM_005514	exon4	c.C636T	p.H212H	GGTCACGTGTGTC	.	PASS	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145641328	145641328	+	Missense_Mutation	SNP	C	C	T	rs17855765	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	63	27	0	0.984375	0	C|0.574;T|0.426	0.426	strong	SLC39A4_ENST00000276833,NS,carcinoma,0,2	SLC39A4	54	2	NM_130849	exon2	c.G340A	p.A114T	CCCGAGCGTCCTC	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541795	12541795	+	Missense_Mutation	SNP	C	C	A	rs35699767	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	47	77	0	0.484536	0	C|0.657;A|0.343	0.343	strong	.	ZNF443	63	.	NM_005815	exon4	c.G1191T	p.Q397H	CCCACACTGCTTG	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46896303	46896303	+	Silent	SNP	C	C	G	rs2230687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	63	82	0	0.984375	0	C|0.793;G|0.207	0.207	strong	.	COL18A1	129	.	NM_030582	exon5	c.C1377G	p.P459P	ACCCCCCGTCACC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509383	195509383	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	2	199	0	0.017094	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C9068A	p.T3023N	AGAGGGGTGGCGT	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911069	29911069	+	Missense_Mutation	SNP	A	A	T	rs1136697	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	55	134	0	0.625	0	A|0.871;T|0.129	0.129	strong	.	HLA-A	89	.	NM_001242758	exon3	c.A368T	p.Y123F	TAATGTATGGCTG	.	PASS	Atlas-SNP
CCDC41	51134	hgsc.bcm.edu	37	12	94769758	94769758	+	Silent	SNP	A	A	G	rs4761611	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	64	0	1	0	A|0.153;G|0.847	0.847	strong	.	CCDC41	59	.	NM_016122	exon8	c.T837C	p.R279R	TTCCAAACGTTCT	.	PASS	Atlas-SNP
APOBEC3G	60489	hgsc.bcm.edu	37	22	39477123	39477123	+	Silent	SNP	T	T	C	rs5757465	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	40	92	0	0.4	0	T|0.692;C|0.308	0.308	strong	APOBEC3G_ENST00000407997,NS,carcinoma,0,1	APOBEC3G	69	1	NM_021822	exon3	c.T357C	p.F119F	CATCTTTGTTGCC	.	PASS	Atlas-SNP
ATE1	11101	hgsc.bcm.edu	37	10	123670575	123670575	+	Silent	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	104	197	0	0.553191	0	.	.	none	ATE1,mouth,carcinoma,0,1	ATE1	67	1	NM_001001976	exon5	c.C429A	p.L143L	ATCACTGAGTGTT	.	PASS	Atlas-SNP
ATRIP	84126	hgsc.bcm.edu	37	3	48501936	48501936	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	2	146	0	0.0141844	0	.	.	none	ATRIP,NS,carcinoma,-2,1	ATRIP	41	1	NM_130384	exon8	c.C1483T	p.L495L	GTCTCCCTATTAC	.	scavenged	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44981883	44981883	+	Missense_Mutation	SNP	C	C	G	rs1897820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	80	141	0	0.487805	0	C|0.530;G|0.470	0.470	strong	.	ZNF180	103	.	NM_013256	exon5	c.G815C	p.C272S	CCATAGCATTTAT	.	PASS	Atlas-SNP
C7orf33	202865	hgsc.bcm.edu	37	7	148288020	148288020	+	Missense_Mutation	SNP	G	G	T	rs62624492	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	28	43	0	0.518519	0	G|0.974;T|0.026	0.026	strong	.	C7orf33	28	.	NM_145304	exon1	c.G3T	p.M1I	CAAAATGCAAGTG	.	PASS	Atlas-SNP
ZMAT4	79698	hgsc.bcm.edu	37	8	40438757	40438757	+	Missense_Mutation	SNP	T	T	C	rs17851751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	84	61	1	0.988235	0.0163934	T|0.790;C|0.210	0.210	strong	ZMAT4,NS,adenoma,0,1	ZMAT4	47	1	NM_024645	exon6	c.A601G	p.T201A	AGATGGTACATCT	.	scavenged	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	37	17	33802156	33802156	+	Missense_Mutation	SNP	T	T	G	rs56070076		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	358	199	363	1	0.555866	0.00275482	.	.	weak	SLFN12L_ENST00000449046,NS,carcinoma,0,6	SLFN12L	140	6	NM_001195790	exon4	c.A1553C	p.Y518S	CTCAAGTAGAAGA	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25981223	25981223	+	Silent	SNP	C	C	G	rs75541743	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	49	98	0	0.590361	0	C|0.981;G|0.019	0.019	strong	.	ATP10A	270	.	NM_024490	exon3	c.G720C	p.L240L	CCTACTCAGGTCG	.	PASS	Atlas-SNP
BMP1	649	hgsc.bcm.edu	37	8	22059323	22059323	+	Silent	SNP	C	C	T	rs61729094	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	22	46	0	0.488889	0	C|0.979;T|0.021	0.021	strong	.	BMP1	131	.	NM_006129	exon16	c.C2115T	p.D705D	CAAGGACGAGTGC	.	PASS	Atlas-SNP
ZNF584	201514	hgsc.bcm.edu	37	19	58928299	58928299	+	Silent	SNP	A	A	T	rs11668757	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	47	106	0	0.51087	0	A|0.846;T|0.154	0.154	strong	.	ZNF584	31	.	NM_173548	exon4	c.A414T	p.A138A	TGGGGCAGCTTTC	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43020983	43020983	+	Missense_Mutation	SNP	G	G	A	rs8023524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	69	128	0	0.463087	0	G|0.749;A|0.251	0.251	strong	.	CDAN1	70	.	NM_138477	exon20	c.C2671T	p.R891C	CCTGGCGCACCAG	.	PASS	Atlas-SNP
CSNK2A2	1459	hgsc.bcm.edu	37	16	58201631	58201631	+	Silent	SNP	G	G	A	rs55748630	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	43	88	0	0.483146	0	G|0.997;A|0.003	0.003	strong	.	CSNK2A2	25	.	NM_001896	exon7	c.C582T	p.A194A	CCTTGAGGCTACA	.	PASS	Atlas-SNP
ZNF175	7728	hgsc.bcm.edu	37	19	52090014	52090014	+	Missense_Mutation	SNP	C	C	T	rs35625154	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	85	181	0	0.464481	0	C|0.918;T|0.082	0.082	strong	.	ZNF175	65	.	NM_007147	exon5	c.C430T	p.R144C	GCTGACCGCACAA	.	PASS	Atlas-SNP
CD163	9332	hgsc.bcm.edu	37	12	7637769	7637769	+	Missense_Mutation	SNP	G	G	A	rs61729512	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	39	58	0	0.609375	0	G|0.905;A|0.095	0.095	strong	CD163,colon,carcinoma,0,1	CD163	221	1	NM_203416	exon11	c.C2702T	p.T901M	CACAGCGTGTCAG	.	PASS	Atlas-SNP
PRRT4	401399	hgsc.bcm.edu	37	7	127999645	127999645	+	Missense_Mutation	SNP	C	C	T	rs56272205	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	36	68	0	0.391304	0	A|0.000;C|0.874;T|0.126	0.126	strong	PRRT4,caecum,carcinoma,0,1	PRRT4	31	1	NM_001174164	exon3	c.G401A	p.R134Q	GAGCGCCGGGATG	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2160503	2160503	+	Silent	SNP	T	T	G	rs71385734	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	50	82	0	0.510204	0	T|0.738;G|0.262	0.262	strong	PKD1,colon,carcinoma,0,1	PKD1	184	1	NM_000296	exon15	c.A4665C	p.A1555A	GCGGCTTGCATTG	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74006317	74006317	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	54	105	0	0.534653	0	.	.	none	.	EVPL	155	.	NM_001988	exon22	c.A2969G	p.Q990R	TCTGCCTGCAGGC	.	PASS	Atlas-SNP
LRRC1	55227	hgsc.bcm.edu	37	6	53762092	53762092	+	Missense_Mutation	SNP	A	A	G	rs9349688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	12	21	0	0.545455	0	A|0.905;G|0.095	0.095	strong	.	LRRC1	59	.	NM_018214	exon7	c.A577G	p.I193V	GAATCAATTGGAG	.	PASS	Atlas-SNP
TRIM55	84675	hgsc.bcm.edu	37	8	67062583	67062583	+	Silent	SNP	G	G	A	rs61738600	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	67	133	0	0.507576	0	G|0.917;A|0.083	0.083	strong	.	TRIM55	91	.	NM_184086	exon7	c.G867A	p.S289S	AATCTCGGAAGCA	.	PASS	Atlas-SNP
UPF1	5976	hgsc.bcm.edu	37	19	18967721	18967721	+	Silent	SNP	C	C	T	rs34677724	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	92	141	0	0.476684	0	C|0.942;T|0.058	0.058	strong	.	UPF1	88	.	NM_002911	exon14	c.C1860T	p.A620A	GGGCGCCGGTGAC	.	PASS	Atlas-SNP
SPECC1L	23384	hgsc.bcm.edu	37	22	24718408	24718408	+	Missense_Mutation	SNP	G	G	A	rs55723436	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	42	105	0	0.461538	0	G|0.993;A|0.007	0.007	strong	.	SPECC1L	85	.	NM_001145468	exon4	c.G1460A	p.R487H	GTGGGCGCTATAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506750	195506750	+	Missense_Mutation	SNP	G	G	C	rs62282471	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	57	23	0	0.76	0	G|0.967;C|0.033	0.033	strong	.	MUC4	1505	.	NM_018406	exon2	c.C11701G	p.H3901D	TGGCGTGACGTGT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73680508	73680508	+	Missense_Mutation	SNP	G	G	C	rs6546839	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	39	76	0	0.5	0	G|0.687;C|0.313	0.313	strong	.	ALMS1	384	.	NM_015120	exon8	c.G6851C	p.R2284P	TTGCCCGTTTCAG	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227954599	227954599	+	Missense_Mutation	SNP	G	G	A	rs2229814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	112	209	0	0.495575	0	G|0.449;T|0.045	.	strong	.	COL4A4	215	.	NM_000092	exon21	c.C1444T	p.P482S	CTTTTGGGCCTCT	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340835	55340835	+	Silent	SNP	C	C	T	rs45459293	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	10	22	0	0.322581	0	C|0.913;T|0.087	0.087	strong	.	KIR3DL1	174	.	NM_013289	exon7	c.C1020T	p.H340H	CCTGCACATTCTG	.	PASS	Atlas-SNP
SLC26A2	1836	hgsc.bcm.edu	37	5	149360630	149360630	+	Missense_Mutation	SNP	C	C	T	rs78676079	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	34	79	0	0.465753	0	C|0.985;T|0.015	0.015	strong	SLC26A2,NS,NS,0,1	SLC26A2	48	1	NM_000112	exon3	c.C1474T	p.R492W	AATCTACGGGGAG	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641075	55641075	+	Missense_Mutation	SNP	A	A	G	rs7301705	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	37	76	0	0.397849	0	A|0.753;G|0.247	0.247	strong	.	OR6C74	52	.	NM_001005490	exon1	c.A4G	p.R2G	ACTATGAGAAACC	.	PASS	Atlas-SNP
STXBP3	6814	hgsc.bcm.edu	37	1	109338861	109338861	+	Silent	SNP	G	G	C	rs1127635	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	259	125	283	0	0.482625	0	G|0.624;C|0.375	0.375	strong	.	STXBP3	44	.	NM_007269	exon14	c.G1116C	p.L372L	GGACCTGGCACTT	.	PASS	Atlas-SNP
SLC7A7	9056	hgsc.bcm.edu	37	14	23282110	23282110	+	Silent	SNP	A	A	G	rs8018462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	46	0	1	0	A|0.461;G|0.539	0.539	strong	.	SLC7A7	36	.	NM_001126105	exon3	c.T498C	p.I166I	CTTACAAATGCAG	.	PASS	Atlas-SNP
NECAB2	54550	hgsc.bcm.edu	37	16	84012104	84012104	+	Silent	SNP	T	T	C	rs925331	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	33	79	0	0.559322	0	T|0.692;C|0.308	0.308	strong	.	NECAB2	36	.	NM_019065	exon3	c.T282C	p.L94L	CGTCCTTAATGAG	.	PASS	Atlas-SNP
DTYMK	1841	hgsc.bcm.edu	37	2	242618050	242618050	+	Silent	SNP	A	A	G	rs1131195	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	32	80	0	0.457143	0	A|0.622;G|0.378	0.378	strong	.	DTYMK	9	.	NM_012145	exon4	c.T345C	p.D115D	ACACCAATCTAGG	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30890483	30890483	+	Missense_Mutation	SNP	G	G	T	rs2074506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	40	85	0	0.506329	0	G|0.734;T|0.266	0.266	strong	.	VARS2	60	.	NM_001167734	exon22	c.G2128T	p.V710L	CCCCAGGTGCTGC	.	PASS	Atlas-SNP
FTSJD1	55783	hgsc.bcm.edu	37	16	71318577	71318577	+	Missense_Mutation	SNP	T	T	C	rs3803704	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	71	124	0	0.554688	0	T|0.735;C|0.265	0.265	strong	FTSJD1,NS,carcinoma,0,1	FTSJD1	70	1	NM_018348	exon3	c.A1247G	p.N416S	CAATTATTTCTGG	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151932990	151932990	+	Missense_Mutation	SNP	C	C	T	rs76844681	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	12	147	1	0.102564	0.00680272	C|0.999;T|0.001	0.001	weak	MLL3_ENST00000355193,NS,malignant_melanoma,+1,4	MLL3	1564	4	NM_170606	exon16	c.G2681A	p.R894Q	GGTCTCCGCTTTC	.	scavenged	Atlas-SNP
RALGAPA2	57186	hgsc.bcm.edu	37	20	20565512	20565512	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	36	64	0	0.48	0	.	.	none	.	RALGAPA2	274	.	NM_020343	exon19	c.A2527T	p.K843X	TACTCTTCTGTCT	.	PASS	Atlas-SNP
VLDLR	7436	hgsc.bcm.edu	37	9	2644799	2644799	+	Missense_Mutation	SNP	T	T	C	rs142885301	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	70	109	0	0.534351	0	T|0.999;C|0.001	0.001	strong	.	VLDLR	68	.	NM_003383	exon8	c.T1132C	p.Y378H	ATAGGCTACGAGT	.	PASS	Atlas-SNP
TIMM17A	10440	hgsc.bcm.edu	37	1	201934578	201934578	+	Missense_Mutation	SNP	G	G	A	rs4648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	79	162	0	0.424731	0	G|0.929;A|0.071	0.071	strong	TIMM17A,NS,carcinoma,0,1	TIMM17A	17	1	NM_006335	exon5	c.G337A	p.V113I	GCCATGGTTGGGT	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77325325	77325325	+	Missense_Mutation	SNP	G	G	T	rs35478105	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	119	108	0	0.983471	0	G|0.665;T|0.335	0.335	strong	ADAMTS18,NS,carcinoma,0,1	ADAMTS18	270	1	NM_199355	exon21	c.C3240A	p.S1080R	CTTCTCGCTGCAC	.	PASS	Atlas-SNP
FNDC9	408263	hgsc.bcm.edu	37	5	156770133	156770133	+	Missense_Mutation	SNP	C	C	T	rs10037485	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	97	107	0	1	0	C|0.765;T|0.235	0.235	strong	.	FNDC9	22	.	NM_001001343	exon2	c.G412A	p.V138I	AACGGACACACCA	.	PASS	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136518097	136518097	+	Silent	SNP	A	A	G	rs77905	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	144	150	0	1	0	G|0.581;N|0.000	0.581	strong	DBH,NS,carcinoma,0,2	DBH	86	2	NM_000787	exon9	c.A1410G	p.T470T	CAACACAGAAGAC	.	PASS	Atlas-SNP
RAB11FIP4	84440	hgsc.bcm.edu	37	17	29857460	29857460	+	Silent	SNP	G	G	A	rs61731602	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	55	93	0	0.528846	0	G|0.878;A|0.122	0.122	strong	.	RAB11FIP4	65	.	NM_032932	exon14	c.G1770A	p.A590A	GGCTGCGGAGATA	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231258150	231258150	+	Missense_Mutation	SNP	C	C	T	rs7590429	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	17	45	0	0.34	0	C|0.605;T|0.395	0.395	strong	.	SP140L	68	.	NM_138402	exon13	c.C1129T	p.P377S	AATCCTCCAAGAA	.	PASS	Atlas-SNP
FKBP5	2289	hgsc.bcm.edu	37	6	35544942	35544942	+	Silent	SNP	G	G	A	rs34866878	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	90	160	0	0.535714	0	G|0.928;A|0.072	0.072	strong	.	FKBP5	64	.	NM_001145775	exon11	c.C1095T	p.N365N	AAACTCGTTCATG	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592601	167592601	+	Missense_Mutation	SNP	G	G	A	rs200019718	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	18	101	0	0.3	0	G|0.941;A|0.059	0.059	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.G760A	p.G254R	GCAGCCGGAGTTG	.	PASS	Atlas-SNP
INCENP	3619	hgsc.bcm.edu	37	11	61908440	61908440	+	Missense_Mutation	SNP	T	T	C	rs2277283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	177	158	1	0.994382	0.00632911	T|0.764;C|0.236;A|0.000	0.236	strong	.	INCENP	122	.	NM_001040694	exon10	c.T1517C	p.M506T	TGCTCATGACCCC	.	PASS	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86904588	86904588	+	Silent	SNP	C	C	T	rs11161830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	20	64	0	0.512821	0	C|0.892;T|0.108	0.108	strong	.	CLCA2	102	.	NM_006536	exon7	c.C1002T	p.A334A	ACAAGCCGCAGAA	.	PASS	Atlas-SNP
OAS3	4940	hgsc.bcm.edu	37	12	113398974	113398974	+	Silent	SNP	C	C	T	rs141839417	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	46	69	0	0.46	0	C|0.999;T|0.001	0.001	strong	.	OAS3	63	.	NM_006187	exon8	c.C1756T	p.L586L	GCAGAGCTGCGGA	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47552449	47552449	+	Missense_Mutation	SNP	A	A	C	rs11910483	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	29	24	0	0.446154	0	A|0.975;C|0.025	0.025	strong	.	COL6A2	351	.	NM_001849	exon28	c.A3043C	p.I1015L	CGCTTCATCCGCT	.	PASS	Atlas-SNP
VPS41	27072	hgsc.bcm.edu	37	7	38765883	38765883	+	Missense_Mutation	SNP	C	C	T	rs1059508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	30	56	0	0.410959	0	C|0.986;T|0.014	0.014	strong	.	VPS41	102	.	NM_014396	exon29	c.G2528A	p.R843H	GGTCCACGGTTCT	.	PASS	Atlas-SNP
C11orf16	56673	hgsc.bcm.edu	37	11	8947586	8947586	+	Missense_Mutation	SNP	C	C	G	rs11042127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	42	58	0	0.545455	0	C|0.787;G|0.213	0.213	strong	.	C11orf16	43	.	NM_020643	exon5	c.G628C	p.V210L	ACTGGACCCCACC	.	PASS	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907708	12907708	+	Silent	SNP	A	A	G	rs4026149	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	16	174	25	0.0784314	0.143678	A|0.667;G|0.333	0.333	strong	HNRNPCL1,NS,carcinoma,-1,1	HNRNPCL1	68	1	NM_001013631	exon2	c.T435C	p.R145R	ACGTTGACGTTTC	.	scavenged	Atlas-SNP
SLC1A5	6510	hgsc.bcm.edu	37	19	47282162	47282162	+	Silent	SNP	G	G	A	rs2070246	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	40	55	0	0.588235	0	G|0.704;A|0.296	0.296	strong	.	SLC1A5	31	.	NM_005628	exon5	c.C828T	p.Y276Y	AGGGGCGTACCTG	.	PASS	Atlas-SNP
PFKP	5214	hgsc.bcm.edu	37	10	3150898	3150898	+	Silent	SNP	C	C	T	rs11251721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	93	174	0	0.547059	0	C|0.826;T|0.174	0.174	strong	.	PFKP	182	.	NM_002627	exon9	c.C876T	p.V292V	GCTTGTCGTCACG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124358498	124358498	+	Missense_Mutation	SNP	T	T	G	rs144489236	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	51	116	0	0.554348	0	T|0.976;G|0.024	0.024	strong	DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	NM_007329	exon26	c.T3165G	p.I1055M	ACCCATTGTCCTG	.	PASS	Atlas-SNP
ATP2C2	9914	hgsc.bcm.edu	37	16	84494275	84494275	+	Silent	SNP	C	C	T	rs2241640	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	50	61	0	0.526316	0	C|0.513;T|0.487	0.487	strong	ATP2C2,colon,carcinoma,+1,1	ATP2C2	75	1	NM_014861	exon24	c.C2349T	p.P783P	AGAGCCCGTTGAC	.	PASS	Atlas-SNP
PRAME	23532	hgsc.bcm.edu	37	22	22899234	22899234	+	Missense_Mutation	SNP	A	A	G	rs1129172	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	36	79	0	0.413793	0	G|0.653;N|0.000	0.653	strong	PRAME,NS,carcinoma,0,4	PRAME	78	4	NM_206954	exon3	c.T19C	p.W7R	TTACCCACAAACG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26612460	26612460	+	Silent	SNP	G	G	A	rs11247900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	125	173	1	0.905797	0.00578035	G|0.862;A|0.138	0.138	strong	.	UBXN11	54	.	NM_183008	exon10	c.C628T	p.L210L	CCACCAGCTCACT	.	PASS	Atlas-SNP
CNR2	1269	hgsc.bcm.edu	37	1	24201162	24201162	+	Missense_Mutation	SNP	G	G	A	rs2229579	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	19	220	0	0.0989583	0	G|0.906;T|0.006	.	strong	.	CNR2	78	.	NM_001841	exon2	c.C946T	p.H316Y	TCCAGTGAGCCAG	.	PASS	Atlas-SNP
RBM20	282996	hgsc.bcm.edu	37	10	112544125	112544125	+	Missense_Mutation	SNP	C	C	T	rs189569984	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	55	85	0	0.518868	0	C|0.999;T|0.001	0.001	strong	RBM20,colon,carcinoma,-1,1	RBM20	50	1	NM_001134363	exon4	c.C1364T	p.S455L	TTGGTTCGGCAGA	.	PASS	Atlas-SNP
WDR25	79446	hgsc.bcm.edu	37	14	100847707	100847707	+	Missense_Mutation	SNP	A	A	G	rs2273800	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	29	80	0	0.527273	0	A|0.330;G|0.670	0.670	strong	.	WDR25	37	.	NM_001161476	exon2	c.A446G	p.H149R	CTTTCCATGCTCA	.	PASS	Atlas-SNP
DNAAF3	352909	hgsc.bcm.edu	37	19	55671374	55671374	+	Silent	SNP	C	C	T	rs891187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	92	107	0	0.968421	0	C|0.700;T|0.300	0.300	strong	.	.	.	.	NM_001256714	exon10	c.G1257A	p.P419P	CGGGGTCGGGGCT	.	PASS	Atlas-SNP
TEX33	339669	hgsc.bcm.edu	37	22	37398195	37398195	+	Missense_Mutation	SNP	C	C	T	rs743749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	27	84	0	0.369863	0	C|0.715;T|0.285	0.285	strong	.	TEX33	25	.	NM_001163857	exon3	c.G172A	p.A58T	CTTGAGCGCTGGC	.	PASS	Atlas-SNP
PSMD2	5708	hgsc.bcm.edu	37	3	184020542	184020542	+	Missense_Mutation	SNP	G	G	T	rs11545169	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	76	109	0	0.571429	0	G|0.896;T|0.104	0.104	strong	.	PSMD2	56	.	NM_002808	exon7	c.G939T	p.E313D	CGAGGAGTATGAG	.	PASS	Atlas-SNP
SIPA1L3	23094	hgsc.bcm.edu	37	19	38673298	38673298	+	Missense_Mutation	SNP	C	C	G	rs3745945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	41	89	0	0.493976	0	C|0.942;G|0.058	0.058	strong	.	SIPA1L3	150	.	NM_015073	exon16	c.C4348G	p.P1450A	AAGCAGCCTGTAC	.	PASS	Atlas-SNP
OR5AK2	390181	hgsc.bcm.edu	37	11	56757021	56757021	+	Silent	SNP	G	G	A	rs61886711	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	386	176	325	0	0.455959	0	G|0.829;A|0.171	0.171	strong	.	OR5AK2	45	.	NM_001005323	exon1	c.G633A	p.G211G	CACTGGGTTGGTC	.	PASS	Atlas-SNP
KRT5	3852	hgsc.bcm.edu	37	12	52912909	52912909	+	Missense_Mutation	SNP	G	G	T	rs641615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	37	144	0	0.318966	0	G|0.790;T|0.210	0.210	strong	.	KRT5	88	.	NM_000424	exon2	c.C591A	p.D197E	CTTGGTGTCCAGA	.	PASS	Atlas-SNP
SETMAR	6419	hgsc.bcm.edu	37	3	4358210	4358210	+	Silent	SNP	A	A	G	rs7647539	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	40	49	0	0.952381	0	A|0.558;G|0.442	0.442	strong	.	SETMAR	30	.	NM_006515	exon3	c.A1335G	p.R445R	CGTTCGACATTTG	.	PASS	Atlas-SNP
TRIM45	80263	hgsc.bcm.edu	37	1	117659352	117659352	+	Missense_Mutation	SNP	C	C	T	rs3738413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	52	114	0	0.504854	0	C|0.909;T|0.091	0.091	strong	.	TRIM45	55	.	NM_025188	exon3	c.G1238A	p.R413Q	TTCTCCCGGGCTC	.	PASS	Atlas-SNP
TYSND1	219743	hgsc.bcm.edu	37	10	71905695	71905695	+	Silent	SNP	A	A	G	rs10999158	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	14	10	0	0.466667	0	A|0.679;G|0.321	0.321	strong	.	TYSND1	20	.	NM_173555	exon1	c.T648C	p.G216G	TGGCGCACCCTTG	.	PASS	Atlas-SNP
PPM1F	9647	hgsc.bcm.edu	37	22	22287862	22287862	+	Silent	SNP	G	G	A	rs2027789	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	26	75	0	0.52	0	G|0.665;A|0.335	0.335	strong	.	PPM1F	34	.	NM_014634	exon5	c.C648T	p.N216N	GGCAGCGTTGGTG	.	PASS	Atlas-SNP
SLC44A4	80736	hgsc.bcm.edu	37	6	31842598	31842598	+	Missense_Mutation	SNP	T	T	A	rs12661281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	59	114	0	0.561905	0	T|0.871;A|0.129	0.129	strong	.	SLC44A4	67	.	NM_025257	exon6	c.A368T	p.D123V	CATGGGTCCTCCG	.	PASS	Atlas-SNP
SLC22A14	9389	hgsc.bcm.edu	37	3	38355225	38355225	+	Missense_Mutation	SNP	G	G	A	rs73064822	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	21	47	0	0.411765	0	G|0.825;A|0.175	0.175	strong	.	SLC22A14	64	.	NM_004803	exon7	c.G1171A	p.V391I	TTTACCGTCAGTT	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	271638	271638	+	Missense_Mutation	SNP	C	C	T	rs506121	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	37	77	0	0.649123	0	C|0.688;T|0.312	0.312	strong	.	DOCK8	401	.	NM_203447	exon2	c.C65T	p.A22V	CTTCAGCGGAAAT	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919237	51919237	+	Silent	SNP	C	C	T	rs199590261	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	33	193	0	0.302752	0	C|0.994;T|0.006	0.006	strong	.	SIGLEC10	112	.	NM_001171157	exon5	c.G939A	p.V313V	AGCCTTCACCCCG	.	PASS	Atlas-SNP
SERPINA1	5265	hgsc.bcm.edu	37	14	94844843	94844843	+	Missense_Mutation	SNP	T	T	G	rs1303	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	283	136	247	1	0.480565	0.00404858	T|0.775;G|0.225	0.225	strong	SERPINA1,NS,carcinoma,0,1	SERPINA1	51	1	NM_001127701	exon7	c.A1200C	p.E400D	ATTTTGTTCAATC	.	PASS	Atlas-SNP
GLCCI1	113263	hgsc.bcm.edu	37	7	8125964	8125964	+	Silent	SNP	C	C	T	rs929509	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	138	172	0	0.992806	0	C|0.255;T|0.745	0.745	strong	GLCCI1,NS,carcinoma,0,1	GLCCI1	50	1	NM_138426	exon8	c.C1440T	p.S480S	GAACTCCCCTAAC	.	PASS	Atlas-SNP
BBS10	79738	hgsc.bcm.edu	37	12	76740149	76740149	+	Missense_Mutation	SNP	G	G	A	rs35676114	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	51	157	1	0.490385	0.00636943	G|0.948;A|0.052	0.052	strong	BBS10,NS,carcinoma,-1,1	BBS10	46	1	NM_024685	exon2	c.C1616T	p.P539L	AGTAATGGTTCAT	.	scavenged	Atlas-SNP
DEFB129	140881	hgsc.bcm.edu	37	20	210306	210306	+	Missense_Mutation	SNP	C	C	G	rs1053783	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	42	64	0	0.512195	0	C|0.798;G|0.202	0.202	strong	.	DEFB129	24	.	NM_080831	exon2	c.C446G	p.T149S	GTAACACCAAAGA	.	PASS	Atlas-SNP
NUDT10	170685	hgsc.bcm.edu	37	X	51076018	51076018	+	Silent	SNP	C	C	T	rs12846945	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	138	117	0	0.951724	0	C|0.864;T|0.136	0.136	strong	.	NUDT10	28	.	NM_153183	exon2	c.C201T	p.Y67Y	GGTGTACGAAGAG	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23098422	23098422	+	Missense_Mutation	SNP	A	A	G	rs13339649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	69	139	0	0.472603	0	A|0.742;G|0.258	0.258	strong	.	USP31	122	.	NM_020718	exon9	c.T1613C	p.I538T	TCTACTATTGGGT	.	PASS	Atlas-SNP
ERO1LB	56605	hgsc.bcm.edu	37	1	236381825	236381825	+	Missense_Mutation	SNP	G	G	C	rs1055851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	84	231	0	0.411765	0	G|0.530;C|0.470	0.470	strong	.	ERO1LB	48	.	NM_019891	exon16	c.C1395G	p.H465Q	CCTACTGTGTTGT	.	PASS	Atlas-SNP
DCPS	28960	hgsc.bcm.edu	37	11	126215285	126215285	+	Missense_Mutation	SNP	G	G	A	rs140377449	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	23	56	0	0.425926	0	G|0.999;A|0.001	0.001	strong	.	DCPS	33	.	NM_014026	exon6	c.G791A	p.R264Q	ATCTGCGAGTATA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47925520	47925520	+	Missense_Mutation	SNP	C	C	T	rs141646493	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	98	145	2	0.505155	0.0137931	C|0.995;T|0.005	0.005	strong	PKD1L1,colon,carcinoma,-1,1	PKD1L1	328	1	NM_138295	exon18	c.G2969A	p.R990Q	GGTTCCCGTGAGA	.	scavenged	Atlas-SNP
LRIT3	345193	hgsc.bcm.edu	37	4	110773067	110773067	+	Missense_Mutation	SNP	G	G	A	rs4698797	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	97	112	0	0.979798	0	G|0.486;A|0.514	0.514	strong	.	LRIT3	107	.	NM_198506	exon2	c.G524A	p.S175N	TGGAGAGCTGGAC	.	PASS	Atlas-SNP
CCPG1	9236	hgsc.bcm.edu	37	15	55664220	55664220	+	Silent	SNP	G	G	A	rs3203152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	36	78	0	0.537313	0	G|0.852;A|0.148	0.148	strong	.	CCPG1	74	.	NM_020739	exon6	c.C477T	p.D159D	TTCATCGTCACTA	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17265507	17265507	+	Missense_Mutation	SNP	C	C	T	rs201951425	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	8	2	0	0.666667	0	C|0.983;T|0.017	0.017	strong	CROCC,NS,carcinoma,0,1	CROCC	185	1	NM_014675	exon12	c.C1478T	p.P493L	GGACCCCGTCCCC	.	scavenged	Atlas-SNP
WNT7A	7476	hgsc.bcm.edu	37	3	13896284	13896284	+	Silent	SNP	C	C	T	rs12639607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	22	31	0	0.6875	0	C|0.826;T|0.174	0.174	strong	WNT7A,caecum,carcinoma,-1,3	WNT7A	70	3	NM_004625	exon3	c.G315A	p.A105A	GGTGAACGCAGCC	.	PASS	Atlas-SNP
CMTM1	113540	hgsc.bcm.edu	37	16	66600479	66600479	+	Silent	SNP	G	G	A	rs7193473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	80	92	0	0.588235	0	G|0.721;A|0.279	0.279	strong	.	CMTM1	34	.	NM_181271	exon1	c.G63A	p.P21P	ACAACCGGAGACT	.	PASS	Atlas-SNP
LAT	27040	hgsc.bcm.edu	37	16	28997997	28997997	+	Silent	SNP	G	G	A	rs1131543	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	52	97	0	0.577778	0	G|0.742;A|0.258	0.258	strong	.	LAT	22	.	NM_001014989	exon8	c.G468A	p.A156A	GGATGCGGATGAG	.	PASS	Atlas-SNP
FGL1	2267	hgsc.bcm.edu	37	8	17731935	17731935	+	Missense_Mutation	SNP	T	T	C	rs35311020	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	70	153	0	0.443038	0	T|0.994;C|0.006	0.006	strong	.	FGL1	31	.	NM_201553	exon5	c.A340G	p.M114V	CGGACATGTCACA	.	PASS	Atlas-SNP
CFP	5199	hgsc.bcm.edu	37	X	47483800	47483800	+	Silent	SNP	G	G	A	rs1048118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	47	67	0	1	0	G|0.777;0|0.004	.	strong	.	CFP	43	.	NM_001145252	exon9	c.C1284T	p.N428N	GGTCACGTTCTTC	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32561340	32561340	+	Missense_Mutation	SNP	G	G	A	rs78337553	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	7	101	0	0.0588235	0	G|0.999;A|0.001	0.001	weak	ARHGAP5,NS,carcinoma,0,1	ARHGAP5	166	1	NM_001173	exon2	c.G1465A	p.E489K	AAAGAAGAGTTTC	.	scavenged	Atlas-SNP
SETD6	79918	hgsc.bcm.edu	37	16	58550484	58550484	+	Silent	SNP	G	G	A	rs3743567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	42	84	0	0.385321	0	G|0.896;A|0.104	0.104	strong	.	SETD6	27	.	NM_001160305	exon4	c.G579A	p.L193L	CGTGCTGCCCTTC	.	PASS	Atlas-SNP
ZNF585A	199704	hgsc.bcm.edu	37	19	37644051	37644051	+	Silent	SNP	T	T	C	rs57916401	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	121	255	0	0.47451	0	T|0.630;C|0.370	0.370	strong	.	ZNF585A	117	.	NM_199126	exon6	c.A585G	p.A195A	TGTGAATGCTTTG	.	PASS	Atlas-SNP
FBXO45	200933	hgsc.bcm.edu	37	3	196295974	196295974	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	27	19	0	0.490909	0	.	.	none	.	FBXO45	18	.	NM_001105573	exon1	c.C119T	p.P40L	GGCTGCCCAGCCG	.	PASS	Atlas-SNP
FBXO46	23403	hgsc.bcm.edu	37	19	46216642	46216642	+	Missense_Mutation	SNP	G	G	T	rs11537711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	37	90	0	0.486842	0	G|0.898;T|0.102	0.102	strong	.	FBXO46	34	.	NM_001080469	exon2	c.C112A	p.P38T	GCTCAGGGCAGGC	.	PASS	Atlas-SNP
EML6	400954	hgsc.bcm.edu	37	2	55119771	55119771	+	Missense_Mutation	SNP	T	T	A	rs200933456	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	41	87	0	0.460674	0	T|0.995;A|0.005	0.005	strong	.	EML6	85	.	NM_001039753	exon18	c.T2720A	p.F907Y	CTGTGTTTGCTAT	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31793087	31793087	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	62	157	1	0.5	0.00636943	.	.	none	PDE1C_ENST00000396193,right_upper_lobe,carcinoma,0,2	PDE1C	465	2	NM_001191058	exon19	c.G2221A	p.D741N	GCTCATCAGTTTT	.	scavenged	Atlas-SNP
PCDHGA11	56105	hgsc.bcm.edu	37	5	140801104	140801104	+	Missense_Mutation	SNP	T	T	C	rs11167744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	82	107	0	0.97619	0	T|0.896;C|0.104	0.104	strong	.	PCDHGA11	128	.	NM_032091	exon1	c.T310C	p.F104L	TCCTGTTTTTTAA	.	PASS	Atlas-SNP
GPIHBP1	338328	hgsc.bcm.edu	37	8	144295154	144295154	+	Silent	SNP	C	C	T	rs61747644	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	190	190	124	0	1	0	C|0.860;T|0.140	0.140	strong	.	GPIHBP1	12	.	NM_178172	exon1	c.C12T	p.L4L	GGCGCTCGGGGCT	.	PASS	Atlas-SNP
EFR3A	23167	hgsc.bcm.edu	37	8	132982824	132982824	+	Missense_Mutation	SNP	A	A	G	rs1051221	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	90	102	0	0.989011	0	A|0.517;C|0.002	.	strong	.	EFR3A	96	.	NM_015137	exon10	c.A1093G	p.N365D	AGTGTCAACTTAA	.	PASS	Atlas-SNP
HAGHL	84264	hgsc.bcm.edu	37	16	778820	778820	+	Silent	SNP	G	G	A	rs12448432	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	53	69	0	0.595506	0	G|0.733;A|0.267	0.267	strong	.	HAGHL	18	.	NM_032304	exon6	c.G525A	p.T175T	GCACACGCTTAGC	.	PASS	Atlas-SNP
FAHD1	81889	hgsc.bcm.edu	37	16	1877494	1877494	+	Silent	SNP	T	T	C	rs3743854	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	34	59	0	0.459459	0	T|0.840;C|0.160	0.160	strong	.	FAHD1	18	.	NM_031208	exon1	c.T264C	p.A88A	CGAGGCTGCGGCC	.	PASS	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605350	84605350	+	Missense_Mutation	SNP	G	G	C	rs367877053		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	70	142	0	0.482759	0	.	.	weak	.	.	.	.	NM_001001670	exon3	c.G251C	p.S84T	GGAAAAGTTTCCA	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151171439	151171439	+	Missense_Mutation	SNP	A	A	C	rs7619322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	134	121	0	1	0	A|0.276;C|0.724	0.724	strong	.	IGSF10	279	.	NM_178822	exon3	c.T448G	p.Y150D	GCCCATAAAAAAC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378977	31378977	+	Missense_Mutation	SNP	G	G	A	rs1051792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	152	160	0	1	0	G|0.653;A|0.347	0.347	strong	.	MICA	21	.	NM_001177519	exon3	c.G454A	p.V152M	TGGACAGTGCCCC	.	PASS	Atlas-SNP
VSTM1	284415	hgsc.bcm.edu	37	19	54545186	54545186	+	Silent	SNP	C	C	T	rs73058793	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	22	58	0	0.37931	0	C|0.755;T|0.245	0.245	strong	.	VSTM1	30	.	NM_198481	exon7	c.G537A	p.P179P	CTGCTCCGGAAGT	.	PASS	Atlas-SNP
CH25H	9023	hgsc.bcm.edu	37	10	90966996	90966996	+	Silent	SNP	C	C	G	rs10887932	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	49	82	0	0.494949	0	C|0.834;G|0.166	0.166	strong	.	CH25H	19	.	NM_003956	exon1	c.G54C	p.L18L	CAGGAACAGCTGC	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143747271	143747271	+	Silent	SNP	C	C	G	rs2978973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	32	76	0	0.390244	0	C|0.634;G|0.366	0.366	strong	.	.	.	.	NM_003724	exon2	c.G207C	p.S69S	GGAGTCCGAGCTG	.	PASS	Atlas-SNP
BBOX1	8424	hgsc.bcm.edu	37	11	27147270	27147270	+	Silent	SNP	G	G	A	rs1044273	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	84	125	1	0.988235	0.008	G|0.866;A|0.134	0.134	strong	BBOX1,right_lower_lobe,carcinoma,+2,1	BBOX1	46	1	NM_003986	exon8	c.G906A	p.V302V	TGATGTGCCTGTT	.	PASS	Atlas-SNP
ST18	9705	hgsc.bcm.edu	37	8	53071461	53071461	+	Silent	SNP	G	G	A	rs2278152	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	70	124	0	0.496454	0	G|0.914;A|0.086	0.086	strong	ST18,NS,carcinoma,-2,1	ST18	212	1	NM_014682	exon15	c.C1803T	p.A601A	TACCTTGGCATGC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679280	73679280	+	Missense_Mutation	SNP	A	A	G	rs6546838	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	29	74	0	0.508772	0	A|0.663;G|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon8	c.A5623G	p.I1875V	AAAGCAATAGGGG	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612989	53612989	+	Silent	SNP	A	A	G	rs1054484	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	285	130	257	0	0.45614	0	A|0.848;G|0.152	0.152	strong	ZNF415,NS,carcinoma,0,1	ZNF415	68	1	NM_018355	exon4	c.T309C	p.D103D	TCTTTCATCATCT	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216229692	216229692	+	Silent	SNP	A	A	G	rs11651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	33	78	1	0.452055	0.0128205	A|0.771;G|0.229	0.229	strong	FN1_ENST00000354785,NS,carcinoma,0,2	FN1	521	2	NM_212482	exon44	c.T7161C	p.Y2387Y	ATCATCATAACAC	.	scavenged	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66725160	66725160	+	Missense_Mutation	SNP	C	C	T	rs1185244	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	29	76	0	0.414286	0	C|0.561;T|0.439	0.439	strong	.	HELB	90	.	NM_033647	exon12	c.C2897T	p.P966L	ATTTTCCGTCCCC	.	PASS	Atlas-SNP
ANGPT2	285	hgsc.bcm.edu	37	8	6377433	6377433	+	Silent	SNP	C	C	T	rs1961222	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	93	197	0	0.422727	0	C|0.786;T|0.214	0.214	strong	.	ANGPT2	126	.	NM_001147	exon5	c.G882A	p.T294T	GCCATTCGTGGTG	.	PASS	Atlas-SNP
TAF6L	10629	hgsc.bcm.edu	37	11	62543326	62543326	+	Missense_Mutation	SNP	C	C	T	rs76769410	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	33	53	0	0.578947	0	C|0.995;T|0.005	0.005	strong	.	TAF6L	39	.	NM_006473	exon2	c.C71T	p.T24M	AGAGCACGGGCCT	.	PASS	Atlas-SNP
JSRP1	126306	hgsc.bcm.edu	37	19	2252990	2252990	+	Missense_Mutation	SNP	C	C	G	rs80043033	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	42	96	0	0.461538	0	C|0.842;G|0.158	0.158	strong	.	JSRP1	18	.	NM_144616	exon6	c.G449C	p.G150A	GCCTCCCCAGGGA	.	PASS	Atlas-SNP
ZSCAN31	64288	hgsc.bcm.edu	37	6	28297368	28297368	+	Silent	SNP	G	G	A	rs41269297	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	60	117	0	0.540541	0	G|0.972;A|0.028	0.028	strong	.	.	.	.	NM_030899	exon2	c.C93T	p.N31N	AGAAAAGTTGTTC	.	PASS	Atlas-SNP
ENPP4	22875	hgsc.bcm.edu	37	6	46108916	46108916	+	Silent	SNP	C	C	G	rs9472696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	51	103	0	0.515152	0	C|0.901;G|0.099	0.099	strong	.	ENPP4	44	.	NM_014936	exon3	c.C954G	p.A318A	GGTTGCCGATGAA	.	PASS	Atlas-SNP
EDA2R	60401	hgsc.bcm.edu	37	X	65824986	65824986	+	Missense_Mutation	SNP	C	C	T	rs1385699	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	81	82	0	0.987805	0	C|0.436;0|0.005	.	strong	.	EDA2R	30	.	NM_001242310	exon2	c.G170A	p.R57K	TGACATCTGTGGT	.	PASS	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183753777	183753777	+	Missense_Mutation	SNP	G	G	A	rs36092077	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	44	88	0	0.458333	0	G|0.763;A|0.237	0.237	strong	.	HTR3D	65	.	NM_001163646	exon3	c.G269A	p.R90Q	ATGCCCGGCCTTG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134691472	134691472	+	Missense_Mutation	SNP	C	C	A	rs181912601	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	66	301	0	0.258824	0	C|0.992;A|0.008	0.008	strong	.	TTC40	100	.	NM_001200049	exon30	c.G4125T	p.K1375N	CCTCTCCTTCTCC	.	PASS	Atlas-SNP
F7	2155	hgsc.bcm.edu	37	13	113773159	113773159	+	Missense_Mutation	SNP	G	G	A	rs6046	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	43	99	0	0.394495	0	T|0.001;G|0.877;C|0.007;A|0.115	0.115	strong	.	F7	49	.	NM_000131	exon9	c.G1238A	p.R413Q	ACTACCGGGGCAC	.	PASS	Atlas-SNP
ZRANB3	84083	hgsc.bcm.edu	37	2	135988416	135988416	+	Missense_Mutation	SNP	C	C	T	rs935615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	106	231	0	0.452991	0	C|0.797;T|0.203	0.203	strong	.	ZRANB3	109	.	NM_032143	exon13	c.G1621A	p.E541K	TTGATTCGTCACA	.	PASS	Atlas-SNP
TTC23L	153657	hgsc.bcm.edu	37	5	34840841	34840841	+	Missense_Mutation	SNP	A	A	G	rs6451173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	59	121	0	0.443609	0	A|0.457;G|0.543	0.543	strong	.	TTC23L	47	.	NM_144725	exon2	c.A65G	p.H22R	GCTTCCATATGTA	.	PASS	Atlas-SNP
OSBPL1A	114876	hgsc.bcm.edu	37	18	21752366	21752366	+	Silent	SNP	A	A	G	rs2077984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	73	113	0	0.55303	0	A|0.894;G|0.106	0.106	strong	.	OSBPL1A	94	.	NM_080597	exon22	c.T2175C	p.Y725Y	ATTGCCATACTGT	.	PASS	Atlas-SNP
MYBPC1	4604	hgsc.bcm.edu	37	12	102036305	102036305	+	Silent	SNP	C	C	T	rs2293468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	47	58	0	1	0	C|0.704;T|0.296	0.296	strong	.	MYBPC1	235	.	NM_206819	exon11	c.C774T	p.D258D	CACCGACCTGCGC	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	37	22	18304891	18304891	+	Missense_Mutation	SNP	C	C	T	rs45544141	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	14	42	0	0.325581	0	C|0.921;G|0.000;T|0.079	0.079	strong	ENSG00000093100,NS,carcinoma,-1,1	MICAL3	53	1	NM_015241	exon24	c.G3353A	p.R1118H	GGCAAACGCAGCT	.	PASS	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169432841	169432841	+	Silent	SNP	G	G	A	rs1806729	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	62	118	0	0.525424	0	G|0.728;A|0.272	0.272	strong	.	PALLD	179	.	NM_001166108	exon2	c.G186A	p.K62K	GGAAAAGGAGATC	.	PASS	Atlas-SNP
C15orf56	644809	hgsc.bcm.edu	37	15	40544617	40544617	+	Missense_Mutation	SNP	G	G	A	rs55863440	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	11	21	0	0.52381	0	G|0.812;A|0.188	0.188	strong	.	C15orf56	3	.	NM_001039905	exon2	c.C355T	p.P119S	CAGGTGGAGAGAA	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	589	6	529	6	0.0101868	0.0113422	.	.	none	POTEC,NS,carcinoma,-1,5	POTEC	129	5	NM_001137671	exon1	c.G492T	p.T164T	CATGTCCGTGTCC	.	scavenged	Atlas-SNP
UBR3	130507	hgsc.bcm.edu	37	2	170917648	170917648	+	Silent	SNP	A	A	G	rs10203212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	78	98	0	0.549296	0	A|0.719;G|0.281	0.281	strong	.	UBR3	182	.	NM_172070	exon34	c.A4845G	p.L1615L	TGAACTATTTAAA	.	PASS	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	37	5	96121524	96121524	+	Silent	SNP	C	C	T	rs469783	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	75	76	0	0.986842	0	C|0.451;T|0.549	0.549	strong	.	ERAP1	59	.	NM_001198541	exon13	c.G1911A	p.A637A	GAGACTCGCCCGA	.	PASS	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167689162	167689162	+	Missense_Mutation	SNP	G	G	A	rs370473451		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	59	117	0	0.472	0	.	.	weak	.	.	.	.	NM_001122679	exon29	c.G7645A	p.G2549S	AAAGCAGGTCACT	.	PASS	Atlas-SNP
OR7G1	125962	hgsc.bcm.edu	37	19	9226192	9226192	+	Missense_Mutation	SNP	A	A	G	rs6511874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	95	186	2	0.524862	0.0107527	A|0.686;G|0.314	0.314	strong	OR7G1,right_lower_lobe,carcinoma,+1,1	OR7G1	53	1	NM_001005192	exon1	c.T248C	p.V83A	ATGTTCACTAGGA	.	scavenged	Atlas-SNP
PNKD	25953	hgsc.bcm.edu	37	2	219206738	219206738	+	Silent	SNP	C	C	A	rs34745867	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	47	127	0	0.460784	0	C|0.982;A|0.018	0.018	strong	.	PNKD	58	.	NM_015488	exon7	c.C652A	p.R218R	GTGGGACGGCTTC	.	PASS	Atlas-SNP
ACAP3	116983	hgsc.bcm.edu	37	1	1231656	1231656	+	Silent	SNP	G	G	A	rs1749951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	9	132	0	0.0743802	0	G|0.963;A|0.037	0.037	strong	.	ACAP3	87	.	NM_030649	exon16	c.C1342T	p.L448L	CACCCAGGCTCCT	.	PASS	Atlas-SNP
OR5P3	120066	hgsc.bcm.edu	37	11	7847472	7847472	+	Silent	SNP	C	C	T	rs1482793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	30	43	0	0.508475	0	C|0.504;T|0.496	0.496	strong	.	OR5P3	44	.	NM_153445	exon1	c.G48A	p.G16G	AGATAACCCCAAA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150905485	150905485	+	Silent	SNP	C	C	T	rs36092108	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	36	65	0	0.439024	0	C|0.954;T|0.046	0.046	strong	.	FAT2	465	.	NM_001447	exon17	c.G10350A	p.L3450L	GTCACTCAGGATC	.	PASS	Atlas-SNP
GPR171	29909	hgsc.bcm.edu	37	3	150917000	150917000	+	Silent	SNP	T	T	G	rs3773614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	86	188	0	0.419512	0	T|0.882;G|0.118	0.118	strong	.	GPR171	36	.	NM_013308	exon3	c.A174C	p.T58T	ATCGGCTGTAAGC	.	PASS	Atlas-SNP
FOXK1	221937	hgsc.bcm.edu	37	7	4802035	4802035	+	Silent	SNP	A	A	G	rs1053753	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	17	35	0	0.62963	0	A|0.728;G|0.272	0.272	strong	.	FOXK1	64	.	NM_001037165	exon9	c.A2142G	p.V714V	TGCTGTAACCACA	.	PASS	Atlas-SNP
PSMB5	5693	hgsc.bcm.edu	37	14	23504021	23504021	+	Missense_Mutation	SNP	G	G	A	rs11543947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	29	75	0	0.391892	0	G|0.946;A|0.054	0.054	strong	.	PSMB5	31	.	NM_001144932	exon1	c.C70T	p.R24C	CTGCACGACCCCC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721320	54721320	+	Missense_Mutation	SNP	C	C	G	rs1053002	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	301	106	381	0	0.352159	0	C|0.891;G|0.109	0.109	strong	LILRB3,NS,carcinoma,-2,1	LILRB3	67	1	NM_001081450	exon12	c.G1620C	p.Q540H	CACTGCCTGGGGG	.	PASS	Atlas-SNP
ZNF589	51385	hgsc.bcm.edu	37	3	48282695	48282695	+	Missense_Mutation	SNP	A	A	G	rs9847953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	112	59	0	1	0	A|0.753;G|0.247	0.247	strong	ZNF589,NS,carcinoma,0,2	ZNF589	20	2	NM_016089	exon1	c.A34G	p.T12A	GGCTGGACTGCGG	.	PASS	Atlas-SNP
SEC14L4	284904	hgsc.bcm.edu	37	22	30888527	30888527	+	Missense_Mutation	SNP	C	C	T	rs17738540	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	57	117	0	0.445312	0	C|0.837;N|0.000	.	strong	.	SEC14L4	43	.	NM_001161368	exon8	c.G598A	p.V200M	AGGCCACGGGGAA	.	PASS	Atlas-SNP
H2BFWT	158983	hgsc.bcm.edu	37	X	103267865	103267865	+	Missense_Mutation	SNP	C	C	T	rs553509	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	84	59	0	0.94382	0	C|0.378;0|0.003	.	strong	.	H2BFWT	33	.	NM_001002916	exon1	c.G368A	p.R123H	GCCAGGCGACCAG	.	PASS	Atlas-SNP
FAM22F	54754	hgsc.bcm.edu	37	9	97082699	97082699	+	Missense_Mutation	SNP	G	G	A	rs10993163	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	59	110	0	0.460938	0	G|0.856;A|0.144	0.144	strong	.	FAM22F	72	.	NM_017561	exon5	c.C1159T	p.P387S	CCTCAGGGACCTT	.	PASS	Atlas-SNP
WASF3	10810	hgsc.bcm.edu	37	13	27250823	27250823	+	Silent	SNP	T	T	C	rs3764108	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	30	71	0	0.526316	0	T|0.660;C|0.340	0.340	strong	.	WASF3	68	.	NM_006646	exon7	c.T678C	p.H226H	GTACCATGGAGCG	.	PASS	Atlas-SNP
NBN	4683	hgsc.bcm.edu	37	8	90990479	90990479	+	Missense_Mutation	SNP	C	C	G	rs1805794	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	85	262	0	0.399061	0	C|0.681;G|0.319	0.319	strong	.	NBN	86	.	NM_002485	exon5	c.G553C	p.E185Q	TGGACTCAACTGC	.	PASS	Atlas-SNP
ALPK1	80216	hgsc.bcm.edu	37	4	113351822	113351822	+	Silent	SNP	G	G	A	rs61747381	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	33	91	0	0.39759	0	G|0.963;A|0.037	0.037	strong	.	ALPK1	125	.	NM_001102406	exon11	c.G1119A	p.G373G	GACAGGGACGGTC	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128477547	128477547	+	Silent	SNP	T	T	C	rs2291561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	34	74	0	0.586207	0	T|0.881;C|0.119	0.119	strong	FLNC,NS,carcinoma,0,1	FLNC	339	1	NM_001127487	exon4	c.T795C	p.G265G	ACCTGGTGCCCCT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152189016	152189016	+	Missense_Mutation	SNP	G	G	A	rs200517377		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	272	16	293	1	0.0588235	0.00341297	.	.	weak	HRNR,NS,carcinoma,0,4	HRNR	403	4	NM_001009931	exon3	c.C5089T	p.R1697C	ACTGACGGGAGCC	.	scavenged	Atlas-SNP
PIK3R6	146850	hgsc.bcm.edu	37	17	8733110	8733110	+	Splice_Site	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	12	44	0	0.342857	0	.	.	none	.	.	.	.	NM_001010855	exon11	c.803-1G>A	.	GGTCACCTGCAGA	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27357927	27357927	+	Missense_Mutation	SNP	C	C	T	rs2234895	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	16	40	0	0.326531	0	C|0.931;T|0.069	0.069	strong	.	IL4R	70	.	NM_001257997	exon5	c.C26T	p.T9M	TGAAAACGACCCG	.	PASS	Atlas-SNP
FAM149A	25854	hgsc.bcm.edu	37	4	187088248	187088248	+	Missense_Mutation	SNP	C	C	T	rs9991339	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	47	109	0	0.516484	0	C|0.931;T|0.069	0.069	strong	.	FAM149A	52	.	NM_001006655	exon11	c.C1291T	p.R431W	ACGTTCCGGGTGG	.	PASS	Atlas-SNP
PDDC1	347862	hgsc.bcm.edu	37	11	772490	772490	+	Silent	SNP	G	G	A	rs12224894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	18	52	0	0.339623	0	G|0.633;A|0.367	0.367	strong	.	PDDC1	16	.	NM_182612	exon5	c.C387T	p.A129A	CAGGGCGGCGACA	.	PASS	Atlas-SNP
SIDT1	54847	hgsc.bcm.edu	37	3	113252042	113252042	+	Silent	SNP	C	C	T	rs3732799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	70	70	0	0.642202	0	C|0.857;T|0.143	0.143	strong	.	SIDT1	99	.	NM_017699	exon1	c.C174T	p.L58L	GAACCTCAGCACC	.	PASS	Atlas-SNP
USP16	10600	hgsc.bcm.edu	37	21	30407208	30407208	+	Silent	SNP	G	G	A	rs61735763	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	85	184	0	0.566667	0	G|0.961;A|0.039	0.039	strong	.	USP16	65	.	NM_006447	exon4	c.G291A	p.T97T	TCTGACGCCAAGA	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46899857	46899857	+	Silent	SNP	C	C	T	rs1131101	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	26	71	0	0.65	0	C|0.888;T|0.112	0.112	strong	.	COL18A1	129	.	NM_030582	exon9	c.C1830T	p.D610D	AGGGGACGTAGGT	.	PASS	Atlas-SNP
TTC18	118491	hgsc.bcm.edu	37	10	75035257	75035257	+	Missense_Mutation	SNP	T	T	C	rs4294502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	46	93	0	0.422018	0	T|0.811;C|0.189	0.189	strong	TTC18,NS,carcinoma,0,1	TTC18	106	1	NM_145170	exon23	c.A2830G	p.N944D	CAAAGTTCTTCTT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155410667	155410667	+	Missense_Mutation	SNP	G	G	A	rs55810732	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	60	98	0	0.618557	0	G|0.837;A|0.163	0.163	strong	DCHS2_ENST00000443500,NS,carcinoma,+1,2	DCHS2	594	2	NM_001142552	exon1	c.C1841T	p.A614V	CTGATCGCACCGC	.	PASS	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	37	8	95541371	95541371	+	Silent	SNP	T	T	A	rs957446	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	193	182	0	0.979695	0	A|0.628;T|0.372	0.628	strong	KIAA1429_ENST00000421249,NS,carcinoma,-1,4	KIAA1429	176	4	NM_015496	exon7	c.A807T	p.R269R	TACTGTTCGTCGA	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912002	45912002	+	Missense_Mutation	SNP	A	A	C	rs735482	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	14	38	0	0.4375	0	A|0.771;C|0.229	0.229	strong	.	CD3EAP	27	.	NM_012099	exon3	c.A776C	p.K259T	AAGGGAAAGAAAC	.	PASS	Atlas-SNP
ERCC6L2	375748	hgsc.bcm.edu	37	9	98638288	98638288	+	Missense_Mutation	SNP	A	A	G	rs690528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	20	27	0	0.434783	0	A|0.717;G|0.283	0.283	strong	C9orf102,NS,carcinoma,0,2	.	.	2	NM_001010895	exon1	c.A1G	p.M1V	TGTTACATGCAGC	.	PASS	Atlas-SNP
KRTAP9-8	83901	hgsc.bcm.edu	37	17	39394674	39394674	+	Missense_Mutation	SNP	A	A	G	rs76766237		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	357	121	297	0	0.338936	0	.	.	weak	.	KRTAP9-8	29	.	NM_031963	exon1	c.A371G	p.N124S	GCTCCAACTGCTG	.	PASS	Atlas-SNP
GALNTL5	168391	hgsc.bcm.edu	37	7	151684256	151684256	+	Missense_Mutation	SNP	A	A	G	rs61729490	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	24	58	0	0.470588	0	A|0.814;G|0.186	0.186	strong	.	GALNTL5	87	.	NM_145292	exon5	c.A548G	p.E183G	TGAAAGAAAAACT	.	PASS	Atlas-SNP
SLC4A1	6521	hgsc.bcm.edu	37	17	42328846	42328846	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	47	133	0	0.34058	0	.	.	none	SLC4A1,NS,carcinoma,+1,2	SLC4A1	104	2	NM_000342	exon18	c.C2422T	p.R808C	AGATGCGGTCAAA	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75282882	75282882	+	Silent	SNP	G	G	A	rs585821	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	36	33	0	0.521739	0	G|0.662;A|0.338	0.338	strong	.	SERPINH1	33	.	NM_001235	exon5	c.G1011A	p.L337L	CGACTTGTCACGC	.	PASS	Atlas-SNP
ACSL1	2180	hgsc.bcm.edu	37	4	185701549	185701549	+	Silent	SNP	G	G	T	rs1803898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	22	44	0	0.488889	0	G|0.787;T|0.213	0.213	strong	.	ACSL1	77	.	NM_001995	exon5	c.C414A	p.I138I	CTTCTGGATCAGT	.	PASS	Atlas-SNP
CABLES1	91768	hgsc.bcm.edu	37	18	20793995	20793995	+	Silent	SNP	G	G	A	rs2304301	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	49	77	0	0.597561	0	G|0.970;A|0.030	0.030	strong	CABLES1,NS,carcinoma,0,1	CABLES1	32	1	NM_001100619	exon4	c.G1065A	p.P355P	GCTGCCGTATCGC	.	PASS	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	37	17	3486702	3486702	+	Missense_Mutation	SNP	G	G	A	rs224534	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	30	69	0	0.375	0	G|0.613;A|0.387	0.387	strong	.	TRPV1	99	.	NM_018727	exon9	c.C1406T	p.T469I	TCTCCAGTTTTTT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912098	29912098	+	Silent	SNP	G	G	A	rs142475339	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	92	319	0	0.538012	0	G|0.871;A|0.129	0.129	strong	.	HLA-A	89	.	NM_001242758	exon4	c.G819A	p.V273V	GGTGGTGCCTTCT	.	PASS	Atlas-SNP
SGCD	6444	hgsc.bcm.edu	37	5	155771579	155771579	+	Silent	SNP	T	T	C	rs1801193	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	245	242	278	0	0.987755	0	T|0.516;C|0.484	0.484	strong	.	SGCD	52	.	NM_000337	exon3	c.T84C	p.Y28Y	GATTTATGGCTGG	.	PASS	Atlas-SNP
CPNE4	131034	hgsc.bcm.edu	37	3	131268824	131268824	+	Silent	SNP	T	T	C	rs11915192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	47	127	0	0.505376	0	T|0.840;C|0.160	0.160	strong	.	CPNE4	112	.	NM_130808	exon14	c.A1269G	p.S423S	TGACGCTGACTTG	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26811045	26811045	+	Silent	SNP	T	T	C	rs12313993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	48	47	0	0.64	0	T|0.814;C|0.186	0.186	strong	.	ITPR2	270	.	NM_002223	exon17	c.A1905G	p.S635S	CAGATCTGACAAA	.	PASS	Atlas-SNP
SSTR5	6755	hgsc.bcm.edu	37	16	1129441	1129441	+	Silent	SNP	G	G	A	rs34608001	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	37	33	0	0.528571	0	G|0.983;A|0.017	0.017	strong	.	SSTR5	36	.	NM_001172560	exon2	c.G573A	p.P191P	CTGGCCGGAGCCC	.	PASS	Atlas-SNP
ANKRD17	26057	hgsc.bcm.edu	37	4	73956736	73956736	+	Silent	SNP	G	G	A	rs6855349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	79	150	0	0.441341	0	G|0.639;A|0.361	0.361	strong	.	ANKRD17	214	.	NM_032217	exon29	c.C6609T	p.L2203L	GACACTGAGGACT	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130830	52130830	+	Silent	SNP	C	C	A	rs8107754	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	44	76	0	0.586667	0	C|0.575;A|0.425	0.425	strong	SIGLEC5,NS,carcinoma,-1,1	SIGLEC5	67	1	NM_003830	exon6	c.G1167T	p.G389G	CCAGGGCCCAGCT	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147481430	147481430	+	Silent	SNP	A	A	G	rs6896303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	103	104	0	1	0	A|0.545;G|0.455	0.455	strong	SPINK5,NS,carcinoma,0,1	SPINK5	245	1	NM_001127699	exon15	c.A1389G	p.G463G	AGATGGAAAAATG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144879090	144879090	+	Missense_Mutation	SNP	T	T	C	rs1778120	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	247	75	231	0	0.303644	0	T|0.003;G|0.264	.	strong	.	PDE4DIP	817	.	NM_014644	exon27	c.A4360G	p.K1454E	CATTTTTTGGGAG	.	PASS	Atlas-SNP
IL10RA	3587	hgsc.bcm.edu	37	11	117859209	117859209	+	Silent	SNP	G	G	A	rs4252249	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	19	62	0	0.404255	0	G|0.876;A|0.124	0.124	strong	.	IL10RA	46	.	NM_001558	exon2	c.G180A	p.A60A	AGTGGCGCTCCTG	.	PASS	Atlas-SNP
DGKH	160851	hgsc.bcm.edu	37	13	42793479	42793479	+	Silent	SNP	G	G	A	rs180870	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	42	122	0	0.512195	0	G|0.337;A|0.663	0.663	strong	.	DGKH	106	.	NM_001204504	exon28	c.G3327A	p.E1109E	AAATGAGGATGAG	.	PASS	Atlas-SNP
OR52K2	119774	hgsc.bcm.edu	37	11	4471473	4471473	+	Missense_Mutation	SNP	C	C	T	rs7934336	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	48	121	0	0.494845	0	C|0.868;T|0.132	0.132	strong	.	OR52K2	61	.	NM_001005172	exon1	c.C904T	p.R302C	CAAATCCGTGAGA	.	PASS	Atlas-SNP
PCDHGB6	56100	hgsc.bcm.edu	37	5	140788264	140788264	+	Silent	SNP	C	C	T	rs58047392	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	69	94	0	1	0	C|0.824;T|0.176	0.176	strong	.	PCDHGB6	120	.	NM_032100	exon1	c.C495T	p.N165N	CATAAACTCAATT	.	PASS	Atlas-SNP
DGKG	1608	hgsc.bcm.edu	37	3	186006566	186006566	+	Silent	SNP	T	T	C	rs710443	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	130	179	0	0.977444	0	T|0.313;C|0.687	0.687	strong	.	DGKG	98	.	NM_001346	exon6	c.A477G	p.V159V	CAGGTATACCACT	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126336703	126336703	+	Silent	SNP	T	T	C	rs17009618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	84	134	0	0.535032	0	T|0.848;C|0.152	0.152	strong	FAT4_ENST00000394329,colon,carcinoma,0,2	FAT4	1752	2	NM_024582	exon5	c.T6585C	p.N2195N	TGTTAATGGTAAT	.	PASS	Atlas-SNP
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	48	30	0	0.685714	0	G|0.746;A|0.254	0.254	strong	TMEM204,NS,carcinoma,0,1	TMEM204	29	1	NM_024600	exon2	c.G321A	p.T107T	GGCCACGGCCGCG	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56482801	56482801	+	Missense_Mutation	SNP	C	C	G	rs6459166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	76	154	0	0.457831	0	C|0.569;G|0.431	0.431	strong	.	DST	1427	.	NM_001723	exon23	c.G6031C	p.V2011L	TCAAAACCTTCAC	.	PASS	Atlas-SNP
GSX1	219409	hgsc.bcm.edu	37	13	28367061	28367061	+	Silent	SNP	A	A	G	rs1231058	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	4	4	0	0	1	.	A|0.104;G|0.896	0.896	strong	.	GSX1	20	.	NM_145657	exon1	c.A234G	p.L78L	GCCTCTACTCAAG	.	PASS	Atlas-SNP
CHFR	55743	hgsc.bcm.edu	37	12	133435716	133435716	+	Silent	SNP	T	T	G	rs35011845	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	35	61	0	0.380435	0	T|0.796;G|0.204	0.204	strong	.	CHFR	83	.	NM_001161344	exon8	c.A885C	p.P295P	CTTGTCTGGCTTC	.	PASS	Atlas-SNP
RTP2	344892	hgsc.bcm.edu	37	3	187419764	187419764	+	Silent	SNP	G	G	A	rs150707467	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	65	124	0	0.524194	0	G|1.000;A|0.000	0.000	weak	RTP2,right_upper_lobe,carcinoma,-2,1	RTP2	38	1	NM_001004312	exon1	c.C153T	p.H51H	TGAGGCGTGCTGC	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20441084	20441084	+	Silent	SNP	T	T	C	rs8063682	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	18	50	0	0.4	0	T|0.550;C|0.450	0.450	strong	ACSM5,right_upper_lobe,carcinoma,+2,1	ACSM5	101	1	NM_017888	exon8	c.T1086C	p.T362T	CCAGACTGGTGTG	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71346701	71346701	+	Missense_Mutation	SNP	C	C	G	rs6826961	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	159	167	0	0.981481	0	C|0.738;G|0.262	0.262	strong	.	MUC7	91	.	NM_001145007	exon4	c.C240G	p.N80K	TAATAACCCCCCC	.	PASS	Atlas-SNP
PEA15	8682	hgsc.bcm.edu	37	1	160182943	160182943	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	6	159	0	0.0291262	0	.	.	none	PEA15,NS,carcinoma,+1,1	PEA15	7	1	NM_003768	exon3	c.T216C	p.R72R	CCGCCGTCCTGAC	.	scavenged	Atlas-SNP
REPIN1	29803	hgsc.bcm.edu	37	7	150068933	150068933	+	Silent	SNP	T	T	C	rs6722	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	26	18	0	1	0	T|0.574;C|0.426	0.426	strong	REPIN1_ENST00000489432,NS,carcinoma,0,2	REPIN1	74	2	NM_001099695	exon3	c.T774C	p.A258A	CGTAGCTGAGGCC	.	PASS	Atlas-SNP
RCN1	5954	hgsc.bcm.edu	37	11	32124978	32124978	+	Silent	SNP	T	T	C	rs79220299		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	185	224	0	0.963542	0	.	.	weak	.	RCN1	37	.	NM_002901	exon5	c.T840C	p.H280H	TGATCATGCACAG	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	31496350	31496350	+	Missense_Mutation	SNP	C	C	T	rs1800280	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	94	102	0	1	0	0|0.014;T|0.929	0.929	strong	.	DMD	2127	.	NM_004006	exon59	c.G8810A	p.R2937Q	AGTTCCCGGAGTC	.	PASS	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60785464	60785464	+	Missense_Mutation	SNP	G	G	A	rs2074233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	12	20	0	0.444444	0	G|0.830;A|0.170	0.170	strong	.	CD6	122	.	NM_006725	exon11	c.G1816A	p.G606S	CTGGCCGGCACCC	.	PASS	Atlas-SNP
RBM33	155435	hgsc.bcm.edu	37	7	155532600	155532600	+	Silent	SNP	C	C	T	rs200834081	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	82	157	0	0.479532	0	C|0.998;T|0.002	0.002	strong	.	RBM33	157	.	NM_053043	exon12	c.C1929T	p.S643S	CCTGTCCGTCCCG	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135429503	135429503	+	Missense_Mutation	SNP	C	C	A	rs4829830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	103	83	0	0.971698	0	0|0.015;A|0.479	0.479	strong	.	GPR112	459	.	NM_153834	exon6	c.C3638A	p.T1213N	ATGAGACCACACC	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102576382	102576382	+	Missense_Mutation	SNP	G	G	A	rs12099177	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	91	200	1	0.471503	0.005	G|0.882;A|0.118	0.118	strong	MMP27,NS,carcinoma,0,1	MMP27	84	1	NM_022122	exon1	c.C64T	p.R22W	TCATCCGGACTAA	.	scavenged	Atlas-SNP
SHC2	25759	hgsc.bcm.edu	37	19	425182	425182	+	Silent	SNP	G	G	A	rs61735134	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	62	98	0	0.492063	0	G|0.950;A|0.050	0.050	strong	.	SHC2	47	.	NM_012435	exon10	c.C1224T	p.D408D	CTCGTGGTCCGGG	.	PASS	Atlas-SNP
TTC5	91875	hgsc.bcm.edu	37	14	20764585	20764585	+	Silent	SNP	A	A	C	rs1953552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	35	121	0	0.304348	0	A|0.575;C|0.425	0.425	strong	TTC5,NS,carcinoma,0,1	TTC5	34	1	NM_138376	exon6	c.T660G	p.A220A	GCTAGAAGCTTTT	.	PASS	Atlas-SNP
PSCA	8000	hgsc.bcm.edu	37	8	143763547	143763547	+	Silent	SNP	C	C	A	rs1045531	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	11	21	0	0.407407	0	C|0.584;A|0.416	0.416	strong	.	PSCA	9	.	NM_005672	exon3	c.C342A	p.L114L	CCAGCTCTAGGCT	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134694391	134694391	+	Missense_Mutation	SNP	A	A	G	rs145022957	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	14	15	0	0.466667	0	A|0.993;G|0.007	0.007	strong	.	TTC40	100	.	NM_001200049	exon28	c.T3773C	p.V1258A	TCAGGGACATCGC	.	PASS	Atlas-SNP
NPVF	64111	hgsc.bcm.edu	37	7	25266400	25266400	+	Silent	SNP	G	G	A	rs2717851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	94	190	0	0.477157	0	G|0.702;A|0.298	0.298	strong	.	NPVF	36	.	NM_022150	exon2	c.C384T	p.P128P	CCTTTGGGGCAGG	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329854	55329854	+	Missense_Mutation	SNP	G	G	A	rs144994606	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	19	28	0	0.558824	0	G|0.854;A|0.146	0.146	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.G155A	p.R52H	ACTATCGTCATAG	.	PASS	Atlas-SNP
USP6NL	9712	hgsc.bcm.edu	37	10	11504752	11504752	+	Silent	SNP	T	T	C	rs12570211	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	56	112	0	0.509091	0	T|0.917;C|0.083	0.083	strong	.	USP6NL	57	.	NM_001080491	exon14	c.A2226G	p.P742P	CACTGGTGGAATG	.	PASS	Atlas-SNP
SH2D4A	63898	hgsc.bcm.edu	37	8	19190491	19190491	+	Silent	SNP	A	A	G	rs1574288	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	30	71	0	0.441176	0	A|0.739;G|0.261	0.261	strong	.	SH2D4A	49	.	NM_022071	exon3	c.A207G	p.K69K	TTGGAAACTTGGA	.	PASS	Atlas-SNP
BAZ1A	11177	hgsc.bcm.edu	37	14	35331288	35331288	+	Silent	SNP	G	G	A	rs17592803	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	70	155	0	0.432099	0	G|0.940;A|0.060	0.060	strong	.	BAZ1A	128	.	NM_182648	exon3	c.C354T	p.V118V	TTCTTCGACAAAA	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25058867	25058867	+	Missense_Mutation	SNP	C	C	T	rs201518768	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	22	115	0	0.170543	0	.	.	weak	PARP4,NS,carcinoma,0,5	PARP4	142	5	NM_006437	exon12	c.G1372A	p.V458I	CCACTACTTTGGG	.	scavenged	Atlas-SNP
PML	5371	hgsc.bcm.edu	37	15	74328206	74328206	+	Missense_Mutation	SNP	G	G	C	rs743582	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	18	30	0	0.461538	0	G|0.888;C|0.112	0.112	strong	.	PML	169	.	NM_033239	exon8	c.G2404C	p.A802P	CTGGAAGCCTCTC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378510	31378510	+	Silent	SNP	G	G	A	rs1063632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	91	118	0	1	0	G|0.927;A|0.073	0.073	strong	.	MICA	21	.	NM_001177519	exon2	c.G261A	p.R87R	GACCAGGGACTTG	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19751301	19751301	+	Silent	SNP	C	C	T	rs140548354		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	10	204	1	0.0442478	0.00490196	C|0.999;T|0.001	0.001	weak	TUBA3C,bladder,carcinoma,-2,1	TUBA3C	166	1	NM_006001	exon4	c.G822A	p.P274P	GATGACCGGGGCG	.	scavenged	Atlas-SNP
DNAJB13	374407	hgsc.bcm.edu	37	11	73670645	73670645	+	Silent	SNP	T	T	C	rs653263	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	48	106	0	0.484848	0	T|0.418;C|0.582	0.582	strong	.	DNAJB13	28	.	NM_153614	exon3	c.T279C	p.H93H	CTTCCATGGCAAA	.	PASS	Atlas-SNP
KCNQ2	3785	hgsc.bcm.edu	37	20	62046277	62046277	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	2	85	0	0.0212766	0	.	.	none	KCNQ2,colon,carcinoma,+2,1	KCNQ2	201	1	NM_172107	exon13	c.G1504A	p.A502T	GTGACGCGGCACC	.	scavenged	Atlas-SNP
ZP3	7784	hgsc.bcm.edu	37	7	76069629	76069629	+	Silent	SNP	G	G	A	rs79425252		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1165	378	504	0	0.324464	0	.	.	weak	.	ZP3	32	.	NM_001110354	exon6	c.G894A	p.K298K	CAACAAGGCCTGT	.	PASS	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	37	19	15299048	15299048	+	Missense_Mutation	SNP	G	G	A	rs114207045	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	16	51	0	0.340426	0	G|0.991;A|0.009	0.009	strong	NOTCH3,rectum,carcinoma,0,1	NOTCH3	340	1	NM_000435	exon9	c.C1490T	p.S497L	TCACCCGAGGGGC	.	PASS	Atlas-SNP
MOCOS	55034	hgsc.bcm.edu	37	18	33828916	33828916	+	Silent	SNP	A	A	G	rs55701019	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	29	56	0	0.491525	0	A|0.995;G|0.005	0.005	strong	.	MOCOS	84	.	NM_017947	exon10	c.A1992G	p.E664E	TGAGGAAAATAGT	.	PASS	Atlas-SNP
ZMYM5	9205	hgsc.bcm.edu	37	13	20413021	20413021	+	Missense_Mutation	SNP	T	T	C	rs41292167	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	93	166	0	0.550296	0	T|0.903;C|0.097	0.097	strong	.	ZMYM5	73	.	NM_001039650	exon5	c.A691G	p.T231A	GGGCTGTAGGCTG	.	PASS	Atlas-SNP
PTX4	390667	hgsc.bcm.edu	37	16	1536499	1536499	+	Missense_Mutation	SNP	G	G	T	rs2745097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	67	135	0	0.471831	0	G|0.692;T|0.308	0.308	strong	.	PTX4	46	.	NM_001013658	exon3	c.C863A	p.A288D	CGCAGGGCAGTGA	.	PASS	Atlas-SNP
FAT2	2196	hgsc.bcm.edu	37	5	150924769	150924769	+	Silent	SNP	G	G	A	rs998076	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	26	60	0	0.5	0	G|0.887;A|0.113	0.113	strong	.	FAT2	465	.	NM_001447	exon9	c.C5919T	p.Y1973Y	TGCCCAGTAGACA	.	PASS	Atlas-SNP
CCBP2	1238	hgsc.bcm.edu	37	3	42906116	42906116	+	Missense_Mutation	SNP	T	T	C	rs2228467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	118	202	1	0.543779	0.00495049	T|0.958;C|0.042	0.042	strong	.	CCBP2	49	.	NM_001296	exon3	c.T122C	p.V41A	ATGCAGTGGTGTC	.	PASS	Atlas-SNP
HS1BP3	64342	hgsc.bcm.edu	37	2	20824559	20824559	+	Silent	SNP	C	C	T	rs2305457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	46	90	0	0.589744	0	C|0.772;T|0.228	0.228	strong	.	HS1BP3	33	.	NM_022460	exon5	c.G717A	p.E239E	GAGCCCCTCATCA	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3639977	3639977	+	Missense_Mutation	SNP	G	G	A	rs3827530	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	59	110	0	0.460938	0	G|0.954;A|0.046	0.046	strong	SLX4,bladder,carcinoma,-1,2	SLX4	173	2	NM_032444	exon12	c.C3662T	p.A1221V	GGCAGCGCCCCCT	.	PASS	Atlas-SNP
CRLF2	64109	hgsc.bcm.edu	37	X	1321349	1321349	+	Missense_Mutation	SNP	C	C	T	rs138899368	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	392	185	257	0	0.471939	0	C|0.987;T|0.013	0.013	strong	.	CRLF2	24	.	NM_022148	exon4	c.G406A	p.V136M	ACGTCACCGTCAC	.	PASS	Atlas-SNP
TMEM99	147184	hgsc.bcm.edu	37	17	38991053	38991053	+	Silent	SNP	T	T	A	rs3169915	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	81	186	0	0.473684	0	T|0.873;A|0.127	0.127	strong	.	TMEM99	21	.	NM_001195386	exon3	c.T285A	p.L95L	AGGACTTCTTCTT	.	PASS	Atlas-SNP
TUBA3D	113457	hgsc.bcm.edu	37	2	132237927	132237927	+	Missense_Mutation	SNP	C	C	A	rs76585620	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	328	54	251	0	0.164634	0	C|0.500;A|0.500	0.500	weak	TUBA3D,trunk,malignant_melanoma,0,1	TUBA3D	60	1	NM_080386	exon4	c.C661A	p.R221S	ATTGAACGTCCCA	.	scavenged	Atlas-SNP
SIM2	6493	hgsc.bcm.edu	37	21	38117040	38117040	+	Silent	SNP	G	G	A	rs2073416	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	30	45	0	0.491803	0	G|0.736;A|0.264	0.264	strong	.	SIM2	55	.	NM_005069	exon10	c.G1179A	p.S393S	CAGCTCGTTCCAA	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	99	253	0	0.432314	0	G|0.761;A|0.239	0.239	strong	PDE1C_ENST00000396191,NS,carcinoma,0,2	PDE1C	465	2	NM_001191058	exon16	c.C1962T	p.A654A	CTTCTCGGCTTTG	.	PASS	Atlas-SNP
C17orf80	55028	hgsc.bcm.edu	37	17	71232990	71232990	+	Missense_Mutation	SNP	C	C	A	rs61729639	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	40	91	0	0.430108	0	C|0.964;A|0.036	0.036	strong	.	C17orf80	37	.	NM_001100621	exon3	c.C1369A	p.R457S	ACTCTTCGCAGCT	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68704264	68704264	+	Silent	SNP	C	C	T	rs546382	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	39	68	0	0.464286	0	C|0.761;T|0.239	0.239	strong	.	IGHMBP2	83	.	NM_002180	exon13	c.C2316T	p.S772S	CAGTTCCGGGGAA	.	PASS	Atlas-SNP
MYH7B	57644	hgsc.bcm.edu	37	20	33581955	33581955	+	Silent	SNP	G	G	A	rs2425012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	61	164	0	0.438849	0	G|0.585;A|0.415	0.415	strong	.	MYH7B	145	.	NM_020884	exon27	c.G2577A	p.A859A	GGATGCGCTGTTC	.	PASS	Atlas-SNP
GLYATL3	389396	hgsc.bcm.edu	37	6	49479750	49479750	+	Missense_Mutation	SNP	T	T	C	rs13193063	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	21	54	0	0.403846	0	C|0.179;N|0.000	0.179	strong	GLYATL3,NS,carcinoma,0,1	GLYATL3	19	1	NM_001010904	exon2	c.T47C	p.M16T	AGAAAATGTTGAA	.	PASS	Atlas-SNP
PDCD1LG2	80380	hgsc.bcm.edu	37	9	5557708	5557708	+	Missense_Mutation	SNP	T	T	C	rs7854413	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	103	256	1	0.453745	0.00390625	T|0.745;C|0.255	0.255	strong	.	PDCD1LG2	16	.	NM_025239	exon5	c.T722C	p.I241T	CAGTGATAGCCCT	.	PASS	Atlas-SNP
SIDT1	54847	hgsc.bcm.edu	37	3	113286405	113286405	+	Silent	SNP	C	C	T	rs2292511	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	58	98	1	0.487395	0.0102041	C|0.717;T|0.283	0.283	strong	SIDT1,NS,carcinoma,0,1	SIDT1	99	1	NM_017699	exon3	c.C363T	p.N121N	CTACAACTATCAA	.	scavenged	Atlas-SNP
SMPD1	6609	hgsc.bcm.edu	37	11	6415463	6415463	+	Missense_Mutation	SNP	G	G	A	rs1050239	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	36	89	0	0.521739	0	G|0.815;A|0.185	0.185	strong	.	SMPD1	108	.	NM_000543	exon6	c.G1522A	p.G508R	TACTCCGGGAGCT	.	PASS	Atlas-SNP
IFT140	9742	hgsc.bcm.edu	37	16	1574863	1574863	+	Silent	SNP	G	G	A	rs2235640	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	48	0	0.478873	0	G|0.803;A|0.197	0.197	strong	.	IFT140	128	.	NM_014714	exon23	c.C2919T	p.A973A	CAGCGCGGCGTCC	.	PASS	Atlas-SNP
CDC20	991	hgsc.bcm.edu	37	1	43825644	43825644	+	Silent	SNP	T	T	C	rs839763	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	98	117	0	1	0	T|0.728;C|0.272	0.272	strong	.	CDC20	34	.	NM_001255	exon5	c.T432C	p.Y144Y	AGGTTATCAGAAC	.	PASS	Atlas-SNP
VPS41	27072	hgsc.bcm.edu	37	7	38805215	38805215	+	Missense_Mutation	SNP	C	C	T	rs62444122	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	10	28	0	0.454545	0	C|0.951;T|0.049	0.049	strong	.	VPS41	102	.	NM_014396	exon16	c.G1294A	p.E432K	AAACTTCATATTC	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99193496	99193496	+	Silent	SNP	C	C	T	rs2230388	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	241	234	193	0	0.970954	0	C|0.753;T|0.247	0.247	strong	.	INPP4A	205	.	NM_001134224	exon25	c.C2691T	p.S897S	CAAGAGCGCTAAG	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519158	48519158	+	Missense_Mutation	SNP	C	C	T	rs34129198	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	38	85	0	0.469136	0	C|0.837;T|0.163	0.163	strong	.	ELSPBP1	29	.	NM_022142	exon4	c.C217T	p.R73C	TACCCACGCTGTA	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713625	32713625	+	Missense_Mutation	SNP	C	C	T	rs116163401	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	344	31	352	0	0.0901163	0	C|0.998;T|0.002	0.002	weak	.	HLA-DQA2	27	.	NM_020056	exon3	c.C389T	p.T130I	CCAACACCCTCAT	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46896294	46896294	+	Silent	SNP	G	G	A	rs2230686	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	28	75	0	0.5	0	G|0.933;A|0.067	0.067	strong	COL18A1,right_upper_lobe,carcinoma,+1,1	COL18A1	129	1	NM_030582	exon5	c.G1368A	p.A456A	CCCCGCGCCACCC	.	PASS	Atlas-SNP
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53639438	53639438	+	Missense_Mutation	SNP	C	C	T	rs3213758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	44	83	0	0.478261	0	C|0.927;T|0.073	0.073	strong	RPGRIP1L,NS,carcinoma,0,1	RPGRIP1L	118	1	NM_015272	exon26	c.G3790A	p.D1264N	ACATGTCGGCAAG	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158534381	158534381	+	Silent	SNP	G	G	C	rs59980573	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	42	91	0	0.403846	0	G|0.740;C|0.260	0.260	strong	.	ESYT2	70	.	NM_020728	exon17	c.C2082G	p.P694P	CTCAGGGGGCTGG	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43817406	43817406	+	Silent	SNP	T	T	C	rs480108	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	58	102	0	0.460317	0	T|0.539;C|0.461	0.461	strong	.	MAP1A	189	.	NM_002373	exon4	c.T3735C	p.D1245D	CGAGGATACCTCT	.	PASS	Atlas-SNP
OR5D13	390142	hgsc.bcm.edu	37	11	55541284	55541284	+	Missense_Mutation	SNP	G	G	A	rs11230983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	323	143	299	0	0.442724	0	G|0.898;A|0.102	0.102	strong	OR5D13,caecum,carcinoma,0,2	OR5D13	96	2	NM_001001967	exon1	c.G371A	p.R124H	ATGACCGTTTTGT	.	PASS	Atlas-SNP
OR10R2	343406	hgsc.bcm.edu	37	1	158450238	158450238	+	Missense_Mutation	SNP	G	G	A	rs3820678	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	96	196	0	0.450704	0	G|0.816;A|0.184	0.184	strong	OR10R2,colon,carcinoma,-1,1	OR10R2	81	1	NM_001004472	exon1	c.G571A	p.A191T	TGTAGCGCCAACA	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558314	140558314	+	Silent	SNP	T	T	C	rs17844487	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	48	985	0	0.234146	0	T|0.929;C|0.071	0.071	strong	.	PCDHB8	199	.	NM_019120	exon1	c.T699C	p.V233V	TGAAGTTGTCGAT	.	PASS	Atlas-SNP
VCX2	51480	hgsc.bcm.edu	37	X	8138080	8138080	+	Missense_Mutation	SNP	G	G	C	rs1058239	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	197	173	0	1	0	G|0.122;C|0.878	0.878	strong	.	VCX2	16	.	NM_016378	exon3	c.C413G	p.T138S	TAGTCGGTGCTCT	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117050998	117050998	+	Missense_Mutation	SNP	G	G	A	rs10982134	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	43	101	0	0.409524	0	G|0.655;A|0.345	0.345	strong	COL27A1,NS,carcinoma,+1,1	COL27A1	200	1	NM_032888	exon43	c.G4061A	p.R1354Q	GTGATCGAGGAGA	.	PASS	Atlas-SNP
WWC2	80014	hgsc.bcm.edu	37	4	184236868	184236868	+	Missense_Mutation	SNP	G	G	A	rs4862155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	64	127	0	0.587156	0	G|0.953;A|0.047	0.047	strong	.	WWC2	78	.	NM_024949	exon23	c.G3565A	p.A1189T	CTGCCAGCTGATG	.	PASS	Atlas-SNP
PFKP	5214	hgsc.bcm.edu	37	10	3155698	3155698	+	Silent	SNP	C	C	T	rs4881086	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	28	55	0	0.411765	0	C|0.734;T|0.266	0.266	strong	PFKP_ENST00000381075,NS,carcinoma,0,2	PFKP	182	2	NM_002627	exon13	c.C1359T	p.F453F	CGGCTTCGCCAAG	.	PASS	Atlas-SNP
OASL	8638	hgsc.bcm.edu	37	12	121471337	121471337	+	Silent	SNP	G	G	A	rs3213545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	56	89	0	0.589474	0	G|0.722;A|0.278	0.278	strong	.	OASL	49	.	NM_198213	exon2	c.C408T	p.L136L	GAAGACGAGAGCA	.	PASS	Atlas-SNP
RXFP2	122042	hgsc.bcm.edu	37	13	32367214	32367214	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	3	50	0	0.0441176	0	.	.	none	RXFP2,colon,carcinoma,0,1	RXFP2	95	1	NM_130806	exon16	c.G1775A	p.G592E	CTCTTGGAATTTT	.	scavenged	Atlas-SNP
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234952	26234952	+	Silent	SNP	A	A	G	rs2050948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	68	196	0	0.472222	0	A|0.855;G|0.145	0.145	strong	.	HIST1H1D	40	.	NM_005320	exon1	c.T210C	p.A70A	GTAGCCAGCAGCC	.	PASS	Atlas-SNP
TUBGCP5	114791	hgsc.bcm.edu	37	15	22846897	22846897	+	Missense_Mutation	SNP	G	G	A	rs145668941	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	22	66	0	0.392857	0	G|0.993;A|0.007	0.007	strong	.	TUBGCP5	82	.	NM_052903	exon8	c.G772A	p.V258I	TTGTATGTTCCAG	.	PASS	Atlas-SNP
SLC5A8	160728	hgsc.bcm.edu	37	12	101552075	101552075	+	Silent	SNP	G	G	A	rs2671444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	27	51	0	0.457627	0	G|0.279;A|0.721	0.721	strong	.	SLC5A8	102	.	NM_145913	exon14	c.C1662T	p.Y554Y	TAGTATGTATCTG	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21042094	21042094	+	Silent	SNP	G	G	A	rs12046928	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	65	64	0	0.984848	0	G|0.810;A|0.190	0.190	strong	.	KIF17	130	.	NM_001122819	exon2	c.C270T	p.Y90Y	CTGGCCGTAGGCA	.	PASS	Atlas-SNP
RNPEP	6051	hgsc.bcm.edu	37	1	201969082	201969082	+	Silent	SNP	G	G	A	rs1130790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	93	119	0	0.547059	0	G|0.652;A|0.348	0.348	strong	RNPEP,NS,carcinoma,0,2	RNPEP	39	2	NM_020216	exon6	c.G1143A	p.Q381Q	GCGTCAGCACATG	.	PASS	Atlas-SNP
PRPF39	55015	hgsc.bcm.edu	37	14	45564675	45564675	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	4	84	0	0.0425532	0	.	.	none	.	PRPF39	46	.	NM_017922	exon2	c.C233T	p.P78L	ATTTCCCTCCAGA	.	PASS	Atlas-SNP
BTRC	8945	hgsc.bcm.edu	37	10	103298099	103298099	+	Missense_Mutation	SNP	G	G	T	rs4151060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	32	82	0	0.516129	0	G|0.972;T|0.028	0.028	strong	.	BTRC	64	.	NM_033637	exon13	c.G1627T	p.A543S	GCTCCTGCAGGGA	.	PASS	Atlas-SNP
GSTM5	2949	hgsc.bcm.edu	37	1	110257836	110257836	+	Silent	SNP	T	T	C	rs67757008	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	473	239	447	2	0.505285	0.00447427	CAAATC|0.500;TAAACT|0.500	.	alt	GSTM5,brain,glioma,0,4	GSTM5	89	4	NM_000851	exon7	c.T541C	p.L181L	CTAAACTTGAAGG	.	PASS	Atlas-SNP
C4orf21	55345	hgsc.bcm.edu	37	4	113524723	113524723	+	Missense_Mutation	SNP	G	G	A	rs17669218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	50	142	0	0.416667	0	G|0.937;A|0.063	0.063	strong	.	C4orf21	223	.	NM_018392	exon10	c.C2933T	p.T978I	TCTGGTGTCTCTG	.	PASS	Atlas-SNP
BACH2	60468	hgsc.bcm.edu	37	6	90660319	90660319	+	Silent	SNP	T	T	C	rs9451298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	38	57	0	0.974359	0	T|0.695;C|0.305	0.305	strong	BACH2_ENST00000257749,NS,carcinoma,0,3	BACH2	224	3	NM_001170794	exon5	c.A1506G	p.V502V	GATTGGTACCGGG	.	PASS	Atlas-SNP
COQ7	10229	hgsc.bcm.edu	37	16	19085298	19085298	+	Missense_Mutation	SNP	C	C	T	rs11074359	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	75	146	0	0.46875	0	C|0.434;T|0.566	0.566	strong	.	COQ7	16	.	NM_016138	exon3	c.C308T	p.T103M	TGGTTACGTTCAG	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135426693	135426693	+	Missense_Mutation	SNP	A	A	G	rs4829829	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	111	110	0	0.991071	0	A|0.517;0|0.025	.	strong	.	GPR112	459	.	NM_153834	exon6	c.A828G	p.I276M	ACCTATATTTGCA	.	PASS	Atlas-SNP
ZNF131	7690	hgsc.bcm.edu	37	5	43161351	43161351	+	Silent	SNP	G	G	A	rs71627581	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	26	67	0	0.433333	0	G|0.937;A|0.063	0.063	strong	.	ZNF131	51	.	NM_003432	exon5	c.G372A	p.R124R	TTTCAGGAACAAA	.	PASS	Atlas-SNP
SERPINC1	462	hgsc.bcm.edu	37	1	173878832	173878832	+	Silent	SNP	T	T	C	rs5878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	96	107	0	1	0	T|0.482;C|0.518	0.518	strong	.	SERPINC1	57	.	NM_000488	exon5	c.A1011G	p.Q337Q	CCACTCTTGCAGC	.	PASS	Atlas-SNP
OR6Q1	219952	hgsc.bcm.edu	37	11	57799183	57799183	+	Silent	SNP	C	C	T	rs7123727	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	89	167	0	0.526627	0	C|0.778;T|0.222	0.222	strong	.	OR6Q1	58	.	NM_001005186	exon1	c.C759T	p.S253S	GGTGAGCCTCTTC	.	PASS	Atlas-SNP
HECTD4	283450	hgsc.bcm.edu	37	12	112600883	112600883	+	Silent	SNP	C	C	T	rs183882784	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	86	164	0	0.483146	0	C|0.995;T|0.005	0.005	strong	.	.	.	.	NM_001109662	exon75	c.G12681A	p.P4227P	GGGGTACGGGGGC	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140554606	140554606	+	Silent	SNP	T	T	C	rs11741863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	52	313	0	0.52	0	T|0.805;C|0.195	0.195	strong	PCDHB7,caecum,carcinoma,0,1	PCDHB7	231	1	NM_018940	exon1	c.T2190C	p.F730F	CCCCTTTCCACGA	.	PASS	Atlas-SNP
TULP4	56995	hgsc.bcm.edu	37	6	158927651	158927651	+	Silent	SNP	A	A	G	rs3828712	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	55	106	0	0.808824	0	A|0.590;G|0.410	0.410	strong	.	TULP4	137	.	NM_020245	exon14	c.A4557G	p.L1519L	CATTCTAGACTTC	.	PASS	Atlas-SNP
AXL	558	hgsc.bcm.edu	37	19	41745608	41745608	+	Missense_Mutation	SNP	A	A	C	rs199928489	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	67	109	0	0.515385	0	A|1.000;C|0.000	0.000	strong	.	AXL	126	.	NM_021913	exon10	c.A1295C	p.Q432P	AAGCACAGCCAGT	.	PASS	Atlas-SNP
LRP5L	91355	hgsc.bcm.edu	37	22	25753321	25753321	+	Silent	SNP	G	G	A	rs9624807	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	81	150	0	0.547297	0	G|0.895;A|0.105	0.105	strong	.	LRP5L	23	.	NM_001135772	exon4	c.C339T	p.R113R	CAGCACGCGCAGC	.	PASS	Atlas-SNP
EPN3	55040	hgsc.bcm.edu	37	17	48619249	48619249	+	Missense_Mutation	SNP	C	C	A	rs4794159	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	15	25	0	0.428571	0	C|0.565;A|0.435	0.435	strong	EPN3,NS,carcinoma,0,1	EPN3	32	1	NM_017957	exon10	c.C1630A	p.P544T	GGCGAGCCGGGCA	.	PASS	Atlas-SNP
HSPB7	27129	hgsc.bcm.edu	37	1	16344402	16344402	+	Silent	SNP	G	G	A	rs945416	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	97	94	0	0.989796	0	G|0.357;A|0.643	0.643	strong	HSPB7,NS,carcinoma,-1,1	HSPB7	17	1	NM_014424	exon1	c.C57T	p.S19S	GGAAGAGGAAGAG	.	PASS	Atlas-SNP
OR6K3	391114	hgsc.bcm.edu	37	1	158687163	158687163	+	Missense_Mutation	SNP	G	G	A	rs28568406	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	57	140	0	0.504425	0	G|0.585;A|0.415	0.415	strong	.	OR6K3	101	.	NM_001005327	exon1	c.C743T	p.P248L	AATATCGGGAAGA	.	PASS	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92548785	92548785	+	Missense_Mutation	SNP	C	C	T	rs1048755	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	69	140	0	0.552	0	C|0.699;T|0.301	0.301	strong	.	ATXN3	46	.	NM_004993	exon8	c.G634A	p.V212M	CTAACACTCGTTC	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	rs11549840	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	57	122	0	0.5	0	G|0.986;C|0.014	0.014	strong	.	.	.	.	NM_014855	exon3	c.G333C	p.Q111H	CCGGCAGCTGAGC	.	PASS	Atlas-SNP
TAF7L	54457	hgsc.bcm.edu	37	X	100532621	100532621	+	Missense_Mutation	SNP	T	T	C	rs35899692	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	68	67	0	1	0	0|0.013;C|0.185	0.185	strong	.	TAF7L	64	.	NM_024885	exon9	c.A922G	p.S308G	TGTGGCTGCTCAT	.	PASS	Atlas-SNP
PRKCD	5580	hgsc.bcm.edu	37	3	53220215	53220215	+	Silent	SNP	G	G	A	rs2230494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	50	91	0	0.471698	0	A|0.289;C|0.000;G|0.710;N|0.000	0.289	strong	PRKCD_ENST00000394729,NS,adenoma,0,2	PRKCD	124	2	NM_212539	exon12	c.G1119A	p.E373E	AGGAGAGTACTTT	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13387904	13387904	+	Silent	SNP	A	A	G	rs16030	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	32	71	0	0.484848	0	A|0.841;G|0.159	0.159	strong	.	CACNA1A	715	.	NM_001127221	exon23	c.T3864C	p.F1288F	AAAGGTAAAGACG	.	PASS	Atlas-SNP
FOLH1	2346	hgsc.bcm.edu	37	11	49227620	49227620	+	Missense_Mutation	SNP	A	A	G	rs202676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	32	90	0	0.516129	0	A|0.657;G|0.343	0.343	strong	.	FOLH1	141	.	NM_004476	exon2	c.T223C	p.Y75H	CTTACTATAAGAA	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152285621	152285621	+	Missense_Mutation	SNP	T	T	A	rs145627745	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	338	184	285	0	0.544379	0	T|0.993;A|0.007	0.007	strong	FLG,NS,carcinoma,+1,1	FLG	900	1	NM_002016	exon3	c.A1741T	p.T581S	GCCTGGTGCCGTC	.	PASS	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3297175	3297175	+	Silent	SNP	T	T	C	rs224207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	86	160	0	0.511905	0	T|0.407;C|0.593	0.593	strong	MEFV_ENST00000541159,NS,carcinoma,-2,2	MEFV	170	2	NM_000243	exon5	c.A1428G	p.Q476Q	ATGCTCTTGCTGC	.	PASS	Atlas-SNP
SRSF6	6431	hgsc.bcm.edu	37	20	42088708	42088708	+	Silent	SNP	G	G	A	rs61733949	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	57	87	0	0.548077	0	G|0.956;A|0.044	0.044	strong	.	SRSF6	37	.	NM_006275	exon4	c.G417A	p.A139A	CTATGCGGATGCC	.	PASS	Atlas-SNP
MSH2	4436	hgsc.bcm.edu	37	2	47637439	47637439	+	Silent	SNP	C	C	T	rs1800151	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	49	79	0	0.5	0	C|0.977;T|0.023	0.023	strong	.	MSH2	198	.	NM_000251	exon3	c.C573T	p.L191L	TCTCCTCATCCAG	.	PASS	Atlas-SNP
KHDRBS2	202559	hgsc.bcm.edu	37	6	62390920	62390920	+	Missense_Mutation	SNP	G	G	A	rs61753606	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	69	157	0	0.784091	0	G|0.987;A|0.013	0.013	strong	KHDRBS2,NS,carcinoma,+1,2	KHDRBS2	103	2	NM_152688	exon9	c.C998T	p.P333L	CTTTGCGGTGGTG	.	PASS	Atlas-SNP
SLC2A4	6517	hgsc.bcm.edu	37	17	7187123	7187123	+	Silent	SNP	T	T	C	rs5435	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	52	78	0	0.547368	0	C|0.701;N|0.001	0.701	strong	.	SLC2A4	44	.	NM_001042	exon4	c.T390C	p.N130N	GGCCAATGCTGCT	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133801990	133801990	+	Silent	SNP	G	G	A	rs375960322		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	84	143	0	0.541936	0	.	.	weak	.	IGSF9B	290	.	NM_014987	exon8	c.C1086T	p.D362D	ACGGCCGTCCTTG	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19751229	19751229	+	Silent	SNP	T	T	C	rs36216108	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	86	209	1	0.38914	0.00478469	T|0.955;C|0.045	0.045	strong	TUBA3C,NS,carcinoma,-1,1	TUBA3C	166	1	NM_006001	exon4	c.A894G	p.P298P	ATTGGCTGGCTCG	.	scavenged	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135956342	135956342	+	Missense_Mutation	SNP	C	C	G	rs72615484	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	240	107	169	0	0.445833	0	C|0.500;G|0.500	0.500	strong	.	RBMX	149	.	NM_002139	exon9	c.G1135C	p.G379R	GGCTTCCTCCACG	.	PASS	Atlas-SNP
CHD9	80205	hgsc.bcm.edu	37	16	53283966	53283966	+	Silent	SNP	G	G	A	rs8052283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	39	77	0	0.438202	0	G|0.692;A|0.308	0.308	strong	.	CHD9	203	.	NM_025134	exon17	c.G3849A	p.Q1283Q	TCCTCAGAATGAT	.	PASS	Atlas-SNP
C6orf170	221322	hgsc.bcm.edu	37	6	121577370	121577370	+	Missense_Mutation	SNP	T	T	C	rs7745023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	6	102	0	0.0857143	0	T|0.674;C|0.326	0.326	strong	C6orf170,NS,carcinoma,0,1	C6orf170	146	1	NM_152730	exon16	c.A1795G	p.I599V	AAAATATAGAAAT	.	PASS	Atlas-SNP
SLC2A1	6513	hgsc.bcm.edu	37	1	43396414	43396414	+	Silent	SNP	G	G	A	rs11537641	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	25	77	0	0.543478	0	G|0.840;A|0.160	0.160	strong	.	SLC2A1	36	.	NM_006516	exon4	c.C399T	p.C133C	CAGGCCGCAGTAC	.	PASS	Atlas-SNP
TMEM132B	114795	hgsc.bcm.edu	37	12	125834095	125834095	+	Silent	SNP	C	C	A	rs1491893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	70	163	0	0.503597	0	C|0.737;A|0.262	0.262	strong	.	TMEM132B	207	.	NM_052907	exon2	c.C150A	p.S50S	GGAGTCCTTTTTC	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117002517	117002517	+	Silent	SNP	C	C	T	rs2014134	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	23	57	0	0.46	0	C|0.700;T|0.300	0.300	strong	.	COL27A1	200	.	NM_032888	exon20	c.C2745T	p.I915I	AGACATCGGCCCC	.	PASS	Atlas-SNP
UBASH3A	53347	hgsc.bcm.edu	37	21	43854985	43854985	+	Silent	SNP	A	A	C	rs17114925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	32	69	0	0.457143	0	A|0.750;C|0.250	0.250	strong	.	UBASH3A	72	.	NM_018961	exon10	c.A1314C	p.P438P	TCTGCCAAGACGG	.	PASS	Atlas-SNP
MRPL19	9801	hgsc.bcm.edu	37	2	75879359	75879359	+	Missense_Mutation	SNP	G	G	A	rs41382847	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	349	177	371	0	0.507163	0	G|0.992;A|0.008	0.008	strong	.	MRPL19	21	.	NM_014763	exon3	c.G313A	p.V105I	AGAAAAGTACTCC	.	PASS	Atlas-SNP
MAK	4117	hgsc.bcm.edu	37	6	10775600	10775600	+	Missense_Mutation	SNP	G	G	A	rs567083	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	98	165	0	0.5	0	A|0.017;C|0.006	0.017	strong	.	MAK	47	.	NM_005906	exon12	c.C1558T	p.P520S	CAACGGGTCCCAG	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964196	88964196	+	Missense_Mutation	SNP	T	T	A	rs801840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	47	116	0	0.474747	0	T|0.483;A|0.517	0.517	strong	.	ZNF804B	322	.	NM_181646	exon4	c.T1900A	p.F634I	TCTAGGTTTAAAA	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115370274	115370274	+	Missense_Mutation	SNP	T	T	C	rs10749138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	57	95	0	0.508929	0	T|0.556;C|0.444	0.444	strong	NRAP,head_neck,carcinoma,0,1	NRAP	208	1	NM_001261463	exon31	c.A3547G	p.I1183V	CTGGAATGACACA	.	PASS	Atlas-SNP
MCM4	4173	hgsc.bcm.edu	37	8	48885436	48885436	+	Missense_Mutation	SNP	T	T	A	rs762679	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	97	106	0	0.989796	0	T|0.104;A|0.896	0.896	strong	.	MCM4	97	.	NM_182746	exon14	c.T1948A	p.L650M	TTCCTCTTGCTGG	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107620867	107620867	+	Missense_Mutation	SNP	C	C	T	rs2230806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	77	137	0	0.562044	0	C|0.587;T|0.413	0.413	strong	ABCA1,NS,carcinoma,0,1	ABCA1	244	1	NM_005502	exon7	c.G656A	p.R219K	TTCTCCCTTGGTA	.	PASS	Atlas-SNP
ZNF354A	6940	hgsc.bcm.edu	37	5	178139442	178139442	+	Silent	SNP	T	T	G	rs76562034		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	13	111	0	0.209677	0	.	.	weak	ZNF354A,NS,carcinoma,0,1	ZNF354A	74	1	NM_005649	exon5	c.A1437C	p.S479S	GAGAGCTGAACTC	.	scavenged	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57539082	57539082	+	Missense_Mutation	SNP	C	C	T	rs1800127	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	57	122	0	0.518182	0	C|0.987;T|0.013	0.013	strong	.	LRP1	428	.	NM_002332	exon6	c.C650T	p.A217V	GTGGGGCCCAGGT	.	PASS	Atlas-SNP
ANKRD36	375248	hgsc.bcm.edu	37	2	97869979	97869979	+	Missense_Mutation	SNP	G	G	T	rs111515821	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	3	29	3	0.12	0.103448	.	.	weak	ANKRD36_ENST00000420699,bladder,carcinoma,0,8	ANKRD36	170	8	NM_001164315	exon50	c.G3040T	p.D1014Y	AAAAAGGATGGAG	.	scavenged	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465399	10465399	+	Missense_Mutation	SNP	T	T	A	rs11782670	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	41	78	0	0.465909	0	T|0.847;A|0.153	0.153	strong	RP1L1,NS,carcinoma,+1,1	RP1L1	453	1	NM_178857	exon4	c.A6209T	p.E2070V	TGGACCTCCCCTT	.	PASS	Atlas-SNP
TMEM119	338773	hgsc.bcm.edu	37	12	108986031	108986031	+	Silent	SNP	C	C	T	rs74504010	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	14	6	0	0.7	0	C|0.827;T|0.173	0.173	strong	TMEM119,NS,carcinoma,0,1	TMEM119	31	1	NM_181724	exon2	c.G129A	p.E43E	CTCGGCCTCCCCA	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1896440	1896440	+	Silent	SNP	G	G	A	rs16824585	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	93	84	0	0.894231	0	G|0.764;A|0.236	0.236	strong	.	KIAA1751	92	.	NM_001080484	exon13	c.C1462T	p.L488L	GCTCCAGGATGTC	.	PASS	Atlas-SNP
CEP135	9662	hgsc.bcm.edu	37	4	56885581	56885581	+	Silent	SNP	T	T	C	rs61753870	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	52	102	0	0.460177	0	T|0.978;C|0.022	0.022	strong	.	CEP135	115	.	NM_025009	exon23	c.T3075C	p.N1025N	TTCAAATGAGAGA	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96166270	96166270	+	Silent	SNP	C	C	T	rs35120448	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	37	68	0	0.536232	0	C|0.961;T|0.039	0.039	strong	UNC5C,NS,carcinoma,-1,1	UNC5C	141	1	NM_003728	exon6	c.G801A	p.T267T	CCACTCCGTCCAG	.	PASS	Atlas-SNP
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967981	49967981	+	Silent	SNP	T	T	G	rs11558188	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	31	78	0	0.430556	0	T|0.692;G|0.308	0.308	strong	.	ALDH16A1	54	.	NM_153329	exon12	c.T1530G	p.V510V	CGCTGTTCCCTCA	.	PASS	Atlas-SNP
LASP1	3927	hgsc.bcm.edu	37	17	37054772	37054772	+	Silent	SNP	C	C	T	rs1130638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	35	83	0	0.443038	0	C|0.731;T|0.269	0.269	strong	LASP1,colon,carcinoma,0,1	LASP1	24	1	NM_006148	exon4	c.C357T	p.N119N	CAGTAACGTGAGC	.	PASS	Atlas-SNP
C15orf52	388115	hgsc.bcm.edu	37	15	40627845	40627845	+	Silent	SNP	G	G	A	rs55641696	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	40	98	0	0.547945	0	G|0.836;A|0.164	0.164	strong	.	C15orf52	47	.	NM_207380	exon11	c.C1119T	p.S373S	CATCCCGCTCTGC	.	PASS	Atlas-SNP
SYT3	84258	hgsc.bcm.edu	37	19	51128661	51128661	+	Silent	SNP	T	T	C	rs16986142	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	40	58	0	0.512821	0	T|0.228;C|0.772	0.772	strong	.	SYT3	85	.	NM_032298	exon6	c.A1563G	p.V521V	GTAGTCTACCACG	.	PASS	Atlas-SNP
HEATR5A	25938	hgsc.bcm.edu	37	14	31858209	31858209	+	Missense_Mutation	SNP	C	C	T	rs7157977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	37	24	0	1	0	C|0.676;N|0.000	.	strong	.	HEATR5A	181	.	NM_015473	exon7	c.G775A	p.A259T	GTGAGGCTGCTAT	.	PASS	Atlas-SNP
PCOLCE	5118	hgsc.bcm.edu	37	7	100205365	100205365	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	61	140	0	0.42069	0	.	.	none	.	PCOLCE	37	.	NM_002593	exon8	c.C1118T	p.S373F	TGCCTTCTCCACC	.	PASS	Atlas-SNP
SLC34A3	142680	hgsc.bcm.edu	37	9	140127051	140127051	+	Missense_Mutation	SNP	G	G	A	rs34372115	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	36	18	0	0.705882	0	G|0.924;A|0.076	0.076	strong	.	SLC34A3	32	.	NM_001177317	exon4	c.G200A	p.R67H	GGCTGCGCCGCGT	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	101166095	101166095	+	Silent	SNP	G	G	A	rs41288423	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	37	52	0	0.925	0	G|0.528;A|0.472	0.472	strong	ASCC3,NS,carcinoma,0,2	ASCC3	205	2	NM_006828	exon12	c.C1935T	p.L645L	CAGTCCGAGAATC	.	PASS	Atlas-SNP
USP17L20	100287441	hgsc.bcm.edu	37	4	9270328	9270328	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	475	11	714	6	0.0231579	0.00840336	.	.	none	RP11-1286E23.17,NS,carcinoma,0,1	.	.	1	NM_001256861	exon1	c.G984A	p.W328X	TGGGTGGAGTTGT	.	scavenged	Atlas-SNP
ACPP	55	hgsc.bcm.edu	37	3	132075554	132075554	+	Silent	SNP	T	T	C	rs3181784	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	37	91	0	0.345794	0	T|0.657;C|0.343	0.343	strong	ACPP_ENST00000351273,NS,carcinoma,0,4	ACPP	118	4	NM_001099	exon10	c.T993C	p.Y331Y	GTACTATCGGAAT	.	PASS	Atlas-SNP
VEZT	55591	hgsc.bcm.edu	37	12	95681554	95681554	+	Silent	SNP	C	C	T	rs12424550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	68	81	0	1	0	C|0.882;T|0.118	0.118	strong	.	VEZT	106	.	NM_017599	exon9	c.C1443T	p.H481H	GCCCCACGTTCAA	.	PASS	Atlas-SNP
CHPF	79586	hgsc.bcm.edu	37	2	220404648	220404648	+	Silent	SNP	C	C	T	rs1043833	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	120	163	0	0.524017	0	C|0.645;T|0.355	0.355	strong	.	CHPF	56	.	NM_024536	exon4	c.G1785A	p.L595L	GAGGCGCAGTGGT	.	PASS	Atlas-SNP
C2orf83	56918	hgsc.bcm.edu	37	2	228476140	228476140	+	Nonsense_Mutation	SNP	C	C	T	rs2176186	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	272	143	248	0	0.525735	0	C|0.703;T|0.297	0.297	strong	.	C2orf83	15	.	NM_020161	exon3	c.G423A	p.W141X	ATGGCTCCAGAGC	.	PASS	Atlas-SNP
CD3EAP	10849	hgsc.bcm.edu	37	19	45912343	45912343	+	Missense_Mutation	SNP	A	A	G	rs762562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	19	46	0	0.633333	0	A|0.774;G|0.226	0.226	strong	CD3EAP,NS,carcinoma,0,1	CD3EAP	27	1	NM_012099	exon3	c.A1117G	p.K373E	GGAGCGAAGCCTC	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57182647	57182647	+	Silent	SNP	G	G	A	rs3822003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	31	60	0	0.525424	0	G|0.773;A|0.227	0.227	strong	.	KIAA1211	178	.	NM_020722	exon8	c.G2979A	p.A993A	CCGAGCGGGGAGG	.	PASS	Atlas-SNP
SLC16A4	9122	hgsc.bcm.edu	37	1	110925550	110925550	+	Silent	SNP	T	T	G	rs35653868	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	53	122	0	0.557895	0	T|0.946;G|0.054	0.054	strong	.	SLC16A4	47	.	NM_001201546	exon3	c.A126C	p.A42A	GAAAATTGCAAAA	.	PASS	Atlas-SNP
C18orf54	162681	hgsc.bcm.edu	37	18	51887123	51887123	+	Silent	SNP	C	C	T	rs1657904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	47	119	0	0.505376	0	C|0.932;T|0.068	0.068	strong	.	C18orf54	40	.	NM_173529	exon2	c.C181T	p.L61L	TTTGATCTAGGCC	.	PASS	Atlas-SNP
SMPD4	55627	hgsc.bcm.edu	37	2	130939163	130939163	+	Missense_Mutation	SNP	G	G	T	rs146359515	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	33	48	0	0.478261	0	G|0.996;T|0.004	0.004	strong	.	SMPD4	67	.	NM_017751	exon1	c.C12A	p.F4L	GGCGCCGAAAGTC	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	37	1	222802376	222802376	+	Missense_Mutation	SNP	A	A	G	rs2936052	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	47	82	0	0.534091	0	A|0.758;G|0.242	0.242	strong	MIA3,NS,carcinoma,0,2	MIA3	167	2	NM_198551	exon4	c.A1814G	p.K605R	GGGCCAAACTGCA	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140530529	140530529	+	Missense_Mutation	SNP	G	G	A	rs3776096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	47	94	0	0.460784	0	G|0.783;A|0.217	0.217	strong	.	PCDHB6	161	.	NM_018939	exon1	c.G691A	p.V231I	ATCCAGGTTTTGG	.	PASS	Atlas-SNP
OR10K2	391107	hgsc.bcm.edu	37	1	158390252	158390252	+	Silent	SNP	T	T	G	rs12239443	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	106	243	0	0.484018	0	T|0.635;G|0.365	0.365	strong	.	OR10K2	69	.	NM_001004476	exon1	c.A405C	p.L135L	TCCCATTAGCACT	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130116684	130116684	+	Missense_Mutation	SNP	G	G	A	rs79867908	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	73	162	0	0.544776	0	G|0.891;A|0.109	0.109	strong	.	COL6A5	205	.	NM_153264	exon9	c.G3826A	p.V1276I	GTCAACGTCAGTG	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104432873	104432873	+	Silent	SNP	T	T	G	rs942142	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	87	109	1	0.988636	0.00917431	T|0.683;G|0.317	0.317	strong	.	GRIN3A	186	.	NM_133445	exon3	c.A1821C	p.A607A	TTTCCATGCTCCA	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79182778	79182778	+	Silent	SNP	T	T	C	rs62075318	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	40	101	0	0.416667	0	T|0.621;C|0.379	0.379	strong	AZI1_ENST00000450824,NS,carcinoma,0,4	AZI1	145	4	NM_014984	exon3	c.A222G	p.R74R	GGATCTTCTAAGG	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36869516	36869516	+	Missense_Mutation	SNP	C	C	A	rs1205434	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	62	57	0	0.96875	0	C|0.710;A|0.290	0.290	strong	.	KIAA1755	145	.	NM_001029864	exon3	c.G1017T	p.K339N	TTCTGGCTTTGTG	.	PASS	Atlas-SNP
VWA5A	4013	hgsc.bcm.edu	37	11	124006972	124006972	+	Missense_Mutation	SNP	G	G	T	rs2276054	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	41	97	0	0.5125	0	G|0.877;T|0.123	0.123	strong	.	VWA5A	102	.	NM_014622	exon12	c.G1496T	p.S499I	TAATCAGCTATGC	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55494651	55494651	+	Missense_Mutation	SNP	A	A	G	rs34804158	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	60	60	0	0.631579	0	A|0.808;G|0.192	0.192	strong	.	NLRP2	161	.	NM_017852	exon6	c.A1585G	p.T529A	GGCCACACCTGGG	.	PASS	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39549983	39549983	+	Silent	SNP	G	G	A	rs3736890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	4	71	0	0.0547945	0	G|0.867;A|0.133	0.133	strong	.	MACF1	909	.	NM_012090	exon3	c.G93A	p.S31S	GCGGTCGGGGAGC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557477	32557477	+	Silent	SNP	G	G	A	rs150644773	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	261	21	278	0	0.0804598	0	G|0.868;A|0.132	0.132	strong	HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.C43T	p.L15L	CTGTCAGCGCTGT	.	PASS	Atlas-SNP
CCDC90A	63933	hgsc.bcm.edu	37	6	13801615	13801615	+	Missense_Mutation	SNP	T	T	C	rs3180196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	35	51	0	0.522388	0	T|0.880;C|0.120	0.120	strong	CCDC90A,NS,carcinoma,0,1	CCDC90A	15	1	NM_001031713	exon4	c.A646G	p.T216A	GAAAAGTGATTTC	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158590740	158590740	+	Missense_Mutation	SNP	A	A	T	rs13233513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	42	81	0	0.482759	0	A|0.887;T|0.113	0.113	strong	.	ESYT2	70	.	NM_020728	exon3	c.T544A	p.C182S	ATTGGCAAATGAA	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190876283	190876283	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	271	20	234	0	0.0738007	0	.	.	none	.	FRG1	76	.	NM_004477	exon5	c.C409A	p.Q137K	AGAGAACAATGGG	.	PASS	Atlas-SNP
LUZP4	51213	hgsc.bcm.edu	37	X	114541197	114541197	+	Missense_Mutation	SNP	A	A	G	rs143490659		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	235	40	218	0	0.170213	0	.	.	weak	.	LUZP4	51	.	NM_016383	exon4	c.A770G	p.K257R	CTCAGAAAGATCT	.	PASS	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57080352	57080352	+	Missense_Mutation	SNP	G	G	A	rs12801000	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	56	112	0	0.411765	0	G|0.968;A|0.032	0.032	strong	TNKS1BP1,caecum,carcinoma,+1,1	TNKS1BP1	148	1	NM_033396	exon5	c.C1810T	p.P604S	CCAGGGGGAGAGG	.	PASS	Atlas-SNP
EXOC6	54536	hgsc.bcm.edu	37	10	94714427	94714427	+	Missense_Mutation	SNP	C	C	G	rs11187225	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	21	21	0	0.538462	0	C|0.912;G|0.088	0.088	strong	.	EXOC6	147	.	NM_019053	exon16	c.C1567G	p.L523V	ACAAATCTGCTGC	.	PASS	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204199614	204199614	+	Missense_Mutation	SNP	C	C	T	rs10900562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	133	117	0	1	0	C|0.466;T|0.534	0.534	strong	PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	NM_014935	exon18	c.G2510A	p.R837K	TTCTCCCTCATGG	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46899872	46899872	+	Silent	SNP	C	C	A	rs1131102	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	24	70	0	0.631579	0	C|0.896;A|0.104	0.104	strong	COL18A1_ENST00000359759,NS,carcinoma,+1,2	COL18A1	129	2	NM_030582	exon9	c.C1845A	p.G615G	CAAGGGCGACAAG	.	PASS	Atlas-SNP
CYP4F2	8529	hgsc.bcm.edu	37	19	15990431	15990431	+	Missense_Mutation	SNP	C	C	T	rs2108622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	60	93	0	0.540541	0	C|0.779;T|0.221	0.221	strong	.	CYP4F2	97	.	NM_001082	exon11	c.G1297A	p.V433M	GCCACACAGCTGG	.	PASS	Atlas-SNP
HEPACAM	220296	hgsc.bcm.edu	37	11	124794688	124794688	+	Silent	SNP	C	C	T	rs112686308	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	72	90	0	0.585366	0	C|0.973;T|0.027	0.027	strong	.	HEPACAM	64	.	NM_152722	exon2	c.G363A	p.E121E	CTCGACCTCATAG	.	PASS	Atlas-SNP
AP4B1	10717	hgsc.bcm.edu	37	1	114438951	114438951	+	Missense_Mutation	SNP	A	A	G	rs1217401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	60	136	0	0.517241	0	A|0.589;G|0.411	0.411	strong	.	AP4B1	72	.	NM_006594	exon9	c.T1439C	p.L480S	CGCAGCAAAGCAG	.	PASS	Atlas-SNP
NKAPL	222698	hgsc.bcm.edu	37	6	28228342	28228342	+	Missense_Mutation	SNP	A	A	G	rs1679709	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	50	43	0	1	0	A|0.162;G|0.838	0.838	strong	.	NKAPL	72	.	NM_001007531	exon1	c.A1193G	p.E398G	CAAAAGAGAAAGA	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115350597	115350597	+	Missense_Mutation	SNP	G	G	A	rs1885434	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	80	158	0	0.56338	0	G|0.640;A|0.360	0.360	strong	.	NRAP	208	.	NM_001261463	exon40	c.C4696T	p.R1566C	CACTGCGGTACCC	.	PASS	Atlas-SNP
ADAM18	8749	hgsc.bcm.edu	37	8	39468070	39468070	+	Missense_Mutation	SNP	A	A	C	rs139114737	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	225	93	208	0	0.413333	0	A|0.997;C|0.003	0.003	strong	.	ADAM18	169	.	NM_001190956	exon6	c.A367C	p.I123L	GAAAATATCAGTT	.	PASS	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	37	10	25312689	25312689	+	Silent	SNP	A	A	G	rs4748997	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	45	59	0	1	0	A|0.746;G|0.254	0.254	strong	.	THNSL1	70	.	NM_024838	exon3	c.A537G	p.G179G	TTCTGGAACATCT	.	PASS	Atlas-SNP
EXOC3L1	283849	hgsc.bcm.edu	37	16	67219107	67219107	+	Missense_Mutation	SNP	G	G	C	rs9939768	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	53	81	0	0.557895	0	G|0.838;C|0.162	0.162	strong	.	EXOC3L1	52	.	NM_178516	exon11	c.C1681G	p.Q561E	CACTTTGCAGGAG	.	PASS	Atlas-SNP
RUFY1	80230	hgsc.bcm.edu	37	5	179036433	179036433	+	Silent	SNP	G	G	A	rs17355294	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	28	52	0	0.538462	0	G|0.620;A|0.380	0.380	strong	.	RUFY1	101	.	NM_025158	exon18	c.G2040A	p.L680L	CGAGCTGGCCCTG	.	PASS	Atlas-SNP
PPP6R1	22870	hgsc.bcm.edu	37	19	55752662	55752662	+	Missense_Mutation	SNP	T	T	C	rs200841391	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	61	126	0	0.476562	0	T|0.998;C|0.002	0.002	strong	.	PPP6R1	63	.	NM_014931	exon9	c.A1106G	p.N369S	GCATCATTGGCGC	.	PASS	Atlas-SNP
PPAP2C	8612	hgsc.bcm.edu	37	19	282753	282753	+	Missense_Mutation	SNP	G	G	A	rs1138439	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	22	46	0	0.415094	0	T|0.071;G|0.466;C|0.124;A|0.339	0.339	strong	PPAP2C_ENST00000269812,caecum,carcinoma,0,5	PPAP2C	38	5	NM_177543	exon4	c.C602T	p.A201V	CTCACCGCCAAGA	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158528269	158528269	+	Silent	SNP	C	C	G	rs35914882	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	28	89	0	0.4375	0	C|0.876;G|0.124	0.124	strong	ESYT2,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ESYT2	70	1	NM_020728	exon20	c.G2511C	p.V837V	CCTCTGCACTTCT	.	PASS	Atlas-SNP
SPRR1B	6699	hgsc.bcm.edu	37	1	153004983	153004983	+	Silent	SNP	C	C	T	rs12195	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	78	126	0	0.493671	0	C|0.493;T|0.507	0.507	strong	.	SPRR1B	18	.	NM_003125	exon2	c.C162T	p.P54P	AGTGCCCGAGCCC	.	PASS	Atlas-SNP
C5orf45	51149	hgsc.bcm.edu	37	5	179267949	179267949	+	Missense_Mutation	SNP	T	T	C	rs248248	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	25	72	0	0.454545	0	T|0.191;C|0.809	0.809	strong	.	C5orf45	23	.	NM_016175	exon6	c.A460G	p.R154G	TGCTCCTGCTCCA	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72139184	72139184	+	Silent	SNP	C	C	A	rs2074626	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	44	108	1	0.564103	0.00925926	C|0.529;A|0.471	0.471	strong	DHX38,NS,carcinoma,0,2	DHX38	91	2	NM_014003	exon17	c.C2316A	p.A772A	GCCTGCCCTGGCT	.	scavenged	Atlas-SNP
PADI2	11240	hgsc.bcm.edu	37	1	17405814	17405814	+	Missense_Mutation	SNP	C	C	T	rs148233687	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	48	65	0	0.842105	0	C|0.999;T|0.001	0.001	strong	.	PADI2	72	.	NM_007365	exon11	c.G1255A	p.V419M	CGTTCACGGTCAC	.	PASS	Atlas-SNP
R3HDML	140902	hgsc.bcm.edu	37	20	42965863	42965863	+	Silent	SNP	C	C	T	rs3746570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	37	62	0	0.528571	0	C|0.845;T|0.155	0.155	strong	.	R3HDML	33	.	NM_178491	exon1	c.C66T	p.N22N	AGTGAACGCCTTG	.	PASS	Atlas-SNP
ARHGEF7	8874	hgsc.bcm.edu	37	13	111870037	111870037	+	Silent	SNP	T	T	C	rs2296354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	87	160	0	0.621429	0	T|0.807;C|0.193	0.193	strong	.	ARHGEF7	157	.	NM_001113511	exon6	c.T543C	p.D181D	GACCGATAATAGC	.	PASS	Atlas-SNP
NDUFS4	4724	hgsc.bcm.edu	37	5	52856504	52856504	+	Silent	SNP	G	G	C	rs2279516	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	56	132	0	0.455285	0	G|0.338;C|0.662	0.662	strong	.	NDUFS4	17	.	NM_002495	exon1	c.G12C	p.V4V	GGCGGTGTCAATG	.	PASS	Atlas-SNP
HEATR4	399671	hgsc.bcm.edu	37	14	73969610	73969610	+	Silent	SNP	G	G	A	rs11626122	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	48	95	0	0.461538	0	G|0.841;A|0.159	0.159	strong	.	HEATR4	126	.	NM_203309	exon10	c.C2094T	p.H698H	TATGTCGTGCACC	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60895697	60895697	+	Missense_Mutation	SNP	C	C	T	rs2297587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	29	24	0	0.517857	0	C|0.805;T|0.195	0.195	strong	.	LAMA5	268	.	NM_005560	exon50	c.G6677A	p.R2226H	TCATGGCGGGGGC	.	PASS	Atlas-SNP
NFE2L3	9603	hgsc.bcm.edu	37	7	26224382	26224382	+	Missense_Mutation	SNP	C	C	T	rs151210268		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	296	30	298	0	0.101351	0	.	.	weak	.	NFE2L3	77	.	NM_004289	exon4	c.C1064T	p.T355I	AGCAAACCCTTCC	.	PASS	Atlas-SNP
GON4L	54856	hgsc.bcm.edu	37	1	155735012	155735012	+	Missense_Mutation	SNP	T	T	C	rs2297775	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	66	216	0	0.372881	0	T|0.667;C|0.333	0.333	strong	GON4L,colon,carcinoma,+2,1	GON4L	392	1	NM_001037533	exon21	c.A4252G	p.M1418V	GATCCATTGAGGA	.	PASS	Atlas-SNP
PBXIP1	57326	hgsc.bcm.edu	37	1	154919080	154919080	+	Missense_Mutation	SNP	C	C	T	rs2061690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	20	34	0	0.540541	0	C|0.565;T|0.435	0.435	strong	.	PBXIP1	59	.	NM_020524	exon10	c.G1070A	p.G357D	CCTCTACCCCCAC	.	PASS	Atlas-SNP
WDR88	126248	hgsc.bcm.edu	37	19	33655144	33655144	+	Silent	SNP	C	C	T	rs1981827	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	68	120	0	0.485714	0	C|0.874;T|0.126	0.126	strong	.	WDR88	50	.	NM_173479	exon9	c.C1122T	p.N374N	CAACAACAAGAAA	.	PASS	Atlas-SNP
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675644	61675644	+	Missense_Mutation	SNP	T	T	C	rs174477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	28	60	0	0.388889	0	T|0.917;C|0.083	0.083	strong	RAB3IL1,NS,carcinoma,0,1	RAB3IL1	39	1	NM_001271686	exon2	c.A287G	p.Q96R	TGGCCTTGGGCCT	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36574063	36574063	+	Silent	SNP	C	C	T	rs45567532	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	48	101	0	0.516129	0	C|0.864;T|0.136	0.136	strong	.	WDR62	102	.	NM_173636	exon11	c.C1470T	p.D490D	CATGGACGTGAAA	.	PASS	Atlas-SNP
AMTN	401138	hgsc.bcm.edu	37	4	71388551	71388551	+	Missense_Mutation	SNP	A	A	G	rs7660807	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	165	142	0	1	0	A|0.919;G|0.081	0.081	strong	.	AMTN	28	.	NM_212557	exon3	c.A134G	p.N45S	AGTCAAATCAGGT	.	PASS	Atlas-SNP
PTCHD2	57540	hgsc.bcm.edu	37	1	11589911	11589911	+	Silent	SNP	G	G	A	rs2076468	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	14	109	0	0.110236	0	G|0.816;A|0.184	0.184	strong	.	PTCHD2	193	.	NM_020780	exon15	c.G2997A	p.P999P	GAAGCCGGCGGTG	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47930148	47930148	+	Silent	SNP	C	C	T	rs118004103	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	25	73	0	0.568182	0	C|0.980;T|0.020	0.020	strong	PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	NM_138295	exon16	c.G2667A	p.S889S	GAACGCCGAGTCA	.	PASS	Atlas-SNP
VARS	7407	hgsc.bcm.edu	37	6	31748820	31748820	+	Silent	SNP	G	G	A	rs707926	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	56	113	0	0.482759	0	G|0.770;A|0.230	0.230	strong	.	VARS	76	.	NM_006295	exon22	c.C2625T	p.D875D	GATGACGTCCAGG	.	PASS	Atlas-SNP
CHMP4C	92421	hgsc.bcm.edu	37	8	82670412	82670412	+	Silent	SNP	G	G	A	rs62514262	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	40	108	0	0.506329	0	G|0.966;A|0.034	0.034	strong	CHMP4C,NS,carcinoma,0,1	CHMP4C	28	1	NM_152284	exon4	c.G519A	p.Q173Q	GGAACAGGAGGAA	.	PASS	Atlas-SNP
PLOD1	5351	hgsc.bcm.edu	37	1	12009955	12009955	+	Silent	SNP	C	C	T	rs7529452	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	92	93	0	0.884615	0	C|0.767;T|0.233	0.233	strong	.	PLOD1	75	.	NM_000302	exon3	c.C294T	p.F98F	TCTCTTCGCAGAC	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43028592	43028592	+	Silent	SNP	G	G	A	rs7167392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	15	14	0	0.5	0	G|0.766;A|0.234	0.234	strong	.	CDAN1	70	.	NM_138477	exon2	c.C477T	p.P159P	GCGGCTGGGGCTG	.	PASS	Atlas-SNP
FDXR	2232	hgsc.bcm.edu	37	17	72862593	72862593	+	Missense_Mutation	SNP	C	C	T	rs690514	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	76	145	0	0.490323	0	C|0.813;T|0.187	0.187	strong	FDXR_ENST00000581530,NS,carcinoma,0,4	FDXR	68	4	NM_001258012	exon4	c.G497A	p.R166Q	GCCTCCCGCAGCT	.	PASS	Atlas-SNP
OR6K6	128371	hgsc.bcm.edu	37	1	158725080	158725080	+	Missense_Mutation	SNP	C	C	T	rs16841001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	71	146	0	0.546154	0	C|0.885;T|0.115	0.115	strong	.	OR6K6	81	.	NM_001005184	exon1	c.C475T	p.R159C	CCACTCCGTTACC	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	276	15	225	3	0.0543478	0.0133333	.	.	none	TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	NM_001039141	exon7	c.A1339G	p.T447A	AGAGCTACACGAG	.	scavenged	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44981375	44981375	+	Silent	SNP	T	T	C	rs954314	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	60	111	0	0.47619	0	T|0.760;C|0.240	0.240	strong	ZNF180,caecum,carcinoma,0,1	ZNF180	103	1	NM_013256	exon5	c.A1323G	p.Q441Q	TCCACATTGATTG	.	PASS	Atlas-SNP
PKLR	5313	hgsc.bcm.edu	37	1	155260383	155260383	+	Silent	SNP	G	G	T	rs1052176	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	21	49	0	0.456522	0	G|0.583;T|0.417	0.417	strong	.	PKLR	70	.	NM_000298	exon11	c.C1705A	p.R569R	GCACCCGCATGAT	.	PASS	Atlas-SNP
SERPINA9	327657	hgsc.bcm.edu	37	14	94935901	94935901	+	Missense_Mutation	SNP	G	G	C	rs12879019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	43	93	0	0.438776	0	G|0.779;C|0.221	0.221	strong	.	SERPINA9	105	.	NM_175739	exon2	c.C331G	p.Q111E	GAATCTGGGTCTT	.	PASS	Atlas-SNP
PRAM1	84106	hgsc.bcm.edu	37	19	8564469	8564469	+	Missense_Mutation	SNP	C	C	G	rs4990821	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	22	59	0	0.360656	0	C|0.656;G|0.344	0.344	strong	.	PRAM1	53	.	NM_032152	exon2	c.G223C	p.E75Q	TGACCTCAGGCGG	.	PASS	Atlas-SNP
MKL1	57591	hgsc.bcm.edu	37	22	40814636	40814636	+	Silent	SNP	C	C	T	rs4821944	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	17	25	0	0.53125	0	C|0.829;T|0.171	0.171	strong	.	MKL1	69	.	NM_020831	exon12	c.G1806A	p.A602A	TGGGGCCGCCAGG	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219602499	219602499	+	Missense_Mutation	SNP	G	G	C	rs3731877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	71	114	0	0.522059	0	G|0.525;C|0.475	0.475	strong	TTLL4,brain,glioma,0,1	TTLL4	96	1	NM_014640	exon3	c.G100C	p.E34Q	CCACCTGAGAAAC	.	PASS	Atlas-SNP
UBR7	55148	hgsc.bcm.edu	37	14	93673655	93673655	+	Missense_Mutation	SNP	G	G	A	rs2286653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	50	35	0	0.649351	0	G|0.886;A|0.114	0.114	strong	.	UBR7	36	.	NM_175748	exon1	c.G19A	p.A7T	GAGGGCGCCGCTG	.	PASS	Atlas-SNP
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T	rs10107826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	44	47	0	0.578947	0	C|0.958;T|0.042	0.042	strong	.	TNFRSF10C	30	.	NM_003841	exon1	c.C20T	p.T7I	CCAAGACCCTAAA	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15839174	15839174	+	Silent	SNP	C	C	T	rs74730938		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	250	110	174	0	0.44	0	T|1.000;|0.000	1.000	weak	.	OR10H2	59	.	NM_013939	exon1	c.C321T	p.F107F	CAGCTTCGGCTTC	.	PASS	Atlas-SNP
XRN1	54464	hgsc.bcm.edu	37	3	142078759	142078759	+	Missense_Mutation	SNP	C	C	T	rs73238159	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	26	33	0	1	0	C|0.901;T|0.099	0.099	strong	.	XRN1	138	.	NM_001042604	exon30	c.G3409A	p.D1137N	GTACATCGGCTTC	.	PASS	Atlas-SNP
TRIML1	339976	hgsc.bcm.edu	37	4	189061036	189061036	+	Silent	SNP	C	C	T	rs76826594	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	86	150	0	0.5375	0	C|0.830;T|0.170	0.170	strong	TRIML1,NS,carcinoma,+1,1	TRIML1	126	1	NM_178556	exon1	c.C324T	p.D108D	CGATGACGAGCAG	.	PASS	Atlas-SNP
LBR	3930	hgsc.bcm.edu	37	1	225603029	225603029	+	Silent	SNP	T	T	C	rs61749339	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	82	131	0	0.463277	0	T|0.991;C|0.009	0.009	strong	.	LBR	54	.	NM_194442	exon7	c.A843G	p.V281V	TCCTTCTACAACC	.	PASS	Atlas-SNP
ARNT2	9915	hgsc.bcm.edu	37	15	80884025	80884025	+	Missense_Mutation	SNP	G	G	A	rs4072568	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	36	140	0	0.342857	0	G|0.856;A|0.144	0.144	strong	ARNT2,NS,carcinoma,-1,1	ARNT2	88	1	NM_014862	exon18	c.G2035A	p.G679S	CAGCCCGGTCAGA	.	PASS	Atlas-SNP
PDDC1	347862	hgsc.bcm.edu	37	11	771034	771034	+	Silent	SNP	A	A	G	rs7930569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	37	80	0	0.430233	0	A|0.556;G|0.444	0.444	strong	.	PDDC1	16	.	NM_182612	exon7	c.T615C	p.T205T	CGGGACAGTGGAG	.	PASS	Atlas-SNP
ITIH5	80760	hgsc.bcm.edu	37	10	7679393	7679393	+	Silent	SNP	C	C	T	rs6602256	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	35	69	0	0.466667	0	C|0.587;T|0.413	0.413	strong	.	ITIH5	343	.	NM_001001851	exon5	c.G450A	p.K150K	TTTGTCCTTGCTG	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46341824	46341824	+	Silent	SNP	C	C	T	rs17850110	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	39	91	0	0.448276	0	C|0.873;G|0.000;T|0.127	0.127	strong	.	SYMPK	104	.	NM_004819	exon10	c.G1137A	p.P379P	CCCCGACGGGCCT	.	PASS	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	37	1	184765072	184765072	+	Missense_Mutation	SNP	A	A	G	rs28927681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	22	66	0	0.44	0	G|0.177;A|0.823	0.177	strong	FAM129A,NS,carcinoma,-1,2	FAM129A	98	2	NM_052966	exon14	c.T1826C	p.L609P	CTACCCAGAACTC	.	PASS	Atlas-SNP
OR51A2	401667	hgsc.bcm.edu	37	11	4976077	4976077	+	Missense_Mutation	SNP	T	T	G	rs2570573	bycluster;byfrequency;bysubmitter;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	39	7	7	0.975	1	T|0.952;G|0.048	0.048	strong	OR51A2,NS,carcinoma,-2,1	OR51A2	40	1	NM_001004748	exon1	c.A867C	p.K289N	AATTGGTTTCATC	.	scavenged	Atlas-SNP
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628948	1628948	+	Missense_Mutation	SNP	G	G	A	rs117085626	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	56	81	0	0.474576	0	G|0.917;A|0.083	0.083	strong	.	KRTAP5-3	33	.	NM_001012708	exon1	c.C668T	p.S223F	TGGGAGGAGCAGG	.	PASS	Atlas-SNP
GABBR1	2550	hgsc.bcm.edu	37	6	29581110	29581110	+	Silent	SNP	A	A	G	rs17854217	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	47	119	0	0.435185	0	A|0.902;G|0.098	0.098	strong	.	GABBR1	95	.	NM_001470	exon12	c.T1476C	p.G492G	GCGCACACCAGAA	.	PASS	Atlas-SNP
NCAPH	23397	hgsc.bcm.edu	37	2	97020049	97020049	+	Silent	SNP	T	T	C	rs3731935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	30	61	0	0.410959	0	T|0.781;C|0.219	0.219	strong	NCAPH,NS,carcinoma,+2,2	NCAPH	67	2	NM_015341	exon9	c.T1131C	p.D377D	CAACGATGAACCT	.	PASS	Atlas-SNP
ABAT	18	hgsc.bcm.edu	37	16	8844389	8844389	+	Silent	SNP	C	C	T	rs2229157	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	58	121	0	0.487395	0	C|0.901;T|0.099	0.099	strong	.	ABAT	46	.	NM_001127448	exon5	c.C309T	p.V103V	CTCTGTCCCCATA	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40652142	40652142	+	Silent	SNP	G	G	A	rs2836972	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	57	120	0	0.483051	0	G|0.693;A|0.307	0.307	strong	BRWD1_ENST00000333229,NS,carcinoma,0,2	BRWD1	325	2	NM_018963	exon9	c.C864T	p.Y288Y	AACCATGTATCTT	.	PASS	Atlas-SNP
IPPK	64768	hgsc.bcm.edu	37	9	95396712	95396712	+	Missense_Mutation	SNP	G	G	A	rs2277170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	41	88	0	0.5	0	G|0.961;A|0.039	0.039	strong	.	IPPK	34	.	NM_022755	exon11	c.C1126T	p.L376F	TGGAAAGGTCAAG	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	37	3	52407041	52407041	+	Silent	SNP	C	C	T	rs1546737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	28	64	0	0.482759	0	C|0.781;T|0.219	0.219	strong	.	DNAH1	534	.	NM_015512	exon44	c.C6957T	p.H2319H	GGACCACGGCGGC	.	PASS	Atlas-SNP
METRNL	284207	hgsc.bcm.edu	37	17	81043039	81043039	+	Silent	SNP	A	A	G	rs9908756	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	59	157	0	0.421429	0	A|0.262;G|0.738	0.738	strong	METRNL,NS,carcinoma,0,1	METRNL	29	1	NM_001004431	exon2	c.A396G	p.P132P	GGTACCAGACGGG	.	PASS	Atlas-SNP
SRPK3	26576	hgsc.bcm.edu	37	X	153049535	153049535	+	Silent	SNP	A	A	G	rs4898444	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	45	49	0	1	0	A|0.477;G|0.523	0.523	strong	.	SRPK3	63	.	NM_014370	exon10	c.A1014G	p.P338P	CGCCCCAGGGGGC	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135722264	135722264	+	Missense_Mutation	SNP	A	A	G	rs17197552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	96	160	0	0.518919	0	A|0.779;G|0.221	0.221	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.A1924G	p.S642G	TGTAGAAGTCCTG	.	PASS	Atlas-SNP
RPTOR	57521	hgsc.bcm.edu	37	17	78919558	78919558	+	Silent	SNP	C	C	T	rs1567962	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	29	64	0	0.408451	0	C|0.632;T|0.368	0.368	strong	.	RPTOR	122	.	NM_020761	exon26	c.C3117T	p.A1039A	CATCGCCGTAGCC	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573442	140573442	+	Silent	SNP	C	C	G	rs622424	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	118	144	0	0.983333	0	C|0.549;G|0.451	0.451	strong	.	PCDHB10	177	.	NM_018930	exon1	c.C1317G	p.V439V	AACGGTCCTGGTC	.	PASS	Atlas-SNP
POLM	27434	hgsc.bcm.edu	37	7	44121936	44121936	+	Silent	SNP	C	C	A	rs3218655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	6	12	0	0.272727	0	C|0.841;A|0.159	0.159	strong	.	POLM	50	.	NM_013284	exon1	c.G102T	p.L34L	CTCGACCAGGTAG	.	PASS	Atlas-SNP
NDUFV2	4729	hgsc.bcm.edu	37	18	9122638	9122638	+	Missense_Mutation	SNP	G	G	C	rs148158107	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	271	18	236	2	0.0664207	0.00847458	G|0.996;C|0.005	0.005	strong	NDUFV2,colon,carcinoma,+1,3	NDUFV2	17	3	NM_021074	exon5	c.G428C	p.R143P	TGCTTCGAAACTC	.	scavenged	Atlas-SNP
PNPLA6	10908	hgsc.bcm.edu	37	19	7614888	7614888	+	Silent	SNP	C	C	G	rs62111288	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	67	127	0	0.563025	0	C|0.990;G|0.010	0.010	strong	.	PNPLA6	163	.	NM_001166111	exon16	c.C1731G	p.P577P	GCAGCCCGGGGAA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168107491	168107491	+	Missense_Mutation	SNP	A	A	G	rs3749004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	54	139	0	0.486486	0	A|0.817;G|0.183	0.183	strong	.	XIRP2	914	.	NM_152381	exon9	c.A9589G	p.I3197V	GGGGCCATCCCAT	.	PASS	Atlas-SNP
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130488	52130488	+	Silent	SNP	G	G	A	rs17740650	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	11	49	0	0.282051	0	G|0.811;A|0.188	0.188	strong	.	SIGLEC5	67	.	NM_003830	exon7	c.C1296T	p.L432L	TGTCCCGAGGTTC	.	PASS	Atlas-SNP
C18orf54	162681	hgsc.bcm.edu	37	18	51888173	51888173	+	Silent	SNP	G	G	A	rs79359715	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	77	180	0	0.420765	0	G|0.959;A|0.041	0.041	strong	.	C18orf54	40	.	NM_173529	exon3	c.G444A	p.T148T	CCGAACGAGCAAG	.	PASS	Atlas-SNP
SYNRG	11276	hgsc.bcm.edu	37	17	35902225	35902225	+	Silent	SNP	C	C	G	rs3110623	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	108	107	1	0.990826	0.00934579	G|0.461;C|0.539	0.461	strong	.	SYNRG	101	.	NM_007247	exon15	c.G3051C	p.P1017P	TTCGTTCGGGGTT	.	PASS	Atlas-SNP
UGT3A1	133688	hgsc.bcm.edu	37	5	35965611	35965611	+	Silent	SNP	A	A	G	rs61733467	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	114	237	0	0.511211	0	A|0.988;G|0.012	0.012	strong	.	UGT3A1	95	.	NM_152404	exon4	c.T720C	p.L240L	CAGTAGAAGATGA	.	PASS	Atlas-SNP
VNN2	8875	hgsc.bcm.edu	37	6	133077063	133077063	+	Silent	SNP	T	T	C	rs1883613	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	12	118	0	0.173913	0	T|0.682;C|0.318	0.318	strong	.	VNN2	83	.	NM_004665	exon3	c.A456G	p.T152T	AGGACATGTGGAG	.	PASS	Atlas-SNP
CCM2	83605	hgsc.bcm.edu	37	7	45113170	45113170	+	Silent	SNP	G	G	A	rs2289367	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	35	55	0	0.514706	0	G|0.779;A|0.221	0.221	strong	CCM2,NS,carcinoma,0,1	CCM2	42	1	NM_001029835	exon8	c.G978A	p.T326T	GCTGACGGTAGGC	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115931593	115931593	+	Silent	SNP	G	G	A	rs1128122	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	67	214	0	0.416149	0	G|0.953;A|0.047	0.047	strong	FKBP15_ENST00000238256,NS,carcinoma,-1,2	FKBP15	128	2	NM_015258	exon26	c.C3396T	p.T1132T	GGGACCGGTGGAG	.	PASS	Atlas-SNP
HK3	3101	hgsc.bcm.edu	37	5	176315822	176315822	+	Silent	SNP	G	G	T	rs61749652	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	31	89	0	0.424658	0	G|0.979;T|0.021	0.021	strong	HK3_ENST00000292432,NS,carcinoma,0,2	HK3	210	2	NM_002115	exon9	c.C958A	p.R320R	CCAGCCGCACCAG	.	PASS	Atlas-SNP
CCT8	10694	hgsc.bcm.edu	37	21	30437344	30437344	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	4	85	0	0.0425532	0	.	.	none	.	CCT8	38	.	NM_006585	exon7	c.A707G	p.D236G	TTTGCATCTTTGA	.	PASS	Atlas-SNP
GPR151	134391	hgsc.bcm.edu	37	5	145894896	145894896	+	Missense_Mutation	SNP	G	G	C	rs7709485	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	83	65	0	1	0	G|0.723;C|0.277	0.277	strong	.	GPR151	35	.	NM_194251	exon1	c.C781G	p.L261V	ACAAGAGAGCAGA	.	PASS	Atlas-SNP
SCN1A	6323	hgsc.bcm.edu	37	2	166903445	166903445	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	127	137	0	0.976923	0	.	.	none	.	SCN1A	641	.	NM_001165964	exon9	c.A1212G	p.V404V	GACCAATACAAAA	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	37	7	82435033	82435033	+	Silent	SNP	C	C	T	rs12668093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	55	135	0	0.413534	0	C|0.773;T|0.227	0.227	strong	.	PCLO	1506	.	NM_033026	exon21	c.G14904A	p.G4968G	AGTCTCCCCTGCA	.	PASS	Atlas-SNP
CADPS	8618	hgsc.bcm.edu	37	3	62578336	62578336	+	Silent	SNP	C	C	T	rs17066673	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	44	87	0	0.468085	0	C|0.946;T|0.054	0.054	strong	CADPS,brain,glioma,-2,1	CADPS	387	1	NM_003716	exon7	c.G1413A	p.A471A	CTCCAACGCCAGG	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78565314	78565314	+	Missense_Mutation	SNP	C	C	G	rs17137261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	9	30	0	0.6	0	C|0.969;G|0.031	0.031	strong	.	.	.	.	NM_001098816	exon12	c.G1516C	p.E506Q	GCGCCTCCTGGGT	.	PASS	Atlas-SNP
LHX8	431707	hgsc.bcm.edu	37	1	75622616	75622616	+	Silent	SNP	C	C	T	rs941032	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	159	149	0	1	0	C|0.598;N|0.000	.	strong	.	LHX8	73	.	NM_001001933	exon9	c.C849T	p.H283H	GAAACACGTCAGT	.	PASS	Atlas-SNP
HLTF	6596	hgsc.bcm.edu	37	3	148759325	148759325	+	Silent	SNP	T	T	C	rs2290725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	50	89	0	0.510204	0	T|0.692;C|0.308	0.308	strong	.	HLTF	87	.	NM_139048	exon20	c.A2328G	p.A776A	TACATGTGCACAA	.	PASS	Atlas-SNP
GALNT7	51809	hgsc.bcm.edu	37	4	174090004	174090004	+	Silent	SNP	G	G	A	rs3733477	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	56	69	0	0.54902	0	T|0.000;G|0.353;A|0.647	0.647	strong	.	GALNT7	61	.	NM_017423	exon1	c.G18A	p.G6G	GATTGGGTTCATC	.	PASS	Atlas-SNP
SULF2	55959	hgsc.bcm.edu	37	20	46365636	46365636	+	Missense_Mutation	SNP	C	C	T	rs56218501	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	99	203	0	0.515625	0	C|0.856;G|0.000;T|0.144	0.144	strong	SULF2,colon,carcinoma,+2,3	SULF2	131	3	NM_001161841	exon3	c.G226A	p.A76T	AGTGCGCCCCGCC	.	PASS	Atlas-SNP
NTNG2	84628	hgsc.bcm.edu	37	9	135073967	135073967	+	Silent	SNP	C	C	T	rs3739930	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	67	149	0	0.503759	0	C|0.909;T|0.091	0.091	strong	NTNG2,NS,carcinoma,0,1	NTNG2	66	1	NM_032536	exon3	c.C828T	p.Y276Y	CTTCTACGCCATC	.	PASS	Atlas-SNP
CPED1	79974	hgsc.bcm.edu	37	7	120776097	120776097	+	Missense_Mutation	SNP	C	C	G	rs41281692	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	31	43	0	0.563636	0	C|0.571;G|0.429	0.429	strong	.	.	.	.	NM_001105533	exon13	c.C1652G	p.A551G	TAGCTGCAGTTCC	.	PASS	Atlas-SNP
NLRP11	204801	hgsc.bcm.edu	37	19	56329334	56329334	+	Silent	SNP	G	G	C	rs8113630	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	69	158	0	0.469388	0	G|0.900;C|0.100	0.100	strong	.	NLRP11	139	.	NM_145007	exon4	c.C207G	p.L69L	GCTGAAGAGCATA	.	PASS	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	37	16	1391150	1391150	+	Missense_Mutation	SNP	A	A	C	rs115198116	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	36	86	0	0.413793	0	A|0.998;C|0.002	0.002	strong	.	BAIAP3	88	.	NM_003933	exon7	c.A594C	p.K198N	CCTGAAAGTCTCT	.	PASS	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	37	2	71654175	71654175	+	Missense_Mutation	SNP	G	G	A	rs1804020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	52	105	0	0.504854	0	G|0.710;A|0.290	0.290	strong	ZNF638,tonsil,carcinoma,0,1	ZNF638	179	1	NM_014497	exon24	c.G5176A	p.V1726M	TCTCAGGTGCCCG	.	PASS	Atlas-SNP
ADAM19	8728	hgsc.bcm.edu	37	5	156918850	156918850	+	Missense_Mutation	SNP	C	C	T	rs2287749	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	108	110	0	0.990826	0	C|0.911;T|0.089	0.089	strong	.	ADAM19	216	.	NM_033274	exon17	c.G1979A	p.G660D	CCATGGCCATTGC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389161	1389161	+	Missense_Mutation	SNP	A	A	G	rs71614973	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	27	100	0	0.293478	0	G|1.000;|0.000	1.000	weak	.	CRIPAK	185	.	NM_175918	exon1	c.A862G	p.S288G	ATGTGGAGTGCCC	.	PASS	Atlas-SNP
SIGLEC6	946	hgsc.bcm.edu	37	19	52033158	52033158	+	Missense_Mutation	SNP	C	C	T	rs35931837	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	55	102	1	0.458333	0.00980392	C|0.914;T|0.086	0.086	strong	SIGLEC6_ENST00000425629,NS,carcinoma,+2,2	SIGLEC6	142	2	NM_001177548	exon5	c.G865A	p.G289S	GGTTGCCGTCAGC	.	scavenged	Atlas-SNP
PRND	23627	hgsc.bcm.edu	37	20	4705718	4705718	+	Missense_Mutation	SNP	C	C	T	rs2245220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	34	53	0	0.447368	0	C|0.492;T|0.508	0.508	strong	PRND,caecum,carcinoma,0,1	PRND	34	1	NM_012409	exon2	c.C521T	p.T174M	GGCTCACGGTGAA	.	PASS	Atlas-SNP
NPW	283869	hgsc.bcm.edu	37	16	2070200	2070200	+	Missense_Mutation	SNP	G	G	C	rs11248906	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	13	12	6	0	0.923077	0	G|0.881;C|0.119	0.119	strong	.	NPW	4	.	NM_001099456	exon1	c.G298C	p.E100Q	CTGTGGGAGACGC	.	PASS	Atlas-SNP
NECAB2	54550	hgsc.bcm.edu	37	16	84030848	84030848	+	Silent	SNP	C	C	T	rs7193267	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	64	108	0	0.481203	0	C|0.992;T|0.008	0.008	strong	.	NECAB2	36	.	NM_019065	exon9	c.C823T	p.L275L	CAGCGCCTGTCAG	.	PASS	Atlas-SNP
C5orf60	285679	hgsc.bcm.edu	37	5	179069912	179069912	+	Missense_Mutation	SNP	C	C	T	rs75942553	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	383	200	307	0	0.522193	0	C|0.934;T|0.066	0.066	strong	.	C5orf60	24	.	NM_001142306	exon4	c.G641A	p.S214N	AGGGTGCTCGCAG	.	PASS	Atlas-SNP
FAM208B	54906	hgsc.bcm.edu	37	10	5784151	5784151	+	Missense_Mutation	SNP	A	A	G	rs45575338	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	62	157	0	0.466165	0	A|0.816;G|0.184	0.184	strong	C10orf18,NS,carcinoma,-2,1	.	.	1	NM_017782	exon14	c.A2419G	p.I807V	AACAAAATCATAC	.	PASS	Atlas-SNP
TMEM187	8269	hgsc.bcm.edu	37	X	153248248	153248248	+	Silent	SNP	G	G	A	rs13397	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	114	104	0	1	0	0|0.003;A|0.194	0.194	strong	.	TMEM187	21	.	NM_003492	exon2	c.G735A	p.T245T	TCTGACGCATTTC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65300143	65300143	+	Missense_Mutation	SNP	G	G	C	rs16895517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	86	170	0	0.966292	0	G|0.909;C|0.091	0.091	strong	.	EYS	527	.	NM_001142800	exon26	c.C5617G	p.L1873V	GTGCCAGAATGGA	.	PASS	Atlas-SNP
HHAT	55733	hgsc.bcm.edu	37	1	210577901	210577901	+	Missense_Mutation	SNP	T	T	C	rs34228541	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	69	81	0	1	0	T|0.874;C|0.126	0.126	strong	HHAT,NS,carcinoma,-2,1	HHAT	66	1	NM_001170587	exon5	c.T565C	p.C189R	GAGCTCTGCTGGC	.	PASS	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792093	8792093	+	Silent	SNP	G	G	A	rs16957702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	12	40	0	0.387097	0	G|0.734;A|0.266	0.266	strong	.	PIK3R5	79	.	NM_001142633	exon10	c.C1011T	p.D337D	GTGCCCGTCAGTT	.	PASS	Atlas-SNP
FAM209A	200232	hgsc.bcm.edu	37	20	55099977	55099977	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	22	240	0	0.121547	0	.	.	none	.	.	.	.	NM_001012971	exon1	c.A113G	p.Y38C	TGCAATACGGAGA	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	37	4	187509931	187509931	+	Missense_Mutation	SNP	C	C	T	rs192609167	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	49	108	0	0.445455	0	C|0.999;T|0.001	0.001	strong	.	FAT1	500	.	NM_005245	exon27	c.G13582A	p.E4528K	GCGCCTCGAAGTG	.	PASS	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136561557	136561557	+	Silent	SNP	G	G	A	rs2304371	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	70	128	0	0.482759	0	G|0.327;A|0.673	0.673	strong	.	LCT	309	.	NM_002299	exon11	c.C4606T	p.L1536L	CATTCAGCGTGAT	.	PASS	Atlas-SNP
HAGH	3029	hgsc.bcm.edu	37	16	1869147	1869147	+	Silent	SNP	G	G	A	rs56316151	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	39	85	0	0.481481	0	G|0.975;A|0.025	0.025	strong	.	HAGH	20	.	NM_005326	exon5	c.C510T	p.P170P	GCCTCCGGGCTTG	.	PASS	Atlas-SNP
CCDC65	85478	hgsc.bcm.edu	37	12	49308284	49308284	+	Missense_Mutation	SNP	A	A	G	rs10747556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	66	54	0	0.985075	0	A|0.685;G|0.315	0.315	strong	.	CCDC65	41	.	NM_033124	exon3	c.A398G	p.H133R	AGAGGCACCGGCT	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26310470	26310470	+	Silent	SNP	C	C	T	rs35010955	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	40	98	0	0.465116	0	C|0.923;T|0.077	0.077	strong	.	MYO3A	371	.	NM_017433	exon8	c.C624T	p.D208D	TTATGACGCCAGA	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99149946	99149946	+	Silent	SNP	G	G	A	rs2278211	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	83	79	0	0.976471	0	G|0.779;N|0.000	.	strong	.	INPP4A	205	.	NM_004027	exon5	c.G258A	p.T86T	ACAGACGGAGATC	.	PASS	Atlas-SNP
GALNT6	11226	hgsc.bcm.edu	37	12	51771040	51771040	+	Silent	SNP	T	T	C	rs2277379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	97	180	0	0.502591	0	T|0.930;C|0.070	0.070	strong	.	GALNT6	63	.	NM_007210	exon4	c.A603G	p.L201L	GGTGTGTAGGACG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40389741	40389741	+	Missense_Mutation	SNP	A	A	G	rs3746009	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	783	325	1136	5	0.41507	0.00440141	A|0.200;G|0.800	0.800	strong	FCGBP,NS,neuroblastoma,0,3	FCGBP	416	3	NM_003890	exon18	c.T8441C	p.V2814A	TTACCCACATGGC	.	scavenged	Atlas-SNP
HOXC4	3221	hgsc.bcm.edu	37	12	54448106	54448106	+	Missense_Mutation	SNP	A	A	G	rs75256744	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	32	76	0	0.351648	0	A|0.880;G|0.120	0.120	strong	.	HOXC4	29	.	NM_014620	exon3	c.A400G	p.I134V	CAACCCATAGTCT	.	PASS	Atlas-SNP
SQSTM1	8878	hgsc.bcm.edu	37	5	179260153	179260153	+	Silent	SNP	C	C	T	rs4935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	43	62	0	0.614286	0	C|0.358;T|0.642	0.642	strong	.	SQSTM1	30	.	NM_003900	exon6	c.C876T	p.D292D	CTCTGACCCCAGC	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25016008	25016008	+	Silent	SNP	C	C	T	rs80008060		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	57	96	0	1	0	.	.	weak	.	PARP4	142	.	NM_006437	exon30	c.G3642A	p.E1214E	TTGGGGCTCCCCC	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130949491	130949491	+	Silent	SNP	G	G	A	rs60154251	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	100	213	0	0.452489	0	G|0.612;A|0.388	0.388	strong	TUBA3E,colon,carcinoma,-2,1	TUBA3E	73	1	NM_207312	exon5	c.C1266T	p.R422R	GTCCTCGCGGGCC	.	PASS	Atlas-SNP
AVL9	23080	hgsc.bcm.edu	37	7	32623477	32623477	+	Silent	SNP	C	C	G	rs34778959	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	115	176	0	0.539906	0	C|0.811;G|0.189	0.189	strong	.	AVL9	66	.	NM_015060	exon16	c.C1905G	p.S635S	CACTTCCACCTCC	.	PASS	Atlas-SNP
FAM53A	152877	hgsc.bcm.edu	37	4	1657281	1657281	+	Silent	SNP	G	G	A	rs79735962	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	61	57	0	0.525862	0	G|0.787;A|0.213	0.213	strong	.	FAM53A	25	.	NM_001013622	exon4	c.C306T	p.T102T	GTCCACGGTGCTG	.	PASS	Atlas-SNP
HABP2	3026	hgsc.bcm.edu	37	10	115341753	115341753	+	Silent	SNP	G	G	A	rs2245056	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	27	76	0	0.435484	0	G|0.601;A|0.399	0.399	strong	.	HABP2	52	.	NM_004132	exon9	c.G957A	p.K319K	CTTTAAGAGCACG	.	PASS	Atlas-SNP
SPG7	6687	hgsc.bcm.edu	37	16	89620328	89620328	+	Missense_Mutation	SNP	G	G	A	rs12960	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	64	85	0	0.561404	0	G|0.871;A|0.129	0.129	strong	.	SPG7	75	.	NM_003119	exon15	c.G2063A	p.R688Q	TCGGGCGGCGCCC	.	PASS	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13190163	13190163	+	Missense_Mutation	SNP	C	C	T	rs4741289	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	39	76	0	0.481481	0	C|0.983;T|0.017	0.017	strong	.	MPDZ	324	.	NM_003829	exon16	c.G2104A	p.E702K	CCAGCTCTATGTG	.	PASS	Atlas-SNP
TOP2B	7155	hgsc.bcm.edu	37	3	25639828	25639828	+	Missense_Mutation	SNP	T	T	A	rs61739570	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	52	162	0	0.468468	0	T|0.952;A|0.048	0.048	strong	.	TOP2B	98	.	NM_001068	exon36	c.A4836T	p.E1612D	ATCATCTTCTTCT	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	46008790	46008790	+	Missense_Mutation	SNP	G	G	A	rs3796375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	42	80	0	0.525	0	G|0.650;A|0.350	0.350	strong	.	FYCO1	115	.	NM_024513	exon8	c.C2036T	p.A679V	AAGCTCGCCTCCA	.	PASS	Atlas-SNP
ZSCAN29	146050	hgsc.bcm.edu	37	15	43658935	43658935	+	Missense_Mutation	SNP	C	C	T	rs3917221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	76	103	0	0.580153	0	C|0.817;T|0.183	0.183	strong	.	ZSCAN29	57	.	NM_152455	exon3	c.G595A	p.G199S	TAGAGCCCAGCAG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134691427	134691427	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	298	23	314	0	0.0771812	0	.	.	none	.	TTC40	100	.	NM_001200049	exon30	c.C4170G	p.D1390E	CTCCTTGTCCTTC	.	PASS	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140475980	140475980	+	Missense_Mutation	SNP	G	G	A	rs17844376	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	39	57	0	0.619048	0	G|0.783;A|0.217	0.217	strong	.	PCDHB2	163	.	NM_018936	exon1	c.G1606A	p.A536T	GGCGCCGCAGACC	.	PASS	Atlas-SNP
SMG8	55181	hgsc.bcm.edu	37	17	57287454	57287454	+	Silent	SNP	A	A	G	rs6503905	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	23	34	0	0.958333	0	A|0.301;G|0.699	0.699	strong	.	SMG8	79	.	NM_018149	exon1	c.A42G	p.A14A	GGGAGCATCAGCC	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	37	17	78178893	78178893	+	Missense_Mutation	SNP	C	C	T	rs11652075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	53	104	0	0.557895	0	C|0.597;T|0.403	0.403	strong	.	CARD14	98	.	NM_024110	exon18	c.C2458T	p.R820W	CTGGTGCGGCCCC	.	PASS	Atlas-SNP
UTRN	7402	hgsc.bcm.edu	37	6	145051594	145051594	+	Silent	SNP	G	G	A	rs4305737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	21	35	0	1	0	G|0.490;A|0.510	0.510	strong	.	UTRN	327	.	NM_007124	exon53	c.G7911A	p.E2637E	TGAAGAGCCAAGA	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48254799	48254799	+	Silent	SNP	T	T	C	rs11538669	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	39	74	0	0.481481	0	T|0.987;C|0.013	0.013	strong	.	GLTSCR2	45	.	NM_015710	exon5	c.T621C	p.V207V	GTTGGTTGGCCAG	.	PASS	Atlas-SNP
YDJC	150223	hgsc.bcm.edu	37	22	21984205	21984205	+	Silent	SNP	A	A	G	rs710177	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	16	28	0	0.313726	0	A|0.605;G|0.395	0.395	strong	YDJC,rectum,carcinoma,0,1	YDJC	8	1	NM_001017964	exon1	c.T99C	p.A33A	GGTCACAGCCCCG	.	PASS	Atlas-SNP
NACA2	342538	hgsc.bcm.edu	37	17	59667953	59667953	+	Nonsense_Mutation	SNP	G	G	A	rs17610181	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	232	111	221	0	0.478448	0	G|0.879;A|0.121	0.121	strong	.	NACA2	33	.	NM_199290	exon1	c.C589T	p.R197X	GAGCTCGGACTGC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537115	88537115	+	Missense_Mutation	SNP	G	G	A	rs201186956		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	5	25	0	0.416667	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.G3301A	p.D1101N	AGCAGCGACAGCA	.	PASS	Atlas-SNP
METTL12	751071	hgsc.bcm.edu	37	11	62434173	62434173	+	Missense_Mutation	SNP	G	G	A	rs11231181	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	40	50	0	0.465116	0	G|0.803;A|0.197	0.197	strong	.	METTL12	11	.	NM_001043229	exon3	c.G373A	p.G125S	GGCCCAGGCCAAA	.	PASS	Atlas-SNP
TESPA1	9840	hgsc.bcm.edu	37	12	55368245	55368245	+	Silent	SNP	G	G	A	rs4758993	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	54	103	0	0.465517	0	G|0.625;A|0.375	0.375	strong	.	.	.	.	NM_001098815	exon2	c.C102T	p.A34A	GGCGGCGGCAGCC	.	PASS	Atlas-SNP
MMS19	64210	hgsc.bcm.edu	37	10	99225645	99225645	+	Missense_Mutation	SNP	G	G	A	rs12360068	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	33	66	0	0.52381	0	G|0.974;A|0.026	0.026	strong	.	MMS19	36	.	NM_022362	exon18	c.C1673T	p.A558V	GACAAGGCTTGCA	.	PASS	Atlas-SNP
PTPRO	5800	hgsc.bcm.edu	37	12	15733669	15733669	+	Silent	SNP	G	G	A	rs3748299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	48	107	0	0.539326	0	G|0.893;A|0.107	0.107	strong	.	PTPRO	148	.	NM_030667	exon22	c.G3036A	p.G1012G	CCAGGGGCCACTG	.	PASS	Atlas-SNP
TNMD	64102	hgsc.bcm.edu	37	X	99849017	99849017	+	Silent	SNP	G	G	A	rs2073162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	133	153	0	0.977941	0	0|0.015;A|0.433	0.433	strong	.	TNMD	40	.	NM_022144	exon3	c.G306A	p.V102V	GGAAGTGCACGAC	.	PASS	Atlas-SNP
GLO1	2739	hgsc.bcm.edu	37	6	38650628	38650628	+	Missense_Mutation	SNP	T	T	G	rs4746	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	62	92	0	0.512397	0	T|0.638;G|0.362	0.362	strong	.	GLO1	12	.	NM_006708	exon4	c.A332C	p.E111A	TGGGTCTCATCAT	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52709880	52709880	+	Silent	SNP	A	A	G	rs2852468	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	26	99	0	0.361111	0	A|0.630;G|0.370	0.370	strong	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon7	c.T1059C	p.A353A	CACCGCAGCTTCC	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99130282	99130282	+	Silent	SNP	T	T	G	rs11189170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	57	109	2	0.518182	0.0183486	T|0.952;G|0.048	0.048	strong	RRP12,NS,carcinoma,-2,1	RRP12	97	1	NM_015179	exon23	c.A2619C	p.A873A	CTTCCGTGCGCCC	.	scavenged	Atlas-SNP
BBX	56987	hgsc.bcm.edu	37	3	107491892	107491892	+	Missense_Mutation	SNP	G	G	A	rs138961599	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	58	86	0	0.517857	0	G|0.993;A|0.007	0.007	strong	.	BBX	156	.	NM_001142568	exon11	c.G1324A	p.A442T	GATCCCGCAGCAT	.	PASS	Atlas-SNP
TBC1D15	64786	hgsc.bcm.edu	37	12	72312268	72312268	+	Silent	SNP	G	G	A	rs11178985	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	66	121	0	0.481752	0	G|0.829;A|0.171	0.171	strong	.	TBC1D15	99	.	NM_022771	exon15	c.G1590A	p.R530R	CTTCAGGTGGCTT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115769	168115769	+	Missense_Mutation	SNP	G	G	C	rs16853344	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	37	121	0	0.544118	0	G|0.841;C|0.159	0.159	strong	.	XIRP2	914	.	NM_001199143	exon11	c.G2812C	p.E938Q	AGCCATGAATGTA	.	PASS	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	37	3	69299233	69299233	+	Missense_Mutation	SNP	C	C	G	rs4361282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	49	79	0	0.515789	0	C|0.742;G|0.258	0.258	strong	.	FRMD4B	90	.	NM_015123	exon6	c.G519C	p.E173D	TTCGCTCTCTACT	.	PASS	Atlas-SNP
ATR	545	hgsc.bcm.edu	37	3	142281612	142281612	+	Missense_Mutation	SNP	A	A	G	rs2227928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	42	66	1	0.488372	0.0151515	A|0.361;G|0.639	0.639	strong	ATR,NS,carcinoma,0,1	ATR	285	1	NM_001184	exon4	c.T632C	p.M211T	AGAACCATTAATA	.	scavenged	Atlas-SNP
DEFB127	140850	hgsc.bcm.edu	37	20	139456	139456	+	Missense_Mutation	SNP	G	G	A	rs12624954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	71	157	0	0.452229	0	G|0.719;A|0.281	0.281	strong	DEFB127,NS,carcinoma,-1,1	DEFB127	15	1	NM_139074	exon2	c.G91A	p.G31R	GTACAAGGACATT	.	PASS	Atlas-SNP
LRFN5	145581	hgsc.bcm.edu	37	14	42360633	42360633	+	Silent	SNP	T	T	C	rs6572117	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	163	216	1	0.993902	0.00462963	T|0.301;C|0.699	0.699	strong	.	LRFN5	269	.	NM_152447	exon4	c.T1566C	p.S522S	GCAGTCTCAGTTT	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3788260	3788260	+	Silent	SNP	G	G	A	rs242016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	28	86	0	0.378378	0	G|0.885;A|0.115	0.115	strong	.	EFCAB4B	100	.	NM_001144958	exon6	c.C345T	p.H115H	GAAGAAGTGACCT	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3647692	3647692	+	Missense_Mutation	SNP	A	A	C	rs74319927	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	42	62	0	0.608696	0	A|0.941;C|0.059	0.059	strong	.	SLX4	173	.	NM_032444	exon7	c.T1371G	p.N457K	ACTTTTATTCTCT	.	PASS	Atlas-SNP
ZCCHC7	84186	hgsc.bcm.edu	37	9	37305550	37305550	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	3	109	0	0.0275229	0	.	.	none	ZCCHC7,NS,carcinoma,0,1	ZCCHC7	56	1	NM_032226	exon5	c.C790G	p.R264G	GTTCGTCGCTGCT	.	scavenged	Atlas-SNP
GFPT2	9945	hgsc.bcm.edu	37	5	179740827	179740827	+	Missense_Mutation	SNP	T	T	C	rs2303007	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	33	20	0	0.970588	0	T|0.789;C|0.211	0.211	strong	GFPT2,NS,carcinoma,0,1	GFPT2	74	1	NM_005110	exon14	c.A1411G	p.I471V	CGCCGATCTCCGG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47836216	47836216	+	Silent	SNP	A	A	G	rs60444527	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	56	133	0	0.424242	0	A|0.818;G|0.182	0.182	strong	.	PCNT	283	.	NM_006031	exon30	c.A6384G	p.T2128T	AGACACATGTGAT	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	37	15	24923129	24923129	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	271	110	280	0	0.405904	0	.	.	none	.	.	.	.	NM_018958	exon1	c.T2115C	p.P705P	TCCTCCTTCCAAG	.	PASS	Atlas-SNP
RPS15	6209	hgsc.bcm.edu	37	19	1440068	1440068	+	Missense_Mutation	SNP	G	G	C	rs61746286	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	3	27	0	0.075	0	G|0.442;C|0.558	0.558	strong	RPS15,extremity,malignant_melanoma,0,1	RPS15	11	1	NM_001018	exon3	c.G140C	p.R47P	TGAACCGGGGCCT	.	scavenged	Atlas-SNP
MTIF3	219402	hgsc.bcm.edu	37	13	28009851	28009851	+	Silent	SNP	G	G	A	rs7669	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	71	150	0	0.493056	0	A|0.137;C|0.000;G|0.863	0.137	strong	.	MTIF3	21	.	NM_001166263	exon6	c.C798T	p.D266D	TCCATGGTCTTTG	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74003846	74003846	+	Missense_Mutation	SNP	G	G	A	rs7342883	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	40	94	0	0.470588	0	G|0.803;A|0.197	0.197	strong	.	EVPL	155	.	NM_001988	exon22	c.C5440T	p.P1814S	AGCTGGGAGAGAA	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48318242	48318242	+	Missense_Mutation	SNP	G	G	A	rs79834369	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	54	108	0	0.54	0	G|0.996;A|0.004	0.004	strong	.	ABCA13	1192	.	NM_152701	exon18	c.G7451A	p.R2484K	TTTCAAGAGCAAG	.	PASS	Atlas-SNP
RAD17	5884	hgsc.bcm.edu	37	5	68695940	68695940	+	Missense_Mutation	SNP	T	T	G	rs1045051	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	384	384	253	0	1	0	T|0.763;G|0.237	0.237	strong	.	RAD17	49	.	NM_133339	exon14	c.T1670G	p.L557R	TATGCCTCCAAAC	.	PASS	Atlas-SNP
HSPA1L	3305	hgsc.bcm.edu	37	6	31777946	31777946	+	Missense_Mutation	SNP	C	C	T	rs2075800	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	97	189	0	0.470874	0	C|0.741;T|0.259	0.259	strong	HSPA1L,NS,carcinoma,+2,1	HSPA1L	185	1	NM_005527	exon2	c.G1804A	p.E602K	TCTGCTCCAATTC	.	PASS	Atlas-SNP
ALCAM	214	hgsc.bcm.edu	37	3	105266274	105266274	+	Silent	SNP	T	T	C	rs16851279	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	72	216	0	0.413793	0	T|0.886;C|0.114	0.114	strong	.	ALCAM	71	.	NM_001627	exon11	c.T1281C	p.S427S	TCCCAGTGGACTA	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	37	20	10620275	10620275	+	Silent	SNP	G	G	A	rs1051421	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	353	179	338	0	0.507082	0	G|0.785;A|0.215	0.215	strong	JAG1_ENST00000254958,NS,carcinoma,0,1	JAG1	213	1	NM_000214	exon26	c.C3528T	p.Y1176Y	CAGCGTGTACGCC	.	PASS	Atlas-SNP
PIGZ	80235	hgsc.bcm.edu	37	3	196675397	196675397	+	Missense_Mutation	SNP	G	G	A	rs144088027	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	44	47	0	0.586667	0	G|0.997;A|0.003	0.003	strong	.	PIGZ	34	.	NM_025163	exon3	c.C371T	p.A124V	AGCAGCGCATAGC	.	PASS	Atlas-SNP
WDR4	10785	hgsc.bcm.edu	37	21	44270229	44270229	+	Missense_Mutation	SNP	C	C	T	rs6586250	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	34	57	0	0.472222	0	C|0.748;T|0.252	0.252	strong	.	WDR4	35	.	NM_018669	exon11	c.G1169A	p.R390Q	GGACTCCGGCGCC	.	PASS	Atlas-SNP
DZANK1	55184	hgsc.bcm.edu	37	20	18393312	18393312	+	Silent	SNP	C	C	G	rs6075337	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	169	175	0	1	0	C|0.389;G|0.611	0.611	strong	.	DZANK1	65	.	NM_001099407	exon13	c.G1410C	p.L470L	GGCTGTCAGGAGG	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50885658	50885658	+	Silent	SNP	C	C	T	rs371139013		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	80	135	0	0.449438	0	.	.	weak	.	SBF1	211	.	NM_002972	exon41	c.G5595A	p.T1865T	GCGACGCGTTGTC	.	PASS	Atlas-SNP
C12orf71	728858	hgsc.bcm.edu	37	12	27234999	27234999	+	Missense_Mutation	SNP	T	T	C	rs708167	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	278	147	207	0	0.528777	0	T|0.788;C|0.212	0.212	strong	.	C12orf71	20	.	NM_001080406	exon1	c.A418G	p.I140V	GAAATATCTGAAA	.	PASS	Atlas-SNP
RD3	343035	hgsc.bcm.edu	37	1	211654619	211654619	+	Missense_Mutation	SNP	G	G	A	rs34049451	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	94	154	0	0.508108	0	G|0.990;A|0.010	0.010	strong	.	RD3	26	.	NM_183059	exon2	c.C139T	p.R47C	TGCTGCGCTCCCG	.	PASS	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139749799	139749799	+	Missense_Mutation	SNP	G	G	T	rs10111520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	47	118	0	0.415929	0	G|0.948;T|0.052	0.052	strong	.	COL22A1	390	.	NM_152888	exon23	c.C2107A	p.P703T	CAGGTGGTCCCAT	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75969335	75969335	+	Missense_Mutation	SNP	C	C	T	rs77237106	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	35	56	0	0.583333	0	C|0.919;T|0.081	0.081	strong	.	CSPG4	175	.	NM_001897	exon10	c.G5525A	p.R1842Q	GTGAGCCGGAGTG	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47538960	47538960	+	Missense_Mutation	SNP	G	G	A	rs2839110	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	227	166	1	0.982684	0.0060241	G|0.256;A|0.744	0.744	strong	.	COL6A2	351	.	NM_058175	exon14	c.G1196A	p.S399N	GCAACAGTGGAGC	.	PASS	Atlas-SNP
DDX31	64794	hgsc.bcm.edu	37	9	135521303	135521303	+	Silent	SNP	C	C	T	rs306537	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	37	58	0	0.569231	0	C|0.927;T|0.073	0.073	strong	.	DDX31	76	.	NM_022779	exon13	c.G1674A	p.L558L	GCCATGCAGCCGT	.	PASS	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806812	33806812	+	Silent	SNP	C	C	T	rs12451876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	71	144	1	0.510791	0.00694444	A|0.000;C|0.891;T|0.109	0.109	strong	SLFN12L_ENST00000449046,NS,carcinoma,0,3	SLFN12L	140	3	NM_001195790	exon2	c.G417A	p.T139T	GCTCAACGTGGCA	.	scavenged	Atlas-SNP
EPC1	80314	hgsc.bcm.edu	37	10	32580205	32580205	+	Missense_Mutation	SNP	C	C	T	rs72789797	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	57	83	0	0.612903	0	C|0.956;T|0.044	0.044	strong	.	EPC1	74	.	NM_025209	exon6	c.G861A	p.M287I	CTGTGCCATAACC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134659626	134659626	+	Missense_Mutation	SNP	A	A	G	rs10870341	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	95	0	0.435644	0	A|0.840;G|0.160	0.160	strong	.	TTC40	100	.	NM_001200049	exon44	c.T6373C	p.C2125R	CTTGGCACCGGAG	.	PASS	Atlas-SNP
USP6NL	9712	hgsc.bcm.edu	37	10	11505175	11505175	+	Silent	SNP	A	A	G	rs3740204	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	15	39	0	0.46875	0	A|0.502;G|0.498	0.498	strong	.	USP6NL	57	.	NM_001080491	exon14	c.T1803C	p.P601P	CGGGCTAGGAGGG	.	PASS	Atlas-SNP
CBX2	84733	hgsc.bcm.edu	37	17	77758691	77758691	+	Silent	SNP	G	G	A	rs3751957	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	31	63	0	0.462687	0	G|0.630;A|0.370	0.370	strong	CBX2,mucosal,malignant_melanoma,+2,1	CBX2	50	1	NM_005189	exon5	c.G1449A	p.P483P	GAACCCGTCAGTG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168106085	168106085	+	Missense_Mutation	SNP	G	G	A	rs16853328	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	55	120	0	0.514019	0	G|0.837;A|0.163	0.163	strong	.	XIRP2	914	.	NM_152381	exon9	c.G8183A	p.S2728N	ACCACAGCTATGA	.	PASS	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	99690450	99690450	+	Silent	SNP	T	T	C	rs12222337	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	18	107	0	0.140625	0	C|0.101;T|0.899	0.101	strong	.	CNTN5	324	.	NM_001243270	exon3	c.T231C	p.Y77Y	TTATTATTCCCCC	.	PASS	Atlas-SNP
BCAM	4059	hgsc.bcm.edu	37	19	45315445	45315445	+	Missense_Mutation	SNP	G	G	A	rs28399653	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	20	21	0	0.465116	0	G|0.977;A|0.023	0.023	strong	.	BCAM	53	.	NM_001013257	exon3	c.G230A	p.R77H	GCCCCCGCCTAGC	.	PASS	Atlas-SNP
WDR72	256764	hgsc.bcm.edu	37	15	54003091	54003091	+	Missense_Mutation	SNP	G	G	A	rs551225	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	34	68	0	0.4	0	G|0.619;A|0.381	0.381	strong	.	WDR72	177	.	NM_182758	exon9	c.C917T	p.P306L	AAATGAGGATAAA	.	PASS	Atlas-SNP
CASD1	64921	hgsc.bcm.edu	37	7	94173803	94173803	+	Silent	SNP	T	T	C	rs13242090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	112	233	0	0.504505	0	T|0.913;C|0.087	0.087	strong	.	CASD1	70	.	NM_022900	exon11	c.T1437C	p.F479F	ATACTTTTGGATA	.	PASS	Atlas-SNP
TAF10	6881	hgsc.bcm.edu	37	11	6632450	6632450	+	Silent	SNP	C	C	T	rs12451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	92	150	0	0.605263	0	C|0.817;T|0.183	0.183	strong	.	TAF10	9	.	NM_006284	exon4	c.G537A	p.T179T	GGAGGCCGTGCCC	.	PASS	Atlas-SNP
NPBWR2	2832	hgsc.bcm.edu	37	20	62737537	62737537	+	Silent	SNP	C	C	A	rs4809400	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	50	90	0	0.568182	0	C|0.908;A|0.092	0.092	strong	.	NPBWR2	36	.	NM_005286	exon1	c.G648T	p.T216T	GACCAACGTGTAG	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56392920	56392920	+	Silent	SNP	C	C	T	rs12975929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	24	57	0	0.421053	0	C|0.817;T|0.183	0.183	strong	.	NLRP4	331	.	NM_134444	exon10	c.C2952T	p.D984D	CACAGACGACTGT	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52843581	52843581	+	Silent	SNP	A	A	G	rs382894		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	244	27	181	0	0.110656	0	A|1.000;|0.000	.	weak	KRT6B,NS,carcinoma,0,5	KRT6B	90	5	NM_005555	exon4	c.T873C	p.L291L	ATCTGTAAGAGTG	.	scavenged	Atlas-SNP
CHD9	80205	hgsc.bcm.edu	37	16	53326860	53326860	+	Silent	SNP	G	G	A	rs2287078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	70	147	0	0.48951	0	G|0.692;A|0.308	0.308	strong	CHD9,NS,carcinoma,0,1	CHD9	203	1	NM_025134	exon29	c.G5406A	p.Q1802Q	AATTCAGCAGATA	.	PASS	Atlas-SNP
COG1	9382	hgsc.bcm.edu	37	17	71197439	71197439	+	Silent	SNP	C	C	T	rs1551036	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	48	100	0	0.539326	0	C|0.867;N|0.001	.	strong	.	COG1	46	.	NM_018714	exon7	c.C1473T	p.S491S	GGTCAGCGTGGCA	.	PASS	Atlas-SNP
RPS6KC1	26750	hgsc.bcm.edu	37	1	213414948	213414948	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	4	100	0	0.0430108	0	.	.	none	.	RPS6KC1	114	.	NM_012424	exon11	c.C2129T	p.P710L	TGGGACCTACTAA	.	PASS	Atlas-SNP
CUEDC1	404093	hgsc.bcm.edu	37	17	55951037	55951037	+	Missense_Mutation	SNP	C	C	T	rs17762338	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	63	93	0	0.529412	0	C|0.897;T|0.103	0.103	strong	.	CUEDC1	37	.	NM_001271875	exon4	c.G506A	p.R169H	CGATAGCGTCTCT	.	PASS	Atlas-SNP
PUS7L	83448	hgsc.bcm.edu	37	12	44130330	44130330	+	Missense_Mutation	SNP	G	G	A	rs116948464	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	74	142	0	0.440476	0	G|0.996;A|0.004	0.004	strong	PUS7L,NS,carcinoma,+1,1	PUS7L	73	1	NM_001098614	exon7	c.C1579T	p.R527C	ATATGCGCATGGA	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	37	19	6472930	6472930	+	Silent	SNP	C	C	A	rs74800876	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	23	54	0	0.418182	0	C|0.984;A|0.016	0.016	strong	DENND1C_ENST00000381480,NS,haematopoietic_neoplasm,0,2	DENND1C	93	2	NM_024898	exon15	c.G1128T	p.R376R	AGCCCGCCGGTGG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134694526	134694526	+	Missense_Mutation	SNP	A	A	G	rs148582169	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	36	58	0	0.545455	0	A|0.993;G|0.007	0.007	strong	.	TTC40	100	.	NM_001200049	exon28	c.T3638C	p.M1213T	CACTCCATCTCAG	.	PASS	Atlas-SNP
SLC46A2	57864	hgsc.bcm.edu	37	9	115652836	115652836	+	Silent	SNP	G	G	A	rs3802492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	14	40	0	0.411765	0	G|0.682;A|0.318	0.318	strong	.	SLC46A2	30	.	NM_033051	exon1	c.C126T	p.L42L	CACCACGAGGAGT	.	PASS	Atlas-SNP
ASB18	401036	hgsc.bcm.edu	37	2	237103697	237103697	+	Missense_Mutation	SNP	G	G	T	rs10177957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	55	113	0	0.491071	0	G|0.894;T|0.106	0.106	strong	.	ASB18	34	.	NM_212556	exon6	c.C1219A	p.H407N	GCTTGTGCATCTG	.	PASS	Atlas-SNP
REPIN1	29803	hgsc.bcm.edu	37	7	150068371	150068371	+	Missense_Mutation	SNP	T	T	C	rs3735165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	57	65	0	0.982759	0	T|0.578;C|0.422	0.422	strong	REPIN1_ENST00000489432,NS,carcinoma,0,2	REPIN1	74	2	NM_001099695	exon3	c.T212C	p.L71P	TGGGCCTGGCCCA	.	PASS	Atlas-SNP
SP100	6672	hgsc.bcm.edu	37	2	231333763	231333763	+	Missense_Mutation	SNP	A	A	G	rs12724	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	41	97	0	0.401961	0	A|0.778;G|0.221;N|0.000;T|0.000	0.221	strong	.	SP100	167	.	NM_001206702	exon14	c.A1297G	p.M433V	GCTCCTATGACTT	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833145	82833145	+	Silent	SNP	G	G	A	rs2548541	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	81	101	0	1	0	G|0.316;A|0.684	0.684	strong	.	VCAN	498	.	NM_004385	exon8	c.G4323A	p.Q1441Q	TTCTCAGAATTTC	.	PASS	Atlas-SNP
KCNK12	56660	hgsc.bcm.edu	37	2	47797123	47797123	+	Silent	SNP	G	G	A	rs139772114	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	7	12	0	0.583333	0	G|0.979;A|0.021	0.021	strong	.	KCNK12	11	.	NM_022055	exon1	c.C348T	p.F116F	GCCGGGGAAGTCC	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274416	39274416	+	Missense_Mutation	SNP	C	C	T	rs408579		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	8	81	1	0.0740741	0.0123457	.	.	weak	KRTAP4-11,NS,carcinoma,0,11	KRTAP4-11	94	11	NM_033059	exon1	c.G152A	p.R51K	TGGGGCCTGCAGC	.	scavenged	Atlas-SNP
FOXF2	2295	hgsc.bcm.edu	37	6	1395043	1395043	+	Silent	SNP	T	T	C	rs2293783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	82	149	0	0.463277	0	T|0.783;C|0.217	0.217	strong	.	FOXF2	28	.	NM_001452	exon2	c.T1284C	p.Y428Y	GTATTATCACCAT	.	PASS	Atlas-SNP
TEX14	56155	hgsc.bcm.edu	37	17	56643109	56643109	+	Silent	SNP	A	A	G	rs34818467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	71	119	0	0.47973	0	A|0.851;G|0.149	0.149	strong	.	TEX14	343	.	NM_001201457	exon28	c.T4101C	p.N1367N	CTTACCATTTGCA	.	PASS	Atlas-SNP
PEAK1	0	hgsc.bcm.edu	37	15	77407114	77407114	+	Missense_Mutation	SNP	C	C	G	rs1867780	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	27	72	0	0.457627	0	C|0.750;G|0.250	0.250	strong	.	.	.	.	NM_024776	exon8	c.G4625C	p.S1542T	GTGGGGCTGGGCT	.	PASS	Atlas-SNP
KRT5	3852	hgsc.bcm.edu	37	12	52912906	52912906	+	Silent	SNP	G	G	T	rs641621	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	37	149	0	0.308333	0	T|0.177;G|0.823	0.177	strong	.	KRT5	88	.	NM_000424	exon2	c.C594A	p.T198T	CCACTTGGTGTCC	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3613904	3613904	+	Missense_Mutation	SNP	C	C	G	rs117213971	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	18	35	0	0.514286	0	C|0.956;G|0.044	0.044	strong	.	NLRC3	103	.	NM_178844	exon5	c.G1034C	p.S345T	GTCCTGCTGCGCC	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737329	248737329	+	Missense_Mutation	SNP	C	C	T	rs75095367	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	324	141	304	1	0.435185	0.00328947	C|0.816;T|0.184	0.184	strong	.	OR2T34	72	.	NM_001001821	exon1	c.G730A	p.A244T	AGGTGGCCAAGGC	.	PASS	Atlas-SNP
FAM208B	54906	hgsc.bcm.edu	37	10	5799613	5799613	+	Missense_Mutation	SNP	A	A	G	rs2275774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	95	200	0	0.527778	0	A|0.887;G|0.113	0.113	strong	.	.	.	.	NM_017782	exon17	c.A6863G	p.K2288R	ATGACAAGATACT	.	PASS	Atlas-SNP
SMOC1	64093	hgsc.bcm.edu	37	14	70477508	70477508	+	Silent	SNP	C	C	T	rs3825739	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	41	67	0	0.427083	0	C|0.825;T|0.175	0.175	strong	SMOC1,colon,carcinoma,+1,1	SMOC1	61	1	NM_001034852	exon8	c.C702T	p.A234A	GAGTGCCCTGGAA	.	PASS	Atlas-SNP
SLIT3	6586	hgsc.bcm.edu	37	5	168180081	168180081	+	Missense_Mutation	SNP	C	C	T	rs10036727	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	70	102	0	0.518519	0	C|0.423;N|0.000	.	strong	.	SLIT3	224	.	NM_001271946	exon18	c.G1852A	p.G618S	CACAGCCGATCAA	.	PASS	Atlas-SNP
C9orf50	375759	hgsc.bcm.edu	37	9	132377900	132377900	+	Missense_Mutation	SNP	C	C	T	rs918165	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	41	45	0	0.97619	0	C|0.491;T|0.509	0.509	strong	.	C9orf50	25	.	NM_199350	exon4	c.G743A	p.R248K	TTGAGCCTGGGGA	.	PASS	Atlas-SNP
IFI44	10561	hgsc.bcm.edu	37	1	79115905	79115905	+	Missense_Mutation	SNP	T	T	C	rs2070123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	77	164	0	0.546099	0	T|0.891;C|0.109	0.109	strong	IFI44,NS,carcinoma,-1,1	IFI44	55	1	NM_006417	exon2	c.T25C	p.W9R	TTGACATGGTTGC	.	PASS	Atlas-SNP
ZNF155	7711	hgsc.bcm.edu	37	19	44501518	44501518	+	Silent	SNP	G	G	A	rs446016	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	19	72	0	0.44186	0	G|0.668;A|0.332	0.332	strong	.	ZNF155	30	.	NM_001260488	exon6	c.G1542A	p.P514P	CCAGCCGAGAGAC	.	PASS	Atlas-SNP
IGLL1	3543	hgsc.bcm.edu	37	22	23915516	23915516	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	3	105	0	0.0241935	0	.	.	none	IGLL1,NS,carcinoma,0,1	IGLL1	27	1	NM_020070	exon3	c.C579T	p.S193S	CTGGCAGCTGTAG	.	scavenged	Atlas-SNP
TRMT6	51605	hgsc.bcm.edu	37	20	5924828	5924828	+	Silent	SNP	A	A	G	rs35861347	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	33	53	0	0.464789	0	A|0.958;G|0.042	0.042	strong	.	TRMT6	28	.	NM_015939	exon4	c.T438C	p.Y146Y	TTTAATATATTTA	.	PASS	Atlas-SNP
CPOX	1371	hgsc.bcm.edu	37	3	98307696	98307696	+	Missense_Mutation	SNP	T	T	G	rs1131857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	46	124	0	0.422018	0	T|0.760;G|0.235	0.235	strong	CPOX,NS,carcinoma,0,1	CPOX	34	1	NM_000097	exon4	c.A814C	p.N272H	GCTTGTTGCCTAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910716	29910716	+	Missense_Mutation	SNP	C	C	G	rs1059455	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	88	154	0	0.854369	0	G|1.000	.	weak	.	HLA-A	89	.	NM_001242758	exon2	c.C256G	p.Q86E	TGGGACCAGGAGA	.	PASS	Atlas-SNP
RPE65	6121	hgsc.bcm.edu	37	1	68903942	68903942	+	Silent	SNP	C	C	T	rs12145904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	18	87	0	0.272727	0	C|0.815;T|0.185	0.185	strong	RPE65,NS,carcinoma,-2,1	RPE65	87	1	NM_000329	exon10	c.G1056A	p.E352E	TTTCACCTCTTCC	.	PASS	Atlas-SNP
TEDDM1	127670	hgsc.bcm.edu	37	1	182369233	182369233	+	Missense_Mutation	SNP	A	A	G	rs6674281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	59	108	0	0.513043	0	A|0.364;G|0.636	0.636	strong	.	TEDDM1	32	.	NM_172000	exon1	c.T388C	p.Y130H	GAGAATAAACGTG	.	PASS	Atlas-SNP
DGKI	9162	hgsc.bcm.edu	37	7	137263068	137263068	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	49	120	0	0.426087	0	.	.	none	DGKI_ENST00000288490,NS,carcinoma,-1,2	DGKI	335	2	NM_004717	exon16	c.C1646A	p.A549E	GGATTTGCTTCTG	.	PASS	Atlas-SNP
HTR1F	3355	hgsc.bcm.edu	37	3	88040545	88040545	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	3	92	1	0.0243902	0.0108696	.	.	none	HTR1F,NS,carcinoma,-2,1	HTR1F	66	1	NM_000866	exon2	c.C646A	p.Q216K	AAGAGACAAGCAA	.	scavenged	Atlas-SNP
ZNF154	7710	hgsc.bcm.edu	37	19	58213743	58213743	+	Nonsense_Mutation	SNP	G	G	A	rs74939505	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	101	169	0	0.487923	0	G|0.993;A|0.007	0.007	strong	.	ZNF154	34	.	NM_001085384	exon3	c.C574T	p.R192X	ACTCTCGACATTC	.	PASS	Atlas-SNP
PRSS53	339105	hgsc.bcm.edu	37	16	31095999	31095999	+	Silent	SNP	G	G	A	rs138417092	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	65	177	1	0.367232	0.00564972	G|0.988;A|0.012	0.012	strong	PRSS53,NS,haematopoietic_neoplasm,0,1	PRSS53	29	1	NM_001039503	exon9	c.C1305T	p.P435P	GGTCACGGGCACT	.	scavenged	Atlas-SNP
PTK2B	2185	hgsc.bcm.edu	37	8	27255146	27255146	+	Silent	SNP	G	G	A	rs1045511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	54	129	0	0.556701	0	G|0.645;A|0.355	0.355	strong	.	PTK2B	304	.	NM_173174	exon7	c.G45A	p.T15T	GGGCACGTTACGC	.	PASS	Atlas-SNP
ACER1	125981	hgsc.bcm.edu	37	19	6333476	6333476	+	Silent	SNP	G	G	A	rs16993553	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	52	46	0	0.58427	0	G|0.938;A|0.062	0.062	strong	ACER1,NS,carcinoma,-2,1	ACER1	38	1	NM_133492	exon1	c.C87T	p.Y29Y	CGTGTTGTAGAAC	.	PASS	Atlas-SNP
IFNB1	3456	hgsc.bcm.edu	37	9	21077716	21077716	+	Silent	SNP	G	G	A	rs1051922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	61	126	0	0.516949	0	G|0.656;N|0.000	.	strong	.	IFNB1	33	.	NM_002176	exon1	c.C153T	p.Y51Y	GAGGCAGTATTCA	.	PASS	Atlas-SNP
FAM162B	221303	hgsc.bcm.edu	37	6	117083182	117083182	+	Silent	SNP	G	G	A	rs41305290	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	15	182	0	0.121951	0	G|0.990;A|0.010	0.010	strong	.	FAM162B	19	.	NM_001085480	exon3	c.C348T	p.L116L	AATTGTGAGTCCA	.	PASS	Atlas-SNP
DGCR6L	85359	hgsc.bcm.edu	37	22	20302276	20302276	+	Missense_Mutation	SNP	A	A	T	rs1056804	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	452	230	473	1	0.50885	0.00211416	A|0.975;T|0.025	0.025	strong	.	DGCR6L	9	.	NM_033257	exon5	c.T585A	p.N195K	GGCTGCATTCCCT	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149511985	149511985	+	Missense_Mutation	SNP	A	A	G	rs10952230	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	88	0	1	0	A|0.139;G|0.861	0.861	strong	.	.	.	.	NM_198455	exon74	c.A10535G	p.N3512S	CTGGGAACCACAC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195516305	195516305	+	Missense_Mutation	SNP	C	C	T	rs3749331	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	62	141	0	0.48062	0	C|0.881;T|0.119	0.119	strong	.	MUC4	1505	.	NM_018406	exon2	c.G2146A	p.A716T	TGGGTGCTGCCTG	.	PASS	Atlas-SNP
SLC7A14	57709	hgsc.bcm.edu	37	3	170198898	170198898	+	Silent	SNP	C	C	T	rs3732449	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	30	79	0	0.410959	0	C|0.688;T|0.312	0.312	strong	.	SLC7A14	110	.	NM_020949	exon7	c.G1173A	p.S391S	GAACCCCGACACG	.	PASS	Atlas-SNP
PCDHGA3	56112	hgsc.bcm.edu	37	5	140725828	140725828	+	Missense_Mutation	SNP	C	C	T	rs7736541	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	161	120	1	1	0.00833333	C|0.492;T|0.508	0.508	strong	.	PCDHGA3	246	.	NM_032011	exon1	c.C2228T	p.A743V	TGGGCGCGGACGG	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	37	1	179414105	179414105	+	Missense_Mutation	SNP	A	A	C	rs11577579	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	25	56	0	0.454545	0	A|0.748;C|0.252	0.252	strong	AXDND1,NS,carcinoma,0,1	AXDND1	142	1	NM_144696	exon16	c.A1564C	p.I522L	CTTTAGATCCTGA	.	PASS	Atlas-SNP
DOPEY2	9980	hgsc.bcm.edu	37	21	37617724	37617724	+	Missense_Mutation	SNP	C	C	A	rs3746866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	30	53	0	0.394737	0	C|0.859;A|0.141	0.141	strong	DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	NM_005128	exon19	c.C3446A	p.P1149H	CCATCCCCATGGG	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128488734	128488734	+	Missense_Mutation	SNP	G	G	A	rs2291569	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	18	56	0	0.45	0	G|0.921;A|0.079	0.079	strong	.	FLNC	339	.	NM_001127487	exon27	c.G4700A	p.R1567Q	ACGCACGGGACGC	.	PASS	Atlas-SNP
SCIN	85477	hgsc.bcm.edu	37	7	12610451	12610451	+	Silent	SNP	G	G	A	rs76096341	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	62	116	0	0.446043	0	G|0.970;A|0.030	0.030	strong	.	SCIN	105	.	NM_001112706	exon1	c.G39A	p.A13A	CCGGGCGGGCAAG	.	PASS	Atlas-SNP
ACSS3	79611	hgsc.bcm.edu	37	12	81627238	81627238	+	Silent	SNP	C	C	T	rs1921038	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	49	128	0	0.371212	0	C|0.811;T|0.189	0.189	strong	.	ACSS3	118	.	NM_024560	exon13	c.C1707T	p.G569G	TGCAGGCGCCATT	.	PASS	Atlas-SNP
MUC7	4589	hgsc.bcm.edu	37	4	71346978	71346978	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	359	4	314	4	0.0111421	0.0127389	.	.	none	MUC7,NS,carcinoma,0,5	MUC7	91	5	NM_001145007	exon4	c.T517C	p.S173P	ACACCTTCTGCAA	.	scavenged	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52845801	52845801	+	Missense_Mutation	SNP	T	T	C	rs61741601	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	68	151	0	0.379888	0	T|0.417;C|0.583	0.583	strong	.	KRT6B	90	.	NM_005555	exon1	c.A62G	p.N21S	GCTGAGTTGGCAC	.	PASS	Atlas-SNP
PRG3	10394	hgsc.bcm.edu	37	11	57146202	57146202	+	Silent	SNP	G	G	A	rs1940145	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	52	85	0	0.641975	0	G|0.966;A|0.034	0.034	strong	.	PRG3	35	.	NM_006093	exon4	c.C459T	p.S153S	GACTGTGCTAGTG	.	PASS	Atlas-SNP
UBQLN1	29979	hgsc.bcm.edu	37	9	86278913	86278913	+	Silent	SNP	C	C	T	rs2781004	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	77	140	0	0.49359	0	C|0.873;T|0.127	0.127	strong	.	UBQLN1	49	.	NM_013438	exon10	c.G1494A	p.S498S	AGTTCCCGAAGAG	.	PASS	Atlas-SNP
FAM109B	150368	hgsc.bcm.edu	37	22	42473860	42473860	+	Missense_Mutation	SNP	C	C	G	rs1807493	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	26	68	0	0.52	0	C|0.837;G|0.163	0.163	strong	.	FAM109B	22	.	NM_001002034	exon3	c.C563G	p.A188G	AAGAAGCGGGCAG	.	PASS	Atlas-SNP
BRSK1	84446	hgsc.bcm.edu	37	19	55817694	55817694	+	Silent	SNP	C	C	T	rs200320831		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	35	56	0	0.492958	0	C|0.999;T|0.001	0.001	weak	BRSK1_ENST00000309383,NS,carcinoma,0,2	BRSK1	192	2	NM_032430	exon17	c.C1965T	p.S655S	CCCCTCCGTCTTC	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5353253	5353253	+	Silent	SNP	G	G	T	rs140781391	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	59	62	0	0.536364	0	G|0.907;T|0.093	0.093	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7269A	p.A2423A	TGCTGGGGCCAGG	.	PASS	Atlas-SNP
GABBR1	2550	hgsc.bcm.edu	37	6	29581113	29581113	+	Silent	SNP	A	A	G	rs17854216	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	48	122	0	0.45283	0	A|0.900;G|0.100	0.100	strong	.	GABBR1	95	.	NM_001470	exon12	c.T1473C	p.S491S	CACACCAGAACGG	.	PASS	Atlas-SNP
KRT35	3886	hgsc.bcm.edu	37	17	39637244	39637244	+	Missense_Mutation	SNP	A	A	G	rs743686	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	31	52	0	0.596154	0	A|0.450;G|0.549	0.549	strong	KRT35,colon,carcinoma,+1,1	KRT35	58	1	NM_002280	exon1	c.T106C	p.S36P	TGCAAGAGCTGCT	.	PASS	Atlas-SNP
GGNBP2	79893	hgsc.bcm.edu	37	17	34942595	34942595	+	Silent	SNP	G	G	A	rs1106908	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	29	53	1	0.508772	0.0188679	G|0.613;A|0.387	0.387	strong	GGNBP2,NS,carcinoma,0,1	GGNBP2	72	1	NM_024835	exon12	c.G1608A	p.K536K	GAAGAAGAAGAAA	.	scavenged	Atlas-SNP
MRPL44	65080	hgsc.bcm.edu	37	2	224824617	224824617	+	Silent	SNP	A	A	G	rs11546405	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	91	126	0	0.590909	0	A|0.912;G|0.088	0.088	strong	.	MRPL44	31	.	NM_022915	exon2	c.A546G	p.E182E	GAGTGAAGAATTC	.	PASS	Atlas-SNP
OR11H6	122748	hgsc.bcm.edu	37	14	20692188	20692188	+	Missense_Mutation	SNP	T	T	C	rs12891553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	42	105	0	0.446809	0	T|0.554;C|0.446	0.446	strong	.	OR11H6	60	.	NM_001004480	exon1	c.T320C	p.I107T	CTGAGATTAAAAC	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	37	15	43767774	43767774	+	Missense_Mutation	SNP	G	G	C	rs560191	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	40	74	0	0.540541	0	G|0.501;C|0.499	0.499	strong	.	TP53BP1	157	.	NM_001141980	exon9	c.C1074G	p.D358E	AAGACTGTCCTGA	.	PASS	Atlas-SNP
NDFIP2	54602	hgsc.bcm.edu	37	13	80095030	80095030	+	Missense_Mutation	SNP	C	C	T	rs11549502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	65	137	0	0.496183	0	C|0.910;G|0.000;T|0.090	0.090	strong	NDFIP2,NS,carcinoma,-1,1	NDFIP2	23	1	NM_019080	exon2	c.C407T	p.A136V	AGGCTGCGTCTTC	.	PASS	Atlas-SNP
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	33	102	0	0.464789	0	G|0.691;T|0.309	0.309	strong	.	DNAJC25	20	.	NM_001015882	exon3	c.G702T	p.G234G	AAAGGGGGGCTAT	.	PASS	Atlas-SNP
OR6V1	346517	hgsc.bcm.edu	37	7	142749919	142749919	+	Missense_Mutation	SNP	G	G	A	rs28563993	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	67	120	0	0.54918	0	G|0.941;A|0.059	0.059	strong	OR6V1_ENST00000418316,NS,carcinoma,-1,2	OR6V1	77	2	NM_001001667	exon1	c.G482A	p.R161Q	TCTCCCGAGCTCA	.	PASS	Atlas-SNP
CYP4F3	4051	hgsc.bcm.edu	37	19	15763721	15763721	+	Silent	SNP	G	G	A	rs1805042	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	47	114	0	0.439252	0	G|0.523;A|0.477	0.477	strong	CYP4F3,NS,carcinoma,0,1	CYP4F3	69	1	NM_001199209	exon9	c.G1074A	p.V358V	GGAGGTGCAAGAG	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079371	31079371	+	Silent	SNP	C	C	G	rs2233983	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	63	110	0	0.443662	0	C|0.932;G|0.068	0.068	strong	.	C6orf15	29	.	NM_014070	exon2	c.G765C	p.R255R	TGGATACCGATTA	.	PASS	Atlas-SNP
PRB3	5544	hgsc.bcm.edu	37	12	11420563	11420563	+	Missense_Mutation	SNP	G	G	T	rs200902635	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	2	133	1	0.0145985	0.0075188	.	.	weak	PRB3_ENST00000538488,NS,carcinoma,0,1	PRB3	84	1	NM_006249	exon3	c.C620A	p.P207Q	GGGGGTGGTCCTT	.	scavenged	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	37	11	57982635	57982635	+	Missense_Mutation	SNP	G	G	A	rs143246332	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	287	138	269	1	0.480836	0.00371747	G|0.989;A|0.011	0.011	strong	OR1S1,NS,carcinoma,-1,1	OR1S1	139	1	NM_001004458	exon1	c.G419A	p.C140Y	CGATCTGCCACCC	.	PASS	Atlas-SNP
CTSB	1508	hgsc.bcm.edu	37	8	11710888	11710888	+	Missense_Mutation	SNP	G	G	C	rs12338	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	27	54	0	0.428571	0	G|0.625;C|0.375	0.375	strong	.	CTSB	24	.	NM_147780	exon4	c.C76G	p.L26V	CCGACAGGGGATG	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55259450	55259450	+	Silent	SNP	C	C	T	rs2229066	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	3	20	0	0.157895	0	C|0.986;T|0.014	0.014	strong	EGFR,NS,carcinoma,0,8	EGFR	20426	8	NM_005228	exon21	c.C2508T	p.R836R	GCACCGCGACCTG	.	scavenged	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444026	20444026	+	Missense_Mutation	SNP	T	T	G	rs3861513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	82	157	0	0.458101	0	T|0.767;G|0.233	0.233	strong	.	OR4K15	82	.	NM_001005486	exon1	c.T349G	p.S117A	ACTATTTCTTTTG	.	PASS	Atlas-SNP
CCDC57	284001	hgsc.bcm.edu	37	17	80159665	80159665	+	Silent	SNP	G	G	A	rs11653797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	99	137	0	0.52381	0	G|0.859;A|0.141	0.141	strong	.	CCDC57	102	.	NM_198082	exon2	c.C156T	p.C52C	CTGCAGGCACCGC	.	PASS	Atlas-SNP
SPATA17	128153	hgsc.bcm.edu	37	1	217915324	217915324	+	Silent	SNP	C	C	T	rs34347452	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	34	44	0	0.62963	0	C|0.870;T|0.130	0.130	strong	.	SPATA17	59	.	NM_138796	exon6	c.C403T	p.L135L	AAGGCACTGGAGG	.	PASS	Atlas-SNP
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441197	39441197	+	Silent	SNP	G	G	A	rs200983508	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	7	138	3	0.0448718	0.0217391	G|0.998;A|0.002	0.002	strong	APOBEC3F,NS,carcinoma,0,1	APOBEC3F	37	1	NM_145298	exon3	c.G423A	p.G141G	GGCAGGGGCCCGC	.	scavenged	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34724796	34724796	+	Missense_Mutation	SNP	T	T	A	rs3739879	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	94	229	1	0.456311	0.00436681	T|1.000;|0.000	.	weak	.	FAM205A	45	.	NM_001141917	exon4	c.A2441T	p.E814V	CTAGGCTCCATCT	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171240249	171240249	+	Silent	SNP	C	C	T	rs11675394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	44	96	0	0.415094	0	C|0.732;T|0.268	0.268	strong	MYO3B_ENST00000408978,rectum,carcinoma,0,6	MYO3B	320	6	NM_001083615	exon12	c.C1215T	p.R405R	GAAACGCGCCTCC	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	37	4	190876268	190876268	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	278	4	247	2	0.0143885	0.00809717	.	.	none	FRG1,trunk,malignant_melanoma,-1,1	FRG1	76	1	NM_004477	exon5	c.A394G	p.I132V	GATGCAATTGGAC	.	scavenged	Atlas-SNP
CACNA1I	8911	hgsc.bcm.edu	37	22	40054948	40054948	+	Silent	SNP	T	T	C	rs5757761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	46	87	0	0.505495	0	T|0.245;C|0.755	0.755	strong	CACNA1I,NS,carcinoma,0,1	CACNA1I	264	1	NM_021096	exon12	c.T2157C	p.I719I	GGAGATTGTGGGG	.	PASS	Atlas-SNP
HK2	3099	hgsc.bcm.edu	37	2	75113789	75113789	+	Silent	SNP	C	C	G	rs2229627	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	29	56	0	0.432836	0	C|0.457;0|0.000	.	strong	HK2,colon,carcinoma,+1,1	HK2	85	1	NM_000189	exon15	c.C2208G	p.P736P	CAACCCCGGCAAG	.	PASS	Atlas-SNP
ACO1	48	hgsc.bcm.edu	37	9	32425910	32425910	+	Silent	SNP	A	A	G	rs3780473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	53	110	0	0.519608	0	G|0.346;N|0.000	0.346	strong	.	ACO1	149	.	NM_002197	exon11	c.A1263G	p.E421E	CACTGAATTCACC	.	PASS	Atlas-SNP
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238705	71238705	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	4	150	1	0.028169	0.00666667	.	.	none	KRTAP5-7,NS,carcinoma,0,3	KRTAP5-7	23	3	NM_001012503	exon1	c.G359A	p.C120Y	AGCCCTGCTGCTG	.	scavenged	Atlas-SNP
MICAL2	9645	hgsc.bcm.edu	37	11	12265542	12265542	+	Silent	SNP	A	A	G	rs2270511	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	97	188	0	0.507853	0	A|0.826;G|0.173	0.173	strong	.	MICAL2	114	.	NM_014632	exon21	c.A2667G	p.L889L	TAAACTACTCTCT	.	PASS	Atlas-SNP
LIPA	3988	hgsc.bcm.edu	37	10	91007360	91007360	+	Missense_Mutation	SNP	T	T	G	rs1051338	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	35	56	0	0.625	0	T|0.740;G|0.254	0.254	strong	.	LIPA	29	.	NM_000235	exon2	c.A46C	p.T16P	GCAGGGTCCAGAG	.	PASS	Atlas-SNP
CEP70	80321	hgsc.bcm.edu	37	3	138218994	138218994	+	Missense_Mutation	SNP	T	T	C	rs35340237	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	258	126	264	0	0.488372	0	T|0.869;C|0.131	0.131	strong	.	CEP70	51	.	NM_024491	exon16	c.A1610G	p.N537S	TGCTCATTCACAT	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15811023	15811023	+	Silent	SNP	C	C	T	rs1050163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	80	0	1	0	C|0.592;T|0.408	0.408	strong	.	MYH11	520	.	NM_001040114	exon39	c.G5499A	p.L1833L	CTCCTCCAGCTGT	.	PASS	Atlas-SNP
GABRB1	2560	hgsc.bcm.edu	37	4	47322219	47322219	+	Silent	SNP	C	C	A	rs6284	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	71	74	0	1	0	C|0.849;A|0.151	0.151	strong	.	GABRB1	107	.	NM_000812	exon5	c.C537A	p.I179I	GGAGATCGAAAGT	.	PASS	Atlas-SNP
INPP5A	3632	hgsc.bcm.edu	37	10	134459388	134459388	+	Missense_Mutation	SNP	A	A	G	rs1133400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	24	50	0	0.533333	0	A|0.804;G|0.196	0.196	strong	.	INPP5A	77	.	NM_005539	exon3	c.A134G	p.K45R	CACACAAGCCGCA	.	PASS	Atlas-SNP
EHMT1	79813	hgsc.bcm.edu	37	9	140611436	140611436	+	Silent	SNP	T	T	C	rs3812497	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	27	39	0	0.529412	0	T|0.785;C|0.215	0.215	strong	.	EHMT1	196	.	NM_001145527	exon3	c.T444C	p.P148P	GCTGCCTGGCCAT	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17270751	17270751	+	Silent	SNP	G	G	A	rs12025984	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	10	5	0	0.588235	0	G|0.762;A|0.238	0.238	strong	.	CROCC	185	.	NM_014675	exon14	c.G1965A	p.A655A	TGGCGCGCGGGTG	.	PASS	Atlas-SNP
CLEC7A	64581	hgsc.bcm.edu	37	12	10271087	10271087	+	Nonsense_Mutation	SNP	A	A	C	rs16910526	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	75	193	0	0.433526	0	A|0.950;C|0.050	0.050	strong	.	CLEC7A	55	.	NM_197947	exon6	c.T714G	p.Y238X	AATACTATATGAG	.	PASS	Atlas-SNP
SMPD3	55512	hgsc.bcm.edu	37	16	68398924	68398924	+	Silent	SNP	C	C	T	rs1868158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	83	68	0	1	0	C|0.368;T|0.632	0.632	strong	.	SMPD3	52	.	NM_018667	exon4	c.G1395A	p.P465P	ACCTTGCGGGGCA	.	PASS	Atlas-SNP
MAPK15	225689	hgsc.bcm.edu	37	8	144804000	144804000	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	22	75	0	0.318841	0	.	.	none	.	MAPK15	32	.	NM_139021	exon13	c.C1408T	p.R470W	CTGATCCGGGGTG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168103304	168103304	+	Missense_Mutation	SNP	G	G	A	rs16853309	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	73	161	0	0.470968	0	G|0.820;A|0.180	0.180	strong	.	XIRP2	914	.	NM_152381	exon9	c.G5402A	p.R1801H	TTGAACGTACTGT	.	PASS	Atlas-SNP
MAGEB10	139422	hgsc.bcm.edu	37	X	27839617	27839617	+	Missense_Mutation	SNP	G	G	A	rs12557898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	35	46	0	1	0	0|0.012;A|0.299	0.299	strong	.	MAGEB10	107	.	NM_182506	exon3	c.G194A	p.R65Q	GACTTCGGGAAGC	.	PASS	Atlas-SNP
TEX35	84066	hgsc.bcm.edu	37	1	178492447	178492447	+	Silent	SNP	T	T	A	rs7527160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	11	7	11	0	0.636364	0	T|0.409;A|0.591	0.591	strong	.	TEX35	15	.	NM_001170722	exon9	c.T621A	p.A207A	ATACGCTGCAGTG	.	PASS	Atlas-SNP
NRF1	4899	hgsc.bcm.edu	37	7	129297332	129297332	+	Silent	SNP	T	T	G	rs1882094	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	35	66	3	0.406977	0.0454545	T|0.531;G|0.469	0.469	strong	NRF1,NS,adenoma,0,1	NRF1	40	1	NM_005011	exon2	c.T141G	p.S47S	TTCTTCTCCCGAG	.	scavenged	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227886773	227886773	+	Missense_Mutation	SNP	A	A	G	rs3752895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	55	167	0	0.491071	0	A|0.523;G|0.477	0.477	strong	.	COL4A4	215	.	NM_000092	exon44	c.T4207C	p.S1403P	GTCCTGAGGGGCC	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449037	89449037	+	Missense_Mutation	SNP	C	C	A	rs200081893	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	486	23	473	0	0.0473251	0	C|0.997;A|0.003	0.003	weak	.	.	.	.	NM_001162536	exon3	c.G473T	p.G158V	GGACCCCCACTTC	.	PASS	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	37	6	3015790	3015790	+	Silent	SNP	A	A	G	rs1049115	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	29	72	0	0.414286	0	A|0.232;G|0.768	0.768	strong	.	NQO2	21	.	NM_000904	exon5	c.A330G	p.P110P	CGTGCCAGCCATC	.	PASS	Atlas-SNP
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107533175	107533175	+	Missense_Mutation	SNP	C	C	G	rs3739741	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	80	181	0	0.451977	0	C|0.851;G|0.149	0.149	strong	NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	NM_018376	exon4	c.C476G	p.A159G	GGCCAGCTCTGTG	.	PASS	Atlas-SNP
GPR153	387509	hgsc.bcm.edu	37	1	6314758	6314758	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	9	115	0	0.0782609	0	.	.	none	.	GPR153	44	.	NM_207370	exon2	c.C208T	p.R70W	GCCGCCGCAGCTG	.	PASS	Atlas-SNP
PTCH2	8643	hgsc.bcm.edu	37	1	45293518	45293518	+	Silent	SNP	A	A	G	rs7525308	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	33	70	0	0.478261	0	A|0.574;G|0.426	0.426	strong	.	PTCH2	96	.	NM_001166292	exon14	c.T2055C	p.A685A	TACCTTAGCATGT	.	PASS	Atlas-SNP
DUSP22	56940	hgsc.bcm.edu	37	6	311938	311938	+	Silent	SNP	C	C	T	rs11242786	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	292	91	231	0	0.311644	0	C|0.938;T|0.062	0.062	strong	DUSP22,right_upper_lobe,carcinoma,+2,1	DUSP22	55	1	NM_020185	exon3	c.C114T	p.H38H	TGTCCACGATAGT	.	PASS	Atlas-SNP
C12orf49	79794	hgsc.bcm.edu	37	12	117175608	117175608	+	Missense_Mutation	SNP	C	C	T	rs73220422	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	44	73	0	0.392857	0	C|0.983;T|0.017	0.017	strong	.	C12orf49	17	.	NM_024738	exon1	c.G98A	p.S33N	AAGGTGCTGCTGA	.	PASS	Atlas-SNP
FAM22G	441457	hgsc.bcm.edu	37	9	99700212	99700212	+	Missense_Mutation	SNP	C	C	T	rs202040012	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	40	87	0	0.434783	0	C|0.977;T|0.023	0.023	strong	.	FAM22G	66	.	NM_001045477	exon6	c.C1369T	p.P457S	CTTTCCCCAGATC	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140605069	140605069	+	Silent	SNP	C	C	T	rs145919831	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	12	17	0	0.8	0	C|0.998;T|0.002	0.002	strong	.	PCDHB14	132	.	NM_018934	exon1	c.C1992T	p.D664D	GGTGGACGGCTTC	.	PASS	Atlas-SNP
CD109	135228	hgsc.bcm.edu	37	6	74521947	74521947	+	Missense_Mutation	SNP	C	C	T	rs2917862	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	16	168	0	0.135593	0	C|0.593;T|0.407	0.407	strong	.	CD109	170	.	NM_133493	exon29	c.C3722T	p.T1241M	AGCCAACGGCAGT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9020154	9020154	+	Silent	SNP	A	A	G	rs11882881	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	74	143	0	0.532374	0	A|0.580;G|0.420	0.420	strong	.	MUC16	4315	.	NM_024690	exon21	c.T37341C	p.S12447S	CTTCTCAGACCTG	.	PASS	Atlas-SNP
FAM160A2	84067	hgsc.bcm.edu	37	11	6238960	6238960	+	Missense_Mutation	SNP	C	C	A	rs3750943	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	45	74	0	0.505618	0	C|0.853;A|0.147	0.147	strong	.	FAM160A2	100	.	NM_032127	exon9	c.G1898T	p.R633L	CCAGCCCGCCCCC	.	PASS	Atlas-SNP
CPM	1368	hgsc.bcm.edu	37	12	69252715	69252715	+	Silent	SNP	A	A	G	rs1143653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	28	36	0	0.482759	0	T|0.153;G|0.175;C|0.041;A|0.631	0.175	strong	.	CPM	30	.	NM_001005502	exon8	c.T1077C	p.S359S	TATATAAGACCCA	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51524403	51524403	+	Silent	SNP	G	G	A	rs34460237	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	36	98	0	0.395604	0	G|0.955;A|0.045	0.045	strong	.	PKHD1	927	.	NM_138694	exon61	c.C10521T	p.H3507H	GAAGACGTGGGGG	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982052	240982052	+	Silent	SNP	C	C	G	rs77588089	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	26	19	0	0.530612	0	C|0.250;G|0.750	0.750	weak	PRR21,pharynx,carcinoma,0,4	PRR21	53	4	NM_001080835	exon1	c.G348C	p.S116S	CATGGACGAAGGG	.	PASS	Atlas-SNP
PSG6	5675	hgsc.bcm.edu	37	19	43420451	43420451	+	Missense_Mutation	SNP	G	G	C	rs3198831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	97	217	0	0.494898	0	G|0.625;C|0.375	0.375	strong	.	PSG6	89	.	NM_001031850	exon2	c.C253G	p.H85D	GACCGTGTACTAC	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112989763	112989763	+	Silent	SNP	C	C	T	rs9819129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	21	82	0	0.323077	0	C|0.974;T|0.026	0.026	strong	.	BOC	139	.	NM_033254	exon6	c.C639T	p.S213S	AACCTCCGGCTCC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918963	12918963	+	Missense_Mutation	SNP	G	G	T	rs9661554	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	337	23	325	0	0.0682493	0	G|0.891;T|0.109	0.109	strong	.	PRAMEF2	85	.	NM_023014	exon2	c.G99T	p.R33S	GCCCAGGGTGCTC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549443	32549443	+	Silent	SNP	G	G	A	rs74867190	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	247	82	385	1	0.331984	0.0025974	G|0.980;A|0.020	0.020	strong	.	HLA-DRB1	41	.	NM_002124	exon3	c.C543T	p.D181D	GGTCCAGTCTCCA	.	PASS	Atlas-SNP
FOCAD	54914	hgsc.bcm.edu	37	9	20953049	20953049	+	Missense_Mutation	SNP	A	A	G	rs3206852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	20	75	0	0.3125	0	G|0.351;A|0.649	0.351	strong	KIAA1797,NS,carcinoma,0,1	.	.	1	NM_017794	exon37	c.A4117G	p.T1373A	TTCATTACAGGAG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79065483	79065483	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	709	69	610	0	0.0973202	0	.	.	none	.	ADAMTS7	142	.	NM_014272	exon14	c.C2073T	p.H691H	GTTGCCGTGGCAC	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30892322	30892322	+	Silent	SNP	C	C	T	rs2532942	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	55	84	0	0.504587	0	C|0.739;T|0.261	0.261	strong	.	VARS2	60	.	NM_001167734	exon26	c.C2748T	p.P916P	CTACCCCAGCGCC	.	PASS	Atlas-SNP
SLC11A2	4891	hgsc.bcm.edu	37	12	51390685	51390685	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	63	132	0	0.425676	0	.	.	none	SLC11A2,caecum,carcinoma,0,1	SLC11A2	51	1	NM_001174125	exon9	c.G833A	p.R278H	GGAGTGCGACAGC	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102587062	102587062	+	Silent	SNP	G	G	A	rs3740938	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	49	92	1	0.475728	0.0108696	G|0.920;A|0.080	0.080	strong	MMP8,colon,carcinoma,0,5	MMP8	68	5	NM_002424	exon6	c.C873T	p.L291L	TCCACGGAGTGTG	.	scavenged	Atlas-SNP
KIF27	55582	hgsc.bcm.edu	37	9	86504005	86504005	+	Missense_Mutation	SNP	C	C	T	rs13289566	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	39	127	0	0.393939	0	C|0.798;T|0.202	0.202	strong	.	KIF27	103	.	NM_017576	exon7	c.G1973A	p.G658E	CTAGTTCCAGATT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228496014	228496014	+	Silent	SNP	G	G	A	rs876180	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	52	81	0	0.477064	0	G|0.776;A|0.224	0.224	strong	OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon58	c.G15540A	p.T5180T	CGTGACGCCCGAG	.	PASS	Atlas-SNP
HTR3D	200909	hgsc.bcm.edu	37	3	183755822	183755822	+	Missense_Mutation	SNP	G	G	A	rs1000952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	58	97	0	0.517857	0	G|0.272;A|0.728	0.728	strong	.	HTR3D	65	.	NM_001163646	exon6	c.G674A	p.R225H	TCAGGCGCAGGTG	.	PASS	Atlas-SNP
CCDC171	203238	hgsc.bcm.edu	37	9	15874585	15874585	+	Missense_Mutation	SNP	T	T	G	rs149814894	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	92	175	0	0.469388	0	T|0.993;G|0.007	0.007	strong	C9orf93_ENST00000380689,NS,lymphoid_neoplasm,0,2	.	.	2	NM_173550	exon24	c.T3524G	p.L1175R	TCACCCTACAGCT	.	PASS	Atlas-SNP
OR9G4	283189	hgsc.bcm.edu	37	11	56511160	56511160	+	Missense_Mutation	SNP	A	A	G	rs11228763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	17	49	0	0.414634	0	A|0.905;G|0.095	0.095	strong	OR9G4,NS,carcinoma,0,1	OR9G4	73	1	NM_001005284	exon1	c.T128C	p.F43S	ACTCCAAATAGAA	.	PASS	Atlas-SNP
LRRC31	79782	hgsc.bcm.edu	37	3	169558025	169558025	+	Missense_Mutation	SNP	C	C	T	rs3732451	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	156	156	0	0.987342	0	C|0.485;T|0.515	0.515	strong	.	LRRC31	66	.	NM_024727	exon9	c.C1404A	p.S468R	CCACCCCGCATCA	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121416650	121416650	+	Missense_Mutation	SNP	A	A	C	rs1169288	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	60	135	0	0.454545	0	T|0.002;G|0.007	.	strong	HNF1A,NS,carcinoma,0,1	HNF1A	302	1	NM_000545	exon1	c.A79C	p.I27L	GCACTGATCCAGG	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141724852	141724852	+	Silent	SNP	C	C	T	rs10255702	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	37	126	0	0.362745	0	C|0.922;T|0.078	0.078	strong	.	MGAM	767	.	NM_004668	exon8	c.C885T	p.N295N	GCAGAACGGAACT	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227915832	227915832	+	Missense_Mutation	SNP	G	G	A	rs1800517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	49	137	0	0.382812	0	T|0.180;G|0.324;C|0.162;N|0.000;A|0.334	0.334	strong	.	COL4A4	215	.	NM_000092	exon33	c.C3011T	p.P1004L	CTTCCCGGCTCTC	.	PASS	Atlas-SNP
MAP3K19	80122	hgsc.bcm.edu	37	2	135745722	135745722	+	Silent	SNP	A	A	G	rs10928526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	35	64	0	0.421687	0	A|0.687;G|0.313	0.313	strong	.	.	.	.	NM_025052	exon7	c.T720C	p.S240S	TGTGAGACTTGGA	.	PASS	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44418693	44418693	+	Missense_Mutation	SNP	T	T	C	rs388706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	126	101	0	1	0	T|0.488;C|0.512	0.512	strong	.	ZNF45	51	.	NM_003425	exon10	c.A895G	p.T299A	TTCCAGTGTGAAC	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135956506	135956506	+	Missense_Mutation	SNP	C	C	G	rs77794331	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	319	130	187	0	0.407524	0	C|0.333;G|0.667	0.667	weak	.	RBMX	149	.	NM_002139	exon9	c.G971C	p.R324P	CTGTCTCGACTTC	.	PASS	Atlas-SNP
ZNF782	158431	hgsc.bcm.edu	37	9	99581343	99581343	+	Missense_Mutation	SNP	C	C	T	rs146058964	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	49	82	0	0.457944	0	C|0.995;T|0.005	0.005	strong	.	ZNF782	64	.	NM_001001662	exon6	c.G962A	p.R321H	GAATTACGGTTGA	.	PASS	Atlas-SNP
OR5H15	403274	hgsc.bcm.edu	37	3	97888337	97888337	+	Missense_Mutation	SNP	C	C	T	rs13082608	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	103	212	0	0.474654	0	C|0.771;T|0.229	0.229	strong	.	OR5H15	70	.	NM_001005515	exon1	c.C794T	p.P265L	CATCTCCGCAAGC	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427516	427516	+	Silent	SNP	T	T	C	rs11649031	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	45	96	0	0.436893	0	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	.	PASS	Atlas-SNP
SAMSN1	64092	hgsc.bcm.edu	37	21	15918577	15918577	+	Silent	SNP	G	G	C	rs7281104	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	47	146	0	0.427273	0	G|0.725;C|0.275	0.275	strong	.	SAMSN1	112	.	NM_022136	exon1	c.C6G	p.L2L	TCTCTTGAGCATT	.	PASS	Atlas-SNP
USP31	57478	hgsc.bcm.edu	37	16	23079408	23079408	+	Missense_Mutation	SNP	T	T	C	rs114976439	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	44	99	0	0.415094	0	T|0.997;C|0.003	0.003	strong	.	USP31	122	.	NM_020718	exon16	c.A4018G	p.S1340G	GCATGCTAGAAGA	.	PASS	Atlas-SNP
KLHL3	26249	hgsc.bcm.edu	37	5	136975604	136975604	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	58	150	0	0.417266	0	.	.	none	.	KLHL3	54	.	NM_017415	exon9	c.C966T	p.F322F	CTCCTCGAAATCA	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82835545	82835545	+	Silent	SNP	A	A	G	rs160279	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	40	95	0	0.540541	0	G|0.496;N|0.000	0.496	strong	VCAN,NS,carcinoma,+2,1	VCAN	498	1	NM_004385	exon8	c.A6723G	p.R2241R	CATGAGACCAACA	.	PASS	Atlas-SNP
DMD	1756	hgsc.bcm.edu	37	X	32380996	32380996	+	Missense_Mutation	SNP	C	C	T	rs1801187	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	115	119	0	1	0	0|0.010;T|0.376	0.376	strong	.	DMD	2127	.	NM_004006	exon37	c.G5234A	p.R1745H	TCACCGCGGTTTG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1269627	1269627	+	Silent	SNP	C	C	T	rs4963056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	313	132	334	1	0.421725	0.00299401	C|0.749;T|0.251	0.251	strong	.	MUC5B	473	.	NM_002458	exon31	c.C11517T	p.T3839T	TACCACCACGGCC	.	PASS	Atlas-SNP
MMP8	4317	hgsc.bcm.edu	37	11	102593248	102593248	+	Missense_Mutation	SNP	T	T	C	rs1940475	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	320	153	244	0	0.478125	0	T|0.417;C|0.583	0.583	strong	MMP8,face,malignant_melanoma,+2,1	MMP8	68	1	NM_002424	exon2	c.A259G	p.K87E	GCTTTTTCATCAT	.	PASS	Atlas-SNP
FILIP1L	11259	hgsc.bcm.edu	37	3	99643176	99643176	+	Missense_Mutation	SNP	C	C	T	rs793440	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	359	184	344	0	0.512535	0	C|0.763;T|0.237	0.237	strong	.	FILIP1L	154	.	NM_182909	exon4	c.G503A	p.R168H	TGCCTACGGGATT	.	PASS	Atlas-SNP
OR7G1	125962	hgsc.bcm.edu	37	19	9225685	9225685	+	Missense_Mutation	SNP	T	T	C	rs2195951	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	23	58	0	0.377049	0	T|0.690;C|0.310	0.310	strong	.	OR7G1	53	.	NM_001005192	exon1	c.A755G	p.Y252C	GTCCCATAGAACA	.	PASS	Atlas-SNP
UNC13C	440279	hgsc.bcm.edu	37	15	54838957	54838957	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	54	112	0	0.406015	0	.	.	none	.	UNC13C	674	.	NM_001080534	exon25	c.C5734A	p.L1912I	ACAGTCCTAAAGC	.	PASS	Atlas-SNP
ZNF10	7556	hgsc.bcm.edu	37	12	133732512	133732512	+	Missense_Mutation	SNP	A	A	G	rs11147259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	60	97	0	0.535714	0	A|0.918;G|0.082	0.082	strong	ZNF10,bladder,carcinoma,+1,1	ZNF10	58	1	NM_015394	exon5	c.A680G	p.Q227R	TTATTCAGTTTGC	.	PASS	Atlas-SNP
FRRS1	391059	hgsc.bcm.edu	37	1	100203693	100203693	+	Silent	SNP	G	G	A	rs7514021	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	112	213	0	0.525822	0	G|0.486;A|0.514	0.514	strong	.	FRRS1	50	.	NM_001013660	exon7	c.C708T	p.S236S	GGGGCCGCTCATT	.	PASS	Atlas-SNP
PRKCA	5578	hgsc.bcm.edu	37	17	64685078	64685078	+	Silent	SNP	G	G	A	rs2227857	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	31	50	0	0.508197	0	G|0.741;A|0.259	0.259	strong	.	PRKCA	82	.	NM_002737	exon8	c.G831A	p.L277L	CAAGTTGCTTAAC	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141727526	141727526	+	Missense_Mutation	SNP	G	G	T	rs2272330	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	21	32	0	0.4375	0	G|0.921;T|0.079	0.079	strong	MGAM_ENST00000549489,NS,carcinoma,+2,3	MGAM	767	3	NM_004668	exon10	c.G1212T	p.Q404H	AGCACAGCTCCCT	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679866	73679866	+	Missense_Mutation	SNP	T	T	C	rs10496192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	51	105	0	0.51	0	T|0.882;C|0.118	0.118	strong	.	ALMS1	384	.	NM_015120	exon8	c.T6209C	p.I2070T	AAGGTATTCTAAA	.	PASS	Atlas-SNP
DCAF13	25879	hgsc.bcm.edu	37	8	104427578	104427578	+	Silent	SNP	T	T	C	rs3134297	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	40	59	0	0.487805	0	T|0.764;C|0.236	0.236	strong	DCAF13,NS,carcinoma,0,1	DCAF13	66	1	NM_015420	exon1	c.T360C	p.S120S	TGGAAGTAGTCTG	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340906	55340906	+	Missense_Mutation	SNP	G	G	A	rs45542639	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	7	13	0	0.35	0	G|0.875;A|0.125	0.125	strong	KIR3DL1_ENST00000391728,NS,carcinoma,+1,1	KIR3DL1	174	1	NM_013289	exon7	c.G1091A	p.C364Y	TCTGGTGCTCCAA	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30888161	30888161	+	Missense_Mutation	SNP	T	T	C	rs2249464	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	35	88	0	0.380435	0	T|0.471;C|0.529	0.529	strong	.	VARS2	60	.	NM_001167734	exon14	c.T1435C	p.W479R	AGTGAATGGGGCC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301211	65301211	+	Missense_Mutation	SNP	T	T	C	rs62415826	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	84	147	0	0.988235	0	T|0.902;C|0.098	0.098	strong	.	EYS	527	.	NM_001142800	exon26	c.A4549G	p.S1517G	TTGTACTGAACCG	.	PASS	Atlas-SNP
ZACN	353174	hgsc.bcm.edu	37	17	74077797	74077797	+	Nonsense_Mutation	SNP	C	C	T	rs1043149	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	43	127	0	0.373913	0	C|0.826;T|0.174	0.174	strong	.	ZACN	29	.	NM_180990	exon7	c.C841T	p.Q281X	CTGGTGCAGGCCC	.	PASS	Atlas-SNP
ZNF501	115560	hgsc.bcm.edu	37	3	44775962	44775962	+	Missense_Mutation	SNP	A	A	G	rs4682752	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	63	98	0	0.508065	0	A|0.329;G|0.671	0.671	strong	.	ZNF501	27	.	NM_001258280	exon3	c.A49G	p.M17V	GTTAACATGCAGA	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373129	5373129	+	Missense_Mutation	SNP	C	C	T	rs5006887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	65	255	0	0.328283	0	C|0.760;T|0.240	0.240	strong	.	OR51B6	53	.	NM_001004750	exon1	c.C392T	p.T131I	GATATACCTCTAT	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52710309	52710309	+	Silent	SNP	G	G	A	rs75619735		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	59	158	0	0.472	0	.	.	weak	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon6	c.C984T	p.N328N	CAGCTCGTTGATC	.	PASS	Atlas-SNP
PRAM1	84106	hgsc.bcm.edu	37	19	8564466	8564466	+	Missense_Mutation	SNP	C	C	A	rs4239540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	20	60	0	0.327869	0	C|0.601;A|0.399	0.399	strong	.	PRAM1	53	.	NM_032152	exon2	c.G226T	p.V76F	CAGTGACCTCAGG	.	PASS	Atlas-SNP
LZTS1	11178	hgsc.bcm.edu	37	8	20110641	20110641	+	Silent	SNP	C	C	T	rs2645386	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	27	62	0	0.473684	0	C|0.631;T|0.369	0.369	strong	.	LZTS1	72	.	NM_021020	exon2	c.G801A	p.E267E	CTTCTGCTCCAGC	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65386206	65386206	+	Missense_Mutation	SNP	C	C	G	rs1193851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	44	80	0	0.578947	0	C|0.734;G|0.266	0.266	strong	.	PCNXL3	140	.	NM_032223	exon6	c.C1373G	p.S458C	AGAGCTCCCGGGG	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77055474	77055474	+	Silent	SNP	A	A	G	rs11097244	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	29	80	0	0.381579	0	A|0.865;G|0.135	0.135	strong	NUP54,colon,carcinoma,-2,1	NUP54	48	1	NM_017426	exon5	c.T564C	p.D188D	TAGCCCATCTTCA	.	PASS	Atlas-SNP
PRAM1	84106	hgsc.bcm.edu	37	19	8564523	8564523	+	Missense_Mutation	SNP	T	T	G	rs4804305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	82	0	0.478873	0	T|0.793;G|0.207	0.207	strong	.	PRAM1	53	.	NM_032152	exon2	c.A169C	p.K57Q	CCTTCTTGGGGTG	.	PASS	Atlas-SNP
GBE1	2632	hgsc.bcm.edu	37	3	81627175	81627175	+	Missense_Mutation	SNP	T	T	C	rs2228389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	43	114	0	0.383929	0	T|0.604;G|0.030;C|0.042;A|0.325	0.042	strong	.	GBE1	111	.	NM_000158	exon12	c.A1519G	p.T507A	AAGGAGTCAGGAC	.	PASS	Atlas-SNP
RASSF4	83937	hgsc.bcm.edu	37	10	45488738	45488738	+	Silent	SNP	G	G	A	rs145503557	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	11	31	0	0.55	0	G|0.999;A|0.001	0.001	strong	.	RASSF4	33	.	NM_032023	exon11	c.G927A	p.T309T	TCTGACGATGCTG	.	PASS	Atlas-SNP
TBC1D4	9882	hgsc.bcm.edu	37	13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	rs557337	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	305	163	307	0	0.534426	0	A|0.827;G|0.173	0.173	strong	.	TBC1D4	142	.	NM_014832	exon21	c.T3824C	p.V1275A	CAATTGACTAGAG	.	PASS	Atlas-SNP
FANCD2	2177	hgsc.bcm.edu	37	3	10088308	10088308	+	Silent	SNP	T	T	C	rs72492998		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	482	129	398	0	0.267635	0	T|0.500;C|0.500	0.500	weak	.	FANCD2	253	.	NM_001018115	exon15	c.T1179C	p.T393T	CAATACTCAGACA	.	PASS	Atlas-SNP
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43816735	43816735	+	Missense_Mutation	SNP	G	G	C	rs200986004	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	837	84	1106	1	0.100358	0.000904159	A|0.002;C|0.002;G|0.995	0.002	strong	CNTNAP3B,right_lower_lobe,carcinoma,-2,1	CNTNAP3B	37	1	NM_001201380	exon6	c.G841C	p.D281H	CTCCTCGACACGC	.	scavenged	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	37	18	72168608	72168608	+	Silent	SNP	G	G	A	rs2303463	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	74	166	0	0.496644	0	G|0.791;A|0.209	0.209	strong	CNDP2,caecum,carcinoma,0,2	CNDP2	55	2	NM_001168499	exon2	c.G105A	p.P35P	GTGGCCGGAGAAG	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609806	32609806	+	Missense_Mutation	SNP	C	C	T	rs707952	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	292	134	169	0	0.458904	0	C|0.785;T|0.215	0.215	strong	.	HLA-DQA1	52	.	NM_002122	exon3	c.C389T	p.T130I	CCAACACCCTCAT	.	PASS	Atlas-SNP
ARL2	402	hgsc.bcm.edu	37	11	64789194	64789194	+	Missense_Mutation	SNP	T	T	C	rs664226	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	23	27	0	0.522727	0	T|0.439;C|0.561	0.561	strong	ARL2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ARL2	11	1	NM_001667	exon5	c.T422C	p.V141A	CCCAGGTCCTGGA	.	PASS	Atlas-SNP
CAPN2	824	hgsc.bcm.edu	37	1	223949900	223949900	+	Missense_Mutation	SNP	G	G	A	rs145816861	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	36	64	0	0.433735	0	G|1.000;A|0.000	0.000	weak	.	CAPN2	69	.	NM_001748	exon14	c.G1579A	p.E527K	ATCAGCGAGGATG	.	PASS	Atlas-SNP
KIF20B	9585	hgsc.bcm.edu	37	10	91488979	91488979	+	Missense_Mutation	SNP	A	A	T	rs3758388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	86	250	0	0.396313	0	A|0.807;T|0.193	0.193	strong	.	KIF20B	191	.	NM_016195	exon18	c.A2246T	p.H749L	AGTCTCATATGGA	.	PASS	Atlas-SNP
SPCS1	28972	hgsc.bcm.edu	37	3	52740182	52740182	+	Missense_Mutation	SNP	C	C	G	rs6617	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	7	6	0	0.4375	0	C|0.512;G|0.488	0.488	strong	SPCS1_ENST00000233025,rectum,carcinoma,0,1	SPCS1	20	1	NM_014041	exon1	c.C121G	p.P41A	ACCTTACCCCTCA	.	PASS	Atlas-SNP
SLC17A9	63910	hgsc.bcm.edu	37	20	61595636	61595636	+	Silent	SNP	C	C	T	rs2248900	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	106	268	1	0.540816	0.00373134	C|0.831;T|0.169	0.169	strong	SLC17A9,caecum,carcinoma,0,1	SLC17A9	54	1	NM_022082	exon8	c.C879T	p.S293S	ATTCAGCGGGTTT	.	PASS	Atlas-SNP
KNTC1	9735	hgsc.bcm.edu	37	12	123032478	123032478	+	Missense_Mutation	SNP	C	C	T	rs61751321	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	14	43	0	0.35	0	C|0.991;T|0.008	0.008	strong	.	KNTC1	182	.	NM_014708	exon12	c.C949T	p.L317F	ACAAATCTCAAAT	.	PASS	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	107	115	0	1	0	G|0.341;A|0.659	0.659	strong	.	NOTCH1	1980	.	NM_017617	exon34	c.C6555T	p.D2185D	CTTGCCGTCCTGG	.	PASS	Atlas-SNP
WWOX	51741	hgsc.bcm.edu	37	16	78466437	78466437	+	Missense_Mutation	SNP	C	C	G	rs3764340	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	48	101	0	0.510638	0	C|0.921;G|0.079	0.079	strong	.	WWOX	98	.	NM_016373	exon8	c.C844G	p.P282A	CTCTCTCCAACAA	.	PASS	Atlas-SNP
RIC3	79608	hgsc.bcm.edu	37	11	8159892	8159892	+	Silent	SNP	G	G	T	rs10839976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	53	99	0	0.469027	0	G|0.727;T|0.273	0.273	strong	.	RIC3	42	.	NM_001206672	exon3	c.C354A	p.L118L	CTTTGAGAGCTGA	.	PASS	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56136536	56136536	+	Silent	SNP	A	A	G	rs1042521	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	35	44	0	1	0	A|0.555;G|0.445	0.445	strong	.	PCK1	95	.	NM_002591	exon2	c.A69G	p.L23L	CAGCCTACCCCAG	.	PASS	Atlas-SNP
C4orf21	55345	hgsc.bcm.edu	37	4	113482146	113482146	+	Missense_Mutation	SNP	G	G	A	rs17605622	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	68	175	0	0.49635	0	G|0.939;A|0.061	0.061	strong	.	C4orf21	223	.	NM_018392	exon19	c.C4703T	p.S1568L	GTTGGCGAAGACC	.	PASS	Atlas-SNP
MAD2L1	4085	hgsc.bcm.edu	37	4	120982045	120982045	+	Silent	SNP	T	T	C	rs61752609	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	64	140	0	0.426667	0	T|0.955;C|0.045	0.045	strong	.	MAD2L1	17	.	NM_002358	exon4	c.A429G	p.P143P	CAACAGTGGCAGA	.	PASS	Atlas-SNP
DDRGK1	65992	hgsc.bcm.edu	37	20	3171337	3171337	+	Missense_Mutation	SNP	C	C	T	rs11591	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	34	63	0	0.523077	0	C|0.885;T|0.115	0.115	strong	.	DDRGK1	21	.	NM_023935	exon9	c.G907A	p.A303T	CCCAGGCGATGAG	.	PASS	Atlas-SNP
SEC14L1	6397	hgsc.bcm.edu	37	17	75190962	75190962	+	Silent	SNP	C	C	T	rs674402	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	81	102	0	0.5	0	C|0.643;T|0.357	0.357	strong	.	SEC14L1	81	.	NM_001204408	exon9	c.C678T	p.S226S	CCCCAGCGCACCT	.	PASS	Atlas-SNP
SERPINA4	5267	hgsc.bcm.edu	37	14	95033356	95033356	+	Silent	SNP	C	C	T	rs5510	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	156	151	0	0.993631	0	C|0.718;T|0.282	0.282	strong	.	SERPINA4	81	.	NM_006215	exon3	c.C699T	p.F233F	AGACTTCTATGTT	.	PASS	Atlas-SNP
C9orf66	157983	hgsc.bcm.edu	37	9	215269	215269	+	Missense_Mutation	SNP	A	A	C	rs636922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	21	28	0	0.583333	0	A|0.824;C|0.176	0.176	strong	.	C9orf66	16	.	NM_152569	exon1	c.T128G	p.L43R	GTCCTCAGCCGCC	.	PASS	Atlas-SNP
KIAA1239	57495	hgsc.bcm.edu	37	4	37445315	37445315	+	Missense_Mutation	SNP	C	C	A	rs4634233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	36	57	0	0.553846	0	C|0.819;A|0.181	0.181	strong	.	KIAA1239	79	.	NM_001144990	exon7	c.C1705A	p.L569M	ATCGAGCTGATTC	.	PASS	Atlas-SNP
ERCC2	2068	hgsc.bcm.edu	37	19	45854919	45854919	+	Missense_Mutation	SNP	T	T	G	rs13181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	38	132	0	0.487179	0	A|0.006;C|0.001	.	strong	.	ERCC2	78	.	NM_000400	exon23	c.A2251C	p.K751Q	TCCTCTTCAGCGT	.	PASS	Atlas-SNP
B3GNTL1	146712	hgsc.bcm.edu	37	17	81006387	81006387	+	Silent	SNP	G	G	A	rs1143006	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	84	148	0	0.477273	0	G|0.721;A|0.279	0.279	strong	.	B3GNTL1	40	.	NM_001009905	exon3	c.C237T	p.H79H	GATCACGTGGACA	.	PASS	Atlas-SNP
C3orf20	84077	hgsc.bcm.edu	37	3	14769980	14769980	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	49	165	0	0.326667	0	.	.	none	.	C3orf20	109	.	NM_032137	exon12	c.G1725A	p.E575E	AAAGGAGGAGGAA	.	PASS	Atlas-SNP
WDYHV1	55093	hgsc.bcm.edu	37	8	124449466	124449466	+	Missense_Mutation	SNP	C	C	T	rs3824250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	97	76	0	0.989796	0	C|0.628;N|0.000	.	strong	.	WDYHV1	30	.	NM_018024	exon5	c.C400T	p.R134C	GTGATCCGTGCAG	.	PASS	Atlas-SNP
ABHD4	63874	hgsc.bcm.edu	37	14	23078810	23078810	+	Silent	SNP	A	A	T	rs72677597	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	33	49	0	0.634615	0	A|0.885;T|0.115	0.115	strong	ABHD4,NS,carcinoma,+2,1	ABHD4	30	1	NM_022060	exon6	c.A933T	p.R311R	TGTCCGAGACATG	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32768428	32768428	+	Missense_Mutation	SNP	G	G	A	rs41292163	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	58	93	0	0.54717	0	G|0.996;A|0.004	0.004	strong	.	FRY	312	.	NM_023037	exon29	c.G3740A	p.G1247E	TGTGTGGAAGCAG	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	37	11	82879825	82879825	+	Silent	SNP	G	G	A	rs75717911	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	79	149	0	0.50641	0	G|0.995;A|0.005	0.005	strong	.	PCF11	220	.	NM_015885	exon8	c.G2448A	p.G816G	AGGTGGGTGTCCT	.	PASS	Atlas-SNP
CACHD1	57685	hgsc.bcm.edu	37	1	65142686	65142686	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	67	161	0	0.39645	0	.	.	none	.	CACHD1	125	.	NM_020925	exon22	c.G2931A	p.L977L	GAGGCTGGAAAGT	.	PASS	Atlas-SNP
LRFN2	57497	hgsc.bcm.edu	37	6	40360492	40360492	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	67	106	0	0.563025	0	.	.	none	.	LRFN2	133	.	NM_020737	exon3	c.G1560A	p.P520P	GCACTGCGGGTAG	.	PASS	Atlas-SNP
RSBN1L	222194	hgsc.bcm.edu	37	7	77365770	77365770	+	Silent	SNP	A	A	G	rs3764824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	105	99	0	0.990566	0	A|0.466;G|0.534	0.534	strong	.	RSBN1L	74	.	NM_198467	exon2	c.A630G	p.E210E	AAAAGAAAGAGAA	.	PASS	Atlas-SNP
BICD1	636	hgsc.bcm.edu	37	12	32481093	32481093	+	Silent	SNP	G	G	C	rs3748275	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	60	128	0	0.483871	0	G|0.767;C|0.233	0.233	strong	BICD1,rectum,carcinoma,0,1	BICD1	89	1	NM_001714	exon5	c.G1704C	p.V568V	GGGTGTGTCATCC	.	PASS	Atlas-SNP
EVC	2121	hgsc.bcm.edu	37	4	5721021	5721021	+	Missense_Mutation	SNP	A	A	C	rs2291157	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	47	78	0	0.415929	0	A|0.908;C|0.092	0.092	strong	.	EVC	90	.	NM_153717	exon2	c.A221C	p.Q74P	ATGCGCAGACCCC	.	PASS	Atlas-SNP
ZNF302	55900	hgsc.bcm.edu	37	19	35175208	35175208	+	Missense_Mutation	SNP	A	A	G	rs2290652	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	251	150	209	0	0.59761	0	A|0.726;G|0.274	0.274	strong	.	ZNF302	27	.	NM_018443	exon5	c.A266G	p.Y89C	ATATTTATGATGA	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17303774	17303774	+	Missense_Mutation	SNP	T	T	G	rs1545620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	53	0	1	0	T|0.363;G|0.637	0.637	strong	MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	NM_001130065	exon21	c.T3031G	p.S1011A	CAGGCCTCATGGA	.	PASS	Atlas-SNP
SMPD1	6609	hgsc.bcm.edu	37	11	6415690	6415690	+	Silent	SNP	G	G	A	rs35098198	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	63	104	0	0.577982	0	G|0.985;A|0.015	0.015	strong	.	SMPD1	108	.	NM_000543	exon6	c.G1749A	p.S583S	ACCCTCGGAGCCC	.	PASS	Atlas-SNP
ATP6V1B1	525	hgsc.bcm.edu	37	2	71163173	71163173	+	Missense_Mutation	SNP	C	C	T	rs17720303	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	312	310	263	1	0.99359	0.00380228	C|0.839;N|0.001	.	strong	.	ATP6V1B1	66	.	NM_001692	exon1	c.C89T	p.T30I	CGGTCACCCGAAA	.	PASS	Atlas-SNP
KIAA0825	285600	hgsc.bcm.edu	37	5	93722050	93722050	+	Silent	SNP	G	G	T	rs29913	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	70	138	0	0.443038	0	G|0.892;T|0.108	0.108	strong	.	KIAA0825	172	.	NM_001145678	exon19	c.C3516A	p.I1172I	AGGTCGGATGGGT	.	PASS	Atlas-SNP
DHX57	90957	hgsc.bcm.edu	37	2	39025555	39025555	+	Silent	SNP	G	G	A	rs1530853	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	66	128	0	0.471429	0	G|0.437;A|0.563	0.563	strong	.	DHX57	127	.	NM_198963	exon24	c.C4047T	p.C1349C	AAGTTCGCAACGA	.	PASS	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	37	8	95531419	95531419	+	Silent	SNP	T	T	C	rs1866844	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	61	110	0	0.521368	0	T|0.715;C|0.285	0.285	strong	KIAA1429,caecum,carcinoma,0,1	KIAA1429	176	1	NM_015496	exon9	c.A2307G	p.Q769Q	AATACATTGCAAT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228506661	228506661	+	Silent	SNP	G	G	A	rs41305126	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	50	151	0	0.34965	0	G|0.986;A|0.014	0.014	strong	.	OBSCN	2142	.	NM_001271223	exon65	c.G17079A	p.L5693L	TGACCTGCACCTA	.	PASS	Atlas-SNP
DHX34	9704	hgsc.bcm.edu	37	19	47858424	47858424	+	Silent	SNP	G	G	A	rs2245046	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	62	117	0	0.512397	0	G|0.897;A|0.103	0.103	strong	.	DHX34	98	.	NM_014681	exon3	c.G834A	p.V278V	GATTGTGGATGAA	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274364	39274364	+	Missense_Mutation	SNP	T	T	G	rs425784	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	15	66	4	0.154639	0.0606061	.	.	weak	KRTAP4-11,caecum,carcinoma,0,2	KRTAP4-11	94	2	NM_033059	exon1	c.A204C	p.R68S	GCAGCATCTGGGG	.	scavenged	Atlas-SNP
C10orf54	64115	hgsc.bcm.edu	37	10	73521578	73521578	+	Silent	SNP	G	G	A	rs3747866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	149	170	0	1	0	G|0.790;A|0.210	0.210	strong	.	C10orf54	29	.	NM_022153	exon2	c.C288T	p.D96D	GTGAAGGTCCTGG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608853	26608853	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	15	24	0	0.394737	0	.	.	none	.	UBXN11	54	.	NM_183008	exon16	c.C1500T	p.G500G	ACTGGGGCCGGGA	.	PASS	Atlas-SNP
LAMB2	3913	hgsc.bcm.edu	37	3	49159152	49159152	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	36	77	0	0.349515	0	.	.	none	.	LAMB2	156	.	NM_002292	exon30	c.G5065T	p.G1689C	CACTGCCTGCCGT	.	PASS	Atlas-SNP
RAPSN	5913	hgsc.bcm.edu	37	11	47463220	47463220	+	Silent	SNP	C	C	T	rs45603036	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	92	170	0	0.446602	0	C|0.891;T|0.109	0.109	strong	.	RAPSN	27	.	NM_005055	exon5	c.G855A	p.Q285Q	CTGCACCTGCCCC	.	PASS	Atlas-SNP
FAHD1	81889	hgsc.bcm.edu	37	16	1877558	1877558	+	Missense_Mutation	SNP	G	G	A	rs3743853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	53	72	0	0.456897	0	G|0.882;A|0.118	0.118	strong	.	FAHD1	18	.	NM_031208	exon1	c.G328A	p.D110N	GTGCAGGACGAGT	.	PASS	Atlas-SNP
TTC7B	145567	hgsc.bcm.edu	37	14	91123575	91123575	+	Silent	SNP	T	T	C	rs3742660	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	67	44	0	1	0	T|0.123;G|0.000;C|0.877	0.877	strong	TTC7B,NS,carcinoma,-2,1	TTC7B	93	1	NM_001010854	exon11	c.A1284G	p.P428P	ATCGTCTGGCTTC	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77227554	77227554	+	Silent	SNP	C	C	T	rs35099556	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	40	93	0	0.384615	0	C|0.988;T|0.012	0.012	strong	.	NFATC1	105	.	NM_172390	exon8	c.C2064T	p.Y688Y	CCAGTACCAGCGT	.	PASS	Atlas-SNP
SCRN3	79634	hgsc.bcm.edu	37	2	175289259	175289259	+	Missense_Mutation	SNP	G	G	T	rs41270195	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	117	237	0	0.517699	0	G|0.971;T|0.029	0.029	strong	.	SCRN3	76	.	NM_024583	exon7	c.G974T	p.S325I	ATACCAGTTCACC	.	PASS	Atlas-SNP
LRP4	4038	hgsc.bcm.edu	37	11	46890197	46890197	+	Silent	SNP	G	G	A	rs2290883	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	31	45	0	0.5	0	G|0.841;A|0.159	0.159	strong	.	LRP4	160	.	NM_002334	exon33	c.C4905T	p.F1635F	ACATACGAAGTCC	.	PASS	Atlas-SNP
TAAR1	134864	hgsc.bcm.edu	37	6	132967002	132967002	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	3	239	0	0.0205479	0	.	.	none	TAAR1,NS,carcinoma,-1,1	TAAR1	41	1	NM_138327	exon1	c.T141C	p.S47S	TGATATAGAAACA	.	scavenged	Atlas-SNP
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382792	24382792	+	Missense_Mutation	SNP	G	G	A	rs5944420	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	120	126	0	0.96	0	G|0.882;A|0.118	0.118	strong	.	.	.	.	NM_001136234	exon1	c.G1915A	p.A639T	GCCCCCGCTCCTG	.	PASS	Atlas-SNP
OPTN	10133	hgsc.bcm.edu	37	10	13168025	13168025	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	26	79	0	0.40625	0	.	.	none	.	OPTN	57	.	NM_001008212	exon11	c.C1228A	p.L410I	GAGGAACTAACAA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919079	12919079	+	Missense_Mutation	SNP	C	C	G	rs9659529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	17	243	0	0.0854271	0	C|0.887;G|0.113	0.113	strong	PRAMEF2,caecum,carcinoma,-1,2	PRAMEF2	85	2	NM_023014	exon2	c.C215G	p.T72R	TGAAGACGCTTCA	.	PASS	Atlas-SNP
C1orf172	126695	hgsc.bcm.edu	37	1	27278553	27278553	+	Missense_Mutation	SNP	G	G	A	rs3010109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	20	137	0	0.13245	0	G|0.894;A|0.106	0.106	strong	.	C1orf172	38	.	NM_152365	exon2	c.C319T	p.R107W	ATCCCCGCACACA	.	PASS	Atlas-SNP
SERPINA3	12	hgsc.bcm.edu	37	14	95080803	95080803	+	Missense_Mutation	SNP	G	G	A	rs4934	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	28	29	0	0.965517	0	G|0.587;A|0.413	0.413	strong	.	SERPINA3	78	.	NM_001085	exon2	c.G25A	p.A9T	CTCCTGGCTCTGG	.	PASS	Atlas-SNP
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	89	165	0	0.421801	0	.	.	weak	KRAS_ENST00000256078,NS,adenocarcinoma,0,25136	KRAS	30930	25136	NM_004985	exon2	c.G35T	p.G12V	ACGCCACCAGCTC	.	PASS	Atlas-SNP
FAM209B	388799	hgsc.bcm.edu	37	20	55108589	55108589	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	260	19	203	0	0.0730769	0	.	.	none	.	.	.	.	NM_001013646	exon1	c.G192T	p.L64F	GCTTTTGTTTGCT	.	PASS	Atlas-SNP
PLA2G4D	283748	hgsc.bcm.edu	37	15	42371752	42371752	+	Missense_Mutation	SNP	A	A	T	rs4924618	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	12	17	0	1	0	A|0.716;T|0.284	0.284	strong	PLA2G4D,NS,carcinoma,0,1	PLA2G4D	72	1	NM_178034	exon13	c.T1300A	p.S434T	GCATGGACTCCAG	.	PASS	Atlas-SNP
SCNN1D	6339	hgsc.bcm.edu	37	1	1222622	1222622	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	75	77	0	0.949367	0	.	.	none	.	SCNN1D	60	.	NM_001130413	exon9	c.G1253A	p.S418N	ACGGGAGCCAGGA	.	PASS	Atlas-SNP
SLC44A5	204962	hgsc.bcm.edu	37	1	75702674	75702674	+	Silent	SNP	G	G	A	rs17096508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	366	161	322	1	0.439891	0.00310559	G|0.845;A|0.155	0.155	strong	.	SLC44A5	231	.	NM_152697	exon11	c.C738T	p.L246L	TTACATGAGAATC	.	PASS	Atlas-SNP
CD79B	974	hgsc.bcm.edu	37	17	62007498	62007498	+	Silent	SNP	A	A	G	rs2070776	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	105	106	0	0.981308	0	A|0.371;G|0.629	0.629	strong	CD79B,NS,carcinoma,0,1	CD79B	38	1	NM_001039933	exon3	c.T369C	p.C123C	CTGCTGACAGAAG	.	PASS	Atlas-SNP
FAM189A1	23359	hgsc.bcm.edu	37	15	29544656	29544656	+	Silent	SNP	T	T	C	rs4583203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	93	160	0	0.486911	0	T|0.529;C|0.471	0.471	strong	FAM189A1,NS,carcinoma,-1,1	FAM189A1	20	1	NM_015307	exon3	c.A303G	p.A101A	ACACACTGCAGAA	.	PASS	Atlas-SNP
MMEL1	79258	hgsc.bcm.edu	37	1	2526746	2526746	+	Missense_Mutation	SNP	A	A	G	rs3748816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	151	156	0	0.993421	0	A|0.529;G|0.471	0.471	strong	.	MMEL1	64	.	NM_033467	exon16	c.T1553C	p.M518T	CTGTTCATCTCCT	.	PASS	Atlas-SNP
GPR126	57211	hgsc.bcm.edu	37	6	142737048	142737048	+	Missense_Mutation	SNP	C	C	T	rs186655757	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	11	95	0	0.2	0	C|0.998;T|0.002	0.002	strong	.	GPR126	192	.	NM_198569	exon20	c.C2785T	p.L929F	GATGGACTTTGCA	.	PASS	Atlas-SNP
C17orf98	388381	hgsc.bcm.edu	37	17	36997461	36997461	+	Missense_Mutation	SNP	G	G	A	rs7210156	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	60	59	0	0.582524	0	G|0.926;A|0.074	0.074	strong	.	C17orf98	34	.	NM_001080465	exon1	c.C182T	p.P61L	AGGGGCGGAACCA	.	PASS	Atlas-SNP
RBM5	10181	hgsc.bcm.edu	37	3	50153356	50153356	+	Silent	SNP	T	T	C	rs1138536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	41	79	0	0.488095	0	T|0.328;C|0.672	0.672	strong	.	RBM5	76	.	NM_005778	exon22	c.T2037C	p.Y679Y	CATCTATCGACGA	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28420676	28420676	+	Silent	SNP	C	C	T	rs139728053		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	49	73	0	0.538462	0	C|1.000;T|0.000	0.000	weak	.	HERC2	501	.	NM_004667	exon64	c.G9813A	p.A3271A	CGTGACCGCCAGG	.	PASS	Atlas-SNP
PCDHGB7	56099	hgsc.bcm.edu	37	5	140797630	140797630	+	Silent	SNP	G	G	T	rs2015825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	142	139	0	0.986111	0	G|0.500;T|0.500	0.500	strong	.	PCDHGB7	117	.	NM_018927	exon1	c.G204T	p.V68V	GCGAGTGAGCGCG	.	PASS	Atlas-SNP
GTDC1	79712	hgsc.bcm.edu	37	2	144899559	144899559	+	Missense_Mutation	SNP	C	C	A	rs3731958	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	59	133	0	0.479675	0	C|0.374;A|0.625	0.625	strong	.	GTDC1	61	.	NM_001006636	exon6	c.G411T	p.M137I	TTTTCCCATGGAA	.	PASS	Atlas-SNP
GRID2IP	392862	hgsc.bcm.edu	37	7	6547902	6547902	+	Missense_Mutation	SNP	G	G	A	rs112305062	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	51	70	0	0.476636	0	G|0.908;A|0.092	0.092	strong	.	GRID2IP	82	.	NM_001145118	exon13	c.C2258T	p.P753L	CTGAGCGGGGGTG	.	PASS	Atlas-SNP
B4GALT2	8704	hgsc.bcm.edu	37	1	44451234	44451234	+	Silent	SNP	C	C	T	rs1061781	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	27	77	0	0.457627	0	C|0.910;T|0.090	0.090	strong	B4GALT2,NS,carcinoma,0,1	B4GALT2	35	1	NM_030587	exon6	c.C996T	p.I332I	CCGAATCGGCCGC	.	PASS	Atlas-SNP
NRDE2	55051	hgsc.bcm.edu	37	14	90756760	90756760	+	Silent	SNP	A	A	T	rs3742671	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	68	96	0	0.60177	0	A|0.861;T|0.139	0.139	strong	.	.	.	.	NM_017970	exon10	c.T2034A	p.T678T	GAAAAAAGTCAAG	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229635521	229635521	+	Silent	SNP	A	A	G	rs10916495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	119	1	1	0.00840336	A|0.813;G|0.187	0.187	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon5	c.T558C	p.Y186Y	TGGCCAATAGCGG	.	PASS	Atlas-SNP
INTS4	92105	hgsc.bcm.edu	37	11	77635882	77635882	+	Silent	SNP	A	A	C	rs7119720	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	348	154	348	0	0.442529	0	A|0.818;C|0.182	0.182	strong	.	INTS4	89	.	NM_033547	exon12	c.T1428G	p.V476V	GGTTGAAACATTA	.	PASS	Atlas-SNP
WDR63	126820	hgsc.bcm.edu	37	1	85594466	85594466	+	Missense_Mutation	SNP	G	G	A	rs709783	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	147	178	1	1	0.00561798	G|0.780;A|0.220	0.220	strong	WDR63,colon,carcinoma,0,1	WDR63	91	1	NM_145172	exon21	c.G2393A	p.R798H	TAAGTCGCCCTTC	.	PASS	Atlas-SNP
RALGAPA1	253959	hgsc.bcm.edu	37	14	36191030	36191030	+	Silent	SNP	A	A	G	rs2296168	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	27	49	0	0.397059	0	A|0.890;G|0.110	0.110	strong	.	RALGAPA1	289	.	NM_194301	exon16	c.T2130C	p.V710V	AACTGAAACTTTC	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88502208	88502208	+	Missense_Mutation	SNP	A	A	T	rs3812954	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	31	62	0	0.469697	0	A|0.944;T|0.056	0.056	strong	.	ZNF469	121	.	NM_001127464	exon2	c.A8246T	p.D2749V	CGGAGGACAGCAG	.	PASS	Atlas-SNP
GRID2	2895	hgsc.bcm.edu	37	4	94137954	94137954	+	Silent	SNP	G	G	A	rs75225211	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	48	112	0	0.5	0	G|0.990;A|0.010	0.010	strong	GRID2,NS,malignant_melanoma,+2,1	GRID2	233	1	NM_001510	exon6	c.G855A	p.R285R	TATTCGGCAGACA	.	PASS	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	37	19	15291576	15291576	+	Missense_Mutation	SNP	C	C	G	rs35769976	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	42	75	0	0.552632	0	C|0.886;G|0.114	0.114	strong	.	NOTCH3	340	.	NM_000435	exon19	c.G3058C	p.A1020P	AATAGGCCCCAGT	.	PASS	Atlas-SNP
HSD17B14	51171	hgsc.bcm.edu	37	19	49334991	49334991	+	Silent	SNP	C	C	T	rs62127966	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	55	132	0	0.381944	0	C|0.873;T|0.127	0.127	strong	.	HSD17B14	25	.	NM_016246	exon5	c.G303A	p.E101E	AGAGGTCTCCTCA	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119938	19119938	+	Silent	SNP	G	G	A	rs1052773	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	18	39	0	0.473684	0	A|0.201;C|0.006	0.201	strong	.	TSSK2	29	.	NM_053006	exon1	c.G1026A	p.R342R	CTCCAGGGCCAAA	.	PASS	Atlas-SNP
GPR133	283383	hgsc.bcm.edu	37	12	131471699	131471699	+	Missense_Mutation	SNP	G	G	A	rs61732860	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	63	133	0	0.488372	0	G|0.985;A|0.015	0.015	strong	GPR133,NS,carcinoma,0,1	GPR133	136	1	NM_198827	exon6	c.G550A	p.V184I	GTCTACGTCAACG	.	PASS	Atlas-SNP
AK8	158067	hgsc.bcm.edu	37	9	135753629	135753629	+	Missense_Mutation	SNP	A	A	G	rs2231400	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	27	51	0	0.473684	0	A|0.871;G|0.129	0.129	strong	.	AK8	45	.	NM_152572	exon1	c.T14C	p.I5T	GGGGCGATAGTGG	.	PASS	Atlas-SNP
RIPK3	11035	hgsc.bcm.edu	37	14	24805463	24805463	+	Missense_Mutation	SNP	G	G	T	rs3212254	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	47	98	0	0.573171	0	G|0.896;T|0.104	0.104	strong	.	RIPK3	43	.	NM_006871	exon10	c.C1475A	p.P492Q	ACTGGTGGGGGGT	.	PASS	Atlas-SNP
FHDC1	85462	hgsc.bcm.edu	37	4	153874666	153874666	+	Missense_Mutation	SNP	G	G	A	rs61753649	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	32	72	0	0.492308	0	G|0.954;A|0.046	0.046	strong	.	FHDC1	102	.	NM_033393	exon2	c.G514A	p.A172T	TTGGATGCAAAAC	.	PASS	Atlas-SNP
SLC26A3	1811	hgsc.bcm.edu	37	7	107423254	107423254	+	Silent	SNP	C	C	T	rs3735605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	47	77	1	0.456311	0.012987	C|0.847;T|0.153	0.153	strong	SLC26A3,caecum,carcinoma,0,1	SLC26A3	120	1	NM_000111	exon11	c.G1299A	p.A433A	TAGAGGCGCCAGG	.	scavenged	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243328887	243328887	+	Nonsense_Mutation	SNP	G	G	T	rs2728433	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	3	166	0	0.0202703	0	T|0.500;G|0.500	0.500	weak	CEP170,extremity,malignant_melanoma,0,1	CEP170	153	1	NM_014812	exon13	c.C2375A	p.S792X	TGTCCTGAATTTT	.	scavenged	Atlas-SNP
PARM1	25849	hgsc.bcm.edu	37	4	75938179	75938179	+	Silent	SNP	G	G	A	rs3775527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	123	151	0	0.991935	0	G|0.698;A|0.302	0.302	strong	PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	NM_015393	exon2	c.G588A	p.P196P	GTCCCCGACAGAG	.	PASS	Atlas-SNP
STEAP2	261729	hgsc.bcm.edu	37	7	89861832	89861832	+	Missense_Mutation	SNP	G	G	A	rs194524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	121	139	0	0.991803	0	G|0.606;A|0.394	0.394	strong	.	STEAP2	78	.	NM_001040665	exon6	c.G1367A	p.R456Q	TAAGCCGAAAGCT	.	PASS	Atlas-SNP
LENG9	94059	hgsc.bcm.edu	37	19	54973307	54973307	+	Missense_Mutation	SNP	C	C	T	rs115799049	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	35	40	0	0.614035	0	C|0.977;T|0.023	0.023	strong	.	LENG9	46	.	NM_198988	exon1	c.G1469A	p.G490E	AAAGGCCCCCCTG	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50678369	50678369	+	Missense_Mutation	SNP	T	T	C	rs2228527	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	403	401	405	1	0.995037	0.00246914	T|0.820;C|0.180	0.180	strong	.	ERCC6	162	.	NM_000124	exon18	c.C3637G	p.L1213V	CGTCTCTGCAATG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093274	1093274	+	Missense_Mutation	SNP	C	C	T	rs11245949	bycluster;by2hit2allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	14	40	0	0.297872	0	C|1.000;|0.000	.	weak	.	MUC2	614	.	NM_002457	exon30	c.C5093T	p.S1698L	CAACATCGACACC	.	PASS	Atlas-SNP
CCDC108	255101	hgsc.bcm.edu	37	2	219895548	219895548	+	Missense_Mutation	SNP	C	C	A	rs56411706	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	45	101	0	0.473684	0	C|0.847;A|0.153	0.153	strong	.	CCDC108	208	.	NM_194302	exon9	c.G1024T	p.A342S	GCTGGGCGCACTT	.	PASS	Atlas-SNP
ZNF628	89887	hgsc.bcm.edu	37	19	55995272	55995272	+	Silent	SNP	G	G	A	rs11550705	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	44	76	0	0.494382	0	G|0.723;A|0.277	0.277	strong	.	ZNF628	75	.	NM_033113	exon3	c.G2712A	p.P904P	TGGCCCGGGCCCC	.	PASS	Atlas-SNP
HKR1	284459	hgsc.bcm.edu	37	19	37854580	37854580	+	Missense_Mutation	SNP	C	C	T	rs3745764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	59	111	0	0.464567	0	C|0.794;T|0.206	0.206	strong	.	HKR1	74	.	NM_181786	exon6	c.C1883T	p.T628I	AGAGGACACATTC	.	PASS	Atlas-SNP
ENPP5	59084	hgsc.bcm.edu	37	6	46135489	46135489	+	Missense_Mutation	SNP	T	T	C	rs6926570	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	31	55	0	0.525424	0	C|0.421;N|0.000	0.421	strong	.	ENPP5	44	.	NM_021572	exon2	c.A511G	p.I171V	ATTCAATAATTTT	.	PASS	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131196062	131196062	+	Silent	SNP	C	C	T	rs17744792	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	55	135	0	0.518868	0	C|0.871;T|0.129	0.129	strong	.	PODXL	53	.	NM_001018111	exon2	c.G231A	p.S77S	CTTGACCGAGGCC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168102774	168102774	+	Missense_Mutation	SNP	G	G	T	rs72884678	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	45	147	0	0.445545	0	G|0.968;T|0.032	0.032	strong	.	XIRP2	914	.	NM_152381	exon9	c.G4872T	p.L1624F	GATTTTGATTAGT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510146	195510146	+	Missense_Mutation	SNP	G	G	C	rs199750921		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	4	212	2	0.0377358	0.00943396	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C8305G	p.L2769V	CAGGAAGAGGGGT	.	scavenged	Atlas-SNP
SCAF8	22828	hgsc.bcm.edu	37	6	155152262	155152262	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	20	25	0	0.952381	0	.	.	none	.	SCAF8	122	.	NM_014892	exon19	c.A2347G	p.N783D	GGTGAAAACACCA	.	PASS	Atlas-SNP
MROH9	80133	hgsc.bcm.edu	37	1	170952652	170952652	+	Missense_Mutation	SNP	C	C	A	rs112394419	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	16	27	0	0.444444	0	C|0.996;A|0.004	0.004	strong	.	.	.	.	NM_025063	exon9	c.C706A	p.Q236K	TTTCAACAAGACG	.	PASS	Atlas-SNP
FAM63B	54629	hgsc.bcm.edu	37	15	59064214	59064214	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	36	79	0	0.439024	0	.	.	none	.	FAM63B	33	.	NM_001040450	exon1	c.G620A	p.G207D	AGGAGGGCGCGGC	.	PASS	Atlas-SNP
CLOCK	9575	hgsc.bcm.edu	37	4	56325365	56325365	+	Missense_Mutation	SNP	G	G	C	rs34897046	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	65	167	0	0.371429	0	G|0.964;C|0.036	0.036	strong	.	CLOCK	81	.	NM_004898	exon10	c.C623G	p.S208C	TAGGTAGATGGCT	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531545	140531545	+	Silent	SNP	C	C	T	rs138345434	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	10	5	8	0	0.5	0	C|0.997;T|0.003	0.003	strong	.	PCDHB6	161	.	NM_018939	exon1	c.C1707T	p.P569P	CGCGCCCTGCACC	.	PASS	Atlas-SNP
AIFM2	84883	hgsc.bcm.edu	37	10	71874048	71874048	+	Silent	SNP	G	G	A	rs1053495	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	29	52	0	0.508772	0	G|0.845;A|0.155	0.155	strong	.	AIFM2	33	.	NM_001198696	exon9	c.C1008T	p.D336D	CACACCGTCATTT	.	PASS	Atlas-SNP
ZCCHC2	54877	hgsc.bcm.edu	37	18	60227833	60227833	+	Silent	SNP	T	T	C	rs17070100	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	137	144	0	1	0	T|0.893;C|0.107	0.107	strong	.	ZCCHC2	64	.	NM_017742	exon8	c.T1506C	p.H502H	GCAGCATGCCATA	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170115672	170115672	+	Silent	SNP	A	A	G	rs33954745	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	69	162	0	0.448052	0	A|0.909;G|0.091	0.091	strong	.	LRP2	751	.	NM_004525	exon17	c.T2376C	p.D792D	AATCCAATCAAAA	.	PASS	Atlas-SNP
SBNO1	55206	hgsc.bcm.edu	37	12	123825559	123825559	+	Silent	SNP	C	C	T	rs12322888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	40	83	0	0.430108	0	C|0.728;T|0.272	0.272	strong	.	SBNO1	138	.	NM_001167856	exon4	c.G627A	p.K209K	CCTCATCTTCATG	.	PASS	Atlas-SNP
GH1	2688	hgsc.bcm.edu	37	17	61995241	61995241	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	2	134	0	0.0142857	0	.	.	none	GH1,NS,carcinoma,0,1	GH1	39	1	NM_000515	exon4	c.G335A	p.W112X	TCCAGCCACGACT	.	scavenged	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58752466	58752466	+	Missense_Mutation	SNP	C	C	T	rs11076256	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	27	62	0	0.415385	0	C|0.948;T|0.052	0.052	strong	.	GOT2	42	.	NM_002080	exon5	c.G562A	p.G188S	CAAAACCGCAAGT	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	14766	14766	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	52	26	0	0.981132	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.C20T	p.T7I	GCAAAACTAACCC	.	PASS	Atlas-SNP
PIK3R5	23533	hgsc.bcm.edu	37	17	8792029	8792029	+	Silent	SNP	A	A	G	rs381309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	19	72	0	0.345455	0	A|0.524;C|0.002	.	strong	.	PIK3R5	79	.	NM_001142633	exon10	c.T1075C	p.L359L	GGGACAAGGTGGA	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7435194	7435194	+	Silent	SNP	G	G	A	rs12498567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	20	48	0	0.4	0	G|0.868;A|0.132	0.132	strong	PSAPL1_ENST00000319098,NS,carcinoma,-1,2	PSAPL1	51	2	NM_001085382	exon1	c.C1413T	p.G471G	CCTGGGGCCGTGG	.	PASS	Atlas-SNP
CCDC164	92749	hgsc.bcm.edu	37	2	26667130	26667130	+	Missense_Mutation	SNP	A	A	G	rs3795958	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	73	125	0	0.540741	0	A|0.858;G|0.142	0.142	strong	.	CCDC164	84	.	NM_145038	exon9	c.A1069G	p.K357E	TATGCCAAGCAAA	.	PASS	Atlas-SNP
C9orf72	203228	hgsc.bcm.edu	37	9	27561628	27561628	+	Missense_Mutation	SNP	T	T	C	rs17769294	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	53	90	0	0.452991	0	T|0.919;C|0.081	0.081	strong	.	C9orf72	48	.	NM_018325	exon5	c.A620G	p.N207S	TCATCATTGAGTA	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104433034	104433034	+	Silent	SNP	A	A	G	rs10512285	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	170	187	0	0.994152	0	A|0.698;G|0.302	0.302	strong	.	GRIN3A	186	.	NM_133445	exon3	c.T1660C	p.L554L	TGTCCAATGTGGA	.	PASS	Atlas-SNP
OR10A7	121364	hgsc.bcm.edu	37	12	55615229	55615229	+	Missense_Mutation	SNP	T	T	C	rs151030005	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	236	114	245	0	0.483051	0	T|0.988;C|0.012	0.012	strong	.	OR10A7	53	.	NM_001005280	exon1	c.T421C	p.C141R	TCCCTATGCTTGT	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746069	143746069	+	Silent	SNP	T	T	C	rs3735999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	11	21	0	0.458333	0	T|0.479;C|0.521	0.521	strong	.	.	.	.	NM_003724	exon3	c.A1407G	p.P469P	AGCTTTTGGAGTC	.	PASS	Atlas-SNP
TLR8	51311	hgsc.bcm.edu	37	X	12924826	12924826	+	Missense_Mutation	SNP	A	A	G	rs3764880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	140	143	0	0.985915	0	A|0.639;0|0.017	.	strong	.	TLR8	134	.	NM_138636	exon1	c.A1G	p.M1V	AGAAACATGGTAA	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238434434	238434434	+	Missense_Mutation	SNP	C	C	T	rs11883500	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	45	112	0	0.463918	0	C|0.832;T|0.168	0.168	strong	.	MLPH	41	.	NM_001042467	exon7	c.C866T	p.T289I	TGGGGACTGCTGC	.	PASS	Atlas-SNP
SPTLC3	55304	hgsc.bcm.edu	37	20	13071816	13071816	+	Silent	SNP	C	C	T	rs6109692	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	83	165	0	0.461111	0	C|0.913;T|0.087	0.087	strong	.	SPTLC3	78	.	NM_018327	exon5	c.C693T	p.F231F	GGGATTCGCAACT	.	PASS	Atlas-SNP
SLC4A11	83959	hgsc.bcm.edu	37	20	3208967	3208967	+	Missense_Mutation	SNP	C	C	T	rs34224785	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	64	170	0	0.410256	0	C|0.988;T|0.012	0.012	strong	.	SLC4A11	188	.	NM_001174090	exon19	c.G2625A	p.M875I	GGAGCTCATGCCG	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170070348	170070348	+	Silent	SNP	T	T	C	rs11886219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	68	123	0	0.523077	0	T|0.827;C|0.173	0.173	strong	.	LRP2	751	.	NM_004525	exon36	c.A5859G	p.R1953R	GATCATTCGATCT	.	PASS	Atlas-SNP
CD82	3732	hgsc.bcm.edu	37	11	44636848	44636848	+	Silent	SNP	G	G	A	rs2303864	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	85	174	0	0.464481	0	G|0.994;A|0.006	0.006	strong	.	CD82	27	.	NM_002231	exon7	c.G363A	p.V121V	CATCGTGACTGAG	.	PASS	Atlas-SNP
CMC2	56942	hgsc.bcm.edu	37	16	81010073	81010073	+	Missense_Mutation	SNP	C	C	T	rs8388		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	8	22	0	0.444444	0	.	.	weak	.	.	.	.	NM_020188	exon4	c.G157A	p.V53I	TTTCTACGTACTG	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125631261	125631261	+	Missense_Mutation	SNP	G	G	A	rs79454313	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	22	61	0	0.468085	0	G|0.996;A|0.004	0.004	strong	.	ANKRD50	136	.	NM_020337	exon2	c.C406T	p.R136C	CACTGCGGCAGAT	.	PASS	Atlas-SNP
CDNF	441549	hgsc.bcm.edu	37	10	14867557	14867557	+	Silent	SNP	T	T	G	rs61843027	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	85	167	0	0.469613	0	T|0.983;G|0.017	0.017	strong	.	CDNF	19	.	NM_001029954	exon3	c.A306C	p.P102P	ACTCATTGGGCGA	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25260931	25260931	+	Silent	SNP	A	A	G	rs2227890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	65	150	1	0.416667	0.00666667	A|0.513;G|0.487	0.487	strong	PYGB,NS,carcinoma,0,1	PYGB	84	1	NM_002862	exon10	c.A1122G	p.A374A	CTGTGCATACACC	.	scavenged	Atlas-SNP
GYLTL1B	120071	hgsc.bcm.edu	37	11	45949746	45949746	+	Silent	SNP	A	A	C	rs11038714	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	33	77	0	0.532258	0	A|0.961;C|0.039	0.039	strong	.	GYLTL1B	45	.	NM_152312	exon13	c.A1773C	p.R591R	GCCCCGAGGCCAC	.	PASS	Atlas-SNP
LMBR1	64327	hgsc.bcm.edu	37	7	156556385	156556385	+	Silent	SNP	G	G	C	rs138255184	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	52	110	0	0.504854	0	G|0.994;C|0.006	0.006	strong	.	LMBR1	35	.	NM_022458	exon6	c.C528G	p.A176A	GCTTGCGGCATCG	.	PASS	Atlas-SNP
CCDC94	55702	hgsc.bcm.edu	37	19	4267681	4267681	+	Missense_Mutation	SNP	C	C	T	rs149224144	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	87	126	0	0.524096	0	C|0.996;T|0.004	0.004	strong	.	CCDC94	28	.	NM_018074	exon7	c.C769T	p.R257W	GGCAGCCGGCCCC	.	PASS	Atlas-SNP
RBP1	5947	hgsc.bcm.edu	37	3	139258411	139258411	+	Silent	SNP	G	G	A	rs11549984	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	44	66	0	0.52381	0	G|0.910;A|0.090	0.090	strong	.	RBP1	39	.	NM_002899	exon1	c.C150T	p.R50R	AAGCGGGCGGGAC	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2092803	2092803	+	Silent	SNP	A	A	G	rs1063523	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	30	46	0	0.47619	0	A|0.741;G|0.259	0.259	strong	.	MYOM2	251	.	NM_003970	exon37	c.A4296G	p.T1432T	CGTGACAGTGAGC	.	PASS	Atlas-SNP
TMIGD2	126259	hgsc.bcm.edu	37	19	4292597	4292597	+	Silent	SNP	C	C	T	rs888932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	31	22	0	0.607843	0	C|0.569;T|0.431	0.431	strong	.	TMIGD2	38	.	NM_144615	exon5	c.G848A	p.X283X	ATCTCTCACTCCT	.	PASS	Atlas-SNP
MMP3	4314	hgsc.bcm.edu	37	11	102713465	102713465	+	Silent	SNP	A	A	G	rs602128	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	77	106	0	0.484277	0	A|0.461;G|0.539	0.539	strong	MMP3,NS,carcinoma,0,1	MMP3	60	1	NM_002422	exon2	c.T288C	p.D96D	ACCAACATCAGGA	.	PASS	Atlas-SNP
ACSM5	54988	hgsc.bcm.edu	37	16	20441053	20441053	+	Missense_Mutation	SNP	C	C	G	rs8062344	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	24	57	0	0.436364	0	C|0.598;G|0.402	0.402	strong	ACSM5,NS,carcinoma,-1,1	ACSM5	101	1	NM_017888	exon8	c.C1055G	p.P352R	TCAACCCTGACGT	.	PASS	Atlas-SNP
TSPYL6	388951	hgsc.bcm.edu	37	2	54482964	54482964	+	Missense_Mutation	SNP	C	C	T	rs843704	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	35	71	0	0.486111	0	C|0.746;T|0.253	0.253	strong	TSPYL6,NS,carcinoma,0,1	TSPYL6	54	1	NM_001003937	exon1	c.G325A	p.G109S	GGCTGCCGTCAGT	.	PASS	Atlas-SNP
ADAM7	8756	hgsc.bcm.edu	37	8	24350715	24350715	+	Silent	SNP	G	G	A	rs12547971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	42	71	0	0.482759	0	G|0.925;A|0.075	0.075	strong	.	ADAM7	165	.	NM_003817	exon16	c.G1815A	p.A605A	GGTGGCGTCAGGA	.	PASS	Atlas-SNP
SYNRG	11276	hgsc.bcm.edu	37	17	35937637	35937637	+	Missense_Mutation	SNP	T	T	C	rs12602536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	150	164	1	0.980392	0.00609756	C|0.151;T|0.849	0.151	strong	SYNRG,NS,carcinoma,0,1	SYNRG	101	1	NM_007247	exon7	c.A664G	p.T222A	CAGAAGTATTTAA	.	PASS	Atlas-SNP
FAM47C	442444	hgsc.bcm.edu	37	X	37029254	37029254	+	Missense_Mutation	SNP	A	A	C	rs1995914	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	85	91	0	1	0	A|0.631;C|0.369	0.369	strong	.	FAM47C	267	.	NM_001013736	exon1	c.A2771C	p.N924T	TCCAGAATGCACC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195517124	195517124	+	Silent	SNP	G	G	A	rs1806440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	77	186	0	0.469512	0	G|0.871;A|0.129	0.129	strong	.	MUC4	1505	.	NM_018406	exon2	c.C1327T	p.L443L	GAGGTAGAGAACT	.	PASS	Atlas-SNP
CXorf36	79742	hgsc.bcm.edu	37	X	45051111	45051111	+	Missense_Mutation	SNP	C	C	T	rs1132201	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	68	0	1	0	0|0.013;T|0.348	0.348	strong	.	CXorf36	53	.	NM_176819	exon2	c.G383A	p.R128K	CAGATTCTCCTGT	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449383	89449383	+	Missense_Mutation	SNP	G	G	A	rs71216132		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	381	66	249	0	0.173228	0	G|0.500;A|0.500	0.500	weak	CCBL2,NS,carcinoma,0,1	.	.	1	NM_001162536	exon3	c.C127T	p.R43C	TTTCACGGTCTTT	.	PASS	Atlas-SNP
ATP8A2	51761	hgsc.bcm.edu	37	13	26273403	26273403	+	Silent	SNP	C	C	A	rs7335858	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	50	92	0	0.515464	0	C|0.913;A|0.087	0.087	strong	ATP8A2,middle_lobe,carcinoma,+1,1	ATP8A2	181	1	NM_016529	exon25	c.C2304A	p.T768T	CCACACCCTGAAG	.	PASS	Atlas-SNP
ANKMY2	57037	hgsc.bcm.edu	37	7	16655387	16655387	+	Silent	SNP	C	C	T	rs11540037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	57	114	0	0.495652	0	T|0.144;G|0.146;C|0.687;A|0.024	0.144	strong	.	ANKMY2	46	.	NM_020319	exon5	c.G513A	p.T171T	AAGATTCGTTGTG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378387	31378387	+	Silent	SNP	T	T	C	rs1063631	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	238	234	215	1	0.983193	0.00465116	T|0.642;C|0.358	0.358	strong	MICA,bladder,carcinoma,0,1	MICA	21	1	NM_001177519	exon2	c.T138C	p.L46L	GTTTCTTGCTGAG	.	PASS	Atlas-SNP
THOC5	8563	hgsc.bcm.edu	37	22	29908072	29908072	+	Missense_Mutation	SNP	C	C	T	rs1049534	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	193	191	0	0.994845	0	C|0.771;T|0.229	0.229	strong	.	THOC5	58	.	NM_001002878	exon19	c.G1735A	p.V579I	GGAAAACAGGTGG	.	PASS	Atlas-SNP
PRMT2	3275	hgsc.bcm.edu	37	21	48071901	48071901	+	Missense_Mutation	SNP	C	C	T	rs77776707	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	70	93	0	0.454545	0	C|0.992;T|0.008	0.008	strong	.	PRMT2	48	.	NM_001242865	exon7	c.C838T	p.P280S	TCCTGGCCCATCT	.	PASS	Atlas-SNP
RSPH4A	345895	hgsc.bcm.edu	37	6	116951678	116951678	+	Missense_Mutation	SNP	A	A	C	rs9488991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	102	165	0	0.87931	0	A|0.888;C|0.112	0.112	strong	.	RSPH4A	54	.	NM_001010892	exon5	c.A1879C	p.N627H	CAATCCAACCTTT	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023444	25023444	+	Missense_Mutation	SNP	G	G	T	rs201546887		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	312	51	237	1	0.163462	0.00421941	.	.	weak	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon12	c.G1066T	p.A356S	CTCCGGGCCCAGA	.	scavenged	Atlas-SNP
ZNF195	7748	hgsc.bcm.edu	37	11	3381369	3381369	+	Missense_Mutation	SNP	G	G	C	rs62619253	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	42	90	0	0.428571	0	G|0.817;C|0.183	0.183	strong	.	ZNF195	77	.	NM_001130520	exon6	c.C869G	p.P290R	TTCTCAGGTTCAG	.	PASS	Atlas-SNP
RSAD1	55316	hgsc.bcm.edu	37	17	48559559	48559559	+	Silent	SNP	A	A	G	rs7210579	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	83	71	0	1	0	A|0.693;G|0.307	0.307	strong	RSAD1,colon,carcinoma,0,1	RSAD1	36	1	NM_018346	exon4	c.A582G	p.V194V	GTCTGTAGACTTG	.	PASS	Atlas-SNP
ISX	91464	hgsc.bcm.edu	37	22	35463249	35463249	+	Missense_Mutation	SNP	C	C	T	rs362090	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	95	81	0	0.989583	0	C|0.453;T|0.547	0.547	strong	.	ISX	62	.	NM_001008494	exon1	c.C169T	p.P57S	GAGGGCCCCGGAG	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951754	130951754	+	Missense_Mutation	SNP	G	G	T	rs76585620	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	401	116	409	1	0.289277	0.00244499	G|0.500;T|0.500	0.500	weak	.	TUBA3E	73	.	NM_207312	exon4	c.C661A	p.R221S	TGGGACGTTCAAT	.	PASS	Atlas-SNP
CASP9	842	hgsc.bcm.edu	37	1	15850603	15850603	+	Silent	SNP	G	G	A	rs4645983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	18	19	0	0.692308	0	G|0.777;A|0.223	0.223	strong	.	CASP9	40	.	NM_001229	exon1	c.C93T	p.S31S	CTCGCGGCTCAGC	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641255	55641255	+	Nonsense_Mutation	SNP	C	C	T	rs4522268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	92	244	0	0.429907	0	C|0.743;N|0.000	.	strong	OR6C74,colon,carcinoma,0,6	OR6C74	52	6	NM_001005490	exon1	c.C184T	p.R62X	TTCCTCCGAAATT	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79041057	79041057	+	Missense_Mutation	SNP	A	A	G	rs12514461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	66	122	0	0.481752	0	A|0.904;G|0.096	0.096	strong	.	CMYA5	643	.	NM_153610	exon4	c.A10747G	p.K3583E	TGTAGTAAAAATG	.	PASS	Atlas-SNP
FAM53A	152877	hgsc.bcm.edu	37	4	1656801	1656801	+	Silent	SNP	A	A	C	rs62287700	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	23	30	0	0.534884	0	A|0.738;C|0.262	0.262	strong	FAM53A,NS,carcinoma,0,1	FAM53A	25	1	NM_001013622	exon4	c.T786G	p.P262P	CACGCAAGGCTGT	.	PASS	Atlas-SNP
SBK1	388228	hgsc.bcm.edu	37	16	28328916	28328916	+	Silent	SNP	C	C	T	rs113394773	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	89	142	0	0.436274	0	C|0.945;T|0.055	0.055	strong	.	SBK1	36	.	NM_001024401	exon2	c.C204T	p.D68D	GGTTGACCTGGTG	.	PASS	Atlas-SNP
RTN4	57142	hgsc.bcm.edu	37	2	55253973	55253973	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	120	232	0	0.528634	0	.	.	none	.	RTN4	189	.	NM_020532	exon3	c.A1262C	p.D421A	TTTTTATCCACTT	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388724	1388724	+	Missense_Mutation	SNP	C	C	G	rs76728908	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	12	24	2	0.307692	0.0833333	C|0.500;G|0.500	0.500	weak	CRIPAK,NS,other,0,1	CRIPAK	185	1	NM_175918	exon1	c.C425G	p.P142R	CGTGCCCATGCGG	.	scavenged	Atlas-SNP
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703248	56703248	+	Missense_Mutation	SNP	G	G	A	rs527025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	39	83	0	0.448276	0	G|0.725;A|0.275	0.275	strong	.	ZSCAN5B	160	.	NM_001080456	exon2	c.C559T	p.P187S	CCCTGGGCAGGAT	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40383905	40383905	+	Silent	SNP	G	G	A	rs75088257	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	409	75	331	1	0.183374	0.00302115	G|0.667;A|0.333	0.333	strong	FCGBP,NS,carcinoma,0,6	FCGBP	416	6	NM_003890	exon21	c.C9705T	p.C3235C	AGGCCCGCAGCGA	.	scavenged	Atlas-SNP
CEP63	80254	hgsc.bcm.edu	37	3	134278270	134278270	+	Missense_Mutation	SNP	C	C	T	rs1127826	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	75	0	0.5	0	C|0.695;T|0.305	0.305	strong	.	CEP63	56	.	NM_025180	exon15	c.C1952T	p.S651L	TATCTTCGGTATG	.	PASS	Atlas-SNP
STON1-GTF2A1L	286749	hgsc.bcm.edu	37	2	48896897	48896897	+	Missense_Mutation	SNP	A	A	G	rs33987892	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	47	118	0	0.382114	0	A|0.985;G|0.015	0.015	strong	.	STON1-GTF2A1L	180	.	NM_001198593	exon9	c.A3127G	p.T1043A	CGGGTTACTGATG	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361452	107361452	+	Silent	SNP	C	C	G	rs75081605		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	390	76	607	0	0.194872	0	.	.	weak	OR13C5,NS,carcinoma,-2,1	OR13C5	60	1	NM_001004482	exon1	c.G243C	p.T81T	CACTAGCGTGGAG	.	PASS	Atlas-SNP
TEC	7006	hgsc.bcm.edu	37	4	48165757	48165757	+	Silent	SNP	G	G	A	rs16861083	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	53	92	0	0.410853	0	G|0.950;A|0.050	0.050	strong	TEC,NS,carcinoma,0,1	TEC	81	1	NM_003215	exon8	c.C699T	p.Y233Y	CGTTACGTAATTA	.	PASS	Atlas-SNP
PDGFA	5154	hgsc.bcm.edu	37	7	552046	552046	+	Silent	SNP	A	A	G	rs1129401	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	67	111	0	0.515385	0	A|0.769;G|0.231	0.231	strong	.	PDGFA	34	.	NM_002607	exon3	c.T207C	p.H69H	AGTGGCATGGACC	.	PASS	Atlas-SNP
LRRC61	65999	hgsc.bcm.edu	37	7	150034378	150034378	+	Missense_Mutation	SNP	A	A	G	rs3735169	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	46	0	1	0	A|0.744;G|0.256	0.256	strong	.	LRRC61	17	.	NM_023942	exon2	c.A428G	p.N143S	GTGCCAACCCCTC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557486	32557486	+	Missense_Mutation	SNP	T	T	A	rs201540428	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	247	22	278	0	0.0890688	0	T|0.848;A|0.152	0.152	strong	HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.A34T	p.M12L	CTGTCATGCAGGA	.	PASS	Atlas-SNP
AXIN1	8312	hgsc.bcm.edu	37	16	396264	396264	+	Silent	SNP	A	A	G	rs1805105	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	51	83	0	0.573034	0	A|0.335;G|0.665	0.665	strong	.	AXIN1	290	.	NM_181050	exon2	c.T762C	p.D254D	GTCCTCATCCATG	.	PASS	Atlas-SNP
PLIN3	10226	hgsc.bcm.edu	37	19	4847868	4847868	+	Silent	SNP	G	G	A	rs10406652	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	59	91	0	0.472	0	G|0.867;A|0.132	0.132	strong	.	PLIN3	36	.	NM_001164189	exon6	c.C669T	p.V223V	GGACGCGACGTCA	.	PASS	Atlas-SNP
OR4M2	390538	hgsc.bcm.edu	37	15	22369290	22369290	+	Missense_Mutation	SNP	A	A	G	rs75045725		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	498	162	408	0	0.325301	0	.	.	weak	OR4M2,NS,carcinoma,0,1	OR4M2	140	1	NM_001004719	exon1	c.A715G	p.M239V	AGGGCCATGTCCA	.	PASS	Atlas-SNP
T	6862	hgsc.bcm.edu	37	6	166571935	166571935	+	Silent	SNP	C	C	T	rs35819705	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	46	83	0	0.766667	0	C|0.771;T|0.229	0.229	strong	.	T	77	.	NM_003181	exon9	c.G1176A	p.A392A	AGAGGGCGCCGAG	.	PASS	Atlas-SNP
NOV	4856	hgsc.bcm.edu	37	8	120431506	120431506	+	Missense_Mutation	SNP	G	G	A	rs11538929	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	24	61	0	0.342857	0	G|0.931;A|0.069	0.069	strong	.	NOV	51	.	NM_002514	exon4	c.G698A	p.R233H	GGAACCGTCAATG	.	PASS	Atlas-SNP
TSSK2	23617	hgsc.bcm.edu	37	22	19119751	19119751	+	Missense_Mutation	SNP	C	C	T	rs1052763	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	36	41	1	0.507042	0.0243902	C|0.762;T|0.238	0.238	strong	TSSK2,NS,carcinoma,-1,1	TSSK2	29	1	NM_053006	exon1	c.C839T	p.T280M	AAGCCACGTCTTC	.	scavenged	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68671477	68671477	+	Silent	SNP	T	T	C	rs1249463	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	60	30	0	1	0	T|0.304;C|0.696	0.696	strong	.	IGHMBP2	83	.	NM_002180	exon1	c.T57C	p.L19L	GGAGCTTGAGAGA	.	PASS	Atlas-SNP
C8B	732	hgsc.bcm.edu	37	1	57409459	57409459	+	Missense_Mutation	SNP	C	C	A	rs139498867	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	74	159	0	0.427746	0	C|0.994;A|0.006	0.006	strong	.	C8B	107	.	NM_000066	exon8	c.G1144T	p.D382Y	TAAAATCATTTTT	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55331308	55331308	+	Missense_Mutation	SNP	C	C	A	rs1065331	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	111	123	0	0.486842	0	C|0.968;A|0.032	0.032	strong	KIR3DL1_ENST00000402254,NS,carcinoma,-1,2	KIR3DL1	174	2	NM_013289	exon4	c.C496A	p.R166S	CCCTCACGCCTCG	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143156	55143156	+	Silent	SNP	T	T	C	rs34880987	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	230	117	240	0	0.508696	0	.	.	alt	.	LILRB1	140	.	NM_001081637	exon4	c.T276C	p.H92H	GGAACATGCAGGG	.	PASS	Atlas-SNP
GLB1L	79411	hgsc.bcm.edu	37	2	220107997	220107997	+	Missense_Mutation	SNP	G	G	A	rs147143842	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	40	130	0	0.412371	0	G|0.991;A|0.009	0.009	strong	.	GLB1L	52	.	NM_024506	exon3	c.C112T	p.R38W	GAAACCGGTCATG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512945	4512945	+	Missense_Mutation	SNP	C	C	T	rs75031432	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	82	324	3	0.987952	0.00925926	C|0.826;T|0.174	0.174	strong	PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	NM_001080400	exon3	c.G985A	p.G329S	TGGCACCAGTCAC	.	scavenged	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	561	73	555	1	0.130125	0.0018018	G|0.987;A|0.013	0.013	strong	OR2T3,NS,carcinoma,0,3	OR2T3	79	3	NM_001005495	exon1	c.G730A	p.A244T	GCCTTGGCCACCT	.	scavenged	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33875262	33875262	+	Missense_Mutation	SNP	T	T	A	rs8073060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	36	68	0	0.610169	0	T|0.694;A|0.306	0.306	strong	.	SLFN14	43	.	NM_001129820	exon4	c.A2735T	p.Y912F	TTTCAGTAGGCTG	.	PASS	Atlas-SNP
OR6K3	391114	hgsc.bcm.edu	37	1	158687224	158687224	+	Missense_Mutation	SNP	G	G	A	rs857703	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	47	120	0	0.474747	0	G|0.696;A|0.304	0.304	strong	OR6K3,NS,carcinoma,0,1	OR6K3	101	1	NM_001005327	exon1	c.C682T	p.P228S	AAGAGGGAATCCT	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383027	39383027	+	Missense_Mutation	SNP	G	G	T	rs71371478	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	8	66	0	0.117647	0	G|0.997;T|0.003	0.003	strong	KRTAP9-2,extremity,malignant_melanoma,0,1	KRTAP9-2	24	1	NM_031961	exon1	c.G121T	p.A41S	CAGCCCGCCTGCT	.	scavenged	Atlas-SNP
HGS	9146	hgsc.bcm.edu	37	17	79663931	79663931	+	Silent	SNP	T	T	C	rs8070488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	107	0	1	0	T|0.742;C|0.258	0.258	strong	.	HGS	54	.	NM_004712	exon18	c.T1785C	p.P595P	CAGCCCTGCCGGC	.	PASS	Atlas-SNP
SPTA1	6708	hgsc.bcm.edu	37	1	158582646	158582646	+	Silent	SNP	T	T	C	rs2251969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	33	82	0	0.407407	0	T|0.458;C|0.542	0.542	strong	SPTA1,NS,carcinoma,-2,2	SPTA1	720	2	NM_003126	exon51	c.A7095G	p.A2365A	GCCCTCTGCCAGG	.	PASS	Atlas-SNP
ITPR1	3708	hgsc.bcm.edu	37	3	4829732	4829732	+	Silent	SNP	A	A	G	rs13079522	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	112	210	0	0.568528	0	A|0.754;G|0.246	0.246	strong	.	ITPR1	659	.	NM_001168272	exon51	c.A6672G	p.T2224T	TACTACAGAGAGA	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632820	32632820	+	Missense_Mutation	SNP	C	C	G	rs1130375	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	16	0	0	0.592593	.	G|0.228;C|0.772	0.228	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.G134C	p.G45A	CACATGCCCTTAA	.	PASS	Atlas-SNP
GNL3	26354	hgsc.bcm.edu	37	3	52727257	52727257	+	Missense_Mutation	SNP	G	G	A	rs2289247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	87	163	0	0.462766	0	G|0.533;A|0.467	0.467	strong	GNL3,caecum,carcinoma,-1,1	GNL3	37	1	NM_014366	exon11	c.G1099A	p.V367M	TTTACTGTGCTTG	.	PASS	Atlas-SNP
NDUFS1	4719	hgsc.bcm.edu	37	2	207008763	207008763	+	Silent	SNP	C	C	A	rs1127566	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	66	70	1	1	0.0142857	C|0.495;A|0.505	0.505	strong	NDUFS1,NS,carcinoma,0,1	NDUFS1	82	1	NM_001199984	exon10	c.G1008T	p.A336A	AGAGAGCGCATCC	.	scavenged	Atlas-SNP
MAML3	55534	hgsc.bcm.edu	37	4	140811117	140811117	+	Silent	SNP	C	C	T	rs62344938		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	14	80	0	0.254545	0	.	.	weak	.	MAML3	192	.	NM_018717	exon2	c.G1473A	p.Q491Q	CTGCTGCTGCTGT	.	PASS	Atlas-SNP
C19orf71	100128569	hgsc.bcm.edu	37	19	3543397	3543397	+	Missense_Mutation	SNP	C	C	T	rs12608919	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	63	40	0	1	0	C|0.611;T|0.389	0.389	strong	C19orf71,colon,carcinoma,0,1	C19orf71	12	1	NM_001135580	exon2	c.C248T	p.P83L	GGGCCCCGGCCAG	.	PASS	Atlas-SNP
POGK	57645	hgsc.bcm.edu	37	1	166818566	166818566	+	Silent	SNP	A	A	G	rs2075946	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	35	65	0	0.530303	0	A|0.786;G|0.214	0.214	strong	.	POGK	54	.	NM_017542	exon5	c.A750G	p.A250A	GCGGGCATTCCGA	.	PASS	Atlas-SNP
LILRA1	11024	hgsc.bcm.edu	37	19	55106288	55106288	+	Missense_Mutation	SNP	A	A	C	rs147848714	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	297	11	232	0	0.037037	0	A|0.996;C|0.004	0.004	strong	LILRA1,colon,carcinoma,0,1	LILRA1	105	1	NM_006863	exon4	c.A229C	p.I77L	CAGGAGATTGTGA	.	scavenged	Atlas-SNP
RNF180	285671	hgsc.bcm.edu	37	5	63665448	63665448	+	Missense_Mutation	SNP	G	G	A	rs76090587	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	86	191	0	0.49711	0	G|0.925;A|0.075	0.075	strong	.	RNF180	94	.	NM_001113561	exon8	c.G1586A	p.R529H	GTTTCCGCAGACA	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11809063	11809063	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	3	117	0	0.0181818	0	.	.	none	DNAH9,mouth,carcinoma,0,1	DNAH9	695	1	NM_001372	exon61	c.G11686A	p.A3896T	GGACCAGCCACTC	.	scavenged	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74897816	74897816	+	Silent	SNP	C	C	T	rs2271905	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	31	94	0	0.3875	0	C|0.809;T|0.191	0.191	strong	ECD,NS,carcinoma,0,1	ECD	50	1	NM_001135752	exon13	c.G1533A	p.E511E	TGGAGCCTCAGAA	.	PASS	Atlas-SNP
SPATA4	132851	hgsc.bcm.edu	37	4	177113956	177113956	+	Silent	SNP	A	A	G	rs2291244	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	42	85	0	0.6	0	A|0.801;G|0.199	0.199	strong	.	SPATA4	44	.	NM_144644	exon4	c.T510C	p.Y170Y	GTAGCTATAGTCC	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248925	48248925	+	Silent	SNP	C	C	A	rs144346550	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	71	100	0	0.452229	0	C|0.981;A|0.019	0.019	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.C109A	p.R37R	AGGCGGCGGCGGC	.	PASS	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152772264	152772264	+	Missense_Mutation	SNP	A	A	G	rs214976	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	62	122	0	0.984127	0	G|0.567;N|0.000	0.567	strong	.	SYNE1	3227	.	NM_033071	exon26	c.T3125C	p.V1042A	TCTTCTACAGAGG	.	PASS	Atlas-SNP
CYP4V2	285440	hgsc.bcm.edu	37	4	187122332	187122332	+	Missense_Mutation	SNP	G	G	A	rs34745240	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	49	93	0	0.563218	0	G|0.961;A|0.039	0.039	strong	.	CYP4V2	49	.	NM_207352	exon7	c.G823A	p.E275K	GCCAATGAAATGA	.	PASS	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	37	3	69271032	69271032	+	Silent	SNP	G	G	A	rs62254461	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	40	79	0	0.454545	0	G|0.928;A|0.072	0.072	strong	.	FRMD4B	90	.	NM_015123	exon9	c.C708T	p.L236L	TCGAGTGAGACCT	.	PASS	Atlas-SNP
HMGCS1	3157	hgsc.bcm.edu	37	5	43297144	43297144	+	Silent	SNP	A	A	G	rs3733769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	92	143	0	0.571429	0	A|0.589;G|0.411	0.411	strong	.	HMGCS1	33	.	NM_001098272	exon5	c.T699C	p.Y233Y	GACAGAATAGCAG	.	PASS	Atlas-SNP
C4orf40	401137	hgsc.bcm.edu	37	4	71024240	71024240	+	Missense_Mutation	SNP	C	C	T	rs1613461	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	106	205	0	0.509615	0	C|0.971;T|0.029	0.029	strong	.	C4orf40	19	.	NM_214711	exon3	c.C271T	p.R91C	CACATCCGTGGTT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264795	1264795	+	Missense_Mutation	SNP	G	G	C	rs200138247	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	322	117	347	0	0.363354	0	.	.	weak	.	MUC5B	473	.	NM_002458	exon31	c.G6685C	p.E2229Q	ATCACAGAGCCTT	.	PASS	Atlas-SNP
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107531152	107531152	+	Missense_Mutation	SNP	G	G	C	rs10761084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	66	148	1	0.507692	0.00675676	G|0.846;C|0.154	0.154	strong	NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	NM_018376	exon3	c.G280C	p.A94P	AATTTTGCTCATC	.	scavenged	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1783027	1783027	+	Missense_Mutation	SNP	T	T	C	rs60482625	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	42	102	0	0.442105	0	T|0.934;C|0.066	0.066	strong	.	ATP8B3	108	.	NM_138813	exon29	c.A3903G	p.X1301W	GAGGTGTCACTGT	.	PASS	Atlas-SNP
ANKUB1	389161	hgsc.bcm.edu	37	3	149484970	149484970	+	Silent	SNP	G	G	A	rs75077284	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	43	84	0	0.425743	0	G|0.975;A|0.025	0.025	strong	.	ANKUB1	27	.	NM_001144960	exon5	c.C1479T	p.N493N	GATTGCGTTCTCC	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1729953	1729953	+	Missense_Mutation	SNP	G	G	A	rs17132047	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	28	55	0	0.482759	0	G|0.827;A|0.173	0.173	strong	TACC3,NS,carcinoma,0,1	TACC3	69	1	NM_006342	exon4	c.G824A	p.C275Y	TGGGCTGCCCTGC	.	PASS	Atlas-SNP
MCF2L2	23101	hgsc.bcm.edu	37	3	183027542	183027542	+	Missense_Mutation	SNP	T	T	G	rs7639705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	73	124	0	0.503448	0	T|0.718;G|0.282	0.282	strong	MCF2L2,NS,carcinoma,0,1	MCF2L2	164	1	NM_015078	exon10	c.A1075C	p.I359L	TAAGAATCTGCTC	.	PASS	Atlas-SNP
MANBA	4126	hgsc.bcm.edu	37	4	103611845	103611845	+	Missense_Mutation	SNP	C	C	T	rs227368	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	148	128	1	1	0.0078125	T|0.377;G|0.002;C|0.617;A|0.004	0.377	strong	.	MANBA	78	.	NM_005908	exon6	c.G757A	p.V253I	TGGCTACGATCAC	.	PASS	Atlas-SNP
TMEM198	130612	hgsc.bcm.edu	37	2	220414019	220414019	+	Silent	SNP	T	T	C	rs13023533	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	94	201	2	0.537143	0.00995025	T|0.559;C|0.441	0.441	strong	TMEM198,NS,carcinoma,0,2	TMEM198	36	2	NM_001005209	exon4	c.T888C	p.P296P	AGACCCTGCTTAT	.	scavenged	Atlas-SNP
SERPINB8	5271	hgsc.bcm.edu	37	18	61654297	61654297	+	Missense_Mutation	SNP	A	A	G	rs3169983	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	58	107	0	0.491525	0	A|0.851;G|0.149	0.149	strong	.	SERPINB8	42	.	NM_198833	exon7	c.A910G	p.T304A	ATGTCAACTGAGA	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1546911	1546911	+	Missense_Mutation	SNP	C	C	G	rs2243603	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	46	42	0	1	0	C|0.188;G|0.812	0.812	strong	.	SIRPB1	83	.	NM_006065	exon5	c.G1087C	p.A363P	GCGCTGCTTCTGG	.	PASS	Atlas-SNP
GLRX5	51218	hgsc.bcm.edu	37	14	96010424	96010424	+	Missense_Mutation	SNP	G	G	A	rs11628901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	42	105	0	0.456522	0	G|0.897;A|0.103	0.103	strong	.	GLRX5	7	.	NM_016417	exon2	c.G436A	p.A146T	CACTCCGCCCTTT	.	PASS	Atlas-SNP
PEBP4	157310	hgsc.bcm.edu	37	8	22570905	22570905	+	Missense_Mutation	SNP	T	T	G	rs79936857	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	59	131	0	0.546296	0	T|0.962;G|0.038	0.038	strong	.	PEBP4	23	.	NM_144962	exon7	c.A662C	p.Q221P	TCCGCCTGGTTTT	.	PASS	Atlas-SNP
VSIG10	54621	hgsc.bcm.edu	37	12	118506186	118506186	+	Silent	SNP	A	A	T	rs67405503	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	115	215	0	0.522727	0	A|0.602;T|0.398	0.398	strong	.	VSIG10	41	.	NM_019086	exon8	c.T1563A	p.L521L	ACCTTGAAGATCC	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84213114	84213114	+	Silent	SNP	C	C	T	rs2230130	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	38	31	0	1	0	C|0.709;T|0.291	0.291	strong	.	TAF1C	60	.	NM_005679	exon14	c.G2043A	p.V681V	GCGGAGCACACCC	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12542654	12542654	+	Missense_Mutation	SNP	T	T	A	rs369138475	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	96	214	0	0.48731	0	.	.	alt	.	ZNF443	63	.	NM_005815	exon4	c.A332T	p.K111I	ATGACTTTTTCTC	.	PASS	Atlas-SNP
ASCC2	84164	hgsc.bcm.edu	37	22	30189642	30189642	+	Missense_Mutation	SNP	C	C	T	rs61736786	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	18	49	0	0.428571	0	C|0.974;T|0.026	0.026	strong	.	ASCC2	53	.	NM_032204	exon16	c.G1712A	p.R571Q	AAACTCCGCGTGT	.	PASS	Atlas-SNP
PJA1	64219	hgsc.bcm.edu	37	X	68382422	68382422	+	Silent	SNP	C	C	T	rs149179614	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	91	89	0	0.98913	0	C|0.999;T|0.001	0.001	strong	.	PJA1	106	.	NM_145119	exon2	c.G660A	p.S220S	CCTCTCCGAGCTG	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65622420	65622420	+	Silent	SNP	G	G	A	rs183814213	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	19	291	0	0.113772	0	G|1.000;A|0.000	0.000	strong	.	EYS	527	.	NM_001142800	exon16	c.C2598T	p.C866C	AGCTAAGCATGTT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911154	29911154	+	Missense_Mutation	SNP	C	C	A	rs1059509	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	139	172	0	0.978873	0	A|0.451;C|0.549	0.451	strong	.	HLA-A	89	.	NM_001242758	exon3	c.C453A	p.N151K	CCTGAACGAGGAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911064	29911064	+	Missense_Mutation	SNP	A	A	G	rs1136695	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	81	125	0	0.975904	0	A|0.399;G|0.601	0.601	strong	.	HLA-A	89	.	NM_001242758	exon3	c.A363G	p.I121M	CCAGATAATGTAT	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124114068	124114068	+	Silent	SNP	G	G	A	rs9841322	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	175	160	0	0.988701	0	G|0.886;A|0.114	0.114	strong	.	KALRN	556	.	NM_003947	exon12	c.G2043A	p.K681K	GATCAAGCAGTTC	.	PASS	Atlas-SNP
KRT6C	286887	hgsc.bcm.edu	37	12	52867190	52867190	+	Missense_Mutation	SNP	C	C	T	rs61914499	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	350	35	369	0	0.1	0	C|0.500;T|0.500	0.500	weak	KRT6C,brain,glioma,0,1	KRT6C	55	1	NM_173086	exon1	c.G332A	p.G111D	CCCAGACCAAAGC	.	scavenged	Atlas-SNP
DIMT1	27292	hgsc.bcm.edu	37	5	61694379	61694379	+	Silent	SNP	T	T	C	rs247264	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	201	198	1	0.990148	0.00505051	T|0.437;C|0.563	0.563	strong	.	.	.	.	NM_014473	exon6	c.A405G	p.S135S	AAAAGGTGAAGAG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373111	5373111	+	Missense_Mutation	SNP	G	G	A	rs7479477	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	62	240	0	0.350282	0	G|0.768;A|0.232	0.232	strong	.	OR51B6	53	.	NM_001004750	exon1	c.G374A	p.R125H	CCATCCGCAGCCC	.	PASS	Atlas-SNP
SDCBP2	27111	hgsc.bcm.edu	37	20	1293046	1293046	+	Missense_Mutation	SNP	G	G	A	rs1048621	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	30	83	0	0.361446	0	G|0.816;A|0.184	0.184	strong	.	SDCBP2	78	.	NM_080489	exon7	c.C667T	p.R223C	CGTTGCGGGCCGC	.	PASS	Atlas-SNP
SIPA1L2	57568	hgsc.bcm.edu	37	1	232568041	232568041	+	Missense_Mutation	SNP	G	G	A	rs1547742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	58	159	0	0.487395	0	G|0.931;A|0.069	0.069	strong	SIPA1L2,colon,carcinoma,0,1	SIPA1L2	218	1	NM_020808	exon14	c.C4208T	p.S1403L	CCCTCCGATTTCT	.	PASS	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44418824	44418824	+	Missense_Mutation	SNP	C	C	T	rs399098	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	134	140	0	1	0	C|0.566;T|0.434	0.434	strong	ZNF45,NS,adenoma,0,1	ZNF45	51	1	NM_003425	exon10	c.G764A	p.R255K	ACATTCCTCCCAC	.	PASS	Atlas-SNP
GGCX	2677	hgsc.bcm.edu	37	2	85780536	85780536	+	Missense_Mutation	SNP	C	C	T	rs699664	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	44	95	0	0.44	0	C|0.580;T|0.420	0.420	strong	.	GGCX	44	.	NM_000821	exon8	c.G974A	p.R325Q	AACCTTCGGGGGC	.	PASS	Atlas-SNP
PRSS50	29122	hgsc.bcm.edu	37	3	46755937	46755937	+	Silent	SNP	C	C	T	rs12492868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	33	67	0	0.471429	0	A|0.000;C|0.703;T|0.296	0.296	strong	.	PRSS50	35	.	NM_013270	exon4	c.G525A	p.T175T	GGTCTGCGTCATC	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36486802	36486802	+	Missense_Mutation	SNP	G	G	A	rs72832277	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	73	0	0.5	0	G|0.964;A|0.036	0.036	strong	.	GPR179	170	.	NM_001004334	exon11	c.C2650T	p.R884W	GCCTCCGCACCAG	.	PASS	Atlas-SNP
KIF20B	9585	hgsc.bcm.edu	37	10	91487649	91487649	+	Missense_Mutation	SNP	A	A	T	rs12572012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	49	73	0	0.480392	0	A|0.813;T|0.187	0.187	strong	.	KIF20B	191	.	NM_016195	exon17	c.A2147T	p.N716I	CATCTAATAAGGT	.	PASS	Atlas-SNP
ZNF227	7770	hgsc.bcm.edu	37	19	44739303	44739303	+	Silent	SNP	T	T	C	rs2279073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	119	0	1	0	T|0.587;C|0.413	0.413	strong	.	ZNF227	62	.	NM_182490	exon6	c.T720C	p.N240N	CTCCAATCAGAAA	.	PASS	Atlas-SNP
RTP2	344892	hgsc.bcm.edu	37	3	187416666	187416666	+	Missense_Mutation	SNP	C	C	T	rs61748316	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	127	167	0	0.590698	0	C|0.839;T|0.161	0.161	strong	RTP2,NS,carcinoma,0,1	RTP2	38	1	NM_001004312	exon2	c.G298A	p.G100S	CCGTGCCGCACTC	.	PASS	Atlas-SNP
HNF1A	6927	hgsc.bcm.edu	37	12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	rs2464196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	62	148	0	0.466165	0	G|0.725;A|0.275	0.275	strong	.	HNF1A	302	.	NM_000545	exon7	c.G1460A	p.S487N	CCCAGAGCCCCTT	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114175038	114175038	+	Missense_Mutation	SNP	G	G	A	rs7319493	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	39	116	0	0.46988	0	G|0.835;A|0.165	0.165	strong	.	TMCO3	77	.	NM_017905	exon8	c.G1333A	p.A445T	GCCAGTGCATCTT	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96127799	96127799	+	Missense_Mutation	SNP	C	C	T	rs146123204	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	51	119	0	0.432203	0	C|0.998;T|0.002	0.002	strong	.	UNC5C	141	.	NM_003728	exon11	c.G1882A	p.A628T	GTGCTGCCTGGTT	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43382374	43382374	+	Missense_Mutation	SNP	C	C	G	rs707744	bycluster;byfrequency;by2hit2allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	94	244	0	0.43318	0	C|0.695;G|0.305	0.305	strong	.	PSG1	196	.	NM_001184826	exon2	c.G121C	p.E41Q	TTGGCTCGGCTTC	.	PASS	Atlas-SNP
TCTE1	202500	hgsc.bcm.edu	37	6	44253765	44253765	+	Missense_Mutation	SNP	A	A	G	rs2297336	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	38	68	0	0.475	0	A|0.842;G|0.158	0.158	strong	.	TCTE1	77	.	NM_182539	exon3	c.T782C	p.F261S	AAGAGGAAGAGAT	.	PASS	Atlas-SNP
PI4K2A	55361	hgsc.bcm.edu	37	10	99410790	99410790	+	Silent	SNP	T	T	C	rs7915721	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	58	107	0	0.537037	0	T|0.663;C|0.337	0.337	strong	PI4K2A_ENST00000555577,NS,carcinoma,0,2	PI4K2A	57	2	NM_018425	exon2	c.T528C	p.P176P	CTGTCCTTGCTGC	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1876631	1876631	+	Silent	SNP	C	C	T	rs2272611	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	45	93	0	0.454545	0	C|0.861;T|0.139	0.139	strong	ARHGEF10_ENST00000398564,colon,carcinoma,0,2	ARHGEF10	255	2	NM_014629	exon24	c.C2736T	p.I912I	TGCCATCGTCTCG	.	PASS	Atlas-SNP
CLSPN	63967	hgsc.bcm.edu	37	1	36202125	36202125	+	Missense_Mutation	SNP	C	C	T	rs115320551	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	132	133	0	0.916667	0	C|0.999;T|0.001	0.001	strong	CLSPN,colon,carcinoma,-1,4	CLSPN	248	4	NM_022111	exon25	c.G3992A	p.R1331Q	ATGCTTCGCGTCA	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39742807	39742807	+	Missense_Mutation	SNP	C	C	T	rs3826550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	52	0	0.478873	0	C|0.705;T|0.295	0.295	strong	.	KRT14	65	.	NM_000526	exon1	c.G280A	p.A94T	AGCCAGCACCAAG	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143067054	143067054	+	Silent	SNP	G	G	A	rs35390852	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	99	192	0	0.473684	0	G|0.911;A|0.089	0.089	strong	.	INPP4B	132	.	NM_003866	exon19	c.C1659T	p.G553G	GTTGCCGCCACTG	.	PASS	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	37	1	201285712	201285712	+	Silent	SNP	C	C	T	rs7514146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	87	192	0	0.511765	0	C|0.863;T|0.137	0.137	strong	.	PKP1	127	.	NM_001005337	exon4	c.C733T	p.L245L	AGTGGGCTGACCA	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079242	31079242	+	Silent	SNP	A	A	G	rs2233985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	41	101	0	0.488095	0	A|0.923;G|0.077	0.077	strong	.	C6orf15	29	.	NM_014070	exon2	c.T894C	p.P298P	GACTCCAGGAGGA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	279	22	543	0	0.078853	0	.	.	weak	SIRPA,brain,glioma,0,4	SIRPA	83	4	NM_001040022	exon3	c.C300A	p.N100K	GAGAAACAACATG	.	scavenged	Atlas-SNP
LILRA4	23547	hgsc.bcm.edu	37	19	54848275	54848275	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	244	3	221	0	0.0122951	0	.	.	none	LILRA4,NS,carcinoma,0,1	LILRA4	91	1	NM_012276	exon6	c.G1092A	p.P364P	ACGCAACGGGGGA	.	scavenged	Atlas-SNP
ZNF283	284349	hgsc.bcm.edu	37	19	44352665	44352665	+	Missense_Mutation	SNP	T	T	C	rs2356437	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	69	86	0	0.985714	0	T|0.341;C|0.659	0.659	strong	ZNF283_ENST00000324461,colon,carcinoma,0,1	ZNF283	83	1	NM_181845	exon7	c.T1912C	p.C638R	TTTACTTGTGGCT	.	PASS	Atlas-SNP
MCM8	84515	hgsc.bcm.edu	37	20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	rs16991638	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	20	44	0	0.384615	0	A|0.934;G|0.066	0.066	strong	.	MCM8	125	.	NM_032485	exon18	c.A2354G	p.N785S	TCAACAACGTTGC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919934	12919934	+	Missense_Mutation	SNP	A	A	G	rs3204805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	9	136	0	0.0756303	0	A|0.846;G|0.154	0.154	strong	.	PRAMEF2	85	.	NM_023014	exon3	c.A674G	p.Y225C	AGCTTTATTGTTA	.	PASS	Atlas-SNP
FAM129B	64855	hgsc.bcm.edu	37	9	130270782	130270782	+	Silent	SNP	G	G	A	rs11545937	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	12	28	0	0.324324	0	G|0.957;C|0.000;A|0.043	0.043	strong	.	FAM129B	84	.	NM_022833	exon11	c.C1353T	p.L451L	GTGCAGGAGGGTC	.	PASS	Atlas-SNP
DNAJC15	29103	hgsc.bcm.edu	37	13	43597865	43597865	+	Missense_Mutation	SNP	A	A	G	rs12015	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	42	74	0	0.506024	0	A|0.735;G|0.265	0.265	strong	DNAJC15_ENST00000379221,NS,carcinoma,0,2	DNAJC15	16	2	NM_013238	exon1	c.A103G	p.R35G	CAGCAGAGACTGG	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132237750	132237750	+	Silent	SNP	C	C	T	rs1051219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	68	127	0	0.419753	0	C|0.832;T|0.168	0.168	strong	.	SFSWAP	69	.	NM_001261411	exon8	c.C1164T	p.D388D	AATCGACGTGACT	.	PASS	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44418680	44418680	+	Missense_Mutation	SNP	G	G	C	rs388685	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	120	99	0	1	0	G|0.566;C|0.433	0.433	strong	.	ZNF45	51	.	NM_003425	exon10	c.C908G	p.P303R	TTATATGGTTTCT	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1900911	1900911	+	Silent	SNP	C	C	T	rs2272608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	48	115	0	0.527473	0	C|0.809;T|0.191	0.191	strong	.	ARHGEF10	255	.	NM_014629	exon28	c.C3438T	p.H1146H	CTGCCACGGATTG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	14	109	0	0.153846	0	.	.	weak	HLA-A,NS,carcinoma,0,5	HLA-A	89	5	NM_001242758	exon2	c.G147C	p.V49V	CGCCGTGGGCTAC	.	PASS	Atlas-SNP
IDI2	91734	hgsc.bcm.edu	37	10	1065710	1065710	+	Nonsense_Mutation	SNP	C	C	T	rs1044261	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	100	207	0	0.483092	0	C|0.949;T|0.051	0.051	strong	.	IDI2	20	.	NM_033261	exon5	c.G431A	p.W144X	TCTCCCCAAATTC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912297	29912297	+	Missense_Mutation	SNP	A	A	G	rs1136949	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	271	150	378	0	0.553506	0	A|0.875;G|0.125	0.125	strong	.	HLA-A	89	.	NM_001242758	exon5	c.A916G	p.I306V	CCCACCATCCCCA	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76112299	76112299	+	Missense_Mutation	SNP	A	A	G	rs145151450	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	266	116	329	1	0.43609	0.00303951	A|0.997;G|0.003	0.003	strong	.	DTX2	64	.	NM_001102596	exon2	c.A743G	p.N248S	CGTACAACAAACC	.	PASS	Atlas-SNP
KIAA1549L	25758	hgsc.bcm.edu	37	11	33631423	33631423	+	Silent	SNP	G	G	A	rs2076622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	74	76	0	1	0	G|0.561;A|0.439	0.439	strong	.	.	.	.	NM_012194	exon14	c.G4299A	p.K1433K	AAGAAAGAAGATG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47831509	47831509	+	Missense_Mutation	SNP	A	A	G	rs35940413	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	29	67	0	0.453125	0	A|0.789;G|0.211	0.211	strong	.	PCNT	283	.	NM_006031	exon28	c.A5522G	p.N1841S	AGCGCAATGTAGC	.	PASS	Atlas-SNP
ZBTB1	22890	hgsc.bcm.edu	37	14	64988279	64988279	+	Silent	SNP	A	A	G	rs28626711	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	57	113	0	0.491379	0	A|0.827;G|0.173	0.173	strong	.	ZBTB1	93	.	NM_014950	exon2	c.A57G	p.E19E	AAGAGAATGGGGT	.	PASS	Atlas-SNP
TRAPPC9	83696	hgsc.bcm.edu	37	8	141263015	141263015	+	Silent	SNP	G	G	A	rs11166965	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	20	39	0	0.392157	0	G|0.914;A|0.086	0.086	strong	.	TRAPPC9	114	.	NM_031466	exon16	c.C2586T	p.G862G	GAAGTCGCCATAC	.	PASS	Atlas-SNP
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362287	105362287	+	Silent	SNP	C	C	G	rs3740472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	42	113	0	0.396226	0	C|0.914;G|0.086	0.086	strong	.	SH3PXD2A	90	.	NM_014631	exon14	c.G2604C	p.L868L	CTCATCCAGCACC	.	PASS	Atlas-SNP
FUS	2521	hgsc.bcm.edu	37	16	31193942	31193942	+	Silent	SNP	C	C	A	rs741810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	83	178	1	0.477012	0.00561798	C|0.783;A|0.217	0.217	strong	FUS,caecum,carcinoma,0,1	FUS	52	1	NM_001170634	exon3	c.C147A	p.G49G	TTCAGGCTATGGC	.	scavenged	Atlas-SNP
CIDEC	63924	hgsc.bcm.edu	37	3	9920138	9920138	+	Silent	SNP	G	G	C	rs17851444	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	74	122	0	0.471338	0	G|0.895;C|0.105	0.105	strong	.	CIDEC	22	.	NM_001199623	exon2	c.C72G	p.L24L	GGGGTAGAGAAGG	.	PASS	Atlas-SNP
LAMP2	3920	hgsc.bcm.edu	37	X	119576455	119576455	+	Silent	SNP	G	G	A	rs73219144	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	44	0	1	0	G|0.975;A|0.025	0.025	strong	.	LAMP2	101	.	NM_013995	exon7	c.C927T	p.S309S	CTTACCGGAGCCA	.	PASS	Atlas-SNP
GALNT15	117248	hgsc.bcm.edu	37	3	16254172	16254172	+	Missense_Mutation	SNP	G	G	A	rs17851238	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	51	109	1	0.455357	0.00917431	G|0.837;A|0.163	0.163	strong	GALNTL2,colon,carcinoma,0,1	.	.	1	NM_054110	exon6	c.G1294A	p.A432T	CAGGAGGCCACCC	.	scavenged	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324603	31324603	+	Missense_Mutation	SNP	C	C	T	rs9266178	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	40	14	0	0.493827	0	C|0.719;T|0.281	0.281	strong	.	HLA-B	54	.	NM_005514	exon2	c.G205A	p.E69K	GCTCCTCTCTCGG	.	PASS	Atlas-SNP
ANKRD22	118932	hgsc.bcm.edu	37	10	90583092	90583092	+	Missense_Mutation	SNP	T	T	G	rs2304804	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	131	127	0	1	0	T|0.911;G|0.089	0.089	strong	.	ANKRD22	23	.	NM_144590	exon5	c.A443C	p.Q148P	AGAGACTGGTTTT	.	PASS	Atlas-SNP
DUOX2	50506	hgsc.bcm.edu	37	15	45398797	45398797	+	Missense_Mutation	SNP	C	C	T	rs373620034		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	72	158	0	0.467532	0	.	.	weak	DUOX2,NS,carcinoma,-1,1	DUOX2	137	1	NM_014080	exon16	c.G1874A	p.R625Q	TGTTCTCGGCCCC	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48259787	48259787	+	Silent	SNP	C	C	T	rs11538664	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	21	40	0	0.4375	0	C|0.984;T|0.016	0.016	strong	.	GLTSCR2	45	.	NM_015710	exon11	c.C1299T	p.P433P	GTAGCCCGAGGGC	.	PASS	Atlas-SNP
GLRX	2745	hgsc.bcm.edu	37	5	95152313	95152313	+	Silent	SNP	A	A	G	rs4561	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	76	129	0	0.524138	0	T|0.018;G|0.347	0.347	strong	GLRX,NS,carcinoma,-1,1	GLRX	11	1	NM_001243659	exon2	c.T225C	p.I75I	TTTACCAATAAAG	.	PASS	Atlas-SNP
PRPF6	24148	hgsc.bcm.edu	37	20	62641575	62641575	+	Silent	SNP	G	G	A	rs2427588	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	37	101	0	0.393617	0	A|0.057;C|0.007	0.057	strong	PRPF6,NS,carcinoma,+1,1	PRPF6	88	1	NM_012469	exon10	c.G1209A	p.S403S	AAACTCGGTTCGC	.	PASS	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371212	58371212	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	250	17	199	0	0.068	0	.	.	none	.	ZNF587	53	.	NM_032828	exon3	c.A1432T	p.S478C	AAGCACAGCGTGA	.	PASS	Atlas-SNP
OR8J3	81168	hgsc.bcm.edu	37	11	55904828	55904828	+	Missense_Mutation	SNP	A	A	G	rs11227321	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	98	162	0	0.566474	0	A|0.901;G|0.099	0.099	strong	OR8J3,NS,carcinoma,0,1	OR8J3	112	1	NM_001004064	exon1	c.T367C	p.Y123H	CCACATAGCGGTC	.	PASS	Atlas-SNP
PCSK1	5122	hgsc.bcm.edu	37	5	95733112	95733112	+	Silent	SNP	A	A	G	rs6233	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	60	145	0	0.465116	0	A|0.628;G|0.372	0.372	strong	.	PCSK1	93	.	NM_000439	exon12	c.T1650C	p.N550N	GTCCCAATTCTTA	.	PASS	Atlas-SNP
RGPD2	729857	hgsc.bcm.edu	37	2	88125212	88125212	+	Missense_Mutation	SNP	C	C	G	rs192443832	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	276	121	136	0	0.438406	0	C|0.975;G|0.025	0.025	strong	.	RGPD2	14	.	NM_001078170	exon1	c.G37C	p.A13P	CCGAGGCGAGGTA	.	PASS	Atlas-SNP
SGOL2	151246	hgsc.bcm.edu	37	2	201437214	201437214	+	Silent	SNP	A	A	G	rs17532679	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	60	165	1	0.4	0.00606061	A|0.865;G|0.135	0.135	strong	SGOL2,NS,carcinoma,0,1	SGOL2	126	1	NM_001160046	exon7	c.A2145G	p.K715K	GCAGAAAGTAAAT	.	scavenged	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155312411	155312411	+	Silent	SNP	G	G	A	rs62331900	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	53	115	0	0.445378	0	G|0.723;A|0.277	0.277	strong	DCHS2,right_upper_lobe,carcinoma,-2,1	DCHS2	594	1	NM_017639	exon1	c.C39T	p.D13D	TTCTCCGTCTTCA	.	PASS	Atlas-SNP
HYI	81888	hgsc.bcm.edu	37	1	43917637	43917637	+	Silent	SNP	G	G	A	rs2251802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	145	157	0	0.993151	0	G|0.679;A|0.321	0.321	strong	.	HYI	23	.	NM_001243526	exon5	c.C549T	p.D183D	CTGGGGGTCAGTG	.	PASS	Atlas-SNP
TRAF7	84231	hgsc.bcm.edu	37	16	2222286	2222286	+	Silent	SNP	C	C	T	rs11547311	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	55	75	0	0.504587	0	C|0.945;T|0.055	0.055	strong	.	TRAF7	158	.	NM_032271	exon8	c.C570T	p.H190H	CCGGCACGGCTGC	.	PASS	Atlas-SNP
FBXO17	115290	hgsc.bcm.edu	37	19	39440966	39440966	+	Silent	SNP	T	T	C	rs2304118	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	11	4	4	0	0.363636	0	T|0.453;C|0.547	0.547	strong	.	FBXO17	42	.	NM_148169	exon2	c.A21G	p.L7L	CTCCAGTAGCCAG	.	PASS	Atlas-SNP
CCDC111	201973	hgsc.bcm.edu	37	4	185578337	185578337	+	Nonsense_Mutation	SNP	C	C	T	rs145651098		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	31	67	0	0.492063	0	C|1.000;T|0.000	0.000	weak	.	CCDC111	43	.	NM_152683	exon3	c.C43T	p.R15X	GAAGAACGAGCAT	.	PASS	Atlas-SNP
HIST1H4E	8367	hgsc.bcm.edu	37	6	26205052	26205052	+	Silent	SNP	G	G	A	rs61910695	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	64	105	0	0.581818	0	G|0.946;A|0.054	0.054	strong	.	HIST1H4E	22	.	NM_003545	exon1	c.G180A	p.K60K	TCTGAAGGTGTTT	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110476993	110476993	+	Silent	SNP	A	A	G	rs1673398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	57	126	0	0.53271	0	A|0.525;G|0.475	0.475	strong	.	PKHD1L1	522	.	NM_177531	exon49	c.A7932G	p.A2644A	GCCTGCACCTGCA	.	PASS	Atlas-SNP
PON1	5444	hgsc.bcm.edu	37	7	94937446	94937446	+	Missense_Mutation	SNP	T	T	C	rs662	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	44	111	0	0.419048	0	T|0.544;C|0.456	0.456	strong	PON1,NS,carcinoma,0,1	PON1	55	1	NM_000446	exon6	c.A575G	p.Q192R	CAGGATTGTAAGT	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118537074	118537074	+	Silent	SNP	A	A	G	rs12031260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	38	74	0	0.447059	0	A|0.919;G|0.081	0.081	strong	.	SPAG17	263	.	NM_206996	exon35	c.T5133C	p.P1711P	ATTAGGAGGGACA	.	PASS	Atlas-SNP
COG8	84342	hgsc.bcm.edu	37	16	69373414	69373414	+	Silent	SNP	T	T	C	rs11542583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	15	31	0	0.454545	0	T|0.711;C|0.289	0.289	strong	.	COG8	32	.	NM_032382	exon1	c.A42G	p.T14T	CGCTGCTGTGGCC	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383012	39383012	+	Missense_Mutation	SNP	C	C	T	rs9903833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	30	67	0	0.441176	0	C|0.448;T|0.552	0.552	strong	.	KRTAP9-2	24	.	NM_031961	exon1	c.C106T	p.P36S	AGCACACCCTGCT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9069892	9069892	+	Missense_Mutation	SNP	A	A	C	rs1862460	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	244	123	221	0	0.504098	0	A|0.755;C|0.245	0.245	strong	.	MUC16	4315	.	NM_024690	exon3	c.T17554G	p.F5852V	TTACAAAAGGAAA	.	PASS	Atlas-SNP
ZRANB3	84083	hgsc.bcm.edu	37	2	135965376	135965376	+	Silent	SNP	T	T	C	rs7578111	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	24	62	0	0.533333	0	T|0.792;C|0.208	0.208	strong	.	ZRANB3	109	.	NM_032143	exon19	c.A2637G	p.P879P	TAGAAATGGGACA	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58757683	58757683	+	Silent	SNP	A	A	G	rs257636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	196	194	0	0.98	0	A|0.308;G|0.692	0.692	strong	.	GOT2	42	.	NM_002080	exon2	c.T213C	p.N71N	CTTTCCATTATCA	.	PASS	Atlas-SNP
DTWD1	56986	hgsc.bcm.edu	37	15	49917401	49917401	+	Missense_Mutation	SNP	G	G	A	rs11539519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	50	86	0	0.50505	0	G|0.982;A|0.018	0.018	strong	.	DTWD1	22	.	NM_001144955	exon2	c.G37A	p.E13K	CGAAGTGAAGAAA	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137619195	137619195	+	Silent	SNP	C	C	T	rs3124299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	48	106	0	0.470588	0	C|0.665;T|0.335	0.335	strong	.	COL5A1	323	.	NM_000093	exon5	c.C738T	p.T246T	TGACACCGCAGTA	.	PASS	Atlas-SNP
NDOR1	27158	hgsc.bcm.edu	37	9	140108857	140108857	+	Silent	SNP	T	T	C	rs73563696	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	50	103	0	0.45045	0	T|0.875;C|0.125	0.125	strong	.	NDOR1	71	.	NM_001144026	exon6	c.T714C	p.S238S	GGGCTCTGGCATC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535869	88535869	+	Silent	SNP	C	C	T	rs200233307		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	20	186	0	0.103093	0	.	.	weak	DSPP,NS,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.C2055T	p.N685N	CAGCAACAGCAGT	.	PASS	Atlas-SNP
MAGEB3	4114	hgsc.bcm.edu	37	X	30254064	30254064	+	Missense_Mutation	SNP	C	C	T	rs201131077	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	129	122	1	0.992308	0.00819672	.	.	weak	.	MAGEB3	54	.	NM_002365	exon5	c.C23T	p.T8M	AGAGTACGCTCCA	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	37	15	43724646	43724646	+	Missense_Mutation	SNP	T	T	G	rs2602141	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	98	178	0	0.462264	0	G|0.508;N|0.000	0.508	strong	.	TP53BP1	157	.	NM_001141980	exon17	c.A3421C	p.K1141Q	TTTCCTTATTAGT	.	PASS	Atlas-SNP
GAK	2580	hgsc.bcm.edu	37	4	843720	843720	+	Missense_Mutation	SNP	T	T	C	rs2306242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	26	61	0	0.472727	0	T|0.963;C|0.037	0.037	strong	.	GAK	104	.	NM_005255	exon27	c.A3794G	p.K1265R	TAGTGCTTCTTCA	.	PASS	Atlas-SNP
FOXN4	121643	hgsc.bcm.edu	37	12	109717697	109717697	+	Silent	SNP	A	A	G	rs10774641	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	46	0	1	0	A|0.660;G|0.340	0.340	strong	.	FOXN4	74	.	NM_213596	exon10	c.T1333C	p.L445L	TGTCCAAGCTGAA	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52821011	52821011	+	Missense_Mutation	SNP	A	A	G	rs1042779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	54	138	0	0.391304	0	A|0.564;G|0.436	0.436	strong	.	ITIH1	108	.	NM_002215	exon14	c.A1784G	p.Q595R	CCCTGCAGATGTC	.	PASS	Atlas-SNP
KRT26	353288	hgsc.bcm.edu	37	17	38927462	38927462	+	Silent	SNP	G	G	A	rs113285472	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	66	118	0	0.515625	0	G|0.997;A|0.003	0.003	strong	.	KRT26	49	.	NM_181539	exon2	c.C468T	p.A156A	AATGCTGGCATTG	.	PASS	Atlas-SNP
OR7G1	125962	hgsc.bcm.edu	37	19	9226017	9226017	+	Missense_Mutation	SNP	C	C	G	rs2217657	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	59	121	0	0.536364	0	G|0.476;C|0.522;A|0.002	0.476	strong	OR7G1,NS,carcinoma,0,3	OR7G1	53	3	NM_001005192	exon1	c.G423C	p.W141C	CAAGCCCCAGAAA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2156021	2156021	+	Silent	SNP	A	A	G	rs28575767	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	12	6	0	0.666667	0	A|0.873;G|0.127	0.127	strong	PKD1,right_upper_lobe,carcinoma,+2,1	PKD1	184	1	NM_000296	exon20	c.T7708C	p.L2570L	TGGCCAAAGACCT	.	scavenged	Atlas-SNP
TESC	54997	hgsc.bcm.edu	37	12	117486947	117486947	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	31	66	0	0.424658	0	.	.	none	.	TESC	16	.	NM_017899	exon4	c.C226A	p.P76T	CACTGGGTCCCTT	.	PASS	Atlas-SNP
VRK1	7443	hgsc.bcm.edu	37	14	97321689	97321689	+	Silent	SNP	C	C	T	rs2230532	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	87	64	0	1	0	C|0.650;T|0.350	0.350	strong	.	VRK1	34	.	NM_003384	exon8	c.C705T	p.G235G	CAATGGCGTGGGT	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56538976	56538976	+	Missense_Mutation	SNP	G	G	C	rs471979	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	30	59	0	0.441176	0	G|0.894;C|0.106	0.106	strong	.	NLRP5	217	.	NM_153447	exon7	c.G1377C	p.M459I	GATCATGAACAAC	.	PASS	Atlas-SNP
OR11H6	122748	hgsc.bcm.edu	37	14	20692643	20692643	+	Missense_Mutation	SNP	T	T	C	rs17277228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	70	185	0	0.414201	0	C|0.445;N|0.001	0.445	strong	.	OR11H6	60	.	NM_001004480	exon1	c.T775C	p.C259R	TCCACATGTGGGT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9048320	9048320	+	Missense_Mutation	SNP	C	C	T	rs56334501	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	52	105	0	0.460177	0	C|0.795;T|0.205	0.205	strong	.	MUC16	4315	.	NM_024690	exon5	c.G33311A	p.S11104N	CTGGAACTAGTGA	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12885088	12885088	+	Silent	SNP	G	G	A	rs79874173		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	3	160	2	0.0171429	0.0125	G|0.500;A|0.500	0.500	weak	PRAMEF11,NS,carcinoma,-2,2	PRAMEF11	72	2	NM_001146344	exon4	c.C1023T	p.N341N	GAAGGTGTTGAGC	.	scavenged	Atlas-SNP
EBF4	57593	hgsc.bcm.edu	37	20	2739583	2739583	+	Silent	SNP	T	T	C	rs2073125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	44	113	0	0.407407	0	T|0.647;C|0.353	0.353	strong	.	.	.	.	NM_001110514	exon17	c.T1755C	p.F585F	CAAGTTTCACTCT	.	PASS	Atlas-SNP
CYP24A1	1591	hgsc.bcm.edu	37	20	52786219	52786219	+	Silent	SNP	G	G	A	rs2296241	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	41	78	0	0.405941	0	G|0.500;A|0.500	0.500	strong	CYP24A1,trunk,malignant_melanoma,-1,1	CYP24A1	75	1	NM_000782	exon4	c.C552T	p.A184A	AAAATCGGCCAAG	.	PASS	Atlas-SNP
AMT	275	hgsc.bcm.edu	37	3	49459683	49459683	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	23	111	0	0.242105	0	.	.	none	.	AMT	22	.	NM_001164712	exon2	c.C112T	p.L38F	CATAGAGCGGTGT	.	PASS	Atlas-SNP
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	Silent	SNP	A	A	G	rs1065178	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	78	152	0	0.52349	0	A|0.622;G|0.378	0.378	strong	.	.	.	.	NM_001206650	exon2	c.T132C	p.I44I	GGTTAAAATCACA	.	PASS	Atlas-SNP
CD2BP2	10421	hgsc.bcm.edu	37	16	30364805	30364805	+	Missense_Mutation	SNP	C	C	T	rs13330462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	30	57	0	0.535714	0	C|0.892;T|0.108	0.108	strong	.	CD2BP2	30	.	NM_006110	exon5	c.G692A	p.G231D	CCCAAACCCTTCA	.	PASS	Atlas-SNP
AHSG	197	hgsc.bcm.edu	37	3	186330969	186330969	+	Silent	SNP	C	C	G	rs4831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	39	104	0	0.40625	0	C|0.798;G|0.202	0.202	strong	AHSG,NS,carcinoma,0,1	AHSG	40	1	NM_001622	exon1	c.C39G	p.L13L	TCAGCTCTGGGGC	.	PASS	Atlas-SNP
PARVB	29780	hgsc.bcm.edu	37	22	44395451	44395451	+	Missense_Mutation	SNP	T	T	C	rs1007863	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	78	128	0	0.537931	0	T|0.506;C|0.494	0.494	strong	PARVB,NS,carcinoma,0,1	PARVB	44	1	NM_001003828	exon2	c.T109C	p.W37R	TGCAGCTGGGGCC	.	PASS	Atlas-SNP
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1814440	1814440	+	Missense_Mutation	SNP	A	A	G	rs2294619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	33	70	0	0.445946	0	A|0.741;G|0.259	0.259	strong	MAPK8IP3_ENST00000250894,NS,carcinoma,0,2	MAPK8IP3	164	2	NM_015133	exon19	c.A2257G	p.T753A	GCCCACACGTCTC	.	PASS	Atlas-SNP
TMPRSS6	164656	hgsc.bcm.edu	37	22	37471290	37471290	+	Silent	SNP	G	G	A	rs881144	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	39	57	0	0.527027	0	G|0.926;A|0.074	0.074	strong	.	TMPRSS6	99	.	NM_153609	exon11	c.C1254T	p.Y418Y	CTCGGCGTAGGGC	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26689997	26689997	+	Silent	SNP	G	G	A	rs149236286	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	31	53	0	0.54386	0	G|0.984;A|0.016	0.016	strong	.	OTOF	524	.	NM_194248	exon35	c.C4332T	p.T1444T	CTCCTCGGTGGAG	.	PASS	Atlas-SNP
ACOXL	55289	hgsc.bcm.edu	37	2	111551725	111551725	+	Missense_Mutation	SNP	G	G	A	rs150003283	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	57	100	0	0.522936	0	G|0.995;A|0.005	0.005	strong	ACOXL_ENST00000439055,colon,carcinoma,0,2	ACOXL	93	2	NM_001142807	exon5	c.G319A	p.E107K	CAGACCGAAGCCA	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110465060	110465060	+	Silent	SNP	G	G	C	rs1673404	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	27	94	0	0.529412	0	G|0.517;C|0.483	0.483	strong	PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	NM_177531	exon43	c.G6621C	p.L2207L	CATTCTGCTGGAT	.	PASS	Atlas-SNP
ADAMTS19	171019	hgsc.bcm.edu	37	5	129001247	129001247	+	Silent	SNP	G	G	A	rs77945368	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	25	83	0	0.403226	0	G|0.993;A|0.007	0.007	strong	ADAMTS19,NS,carcinoma,0,1	ADAMTS19	216	1	NM_133638	exon16	c.G2463A	p.E821E	TGTGGAGGAAAAG	.	PASS	Atlas-SNP
TM4SF20	79853	hgsc.bcm.edu	37	2	228228462	228228462	+	Missense_Mutation	SNP	T	T	G	rs137891000	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	42	70	0	0.5	0	T|0.995;G|0.005	0.005	strong	.	TM4SF20	24	.	NM_024795	exon4	c.A668C	p.K223T	CTTCGCTTAGAGA	.	PASS	Atlas-SNP
KCNQ4	9132	hgsc.bcm.edu	37	1	41285591	41285591	+	Silent	SNP	A	A	G	rs12143503	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	155	181	1	0.933735	0.00552486	A|0.918;G|0.082	0.082	strong	.	KCNQ4	58	.	NM_004700	exon6	c.A879G	p.T293T	GCACACATGGCTG	.	PASS	Atlas-SNP
TIMP1	7076	hgsc.bcm.edu	37	X	47444985	47444985	+	Silent	SNP	T	T	C	rs4898	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	56	72	0	0.982456	0	T|0.536;C|0.464	0.464	strong	.	TIMP1	12	.	NM_003254	exon5	c.T372C	p.F124F	CAGTTTTGTGGCT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072975	9072975	+	Missense_Mutation	SNP	G	G	A	rs17000816	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	357	174	350	1	0.487395	0.00285714	G|0.810;A|0.190	0.190	strong	MUC16_ENST00000397910,rectum,carcinoma,0,3	MUC16	4315	3	NM_024690	exon3	c.C14471T	p.T4824M	GGATGCGTTGTCT	.	PASS	Atlas-SNP
C19orf59	199675	hgsc.bcm.edu	37	19	7743821	7743821	+	Missense_Mutation	SNP	A	A	G	rs72996468	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	93	168	0	0.453659	0	A|0.897;G|0.103	0.103	strong	.	C19orf59	15	.	NM_174918	exon6	c.A499G	p.I167V	AAAAACATTGACA	.	PASS	Atlas-SNP
CARD6	84674	hgsc.bcm.edu	37	5	40841741	40841741	+	Missense_Mutation	SNP	C	C	T	rs10512747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	44	143	0	0.376068	0	C|0.922;T|0.078	0.078	strong	.	CARD6	141	.	NM_032587	exon1	c.C257T	p.S86L	CACAGTCAGCTGC	.	PASS	Atlas-SNP
TRIM5	85363	hgsc.bcm.edu	37	11	5701001	5701001	+	Missense_Mutation	SNP	C	C	T	rs10838525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	49	93	0	0.538462	0	C|0.763;T|0.237	0.237	strong	TRIM5_ENST00000380034,NS,carcinoma,0,1	TRIM5	111	1	NM_033093	exon2	c.G407A	p.R136Q	TACTCCCGGGCAA	.	PASS	Atlas-SNP
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152257	151152257	+	Silent	SNP	A	A	G	rs926624	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	8	94	0	0.150943	0	A|0.733;G|0.267	0.267	strong	PLEKHG1,NS,carcinoma,0,2	PLEKHG1	97	2	NM_001029884	exon16	c.A2010G	p.K670K	CTTAAAACTAATG	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234218	8234218	+	Silent	SNP	C	C	T	rs4840954	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	14	39	0	0.341463	0	C|0.631;T|0.369	0.369	strong	.	.	.	.	NM_001080826	exon2	c.G1701A	p.P567P	AGCCAGCGGTGAC	.	PASS	Atlas-SNP
PCDHB12	56124	hgsc.bcm.edu	37	5	140590641	140590641	+	Missense_Mutation	SNP	C	C	G	rs150562956	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	46	53	0	0.511111	0	C|0.998;G|0.002;T|0.000	0.002	strong	PCDHB12,colon,carcinoma,0,1	PCDHB12	179	1	NM_018932	exon1	c.C2162G	p.P721R	CGGCCCCGGTCGG	.	PASS	Atlas-SNP
NEK1	4750	hgsc.bcm.edu	37	4	170506525	170506525	+	Missense_Mutation	SNP	C	C	T	rs200161705	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	63	172	0	0.473684	0	C|0.999;T|0.001	0.001	strong	NEK1_ENST00000507142,NS,carcinoma,0,2	NEK1	203	2	NM_001199399	exon10	c.G782A	p.R261H	TCAATGCGTTTGG	.	PASS	Atlas-SNP
CHRNA3	1136	hgsc.bcm.edu	37	15	78894339	78894339	+	Silent	SNP	G	G	A	rs1051730	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	229	216	0	0.991342	0	G|0.754;A|0.246	0.246	strong	.	CHRNA3	56	.	NM_000743	exon5	c.C645T	p.Y215Y	GTGTTTGTAGCCT	.	PASS	Atlas-SNP
ZNF770	54989	hgsc.bcm.edu	37	15	35273620	35273620	+	Silent	SNP	C	C	T	rs4923849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	45	67	0	0.548781	0	C|0.523;T|0.477	0.477	strong	.	ZNF770	64	.	NM_014106	exon3	c.G2016A	p.Q672Q	AGTAAGCTGATGT	.	PASS	Atlas-SNP
CNTN1	1272	hgsc.bcm.edu	37	12	41330611	41330611	+	Silent	SNP	T	T	C	rs935105	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	34	118	0	0.350515	0	T|0.868;C|0.132	0.132	strong	.	CNTN1	207	.	NM_001256063	exon10	c.T1014C	p.N338N	CATCAATGACACA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9049910	9049910	+	Missense_Mutation	SNP	C	C	T	rs56307190	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	298	163	248	0	0.54698	0	C|0.794;T|0.206	0.206	strong	.	MUC16	4315	.	NM_024690	exon5	c.G31721A	p.R10574H	CCAGAACGAGAGA	.	PASS	Atlas-SNP
ZNF585A	199704	hgsc.bcm.edu	37	19	37642917	37642917	+	Silent	SNP	G	G	A	rs77675231	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	89	210	0	0.375527	0	G|0.497;A|0.503	0.503	strong	.	ZNF585A	117	.	NM_199126	exon6	c.C1719T	p.H573H	TCCTGTGTGAACT	.	PASS	Atlas-SNP
OR2G3	81469	hgsc.bcm.edu	37	1	247769752	247769752	+	Missense_Mutation	SNP	A	A	G	rs61730407	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	45	128	0	0.463918	0	A|0.629;G|0.371	0.371	strong	.	OR2G3	108	.	NM_001001914	exon1	c.A865G	p.I289V	CCTATCATCTATA	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76922946	76922946	+	Silent	SNP	G	G	A	rs11237123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	73	61	0	1	0	G|0.785;A|0.215	0.215	strong	.	MYO7A	164	.	NM_000260	exon46	c.G6318A	p.K2106K	CTTCAAGTGGCCC	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52643685	52643685	+	Silent	SNP	T	T	C	rs3755806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	75	144	0	0.460123	0	T|0.658;C|0.342	0.342	strong	PBRM1_ENST00000356770,rectum,carcinoma,0,3	PBRM1	1252	3	NM_018313	exon17	c.A2211G	p.T737T	ATTGTATGTACAG	.	PASS	Atlas-SNP
LRRC8E	80131	hgsc.bcm.edu	37	19	7963976	7963976	+	Missense_Mutation	SNP	T	T	C	rs2115108	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	30	73	0	0.454545	0	T|0.676;C|0.324	0.324	strong	.	LRRC8E	67	.	NM_001268284	exon4	c.T569C	p.M190T	TGGCCATGGCAGG	.	PASS	Atlas-SNP
ANKIB1	54467	hgsc.bcm.edu	37	7	92027537	92027537	+	Silent	SNP	C	C	G	rs1861635	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	47	95	0	0.479592	0	C|0.845;G|0.155	0.155	strong	.	ANKIB1	92	.	NM_019004	exon20	c.C2544G	p.S848S	GAGTTCCTTGGAT	.	PASS	Atlas-SNP
ZNF681	148213	hgsc.bcm.edu	37	19	23927345	23927345	+	Missense_Mutation	SNP	T	T	C	rs7245561	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	16	67	1	0.301887	0.0149254	T|0.849;C|0.151	0.151	strong	ZNF681,NS,carcinoma,+1,2	ZNF681	76	2	NM_138286	exon4	c.A1007G	p.K336R	TAGGGTTTCTCTC	.	scavenged	Atlas-SNP
PRDM14	63978	hgsc.bcm.edu	37	8	70981451	70981451	+	Silent	SNP	G	G	A	rs9969435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	58	113	0	0.5	0	G|0.951;A|0.049	0.049	strong	.	PRDM14	102	.	NM_024504	exon2	c.C645T	p.H215H	GGCTGGGTGCTCC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45122464	45122464	+	Missense_Mutation	SNP	A	A	C	rs10243185	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	23	47	0	0.489362	0	A|0.565;C|0.435	0.435	strong	.	NACAD	44	.	NM_001146334	exon2	c.T3315G	p.D1105E	AGGCGCATCGGGG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511890	4511890	+	Silent	SNP	G	G	A	rs200897749	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	307	61	265	0	0.198697	0	G|0.982;A|0.018	0.018	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C2040T	p.T680T	GGTGCCGGTCAGC	.	PASS	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	37	4	169158489	169158489	+	Silent	SNP	G	G	C	rs3828560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	61	137	0	0.495935	0	G|0.938;C|0.062	0.062	strong	.	DDX60	304	.	NM_017631	exon32	c.C4359G	p.V1453V	AAAACTGACAAAA	.	PASS	Atlas-SNP
GRAMD3	65983	hgsc.bcm.edu	37	5	125802027	125802027	+	Missense_Mutation	SNP	G	G	A	rs62394179	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	73	156	0	0.557252	0	G|0.787;A|0.213	0.213	strong	.	GRAMD3	30	.	NM_001146321	exon3	c.G226A	p.E76K	GACCAAGAGTAAG	.	PASS	Atlas-SNP
PRLR	5618	hgsc.bcm.edu	37	5	35084647	35084647	+	Missense_Mutation	SNP	T	T	C	rs2228482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	75	180	0	0.457317	0	T|0.899;G|0.003	.	strong	.	PRLR	90	.	NM_000949	exon5	c.A298G	p.I100V	TCATGATGTATGT	.	PASS	Atlas-SNP
KRTAP15-1	254950	hgsc.bcm.edu	37	21	31812828	31812828	+	Silent	SNP	C	C	T	rs35857034	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	65	151	0	0.481481	0	C|0.967;T|0.033	0.033	strong	.	KRTAP15-1	35	.	NM_181623	exon1	c.C183T	p.C61C	CAGCTGCCAGACA	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25052321	25052321	+	Silent	SNP	A	A	G	rs149727830	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	11	97	0	0.112245	0	A|1.000;C|0.000	.	alt	PARP4,rectum,carcinoma,0,1	PARP4	142	1	NM_006437	exon13	c.T1542C	p.H514H	CTTCTCATGTAAG	.	scavenged	Atlas-SNP
TMEM38B	55151	hgsc.bcm.edu	37	9	108536246	108536246	+	Missense_Mutation	SNP	G	G	C	rs35232724	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	37	79	0	0.569231	0	G|0.960;C|0.040	0.040	strong	.	TMEM38B	31	.	NM_018112	exon6	c.G761C	p.C254S	CATCATGTGAGAA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895951	1895951	+	Missense_Mutation	SNP	C	C	T	rs149634649	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	262	25	502	0	0.0954198	0	C|0.697;T|0.304	0.304	strong	.	SIRPA	83	.	NM_001040022	exon3	c.C286T	p.L96F	TCAGACCTCACAA	.	PASS	Atlas-SNP
MFSD1	64747	hgsc.bcm.edu	37	3	158538056	158538056	+	Silent	SNP	T	T	C	rs4680469	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	190	75	186	0	0.394737	0	T|0.820;C|0.180	0.180	strong	.	MFSD1	88	.	NM_022736	exon9	c.T951C	p.L317L	GTGGCTTATATTT	.	PASS	Atlas-SNP
PSMD3	5709	hgsc.bcm.edu	37	17	38146154	38146154	+	Silent	SNP	T	T	C	rs9916279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	25	51	0	0.416667	0	T|0.798;C|0.202	0.202	strong	.	PSMD3	56	.	NM_002809	exon5	c.T849C	p.N283N	CAACAATGAGTGG	.	PASS	Atlas-SNP
DNAJB11	51726	hgsc.bcm.edu	37	3	186301703	186301703	+	Missense_Mutation	SNP	A	A	G	rs8147	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	36	65	0	0.580645	0	A|0.723;G|0.277	0.277	strong	.	DNAJB11	42	.	NM_016306	exon8	c.A790G	p.I264V	GTGACAATCTCAT	.	PASS	Atlas-SNP
ICAM3	3385	hgsc.bcm.edu	37	19	10450285	10450285	+	Silent	SNP	G	G	A	rs281414	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	41	40	0	0.97619	0	G|0.827;A|0.173	0.173	strong	.	ICAM3	29	.	NM_002162	exon1	c.C6T	p.A2A	CATGGTGGCCATT	.	PASS	Atlas-SNP
CEP85	64793	hgsc.bcm.edu	37	1	26582091	26582091	+	Missense_Mutation	SNP	G	G	A	rs3795686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	7	103	0	0.0530303	0	G|0.777;A|0.223	0.223	strong	.	CEP85	61	.	NM_022778	exon4	c.G638A	p.S213N	GAACCAGCACAAG	.	PASS	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	37	16	1388909	1388909	+	Silent	SNP	C	C	T	rs77633104	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	31	54	0	0.455882	0	C|0.962;T|0.038	0.038	strong	BAIAP3,NS,carcinoma,0,1	BAIAP3	88	1	NM_003933	exon3	c.C243T	p.P81P	GAAACCCGGGGAT	.	PASS	Atlas-SNP
GPC1	2817	hgsc.bcm.edu	37	2	241401741	241401741	+	Silent	SNP	C	C	T	rs1042829	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	53	125	0	0.430894	0	C|0.820;T|0.180	0.180	strong	GPC1,NS,carcinoma,0,1	GPC1	32	1	NM_002081	exon3	c.C459T	p.R153R	CTACCGCGGTGCC	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592215	1592215	+	Missense_Mutation	SNP	C	C	G	rs41289057	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	27	379	0	0.964286	0	C|0.624;G|0.376	0.376	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.G221C	p.G74A	TCCCGGCCTGGTC	.	PASS	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26697422	26697422	+	Missense_Mutation	SNP	C	C	G	rs80356574	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	30	93	0	0.405405	0	C|0.983;G|0.017	0.017	strong	.	OTOF	524	.	NM_194248	exon26	c.G3247C	p.A1083P	CTGTGGCGTTGCC	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784427	140784427	+	Silent	SNP	T	T	C	rs3749769	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	195	202	0	1	0	T|0.875;C|0.125	0.125	strong	.	PCDHGA9	110	.	NM_032089	exon1	c.T1908C	p.D636D	TAGAGATGCGCTC	.	PASS	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32754306	32754306	+	Missense_Mutation	SNP	T	T	C	rs16987625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	273	143	248	0	0.52381	0	T|0.910;C|0.090	0.090	strong	.	RFPL3	91	.	NM_001098535	exon1	c.T248C	p.M83T	GTTCCATGGTCTC	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29274720	29274720	+	Missense_Mutation	SNP	A	A	G	rs895591	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	135	132	1	1	0.00757576	A|0.416;G|0.584	0.584	strong	FAM179A,NS,carcinoma,0,1	FAM179A	106	1	NM_199280	exon20	c.A2821G	p.T941A	AATGGCACCCTGC	.	PASS	Atlas-SNP
SLC39A14	23516	hgsc.bcm.edu	37	8	22262418	22262418	+	Silent	SNP	A	A	G	rs2293144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	90	98	0	1	0	A|0.386;G|0.614	0.614	strong	.	SLC39A14	59	.	NM_001135153	exon2	c.A195G	p.L65L	GGCCCTACTCAAC	.	PASS	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	37	5	476353	476353	+	Silent	SNP	C	C	T	rs2230437	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	44	87	0	0.517647	0	C|0.706;T|0.294	0.294	strong	SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	NM_004174	exon13	c.G2031A	p.A677A	CTTGGCCGCCTTC	.	PASS	Atlas-SNP
ANKRD27	84079	hgsc.bcm.edu	37	19	33117666	33117666	+	Silent	SNP	T	T	C	rs6510271	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	63	53	0	0.984375	0	T|0.335;C|0.665	0.665	strong	ANKRD27,NS,carcinoma,-1,1	ANKRD27	86	1	NM_032139	exon16	c.A1488G	p.G496G	AGTGGCTCCATGG	.	PASS	Atlas-SNP
HSF5	124535	hgsc.bcm.edu	37	17	56540267	56540267	+	Missense_Mutation	SNP	C	C	T	rs3803752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	114	213	0	0.481013	0	C|0.850;T|0.150	0.150	strong	.	HSF5	51	.	NM_001080439	exon4	c.G1418A	p.S473N	ATTGTGCTATTTT	.	PASS	Atlas-SNP
ANP32C	23520	hgsc.bcm.edu	37	4	165118652	165118652	+	Missense_Mutation	SNP	C	C	T	rs2288675	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	90	230	0	0.447761	0	C|0.676;T|0.324	0.324	strong	.	ANP32C	59	.	NM_012403	exon1	c.G212A	p.R71K	GAGACTCTTAGTT	.	PASS	Atlas-SNP
ASTN1	460	hgsc.bcm.edu	37	1	176833427	176833427	+	Missense_Mutation	SNP	T	T	C	rs61756323	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	26	56	0	0.433333	0	T|0.998;C|0.002	0.002	strong	.	ASTN1	314	.	NM_004319	exon23	c.A3878G	p.E1293G	TAGATCTCTTTGC	.	PASS	Atlas-SNP
ZFYVE26	23503	hgsc.bcm.edu	37	14	68257352	68257352	+	Missense_Mutation	SNP	T	T	A	rs17192170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	94	249	1	0.437209	0.00401606	T|0.932;A|0.068	0.068	strong	.	ZFYVE26	223	.	NM_015346	exon15	c.A2692T	p.T898S	GAATGGTGCTGCT	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1082605	1082605	+	Silent	SNP	G	G	A	rs41480348	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	58	95	0	0.495726	0	G|0.952;A|0.048	0.048	strong	.	MUC2	614	.	NM_002457	exon15	c.G1854A	p.T618T	TGACACGTGTAAC	.	PASS	Atlas-SNP
MLL5	55904	hgsc.bcm.edu	37	7	104717517	104717517	+	Silent	SNP	C	C	T	rs2240455	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	170	153	0	0.994152	0	C|0.620;T|0.380	0.380	strong	.	MLL5	173	.	NM_018682	exon9	c.C876T	p.Y292Y	CCAGTACAGTGAG	.	PASS	Atlas-SNP
GSTO2	119391	hgsc.bcm.edu	37	10	106058901	106058901	+	Silent	SNP	G	G	T	rs3758572	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	43	91	0	0.477778	0	G|0.938;T|0.062	0.062	strong	.	GSTO2	23	.	NM_183239	exon7	c.G591T	p.T197T	CCACACGCCAGCC	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	251469	251469	+	Silent	SNP	G	G	A	rs1139449	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	348	81	361	4	0.232759	0.0110803	A|1.000;|0.000	1.000	weak	SDHA,NS,malignant_melanoma,+1,1	SDHA	80	1	NM_004168	exon13	c.G1680A	p.T560T	GAACACGGACCTG	.	scavenged	Atlas-SNP
C19orf53	28974	hgsc.bcm.edu	37	19	13885309	13885309	+	Silent	SNP	C	C	T	rs1128749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	42	100	0	0.6	0	A|0.000;C|0.661;G|0.000;T|0.338	0.338	strong	C19orf53,NS,carcinoma,0,1	C19orf53	14	1	NM_014047	exon1	c.C18T	p.R6R	GCAGCGCAAGTTT	.	PASS	Atlas-SNP
BARD1	580	hgsc.bcm.edu	37	2	215645545	215645545	+	Silent	SNP	C	C	G	rs2070096	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	51	94	0	0.495146	0	C|0.803;G|0.197	0.197	strong	.	BARD1	138	.	NM_000465	exon4	c.G1053C	p.T351T	GGGCACCGTTTGC	.	PASS	Atlas-SNP
SLC23A2	9962	hgsc.bcm.edu	37	20	4855309	4855309	+	Silent	SNP	G	G	A	rs41282100	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	36	58	0	0.45	0	G|0.990;A|0.010	0.010	strong	.	SLC23A2	62	.	NM_203327	exon10	c.C858T	p.Y286Y	TCTGGCGTATTGA	.	PASS	Atlas-SNP
ENPP3	5169	hgsc.bcm.edu	37	6	132061420	132061420	+	Missense_Mutation	SNP	G	G	A	rs17601580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	40	77	0	0.851064	0	G|0.897;A|0.103	0.103	strong	.	ENPP3	117	.	NM_005021	exon24	c.G2357A	p.S786N	TGACCAGTTGTAA	.	PASS	Atlas-SNP
EFCAB4B	84766	hgsc.bcm.edu	37	12	3805977	3805977	+	Missense_Mutation	SNP	A	A	C	rs144314920	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	42	66	0	0.494118	0	A|1.000;C|0.000	0.000	strong	.	EFCAB4B	100	.	NM_001144958	exon4	c.T189G	p.D63E	TTCAGCATCACAG	.	PASS	Atlas-SNP
UNC79	57578	hgsc.bcm.edu	37	14	94088369	94088369	+	Missense_Mutation	SNP	T	T	C	rs28670114	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	50	96	0	0.446429	0	T|0.833;C|0.167	0.167	strong	.	UNC79	366	.	NM_020818	exon30	c.T4259C	p.V1420A	CGCCGGTAAAGCC	.	PASS	Atlas-SNP
NFATC2	4773	hgsc.bcm.edu	37	20	50140627	50140627	+	Silent	SNP	G	G	C	rs3746420	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	35	67	0	0.583333	0	G|0.939;C|0.061	0.061	strong	.	NFATC2	112	.	NM_012340	exon2	c.C153G	p.V51V	GCTGGCGACCTTA	.	PASS	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74759006	74759006	+	Missense_Mutation	SNP	C	C	T	rs3742801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	26	53	0	0.393939	0	C|0.710;T|0.290	0.290	strong	.	ABCD4	54	.	NM_005050	exon11	c.G1102A	p.E368K	CCCACTCGCTCTC	.	PASS	Atlas-SNP
ZNF480	147657	hgsc.bcm.edu	37	19	52825032	52825032	+	Missense_Mutation	SNP	C	C	T	rs13343641	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	240	121	230	1	0.504167	0.00434783	C|0.820;T|0.180	0.180	strong	.	ZNF480	123	.	NM_144684	exon5	c.C529T	p.P177S	AAAACCCCCATTT	.	PASS	Atlas-SNP
CENPN	55839	hgsc.bcm.edu	37	16	81056441	81056441	+	Missense_Mutation	SNP	T	T	G	rs3743503	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	30	67	0	0.394737	0	T|0.878;G|0.122	0.122	strong	.	CENPN	84	.	NM_018455	exon7	c.T613G	p.X205E	TGCAATTAGTGAA	.	PASS	Atlas-SNP
CKAP2L	150468	hgsc.bcm.edu	37	2	113498566	113498566	+	Missense_Mutation	SNP	A	A	G	rs3811040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	64	118	0	0.421053	0	A|0.592;G|0.408	0.408	strong	.	CKAP2L	54	.	NM_152515	exon8	c.T1841C	p.L614S	GCAACTAAAGAGT	.	PASS	Atlas-SNP
ITGBL1	9358	hgsc.bcm.edu	37	13	102366825	102366825	+	Silent	SNP	A	A	G	rs2281991	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	112	241	1	0.506787	0.00414938	A|0.829;G|0.171	0.171	strong	.	ITGBL1	83	.	NM_004791	exon10	c.A1317G	p.E439E	TGCTGAAGAGTGG	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531193	140531193	+	Missense_Mutation	SNP	C	C	T	rs149392351	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	49	88	0	0.433628	0	C|0.997;T|0.003	0.003	strong	.	PCDHB6	161	.	NM_018939	exon1	c.C1355T	p.T452I	CCCAAACCTCCTA	.	PASS	Atlas-SNP
C15orf55	256646	hgsc.bcm.edu	37	15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	rs149177074	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	26	56	0	0.472727	0	G|0.998;A|0.002	0.002	strong	C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	NM_175741	exon7	c.G3043A	p.E1015K	GAGGATGAGGAAC	.	PASS	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	709567	709567	+	Missense_Mutation	SNP	G	G	A	rs12283031	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	37	69	0	0.552239	0	G|0.963;A|0.037	0.037	strong	.	EPS8L2	42	.	NM_022772	exon3	c.G59A	p.R20Q	TGGGCCGGTCCGA	.	PASS	Atlas-SNP
ANAPC1	64682	hgsc.bcm.edu	37	2	112619981	112619981	+	Missense_Mutation	SNP	G	G	A	rs201128090	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	33	145	1	0.181319	0.00689655	G|0.940;A|0.060	0.060	strong	ANAPC1,NS,carcinoma,0,2	ANAPC1	116	2	NM_022662	exon10	c.C1247T	p.T416M	GTAATCGTTTCTG	.	scavenged	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52841765	52841765	+	Silent	SNP	G	G	A	rs388626	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	76	133	0	0.466258	0	G|0.488;A|0.512	0.512	strong	.	KRT6B	90	.	NM_005555	exon7	c.C1221T	p.A407A	AATGGCGGCCTGT	.	PASS	Atlas-SNP
PGAM1	5223	hgsc.bcm.edu	37	10	99190185	99190185	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	41	82	0	0.506173	0	.	.	none	PGAM1,caecum,carcinoma,+1,1	PGAM1	11	1	NM_002629	exon2	c.G189A	p.A63A	GAGAGCGATCCGG	.	PASS	Atlas-SNP
DOT1L	84444	hgsc.bcm.edu	37	19	2226676	2226676	+	Missense_Mutation	SNP	G	G	A	rs3815308	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	16	4	0	1	0	G|0.722;A|0.278	0.278	strong	.	DOT1L	205	.	NM_032482	exon27	c.G4156A	p.G1386S	AGCCGCGGCAAGG	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31122330	31122330	+	Silent	SNP	G	G	A	rs130077	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	138	132	0	1	0	G|0.860;A|0.140	0.140	strong	.	CCHCR1	68	.	NM_001105564	exon4	c.C744T	p.N248N	TTCCAAGTTCTTC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6549995	6549995	+	Missense_Mutation	SNP	A	A	G	rs7480644	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	70	63	0	1	0	A|0.284;G|0.716	0.716	strong	DNHD1,colon,carcinoma,0,1	DNHD1	198	1	NM_144666	exon11	c.A2081G	p.N694S	CACTGAATATACA	.	PASS	Atlas-SNP
ABI3BP	25890	hgsc.bcm.edu	37	3	100617668	100617668	+	Silent	SNP	G	G	T	rs34999788	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	45	79	0	0.576923	0	G|0.913;T|0.087	0.087	strong	.	ABI3BP	305	.	NM_015429	exon4	c.C420A	p.S140S	ACCCCAGGACAGG	.	PASS	Atlas-SNP
PINK1	65018	hgsc.bcm.edu	37	1	20977000	20977000	+	Missense_Mutation	SNP	A	A	C	rs1043424	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	87	87	0	0.87	0	A|0.725;C|0.275	0.275	strong	.	PINK1	37	.	NM_032409	exon8	c.A1562C	p.N521T	TGAAGAATCTGAA	.	PASS	Atlas-SNP
NLRP14	338323	hgsc.bcm.edu	37	11	7091569	7091569	+	Missense_Mutation	SNP	C	C	T	rs17280682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	70	126	0	0.47619	0	C|0.850;T|0.150	0.150	strong	.	NLRP14	187	.	NM_176822	exon11	c.C3028T	p.L1010F	TCTGCTCTTATCT	.	PASS	Atlas-SNP
ZSCAN29	146050	hgsc.bcm.edu	37	15	43661802	43661802	+	Missense_Mutation	SNP	T	T	C	rs3809482	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	67	189	0	0.372222	0	T|0.485;C|0.515	0.515	strong	.	ZSCAN29	57	.	NM_152455	exon1	c.A310G	p.R104G	AAGATCTAGGTCT	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	37	10	126714966	126714966	+	Missense_Mutation	SNP	A	A	G	rs3012075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	42	66	0	0.451613	0	A|0.547;G|0.453	0.453	strong	.	CTBP2	100	.	NM_022802	exon1	c.T1363C	p.Y455H	GGGGGTACGTGGG	.	PASS	Atlas-SNP
HIST1H2BG	8339	hgsc.bcm.edu	37	6	26216584	26216584	+	Silent	SNP	C	C	T	rs16891427	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	61	118	0	0.586538	0	C|0.948;T|0.052	0.052	strong	.	HIST1H2BG	25	.	NM_003518	exon1	c.G288A	p.Q96Q	GGCGGTCTGGATC	.	PASS	Atlas-SNP
ZNF853	54753	hgsc.bcm.edu	37	7	6661256	6661256	+	Missense_Mutation	SNP	C	C	G	rs11971880	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	209	202	0	0.981221	0	C|0.905;G|0.095	0.095	strong	.	ZNF853	32	.	NM_017560	exon3	c.C634G	p.Q212E	CAGTTACAGCAGC	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100686291	100686291	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	55	99	0	0.544554	0	.	.	none	MUC17,NS,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G11594A	p.R3865H	CCATACGTATTTC	.	PASS	Atlas-SNP
CLCN7	1186	hgsc.bcm.edu	37	16	1509123	1509123	+	Silent	SNP	G	G	A	rs12923538	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	190	74	201	0	0.389474	0	G|0.854;A|0.146	0.146	strong	CLCN7,colon,carcinoma,-1,1	CLCN7	53	1	NM_001287	exon7	c.C660T	p.H220H	CACCACGTGGGGG	.	PASS	Atlas-SNP
TRIM22	10346	hgsc.bcm.edu	37	11	5718517	5718517	+	Missense_Mutation	SNP	G	G	A	rs7935564	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	54	85	0	0.586957	0	G|0.528;A|0.472	0.472	strong	.	TRIM22	66	.	NM_001199573	exon3	c.G463A	p.D155N	AAGGAGGATCAAG	.	PASS	Atlas-SNP
ANXA7	310	hgsc.bcm.edu	37	10	75148116	75148116	+	Silent	SNP	A	A	G	rs2234965	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	51	64	0	0.414634	0	A|0.871;G|0.129	0.129	strong	ANXA7,NS,carcinoma,-2,2	ANXA7	50	2	NM_004034	exon7	c.T558C	p.D186D	TATAGCATCGAAG	.	PASS	Atlas-SNP
C7	730	hgsc.bcm.edu	37	5	40964852	40964852	+	Missense_Mutation	SNP	A	A	C	rs13157656	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	94	166	0	0.556213	0	A|0.817;C|0.182	0.182	strong	.	C7	136	.	NM_000587	exon14	c.A1759C	p.T587P	GAAGGTACAATGT	.	PASS	Atlas-SNP
CRK	1398	hgsc.bcm.edu	37	17	1359363	1359363	+	Silent	SNP	T	T	G	rs2229075	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	64	40	0	0.984615	0	T|0.252;G|0.748;C|0.000	0.748	strong	.	CRK	14	.	NM_016823	exon1	c.A49C	p.R17R	TCAACCTCCCCCA	.	PASS	Atlas-SNP
SLC6A11	6538	hgsc.bcm.edu	37	3	10976876	10976876	+	Silent	SNP	A	A	G	rs2245532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	63	137	0	0.45	0	A|0.595;G|0.405	0.405	strong	.	SLC6A11	87	.	NM_014229	exon13	c.A1737G	p.T579T	GGGGACACTGCCC	.	PASS	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	37	19	39229089	39229089	+	Missense_Mutation	SNP	A	A	G	rs12983010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	24	38	0	0.48	0	A|0.915;G|0.085	0.085	strong	.	CAPN12	43	.	NM_144691	exon7	c.T859C	p.C287R	CCACGCAGCCCCA	.	PASS	Atlas-SNP
RMND1	55005	hgsc.bcm.edu	37	6	151766822	151766822	+	Missense_Mutation	SNP	C	C	A	rs11550103	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	96	0	1	0	C|0.912;A|0.088	0.088	strong	RMND1,lymph_node,lymphoid_neoplasm,0,1	RMND1	32	1	NM_017909	exon2	c.G125T	p.S42I	AGTGTGCTGCATG	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115933885	115933885	+	Silent	SNP	A	A	C	rs1128118	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	75	116	0	0.510204	0	A|0.938;C|0.062	0.062	strong	.	FKBP15	128	.	NM_015258	exon24	c.T2634G	p.A878A	TGCAGCAGCTTCA	.	PASS	Atlas-SNP
ADAM28	10863	hgsc.bcm.edu	37	8	24171051	24171051	+	Silent	SNP	C	C	T	rs6996616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	93	178	0	0.447115	0	C|0.809;T|0.191	0.191	strong	.	ADAM28	100	.	NM_014265	exon6	c.C534T	p.H178H	GGCCCACGATTTG	.	PASS	Atlas-SNP
METTL3	56339	hgsc.bcm.edu	37	14	21967916	21967916	+	Silent	SNP	A	A	G	rs1139130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	124	129	0	1	0	A|0.488;G|0.512	0.512	strong	.	METTL3	48	.	NM_019852	exon7	c.T1335C	p.N445N	CCAGAGATTTAGA	.	PASS	Atlas-SNP
FDXR	2232	hgsc.bcm.edu	37	17	72863030	72863030	+	Missense_Mutation	SNP	T	T	C	rs1688149	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	76	116	0	0.490323	0	T|0.781;C|0.219	0.219	strong	.	FDXR	68	.	NM_001258012	exon3	c.A275G	p.D92G	GTGGGGTCGAGAG	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16278863	16278863	+	Missense_Mutation	SNP	G	G	T	rs8058694	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	126	124	0	0.992126	0	G|0.607;T|0.393	0.393	strong	.	ABCC6	110	.	NM_001171	exon15	c.C1896A	p.H632Q	GGCACTGTGTATG	.	PASS	Atlas-SNP
PRR15	222171	hgsc.bcm.edu	37	7	29606316	29606316	+	Missense_Mutation	SNP	C	C	A	rs112093295	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	44	88	0	0.55	0	A|0.036;C|0.963;G|0.000	0.036	strong	PRR15,NS,carcinoma,0,3	PRR15	6	3	NM_175887	exon2	c.C371A	p.P124H	GTGACCCCCACGA	.	PASS	Atlas-SNP
MANEAL	149175	hgsc.bcm.edu	37	1	38265653	38265653	+	Silent	SNP	T	T	C	rs41267339	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	118	128	1	0.944	0.0078125	T|0.982;C|0.018	0.018	strong	.	MANEAL	43	.	NM_001113482	exon4	c.T1152C	p.Y384Y	GTACTATGAGACG	.	PASS	Atlas-SNP
NLRP1	22861	hgsc.bcm.edu	37	17	5462240	5462240	+	Silent	SNP	C	C	T	rs61753142	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	60	102	0	0.582524	0	C|0.937;T|0.063	0.063	strong	.	NLRP1	358	.	NM_033007	exon4	c.G1776A	p.R592R	ATGCTTCCTGAGG	.	PASS	Atlas-SNP
ELF3	1999	hgsc.bcm.edu	37	1	201981218	201981218	+	Silent	SNP	C	C	G	rs11543979	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	66	97	0	0.481752	0	C|0.695;G|0.305	0.305	strong	ELF3,NS,carcinoma,0,1	ELF3	92	1	NM_001114309	exon3	c.C297G	p.G99G	GGATGGCGCCACC	.	PASS	Atlas-SNP
SHROOM2	357	hgsc.bcm.edu	37	X	9859098	9859098	+	Silent	SNP	A	A	G	rs6640543	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	149	145	0	0.993333	0	A|0.147;G|0.853	0.853	strong	.	SHROOM2	139	.	NM_001649	exon3	c.A399G	p.P133P	CTCCCCATTCACC	.	PASS	Atlas-SNP
USP26	83844	hgsc.bcm.edu	37	X	132161673	132161673	+	Silent	SNP	C	C	T	rs41304540	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	130	146	1	0.984848	0.00684932	C|0.677;T|0.323	0.323	strong	.	USP26	135	.	NM_031907	exon1	c.G576A	p.E192E	GAATTCCTCATTC	.	PASS	Atlas-SNP
SSH2	85464	hgsc.bcm.edu	37	17	27963141	27963141	+	Missense_Mutation	SNP	T	T	C	rs61737983	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	97	145	0	0.598765	0	T|0.984;C|0.016	0.016	strong	SSH2,NS,carcinoma,+2,1	SSH2	107	1	NM_033389	exon14	c.A2026G	p.M676V	CCTCCATCCTTGA	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449483	89449483	+	Missense_Mutation	SNP	C	C	G	rs74100106	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	440	58	319	0	0.131818	0	C|0.904;G|0.096	0.096	strong	.	.	.	.	NM_001162536	exon3	c.G27C	p.K9N	GAAGAGCTTTCCT	.	PASS	Atlas-SNP
CHRNA2	1135	hgsc.bcm.edu	37	8	27324844	27324844	+	Silent	SNP	G	G	A	rs2565061	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	63	127	0	0.484615	0	G|0.788;A|0.212	0.212	strong	.	CHRNA2	48	.	NM_000742	exon5	c.C351T	p.D117D	TTTGTAGTCGCTC	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121747406	121747406	+	Missense_Mutation	SNP	G	G	A	rs12711538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	77	163	0	0.411765	0	G|0.360;A|0.640	0.640	strong	.	GLI2	187	.	NM_005270	exon13	c.G3916A	p.D1306N	GTCCCCGATTCAG	.	PASS	Atlas-SNP
ENTPD6	955	hgsc.bcm.edu	37	20	25193949	25193949	+	Silent	SNP	G	G	A	rs2076561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	33	73	0	0.515625	0	G|0.708;A|0.292	0.292	strong	ENTPD6,face,carcinoma,+2,1	ENTPD6	57	1	NM_001247	exon5	c.G504A	p.P168P	CATTCCGTTCGAC	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158536345	158536345	+	Missense_Mutation	SNP	A	A	G	rs2305475	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	30	88	0	0.441176	0	A|0.737;C|0.000;G|0.262;T|0.000	0.262	strong	.	ESYT2	70	.	NM_020728	exon16	c.T1750C	p.S584P	CCAGGGAACACTG	.	PASS	Atlas-SNP
BPTF	2186	hgsc.bcm.edu	37	17	65955758	65955758	+	Silent	SNP	T	T	C	rs202116659	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	20	143	5	0.16	0.034965	.	.	weak	BPTF_ENST00000335221,rectum,carcinoma,0,2	BPTF	415	2	NM_182641	exon24	c.T8028C	p.A2676A	ACCAGCTCCTCCA	.	scavenged	Atlas-SNP
SF3A1	10291	hgsc.bcm.edu	37	22	30733111	30733111	+	Silent	SNP	C	C	A	rs2229807	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	92	104	0	0.968421	0	C|0.795;A|0.205	0.205	strong	.	SF3A1	61	.	NM_005877	exon13	c.G2010T	p.V670V	GGGATGCACAGGG	.	PASS	Atlas-SNP
SOGA3	387104	hgsc.bcm.edu	37	6	127797179	127797179	+	Silent	SNP	G	G	A	rs3734448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	7	67	0	0.2	0	G|0.657;A|0.343	0.343	strong	.	.	.	.	NM_001012279	exon6	c.C1992T	p.A664A	CAGGTCGGCCACG	.	PASS	Atlas-SNP
KRTAP11-1	337880	hgsc.bcm.edu	37	21	32253629	32253629	+	Missense_Mutation	SNP	C	C	T	rs71321355	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	55	74	0	0.495495	0	C|0.841;T|0.159	0.159	strong	.	KRTAP11-1	46	.	NM_175858	exon1	c.G215A	p.R72Q	GTTCGCCGGTAAC	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1431048	1431048	+	Missense_Mutation	SNP	A	A	G	rs201429000		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	9	119	2	0.0612245	0.0168067	.	.	weak	ATAD3B,NS,neuroblastoma,0,1	ATAD3B	68	1	NM_031921	exon16	c.A1798G	p.T600A	CTGGCCACGGACC	.	scavenged	Atlas-SNP
AHSG	197	hgsc.bcm.edu	37	3	186337713	186337713	+	Missense_Mutation	SNP	T	T	C	rs4917	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	64	79	0	0.969697	0	T|0.293;C|0.707	0.707	strong	.	AHSG	40	.	NM_001622	exon6	c.T743C	p.M248T	CCTGCATGGTGTT	.	PASS	Atlas-SNP
SLC12A8	84561	hgsc.bcm.edu	37	3	124896668	124896668	+	Missense_Mutation	SNP	G	G	A	rs2993631	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	40	76	0	0.408163	0	G|0.964;A|0.036	0.036	strong	.	SLC12A8	81	.	NM_024628	exon5	c.C541T	p.R181C	GGAGGCGGATTAT	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121747429	121747429	+	Silent	SNP	A	A	G	rs10167980	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	84	159	0	0.454054	0	A|0.400;G|0.600	0.600	strong	.	GLI2	187	.	NM_005270	exon13	c.A3939G	p.P1313P	AGTGCCACCACCT	.	PASS	Atlas-SNP
OR2H1	26716	hgsc.bcm.edu	37	6	29429766	29429766	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	93	206	0	0.458128	0	.	.	none	.	OR2H1	38	.	NM_030883	exon3	c.A220G	p.S74G	ACCACAAGTTGTG	.	PASS	Atlas-SNP
DNPH1	10591	hgsc.bcm.edu	37	6	43193877	43193877	+	Silent	SNP	G	G	A	rs7832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	16	34	0	0.516129	0	G|0.942;A|0.058	0.058	strong	C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	NM_006443	exon3	c.C270T	p.V90V	TGCCACGACCACT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60897488	60897488	+	Silent	SNP	G	G	A	rs2274933	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	35	30	0	0.522388	0	G|0.817;C|0.000;A|0.183	0.183	strong	.	LAMA5	268	.	NM_005560	exon47	c.C6183T	p.F2061F	GCCATCGAAACCA	.	PASS	Atlas-SNP
MTUS1	57509	hgsc.bcm.edu	37	8	17513484	17513484	+	Missense_Mutation	SNP	T	T	C	rs61733708	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	110	245	0	0.526316	0	T|0.992;C|0.008	0.008	strong	.	MTUS1	144	.	NM_001001924	exon9	c.A2996G	p.E999G	GTTTTTTCAGCCT	.	PASS	Atlas-SNP
E2F7	144455	hgsc.bcm.edu	37	12	77419593	77419593	+	Silent	SNP	A	A	G	rs310830	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	45	66	0	0.608108	0	A|0.919;G|0.081	0.081	strong	.	E2F7	201	.	NM_203394	exon12	c.T2310C	p.S770S	AAGAGTAGAAGAA	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44157746	44157746	+	Missense_Mutation	SNP	C	C	A	rs35088381	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	45	85	0	0.511364	0	C|0.984;A|0.016	0.016	strong	.	LOXHD1	367	.	NM_144612	exon14	c.G1894T	p.G632C	ACCAGCCGCTGCC	.	PASS	Atlas-SNP
OXTR	5021	hgsc.bcm.edu	37	3	8809703	8809703	+	Silent	SNP	G	G	A	rs2228485	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	41	36	0	1	0	G|0.297;A|0.703	0.703	strong	.	OXTR	31	.	NM_000916	exon3	c.C171T	p.N57N	ACACGCGTTCCCG	.	PASS	Atlas-SNP
GALNT16	57452	hgsc.bcm.edu	37	14	69727121	69727121	+	Silent	SNP	G	G	A	rs150774678	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	37	33	0	0.528571	0	G|0.960;A|0.040	0.040	strong	.	GALNT16	8	.	NM_001168368	exon1	c.G114A	p.R38R	CGGCCGGGGCGCG	.	PASS	Atlas-SNP
RNASE11	122651	hgsc.bcm.edu	37	14	21052414	21052414	+	Missense_Mutation	SNP	T	T	A	rs35818240	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	120	200	0	0.547945	0	T|0.926;A|0.074	0.074	strong	.	RNASE11	44	.	NM_145250	exon3	c.A220T	p.T74S	GTAATGTGGAAGA	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549548	32549548	+	Silent	SNP	G	G	A	rs112201403	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	54	431	0	0.305085	0	G|0.500;A|0.500	0.500	strong	.	HLA-DRB1	41	.	NM_002124	exon3	c.C438T	p.C146C	CACAGAGCAGACC	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	140788	140788	+	Silent	SNP	A	A	G	rs12516245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	31	56	0	0.455882	0	A|0.830;G|0.170	0.170	strong	.	PLEKHG4B	167	.	NM_052909	exon1	c.A366G	p.P122P	GACCCCAAACTGT	.	PASS	Atlas-SNP
ATP2B2	491	hgsc.bcm.edu	37	3	10379923	10379923	+	Silent	SNP	C	C	T	rs35678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	40	81	0	0.57971	0	C|0.505;T|0.495	0.495	strong	.	ATP2B2	304	.	NM_001001331	exon22	c.G3357A	p.A1119A	CCGCTCCGCGTGG	.	PASS	Atlas-SNP
RGS22	26166	hgsc.bcm.edu	37	8	100990177	100990177	+	Silent	SNP	A	A	G	rs7841915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	245	119	238	0	0.485714	0	A|0.924;G|0.076	0.076	strong	.	RGS22	319	.	NM_015668	exon23	c.T3487C	p.L1163L	CTGCCAATTTTTT	.	PASS	Atlas-SNP
PCDH1	5097	hgsc.bcm.edu	37	5	141244356	141244356	+	Missense_Mutation	SNP	C	C	T	rs3822357	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	96	192	0	0.542373	0	C|0.935;T|0.065	0.065	strong	.	PCDH1	119	.	NM_032420	exon3	c.G1540A	p.A514T	GGAAGGCGACCTC	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79639708	79639708	+	Missense_Mutation	SNP	C	C	T	rs11546631	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	49	128	0	0.556818	0	C|0.877;T|0.123	0.123	strong	.	CCDC137	27	.	NM_199287	exon6	c.C844T	p.R282W	ACTTCCCGGAAGA	.	PASS	Atlas-SNP
RECK	8434	hgsc.bcm.edu	37	9	36107981	36107981	+	Missense_Mutation	SNP	C	C	G	rs148296262	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	45	97	0	0.48913	0	C|0.997;G|0.003	0.003	strong	.	RECK	73	.	NM_021111	exon14	c.C1585G	p.L529V	TGCAAACTGGGAG	.	PASS	Atlas-SNP
ZNF677	342926	hgsc.bcm.edu	37	19	53741068	53741068	+	Silent	SNP	C	C	T	rs12984188	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	49	103	0	0.475728	0	C|0.591;T|0.409	0.409	strong	ZNF677,rectum,carcinoma,-1,3	ZNF677	94	3	NM_182609	exon5	c.G912A	p.S304S	GAGGTTCGAACAC	.	PASS	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1789721	1789721	+	Silent	SNP	T	T	C	rs56335545	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	10	11	0	0.434783	0	T|0.914;C|0.086	0.086	strong	ATP8B3,NS,lymphoid_neoplasm,0,1	ATP8B3	108	1	NM_138813	exon23	c.A2484G	p.K828K	CAGCAGTTTGTCC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8145921	8145921	+	Silent	SNP	C	C	T	rs2303168	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	39	22	0	1	0	C|0.386;T|0.614	0.614	strong	.	FBN3	300	.	NM_032447	exon58	c.G7419A	p.P2473P	GCCGGGCGGACAG	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23542290	23542290	+	Missense_Mutation	SNP	A	A	G	rs428549	bycluster;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	13	38	0	0.433333	0	A|0.713;G|0.287	0.287	strong	.	ZNF91	349	.	NM_003430	exon4	c.T3491C	p.L1164P	CAAAGTAGTGGGA	.	PASS	Atlas-SNP
MSLN	10232	hgsc.bcm.edu	37	16	818559	818559	+	Missense_Mutation	SNP	A	A	G	rs1135210	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	69	58	2	1	0.0344828	A|0.678;G|0.322	0.322	strong	MSLN_ENST00000446427,NS,carcinoma,0,2	MSLN	109	2	NM_013404	exon16	c.A1801G	p.M601V	CTCAGCATGCAAG	.	scavenged	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	260142	260142	+	Silent	SNP	G	G	T	rs7503725	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	5	0	0	1	.	G|0.658;T|0.342	0.342	strong	.	C17orf97	76	.	NM_001013672	exon1	c.G9T	p.T3T	GGAGACGCGTGGC	.	PASS	Atlas-SNP
CLCA4	22802	hgsc.bcm.edu	37	1	87045902	87045902	+	Silent	SNP	A	A	T	rs1932809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	46	2	0	0.442308	0	A|0.601;T|0.399	0.399	strong	.	CLCA4	131	.	NM_012128	exon14	c.A2634T	p.T878T	TCCTACACCTACT	.	PASS	Atlas-SNP
SLC22A20	440044	hgsc.bcm.edu	37	11	64981818	64981818	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	45	62	0	0.625	0	.	.	none	.	SLC22A20	36	.	NM_001004326	exon2	c.C403T	p.R135C	GAGGCCCGCACTC	.	PASS	Atlas-SNP
RDH5	5959	hgsc.bcm.edu	37	12	56115585	56115585	+	Silent	SNP	C	C	T	rs3138142	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	17	46	0	0.435897	0	C|0.865;T|0.135	0.135	strong	.	RDH5	25	.	NM_001199771	exon3	c.C423T	p.I141I	TCCCATCGGGGTC	.	PASS	Atlas-SNP
OR5D18	219438	hgsc.bcm.edu	37	11	55587914	55587914	+	Missense_Mutation	SNP	A	A	G	rs55832853	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	76	109	0	0.608	0	A|0.774;G|0.226	0.226	strong	OR5D18,NS,carcinoma,-1,1	OR5D18	121	1	NM_001001952	exon1	c.A809G	p.H270R	CCAGGCACACAGT	.	PASS	Atlas-SNP
ZNF644	84146	hgsc.bcm.edu	37	1	91404256	91404256	+	Missense_Mutation	SNP	C	C	A	rs41286761	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	49	119	0	0.462264	0	C|0.981;A|0.019	0.019	strong	.	ZNF644	120	.	NM_201269	exon3	c.G2655T	p.E885D	TACATGCTCTTGA	.	PASS	Atlas-SNP
ETV3	2117	hgsc.bcm.edu	37	1	157095470	157095470	+	Silent	SNP	A	A	G	rs2231856	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	41	111	0	0.431579	0	A|0.792;G|0.208	0.208	strong	.	ETV3	50	.	NM_001145312	exon5	c.T702C	p.F234F	CCTAGCAAACAGA	.	PASS	Atlas-SNP
KCNH4	23415	hgsc.bcm.edu	37	17	40312349	40312349	+	Silent	SNP	G	G	A	rs138917401	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	50	122	0	0.454545	0	G|0.996;A|0.004	0.004	strong	.	KCNH4	105	.	NM_012285	exon16	c.C2763T	p.S921S	CCAAGCGGAGCCT	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13811775	13811775	+	Missense_Mutation	SNP	T	T	C	rs10078391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	54	121	0	0.593407	0	T|0.764;C|0.236	0.236	strong	DNAH5,right_upper_lobe,carcinoma,-1,1	DNAH5	868	1	NM_001369	exon44	c.A7388G	p.Q2463R	AGGCCTTGAAGCA	.	PASS	Atlas-SNP
USP42	84132	hgsc.bcm.edu	37	7	6193752	6193752	+	Missense_Mutation	SNP	G	G	A	rs61753119	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	10	3	0	0.588235	0	G|0.919;A|0.081	0.081	strong	USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	NM_032172	exon15	c.G2567A	p.S856N	GGTTGAGTCCGGC	.	PASS	Atlas-SNP
USP42	84132	hgsc.bcm.edu	37	7	6194383	6194383	+	Silent	SNP	C	C	T	rs73058659	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	9	16	0	0.473684	0	C|0.929;T|0.071	0.071	strong	USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	NM_032172	exon15	c.C3198T	p.Y1066Y	CAGGTACGCCCTG	.	PASS	Atlas-SNP
ZNF587B	100293516	hgsc.bcm.edu	37	19	58353003	58353003	+	Missense_Mutation	SNP	G	G	A	rs34871842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	12	25	0	0.666667	0	G|0.956;A|0.044	0.044	strong	.	.	.	.	NM_001204818	exon3	c.G961A	p.A321T	GTTCACGCTGGAA	.	PASS	Atlas-SNP
UNC13A	23025	hgsc.bcm.edu	37	19	17746940	17746940	+	Silent	SNP	C	C	T	rs77267738	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	94	158	0	0.516484	0	C|0.958;T|0.042	0.042	strong	.	UNC13A	299	.	NM_001080421	exon25	c.G3108A	p.E1036E	CTGTTCCTCTGGG	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	37	MT	11719	11719	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	7	4	0	1	0	.	.	none	.	.	.	.	ENST00000361381	exon1	c.G960A	p.G320G	CCACGGGCTTACA	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	83	203	0	0.425641	0	G|0.747;C|0.253	0.253	strong	PCDHB6,NS,carcinoma,+2,1	PCDHB6	161	1	NM_018939	exon1	c.G1014C	p.V338V	GGACGTGAATGAC	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234219	8234219	+	Missense_Mutation	SNP	G	G	A	rs4840955	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	14	39	0	0.358974	0	G|0.631;A|0.369	0.369	strong	.	.	.	.	NM_001080826	exon2	c.C1700T	p.P567L	GCCAGCGGTGACA	.	PASS	Atlas-SNP
MYO1E	4643	hgsc.bcm.edu	37	15	59500970	59500970	+	Silent	SNP	C	C	T	rs117265950	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	63	152	0	0.398734	0	C|0.991;T|0.009	0.009	strong	.	MYO1E	99	.	NM_004998	exon14	c.G1440A	p.T480T	GAGCAGCGTCTGA	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132250712	132250712	+	Silent	SNP	G	G	C	rs1051233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	20	34	0	0.4	0	G|0.840;C|0.160	0.160	strong	.	SFSWAP	69	.	NM_001261411	exon13	c.G2001C	p.L667L	AAAGCTGGCCCAG	.	PASS	Atlas-SNP
PIGX	54965	hgsc.bcm.edu	37	3	196460680	196460680	+	Silent	SNP	C	C	T	rs34830136	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	49	138	0	0.352518	0	C|0.811;T|0.189	0.189	strong	.	PIGX	16	.	NM_001166304	exon7	c.C738T	p.T246T	ACATACCTCTCTA	.	PASS	Atlas-SNP
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20740129	20740129	+	Missense_Mutation	SNP	G	G	A	rs199932545	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	422	209	816	0	0.495261	0	.	.	weak	.	GOLGA6L6	37	.	NM_001145004	exon8	c.C1621T	p.R541W	GCTCCCGTATCTT	.	PASS	Atlas-SNP
CTNNA2	1496	hgsc.bcm.edu	37	2	80801346	80801346	+	Silent	SNP	T	T	C	rs2228460	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	182	173	0	0.983784	0	T|0.724;C|0.276	0.276	strong	.	CTNNA2	462	.	NM_001164883	exon13	c.T1800C	p.V600V	CAACGTTCCTCAA	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76423151	76423151	+	Silent	SNP	C	C	T	rs3209030	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	34	73	0	0.4	0	C|0.914;T|0.086	0.086	strong	.	DNAH17	347	.	NM_173628	exon78	c.G12627A	p.P4209P	AGTCTCCGGAATC	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1896060	1896060	+	Missense_Mutation	SNP	T	T	C	rs114499682	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	32	360	1	0.15311	0.00277778	T|0.684;C|0.317	0.317	strong	SIRPA,caecum,carcinoma,+1,2	SIRPA	83	2	NM_001040022	exon3	c.T395C	p.V132A	ATGACGTGGAGTT	.	scavenged	Atlas-SNP
EPB41L2	2037	hgsc.bcm.edu	37	6	131186718	131186718	+	Silent	SNP	T	T	A	rs149001048	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	19	247	0	0.123377	0	T|1.000;A|0.000	0.000	strong	.	EPB41L2	96	.	NM_001431	exon17	c.A2787T	p.T929T	CTCAGATGTGATG	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143491	55143491	+	Missense_Mutation	SNP	G	G	T	rs1061681	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	93	186	1	0.534483	0.00537634	G|0.602;T|0.398	0.398	strong	LILRB1,colon,carcinoma,0,1	LILRB1	140	1	NM_001081637	exon5	c.G464T	p.S155I	GCTTCAGTCTGTG	.	scavenged	Atlas-SNP
HEG1	57493	hgsc.bcm.edu	37	3	124746237	124746237	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	106	199	0	0.497653	0	.	.	none	.	HEG1	109	.	NM_020733	exon3	c.T725A	p.L242Q	TCTGACAGCCCCA	.	PASS	Atlas-SNP
FAM5B	57795	hgsc.bcm.edu	37	1	177247854	177247854	+	Missense_Mutation	SNP	C	C	G	rs3176443	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	54	117	0	0.519231	0	C|0.730;G|0.270	0.270	strong	.	FAM5B	191	.	NM_021165	exon7	c.C1168G	p.L390V	CGGATCCTACGCC	.	PASS	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	37	14	71444788	71444788	+	Silent	SNP	G	G	A	rs3814871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	47	78	0	0.573171	0	G|0.604;A|0.396	0.396	strong	PCNX,NS,carcinoma,0,1	PCNX	198	1	NM_014982	exon6	c.G1734A	p.R578R	GCATAGGGACTAT	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6550004	6550004	+	Missense_Mutation	SNP	A	A	G	rs2344828	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	69	61	0	1	0	A|0.275;G|0.725	0.725	strong	DNHD1,colon,carcinoma,0,1	DNHD1	198	1	NM_144666	exon11	c.A2090G	p.Q697R	TACAACAGGTGCT	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79031558	79031558	+	Missense_Mutation	SNP	G	G	A	rs62621912	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	61	128	0	0.521368	0	A|0.166;C|0.000;G|0.834	0.166	strong	.	CMYA5	643	.	NM_153610	exon2	c.G6970A	p.G2324S	CTAATCGGTGAGA	.	PASS	Atlas-SNP
ISOC1	51015	hgsc.bcm.edu	37	5	128430757	128430757	+	Silent	SNP	T	T	C	rs1127827	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	11	26	0	0.392857	0	T|0.232;C|0.768	0.768	strong	.	ISOC1	26	.	NM_016048	exon1	c.T298C	p.L100L	GTGCCGTTGCAGA	.	PASS	Atlas-SNP
MRPL40	64976	hgsc.bcm.edu	37	22	19423257	19423257	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	5	118	0	0.0416667	0	.	.	none	.	MRPL40	13	.	NM_003776	exon4	c.G393A	p.M131I	TAAGATGGAGAGG	.	PASS	Atlas-SNP
PIGB	9488	hgsc.bcm.edu	37	15	55647492	55647492	+	Silent	SNP	C	C	T	rs8043415	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	64	152	0	0.512	0	C|0.909;T|0.091	0.091	strong	PIGB,NS,carcinoma,+1,1	PIGB	36	1	NM_004855	exon12	c.C1527T	p.S509S	AATAAGCGCTTTC	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50098740	50098740	+	Silent	SNP	T	T	A	rs41283285	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	110	176	0	0.601093	0	T|0.974;A|0.026	0.026	strong	.	WDFY4	205	.	NM_020945	exon44	c.T7284A	p.G2428G	CACGGGTGATGTC	.	PASS	Atlas-SNP
LIPK	643414	hgsc.bcm.edu	37	10	90503075	90503075	+	Silent	SNP	T	T	C	rs390152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	36	57	0	0.62069	0	T|0.754;C|0.246	0.246	strong	LIPK_ENST00000404190,colon,carcinoma,0,2	LIPK	50	2	NM_001080518	exon8	c.T957C	p.H319H	CTTCCATCAGGTA	.	PASS	Atlas-SNP
VEGFB	7423	hgsc.bcm.edu	37	11	64004692	64004692	+	Silent	SNP	C	C	T	rs12366035	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	41	128	0	0.366071	0	C|0.792;T|0.208	0.208	strong	VEGFB,NS,carcinoma,0,1	VEGFB	18	1	NM_003377	exon5	c.C408T	p.D136D	GCCAGACAGGTGA	.	PASS	Atlas-SNP
OTOP3	347741	hgsc.bcm.edu	37	17	72943184	72943184	+	Missense_Mutation	SNP	C	C	T	rs142183564	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	42	66	0	0.506024	0	C|0.999;T|0.001	0.001	strong	.	OTOP3	64	.	NM_178233	exon6	c.C1234T	p.R412C	CCTACCCGCAGCC	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	37	12	53670545	53670545	+	Missense_Mutation	SNP	C	C	A	rs1318648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	33	44	0	0.532258	0	C|0.400;N|0.000	.	strong	.	ESPL1	158	.	NM_012291	exon8	c.C1842A	p.S614R	GCTGAGCCCCGAG	.	PASS	Atlas-SNP
ABLIM3	22885	hgsc.bcm.edu	37	5	148596547	148596547	+	Missense_Mutation	SNP	C	C	T	rs116226381	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	39	106	0	0.493671	0	C|0.997;T|0.003	0.003	strong	.	ABLIM3	91	.	NM_014945	exon8	c.C695T	p.T232I	ACCCAACCTGTGC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45125466	45125466	+	Missense_Mutation	SNP	G	G	C	rs11760885	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	38	48	0	0.513514	0	G|0.970;C|0.030	0.030	strong	.	NACAD	44	.	NM_001146334	exon2	c.C313G	p.L105V	TGGACAGAGCCTG	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5039138	5039138	+	Silent	SNP	C	C	T	rs3213878	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	7	12	0	0.5	0	C|0.883;T|0.117	0.117	strong	.	USP6	213	.	NM_004505	exon9	c.C579T	p.T193T	CATCACCGCCTTG	.	PASS	Atlas-SNP
ART3	419	hgsc.bcm.edu	37	4	77003484	77003484	+	Missense_Mutation	SNP	G	G	A	rs142545952	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	40	77	0	0.416667	0	G|1.000;A|0.000	0.000	strong	ART3,NS,carcinoma,0,1	ART3	34	1	NM_001130017	exon3	c.G577A	p.A193T	CCTCAGGCTGCTA	.	PASS	Atlas-SNP
OR2B11	127623	hgsc.bcm.edu	37	1	247614896	247614896	+	Missense_Mutation	SNP	A	A	C	rs11583410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	27	77	0	0.391304	0	A|0.630;C|0.370	0.370	strong	.	OR2B11	102	.	NM_001004492	exon1	c.T389G	p.I130S	TTGCAGATGGCCA	.	PASS	Atlas-SNP
MCM3	4172	hgsc.bcm.edu	37	6	52129484	52129484	+	Missense_Mutation	SNP	C	C	T	rs2230240	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	60	99	0	0.454545	0	C|0.841;T|0.159	0.159	strong	.	MCM3	63	.	NM_002388	exon17	c.G2464A	p.E822K	GCTCTTCGCTGTC	.	PASS	Atlas-SNP
TBC1D16	125058	hgsc.bcm.edu	37	17	77925393	77925393	+	Silent	SNP	G	G	A	rs35286723	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	38	67	0	0.487179	0	G|0.883;A|0.117	0.117	strong	.	TBC1D16	48	.	NM_019020	exon5	c.C945T	p.D315D	GGCCTCGTCGCTG	.	PASS	Atlas-SNP
TXNDC2	84203	hgsc.bcm.edu	37	18	9887546	9887546	+	Missense_Mutation	SNP	G	G	A	rs2240906	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	33	78	0	0.445946	0	G|0.562;A|0.438	0.438	strong	TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	NM_001098529	exon2	c.G1070A	p.G357D	AGAAGGGTGACAT	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157102159	157102159	+	Missense_Mutation	SNP	G	G	A	rs10051838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	95	130	0	0.979381	0	G|0.823;A|0.177	0.177	strong	C5orf52,NS,carcinoma,+1,1	C5orf52	17	1	NM_001145132	exon2	c.G272A	p.R91Q	TATCTCGGGTGAT	.	PASS	Atlas-SNP
ZUFSP	221302	hgsc.bcm.edu	37	6	116973182	116973182	+	Missense_Mutation	SNP	T	T	C	rs4946188	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	34	86	0	0.829268	0	T|0.640;C|0.360	0.360	strong	ZUFSP,NS,carcinoma,0,1	ZUFSP	46	1	NM_145062	exon6	c.A1135G	p.N379D	AATCGTTGTAAGC	.	PASS	Atlas-SNP
CA9	768	hgsc.bcm.edu	37	9	35674053	35674053	+	Missense_Mutation	SNP	G	G	A	rs2071676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	51	100	0	0.490385	0	G|0.707;A|0.293	0.293	strong	.	CA9	48	.	NM_001216	exon1	c.G97A	p.V33M	CTTCTGGTGCCTG	.	PASS	Atlas-SNP
PRB2	653247	hgsc.bcm.edu	37	12	11546495	11546495	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	17	213	8	0.0752212	0.0375587	.	.	none	PRB2_ENST00000389362,colon,carcinoma,+1,2	PRB2	168	2	NM_006248	exon3	c.T517C	p.S173P	ATCGAGAACTTCG	.	scavenged	Atlas-SNP
ZFP91	80829	hgsc.bcm.edu	37	11	58378424	58378424	+	Missense_Mutation	SNP	A	A	G	rs8373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	10	40	0	0.434783	0	A|0.780;G|0.220	0.220	strong	.	ZFP91	66	.	NM_053023	exon5	c.A619G	p.S207G	TTTAGTAGTGAAG	.	PASS	Atlas-SNP
SLC12A9	56996	hgsc.bcm.edu	37	7	100464053	100464053	+	Silent	SNP	G	G	A	rs199582669	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	8	16	0	0.444444	0	G|0.995;A|0.005	0.005	strong	.	SLC12A9	81	.	NM_020246	exon14	c.G2571A	p.E857E	GCCGGAGGGTGGG	.	PASS	Atlas-SNP
NRN1L	123904	hgsc.bcm.edu	37	16	67920049	67920049	+	Missense_Mutation	SNP	G	G	A	rs73594554	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	19	37	0	0.527778	0	G|0.854;A|0.146	0.146	strong	NRN1L,colon,carcinoma,0,1	NRN1L	13	1	NM_198443	exon3	c.G385A	p.E129K	GGCTCCGAAACCA	.	PASS	Atlas-SNP
ND6	0	hgsc.bcm.edu	37	MT	14311	14311	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	8	8	7	0	1	0	.	.	none	.	.	.	.	ENST00000361681	exon1	c.A363G	p.V121V	GCTTCCTACACTA	.	PASS	Atlas-SNP
PPP1R21	129285	hgsc.bcm.edu	37	2	48713777	48713777	+	Silent	SNP	C	C	T	rs33994624	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	63	150	0	0.538462	0	C|0.914;T|0.086	0.086	strong	.	PPP1R21	47	.	NM_152994	exon14	c.C1326T	p.S442S	TATTTCCAAACAT	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75279846	75279846	+	Silent	SNP	C	C	T	rs649257	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	56	116	0	0.444444	0	C|0.660;T|0.340	0.340	strong	SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	NM_001235	exon3	c.C693T	p.T231T	CTATACCGTGGGT	.	PASS	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3329037	3329037	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	77	70	0	0.905882	0	.	.	none	PRDM16,NS,lymphoid_neoplasm,+1,1	PRDM16	147	1	NM_022114	exon9	c.G2276A	p.R759Q	CACCCCGGGACGC	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176304	57176304	+	Missense_Mutation	SNP	T	T	G	rs12460400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	38	94	0	0.558824	0	T|0.628;G|0.372	0.372	strong	.	ZNF835	106	.	NM_001005850	exon2	c.A263C	p.E88A	GGGCTCTCCCCAG	.	PASS	Atlas-SNP
CPO	130749	hgsc.bcm.edu	37	2	207827220	207827220	+	Missense_Mutation	SNP	G	G	A	rs62617140	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	88	146	0	0.505747	0	G|0.965;A|0.035	0.035	strong	.	CPO	42	.	NM_173077	exon7	c.G659A	p.S220N	TTGCCAGCTTCAT	.	PASS	Atlas-SNP
RRN3	54700	hgsc.bcm.edu	37	16	15185186	15185186	+	Missense_Mutation	SNP	C	C	T	rs151006368	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	737	557	551	1	0.755767	0.00181488	C|0.988;T|0.012	0.012	strong	.	RRN3	36	.	NM_018427	exon3	c.G238A	p.D80N	CTGGATCTAACAG	.	PASS	Atlas-SNP
TTC7B	145567	hgsc.bcm.edu	37	14	91084338	91084338	+	Silent	SNP	C	C	T	rs754247	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	80	104	0	0.97561	0	C|0.578;T|0.422	0.422	strong	.	TTC7B	93	.	NM_001010854	exon16	c.G1803A	p.E601E	CAGTGCCTCGTCC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54726237	54726237	+	Missense_Mutation	SNP	C	C	G	rs16985555	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	240	6	635	0	0.025	0	C|0.333;G|0.667	0.667	strong	LILRB3,NS,carcinoma,0,1	LILRB3	67	1	NM_006864	exon3	c.G268C	p.E90Q	GGTGCTCTGTCAT	.	scavenged	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	37	8	98954108	98954108	+	Silent	SNP	G	G	T	rs35407519	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	256	114	248	0	0.445312	0	G|0.905;T|0.095	0.095	strong	.	MATN2	165	.	NM_002380	exon4	c.G816T	p.S272S	CAACTCGGATCAG	.	PASS	Atlas-SNP
KRTAP10-5	386680	hgsc.bcm.edu	37	21	46000367	46000367	+	Missense_Mutation	SNP	G	G	T	rs149326833	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	67	93	0	0.553719	0	G|0.971;T|0.029	0.029	strong	KRTAP10-5,NS,carcinoma,-1,1	KRTAP10-5	43	1	NM_198694	exon1	c.C89A	p.P30H	CCGCAGGGGGGCT	.	PASS	Atlas-SNP
IKBIP	121457	hgsc.bcm.edu	37	12	99007411	99007411	+	Silent	SNP	C	C	T	rs201283576	bycluster;by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	15	45	0	0.319149	0	C|0.999;A|0.001	.	alt	.	IKBIP	46	.	NM_201612	exon3	c.G1005A	p.E335E	CTTAATCTCAGCT	.	PASS	Atlas-SNP
QPRT	23475	hgsc.bcm.edu	37	16	29706444	29706444	+	Missense_Mutation	SNP	C	C	T	rs2303255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	42	68	0	0.494118	0	C|0.895;T|0.105	0.105	strong	.	QPRT	19	.	NM_014298	exon2	c.C473T	p.A158V	GGGCCGCCTCGCA	.	PASS	Atlas-SNP
TMEM72	643236	hgsc.bcm.edu	37	10	45430462	45430462	+	Silent	SNP	C	C	T	rs17417442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	60	106	0	0.566038	0	C|0.634;T|0.366	0.366	strong	.	TMEM72	25	.	NM_001123376	exon5	c.C708T	p.A236A	CCTCGCCGAAGGT	.	PASS	Atlas-SNP
LMTK3	114783	hgsc.bcm.edu	37	19	49003060	49003060	+	Silent	SNP	C	C	A	rs201659713	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	15	6	0	0.75	0	C|0.987;A|0.013	0.013	strong	.	LMTK3	125	.	NM_001080434	exon12	c.G1353T	p.P451P	GGGTGGCGGCGGT	.	PASS	Atlas-SNP
EID3	493861	hgsc.bcm.edu	37	12	104698208	104698208	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	2	105	1	0.0190476	0.00952381	.	.	none	EID3,NS,carcinoma,0,2	EID3	28	2	NM_001008394	exon1	c.G496A	p.E166K	AAAGCTGAGACAT	.	scavenged	Atlas-SNP
PDCD4	27250	hgsc.bcm.edu	37	10	112647433	112647433	+	Missense_Mutation	SNP	G	G	A	rs41292600	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	36	73	0	0.467532	0	G|0.993;A|0.007	0.007	strong	.	PDCD4	39	.	NM_014456	exon6	c.G566A	p.R189K	TGTTAAGAGATTT	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90418262	90418262	+	Silent	SNP	C	C	T	rs2026634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	66	102	1	0.985075	0.00980392	C|0.152;T|0.848	0.848	strong	.	MDN1	478	.	NM_014611	exon51	c.G7851A	p.T2617T	CTGGTCCGTTTGT	.	PASS	Atlas-SNP
DDHD1	80821	hgsc.bcm.edu	37	14	53619500	53619500	+	Missense_Mutation	SNP	C	C	G	rs117525276	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	47	52	0	0.54023	0	C|0.928;G|0.072	0.072	strong	.	DDHD1	202	.	NM_001160147	exon1	c.G317C	p.G106A	CTCTCACCCTCGC	.	PASS	Atlas-SNP
CFHR5	81494	hgsc.bcm.edu	37	1	196952092	196952092	+	Missense_Mutation	SNP	C	C	T	rs12097550	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	260	103	268	1	0.396154	0.00373134	C|0.986;T|0.014	0.014	strong	.	CFHR5	150	.	NM_030787	exon2	c.C136T	p.P46S	CAAGTTCCTACAG	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60913127	60913127	+	Silent	SNP	A	A	G	rs8124907	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	73	100	1	0.486667	0.01	A|0.749;G|0.251	0.251	strong	LAMA5,NS,carcinoma,0,3	LAMA5	268	3	NM_005560	exon14	c.T1836C	p.A612A	AGGTCCAGCAAAC	.	scavenged	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537035	88537035	+	Missense_Mutation	SNP	A	A	G	rs202210195	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	38	129	1	0.348624	0.00775194	.	.	weak	DSPP,NS,carcinoma,-1,1	DSPP	174	1	NM_014208	exon5	c.A3221G	p.D1074G	GCAGTGACAGCAG	.	scavenged	Atlas-SNP
TG	7038	hgsc.bcm.edu	37	8	133899575	133899575	+	Missense_Mutation	SNP	G	G	A	rs2069548	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	60	160	0	0.397351	0	G|0.991;A|0.009	0.009	strong	.	TG	416	.	NM_003235	exon9	c.G1958A	p.G653D	TCAGAGGTGGACA	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	37	10	126715075	126715075	+	Silent	SNP	T	T	C	rs3781413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	47	99	0	0.419643	0	T|0.892;C|0.108	0.108	strong	CTBP2,NS,carcinoma,0,1	CTBP2	100	1	NM_022802	exon1	c.A1254G	p.A418A	GGTGGCTGCCGTC	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	37	17	62020348	62020348	+	Missense_Mutation	SNP	T	T	C	rs2058194	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	218	240	1	0.990909	0.00416667	T|0.407;C|0.593	0.593	strong	SCN4A,NS,carcinoma,0,1	SCN4A	205	1	NM_000334	exon23	c.A4126G	p.N1376D	TCTGGTTGTCTGT	.	PASS	Atlas-SNP
OR8H1	219469	hgsc.bcm.edu	37	11	56058197	56058197	+	Silent	SNP	G	G	A	rs1842674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	88	189	0	0.483516	0	G|0.650;A|0.350	0.350	strong	OR8H1,NS,carcinoma,-1,1	OR8H1	89	1	NM_001005199	exon1	c.C342T	p.L114L	TGATGAGAGAAGA	.	PASS	Atlas-SNP
MTMR1	8776	hgsc.bcm.edu	37	X	149931106	149931106	+	Silent	SNP	C	C	T	rs16995747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	163	150	0	0.976048	0	C|0.180;0|0.003	.	strong	.	MTMR1	82	.	NM_003828	exon15	c.C1902T	p.G634G	GGAGGGCCTACAG	.	PASS	Atlas-SNP
LCE1C	353133	hgsc.bcm.edu	37	1	152777868	152777868	+	Silent	SNP	A	A	G	rs36107483	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	201	194	0	0.995049	0	A|0.738;G|0.262	0.262	strong	.	LCE1C	40	.	NM_178351	exon2	c.T87C	p.C29C	TGGGGGACACTTT	.	PASS	Atlas-SNP
FNBP4	23360	hgsc.bcm.edu	37	11	47745696	47745696	+	Missense_Mutation	SNP	G	G	C	rs138653244	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	41	61	0	0.539474	0	G|0.995;C|0.005	0.005	strong	.	FNBP4	99	.	NM_015308	exon14	c.C2348G	p.S783C	GAAGAAGAACTAG	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127597518	127597518	+	Silent	SNP	G	G	A	rs10070365	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	79	148	0	0.441341	0	G|0.871;A|0.129	0.129	strong	.	FBN2	858	.	NM_001999	exon64	c.C8274T	p.S2758S	TTCTGGGGACAGA	.	PASS	Atlas-SNP
ATIC	471	hgsc.bcm.edu	37	2	216190020	216190020	+	Missense_Mutation	SNP	C	C	G	rs2372536	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	77	151	0	0.534722	0	C|0.763;G|0.237	0.237	strong	.	ATIC	84	.	NM_004044	exon5	c.C347G	p.T116S	GTGTAACTGTTGA	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21031046	21031046	+	Silent	SNP	C	C	T	rs2296226	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	240	223	169	0	0.929167	0	C|0.878;T|0.122	0.122	strong	KIF17,colon,carcinoma,0,1	KIF17	130	1	NM_001122819	exon5	c.G1017A	p.P339P	GATGCGCGGCTTG	.	PASS	Atlas-SNP
NBPF15	284565	hgsc.bcm.edu	37	1	148594455	148594455	+	Missense_Mutation	SNP	A	A	G	rs1043751	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	318	39	297	30	0.122642	0.10101	A|0.996;G|0.004	0.004	strong	NBPF15,NS,carcinoma,-1,1	NBPF15	20	1	NM_173638	exon19	c.A1828G	p.R610G	CTGGATAGATGTT	.	scavenged	Atlas-SNP
TCF20	6942	hgsc.bcm.edu	37	22	42606257	42606257	+	Silent	SNP	C	C	T	rs2070116	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	76	149	0	0.506667	0	C|0.788;T|0.212	0.212	strong	.	TCF20	164	.	NM_181492	exon1	c.G5055A	p.S1685S	AAAGGACGAGGCC	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604721	140604721	+	Silent	SNP	C	C	A	rs2910003	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	76	65	0	0.612903	0	C|0.642;A|0.358	0.358	strong	PCDHB14,NS,carcinoma,+2,1	PCDHB14	132	1	NM_018934	exon1	c.C1644A	p.R548R	GGTGCGCGTGCTG	.	PASS	Atlas-SNP
POLR2B	5431	hgsc.bcm.edu	37	4	57889677	57889677	+	Silent	SNP	C	C	T	rs1056364	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	121	94	0	0.98374	0	C|0.436;T|0.564	0.564	strong	POLR2B,NS,carcinoma,0,1	POLR2B	108	1	NM_000938	exon19	c.C2697T	p.S899S	AACTAGCGAGACG	.	PASS	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39137297	39137297	+	Missense_Mutation	SNP	C	C	T	rs721957	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	190	90	201	0	0.473684	0	T|0.613;G|0.022	0.613	strong	.	KRT40	27	.	NM_182497	exon6	c.G794A	p.C265Y	GTTTCACACTGAC	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56539240	56539240	+	Silent	SNP	C	C	T	rs397977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	74	127	0	0.544118	0	C|0.671;N|0.000	.	strong	NLRP5,NS,carcinoma,0,1	NLRP5	217	1	NM_153447	exon7	c.C1641T	p.D547D	GTTTGACGGTGAC	.	PASS	Atlas-SNP
ILVBL	10994	hgsc.bcm.edu	37	19	15227030	15227030	+	Silent	SNP	G	G	A	rs2074263	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	47	78	0	0.573171	0	G|0.293;A|0.707	0.707	strong	.	ILVBL	54	.	NM_006844	exon12	c.C1404T	p.G468G	GTCCCCGCCATCC	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	37	1	152732436	152732436	+	Silent	SNP	G	G	C	rs4845480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	241	237	268	1	0.983402	0.00373134	G|0.490;C|0.510	0.510	strong	KPRP,NS,carcinoma,+1,1	KPRP	152	1	NM_001025231	exon2	c.G372C	p.A124A	CGAAGCGTCACAA	.	PASS	Atlas-SNP
SCAF4	57466	hgsc.bcm.edu	37	21	33068962	33068962	+	Silent	SNP	T	T	C	rs7280330	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	36	104	0	0.356436	0	T|0.831;C|0.169	0.169	strong	SCAF4,NS,carcinoma,0,2	SCAF4	142	2	NM_020706	exon8	c.A879G	p.A293A	GGGTACTGCGGCA	.	PASS	Atlas-SNP
CPM	1368	hgsc.bcm.edu	37	12	69265578	69265578	+	Silent	SNP	A	A	G	rs2228654	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	79	188	0	0.434066	0	T|0.108;G|0.403	0.403	strong	.	CPM	30	.	NM_001005502	exon4	c.T417C	p.Y139Y	GCTGTAATAACAG	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	82	96	0	1	0	C|0.213;N|0.000	0.213	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon7	c.A880G	p.I294V	TACTGATGTTTGA	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110397780	110397780	+	Missense_Mutation	SNP	A	A	G	rs62508075	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	31	41	0	0.574074	0	A|0.975;G|0.025	0.025	strong	.	PKHD1L1	522	.	NM_177531	exon6	c.A490G	p.I164V	ATAACAATCCAAG	.	PASS	Atlas-SNP
C7orf10	79783	hgsc.bcm.edu	37	7	40899967	40899967	+	Silent	SNP	G	G	C	rs2010706	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	135	126	0	0.992647	0	G|0.556;C|0.444	0.444	strong	.	C7orf10	99	.	NM_001193311	exon15	c.G1305C	p.P435P	GCCCCCGCTGCTC	.	PASS	Atlas-SNP
APOL2	23780	hgsc.bcm.edu	37	22	36624231	36624231	+	Missense_Mutation	SNP	C	C	T	rs118097350	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	48	87	0	0.551724	0	C|0.994;T|0.006	0.006	strong	APOL2,NS,carcinoma,0,1	APOL2	20	1	NM_030882	exon5	c.G233A	p.R78K	CACTGCCTGTGCT	.	PASS	Atlas-SNP
OR6S1	341799	hgsc.bcm.edu	37	14	21108909	21108909	+	Silent	SNP	G	G	A	rs17277515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	64	169	0	0.357542	0	A|0.090;C|0.000;G|0.910	0.090	strong	.	OR6S1	49	.	NM_001001968	exon1	c.C942T	p.G314G	TAAAACGCCTGCC	.	PASS	Atlas-SNP
CES3	23491	hgsc.bcm.edu	37	16	67006838	67006838	+	Silent	SNP	G	G	A	rs3848289	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	79	118	0	0.519737	0	G|0.955;A|0.045	0.045	strong	.	CES3	56	.	NM_024922	exon13	c.G1602A	p.R534R	GCCACGGGCCGGA	.	PASS	Atlas-SNP
RAVER1	125950	hgsc.bcm.edu	37	19	10431799	10431799	+	Silent	SNP	G	G	T	rs281425	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	11	11	0	0.916667	0	G|0.798;T|0.202	0.202	strong	.	RAVER1	67	.	NM_133452	exon8	c.C1449A	p.P483P	AGGGGCGGGGGGA	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	71002893	71002893	+	Missense_Mutation	SNP	C	C	T	rs2252784	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	254	106	302	0	0.417323	0	C|0.424;T|0.576	0.576	strong	.	PTPRB	676	.	NM_001109754	exon4	c.G935A	p.R312K	ATAATCCTGAAGT	.	PASS	Atlas-SNP
NALCN	259232	hgsc.bcm.edu	37	13	101747984	101747984	+	Silent	SNP	G	G	A	rs9513851	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	21	70	0	0.403846	0	G|0.939;A|0.061	0.061	strong	.	NALCN	431	.	NM_052867	exon28	c.C3210T	p.N1070N	ATTTAAGTTCTTT	.	PASS	Atlas-SNP
LAMA5	3911	hgsc.bcm.edu	37	20	60903419	60903419	+	Silent	SNP	C	C	T	rs7262393	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	42	36	0	0.552632	0	C|0.782;T|0.218	0.218	strong	LAMA5,colon,carcinoma,0,1	LAMA5	268	1	NM_005560	exon35	c.G4530A	p.L1510L	GCACAGCAGGCAG	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32914126	32914126	+	Missense_Mutation	SNP	C	C	G	rs80358784	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	27	81	0	0.442623	0	C|0.999;T|0.001	.	weak	.	BRCA2	812	.	NM_000059	exon11	c.C5634G	p.N1878K	AAACAACGAGAAT	.	PASS	Atlas-SNP
PFAS	5198	hgsc.bcm.edu	37	17	8166458	8166458	+	Missense_Mutation	SNP	T	T	A	rs35217368	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	25	88	0	0.490196	0	T|0.955;A|0.045	0.045	strong	.	PFAS	91	.	NM_012393	exon13	c.T1442A	p.F481Y	TGGACTTTGGGGC	.	PASS	Atlas-SNP
CLSTN2	64084	hgsc.bcm.edu	37	3	140178485	140178485	+	Missense_Mutation	SNP	G	G	A	rs7632885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	93	97	0	1	0	G|0.425;A|0.574	0.574	strong	.	CLSTN2	190	.	NM_022131	exon7	c.G1096A	p.V366I	GCCAAAGTCCCCG	.	PASS	Atlas-SNP
SMYD3	64754	hgsc.bcm.edu	37	1	246078851	246078851	+	Missense_Mutation	SNP	C	C	T	rs61762672	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	43	83	0	0.417476	0	C|0.999;T|0.001	0.001	strong	.	SMYD3	77	.	NM_001167740	exon8	c.G794A	p.R265H	TGGCAACGGAAAC	.	PASS	Atlas-SNP
NCAPH	23397	hgsc.bcm.edu	37	2	97030247	97030247	+	Missense_Mutation	SNP	T	T	C	rs2305935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	71	171	0	0.430303	0	T|0.688;C|0.312	0.312	strong	NCAPH,NS,carcinoma,0,1	NCAPH	67	1	NM_015341	exon13	c.T1616C	p.V539A	ATAGGGTAGAGAC	.	PASS	Atlas-SNP
ZNF407	55628	hgsc.bcm.edu	37	18	72346701	72346701	+	Silent	SNP	T	T	C	rs146635665	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	27	72	0	0.465517	0	T|0.997;C|0.003	0.003	strong	.	ZNF407	231	.	NM_001146190	exon1	c.T3726C	p.G1242G	TGGAGGTGTTGTC	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43817404	43817404	+	Missense_Mutation	SNP	G	G	A	rs71471869	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	55	103	0	0.433071	0	GAT|0.500;AAC|0.500	.	alt	.	MAP1A	189	.	NM_002373	exon4	c.G3733A	p.D1245N	GCCGAGGATACCT	.	PASS	Atlas-SNP
GDF9	2661	hgsc.bcm.edu	37	5	132198199	132198199	+	Silent	SNP	G	G	A	rs254286	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	34	30	0	1	0	G|0.516;A|0.484	0.484	strong	.	GDF9	50	.	NM_005260	exon2	c.C447T	p.T149T	TTCAACGGTAGTA	.	PASS	Atlas-SNP
CELA1	1990	hgsc.bcm.edu	37	12	51737562	51737562	+	Missense_Mutation	SNP	T	T	C	rs17860300	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	43	117	0	0.43	0	T|0.788;C|0.212	0.212	strong	CELA1,NS,carcinoma,+2,1	CELA1	39	1	NM_001971	exon3	c.A175G	p.M59V	CTGTCATCACCCA	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379931	31379931	+	Missense_Mutation	SNP	G	G	A	rs1063635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	99	111	0	0.99	0	G|0.488;A|0.512	0.512	strong	.	MICA	21	.	NM_001177519	exon4	c.G821A	p.R274Q	TTTGCCGAGGAGA	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	17113563	17113563	+	Silent	SNP	C	C	T	rs1801225	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	18	25	0	0.666667	0	C|0.657;T|0.343	0.343	strong	.	CUBN	515	.	NM_001081	exon19	c.G2487A	p.S829S	AAAAGGCGAGCGA	.	PASS	Atlas-SNP
MARCH10	162333	hgsc.bcm.edu	37	17	60813627	60813627	+	Silent	SNP	G	G	A	rs2041283	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	65	130	0	0.631068	0	G|0.692;A|0.308	0.308	strong	.	MARCH10	102	.	NM_001100875	exon6	c.C1602T	p.N534N	TGCACTGTTTACT	.	PASS	Atlas-SNP
GRM7	2917	hgsc.bcm.edu	37	3	7620168	7620168	+	Silent	SNP	A	A	G	rs34373930	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	107	204	1	0.511962	0.00490196	A|0.788;G|0.212	0.212	strong	.	GRM7	223	.	NM_000844	exon8	c.A1575G	p.L525L	CACACTACCATGT	.	PASS	Atlas-SNP
CRYL1	51084	hgsc.bcm.edu	37	13	21063524	21063524	+	Silent	SNP	A	A	G	rs14236	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	29	58	0	0.42029	0	A|0.737;G|0.263	0.263	strong	CRYL1,mouth,carcinoma,-1,1	CRYL1	28	1	NM_015974	exon3	c.T261C	p.G87G	CATGGCACCCTCT	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134680921	134680921	+	Silent	SNP	A	A	G	rs141926275	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	71	143	0	0.467105	0	A|0.985;G|0.015	0.015	strong	.	TTC40	100	.	NM_001200049	exon34	c.T4701C	p.P1567P	CTGGACAGGAAGT	.	PASS	Atlas-SNP
KCNA5	3741	hgsc.bcm.edu	37	12	5155046	5155046	+	Missense_Mutation	SNP	G	G	A	rs12720445	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	26	47	0	0.541667	0	G|0.993;A|0.007	0.007	strong	.	KCNA5	138	.	NM_002234	exon1	c.G1733A	p.R578K	CCCGAAGGGGCAG	.	PASS	Atlas-SNP
IL22RA1	58985	hgsc.bcm.edu	37	1	24447468	24447468	+	Missense_Mutation	SNP	G	G	C	rs3795299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	16	139	0	0.0969697	0	G|0.599;C|0.401	0.401	strong	.	IL22RA1	62	.	NM_021258	exon7	c.C1552G	p.R518G	ATGGACGGGAAGG	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327330	16327330	+	Silent	SNP	T	T	C	rs2075974	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	25	52	0	0.520833	0	T|0.695;C|0.305	0.305	strong	.	ATXN1	117	.	NM_001128164	exon7	c.A1212G	p.E404E	GGAGGCTTCACGA	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	37	16	2348528	2348528	+	Silent	SNP	G	G	C	rs323043	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	49	96	0	0.538462	0	G|0.858;C|0.142	0.142	strong	.	ABCA3	176	.	NM_001089	exon15	c.C1755G	p.P585P	ACTGGTGGGGGGA	.	PASS	Atlas-SNP
DNAH7	56171	hgsc.bcm.edu	37	2	196825256	196825256	+	Silent	SNP	G	G	C	rs115124743	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	74	161	0	0.453988	0	G|0.969;C|0.031	0.031	strong	.	DNAH7	512	.	NM_018897	exon18	c.C2619G	p.V873V	AGAGGAGACTGTG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373646	5373646	+	Silent	SNP	T	T	C	rs5024041	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	24	65	0	0.428571	0	T|0.407;C|0.593	0.593	strong	OR51B6,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	OR51B6	53	1	NM_001004750	exon1	c.T909C	p.R303R	ACTTCGTTTATTC	.	PASS	Atlas-SNP
DNAJC5B	85479	hgsc.bcm.edu	37	8	66992737	66992737	+	Silent	SNP	G	G	A	rs7006209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	48	112	0	0.413793	0	G|0.909;A|0.091	0.091	strong	.	DNAJC5B	42	.	NM_033105	exon5	c.G459A	p.V153V	CTATGTGTCCCCA	.	PASS	Atlas-SNP
GOLT1A	127845	hgsc.bcm.edu	37	1	204172090	204172090	+	Silent	SNP	G	G	A	rs13334	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	100	172	0	0.471698	0	A|0.016;G|0.984	0.016	strong	.	GOLT1A	15	.	NM_198447	exon2	c.C51T	p.F17F	GATGCCGAAACCG	.	PASS	Atlas-SNP
CSTL1	128817	hgsc.bcm.edu	37	20	23421101	23421101	+	Missense_Mutation	SNP	G	G	A	rs17757442	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	60	164	0	0.434783	0	G|0.906;A|0.094	0.094	strong	.	CSTL1	30	.	NM_138283	exon2	c.G197A	p.R66K	TCCAGAGGCTAAT	.	PASS	Atlas-SNP
CDH13	1012	hgsc.bcm.edu	37	16	83065664	83065664	+	Silent	SNP	G	G	A	rs6565105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	42	116	0	0.392523	0	A|0.532;C|0.000;G|0.467	0.532	strong	.	CDH13	97	.	NM_001220488	exon4	c.G348A	p.S116S	GGTCTCGAGCCCA	.	PASS	Atlas-SNP
ERC2	26059	hgsc.bcm.edu	37	3	55922561	55922561	+	Missense_Mutation	SNP	T	T	G	rs61745935	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	117	213	0	0.517699	0	T|0.999;G|0.001	0.001	strong	ERC2_ENST00000288221,NS,carcinoma,+1,2	ERC2	221	2	NM_015576	exon13	c.A2414C	p.N805T	AGTGCATTCATCA	.	PASS	Atlas-SNP
IL31RA	133396	hgsc.bcm.edu	37	5	55147405	55147405	+	Missense_Mutation	SNP	A	A	C	rs75528518	bycluster;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	69	133	0	0.43125	0	.	.	alt	.	IL31RA	84	.	NM_001242637	exon1	c.A7C	p.I3L	ATGTGCATCAGGC	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128495338	128495338	+	Silent	SNP	C	C	T	rs3816885	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	38	96	0	0.506667	0	C|0.813;T|0.187	0.187	strong	.	FLNC	339	.	NM_001458	exon43	c.C7221T	p.D2407D	GGATGACGCTCGC	.	PASS	Atlas-SNP
RDH8	50700	hgsc.bcm.edu	37	19	10124257	10124257	+	Silent	SNP	C	C	T	rs150712129	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	16	28	0	0.432432	0	C|1.000;T|0.000	0.000	strong	.	RDH8	51	.	NM_015725	exon1	c.C144T	p.D48D	CCATGACCCCAAG	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110460488	110460488	+	Missense_Mutation	SNP	G	G	T	rs1673407	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	54	97	0	0.432	0	G|0.427;T|0.573	0.573	strong	PKHD1L1,colon,carcinoma,0,1	PKHD1L1	522	1	NM_177531	exon39	c.G5893T	p.V1965L	AGTGTGGTGCAGT	.	PASS	Atlas-SNP
MEIOB	254528	hgsc.bcm.edu	37	16	1894961	1894961	+	Missense_Mutation	SNP	A	A	G	rs9806945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	52	149	0	0.396947	0	A|0.839;G|0.161	0.161	strong	.	.	.	.	NM_001163560	exon10	c.T782C	p.I261T	TCTGGTATATCTT	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134671154	134671154	+	Silent	SNP	G	G	A	rs189775198	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	60	131	0	0.454545	0	G|0.991;A|0.009	0.009	strong	.	TTC40	100	.	NM_001200049	exon39	c.C5514T	p.G1838G	CATGGCGCCCTGG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104679	168104679	+	Silent	SNP	T	T	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	60	196	0	0.340909	0	.	.	none	.	XIRP2	914	.	NM_152381	exon9	c.T6777G	p.T2259T	AAATACTTCCACA	.	PASS	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145737123	145737123	+	Missense_Mutation	SNP	G	G	A	rs35346077	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	50	57	0	0.632911	0	G|0.995;A|0.005	0.005	weak	.	RECQL4	75	.	NM_004260	exon21	c.C3443T	p.S1148F	CTCAGGGACAGGA	.	PASS	Atlas-SNP
ARHGEF38	54848	hgsc.bcm.edu	37	4	106474078	106474078	+	Silent	SNP	G	G	A	rs10032241	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	64	119	0	0.460432	0	G|0.830;A|0.170	0.170	strong	.	ARHGEF38	52	.	NM_001242729	exon1	c.G156A	p.R52R	GAGGAGGAGCCAA	.	PASS	Atlas-SNP
OR5T1	390155	hgsc.bcm.edu	37	11	56044050	56044050	+	Silent	SNP	A	A	G	rs148135770	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	53	121	0	0.490741	0	A|0.999;G|0.001	0.001	strong	OR5T1,right_upper_lobe,carcinoma,+1,1	OR5T1	95	1	NM_001004745	exon1	c.A936G	p.A312A	GGAGGCAATCAAA	.	PASS	Atlas-SNP
AQP11	282679	hgsc.bcm.edu	37	11	77301385	77301385	+	Silent	SNP	G	G	A	rs145642525	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	51	85	0	0.451327	0	G|0.998;A|0.002	0.002	strong	.	AQP11	14	.	NM_173039	exon1	c.G348A	p.T116T	CGAGACGGGTGCG	.	PASS	Atlas-SNP
CYFIP1	23191	hgsc.bcm.edu	37	15	22925851	22925851	+	Silent	SNP	C	C	T	rs4134802	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	54	88	0	0.514286	0	C|0.769;T|0.231	0.231	strong	.	CYFIP1	159	.	NM_014608	exon2	c.C69T	p.P23P	CCTGCCCGACCAG	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121416623	121416623	+	Missense_Mutation	SNP	G	G	C	rs3732407	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	79	169	0	0.49375	0	G|0.843;C|0.157	0.157	strong	.	GOLGB1	319	.	NM_001256486	exon13	c.C2747G	p.T916S	TTCTCAGTCATAC	.	PASS	Atlas-SNP
ADAMTS9	56999	hgsc.bcm.edu	37	3	64606840	64606840	+	Silent	SNP	C	C	A	rs149253049	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	98	170	0	0.471154	0	A|0.001;C|0.999;G|0.000	0.001	strong	.	ADAMTS9	206	.	NM_182920	exon19	c.G2763T	p.L921L	CTGGGGCAGCCGA	.	PASS	Atlas-SNP
ELOVL5	60481	hgsc.bcm.edu	37	6	53159090	53159090	+	Silent	SNP	G	G	T	rs2294857	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	61	116	0	0.491935	0	G|0.922;T|0.078	0.078	strong	.	ELOVL5	25	.	NM_001242831	exon3	c.C258A	p.A86A	GGCAGGGGCATGT	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202287156	202287156	+	Silent	SNP	C	C	T	rs12123010	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	95	130	0	0.539773	0	C|0.899;T|0.101	0.101	strong	.	LGR6	102	.	NM_001017403	exon18	c.C1725T	p.S575S	GCTCTCCGTGCTC	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36841756	36841756	+	Silent	SNP	T	T	C	rs1534967	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	68	70	1	0.971429	0.0142857	T|0.603;C|0.397	0.397	strong	KIAA1755,NS,carcinoma,0,1	KIAA1755	145	1	NM_001029864	exon14	c.A3291G	p.S1097S	GCCCAGTGAGTCT	.	scavenged	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17446991	17446991	+	Silent	SNP	C	C	T	rs4819925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	61	142	0	0.465649	0	C|0.190;T|0.810	0.810	strong	GAB4,NS,carcinoma,0,1	GAB4	95	1	NM_001037814	exon6	c.G1287A	p.K429K	CTTACCCTTCTGG	.	PASS	Atlas-SNP
ZNF568	374900	hgsc.bcm.edu	37	19	37441365	37441365	+	Missense_Mutation	SNP	T	T	C	rs547483	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	14	26	0	0.451613	0	T|0.698;C|0.302	0.302	strong	.	ZNF568	106	.	NM_198539	exon7	c.T1310C	p.M437T	TACATATGCGAAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509353	195509353	+	Missense_Mutation	SNP	G	G	A	rs200052949	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	11	160	4	0.104762	0.025	.	.	weak	MUC4_ENST00000463781,uveal_tract,malignant_melanoma,-1,4	MUC4	1505	4	NM_018406	exon2	c.C9098T	p.A3033V	GTGGATGCTGAGG	.	scavenged	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48597064	48597064	+	Silent	SNP	A	A	G	rs17224828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	22	40	0	0.478261	0	A|0.939;G|0.061	0.061	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.T12C	p.N4N	GCTGCCATTCCTT	.	PASS	Atlas-SNP
PPFIA4	8497	hgsc.bcm.edu	37	1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	rs12130501	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	11	6	14	0	0.545455	0	G|0.992;A|0.008	0.008	strong	PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	NM_015053	exon16	c.G1948A	p.G650S	GGTCGCGGCGGCA	.	PASS	Atlas-SNP
RAPGEF3	10411	hgsc.bcm.edu	37	12	48151822	48151822	+	Missense_Mutation	SNP	C	C	G	rs11168230	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	44	105	0	0.37931	0	C|0.721;G|0.279	0.279	strong	.	RAPGEF3	98	.	NM_001098531	exon2	c.G46C	p.A16P	CCACAGCCAGGCC	.	PASS	Atlas-SNP
OR10H3	26532	hgsc.bcm.edu	37	19	15852872	15852872	+	Missense_Mutation	SNP	G	G	A	rs2240228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	279	147	236	0	0.526882	0	G|0.797;A|0.203	0.203	strong	OR10H3,NS,carcinoma,0,1	OR10H3	53	1	NM_013938	exon1	c.G670A	p.V224M	TTCATTGTGGCTG	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	37	2	185801103	185801103	+	Missense_Mutation	SNP	A	A	C	rs61739291	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	292	128	271	1	0.438356	0.00369004	A|0.984;C|0.016	0.016	strong	.	ZNF804A	322	.	NM_194250	exon4	c.A980C	p.N327T	GTCAAAATTCAGT	.	PASS	Atlas-SNP
DNAAF3	352909	hgsc.bcm.edu	37	19	55672470	55672470	+	Missense_Mutation	SNP	T	T	C	rs2365725	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	55	45	0	0.964912	0	T|0.756;C|0.244	0.244	strong	C19orf51,rectum,carcinoma,0,3	.	.	3	NM_001256714	exon8	c.A1079G	p.E360G	AGGCTCTCGTCGT	.	PASS	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367008	107367008	+	Missense_Mutation	SNP	T	T	C	rs10156474	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	112	186	0	0.533333	0	T|0.639;C|0.361	0.361	strong	.	OR13C2	46	.	NM_001004481	exon1	c.A901G	p.K301E	CATCCTTGTTTCT	.	PASS	Atlas-SNP
FABP2	2169	hgsc.bcm.edu	37	4	120240238	120240238	+	Silent	SNP	T	T	C	rs1511025	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	87	181	0	0.5	0	T|0.654;C|0.346	0.346	strong	FABP2,NS,carcinoma,-1,1	FABP2	21	1	NM_000134	exon4	c.A357G	p.V119V	TTCATATACATAA	.	PASS	Atlas-SNP
PTGDR	5729	hgsc.bcm.edu	37	14	52735108	52735108	+	Silent	SNP	C	C	T	rs34968651	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	26	49	0	0.40625	0	C|0.932;T|0.068	0.068	strong	.	PTGDR	58	.	NM_000953	exon1	c.C576T	p.G192G	GGAGGGCTCGCTG	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279866	46279866	+	Silent	SNP	A	A	G	rs28529067	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	45	97	0	0.523256	0	A|0.870;G|0.130	0.130	strong	NCOA3,colon,carcinoma,0,1	NCOA3	156	1	NM_181659	exon20	c.A3792G	p.Q1264Q	GCAGCAACAGCAA	.	PASS	Atlas-SNP
MYO16	23026	hgsc.bcm.edu	37	13	109613929	109613929	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	4	137	0	0.040404	0	.	.	none	.	MYO16	285	.	NM_001198950	exon18	c.C2080T	p.L694F	TTGCACCTTGGAG	.	PASS	Atlas-SNP
CCDC41	51134	hgsc.bcm.edu	37	12	94772742	94772742	+	Missense_Mutation	SNP	C	C	T	rs2271979	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	101	101	0	1	0	C|0.864;T|0.136	0.136	strong	CCDC41,caecum,carcinoma,0,1	CCDC41	59	1	NM_016122	exon7	c.G626A	p.R209Q	TCCACTCGTTTGC	.	PASS	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920196	51920196	+	Missense_Mutation	SNP	G	G	T	rs77553517	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	37	148	0	0.205556	0	.	.	weak	.	SIGLEC10	112	.	NM_001171157	exon3	c.C430A	p.Q144K	GCTTCTGAGTCAG	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1552430	1552430	+	Missense_Mutation	SNP	T	T	C	rs2253427	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	413	409	446	1	0.990315	0.00224215	C|0.824;N|0.000	0.824	strong	SIRPB1,NS,carcinoma,0,1	SIRPB1	83	1	NM_006065	exon3	c.A687G	p.I229M	GTGGGCTATCTCG	.	PASS	Atlas-SNP
ANO3	63982	hgsc.bcm.edu	37	11	26621117	26621117	+	Silent	SNP	A	A	C	rs11604868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	110	257	0	0.486726	0	A|0.835;C|0.165	0.165	strong	.	ANO3	145	.	NM_031418	exon17	c.A1692C	p.A564A	CACTGCAGTGTTT	.	PASS	Atlas-SNP
PCDHGB2	56103	hgsc.bcm.edu	37	5	140739779	140739779	+	Missense_Mutation	SNP	C	C	G	rs17097231	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	141	132	0	0.979167	0	C|0.880;G|0.120	0.120	strong	.	PCDHGB2	196	.	NM_018923	exon1	c.C77G	p.P26R	TGTTCCCCGGGGC	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33628239	33628239	+	Silent	SNP	G	G	A	rs9527026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	46	127	0	0.386555	0	G|0.844;A|0.156	0.156	strong	.	KL	106	.	NM_004795	exon2	c.G1155A	p.K385K	CATGAAGTTCCGC	.	PASS	Atlas-SNP
EPS8L2	64787	hgsc.bcm.edu	37	11	721570	721570	+	Silent	SNP	C	C	T	rs7635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	36	86	0	0.461538	0	C|0.687;T|0.313	0.313	strong	EPS8L2,colon,carcinoma,0,1	EPS8L2	42	1	NM_022772	exon10	c.C774T	p.I258I	GCAAATCCTCAAC	.	PASS	Atlas-SNP
GNB2	2783	hgsc.bcm.edu	37	7	100276355	100276355	+	Silent	SNP	C	C	T	rs17850902	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	83	145	0	0.564626	0	C|0.995;T|0.005	0.005	strong	.	GNB2	29	.	NM_005273	exon10	c.C954T	p.L318L	CTGCCTCGGGGTC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379795	31379795	+	Missense_Mutation	SNP	A	A	G	rs1131898	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	60	130	0	1	0	A|0.700;G|0.300	0.300	strong	.	MICA	21	.	NM_001177519	exon4	c.A685G	p.S229G	GCTTCCAGCTTCT	.	PASS	Atlas-SNP
POU2F2	5452	hgsc.bcm.edu	37	19	42600030	42600030	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	31	30	0	0.392405	0	.	.	none	POU2F2_ENST00000292077,NS,lymphoid_neoplasm,0,8	POU2F2	106	8	NM_001207025	exon9	c.A715G	p.T239A	TGGTCGTCTGGCT	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7012123	7012123	+	Silent	SNP	A	A	G	rs9946794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	27	53	0	0.642857	0	A|0.528;G|0.472	0.472	strong	LAMA1,NS,carcinoma,0,1	LAMA1	458	1	NM_005559	exon24	c.T3378C	p.G1126G	CTGAGGACCAAAG	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026491	176026491	+	Silent	SNP	G	G	A	rs35847475	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	25	76	0	0.409836	0	G|0.984;A|0.016	0.016	strong	.	GPRIN1	77	.	NM_052899	exon2	c.C345T	p.A115A	GATGGAGGCTCCA	.	PASS	Atlas-SNP
ACADL	33	hgsc.bcm.edu	37	2	211085491	211085491	+	Missense_Mutation	SNP	G	G	A	rs61731470	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	25	44	0	0.641026	0	G|0.976;A|0.024	0.024	strong	.	ACADL	38	.	NM_001608	exon2	c.C113T	p.T38I	GAAGGAGTTTCTA	.	PASS	Atlas-SNP
PIK3C2B	5287	hgsc.bcm.edu	37	1	204399061	204399061	+	Silent	SNP	A	A	G	rs2271419	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	13	34	0	0.464286	0	A|0.866;G|0.134	0.134	strong	.	PIK3C2B	142	.	NM_002646	exon30	c.T4386C	p.P1462P	CACCTCAGGGGGT	.	PASS	Atlas-SNP
DNMT3B	1789	hgsc.bcm.edu	37	20	31367948	31367948	+	Silent	SNP	C	C	T	rs6058885	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	81	0	1	0	C|0.921;T|0.079	0.079	strong	.	DNMT3B	196	.	NM_175850	exon1	c.C27T	p.S9S	TCCAAGCTTGGTG	.	PASS	Atlas-SNP
GALC	2581	hgsc.bcm.edu	37	14	88459434	88459434	+	Silent	SNP	G	G	T	rs111976362	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	16	7	0	1	0	G|0.907;T|0.093	0.093	strong	GALC,NS,carcinoma,0,1	GALC	48	1	NM_000153	exon1	c.C75A	p.G25G	GGCGCGGCCCGCC	.	PASS	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	37	9	35705759	35705759	+	Silent	SNP	G	G	A	rs11541908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	25	54	0	0.510204	0	G|0.806;A|0.194	0.194	strong	.	TLN1	185	.	NM_006289	exon42	c.C5601T	p.T1867T	CTGAACGGTCACT	.	PASS	Atlas-SNP
TRIM64C	646754	hgsc.bcm.edu	37	11	49080565	49080565	+	Missense_Mutation	SNP	A	A	C	rs7932738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	112	243	0	0.495575	0	A|0.844;C|0.156	0.156	strong	TRIM64C,NS,carcinoma,0,1	TRIM64C	18	1	NM_001206631	exon1	c.T100G	p.F34V	TGCAAAAGCTGTG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388324	1388324	+	Missense_Mutation	SNP	A	A	C	rs74377230	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	11	191	0	0.0662651	0	A|0.833;C|0.167	0.167	weak	CRIPAK,caecum,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.A25C	p.N9H	TGTGCCAATGTGG	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12187861	12187861	+	Missense_Mutation	SNP	T	T	G	rs10426017	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	29	50	0	0.439394	0	T|0.746;G|0.254	0.254	strong	.	ZNF844	69	.	NM_001136501	exon4	c.T1926G	p.I642M	CCATATTAATGTA	.	PASS	Atlas-SNP
TSHR	7253	hgsc.bcm.edu	37	14	81610504	81610504	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	2	161	1	0.0125786	0.00621118	.	.	none	TSHR,colon,carcinoma,+1,1	TSHR	462	1	NM_000369	exon10	c.G2102A	p.R701H	GTAAACGCCAGGC	.	scavenged	Atlas-SNP
KRTAP25-1	100131902	hgsc.bcm.edu	37	21	31661691	31661691	+	Missense_Mutation	SNP	A	A	G	rs8127420	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	105	245	1	0.525	0.00408163	A|0.520;G|0.480	0.480	strong	.	KRTAP25-1	13	.	NM_001128598	exon1	c.T118C	p.S40P	TCCTGGACACAAA	.	PASS	Atlas-SNP
RAET1E	135250	hgsc.bcm.edu	37	6	150212003	150212003	+	Missense_Mutation	SNP	C	C	T	rs9383583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	31	65	0	0.911765	0	C|0.783;T|0.217	0.217	strong	.	RAET1E	20	.	NM_139165	exon1	c.G35A	p.R12H	AGAAGGCGCACAG	.	PASS	Atlas-SNP
TMEM175	84286	hgsc.bcm.edu	37	4	946226	946226	+	Silent	SNP	T	T	C	rs11552301	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	49	45	0	1	0	T|0.369;C|0.631	0.631	strong	.	TMEM175	44	.	NM_032326	exon7	c.T450C	p.I150I	CGCCATTGGGGTC	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157369324	157369324	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	20	45	0	0.350877	0	.	.	none	.	PTPRN2	243	.	NM_002847	exon19	c.T2764C	p.S922P	GGAGGGACCTTGA	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121415720	121415720	+	Missense_Mutation	SNP	T	T	C	rs3732410	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	382	185	305	0	0.484293	0	T|0.787;C|0.213	0.213	strong	GOLGB1,NS,carcinoma,0,1	GOLGB1	319	1	NM_001256486	exon13	c.A3650G	p.Y1217C	CGATTATAGTCAT	.	PASS	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	37	2	220331911	220331911	+	Missense_Mutation	SNP	G	G	A	rs34861443	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	36	59	0	0.514286	0	G|0.988;A|0.012	0.012	strong	.	SPEG	272	.	NM_005876	exon10	c.G2897A	p.R966Q	AAAGCCGGTCCCT	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33772658	33772658	+	Nonsense_Mutation	SNP	G	G	T	rs8072510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	48	110	0	0.384	0	G|0.896;T|0.104	0.104	strong	.	SLFN13	79	.	NM_144682	exon3	c.C42A	p.Y14X	GTCTGGGTAAGAT	.	PASS	Atlas-SNP
OR4C16	219428	hgsc.bcm.edu	37	11	55339798	55339798	+	Silent	SNP	C	C	T	rs557667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	61	191	0	0.401316	0	C|0.755;T|0.245	0.245	strong	.	OR4C16	104	.	NM_001004701	exon1	c.C195T	p.S65S	CTTATCCTTATCT	.	PASS	Atlas-SNP
ZNF70	7621	hgsc.bcm.edu	37	22	24087319	24087319	+	Silent	SNP	A	A	C	rs2070451	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	58	82	0	0.557692	0	A|0.865;C|0.135	0.135	strong	.	ZNF70	49	.	NM_021916	exon2	c.T9G	p.V3V	TGGGGGAACCTCC	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	37	12	133384864	133384864	+	Missense_Mutation	SNP	G	G	A	rs3741486	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	82	202	0	0.453039	0	G|0.802;A|0.198	0.198	strong	.	GOLGA3	234	.	NM_001172557	exon5	c.C791T	p.P264L	GGAGCCGGGACAT	.	PASS	Atlas-SNP
PPP1R3A	5506	hgsc.bcm.edu	37	7	113518434	113518434	+	Missense_Mutation	SNP	C	C	A	rs1799999	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	33	75	0	0.515625	0	C|0.769;N|0.000	.	strong	.	PPP1R3A	317	.	NM_002711	exon4	c.G2713T	p.D905Y	TAGTGTCTGAGTT	.	PASS	Atlas-SNP
EFCAB6	64800	hgsc.bcm.edu	37	22	44083442	44083442	+	Missense_Mutation	SNP	T	T	C	rs5764214	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	70	150	0	0.482759	0	T|0.603;C|0.397	0.397	strong	.	EFCAB6	177	.	NM_022785	exon11	c.A1051G	p.T351A	TTTTAGTGGTGGC	.	PASS	Atlas-SNP
ZNF761	388561	hgsc.bcm.edu	37	19	53959568	53959568	+	Missense_Mutation	SNP	G	G	C	rs76363078		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	37	66	0	0.560606	0	.	.	weak	ZNF761,rectum,carcinoma,0,1	ZNF761	104	1	NM_001008401	exon7	c.G1807C	p.E603Q	ACTGAAGAGAATC	.	PASS	Atlas-SNP
SLC4A4	8671	hgsc.bcm.edu	37	4	72433545	72433545	+	Missense_Mutation	SNP	A	A	C	rs1062677	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	90	168	0	0.526316	0	A|0.847;C|0.153	0.153	strong	.	SLC4A4	269	.	NM_001134742	exon25	c.A3220C	p.I1074L	ATTAGAATAGAAC	.	PASS	Atlas-SNP
TMEM161A	54929	hgsc.bcm.edu	37	19	19230816	19230816	+	Missense_Mutation	SNP	T	T	C	rs45467802	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	72	143	0	0.510638	0	T|0.911;C|0.089	0.089	strong	.	TMEM161A	37	.	NM_017814	exon12	c.A1363G	p.I455V	ACCAGATGAGGTA	.	PASS	Atlas-SNP
OCEL1	79629	hgsc.bcm.edu	37	19	17337928	17337928	+	Silent	SNP	C	C	T	rs1045201	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	46	81	0	0.516854	0	C|0.914;T|0.086	0.086	strong	OCEL1,colon,carcinoma,0,1	OCEL1	20	1	NM_024578	exon3	c.C372T	p.A124A	CCAGGCCCTCCTG	.	PASS	Atlas-SNP
C5orf45	51149	hgsc.bcm.edu	37	5	179264731	179264731	+	Missense_Mutation	SNP	T	T	C	rs10277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	68	178	2	0.433121	0.011236	T|0.352;C|0.648	0.648	strong	C5orf45,NS,carcinoma,0,1	C5orf45	23	1	NM_016175	exon7	c.A692G	p.Q231R	ACAAATTGCGCCC	.	scavenged	Atlas-SNP
DGCR6L	85359	hgsc.bcm.edu	37	22	20303664	20303664	+	Missense_Mutation	SNP	G	G	A	rs113468394	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	86	153	0	0.469945	0	G|0.974;A|0.026	0.026	strong	.	DGCR6L	9	.	NM_033257	exon3	c.C350T	p.A117V	TGAGCCGCCTGAA	.	PASS	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	37	19	12501852	12501852	+	Missense_Mutation	SNP	C	C	T	rs200077318		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	3	117	0	0.0294118	0	.	.	weak	ZNF799_ENST00000430385,head_neck,carcinoma,0,2	ZNF799	111	2	NM_001080821	exon4	c.G1360A	p.G454R	CTTTCCCACATTT	.	scavenged	Atlas-SNP
TTC18	118491	hgsc.bcm.edu	37	10	75095253	75095253	+	Silent	SNP	G	G	A	rs7910541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	62	121	0	0.427586	0	G|0.871;A|0.129	0.129	strong	TTC18,NS,carcinoma,0,1	TTC18	106	1	NM_145170	exon8	c.C822T	p.C274C	CTTTATGCACTCT	.	PASS	Atlas-SNP
COL9A1	1297	hgsc.bcm.edu	37	6	70963124	70963124	+	Silent	SNP	A	A	C	rs9346373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	21	210	0	0.162791	0	A|0.831;C|0.169	0.169	strong	.	COL9A1	228	.	NM_001851	exon26	c.T1728G	p.P576P	AATTCCAGGTACA	.	PASS	Atlas-SNP
ZNF419	79744	hgsc.bcm.edu	37	19	58002964	58002964	+	Silent	SNP	G	G	C	rs8108040	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	175	148	0	0.961538	0	G|0.730;C|0.270	0.270	strong	.	ZNF419	134	.	NM_001098494	exon3	c.G201C	p.L67L	CTCTCTGGGTAAG	.	PASS	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	37	17	33805180	33805180	+	Missense_Mutation	SNP	G	G	C	rs2304967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	35	85	0	0.421687	0	G|0.810;C|0.190	0.190	strong	SLFN12L_ENST00000449046,NS,carcinoma,0,3	SLFN12L	140	3	NM_001195790	exon3	c.C1118G	p.A373G	GTACTTGCTGGAG	.	PASS	Atlas-SNP
ACSF2	80221	hgsc.bcm.edu	37	17	48539035	48539035	+	Silent	SNP	T	T	C	rs9674937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	170	180	0	0.982659	0	T|0.644;C|0.356	0.356	strong	.	ACSF2	46	.	NM_025149	exon4	c.T495C	p.Y165Y	GGAGTATGTCCTC	.	PASS	Atlas-SNP
CHRNE	1145	hgsc.bcm.edu	37	17	4802329	4802329	+	Silent	SNP	G	G	A	rs33978919	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	40	49	0	0.571429	0	G|0.820;A|0.180	0.180	strong	.	CHRNE	25	.	NM_000080	exon11	c.C1293T	p.A431A	GCTCTCGGCCACG	.	PASS	Atlas-SNP
CARD8	22900	hgsc.bcm.edu	37	19	48722180	48722180	+	Silent	SNP	C	C	T	rs10500299	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	163	150	0	1	0	C|0.758;T|0.242	0.242	strong	.	CARD8	53	.	NM_001184900	exon9	c.G1251A	p.E417E	AGTAATCTCAAGT	.	PASS	Atlas-SNP
ATP8B4	79895	hgsc.bcm.edu	37	15	50212572	50212572	+	Silent	SNP	G	G	T	rs72733094	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	92	199	1	0.528736	0.00502513	G|0.994;T|0.006	0.006	strong	.	ATP8B4	173	.	NM_024837	exon18	c.C1794A	p.I598I	GTATGCGATGGCC	.	PASS	Atlas-SNP
MMRN1	22915	hgsc.bcm.edu	37	4	90857479	90857479	+	Missense_Mutation	SNP	G	G	A	rs12646270	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	49	108	0	0.449541	0	G|0.939;A|0.061	0.061	strong	MMRN1,NS,carcinoma,0,2	MMRN1	174	2	NM_007351	exon6	c.G2648A	p.G883D	AAAAAGGCAGTGT	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58577421	58577421	+	Silent	SNP	C	C	T	rs41260	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	28	54	0	0.518519	0	C|0.186;T|0.814	0.814	strong	CNOT1_ENST00000441024,colon,carcinoma,-1,1	CNOT1	359	1	NM_206999	exon31	c.G4524A	p.A1508A	TGGTAACGCCCAG	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	662838	662838	+	Silent	SNP	T	T	C	rs3087639		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	27	69	0	0.397059	0	.	.	weak	.	B4GALNT3	64	.	NM_173593	exon14	c.T1749C	p.P583P	GGCCCCTGGAAGG	.	PASS	Atlas-SNP
C7orf66	154907	hgsc.bcm.edu	37	7	108524494	108524494	+	Missense_Mutation	SNP	C	C	T	rs141228190	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	41	82	0	0.569444	0	C|0.999;T|0.001	0.001	strong	.	C7orf66	29	.	NM_001024607	exon1	c.G96A	p.M32I	AAACAGCATTGCA	.	PASS	Atlas-SNP
NUAK2	81788	hgsc.bcm.edu	37	1	205273142	205273142	+	Silent	SNP	G	G	C	rs41264881	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	45	126	1	0.463918	0.00793651	G|0.874;C|0.126	0.126	strong	NUAK2_ENST00000367157,NS,carcinoma,0,2	NUAK2	107	2	NM_030952	exon7	c.C1323G	p.P441P	GAGCAGGGGGGCA	.	scavenged	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971299	45971299	+	Missense_Mutation	SNP	T	T	C	rs233240	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	71	108	0	0.572581	0	T|0.767;C|0.233	0.233	strong	KRTAP10-2,bladder,carcinoma,0,3	KRTAP10-2	21	3	NM_198693	exon1	c.A43G	p.N15D	AGGAGTTGGTGCA	.	PASS	Atlas-SNP
PLCD1	5333	hgsc.bcm.edu	37	3	38052725	38052725	+	Missense_Mutation	SNP	C	C	T	rs933135	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	31	48	0	0.508197	0	C|0.958;A|0.000	.	strong	.	PLCD1	87	.	NM_001130964	exon5	c.G833A	p.R278H	TCGTAGCGCTCAA	.	PASS	Atlas-SNP
TMEM99	147184	hgsc.bcm.edu	37	17	38991052	38991052	+	Missense_Mutation	SNP	T	T	G	rs1044806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	83	190	0	0.479769	0	T|0.907;G|0.093	0.093	strong	.	TMEM99	21	.	NM_001195386	exon3	c.T284G	p.L95R	AAGGACTTCTTCT	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15811062	15811062	+	Silent	SNP	C	C	T	rs1050162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	91	90	0	1	0	C|0.596;T|0.404	0.404	strong	MYH11_ENST00000396324,NS,neuroblastoma,-1,2	MYH11	520	2	NM_001040114	exon39	c.G5460A	p.K1820K	GGTGGACTTGAAC	.	PASS	Atlas-SNP
GLIS3	169792	hgsc.bcm.edu	37	9	4118111	4118111	+	Missense_Mutation	SNP	G	G	T	rs6415788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	14	5	0	1	0	G|0.313;T|0.687	0.687	strong	.	GLIS3	152	.	NM_001042413	exon4	c.C1367A	p.P456Q	GGGCCTGGGGGCG	.	PASS	Atlas-SNP
TRAPPC5	126003	hgsc.bcm.edu	37	19	7747293	7747293	+	Missense_Mutation	SNP	T	T	G	rs6952	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	7	2	0	1	0	T|0.657;G|0.343	0.343	strong	TRAPPC5,NS,carcinoma,0,1	TRAPPC5	11	1	NM_001042461	exon2	c.T154G	p.S52A	CTGCAGTCGCGCC	.	PASS	Atlas-SNP
ZIM3	114026	hgsc.bcm.edu	37	19	57649900	57649900	+	Missense_Mutation	SNP	C	C	T	rs2370134	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	60	91	0	0.540541	0	C|0.856;T|0.143	0.143	strong	.	ZIM3	107	.	NM_052882	exon3	c.G82A	p.E28K	TCTGTTCGGGATT	.	PASS	Atlas-SNP
GOLGA5	9950	hgsc.bcm.edu	37	14	93275841	93275841	+	Silent	SNP	A	A	G	rs17128583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	33	83	0	0.445946	0	A|0.925;G|0.075	0.075	strong	.	GOLGA5	84	.	NM_005113	exon4	c.A969G	p.E323E	ATTAGAAGCCTTA	.	PASS	Atlas-SNP
DCSTAMP	81501	hgsc.bcm.edu	37	8	105361354	105361354	+	Missense_Mutation	SNP	G	G	C	rs67114147	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	23	41	0	0.547619	0	G|0.883;C|0.117	0.117	strong	.	.	.	.	NM_001257317	exon2	c.G574C	p.E192Q	AAAGGGGAAGTCC	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	233734	233734	+	Silent	SNP	C	C	G	rs1041949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	36	107	0	0.409091	0	C|0.725;G|0.275	0.275	strong	.	SDHA	80	.	NM_004168	exon8	c.C1038G	p.S346S	TCGGTCCATGACT	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558326	140558326	+	Silent	SNP	T	T	C	rs2910317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	198	924	2	0.965854	0.0021645	T|0.573;C|0.427	0.427	strong	.	PCDHB8	199	.	NM_019120	exon1	c.T711C	p.N237N	TGTCAATGATAAT	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118790	93118790	+	Missense_Mutation	SNP	A	A	C	rs139248637	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	34	85	0	0.409639	0	A|0.998;C|0.002	0.002	strong	.	RIN3	81	.	NM_024832	exon6	c.A1396C	p.I466L	AAACGGATCTCTC	.	PASS	Atlas-SNP
ATP6V1B1	525	hgsc.bcm.edu	37	2	71190384	71190384	+	Silent	SNP	C	C	T	rs2072462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	92	84	0	0.989247	0	C|0.602;T|0.398	0.398	strong	.	ATP6V1B1	66	.	NM_001692	exon10	c.C1002T	p.R334R	GGGCCGCGTGGAG	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239622	31239622	+	Missense_Mutation	SNP	C	C	G	rs9264668	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	11	25	0	0.189655	0	A|0.575;C|0.423;G|0.002	0.002	strong	HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	NM_002117	exon2	c.G97C	p.D33H	CGGTGTCGAAATA	.	scavenged	Atlas-SNP
MEP1A	4224	hgsc.bcm.edu	37	6	46803102	46803102	+	Missense_Mutation	SNP	A	A	G	rs2297019	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	66	112	0	0.519685	0	A|0.676;G|0.324	0.324	strong	.	MEP1A	93	.	NM_005588	exon13	c.A1900G	p.M634V	AAGGCCATGTTAG	.	PASS	Atlas-SNP
SCUBE1	80274	hgsc.bcm.edu	37	22	43619200	43619200	+	Silent	SNP	G	G	A	rs6003114	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	24	60	0	0.470588	0	G|0.765;A|0.235	0.235	strong	.	SCUBE1	105	.	NM_173050	exon11	c.C1230T	p.R410R	CTTGGCGCGAGAA	.	PASS	Atlas-SNP
CCDC108	255101	hgsc.bcm.edu	37	2	219900068	219900068	+	Missense_Mutation	SNP	C	C	T	rs17852959	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	33	121	0	0.336735	0	C|0.904;T|0.096	0.096	strong	CCDC108_ENST00000295729,NS,carcinoma,0,1	CCDC108	208	1	NM_152389	exon4	c.G481A	p.V161M	ACTGCACGTATTT	.	PASS	Atlas-SNP
TUBGCP6	85378	hgsc.bcm.edu	37	22	50658698	50658698	+	Missense_Mutation	SNP	T	T	A	rs5771107	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	42	101	0	0.506024	0	T|0.857;A|0.143	0.143	strong	.	TUBGCP6	132	.	NM_020461	exon16	c.A4090T	p.S1364C	AGACACTGTCTCC	.	PASS	Atlas-SNP
PPIAL4G	644591	hgsc.bcm.edu	37	1	143767466	143767466	+	Missense_Mutation	SNP	G	G	A	rs77641628	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	8	63	0	0.145455	0	G|0.982;A|0.018	0.018	strong	PPIAL4G,NS,carcinoma,0,2	PPIAL4G	22	2	NM_001123068	exon1	c.C383T	p.A128V	CCAAAGGCCACAT	.	PASS	Atlas-SNP
CREBZF	58487	hgsc.bcm.edu	37	11	85374993	85374993	+	Silent	SNP	C	C	T	rs1192	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	48	74	0	0.457143	0	C|0.837;T|0.163	0.163	strong	.	CREBZF	26	.	NM_001039618	exon1	c.G927A	p.P309P	TCCCACCGGCAGA	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4830971	4830971	+	Silent	SNP	G	G	T	rs77393809	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	73	109	0	0.532847	0	G|0.985;T|0.015	0.015	strong	.	.	.	.	NM_014855	exon17	c.G2379T	p.T793T	GCGCACGGTCAGC	.	PASS	Atlas-SNP
NCK1	4690	hgsc.bcm.edu	37	3	136646930	136646930	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	3	178	0	0.015873	0	.	.	none	NCK1,colon,carcinoma,0,1	NCK1	26	1	NM_006153	exon2	c.A87G	p.L29L	GAGATTATGGCTT	.	scavenged	Atlas-SNP
CACNA1S	779	hgsc.bcm.edu	37	1	201046058	201046058	+	Missense_Mutation	SNP	C	C	T	rs142356235	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	260	123	257	0	0.473077	0	C|0.993;T|0.007	0.007	strong	.	CACNA1S	249	.	NM_000069	exon12	c.G1817A	p.S606N	AAGACGCTGATGA	.	PASS	Atlas-SNP
GPR111	222611	hgsc.bcm.edu	37	6	47649265	47649265	+	Missense_Mutation	SNP	T	T	A	rs17541107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	89	90	0	0.988889	0	T|0.577;A|0.423	0.423	strong	.	GPR111	123	.	NM_153839	exon7	c.T766A	p.L256M	AGAGTGTTGATCA	.	PASS	Atlas-SNP
GABBR2	9568	hgsc.bcm.edu	37	9	101056122	101056122	+	Missense_Mutation	SNP	T	T	C	rs10985765	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	82	141	0	0.458101	0	T|0.756;C|0.244	0.244	strong	.	GABBR2	126	.	NM_005458	exon18	c.A2605G	p.T869A	GCTCTGTTGTGTT	.	PASS	Atlas-SNP
STAC	6769	hgsc.bcm.edu	37	3	36422216	36422216	+	Silent	SNP	T	T	C	rs73052248	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	20	53	0	0.540541	0	T|0.823;C|0.177	0.177	strong	STAC,caecum,carcinoma,0,1	STAC	78	1	NM_003149	exon1	c.T81C	p.S27S	GCCCTCTCCTGCA	.	PASS	Atlas-SNP
KIAA1549L	25758	hgsc.bcm.edu	37	11	33680371	33680371	+	Silent	SNP	C	C	T	rs12280103	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	99	109	0	0.970588	0	C|0.716;T|0.284	0.284	strong	.	.	.	.	NM_012194	exon18	c.C5043T	p.S1681S	CGACAGCGCCTCC	.	PASS	Atlas-SNP
CARS	833	hgsc.bcm.edu	37	11	3028140	3028140	+	Silent	SNP	G	G	A	rs729662	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	25	46	0	0.416667	0	G|0.727;A|0.273	0.273	strong	.	CARS	114	.	NM_001014437	exon19	c.C2118T	p.P706P	AAGCTCGGGCAGG	.	PASS	Atlas-SNP
CXorf22	170063	hgsc.bcm.edu	37	X	35938045	35938045	+	Silent	SNP	C	C	T	rs6629019	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	92	69	0	1	0	C|0.834;T|0.166	0.166	strong	.	CXorf22	272	.	NM_152632	exon1	c.C129T	p.I43I	GGTGATCCCGGCT	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51359497	51359497	+	Silent	SNP	T	T	C	rs11573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	52	92	0	0.514852	0	T|0.629;C|0.371	0.371	strong	.	KLK3	76	.	NM_001030050	exon2	c.T48C	p.G16G	TGCAGGTGCTGCA	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8160897	8160897	+	Missense_Mutation	SNP	G	G	C	rs12150963	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	72	120	0	0.483221	0	G|0.880;C|0.120	0.120	strong	.	FBN3	300	.	NM_032447	exon44	c.C5607G	p.N1869K	GAGGCAGTTGTAG	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	37	11	77412851	77412851	+	Missense_Mutation	SNP	A	A	G	rs7950873	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	89	142	0	0.593333	0	A|0.846;G|0.154	0.154	strong	.	RSF1	105	.	NM_016578	exon6	c.T1423C	p.S475P	CCTTAGAGGGGCT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228494696	228494696	+	Silent	SNP	G	G	A	rs4653939	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	235	126	195	0	0.53617	0	G|0.667;A|0.333	0.333	strong	.	OBSCN	2142	.	NM_001271223	exon56	c.G14892A	p.A4964A	GGGTGCGAGCGTG	.	PASS	Atlas-SNP
OR1B1	347169	hgsc.bcm.edu	37	9	125391369	125391369	+	Missense_Mutation	SNP	A	A	G	rs1536929	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	20	62	0	0.392157	0	G|0.645;N|0.000	0.645	strong	.	OR1B1	48	.	NM_001004450	exon1	c.T446C	p.L149S	CAGCTCAAGGCTA	.	PASS	Atlas-SNP
MROH9	80133	hgsc.bcm.edu	37	1	170959029	170959029	+	Silent	SNP	C	C	T	rs16863922	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	53	141	0	0.40458	0	C|0.806;T|0.194	0.194	strong	.	.	.	.	NM_025063	exon11	c.C913T	p.L305L	AGGCAACTGTGTG	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262122	39262122	+	Missense_Mutation	SNP	G	G	A	rs188946528	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	39	67	0	0.419355	0	G|0.972;A|0.028	0.028	strong	KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-9	110	2	NM_001146041	exon1	c.G482A	p.R161H	GCTGCCGCCCCTC	.	PASS	Atlas-SNP
VAMP8	8673	hgsc.bcm.edu	37	2	85808737	85808737	+	Silent	SNP	A	A	G	rs1009	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	230	110	277	0	0.478261	0	A|0.547;G|0.453	0.453	strong	VAMP8,NS,carcinoma,0,1	VAMP8	10	1	NM_003761	exon3	c.A201G	p.R67R	GGCTCGAAAATTC	.	PASS	Atlas-SNP
LRRC8C	84230	hgsc.bcm.edu	37	1	90179532	90179532	+	Missense_Mutation	SNP	A	A	G	rs12032393	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	46	63	0	0.978723	0	A|0.869;G|0.131	0.131	strong	.	LRRC8C	73	.	NM_032270	exon3	c.A1403G	p.N468S	TAGACAATCTTCA	.	PASS	Atlas-SNP
ERCC8	1161	hgsc.bcm.edu	37	5	60200665	60200665	+	Silent	SNP	A	A	G	rs4647100	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	100	178	0	0.507614	0	A|0.820;G|0.180	0.180	strong	.	ERCC8	31	.	NM_000082	exon5	c.T435C	p.Y145Y	ATGACTATAAACT	.	PASS	Atlas-SNP
FAM187B	148109	hgsc.bcm.edu	37	19	35719020	35719020	+	Nonsense_Mutation	SNP	C	C	T	rs541169	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	53	98	0	0.434426	0	C|0.697;T|0.303	0.303	strong	.	FAM187B	28	.	NM_152481	exon1	c.G564A	p.W188X	GCTAGACCACACC	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145368461	145368461	+	Missense_Mutation	SNP	A	A	C	rs12128680	bycluster;byfrequency;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	302	123	288	0	0.407285	0	A|0.899;C|0.101	0.101	strong	.	NBPF10	221	.	NM_001039703	exon84	c.A10439C	p.E3480A	TGATGGAAGTGGA	.	PASS	Atlas-SNP
KCNH2	3757	hgsc.bcm.edu	37	7	150645534	150645534	+	Missense_Mutation	SNP	T	T	G	rs1805123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	32	24	0	1	0	T|0.855;G|0.145	0.145	strong	KCNH2,colon,carcinoma,0,1	KCNH2	157	1	NM_000238	exon11	c.A2690C	p.K897T	TCACCCTTGTCCG	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882952	152882952	+	Missense_Mutation	SNP	G	G	C	rs11807064	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	9	82	0	0.108434	0	G|0.995;C|0.005	0.005	strong	IVL,caecum,carcinoma,0,3	IVL	100	3	NM_005547	exon2	c.G679C	p.E227Q	CTCCCAGAGCAGC	.	scavenged	Atlas-SNP
NLRP13	126204	hgsc.bcm.edu	37	19	56424532	56424532	+	Silent	SNP	G	G	A	rs731338	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	61	115	0	0.438849	0	G|0.891;A|0.109	0.109	strong	.	NLRP13	220	.	NM_176810	exon5	c.C651T	p.R217R	CAGTAGGCGCTGC	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	37	16	81922813	81922813	+	Missense_Mutation	SNP	C	C	T	rs1143687	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	86	163	0	0.558442	0	C|0.959;T|0.041	0.041	strong	.	PLCG2	276	.	NM_002661	exon10	c.C802T	p.R268W	CGTGAGCGGATGA	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	37	2	220285666	220285666	+	Silent	SNP	G	G	C	rs12920	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	23	43	0	0.479167	0	G|0.635;C|0.365	0.365	strong	.	DES	53	.	NM_001927	exon5	c.G1014C	p.L338L	CGCCCTGAAGGGC	.	PASS	Atlas-SNP
XYLT2	64132	hgsc.bcm.edu	37	17	48437456	48437456	+	Missense_Mutation	SNP	C	C	G	rs6504649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	157	195	0	0.987421	0	C|0.688;G|0.312	0.312	strong	XYLT2,colon,carcinoma,0,1	XYLT2	51	1	NM_022167	exon11	c.C2402G	p.T801R	GGCACACACAGCT	.	PASS	Atlas-SNP
LRRC61	65999	hgsc.bcm.edu	37	7	150034184	150034184	+	Silent	SNP	T	T	C	rs3735170	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	52	53	0	1	0	T|0.745;C|0.255	0.255	strong	LRRC61,rectum,carcinoma,0,1	LRRC61	17	1	NM_023942	exon2	c.T234C	p.A78A	GCTAGCTGTGCTC	.	PASS	Atlas-SNP
PACS2	23241	hgsc.bcm.edu	37	14	105833623	105833623	+	Missense_Mutation	SNP	C	C	T	rs111376436	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	111	228	1	0.497758	0.00438596	C|0.985;T|0.015	0.015	strong	.	PACS2	75	.	NM_001100913	exon5	c.C497T	p.A166V	TCAAGGCGGCCGA	.	PASS	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	37	10	64974537	64974537	+	Missense_Mutation	SNP	A	A	T	rs10761725	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	103	121	0	0.980952	0	A|0.395;T|0.605	0.605	strong	JMJD1C_ENST00000399262,NS,carcinoma,+2,2	JMJD1C	347	2	NM_032776	exon8	c.T1390A	p.S464T	CTGACGAATGAAT	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17317955	17317955	+	Silent	SNP	A	A	G	rs8110964	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	169	202	2	0.988304	0.00990099	A|0.384;G|0.616	0.616	strong	MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	NM_001130065	exon35	c.A5526G	p.S1842S	CATGTCACCTGGG	.	scavenged	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433327	169433327	+	Missense_Mutation	SNP	G	G	A	rs7671781	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	23	78	0	0.418182	0	G|0.733;A|0.267	0.267	strong	.	PALLD	179	.	NM_001166108	exon2	c.G672A	p.M224I	CCCTATGGAAGAC	.	PASS	Atlas-SNP
NPW	283869	hgsc.bcm.edu	37	16	2070568	2070568	+	Missense_Mutation	SNP	A	A	C	rs2286472	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	22	34	0	0.407407	0	A|0.624;C|0.376	0.376	strong	NPW,NS,carcinoma,0,2	NPW	4	2	NM_001099456	exon2	c.A446C	p.D149A	CGGTGGACCCCGC	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138738204	138738204	+	Silent	SNP	G	G	A	rs11977775	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	40	103	0	0.470588	0	G|0.898;A|0.102	0.102	strong	.	ZC3HAV1	75	.	NM_020119	exon12	c.C2442T	p.Y814Y	TTTTCCGTATTTG	.	PASS	Atlas-SNP
ABP1	26	hgsc.bcm.edu	37	7	150556002	150556002	+	Silent	SNP	T	T	C	rs1049748	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	71	124	0	0.525926	0	T|0.510;C|0.490	0.490	strong	.	ABP1	92	.	NM_001091	exon3	c.T1722C	p.P574P	GCTGCCTAAGTAC	.	PASS	Atlas-SNP
CYFIP1	23191	hgsc.bcm.edu	37	15	22960868	22960868	+	Silent	SNP	G	G	C	rs2289818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	105	91	0	1	0	G|0.543;C|0.457	0.457	strong	.	CYFIP1	159	.	NM_014608	exon18	c.G2061C	p.L687L	GTTCCTGTACGAC	.	PASS	Atlas-SNP
PLXND1	23129	hgsc.bcm.edu	37	3	129303236	129303236	+	Missense_Mutation	SNP	G	G	C	rs201334507	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	40	93	0	0.571429	0	.	.	weak	.	PLXND1	149	.	NM_015103	exon6	c.C2021G	p.P674R	TGGTTGGGGGGGA	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15818141	15818141	+	Silent	SNP	A	A	C	rs2075511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	147	173	1	1	0.00578035	A|0.589;C|0.411	0.411	strong	.	MYH11	520	.	NM_001040114	exon32	c.T4263G	p.A1421A	ATCATAAGCGGCC	.	PASS	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219508372	219508372	+	Missense_Mutation	SNP	A	A	T	rs3770213	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	57	118	0	0.483051	0	A|0.741;N|0.000	.	strong	.	ZNF142	190	.	NM_001105537	exon8	c.T2867A	p.L956H	GTGGCAAGAGGCT	.	PASS	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	37	2	121746956	121746956	+	Missense_Mutation	SNP	G	G	T	rs3738880	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	36	106	0	0.493151	0	G|0.411;T|0.589	0.589	strong	.	GLI2	187	.	NM_005270	exon13	c.G3466T	p.A1156S	GTAGACGCCCTGG	.	PASS	Atlas-SNP
GPR20	2843	hgsc.bcm.edu	37	8	142367400	142367400	+	Silent	SNP	G	G	A	rs11167054	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	3	3	5	1	1	0.2	G|0.248;A|0.752	0.752	strong	GPR20,NS,carcinoma,0,2	GPR20	43	2	NM_005293	exon2	c.C624T	p.P208P	CAGCAGGGGCAGC	.	scavenged	Atlas-SNP
CYBRD1	79901	hgsc.bcm.edu	37	2	172411273	172411273	+	Missense_Mutation	SNP	G	G	A	rs10455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	148	141	1	1	0.0070922	A|0.688;C|0.004	0.688	strong	.	CYBRD1	16	.	NM_024843	exon4	c.G797A	p.S266N	TAAACAGTGAAGT	.	PASS	Atlas-SNP
ACOXL	55289	hgsc.bcm.edu	37	2	111598958	111598958	+	Missense_Mutation	SNP	C	C	T	rs1554005	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	57	93	0	0.548077	0	C|0.823;N|0.000	.	strong	.	ACOXL	93	.	NM_001142807	exon10	c.C764T	p.T255M	GGTTGACGATAGC	.	PASS	Atlas-SNP
UNC5C	8633	hgsc.bcm.edu	37	4	96127798	96127798	+	Missense_Mutation	SNP	G	G	T	rs141976218	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	50	119	0	0.42735	0	G|0.998;T|0.002	0.002	strong	.	UNC5C	141	.	NM_003728	exon11	c.C1883A	p.A628E	TGTGCTGCCTGGT	.	PASS	Atlas-SNP
OR2L5	81466	hgsc.bcm.edu	37	1	248185883	248185883	+	Missense_Mutation	SNP	G	G	A	rs55982561	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	396	185	324	0	0.467172	0	G|0.977;A|0.023	0.023	strong	.	.	.	.	NM_001258284	exon1	c.G634A	p.G212S	TTCACTGGCATTG	.	PASS	Atlas-SNP
PAPPA	5069	hgsc.bcm.edu	37	9	119106881	119106881	+	Missense_Mutation	SNP	C	C	A	rs7020782	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	94	99	0	1	0	C|0.420;A|0.580	0.580	strong	.	PAPPA	243	.	NM_002581	exon14	c.C3671A	p.S1224Y	ATGCTTCTCTCAA	.	PASS	Atlas-SNP
OR56A3	390083	hgsc.bcm.edu	37	11	5969185	5969185	+	Silent	SNP	A	A	G	rs10769378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	38	101	0	0.436782	0	A|0.777;G|0.223	0.223	strong	OR56A3,NS,carcinoma,+2,1	OR56A3	81	1	NM_001003443	exon1	c.A609G	p.Q203Q	TTACCAATTTGCT	.	PASS	Atlas-SNP
EP300	2033	hgsc.bcm.edu	37	22	41548008	41548008	+	Missense_Mutation	SNP	A	A	G	rs20551	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	71	183	0	0.430303	0	A|0.802;G|0.198	0.198	strong	.	EP300	367	.	NM_001429	exon15	c.A2989G	p.I997V	GAGGATATTTCAG	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104153004	104153004	+	Missense_Mutation	SNP	C	C	G	rs2271637	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	20	69	0	0.37037	0	C|0.734;G|0.266	0.266	strong	.	STAB2	370	.	NM_017564	exon65	c.C7201G	p.L2401V	ACGAGGCTGGGAA	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140594466	140594466	+	Silent	SNP	G	G	A	rs17844608	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	19	270	1	0.0785124	0.0037037	.	.	weak	PCDHB13,rectum,carcinoma,+1,1	PCDHB13	142	1	NM_018933	exon1	c.G771A	p.P257P	CAGTCCGGTAGGC	.	scavenged	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125591423	125591423	+	Silent	SNP	A	A	T	rs3822116	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	57	131	0	0.513514	0	A|0.940;T|0.060	0.060	strong	.	ANKRD50	136	.	NM_020337	exon4	c.T3009A	p.A1003A	GACGTCAGCATGG	.	PASS	Atlas-SNP
SMCR9	140776	hgsc.bcm.edu	37	17	17326363	17326363	+	Missense_Mutation	SNP	G	G	A	rs35590625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	11	22	0	0.407407	0	G|0.747;A|0.253	0.253	strong	.	.	.	.	NM_001243312	exon3	c.G178A	p.V60I	TTGAGTGTTCTTC	.	PASS	Atlas-SNP
TGM3	7053	hgsc.bcm.edu	37	20	2297790	2297790	+	Missense_Mutation	SNP	G	G	A	rs214814	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	23	58	0	0.469388	0	G|0.863;A|0.136	0.136	strong	.	TGM3	105	.	NM_003245	exon6	c.G746A	p.S249N	CAAGGAGCTGGAA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90482397	90482397	+	Missense_Mutation	SNP	T	T	C	rs12110451	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	50	71	0	0.769231	0	T|0.817;C|0.183	0.183	strong	.	MDN1	478	.	NM_014611	exon14	c.A1978G	p.I660V	GCTCGATGAGAAC	.	PASS	Atlas-SNP
ZNF155	7711	hgsc.bcm.edu	37	19	44496070	44496070	+	Silent	SNP	A	A	G	rs431509	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	47	97	0	0.489583	0	A|0.624;G|0.376	0.376	strong	.	ZNF155	30	.	NM_001260488	exon5	c.A252G	p.Q84Q	AACCCAAAGAGAA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511746	4511746	+	Missense_Mutation	SNP	A	A	T	rs62115192	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	42	185	0	0.185022	0	A|0.333;T|0.667	0.667	strong	.	PLIN4	191	.	NM_001080400	exon3	c.T2184A	p.N728K	GGCCACATTCGCA	.	PASS	Atlas-SNP
ARHGEF39	84904	hgsc.bcm.edu	37	9	35662251	35662251	+	Missense_Mutation	SNP	T	T	C	rs2297879	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	61	114	0	0.521368	0	T|0.720;C|0.280	0.280	strong	.	.	.	.	NM_032818	exon8	c.A917G	p.H306R	TTCTCATGAGGGA	.	PASS	Atlas-SNP
ING3	54556	hgsc.bcm.edu	37	7	120610901	120610901	+	Silent	SNP	C	C	T	rs2525725	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	36	83	0	0.571429	0	C|0.812;A|0.001	.	strong	.	ING3	36	.	NM_019071	exon10	c.C1068T	p.D356D	TTACGACCCAAAT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152281142	152281142	+	Missense_Mutation	SNP	C	C	G	rs141120727	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	297	150	388	0	0.50505	0	C|0.993;G|0.007	0.007	strong	FLG,NS,lymphoid_neoplasm,0,1	FLG	900	1	NM_002016	exon3	c.G6220C	p.E2074Q	CGGACTCTTTGTG	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112991959	112991959	+	Silent	SNP	C	C	T	rs11710894	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	60	152	0	0.437956	0	C|0.773;T|0.227	0.227	strong	.	BOC	139	.	NM_033254	exon8	c.C1005T	p.P335P	CATCCCCTGGGGC	.	PASS	Atlas-SNP
SAMSN1	64092	hgsc.bcm.edu	37	21	15954593	15954593	+	Missense_Mutation	SNP	G	G	A	rs2822786	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	92	136	1	0.989247	0.00735294	G|0.766;A|0.234	0.234	strong	.	SAMSN1	112	.	NM_001256370	exon2	c.C125T	p.P42L	GGAAAAGGCTTCC	.	PASS	Atlas-SNP
RNF6	6049	hgsc.bcm.edu	37	13	26788114	26788114	+	Silent	SNP	A	A	G	rs301047	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	81	175	0	0.496933	0	A|0.796;G|0.204	0.204	strong	.	RNF6	68	.	NM_183043	exon5	c.T1905C	p.C635C	ACTAATACAAACA	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592284	1592284	+	Missense_Mutation	SNP	G	G	A	rs1135196	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	38	253	0	0.974359	0	G|0.420;A|0.580	0.580	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.C152T	p.T51I	TGCAGAGTGGCCG	.	PASS	Atlas-SNP
EEF2	1938	hgsc.bcm.edu	37	19	3983184	3983184	+	Silent	SNP	A	A	G	rs2230560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	56	109	1	0.455285	0.00917431	T|0.000;G|0.239;C|0.000;A|0.760	0.239	strong	EEF2,NS,carcinoma,0,2	EEF2	57	2	NM_001961	exon3	c.T324C	p.H108H	GTCGACATGCCCG	.	scavenged	Atlas-SNP
OTOF	9381	hgsc.bcm.edu	37	2	26739423	26739423	+	Silent	SNP	T	T	C	rs11687696	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	14	37	0	0.5	0	T|0.761;C|0.239	0.239	strong	.	OTOF	524	.	NM_194248	exon5	c.A372G	p.T124T	GCCCACTGTGCCG	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380414	107380414	+	Missense_Mutation	SNP	C	C	A	rs2900373	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	264	123	287	0	0.465909	0	A|0.365;C|0.635	0.365	strong	.	OR13C9	42	.	NM_001001956	exon1	c.G72T	p.E24D	GAGTAACTCAAGC	.	PASS	Atlas-SNP
NSA2	10412	hgsc.bcm.edu	37	5	74069863	74069863	+	Silent	SNP	A	A	G	rs6874609	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	38	68	1	0.457831	0.0147059	A|0.624;G|0.376	0.376	strong	NSA2,NS,carcinoma,+1,1	NSA2	18	1	NM_014886	exon5	c.A693G	p.T231T	TGTGACACAAGGA	.	scavenged	Atlas-SNP
BTN1A1	696	hgsc.bcm.edu	37	6	26501897	26501897	+	Silent	SNP	T	T	C	rs1321479	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	89	59	0	1	0	T|0.485;C|0.515	0.515	strong	BTN1A1,colon,carcinoma,0,1	BTN1A1	68	1	NM_001732	exon2	c.T159C	p.S53S	CCTGTCTCCGAAC	.	PASS	Atlas-SNP
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67242087	67242087	+	Splice_Site	SNP	G	G	A	rs3816989	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	94	158	0	0.51087	0	G|0.879;A|0.121	0.121	strong	.	TCTEX1D1	27	.	NM_152665	exon4	c.336+1G>A	.	TCTGAGGTACGTG	.	PASS	Atlas-SNP
CTBP2	1488	hgsc.bcm.edu	37	10	126714714	126714714	+	Missense_Mutation	SNP	G	G	C	rs2946994	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	63	129	1	0.488372	0.00775194	G|0.533;C|0.467	0.467	strong	CTBP2,colon,carcinoma,0,1	CTBP2	100	1	NM_022802	exon1	c.C1615G	p.Q539E	CCTTCTGGTACGG	.	scavenged	Atlas-SNP
TMC4	147798	hgsc.bcm.edu	37	19	54675643	54675643	+	Missense_Mutation	SNP	G	G	A	rs77215230	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	48	96	0	0.539326	0	G|0.876;A|0.124	0.124	strong	.	TMC4	89	.	NM_001145303	exon2	c.C307T	p.H103Y	ACCTGTGTGCCCG	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45123859	45123859	+	Silent	SNP	G	G	A	rs72497819	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	6	19	0	0.315789	0	G|0.792;A|0.208	0.208	strong	.	NACAD	44	.	NM_001146334	exon2	c.C1920T	p.S640S	CATAACGGAGTCC	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57176198	57176198	+	Silent	SNP	T	T	G	rs8108756	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	29	59	0	0.483333	0	T|0.587;G|0.413	0.413	strong	.	ZNF835	106	.	NM_001005850	exon2	c.A369C	p.S123S	GAACGCTGAACAG	.	PASS	Atlas-SNP
OR8S1	341568	hgsc.bcm.edu	37	12	48920073	48920073	+	Missense_Mutation	SNP	G	G	A	rs61941963	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	251	136	215	1	0.541833	0.00465116	G|0.873;A|0.127	0.127	strong	.	OR8S1	47	.	NM_001005203	exon1	c.G659A	p.R220H	ACACCCGTATAAT	.	PASS	Atlas-SNP
HGFAC	3083	hgsc.bcm.edu	37	4	3444503	3444503	+	Silent	SNP	G	G	A	rs2073505	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	107	228	0	0.481982	0	G|0.898;A|0.102	0.102	strong	HGFAC,caecum,adenoma,+1,1	HGFAC	69	1	NM_001528	exon2	c.G162A	p.A54A	CCCTGCGATCCCC	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79432455	79432455	+	Silent	SNP	A	A	C	rs3749488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	258	123	237	0	0.476744	0	A|0.628;C|0.372	0.372	strong	.	FRAS1	779	.	NM_025074	exon64	c.A9808C	p.R3270R	AGCCGGAGGTTCC	.	PASS	Atlas-SNP
SCN3A	6328	hgsc.bcm.edu	37	2	165987772	165987772	+	Silent	SNP	T	T	G	rs62174900	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	76	165	0	0.517007	0	T|0.828;G|0.172	0.172	strong	.	SCN3A	544	.	NM_006922	exon16	c.A2547C	p.V849V	TCGCAGTACAGAC	.	PASS	Atlas-SNP
OR7A5	26659	hgsc.bcm.edu	37	19	14938184	14938184	+	Silent	SNP	A	A	G	rs200531878		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	8	66	0	0.0707965	0	A|0.999;G|0.001	0.001	weak	OR7A5,NS,carcinoma,0,1	OR7A5	43	1	NM_017506	exon1	c.T870C	p.Y290Y	CAGACTATAGATA	.	PASS	Atlas-SNP
CCDC61	729440	hgsc.bcm.edu	37	19	46518682	46518682	+	Missense_Mutation	SNP	G	G	A	rs7271	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	13	30	0	0.393939	0	G|0.900;A|0.100	0.100	strong	.	CCDC61	32	.	NM_001267723	exon7	c.G842A	p.R281K	ACAAGAGGGGGTG	.	PASS	Atlas-SNP
MYH8	4626	hgsc.bcm.edu	37	17	10312472	10312472	+	Missense_Mutation	SNP	G	G	A	rs34693726	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	64	150	0	0.405063	0	G|0.944;A|0.056	0.056	strong	MYH8,NS,carcinoma,+1,1	MYH8	346	1	NM_002472	exon17	c.C1907T	p.A636V	TTCTTCGCGCTGC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241791	3241791	+	Silent	SNP	G	G	A	rs1635250	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	147	153	0	1	0	0|0.003;A|0.487	0.487	strong	.	MXRA5	815	.	NM_015419	exon5	c.C1935T	p.D645D	ACCACTGTCACTG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373114	5373114	+	Missense_Mutation	SNP	G	G	A	rs5006888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	60	243	0	0.340909	0	G|0.408;A|0.592	0.592	strong	.	OR51B6	53	.	NM_001004750	exon1	c.G377A	p.S126N	TCCGCAGCCCCTT	.	PASS	Atlas-SNP
MTMR7	9108	hgsc.bcm.edu	37	8	17157677	17157677	+	Missense_Mutation	SNP	T	T	G	rs3764796	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	70	163	0	0.482759	0	T|0.909;G|0.091	0.091	strong	.	MTMR7	75	.	NM_004686	exon14	c.A1677C	p.Q559H	CTCACTTTGCTTA	.	PASS	Atlas-SNP
GRHL3	57822	hgsc.bcm.edu	37	1	24680915	24680915	+	Silent	SNP	C	C	T	rs12030057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	57	53	0	0.904762	0	C|0.754;T|0.246	0.246	strong	.	GRHL3	69	.	NM_021180	exon16	c.C1761T	p.V587V	CCACGTCGCCTTC	.	PASS	Atlas-SNP
GGCX	2677	hgsc.bcm.edu	37	2	85780131	85780131	+	Silent	SNP	G	G	A	rs2592551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	83	232	0	0.456044	0	G|0.693;A|0.307	0.307	strong	GGCX,NS,carcinoma,0,1	GGCX	44	1	NM_000821	exon9	c.C1218T	p.R406R	GTGGGAGCGGGAG	.	PASS	Atlas-SNP
VDAC3	7419	hgsc.bcm.edu	37	8	42259418	42259418	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	5	193	0	0.025	0	.	.	none	VDAC3,NS,carcinoma,-2,1	VDAC3	17	1	NM_001135694	exon7	c.T439C	p.F147L	TTGGCCTTCGAAG	.	scavenged	Atlas-SNP
FAM154B	283726	hgsc.bcm.edu	37	15	82574461	82574461	+	Silent	SNP	C	C	T	rs76375505	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	69	97	0	0.6	0	C|0.977;T|0.023	0.023	strong	.	FAM154B	50	.	NM_001008226	exon3	c.C255T	p.D85D	TCAAGACGATTAT	.	PASS	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	37	16	15131974	15131974	+	Missense_Mutation	SNP	G	G	T	rs1136001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	129	117	0	0.992308	0	G|0.706;T|0.294	0.294	strong	.	NTAN1	21	.	NM_173474	exon10	c.C847A	p.H283N	GTGTGTGAGCTGG	.	PASS	Atlas-SNP
LRRC56	115399	hgsc.bcm.edu	37	11	551235	551235	+	Silent	SNP	G	G	A	rs35537971	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	84	111	0	0.521739	0	G|0.835;A|0.165	0.165	strong	.	LRRC56	23	.	NM_198075	exon9	c.G729A	p.P243P	CCCCCCGCGGCTG	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585334	43585334	+	Silent	SNP	T	T	G	rs79582550	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	291	23	264	0	0.0790378	0	T|0.944;G|0.056	0.056	strong	PSG2,NS,carcinoma,-1,2	PSG2	84	2	NM_031246	exon2	c.A129C	p.P43P	AACTTTTGGTGGC	.	scavenged	Atlas-SNP
BRSK1	84446	hgsc.bcm.edu	37	19	55815159	55815159	+	Silent	SNP	C	C	A	rs17851415	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	48	87	0	0.527473	0	C|0.936;A|0.064	0.064	strong	.	BRSK1	192	.	NM_032430	exon12	c.C1251A	p.T417T	ACCCACCCGACGG	.	PASS	Atlas-SNP
SLC52A3	113278	hgsc.bcm.edu	37	20	744570	744570	+	Silent	SNP	G	G	A	rs6054605	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	30	77	0	0.405405	0	G|0.908;A|0.092	0.092	strong	.	.	.	.	NM_033409	exon3	c.C645T	p.P215P	GTGGGCGGGAAGG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	rs7284177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	19	60	0	0.387755	0	G|0.931;A|0.069	0.069	strong	.	MYO18B	322	.	NM_032608	exon43	c.G7537A	p.G2513S	TCCTCCGGCTCCA	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140604475	140604475	+	Silent	SNP	C	C	T	rs149933809	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	77	131	0	0.562044	0	C|0.997;T|0.003	0.003	strong	.	PCDHB14	132	.	NM_018934	exon1	c.C1398T	p.P466P	CAGCCCCGCCCTG	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128484816	128484816	+	Silent	SNP	A	A	G	rs3734973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	110	74	1	1	0.0135135	A|0.663;G|0.337	0.337	strong	FLNC,caecum,carcinoma,+2,1	FLNC	339	1	NM_001127487	exon21	c.A3297G	p.V1099V	GACCGTAGAGGGC	.	scavenged	Atlas-SNP
B4GALT2	8704	hgsc.bcm.edu	37	1	44447413	44447413	+	Missense_Mutation	SNP	G	G	C	rs1859728	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	67	134	0	0.449664	0	G|0.928;C|0.072	0.072	strong	.	B4GALT2	35	.	NM_030587	exon3	c.G453C	p.Q151H	GGTGCAGAGGGAG	.	PASS	Atlas-SNP
PEX16	9409	hgsc.bcm.edu	37	11	45937306	45937306	+	Missense_Mutation	SNP	C	C	T	rs11553094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	232	118	236	0	0.508621	0	C|0.980;T|0.020	0.020	strong	.	PEX16	24	.	NM_004813	exon4	c.G307A	p.V103M	CCCACACCTTGGC	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52825585	52825585	+	Silent	SNP	T	T	C	rs9324	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	22	61	0	0.488889	0	T|0.568;C|0.432	0.432	strong	.	ITIH1	108	.	NM_002215	exon21	c.T2547C	p.S849S	AGGCTCTGACCCC	.	PASS	Atlas-SNP
ACPT	93650	hgsc.bcm.edu	37	19	51293955	51293955	+	Silent	SNP	G	G	A	rs2162784	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	26	35	0	0.509804	0	G|0.892;A|0.108	0.108	strong	.	ACPT	43	.	NM_033068	exon2	c.G216A	p.T72T	GACCACGGTGAGA	.	PASS	Atlas-SNP
SSRP1	6749	hgsc.bcm.edu	37	11	57102096	57102096	+	Silent	SNP	A	A	G	rs2230649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	25	52	0	0.471698	0	A|0.799;G|0.201	0.201	strong	.	SSRP1	75	.	NM_003146	exon3	c.T81C	p.R27R	GCCCTGACGGCTC	.	PASS	Atlas-SNP
MMP27	64066	hgsc.bcm.edu	37	11	102576358	102576358	+	Missense_Mutation	SNP	T	T	C	rs2846707	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	178	194	0	0.988889	0	T|0.229;C|0.771	0.771	strong	.	MMP27	84	.	NM_022122	exon1	c.A88G	p.M30V	GTTGCATATTTTC	.	PASS	Atlas-SNP
ITIH1	3697	hgsc.bcm.edu	37	3	52820981	52820981	+	Missense_Mutation	SNP	A	A	T	rs678	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	56	150	0	0.4	0	A|0.681;T|0.319	0.319	strong	.	ITIH1	108	.	NM_002215	exon14	c.A1754T	p.E585V	GGGAGGAGAGGGC	.	PASS	Atlas-SNP
RND1	27289	hgsc.bcm.edu	37	12	49255798	49255798	+	Silent	SNP	G	G	C	rs1565933	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	106	111	0	1	0	G|0.576;C|0.424	0.424	strong	.	RND1	26	.	NM_014470	exon3	c.C312G	p.L104L	CTTCTTGAGTGCG	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	661656	661656	+	Missense_Mutation	SNP	A	A	G	rs7298766	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	292	145	250	0	0.496575	0	A|0.704;G|0.296	0.296	strong	.	B4GALNT3	64	.	NM_173593	exon13	c.A1232G	p.K411R	ACATCAAGATTGA	.	PASS	Atlas-SNP
CNKSR3	154043	hgsc.bcm.edu	37	6	154763401	154763401	+	Silent	SNP	G	G	A	rs6557351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	33	75	1	1	0.0133333	G|0.660;A|0.340	0.340	strong	CNKSR3,NS,carcinoma,0,1	CNKSR3	56	1	NM_173515	exon3	c.C240T	p.N80N	CTTCATGTTATCA	.	scavenged	Atlas-SNP
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	390	82	215	0	0.210256	0	G|0.822;T|0.178	0.178	strong	ZNF587,NS,carcinoma,+2,1	ZNF587	53	1	NM_032828	exon3	c.G1494T	p.G498G	ATGTGGGAAATCA	.	PASS	Atlas-SNP
VCX2	51480	hgsc.bcm.edu	37	X	8138171	8138171	+	Missense_Mutation	SNP	T	T	C	rs78723459	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	72	120	1	0.888889	0.00833333	T|0.364;C|0.636	0.636	strong	.	VCX2	16	.	NM_016378	exon3	c.A322G	p.S108G	CCTCGCTCTCCTG	.	PASS	Atlas-SNP
PIGC	5279	hgsc.bcm.edu	37	1	172410967	172410967	+	Missense_Mutation	SNP	G	G	A	rs1063412	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	57	126	0	0.518182	0	G|0.552;A|0.448	0.448	strong	.	PIGC	24	.	NM_153747	exon2	c.C796T	p.P266S	AGAATGGACACAG	.	PASS	Atlas-SNP
COL8A2	1296	hgsc.bcm.edu	37	1	36563509	36563509	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	67	46	0	0.971014	0	.	.	none	.	COL8A2	41	.	NM_005202	exon2	c.C1773T	p.P591P	TTTCACGGGCATG	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	216258213	216258213	+	Missense_Mutation	SNP	A	A	G	rs56222536	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	36	84	0	0.418605	0	A|0.892;G|0.108	0.108	strong	.	USH2A	1168	.	NM_206933	exon25	c.T4994C	p.I1665T	TTTTGGATTATCT	.	PASS	Atlas-SNP
GALNT12	79695	hgsc.bcm.edu	37	9	101611335	101611335	+	Silent	SNP	G	G	C	rs2273846	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	58	94	0	0.542056	0	G|0.886;C|0.114	0.114	strong	.	GALNT12	37	.	NM_024642	exon10	c.G1707C	p.S569S	CAACTCGGATCAT	.	PASS	Atlas-SNP
ADAM15	8751	hgsc.bcm.edu	37	1	155033918	155033918	+	Missense_Mutation	SNP	C	C	T	rs41264285	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	62	155	0	0.525424	0	C|0.818;T|0.182	0.182	strong	.	ADAM15	92	.	NM_207194	exon20	c.C2305T	p.P769S	CCGGCCCCCCCTT	.	PASS	Atlas-SNP
LTN1	26046	hgsc.bcm.edu	37	21	30339120	30339120	+	Missense_Mutation	SNP	C	C	A	rs34191159	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	55	73	0	0.982143	0	C|0.836;A|0.164	0.164	strong	.	LTN1	141	.	NM_015565	exon10	c.G1831T	p.G611C	CCCAGCCTTCAAT	.	PASS	Atlas-SNP
SCLY	51540	hgsc.bcm.edu	37	2	238990388	238990388	+	Missense_Mutation	SNP	G	G	A	rs3210400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	59	100	0	0.526786	0	G|0.715;A|0.285	0.285	strong	.	SCLY	51	.	NM_016510	exon5	c.G547A	p.A183T	GGGCAGGCAGAGG	.	PASS	Atlas-SNP
FFAR3	2865	hgsc.bcm.edu	37	19	35849926	35849926	+	Missense_Mutation	SNP	G	G	A	rs79251979	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	656	245	579	2	0.373476	0.00345423	G|0.800;A|0.200	0.200	strong	FFAR3,NS,carcinoma,0,1	FFAR3	40	1	NM_005304	exon2	c.G134A	p.R45H	TGCAGCGCCGCCC	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10116375	10116375	+	Silent	SNP	G	G	T	rs2303099	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	87	91	0	0.988636	0	G|0.490;T|0.510	0.510	strong	.	COL5A3	243	.	NM_015719	exon4	c.C453A	p.A151A	GCTGACGGCCACA	.	PASS	Atlas-SNP
OR7G3	390883	hgsc.bcm.edu	37	19	9237542	9237542	+	Missense_Mutation	SNP	T	T	C	rs10414255	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	65	132	0	0.365169	0	T|0.569;C|0.431	0.431	strong	.	OR7G3	41	.	NM_001001958	exon1	c.A85G	p.M29V	ACAGCATGAAGAG	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82835724	82835724	+	Missense_Mutation	SNP	T	T	A	rs160278	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	49	80	0	0.532609	0	T|0.507;G|0.000;N|0.000;A|0.493	0.493	strong	.	VCAN	498	.	NM_004385	exon8	c.T6902A	p.F2301Y	AAGACTTTAACAG	.	PASS	Atlas-SNP
AGRP	181	hgsc.bcm.edu	37	16	67516605	67516605	+	Silent	SNP	G	G	C	rs34730014	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	63	138	0	0.428571	0	G|0.997;C|0.003	0.003	strong	.	AGRP	8	.	NM_001138	exon4	c.C333G	p.R111R	GAAGAAGCGGCAG	.	PASS	Atlas-SNP
VCX2	51480	hgsc.bcm.edu	37	X	8138160	8138160	+	Silent	SNP	T	T	C	rs1058238	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	98	132	0	0.942308	0	T|0.239;C|0.761	0.761	strong	.	VCX2	16	.	NM_016378	exon3	c.A333G	p.E111E	TGGTTCTTCCACC	.	PASS	Atlas-SNP
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407887	75407887	+	Missense_Mutation	SNP	G	G	T	rs57006992	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	19	20	0	0.5	0	G|0.933;T|0.067	0.067	strong	.	SYNPO2L	118	.	NM_001114133	exon4	c.C1523A	p.P508H	AAGAAGGGGGGTG	.	PASS	Atlas-SNP
USH2A	7399	hgsc.bcm.edu	37	1	215848587	215848587	+	Silent	SNP	T	T	C	rs2797234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	72	180	0	0.48	0	T|0.680;C|0.320	0.320	strong	USH2A,NS,carcinoma,0,2	USH2A	1168	2	NM_206933	exon63	c.A12666G	p.T4222T	CATAAATGTATTC	.	PASS	Atlas-SNP
C5orf54	63920	hgsc.bcm.edu	37	5	159820931	159820931	+	Missense_Mutation	SNP	C	C	A	rs10515808	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	78	140	0	0.478528	0	C|0.943;A|0.057	0.057	strong	C5orf54,NS,carcinoma,+1,1	C5orf54	46	1	NM_022090	exon2	c.G1567T	p.A523S	GAAATGCTGTGAA	.	PASS	Atlas-SNP
TAF1A	9015	hgsc.bcm.edu	37	1	222734803	222734803	+	Silent	SNP	G	G	C	rs1134898	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	69	168	0	0.381215	0	G|0.637;C|0.363	0.363	strong	.	TAF1A	35	.	NM_001201536	exon10	c.C1143G	p.G381G	ATGAAAGCCTGGC	.	PASS	Atlas-SNP
IGF1R	3480	hgsc.bcm.edu	37	15	99465473	99465473	+	Silent	SNP	C	C	T	rs3743262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	43	85	0	0.494253	0	C|0.921;T|0.079	0.079	strong	.	IGF1R	147	.	NM_000875	exon11	c.C2298T	p.T766T	CATCACCGACCCG	.	PASS	Atlas-SNP
FTCD	10841	hgsc.bcm.edu	37	21	47557222	47557222	+	Silent	SNP	G	G	A	rs10432965	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	38	46	0	0.535211	0	G|0.872;A|0.128	0.128	strong	.	FTCD	59	.	NM_206965	exon13	c.C1470T	p.G490G	AAACACGCCCATC	.	PASS	Atlas-SNP
RIOK2	55781	hgsc.bcm.edu	37	5	96513471	96513471	+	Missense_Mutation	SNP	G	G	C	rs2544773	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	65	100	0	0.436242	0	G|0.673;C|0.327	0.327	strong	.	RIOK2	82	.	NM_001159749	exon3	c.C287G	p.S96C	CCAACAGACTCAA	.	PASS	Atlas-SNP
CCDC136	64753	hgsc.bcm.edu	37	7	128455916	128455916	+	Silent	SNP	G	G	A	rs2270590	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	42	74	0	0.477273	0	G|0.609;A|0.391	0.391	strong	.	CCDC136	170	.	NM_022742	exon16	c.G3294A	p.E1098E	GGAGGAGGATGAC	.	PASS	Atlas-SNP
OR8D2	283160	hgsc.bcm.edu	37	11	124189729	124189729	+	Missense_Mutation	SNP	C	C	T	rs2512219	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	26	44	0	0.440678	0	C|0.749;T|0.250	0.250	strong	.	OR8D2	65	.	NM_001002918	exon1	c.G365A	p.R122H	ACATAACGGTCAT	.	PASS	Atlas-SNP
ANAPC1	64682	hgsc.bcm.edu	37	2	112592265	112592265	+	Missense_Mutation	SNP	T	T	C	rs71277799	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	448	52	319	2	0.116071	0.00626959	CGAAGAACG|0.500;TGAAGAACA|0.500	.	alt	ANAPC1,NS,carcinoma,0,1	ANAPC1	116	1	NM_022662	exon19	c.A2300G	p.H767R	ACAAGGTGAAGAA	.	scavenged	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557479	32557479	+	Missense_Mutation	SNP	G	G	A	rs9270302	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	259	51	278	0	0.196911	0	A|0.267;C|0.015;G|0.718	0.267	strong	.	HLA-DRB1	41	.	NM_002124	exon1	c.C41T	p.A14V	GTCAGCGCTGTCA	.	PASS	Atlas-SNP
CYTL1	54360	hgsc.bcm.edu	37	4	5021086	5021086	+	Silent	SNP	G	G	T	rs10006676	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	28	42	0	0.54902	0	G|0.898;T|0.102	0.102	strong	.	CYTL1	20	.	NM_018659	exon1	c.C87A	p.S29S	CATGCGGGAGTAG	.	PASS	Atlas-SNP
DLK2	65989	hgsc.bcm.edu	37	6	43418733	43418733	+	Silent	SNP	G	G	A	rs1214749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	46	73	0	0.442308	0	G|0.662;A|0.338	0.338	strong	.	DLK2	22	.	NM_023932	exon6	c.C696T	p.H232H	GAAGTCGTGGACA	.	PASS	Atlas-SNP
OGDHL	55753	hgsc.bcm.edu	37	10	50960209	50960209	+	Silent	SNP	G	G	A	rs1258184	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	47	90	0	0.5	0	G|0.567;A|0.433	0.433	strong	.	OGDHL	149	.	NM_018245	exon5	c.C564T	p.L188L	CAGAGAGAGGGTG	.	PASS	Atlas-SNP
KIF17	57576	hgsc.bcm.edu	37	1	21011346	21011346	+	Silent	SNP	A	A	G	rs12028811	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	162	185	1	0.94186	0.00540541	A|0.831;G|0.169	0.169	strong	KIF17,caecum,carcinoma,-1,1	KIF17	130	1	NM_001122819	exon10	c.T2187C	p.T729T	GTCATCAGTCAGC	.	PASS	Atlas-SNP
CCDC39	339829	hgsc.bcm.edu	37	3	180334623	180334623	+	Silent	SNP	C	C	T	rs7612917	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	41	99	0	0.506173	0	C|0.838;T|0.162	0.162	strong	CCDC39_ENST00000442201,NS,carcinoma,-2,1	CCDC39	242	1	NM_181426	exon17	c.G2397A	p.V799V	TTTGGTCACTCTT	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52709883	52709883	+	Silent	SNP	T	T	C	rs2248473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	26	103	1	0.356164	0.00970874	T|0.629;C|0.371	0.371	strong	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon7	c.A1056G	p.E352E	CGCAGCTTCCAGC	.	scavenged	Atlas-SNP
TAF7L	54457	hgsc.bcm.edu	37	X	100547804	100547804	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	45	52	0	0.957447	0	.	.	none	.	TAF7L	64	.	NM_024885	exon1	c.C230G	p.A77G	TCTGGGGCCTGGG	.	PASS	Atlas-SNP
RAB36	9609	hgsc.bcm.edu	37	22	23503170	23503170	+	Missense_Mutation	SNP	A	A	G	rs5759612	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	41	67	0	0.506173	0	A|0.466;G|0.534	0.534	strong	.	RAB36	26	.	NM_004914	exon10	c.A922G	p.N308D	GTCGGCAATGGAG	.	PASS	Atlas-SNP
LRRC7	57554	hgsc.bcm.edu	37	1	70504360	70504360	+	Silent	SNP	C	C	T	rs77157341	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	22	74	0	0.37931	0	C|0.990;T|0.010	0.010	strong	.	LRRC7	400	.	NM_020794	exon19	c.C2739T	p.H913H	AATCCACTGCCGC	.	PASS	Atlas-SNP
PRC1	9055	hgsc.bcm.edu	37	15	91525197	91525197	+	Silent	SNP	C	C	T	rs2301826	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	158	186	1	1	0.00537634	C|0.592;T|0.408	0.408	strong	PRC1,NS,carcinoma,-1,1	PRC1	51	1	NM_199413	exon4	c.G282A	p.T94T	GATGGTCGTCTCT	.	PASS	Atlas-SNP
BIN3	55909	hgsc.bcm.edu	37	8	22526559	22526559	+	Silent	SNP	G	G	A	rs11550509	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	36	44	0	0.493151	0	G|0.877;A|0.123	0.123	strong	.	BIN3	16	.	NM_018688	exon1	c.C6T	p.S2S	TCACCAGCTCATG	.	PASS	Atlas-SNP
TAS2R4	50832	hgsc.bcm.edu	37	7	141478800	141478800	+	Missense_Mutation	SNP	G	G	A	rs2234002	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	87	240	0	0.465241	0	G|0.543;A|0.457	0.457	strong	.	TAS2R4	25	.	NM_016944	exon1	c.G512A	p.S171N	ATATCAGTGAGGG	.	PASS	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	37	12	50744581	50744581	+	Missense_Mutation	SNP	A	A	T	rs73108300	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	65	109	0	0.507812	0	A|0.986;T|0.014	0.014	strong	FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	NM_001145475	exon4	c.T6034A	p.F2012I	TTCTAAATGATTC	.	PASS	Atlas-SNP
UMODL1	89766	hgsc.bcm.edu	37	21	43539293	43539293	+	Missense_Mutation	SNP	G	G	A	rs220146	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	78	138	0	0.478528	0	G|0.780;A|0.220	0.220	strong	.	UMODL1	186	.	NM_173568	exon14	c.G2932A	p.V978I	GTCAGCGTCACCA	.	PASS	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74766352	74766352	+	Silent	SNP	A	A	G	rs2301345	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	69	143	0	0.522727	0	A|0.717;G|0.283	0.283	strong	.	ABCD4	54	.	NM_005050	exon3	c.T184C	p.L62L	GGATCAAGCCAAC	.	PASS	Atlas-SNP
SPATC1L	84221	hgsc.bcm.edu	37	21	47588427	47588427	+	Silent	SNP	G	G	A	rs74486947	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	42	52	0	0.466667	0	G|0.966;A|0.034	0.034	strong	.	.	.	.	NM_001142854	exon3	c.C339T	p.P113P	CTTGAAGGGTGCC	.	PASS	Atlas-SNP
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806332	33806332	+	Silent	SNP	C	C	T	rs8066132	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	85	179	0	0.5	0	C|0.865;T|0.135	0.135	strong	.	SLFN12L	140	.	NM_001195790	exon2	c.G897A	p.G299G	TATCGTCCCCTTC	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176721272	176721272	+	Silent	SNP	G	G	C	rs11740250	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	23	55	0	0.522727	0	G|0.836;C|0.164	0.164	strong	.	NSD1	416	.	NM_022455	exon23	c.G6903C	p.G2301G	CGCTGGGTCAGGG	.	PASS	Atlas-SNP
FANCD2	2177	hgsc.bcm.edu	37	3	10088299	10088299	+	Silent	SNP	C	C	T	rs112887807	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	471	120	375	0	0.254777	0	C|0.500;T|0.500	0.500	weak	.	FANCD2	253	.	NM_001018115	exon15	c.C1170T	p.S390S	CTATAGCACCAAT	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153222835	153222835	+	Silent	SNP	G	G	C	rs2071134	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	95	142	0	0.969388	0	G|0.665;C|0.335	0.335	strong	.	HCFC1	284	.	NM_005334	exon13	c.C2283G	p.T761T	GGGCTTGGTGGTA	.	PASS	Atlas-SNP
CACNA1I	8911	hgsc.bcm.edu	37	22	40057273	40057273	+	Silent	SNP	T	T	C	rs136852	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	29	74	0	0.467742	0	T|0.284;C|0.716	0.716	strong	.	CACNA1I	264	.	NM_021096	exon16	c.T2859C	p.S953S	GAGCAGTGTCATG	.	PASS	Atlas-SNP
CORIN	10699	hgsc.bcm.edu	37	4	47605505	47605505	+	Silent	SNP	G	G	A	rs61759670	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	54	108	0	0.45	0	G|0.986;A|0.014	0.014	strong	.	CORIN	154	.	NM_006587	exon20	c.C2721T	p.Y907Y	CCGGACGTAGCCA	.	PASS	Atlas-SNP
NLRP3	114548	hgsc.bcm.edu	37	1	247588053	247588053	+	Silent	SNP	C	C	T	rs34298354	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	33	67	0	0.407407	0	C|0.912;T|0.088	0.088	strong	NLRP3,NS,carcinoma,+1,1	NLRP3	286	1	NM_183395	exon3	c.C1308T	p.S436S	GACATCCAAGACC	.	PASS	Atlas-SNP
SYNPO2	171024	hgsc.bcm.edu	37	4	119952955	119952955	+	Missense_Mutation	SNP	C	C	T	rs61732241	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	91	153	0	0.502762	0	C|0.932;T|0.068	0.068	strong	.	SYNPO2	353	.	NM_001128934	exon4	c.C3025T	p.R1009W	CCTCCCCGGCCAG	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444588	20444588	+	Missense_Mutation	SNP	T	T	C	rs2153466	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	114	183	0	0.530233	0	T|0.613;C|0.387	0.387	strong	.	OR4K15	82	.	NM_001005486	exon1	c.T911C	p.L304P	TCACGCTTATTTT	.	PASS	Atlas-SNP
TSPAN16	26526	hgsc.bcm.edu	37	19	11407019	11407019	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	57	126	0	0.471074	0	.	.	none	.	TSPAN16	22	.	NM_012466	exon1	c.T46C	p.S16P	CTGTTATCTTTAC	.	PASS	Atlas-SNP
LSS	4047	hgsc.bcm.edu	37	21	47635686	47635686	+	Missense_Mutation	SNP	C	C	T	rs143692945	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	64	87	0	0.542373	0	C|0.997;T|0.003	0.003	strong	.	LSS	50	.	NM_001001438	exon8	c.G805A	p.A269T	TGCTGGCGAAGTC	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77053834	77053834	+	Missense_Mutation	SNP	T	T	C	rs61750814	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	82	180	0	0.429319	0	T|0.836;C|0.164	0.164	strong	.	NUP54	48	.	NM_017426	exon6	c.A749G	p.N250S	GTACCATTTGGCG	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43816917	43816917	+	Silent	SNP	G	G	A	rs1060939	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	58	90	0	0.495726	0	G|0.497;A|0.503	0.503	strong	.	MAP1A	189	.	NM_002373	exon4	c.G3246A	p.G1082G	TGAGGGGCTTACA	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	804142	804142	+	Silent	SNP	A	A	G	rs61757783	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	29	63	0	0.42029	0	A|0.989;G|0.011	0.011	strong	.	PTBP1	43	.	NM_031990	exon4	c.A222G	p.E74E	GGGGGAAGTCATC	.	PASS	Atlas-SNP
DDO	8528	hgsc.bcm.edu	37	6	110714205	110714205	+	Missense_Mutation	SNP	C	C	T	rs35697832	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	55	129	0	0.833333	0	C|0.907;T|0.093	0.093	strong	.	DDO	51	.	NM_003649	exon5	c.G883A	p.G295R	AGGCTCCGTGGAG	.	PASS	Atlas-SNP
HIVEP1	3096	hgsc.bcm.edu	37	6	12124587	12124587	+	Missense_Mutation	SNP	C	C	G	rs2228212	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	84	93	0	0.988235	0	C|0.714;G|0.286	0.286	strong	.	HIVEP1	242	.	NM_002114	exon4	c.C4559G	p.A1520G	TCCATGCACCGCC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1258184	1258184	+	Silent	SNP	C	C	T	rs55703838	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	21	48	0	0.477273	0	C|0.993;T|0.007	0.007	strong	.	MUC5B	473	.	NM_002458	exon25	c.C3087T	p.F1029F	GAACTTCGACGAC	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1559259	1559259	+	Missense_Mutation	SNP	C	C	T	rs2746603	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	167	163	0	0.988166	0	C|0.952;T|0.048	0.048	strong	SIRPB1,NS,carcinoma,0,2	SIRPB1	83	2	NM_001083910	exon2	c.G158A	p.R53H	GCACAGCGCAGAG	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43826204	43826204	+	Missense_Mutation	SNP	C	C	T	rs7297737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	66	181	0	0.434211	0	C|0.968;T|0.032	0.032	strong	ADAMTS20_ENST00000389420,colon,carcinoma,-1,1	ADAMTS20	635	1	NM_025003	exon21	c.G2999A	p.R1000H	GCAAGACGATGGC	.	PASS	Atlas-SNP
SPHK1	8877	hgsc.bcm.edu	37	17	74381555	74381555	+	Missense_Mutation	SNP	G	G	A	rs2247856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	7	5	2	1	0.4	G|0.716;A|0.284	0.284	strong	SPHK1,NS,carcinoma,0,1	SPHK1	24	1	NM_182965	exon2	c.G88A	p.A30T	AATGACGCCGGTG	.	scavenged	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4722785	4722785	+	Silent	SNP	G	G	A	rs1052751	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	35	65	0	0.514706	0	G|0.863;A|0.137	0.137	strong	.	PLD2	138	.	NM_001243108	exon23	c.G2370A	p.L790L	CGTGCTGATCGAG	.	PASS	Atlas-SNP
STAT1	6772	hgsc.bcm.edu	37	2	191874667	191874667	+	Silent	SNP	A	A	G	rs2066802	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	92	184	0	0.528736	0	A|0.909;G|0.091	0.091	strong	.	STAT1	93	.	NM_007315	exon3	c.T63C	p.L21L	ATCATAAAGCTGG	.	PASS	Atlas-SNP
VWA3B	200403	hgsc.bcm.edu	37	2	98779439	98779439	+	Nonsense_Mutation	SNP	G	G	T	rs62154921	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	42	87	0	0.477273	0	G|0.971;T|0.029	0.029	strong	.	VWA3B	138	.	NM_144992	exon8	c.G1114T	p.E372X	GACTGCGGTTGGT	.	PASS	Atlas-SNP
PSMC4	5704	hgsc.bcm.edu	37	19	40478362	40478362	+	Silent	SNP	T	T	C	rs35555615	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	15	43	0	0.333333	0	T|0.976;C|0.024	0.024	strong	.	PSMC4	48	.	NM_006503	exon3	c.T222C	p.H74H	TCTCCATGCCCAG	.	PASS	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31084639	31084639	+	Silent	SNP	C	C	T	rs4713436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	45	0	1	0	C|0.838;T|0.162	0.162	strong	.	CDSN	48	.	NM_001264	exon2	c.G753A	p.R251R	CACAGGCCTCTGA	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234192	8234192	+	Missense_Mutation	SNP	G	G	C	rs4840953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	19	49	0	0.358491	0	G|0.602;C|0.398	0.398	strong	.	.	.	.	NM_001080826	exon2	c.C1727G	p.S576C	CCGCCAGAGCTCC	.	PASS	Atlas-SNP
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969085	49969085	+	Silent	SNP	C	C	T	rs10853810	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	38	100	1	0.404255	0.01	C|0.695;T|0.305	0.305	strong	ALDH16A1,colon,carcinoma,0,1	ALDH16A1	54	1	NM_153329	exon13	c.C1659T	p.N553N	TGGCAACCTCCAT	.	scavenged	Atlas-SNP
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	105	209	1	0.495283	0.00478469	C|0.686;T|0.314	0.314	strong	.	DDX47	37	.	NM_201224	exon2	c.C150T	p.I50I	CAAGATCCAGATT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506760	195506760	+	Silent	SNP	T	T	A	rs62282473	byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	49	32	0	0.720588	0	T|0.967;A|0.033	0.033	strong	.	MUC4	1505	.	NM_018406	exon2	c.A11691T	p.A3897A	TGTGGATGCTGAG	.	PASS	Atlas-SNP
IMPG1	3617	hgsc.bcm.edu	37	6	76640781	76640781	+	Missense_Mutation	SNP	C	C	T	rs3734313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	10	139	1	0.136986	0.00719424	C|0.826;T|0.174	0.174	strong	IMPG1,NS,carcinoma,-1,1	IMPG1	143	1	NM_001563	exon15	c.G2132A	p.R711H	TTGCAGCGACACT	.	scavenged	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52325767	52325767	+	Missense_Mutation	SNP	T	T	G	rs16916207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	30	66	0	0.6	0	T|0.846;G|0.154	0.154	strong	.	PXDNL	414	.	NM_144651	exon15	c.A1847C	p.D616A	ACAGCATCAAGAA	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158534372	158534372	+	Silent	SNP	G	G	A	rs57686648	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	41	80	0	0.405941	0	G|0.759;A|0.241	0.241	strong	ESYT2,NS,malignant_melanoma,-1,1	ESYT2	70	1	NM_020728	exon17	c.C2091T	p.A697A	AGGGCCGGCCTCA	.	PASS	Atlas-SNP
DYDC1	143241	hgsc.bcm.edu	37	10	82098881	82098881	+	Missense_Mutation	SNP	A	A	T	rs35605779	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	51	111	0	0.455357	0	A|0.994;T|0.006	0.006	strong	.	DYDC1	15	.	NM_001269053	exon5	c.T371A	p.V124D	TTCCTAACTAGAT	.	PASS	Atlas-SNP
GIPR	2696	hgsc.bcm.edu	37	19	46177997	46177997	+	Silent	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	48	89	0	0.5	0	.	.	none	.	GIPR	36	.	NM_000164	exon7	c.G546T	p.L182L	CATGCTGCGAGCT	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406516	3406516	+	Silent	SNP	A	A	G	rs11643487	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	19	49	0	0.339286	0	A|0.659;G|0.341	0.341	strong	.	OR2C1	38	.	NM_012368	exon1	c.A576G	p.T192T	CGACACAAGTCTC	.	PASS	Atlas-SNP
NDST1	3340	hgsc.bcm.edu	37	5	149907533	149907533	+	Silent	SNP	T	T	G	rs2273235	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	30	80	0	0.447761	0	T|0.626;G|0.374	0.374	strong	.	NDST1	79	.	NM_001543	exon3	c.T681G	p.V227V	GACGGTTTTCCAG	.	PASS	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74923562	74923562	+	Missense_Mutation	SNP	C	C	T	rs3812619	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	97	176	0	0.47549	0	C|0.811;T|0.189	0.189	strong	.	ECD	50	.	NM_001135752	exon2	c.G134A	p.R45Q	GCAAACCGAGTGA	.	PASS	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44418544	44418544	+	Silent	SNP	A	A	G	rs425221	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	107	106	0	0.981651	0	A|0.488;G|0.512	0.512	strong	.	ZNF45	51	.	NM_003425	exon10	c.T1044C	p.N348N	ATGAATATTAAGG	.	PASS	Atlas-SNP
POM121C	100101267	hgsc.bcm.edu	37	7	75053499	75053499	+	Missense_Mutation	SNP	G	G	A	rs113744930	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	468	228	401	0	0.487179	0	G|0.881;A|0.119	0.119	strong	POM121C,NS,carcinoma,+1,1	POM121C	46	1	NM_001099415	exon12	c.C881T	p.S294L	GAGTTCGAGGCAG	.	PASS	Atlas-SNP
CDRT1	374286	hgsc.bcm.edu	37	17	15496730	15496730	+	Missense_Mutation	SNP	A	A	G	rs8078150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	111	221	0	0.468354	0	A|0.688;G|0.312	0.312	strong	.	CDRT1	83	.	NM_006382	exon11	c.T1927C	p.F643L	CATTGAAGAAATT	.	PASS	Atlas-SNP
MICB	4277	hgsc.bcm.edu	37	6	31473561	31473561	+	Missense_Mutation	SNP	A	A	G	rs1065075	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	43	99	0	0.483146	0	A|0.712;G|0.288	0.288	strong	.	MICB	26	.	NM_005931	exon2	c.A238G	p.K80E	GGAGCTAAGACCT	.	PASS	Atlas-SNP
HNF4A	3172	hgsc.bcm.edu	37	20	43048368	43048368	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	24	58	0	0.444444	0	.	.	none	.	HNF4A	150	.	NM_178849	exon7	c.C744T	p.D248D	CAATGACTACATT	.	PASS	Atlas-SNP
NDUFA6	4700	hgsc.bcm.edu	37	22	42486723	42486723	+	Missense_Mutation	SNP	G	G	A	rs1801311	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	51	79	0	0.5	0	G|0.625;A|0.375	0.375	strong	.	NDUFA6	13	.	NM_002490	exon1	c.C104T	p.A35V	GAAGTAGCTTGGC	.	PASS	Atlas-SNP
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458765	39458765	+	Silent	SNP	A	A	G	rs1005197	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	36	56	0	0.642857	0	A|0.331;G|0.669	0.669	strong	.	KRTAP29-1	2	.	NM_001257309	exon1	c.T339C	p.S113S	ACAAGTAGATTCC	.	PASS	Atlas-SNP
EHD2	30846	hgsc.bcm.edu	37	19	48229169	48229169	+	Silent	SNP	A	A	G	rs8111184	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	31	65	0	0.455882	0	A|0.861;G|0.139	0.139	strong	.	EHD2	59	.	NM_014601	exon4	c.A603G	p.S201S	GTTCTCAGAGGCC	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626117	140626117	+	Missense_Mutation	SNP	G	G	C	rs147373970	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	55	166	0	0.361842	0	G|0.997;C|0.003	0.003	strong	.	PCDHB15	138	.	NM_018935	exon1	c.G971C	p.G324A	CTGATGGCGGGGG	.	PASS	Atlas-SNP
BNC2	54796	hgsc.bcm.edu	37	9	16419519	16419519	+	Missense_Mutation	SNP	G	G	A	rs117452684	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	46	116	0	0.516854	0	G|0.979;A|0.021	0.021	strong	.	BNC2	166	.	NM_017637	exon7	c.C2768T	p.A923V	TGCTGGGCACCAT	.	PASS	Atlas-SNP
ARHGEF18	23370	hgsc.bcm.edu	37	19	7505147	7505147	+	Missense_Mutation	SNP	G	G	T	rs201598844		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	52	74	0	0.448276	0	G|0.999;T|0.001	0.001	weak	.	ARHGEF18	129	.	NM_001130955	exon1	c.G321T	p.Q107H	GCCGCAGTCGGAG	.	PASS	Atlas-SNP
ZNF235	9310	hgsc.bcm.edu	37	19	44792701	44792701	+	Missense_Mutation	SNP	T	T	G	rs2125579	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	141	164	0	0.992958	0	G|0.429;N|0.000	0.429	strong	.	ZNF235	60	.	NM_004234	exon5	c.A887C	p.H296P	TTCTCATGTGTAC	.	PASS	Atlas-SNP
PKN1	5585	hgsc.bcm.edu	37	19	14580197	14580197	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	82	150	0	0.577465	0	.	.	none	.	PKN1	99	.	NM_213560	exon16	c.G2039T	p.G680V	GTGCGGGACACCC	.	PASS	Atlas-SNP
FAM210A	125228	hgsc.bcm.edu	37	18	13681962	13681962	+	Missense_Mutation	SNP	A	A	T	rs35493157	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	47	84	0	0.522222	0	A|0.971;T|0.029	0.029	strong	.	.	.	.	NM_001098801	exon3	c.T115A	p.Y39N	CATTGTATAAAAG	.	PASS	Atlas-SNP
MCM3AP	8888	hgsc.bcm.edu	37	21	47695220	47695220	+	Silent	SNP	A	A	G	rs2839190	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	42	65	0	0.477273	0	A|0.864;G|0.136	0.136	strong	.	MCM3AP	146	.	NM_003906	exon6	c.T1878C	p.D626D	GTCCAGATCGGTT	.	PASS	Atlas-SNP
MCM8	84515	hgsc.bcm.edu	37	20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	rs6117014	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	36	87	0	0.36	0	A|0.936;C|0.064	0.064	strong	.	MCM8	125	.	NM_032485	exon4	c.A303C	p.K101N	TGAAAAATTTTTC	.	PASS	Atlas-SNP
IL6ST	3572	hgsc.bcm.edu	37	5	55272085	55272085	+	Missense_Mutation	SNP	G	G	C	rs1063560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	82	163	0	0.455556	0	G|0.989;C|0.011	0.011	strong	.	IL6ST	75	.	NM_175767	exon3	c.C22G	p.L8V	GCACTAGCCAAGT	.	PASS	Atlas-SNP
UEVLD	55293	hgsc.bcm.edu	37	11	18555949	18555949	+	Silent	SNP	T	T	C	rs55999230	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	24	62	0	0.444444	0	T|0.793;C|0.207	0.207	strong	.	UEVLD	58	.	NM_001040697	exon11	c.A1176G	p.L392L	TACTGATAGTCCA	.	PASS	Atlas-SNP
CPZ	8532	hgsc.bcm.edu	37	4	8621269	8621269	+	Silent	SNP	C	C	T	rs61734024	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	18	30	0	0.642857	0	C|0.987;T|0.013	0.013	strong	.	CPZ	95	.	NM_001014447	exon11	c.C1884T	p.D628D	GGCCGACGGGAGT	.	PASS	Atlas-SNP
ITSN2	50618	hgsc.bcm.edu	37	2	24439048	24439048	+	Missense_Mutation	SNP	A	A	G	rs3731625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	66	109	0	0.52381	0	A|0.924;G|0.076	0.076	strong	ITSN2,NS,carcinoma,0,1	ITSN2	224	1	NM_006277	exon32	c.T3860C	p.I1287T	TCCCCAATCATCT	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73569749	73569749	+	Silent	SNP	C	C	T	rs11000009	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	29	54	0	0.630435	0	C|0.909;T|0.091	0.091	strong	.	CDH23	365	.	NM_022124	exon59	c.C8895T	p.P2965P	GATCCCCGACCGT	.	PASS	Atlas-SNP
BAGE3	85318	hgsc.bcm.edu	37	21	11049616	11049616	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	388	27	430	0	0.0695876	0	.	.	none	.	.	.	.	NM_182481	exon4	c.G285A	p.R95R	CATCTTCCTTCGC	.	PASS	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3297181	3297181	+	Silent	SNP	C	C	T	rs224208	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	76	154	0	0.477987	0	C|0.414;T|0.586	0.586	strong	.	MEFV	170	.	NM_000243	exon5	c.G1422A	p.E474E	TTGCTGCTCCAGG	.	PASS	Atlas-SNP
STK10	6793	hgsc.bcm.edu	37	5	171482633	171482633	+	Missense_Mutation	SNP	C	C	T	rs115040416	byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	270	3	233	0	0.0111111	0	C|0.990;T|0.010	0.010	strong	STK10,NS,carcinoma,0,1	STK10	100	1	NM_005990	exon16	c.G2485A	p.G829S	CCCCGCCGTTGAT	.	scavenged	Atlas-SNP
USP18	11274	hgsc.bcm.edu	37	22	18650682	18650682	+	Missense_Mutation	SNP	C	C	T	rs3180408	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	243	122	191	1	0.502058	0.0052356	C|0.674;N|0.000	.	strong	USP18,NS,carcinoma,0,1	USP18	22	1	NM_017414	exon6	c.C506T	p.T169M	TGTATACGATCCG	.	scavenged	Atlas-SNP
SSRP1	6749	hgsc.bcm.edu	37	11	57099661	57099661	+	Silent	SNP	T	T	C	rs2230648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	19	73	0	0.395833	0	T|0.967;C|0.033;A|0.000	0.033	strong	.	SSRP1	75	.	NM_003146	exon8	c.A966G	p.V322V	GCGGTTTACCAGT	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3640784	3640784	+	Missense_Mutation	SNP	G	G	A	rs78637028	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	62	129	0	0.512397	0	G|0.955;A|0.045	0.045	strong	SLX4,NS,carcinoma,+1,1	SLX4	173	1	NM_032444	exon12	c.C2855T	p.A952V	CCAAGCGCCTCCT	.	PASS	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	37	6	42571346	42571346	+	Silent	SNP	A	A	T	rs16895863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	24	47	0	0.461538	0	A|0.793;T|0.207	0.207	strong	.	UBR2	134	.	NM_001184801	exon5	c.A552T	p.S184S	TTTATCAGAAGAT	.	PASS	Atlas-SNP
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	243	112	248	0	0.460905	0	C|0.495;T|0.505	0.505	strong	.	ZNF280D	82	.	NM_017661	exon15	c.G1702A	p.V568I	ATTTGACTGTATT	.	PASS	Atlas-SNP
CENPB	1059	hgsc.bcm.edu	37	20	3766885	3766885	+	Silent	SNP	G	G	A	rs140023764	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	16	29	0	0.457143	0	G|0.997;A|0.003	0.003	strong	.	CENPB	24	.	NM_001810	exon1	c.C246T	p.I82I	CCAGGCGATGAGC	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1018316	1018316	+	Silent	SNP	G	G	A	rs201954368		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	420	22	340	0	0.052381	0	.	.	weak	MUC6_ENST00000421673,NS,carcinoma,0,4	MUC6	408	4	NM_005961	exon31	c.C4485T	p.S1495S	GTGGGTGGACCCT	.	PASS	Atlas-SNP
PARD6B	84612	hgsc.bcm.edu	37	20	49366879	49366879	+	Silent	SNP	C	C	T	rs41283606	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	98	165	0	0.505155	0	C|0.996;T|0.004	0.004	strong	.	PARD6B	31	.	NM_032521	exon3	c.C973T	p.L325L	ATAGAGCTAAGCT	.	PASS	Atlas-SNP
SMPD4	55627	hgsc.bcm.edu	37	2	130925088	130925088	+	Silent	SNP	C	C	T	rs10909567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	38	46	0	0.520548	0	C|0.662;T|0.338	0.338	strong	.	SMPD4	67	.	NM_017751	exon9	c.G852A	p.T284T	CACAGACGTCTGA	.	PASS	Atlas-SNP
ZBTB42	100128927	hgsc.bcm.edu	37	14	105267579	105267579	+	Silent	SNP	A	A	G	rs12878684	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	5	0	0	1	.	A|0.292;G|0.708	0.708	strong	.	ZBTB42	10	.	NM_001137601	exon2	c.A45G	p.R15R	CCTGAGACAGCAG	.	PASS	Atlas-SNP
SGCD	6444	hgsc.bcm.edu	37	5	155935708	155935708	+	Missense_Mutation	SNP	G	G	A	rs45559835	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	26	60	0	0.42623	0	G|0.972;A|0.028	0.028	strong	SGCD,NS,carcinoma,+1,1	SGCD	52	1	NM_000337	exon4	c.G290A	p.R97Q	AGTCCCGACCAGT	.	PASS	Atlas-SNP
NIM1	0	hgsc.bcm.edu	37	5	43245922	43245922	+	Silent	SNP	C	C	T	rs13176855	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	117	121	0	1	0	C|0.645;T|0.355	0.355	strong	.	.	.	.	NM_153361	exon2	c.C45T	p.H15H	CCCCCACTATGCC	.	PASS	Atlas-SNP
OR7E24	26648	hgsc.bcm.edu	37	19	9362443	9362443	+	Missense_Mutation	SNP	C	C	T	rs2240928	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	22	66	0	0.431373	0	C|0.537;T|0.463	0.463	strong	.	OR7E24	48	.	NM_001079935	exon1	c.C724T	p.P242S	GTTTCCCCCATTC	.	PASS	Atlas-SNP
TRIM10	10107	hgsc.bcm.edu	37	6	30128442	30128442	+	Missense_Mutation	SNP	C	C	T	rs12212092	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	86	149	0	0.477778	0	C|0.895;T|0.105	0.105	strong	.	TRIM10	65	.	NM_052828	exon1	c.G194A	p.R65H	CCAGGACGGAAGG	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301217	65301217	+	Missense_Mutation	SNP	G	G	A	rs62415827	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	90	144	0	1	0	G|0.902;A|0.098	0.098	strong	.	EYS	527	.	NM_001142800	exon26	c.C4543T	p.R1515W	TGAACCGGTGCAG	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140627225	140627225	+	Silent	SNP	A	A	G	rs141485224	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	18	53	0	0.333333	0	A|0.997;G|0.003	0.003	strong	.	PCDHB15	138	.	NM_018935	exon1	c.A2079G	p.A693A	GGTGGCATTGGCC	.	PASS	Atlas-SNP
PGM1	5236	hgsc.bcm.edu	37	1	64097432	64097432	+	Missense_Mutation	SNP	C	C	T	rs1126728	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	55	107	0	0.436508	0	C|0.767;T|0.233	0.233	strong	PGM1_ENST00000371083,NS,carcinoma,-1,2	PGM1	75	2	NM_001172818	exon4	c.C715T	p.R239C	AAGATCCGTATTG	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34723935	34723935	+	Missense_Mutation	SNP	C	C	T	rs77983392		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	45	97	0	0.412844	0	T|1.000;|0.000	1.000	weak	.	FAM205A	45	.	NM_001141917	exon4	c.G3302A	p.R1101H	AAGCTACGGCTCC	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109623516	109623516	+	Missense_Mutation	SNP	G	G	A	rs2300455	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	20	30	0	0.5	0	G|0.846;A|0.154	0.154	strong	ACACB,colon,carcinoma,0,1	ACACB	330	1	NM_001093	exon11	c.G1951A	p.A651T	ATTGCCGCCAGAA	.	PASS	Atlas-SNP
ZCCHC9	84240	hgsc.bcm.edu	37	5	80604430	80604430	+	Silent	SNP	C	C	T	rs1055383	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	59	167	1	0.371069	0.00598802	C|0.842;T|0.158	0.158	strong	ZCCHC9,caecum,carcinoma,+1,1	ZCCHC9	26	1	NM_001131036	exon3	c.C435T	p.A145A	CCCCGCCGCCCTT	.	scavenged	Atlas-SNP
TRPV1	7442	hgsc.bcm.edu	37	17	3480447	3480447	+	Missense_Mutation	SNP	T	T	C	rs8065080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	48	87	0	0.340426	0	T|0.625;C|0.375	0.375	strong	.	TRPV1	99	.	NM_018727	exon12	c.A1753G	p.I585V	AGACGATGTAGAC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228526011	228526011	+	Silent	SNP	C	C	T	rs11577699	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	37	50	0	0.521127	0	C|0.879;T|0.121	0.121	strong	.	OBSCN	2142	.	NM_001271223	exon79	c.C19893T	p.A6631A	GGGGGCCGCTGAG	.	PASS	Atlas-SNP
SPICE1	152185	hgsc.bcm.edu	37	3	113175984	113175984	+	Silent	SNP	G	G	A	rs146846950	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	24	46	0	0.533333	0	G|0.995;A|0.005	0.005	strong	SPICE1_ENST00000295872,NS,carcinoma,0,2	SPICE1	130	2	NM_144718	exon13	c.C1656T	p.D552D	CTTACCGTCCTGA	.	PASS	Atlas-SNP
POLR1D	51082	hgsc.bcm.edu	37	13	28240075	28240075	+	Silent	SNP	G	G	T	rs75314566	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	24	43	0	0.545455	0	G|0.967;T|0.033	0.033	strong	POLR1D,NS,carcinoma,+1,1	POLR1D	31	1	NM_152705	exon3	c.G354T	p.R118R	AAAGCGGTCCAAC	.	PASS	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113479813	113479813	+	Silent	SNP	G	G	A	rs9549564	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	157	216	1	0.993671	0.00462963	G|0.774;A|0.226	0.226	strong	.	ATP11A	225	.	NM_032189	exon11	c.G942A	p.L314L	TGTGCTGAAATAC	.	PASS	Atlas-SNP
SUN5	140732	hgsc.bcm.edu	37	20	31590686	31590686	+	Missense_Mutation	SNP	C	C	A	rs1133358	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	70	106	0	0.526316	0	T|0.002;G|0.005	.	strong	.	SUN5	63	.	NM_080675	exon2	c.G117T	p.E39D	GGTGTCCTCTGCC	.	PASS	Atlas-SNP
TCP10L2	401285	hgsc.bcm.edu	37	6	167592606	167592606	+	Silent	SNP	T	T	A	rs201866116	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	20	97	0	0.344828	0	T|0.927;A|0.073	0.073	strong	.	TCP10L2	41	.	NM_001145121	exon6	c.T765A	p.V255V	CGGAGTTGCTGGT	.	PASS	Atlas-SNP
ADAMTS4	9507	hgsc.bcm.edu	37	1	161168004	161168004	+	Silent	SNP	C	C	T	rs33941127	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	43	88	0	0.425743	0	C|0.720;T|0.280	0.280	strong	.	ADAMTS4	171	.	NM_005099	exon1	c.G414A	p.S138S	TGCCACCGACTCC	.	PASS	Atlas-SNP
TEKT3	64518	hgsc.bcm.edu	37	17	15217437	15217437	+	Missense_Mutation	SNP	C	C	G	rs230898	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	275	132	251	0	0.48	0	C|0.581;G|0.419	0.419	strong	.	TEKT3	64	.	NM_031898	exon6	c.G845C	p.G282A	AAGTAGCCGACAC	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125453115	125453115	+	Missense_Mutation	SNP	C	C	T	rs11057939	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	24	34	0	0.5	0	C|0.906;T|0.094	0.094	strong	.	DHX37	114	.	NM_032656	exon10	c.G1373A	p.R458Q	ACCTTCCGGAAGC	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160453978	160453978	+	Silent	SNP	A	A	G	rs1570070	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	23	53	0	0.92	0	A|0.643;G|0.357	0.357	strong	.	IGF2R	251	.	NM_000876	exon9	c.A1050G	p.S350S	AGGTTCATCCTAT	.	PASS	Atlas-SNP
FAM83G	644815	hgsc.bcm.edu	37	17	18874720	18874720	+	Silent	SNP	C	C	G	rs916823	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	66	77	0	0.985075	0	C|0.359;G|0.641	0.641	strong	.	FAM83G	51	.	NM_001039999	exon6	c.G2424C	p.S808S	AGAATCCGATGAG	.	PASS	Atlas-SNP
PDK2	5164	hgsc.bcm.edu	37	17	48174908	48174908	+	Silent	SNP	C	C	T	rs9839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	21	23	0	0.456522	0	C|0.639;T|0.361	0.361	strong	PDK2,NS,carcinoma,0,1	PDK2	41	1	NM_002611	exon2	c.C240T	p.S80S	ACCCTCCGTGCAG	.	PASS	Atlas-SNP
TRIT1	54802	hgsc.bcm.edu	37	1	40349131	40349131	+	Silent	SNP	G	G	A	rs3845570	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	7	54	0	0.0886076	0	G|0.541;A|0.459	0.459	strong	TRIT1,NS,carcinoma,0,2	TRIT1	40	2	NM_017646	exon1	c.C33T	p.P11P	GCCCACGGGAACT	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301167	65301167	+	Silent	SNP	C	C	T	rs62415825	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	98	179	0	1	0	C|0.902;T|0.098	0.098	strong	.	EYS	527	.	NM_001142800	exon26	c.G4593A	p.E1531E	TGAAGCCTCAGTA	.	PASS	Atlas-SNP
ZNF154	7710	hgsc.bcm.edu	37	19	58213969	58213969	+	Silent	SNP	T	T	G	rs11878316	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	64	139	0	0.460432	0	T|0.862;G|0.138	0.138	strong	.	ZNF154	34	.	NM_001085384	exon3	c.A348C	p.S116S	GCTATTTGATTGC	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784055	140784055	+	Silent	SNP	T	T	C	rs3749770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	128	132	0	0.984615	0	T|0.697;C|0.303	0.303	strong	.	PCDHGA9	110	.	NM_032089	exon1	c.T1536C	p.G512G	CACTGGTGTGCTG	.	PASS	Atlas-SNP
SLC39A8	64116	hgsc.bcm.edu	37	4	103228734	103228734	+	Silent	SNP	C	C	T	rs35411892	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	270	142	229	0	0.525926	0	C|0.841;T|0.159	0.159	strong	.	SLC39A8	24	.	NM_022154	exon3	c.G411A	p.T137T	AATAATCGTCACT	.	PASS	Atlas-SNP
ADCY2	108	hgsc.bcm.edu	37	5	7520881	7520881	+	Missense_Mutation	SNP	G	G	T	rs13166360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	65	147	0	0.398773	0	G|0.850;T|0.150	0.150	strong	.	ADCY2	337	.	NM_020546	exon3	c.G439T	p.V147L	TTCGTGGTGTACA	.	PASS	Atlas-SNP
PTCRA	171558	hgsc.bcm.edu	37	6	42893254	42893254	+	Missense_Mutation	SNP	G	G	A	rs146531157	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	25	52	0	0.555556	0	G|0.999;A|0.001	0.001	strong	.	PTCRA	24	.	NM_001243168	exon4	c.G725A	p.R242Q	CGGGTCGGAAGCC	.	PASS	Atlas-SNP
COL5A3	50509	hgsc.bcm.edu	37	19	10078589	10078589	+	Silent	SNP	T	T	C	rs3815748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	38	60	0	0.475	0	T|0.837;C|0.163	0.163	strong	.	COL5A3	243	.	NM_015719	exon61	c.A4395G	p.K1465K	AGACCCTTTTGAG	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057666	46057666	+	Missense_Mutation	SNP	A	A	T	rs116100696	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	90	140	0	0.6	0	A|0.982;T|0.018	0.018	strong	.	KRTAP10-10	37	.	NM_181688	exon1	c.A332T	p.K111M	GTAACAAGCCTGT	.	PASS	Atlas-SNP
SEC24C	9632	hgsc.bcm.edu	37	10	75527708	75527708	+	Silent	SNP	A	A	G	rs4746147	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	216	129	193	1	0.597222	0.00518135	A|0.856;G|0.144	0.144	strong	SEC24C,NS,carcinoma,0,1	SEC24C	86	1	NM_198597	exon15	c.A2124G	p.T708T	GGCCACACTCTCT	.	PASS	Atlas-SNP
MAP1A	4130	hgsc.bcm.edu	37	15	43815999	43815999	+	Silent	SNP	C	C	T	rs3862138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	41	76	0	0.476744	0	C|0.837;T|0.163	0.163	strong	.	MAP1A	189	.	NM_002373	exon4	c.C2328T	p.P776P	CCTGCCCGGGCCT	.	PASS	Atlas-SNP
R3HDML	140902	hgsc.bcm.edu	37	20	42966025	42966025	+	Silent	SNP	T	T	C	rs1884612	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	62	87	0	0.488189	0	T|0.730;C|0.270	0.270	strong	.	R3HDML	33	.	NM_178491	exon1	c.T228C	p.S76S	GGCCAGTGTGTAC	.	PASS	Atlas-SNP
EPHB2	2048	hgsc.bcm.edu	37	1	23208925	23208925	+	Silent	SNP	G	G	A	rs2229872	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	85	92	0	0.934066	0	G|0.854;A|0.146	0.146	strong	EPHB2_ENST00000374632,NS,adenoma,0,1	EPHB2	257	1	NM_004442	exon6	c.G1377A	p.P459P	CCAGCCGGACCAG	.	PASS	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31083945	31083945	+	Missense_Mutation	SNP	C	C	T	rs145583110	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	70	132	0	0.496454	0	C|0.995;T|0.005	0.005	strong	.	CDSN	48	.	NM_001264	exon2	c.G1447A	p.A483T	GCTTGGCACCAGC	.	PASS	Atlas-SNP
ALPP	250	hgsc.bcm.edu	37	2	233243586	233243586	+	Missense_Mutation	SNP	C	C	T	rs41415150		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	67	144	0	0.432258	0	C|1.000;|0.000	.	weak	.	ALPP	53	.	NM_001632	exon1	c.C74T	p.P25L	TCATCCCAGGTAA	.	PASS	Atlas-SNP
OR56A3	390083	hgsc.bcm.edu	37	11	5968728	5968728	+	Missense_Mutation	SNP	T	T	C	rs1840178	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	77	159	0	0.442529	0	T|0.447;C|0.553	0.553	strong	.	OR56A3	81	.	NM_001003443	exon1	c.T152C	p.M51T	TCCTGATGACCAT	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71780215	71780215	+	Silent	SNP	T	T	C	rs2303596	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	154	173	0	0.987179	0	T|0.328;C|0.672	0.672	strong	.	DYSF	536	.	NM_001130982	exon21	c.T1923C	p.D641D	GGATGATGCCATC	.	PASS	Atlas-SNP
SEC14L4	284904	hgsc.bcm.edu	37	22	30888494	30888494	+	Missense_Mutation	SNP	C	C	T	rs17738527	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	60	132	0	0.451128	0	C|0.841;T|0.159	0.159	strong	.	SEC14L4	43	.	NM_001161368	exon8	c.G631A	p.E211K	TCTCCTCACTCAT	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74005476	74005476	+	Silent	SNP	G	G	A	rs7225323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	39	83	0	0.464286	0	G|0.810;A|0.190	0.190	strong	.	EVPL	155	.	NM_001988	exon22	c.C3810T	p.I1270I	GCGGTCGATCTCA	.	PASS	Atlas-SNP
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23060256	23060256	+	Missense_Mutation	SNP	T	T	C	rs17620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	61	160	0	0.412162	0	T|0.514;C|0.486	0.486	strong	.	TNFRSF10A	40	.	NM_003844	exon3	c.A422G	p.H141R	CCAGGATGTTCTG	.	PASS	Atlas-SNP
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58345606	58345606	+	Silent	SNP	T	T	C	rs17120203	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	84	159	0	0.449198	0	T|0.861;C|0.139	0.139	strong	.	XRCC6BP1	22	.	NM_033276	exon4	c.T381C	p.L127L	CGAGCTTATTCAT	.	PASS	Atlas-SNP
BAZ1A	11177	hgsc.bcm.edu	37	14	35231108	35231108	+	Missense_Mutation	SNP	A	A	T	rs1044140	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	345	168	337	0	0.486957	0	A|0.941;T|0.059	0.059	strong	.	BAZ1A	128	.	NM_013448	exon24	c.T4098A	p.N1366K	TGGTGTATTATTA	.	PASS	Atlas-SNP
PIK3C2B	5287	hgsc.bcm.edu	37	1	204399064	204399064	+	Silent	SNP	G	G	A	rs2271420	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	15	37	0	0.5	0	G|0.866;A|0.134	0.134	strong	.	PIK3C2B	142	.	NM_002646	exon30	c.C4383T	p.P1461P	CTCAGGGGGTGCG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1247458	1247458	+	Missense_Mutation	SNP	C	C	T	rs2075853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	40	73	0	0.487805	0	C|0.812;T|0.188	0.188	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon3	c.C151T	p.R51W	CCCACCCGGCGCG	.	PASS	Atlas-SNP
TTF1	7270	hgsc.bcm.edu	37	9	135277007	135277007	+	Missense_Mutation	SNP	C	C	T	rs3739916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	243	107	265	0	0.440329	0	C|0.959;T|0.041	0.041	strong	TTF1,NS,carcinoma,0,2	TTF1	82	2	NM_007344	exon2	c.G1202A	p.R401Q	GACACTCGTGCCC	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187088903	187088903	+	Silent	SNP	C	C	A	rs1533595	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	43	104	0	0.452632	0	C|0.669;A|0.331	0.331	strong	.	RTP4	20	.	NM_022147	exon2	c.C483A	p.I161I	GGGCATCTGTGGA	.	PASS	Atlas-SNP
SEMA3C	10512	hgsc.bcm.edu	37	7	80387766	80387766	+	Silent	SNP	C	C	T	rs1058425	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	47	103	0	0.447619	0	C|0.633;T|0.367	0.367	strong	.	SEMA3C	106	.	NM_006379	exon15	c.G1524A	p.Q508Q	AGATACCTGGGAA	.	PASS	Atlas-SNP
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534523	16534523	+	Missense_Mutation	SNP	G	G	A	rs141036884	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	126	125	0	0.940298	0	G|0.999;A|0.001	0.001	strong	ARHGEF19,NS,carcinoma,+1,1	ARHGEF19	49	1	NM_153213	exon3	c.C610T	p.R204W	GCAGCCGGGTCAT	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596890	48596890	+	Silent	SNP	G	G	A	rs17823193	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	100	175	0	0.490196	0	G|0.939;A|0.061	0.061	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.C186T	p.F62F	GAGGAAGAAGTAC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4511365	4511365	+	Silent	SNP	C	C	G	rs116973517	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	97	230	0	0.41453	0	C|0.937;G|0.063	0.063	strong	.	PLIN4	191	.	NM_001080400	exon3	c.G2565C	p.V855V	ACCGGTCACCCCA	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238249108	238249108	+	Silent	SNP	T	T	C	rs61729844	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	52	39	0	0.981132	0	A|0.000;C|0.070;T|0.930	0.070	strong	.	COL6A3	608	.	NM_004369	exon38	c.A8451G	p.P2817P	GAAGGATGGCAAC	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs71354064		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	277	219	256	0	0.790614	0	C|0.500;A|0.500	0.500	weak	ZNF417,NS,carcinoma,0,1	ZNF417	44	1	NM_152475	exon3	c.G947T	p.R316L	TGAACACGCTGAT	.	PASS	Atlas-SNP
CCDC168	643677	hgsc.bcm.edu	37	13	103388370	103388370	+	Missense_Mutation	SNP	C	C	T	rs9518825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	109	225	2	0.502304	0.00888889	C|0.737;T|0.263	0.263	strong	Q8N800_HUMAN,NS,carcinoma,0,2	.	.	2	NM_001146197	exon4	c.G14677A	p.G4893S	TTCTACCTTCCCT	.	scavenged	Atlas-SNP
CLIP4	79745	hgsc.bcm.edu	37	2	29356669	29356669	+	Silent	SNP	A	A	G	rs3100232	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	37	89	0	0.474359	0	A|0.551;G|0.449	0.449	strong	.	CLIP4	69	.	NM_024692	exon5	c.A516G	p.T172T	GAAAACATCGAAA	.	PASS	Atlas-SNP
NUP54	53371	hgsc.bcm.edu	37	4	77065580	77065580	+	Silent	SNP	T	T	C	rs11558469	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	70	145	0	0.546875	0	T|0.865;C|0.135	0.135	strong	NUP54,NS,carcinoma,0,1	NUP54	48	1	NM_017426	exon2	c.A114G	p.A38A	GCTGAATGCAGAA	.	PASS	Atlas-SNP
IFRD1	3475	hgsc.bcm.edu	37	7	112102355	112102355	+	Silent	SNP	T	T	G	rs2253962	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	59	125	0	0.513043	0	T|0.746;G|0.254	0.254	strong	.	IFRD1	46	.	NM_001007245	exon9	c.T828G	p.S276S	CCTCTCTTGTGAT	.	PASS	Atlas-SNP
GZMB	3002	hgsc.bcm.edu	37	14	25101589	25101589	+	Missense_Mutation	SNP	G	G	C	rs11539752	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	304	78	391	0	0.256579	0	G|0.724;C|0.276	0.276	strong	GZMB,NS,carcinoma,0,1	GZMB	73	1	NM_004131	exon3	c.C280G	p.P94A	GGATGGGTCTTTT	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21319488	21319488	+	Silent	SNP	C	C	T	rs77176173	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	18	218	40	0.0967742	0.183486	C|0.625;T|0.375	0.375	strong	KCNJ12,NS,carcinoma,0,1	.	.	1	NM_001194958	exon3	c.C834T	p.S278S	GGCCAGCCCGCTC	.	scavenged	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039896	239039896	+	Silent	SNP	G	G	C	rs10182906	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	29	55	0	0.483333	0	G|0.154;C|0.846	0.846	strong	.	ESPNL	63	.	NM_194312	exon9	c.G2541C	p.P847P	GGCTCCGGTGCCC	.	PASS	Atlas-SNP
MRPL39	54148	hgsc.bcm.edu	37	21	26965148	26965148	+	Silent	SNP	G	G	A	rs1135638	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	21	85	0	0.28	0	G|0.221;A|0.779	0.779	strong	.	MRPL39	61	.	NM_017446	exon8	c.C897T	p.G299G	AGACACGCCCTGG	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1047002	1047002	+	Silent	SNP	A	A	G	rs3752234	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	28	28	0	1	0	A|0.401;G|0.599	0.599	strong	ABCA7,NS,carcinoma,0,1	ABCA7	174	1	NM_019112	exon14	c.A1824G	p.A608A	CGCCGCACTGCTG	.	PASS	Atlas-SNP
ATP10B	23120	hgsc.bcm.edu	37	5	159992697	159992697	+	Silent	SNP	C	C	T	rs4921302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	46	112	0	0.418182	0	C|0.920;T|0.080	0.080	strong	.	ATP10B	201	.	NM_025153	exon26	c.G4149A	p.K1383K	AGAGCTCTTTGGG	.	PASS	Atlas-SNP
PPARGC1B	133522	hgsc.bcm.edu	37	5	149200043	149200043	+	Silent	SNP	T	T	C	rs32588	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	13	34	0	0.433333	0	T|0.802;C|0.198	0.198	strong	PPARGC1B,NS,carcinoma,0,1	PPARGC1B	74	1	NM_133263	exon2	c.T126C	p.L42L	AGAACTTGACCTC	.	PASS	Atlas-SNP
SERPINB13	5275	hgsc.bcm.edu	37	18	61264298	61264298	+	Missense_Mutation	SNP	G	G	A	rs1020694	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	127	111	0	0.984496	0	G|0.178;A|0.822	0.822	strong	.	SERPINB13	51	.	NM_012397	exon8	c.G877A	p.G293S	GAGGACGGTTACG	.	PASS	Atlas-SNP
ACSL3	2181	hgsc.bcm.edu	37	2	223799388	223799388	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	113	0	0.435644	0	.	.	none	.	ACSL3	107	.	NM_203372	exon15	c.C1988T	p.S663F	TGCTTTCCGAAGC	.	PASS	Atlas-SNP
FAM154B	283726	hgsc.bcm.edu	37	15	82574879	82574879	+	Missense_Mutation	SNP	T	T	C	rs11630197	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	62	137	0	0.476923	0	T|0.779;C|0.221	0.221	strong	.	FAM154B	50	.	NM_001008226	exon3	c.T673C	p.W225R	CAACCATGGGAAA	.	PASS	Atlas-SNP
ZFP90	146198	hgsc.bcm.edu	37	16	68598007	68598007	+	Silent	SNP	A	A	G	rs1177648	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	103	97	1	0.990385	0.0103093	A|0.462;G|0.538	0.538	strong	ZFP90,NS,carcinoma,+1,1	ZFP90	67	1	NM_133458	exon4	c.A1317G	p.Q439Q	CACTCAAGATGAA	.	scavenged	Atlas-SNP
CAPN14	440854	hgsc.bcm.edu	37	2	31399988	31399988	+	Missense_Mutation	SNP	C	C	T	rs4592896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	72	125	0	0.464516	0	C|0.689;T|0.311	0.311	strong	.	CAPN14	36	.	NM_001145122	exon20	c.G1876A	p.V626I	GACAGACGTCATC	.	PASS	Atlas-SNP
TMC7	79905	hgsc.bcm.edu	37	16	19067933	19067933	+	Silent	SNP	G	G	A	rs17854511	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	102	169	0	0.459459	0	G|0.511;A|0.489	0.489	strong	.	TMC7	75	.	NM_024847	exon14	c.G1941A	p.T647T	CAAGACGGTGAGC	.	PASS	Atlas-SNP
SLU7	10569	hgsc.bcm.edu	37	5	159840980	159840980	+	Missense_Mutation	SNP	T	T	C	rs17856338	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	34	72	0	0.492754	0	T|0.995;C|0.005	0.005	strong	.	SLU7	35	.	NM_006425	exon4	c.A331G	p.I111V	TAATTATGGAATT	.	PASS	Atlas-SNP
ICAM1	3383	hgsc.bcm.edu	37	19	10385540	10385540	+	Missense_Mutation	SNP	A	A	T	rs5491	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	51	78	0	0.520408	0	A|0.924;T|0.076	0.076	strong	.	ICAM1	32	.	NM_000201	exon2	c.A167T	p.K56M	AGCCCAAGTTGTT	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549452	32549452	+	Missense_Mutation	SNP	C	C	G	rs77637983	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	89	409	0	0.367769	0	C|0.500;G|0.500	0.500	weak	HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon3	c.G534C	p.Q178H	TCCATTCTGGATC	.	PASS	Atlas-SNP
SMEK1	55671	hgsc.bcm.edu	37	14	91948043	91948043	+	Silent	SNP	T	T	C	rs17127374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	264	125	274	0	0.473485	0	T|0.932;C|0.068	0.068	strong	.	SMEK1	94	.	NM_032560	exon5	c.A792G	p.T264T	TCTGTATGTCTGA	.	PASS	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41383153	41383153	+	Missense_Mutation	SNP	A	A	G	rs2261144	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	138	225	2	0.560976	0.00888889	A|0.704;G|0.296	0.296	strong	CYP2A7,colon,carcinoma,0,1	CYP2A7	71	1	NM_000764	exon7	c.T1103C	p.M368T	AAACTCATGGGGA	.	scavenged	Atlas-SNP
PRKAG3	53632	hgsc.bcm.edu	37	2	219695487	219695487	+	Missense_Mutation	SNP	G	G	C	rs692243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	57	120	1	0.478992	0.00833333	G|0.835;C|0.165	0.165	strong	PRKAG3,NS,carcinoma,+1,1	PRKAG3	47	1	NM_017431	exon3	c.C211G	p.P71A	CTGGTGGCTCCCC	.	scavenged	Atlas-SNP
TMEM30A	55754	hgsc.bcm.edu	37	6	75965985	75965985	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	41	83	0	0.745455	0	.	.	none	TMEM30A,NS,carcinoma,+1,3	TMEM30A	40	3	NM_018247	exon7	c.C919T	p.R307X	GTTTTCGTCCATC	.	PASS	Atlas-SNP
SLC47A2	146802	hgsc.bcm.edu	37	17	19617236	19617236	+	Silent	SNP	G	G	T	rs4924792	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	112	75	0	0.982456	0	G|0.682;T|0.318	0.318	strong	SLC47A2_ENST00000350657,NS,carcinoma,-2,2	SLC47A2	61	2	NM_152908	exon4	c.C345A	p.G115G	CAGCGCGCCCCGC	.	PASS	Atlas-SNP
MCM3AP	8888	hgsc.bcm.edu	37	21	47676711	47676711	+	Silent	SNP	G	G	A	rs2839173	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	85	106	0	0.582192	0	G|0.614;A|0.386	0.386	strong	.	MCM3AP	146	.	NM_003906	exon17	c.C3924T	p.S1308S	GGTGCAGGAGATG	.	PASS	Atlas-SNP
OR8U1	219417	hgsc.bcm.edu	37	11	56143592	56143592	+	Missense_Mutation	SNP	C	C	T	rs17150411	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	45	273	0	0.214286	0	C|0.653;N|0.000	.	strong	OR8U1,colon,carcinoma,0,1	OR8U1	59	1	NM_001005204	exon1	c.C493T	p.R165C	ACCTTCCGCCTCT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801493	27801493	+	Missense_Mutation	SNP	T	T	C	rs1919127	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	69	175	0	0.442308	0	T|0.680;C|0.320	0.320	strong	.	C2orf16	357	.	NM_032266	exon1	c.T2054C	p.V685A	AGGCTGTGAAATC	.	PASS	Atlas-SNP
KIF1C	10749	hgsc.bcm.edu	37	17	4904564	4904564	+	Silent	SNP	T	T	C	rs17707385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	96	224	0	0.434389	0	C|0.070;N|0.000	0.070	strong	.	KIF1C	70	.	NM_006612	exon5	c.T231C	p.I77I	GGACATTGGAGAA	.	PASS	Atlas-SNP
ARHGEF40	55701	hgsc.bcm.edu	37	14	21551058	21551058	+	Silent	SNP	G	G	A	rs1958395	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	33	50	0	0.515625	0	G|0.422;A|0.578	0.578	strong	.	ARHGEF40	84	.	NM_018071	exon16	c.G3555A	p.A1185A	GGCTGCGCTCAGT	.	PASS	Atlas-SNP
ZNF286A	57335	hgsc.bcm.edu	37	17	15611495	15611495	+	Missense_Mutation	SNP	T	T	C	rs3760299	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	39	64	0	0.534247	0	T|0.541;C|0.459	0.459	strong	ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	NM_020652	exon5	c.T268C	p.Y90H	GAGAGCTACAACT	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107360851	107360851	+	Missense_Mutation	SNP	T	T	C	rs1523678	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	72	197	0	0.464516	0	T|0.634;C|0.366	0.366	strong	.	OR13C5	60	.	NM_001004482	exon1	c.A844G	p.I282V	AGAATATGAATAT	.	PASS	Atlas-SNP
HSPB7	27129	hgsc.bcm.edu	37	1	16344360	16344360	+	Silent	SNP	A	A	G	rs732286	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	146	132	0	1	0	A|0.366;G|0.634	0.634	strong	.	HSPB7	17	.	NM_014424	exon1	c.T99C	p.A33A	CGGGAGAGCACGG	.	PASS	Atlas-SNP
WDR17	116966	hgsc.bcm.edu	37	4	177089839	177089839	+	Missense_Mutation	SNP	C	C	G	rs140459637	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	51	150	0	0.389313	0	C|0.995;G|0.005	0.005	strong	.	WDR17	198	.	NM_170710	exon25	c.C3124G	p.L1042V	GCTGATCTTCTTC	.	PASS	Atlas-SNP
CFB	629	hgsc.bcm.edu	37	6	31914179	31914179	+	Missense_Mutation	SNP	C	C	T	rs12614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	61	131	0	0.462121	0	C|0.824;T|0.176	0.176	strong	.	CFB	33	.	NM_001710	exon2	c.C94T	p.R32W	TTGGCCCGGCCCC	.	PASS	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305646	39305646	+	Missense_Mutation	SNP	C	C	T	rs1846044	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	47	54	0	0.580247	0	C|0.949;T|0.051	0.051	strong	.	KRTAP4-5	34	.	NM_033188	exon1	c.G374A	p.C125Y	ATGCAGCAGCTGG	.	PASS	Atlas-SNP
TLN1	7094	hgsc.bcm.edu	37	9	35712003	35712003	+	Missense_Mutation	SNP	G	G	A	rs2295795	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	13	28	0	0.351351	0	G|0.785;A|0.215	0.215	strong	.	TLN1	185	.	NM_006289	exon28	c.C3680T	p.S1227L	CCTACCGAGTCAC	.	PASS	Atlas-SNP
TNFRSF1A	7132	hgsc.bcm.edu	37	12	6450945	6450945	+	Silent	SNP	T	T	C	rs767455	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	56	103	0	0.504505	0	T|0.619;C|0.381	0.381	strong	TNFRSF1A,NS,carcinoma,0,1	TNFRSF1A	39	1	NM_001065	exon1	c.A36G	p.P12P	CACCAGTGGCAGC	.	PASS	Atlas-SNP
RASGEF1C	255426	hgsc.bcm.edu	37	5	179563435	179563435	+	Silent	SNP	T	T	C	rs11546322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	79	162	1	0.389163	0.00617284	T|0.588;C|0.412	0.412	strong	RASGEF1C_ENST00000393371,NS,carcinoma,0,2	RASGEF1C	81	2	NM_175062	exon4	c.A381G	p.E127E	CGACTCTTCCTGG	.	scavenged	Atlas-SNP
OR5W2	390148	hgsc.bcm.edu	37	11	55681865	55681865	+	Missense_Mutation	SNP	T	T	C	rs12419022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	82	139	0	0.535948	0	T|0.900;C|0.100	0.100	strong	.	OR5W2	112	.	NM_001001960	exon1	c.A194G	p.H65R	GACAGATGACTGA	.	PASS	Atlas-SNP
ATG10	83734	hgsc.bcm.edu	37	5	81549216	81549216	+	Missense_Mutation	SNP	C	C	T	rs1864183	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	70	128	0	0.460526	0	C|0.552;T|0.448	0.448	strong	.	ATG10	23	.	NM_001131028	exon8	c.C635T	p.T212M	AAGCAACGTCTCA	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91811749	91811749	+	Silent	SNP	G	G	A	rs3743444	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	54	151	0	0.391304	0	G|0.848;A|0.152	0.152	strong	.	SV2B	98	.	NM_014848	exon10	c.G1287A	p.V429V	GAAGGTGTTTTTT	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50894987	50894987	+	Silent	SNP	G	G	A	rs79468232	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	20	51	0	0.487805	0	G|0.963;A|0.037	0.037	strong	.	SBF1	211	.	NM_002972	exon30	c.C4020T	p.P1340P	CGGGTCGGGAGGG	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626767	140626767	+	Silent	SNP	C	C	T	rs3096081	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	3	141	0	0.0153846	0	C|0.770;T|0.230	0.230	strong	PCDHB15,NS,carcinoma,-2,1	PCDHB15	138	1	NM_018935	exon1	c.C1621T	p.L541L	CCGGCGCTGAGCA	.	scavenged	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113527967	113527967	+	Silent	SNP	G	G	A	rs1320525	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	57	193	0	0.44186	0	G|0.623;A|0.377	0.377	strong	.	ATP11A	225	.	NM_032189	exon27	c.G3138A	p.S1046S	CTTTTCGCTTCTC	.	PASS	Atlas-SNP
GALC	2581	hgsc.bcm.edu	37	14	88459467	88459467	+	Silent	SNP	C	C	G	rs112992946	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	32	19	0	1	0	C|0.909;G|0.091	0.091	strong	.	GALC	48	.	NM_000153	exon1	c.G42C	p.A14A	AGCTTTCGCTCGG	.	PASS	Atlas-SNP
MMP20	9313	hgsc.bcm.edu	37	11	102477377	102477377	+	Missense_Mutation	SNP	G	G	T	rs1784424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	142	143	0	0.993007	0	G|0.598;T|0.402	0.402	strong	.	MMP20	52	.	NM_004771	exon6	c.C842A	p.T281N	GGCAGAGTGGGCT	.	PASS	Atlas-SNP
OR8J3	81168	hgsc.bcm.edu	37	11	55904382	55904382	+	Missense_Mutation	SNP	A	A	C	rs17150102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	103	202	1	0.481308	0.00495049	A|0.900;C|0.100	0.100	strong	OR8J3,NS,carcinoma,0,1	OR8J3	112	1	NM_001004064	exon1	c.T813G	p.D271E	CATCTTATCAGTA	.	scavenged	Atlas-SNP
SPDYE4	388333	hgsc.bcm.edu	37	17	8658901	8658901	+	Missense_Mutation	SNP	G	G	A	rs74844184	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	36	72	0	0.371134	0	G|0.952;A|0.048	0.048	strong	.	SPDYE4	22	.	NM_001128076	exon4	c.C422T	p.A141V	AAATACGCTATGA	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107040572	107040572	+	Missense_Mutation	SNP	T	T	C	rs3870235		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	175	969	1	0.94086	0.00103199	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,4	RGPD3	316	4	NM_001144013	exon20	c.A3851G	p.H1284R	TCAAAGTGGAAAA	.	scavenged	Atlas-SNP
AGAP1	116987	hgsc.bcm.edu	37	2	236708166	236708166	+	Silent	SNP	C	C	T	rs2292708	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	33	75	0	0.55	0	C|0.787;T|0.213	0.213	strong	AGAP1,NS,carcinoma,0,1	AGAP1	95	1	NM_014914	exon8	c.C957T	p.T319T	GTTCACCGTGAGT	.	PASS	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	37	17	32957114	32957114	+	Missense_Mutation	SNP	G	G	A	rs56879769	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	84	131	0	0.518519	0	G|0.952;A|0.048	0.048	strong	.	TMEM132E	122	.	NM_207313	exon6	c.G1156A	p.V386I	GGCCTCGTCCTGG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506627	195506627	+	Missense_Mutation	SNP	T	T	G	rs145875920	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	21	23	8	0.160305	0.347826	T|0.808;G|0.192	0.192	strong	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.A11824C	p.T3942P	AGGAAGTGCTGGT	.	scavenged	Atlas-SNP
CNOT6	57472	hgsc.bcm.edu	37	5	179996111	179996111	+	Silent	SNP	C	C	T	rs6877400	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	88	74	0	1	0	C|0.128;T|0.872	0.872	strong	.	CNOT6	47	.	NM_015455	exon10	c.C1029T	p.S343S	TGTAGCCGGAAAG	.	PASS	Atlas-SNP
TTC21B	79809	hgsc.bcm.edu	37	2	166773971	166773971	+	Silent	SNP	G	G	A	rs6750044	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	78	217	0	0.503226	0	G|0.668;A|0.332	0.332	strong	.	TTC21B	130	.	NM_024753	exon14	c.C1695T	p.Y565Y	CAAATGGTATAAA	.	PASS	Atlas-SNP
KTN1	3895	hgsc.bcm.edu	37	14	56096731	56096731	+	Silent	SNP	A	A	G	rs2274075	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	70	121	0	0.496454	0	A|0.925;G|0.075	0.075	strong	KTN1_ENST00000416613,NS,carcinoma,+1,1	KTN1	147	1	NM_004986	exon7	c.A1137G	p.R379R	AGATCGAATTGGA	.	PASS	Atlas-SNP
AK4	205	hgsc.bcm.edu	37	1	65690461	65690461	+	Silent	SNP	G	G	A	rs4915685	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	73	141	0	0.506944	0	G|0.726;A|0.274	0.274	strong	.	AK4	22	.	NM_203464	exon5	c.G465A	p.P155P	TGAACCGTTAGTC	.	PASS	Atlas-SNP
DUXA	503835	hgsc.bcm.edu	37	19	57669827	57669827	+	Missense_Mutation	SNP	G	G	A	rs140589597	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	37	100	0	0.4625	0	G|0.999;A|0.001	0.001	strong	DUXA,NS,carcinoma,+1,3	DUXA	46	3	NM_001012729	exon4	c.C307T	p.R103W	GACACCGTCTGGC	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	37	13	32912299	32912299	+	Silent	SNP	T	T	C	rs543304	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	27	43	0	0.490909	0	C|0.187;N|0.000;T|0.813	0.187	strong	.	BRCA2	812	.	NM_000059	exon11	c.T3807C	p.V1269V	TTCTGTTGTTTCA	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3176063	3176063	+	Silent	SNP	C	C	T	rs2230162	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	115	93	0	1	0	T|0.164;G|0.282	0.164	strong	.	MYOM1	192	.	NM_003803	exon6	c.G999A	p.G333G	GTGCATCCCATAT	.	PASS	Atlas-SNP
SLC22A18	5002	hgsc.bcm.edu	37	11	2929502	2929502	+	Missense_Mutation	SNP	G	G	T	rs143044180	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	45	92	0	0.555556	0	G|0.998;T|0.002	0.002	strong	SLC22A18,NS,carcinoma,0,1	SLC22A18	20	1	NM_002555	exon3	c.G184T	p.G62C	GCCTTCGGCTACC	.	PASS	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285611	16285611	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	4	125	2	0.031746	0.016	.	.	none	UBB,rectum,carcinoma,+2,2	UBB	30	2	NM_018955	exon2	c.C390T	p.R130R	TGGCCGCACTCTT	.	scavenged	Atlas-SNP
MTUS2	23281	hgsc.bcm.edu	37	13	29675049	29675049	+	Silent	SNP	A	A	T	rs140464903	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	40	72	0	0.45977	0	A|0.965;T|0.035	0.035	strong	MTUS2_ENST00000431530,NS,carcinoma,0,1	MTUS2	279	1	NM_001033602	exon3	c.A2616T	p.S872S	CTCCTCAGTCTCC	.	PASS	Atlas-SNP
FGD6	55785	hgsc.bcm.edu	37	12	95602805	95602805	+	Missense_Mutation	SNP	C	C	A	rs117209224	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	78	202	0	0.445714	0	C|0.993;A|0.007	0.007	strong	.	FGD6	127	.	NM_018351	exon2	c.G2255T	p.R752L	TAATGGCGTATAT	.	PASS	Atlas-SNP
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42832683	42832683	+	Silent	SNP	G	G	A	rs10456519	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	28	40	0	0.474576	0	G|0.989;A|0.011	0.011	strong	.	.	.	.	NM_015349	exon12	c.G2739A	p.Q913Q	AGTGCAGTACCAG	.	PASS	Atlas-SNP
N4BP2	55728	hgsc.bcm.edu	37	4	40119501	40119501	+	Silent	SNP	T	T	C	rs1128372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	31	71	0	0.469697	0	T|0.851;C|0.149	0.149	strong	.	N4BP2	166	.	NM_018177	exon8	c.T1677C	p.H559H	CATTCATGGGGTA	.	PASS	Atlas-SNP
ACTN4	81	hgsc.bcm.edu	37	19	39219780	39219780	+	Silent	SNP	T	T	C	rs1136956	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	61	144	0	0.451852	0	T|0.788;C|0.212	0.212	strong	.	ACTN4	69	.	NM_004924	exon20	c.T2563C	p.L855L	AAGGTCTTAGCAG	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50533841	50533841	+	Missense_Mutation	SNP	G	G	C	rs11101094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	33	95	0	0.478261	0	G|0.907;C|0.093	0.093	strong	.	C10orf71	179	.	NM_001135196	exon3	c.G3251C	p.G1084A	CCCCTGGAGGACC	.	PASS	Atlas-SNP
PTBP1	5725	hgsc.bcm.edu	37	19	808577	808577	+	Silent	SNP	C	C	T	rs148751202	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	33	56	0	0.532258	0	C|0.988;T|0.012	0.012	strong	.	PTBP1	43	.	NM_002819	exon13	c.C1278T	p.H426H	GCTGCACGGGAAG	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115933980	115933980	+	Missense_Mutation	SNP	C	C	A	rs1128116	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	43	103	0	0.467391	0	C|0.940;A|0.060	0.060	strong	.	FKBP15	128	.	NM_015258	exon24	c.G2539T	p.A847S	GGAGGGCTAAACA	.	PASS	Atlas-SNP
CHRNA5	1138	hgsc.bcm.edu	37	15	78882925	78882925	+	Missense_Mutation	SNP	G	G	A	rs16969968	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	87	106	0	0.977528	0	G|0.771;A|0.229	0.229	strong	.	CHRNA5	48	.	NM_000745	exon5	c.G1192A	p.D398N	GCGCTCGATTCTA	.	PASS	Atlas-SNP
ADCK1	57143	hgsc.bcm.edu	37	14	78374172	78374172	+	Silent	SNP	C	C	T	rs34272020	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	46	76	0	0.505495	0	C|0.893;T|0.107	0.107	strong	.	ADCK1	81	.	NM_020421	exon7	c.C768T	p.S256S	CCTGTCCACGGAG	.	PASS	Atlas-SNP
NSD1	64324	hgsc.bcm.edu	37	5	176721879	176721879	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	17	34	0	0.404762	0	.	.	none	.	NSD1	416	.	NM_022455	exon23	c.G7510A	p.V2504I	AGAGCTGTTGAGA	.	PASS	Atlas-SNP
CRAMP1L	57585	hgsc.bcm.edu	37	16	1706435	1706435	+	Silent	SNP	C	C	T	rs61739874	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	18	32	0	0.6	0	C|0.900;T|0.100	0.100	strong	.	CRAMP1L	60	.	NM_020825	exon9	c.C1677T	p.D559D	TCTAGACCCCTTG	.	PASS	Atlas-SNP
ANO1	55107	hgsc.bcm.edu	37	11	69933891	69933891	+	Missense_Mutation	SNP	G	G	A	rs76718681	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	76	113	0	0.481013	0	G|0.951;A|0.049	0.049	strong	ANO1_ENST00000355303,NS,carcinoma,-2,2	ANO1	156	2	NM_018043	exon2	c.G142A	p.E48K	GATGCCGAGTGCA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144857010	144857010	+	Missense_Mutation	SNP	T	T	C	rs3853916	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	846	23	862	6	0.0271868	0.00696056	.	.	weak	PDE4DIP,NS,carcinoma,0,1	PDE4DIP	817	1	NM_014644	exon40	c.A6475G	p.T2159A	GAGGGGTCTTCAT	.	scavenged	Atlas-SNP
CPZ	8532	hgsc.bcm.edu	37	4	8616096	8616096	+	Silent	SNP	T	T	C	rs1131140	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	91	86	0	0.98913	0	T|0.457;C|0.543	0.543	strong	.	CPZ	95	.	NM_001014447	exon9	c.T1374C	p.D458D	GTCCGATTTCAAC	.	PASS	Atlas-SNP
SCAF4	57466	hgsc.bcm.edu	37	21	33044378	33044378	+	Silent	SNP	G	G	A	rs73201505	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	35	54	0	0.603448	0	G|0.986;A|0.014	0.014	strong	.	SCAF4	142	.	NM_020706	exon20	c.C2778T	p.G926G	CCCTGGGCCCCCG	.	PASS	Atlas-SNP
MTR	4548	hgsc.bcm.edu	37	1	237058744	237058744	+	Silent	SNP	C	C	A	rs12070777	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	52	157	0	0.412698	0	C|0.658;A|0.342	0.342	strong	.	MTR	127	.	NM_000254	exon31	c.C3492A	p.R1164R	CCTGCGCAGGCTG	.	PASS	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62848445	62848445	+	Silent	SNP	A	A	G	rs11231340	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	59	122	0	0.450382	0	A|0.539;G|0.460	0.460	strong	SLC22A24_ENST00000417740,NS,carcinoma,0,1	SLC22A24	31	1	NM_001136506	exon9	c.T1545C	p.L515L	TTCTGGAAGGAGG	.	PASS	Atlas-SNP
CCNT1	904	hgsc.bcm.edu	37	12	49087656	49087656	+	Silent	SNP	G	G	C	rs3013	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	50	108	0	0.520833	0	G|0.788;C|0.212	0.212	strong	.	CCNT1	55	.	NM_001240	exon9	c.C1341G	p.P447P	CCGCTCGGGGTTT	.	PASS	Atlas-SNP
WDFY4	57705	hgsc.bcm.edu	37	10	50040722	50040722	+	Silent	SNP	C	C	A	rs12761517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	57	63	0	0.612903	0	A|0.092;C|0.908;T|0.000	0.092	strong	WDFY4,cerebellum,primitive_neuroectodermal_tumour-medulloblastoma,0,3	WDFY4	205	3	NM_020945	exon39	c.C6631A	p.R2211R	CCCGGGCGGCAGG	.	PASS	Atlas-SNP
ZNF142	7701	hgsc.bcm.edu	37	2	219513782	219513782	+	Silent	SNP	T	T	C	rs4674322	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	31	61	0	0.5	0	T|0.861;C|0.139	0.139	strong	.	ZNF142	190	.	NM_001105537	exon6	c.A849G	p.P283P	GGGTAATGGCTCT	.	PASS	Atlas-SNP
TMEM106B	54664	hgsc.bcm.edu	37	7	12269417	12269417	+	Missense_Mutation	SNP	C	C	G	rs3173615	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	274	273	286	0	0.99635	0	C|0.481;G|0.519	0.519	strong	TMEM106B,NS,adenoma,0,1	TMEM106B	34	1	NM_001134232	exon5	c.C554G	p.T185S	ACATAACCATTAT	.	PASS	Atlas-SNP
CEACAM3	1084	hgsc.bcm.edu	37	19	42312933	42312933	+	Silent	SNP	G	G	A	rs3752172	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	110	244	1	0.526316	0.00409836	G|0.840;A|0.160	0.160	strong	.	CEACAM3	37	.	NM_001815	exon3	c.G507A	p.A169A	GGCCGCGCTGGTG	.	PASS	Atlas-SNP
CELA2A	63036	hgsc.bcm.edu	37	1	15793913	15793913	+	Silent	SNP	G	G	A	rs1042010	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	61	39	0	0.953125	0	G|0.799;A|0.201	0.201	strong	.	CELA2A	32	.	NM_033440	exon7	c.G672A	p.A224A	TCAGGCGTCTGAC	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117848201	117848201	+	Silent	SNP	T	T	C	rs3827815	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	64	112	0	0.561404	0	T|0.907;C|0.093	0.093	strong	TNC,NS,carcinoma,0,1	TNC	282	1	NM_002160	exon3	c.A1809G	p.Q603Q	GACGCATTGTCCT	.	PASS	Atlas-SNP
PDGFRB	5159	hgsc.bcm.edu	37	5	149499672	149499672	+	Silent	SNP	T	T	C	rs246395	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	20	49	0	0.425532	0	T|0.745;C|0.255	0.255	strong	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	NM_002609	exon19	c.A2601G	p.L867L	CCACTTTAAAGGC	.	PASS	Atlas-SNP
TMEM244	253582	hgsc.bcm.edu	37	6	130152479	130152479	+	Silent	SNP	T	T	C	rs7758540	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	121	181	0	0.98374	0	T|0.428;C|0.572	0.572	strong	C6orf191,NS,carcinoma,-1,1	.	.	1	NM_001010876	exon5	c.A372G	p.S124S	CAATTTTGATATA	.	PASS	Atlas-SNP
LRIF1	55791	hgsc.bcm.edu	37	1	111494194	111494194	+	Missense_Mutation	SNP	C	C	T	rs2232041	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	60	108	0	0.517241	0	C|0.813;T|0.187	0.187	strong	.	LRIF1	65	.	NM_018372	exon2	c.G1312A	p.A438T	GATTGGCCATGGA	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26749831	26749831	+	Silent	SNP	G	G	A	rs2230377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	65	75	0	1	0	G|0.780;A|0.220	0.220	strong	.	ITPR2	270	.	NM_002223	exon31	c.C4239T	p.D1413D	GCAGTCGTCATGG	.	PASS	Atlas-SNP
POLRMT	5442	hgsc.bcm.edu	37	19	621148	621148	+	Silent	SNP	C	C	T	rs143192895	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	26	74	0	0.302326	0	C|0.997;T|0.003	0.003	strong	.	POLRMT	91	.	NM_005035	exon10	c.G2550A	p.G850G	CTTCAACCCCGTG	.	PASS	Atlas-SNP
ZFYVE9	9372	hgsc.bcm.edu	37	1	52803595	52803595	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	73	145	0	0.570312	0	.	.	none	.	ZFYVE9	131	.	NM_004799	exon16	c.C3822T	p.N1274N	CAAGAACGTTAGC	.	PASS	Atlas-SNP
CTNNA1	1495	hgsc.bcm.edu	37	5	138266546	138266546	+	Silent	SNP	G	G	A	rs1059110	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	176	231	1	0.988764	0.004329	G|0.693;A|0.307	0.307	strong	.	CTNNA1	114	.	NM_001903	exon16	c.G2220A	p.S740S	TACATCGGATGTC	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4821300	4821300	+	Missense_Mutation	SNP	C	C	G	rs11549839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	70	130	0	0.555556	0	C|0.987;G|0.013	0.013	strong	.	.	.	.	NM_014855	exon3	c.C281G	p.S94C	AGATGTCCCCCTC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168103863	168103863	+	Silent	SNP	G	G	A	rs7581012	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	79	127	0	0.593985	0	G|0.836;A|0.164	0.164	strong	XIRP2,right_upper_lobe,carcinoma,+1,1	XIRP2	914	1	NM_152381	exon9	c.G5961A	p.A1987A	GCCAGCGGCCAAG	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	56000471	56000471	+	Missense_Mutation	SNP	G	G	A	rs11227599	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	41	83	0	0.554054	0	G|0.820;A|0.180	0.180	strong	OR5T2,NS,carcinoma,0,1	OR5T2	107	1	NM_001004746	exon1	c.C191T	p.T64I	AAGATAGTCTGCA	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169362557	169362557	+	Missense_Mutation	SNP	C	C	G	rs13151700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	69	173	0	0.445161	0	C|0.615;G|0.385	0.385	strong	.	DDX60L	116	.	NM_001012967	exon10	c.G1225C	p.V409L	TTCCAACGTTAAA	.	PASS	Atlas-SNP
COL6A2	1292	hgsc.bcm.edu	37	21	47545913	47545913	+	Silent	SNP	G	G	A	rs2839114	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	59	103	0	0.556604	0	G|0.690;A|0.310	0.310	strong	.	COL6A2	351	.	NM_058175	exon26	c.G2184A	p.V728V	TGCGGTGGTCATC	.	PASS	Atlas-SNP
LMOD1	25802	hgsc.bcm.edu	37	1	201869257	201869257	+	Missense_Mutation	SNP	G	G	A	rs2820312	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	283	141	272	0	0.498233	0	G|0.763;A|0.237	0.237	strong	.	LMOD1	59	.	NM_012134	exon2	c.C884T	p.T295M	CTGGGCGTCTGTT	.	PASS	Atlas-SNP
GNRH1	2796	hgsc.bcm.edu	37	8	25279148	25279148	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	67	195	0	0.446667	0	.	.	none	.	GNRH1	8	.	NM_000825	exon2	c.C190T	p.R64C	CGAAGCGTTGGGT	.	PASS	Atlas-SNP
FAM171B	165215	hgsc.bcm.edu	37	2	187615953	187615953	+	Missense_Mutation	SNP	G	G	A	rs201119796		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	29	83	0	0.376623	0	G|0.999;A|0.001	0.001	weak	FAM171B,rectum,carcinoma,-1,2	FAM171B	146	2	NM_177454	exon5	c.G817A	p.V273I	ATTCAAGTTTCTC	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	125115420	125115420	+	Missense_Mutation	SNP	G	G	A	rs56132579	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	34	77	0	0.4	0	G|0.947;A|0.053	0.053	strong	.	FER1L6	268	.	NM_001039112	exon39	c.G5159A	p.R1720Q	TCCCTCGAGCAGC	.	PASS	Atlas-SNP
ADORA3	140	hgsc.bcm.edu	37	1	112042787	112042787	+	Missense_Mutation	SNP	T	T	G	rs35511654	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	75	167	0	0.524476	0	T|0.898;G|0.102	0.102	strong	ADORA3,caecum,carcinoma,0,1	ADORA3	104	1	NM_000677	exon2	c.A742C	p.I248L	TGATGATAGATAA	.	PASS	Atlas-SNP
ZNF568	374900	hgsc.bcm.edu	37	19	37441462	37441462	+	Silent	SNP	T	T	C	rs546589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	21	40	0	0.525	0	T|0.450;C|0.550	0.550	strong	.	ZNF568	106	.	NM_198539	exon7	c.T1407C	p.T469T	TCACACTGGAGAG	.	PASS	Atlas-SNP
KRT27	342574	hgsc.bcm.edu	37	17	38935812	38935812	+	Missense_Mutation	SNP	A	A	G	rs981684	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	40	66	0	0.5	0	A|0.443;G|0.557	0.557	strong	.	KRT27	41	.	NM_181537	exon5	c.T914C	p.I305T	ATCTCGATAAGCT	.	PASS	Atlas-SNP
MYB	4602	hgsc.bcm.edu	37	6	135518402	135518402	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	70	105	0	0.972222	0	.	.	none	.	MYB	137	.	NM_001130173	exon10	c.G1507A	p.V503I	GCTGACGTCAGCA	.	PASS	Atlas-SNP
ANK1	286	hgsc.bcm.edu	37	8	41585438	41585438	+	Silent	SNP	G	G	A	rs2304871	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	56	72	0	0.509091	0	G|0.763;A|0.237	0.237	strong	.	ANK1	497	.	NM_001142446	exon4	c.C414T	p.N138N	CTGGGCGTTGACG	.	PASS	Atlas-SNP
OR56A5	390084	hgsc.bcm.edu	37	11	5989282	5989282	+	Missense_Mutation	SNP	G	G	A	rs116908319	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	42	98	0	0.442105	0	G|0.980;A|0.020	0.020	strong	.	.	.	.	NM_001146033	exon1	c.C443T	p.A148V	AAGATGGCAGCCC	.	PASS	Atlas-SNP
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105897003	105897003	+	Silent	SNP	G	G	A	rs2241799	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	97	200	0	0.497436	0	G|0.853;A|0.147	0.147	strong	.	TGFBRAP1	70	.	NM_004257	exon6	c.C1299T	p.N433N	GACCTCGTTCAGG	.	PASS	Atlas-SNP
ATF4	468	hgsc.bcm.edu	37	22	39917787	39917787	+	Missense_Mutation	SNP	T	T	G	rs141575018	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	30	76	0	0.491803	0	T|1.000;G|0.000	0.000	weak	.	ATF4	27	.	NM_001675	exon2	c.T236G	p.F79C	ATGCCTTCTCCGG	.	PASS	Atlas-SNP
TOPAZ1	375337	hgsc.bcm.edu	37	3	44284584	44284584	+	Missense_Mutation	SNP	G	G	A	rs9284879	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	41	85	0	0.506173	0	G|0.462;A|0.538	0.538	strong	C3orf77_ENST00000309765,NS,carcinoma,0,2	.	.	2	NM_001145030	exon2	c.G586A	p.V196I	ATTAAGGTTGAAT	.	PASS	Atlas-SNP
POU5F1B	5462	hgsc.bcm.edu	37	8	128428656	128428656	+	Missense_Mutation	SNP	A	A	C	rs13273814	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	116	107	0	0.983051	0	A|0.823;C|0.177	0.177	strong	.	POU5F1B	32	.	NM_001159542	exon1	c.A545C	p.K182T	GCCAAAAGACCAT	.	PASS	Atlas-SNP
GYLTL1B	120071	hgsc.bcm.edu	37	11	45948962	45948962	+	Silent	SNP	C	C	T	rs138897549	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	32	84	0	0.385542	0	C|1.000;T|0.000	0.000	strong	.	GYLTL1B	45	.	NM_152312	exon11	c.C1422T	p.F474F	GCATTTCGTCGAG	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56466227	56466227	+	Missense_Mutation	SNP	A	A	G	rs7259764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	76	125	1	0.5	0.008	A|0.922;G|0.078	0.078	strong	NLRP8_ENST00000291971,NS,carcinoma,+1,2	NLRP8	225	2	NM_176811	exon3	c.A803G	p.Q268R	GATCTCAGGACCT	.	scavenged	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57076895	57076895	+	Missense_Mutation	SNP	T	T	C	rs35950335	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	34	75	0	0.566667	0	T|0.968;C|0.032	0.032	strong	.	TNKS1BP1	148	.	NM_033396	exon6	c.A3290G	p.Q1097R	TCTCGCTGGGGGC	.	PASS	Atlas-SNP
TECTA	7007	hgsc.bcm.edu	37	11	121030874	121030874	+	Missense_Mutation	SNP	A	A	G	rs147354818	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	65	97	0	0.524194	0	A|0.999;G|0.001	0.001	strong	.	TECTA	329	.	NM_005422	exon14	c.A4720G	p.I1574V	CCATTTATAACTG	.	PASS	Atlas-SNP
TTC29	83894	hgsc.bcm.edu	37	4	147788709	147788709	+	Missense_Mutation	SNP	C	C	T	rs10013280	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	204	263	0	0.985507	0	C|0.648;T|0.352	0.352	strong	TTC29,NS,carcinoma,0,1	TTC29	63	1	NM_031956	exon8	c.G826A	p.A276T	AAGAGGCTTCCGC	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080336	194080336	+	Silent	SNP	G	G	A	rs4974533	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	125	203	0	0.527426	0	G|0.792;A|0.208	0.208	strong	LRRC15_ENST00000439944,NS,adenoma,0,1	LRRC15	137	1	NM_001135057	exon3	c.C1455T	p.P485P	CACCTCGGGGACA	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31090094	31090094	+	Missense_Mutation	SNP	G	G	A	rs78522165	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	58	131	0	0.504348	0	A|0.052;C|0.000;G|0.948	0.052	strong	.	ZNF646	133	.	NM_014699	exon2	c.G2449A	p.A817T	TGGCAGGCTGGGG	.	PASS	Atlas-SNP
OR2J2	26707	hgsc.bcm.edu	37	6	29142054	29142054	+	Silent	SNP	C	C	G	rs3129159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	314	155	306	1	0.493631	0.00326797	C|0.567;G|0.433	0.433	strong	.	OR2J2	51	.	NM_030905	exon1	c.C642G	p.L214L	CATTCTCATTCTC	.	PASS	Atlas-SNP
SPSB1	80176	hgsc.bcm.edu	37	1	9416151	9416151	+	Silent	SNP	G	G	A	rs9435243	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	6	107	0	0.0666667	0	G|0.765;A|0.235	0.235	strong	.	SPSB1	22	.	NM_025106	exon2	c.G201A	p.V67V	CTTTGTGAAGGAG	.	PASS	Atlas-SNP
DOCK6	57572	hgsc.bcm.edu	37	19	11347493	11347493	+	Silent	SNP	T	T	C	rs737337	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	31	68	0	0.476923	0	T|0.740;C|0.260	0.260	strong	.	DOCK6	104	.	NM_020812	exon19	c.A2136G	p.T712T	CACGGCTGTGAGC	.	PASS	Atlas-SNP
APOBEC1	339	hgsc.bcm.edu	37	12	7805154	7805154	+	Missense_Mutation	SNP	G	G	A	rs61753204	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	44	86	0	0.55	0	G|0.989;A|0.011	0.011	strong	.	APOBEC1	43	.	NM_001644	exon3	c.C322T	p.P108S	CACCAGGGTGCCG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8176919	8176919	+	Silent	SNP	C	C	T	rs4804264	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	147	133	0	0.986577	0	C|0.388;N|0.000	.	strong	.	FBN3	300	.	NM_032447	exon30	c.G3903A	p.P1301P	ACTCCCCGGGATG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168099775	168099775	+	Missense_Mutation	SNP	C	C	G	rs16853305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	258	121	282	0	0.468992	0	C|0.784;G|0.216	0.216	strong	.	XIRP2	914	.	NM_152381	exon9	c.C1873G	p.P625A	ACCCAACCCATCG	.	PASS	Atlas-SNP
SRP14	6727	hgsc.bcm.edu	37	15	40330518	40330518	+	Silent	SNP	T	T	G	rs1059395	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	47	83	0	0.516484	0	T|0.867;G|0.133	0.133	strong	.	SRP14	11	.	NM_003134	exon3	c.A175C	p.R59R	TAGCTCTTAACAG	.	PASS	Atlas-SNP
LRRC29	26231	hgsc.bcm.edu	37	16	67241930	67241930	+	Missense_Mutation	SNP	C	C	T	rs34595673	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	54	90	0	0.486486	0	C|0.909;T|0.091	0.091	strong	.	LRRC29	13	.	NM_001004055	exon5	c.G349A	p.G117S	CCAAGCCGTTGTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228412227	228412227	+	Silent	SNP	T	T	C	rs1771480	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	100	202	1	0.497512	0.00495049	T|0.612;C|0.388	0.388	strong	.	OBSCN	2142	.	NM_001271223	exon10	c.T2997C	p.S999S	AGCCAGTGCCACA	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37455583	37455583	+	Silent	SNP	G	G	A	rs75413857	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	621	16	722	1	0.0257649	0.00138504	A|1.000;|0.000	1.000	weak	ANKRD30A,NS,haematopoietic_neoplasm,+1,1	ANKRD30A	448	1	NM_052997	exon19	c.G1947A	p.A649A	GGCTGCGCATCAA	.	scavenged	Atlas-SNP
MACF1	23499	hgsc.bcm.edu	37	1	39549942	39549942	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	74	76	0	0.925	0	.	.	none	MACF1_ENST00000361689,caecum,carcinoma,-1,1	MACF1	909	1	NM_012090	exon3	c.C52T	p.R18W	AGTGAGCGGTCTT	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248084440	248084440	+	Missense_Mutation	SNP	T	T	G	rs111379878	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	578	21	494	0	0.0363322	0	T|0.988;G|0.012	0.012	strong	OR2T8,NS,other,0,1	OR2T8	67	1	NM_001005522	exon1	c.T121G	p.S41A	GGCAATTCCCTCA	.	scavenged	Atlas-SNP
FHOD1	29109	hgsc.bcm.edu	37	16	67265360	67265360	+	Silent	SNP	C	C	A	rs6499118	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	63	145	0	0.529412	0	C|0.755;A|0.245	0.245	strong	.	FHOD1	86	.	NM_013241	exon16	c.G2478T	p.A826A	GCCCACCGCTAGG	.	PASS	Atlas-SNP
ZCCHC14	23174	hgsc.bcm.edu	37	16	87446368	87446368	+	Silent	SNP	C	C	T	rs2241615	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	84	159	0	0.502994	0	C|0.858;T|0.142	0.142	strong	.	ZCCHC14	87	.	NM_015144	exon12	c.G1548A	p.P516P	TCTTTCCGGCTTG	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5352949	5352949	+	Missense_Mutation	SNP	G	G	C	rs76882791	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	13	34	0	0.393939	0	G|0.869;C|0.131	0.131	strong	.	TNRC18	311	.	NM_001080495	exon27	c.C7573G	p.L2525V	GGGCGAGGTCCCC	.	PASS	Atlas-SNP
SLC38A10	124565	hgsc.bcm.edu	37	17	79220224	79220224	+	Missense_Mutation	SNP	G	G	C	rs2725405	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	41	59	0	0.66129	0	G|0.561;C|0.439	0.439	strong	.	SLC38A10	133	.	NM_001037984	exon16	c.C2492G	p.A831G	AGCTTGGCCTGGG	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605266	32605266	+	Missense_Mutation	SNP	G	G	A	rs1047992	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	23	108	0	0.237113	0	G|0.879;A|0.121	0.121	strong	.	HLA-DQA1	52	.	NM_002122	exon1	c.G31A	p.A11T	CTGGGGGCCCTCG	.	PASS	Atlas-SNP
KDM8	79831	hgsc.bcm.edu	37	16	27231740	27231740	+	Silent	SNP	G	G	C	rs34577370	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	106	124	1	0.990654	0.00806452	G|0.891;C|0.109	0.109	strong	.	.	.	.	NM_001145348	exon7	c.G1134C	p.L378L	CCGGCTGTATTCC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632781	32632781	+	Missense_Mutation	SNP	A	A	T	rs74184882	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	22	0	0	0.666667	.	CCC|1.000;|0.000	.	alt	.	HLA-DQB1	15	.	NM_002123	exon2	c.T173A	p.L58H	GTCACAAGACGCA	.	PASS	Atlas-SNP
IDUA	3425	hgsc.bcm.edu	37	4	995868	995868	+	Silent	SNP	C	C	T	rs114806891	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	18	30	0	0.428571	0	C|0.965;T|0.035	0.035	strong	.	IDUA	33	.	NM_000203	exon7	c.C891T	p.N297N	TTACAACGACGAG	.	PASS	Atlas-SNP
FABP2	2169	hgsc.bcm.edu	37	4	120241849	120241849	+	Silent	SNP	A	A	G	rs4834770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	16	42	0	0.5	0	A|0.422;G|0.578	0.578	strong	.	FABP2	21	.	NM_000134	exon2	c.T216C	p.N72N	TGCTAGATTGTAA	.	PASS	Atlas-SNP
ANKRD6	22881	hgsc.bcm.edu	37	6	90340276	90340276	+	Silent	SNP	G	G	A	rs3210511	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	73	117	0	1	0	G|0.381;A|0.619	0.619	strong	.	ANKRD6	51	.	NM_001242809	exon16	c.G1737A	p.S579S	GCTGTCGTCTTCT	.	PASS	Atlas-SNP
CRB2	286204	hgsc.bcm.edu	37	9	126133497	126133497	+	Silent	SNP	C	C	T	rs13290763	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	97	139	0	0.487437	0	C|0.763;T|0.237	0.237	strong	.	CRB2	86	.	NM_173689	exon8	c.C2076T	p.S692S	TGACTCCGCAGCT	.	PASS	Atlas-SNP
GSTA4	2941	hgsc.bcm.edu	37	6	52849325	52849325	+	Silent	SNP	C	C	T	rs1802061	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	61	151	0	0.417808	0	C|0.959;T|0.041	0.041	strong	.	GSTA4	20	.	NM_001512	exon5	c.G351A	p.Q117Q	CTTTTGCTGATCA	.	PASS	Atlas-SNP
FANCD2	2177	hgsc.bcm.edu	37	3	10088404	10088404	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	349	38	288	1	0.108883	0.00347222	.	.	none	FANCD2_ENST00000419585,caecum,carcinoma,0,2	FANCD2	253	2	NM_001018115	exon15	c.C1275T	p.Y425Y	TCATTACTTAGTA	.	scavenged	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	37	12	657404	657404	+	Missense_Mutation	SNP	G	G	A	rs11063529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	42	137	0	0.403846	0	G|0.799;A|0.201	0.201	strong	.	B4GALNT3	64	.	NM_173593	exon9	c.G794A	p.R265Q	GGCGACGGAACGA	.	PASS	Atlas-SNP
TJP3	27134	hgsc.bcm.edu	37	19	3728609	3728609	+	Missense_Mutation	SNP	G	G	A	rs2067019	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	65	59	0	0.984848	0	G|0.787;A|0.213	0.213	strong	TJP3,colon,carcinoma,0,1	TJP3	79	1	NM_001267561	exon3	c.G83A	p.R28H	ACCCCCGCCGGGG	.	PASS	Atlas-SNP
DUS2L	54920	hgsc.bcm.edu	37	16	68088485	68088485	+	Silent	SNP	A	A	G	rs11555011	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	299	132	269	0	0.441472	0	A|0.876;G|0.124	0.124	strong	.	DUS2L	39	.	NM_001271762	exon5	c.A273G	p.S91S	GACTTCAGACGCA	.	PASS	Atlas-SNP
USP49	25862	hgsc.bcm.edu	37	6	41773735	41773735	+	Silent	SNP	G	G	A	rs6926173	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	14	53	0	0.388889	0	G|0.764;A|0.236	0.236	strong	.	USP49	58	.	NM_018561	exon4	c.C987T	p.G329G	GCAGAAGCCCTCC	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44118191	44118191	+	Missense_Mutation	SNP	G	G	A	rs34163641	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	32	44	0	1	0	G|0.784;A|0.216	0.216	strong	.	SRRM5	38	.	NM_001145641	exon1	c.G1918A	p.D640N	GAGAGCGACCCCA	.	PASS	Atlas-SNP
SERPINH1	871	hgsc.bcm.edu	37	11	75277757	75277757	+	Silent	SNP	C	C	G	rs650241	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	23	45	0	0.377049	0	C|0.668;G|0.332	0.332	strong	SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	NM_001235	exon2	c.C363G	p.S121S	CAACTCCACGGCG	.	PASS	Atlas-SNP
ZNF77	58492	hgsc.bcm.edu	37	19	2936535	2936535	+	Nonsense_Mutation	SNP	G	G	A	rs35699176	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	43	74	0	0.52439	0	G|0.965;A|0.035	0.035	strong	.	ZNF77	47	.	NM_021217	exon3	c.C298T	p.Q100X	GCCTCTGTGGGAT	.	PASS	Atlas-SNP
OGFRL1	79627	hgsc.bcm.edu	37	6	72006512	72006512	+	Silent	SNP	T	T	C	rs2273888	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	13	115	0	0.164557	0	T|0.820;C|0.180	0.180	strong	.	OGFRL1	44	.	NM_024576	exon6	c.T684C	p.H228H	TCAGCATCTGAAT	.	PASS	Atlas-SNP
TCF7	6932	hgsc.bcm.edu	37	5	133451683	133451683	+	Missense_Mutation	SNP	C	C	A	rs5742913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	225	93	190	0	0.413333	0	A|0.060;C|0.931;T|0.009	0.060	strong	.	TCF7	81	.	NM_003202	exon3	c.C400A	p.P134T	CCACCCCCCTCGG	.	PASS	Atlas-SNP
CNOT1	23019	hgsc.bcm.edu	37	16	58579274	58579274	+	Silent	SNP	C	C	T	rs246258	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	96	187	0	0.432432	0	C|0.754;T|0.246	0.246	strong	.	CNOT1	359	.	NM_206999	exon30	c.G4128A	p.L1376L	TGGATTCAGAGTA	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68682402	68682402	+	Missense_Mutation	SNP	A	A	G	rs10896380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	74	155	1	0.528571	0.00645161	A|0.824;G|0.176	0.176	strong	IGHMBP2,NS,carcinoma,-1,2	IGHMBP2	83	2	NM_002180	exon6	c.A823G	p.I275V	GAGTCCATTCAGC	.	scavenged	Atlas-SNP
MTUS2	23281	hgsc.bcm.edu	37	13	29933450	29933450	+	Missense_Mutation	SNP	C	C	T	rs114541586	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	66	151	0	0.428571	0	C|0.990;T|0.010	0.010	strong	.	MTUS2	279	.	NM_001033602	exon6	c.C2987T	p.P996L	CCAAGCCGGACCC	.	PASS	Atlas-SNP
EVC	2121	hgsc.bcm.edu	37	4	5743512	5743512	+	Missense_Mutation	SNP	T	T	C	rs6414624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	108	98	0	1	0	T|0.274;C|0.726	0.726	strong	.	EVC	90	.	NM_153717	exon6	c.T772C	p.Y258H	GAACTATACCAGA	.	PASS	Atlas-SNP
RBM5	10181	hgsc.bcm.edu	37	3	50144951	50144951	+	Silent	SNP	T	T	C	rs1061474	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	100	154	0	0.510204	0	T|0.327;C|0.673	0.673	strong	.	RBM5	76	.	NM_005778	exon12	c.T990C	p.A330A	CAGCGCTTTCTCT	.	PASS	Atlas-SNP
KLHL7	55975	hgsc.bcm.edu	37	7	23164701	23164701	+	Silent	SNP	C	C	T	rs15775	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	65	124	0	0.492424	0	C|0.553;T|0.447	0.447	strong	.	KLHL7	102	.	NM_001172428	exon4	c.C352T	p.L118L	TCTTTGCTGGATG	.	PASS	Atlas-SNP
ZNF491	126069	hgsc.bcm.edu	37	19	11916914	11916914	+	Missense_Mutation	SNP	A	A	G	rs141870350	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	78	0	0.5	0	A|0.997;G|0.003	0.003	strong	.	ZNF491	61	.	NM_152356	exon3	c.A146G	p.Y49C	TGGGATATTCATC	.	PASS	Atlas-SNP
KRT9	3857	hgsc.bcm.edu	37	17	39724810	39724810	+	Missense_Mutation	SNP	G	G	A	rs116216460	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	68	114	0	0.548387	0	G|0.998;A|0.002	0.002	strong	.	KRT9	78	.	NM_000226	exon5	c.C1120T	p.R374W	CGTGCCGGAGCTG	.	PASS	Atlas-SNP
NUB1	51667	hgsc.bcm.edu	37	7	151074296	151074296	+	Silent	SNP	A	A	G	rs2159158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	75	88	0	0.974026	0	A|0.597;G|0.403	0.403	strong	.	NUB1	31	.	NM_001243351	exon15	c.A1905G	p.A635A	GTCAGCAACAAAG	.	PASS	Atlas-SNP
IHH	3549	hgsc.bcm.edu	37	2	219920565	219920565	+	Silent	SNP	C	C	T	rs3731878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	22	35	0	0.55	0	C|0.902;T|0.098	0.098	strong	.	IHH	33	.	NM_002181	exon3	c.G600A	p.T200T	GCCGCCCGTCTTG	.	PASS	Atlas-SNP
RBM15	64783	hgsc.bcm.edu	37	1	110883569	110883569	+	Silent	SNP	A	A	T	rs3738752	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	36	71	0	0.404494	0	A|0.840;T|0.160	0.160	strong	RBM15_ENST00000369784,NS,carcinoma,0,1	RBM15	93	1	NM_022768	exon1	c.A1542T	p.P514P	CTTCCCACTTGGT	.	PASS	Atlas-SNP
KPNA4	3840	hgsc.bcm.edu	37	3	160227606	160227606	+	Silent	SNP	A	A	G	rs2305401	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	18	35	0	0.375	0	A|0.952;G|0.048	0.048	strong	.	KPNA4	50	.	NM_002268	exon14	c.T1191C	p.I397I	TCCACTAATTGTT	.	PASS	Atlas-SNP
SCN1B	6324	hgsc.bcm.edu	37	19	35524939	35524939	+	Missense_Mutation	SNP	C	C	A	rs67701503	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	117	211	0	0.506494	0	C|0.866;A|0.134	0.134	strong	.	SCN1B	32	.	NM_199037	exon3	c.C744A	p.S248R	TCTGAGCCAAAGG	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169369920	169369920	+	Missense_Mutation	SNP	C	C	T	rs12507582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	190	97	177	0	0.510526	0	C|0.632;T|0.368	0.368	strong	.	DDX60L	116	.	NM_001012967	exon9	c.G1007A	p.C336Y	TATTCACACCACT	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080648	194080648	+	Silent	SNP	G	G	A	rs9682540	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	66	98	0	0.55	0	G|0.808;A|0.192	0.192	strong	.	LRRC15	137	.	NM_001135057	exon3	c.C1143T	p.N381N	GAGGCGGTTGTTC	.	PASS	Atlas-SNP
LMBRD1	55788	hgsc.bcm.edu	37	6	70407465	70407465	+	Missense_Mutation	SNP	A	A	T	rs12648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	25	38	0	0.862069	0	A|0.653;T|0.347	0.347	strong	.	LMBRD1	61	.	NM_018368	exon14	c.T1407A	p.D469E	AGGAGCATCTGCA	.	PASS	Atlas-SNP
PPM1N	147699	hgsc.bcm.edu	37	19	46002456	46002456	+	Silent	SNP	G	G	T	rs3745821	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	11	26	0	0.392857	0	G|0.895;T|0.105	0.105	strong	PPM1N,rectum,carcinoma,+1,1	PPM1N	25	1	NM_001080401	exon1	c.G726T	p.P242P	GGCTCCGGGGAGG	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912386	29912386	+	Missense_Mutation	SNP	G	G	C	rs1137160	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	262	176	364	0	0.671756	0	G|0.868;C|0.132	0.132	strong	HLA-A,colon,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon5	c.G1005C	p.K335N	GAGGAAGAGCTCA	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	66112409	66112409	+	Silent	SNP	A	A	G	rs974110	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	18	176	0	0.191489	0	A|0.498;G|0.502	0.502	strong	.	EYS	527	.	NM_001142801	exon7	c.T1146C	p.N382N	TGTAGCATTATTC	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19748038	19748038	+	Missense_Mutation	SNP	C	C	T	rs1803092	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	68	141	0	0.515152	0	C|0.957;T|0.043	0.043	strong	.	TUBA3C	166	.	NM_006001	exon5	c.G1318A	p.V440M	CTTCCACGGAATC	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512886	4512886	+	Silent	SNP	G	G	A	rs112609940	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	55	289	1	0.964912	0.00346021	G|0.931;A|0.069	0.069	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C1044T	p.V348V	AGTTAGGACAGTC	.	PASS	Atlas-SNP
FPGS	2356	hgsc.bcm.edu	37	9	130566678	130566678	+	Missense_Mutation	SNP	C	C	T	rs41306702	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	54	96	0	0.580645	0	C|0.997;T|0.003	0.003	strong	.	FPGS	30	.	NM_004957	exon2	c.C253T	p.R85W	CTGGCACGGAGTG	.	PASS	Atlas-SNP
KIFAP3	22920	hgsc.bcm.edu	37	1	169951997	169951997	+	Silent	SNP	C	C	T	rs33943686	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	59	74	0	1	0	C|0.728;T|0.272	0.272	strong	.	KIFAP3	102	.	NM_014970	exon14	c.G1518A	p.G506G	AAGGTCCCCAACA	.	PASS	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	37	17	38955961	38955961	+	Missense_Mutation	SNP	G	G	A	rs4624233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	31	69	0	0.469697	0	G|0.752;A|0.248	0.248	strong	.	KRT28	65	.	NM_181535	exon1	c.C185T	p.A62V	CCACCAGCATGGC	.	PASS	Atlas-SNP
TBC1D19	55296	hgsc.bcm.edu	37	4	26585881	26585881	+	Silent	SNP	C	C	T	rs4692549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	45	53	0	0.48913	0	C|0.679;T|0.321	0.321	strong	.	TBC1D19	53	.	NM_018317	exon1	c.C66T	p.S22S	GGGCTCCAATTTG	.	PASS	Atlas-SNP
ZSWIM8	23053	hgsc.bcm.edu	37	10	75552298	75552298	+	Silent	SNP	T	T	C	rs200674189	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	63	144	0	0.446809	0	T|0.997;C|0.003	0.003	strong	.	.	.	.	NM_001242488	exon10	c.T2001C	p.Y667Y	TACTTATGAAGAA	.	PASS	Atlas-SNP
TNKS	8658	hgsc.bcm.edu	37	8	9609331	9609331	+	Silent	SNP	G	G	A	rs13265931	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	22	49	0	0.44898	0	G|0.844;A|0.156	0.156	strong	.	TNKS	198	.	NM_003747	exon19	c.G3045A	p.A1015A	CGCCGCGGGAACA	.	PASS	Atlas-SNP
DNAJC9	23234	hgsc.bcm.edu	37	10	75006932	75006932	+	Missense_Mutation	SNP	G	G	T	rs201308148	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	27	42	0	0.442623	0	.	.	weak	.	DNAJC9	19	.	NM_015190	exon1	c.C16A	p.L6I	CGCAAAGGTCCAG	.	PASS	Atlas-SNP
OR8K1	390157	hgsc.bcm.edu	37	11	56113593	56113593	+	Missense_Mutation	SNP	C	C	A	rs10896272	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	51	147	0	0.504951	0	C|0.621;A|0.379	0.379	strong	.	OR8K1	93	.	NM_001002907	exon1	c.C79A	p.P27T	GACAACCCTGGGC	.	PASS	Atlas-SNP
LRPAP1	4043	hgsc.bcm.edu	37	4	3520701	3520701	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	43	97	0	0.511905	0	.	.	none	.	LRPAP1	29	.	NM_002337	exon4	c.A489G	p.K163K	GGAGAATTTCCCA	.	PASS	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	37	22	50878196	50878196	+	Missense_Mutation	SNP	G	G	A	rs13057311	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	45	139	0	0.354331	0	G|0.783;A|0.217	0.217	strong	.	PPP6R2	71	.	NM_001242898	exon20	c.G2195A	p.R732K	TGGTGAGGGACGT	.	PASS	Atlas-SNP
SOCS4	122809	hgsc.bcm.edu	37	14	55510110	55510110	+	Silent	SNP	G	G	A	rs17128136	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	39	62	0	0.557143	0	G|0.944;A|0.056	0.056	strong	.	SOCS4	34	.	NM_080867	exon2	c.G351A	p.P117P	GCTTCCGTCTAAA	.	PASS	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347053	140347053	+	Silent	SNP	C	C	T	rs155807	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	57	105	0	0.478992	0	C|0.679;T|0.321	0.321	strong	.	PCDHAC2	142	.	NM_031883	exon1	c.C702T	p.I234I	GGGCATCCCAGCC	.	PASS	Atlas-SNP
POM121	9883	hgsc.bcm.edu	37	7	72418963	72418963	+	Missense_Mutation	SNP	T	T	C	rs7056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	63	157	0	0.508065	0	T|0.473;C|0.527	0.527	strong	.	POM121	131	.	NM_001257190	exon16	c.T2954C	p.L985P	AGGGTCTTCCACG	.	PASS	Atlas-SNP
CLEC4A	50856	hgsc.bcm.edu	37	12	8278181	8278181	+	Missense_Mutation	SNP	A	A	T	rs2024301	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	96	113	0	0.989691	0	T|0.573;N|0.000	0.573	strong	.	CLEC4A	28	.	NM_016184	exon2	c.A107T	p.H36L	CCCCTCACAAAAG	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17794494	17794494	+	Silent	SNP	G	G	A	rs3734234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	34	97	0	0.404762	0	G|0.609;A|0.391	0.391	strong	.	KIF13A	276	.	NM_001105567	exon25	c.C3208T	p.L1070L	TGTCCAGCCCTCT	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52508842	52508842	+	Missense_Mutation	SNP	C	C	A	rs61747585	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	35	85	1	0.454545	0.0117647	C|0.953;A|0.047	0.047	strong	NID2,NS,carcinoma,-2,1	NID2	201	1	NM_007361	exon7	c.G1806T	p.E602D	GCCGTTCTCAGAG	.	scavenged	Atlas-SNP
CA5B	11238	hgsc.bcm.edu	37	X	15800751	15800751	+	Silent	SNP	G	G	A	rs1808	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	87	81	0	1	0	G|0.655;0|0.003	.	strong	.	CA5B	23	.	NM_007220	exon8	c.G918A	p.A306A	ACAAGCGAAACCC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6585032	6585032	+	Missense_Mutation	SNP	G	G	A	rs11604232	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	27	48	0	0.457627	0	G|0.978;A|0.022	0.022	strong	.	DNHD1	198	.	NM_144666	exon31	c.G9962A	p.R3321Q	TGAGCCGACCTGC	.	PASS	Atlas-SNP
SGTA	6449	hgsc.bcm.edu	37	19	2761500	2761500	+	Silent	SNP	G	G	A	rs111283489	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	41	58	0	0.602941	0	G|0.997;A|0.003	0.003	strong	.	SGTA	19	.	NM_003021	exon8	c.C657T	p.F219F	GATGTCGAAGCTG	.	PASS	Atlas-SNP
NEK11	79858	hgsc.bcm.edu	37	3	130947466	130947466	+	Silent	SNP	G	G	A	rs138864243	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	21	51	0	0.5	0	G|0.998;A|0.002	0.002	strong	.	NEK11	76	.	NM_024800	exon15	c.G1494A	p.A498A	AATAGCGTTAGAA	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12186611	12186611	+	Missense_Mutation	SNP	A	A	G	rs7259684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	28	41	0	0.444444	0	A|0.854;G|0.146	0.146	strong	.	ZNF844	69	.	NM_001136501	exon4	c.A676G	p.K226E	CCATATAAATGTA	.	PASS	Atlas-SNP
ATAD3B	83858	hgsc.bcm.edu	37	1	1425700	1425700	+	Silent	SNP	T	T	C	rs819980	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	128	149	1	0.876712	0.00671141	T|0.629;C|0.371	0.371	strong	ATAD3B,NS,carcinoma,0,2	ATAD3B	68	2	NM_031921	exon14	c.T1401C	p.I467I	CCGCATTGACGTG	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55331419	55331419	+	Missense_Mutation	SNP	C	C	T	rs2273731	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	49	58	0	0.462264	0	C|0.250;T|0.750	0.750	weak	KIR3DL1_ENST00000402254,NS,neuroblastoma,0,2	KIR3DL1	174	2	NM_013289	exon4	c.C607T	p.P203S	CACACCCCCTATC	.	PASS	Atlas-SNP
SCN3A	6328	hgsc.bcm.edu	37	2	166003479	166003479	+	Silent	SNP	G	G	A	rs16850131	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	170	204	1	0.977012	0.00490196	G|0.756;A|0.244	0.244	strong	.	SCN3A	544	.	NM_001081676	exon12	c.C1441T	p.L481L	CCAACAGCTCTCC	.	PASS	Atlas-SNP
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105363289	105363289	+	Silent	SNP	T	T	C	rs3740471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	36	76	0	0.610169	0	T|0.835;C|0.165	0.165	strong	.	SH3PXD2A	90	.	NM_014631	exon14	c.A1602G	p.A534A	GCCGAATGCAGGG	.	PASS	Atlas-SNP
IL12RB1	3594	hgsc.bcm.edu	37	19	18180451	18180451	+	Missense_Mutation	SNP	A	A	G	rs375947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	29	78	0	0.358025	0	A|0.701;G|0.299	0.299	strong	.	IL12RB1	92	.	NM_005535	exon10	c.T1094C	p.M365T	TACGTCATGCTCT	.	PASS	Atlas-SNP
AHDC1	27245	hgsc.bcm.edu	37	1	27875055	27875055	+	Missense_Mutation	SNP	C	C	T	rs146401682	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	50	66	0	0.892857	0	C|0.999;T|0.001	0.001	strong	.	AHDC1	98	.	NM_001029882	exon6	c.G3572A	p.S1191N	TCACTACTTGAGG	.	PASS	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	37	14	45650900	45650900	+	Missense_Mutation	SNP	A	A	G	rs78211950	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	29	61	0	0.414286	0	A|0.918;G|0.082	0.082	strong	.	FANCM	225	.	NM_020937	exon16	c.A4378G	p.I1460V	TTTCCTATAAACA	.	PASS	Atlas-SNP
CD27	939	hgsc.bcm.edu	37	12	6554628	6554628	+	Missense_Mutation	SNP	G	G	A	rs25680	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	37	60	0	0.474359	0	G|0.844;A|0.156	0.156	strong	.	CD27	17	.	NM_001242	exon2	c.G175A	p.A59T	AGAAAGGCTGCTC	.	PASS	Atlas-SNP
PTCH1	5727	hgsc.bcm.edu	37	9	98238358	98238358	+	Silent	SNP	G	G	A	rs2066836	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	17	40	0	0.459459	0	G|0.865;A|0.135	0.135	strong	.	PTCH1	1850	.	NM_000264	exon12	c.C1686T	p.A562A	TAACGCGGCCATG	.	PASS	Atlas-SNP
MATN4	8785	hgsc.bcm.edu	37	20	43933163	43933163	+	Silent	SNP	T	T	C	rs2233094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	46	67	0	1	0	T|0.676;C|0.324	0.324	strong	MATN4,NS,carcinoma,0,1	MATN4	57	1	NM_030592	exon3	c.A348G	p.A116A	CTGGATTGCCAGT	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274235	39274235	+	Silent	SNP	G	G	A	rs11654403	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	29	69	0	0.353659	0	G|0.724;A|0.276	0.276	strong	KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	NM_033059	exon1	c.C333T	p.R111R	GCTGGGGCGACAG	.	PASS	Atlas-SNP
LAMB2	3913	hgsc.bcm.edu	37	3	49166460	49166460	+	Missense_Mutation	SNP	C	C	T	rs61729152	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	14	33	1	0.411765	0.030303	C|0.991;T|0.009	0.009	strong	LAMB2,NS,carcinoma,-1,1	LAMB2	156	1	NM_002292	exon13	c.G1724A	p.R575Q	TGCCCTCGGGTGT	.	scavenged	Atlas-SNP
NCOA7	135112	hgsc.bcm.edu	37	6	126249914	126249914	+	Missense_Mutation	SNP	T	T	G	rs1567	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	39	47	0	0.847826	0	T|0.829;G|0.171	0.171	strong	.	NCOA7	92	.	NM_001199619	exon17	c.T2826G	p.D942E	ATTTGATTGAAAT	.	PASS	Atlas-SNP
WFIKKN2	124857	hgsc.bcm.edu	37	17	48918275	48918275	+	Silent	SNP	C	C	T	rs139049586	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	56	139	1	0.482759	0.00719424	C|0.997;T|0.003	0.003	strong	WFIKKN2,colon,carcinoma,0,1	WFIKKN2	69	1	NM_175575	exon2	c.C1626T	p.P542P	GCGCCCCGATAGC	.	scavenged	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100139161	100139161	+	Silent	SNP	A	A	G	rs11581	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	30	43	0	0.555556	0	A|0.654;G|0.346	0.346	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon37	c.A5091G	p.Q1697Q	TATCCAAGGCCTG	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4874729	4874729	+	Missense_Mutation	SNP	C	C	G	rs144507770	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	21	27	0	0.512195	0	C|0.987;G|0.013	0.013	strong	.	RADIL	110	.	NM_018059	exon4	c.G925C	p.G309R	CCTGGCCGCTGTC	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137642654	137642654	+	Missense_Mutation	SNP	G	G	A	rs61735045	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	41	85	0	0.482353	0	G|0.971;A|0.029	0.029	strong	COL5A1,NS,carcinoma,-2,2	COL5A1	323	2	NM_000093	exon13	c.G1588A	p.G530S	GGTGGCGGCGATG	.	PASS	Atlas-SNP
ITGBL1	9358	hgsc.bcm.edu	37	13	102227872	102227872	+	Silent	SNP	C	C	T	rs3916912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	78	150	0	0.4875	0	C|0.831;T|0.169	0.169	strong	.	ITGBL1	83	.	NM_004791	exon4	c.C561T	p.D187D	CATAGACGATGAA	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52712975	52712975	+	Silent	SNP	G	G	A	rs56040851		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	281	143	283	0	0.508897	0	.	.	weak	.	KRT83	64	.	NM_002282	exon2	c.C558T	p.N186N	CACGTGGTTGAGC	.	PASS	Atlas-SNP
CATSPERB	79820	hgsc.bcm.edu	37	14	92159558	92159558	+	Missense_Mutation	SNP	A	A	G	rs72629402	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	103	104	1	1	0.00961538	A|0.955;G|0.045	0.045	strong	.	CATSPERB	114	.	NM_024764	exon9	c.T743C	p.V248A	GTTAAAACCATAT	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125434716	125434716	+	Silent	SNP	G	G	A	rs4078216	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	41	111	0	0.450549	0	G|0.776;N|0.000	.	strong	DHX37,NS,carcinoma,0,1	DHX37	114	1	NM_032656	exon24	c.C3195T	p.A1065A	GAACCGGGCAAAG	.	PASS	Atlas-SNP
MED12	9968	hgsc.bcm.edu	37	X	70349947	70349947	+	Silent	SNP	A	A	C	rs5030619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	185	197	0	0.989305	0	A|0.853;0|0.007	.	strong	.	MED12	984	.	NM_005120	exon28	c.A3930C	p.P1310P	AGACCCAGTGTTG	.	PASS	Atlas-SNP
C6orf52	347744	hgsc.bcm.edu	37	6	10687746	10687746	+	Missense_Mutation	SNP	G	G	T	rs7749306	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	32	70	0	0.450704	0	A|0.000;G|0.781;T|0.219	0.219	strong	.	C6orf52	9	.	NM_001145020	exon2	c.C38A	p.A13D	TGTTGAGCTATGC	.	PASS	Atlas-SNP
COBL	23242	hgsc.bcm.edu	37	7	51094269	51094269	+	Missense_Mutation	SNP	G	G	A	rs61737954	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	43	87	0	0.452632	0	G|0.947;A|0.053	0.053	strong	.	COBL	167	.	NM_015198	exon11	c.C3478T	p.H1160Y	CGCTGTGCCCGCG	.	PASS	Atlas-SNP
PLEKHG4	25894	hgsc.bcm.edu	37	16	67322414	67322414	+	Silent	SNP	G	G	A	rs11556908	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	36	80	0	0.473684	0	G|0.971;A|0.029	0.029	strong	PLEKHG4,colon,carcinoma,+1,1	PLEKHG4	94	1	NM_001129728	exon21	c.G3477A	p.S1159S	GATCTCGTCCCAA	.	PASS	Atlas-SNP
WSCD1	23302	hgsc.bcm.edu	37	17	5991344	5991344	+	Silent	SNP	C	C	T	rs2302836	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	98	94	0	0.98	0	C|0.529;T|0.471	0.471	strong	.	WSCD1	84	.	NM_015253	exon3	c.C462T	p.H154H	TGGCCACGAGAGG	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56327849	56327849	+	Missense_Mutation	SNP	C	C	T	rs11758339	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	63	121	0	0.492188	0	C|0.788;T|0.212	0.212	strong	.	DST	1427	.	NM_015548	exon82	c.G15124A	p.A5042T	CCTCTGCAGATGG	.	PASS	Atlas-SNP
TNN	63923	hgsc.bcm.edu	37	1	175097864	175097864	+	Silent	SNP	G	G	A	rs12022593	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	46	85	0	0.5	0	G|0.813;A|0.187	0.187	strong	TNN,right_upper_lobe,carcinoma,+1,1	TNN	297	1	NM_022093	exon15	c.G3312A	p.T1104T	GGAAACGGACGGA	.	PASS	Atlas-SNP
CXXC1	30827	hgsc.bcm.edu	37	18	47811374	47811374	+	Silent	SNP	G	G	A	rs17660776	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	146	151	1	0.986486	0.00662252	G|0.886;A|0.114	0.114	strong	.	CXXC1	50	.	NM_001101654	exon7	c.C910T	p.L304L	TCACCAGGCCATG	.	PASS	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3627840	3627840	+	Missense_Mutation	SNP	G	G	A	rs220462	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	122	129	0	1	0	G|0.759;A|0.241	0.241	strong	.	GSG2	48	.	NM_031965	exon1	c.G611A	p.G204D	CGAGCGGCCTCCA	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	69	81	0	1	0	C|0.507;0|0.003	.	strong	.	GPR112	459	.	NM_153834	exon6	c.C5493T	p.P1831P	TCTACCCTCTTTG	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32024395	32024395	+	Missense_Mutation	SNP	C	C	T	rs10947230	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	118	231	1	0.473896	0.004329	C|0.895;T|0.105	0.105	strong	TNXB_ENST00000375247,caecum,carcinoma,+1,2	TNXB	553	2	NM_019105	exon23	c.G8111A	p.R2704H	CCCACGCGCTGGC	.	PASS	Atlas-SNP
DLGAP1	9229	hgsc.bcm.edu	37	18	3814148	3814148	+	Silent	SNP	C	C	G	rs3786431	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	63	98	0	0.533898	0	C|0.896;G|0.104	0.104	strong	.	DLGAP1	201	.	NM_001242761	exon5	c.G1083C	p.T361T	AGGACTCGTGTCT	.	PASS	Atlas-SNP
LRRC69	100130742	hgsc.bcm.edu	37	8	92136728	92136728	+	Missense_Mutation	SNP	C	C	T	rs11785003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	9	30	0	0.321429	0	C|0.555;T|0.445	0.445	strong	.	LRRC69	24	.	NM_001129890	exon2	c.C191T	p.T64I	TGACAACACTAAA	.	PASS	Atlas-SNP
OR2J3	442186	hgsc.bcm.edu	37	6	29079925	29079925	+	Silent	SNP	C	C	G	rs140877389	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	315	169	270	1	0.536508	0.0037037	C|0.992;G|0.008	0.008	strong	OR2J3,NS,carcinoma,0,1	OR2J3	53	1	NM_001005216	exon1	c.C258G	p.V86V	GCTGGTCAATCTC	.	PASS	Atlas-SNP
SPRR1B	6699	hgsc.bcm.edu	37	1	153004853	153004853	+	Missense_Mutation	SNP	C	C	T	rs3795382	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	98	191	0	0.487562	0	C|0.497;T|0.503	0.503	strong	SPRR1B,head_neck,carcinoma,0,1	SPRR1B	18	1	NM_003125	exon2	c.C32T	p.T11I	CTTGCACCCCACC	.	PASS	Atlas-SNP
NDUFV2	4729	hgsc.bcm.edu	37	18	9122591	9122591	+	Silent	SNP	T	T	C	rs76552443	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	36	203	0	0.144578	0	T|0.879;C|0.121	0.121	strong	NDUFV2,NS,carcinoma,0,1	NDUFV2	17	1	NM_021074	exon5	c.T381C	p.V127V	GCCAGTTGGAAAG	.	scavenged	Atlas-SNP
PRKCSH	5589	hgsc.bcm.edu	37	19	11558275	11558275	+	Missense_Mutation	SNP	G	G	A	rs11557488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	64	121	0	0.435374	0	A|0.141;C|0.000;G|0.859	0.141	strong	.	PRKCSH	55	.	NM_001001329	exon11	c.G871A	p.A291T	CTTCCAGCACCTT	.	PASS	Atlas-SNP
OR52R1	119695	hgsc.bcm.edu	37	11	4825349	4825349	+	Missense_Mutation	SNP	A	A	G	rs17327254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	49	99	0	0.485149	0	A|0.937;G|0.063	0.063	strong	.	OR52R1	81	.	NM_001005177	exon1	c.T262C	p.F88L	ACCAGAATATGGC	.	PASS	Atlas-SNP
RREB1	6239	hgsc.bcm.edu	37	6	7229346	7229346	+	Silent	SNP	T	T	C	rs2714315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	42	88	0	0.477273	0	T|0.555;C|0.445	0.445	strong	.	RREB1	242	.	NM_001003700	exon10	c.T1014C	p.H338H	GACCCATGTGGCG	.	PASS	Atlas-SNP
CHPF	79586	hgsc.bcm.edu	37	2	220405230	220405230	+	Silent	SNP	G	G	A	rs6436154	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	55	86	0	0.491071	0	G|0.613;A|0.387	0.387	strong	.	CHPF	56	.	NM_024536	exon4	c.C1203T	p.H401H	GAAAGCGTGCTGC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549481	32549481	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	69	422	1	0.338235	0.00236967	.	.	none	.	HLA-DRB1	41	.	NM_002124	exon3	c.G505A	p.A169T	TCCCAGCCTTCTC	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52710721	52710721	+	Missense_Mutation	SNP	G	G	C	rs2852464	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	74	183	0	0.422857	0	G|0.638;C|0.362	0.362	strong	KRT83,NS,carcinoma,-1,2	KRT83	64	2	NM_002282	exon5	c.C837G	p.I279M	GGCAACGATGCAG	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138764233	138764233	+	Missense_Mutation	SNP	C	C	T	rs2236426	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	57	142	0	0.419118	0	C|0.799;T|0.201	0.201	strong	.	ZC3HAV1	75	.	NM_024625	exon4	c.G1454A	p.R485K	GCTACTCTTGGGT	.	PASS	Atlas-SNP
UNC80	285175	hgsc.bcm.edu	37	2	210658517	210658517	+	Missense_Mutation	SNP	G	G	A	rs146565598	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	2	112	0	0.015873	0	G|1.000;A|0.000	0.000	strong	UNC80_ENST00000439458,NS,carcinoma,+1,2	UNC80	280	2	NM_182587	exon7	c.G872A	p.R291Q	GTCACCGAGGAAA	.	scavenged	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76395464	76395464	+	Missense_Mutation	SNP	C	C	T	rs41286126	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	50	72	0	0.609756	0	C|0.935;T|0.065	0.065	strong	.	LMO7	334	.	NM_015842	exon11	c.C1660T	p.P554S	ACTTATCCTTCAG	.	PASS	Atlas-SNP
ZDHHC1	29800	hgsc.bcm.edu	37	16	67434917	67434917	+	Missense_Mutation	SNP	C	C	T	rs34229857	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	89	120	0	0.542683	0	C|0.983;T|0.017	0.017	strong	.	ZDHHC1	28	.	NM_013304	exon4	c.G371A	p.R124Q	TGGCTTCGGTTGA	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114282496	114282496	+	Missense_Mutation	SNP	C	C	T	rs2075387	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	27	38	0	0.529412	0	C|0.781;T|0.219	0.219	strong	.	RBM19	117	.	NM_001146699	exon23	c.G2762A	p.R921Q	GTCTTCCGCCGCA	.	PASS	Atlas-SNP
CDAN1	146059	hgsc.bcm.edu	37	15	43023482	43023482	+	Missense_Mutation	SNP	T	T	C	rs12917189	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	84	179	0	0.482759	0	C|0.419;N|0.000	0.419	strong	.	CDAN1	70	.	NM_138477	exon12	c.A1787G	p.Q596R	AGCTCCTGGATCT	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737167	248737167	+	Missense_Mutation	SNP	G	G	A	rs74984555	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	55	213	1	0.220884	0.00469484	G|0.500;A|0.500	0.500	strong	OR2T34,NS,carcinoma,+2,1	OR2T34	72	1	NM_001001821	exon1	c.C892T	p.R298C	TGTTGCGGAGACT	.	scavenged	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76409436	76409436	+	Silent	SNP	A	A	G	rs2273997	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	44	84	0	0.473118	0	G|0.263;N|0.000	0.263	strong	LMO7_ENST00000465261,NS,carcinoma,0,3	LMO7	334	3	NM_015842	exon15	c.A2595G	p.L865L	AAATCTATCTGTA	.	PASS	Atlas-SNP
MARVELD2	153562	hgsc.bcm.edu	37	5	68715310	68715310	+	Missense_Mutation	SNP	C	C	T	rs1185246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	155	131	0	1	0	C|0.528;A|0.003	.	strong	.	MARVELD2	49	.	NM_001244734	exon2	c.C98T	p.T33I	ACCCAACTCTTCA	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186050417	186050417	+	Missense_Mutation	SNP	A	A	G	rs10798035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	73	98	0	0.618644	0	A|0.425;G|0.575	0.575	strong	HMCN1,NS,carcinoma,0,2	HMCN1	797	2	NM_031935	exon56	c.A8678G	p.E2893G	TGATAGAGTGTTT	.	PASS	Atlas-SNP
POFUT2	23275	hgsc.bcm.edu	37	21	46705621	46705621	+	Silent	SNP	G	G	A	rs2297285	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	27	110	2	0.355263	0.0181818	G|0.821;A|0.179	0.179	strong	POFUT2,NS,carcinoma,-1,1	POFUT2	77	1	NM_015227	exon2	c.C354T	p.P118P	GATGACGGGGATG	.	scavenged	Atlas-SNP
RRP1	8568	hgsc.bcm.edu	37	21	45209559	45209559	+	Silent	SNP	C	C	T	rs78489660	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	65	82	0	0.570175	0	C|0.949;T|0.051	0.051	strong	.	RRP1	23	.	NM_003683	exon1	c.C49T	p.L17L	CAGCGCCTGGCGG	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79048562	79048562	+	Silent	SNP	C	C	T	rs1366272	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	35	52	0	0.5	0	C|0.753;T|0.247	0.247	strong	CMYA5,NS,carcinoma,0,1	CMYA5	643	1	NM_153610	exon6	c.C11055T	p.F3685F	CCTTTTCGAACAT	.	PASS	Atlas-SNP
C12orf54	121273	hgsc.bcm.edu	37	12	48888689	48888689	+	Silent	SNP	C	C	G	rs9268	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	34	75	0	0.43038	0	C|0.533;G|0.467	0.467	strong	.	C12orf54	11	.	NM_152319	exon8	c.C351G	p.L117L	ACAGCTCTTCAGT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115710	168115710	+	Missense_Mutation	SNP	T	T	G	rs3749006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	38	119	0	0.417582	0	T|0.808;G|0.192	0.192	strong	XIRP2_ENST00000409728,NS,carcinoma,0,1	XIRP2	914	1	NM_001199143	exon11	c.T2753G	p.V918G	GGCATGTTGAAAC	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17700792	17700792	+	Silent	SNP	C	C	T	rs35686634	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	70	144	0	0.510949	0	C|0.916;T|0.084	0.084	strong	.	RAI1	121	.	NM_030665	exon3	c.C4530T	p.P1510P	CCAGCCCCCGGAG	.	PASS	Atlas-SNP
AKR1E2	83592	hgsc.bcm.edu	37	10	4889403	4889403	+	Nonsense_Mutation	SNP	C	C	T	rs12240276	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	97	194	0	0.535912	0	C|0.901;T|0.099	0.099	strong	.	AKR1E2	30	.	NM_001040177	exon9	c.C901T	p.R301X	AATCTCCGACTGG	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219602819	219602819	+	Silent	SNP	G	G	A	rs3731876	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	36	60	0	0.734694	0	G|0.459;A|0.541	0.541	strong	.	TTLL4	96	.	NM_014640	exon3	c.G420A	p.P140P	GAGCCCGTCAGAA	.	PASS	Atlas-SNP
OR12D3	81797	hgsc.bcm.edu	37	6	29342825	29342825	+	Silent	SNP	G	G	A	rs3749970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	34	75	0	0.404762	0	G|0.667;A|0.333	0.333	strong	OR12D3,NS,carcinoma,0,1	OR12D3	55	1	NM_030959	exon1	c.C240T	p.L80L	GTTTACGAGCAGC	.	PASS	Atlas-SNP
MSH6	2956	hgsc.bcm.edu	37	2	48025764	48025764	+	Silent	SNP	C	C	T	rs1800937	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	11	20	0	0.5	0	C|0.942;T|0.058	0.058	strong	.	MSH6	341	.	NM_000179	exon4	c.C642T	p.Y214Y	AACTTACGTAACA	.	PASS	Atlas-SNP
SERPINF2	5345	hgsc.bcm.edu	37	17	1649022	1649022	+	Silent	SNP	C	C	T	rs35259159	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	35	73	0	0.522388	0	C|0.960;T|0.040	0.040	strong	.	SERPINF2	33	.	NM_000934	exon5	c.C186T	p.A62A	GACTGCCCTGAAG	.	PASS	Atlas-SNP
A2ML1	144568	hgsc.bcm.edu	37	12	9013755	9013755	+	Missense_Mutation	SNP	C	C	T	rs1860967	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	87	136	0	0.508772	0	C|0.568;T|0.432	0.432	strong	A2ML1,NS,lymphoid_neoplasm,-2,1	A2ML1	199	1	NM_144670	exon28	c.C3364T	p.R1122W	GGTCTACGGTGTC	.	PASS	Atlas-SNP
LETM2	137994	hgsc.bcm.edu	37	8	38250202	38250202	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	37	79	0	0.521127	0	.	.	none	.	LETM2	57	.	NM_001199659	exon3	c.A49G	p.N17D	CCAGGCAATACAG	.	PASS	Atlas-SNP
NDUFS2	4720	hgsc.bcm.edu	37	1	161182208	161182208	+	Missense_Mutation	SNP	C	C	G	rs11576415	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	23	42	0	0.442308	0	C|0.937;G|0.063	0.063	strong	NDUFS2,lymph_node,lymphoid_neoplasm,0,1	NDUFS2	33	1	NM_001166159	exon10	c.C1054G	p.P352A	AAGATGCCTCCTG	.	PASS	Atlas-SNP
TBC1D8	11138	hgsc.bcm.edu	37	2	101627925	101627925	+	Missense_Mutation	SNP	C	C	T	rs1062062	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	30	58	0	0.483871	0	C|0.941;T|0.059	0.059	strong	TBC1D8,NS,carcinoma,+1,2	TBC1D8	169	2	NM_001102426	exon18	c.G2860A	p.G954R	GTTTCCCGAAAAC	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487172	32487172	+	Silent	SNP	C	C	T	rs72508430	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	52	110	0	0.509804	0	C|0.764;T|0.235	0.235	strong	HLA-DRB5,NS,carcinoma,-2,1	HLA-DRB5	31	1	NM_002125	exon3	c.G627A	p.V209V	GCTCGTCACGCTT	.	scavenged	Atlas-SNP
ZNF358	140467	hgsc.bcm.edu	37	19	7584223	7584223	+	Missense_Mutation	SNP	A	A	G	rs11555037	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	53	41	0	1	0	A|0.768;G|0.231;T|0.000	0.231	strong	.	ZNF358	41	.	NM_018083	exon2	c.A95G	p.N32S	ACCCCAATCCTGA	.	PASS	Atlas-SNP
C1RL	51279	hgsc.bcm.edu	37	12	7252597	7252597	+	Silent	SNP	G	G	A	rs61917913	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	17	46	0	0.346939	0	G|0.976;A|0.024	0.024	strong	C1RL,colon,carcinoma,0,1	C1RL	39	1	NM_016546	exon4	c.C516T	p.S172S	GGCCTCGCTGATG	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47927744	47927744	+	Missense_Mutation	SNP	C	C	T	rs56100904	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	35	84	0	0.421687	0	C|0.902;T|0.098	0.098	strong	.	PKD1L1	328	.	NM_138295	exon17	c.G2680A	p.V894I	TGTGGACGAATCT	.	PASS	Atlas-SNP
LGALS14	56891	hgsc.bcm.edu	37	19	40195183	40195183	+	Silent	SNP	C	C	T	rs117106744	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	103	199	0	0.481308	0	C|0.996;T|0.004	0.004	strong	.	LGALS14	38	.	NM_020129	exon1	c.C15T	p.P5P	ACTACCCGTGAGT	.	PASS	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	37	16	3254972	3254972	+	Silent	SNP	T	T	C	rs2075851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	64	168	0	0.410256	0	T|0.618;C|0.382	0.382	strong	.	OR1F1	36	.	NM_012360	exon1	c.T726C	p.G242G	CTGTGGTTCTCAC	.	PASS	Atlas-SNP
KIF4B	285643	hgsc.bcm.edu	37	5	154396017	154396017	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	216	4	227	1	0.0185185	0.00440529	.	.	none	KIF4B_ENST00000435029,NS,carcinoma,0,2	KIF4B	307	2	NM_001099293	exon1	c.C2598T	p.A866A	GTGTGCCCTGAAA	.	scavenged	Atlas-SNP
MBTPS1	8720	hgsc.bcm.edu	37	16	84115483	84115483	+	Silent	SNP	G	G	A	rs3743631	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	56	69	0	1	0	G|0.504;A|0.496	0.496	strong	MBTPS1,NS,carcinoma,0,1	MBTPS1	85	1	NM_003791	exon11	c.C1317T	p.P439P	ACTGGCGGGATTC	.	PASS	Atlas-SNP
RTBDN	83546	hgsc.bcm.edu	37	19	12936693	12936693	+	Missense_Mutation	SNP	C	C	T	rs148952767	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	59	84	0	0.464567	0	C|0.993;T|0.007	0.007	strong	.	RTBDN	26	.	NM_031429	exon7	c.G613A	p.V205M	CAGCCACCGGTAG	.	PASS	Atlas-SNP
RPL13	6137	hgsc.bcm.edu	37	16	89627460	89627460	+	Silent	SNP	T	T	G	rs4874	by2hit2allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	26	21	0	0.464286	0	G|1.000;|0.000	1.000	weak	RPL13,colon,carcinoma,0,1	RPL13	11	1	NM_001243131	exon2	c.T93G	p.R31R	GGCCCGTAAGATC	.	PASS	Atlas-SNP
WDYHV1	55093	hgsc.bcm.edu	37	8	124440174	124440174	+	Missense_Mutation	SNP	A	A	G	rs6999234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	54	29	0	1	0	A|0.626;G|0.374	0.374	strong	WDYHV1,NS,carcinoma,0,2	WDYHV1	30	2	NM_018024	exon2	c.A94G	p.I32V	GAAAATATTTGGA	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36486004	36486004	+	Missense_Mutation	SNP	T	T	C	rs55727040	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	30	93	0	0.416667	0	T|0.897;C|0.103	0.103	strong	.	GPR179	170	.	NM_001004334	exon11	c.A3448G	p.K1150E	ACTCCTTGTCATC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9085004	9085004	+	Missense_Mutation	SNP	T	T	C	rs11085805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	54	114	0	0.495413	0	T|0.812;C|0.188	0.188	strong	MUC16_ENST00000397910,NS,carcinoma,+1,2	MUC16	4315	2	NM_024690	exon1	c.A6811G	p.T2271A	AATGAGTTGTCTT	.	PASS	Atlas-SNP
ARHGAP5	394	hgsc.bcm.edu	37	14	32562733	32562733	+	Missense_Mutation	SNP	A	A	G	rs151151743	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	44	98	0	0.478261	0	A|0.993;G|0.007	0.007	strong	.	ARHGAP5	166	.	NM_001173	exon2	c.A2858G	p.N953S	CTGATAATACAAG	.	PASS	Atlas-SNP
MORC4	79710	hgsc.bcm.edu	37	X	106221323	106221323	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	61	67	0	0.859155	0	.	.	none	.	MORC4	155	.	NM_001085354	exon8	c.G1043T	p.G348V	TGGCACCCCACCT	.	PASS	Atlas-SNP
FKBP1A	2280	hgsc.bcm.edu	37	20	1350709	1350709	+	Silent	SNP	T	T	C	rs8392	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	25	78	0	0.510204	0	T|0.408;G|0.125;C|0.192;A|0.276	0.192	strong	.	FKBP1A	6	.	NM_001199786	exon4	c.A258G	p.P86P	CCTCCATGGCAGA	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	226160	226160	+	Silent	SNP	A	A	C	rs6555055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	55	118	0	0.429688	0	A|0.751;C|0.249	0.249	strong	.	SDHA	80	.	NM_004168	exon5	c.A619C	p.R207R	TATGGAAGGGTAA	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47836395	47836395	+	Missense_Mutation	SNP	T	T	G	rs1044998	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	44	107	0	0.468085	0	T|0.820;G|0.180	0.180	strong	.	PCNT	283	.	NM_006031	exon30	c.T6563G	p.M2188R	AGGACATGTCTCT	.	PASS	Atlas-SNP
WDR92	116143	hgsc.bcm.edu	37	2	68364478	68364478	+	Missense_Mutation	SNP	T	T	C	rs13009282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	66	122	0	0.568965	0	T|0.804;C|0.196	0.196	strong	WDR92,NS,carcinoma,0,1	WDR92	21	1	NM_001256476	exon6	c.A721G	p.M241V	TTCTCATGTCAAA	.	PASS	Atlas-SNP
MCC	4163	hgsc.bcm.edu	37	5	112399791	112399791	+	Silent	SNP	G	G	A	rs2227947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	117	98	0	0.991525	0	G|0.494;A|0.506	0.506	strong	.	MCC	234	.	NM_001085377	exon14	c.C2103T	p.N701N	GGCAGCGTTCTCA	.	PASS	Atlas-SNP
ABCD3	5825	hgsc.bcm.edu	37	1	94930345	94930345	+	Silent	SNP	G	G	A	rs16946	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	154	165	0	0.980892	0	G|0.652;A|0.348	0.348	strong	.	ABCD3	62	.	NM_002858	exon3	c.G162A	p.K54K	GAAAAAGGAGCGA	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362745	32362745	+	Missense_Mutation	SNP	G	G	A	rs28362678	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	46	129	0	0.403509	0	G|0.859;A|0.141	0.141	strong	.	BTNL2	50	.	NM_019602	exon6	c.C1136T	p.P379L	CACATCGGCTGCA	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145293515	145293515	+	Missense_Mutation	SNP	A	A	G	rs12565078	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	28	101	0	0.297872	0	A|0.731;G|0.269	0.269	strong	.	NBPF10	221	.	NM_001039703	exon1	c.A110G	p.N37S	TCAGAAACCTCAA	.	PASS	Atlas-SNP
C10orf120	399814	hgsc.bcm.edu	37	10	124457906	124457906	+	Silent	SNP	C	C	T	rs2901343	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	82	189	0	0.420513	0	C|0.580;T|0.420	0.420	strong	.	C10orf120	55	.	NM_001010912	exon3	c.G351A	p.P117P	GTAGTCCGGAGAC	.	PASS	Atlas-SNP
MYO9A	4649	hgsc.bcm.edu	37	15	72180440	72180440	+	Silent	SNP	C	C	T	rs148060237	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	45	76	0	0.48913	0	C|0.983;T|0.017	0.017	strong	.	MYO9A	203	.	NM_006901	exon27	c.G5160A	p.S1720S	AACTGACGAAAAT	.	PASS	Atlas-SNP
FLT4	2324	hgsc.bcm.edu	37	5	180043388	180043388	+	Silent	SNP	G	G	A	rs1130378	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	64	120	0	0.484848	0	G|0.751;A|0.249	0.249	strong	.	FLT4	356	.	NM_182925	exon23	c.C3198T	p.P1066P	GTAGTCGGGGTCT	.	PASS	Atlas-SNP
KCNQ1	3784	hgsc.bcm.edu	37	11	2869086	2869086	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	36	31	0	0.545455	0	.	.	none	.	KCNQ1	60	.	NM_000218	exon16	c.C1884T	p.G628G	CAGCGGCGGCCCC	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634313	32634313	+	Missense_Mutation	SNP	C	C	G	rs1049059	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	23	4	0	0.766667	0	C|0.813;G|0.187	0.187	strong	.	HLA-DQB1	15	.	NM_002123	exon1	c.G72C	p.M24I	GCTCAGCATCGCC	.	PASS	Atlas-SNP
IL17RC	84818	hgsc.bcm.edu	37	3	9965582	9965582	+	Missense_Mutation	SNP	G	G	A	rs75692599	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	54	117	0	0.432	0	G|0.988;A|0.012	0.012	strong	.	IL17RC	55	.	NM_153461	exon8	c.G853A	p.V285M	CTCAACGTGTCAG	.	PASS	Atlas-SNP
KCNMB1	3779	hgsc.bcm.edu	37	5	169805956	169805956	+	Missense_Mutation	SNP	C	C	G	rs2301149	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	60	95	0	0.594059	0	C|0.898;G|0.102	0.102	strong	KCNMB1,NS,carcinoma,0,1	KCNMB1	38	1	NM_004137	exon4	c.G328C	p.E110Q	TGTCCACGCTGCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506752	195506752	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	23	25	0	0.328571	0	.	.	none	.	MUC4	1505	.	NM_018406	exon2	c.G11699A	p.R3900H	GCGTGACGTGTGG	.	PASS	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	37	17	33690619	33690619	+	Missense_Mutation	SNP	G	G	T	rs72825958	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	74	119	0	0.486842	0	G|0.859;T|0.141	0.141	strong	.	SLFN11	112	.	NM_152270	exon2	c.C208A	p.P70T	CCACGGGATGCTC	.	PASS	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	37	2	113943470	113943470	+	Silent	SNP	A	A	G	rs2241976	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	159	177	1	0.969512	0.00564972	A|0.460;G|0.540	0.540	strong	.	PSD4	74	.	NM_012455	exon5	c.A1266G	p.G422G	GGGTGGACACCCC	.	PASS	Atlas-SNP
R3HDM4	91300	hgsc.bcm.edu	37	19	899444	899444	+	Silent	SNP	C	C	T	rs2965284	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	36	69	0	0.493151	0	C|0.877;T|0.123	0.123	strong	C19orf22,NS,carcinoma,0,1	.	.	1	NM_138774	exon7	c.G699A	p.S233S	ACTGGCCGAGATG	.	PASS	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117122130	117122130	+	Missense_Mutation	SNP	T	T	C	rs6703791	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	108	0	0.435644	0	T|0.725;C|0.275	0.275	strong	.	IGSF3	294	.	NM_001542	exon11	c.A3278G	p.Q1093R	GTATCTTGGGGGC	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126237971	126237971	+	Silent	SNP	C	C	T	rs72928772	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	56	76	0	1	0	C|0.831;T|0.169	0.169	strong	.	FAT4	1752	.	NM_024582	exon1	c.C405T	p.F135F	CGTTTTCCCGGAC	.	PASS	Atlas-SNP
QRFPR	84109	hgsc.bcm.edu	37	4	122301622	122301622	+	Missense_Mutation	SNP	A	A	C	rs17438900	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	165	166	0	0.993976	0	A|0.852;C|0.147	0.147	strong	QRFPR,NS,carcinoma,0,1	QRFPR	65	1	NM_198179	exon1	c.T181G	p.F61V	TGCCAAAGAGCGC	.	PASS	Atlas-SNP
FSD1L	83856	hgsc.bcm.edu	37	9	108230553	108230553	+	Missense_Mutation	SNP	G	G	T	rs41316532	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	77	109	0	0.49359	0	G|0.992;T|0.008	0.008	strong	.	FSD1L	31	.	NM_001145313	exon4	c.G287T	p.S96I	AAGAAAGTATGAT	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71025245	71025245	+	Silent	SNP	C	C	T	rs1774516	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	19	140	6	0.103261	0.0428571	C|0.977;T|0.023	0.023	strong	LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	NM_001270974	exon25	c.G3840A	p.T1280T	AGCTTTCGTTTTT	.	scavenged	Atlas-SNP
BEND7	222389	hgsc.bcm.edu	37	10	13534851	13534851	+	Silent	SNP	A	A	G	rs2251555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	52	85	0	0.626506	0	A|0.476;G|0.524	0.524	strong	BEND7_ENST00000378605,colon,carcinoma,0,4	BEND7	85	4	NM_001100912	exon4	c.T480C	p.P160P	AATTGGAGGTTGT	.	PASS	Atlas-SNP
FAM129A	116496	hgsc.bcm.edu	37	1	184801065	184801065	+	Silent	SNP	T	T	C	rs487675	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	63	123	0	0.473684	0	T|0.682;C|0.318	0.318	strong	FAM129A,colon,carcinoma,0,1	FAM129A	98	1	NM_052966	exon6	c.A633G	p.Q211Q	AAAGGCTTGGGCT	.	PASS	Atlas-SNP
VEZF1	7716	hgsc.bcm.edu	37	17	56056550	56056550	+	Silent	SNP	C	C	G	rs1135655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	106	242	0	0.430894	0	C|0.907;G|0.093	0.093	strong	.	VEZF1	50	.	NM_007146	exon5	c.G1101C	p.L367L	CAGTCTCAGTGTT	.	PASS	Atlas-SNP
PCDHAC1	56135	hgsc.bcm.edu	37	5	140307746	140307746	+	Silent	SNP	C	C	G	rs155820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	31	47	0	0.62	0	C|0.680;G|0.320	0.320	strong	.	PCDHAC1	141	.	NM_031882	exon1	c.C1269G	p.P423P	CTCACCCCCACTT	.	PASS	Atlas-SNP
USP14	9097	hgsc.bcm.edu	37	18	166819	166819	+	Silent	SNP	T	T	C	rs563155	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	32	31	0	1	0	T|0.812;C|0.188	0.188	strong	.	USP14	41	.	NM_001037334	exon3	c.T195C	p.N65N	AAAAAATGTAAGT	.	PASS	Atlas-SNP
ZNF543	125919	hgsc.bcm.edu	37	19	57838018	57838018	+	Missense_Mutation	SNP	C	C	G	rs6510057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	48	95	0	0.432432	0	C|0.496;G|0.504	0.504	strong	.	ZNF543	61	.	NM_213598	exon3	c.C163G	p.P55A	TTCAAACCAGAGC	.	PASS	Atlas-SNP
STAP2	55620	hgsc.bcm.edu	37	19	4324564	4324564	+	Silent	SNP	C	C	T	rs57455784	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	29	62	0	0.591837	0	C|0.906;T|0.094	0.094	strong	STAP2,NS,carcinoma,-2,1	STAP2	38	1	NM_017720	exon12	c.G1173A	p.V391V	GTGGCTCACGCCG	.	PASS	Atlas-SNP
DCBLD2	131566	hgsc.bcm.edu	37	3	98619997	98619997	+	Silent	SNP	G	G	C	rs17852693	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	14	37	0	0.538462	0	G|0.859;C|0.141	0.141	strong	.	DCBLD2	62	.	NM_080927	exon1	c.C174G	p.L58L	CAGCAGGAGCAGG	.	PASS	Atlas-SNP
AGMAT	79814	hgsc.bcm.edu	37	1	15905501	15905501	+	Silent	SNP	G	G	A	rs41270261	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	78	90	0	0.928571	0	G|0.883;A|0.117	0.117	strong	AGMAT,colon,carcinoma,0,1	AGMAT	25	1	NM_024758	exon4	c.C573T	p.T191T	CTTGTCGGTCGTG	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197432029	197432029	+	Silent	SNP	C	C	A	rs60457064	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	33	62	0	0.507692	0	C|0.877;A|0.123	0.123	strong	.	KIAA0226	136	.	NM_014687	exon3	c.G237T	p.T79T	GTAATCCGTCTGG	.	PASS	Atlas-SNP
VEPH1	79674	hgsc.bcm.edu	37	3	157131788	157131788	+	Missense_Mutation	SNP	A	A	C	rs1378796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	66	117	0	0.5	0	A|0.850;C|0.150	0.150	strong	.	VEPH1	129	.	NM_001167911	exon6	c.T788G	p.V263G	TCATAGACTGCTA	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53990002	53990002	+	Silent	SNP	G	G	A	rs77810160	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	15	21	0	0.288462	0	G|0.500;A|0.500	0.500	strong	.	ZNF813	81	.	NM_001004301	exon3	c.G132A	p.L44L	GAACCTGGTCTCC	.	PASS	Atlas-SNP
MAP10	54627	hgsc.bcm.edu	37	1	232941354	232941354	+	Silent	SNP	G	G	T	rs12567597	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	8	13	0	0.444444	0	G|0.858;T|0.142	0.142	strong	.	.	.	.	NM_019090	exon1	c.G585T	p.L195L	CGGTCTGTGCCCC	.	PASS	Atlas-SNP
XPC	7508	hgsc.bcm.edu	37	3	14187449	14187449	+	Missense_Mutation	SNP	G	G	T	rs2228001	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	76	0	1	0	G|0.341;T|0.659	0.659	strong	.	XPC	60	.	NM_004628	exon16	c.C2815A	p.Q939K	ACAGCTGCTCAAA	.	PASS	Atlas-SNP
HLA-F	3134	hgsc.bcm.edu	37	6	29693019	29693019	+	Silent	SNP	G	G	A	rs201844059	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	60	191	0	0.384615	0	G|0.999;A|0.001	0.001	weak	.	HLA-F	41	.	NM_001098479	exon4	c.G822A	p.E274E	TGGAGAGGAACAG	.	PASS	Atlas-SNP
FAM131C	348487	hgsc.bcm.edu	37	1	16385042	16385042	+	Missense_Mutation	SNP	G	G	A	rs77667563	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	36	41	0	0.6	0	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	.	PASS	Atlas-SNP
EEF2K	29904	hgsc.bcm.edu	37	16	22237273	22237273	+	Missense_Mutation	SNP	C	C	G	rs17841292	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	31	56	0	0.484375	0	C|0.912;G|0.088	0.088	strong	EEF2K_ENST00000263026,NS,carcinoma,0,2	EEF2K	142	2	NM_013302	exon2	c.C223G	p.P75A	GGGTCCCCGGCAA	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128487893	128487893	+	Silent	SNP	G	G	A	rs2291568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	38	79	0	0.567164	0	A|0.179;C|0.011	0.179	strong	.	FLNC	339	.	NM_001127487	exon25	c.G4431A	p.L1477L	GCCCCTGCAGGTG	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115968797	115968797	+	Missense_Mutation	SNP	C	C	T	rs1133618	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	38	99	0	0.447059	0	C|0.805;T|0.195	0.195	strong	.	FKBP15	128	.	NM_015258	exon4	c.G316A	p.A106T	CTCTGGCTGTGTG	.	PASS	Atlas-SNP
ARPP21	10777	hgsc.bcm.edu	37	3	35778773	35778773	+	Silent	SNP	A	A	G	rs2278757	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	36	79	0	0.455696	0	A|0.525;G|0.475	0.475	strong	.	ARPP21	153	.	NM_016300	exon16	c.A1563G	p.P521P	GCAGCCACCACAG	.	PASS	Atlas-SNP
KIAA0753	9851	hgsc.bcm.edu	37	17	6538355	6538355	+	Silent	SNP	G	G	A	rs2301873	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	59	80	0	0.983333	0	G|0.637;A|0.363	0.363	strong	KIAA0753,NS,carcinoma,0,1	KIAA0753	63	1	NM_014804	exon2	c.C69T	p.S23S	GGGGTCGCTCCTC	.	PASS	Atlas-SNP
CCDC65	85478	hgsc.bcm.edu	37	12	49314862	49314862	+	Silent	SNP	C	C	A	rs10875894	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	49	56	1	1	0.0178571	C|0.681;A|0.319	0.319	strong	CCDC65,NS,carcinoma,+1,2	CCDC65	41	2	NM_033124	exon7	c.C1176A	p.T392T	GCTCACCAAGGTA	.	scavenged	Atlas-SNP
C19orf53	28974	hgsc.bcm.edu	37	19	13885484	13885484	+	Missense_Mutation	SNP	A	A	G	rs10104	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	111	266	0	0.451219	0	A|0.669;G|0.331	0.331	strong	.	C19orf53	14	.	NM_014047	exon2	c.A116G	p.K39R	CTCCCAAGAAGGC	.	PASS	Atlas-SNP
DCHS1	8642	hgsc.bcm.edu	37	11	6644600	6644600	+	Silent	SNP	C	C	T	rs72911011	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	24	61	0	0.470588	0	C|0.839;T|0.161	0.161	strong	.	DCHS1	277	.	NM_003737	exon21	c.G8307A	p.A2769A	CACTCGCGCACGC	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133236000	133236000	+	Silent	SNP	C	C	T	rs5744857	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	63	112	1	0.520661	0.00892857	C|0.443;T|0.557	0.557	strong	POLE_ENST00000320574,caecum,carcinoma,-1,2	POLE	416	2	NM_006231	exon26	c.G3156A	p.T1052T	GATGGACGTAGAC	.	scavenged	Atlas-SNP
CEBPZ	10153	hgsc.bcm.edu	37	2	37441091	37441091	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	32	121	0	0.421053	0	.	.	none	.	CEBPZ	68	.	NM_005760	exon10	c.G2461T	p.V821F	CAGCAACTTTTTT	.	PASS	Atlas-SNP
GSG2	83903	hgsc.bcm.edu	37	17	3628212	3628212	+	Missense_Mutation	SNP	T	T	C	rs220461	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	31	46	0	1	0	T|0.769;C|0.230	0.230	strong	.	GSG2	48	.	NM_031965	exon1	c.T983C	p.I328T	GGGGAATAGACAG	.	PASS	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	37	4	169158471	169158471	+	Silent	SNP	T	T	G	rs6552559	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	47	107	0	0.494737	0	T|0.825;G|0.175	0.175	strong	.	DDX60	304	.	NM_017631	exon32	c.A4377C	p.G1459G	GAAGAGTCCATTT	.	PASS	Atlas-SNP
TEX33	339669	hgsc.bcm.edu	37	22	37398201	37398201	+	Missense_Mutation	SNP	C	C	A	rs743750	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	27	85	0	0.36	0	C|0.716;A|0.284	0.284	strong	.	TEX33	25	.	NM_001163857	exon3	c.G166T	p.A56S	CGCTGGCTCCCAG	.	PASS	Atlas-SNP
TNC	3371	hgsc.bcm.edu	37	9	117819436	117819436	+	Silent	SNP	C	C	T	rs17819466	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	28	45	0	0.518519	0	C|0.913;T|0.087	0.087	strong	.	TNC	282	.	NM_002160	exon15	c.G4575A	p.T1525T	ACCTGTCGTGGCT	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3640785	3640785	+	Missense_Mutation	SNP	C	C	T	rs59939128	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	62	128	0	0.521008	0	C|0.927;T|0.073	0.073	strong	SLX4,NS,carcinoma,+2,1	SLX4	173	1	NM_032444	exon12	c.G2854A	p.A952T	CAAGCGCCTCCTC	.	PASS	Atlas-SNP
PRG4	10216	hgsc.bcm.edu	37	1	186275564	186275564	+	Missense_Mutation	SNP	C	C	T	rs12128607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	37	89	0	0.544118	0	C|0.969;T|0.031	0.031	strong	.	PRG4	259	.	NM_005807	exon7	c.C713T	p.T238M	CTGACACGTCTAC	.	PASS	Atlas-SNP
SMG8	55181	hgsc.bcm.edu	37	17	57290383	57290383	+	Silent	SNP	G	G	A	rs3744383	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	54	94	0	0.514286	0	G|0.551;A|0.449	0.449	strong	.	SMG8	79	.	NM_018149	exon3	c.G2199A	p.R733R	GAAGAGGCCAAAC	.	PASS	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139399213	139399213	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	10	25	0	0.5	0	.	.	none	NOTCH1,NS,lymphoid_neoplasm,+2,1	NOTCH1	1980	1	NM_017617	exon26	c.C4930T	p.L1644L	CCAGCAGGGCGTC	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	6978233	6978233	+	Missense_Mutation	SNP	C	C	T	rs145781920	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	85	179	0	0.488506	0	C|0.999;T|0.001	0.001	strong	.	LAMA1	458	.	NM_005559	exon43	c.G6152A	p.R2051Q	GTCTCTCGTAATG	.	PASS	Atlas-SNP
TONSL	4796	hgsc.bcm.edu	37	8	145665407	145665407	+	Missense_Mutation	SNP	C	C	T	rs2229315	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	123	108	0	0.984	0	T|0.531;G|0.000;C|0.469	0.531	strong	.	TONSL	128	.	NM_013432	exon11	c.G1477A	p.G493S	CACCGCCCTCTGA	.	PASS	Atlas-SNP
MARCH10	162333	hgsc.bcm.edu	37	17	60814273	60814273	+	Missense_Mutation	SNP	A	A	G	rs9891498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	71	173	0	0.435583	0	A|0.682;G|0.318	0.318	strong	.	MARCH10	102	.	NM_001100875	exon6	c.T956C	p.F319S	CCCCCAAATCTAC	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	62923326	62923326	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	262	6	235	1	0.0229008	0.00425532	.	.	none	DOCK7,rectum,carcinoma,+1,1	DOCK7	184	1	NM_001271999	exon48	c.A6230G	p.K2077R	TACTCCTTTTGAT	.	scavenged	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	37	4	169208334	169208334	+	Missense_Mutation	SNP	C	C	T	rs72693161	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	40	128	0	0.36036	0	C|0.970;T|0.030	0.030	strong	.	DDX60	304	.	NM_017631	exon10	c.G1204A	p.D402N	TGGTATCTCCCAA	.	PASS	Atlas-SNP
CCT8L2	150160	hgsc.bcm.edu	37	22	17072411	17072411	+	Missense_Mutation	SNP	G	G	T	rs41277596	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	52	95	0	0.547368	0	G|0.994;T|0.006	0.006	strong	.	CCT8L2	150	.	NM_014406	exon1	c.C1030A	p.P344T	TGCCTGGCCTCTG	.	PASS	Atlas-SNP
SYT3	84258	hgsc.bcm.edu	37	19	51133356	51133356	+	Silent	SNP	C	C	G	rs10407511	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	52	86	0	0.52	0	C|0.328;G|0.672	0.672	strong	.	SYT3	85	.	NM_032298	exon3	c.G747C	p.R249R	AGGTGGCCGCTCC	.	PASS	Atlas-SNP
POR	5447	hgsc.bcm.edu	37	7	75615006	75615006	+	Missense_Mutation	SNP	C	C	T	rs1057868	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	59	46	0	0.621053	0	C|0.723;T|0.277	0.277	strong	.	POR	46	.	NM_000941	exon13	c.C1508T	p.A503V	AGCCTGCCGGGGA	.	PASS	Atlas-SNP
CPA6	57094	hgsc.bcm.edu	37	8	68421768	68421768	+	Missense_Mutation	SNP	G	G	C	rs17853192	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	60	142	0	0.594059	0	G|0.925;C|0.075	0.075	strong	.	CPA6	69	.	NM_020361	exon5	c.C518G	p.S173C	AAAAGAGATCTTC	.	PASS	Atlas-SNP
KIF21A	55605	hgsc.bcm.edu	37	12	39735348	39735348	+	Missense_Mutation	SNP	C	C	A	rs79089655	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	59	144	0	0.522124	0	C|0.971;A|0.029	0.029	strong	.	KIF21A	238	.	NM_001173464	exon14	c.G1880T	p.G627V	CTTTCACCCCCAT	.	PASS	Atlas-SNP
XRN1	54464	hgsc.bcm.edu	37	3	142123841	142123841	+	Silent	SNP	C	C	T	rs2306700	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	247	245	273	1	0.991903	0.003663	C|0.867;T|0.133	0.133	strong	.	XRN1	138	.	NM_001042604	exon16	c.G1791A	p.E597E	TAGGCACTCACTA	.	PASS	Atlas-SNP
TRRAP	8295	hgsc.bcm.edu	37	7	98580987	98580987	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	2	120	0	0.0128205	0	.	.	none	TRRAP_ENST00000359863,NS,carcinoma,+1,2	TRRAP	863	2	NM_001244580	exon59	c.C8906T	p.T2969M	TGAAGACGGTGGT	.	scavenged	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74759477	74759477	+	Missense_Mutation	SNP	C	C	T	rs4148077	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	48	77	0	0.45283	0	C|0.709;T|0.291	0.291	strong	.	ABCD4	54	.	NM_005050	exon9	c.G910A	p.A304T	GCTCTGCGGGACT	.	PASS	Atlas-SNP
DCK	1633	hgsc.bcm.edu	37	4	71888240	71888240	+	Missense_Mutation	SNP	C	C	T	rs67437265	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	14	44	0	0.482759	0	C|0.975;T|0.025	0.025	strong	.	DCK	23	.	NM_000788	exon3	c.C364T	p.P122S	GAGAAACCTGTAT	.	PASS	Atlas-SNP
RSAD1	55316	hgsc.bcm.edu	37	17	48557326	48557326	+	Missense_Mutation	SNP	G	G	A	rs2290862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	115	109	0	0.991379	0	G|0.331;A|0.669	0.669	strong	.	RSAD1	36	.	NM_018346	exon3	c.G355A	p.A119T	GCACAGGCAGCCC	.	PASS	Atlas-SNP
VPS13A	23230	hgsc.bcm.edu	37	9	79985181	79985181	+	Silent	SNP	C	C	T	rs117485827	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	51	106	0	0.536842	0	C|0.993;T|0.007	0.007	strong	.	VPS13A	735	.	NM_001018038	exon64	c.C8676T	p.I2892I	AGCCATCCAGGGT	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379109	31379109	+	Missense_Mutation	SNP	G	G	A	rs1051794	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	88	83	0	0.988764	0	G|0.642;A|0.358	0.358	strong	.	MICA	21	.	NM_001177519	exon3	c.G586A	p.E196K	TATCTAGAATCCG	.	PASS	Atlas-SNP
STON1-GTF2A1L	286749	hgsc.bcm.edu	37	2	48873662	48873662	+	Silent	SNP	T	T	C	rs13396590	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	259	112	213	0	0.432432	0	T|0.899;C|0.101	0.101	strong	.	STON1-GTF2A1L	180	.	NM_001198593	exon8	c.T2571C	p.H857H	TCAGCATCCAATT	.	PASS	Atlas-SNP
EEF2K	29904	hgsc.bcm.edu	37	16	22237118	22237118	+	Missense_Mutation	SNP	A	A	G	rs9935059	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	45	77	0	0.511364	0	A|0.816;G|0.184	0.184	strong	.	EEF2K	142	.	NM_013302	exon2	c.A68G	p.H23R	CTGGCCATGATGG	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38345455	38345455	+	Silent	SNP	A	A	G	rs12242343	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	40	84	0	0.56338	0	A|0.968;G|0.032	0.032	strong	.	ZNF33A	103	.	NM_006954	exon5	c.A2403G	p.G801G	CTGTGGAGAAAGC	.	PASS	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43837052	43837052	+	Missense_Mutation	SNP	C	C	A	rs199672858	by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	2	149	0	0.0145985	0	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
ZMYND11	10771	hgsc.bcm.edu	37	10	267222	267222	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	353	4	400	0	0.0113314	0	.	.	none	ZMYND11_ENST00000397962,NS,carcinoma,-1,3	ZMYND11	72	3	NM_212479	exon4	c.T364C	p.Y122H	CGTGTGTATCATT	.	scavenged	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329922	55329922	+	Missense_Mutation	SNP	A	A	T	rs1049150	bycluster;byfrequency;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	30	31	0	0.535714	0	A|0.545;T|0.455	0.455	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.A223T	p.I75L	GGCAGAATATTCC	.	PASS	Atlas-SNP
CDC37L1	55664	hgsc.bcm.edu	37	9	4679847	4679847	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	38	78	0	0.361905	0	.	.	none	.	CDC37L1	19	.	NM_017913	exon1	c.A80C	p.D27A	ACTTCGACGTGTT	.	PASS	Atlas-SNP
UQCRC1	7384	hgsc.bcm.edu	37	3	48638801	48638801	+	Missense_Mutation	SNP	C	C	T	rs62618742	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	73	149	0	0.483444	0	C|0.979;T|0.021	0.021	strong	UQCRC1,NS,carcinoma,-1,2	UQCRC1	42	2	NM_003365	exon7	c.G806A	p.R269H	GTGAAGCGGCATG	.	PASS	Atlas-SNP
GFM2	84340	hgsc.bcm.edu	37	5	74017499	74017499	+	Missense_Mutation	SNP	C	C	T	rs1048167	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	44	81	0	0.488889	0	C|0.856;T|0.144	0.144	strong	.	GFM2	38	.	NM_032380	exon21	c.G2321A	p.R774Q	CTTCTCCGGTTGA	.	PASS	Atlas-SNP
MTA1	9112	hgsc.bcm.edu	37	14	105930406	105930406	+	Missense_Mutation	SNP	G	G	A	rs4983413	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	84	127	1	0.512195	0.00787402	G|0.782;A|0.218	0.218	strong	MTA1,NS,carcinoma,0,1	MTA1	61	1	NM_004689	exon13	c.G1114A	p.V372I	AACAACGTCAAGG	.	scavenged	Atlas-SNP
IRF2BP1	26145	hgsc.bcm.edu	37	19	46388379	46388379	+	Silent	SNP	C	C	G	rs3826892	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	16	31	0	0.5	0	C|0.899;G|0.101	0.101	strong	IRF2BP1,NS,carcinoma,0,1	IRF2BP1	23	1	NM_015649	exon1	c.G654C	p.R218R	CTCTGCCCGGCCT	.	PASS	Atlas-SNP
SORCS3	22986	hgsc.bcm.edu	37	10	106974224	106974224	+	Missense_Mutation	SNP	C	C	A	rs200098588	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	62	112	0	0.504065	0	C|1.000;A|0.000	0.000	strong	.	SORCS3	282	.	NM_014978	exon18	c.C2400A	p.N800K	CAACAACTGCACA	.	PASS	Atlas-SNP
PHF10	55274	hgsc.bcm.edu	37	6	170115902	170115902	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	16	161	0	0.131148	0	.	.	none	PHF10_ENST00000339209,NS,carcinoma,0,3	PHF10	76	3	NM_018288	exon6	c.T595G	p.Y199D	TAATATACTCAGG	.	scavenged	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	37	10	101716484	101716484	+	Silent	SNP	G	G	A	rs3750715	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	37	57	0	0.552239	0	G|0.963;N|0.001	.	strong	.	DNMBP	173	.	NM_015221	exon4	c.C747T	p.V249V	CAGGGCGACCCCA	.	PASS	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126372742	126372742	+	Missense_Mutation	SNP	G	G	A	rs1567047	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	139	178	0	0.992857	0	G|0.769;A|0.231	0.231	strong	.	FAT4	1752	.	NM_024582	exon9	c.G10571A	p.G3524D	GGCCAGGCACTTT	.	PASS	Atlas-SNP
CUL5	8065	hgsc.bcm.edu	37	11	107965639	107965639	+	Silent	SNP	G	G	A	rs146843253	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	53	72	0	0.576087	0	G|1.000;A|0.000	0.000	strong	.	CUL5	71	.	NM_003478	exon15	c.G1668A	p.P556P	GATACCGGAAGTA	.	PASS	Atlas-SNP
OTOP3	347741	hgsc.bcm.edu	37	17	72943434	72943434	+	Missense_Mutation	SNP	G	G	A	rs35702634	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	56	85	0	0.554455	0	G|0.989;A|0.011	0.011	strong	OTOP3,NS,carcinoma,+1,1	OTOP3	64	1	NM_178233	exon6	c.G1484A	p.R495H	CTCCCCGCAGAGG	.	PASS	Atlas-SNP
PTPN5	84867	hgsc.bcm.edu	37	11	18751041	18751041	+	Silent	SNP	C	C	T	rs1550870	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	38	26	0	0.95	0	C|0.633;T|0.367	0.367	strong	.	PTPN5	163	.	NM_032781	exon14	c.G1563A	p.V521V	GTCCACCACACCC	.	PASS	Atlas-SNP
LIPI	149998	hgsc.bcm.edu	37	21	15481365	15481365	+	Missense_Mutation	SNP	G	G	T	rs7278737	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	35	94	0	0.416667	0	G|0.501;T|0.499	0.499	strong	LIPI,caecum,carcinoma,-2,1	LIPI	95	1	NM_198996	exon10	c.C1395A	p.D465E	CTCTCTGTCTTTA	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940267	144940267	+	Silent	SNP	G	G	A	rs28441354	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	13	184	0	0.0572687	0	G|0.995;A|0.005	0.005	weak	.	EPPK1	199	.	NM_031308	exon1	c.C7155T	p.G2385G	GAAGAAGCCCTTG	.	PASS	Atlas-SNP
KRT8	3856	hgsc.bcm.edu	37	12	53294381	53294381	+	Silent	SNP	T	T	C	rs8608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	27	48	0	0.442623	0	T|0.483;C|0.517	0.517	strong	.	KRT8	41	.	NM_001256282	exon5	c.A765G	p.L255L	TTCATATAGCTGC	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54724457	54724457	+	Missense_Mutation	SNP	T	T	C	rs1052995	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	39	106	0	0.448276	0	T|1.000;|0.000	.	strong	.	LILRB3	67	.	NM_006864	exon6	c.A1199G	p.Y400C	GAGCTGTATGAGC	.	PASS	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100995721	100995721	+	Missense_Mutation	SNP	A	A	G	rs879369	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	36	81	0	0.610169	0	T|0.000;G|0.439;C|0.000;A|0.561	0.439	strong	.	TBC1D2	70	.	NM_001267571	exon4	c.T758C	p.L253S	GAGGCCAAGGGCT	.	PASS	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161139480	161139480	+	Silent	SNP	C	C	T	rs1130656	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	25	81	0	1	0	C|0.636;T|0.364	0.364	strong	PLG,NS,carcinoma,0,1	PLG	150	1	NM_000301	exon8	c.C942T	p.F314F	AAACTTCCCCTGC	.	PASS	Atlas-SNP
GOLGA3	2802	hgsc.bcm.edu	37	12	133389998	133389998	+	Silent	SNP	T	T	C	rs7134809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	44	90	0	0.478261	0	T|0.897;C|0.103	0.103	strong	.	GOLGA3	234	.	NM_001172557	exon4	c.A414G	p.T138T	AGAATCTGTAGAG	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	5	81	3	0.0462963	0.037037	.	.	weak	KRTAP4-11,NS,carcinoma,-1,11	KRTAP4-11	94	11	NM_033059	exon1	c.G153A	p.R51R	CTGGGGCCTGCAG	.	scavenged	Atlas-SNP
CTCFL	140690	hgsc.bcm.edu	37	20	56098733	56098733	+	Missense_Mutation	SNP	T	T	C	rs6025606	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	114	97	0	0.991304	0	T|0.260;C|0.740	0.740	strong	.	CTCFL	97	.	NM_001269044	exon1	c.A529G	p.T177A	GTCCAGTAGTTTC	.	PASS	Atlas-SNP
TAS2R3	50831	hgsc.bcm.edu	37	7	141464765	141464765	+	Silent	SNP	C	C	T	rs2270009	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	76	155	0	0.531469	0	C|0.568;N|0.000	.	strong	.	TAS2R3	40	.	NM_016943	exon1	c.C807T	p.G269G	GATTGGCGAAGTA	.	PASS	Atlas-SNP
APLF	200558	hgsc.bcm.edu	37	2	68753240	68753240	+	Missense_Mutation	SNP	T	T	A	rs35002937	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	76	159	0	0.45509	0	T|0.754;A|0.246	0.246	strong	APLF,colon,carcinoma,0,1	APLF	69	1	NM_173545	exon6	c.T670A	p.S224T	GATAAATCCCAGC	.	PASS	Atlas-SNP
KRT7	3855	hgsc.bcm.edu	37	12	52635360	52635360	+	Silent	SNP	G	G	A	rs999665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	91	95	0	0.968085	0	G|0.514;A|0.486	0.486	strong	KRT7,NS,carcinoma,0,1	KRT7	48	1	NM_005556	exon5	c.G798A	p.A266A	CAAGGCGCAGTAT	.	PASS	Atlas-SNP
MMEL1	79258	hgsc.bcm.edu	37	1	2541269	2541269	+	Silent	SNP	A	A	G	rs10797440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	97	93	0	0.979798	0	A|0.542;G|0.458	0.458	strong	.	MMEL1	64	.	NM_033467	exon5	c.T294C	p.A98A	CCTGGCAGCTGCT	.	PASS	Atlas-SNP
C5orf48	389320	hgsc.bcm.edu	37	5	125968301	125968301	+	Silent	SNP	C	C	T	rs6887295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	43	89	0	0.551282	0	C|0.870;T|0.130	0.130	strong	.	C5orf48	21	.	NM_207408	exon2	c.C150T	p.V50V	TTATGTCATGCCT	.	PASS	Atlas-SNP
RNF123	63891	hgsc.bcm.edu	37	3	49740895	49740895	+	Missense_Mutation	SNP	A	A	G	rs35726701	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	106	184	0	0.538071	0	A|0.986;G|0.014	0.014	strong	.	RNF123	100	.	NM_022064	exon21	c.A1786G	p.K596E	AATGGCAAGGTGG	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47961711	47961711	+	Silent	SNP	G	G	A	rs2070435	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	32	55	0	0.438356	0	G|0.580;A|0.420	0.420	strong	.	DIP2A	332	.	NM_206891	exon18	c.G2079A	p.L693L	AGTCCTGTCGATG	.	PASS	Atlas-SNP
C1QTNF8	390664	hgsc.bcm.edu	37	16	1143605	1143605	+	Missense_Mutation	SNP	C	C	A	rs116934818	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	15	13	0	0.416667	0	C|0.987;A|0.013	0.013	strong	.	C1QTNF8	15	.	NM_207419	exon4	c.G655T	p.V219L	TGCGCACCCAGAC	.	PASS	Atlas-SNP
NUGGC	389643	hgsc.bcm.edu	37	8	27898580	27898580	+	Silent	SNP	T	T	C	rs17058502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	33	56	0	0.568965	0	T|0.884;C|0.116	0.116	strong	.	.	.	.	NM_001010906	exon13	c.A1599G	p.R533R	GCATGCTCTGAGG	.	PASS	Atlas-SNP
UBXN2B	137886	hgsc.bcm.edu	37	8	59358556	59358556	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	30	78	0	0.483871	0	.	.	none	.	UBXN2B	36	.	NM_001077619	exon7	c.G762A	p.V254V	TTCAGTGCCAACA	.	PASS	Atlas-SNP
WLS	79971	hgsc.bcm.edu	37	1	68624878	68624878	+	Silent	SNP	C	C	T	rs3748705	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	40	108	0	0.449438	0	C|0.664;T|0.336	0.336	strong	.	WLS	97	.	NM_024911	exon3	c.G432A	p.A144A	AGCAAACGCGTCA	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76567708	76567708	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	73	111	0	0.51049	0	.	.	none	.	DNAH17	347	.	NM_173628	exon4	c.C696T	p.D232D	CCGAGTGTCCCAG	.	PASS	Atlas-SNP
NEU2	4759	hgsc.bcm.edu	37	2	233899126	233899126	+	Missense_Mutation	SNP	C	C	A	rs2233391	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	58	89	0	0.542056	0	C|0.668;A|0.332	0.332	strong	.	NEU2	42	.	NM_005383	exon2	c.C502A	p.H168N	CAGCTTCACGACA	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248924	48248924	+	Silent	SNP	G	G	A	rs3181870	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	71	99	0	0.455128	0	G|0.981;A|0.019	0.019	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.G108A	p.R36R	GAGGCGGCGGCGG	.	PASS	Atlas-SNP
KIAA1671	85379	hgsc.bcm.edu	37	22	25577667	25577667	+	Silent	SNP	G	G	A	rs199924926		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	49	98	0	0.526882	0	.	.	weak	.	KIAA1671	28	.	NM_001145206	exon8	c.G5076A	p.E1692E	AACAGAGGAGAAA	.	PASS	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64216815	64216815	+	Missense_Mutation	SNP	C	C	T	rs8178847	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	79	115	0	0.533784	0	C|0.927;T|0.073	0.073	strong	.	APOH	45	.	NM_000042	exon5	c.G461A	p.R154H	TAAACACGAAGTG	.	PASS	Atlas-SNP
RALGAPA1	253959	hgsc.bcm.edu	37	14	36153177	36153177	+	Missense_Mutation	SNP	T	T	C	rs2274068	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	146	205	1	1	0.00487805	T|0.603;C|0.397	0.397	strong	.	RALGAPA1	289	.	NM_194301	exon20	c.A2791G	p.T931A	TGTCGGTTCCAAA	.	PASS	Atlas-SNP
DNER	92737	hgsc.bcm.edu	37	2	230456365	230456365	+	Silent	SNP	C	C	T	rs138325902	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	2	136	1	0.0124224	0.00735294	C|1.000;T|0.000	0.000	strong	DNER,colon,carcinoma,-1,2	DNER	129	2	NM_139072	exon2	c.G516A	p.T172T	TGTCACCGTTGCC	.	scavenged	Atlas-SNP
RASGRP3	25780	hgsc.bcm.edu	37	2	33759395	33759395	+	Silent	SNP	C	C	T	rs35933402	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	42	84	0	0.371681	0	C|0.890;T|0.110	0.110	strong	.	RASGRP3	87	.	NM_170672	exon12	c.C1089T	p.S363S	GCTTTCCCTGGAC	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36842086	36842086	+	Silent	SNP	G	G	A	rs112401596	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	39	73	0	0.47561	0	G|0.986;A|0.014	0.014	strong	.	KIAA1755	145	.	NM_001029864	exon14	c.C2961T	p.T987T	CCTTGAGGTCTTG	.	PASS	Atlas-SNP
ZNF790	388536	hgsc.bcm.edu	37	19	37310344	37310344	+	Missense_Mutation	SNP	T	T	C	rs3745775	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	18	42	0	0.409091	0	T|0.723;C|0.277	0.277	strong	.	ZNF790	89	.	NM_206894	exon5	c.A902G	p.Q301R	ATTCTCTGATGTC	.	PASS	Atlas-SNP
C8B	732	hgsc.bcm.edu	37	1	57415310	57415310	+	Missense_Mutation	SNP	G	G	A	rs12085435	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	59	104	0	0.483607	0	G|0.944;A|0.056	0.056	strong	.	C8B	107	.	NM_000066	exon6	c.C782T	p.P261L	ATTCCAGGTATTT	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017673	109017673	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	34	178	2	0.228188	0.011236	.	.	none	SELPLG_ENST00000550948,NS,carcinoma,-1,7	SELPLG	138	7	NM_001206609	exon2	c.G459A	p.V153V	CGTGGGCACTGGT	.	scavenged	Atlas-SNP
KCTD15	79047	hgsc.bcm.edu	37	19	34302280	34302280	+	Silent	SNP	C	C	G	rs10426916	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	7	3	0	0.368421	0	C|0.880;G|0.120	0.120	strong	KCTD15,NS,carcinoma,0,1	KCTD15	18	1	NM_001129995	exon6	c.C516G	p.R172R	GGTGCGCGTCACG	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32776616	32776616	+	Missense_Mutation	SNP	T	T	A	rs61750791	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	61	90	0	0.525862	0	T|0.916;A|0.084	0.084	strong	.	FRY	312	.	NM_023037	exon31	c.T3970A	p.C1324S	TTGTCATGTGAGC	.	PASS	Atlas-SNP
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234883	26234883	+	Silent	SNP	A	A	G	rs2050950	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	73	198	0	0.439759	0	A|0.854;G|0.146	0.146	strong	.	HIST1H1D	40	.	NM_005320	exon1	c.T279C	p.T93T	CACCAGAGTACCT	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53995004	53995004	+	Silent	SNP	G	G	A	rs2708845	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	87	94	1	1	0.0106383	G|0.248;A|0.752	0.752	strong	ZNF813_ENST00000396403,colon,carcinoma,+1,1	ZNF813	81	1	NM_001004301	exon4	c.G1518A	p.R506R	TAATCGGAAAACA	.	scavenged	Atlas-SNP
AQR	9716	hgsc.bcm.edu	37	15	35198879	35198879	+	Silent	SNP	G	G	A	rs80093103	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	42	93	0	0.56	0	G|0.946;A|0.054	0.054	strong	.	AQR	139	.	NM_014691	exon18	c.C1698T	p.T566T	ACGTACGGTAATT	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3613928	3613928	+	Missense_Mutation	SNP	A	A	G	rs45483498	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	11	37	0	0.578947	0	A|0.926;G|0.074	0.074	strong	.	NLRC3	103	.	NM_178844	exon5	c.T1010C	p.M337T	AGCGCCATCCCCG	.	PASS	Atlas-SNP
GPR156	165829	hgsc.bcm.edu	37	3	119886101	119886101	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	46	81	0	0.484211	0	.	.	none	.	GPR156	85	.	NM_153002	exon9	c.C2223T	p.H741H	ATAGCTGTGTTGA	.	PASS	Atlas-SNP
ATP8B3	148229	hgsc.bcm.edu	37	19	1785185	1785185	+	Missense_Mutation	SNP	C	C	T	rs16994563	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	24	59	0	0.338028	0	C|0.954;T|0.046	0.046	strong	.	ATP8B3	108	.	NM_138813	exon27	c.G3505A	p.V1169I	GGGATACTCTGAA	.	PASS	Atlas-SNP
RRBP1	6238	hgsc.bcm.edu	37	20	17602571	17602571	+	Missense_Mutation	SNP	A	A	G	rs2229886	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	36	44	0	0.571429	0	A|0.964;G|0.036	0.036	strong	.	RRBP1	157	.	NM_004587	exon14	c.T1870C	p.C624R	TCAGACAGAGCTG	.	PASS	Atlas-SNP
AMBRA1	55626	hgsc.bcm.edu	37	11	46431914	46431914	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	34	56	0	0.390805	0	.	.	none	.	AMBRA1	201	.	NM_001267782	exon18	c.T3130G	p.L1044V	AGTTTAAGGCCCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910752	29910752	+	Missense_Mutation	SNP	G	G	C	rs1136683	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	41	147	0	0.5125	0	C|0.195;G|0.805	0.195	strong	HLA-A,NS,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon2	c.G292C	p.D98H	CAGACTGACCGAG	.	PASS	Atlas-SNP
RAB6B	51560	hgsc.bcm.edu	37	3	133547692	133547692	+	Silent	SNP	G	G	A	rs2293373	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	16	41	0	0.340426	0	G|0.856;A|0.144	0.144	strong	.	RAB6B	36	.	NM_016577	exon8	c.C567T	p.I189I	GATGTCGATCACT	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	37	16	2812647	2812647	+	Silent	SNP	C	C	T	rs2240142	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	25	63	0	0.390625	0	C|0.826;T|0.174	0.174	strong	SRRM2,NS,lymphoid_neoplasm,0,1	SRRM2	263	1	NM_016333	exon11	c.C2118T	p.S706S	TAGAAGCTTAGTT	.	PASS	Atlas-SNP
SFTPD	6441	hgsc.bcm.edu	37	10	81706324	81706324	+	Missense_Mutation	SNP	A	A	G	rs721917	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	69	116	0	0.479167	0	A|0.559;G|0.441	0.441	strong	SFTPD,NS,carcinoma,+1,1	SFTPD	43	1	NM_003019	exon2	c.T92C	p.M31T	CTGGGCATTGTTC	.	PASS	Atlas-SNP
CIITA	4261	hgsc.bcm.edu	37	16	11001770	11001770	+	Silent	SNP	G	G	T	rs34654419	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	22	27	0	0.458333	0	T|0.193;G|0.806;C|0.000	0.193	strong	CIITA_ENST00000324288,NS,lymphoid_neoplasm,0,1	CIITA	92	1	NM_000246	exon11	c.G2421T	p.L807L	GCTGCTGGAGCTG	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46895427	46895427	+	Missense_Mutation	SNP	G	G	T	rs62000965	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	65	141	0	0.439189	0	G|0.976;T|0.024	0.024	strong	.	COL18A1	129	.	NM_030582	exon4	c.G1316T	p.R439L	ACGCCCGGGAGCT	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324574	31324574	+	Silent	SNP	C	C	T	rs9266175	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	89	20	0	1	0	C|0.970;T|0.030	0.030	strong	.	HLA-B	54	.	NM_005514	exon2	c.G234A	p.Q78Q	CCCCTCCTGCTCT	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38798171	38798171	+	Silent	SNP	C	C	T	rs62244070	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	40	36	0	1	0	C|0.785;T|0.215	0.215	strong	.	SCN10A	359	.	NM_006514	exon9	c.G1284A	p.E428E	CTCCTGCTCCTTC	.	PASS	Atlas-SNP
NUP98	4928	hgsc.bcm.edu	37	11	3723941	3723941	+	Silent	SNP	C	C	T	rs35488940	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	72	167	0	0.409091	0	C|0.951;T|0.049	0.049	strong	.	NUP98	149	.	NM_016320	exon23	c.G3264A	p.P1088P	TTTCAACGGAACC	.	PASS	Atlas-SNP
C11orf21	29125	hgsc.bcm.edu	37	11	2323089	2323089	+	Missense_Mutation	SNP	C	C	T	rs188839109	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	34	54	0	0.485714	0	C|0.993;T|0.007	0.007	strong	.	C11orf21	11	.	NM_001142946	exon1	c.G3A	p.M1I	CGAGGCCATGTCT	.	PASS	Atlas-SNP
TTC8	123016	hgsc.bcm.edu	37	14	89319359	89319359	+	Silent	SNP	G	G	A	rs141304350	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	73	139	0	0.483444	0	G|1.000;A|0.000	0.000	strong	.	TTC8	42	.	NM_144596	exon8	c.G669A	p.K223K	GTACAAGGACTGG	.	PASS	Atlas-SNP
EMR1	2015	hgsc.bcm.edu	37	19	6913707	6913707	+	Missense_Mutation	SNP	C	C	T	rs466876	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	45	102	0	0.445545	0	C|0.824;T|0.176	0.176	strong	.	EMR1	153	.	NM_001256253	exon11	c.C1166T	p.T389M	TATCCACGTGGAC	.	PASS	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	37	19	39230748	39230748	+	Silent	SNP	C	C	G	rs34911882	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	24	55	0	0.5	0	C|0.943;G|0.057	0.057	strong	.	CAPN12	43	.	NM_144691	exon5	c.G672C	p.L224L	AGAGAACAGCCCC	.	PASS	Atlas-SNP
ZNF354A	6940	hgsc.bcm.edu	37	5	178139355	178139355	+	Silent	SNP	T	T	C	rs113805764	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	16	133	0	0.207792	0	T|0.988;C|0.012	0.012	strong	.	ZNF354A	74	.	NM_005649	exon5	c.A1524G	p.S508S	ACTAAGTGATGAG	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113234507	113234507	+	Missense_Mutation	SNP	T	T	C	rs10817025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	182	151	0	1	0	T|0.798;C|0.202	0.202	strong	.	SVEP1	326	.	NM_153366	exon15	c.A2696G	p.K899R	GAGGACTTGGCAT	.	PASS	Atlas-SNP
OR2G2	81470	hgsc.bcm.edu	37	1	247752019	247752019	+	Missense_Mutation	SNP	G	G	C	rs1151687	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	292	125	282	1	0.428082	0.0035461	G|0.435;C|0.565	0.565	strong	OR2G2,NS,adenoma,0,2	OR2G2	88	2	NM_001001915	exon1	c.G358C	p.V120L	CCGGCTGTGATGT	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	220	142	0	0.990991	0	C|0.840;G|0.160	0.160	strong	.	HLA-C	92	.	NM_002117	exon2	c.G270C	p.K90N	CTTGTACTTCTGT	.	PASS	Atlas-SNP
PCDHGB5	56101	hgsc.bcm.edu	37	5	140778256	140778256	+	Missense_Mutation	SNP	G	G	A	rs6867460	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	110	131	1	0.990991	0.00763359	G|0.804;A|0.196	0.196	strong	.	.	.	.	NM_018925	exon1	c.G562A	p.G188S	CAGGATGGTAGTA	.	PASS	Atlas-SNP
RNF20	56254	hgsc.bcm.edu	37	9	104324545	104324545	+	Silent	SNP	G	G	A	rs10521057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	92	84	0	1	0	G|0.836;A|0.164	0.164	strong	RNF20,NS,carcinoma,0,1	RNF20	110	1	NM_019592	exon20	c.G2769A	p.P923P	CTGTCCGTGCTGT	.	PASS	Atlas-SNP
OR10K2	391107	hgsc.bcm.edu	37	1	158390501	158390501	+	Silent	SNP	G	G	A	rs34616883	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	245	119	261	0	0.485714	0	G|0.643;A|0.357	0.357	strong	OR10K2,NS,carcinoma,0,1	OR10K2	69	1	NM_001004476	exon1	c.C156T	p.D52D	GGCCCTGTCCAGG	.	PASS	Atlas-SNP
SLC4A1	6521	hgsc.bcm.edu	37	17	42335135	42335135	+	Silent	SNP	C	C	T	rs5017	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	52	99	0	0.448276	0	C|0.948;T|0.052	0.052	strong	.	SLC4A1	104	.	NM_000342	exon12	c.G1323A	p.L441L	GGAGATCAGCAGC	.	PASS	Atlas-SNP
UTP15	84135	hgsc.bcm.edu	37	5	72874907	72874907	+	Silent	SNP	A	A	C	rs343122	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	54	129	0	0.473684	0	A|0.839;C|0.161	0.161	strong	.	UTP15	30	.	NM_032175	exon11	c.A1212C	p.G404G	AAGAGGAGTCCTT	.	PASS	Atlas-SNP
OR7D4	125958	hgsc.bcm.edu	37	19	9325116	9325116	+	Missense_Mutation	SNP	G	G	A	rs5020278	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	69	114	0	0.43949	0	G|0.845;A|0.155	0.155	strong	.	OR7D4	66	.	NM_001005191	exon1	c.C398T	p.T133M	ATGACCGTGTAGT	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537258	88537258	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	20	142	4	0.130719	0.028169	.	.	none	DSPP,NS,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.T3444C	p.S1148S	CAGCAGTGAAAGC	.	scavenged	Atlas-SNP
APOH	350	hgsc.bcm.edu	37	17	64208285	64208285	+	Missense_Mutation	SNP	C	C	G	rs1801690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	53	120	0	0.514563	0	C|0.960;G|0.040	0.040	strong	APOH,rectum,carcinoma,+1,1	APOH	45	1	NM_000042	exon8	c.G1004C	p.W335S	GTTTTCCAAAAAG	.	PASS	Atlas-SNP
B3GALNT1	8706	hgsc.bcm.edu	37	3	160804167	160804167	+	Missense_Mutation	SNP	C	C	T	rs2231257	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	29	58	0	0.42029	0	C|0.973;T|0.027	0.027	strong	.	B3GALNT1	34	.	NM_001038628	exon8	c.G376A	p.D126N	TTTTGTCTTCCTT	.	PASS	Atlas-SNP
TOPBP1	11073	hgsc.bcm.edu	37	3	133327457	133327457	+	Silent	SNP	T	T	C	rs1051772	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	49	105	0	0.415254	0	T|0.900;C|0.100	0.100	strong	.	TOPBP1	218	.	NM_007027	exon27	c.A4347G	p.S1449S	AACTCCTGAGTCA	.	PASS	Atlas-SNP
CXXC1	30827	hgsc.bcm.edu	37	18	47813157	47813157	+	Silent	SNP	C	C	A	rs375253589		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	62	114	0	0.449275	0	.	.	weak	.	CXXC1	50	.	NM_001101654	exon2	c.G75T	p.A25A	GATGGGCGCATTC	.	PASS	Atlas-SNP
SNED1	25992	hgsc.bcm.edu	37	2	241991198	241991198	+	Silent	SNP	C	C	T	rs138612536	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	64	86	0	0.537815	0	C|0.999;T|0.001	0.001	strong	.	SNED1	76	.	NM_001080437	exon13	c.C1773T	p.N591N	CCGGAACGGGGGC	.	PASS	Atlas-SNP
DEFA5	1670	hgsc.bcm.edu	37	8	6913031	6913031	+	Silent	SNP	G	G	A	rs2272719	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	27	41	0	0.473684	0	G|0.682;A|0.318	0.318	strong	DEFA5,NS,carcinoma,0,1	DEFA5	17	1	NM_021010	exon2	c.C207T	p.T69T	ACGGCCGGTTCGG	.	PASS	Atlas-SNP
ZNF442	79973	hgsc.bcm.edu	37	19	12462839	12462839	+	Missense_Mutation	SNP	G	G	A	rs117612375	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	53	102	0	0.392593	0	G|0.985;A|0.015	0.015	strong	.	ZNF442	102	.	NM_030824	exon5	c.C251T	p.P84L	CTCCTGGGATTTC	.	PASS	Atlas-SNP
TOMM40	10452	hgsc.bcm.edu	37	19	45397229	45397229	+	Silent	SNP	G	G	A	rs1160983	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	43	91	0	0.530864	0	G|0.950;A|0.050	0.050	strong	.	TOMM40	13	.	NM_001128917	exon5	c.G549A	p.S183S	GCAGTCGAAGTTT	.	PASS	Atlas-SNP
EFHB	151651	hgsc.bcm.edu	37	3	19975139	19975139	+	Silent	SNP	C	C	T	rs17180771	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	96	239	0	0.448598	0	C|0.881;T|0.119	0.119	strong	.	EFHB	186	.	NM_144715	exon1	c.G372A	p.R124R	TATTATCCGTTCA	.	PASS	Atlas-SNP
CCDC138	165055	hgsc.bcm.edu	37	2	109408208	109408208	+	Missense_Mutation	SNP	G	G	A	rs6740879	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	12	43	0	0.444444	0	G|0.747;A|0.253	0.253	strong	CCDC138,NS,carcinoma,0,1	CCDC138	49	1	NM_144978	exon4	c.G344A	p.R115K	ATTATAGAGTTAG	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214787130	214787130	+	Silent	SNP	G	G	A	rs2070064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	94	218	0	0.458537	0	G|0.653;A|0.345	0.345	strong	CENPF,NS,carcinoma,0,1	CENPF	321	1	NM_016343	exon2	c.G33A	p.G11G	AGAAGGGCTGCCT	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238427194	238427194	+	Missense_Mutation	SNP	T	T	C	rs3751109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	107	193	0	0.504717	0	T|0.795;C|0.205	0.205	strong	.	MLPH	41	.	NM_001042467	exon5	c.T458C	p.L153P	CTGAACTGATATC	.	PASS	Atlas-SNP
OR51B5	282763	hgsc.bcm.edu	37	11	5364450	5364450	+	Missense_Mutation	SNP	A	A	G	rs11036912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	18	36	0	0.45	0	A|0.645;G|0.355	0.355	strong	.	OR51B5	60	.	NM_001005567	exon5	c.T305C	p.I102T	GAGTGTATAAAGT	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25000617	25000617	+	Missense_Mutation	SNP	C	C	G	rs7571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	267	264	309	0	0.988764	0	C|0.568;G|0.432	0.432	strong	PARP4,NS,carcinoma,0,1	PARP4	142	1	NM_006437	exon33	c.G4966C	p.A1656P	TAGAAGCGTCATC	.	PASS	Atlas-SNP
ZNF45	7596	hgsc.bcm.edu	37	19	44417575	44417575	+	Silent	SNP	A	A	G	rs417699	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	70	62	0	0.985915	0	A|0.474;G|0.526	0.526	strong	ZNF45,NS,carcinoma,-2,2	ZNF45	51	2	NM_003425	exon10	c.T2013C	p.F671F	TGAAGGAAAGTCC	.	PASS	Atlas-SNP
GYS2	2998	hgsc.bcm.edu	37	12	21690035	21690035	+	Missense_Mutation	SNP	C	C	G	rs117639846	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	328	158	260	0	0.481707	0	C|0.978;G|0.022	0.022	strong	.	GYS2	110	.	NM_021957	exon16	c.G1965C	p.Q655H	ACTGCTCTGAGGA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9088017	9088017	+	Missense_Mutation	SNP	T	T	G	rs1596797	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	230	133	217	1	0.578261	0.00460829	T|0.205;G|0.795	0.795	strong	.	MUC16	4315	.	NM_024690	exon1	c.A3798C	p.K1266N	GGTAAGTTTGATG	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36979265	36979265	+	Silent	SNP	T	T	C	rs2232582	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	33	45	0	0.568965	0	T|0.792;C|0.208	0.208	strong	.	LBP	60	.	NM_004139	exon3	c.T291C	p.P97P	TGTCCCTGGCCAG	.	PASS	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99172244	99172244	+	Missense_Mutation	SNP	A	A	G	rs2278206	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	60	52	0	1	0	A|0.729;G|0.271	0.271	strong	.	INPP4A	205	.	NM_001134224	exon17	c.A1810G	p.T604A	CCCTCCACTGCAT	.	PASS	Atlas-SNP
COL27A1	85301	hgsc.bcm.edu	37	9	117033022	117033022	+	Silent	SNP	T	T	C	rs4143245	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	135	121	0	0.985401	0	T|0.601;C|0.399	0.399	strong	.	COL27A1	200	.	NM_032888	exon36	c.T3570C	p.L1190L	AGGCCTTGAGGGT	.	PASS	Atlas-SNP
MLC1	23209	hgsc.bcm.edu	37	22	50512732	50512732	+	Silent	SNP	G	G	A	rs138153307	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	32	82	0	0.484848	0	G|0.999;A|0.001	0.001	strong	.	MLC1	48	.	NM_015166	exon8	c.C627T	p.A209A	GAGGACGGCAGAG	.	PASS	Atlas-SNP
CLTCL1	8218	hgsc.bcm.edu	37	22	19263266	19263266	+	Missense_Mutation	SNP	C	C	A	rs34869740	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	58	124	0	0.453125	0	C|0.994;A|0.006	0.006	strong	.	CLTCL1	115	.	NM_001835	exon2	c.G130T	p.V44F	CACCAACTTTCTC	.	PASS	Atlas-SNP
C11orf45	219833	hgsc.bcm.edu	37	11	128772452	128772452	+	Silent	SNP	C	C	T	rs11221503	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	29	71	0	0.402778	0	C|0.869;T|0.131	0.131	strong	.	C11orf45	14	.	NM_145013	exon4	c.G438A	p.X146X	ACAGGGCTAGTTA	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52555957	52555957	+	Silent	SNP	T	T	C	rs9853056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	45	112	0	0.459184	0	T|0.399;C|0.601	0.601	strong	STAB1,NS,carcinoma,0,1	STAB1	178	1	NM_015136	exon58	c.T6261C	p.R2087R	TGGCCGTGTGTGT	.	PASS	Atlas-SNP
TAB2	23118	hgsc.bcm.edu	37	6	149700491	149700491	+	Silent	SNP	G	G	A	rs3734296	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	44	93	0	0.916667	0	G|0.856;A|0.144	0.144	strong	.	TAB2	55	.	NM_015093	exon5	c.G1440A	p.V480V	AGGGGTGGTGTCC	.	PASS	Atlas-SNP
TNRC6A	27327	hgsc.bcm.edu	37	16	24834233	24834233	+	Silent	SNP	C	C	T	rs2303085	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	53	77	0	0.490741	0	C|0.816;T|0.184	0.184	strong	TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	NM_014494	exon24	c.C5412T	p.H1804H	GCAGCACGGCCCG	.	PASS	Atlas-SNP
ZNF774	342132	hgsc.bcm.edu	37	15	90903502	90903502	+	Missense_Mutation	SNP	G	G	A	rs11854320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	42	69	0	0.461538	0	G|0.879;A|0.121	0.121	strong	ZNF774,NS,carcinoma,0,1	ZNF774	35	1	NM_001004309	exon4	c.G439A	p.V147I	GGATATGTAGGAG	.	PASS	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139703107	139703107	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	3	92	0	0.026087	0	.	.	none	COL22A1,caecum,carcinoma,-1,2	COL22A1	390	2	NM_152888	exon36	c.G2765A	p.G922E	ACATGTCCGGGAG	.	scavenged	Atlas-SNP
SPTBN4	57731	hgsc.bcm.edu	37	19	41008049	41008049	+	Silent	SNP	A	A	G	rs814526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	34	61	0	0.507463	0	A|0.581;G|0.419	0.419	strong	.	SPTBN4	213	.	NM_020971	exon9	c.A912G	p.V304V	CCAGGTATTGGAG	.	PASS	Atlas-SNP
FBXO39	162517	hgsc.bcm.edu	37	17	6690161	6690161	+	Silent	SNP	C	C	T	rs17853331	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	63	135	0	0.379518	0	C|0.771;T|0.229	0.229	strong	.	FBXO39	50	.	NM_153230	exon3	c.C1086T	p.I362I	CCTCATCATATCC	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4721376	4721376	+	Missense_Mutation	SNP	A	A	G	rs17854914	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	34	77	0	0.453333	0	A|0.896;G|0.104	0.104	strong	PLD2,NS,carcinoma,0,1	PLD2	138	1	NM_001243108	exon18	c.A1895G	p.E632G	TCAGGGAGAGCCA	.	PASS	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	37	2	167128972	167128972	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	78	180	0	0.52	0	.	.	none	SCN9A,colon,carcinoma,0,1	SCN9A	296	1	NM_002977	exon17	c.C3255T	p.S1085S	CAAATCGGATTCC	.	PASS	Atlas-SNP
TET3	200424	hgsc.bcm.edu	37	2	74300717	74300717	+	Silent	SNP	T	T	C	rs7560668	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	34	44	0	0.576271	0	T|0.639;C|0.361	0.361	strong	TET3,NS,carcinoma,0,1	TET3	101	1	NM_144993	exon2	c.T2131C	p.L711L	ACTCACTTGGGAT	.	PASS	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18064730	18064730	+	Silent	SNP	C	C	T	rs8077577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	56	47	0	1	0	C|0.806;T|0.194	0.194	strong	.	MYO15A	268	.	NM_016239	exon56	c.C9486T	p.D3162D	CCAAGACGTGAGC	.	PASS	Atlas-SNP
MYBPC1	4604	hgsc.bcm.edu	37	12	102045163	102045163	+	Missense_Mutation	SNP	C	C	G	rs3817552	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	106	94	0	1	0	C|0.844;G|0.156	0.156	strong	.	MYBPC1	235	.	NM_206819	exon16	c.C1518G	p.H506Q	GGTTCACAAGGGA	.	PASS	Atlas-SNP
KRT33B	3884	hgsc.bcm.edu	37	17	39521058	39521058	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	57	118	0	0.495652	0	.	.	none	KRT33B,NS,carcinoma,-1,1	KRT33B	46	1	NM_002279	exon6	c.G1070C	p.R357P	AGGCTCCGGTATG	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31769763	31769763	+	Silent	SNP	G	G	A	rs12461253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	52	132	0	0.485981	0	G|0.689;A|0.311	0.311	strong	.	TSHZ3	549	.	NM_020856	exon2	c.C936T	p.V312V	GGCGGCGACAGGA	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52708420	52708420	+	Missense_Mutation	SNP	G	G	A	rs2857671	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	163	131	1	0.964497	0.00763359	G|0.240;A|0.760	0.760	strong	KRT83,NS,carcinoma,0,1	KRT83	64	1	NM_002282	exon9	c.C1477T	p.H493Y	CTTAATGCCTCCC	.	PASS	Atlas-SNP
FAM25A	643161	hgsc.bcm.edu	37	10	88782100	88782100	+	Missense_Mutation	SNP	G	G	C	rs7079587	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	13	5	0	0.619048	0	G|0.964;C|0.036	0.036	strong	.	FAM25A	4	.	NM_001146157	exon2	c.G103C	p.V35L	AAGGAGGTGGTGG	.	PASS	Atlas-SNP
PLEKHF1	79156	hgsc.bcm.edu	37	19	30165157	30165157	+	Silent	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	7	10	0	0.466667	0	.	.	none	.	PLEKHF1	16	.	NM_024310	exon2	c.G411T	p.T137T	GGCCACGGGCCGC	.	PASS	Atlas-SNP
BSN	8927	hgsc.bcm.edu	37	3	49690627	49690627	+	Missense_Mutation	SNP	G	G	A	rs35762866	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	39	33	0	0.565217	0	G|0.940;A|0.060	0.060	strong	.	BSN	272	.	NM_003458	exon5	c.G3638A	p.G1213D	CCCATGGCGGCCC	.	PASS	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	37	10	25313818	25313818	+	Silent	SNP	C	C	T	rs7086282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	43	68	1	0.955556	0.0147059	C|0.530;T|0.470	0.470	strong	THNSL1,NS,carcinoma,0,1	THNSL1	70	1	NM_024838	exon3	c.C1666T	p.L556L	AGAAAACTAGCAC	.	scavenged	Atlas-SNP
MAP3K5	4217	hgsc.bcm.edu	37	6	137026266	137026266	+	Silent	SNP	T	T	G	rs9321567	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	37	105	0	0.925	0	T|0.413;G|0.587	0.587	strong	.	MAP3K5	136	.	NM_005923	exon3	c.A594C	p.I198I	GCAAATTATTTCC	.	PASS	Atlas-SNP
PRMT10	90826	hgsc.bcm.edu	37	4	148560193	148560193	+	Missense_Mutation	SNP	C	C	T	rs11557361	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	47	104	0	0.456311	0	C|0.981;T|0.019	0.019	strong	.	PRMT10	68	.	NM_138364	exon11	c.G2240A	p.C747Y	GGTATACAGGGCA	.	PASS	Atlas-SNP
SLC16A13	201232	hgsc.bcm.edu	37	17	6942111	6942111	+	Silent	SNP	G	G	T	rs33979567	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	56	91	0	0.543689	0	G|0.773;T|0.227	0.227	strong	SLC16A13,colon,carcinoma,0,1	SLC16A13	28	1	NM_201566	exon3	c.G984T	p.V328V	CTCCGTGCTGCCT	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641295	55641295	+	Missense_Mutation	SNP	A	A	G	rs4388990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	88	227	0	0.433498	0	A|0.750;G|0.250	0.250	strong	.	OR6C74	52	.	NM_001005490	exon1	c.A224G	p.Y75C	CTGTCTACATTCC	.	PASS	Atlas-SNP
PLA2G4E	123745	hgsc.bcm.edu	37	15	42281719	42281719	+	Silent	SNP	G	G	A	rs1668579	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	78	56	0	0.987342	0	G|0.630;A|0.370	0.370	strong	.	PLA2G4E	60	.	NM_001206670	exon15	c.C1617T	p.G539G	CTGCAGGCCCACC	.	PASS	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	37	4	77631425	77631425	+	Missense_Mutation	SNP	T	T	A	rs3821979	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	42	125	0	0.378378	0	T|0.843;A|0.157	0.157	strong	.	SHROOM3	134	.	NM_020859	exon3	c.T440A	p.L147H	TTAAACTTCGGCT	.	PASS	Atlas-SNP
HAGHL	84264	hgsc.bcm.edu	37	16	778024	778024	+	Silent	SNP	T	T	C	rs1406814	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	66	0	0.478873	0	T|0.616;C|0.384	0.384	strong	HAGHL,NS,carcinoma,0,1	HAGHL	18	1	NM_032304	exon2	c.T165C	p.H55H	CCACCATCACTGG	.	PASS	Atlas-SNP
FRY	10129	hgsc.bcm.edu	37	13	32776153	32776153	+	Silent	SNP	T	T	C	rs9567420	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	35	92	0	0.492958	0	T|0.918;C|0.082	0.082	strong	.	FRY	312	.	NM_023037	exon30	c.T3822C	p.Y1274Y	GATTTATGAAATC	.	PASS	Atlas-SNP
BRD8	10902	hgsc.bcm.edu	37	5	137475787	137475787	+	Silent	SNP	C	C	T	rs423258	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	84	147	0	0.515337	0	C|0.714;T|0.286	0.286	strong	BRD8,NS,carcinoma,0,1	BRD8	192	1	NM_139199	exon27	c.G3684A	p.V1228V	ATCATCCACTGGG	.	PASS	Atlas-SNP
EFHB	151651	hgsc.bcm.edu	37	3	19930003	19930003	+	Silent	SNP	G	G	A	rs4858714	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	47	88	0	0.489583	0	G|0.728;A|0.272	0.272	strong	.	EFHB	186	.	NM_144715	exon10	c.C1866T	p.F622F	ATTTGCGAATTCC	.	PASS	Atlas-SNP
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	69	135	0	0.396552	0	T|0.119;G|0.156;C|0.699;A|0.025	0.119	strong	.	MED24	89	.	NM_014815	exon13	c.G1161A	p.A387A	TCGGTCCGCTTTG	.	PASS	Atlas-SNP
CD6	923	hgsc.bcm.edu	37	11	60776186	60776186	+	Missense_Mutation	SNP	C	C	T	rs11230562	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	35	41	0	0.522388	0	C|0.852;T|0.148	0.148	strong	.	CD6	122	.	NM_006725	exon4	c.C650T	p.T217M	ACTTCACGCCCGG	.	PASS	Atlas-SNP
TBX1	6899	hgsc.bcm.edu	37	22	19766782	19766782	+	Missense_Mutation	SNP	C	C	T	rs4819522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	49	72	0	1	0	C|0.829;T|0.171	0.171	strong	TBX1_ENST00000329705,colon,carcinoma,0,1	TBX1	62	1	NM_080646	exon9	c.C1049T	p.T350M	CTGAGACGTCTAG	.	PASS	Atlas-SNP
ETFDH	2110	hgsc.bcm.edu	37	4	159627845	159627845	+	Silent	SNP	T	T	C	rs77484245	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	38	91	0	0.417582	0	T|0.996;C|0.004	0.004	strong	.	ETFDH	57	.	NM_004453	exon12	c.T1533C	p.D511D	ACCCGATGGACAG	.	PASS	Atlas-SNP
PROP1	5626	hgsc.bcm.edu	37	5	177422908	177422908	+	Silent	SNP	A	A	G	rs1135320	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	39	72	0	0.47561	0	A|0.580;G|0.420	0.420	strong	.	PROP1	28	.	NM_006261	exon1	c.T27C	p.A9A	CTTCTCAGCCTGG	.	PASS	Atlas-SNP
SRSF6	6431	hgsc.bcm.edu	37	20	42087079	42087079	+	Silent	SNP	C	C	G	rs147967864	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	15	3	0	0.652174	0	C|0.972;G|0.028	0.028	strong	.	SRSF6	37	.	NM_006275	exon2	c.C186G	p.G62G	CTGCGGCGAGCGC	.	PASS	Atlas-SNP
NCAPD2	9918	hgsc.bcm.edu	37	12	6638116	6638116	+	Silent	SNP	C	C	T	rs740850	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	66	127	0	0.515625	0	C|0.653;T|0.347	0.347	strong	.	NCAPD2	99	.	NM_014865	exon27	c.C3483T	p.N1161N	GGGCAACGCAATC	.	PASS	Atlas-SNP
KLRG2	346689	hgsc.bcm.edu	37	7	139138950	139138950	+	Missense_Mutation	SNP	C	C	G	rs17160911	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	14	36	0	0.4	0	C|0.832;G|0.166	0.166	strong	KLRG2,NS,carcinoma,0,3	KLRG2	22	3	NM_198508	exon4	c.G1016C	p.G339A	TATCTGCCCAGGA	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17062905	17062905	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	31	63	0	0.54386	0	.	.	none	.	CPAMD8	192	.	NM_015692	exon20	c.C2523T	p.A841A	GGGCTCGGCGATG	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	71002865	71002865	+	Silent	SNP	T	T	A	rs2717430	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	238	96	289	0	0.403361	0	T|0.423;A|0.577	0.577	strong	.	PTPRB	676	.	NM_001109754	exon4	c.A963T	p.T321T	GACCACTGTTCTC	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43074430	43074430	+	Silent	SNP	A	A	G	rs2948619	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	34	97	0	0.419753	0	A|0.349;G|0.651	0.651	strong	.	FAM198A	23	.	NM_001129908	exon2	c.A675G	p.G225G	CTCAGGAGCTCAT	.	PASS	Atlas-SNP
OR8K1	390157	hgsc.bcm.edu	37	11	56113575	56113575	+	Missense_Mutation	SNP	A	A	G	rs10896271	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	48	130	0	0.516129	0	A|0.616;G|0.384	0.384	strong	.	OR8K1	93	.	NM_001002907	exon1	c.A61G	p.M21V	ATTCTCATGGGGA	.	PASS	Atlas-SNP
MLLT6	4302	hgsc.bcm.edu	37	17	36873149	36873149	+	Silent	SNP	C	C	T	rs9892493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	47	97	0	0.465347	0	C|0.869;T|0.131	0.131	strong	.	MLLT6	80	.	NM_005937	exon10	c.C1566T	p.S522S	CAGCTCCGGCCTG	.	PASS	Atlas-SNP
EVPL	2125	hgsc.bcm.edu	37	17	74003463	74003463	+	Silent	SNP	G	G	A	rs17886642	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	45	98	0	0.483871	0	G|0.945;A|0.055	0.055	strong	.	EVPL	155	.	NM_001988	exon22	c.C5823T	p.T1941T	CCCCCCGGTCAGG	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152919	103152919	+	Silent	SNP	G	G	A	rs12574626	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	11	48	0	0.275	0	G|0.808;A|0.192	0.192	strong	.	DYNC2H1	246	.	NM_001080463	exon73	c.G10794A	p.T3598T	GGATACGTTTACA	.	PASS	Atlas-SNP
FBXO32	114907	hgsc.bcm.edu	37	8	124553222	124553222	+	Silent	SNP	G	G	C	rs4871385	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	90	58	0	0.731707	0	G|0.855;C|0.145	0.145	strong	.	FBXO32	39	.	NM_001242463	exon1	c.C33G	p.P11P	CTGCCCGGGGGAC	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383041	39383041	+	Silent	SNP	C	C	T	rs71371479		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	4	60	0	0.0547945	0	C|0.500;T|0.500	0.500	weak	KRTAP9-2,NS,carcinoma,0,1	KRTAP9-2	24	1	NM_031961	exon1	c.C135T	p.S45S	TGTGTCCAGCTGC	.	scavenged	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3640274	3640274	+	Missense_Mutation	SNP	G	G	A	rs714181	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	56	137	0	0.491228	0	G|0.785;N|0.000	.	strong	.	SLX4	173	.	NM_032444	exon12	c.C3365T	p.P1122L	ATAGACGGAGATT	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	37	2	170150671	170150671	+	Silent	SNP	G	G	A	rs2229266	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	315	145	261	0	0.460317	0	G|0.567;T|0.068	.	strong	.	LRP2	751	.	NM_004525	exon6	c.C639T	p.D213D	ATGTTCGTCACTG	.	PASS	Atlas-SNP
FDX1L	112812	hgsc.bcm.edu	37	19	10426422	10426422	+	Silent	SNP	A	A	C	rs378395	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	17	15	4	0.944444	0.266667	A|0.532;C|0.468	0.468	strong	FDX1L,NS,carcinoma,0,1	FDX1L	21	1	NM_001031734	exon2	c.T159G	p.A53A	CTCTCCAGCCGGG	.	scavenged	Atlas-SNP
BANP	54971	hgsc.bcm.edu	37	16	88071611	88071611	+	Silent	SNP	C	C	T	rs149196674	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	69	151	0	0.530769	0	C|0.999;T|0.001	0.001	strong	.	BANP	67	.	NM_001173542	exon11	c.C1305T	p.D435D	GCAGGACGGTCAG	.	PASS	Atlas-SNP
CACNA1H	8912	hgsc.bcm.edu	37	16	1270111	1270111	+	Missense_Mutation	SNP	G	G	A	rs1054644	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	21	33	0	0.5	0	G|0.936;A|0.064	0.064	strong	.	CACNA1H	317	.	NM_021098	exon35	c.G6179A	p.R2060H	CACCACGCTCCCC	.	PASS	Atlas-SNP
F13A1	2162	hgsc.bcm.edu	37	6	6152137	6152137	+	Missense_Mutation	SNP	C	C	G	rs5988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	50	55	0	0.568182	0	C|0.786;G|0.214	0.214	strong	.	F13A1	135	.	NM_000129	exon14	c.G1954C	p.E652Q	TAAACTCAACTGT	.	PASS	Atlas-SNP
CASZ1	54897	hgsc.bcm.edu	37	1	10713997	10713997	+	Missense_Mutation	SNP	G	G	A	rs61736955	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	3	31	0	0.038961	0	G|0.998;A|0.002	0.002	strong	CASZ1,caecum,carcinoma,+1,1	CASZ1	150	1	NM_001079843	exon11	c.C2117T	p.P706L	GAGGGCGGCAGCC	.	scavenged	Atlas-SNP
ENTHD2	146705	hgsc.bcm.edu	37	17	79202956	79202956	+	Silent	SNP	T	T	C	rs2048057	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	30	92	0	0.379747	0	A|0.000;C|0.395;T|0.605	0.395	strong	C17orf56,colon,carcinoma,0,1	.	.	1	NM_144679	exon12	c.A1350G	p.P450P	GCCCCCTGGGATC	.	PASS	Atlas-SNP
DDX28	55794	hgsc.bcm.edu	37	16	68055495	68055495	+	Silent	SNP	G	G	C	rs13816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	34	91	0	0.43038	0	T|0.000;G|0.812;C|0.188	0.188	strong	DDX28,NS,carcinoma,0,1	DDX28	29	1	NM_018380	exon1	c.C1611G	p.P537P	TGCTTGGGGCAAA	.	PASS	Atlas-SNP
TRPM5	29850	hgsc.bcm.edu	37	11	2432666	2432666	+	Missense_Mutation	SNP	C	C	T	rs34364959	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	37	62	0	0.506849	0	C|0.930;T|0.070	0.070	strong	.	TRPM5	86	.	NM_014555	exon18	c.G2698A	p.G900S	GGCGGCCGTCATG	.	PASS	Atlas-SNP
CHGB	1114	hgsc.bcm.edu	37	20	5904040	5904040	+	Missense_Mutation	SNP	G	G	A	rs742711	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	19	43	0	0.452381	0	G|0.775;A|0.225	0.225	strong	CHGB,NS,carcinoma,0,1	CHGB	112	1	NM_001819	exon4	c.G1250A	p.R417H	AGGGACGCCATCA	.	PASS	Atlas-SNP
MRPL39	54148	hgsc.bcm.edu	37	21	26965205	26965205	+	Silent	SNP	T	T	C	rs1057885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	26	88	0	0.333333	0	T|0.211;C|0.789	0.789	strong	.	MRPL39	61	.	NM_017446	exon8	c.A840G	p.V280V	TGCTGATACTTCA	.	PASS	Atlas-SNP
WDR81	124997	hgsc.bcm.edu	37	17	1640709	1640709	+	Silent	SNP	C	C	T	rs1045794	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	44	102	0	0.458333	0	C|0.826;N|0.001	.	strong	WDR81_ENST00000437219,NS,carcinoma,+1,3	WDR81	180	3	NM_001163809	exon10	c.C5556T	p.T1852T	CTTGACCGTCTGG	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	37	2	29416615	29416615	+	Silent	SNP	G	G	A	rs56132472	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	40	133	0	0.465116	0	G|0.903;A|0.097	0.097	strong	.	ALK	533	.	NM_004304	exon29	c.C4338T	p.T1446T	GGAGGTGGTAGGC	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13762972	13762972	+	Silent	SNP	T	T	C	rs6554812	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	85	0	0.435644	0	T|0.714;C|0.286	0.286	strong	DNAH5,NS,carcinoma,-2,1	DNAH5	868	1	NM_001369	exon60	c.A10140G	p.E3380E	CAAAAATTCTATC	.	PASS	Atlas-SNP
ZNF518B	85460	hgsc.bcm.edu	37	4	10447168	10447168	+	Missense_Mutation	SNP	C	C	G	rs66538112	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	54	91	0	0.524272	0	C|0.795;G|0.205	0.205	strong	.	ZNF518B	116	.	NM_053042	exon3	c.G785C	p.G262A	GAGAAACCTGACA	.	PASS	Atlas-SNP
ZNF175	7728	hgsc.bcm.edu	37	19	52085095	52085095	+	Silent	SNP	G	G	A	rs35431178	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	37	58	0	0.486842	0	G|0.916;A|0.084	0.084	strong	.	ZNF175	65	.	NM_007147	exon4	c.G255A	p.P85P	GGAGCCGCGTGTG	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5427652	5427652	+	Silent	SNP	G	G	A	rs4720623	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	29	31	0	0.491525	0	G|0.633;A|0.367	0.367	strong	.	TNRC18	311	.	NM_001080495	exon5	c.C1803T	p.A601A	GCGCACGGCCACG	.	PASS	Atlas-SNP
KIAA1432	57589	hgsc.bcm.edu	37	9	5774225	5774225	+	Silent	SNP	T	T	G	rs3739648	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	40	104	0	0.43956	0	T|0.717;G|0.283	0.283	strong	KIAA1432,NS,carcinoma,+2,1	KIAA1432	97	1	NM_020829	exon26	c.T4251G	p.T1417T	TGGGACTTACGAC	.	PASS	Atlas-SNP
CLEC4D	338339	hgsc.bcm.edu	37	12	8667897	8667897	+	Missense_Mutation	SNP	A	A	G	rs4304840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	244	106	232	0	0.434426	0	A|0.678;G|0.322	0.322	strong	.	CLEC4D	46	.	NM_080387	exon2	c.A94G	p.S32G	CTTCTCAGTGTCT	.	PASS	Atlas-SNP
DNAH10	196385	hgsc.bcm.edu	37	12	124366300	124366300	+	Silent	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	43	101	0	0.467391	0	.	.	none	.	DNAH10	888	.	NM_207437	exon50	c.G8409T	p.G2803G	GGTCGGGGTAGGG	.	PASS	Atlas-SNP
INO80C	125476	hgsc.bcm.edu	37	18	33048617	33048617	+	Silent	SNP	G	G	A	rs34130630	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	38	80	0	0.584615	0	G|0.986;A|0.014	0.014	strong	.	INO80C	18	.	NM_001098817	exon7	c.C645T	p.T215T	GTAGCCGGTGACG	.	PASS	Atlas-SNP
TYK2	7297	hgsc.bcm.edu	37	19	10475649	10475649	+	Missense_Mutation	SNP	C	C	T	rs2304255	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	30	53	0	0.526316	0	C|0.948;T|0.052	0.052	strong	.	TYK2	126	.	NM_003331	exon8	c.G1087A	p.G363S	GCTGGCCGACTGC	.	PASS	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	37	6	3012778	3012778	+	Missense_Mutation	SNP	G	G	A	rs17300141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	58	103	0	0.483333	0	G|0.978;A|0.022	0.022	strong	.	NQO2	21	.	NM_000904	exon4	c.G173A	p.G58D	CGACAGGTACTCT	.	PASS	Atlas-SNP
EMC10	284361	hgsc.bcm.edu	37	19	50983930	50983930	+	Silent	SNP	C	C	T	rs10409679	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	44	29	1	0.956522	0.0344828	C|0.493;T|0.507	0.507	strong	C19orf63_ENST00000376918,rectum,carcinoma,0,2	.	.	2	NM_175063	exon5	c.C495T	p.P165P	GCACCCCGGGGGC	.	scavenged	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541214	12541214	+	Missense_Mutation	SNP	G	G	T	rs7256321	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	79	150	0	0.478788	0	G|0.659;T|0.341	0.341	strong	.	ZNF443	63	.	NM_005815	exon4	c.C1772A	p.P591Q	CATTGTGGACATT	.	PASS	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16349137	16349137	+	Missense_Mutation	SNP	G	G	A	rs9442189	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	7	95	0	0.0546875	0	G|0.989;A|0.011	0.011	strong	.	CLCNKA	56	.	NM_004070	exon2	c.G23A	p.R8H	GGCTGCGTGAGGG	.	PASS	Atlas-SNP
AGRN	375790	hgsc.bcm.edu	37	1	978800	978800	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	4	43	0	0.05	0	.	.	none	.	AGRN	110	.	NM_198576	exon8	c.C1566T	p.L522L	TACCCTCGGGCGG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264941	1264941	+	Silent	SNP	G	G	A	rs200834421	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	607	179	537	0	0.294893	0	G|0.988;A|0.012	0.012	strong	MUC5B,NS,carcinoma,+1,2	MUC5B	473	2	NM_002458	exon31	c.G6831A	p.T2277T	CACCACGGCCACC	.	PASS	Atlas-SNP
RHOBTB3	22836	hgsc.bcm.edu	37	5	95091201	95091201	+	Missense_Mutation	SNP	A	A	G	rs34899	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	218	222	0	0.990909	0	A|0.561;G|0.439	0.439	strong	.	RHOBTB3	43	.	NM_014899	exon6	c.A784G	p.N262D	AACCCCAATTTAA	.	PASS	Atlas-SNP
ACTR3C	653857	hgsc.bcm.edu	37	7	149990455	149990455	+	Silent	SNP	T	T	C	rs2689611		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	558	13	545	3	0.0232975	0.00550459	.	.	weak	Q9C0K3_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001164459	exon3	c.A99G	p.T33T	CGTTAATGTACGT	.	scavenged	Atlas-SNP
CD2AP	23607	hgsc.bcm.edu	37	6	47563608	47563608	+	Missense_Mutation	SNP	A	A	G	rs138727736	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	16	24	0	0.551724	0	A|0.995;G|0.005	0.005	strong	.	CD2AP	43	.	NM_012120	exon12	c.A1120G	p.T374A	AAATCAACACTGG	.	PASS	Atlas-SNP
VPS13D	55187	hgsc.bcm.edu	37	1	12443033	12443033	+	Splice_Site	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	3	228	0	0.0143541	0	.	.	none	VPS13D,NS,carcinoma,0,1	VPS13D	316	1	NM_015378	exon58	c.11191-2A>G	.	TCTTTTAGGCCAA	.	scavenged	Atlas-SNP
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751128	140751128	+	Missense_Mutation	SNP	C	C	G	rs2240697	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	59	91	0	1	0	C|0.477;G|0.523	0.523	strong	.	PCDHGB3	168	.	NM_018924	exon1	c.C1167G	p.N389K	AGGAAACTTCCCC	.	PASS	Atlas-SNP
AKAP6	9472	hgsc.bcm.edu	37	14	33004975	33004975	+	Silent	SNP	G	G	A	rs35436895	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	85	131	0	0.464481	0	G|0.924;A|0.076	0.076	strong	.	AKAP6	308	.	NM_004274	exon3	c.G540A	p.T180T	GCAGACGGACATT	.	PASS	Atlas-SNP
SP1	6667	hgsc.bcm.edu	37	12	53777171	53777171	+	Silent	SNP	A	A	G	rs3741651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	86	138	0	0.5375	0	A|0.814;G|0.186	0.186	strong	.	SP1	57	.	NM_138473	exon3	c.A1440G	p.Q480Q	AGCCCAAACAATC	.	PASS	Atlas-SNP
CYP26C1	340665	hgsc.bcm.edu	37	10	94824166	94824166	+	Missense_Mutation	SNP	G	G	A	rs11187265	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	43	78	0	0.425743	0	G|0.914;A|0.086	0.086	strong	.	CYP26C1	25	.	NM_183374	exon4	c.G734A	p.R245Q	TGCATCGGCACCT	.	PASS	Atlas-SNP
CPNE3	8895	hgsc.bcm.edu	37	8	87567193	87567193	+	Missense_Mutation	SNP	C	C	T	rs2304789	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	40	90	0	0.526316	0	C|0.730;T|0.270	0.270	strong	.	CPNE3	65	.	NM_003909	exon15	c.C1235T	p.T412M	CAGCCACGCAACA	.	PASS	Atlas-SNP
C5orf45	51149	hgsc.bcm.edu	37	5	179280379	179280379	+	Missense_Mutation	SNP	T	T	C	rs1650893	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	14	26	0	0.4375	0	T|0.318;C|0.682	0.682	strong	.	C5orf45	23	.	NM_016175	exon2	c.A125G	p.Q42R	CTCACCTGCAAAA	.	PASS	Atlas-SNP
KCNH8	131096	hgsc.bcm.edu	37	3	19498417	19498417	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	3	199	0	0.0160428	0	.	.	none	KCNH8,rectum,carcinoma,0,2	KCNH8	189	2	NM_144633	exon11	c.C1983T	p.F661F	CAAATTCGTGGAA	.	scavenged	Atlas-SNP
FAM187B	148109	hgsc.bcm.edu	37	19	35718938	35718938	+	Missense_Mutation	SNP	C	C	T	rs564117	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	95	141	0	0.477387	0	C|0.811;T|0.189	0.189	strong	FAM187B,caecum,carcinoma,0,1	FAM187B	28	1	NM_152481	exon1	c.G646A	p.V216I	AAATGACGTAATC	.	PASS	Atlas-SNP
TEKT1	83659	hgsc.bcm.edu	37	17	6716242	6716242	+	Missense_Mutation	SNP	G	G	A	rs3744395	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	89	145	0	0.546012	0	G|0.790;A|0.210	0.210	strong	.	TEKT1	49	.	NM_053285	exon6	c.C760T	p.R254C	GCTTGCGCAGATC	.	PASS	Atlas-SNP
C14orf182	283551	hgsc.bcm.edu	37	14	50472405	50472405	+	Missense_Mutation	SNP	G	G	A	rs6572635	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	100	192	0	0.44843	0	G|0.739;A|0.261	0.261	strong	C14orf182,bladder,carcinoma,+1,1	C14orf182	8	1	NM_001012706	exon1	c.C113T	p.P38L	CCTCTCGGTTCGT	.	PASS	Atlas-SNP
ACADL	33	hgsc.bcm.edu	37	2	211068100	211068100	+	Silent	SNP	A	A	G	rs148069105	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	30	64	0	0.375	0	A|0.999;G|0.001	0.001	strong	.	ACADL	38	.	NM_001608	exon8	c.T939C	p.Y313Y	TTTAACATAGTTC	.	PASS	Atlas-SNP
GTDC2	84892	hgsc.bcm.edu	37	3	43121743	43121743	+	Missense_Mutation	SNP	C	C	T	rs199612856	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	92	184	0	0.497297	0	C|1.000;T|0.000	0.000	strong	.	.	.	.	NM_032806	exon2	c.G1181A	p.R394Q	ATGTTCCGCCAGG	.	PASS	Atlas-SNP
MYBPC2	4606	hgsc.bcm.edu	37	19	50967640	50967640	+	Missense_Mutation	SNP	G	G	A	rs25667	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	23	51	0	0.403509	0	A|0.143;C|0.000;G|0.857	0.143	strong	.	MYBPC2	103	.	NM_004533	exon27	c.G3266A	p.R1089H	AAATCCGTGAAGA	.	PASS	Atlas-SNP
CLRN2	645104	hgsc.bcm.edu	37	4	17524570	17524570	+	Missense_Mutation	SNP	C	C	G	rs13147559	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	45	106	0	0.494505	0	C|0.904;G|0.095	0.095	strong	.	CLRN2	40	.	NM_001079827	exon2	c.C337G	p.L113V	CTGGCTCTGGTCA	.	PASS	Atlas-SNP
ESPN	83715	hgsc.bcm.edu	37	1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	rs200602012	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	11	7	0	0.6875	0	G|0.991;A|0.010	0.010	weak	.	ESPN	32	.	NM_031475	exon4	c.G752A	p.G251D	GCCGCGGCCACAC	.	PASS	Atlas-SNP
TRPC1	7220	hgsc.bcm.edu	37	3	142524858	142524858	+	Silent	SNP	G	G	A	rs1132030	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	69	161	0	0.482517	0	A|0.353;G|0.647;T|0.000	0.353	strong	.	TRPC1	82	.	NM_001251845	exon13	c.G2163A	p.R721R	ATGGAGGAATTTG	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55523860	55523860	+	Missense_Mutation	SNP	A	A	C	rs7305779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	34	86	0	0.472222	0	A|0.677;C|0.323	0.323	strong	.	OR9K2	63	.	NM_001005243	exon1	c.A308C	p.E103A	TTATTGAACCCAA	.	PASS	Atlas-SNP
LGALS3BP	3959	hgsc.bcm.edu	37	17	76970803	76970803	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	46	126	0	0.393162	0	.	.	none	.	LGALS3BP	47	.	NM_005567	exon4	c.C343T	p.H115Y	TCTCGTGCCTGCA	.	PASS	Atlas-SNP
ZFP28	140612	hgsc.bcm.edu	37	19	57065189	57065189	+	Silent	SNP	T	T	C	rs145011	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	72	100	0	0.553846	0	T|0.798;C|0.202	0.202	strong	ZFP28,NS,carcinoma,0,1	ZFP28	99	1	NM_020828	exon8	c.T1035C	p.F345F	TGTGTTTGGAAGG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392802	40392802	+	Missense_Mutation	SNP	C	C	T	rs149844303	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	404	107	378	0	0.264851	0	.	.	weak	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon16	c.G7702A	p.A2568T	CGTAGGCCACACG	.	scavenged	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169282355	169282355	+	Missense_Mutation	SNP	T	T	C	rs2684348	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	49	101	0	0.515789	0	T|0.390;C|0.610	0.610	strong	.	DDX60L	116	.	NM_001012967	exon37	c.A4936G	p.M1646V	GTCCCATACGCAT	.	PASS	Atlas-SNP
LRRN2	10446	hgsc.bcm.edu	37	1	204589066	204589066	+	Missense_Mutation	SNP	C	C	T	rs36012907	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	34	100	0	0.515152	0	C|0.942;T|0.058	0.058	strong	.	LRRN2	81	.	NM_006338	exon3	c.G55A	p.A19T	GCACAGCGGCAGT	.	PASS	Atlas-SNP
ATG4D	84971	hgsc.bcm.edu	37	19	10659659	10659659	+	Silent	SNP	C	C	T	rs2304165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	61	82	0	0.491935	0	C|0.875;T|0.125	0.125	strong	.	ATG4D	47	.	NM_032885	exon6	c.C915T	p.P305P	GGTGCCCGTGCGA	.	PASS	Atlas-SNP
NAGPA	51172	hgsc.bcm.edu	37	16	5075633	5075633	+	Missense_Mutation	SNP	G	G	A	rs7188856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	110	156	0	0.547264	0	G|0.758;A|0.242	0.242	strong	.	NAGPA	30	.	NM_016256	exon10	c.C1394T	p.T465I	GCTGCAGTGCTGA	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2048831	2048831	+	Missense_Mutation	SNP	A	A	G	rs968381	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	96	112	1	1	0.00892857	A|0.561;G|0.439	0.439	strong	MYOM2,NS,carcinoma,0,1	MYOM2	251	1	NM_003970	exon20	c.A2606G	p.N869S	CAGCCAACCGTTA	.	PASS	Atlas-SNP
BCHE	590	hgsc.bcm.edu	37	3	165491280	165491280	+	Missense_Mutation	SNP	C	C	T	rs1803274	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	53	120	0	0.552083	0	C|0.822;T|0.178	0.178	strong	.	BCHE	136	.	NM_000055	exon4	c.G1699A	p.A567T	ATTCTGCTTCATC	.	PASS	Atlas-SNP
LRRC45	201255	hgsc.bcm.edu	37	17	79983367	79983367	+	Silent	SNP	C	C	T	rs117200853	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	29	42	0	0.47541	0	C|0.997;T|0.003	0.003	strong	.	LRRC45	22	.	NM_144999	exon5	c.C645T	p.D215D	TGGAGACGTCCTC	.	PASS	Atlas-SNP
F5	2153	hgsc.bcm.edu	37	1	169511403	169511403	+	Silent	SNP	G	G	A	rs41272457	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	47	97	0	0.505376	0	G|0.986;A|0.014	0.014	strong	F5,NS,carcinoma,-2,1	F5	301	1	NM_000130	exon13	c.C2925T	p.P975P	ATTCTGGGGGCTG	.	PASS	Atlas-SNP
AMY2A	279	hgsc.bcm.edu	37	1	104166590	104166590	+	Missense_Mutation	SNP	C	C	G	rs1832269	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	492	93	468	0	0.189024	0	.	.	weak	AMY2A,colon,carcinoma,0,1	AMY2A	36	1	NM_000699	exon8	c.C1204G	p.R402G	GAACATCGATGGC	.	scavenged	Atlas-SNP
GABRG3	2567	hgsc.bcm.edu	37	15	27772676	27772676	+	Silent	SNP	C	C	T	rs140679	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	67	105	0	0.523438	0	C|0.472;T|0.528	0.528	strong	.	GABRG3	115	.	NM_033223	exon8	c.C963T	p.T321T	TGTGACCGTGTGC	.	PASS	Atlas-SNP
POLK	51426	hgsc.bcm.edu	37	5	74877266	74877266	+	Silent	SNP	C	C	T	rs3213801	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	97	90	0	1	0	C|0.762;T|0.238	0.238	strong	.	POLK	123	.	NM_016218	exon7	c.C927T	p.A309A	GACAGCCAGTGCA	.	PASS	Atlas-SNP
SNTB2	6645	hgsc.bcm.edu	37	16	69221510	69221510	+	Silent	SNP	C	C	G	rs10650	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	15	18	0	0.535714	0	C|0.815;G|0.185	0.185	strong	.	SNTB2	22	.	NM_006750	exon1	c.C441G	p.P147P	CTTCCCCGGGCTG	.	PASS	Atlas-SNP
GAS2L3	283431	hgsc.bcm.edu	37	12	101017839	101017839	+	Missense_Mutation	SNP	C	C	T	rs148236676	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	44	102	0	0.431373	0	C|0.995;T|0.005	0.005	strong	.	GAS2L3	76	.	NM_174942	exon10	c.C1256T	p.P419L	CTTCACCAGCTTT	.	PASS	Atlas-SNP
ABCD4	5826	hgsc.bcm.edu	37	14	74759301	74759301	+	Silent	SNP	G	G	T	rs4148078	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	30	73	0	0.365854	0	G|0.719;T|0.281	0.281	strong	.	ABCD4	54	.	NM_005050	exon10	c.C981A	p.L327L	GTCGATGAGCTGG	.	PASS	Atlas-SNP
HOXB1	3211	hgsc.bcm.edu	37	17	46607958	46607958	+	Missense_Mutation	SNP	T	T	A	rs12939811	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	13	32	0	0.342105	0	T|0.866;A|0.134	0.134	strong	.	HOXB1	67	.	NM_002144	exon1	c.A309T	p.Q103H	TTCTGATTGACCC	.	PASS	Atlas-SNP
NDUFS1	4719	hgsc.bcm.edu	37	2	207006676	207006676	+	Silent	SNP	T	T	C	rs1801318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	43	99	0	0.377193	0	T|0.644;C|0.356;A|0.000	0.356	strong	.	NDUFS1	82	.	NM_001199984	exon12	c.A1293G	p.R431R	TCGAATTCTAGCA	.	PASS	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118668	93118668	+	Missense_Mutation	SNP	C	C	T	rs3742717	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	56	90	0	0.543689	0	C|0.777;T|0.223	0.223	strong	RIN3,rectum,carcinoma,-1,1	RIN3	81	1	NM_024832	exon6	c.C1274T	p.T425M	AGGACACGCCCCG	.	PASS	Atlas-SNP
BTN1A1	696	hgsc.bcm.edu	37	6	26505362	26505362	+	Missense_Mutation	SNP	G	G	A	rs3736781	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	122	136	0	1	0	G|0.485;A|0.515	0.515	strong	.	BTN1A1	68	.	NM_001732	exon3	c.G637A	p.A213T	ACTTCTGCGAAAA	.	PASS	Atlas-SNP
BTBD6	90135	hgsc.bcm.edu	37	14	105716377	105716377	+	Silent	SNP	C	C	T	rs45452103	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	23	43	0	0.5	0	C|0.983;T|0.017	0.017	strong	.	BTBD6	24	.	NM_033271	exon5	c.C826T	p.L276L	CATGTTCTGGGGC	.	PASS	Atlas-SNP
MMP10	4319	hgsc.bcm.edu	37	11	102650246	102650246	+	Silent	SNP	G	G	A	rs17860949	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	53	130	0	0.441667	0	G|0.872;A|0.128	0.128	strong	.	MMP10	44	.	NM_002425	exon2	c.C336T	p.H112H	TGTAAGGTGGGTT	.	PASS	Atlas-SNP
SEC14L4	284904	hgsc.bcm.edu	37	22	30887919	30887919	+	Silent	SNP	G	G	A	rs61741444	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	38	103	0	0.372549	0	G|0.962;A|0.038	0.038	strong	.	SEC14L4	43	.	NM_001161368	exon10	c.C813T	p.C271C	CTGCTCGCACAGG	.	PASS	Atlas-SNP
TIMELESS	8914	hgsc.bcm.edu	37	12	56814653	56814653	+	Missense_Mutation	SNP	G	G	A	rs2291739	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	110	111	0	1	0	G|0.548;A|0.452	0.452	strong	.	TIMELESS	107	.	NM_003920	exon25	c.C3053T	p.P1018L	AGGAGCGGGATAG	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17312992	17312992	+	Silent	SNP	C	C	T	rs2305765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	64	62	0	0.984615	0	C|0.436;T|0.564	0.564	strong	MYO9B_ENST00000319396,NS,carcinoma,+2,2	MYO9B	264	2	NM_001130065	exon28	c.C4716T	p.V1572V	GATCGTCGTCAGC	.	PASS	Atlas-SNP
MYO9B	4650	hgsc.bcm.edu	37	19	17305440	17305440	+	Silent	SNP	T	T	C	rs1064305	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	98	103	1	0.98	0.00970874	T|0.392;C|0.608	0.608	strong	.	MYO9B	264	.	NM_001130065	exon22	c.T3204C	p.G1068G	AGCAGGTGCTGAG	.	PASS	Atlas-SNP
SOGA1	140710	hgsc.bcm.edu	37	20	35414905	35414905	+	Missense_Mutation	SNP	G	G	T	rs73109216	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	9	23	0	0.391304	0	G|0.950;T|0.050	0.050	strong	.	SOGA1	136	.	NM_080627	exon15	c.C4969A	p.L1657I	GGGGGAGTGCCCT	.	PASS	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77327042	77327042	+	Silent	SNP	C	C	T	rs61754842	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	39	59	0	0.639344	0	C|0.995;T|0.005	0.005	strong	ADAMTS18,breast,lymphoid_neoplasm,-2,1	ADAMTS18	270	1	NM_199355	exon20	c.G3120A	p.Q1040Q	GCCCTCCTGCAGC	.	PASS	Atlas-SNP
IP6K3	117283	hgsc.bcm.edu	37	6	33703230	33703230	+	Silent	SNP	G	G	A	rs545787	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	24	52	0	0.5	0	G|0.598;A|0.402	0.402	strong	IP6K3_ENST00000451316,NS,carcinoma,0,2	IP6K3	52	2	NM_001142883	exon3	c.C24T	p.D8D	CCCGGCGTCTGCG	.	PASS	Atlas-SNP
RAI1	10743	hgsc.bcm.edu	37	17	17700573	17700573	+	Silent	SNP	T	T	C	rs4925112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	19	58	0	0.395833	0	T|0.888;C|0.112	0.112	strong	.	RAI1	121	.	NM_030665	exon3	c.T4311C	p.P1437P	GCAGCCTGGGGGG	.	PASS	Atlas-SNP
OR2T5	401993	hgsc.bcm.edu	37	1	248651959	248651959	+	Nonsense_Mutation	SNP	C	C	T	rs76332972	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	800	132	727	0	0.165	0	C|0.983;T|0.016	0.016	strong	OR2T5,lymph_node,lymphoid_neoplasm,0,1	OR2T5	17	1	NM_001004697	exon1	c.C70T	p.R24X	TTCAGACGATCCA	.	scavenged	Atlas-SNP
SCARA3	51435	hgsc.bcm.edu	37	8	27528446	27528446	+	Missense_Mutation	SNP	T	T	C	rs17057523	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	28	60	0	0.41791	0	T|0.908;C|0.092	0.092	strong	.	SCARA3	93	.	NM_016240	exon6	c.T1399C	p.F467L	AGAGGATTCAAAG	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25009297	25009297	+	Missense_Mutation	SNP	G	G	T	rs1050112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	125	167	1	0.961538	0.00598802	G|0.603;T|0.397	0.397	strong	.	PARP4	142	.	NM_006437	exon31	c.C3982A	p.P1328T	TCGGGGGAAGATA	.	PASS	Atlas-SNP
TTC5	91875	hgsc.bcm.edu	37	14	20770036	20770036	+	Missense_Mutation	SNP	T	T	C	rs3742945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	98	215	2	0.451613	0.00930233	T|0.243;C|0.757	0.757	strong	TTC5,NS,adenoma,0,1	TTC5	34	1	NM_138376	exon2	c.A140G	p.Q47R	TCCTTCTGCACAT	.	scavenged	Atlas-SNP
KCTD19	146212	hgsc.bcm.edu	37	16	67327642	67327642	+	Missense_Mutation	SNP	C	C	T	rs145649592	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	30	96	0	0.428571	0	C|0.997;T|0.003	0.003	strong	.	KCTD19	82	.	NM_001100915	exon12	c.G2023A	p.E675K	CAGCCTCGCTTCC	.	PASS	Atlas-SNP
C9orf135	138255	hgsc.bcm.edu	37	9	72472831	72472831	+	Silent	SNP	C	C	T	rs10780682	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	53	0	1	0	C|0.722;T|0.278	0.278	strong	.	C9orf135	25	.	NM_001010940	exon4	c.C387T	p.T129T	GGTCACCGGATTG	.	PASS	Atlas-SNP
TTC27	55622	hgsc.bcm.edu	37	2	32983526	32983526	+	Silent	SNP	C	C	T	rs2273665	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	62	116	0	0.496	0	C|0.676;N|0.000	.	strong	TTC27,NS,carcinoma,0,1	TTC27	71	1	NM_017735	exon13	c.C1620T	p.N540N	TCGGAACAAGGAG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90497589	90497589	+	Missense_Mutation	SNP	A	A	C	rs4707569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	12	19	0	0.857143	0	A|0.832;C|0.168	0.168	strong	.	MDN1	478	.	NM_014611	exon8	c.T1318G	p.F440V	CAAAAAACTGAAA	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33757947	33757947	+	Missense_Mutation	SNP	A	A	T	rs58978310	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	67	110	0	0.507576	0	A|0.887;T|0.113	0.113	strong	.	URB1	176	.	NM_014825	exon2	c.T189A	p.D63E	ATACACATCTTCT	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080916	194080916	+	Missense_Mutation	SNP	G	G	A	rs13070515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	190	106	164	0	0.557895	0	G|0.843;A|0.157	0.157	strong	.	LRRC15	137	.	NM_001135057	exon3	c.C875T	p.P292L	ATCCCCGGAGAGA	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31092075	31092075	+	Missense_Mutation	SNP	G	G	A	rs7196726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	25	47	0	0.568182	0	G|0.587;A|0.413	0.413	strong	.	ZNF646	133	.	NM_014699	exon2	c.G4430A	p.G1477D	GTGGAGGCTGGGT	.	PASS	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57076080	57076080	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	26	45	0	0.40625	0	.	.	none	.	TNKS1BP1	148	.	NM_033396	exon6	c.G4105A	p.G1369R	TCACCCCGCCCAC	.	PASS	Atlas-SNP
DOC2A	8448	hgsc.bcm.edu	37	16	30017536	30017536	+	Missense_Mutation	SNP	G	G	C	rs202062683	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	50	72	0	0.555556	0	.	.	weak	.	DOC2A	40	.	NM_003586	exon11	c.C1174G	p.P392A	CCGCAGGGGGCAG	.	PASS	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	37	18	14850375	14850375	+	Silent	SNP	G	G	A	rs66708488	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	115	168	1	0.982906	0.00595238	G|0.167;A|0.833	0.833	weak	.	ANKRD30B	237	.	NM_001145029	exon35	c.G3201A	p.L1067L	TAATTTGAATCAG	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113364696	113364696	+	Silent	SNP	A	A	G	rs11778209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	77	149	0	0.596899	0	A|0.790;G|0.210	0.210	strong	CSMD3_ENST00000343508,NS,carcinoma,-1,2	CSMD3	2325	2	NM_198123	exon39	c.T6204C	p.Y2068Y	AACCATATATCTG	.	PASS	Atlas-SNP
NPVF	64111	hgsc.bcm.edu	37	7	25267934	25267934	+	Missense_Mutation	SNP	T	T	C	rs877834	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	61	130	0	0.429577	0	C|0.206;N|0.000	0.206	strong	.	NPVF	36	.	NM_022150	exon1	c.A125G	p.D42G	TATTTGTCATAAT	.	PASS	Atlas-SNP
RWDD3	25950	hgsc.bcm.edu	37	1	95699829	95699829	+	Missense_Mutation	SNP	A	A	G	rs142820652	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	77	88	0	0.52027	0	A|0.993;G|0.007	0.007	strong	.	RWDD3	24	.	NM_015485	exon1	c.A43G	p.I15V	GCCGCGATTTTCT	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43329572	43329572	+	Silent	SNP	T	T	C	rs61735800	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	82	0	0.43662	0	T|0.968;C|0.032	0.032	strong	.	C2CD2	47	.	NM_015500	exon8	c.A1014G	p.S338S	ACCTTCTGAGGAT	.	PASS	Atlas-SNP
HERPUD1	9709	hgsc.bcm.edu	37	16	56969148	56969148	+	Missense_Mutation	SNP	G	G	A	rs2217332	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	84	149	2	0.502994	0.0134228	G|0.870;A|0.130	0.130	strong	HERPUD1,NS,carcinoma,0,1	HERPUD1	28	1	NM_014685	exon2	c.G149A	p.R50H	ATCAGCGTCCAGA	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515568	195515568	+	Silent	SNP	C	C	T	rs62282504	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	267	127	224	0	0.475655	0	C|0.783;T|0.217	0.217	strong	.	MUC4	1505	.	NM_018406	exon2	c.G2883A	p.G961G	ACCAGACCCTGAA	.	PASS	Atlas-SNP
EXT1	2131	hgsc.bcm.edu	37	8	118832020	118832020	+	Silent	SNP	G	G	A	rs17439693	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	95	120	0	0.579268	0	G|0.849;A|0.151	0.151	strong	.	EXT1	98	.	NM_000127	exon6	c.C1431T	p.P477P	TTTGGAGGGGGGC	.	PASS	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	37	12	52822258	52822258	+	Silent	SNP	A	A	G	rs401926	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	43	67	0	0.477778	0	A|0.368;G|0.632	0.632	strong	.	KRT75	75	.	NM_004693	exon7	c.T1164C	p.C388C	GCTGGAACACTGT	.	PASS	Atlas-SNP
GPR116	221395	hgsc.bcm.edu	37	6	46827239	46827239	+	Missense_Mutation	SNP	C	C	T	rs9395218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	60	124	0	0.437956	0	C|0.761;T|0.239	0.239	strong	.	GPR116	133	.	NM_015234	exon17	c.G2401A	p.V801I	GGATGACATTAAC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40360928	40360928	+	Silent	SNP	G	G	A	rs1053686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	46	120	0	0.442308	0	G|0.865;N|0.000	.	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon33	c.C15480T	p.R5160R	CAGGAAGCGGTCG	.	PASS	Atlas-SNP
HTT	3064	hgsc.bcm.edu	37	4	3215835	3215835	+	Missense_Mutation	SNP	T	T	C	rs362331	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	61	122	0	0.508333	0	C|0.453;N|0.000	0.453	strong	HTT,NS,carcinoma,0,1	HTT	221	1	NM_002111	exon50	c.T6925C	p.Y2309H	CTCATCTACTGTG	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	37	16	51173710	51173710	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	2	161	0	0.0108108	0	.	.	none	SALL1,NS,carcinoma,0,1	SALL1	301	1	NM_002968	exon2	c.C2423T	p.S808F	GTGTCAGACTCCA	.	scavenged	Atlas-SNP
ZNF544	27300	hgsc.bcm.edu	37	19	58774071	58774071	+	Missense_Mutation	SNP	A	A	G	rs260462	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	30	72	0	0.434783	0	A|0.455;G|0.545	0.545	strong	.	ZNF544	57	.	NM_014480	exon7	c.A2099G	p.Q700R	GGCAGCAATCTCA	.	PASS	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145639726	145639726	+	Missense_Mutation	SNP	T	T	C	rs2272662	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	358	357	226	1	0.997207	0.00442478	T|0.606;C|0.394	0.394	strong	SLC39A4,NS,carcinoma,0,1	SLC39A4	54	1	NM_130849	exon6	c.A1069G	p.T357A	AGTGGGTGACCCC	.	PASS	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3886847	3886847	+	Silent	SNP	G	G	C	rs3749349	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	42	113	0	0.477273	0	G|0.820;C|0.180	0.180	strong	.	LRRN1	82	.	NM_020873	exon2	c.G522C	p.L174L	CCACCTGAACTCC	.	PASS	Atlas-SNP
KCNQ3	3786	hgsc.bcm.edu	37	8	133153451	133153451	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	41	97	0	0.330645	0	.	.	none	.	KCNQ3	164	.	NM_004519	exon10	c.G1390A	p.V464I	AGCCAACAGGCTT	.	PASS	Atlas-SNP
RNF43	54894	hgsc.bcm.edu	37	17	56492800	56492800	+	Missense_Mutation	SNP	T	T	C	rs3744093	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	46	69	0	0.505495	0	T|0.651;C|0.349	0.349	strong	.	RNF43	157	.	NM_017763	exon2	c.A139G	p.I47V	TGATAATAGCTTT	.	PASS	Atlas-SNP
LRIT3	345193	hgsc.bcm.edu	37	4	110790911	110790911	+	Missense_Mutation	SNP	A	A	T	rs764205	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	188	210	0	0.979167	0	T|0.561;N|0.000	0.561	strong	LRIT3_ENST00000379920,NS,carcinoma,0,2	LRIT3	107	2	NM_198506	exon4	c.A1006T	p.M336L	GCTGGGATGTCAG	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48056050	48056050	+	Missense_Mutation	SNP	G	G	A	rs151039709	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	62	133	0	0.473282	0	G|1.000;A|0.000	0.000	strong	.	SEMA6D	322	.	NM_153617	exon10	c.G751A	p.V251M	CAGGCTGTGTATT	.	PASS	Atlas-SNP
OR2J2	26707	hgsc.bcm.edu	37	6	29141632	29141632	+	Missense_Mutation	SNP	T	T	C	rs3116855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	117	254	0	0.47561	0	T|0.593;C|0.407	0.407	strong	.	OR2J2	51	.	NM_030905	exon1	c.T220C	p.Y74H	CTCTGCTACACCA	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47869038	47869038	+	Silent	SNP	T	T	C	rs7788583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	40	58	0	0.634921	0	T|0.785;C|0.215	0.215	strong	PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	NM_138295	exon44	c.A6720G	p.A2240A	CTCGCCTGCACAG	.	PASS	Atlas-SNP
RILPL1	353116	hgsc.bcm.edu	37	12	124017850	124017850	+	Silent	SNP	G	G	C	rs28492040	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	17	32	0	0.459459	0	G|0.882;C|0.118	0.118	strong	RILPL1,NS,carcinoma,0,1	RILPL1	23	1	NM_178314	exon1	c.C180G	p.V60V	CTCCAGGACGCGC	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	37	2	37289177	37289177	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	11	52	0	0.275	0	.	.	none	.	HEATR5B	185	.	NM_019024	exon11	c.C1601A	p.A534D	TCTTCAGCAATAC	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202288293	202288293	+	Silent	SNP	C	C	T	rs56234832	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	64	138	0	0.520325	0	C|0.914;T|0.086	0.086	strong	.	LGR6	102	.	NM_001017403	exon18	c.C2862T	p.G954G	GGGTGGCGGCTTT	.	PASS	Atlas-SNP
COL5A2	1290	hgsc.bcm.edu	37	2	189904233	189904233	+	Silent	SNP	T	T	G	rs10197596	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	41	103	0	0.532468	0	T|0.896;G|0.104	0.104	strong	.	COL5A2	230	.	NM_000393	exon51	c.A3690C	p.T1230T	AGCAGCTGTAAGG	.	PASS	Atlas-SNP
WT1	7490	hgsc.bcm.edu	37	11	32417945	32417945	+	Silent	SNP	T	T	C	rs16754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	9	41	0	0.375	0	T|0.782;C|0.218	0.218	strong	WT1_ENST00000379079,colon,carcinoma,0,7	WT1	744	7	NM_024424	exon7	c.A1107G	p.R369R	CACACGTCGCACA	.	PASS	Atlas-SNP
RANBP6	26953	hgsc.bcm.edu	37	9	6012734	6012734	+	Silent	SNP	A	A	C	rs106033	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	37	95	0	0.445783	0	A|0.647;C|0.353	0.353	strong	.	RANBP6	127	.	NM_012416	exon1	c.T2874G	p.L958L	TACCAGAAGTGGA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912147	29912147	+	Silent	SNP	C	C	T	rs1059686	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	57	304	0	0.314917	0	C|0.711;T|0.289	0.289	strong	.	HLA-A	89	.	NM_001242758	exon4	c.C868T	p.L290L	GAGGGTCTGCCCA	.	PASS	Atlas-SNP
STEAP2	261729	hgsc.bcm.edu	37	7	89854446	89854446	+	Missense_Mutation	SNP	T	T	G	rs194520	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	129	151	0	1	0	T|0.602;G|0.398	0.398	strong	.	STEAP2	78	.	NM_001244946	exon3	c.T50G	p.F17C	AAACTTTTTTACC	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56549532	56549532	+	Silent	SNP	A	A	G	rs306447	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	66	140	0	0.409938	0	A|0.693;G|0.307	0.307	strong	NLRP5,NS,carcinoma,0,1	NLRP5	217	1	NM_153447	exon10	c.A2757G	p.R919R	CTTGAGAGTCTCC	.	PASS	Atlas-SNP
FBXO42	54455	hgsc.bcm.edu	37	1	16641899	16641899	+	Silent	SNP	C	C	T	rs2273311	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	8	139	0	0.0516129	0	C|0.658;T|0.342	0.342	strong	.	FBXO42	53	.	NM_018994	exon2	c.G15A	p.S5S	ACTGTCCGAGGAG	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128491603	128491603	+	Silent	SNP	T	T	C	rs3816884	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	97	175	1	0.521505	0.00571429	T|0.793;C|0.207	0.207	strong	FLNC,NS,lymphoid_neoplasm,+1,1	FLNC	339	1	NM_001458	exon35	c.T5763C	p.T1921T	GCCGACTGCGCCT	.	scavenged	Atlas-SNP
C1QTNF1	114897	hgsc.bcm.edu	37	17	77040185	77040185	+	Silent	SNP	G	G	C	rs4789853	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	20	47	0	0.47619	0	G|0.616;C|0.384	0.384	strong	.	C1QTNF1	62	.	NM_030968	exon2	c.G135C	p.S45S	GCCGTCGCCTCCG	.	PASS	Atlas-SNP
SDC2	6383	hgsc.bcm.edu	37	8	97605800	97605800	+	Silent	SNP	C	C	T	rs1126681	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	32	53	1	0.551724	0.0188679	C|0.804;T|0.196	0.196	strong	SDC2,NS,carcinoma,0,2	SDC2	33	2	NM_002998	exon2	c.C153T	p.Y51Y	TGACTACGCTTCT	.	scavenged	Atlas-SNP
PPP6R2	9701	hgsc.bcm.edu	37	22	50873497	50873497	+	Silent	SNP	C	C	T	rs1134848	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	14	55	0	0.28	0	C|0.920;T|0.080	0.080	strong	PPP6R2,NS,carcinoma,0,1	PPP6R2	71	1	NM_001242899	exon13	c.C1506T	p.S502S	CATCAGCGAGGTC	.	PASS	Atlas-SNP
SCUBE2	57758	hgsc.bcm.edu	37	11	9051475	9051475	+	Missense_Mutation	SNP	G	G	C	rs3751057	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	116	266	0	0.485356	0	G|0.908;C|0.092	0.092	strong	.	SCUBE2	102	.	NM_020974	exon18	c.C2288G	p.T763S	GTCGTAGTATTTC	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057711	46057711	+	Missense_Mutation	SNP	G	G	C	rs4818948	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	73	137	0	0.470968	0	G|0.711;C|0.289	0.289	strong	KRTAP10-10,NS,carcinoma,0,1	KRTAP10-10	37	1	NM_181688	exon1	c.G377C	p.C126S	CTTCATGCTGCCA	.	PASS	Atlas-SNP
MAP3K2	10746	hgsc.bcm.edu	37	2	128079806	128079806	+	Silent	SNP	A	A	G	rs3732209	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	20	69	0	0.425532	0	A|0.788;G|0.212	0.212	strong	.	MAP3K2	78	.	NM_006609	exon11	c.T861C	p.A287A	CCTTCTAGCTCTT	.	PASS	Atlas-SNP
UBASH3A	53347	hgsc.bcm.edu	37	21	43863521	43863521	+	Silent	SNP	A	A	G	rs868092	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	19	48	0	0.38	0	A|0.359;G|0.641	0.641	strong	.	UBASH3A	72	.	NM_018961	exon13	c.A1731G	p.P577P	CTGTCCACAGGAC	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14991459	14991459	+	Missense_Mutation	SNP	C	C	T	rs13345394	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	35	55	0	0.5	0	C|0.959;T|0.041	0.041	strong	.	OR7A17	37	.	NM_030901	exon1	c.G709A	p.A237T	AAAATGCCTTGTA	.	PASS	Atlas-SNP
ADCK4	79934	hgsc.bcm.edu	37	19	41209477	41209477	+	Silent	SNP	C	C	T	rs11538385	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	54	102	0	0.545455	0	C|0.773;T|0.227	0.227	strong	ADCK4_ENST00000324464,colon,carcinoma,-1,6	ADCK4	92	6	NM_024876	exon9	c.G768A	p.A256A	GAGTACCGCCAGC	.	PASS	Atlas-SNP
ERCC4	2072	hgsc.bcm.edu	37	16	14041958	14041958	+	Silent	SNP	T	T	C	rs1799801	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	37	105	0	0.420455	0	T|0.754;C|0.246	0.246	strong	.	ERCC4	100	.	NM_005236	exon11	c.T2505C	p.S835S	AGATTCTGAAACC	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140553581	140553581	+	Missense_Mutation	SNP	G	G	C	rs2910313	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	88	80	1	0.988764	0.0125	G|0.392;C|0.608	0.608	strong	PCDHB7,colon,carcinoma,0,1	PCDHB7	231	1	NM_018940	exon1	c.G1165C	p.V389L	GACGATGTCCCCT	.	scavenged	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41870083	41870083	+	Splice_Site	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	3	37	0	0.0681818	0	.	.	none	TYRO3_ENST00000263798,colon,carcinoma,0,4	TYRO3	169	4	NM_006293	exon19	c.2283-1G>T	.	ACCCCAGGTATGA	.	scavenged	Atlas-SNP
MSH5	4439	hgsc.bcm.edu	37	6	31708328	31708328	+	Missense_Mutation	SNP	C	C	T	rs2075789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	49	70	0	0.526882	0	C|0.881;T|0.119	0.119	strong	.	MSH5	108	.	NM_172165	exon2	c.C85T	p.P29S	CCGGCCCCAGTGC	.	PASS	Atlas-SNP
CRB2	286204	hgsc.bcm.edu	37	9	126132919	126132919	+	Silent	SNP	G	G	A	rs33984675	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	14	33	0	0.318182	0	G|0.766;A|0.234	0.234	strong	.	CRB2	86	.	NM_173689	exon7	c.G1587A	p.A529A	TCTAGCGACCCTG	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135958730	135958730	+	Missense_Mutation	SNP	C	C	A	rs78702689	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	342	73	233	0	0.21345	0	.	.	weak	.	RBMX	149	.	NM_002139	exon5	c.G473T	p.G158V	GGACCCCCACTTC	.	PASS	Atlas-SNP
YDJC	150223	hgsc.bcm.edu	37	22	21982892	21982892	+	Missense_Mutation	SNP	C	C	T	rs2298428	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	20	18	0	0.645161	0	C|0.795;T|0.205	0.205	strong	.	YDJC	8	.	NM_001017964	exon5	c.G787A	p.A263T	AGAAAGCGTCGGG	.	PASS	Atlas-SNP
NMNAT2	23057	hgsc.bcm.edu	37	1	183255908	183255908	+	Missense_Mutation	SNP	T	T	C	rs41314643	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	216	99	229	0	0.458333	0	T|0.989;C|0.011	0.011	strong	.	NMNAT2	48	.	NM_015039	exon5	c.A337G	p.I113V	AGAGGATGCAGCC	.	PASS	Atlas-SNP
MAGEB10	139422	hgsc.bcm.edu	37	X	27839572	27839572	+	Missense_Mutation	SNP	T	T	C	rs1368769	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	51	60	0	1	0	0|0.029;C|0.421	0.421	strong	.	MAGEB10	107	.	NM_182506	exon3	c.T149C	p.F50S	ATGTTTTCCAGAG	.	PASS	Atlas-SNP
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67236097	67236097	+	Missense_Mutation	SNP	A	A	T	rs1060575	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	27	42	0	0.355263	0	A|0.878;N|0.000	.	strong	.	TCTEX1D1	27	.	NM_152665	exon3	c.A147T	p.E49D	TATGGAAGAACCC	.	PASS	Atlas-SNP
FMN1	342184	hgsc.bcm.edu	37	15	33091079	33091079	+	Silent	SNP	A	A	G	rs7162695	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	32	71	0	0.5	0	A|0.853;G|0.147	0.147	strong	.	FMN1	174	.	NM_001103184	exon15	c.T3387C	p.F1129F	CACCATAAACACG	.	PASS	Atlas-SNP
EXOSC3	51010	hgsc.bcm.edu	37	9	37782111	37782111	+	Silent	SNP	C	C	T	rs7158	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	47	109	0	0.447619	0	C|0.471;T|0.529	0.529	strong	.	EXOSC3	8	.	NM_016042	exon3	c.G498A	p.Q166Q	CACAAACTGGCCA	.	PASS	Atlas-SNP
DIP2A	23181	hgsc.bcm.edu	37	21	47910523	47910523	+	Silent	SNP	A	A	G	rs7279002	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	68	129	0	0.485714	0	A|0.634;G|0.366	0.366	strong	.	DIP2A	332	.	NM_206891	exon3	c.A174G	p.P58P	AGACCCATCTCTG	.	PASS	Atlas-SNP
ZNF677	342926	hgsc.bcm.edu	37	19	53740822	53740822	+	Silent	SNP	T	T	C	rs8113436	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	53	108	0	0.469027	0	T|0.600;C|0.400	0.400	strong	ZNF677,NS,carcinoma,0,1	ZNF677	94	1	NM_182609	exon5	c.A1158G	p.E386E	TGAACGTTCAGCA	.	PASS	Atlas-SNP
NIN	51199	hgsc.bcm.edu	37	14	51224658	51224658	+	Silent	SNP	T	T	A	rs2073348	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	81	206	0	0.419689	0	A|0.311;N|0.000	0.311	strong	.	NIN	475	.	NM_020921	exon18	c.A3090T	p.S1030S	AAGCATTGAGAGA	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	37	22	46805772	46805772	+	Missense_Mutation	SNP	C	C	T	rs11704506	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	43	39	0	0.614286	0	C|0.979;T|0.021	0.021	strong	.	CELSR1	242	.	NM_014246	exon8	c.G4939A	p.A1647T	GAGCAGCGCAGCC	.	PASS	Atlas-SNP
C16orf89	146556	hgsc.bcm.edu	37	16	5106184	5106184	+	Silent	SNP	C	C	T	rs741164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	58	101	0	0.491525	0	C|0.432;T|0.568	0.568	strong	.	C16orf89	64	.	NM_001098514	exon5	c.G633A	p.G211G	TGTGCACCCCCTC	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505179	37505179	+	Silent	SNP	T	T	C	rs57914746	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	65	222	0	0.384615	0	T|0.822;C|0.178	0.178	strong	.	ANKRD30A	448	.	NM_052997	exon32	c.T2772C	p.D924D	AAAAGATCACTGT	.	PASS	Atlas-SNP
DHCR24	1718	hgsc.bcm.edu	37	1	55319902	55319902	+	Silent	SNP	A	A	G	rs718265	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	79	79	0	1	0	A|0.363;G|0.637	0.637	strong	.	DHCR24	31	.	NM_014762	exon7	c.T1026C	p.I342I	GGGGATAATGTCC	.	PASS	Atlas-SNP
SPG7	6687	hgsc.bcm.edu	37	16	89613123	89613123	+	Missense_Mutation	SNP	A	A	G	rs2292954	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	42	95	0	0.424242	0	G|0.121;N|0.000	0.121	strong	.	SPG7	75	.	NM_003119	exon11	c.A1507G	p.T503A	TCCAGCACCTTTT	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100071728	100071728	+	Silent	SNP	G	G	A	rs3747507	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	35	91	0	0.416667	0	G|0.774;A|0.226	0.226	strong	.	.	.	.	NM_020893	exon3	c.G234A	p.R78R	CACCAGGAAGCGG	.	PASS	Atlas-SNP
TRIM51	84767	hgsc.bcm.edu	37	11	55652963	55652963	+	Missense_Mutation	SNP	A	A	G	rs2063276	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	196	236	0	0.989899	0	A|0.360;G|0.640	0.640	strong	.	.	.	.	NM_032681	exon2	c.A59G	p.N20S	GCATGAACTACTT	.	PASS	Atlas-SNP
SLC17A1	6568	hgsc.bcm.edu	37	6	25820126	25820126	+	Missense_Mutation	SNP	C	C	A	rs149708935	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	27	53	0	0.397059	0	C|1.000;A|0.000	0.000	weak	.	SLC17A1	71	.	NM_005074	exon4	c.G225T	p.W75C	TGGGCTCCAATTA	.	PASS	Atlas-SNP
SERPINA11	256394	hgsc.bcm.edu	37	14	94912896	94912896	+	Missense_Mutation	SNP	T	T	G	rs1885137	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	140	176	0	0.985915	0	G|0.312;N|0.000	0.312	strong	.	SERPINA11	53	.	NM_001080451	exon3	c.A689C	p.E230A	AAACTTTCCTGCT	.	PASS	Atlas-SNP
KRT32	3882	hgsc.bcm.edu	37	17	39619115	39619115	+	Missense_Mutation	SNP	G	G	A	rs2071563	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	55	80	0	0.597826	0	G|0.611;A|0.389	0.389	strong	.	KRT32	57	.	NM_002278	exon6	c.C1184T	p.T395M	CGGTACGTGTTGA	.	PASS	Atlas-SNP
BST1	683	hgsc.bcm.edu	37	4	15709252	15709252	+	Missense_Mutation	SNP	G	G	A	rs2302464	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	99	152	0	0.55	0	G|0.944;A|0.056	0.056	strong	BST1,NS,carcinoma,0,1	BST1	30	1	NM_004334	exon3	c.G434A	p.R145Q	GGTGTCGACAGAA	.	PASS	Atlas-SNP
PARM1	25849	hgsc.bcm.edu	37	4	75937971	75937971	+	Missense_Mutation	SNP	C	C	T	rs3822109	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	111	118	0	0.991071	0	C|0.691;T|0.309	0.309	strong	PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	NM_015393	exon2	c.C380T	p.S127L	ACAGCTCGGGCAC	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11835331	11835331	+	Missense_Mutation	SNP	G	G	A	rs17612861	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	91	195	0	0.4375	0	G|0.766;A|0.233	0.233	strong	.	DNAH9	695	.	NM_001372	exon64	c.G12106A	p.D4036N	TTTCAGGACACTC	.	PASS	Atlas-SNP
GATA5	140628	hgsc.bcm.edu	37	20	61040453	61040453	+	Silent	SNP	C	C	G	rs6061243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	16	49	0	0.470588	0	C|0.467;G|0.533	0.533	strong	GATA5,NS,carcinoma,-1,1	GATA5	22	1	NM_080473	exon6	c.G981C	p.S327S	GGCTTTCGAAGTG	.	PASS	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145641564	145641564	+	Missense_Mutation	SNP	T	T	G	rs2280839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	23	23	0	1	0	T|0.522;G|0.478	0.478	strong	.	SLC39A4	54	.	NM_017767	exon1	c.A29C	p.E10A	CCTGTTTCCCTTT	.	PASS	Atlas-SNP
ZDHHC8	29801	hgsc.bcm.edu	37	22	20134739	20134739	+	Silent	SNP	C	C	T	rs9605070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	34	29	0	1	0	C|0.880;T|0.120	0.120	strong	ZDHHC8_ENST00000405930,rectum,carcinoma,0,1	ZDHHC8	77	1	NM_001185024	exon11	c.C2322T	p.S774S	CCCCAGCCTCTCG	.	PASS	Atlas-SNP
TUBB8	347688	hgsc.bcm.edu	37	10	93714	93714	+	Silent	SNP	A	A	C	rs41288743		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	9	41	0	0.155172	0	.	.	weak	TUBB8,NS,carcinoma,0,1	TUBB8	62	1	NM_177987	exon4	c.T618G	p.A206A	ATACAGAGCTTCG	.	scavenged	Atlas-SNP
KIFC3	3801	hgsc.bcm.edu	37	16	57794643	57794643	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	4	87	0	0.045977	0	.	.	none	.	KIFC3	55	.	NM_001130100	exon16	c.G2227A	p.V743I	CCTGTACCACCAT	.	PASS	Atlas-SNP
HOXC6	3223	hgsc.bcm.edu	37	12	54422479	54422479	+	Silent	SNP	G	G	A	rs145731630	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	58	97	0	0.517857	0	G|0.997;A|0.003	0.003	strong	.	HOXC6	30	.	NM_004503	exon1	c.G174A	p.Q58Q	GCCACAGGAGAAT	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	37	11	119043656	119043656	+	Missense_Mutation	SNP	C	C	T	rs643423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	39	55	0	0.6	0	C|0.405;T|0.595	0.595	strong	.	NLRX1	128	.	NM_024618	exon4	c.C187T	p.P63S	CCCCCACCCGGGA	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89417238	89417238	+	Missense_Mutation	SNP	A	A	G	rs1126823	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	29	41	0	0.557692	0	A|0.613;G|0.387	0.387	strong	.	ACAN	220	.	NM_013227	exon17	c.A7499G	p.Q2500R	AGCCTCAGATCAC	.	PASS	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	37	18	72178161	72178161	+	Silent	SNP	T	T	C	rs2278159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	53	110	0	0.456897	0	T|0.825;C|0.175	0.175	strong	CNDP2,NS,carcinoma,0,1	CNDP2	55	1	NM_018235	exon6	c.T570C	p.Y190Y	GGACTATGTCTGC	.	PASS	Atlas-SNP
FAS	355	hgsc.bcm.edu	37	10	90771829	90771829	+	Silent	SNP	T	T	C	rs2234978	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	81	54	0	0.975904	0	T|0.261;C|0.739	0.739	strong	.	FAS	47	.	NM_152872	exon7	c.T642C	p.T214T	TCCAACTTTAAAT	.	PASS	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	37	2	1642697	1642697	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	65	113	0	0.481481	0	.	.	none	PXDN,NS,carcinoma,0,1	PXDN	255	1	NM_012293	exon21	c.G4127A	p.R1376H	TCTGAGCGTGTGC	.	PASS	Atlas-SNP
C5orf52	100190949	hgsc.bcm.edu	37	5	157102185	157102185	+	Missense_Mutation	SNP	A	A	G	rs6884959	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	87	113	0	0.988636	0	A|0.478;G|0.522	0.522	strong	.	C5orf52	17	.	NM_001145132	exon2	c.A298G	p.T100A	CGCATCACACAAC	.	PASS	Atlas-SNP
PNMA3	29944	hgsc.bcm.edu	37	X	152226542	152226542	+	Missense_Mutation	SNP	T	T	C	rs6526155	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	35	43	0	0.972222	0	0|0.013;C|0.892	0.892	strong	.	PNMA3	81	.	NM_013364	exon2	c.T1130C	p.V377A	TTGATGTGAGGCC	.	PASS	Atlas-SNP
GSDMA	284110	hgsc.bcm.edu	37	17	38131187	38131187	+	Missense_Mutation	SNP	C	C	A	rs56030650	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	92	75	0	0.989247	0	C|0.572;A|0.428	0.428	strong	.	GSDMA	26	.	NM_178171	exon10	c.C941A	p.T314N	AAGTGACCCTGGA	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84212571	84212571	+	Silent	SNP	C	C	A	rs1804500	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	23	51	0	0.958333	0	C|0.709;A|0.291	0.291	strong	TAF1C,NS,carcinoma,0,1	TAF1C	60	1	NM_005679	exon14	c.G2586T	p.R862R	CTTCTTCCGGAGG	.	PASS	Atlas-SNP
NACA2	342538	hgsc.bcm.edu	37	17	59668021	59668021	+	Missense_Mutation	SNP	G	G	C	rs61739273	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	99	173	0	0.502538	0	G|0.868;C|0.132	0.132	strong	NACA2,NS,carcinoma,0,2	NACA2	33	2	NM_199290	exon1	c.C521G	p.T174R	ACACCTGTTTCAT	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786832	75786832	+	Missense_Mutation	SNP	C	C	T	rs11122676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	40	44	0	0.533333	0	C|0.574;T|0.426	0.426	strong	.	ZNF717	160	.	NM_001128223	exon5	c.G1942A	p.V648I	TACATACGTAAGG	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	37	2	33540248	33540248	+	Silent	SNP	G	G	A	rs1058840	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	46	117	0	0.429907	0	G|0.480;A|0.519	0.519	strong	.	LTBP1	317	.	NM_206943	exon24	c.G3642A	p.P1214P	TGGTCCGCAAGGG	.	PASS	Atlas-SNP
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46102015	46102015	+	Silent	SNP	C	C	T	rs7283084	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	79	116	0	0.490683	0	C|0.871;T|0.129	0.129	strong	.	KRTAP12-1	9	.	NM_181686	exon1	c.G24A	p.S8S	GCAGCCCGAGGAG	.	PASS	Atlas-SNP
AEN	64782	hgsc.bcm.edu	37	15	89169484	89169484	+	Missense_Mutation	SNP	C	C	T	rs3743477	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	14	29	0	0.378378	0	C|0.930;T|0.070	0.070	strong	.	AEN	29	.	NM_022767	exon2	c.C44T	p.P15L	TGTGCCCTTCCCT	.	PASS	Atlas-SNP
BCKDHA	593	hgsc.bcm.edu	37	19	41920030	41920030	+	Missense_Mutation	SNP	C	C	T	rs34442879	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	60	86	0	0.560748	0	C|0.993;T|0.007	0.007	strong	.	BCKDHA	36	.	NM_000709	exon4	c.C452T	p.T151M	ACAACACGGACCT	.	PASS	Atlas-SNP
DROSHA	29102	hgsc.bcm.edu	37	5	31409252	31409252	+	Silent	SNP	A	A	G	rs2241337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	83	231	1	0.458564	0.004329	A|0.696;G|0.304	0.304	strong	.	DROSHA	130	.	NM_013235	exon32	c.T3765C	p.N1255N	ATCCTGATTCAAA	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68704028	68704028	+	Missense_Mutation	SNP	C	C	T	rs2236654	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	24	55	0	0.545455	0	C|0.807;T|0.193	0.193	strong	.	IGHMBP2	83	.	NM_002180	exon13	c.C2080T	p.R694W	CAGGGCCGGAAGA	.	PASS	Atlas-SNP
SWSAP1	126074	hgsc.bcm.edu	37	19	11486514	11486514	+	Missense_Mutation	SNP	A	A	G	rs317926	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	26	49	0	0.433333	0	A|0.984;G|0.016	0.016	strong	C19orf39,NS,carcinoma,0,1	.	.	1	NM_175871	exon2	c.A512G	p.D171G	AGCCAGATGCACC	.	PASS	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57070170	57070170	+	Silent	SNP	C	C	T	rs34905018	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	29	39	0	0.557692	0	C|0.987;T|0.013	0.013	strong	.	TNKS1BP1	148	.	NM_033396	exon7	c.G4446A	p.L1482L	CTCCTCCAACAGG	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127215772	127215772	+	Missense_Mutation	SNP	C	C	G	rs72616654	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	16	6	0	1	0	C|0.491;G|0.509	0.509	strong	.	GPR144	33	.	NM_001161808	exon4	c.C796G	p.H266D	GTGCGTCACGCCC	.	PASS	Atlas-SNP
XPC	7508	hgsc.bcm.edu	37	3	14214524	14214524	+	Missense_Mutation	SNP	G	G	A	rs2229089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	84	175	0	0.488372	0	G|0.985;A|0.015	0.015	strong	.	XPC	60	.	NM_004628	exon2	c.C142T	p.L48F	TGGAGAGAAGGCT	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612757	53612757	+	Missense_Mutation	SNP	T	T	G	rs1054485	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	141	115	0	0.992958	0	T|0.487;G|0.508	0.508	strong	.	ZNF415	68	.	NM_018355	exon4	c.A541C	p.I181L	AAGAAATTATTTG	.	PASS	Atlas-SNP
MAGEA6	4105	hgsc.bcm.edu	37	X	151870117	151870117	+	Silent	SNP	T	T	C	rs369345489		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	91	119	0	0.98913	0	.	.	weak	.	MAGEA6	53	.	NM_005363	exon3	c.T807C	p.Y269Y	ATGCTATGAGTTC	.	PASS	Atlas-SNP
DUSP4	1846	hgsc.bcm.edu	37	8	29197685	29197685	+	Missense_Mutation	SNP	G	G	A	rs371579846		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	20	47	0	0.384615	0	.	.	weak	.	DUSP4	58	.	NM_001394	exon2	c.C509T	p.P170L	GGAACCGGGGGTG	.	PASS	Atlas-SNP
CHD3	1107	hgsc.bcm.edu	37	17	7807904	7807904	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	55	95	0	0.539216	0	.	.	none	.	CHD3	169	.	NM_001005271	exon25	c.G4216A	p.V1406I	AAGCAAGTTAACT	.	PASS	Atlas-SNP
POFUT2	23275	hgsc.bcm.edu	37	21	46707778	46707778	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	12	11	0	0.6	0	.	.	none	.	POFUT2	77	.	NM_015227	exon1	c.A9G	p.T3T	GCTGAGTGTCGCC	.	PASS	Atlas-SNP
FAM198A	729085	hgsc.bcm.edu	37	3	43073761	43073761	+	Silent	SNP	G	G	A	rs658958	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	44	105	0	0.494382	0	G|0.533;A|0.467	0.467	strong	FAM198A_ENST00000430121,caecum,carcinoma,0,1	FAM198A	23	1	NM_001129908	exon2	c.G6A	p.A2A	TCAGGCGTCTTGG	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152192395	152192395	+	Silent	SNP	G	G	A	rs61814946	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	91	167	0	0.50838	0	G|0.895;A|0.105	0.105	strong	HRNR,NS,carcinoma,0,1	HRNR	403	1	NM_001009931	exon3	c.C1710T	p.S570S	GCCACGGCTTGAA	.	PASS	Atlas-SNP
CCNG1	900	hgsc.bcm.edu	37	5	162868910	162868910	+	Missense_Mutation	SNP	T	T	G	rs11541970	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	80	251	0	0.462428	0	T|0.977;G|0.023	0.023	strong	.	CCNG1	28	.	NM_199246	exon5	c.T537G	p.F179L	TAATTTTGAAAGA	.	PASS	Atlas-SNP
NPLOC4	55666	hgsc.bcm.edu	37	17	79526402	79526402	+	Silent	SNP	G	G	C	rs4073997	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	254	128	239	2	0.503937	0.0083682	G|0.821;C|0.179	0.179	strong	NPLOC4,NS,carcinoma,0,1	NPLOC4	27	1	NM_017921	exon17	c.C1710G	p.G570G	GACGGCGCCGTAC	.	scavenged	Atlas-SNP
DPP4	1803	hgsc.bcm.edu	37	2	162929979	162929979	+	Silent	SNP	A	A	G	rs17574	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	46	88	0	0.469388	0	A|0.720;G|0.280	0.280	strong	.	DPP4	90	.	NM_001935	exon2	c.T24C	p.L8L	TCCCAGAAGAACC	.	PASS	Atlas-SNP
NUMA1	4926	hgsc.bcm.edu	37	11	71725281	71725281	+	Silent	SNP	G	G	A	rs200298289	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	104	167	0	0.497608	0	A|0.001;G|0.999	0.001	weak	.	NUMA1	142	.	NM_006185	exon15	c.C3268T	p.L1090L	CCTTCAGTTGCTT	.	PASS	Atlas-SNP
SLC25A13	10165	hgsc.bcm.edu	37	7	95800820	95800820	+	Silent	SNP	T	T	C	rs2301629	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	93	140	0	0.502703	0	T|0.645;C|0.355	0.355	strong	SLC25A13,caecum,carcinoma,0,1	SLC25A13	131	1	NM_001160210	exon12	c.A1197G	p.L399L	TCCCAATAACTGT	.	PASS	Atlas-SNP
P2RX3	5024	hgsc.bcm.edu	37	11	57114109	57114109	+	Missense_Mutation	SNP	G	G	A	rs34572680	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	39	92	0	0.46988	0	G|0.971;A|0.029	0.029	strong	.	P2RX3	55	.	NM_002559	exon2	c.G211A	p.A71T	CTCTACGCCAACA	.	PASS	Atlas-SNP
TRDMT1	1787	hgsc.bcm.edu	37	10	17199778	17199778	+	Silent	SNP	C	C	A	rs11254408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	20	28	0	0.625	0	C|0.884;A|0.116	0.116	strong	.	TRDMT1	46	.	NM_004412	exon8	c.G549T	p.L183L	CTCCATCAGTACC	.	PASS	Atlas-SNP
PRMT6	55170	hgsc.bcm.edu	37	1	107599918	107599918	+	Missense_Mutation	SNP	C	C	T	rs2232016	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	55	70	0	0.539216	0	C|0.849;T|0.151	0.151	strong	.	PRMT6	55	.	NM_018137	exon1	c.C581T	p.A194V	TCATAGCCCCCAT	.	PASS	Atlas-SNP
ELF3	1999	hgsc.bcm.edu	37	1	201981774	201981774	+	Missense_Mutation	SNP	G	G	A	rs55729978	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	40	71	0	0.416667	0	G|0.938;A|0.062	0.062	strong	ELF3_ENST00000359651,NS,carcinoma,0,2	ELF3	92	2	NM_001114309	exon5	c.G485A	p.G162D	ACCAGGGCAGCCC	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37455581	37455581	+	Missense_Mutation	SNP	G	G	A	rs71283286	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	633	12	732	0	0.0189573	0	GCG|0.500;ACA|0.500	.	alt	ANKRD30A,NS,haematopoietic_neoplasm,-1,1	ANKRD30A	448	1	NM_052997	exon19	c.G1945A	p.A649T	AAGGCTGCGCATC	.	scavenged	Atlas-SNP
TAF5L	27097	hgsc.bcm.edu	37	1	229730452	229730452	+	Silent	SNP	G	G	A	rs2295625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	68	111	0	0.548387	0	G|0.674;A|0.326	0.326	strong	.	TAF5L	76	.	NM_014409	exon5	c.C1362T	p.S454S	CTGAGCGCTCCAC	.	PASS	Atlas-SNP
ITGAE	3682	hgsc.bcm.edu	37	17	3632836	3632836	+	Missense_Mutation	SNP	G	G	A	rs1716	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	129	157	0	0.969925	0	G|0.755;A|0.245	0.245	strong	.	ITGAE	96	.	NM_002208	exon24	c.C2848T	p.R950W	AAGACCGTCTTTC	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	37	6	51491884	51491884	+	Missense_Mutation	SNP	T	T	C	rs4715227	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	167	188	1	0.994048	0.00531915	T|0.467;C|0.533	0.533	strong	.	PKHD1	927	.	NM_138694	exon66	c.A11696G	p.Q3899R	TTAGTCTGGGATT	.	PASS	Atlas-SNP
TAMM41	132001	hgsc.bcm.edu	37	3	11880760	11880760	+	Missense_Mutation	SNP	T	T	C	rs7641243	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	24	56	0	0.444444	0	T|0.854;C|0.146	0.146	strong	.	.	.	.	NM_138807	exon3	c.A347G	p.N116S	AGAACGTTAGTGC	.	PASS	Atlas-SNP
DENND5A	23258	hgsc.bcm.edu	37	11	9225486	9225486	+	Missense_Mutation	SNP	C	C	G	rs952374	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	48	86	0	0.40678	0	C|0.715;G|0.285	0.285	strong	.	DENND5A	84	.	NM_015213	exon4	c.G670C	p.E224Q	GTTGCTCCAGCAC	.	PASS	Atlas-SNP
TBC1D10A	83874	hgsc.bcm.edu	37	22	30700607	30700607	+	Silent	SNP	T	T	G	rs4823089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	90	92	0	1	0	T|0.801;G|0.199	0.199	strong	.	TBC1D10A	49	.	NM_001204240	exon2	c.A243C	p.V81V	CAGGGGTACTTCC	.	PASS	Atlas-SNP
CPED1	79974	hgsc.bcm.edu	37	7	120764477	120764477	+	Silent	SNP	G	G	C	rs1524498	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	52	92	0	0.481481	0	G|0.561;C|0.439	0.439	strong	.	.	.	.	NM_001105533	exon7	c.G1011C	p.A337A	GCTAGCGGCTGAA	.	PASS	Atlas-SNP
MAT2A	4144	hgsc.bcm.edu	37	2	85769711	85769711	+	Silent	SNP	C	C	G	rs1078004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	88	175	1	0.460733	0.00571429	C|0.483;G|0.517	0.517	strong	MAT2A,NS,carcinoma,0,1	MAT2A	23	1	NM_005911	exon7	c.C792G	p.R264R	TGGACGCAAAATC	.	scavenged	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168104370	168104370	+	Silent	SNP	A	A	C	rs61748715	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	34	87	0	0.404762	0	A|0.860;C|0.140	0.140	strong	.	XIRP2	914	.	NM_152381	exon9	c.A6468C	p.T2156T	TGATACACAAAGC	.	PASS	Atlas-SNP
DOC2A	8448	hgsc.bcm.edu	37	16	30017985	30017985	+	Missense_Mutation	SNP	C	C	T	rs201869632	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	2	115	0	0.015873	0	C|1.000;T|0.000	0.000	strong	DOC2A,caecum,carcinoma,+2,1	DOC2A	40	1	NM_003586	exon9	c.G892A	p.D298N	CCACATCGGGCCT	.	scavenged	Atlas-SNP
FAM65B	9750	hgsc.bcm.edu	37	6	24828490	24828490	+	Missense_Mutation	SNP	C	C	T	rs9461073	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	12	33	0	0.315789	0	C|0.769;G|0.000;T|0.230	0.230	strong	.	FAM65B	134	.	NM_014722	exon19	c.G2603A	p.R868Q	TCAGCCCGGTCCA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73679990	73679990	+	Missense_Mutation	SNP	T	T	A	rs6724782	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	28	78	0	0.388889	0	T|0.691;A|0.309	0.309	strong	.	ALMS1	384	.	NM_015120	exon8	c.T6333A	p.S2111R	AGGTAGTCATGTA	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721036	135721036	+	Silent	SNP	C	C	T	rs34629706	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	20	36	0	0.454545	0	C|0.945;T|0.055	0.055	strong	PPP2R3A,colon,carcinoma,+1,1	PPP2R3A	114	1	NM_002718	exon2	c.C696T	p.C232C	GATGTGCTTGGAC	.	PASS	Atlas-SNP
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46101939	46101939	+	Missense_Mutation	SNP	C	C	T	rs9984476	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	80	129	0	0.479042	0	C|0.877;T|0.123	0.123	strong	.	KRTAP12-1	9	.	NM_181686	exon1	c.G100A	p.V34M	CGCACACGGAGGA	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733102	52733102	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	328	6	266	0	0.0182927	0	.	.	none	PCMTD1,extremity,malignant_melanoma,0,3	PCMTD1	73	3	NM_052937	exon6	c.C883T	p.L295F	GAATAAGCTGATT	.	scavenged	Atlas-SNP
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75785100	75785100	+	Silent	SNP	C	C	T	rs11180483	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	66	136	0	0.442953	0	C|0.653;T|0.347	0.347	strong	.	GLIPR1L2	54	.	NM_152436	exon1	c.C204T	p.V68V	CGACGTCATTCCC	.	PASS	Atlas-SNP
SPP1	6696	hgsc.bcm.edu	37	4	88902692	88902692	+	Silent	SNP	T	T	C	rs4754	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	77	160	0	0.401042	0	T|0.713;C|0.287	0.287	strong	SPP1,NS,carcinoma,0,1	SPP1	35	1	NM_001251830	exon7	c.T321C	p.D107D	TGATGATGACCAT	.	PASS	Atlas-SNP
PCDHGA7	56108	hgsc.bcm.edu	37	5	140763029	140763029	+	Missense_Mutation	SNP	A	A	G	rs2072315	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	187	162	0	0.994681	0	A|0.473;G|0.527	0.527	strong	.	PCDHGA7	130	.	NM_032087	exon1	c.A563G	p.E188G	ACGATGAAACTAA	.	PASS	Atlas-SNP
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39412119	39412119	+	Missense_Mutation	SNP	C	C	A	rs77134625	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	224	10	171	1	0.0446429	0.00584795	C|0.946;A|0.054	0.054	strong	KRTAP9-9,extremity,malignant_melanoma,0,2	KRTAP9-9	24	2	NM_030975	exon1	c.C482A	p.S161Y	GTGTGTCCAGCTG	.	scavenged	Atlas-SNP
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	3	110	0	0.0238095	0	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
NAT8	9027	hgsc.bcm.edu	37	2	73868328	73868328	+	Missense_Mutation	SNP	A	A	G	rs13538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	60	123	0	0.530973	0	A|0.708;G|0.292	0.292	strong	.	NAT8	26	.	NM_003960	exon2	c.T428C	p.F143S	TCCACAAAGAGAT	.	PASS	Atlas-SNP
SHD	56961	hgsc.bcm.edu	37	19	4288332	4288332	+	Missense_Mutation	SNP	A	A	G	rs888930	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	36	68	0	0.439024	0	A|0.552;G|0.446	0.446	strong	SHD,NS,carcinoma,0,3	SHD	33	3	NM_020209	exon5	c.A809G	p.N270S	AGACCAACCCCCA	.	PASS	Atlas-SNP
HGD	3081	hgsc.bcm.edu	37	3	120389316	120389316	+	Missense_Mutation	SNP	T	T	A	rs2255543	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	25	84	0	0.384615	0	T|0.269;A|0.731	0.731	strong	.	HGD	65	.	NM_000187	exon4	c.A240T	p.Q80H	AGTGACTTGGCCT	.	PASS	Atlas-SNP
KIAA0391	9692	hgsc.bcm.edu	37	14	35735967	35735967	+	Missense_Mutation	SNP	A	A	G	rs11156878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	95	187	0	0.46798	0	A|0.882;G|0.118	0.118	strong	.	KIAA0391	35	.	NM_014672	exon6	c.A1310G	p.N437S	AACGGAATCTGCG	.	PASS	Atlas-SNP
EVC	2121	hgsc.bcm.edu	37	4	5733236	5733236	+	Missense_Mutation	SNP	C	C	G	rs146729456	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	76	181	0	0.457831	0	C|0.995;G|0.005	0.005	strong	.	EVC	90	.	NM_153717	exon4	c.C469G	p.P157A	GCCTCTCCTTCCA	.	PASS	Atlas-SNP
ADAM21	8747	hgsc.bcm.edu	37	14	70924507	70924507	+	Silent	SNP	A	A	C	rs3751524	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	115	124	1	0.737179	0.00806452	A|0.780;C|0.220	0.220	strong	ADAM21,NS,carcinoma,0,1	ADAM21	181	1	NM_003813	exon2	c.A291C	p.A97A	CCGTGCACTCCTG	.	scavenged	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420152	58420152	+	Silent	SNP	C	C	A	rs17845779	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	139	248	0	0.972028	0	C|0.765;A|0.235	0.235	strong	ZNF417,NS,carcinoma,0,1	ZNF417	44	1	NM_152475	exon3	c.G1494T	p.G498G	TGATTTCCCACAT	.	PASS	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	37	18	14851756	14851756	+	Silent	SNP	G	G	A	rs9676225	bycluster;byfrequency;by2hit2allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	147	290	0	0.986577	0	G|0.500;A|0.500	0.500	strong	ANKRD30B_ENST00000358984,NS,carcinoma,+2,1	ANKRD30B	237	1	NM_001145029	exon36	c.G3456A	p.T1152T	TCTGACGGCAGAG	.	scavenged	Atlas-SNP
ZNF700	90592	hgsc.bcm.edu	37	19	12060627	12060627	+	Silent	SNP	A	A	G	rs78201704	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	21	34	0	0.538462	0	A|0.979;G|0.021	0.021	strong	ZNF700,NS,carcinoma,0,1	ZNF700	81	1	NM_001271848	exon4	c.A1797G	p.Q599Q	TAAGCAATGTGGG	.	PASS	Atlas-SNP
PCDHB16	57717	hgsc.bcm.edu	37	5	140563579	140563579	+	Missense_Mutation	SNP	C	C	T	rs61745657	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	44	25	0	0.37931	0	C|0.878;T|0.122	0.122	strong	.	PCDHB16	159	.	NM_020957	exon1	c.C1445T	p.T482I	CAGGCACCAACGC	.	PASS	Atlas-SNP
PRR4	11272	hgsc.bcm.edu	37	12	10999780	10999780	+	Missense_Mutation	SNP	C	C	T	rs1063193	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	178	154	0	0.988889	0	C|0.469;T|0.531	0.531	strong	.	PRR4	17	.	NM_007244	exon3	c.G287A	p.R96Q	CCTCGTCGGGGTG	.	PASS	Atlas-SNP
WDR5	11091	hgsc.bcm.edu	37	9	137017126	137017126	+	Silent	SNP	A	A	G	rs34523253	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	74	136	0	0.496644	0	A|0.920;G|0.080	0.080	strong	WDR5,NS,carcinoma,+1,1	WDR5	29	1	NM_052821	exon8	c.A606G	p.S202S	CGCCTCAGGCCAG	.	PASS	Atlas-SNP
CATSPERD	257062	hgsc.bcm.edu	37	19	5772950	5772950	+	Missense_Mutation	SNP	G	G	A	rs61180947	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	43	66	0	0.641791	0	G|0.749;A|0.251	0.251	strong	.	.	.	.	NM_152784	exon20	c.G1915A	p.G639R	GAATTCGGGGGGC	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139371700	139371700	+	Missense_Mutation	SNP	G	G	A	rs371074782		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	10	140	0	0.0847458	0	.	.	weak	.	SEC16A	249	.	NM_014866	exon3	c.C368T	p.P123L	GAAAACGGACTGG	.	PASS	Atlas-SNP
AKD1	221264	hgsc.bcm.edu	37	6	109837147	109837147	+	Silent	SNP	A	A	G	rs150078049	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	11	135	0	0.0948276	0	A|0.990;G|0.010	0.010	strong	.	AKD1	223	.	NM_001145128	exon31	c.T3978C	p.C1326C	TGGATGACATTTC	.	PASS	Atlas-SNP
RIMS2	9699	hgsc.bcm.edu	37	8	105261725	105261725	+	Silent	SNP	G	G	A	rs59975412		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	34	65	0	0.465753	0	.	.	weak	.	RIMS2	1357	.	NM_001100117	exon22	c.G3600A	p.Q1200Q	CATTCAGGTAGGA	.	PASS	Atlas-SNP
TUBA8	51807	hgsc.bcm.edu	37	22	18613739	18613739	+	Missense_Mutation	SNP	G	G	T	rs146821364		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	61	130	0	0.426573	0	G|1.000;T|0.000	0.000	weak	TUBA8,NS,carcinoma,0,1	TUBA8	36	1	NM_018943	exon5	c.G1186T	p.D396Y	AAGTTCGACCTCA	.	PASS	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	37	17	27424316	27424316	+	Silent	SNP	G	G	A	rs8067806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	33	75	0	0.44	0	G|0.745;A|0.255	0.255	strong	.	MYO18A	217	.	NM_078471	exon27	c.C4155T	p.T1385T	TTTCTTGGTGAAG	.	PASS	Atlas-SNP
LEPRE1	64175	hgsc.bcm.edu	37	1	43228049	43228049	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	51	102	0	0.435897	0	.	.	none	.	LEPRE1	130	.	NM_001146289	exon2	c.C563T	p.T188I	GACATGGTTTGGT	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2152387	2152387	+	Missense_Mutation	SNP	A	A	G	rs9925969	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	37	87	0	0.381443	0	A|0.500;G|0.500	0.500	weak	.	PKD1	184	.	NM_000296	exon25	c.T9196C	p.F3066L	CAGGAAACACAAA	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4720522	4720522	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	79	129	0	0.42246	0	.	.	none	.	PLD2	138	.	NM_001243108	exon17	c.A1783T	p.T595S	CCCTTCACACTTC	.	PASS	Atlas-SNP
ABAT	18	hgsc.bcm.edu	37	16	8868776	8868776	+	Silent	SNP	C	C	A	rs1641022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	86	77	0	0.988506	0	C|0.674;A|0.326	0.326	strong	.	ABAT	46	.	NM_001127448	exon13	c.C984A	p.V328V	CGAGGTCCAGACC	.	PASS	Atlas-SNP
FDFT1	2222	hgsc.bcm.edu	37	8	11667179	11667179	+	Silent	SNP	C	C	T	rs8417	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	51	79	0	0.463636	0	C|0.809;T|0.191	0.191	strong	.	FDFT1	25	.	NM_004462	exon3	c.C201T	p.N67N	CAGCAACGCAGTG	.	PASS	Atlas-SNP
HSPA6	3310	hgsc.bcm.edu	37	1	161496134	161496134	+	Missense_Mutation	SNP	C	C	G	rs753856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	232	225	291	0	0.969828	0	C|0.914;G|0.086	0.086	strong	.	HSPA6	53	.	NM_002155	exon1	c.C1686G	p.D562E	TAGGGACAAGATT	.	PASS	Atlas-SNP
TMEM2	23670	hgsc.bcm.edu	37	9	74360096	74360096	+	Missense_Mutation	SNP	C	C	T	rs25689	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	59	126	0	0.495798	0	T|0.248;C|0.752	0.248	strong	.	TMEM2	112	.	NM_001135820	exon4	c.G872A	p.R291H	TCATTGCGGTATT	.	PASS	Atlas-SNP
RHOD	29984	hgsc.bcm.edu	37	11	66834252	66834252	+	Silent	SNP	C	C	T	rs2282502	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	45	90	0	0.463918	0	C|0.683;G|0.000;T|0.317	0.317	strong	.	RHOD	8	.	NM_014578	exon3	c.C264T	p.D88D	CCCTGACGCCAGC	.	PASS	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	37	7	4153824	4153824	+	Silent	SNP	A	A	G	rs2141076	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	53	119	0	0.486239	0	A|0.851;G|0.149	0.149	strong	.	SDK1	361	.	NM_152744	exon25	c.A3741G	p.E1247E	GATGGAATACGAG	.	PASS	Atlas-SNP
FAM188B	84182	hgsc.bcm.edu	37	7	30880413	30880413	+	Missense_Mutation	SNP	G	G	A	rs34970833	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	53	90	0	0.509615	0	G|0.973;A|0.027	0.027	strong	.	FAM188B	62	.	NM_032222	exon9	c.G1394A	p.C465Y	AAGGCTGTGTCCT	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	37	16	72130815	72130815	+	Silent	SNP	C	C	A	rs1050362	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	61	85	0	0.535088	0	C|0.529;A|0.471	0.471	strong	DHX38,right_upper_lobe,carcinoma,-2,2	DHX38	91	2	NM_014003	exon3	c.C418A	p.R140R	GAGCGGCGGGAAC	.	PASS	Atlas-SNP
SORD	6652	hgsc.bcm.edu	37	15	45361180	45361180	+	Missense_Mutation	SNP	A	A	T	rs55739437	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	90	219	0	0.39823	0	A|0.734;T|0.266	0.266	strong	.	SORD	24	.	NM_003104	exon7	c.A716T	p.Q239L	AAGGTCAGCTGGG	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	37	22	18304821	18304821	+	Silent	SNP	G	G	A	rs45514595	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	11	47	0	0.289474	0	G|0.921;A|0.079	0.079	strong	.	MICAL3	53	.	NM_015241	exon24	c.C3423T	p.P1141P	TGAGGCGGGCAGC	.	PASS	Atlas-SNP
IL20RA	53832	hgsc.bcm.edu	37	6	137323213	137323213	+	Missense_Mutation	SNP	G	G	A	rs1342642	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	64	129	0	0.810127	0	G|0.794;N|0.001	.	strong	.	IL20RA	54	.	NM_014432	exon7	c.C1144T	p.L382F	GGGTGAGAGAAGT	.	PASS	Atlas-SNP
APCDD1L	164284	hgsc.bcm.edu	37	20	57045667	57045667	+	Silent	SNP	T	T	C	rs1980576	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	51	53	0	0.980769	0	T|0.564;C|0.436	0.436	strong	.	APCDD1L	48	.	NM_153360	exon2	c.A186G	p.T62T	TTACCCTGTGGAG	.	PASS	Atlas-SNP
STAB1	23166	hgsc.bcm.edu	37	3	52558133	52558133	+	Silent	SNP	T	T	C	rs13621	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	68	139	0	0.492754	0	A|0.000;C|0.428;G|0.000;T|0.572	0.428	strong	.	STAB1	178	.	NM_015136	exon68	c.T7560C	p.D2520D	TGCTGATGACGAC	.	PASS	Atlas-SNP
C1orf123	54987	hgsc.bcm.edu	37	1	53681699	53681699	+	Silent	SNP	T	T	G	rs1134688	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	43	87	0	0.551282	0	T|0.843;G|0.157	0.157	strong	.	C1orf123	9	.	NM_017887	exon7	c.A369C	p.S123S	TGTCCCTGACTCC	.	PASS	Atlas-SNP
ZNF341	84905	hgsc.bcm.edu	37	20	32376745	32376745	+	Silent	SNP	C	C	T	rs140105337	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	78	163	0	0.472727	0	C|0.983;T|0.017	0.017	strong	.	ZNF341	73	.	NM_032819	exon13	c.C1908T	p.I636I	GTTGATCCACGAG	.	PASS	Atlas-SNP
HR	55806	hgsc.bcm.edu	37	8	21984945	21984945	+	Missense_Mutation	SNP	C	C	T	rs12675375	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	55	139	0	0.509259	0	C|0.723;T|0.277	0.277	strong	HR,NS,carcinoma,0,1	HR	71	1	NM_018411	exon3	c.G1010A	p.G337D	CCAAGACCCCCAC	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52844243	52844243	+	Silent	SNP	A	A	G	rs28414881	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	388	62	290	0	0.159794	0	A|0.959;G|0.041	0.041	strong	KRT6B,NS,carcinoma,-1,1	KRT6B	90	1	NM_005555	exon2	c.T702C	p.R234R	GTCCAGACGACCC	.	scavenged	Atlas-SNP
MNX1	3110	hgsc.bcm.edu	37	7	156802363	156802363	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	22	15	0	0.511628	0	.	.	none	.	MNX1	17	.	NM_005515	exon1	c.G682A	p.D228N	TGAAGTCGGGCAT	.	PASS	Atlas-SNP
OR2T5	401993	hgsc.bcm.edu	37	1	248652011	248652011	+	Missense_Mutation	SNP	A	A	T	rs9439338	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	734	109	747	2	0.148501	0.00267738	A|0.250;T|0.750	0.750	weak	OR2T5,NS,other,0,1	OR2T5	17	1	NM_001004697	exon1	c.A122T	p.K41M	TCCTGAAGGCGTT	.	scavenged	Atlas-SNP
COL14A1	7373	hgsc.bcm.edu	37	8	121222046	121222046	+	Missense_Mutation	SNP	G	G	A	rs61753752	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	56	93	0	0.491228	0	G|0.998;A|0.002	0.002	strong	COL14A1,NS,carcinoma,-1,1	COL14A1	292	1	NM_021110	exon12	c.G1373A	p.S458N	AGAACAGCATGCG	.	PASS	Atlas-SNP
MEF2D	4209	hgsc.bcm.edu	37	1	156450719	156450719	+	Silent	SNP	G	G	A	rs1185700	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	121	105	1	0.975806	0.00952381	G|0.766;A|0.234	0.234	strong	.	MEF2D	43	.	NM_005920	exon4	c.C303T	p.P101P	CCCGTCGGGCTCG	.	PASS	Atlas-SNP
CEP164	22897	hgsc.bcm.edu	37	11	117209340	117209340	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	5	111	0	0.0328947	0	.	.	none	CEP164,colon,carcinoma,0,1	CEP164	121	1	NM_001271933	exon2	c.T38C	p.V13A	AGCTGGTTCTGGA	.	scavenged	Atlas-SNP
UBXN6	80700	hgsc.bcm.edu	37	19	4457650	4457650	+	Silent	SNP	C	C	T	rs1044510	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	13	15	0	0.481481	0	C|0.660;T|0.340	0.340	strong	.	UBXN6	27	.	NM_025241	exon1	c.G45A	p.K15K	CGCGCTCTTGAAC	.	PASS	Atlas-SNP
NXPE4	54827	hgsc.bcm.edu	37	11	114442103	114442103	+	Missense_Mutation	SNP	A	A	G	rs550897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	95	96	0	0.989583	0	T|0.007;G|0.608	0.608	strong	.	.	.	.	NM_001077639	exon6	c.T1192C	p.Y398H	AACAATATTTTTG	.	PASS	Atlas-SNP
SLCO1C1	53919	hgsc.bcm.edu	37	12	20854303	20854303	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	74	179	0	0.413408	0	.	.	none	.	SLCO1C1	216	.	NM_017435	exon3	c.G181T	p.G61C	GCAGAAGGCTATC	.	PASS	Atlas-SNP
TRAF5	7188	hgsc.bcm.edu	37	1	211533352	211533352	+	Silent	SNP	A	A	G	rs2230779	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	63	122	0	0.538462	0	A|0.954;G|0.046	0.046	strong	.	TRAF5	64	.	NM_004619	exon5	c.A477G	p.A159A	GAGTGCATCCTGT	.	PASS	Atlas-SNP
CNTN5	53942	hgsc.bcm.edu	37	11	99690461	99690461	+	Missense_Mutation	SNP	A	A	G	rs10893933	bycluster;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	16	97	0	0.141593	0	A|1.000;|0.000	.	strong	.	CNTN5	324	.	NM_001243270	exon3	c.A242G	p.N81S	CCATCAATCTTTA	.	PASS	Atlas-SNP
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138761034	138761034	+	Missense_Mutation	SNP	G	G	C	rs2297241	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	96	203	0	0.48	0	G|0.797;C|0.203	0.203	strong	.	ZC3HAV1	75	.	NM_024625	exon6	c.C1695G	p.H565Q	TTACAGGTGGATT	.	PASS	Atlas-SNP
ANKRD27	84079	hgsc.bcm.edu	37	19	33106621	33106621	+	Silent	SNP	C	C	T	rs405858	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	136	121	0	1	0	C|0.445;T|0.555	0.555	strong	ANKRD27,NS,carcinoma,-1,1	ANKRD27	86	1	NM_032139	exon22	c.G2118A	p.A706A	GGGGTCCGCTGCA	.	PASS	Atlas-SNP
SLFN13	146857	hgsc.bcm.edu	37	17	33768334	33768334	+	Missense_Mutation	SNP	T	T	G	rs75812929	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	17	74	0	0.346939	0	T|0.900;G|0.100	0.100	strong	.	SLFN13	79	.	NM_144682	exon6	c.A1974C	p.K658N	TTCAAATTTTTCT	.	PASS	Atlas-SNP
ZNF212	7988	hgsc.bcm.edu	37	7	148950895	148950895	+	Missense_Mutation	SNP	C	C	T	rs34185245	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	43	56	0	0.494253	0	C|0.982;T|0.018	0.018	strong	.	ZNF212	28	.	NM_012256	exon5	c.C877T	p.H293Y	AAATCTCATAGGC	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17273443	17273443	+	Missense_Mutation	SNP	C	C	T	rs74657070	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	7	42	0	0.0578512	0	C|0.974;T|0.026	0.026	strong	CROCC,NS,carcinoma,-1,1	CROCC	185	1	NM_014675	exon17	c.C2471T	p.T824M	TCCCCACGCTGCG	.	PASS	Atlas-SNP
FIP1L1	81608	hgsc.bcm.edu	37	4	54324914	54324914	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	92	194	0	0.431925	0	.	.	none	.	FIP1L1	60	.	NM_030917	exon17	c.C1594T	p.R532X	GAAAGACGACACA	.	PASS	Atlas-SNP
SYN1	6853	hgsc.bcm.edu	37	X	47466361	47466361	+	Silent	SNP	A	A	G	rs1142636	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	81	75	0	1	0	T|0.141;G|0.294;C|0.097;A|0.468	0.294	strong	.	SYN1	84	.	NM_006950	exon3	c.T510C	p.N170N	CACCCCATTCCGA	.	PASS	Atlas-SNP
LILRB5	10990	hgsc.bcm.edu	37	19	54754778	54754778	+	Missense_Mutation	SNP	G	G	A	rs150660840	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	8	202	0	0.0414508	0	G|0.994;A|0.006	0.006	strong	LILRB5,NS,carcinoid-endocrine_tumour,+1,1	LILRB5	176	1	NM_001081442	exon13	c.C1648T	p.P550S	CCTGGGGGGCTTC	.	scavenged	Atlas-SNP
NTF3	4908	hgsc.bcm.edu	37	12	5603935	5603935	+	Silent	SNP	C	C	T	rs10849277	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	20	49	0	0.416667	0	C|0.874;T|0.126	0.126	strong	.	NTF3	50	.	NM_001102654	exon2	c.C594T	p.P198P	CTCTCCCGTCAAA	.	PASS	Atlas-SNP
DEFB108B	245911	hgsc.bcm.edu	37	11	71548520	71548520	+	Missense_Mutation	SNP	A	A	T	rs12285495	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	238	108	284	1	0.453782	0.00352113	A|0.486;T|0.514	0.514	strong	.	DEFB108B	6	.	NM_001002035	exon2	c.A134T	p.H45L	AAATCCATGTTGG	.	PASS	Atlas-SNP
SH3BP5	9467	hgsc.bcm.edu	37	3	15373858	15373858	+	Missense_Mutation	SNP	C	C	T	rs115738660	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	13	19	0	0.52	0	C|0.973;T|0.027	0.027	strong	SH3BP5,NS,carcinoma,0,1	SH3BP5	32	1	NM_004844	exon1	c.G58A	p.A20T	CCCGGGCAGGCGG	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	37	16	84224967	84224967	+	Missense_Mutation	SNP	G	G	A	rs8044695	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	4	4	1	0	1	0	G|0.291;A|0.709	0.709	strong	.	ADAD2	46	.	NM_001145400	exon1	c.G131A	p.G44E	CCTGGGGGCCCGC	.	PASS	Atlas-SNP
TMC1	117531	hgsc.bcm.edu	37	9	75303653	75303653	+	Silent	SNP	C	C	T	rs2589615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	23	46	0	0.433962	0	C|0.478;T|0.522	0.522	strong	.	TMC1	87	.	NM_138691	exon6	c.C45T	p.D15D	AGAAGACGAGACT	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76111994	76111994	+	Silent	SNP	C	C	G	rs75035622	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	236	118	163	0	0.5	0	.	.	weak	DTX2,NS,carcinoma,0,1	DTX2	64	1	NM_001102596	exon2	c.C438G	p.A146A	CTTGGCCCCCCTG	.	PASS	Atlas-SNP
ORC1	4998	hgsc.bcm.edu	37	1	52854961	52854961	+	Missense_Mutation	SNP	G	G	A	rs3087476	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	76	143	0	0.510067	0	G|0.984;A|0.016	0.016	strong	.	ORC1	79	.	NM_004153	exon7	c.C1115T	p.A372V	GAGGTCGCTTCAT	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128486446	128486446	+	Silent	SNP	C	C	T	rs75770585	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	19	54	0	0.413043	0	C|0.890;T|0.110	0.110	strong	FLNC,NS,carcinoma,+1,1	FLNC	339	1	NM_001127487	exon23	c.C4056T	p.R1352R	CACCCGCGTCCGA	.	PASS	Atlas-SNP
POM121L2	94026	hgsc.bcm.edu	37	6	27279852	27279852	+	Missense_Mutation	SNP	T	T	C	rs2235233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	41	71	0	0.546667	0	T|0.762;C|0.238	0.238	strong	.	POM121L2	61	.	NM_033482	exon1	c.A98G	p.Q33R	AGGGGCTGAGGTG	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104641612	104641612	+	Silent	SNP	T	T	C	rs4906422	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	15	25	0	0.428571	0	T|0.708;C|0.292	0.292	strong	KIF26A,NS,carcinoma,0,1	KIF26A	84	1	NM_015656	exon12	c.T2487C	p.G829G	CAAGGGTCCCCGA	.	PASS	Atlas-SNP
CR1	1378	hgsc.bcm.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	262	9	235	2	0.0343511	0.00851064	.	.	none	CR1_ENST00000367049,NS,carcinoma,0,12	CR1	354	12	NM_000651	exon40	c.G6658T	p.E2220X	GTGTGTGAACGTG	.	scavenged	Atlas-SNP
CDK2	1017	hgsc.bcm.edu	37	12	56360876	56360876	+	Silent	SNP	G	G	A	rs2069398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	21	45	0	0.477273	0	G|0.871;A|0.129	0.129	strong	.	CDK2	27	.	NM_052827	exon1	c.G84A	p.E28E	GGGAGAGGTGGTG	.	PASS	Atlas-SNP
MRPS30	10884	hgsc.bcm.edu	37	5	44815069	44815069	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	3	110	0	0.025	0	.	.	none	MRPS30_ENST00000507110,NS,carcinoma,+1,2	MRPS30	90	2	NM_016640	exon5	c.C1085A	p.T362K	TGATCACAGATGG	.	scavenged	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134671150	134671150	+	Missense_Mutation	SNP	T	T	C	rs148181302	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	55	131	0	0.44	0	T|0.991;C|0.009	0.009	strong	.	TTC40	100	.	NM_001200049	exon39	c.A5518G	p.M1840V	CAGCCATGGCGCC	.	PASS	Atlas-SNP
CENPF	1063	hgsc.bcm.edu	37	1	214814059	214814059	+	Missense_Mutation	SNP	T	T	G	rs61732042	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	51	130	0	0.459459	0	T|0.968;G|0.032	0.032	strong	.	CENPF	321	.	NM_016343	exon12	c.T2378G	p.M793R	CTGCCATGCATCA	.	PASS	Atlas-SNP
CCDC6	8030	hgsc.bcm.edu	37	10	61665886	61665886	+	Silent	SNP	C	C	A	rs1171830	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	24	20	0	0.55814	0	C|0.638;A|0.362	0.362	strong	.	CCDC6	44	.	NM_005436	exon1	c.G297T	p.V99V	GATGGTCACGCTG	.	PASS	Atlas-SNP
HIST4H4	121504	hgsc.bcm.edu	37	12	14923988	14923988	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	38	69	0	0.506667	0	.	.	none	.	HIST4H4	13	.	NM_175054	exon1	c.C31A	p.L11M	TACCCAGCCCCTT	.	PASS	Atlas-SNP
C21orf58	54058	hgsc.bcm.edu	37	21	47734777	47734777	+	Silent	SNP	G	G	A	rs56036022	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	40	74	0	0.43956	0	G|0.975;A|0.025	0.025	strong	.	C21orf58	25	.	NM_058180	exon5	c.C462T	p.D154D	GAGCTCGTCCAGG	.	PASS	Atlas-SNP
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950690	59950690	+	Silent	SNP	A	A	C	rs2296842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	5	6	0	0.555556	0	A|0.786;C|0.214	0.214	strong	C14orf149,NS,carcinoma,0,1	.	.	1	NM_144581	exon1	c.T345G	p.A115A	GTCCAAAGCGAAG	.	PASS	Atlas-SNP
NPHP3	27031	hgsc.bcm.edu	37	3	132409455	132409455	+	Silent	SNP	C	C	T	rs16839515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	72	166	0	0.470588	0	C|0.950;T|0.050	0.050	strong	.	NPHP3	110	.	NM_153240	exon19	c.G2610A	p.P870P	AAGCCACGGGAGT	.	PASS	Atlas-SNP
VRK3	51231	hgsc.bcm.edu	37	19	50484234	50484234	+	Silent	SNP	G	G	A	rs16981617	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	18	26	0	0.545455	0	G|0.883;A|0.117	0.117	strong	VRK3,NS,carcinoma,0,1	VRK3	49	1	NM_016440	exon13	c.C1254T	p.C418C	GTGACCGCAGGGT	.	PASS	Atlas-SNP
RPL9	6133	hgsc.bcm.edu	37	4	39458051	39458051	+	Silent	SNP	A	A	G	rs2125313	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	332	330	344	0	0.993976	0	A|0.341;G|0.659	0.659	strong	.	RPL9	16	.	NM_000661	exon5	c.T366C	p.Y122Y	GCGGATATATTTT	.	PASS	Atlas-SNP
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383073	39383073	+	Missense_Mutation	SNP	G	G	C	rs9902235	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	39	60	0	0.47561	0	G|0.287;C|0.713	0.713	strong	.	KRTAP9-2	24	.	NM_031961	exon1	c.G167C	p.C56S	CAACTTGCTGTCA	.	PASS	Atlas-SNP
GRID1	2894	hgsc.bcm.edu	37	10	88126071	88126071	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	13	3	0	0.65	0	.	.	none	.	GRID1	204	.	NM_017551	exon1	c.G79A	p.G27S	GCTTACCGATGTG	.	PASS	Atlas-SNP
SLC12A8	84561	hgsc.bcm.edu	37	3	124802881	124802881	+	Silent	SNP	A	A	G	rs2981483	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	133	129	1	1	0.00775194	A|0.406;G|0.594	0.594	strong	.	SLC12A8	81	.	NM_024628	exon14	c.T1998C	p.P666P	CTCCTGAGGGGAC	.	PASS	Atlas-SNP
POLG	5428	hgsc.bcm.edu	37	15	89859994	89859994	+	Missense_Mutation	SNP	C	C	A	rs3087374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	58	130	0	0.47541	0	C|0.950;A|0.050	0.050	strong	.	POLG	75	.	NM_002693	exon23	c.G3708T	p.Q1236H	TCCAGGCTGGCTT	.	PASS	Atlas-SNP
IFRD1	3475	hgsc.bcm.edu	37	7	112112279	112112279	+	Silent	SNP	G	G	A	rs2074796	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	118	0	0.435644	0	G|0.736;A|0.264	0.264	strong	IFRD1,NS,carcinoma,+1,2	IFRD1	46	2	NM_001007245	exon11	c.G1047A	p.R349R	GGAACGGGATTTT	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296616	39296616	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	4	75	0	0.0487805	0	.	.	none	KRTAP4-6,bladder,carcinoma,+2,3	KRTAP4-6	46	3	NM_030976	exon1	c.G124A	p.V42M	TGGACACACAGCA	.	scavenged	Atlas-SNP
ALS2CL	259173	hgsc.bcm.edu	37	3	46729757	46729757	+	Missense_Mutation	SNP	C	C	G	rs7642448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	102	105	0	0.990291	0	C|0.587;G|0.413	0.413	strong	.	ALS2CL	78	.	NM_001190707	exon3	c.G133C	p.E45Q	GGCACTCTCTGCC	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746050	143746050	+	Missense_Mutation	SNP	C	C	T	rs2976399	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	14	22	0	0.4	0	C|0.577;T|0.423	0.423	strong	.	.	.	.	NM_003724	exon3	c.G1426A	p.G476R	CTCCTCCGCCGTC	.	PASS	Atlas-SNP
USP10	9100	hgsc.bcm.edu	37	16	84778766	84778766	+	Missense_Mutation	SNP	C	C	T	rs139338093	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	42	108	0	0.392523	0	C|0.985;T|0.015	0.015	strong	USP10,NS,carcinoma,0,1	USP10	51	1	NM_001272075	exon5	c.C691T	p.P231S	GACAGTCCTTTCC	.	PASS	Atlas-SNP
SMCO2	0	hgsc.bcm.edu	37	12	27654898	27654898	+	Silent	SNP	C	C	T	rs61731840	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	56	110	0	0.448	0	C|0.842;T|0.158	0.158	strong	.	.	.	.	NM_001145010	exon9	c.C876T	p.T292T	CCTCACCGTCACT	.	PASS	Atlas-SNP
ELMO2	63916	hgsc.bcm.edu	37	20	45003211	45003211	+	Silent	SNP	C	C	T	rs8124302	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	60	106	0	0.5	0	C|0.997;T|0.003	0.003	strong	.	ELMO2	51	.	NM_182764	exon13	c.G1134A	p.L378L	CAAGTACAGCATG	.	PASS	Atlas-SNP
ADAMTS12	81792	hgsc.bcm.edu	37	5	33549387	33549387	+	Silent	SNP	G	G	A	rs61748195	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	37	72	1	0.45679	0.0138889	G|0.923;A|0.077	0.077	strong	ADAMTS12,colon,carcinoma,0,1	ADAMTS12	464	1	NM_030955	exon21	c.C4227T	p.A1409A	AATGCCGGCCAGG	.	scavenged	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129901066	129901066	+	Missense_Mutation	SNP	C	C	A	rs114687140	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	136	181	1	0.985507	0.00552486	C|0.955;A|0.045	0.045	strong	.	MKI67	363	.	NM_002417	exon13	c.G9038T	p.R3013L	ATGCAGCGCAGCC	.	PASS	Atlas-SNP
DDX5	1655	hgsc.bcm.edu	37	17	62496670	62496670	+	Missense_Mutation	SNP	A	A	C	rs1140409	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	68	162	0	0.468966	0	A|0.953;C|0.047	0.047	strong	.	DDX5	101	.	NM_004396	exon12	c.T1438G	p.S480A	TACCTGAACCTCT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912086	29912086	+	Silent	SNP	G	G	A	rs2231092	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	92	301	0	0.541176	0	G|0.580;A|0.420	0.420	strong	.	HLA-A	89	.	NM_001242758	exon4	c.G807A	p.A269A	GTGGGCGGCTGTG	.	PASS	Atlas-SNP
OR2H2	7932	hgsc.bcm.edu	37	6	29555778	29555778	+	Silent	SNP	A	A	G	rs2235698	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	97	218	1	0.459716	0.00458716	A|0.764;G|0.236	0.236	strong	OR2H2,NS,carcinoma,+1,1	OR2H2	29	1	NM_007160	exon1	c.A57G	p.P19P	ACACCCAGGGCTG	.	PASS	Atlas-SNP
RYR3	6263	hgsc.bcm.edu	37	15	33905410	33905410	+	Missense_Mutation	SNP	A	A	G	rs2229116	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	65	153	1	0.532787	0.00653595	A|0.790;G|0.210	0.210	strong	RYR3,colon,carcinoma,0,1	RYR3	760	1	NM_001243996	exon19	c.A2191G	p.I731V	GCTTCCATCAACC	.	scavenged	Atlas-SNP
OR8H2	390151	hgsc.bcm.edu	37	11	55873149	55873149	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	3	220	0	0.0170455	0	.	.	none	OR8H2,colon,carcinoma,0,1	OR8H2	117	1	NM_001005200	exon1	c.C631T	p.L211F	GTGTCCCTTTTCA	.	scavenged	Atlas-SNP
TMEM187	8269	hgsc.bcm.edu	37	X	153247954	153247954	+	Silent	SNP	C	C	T	rs6571303	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	28	17	0	1	0	C|0.755;0|0.003	.	strong	.	TMEM187	21	.	NM_003492	exon2	c.C441T	p.C147C	TGAGTGCGTCTCC	.	PASS	Atlas-SNP
VKORC1	79001	hgsc.bcm.edu	37	16	31106015	31106015	+	Silent	SNP	C	C	T	rs55894764	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	27	18	0	0.574468	0	C|0.990;T|0.010	0.010	strong	.	VKORC1	9	.	NM_024006	exon1	c.G36A	p.R12R	AGCGAGCCGCACC	.	PASS	Atlas-SNP
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519244	48519244	+	Silent	SNP	A	A	G	rs35792818	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	53	106	0	0.417323	0	A|0.837;G|0.163	0.163	strong	ELSPBP1,NS,NS,+1,1	ELSPBP1	29	1	NM_022142	exon4	c.A303G	p.S101S	GTGCTCAGTCACC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179580418	179580418	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	45	118	0	0.387931	0	.	.	none	.	TTN	18412	.	NM_001267550	exon89	c.G25723A	p.G8575R	GAGACCCACCGAT	.	PASS	Atlas-SNP
D2HGDH	728294	hgsc.bcm.edu	37	2	242690675	242690675	+	Missense_Mutation	SNP	G	G	A	rs1106639	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	96	133	1	0.52459	0.0075188	G|0.742;A|0.258	0.258	strong	D2HGDH,caecum,carcinoma,0,1	D2HGDH	39	1	NM_152783	exon8	c.G1012A	p.V338I	TTTTACGTCCTCA	.	scavenged	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228525008	228525008	+	Missense_Mutation	SNP	G	G	A	rs3795809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	115	228	0	0.491453	0	G|0.913;A|0.087	0.087	strong	OBSCN_ENST00000570156,caecum,carcinoma,0,3	OBSCN	2142	3	NM_001271223	exon77	c.G19595A	p.R6532H	CCCCCCGCCATGG	.	PASS	Atlas-SNP
EPHB3	2049	hgsc.bcm.edu	37	3	184289152	184289152	+	Silent	SNP	A	A	G	rs13069661	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	336	165	281	0	0.491071	0	A|0.802;G|0.198	0.198	strong	EPHB3,NS,adenoma,0,1	EPHB3	114	1	NM_004443	exon2	c.A165G	p.T55T	GTGGACATCTCAT	.	PASS	Atlas-SNP
GRM7	2917	hgsc.bcm.edu	37	3	6903297	6903297	+	Silent	SNP	C	C	T	rs3749380	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	76	86	0	0.974359	0	C|0.630;T|0.370	0.370	strong	GRM7,caecum,carcinoma,0,1	GRM7	223	1	NM_000844	exon1	c.C222T	p.N74N	GGAAAACGGGATC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144931461	144931461	+	Missense_Mutation	SNP	A	A	T	rs41315685	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	39	159	0	0.186603	0	A|0.382;T|0.618	0.618	strong	.	PDE4DIP	817	.	NM_001002811	exon1	c.T248A	p.L83Q	TCCAGTAGCAGCT	.	PASS	Atlas-SNP
ZNF713	349075	hgsc.bcm.edu	37	7	56007498	56007498	+	Silent	SNP	A	A	G	rs112798657	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	41	63	0	0.569444	0	A|0.998;G|0.002	0.002	strong	.	ZNF713	47	.	NM_182633	exon4	c.A1092G	p.K364K	TGGCAAAGCCTTC	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243329211	243329211	+	Missense_Mutation	SNP	G	G	T	rs2728430		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	247	34	203	0	0.137652	0	.	.	weak	CEP170,NS,carcinoma,-1,1	CEP170	153	1	NM_014812	exon13	c.C2051A	p.T684K	ACCTGTGTAGGTG	.	scavenged	Atlas-SNP
BCAM	4059	hgsc.bcm.edu	37	19	45316588	45316588	+	Missense_Mutation	SNP	G	G	A	rs28399654	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	42	51	0	0.626866	0	G|0.983;A|0.017	0.017	strong	.	BCAM	53	.	NM_001013257	exon5	c.G586A	p.V196I	GTGCCCGTAGAGA	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73746923	73746923	+	Silent	SNP	C	C	T	rs11884776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	58	135	0	0.394558	0	C|0.742;T|0.258	0.258	strong	.	ALMS1	384	.	NM_015120	exon11	c.C9558T	p.T3186T	GAAGACCCCACTT	.	PASS	Atlas-SNP
CCDC85C	317762	hgsc.bcm.edu	37	14	99988570	99988570	+	Missense_Mutation	SNP	C	C	G	rs75827961	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	14	22	0	0.518519	0	C|0.930;G|0.070	0.070	strong	.	CCDC85C	3	.	NM_001144995	exon3	c.G875C	p.G292A	CCGGAGCCTGCCT	.	PASS	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	105	113	0	0.990566	0	G|0.656;T|0.344	0.344	strong	.	OR10G3	40	.	NM_001005465	exon1	c.C351A	p.T117T	CATTAGGGTGTAG	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47783655	47783655	+	Silent	SNP	C	C	G	rs61407822	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	55	118	0	0.495495	0	C|0.868;G|0.132	0.132	strong	.	PCNT	283	.	NM_006031	exon14	c.C2415G	p.A805A	GGCAGCCCAGATC	.	PASS	Atlas-SNP
ZNF443	10224	hgsc.bcm.edu	37	19	12541544	12541544	+	Missense_Mutation	SNP	A	A	C	rs35055629	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	33	83	0	0.423077	0	A|0.687;C|0.313	0.313	strong	.	ZNF443	63	.	NM_005815	exon4	c.T1442G	p.L481R	TTCCCAAGTTTGC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81211496	81211496	+	Missense_Mutation	SNP	C	C	A	rs9935113	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	22	48	0	0.407407	0	C|0.823;A|0.177	0.177	strong	.	PKD1L2	361	.	NM_001076780	exon14	c.G2353T	p.G785C	CGGTGCCCTCCTC	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	37	21	28315841	28315841	+	Silent	SNP	G	G	A	rs61088614	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	55	100	0	0.482456	0	G|0.957;A|0.043	0.043	strong	.	ADAMTS5	184	.	NM_007038	exon3	c.C1263T	p.D421D	GGAATCGTCATGG	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444193	20444193	+	Silent	SNP	A	A	C	rs2318556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	103	176	0	0.488152	0	A|0.619;C|0.380;G|0.001	0.380	strong	.	OR4K15	82	.	NM_001005486	exon1	c.A516C	p.S172S	CATTTCATGGTTT	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135956411	135956411	+	Missense_Mutation	SNP	C	C	A	rs35085326	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	398	168	231	0	0.422111	0	C|0.989;A|0.011	0.011	strong	.	RBMX	149	.	NM_002139	exon9	c.G1066T	p.G356W	GGTACCCCCTTTC	.	PASS	Atlas-SNP
POLR2J3	548644	hgsc.bcm.edu	37	7	102212939	102212939	+	Missense_Mutation	SNP	G	G	C	rs139049967	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1015	180	679	0	0.17734	0	G|0.980;C|0.020	0.020	strong	.	POLR2J3	2	.	NM_001097615	exon1	c.C30G	p.F10L	GAGCAAGAACGAC	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234569192	234569192	+	Silent	SNP	T	T	C	rs3754311	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	49	85	0	0.515789	0	T|0.848;C|0.152	0.152	strong	.	TARBP1	111	.	NM_005646	exon14	c.A2358G	p.A786A	AATGGATGCATTT	.	PASS	Atlas-SNP
TSPYL5	85453	hgsc.bcm.edu	37	8	98289714	98289714	+	Missense_Mutation	SNP	G	G	C	rs2635164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	37	69	0	0.5	0	G|0.810;C|0.190	0.190	strong	.	TSPYL5	48	.	NM_033512	exon1	c.C359G	p.T120S	AAGACAGTGTCTG	.	PASS	Atlas-SNP
RBMXL2	27288	hgsc.bcm.edu	37	11	7110548	7110548	+	Missense_Mutation	SNP	C	C	T	rs11041170	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	25	65	0	0.378788	0	C|0.795;T|0.205	0.205	strong	.	RBMXL2	47	.	NM_014469	exon1	c.C197T	p.A66V	CCGCCGCCAGAGA	.	PASS	Atlas-SNP
IRAK4	51135	hgsc.bcm.edu	37	12	44177511	44177511	+	Missense_Mutation	SNP	G	G	A	rs55944915	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	35	53	0	0.603448	0	G|0.989;A|0.011	0.011	strong	.	IRAK4	77	.	NM_016123	exon10	c.G1172A	p.R391H	AACACCGTGAACC	.	PASS	Atlas-SNP
CREB3L2	64764	hgsc.bcm.edu	37	7	137600690	137600690	+	Missense_Mutation	SNP	C	C	T	rs273957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	107	193	0	0.509524	0	C|0.243;T|0.757	0.757	strong	.	CREB3L2	62	.	NM_001253775	exon3	c.G388A	p.V130I	CTGTAACTGGCTC	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58743454	58743454	+	Missense_Mutation	SNP	A	A	C	rs30842	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	48	60	0	1	0	A|0.252;C|0.748	0.748	strong	.	GOT2	42	.	NM_002080	exon9	c.T1037G	p.V346G	GCCATGACTTTCA	.	PASS	Atlas-SNP
DAGLB	221955	hgsc.bcm.edu	37	7	6452461	6452461	+	Missense_Mutation	SNP	G	G	A	rs1133850	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	49	99	0	0.526882	0	G|0.971;A|0.029	0.029	strong	.	DAGLB	74	.	NM_139179	exon13	c.C1550T	p.A517V	CAGTGCGCGACCA	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	37	7	31920395	31920395	+	Silent	SNP	G	G	A	rs61729940	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	81	0	0.43662	0	A|0.094;G|0.906;T|0.000	0.094	strong	.	PDE1C	465	.	NM_001191058	exon4	c.C387T	p.A129A	CACTGTGGCTGCA	.	PASS	Atlas-SNP
RAD23B	5887	hgsc.bcm.edu	37	9	110084328	110084328	+	Missense_Mutation	SNP	C	C	T	rs1805329	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	71	143	0	0.507143	0	C|0.850;T|0.150	0.150	strong	.	RAD23B	31	.	NM_002874	exon7	c.C746T	p.A249V	CTGGGGCTCCTCA	.	PASS	Atlas-SNP
C14orf178	283579	hgsc.bcm.edu	37	14	78234796	78234796	+	Missense_Mutation	SNP	C	C	T	rs8015313	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	25	67	0	0.409836	0	C|0.835;T|0.165	0.165	strong	.	C14orf178	11	.	NM_174943	exon2	c.C76T	p.H26Y	TACAGGCATGATC	.	PASS	Atlas-SNP
DLST	1743	hgsc.bcm.edu	37	14	75359670	75359670	+	Silent	SNP	G	G	A	rs2230237	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	55	102	0	0.416667	0	G|0.365;A|0.635	0.635	strong	DLST,colon,carcinoma,0,1	DLST	42	1	NM_001933	exon8	c.G576A	p.Q192Q	CTCACAGCCTCCT	.	PASS	Atlas-SNP
IL17RC	84818	hgsc.bcm.edu	37	3	9962634	9962634	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	332	176	317	0	0.53012	0	.	.	none	.	IL17RC	55	.	NM_153461	exon7	c.C816T	p.N272N	CTGGAACAGCATC	.	PASS	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57070089	57070089	+	Silent	SNP	C	C	T	rs34498883	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	24	57	0	0.40678	0	C|0.969;T|0.031	0.031	strong	.	TNKS1BP1	148	.	NM_033396	exon7	c.G4527A	p.P1509P	AGGCTGCGGCCTC	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25264814	25264814	+	Silent	SNP	T	T	C	rs2227892	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	41	100	0	0.431579	0	T|0.523;C|0.477	0.477	strong	.	PYGB	84	.	NM_002862	exon14	c.T1695C	p.D565D	GTTCGATGTGCAT	.	PASS	Atlas-SNP
DLK2	65989	hgsc.bcm.edu	37	6	43418691	43418691	+	Silent	SNP	G	G	A	rs1214748	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	51	113	0	0.421488	0	A|0.330;C|0.006	0.330	strong	.	DLK2	22	.	NM_023932	exon6	c.C738T	p.T246T	CTCACAGGTCTTG	.	PASS	Atlas-SNP
OR1B1	347169	hgsc.bcm.edu	37	9	125391127	125391127	+	Missense_Mutation	SNP	C	C	T	rs1476859	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	29	65	0	0.414286	0	C|0.691;T|0.309	0.309	strong	.	OR1B1	48	.	NM_001004450	exon1	c.G688A	p.A230T	GAATAGCGGCCCC	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17017878	17017878	+	Missense_Mutation	SNP	G	G	A	rs56408444	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	127	107	1	0.992188	0.00934579	G|0.803;A|0.197	0.197	strong	CPAMD8,NS,carcinoma,0,1	CPAMD8	192	1	NM_015692	exon30	c.C4052T	p.A1351V	AGGGGCGCAGCAG	.	PASS	Atlas-SNP
GAREML	150946	hgsc.bcm.edu	37	2	26407120	26407120	+	Missense_Mutation	SNP	A	A	T	rs116239749	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	77	135	0	0.542253	0	A|0.997;T|0.003	0.003	strong	.	.	.	.	NM_001168241	exon4	c.A403T	p.S135C	GAGTTCAGCGAGG	.	PASS	Atlas-SNP
DOCK6	57572	hgsc.bcm.edu	37	19	11332570	11332570	+	Silent	SNP	T	T	A	rs3810307	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	54	96	0	0.453782	0	T|0.723;A|0.277	0.277	strong	.	DOCK6	104	.	NM_020812	exon28	c.A3507T	p.L1169L	AATCGATAGCAGT	.	PASS	Atlas-SNP
EXTL1	2134	hgsc.bcm.edu	37	1	26349245	26349245	+	Silent	SNP	C	C	T	rs35744844	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	6	109	0	0.0606061	0	C|0.943;T|0.057	0.057	strong	.	EXTL1	61	.	NM_004455	exon1	c.C108T	p.P36P	GCCTCCCAGACCT	.	PASS	Atlas-SNP
GPR174	84636	hgsc.bcm.edu	37	X	78426988	78426988	+	Missense_Mutation	SNP	T	T	C	rs3827440	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	135	148	1	1	0.00675676	T|0.495;0|0.014	.	strong	.	GPR174	79	.	NM_032553	exon1	c.T484C	p.S162P	GATACCTCTGGCA	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144922252	144922252	+	Missense_Mutation	SNP	C	C	G	rs147451175	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	26	132	0	0.180556	0	C|0.996;G|0.004	0.004	strong	.	PDE4DIP	817	.	NM_001002811	exon4	c.G1405C	p.G469R	TTTGACCTTCAAT	.	PASS	Atlas-SNP
GZMB	3002	hgsc.bcm.edu	37	14	25101548	25101548	+	Silent	SNP	G	G	A	rs41469548	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	248	54	337	1	0.217742	0.00296736	G|0.721;A|0.279	0.279	strong	GZMB_ENST00000382542,brain,glioma,0,3	GZMB	73	3	NM_004131	exon3	c.C321T	p.N107N	GATGTCGTTGGAG	.	scavenged	Atlas-SNP
FAM208B	54906	hgsc.bcm.edu	37	10	5790738	5790738	+	Missense_Mutation	SNP	G	G	A	rs183849963	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	41	91	0	0.386792	0	G|0.999;A|0.001	0.001	strong	.	.	.	.	NM_017782	exon15	c.G5354A	p.C1785Y	CTGTTTGTGGAAT	.	PASS	Atlas-SNP
MYOM2	9172	hgsc.bcm.edu	37	8	2071174	2071174	+	Missense_Mutation	SNP	T	T	C	rs17854780	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	50	87	0	0.446429	0	T|0.900;C|0.100	0.100	strong	.	MYOM2	251	.	NM_003970	exon29	c.T3503C	p.V1168A	ATGATGTTCTGTA	.	PASS	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50755782	50755782	+	Silent	SNP	G	G	A	rs145811594	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	41	87	1	0.5	0.0114943	G|0.992;A|0.008	0.008	strong	FAM116B,colon,carcinoma,0,1	.	.	1	NM_001001794	exon5	c.C393T	p.F131F	GTAGCCGAAGTAG	.	scavenged	Atlas-SNP
FMN2	56776	hgsc.bcm.edu	37	1	240492734	240492734	+	Missense_Mutation	SNP	G	G	A	rs3795677	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	115	228	0	0.461847	0	G|0.684;A|0.316	0.316	strong	FMN2,NS,carcinoma,+1,1	FMN2	451	1	NM_020066	exon10	c.G4403A	p.R1468H	CAATTCGTCGCAA	.	PASS	Atlas-SNP
MYO15A	51168	hgsc.bcm.edu	37	17	18055229	18055229	+	Silent	SNP	G	G	A	rs854772	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	107	67	0	0.990741	0	G|0.577;A|0.423	0.423	strong	MYO15A,NS,carcinoma,0,1	MYO15A	268	1	NM_016239	exon40	c.G7857A	p.G2619G	GAAAGGGCAGATG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118530796	118530796	+	Silent	SNP	C	C	T	rs12040811	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	53	114	0	0.557895	0	C|0.915;T|0.085	0.085	strong	.	SPAG17	263	.	NM_206996	exon39	c.G5553A	p.Q1851Q	CAAAGACTGCTTG	.	PASS	Atlas-SNP
SSR1	6745	hgsc.bcm.edu	37	6	7310259	7310259	+	Missense_Mutation	SNP	A	A	G	rs10004	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	42	63	0	0.461538	0	T|0.123;G|0.260	0.260	strong	SSR1,NS,carcinoma,0,1	SSR1	21	1	NM_003144	exon2	c.T83C	p.L28S	GCTAACAAGCCTA	.	PASS	Atlas-SNP
LRIG3	121227	hgsc.bcm.edu	37	12	59282702	59282702	+	Silent	SNP	T	T	C	rs17533647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	50	137	0	0.378788	0	T|0.928;C|0.072	0.072	strong	LRIG3,NS,carcinoma,-2,1	LRIG3	120	1	NM_153377	exon6	c.A702G	p.T234T	TTGGAATGTCAGT	.	PASS	Atlas-SNP
C6orf15	29113	hgsc.bcm.edu	37	6	31079236	31079236	+	Silent	SNP	G	G	A	rs1265055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	87	98	0	1	0	G|0.484;A|0.516	0.516	strong	.	C6orf15	29	.	NM_014070	exon2	c.C900T	p.V300V	GCGGAGGACTCCA	.	PASS	Atlas-SNP
CCDC28B	79140	hgsc.bcm.edu	37	1	32669645	32669645	+	Silent	SNP	C	C	T	rs41263993	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	5	56	0	0.102041	0	C|0.987;T|0.013	0.013	strong	.	CCDC28B	21	.	NM_024296	exon3	c.C330T	p.F110F	GGCCTTCGGTGAG	.	PASS	Atlas-SNP
EPN3	55040	hgsc.bcm.edu	37	17	48618360	48618360	+	Missense_Mutation	SNP	C	C	T	rs78111408	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	16	30	0	0.533333	0	C|0.964;T|0.036	0.036	strong	.	EPN3	32	.	NM_017957	exon7	c.C1186T	p.H396Y	CCCCACCACAAAC	.	PASS	Atlas-SNP
PALM2-AKAP2	445815	hgsc.bcm.edu	37	9	112900466	112900466	+	Missense_Mutation	SNP	C	C	T	rs61735424	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	28	66	0	0.491228	0	C|0.969;T|0.031	0.031	strong	.	PALM2-AKAP2	117	.	NM_007203	exon8	c.C2642T	p.A881V	ACAGGGCGCTCAG	.	PASS	Atlas-SNP
FBXO6	26270	hgsc.bcm.edu	37	1	11728894	11728894	+	Missense_Mutation	SNP	G	G	A	rs56331446		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	10	151	0	0.0609756	0	.	.	weak	FBXO6,NS,carcinoma,0,1	FBXO6	17	1	NM_018438	exon2	c.G179A	p.R60Q	GCCTGCGAGAGGG	.	PASS	Atlas-SNP
TOPORS	10210	hgsc.bcm.edu	37	9	32541532	32541532	+	Silent	SNP	A	A	G	rs12348918	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	51	141	1	0.459459	0.0070922	A|0.832;G|0.168	0.168	strong	TOPORS_ENST00000360538,NS,carcinoma,0,2	TOPORS	127	2	NM_005802	exon3	c.T2991C	p.D997D	TCTTACATCGAGA	.	scavenged	Atlas-SNP
NOD2	64127	hgsc.bcm.edu	37	16	50733859	50733859	+	Silent	SNP	C	C	G	rs2067085	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	9	31	0	0.5625	0	C|0.673;G|0.327	0.327	strong	NOD2,NS,carcinoma,0,1	NOD2	118	1	NM_022162	exon2	c.C534G	p.S178S	ACCGTCCCAGAGG	.	PASS	Atlas-SNP
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159254	18159254	+	Missense_Mutation	SNP	A	A	G	rs4274188	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	174	143	0	1	0	A|0.278;G|0.722	0.722	strong	.	MRGPRX3	59	.	NM_054031	exon3	c.A505G	p.N169D	GGTGCTAATTCTG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134698626	134698626	+	Missense_Mutation	SNP	T	T	C	rs73393250	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	36	75	0	0.404494	0	T|0.913;C|0.087	0.087	strong	.	TTC40	100	.	NM_001200049	exon27	c.A3608G	p.N1203S	ATGGCGTTGTTGT	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227920747	227920747	+	Missense_Mutation	SNP	C	C	T	rs150979437	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	57	95	0	0.527778	0	C|0.930;T|0.070	0.070	strong	.	COL4A4	215	.	NM_000092	exon30	c.G2630A	p.R877Q	CCAGGCCGTCCTG	.	PASS	Atlas-SNP
MORN4	118812	hgsc.bcm.edu	37	10	99376152	99376152	+	Silent	SNP	A	A	G	rs3814556	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	22	77	0	0.44	0	A|0.673;G|0.327	0.327	strong	MORN4_ENST00000307450,NS,carcinoma,0,2	MORN4	24	2	NM_001098831	exon5	c.T309C	p.P103P	ACCATCAGGGAAA	.	PASS	Atlas-SNP
C21orf91	54149	hgsc.bcm.edu	37	21	19169155	19169155	+	Missense_Mutation	SNP	G	G	C	rs1047978	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	43	99	0	0.530864	0	G|0.690;C|0.310	0.310	strong	.	C21orf91	21	.	NM_017447	exon3	c.C408G	p.D136E	TTGGGAGTCAAAC	.	PASS	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	37	12	52824352	52824352	+	Silent	SNP	G	G	A	rs395623	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	50	111	0	0.442478	0	G|0.709;A|0.291	0.291	strong	.	KRT75	75	.	NM_004693	exon5	c.C1008T	p.A336A	AGCCTCGGCCCGG	.	PASS	Atlas-SNP
SLC39A4	55630	hgsc.bcm.edu	37	8	145641417	145641417	+	Missense_Mutation	SNP	G	G	A	rs117535951	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	18	6	0	0.72	0	G|0.980;A|0.020	0.020	strong	.	SLC39A4	54	.	NM_130849	exon2	c.C251T	p.P84L	GGGCCCGGGGGCA	.	PASS	Atlas-SNP
JAKMIP1	152789	hgsc.bcm.edu	37	4	6114561	6114561	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	2	82	1	0.027027	0.0121951	.	.	none	JAKMIP1_ENST00000409021,caecum,carcinoma,0,6	JAKMIP1	250	6	NM_001099433	exon2	c.G17A	p.R6Q	TTGCTCCGGCCTT	.	scavenged	Atlas-SNP
C12orf71	728858	hgsc.bcm.edu	37	12	27234200	27234200	+	Silent	SNP	T	T	C	rs708165	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	25	39	0	0.454545	0	T|0.739;C|0.261	0.261	strong	.	C12orf71	20	.	NM_001080406	exon2	c.A717G	p.K239K	GGGACTTTTGGTG	.	PASS	Atlas-SNP
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417718	138417718	+	Silent	SNP	A	A	G	rs3807154	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	85	0	1	0	A|0.340;G|0.660	0.660	strong	.	ATP6V0A4	93	.	NM_130841	exon16	c.T1812C	p.H604H	AGATACATGGACG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632782	32632782	+	Missense_Mutation	SNP	G	G	A	rs12722115	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	22	0	0	0.666667	.	G|0.644;C|0.073;A|0.283	0.283	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.C172T	p.L58F	TCACAAGACGCAC	.	PASS	Atlas-SNP
FAM129C	199786	hgsc.bcm.edu	37	19	17650053	17650053	+	Silent	SNP	G	G	A	rs74546231	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	33	0	0.43662	0	G|0.962;A|0.038	0.038	strong	FAM129C_ENST00000332386,NS,carcinoma,0,2	FAM129C	110	2	NM_001098524	exon7	c.G783A	p.V261V	CGACGTGACCCTA	.	PASS	Atlas-SNP
AEN	64782	hgsc.bcm.edu	37	15	89169653	89169653	+	Silent	SNP	G	G	A	rs34649587	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	33	62	0	0.458333	0	G|0.963;A|0.037	0.037	strong	.	AEN	29	.	NM_022767	exon2	c.G213A	p.A71A	GGCAGCGACAGCA	.	PASS	Atlas-SNP
CCDC68	80323	hgsc.bcm.edu	37	18	52605188	52605188	+	Silent	SNP	C	C	T	rs1344011	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	99	245	0	0.478261	0	C|0.784;T|0.216	0.216	strong	.	CCDC68	38	.	NM_025214	exon5	c.G345A	p.K115K	TCATACCTTGATT	.	PASS	Atlas-SNP
ANKHD1	54882	hgsc.bcm.edu	37	5	139838786	139838786	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	70	188	0	0.466667	0	.	.	none	ANKHD1-EIF4EBP3,rectum,carcinoma,+2,2	ANKHD1	233	2	NM_024668	exon9	c.A1518C	p.E506D	TCAAGAAACTGCT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195510133	195510133	+	Missense_Mutation	SNP	T	T	C	rs371587475		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	7	229	5	0.0569106	0.0218341	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	NM_018406	exon2	c.A8318G	p.N2773S	GAAGTGTTGGTGA	.	scavenged	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9072875	9072875	+	Silent	SNP	G	G	A	rs73009098	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	441	204	442	0	0.462585	0	G|0.809;A|0.191	0.191	strong	.	MUC16	4315	.	NM_024690	exon3	c.C14571T	p.V4857V	AGATGTGACTTTA	.	PASS	Atlas-SNP
RNF43	54894	hgsc.bcm.edu	37	17	56435885	56435885	+	Missense_Mutation	SNP	G	G	T	rs2526374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	55	138	0	0.474138	0	G|0.612;T|0.388	0.388	strong	.	RNF43	157	.	NM_017763	exon9	c.C1252A	p.L418M	GGCTCAGTCCCCA	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88536919	88536919	+	Silent	SNP	T	T	C	rs369387818	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	26	143	0	0.19403	0	.	.	weak	DSPP,NS,carcinoma,0,3	DSPP	174	3	NM_014208	exon5	c.T3105C	p.D1035D	CAGCGATAGCAGT	.	PASS	Atlas-SNP
SOLH	6650	hgsc.bcm.edu	37	16	602313	602313	+	Silent	SNP	C	C	A	rs9930550	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	5	3	0	1	0	C|0.433;A|0.567	0.567	strong	SOLH,NS,carcinoma,0,2	SOLH	47	2	NM_005632	exon11	c.C2520A	p.A840A	GGACGCCGTGGAC	.	scavenged	Atlas-SNP
CHST12	55501	hgsc.bcm.edu	37	7	2472429	2472429	+	Missense_Mutation	SNP	C	C	A	rs3735099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	39	32	0	0.6	0	C|0.957;A|0.043	0.043	strong	.	CHST12	39	.	NM_018641	exon2	c.C155A	p.P52H	CCACGCCCGGGCC	.	PASS	Atlas-SNP
FBF1	85302	hgsc.bcm.edu	37	17	73910027	73910027	+	Silent	SNP	C	C	T	rs61736662	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	45	28	0	0.681818	0	C|0.964;T|0.036	0.036	strong	.	FBF1	48	.	NM_001080542	exon26	c.G3051A	p.E1017E	CAGCCGCTCCTGC	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81598269	81598269	+	Missense_Mutation	SNP	T	T	G	rs11556218	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	39	49	0	0.46988	0	T|0.860;G|0.140	0.140	strong	.	IL16	254	.	NM_001172128	exon17	c.T3441G	p.N1147K	TCCAAATGGGCTG	.	PASS	Atlas-SNP
OR5AK2	390181	hgsc.bcm.edu	37	11	56756516	56756516	+	Missense_Mutation	SNP	G	G	C	rs12420424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	254	136	282	0	0.535433	0	G|0.938;C|0.062	0.062	strong	.	OR5AK2	45	.	NM_001005323	exon1	c.G128C	p.S43T	GTAATAGTGGAAT	.	PASS	Atlas-SNP
FDXACB1	91893	hgsc.bcm.edu	37	11	111747297	111747297	+	Silent	SNP	A	A	G	rs7124696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	44	94	0	0.468085	0	A|0.738;G|0.262	0.262	strong	.	FDXACB1	74	.	NM_138378	exon4	c.T600C	p.F200F	ACCTTCAAAAGGT	.	PASS	Atlas-SNP
NRAP	4892	hgsc.bcm.edu	37	10	115352005	115352005	+	Missense_Mutation	SNP	A	A	G	rs11196389	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	63	109	0	0.6	0	A|0.904;G|0.095	0.095	strong	.	NRAP	208	.	NM_001261463	exon39	c.T4592C	p.L1531P	GCATCCAGCCTGA	.	PASS	Atlas-SNP
ANKRD30A	91074	hgsc.bcm.edu	37	10	37488689	37488689	+	Missense_Mutation	SNP	G	G	C	rs1209750	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	265	264	356	0	0.996226	0	A|0.002;C|0.510;G|0.489	0.510	strong	.	ANKRD30A	448	.	NM_052997	exon30	c.G2583C	p.K861N	AAAGAAGGTTGAA	.	PASS	Atlas-SNP
PHIP	55023	hgsc.bcm.edu	37	6	79692751	79692751	+	Missense_Mutation	SNP	G	G	A	rs11547228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	42	112	0	0.792453	0	G|0.923;A|0.077	0.077	strong	.	PHIP	177	.	NM_017934	exon23	c.C2621T	p.T874I	TTCTTGGTTTTAT	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713821	32713821	+	Silent	SNP	C	C	A	rs34005994	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	475	35	513	1	0.0736842	0.00194932	C|0.778;A|0.222	0.222	strong	HLA-DQA2,NS,carcinoma,+2,1	HLA-DQA2	27	1	NM_020056	exon3	c.C585A	p.G195G	CTGGGGCCTGGAC	.	scavenged	Atlas-SNP
ESYT3	83850	hgsc.bcm.edu	37	3	138191448	138191448	+	Missense_Mutation	SNP	A	A	T	rs35537868	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	56	117	0	0.57732	0	A|0.902;T|0.098	0.098	strong	.	ESYT3	64	.	NM_031913	exon18	c.A1984T	p.T662S	CAAGAGACAGGCC	.	PASS	Atlas-SNP
BPIFB6	128859	hgsc.bcm.edu	37	20	31619515	31619515	+	Missense_Mutation	SNP	G	G	A	rs41293138	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	50	138	0	0.30303	0	G|0.995;A|0.005	0.005	strong	.	.	.	.	NM_174897	exon1	c.G62A	p.G21E	ACCCTGGGGCACT	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338298	28338298	+	Missense_Mutation	SNP	C	C	G	rs457947	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	70	99	0	0.542636	0	C|0.834;G|0.166	0.166	strong	.	ADAMTS5	184	.	NM_007038	exon1	c.G413C	p.G138A	GGACTACCGTCCA	.	PASS	Atlas-SNP
HHLA1	10086	hgsc.bcm.edu	37	8	133092138	133092138	+	Missense_Mutation	SNP	G	G	A	rs2403730	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	400	163	342	1	0.4075	0.00292398	G|0.754;A|0.246	0.246	strong	HHLA1,NS,carcinoma,0,1	HHLA1	35	1	NM_001145095	exon10	c.C752T	p.P251L	TGTCCGGGGCTTG	.	PASS	Atlas-SNP
TNXB	7148	hgsc.bcm.edu	37	6	32017173	32017173	+	Missense_Mutation	SNP	G	G	C	rs41270450	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	106	215	1	0.479638	0.00465116	G|0.940;C|0.060	0.060	strong	.	TNXB	553	.	NM_019105	exon28	c.C9625G	p.R3209G	TGACACGCACCAC	.	PASS	Atlas-SNP
OR2L3	391192	hgsc.bcm.edu	37	1	248224746	248224746	+	Missense_Mutation	SNP	G	G	T	rs74579079		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	249	116	226	1	0.465863	0.00442478	.	.	weak	.	OR2L3	97	.	NM_001004687	exon1	c.G763T	p.V255F	CCTTTTGTCTACA	.	PASS	Atlas-SNP
RPGRIP1	57096	hgsc.bcm.edu	37	14	21790040	21790040	+	Missense_Mutation	SNP	G	G	T	rs10151259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	85	107	0	0.988372	0	A|0.059;C|0.298	.	strong	.	RPGRIP1	213	.	NM_020366	exon13	c.G1639T	p.A547S	ACAAAAGCTGACA	.	PASS	Atlas-SNP
PSD4	23550	hgsc.bcm.edu	37	2	113940681	113940681	+	Silent	SNP	T	T	C	rs3748914	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	77	72	0	1	0	C|0.529;N|0.000	0.529	strong	PSD4,NS,carcinoma,0,1	PSD4	74	1	NM_012455	exon2	c.T648C	p.S216S	CAGCAGTGAGCCT	.	PASS	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136029138	136029138	+	Silent	SNP	G	G	A	rs35902535	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	52	102	0	0.52	0	G|0.944;A|0.056	0.056	strong	.	GBGT1	25	.	NM_021996	exon7	c.C870T	p.G290G	CATGATGCCATTG	.	PASS	Atlas-SNP
SS18L1	26039	hgsc.bcm.edu	37	20	60738566	60738566	+	Silent	SNP	C	C	T	rs73309164	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	77	116	1	0.516779	0.00862069	C|0.928;T|0.072	0.072	strong	SS18L1_ENST00000331758,NS,carcinoma,0,1	SS18L1	37	1	NM_198935	exon6	c.C609T	p.G203G	GCAGGGCGGCAGC	.	scavenged	Atlas-SNP
CCM2	83605	hgsc.bcm.edu	37	7	45104131	45104131	+	Missense_Mutation	SNP	G	G	A	rs11552377	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	33	37	0	0.647059	0	G|0.879;A|0.121	0.121	strong	.	CCM2	42	.	NM_001029835	exon4	c.G421A	p.V141I	TACAACGTCAAGC	.	PASS	Atlas-SNP
ZNF232	7775	hgsc.bcm.edu	37	17	5012935	5012935	+	Missense_Mutation	SNP	A	A	C	rs200108859	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	86	186	0	0.467391	0	.	.	weak	.	ZNF232	42	.	NM_014519	exon3	c.T252G	p.H84Q	GCGGAGATGCCTG	.	PASS	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	37	18	14803745	14803745	+	Missense_Mutation	SNP	A	A	G	rs45533337	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	372	103	315	0	0.276882	0	A|1.000;|0.000	.	weak	ANKRD30B_ENST00000358984,NS,carcinoma,0,2	ANKRD30B	237	2	NM_001145029	exon24	c.A2206G	p.T736A	CTTGAGACTCTCT	.	scavenged	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74916173	74916173	+	Silent	SNP	T	T	A	rs12241093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	49	134	0	0.426087	0	T|0.885;A|0.115	0.115	strong	.	ECD	50	.	NM_001135752	exon5	c.A450T	p.A150A	TCTTGGTGCAGGG	.	PASS	Atlas-SNP
CCDC69	26112	hgsc.bcm.edu	37	5	150578574	150578574	+	Silent	SNP	A	A	G	rs3734038	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	99	98	0	0.99	0	A|0.820;G|0.180	0.180	strong	.	CCDC69	30	.	NM_015621	exon4	c.T303C	p.N101N	CTCTTCATTCTTT	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65392695	65392695	+	Silent	SNP	C	C	T	rs1205259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	36	74	0	0.580645	0	C|0.733;T|0.267	0.267	strong	.	PCNXL3	140	.	NM_032223	exon17	c.C2973T	p.L991L	TGGCCTCCTGGTG	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1250488	1250488	+	Silent	SNP	C	C	T	rs2075859	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	69	117	0	0.475862	0	C|0.604;T|0.396	0.396	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon9	c.C1065T	p.C355C	GCTCTGCGAGGAC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1051214	1051214	+	Silent	SNP	A	A	G	rs3752240	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	55	101	0	0.5	0	A|0.653;G|0.347	0.347	strong	.	ABCA7	174	.	NM_019112	exon20	c.A2745G	p.V915V	CGCTGTAGTGGGC	.	PASS	Atlas-SNP
SLIRP	81892	hgsc.bcm.edu	37	14	78182188	78182188	+	Missense_Mutation	SNP	T	T	A	rs199752740	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	102	238	0	0.459459	0	T|0.999;A|0.001	0.001	weak	.	SLIRP	6	.	NM_001267864	exon3	c.T230A	p.L77Q	ATGCACTACAACA	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	254599	254599	+	Missense_Mutation	SNP	A	A	T	rs6960	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	565	173	635	3	0.306195	0.00472441	A|0.865;T|0.135	0.135	strong	SDHA,adrenal_gland,pheochromocytoma,0,1	SDHA	80	1	NM_004168	exon14	c.A1886T	p.Y629F	TGTCCTATGTGGA	.	scavenged	Atlas-SNP
NPBWR2	2832	hgsc.bcm.edu	37	20	62737568	62737568	+	Missense_Mutation	SNP	T	T	C	rs4809401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	52	106	0	0.547368	0	T|0.908;C|0.092	0.092	strong	NPBWR2,NS,carcinoma,0,1	NPBWR2	36	1	NM_005286	exon1	c.A617G	p.Q206R	CAGACCTGCTCGG	.	PASS	Atlas-SNP
FLII	2314	hgsc.bcm.edu	37	17	18148485	18148485	+	Silent	SNP	G	G	A	rs7498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	123	104	0	1	0	G|0.728;A|0.272	0.272	strong	.	FLII	79	.	NM_002018	exon30	c.C3777T	p.H1259H	CCAGGCGTGGAAG	.	PASS	Atlas-SNP
ATP1A4	480	hgsc.bcm.edu	37	1	160136350	160136350	+	Silent	SNP	G	G	A	rs7529215	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	167	175	0	0.982353	0	G|0.522;A|0.478	0.478	strong	.	ATP1A4	167	.	NM_144699	exon8	c.G1080A	p.A360A	CATGGCGCGGAAG	.	PASS	Atlas-SNP
PER3	8863	hgsc.bcm.edu	37	1	7880683	7880683	+	Missense_Mutation	SNP	T	T	G	rs10462020	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	123	120	0	0.891304	0	T|0.862;G|0.138	0.138	strong	.	PER3	95	.	NM_016831	exon15	c.T1916G	p.V639G	TCCATGTCCCACC	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378388	31378388	+	Missense_Mutation	SNP	G	G	A	rs1051785	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	232	214	1	0.978903	0.0046729	G|0.934;A|0.066	0.066	strong	MICA,bladder,carcinoma,+1,1	MICA	21	1	NM_001177519	exon2	c.G139A	p.A47T	TTTCTTGCTGAGG	.	PASS	Atlas-SNP
NCKAP5	344148	hgsc.bcm.edu	37	2	133540708	133540708	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	5	252	0	0.025641	0	.	.	none	NCKAP5,NS,carcinoma,0,1	NCKAP5	322	1	NM_207363	exon14	c.G3676A	p.E1226K	CTGTTTCCAGGGG	.	scavenged	Atlas-SNP
TTLL10	254173	hgsc.bcm.edu	37	1	1115503	1115503	+	Missense_Mutation	SNP	T	T	C	rs111751804	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	66	86	0	0.916667	0	T|0.985;C|0.015	0.015	strong	.	TTLL10	66	.	NM_001130045	exon6	c.T289C	p.C97R	GGACACTGTGGGC	.	PASS	Atlas-SNP
AKAP9	10142	hgsc.bcm.edu	37	7	91708898	91708898	+	Missense_Mutation	SNP	A	A	G	rs35759833	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	27	57	0	0.5625	0	A|0.911;G|0.089	0.089	strong	AKAP9_ENST00000356239,colon,carcinoma,0,2	AKAP9	788	2	NM_005751	exon31	c.A7451G	p.K2484R	ACTTCAAATCTTT	.	PASS	Atlas-SNP
TSHZ3	57616	hgsc.bcm.edu	37	19	31768416	31768416	+	Silent	SNP	A	A	G	rs3745784	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	56	146	0	0.486957	0	A|0.717;G|0.283	0.283	strong	.	TSHZ3	549	.	NM_020856	exon2	c.T2283C	p.A761A	CACAGCAGCCTTC	.	PASS	Atlas-SNP
DNAAF1	123872	hgsc.bcm.edu	37	16	84203939	84203939	+	Missense_Mutation	SNP	C	C	T	rs11644164	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	35	45	0	1	0	C|0.703;T|0.297	0.297	strong	.	DNAAF1	81	.	NM_178452	exon8	c.C1505T	p.P502L	CACCACCGCCCCT	.	PASS	Atlas-SNP
OR7D4	125958	hgsc.bcm.edu	37	19	9325252	9325252	+	Missense_Mutation	SNP	G	G	A	rs61729907	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	76	143	0	0.490323	0	G|0.845;A|0.155	0.155	strong	.	OR7D4	66	.	NM_001005191	exon1	c.C262T	p.R88W	TGCTCCGTGCCTG	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135958704	135958704	+	Missense_Mutation	SNP	G	G	C	rs112089728	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	340	54	251	0	0.158824	0	.	.	weak	.	RBMX	149	.	NM_002139	exon5	c.C499G	p.P167A	CTGAAGGTGCAGA	.	PASS	Atlas-SNP
FGD4	121512	hgsc.bcm.edu	37	12	32735236	32735236	+	Silent	SNP	C	C	T	rs904582	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	47	97	0	0.505376	0	C|0.515;T|0.485	0.485	strong	.	FGD4	86	.	NM_139241	exon4	c.C435T	p.D145D	AACAGACAGCTGT	.	PASS	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	37	21	33371123	33371123	+	Missense_Mutation	SNP	C	C	T	rs10775648	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	43	91	0	0.511905	0	C|0.807;T|0.193	0.193	strong	.	HUNK	74	.	NM_014586	exon11	c.C1771T	p.R591C	TTGGCTCGCAGAA	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626627	140626627	+	Missense_Mutation	SNP	G	G	A	rs618096	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	233	229	216	2	0.982833	0.00925926	G|0.364;A|0.636	0.636	strong	.	PCDHB15	138	.	NM_018935	exon1	c.G1481A	p.R494Q	CGCCCCGGGACCC	.	PASS	Atlas-SNP
JPH2	57158	hgsc.bcm.edu	37	20	42743454	42743454	+	Silent	SNP	A	A	G	rs6093935	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	65	100	0	0.575221	0	A|0.685;G|0.315	0.315	strong	.	JPH2	86	.	NM_020433	exon5	c.T2073C	p.F691F	GTGAACAAAGAGG	.	PASS	Atlas-SNP
GSTM5	2949	hgsc.bcm.edu	37	1	110257831	110257831	+	Missense_Mutation	SNP	T	T	C	rs2227963	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	472	234	447	2	0.495763	0.00447427	T|0.847;C|0.153	0.153	strong	GSTM5,scalp,carcinoma,0,13	GSTM5	89	13	NM_000851	exon7	c.T536C	p.L179P	CCTTCCTAAACTT	.	PASS	Atlas-SNP
COL4A2	1284	hgsc.bcm.edu	37	13	111119396	111119396	+	Missense_Mutation	SNP	G	G	C	rs3803230	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	55	152	0	0.561224	0	G|0.898;C|0.102	0.102	strong	.	COL4A2	178	.	NM_001846	exon27	c.G2048C	p.G683A	GCATAGGAGGGCC	.	PASS	Atlas-SNP
TRIM31	11074	hgsc.bcm.edu	37	6	30075864	30075864	+	Silent	SNP	A	A	G	rs2023472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	72	173	0	0.473684	0	A|0.348;G|0.652	0.652	strong	TRIM31,NS,carcinoma,0,1	TRIM31	40	1	NM_007028	exon6	c.T849C	p.H283H	GGAGTCATGTCTT	.	PASS	Atlas-SNP
DIS3L	115752	hgsc.bcm.edu	37	15	66625161	66625161	+	Silent	SNP	A	A	G	rs11071885	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	58	117	0	0.453125	0	A|0.924;G|0.076	0.076	strong	.	DIS3L	175	.	NM_001143688	exon16	c.A2769G	p.P923P	GAAACCAGGATCC	.	PASS	Atlas-SNP
TREM1	54210	hgsc.bcm.edu	37	6	41250179	41250179	+	Silent	SNP	C	C	T	rs2234239	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	65	182	0	0.457746	0	C|0.964;T|0.036	0.036	strong	.	TREM1	38	.	NM_001242590	exon2	c.G360A	p.K120K	AGGCTCCTTGGGA	.	PASS	Atlas-SNP
KHK	3795	hgsc.bcm.edu	37	2	27315252	27315252	+	Missense_Mutation	SNP	G	G	A	rs2304681	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	27	47	0	0.509434	0	G|0.649;A|0.351	0.351	strong	KHK_ENST00000260598,colon,carcinoma,0,2	KHK	60	2	NM_006488	exon2	c.G145A	p.V49I	TGCACCGTTCTCT	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	37	12	70983895	70983895	+	Missense_Mutation	SNP	A	A	C	rs2165627	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	95	201	0	0.470297	0	A|0.905;C|0.095	0.095	strong	.	PTPRB	676	.	NM_001109754	exon8	c.T1899G	p.D633E	CACAGAATCATTG	.	PASS	Atlas-SNP
HAS1	3036	hgsc.bcm.edu	37	19	52222552	52222552	+	Silent	SNP	G	G	A	rs11084112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	10	17	0	0.384615	0	G|0.658;A|0.342	0.342	strong	HAS1,NS,lymphoid_neoplasm,0,1	HAS1	61	1	NM_001523	exon2	c.C609T	p.R203R	GCACCTGCGAGTC	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75982058	75982058	+	Missense_Mutation	SNP	T	T	A	rs147116973	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	21	141	0	0.105528	0	T|0.988;A|0.013	0.013	strong	CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	NM_001897	exon3	c.A1348T	p.R450W	CATGCCTCCACTC	.	scavenged	Atlas-SNP
COX18	285521	hgsc.bcm.edu	37	4	73930552	73930552	+	Silent	SNP	G	G	A	rs3762883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	106	192	0	0.527363	0	G|0.650;C|0.000;A|0.350	0.350	strong	.	COX18	20	.	NM_173827	exon4	c.C663T	p.P221P	GGAGTCGGGTGCA	.	PASS	Atlas-SNP
LRCH3	84859	hgsc.bcm.edu	37	3	197566254	197566254	+	Silent	SNP	T	T	C	rs17850206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	52	108	0	0.490566	0	T|0.669;C|0.331	0.331	strong	.	LRCH3	96	.	NM_032773	exon10	c.T1314C	p.Y438Y	AAGATATTTACAT	.	PASS	Atlas-SNP
MYL10	93408	hgsc.bcm.edu	37	7	101256833	101256833	+	Silent	SNP	T	T	C	rs2240389	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	139	138	0	1	0	T|0.742;C|0.258	0.258	strong	.	MYL10	32	.	NM_138403	exon8	c.A603G	p.A201A	GGGAAATGCTGCA	.	PASS	Atlas-SNP
GZMB	3002	hgsc.bcm.edu	37	14	25101629	25101629	+	Silent	SNP	T	T	C	rs10909625	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	286	89	343	0	0.311189	0	T|0.742;C|0.258	0.258	strong	GZMB,NS,carcinoma,0,1	GZMB	73	1	NM_004131	exon3	c.A240G	p.K80K	CTGTTCTTTGATA	.	PASS	Atlas-SNP
HRH2	3274	hgsc.bcm.edu	37	5	175110379	175110379	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	260	6	257	0	0.0230769	0	.	.	none	HRH2_ENST00000377291,colon,carcinoma,+1,2	HRH2	108	2	NM_001131055	exon2	c.G143A	p.R48Q	ACCGCCGGCTCCG	.	scavenged	Atlas-SNP
SLC25A47	283600	hgsc.bcm.edu	37	14	100795139	100795139	+	Missense_Mutation	SNP	G	G	T	rs35007880	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	55	72	1	0.447154	0.0138889	G|0.667;T|0.333	0.333	strong	SLC25A47,NS,carcinoma,0,1	SLC25A47	36	1	NM_207117	exon5	c.G404T	p.R135L	AGCGGCGGCTTTC	.	scavenged	Atlas-SNP
SERPINF1	5176	hgsc.bcm.edu	37	17	1680002	1680002	+	Silent	SNP	T	T	C	rs6828	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	106	122	0	1	0	C|0.782;G|0.000;N|0.000;T|0.218	0.782	strong	.	SERPINF1	31	.	NM_002615	exon7	c.T963C	p.Y321Y	GAGTTATGAAGGC	.	PASS	Atlas-SNP
ADAMTS19	171019	hgsc.bcm.edu	37	5	128863518	128863518	+	Silent	SNP	A	A	G	rs61749629	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	89	210	0	0.427885	0	A|0.968;G|0.032	0.032	strong	.	ADAMTS19	216	.	NM_133638	exon5	c.A1146G	p.E382E	CCATGAAACTCCA	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16251599	16251599	+	Missense_Mutation	SNP	C	C	T	rs2238472	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	38	0	1	0	C|0.810;T|0.190	0.190	strong	.	ABCC6	110	.	NM_001171	exon27	c.G3803A	p.R1268Q	AAGTCCCGGAACT	.	PASS	Atlas-SNP
GRIN3B	116444	hgsc.bcm.edu	37	19	1004808	1004808	+	Silent	SNP	C	C	T	rs61736783	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	34	23	0	0.618182	0	C|0.936;T|0.064	0.064	strong	.	GRIN3B	46	.	NM_138690	exon3	c.C1308T	p.D436D	CGAAGACGGGCAG	.	PASS	Atlas-SNP
SELP	6403	hgsc.bcm.edu	37	1	169563951	169563951	+	Missense_Mutation	SNP	T	T	G	rs6136	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	103	213	0	0.466063	0	T|0.930;G|0.070	0.070	strong	.	SELP	132	.	NM_003005	exon13	c.A2266C	p.T756P	CGGTAGTTGACCA	.	PASS	Atlas-SNP
ZNF25	219749	hgsc.bcm.edu	37	10	38241220	38241220	+	Silent	SNP	T	T	C	rs146555827	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	51	78	0	0.554348	0	T|0.999;C|0.001	0.001	strong	.	ZNF25	66	.	NM_145011	exon6	c.A1206G	p.E402E	CCCACATTCCTTG	.	PASS	Atlas-SNP
CHGA	1113	hgsc.bcm.edu	37	14	93399101	93399101	+	Missense_Mutation	SNP	C	C	T	rs729940	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	33	35	0	0.540984	0	C|0.876;T|0.124	0.124	strong	.	CHGA	32	.	NM_001275	exon7	c.C1195T	p.R399W	TCCTCCCGGGAGG	.	PASS	Atlas-SNP
FAM209A	200232	hgsc.bcm.edu	37	20	55099978	55099978	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	22	241	0	0.120219	0	.	.	none	.	.	.	.	NM_001012971	exon1	c.C114T	p.Y38Y	GCAATACGGAGAG	.	PASS	Atlas-SNP
PODXL2	50512	hgsc.bcm.edu	37	3	127379635	127379635	+	Missense_Mutation	SNP	C	C	T	rs34691761	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	49	127	0	0.398374	0	C|0.995;T|0.005	0.005	strong	.	PODXL2	53	.	NM_015720	exon3	c.C764T	p.P255L	TGACTCCGGGGGA	.	PASS	Atlas-SNP
C2orf71	388939	hgsc.bcm.edu	37	2	29295476	29295476	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	52	115	0	0.504854	0	.	.	none	.	C2orf71	146	.	NM_001029883	exon1	c.G1652A	p.R551K	TTGATCCTTTCGC	.	PASS	Atlas-SNP
PCDHB11	56125	hgsc.bcm.edu	37	5	140579367	140579367	+	Missense_Mutation	SNP	G	G	A	rs917535	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	32	91	0	0.533333	0	G|0.931;A|0.069	0.069	strong	PCDHB11,NS,carcinoma,+1,1	PCDHB11	162	1	NM_018931	exon1	c.G20A	p.R7H	GGACACGCACTCA	.	PASS	Atlas-SNP
DHX33	56919	hgsc.bcm.edu	37	17	5366947	5366947	+	Missense_Mutation	SNP	G	G	A	rs8069315	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	41	68	0	0.488095	0	G|0.856;A|0.144	0.144	strong	.	DHX33	41	.	NM_020162	exon2	c.C352T	p.R118C	CCTGGCGGCTGAT	.	PASS	Atlas-SNP
ANKRD66	100287718	hgsc.bcm.edu	37	6	46726500	46726500	+	Missense_Mutation	SNP	C	C	A	rs9472839	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	28	51	0	0.430769	0	C|0.903;A|0.097	0.097	strong	.	.	.	.	NM_001162435	exon5	c.C598A	p.Q200K	GCCCAGCAGAAGG	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373311	5373311	+	Missense_Mutation	SNP	T	T	C	rs5006883	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	70	221	0	0.404624	0	T|0.772;C|0.228	0.228	strong	OR51B6,NS,carcinoma,-1,1	OR51B6	53	1	NM_001004750	exon1	c.T574C	p.F192L	ATCACCTTCAACC	.	PASS	Atlas-SNP
CRX	1406	hgsc.bcm.edu	37	19	48342985	48342985	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	2	51	0	0.031746	0	.	.	none	CRX,NS,carcinoma,-2,1	CRX	52	1	NM_000554	exon4	c.T661A	p.Y221N	GACCCCTACCTTT	.	scavenged	Atlas-SNP
CILP2	148113	hgsc.bcm.edu	37	19	19653231	19653231	+	Missense_Mutation	SNP	T	T	A	rs186322474	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	33	56	0	0.532258	0	T|0.999;A|0.001	0.001	weak	.	CILP2	84	.	NM_153221	exon5	c.T640A	p.S214T	CTGGGCTCGGTGG	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38375666	38375666	+	Missense_Mutation	SNP	C	C	T	rs73027451	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	97	110	0	0.979798	0	C|0.835;T|0.166	0.166	strong	.	WDR87	191	.	NM_031951	exon6	c.G8528A	p.R2843Q	CCATACCGGGCAA	.	PASS	Atlas-SNP
PSG2	5670	hgsc.bcm.edu	37	19	43585253	43585253	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	4	190	4	0.0192308	0.0210526	.	.	none	PSG2,NS,carcinoma,0,2	PSG2	84	2	NM_031246	exon2	c.G210A	p.G70G	GATTTGCCCTTTG	.	scavenged	Atlas-SNP
KDM1B	221656	hgsc.bcm.edu	37	6	18213988	18213988	+	Silent	SNP	C	C	T	rs6903583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	102	201	0	0.426778	0	C|0.808;T|0.192	0.192	strong	.	KDM1B	58	.	NM_153042	exon15	c.C1389T	p.A463A	TTTTGCCGTGTTC	.	PASS	Atlas-SNP
COX11	1353	hgsc.bcm.edu	37	17	53038654	53038654	+	Missense_Mutation	SNP	A	A	C	rs1802212	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	82	82	0	1	0	A|0.835;C|0.165	0.165	strong	.	COX11	16	.	NM_001162861	exon4	c.T682G	p.S228A	ACGTAGACTCTGT	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40406019	40406019	+	Silent	SNP	G	G	A	rs2355719	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	560	366	691	1	0.653571	0.00144718	G|0.717;A|0.283	0.283	strong	.	FCGBP	416	.	NM_003890	exon10	c.C4827T	p.C1609C	GCACGTGCACTGC	.	PASS	Atlas-SNP
CD93	22918	hgsc.bcm.edu	37	20	23065209	23065209	+	Missense_Mutation	SNP	G	G	A	rs3746731	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	31	51	0	0.574074	0	G|0.481;A|0.519	0.519	strong	.	CD93	84	.	NM_012072	exon1	c.C1621T	p.P541S	CGCCTGGGGACCC	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80764360	80764360	+	Missense_Mutation	SNP	C	C	T	rs146572555	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	29	67	0	0.617021	0	C|0.997;T|0.003	0.003	strong	.	OTOGL	235	.	NM_173591	exon55	c.C6599T	p.T2200I	GGAGTACCTGGCA	.	PASS	Atlas-SNP
MYPN	84665	hgsc.bcm.edu	37	10	69926319	69926319	+	Silent	SNP	C	C	A	rs61854624	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	44	97	0	0.458333	0	A|0.133;C|0.867;G|0.000	0.133	strong	MYPN,NS,carcinoma,+1,1	MYPN	189	1	NM_032578	exon10	c.C1869A	p.T623T	ACAGACCAGGCCC	.	PASS	Atlas-SNP
MRPS5	64969	hgsc.bcm.edu	37	2	95775761	95775761	+	Silent	SNP	G	G	A	rs113259652	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	357	348	398	0	0.97479	0	G|0.968;A|0.032	0.032	strong	.	MRPS5	52	.	NM_031902	exon4	c.C303T	p.G101G	TAAAGCGCCTTTC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3241317	3241317	+	Silent	SNP	T	T	C	rs1635249	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	78	85	0	1	0	0|0.003;C|0.737	0.737	strong	.	MXRA5	815	.	NM_015419	exon5	c.A2409G	p.P803P	AATCAATGGGGGT	.	PASS	Atlas-SNP
SIGLEC7	27036	hgsc.bcm.edu	37	19	51650520	51650520	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	79	134	0	0.512987	0	.	.	none	.	SIGLEC7	74	.	NM_014385	exon6	c.C1167T	p.D389D	AGCGGACGTGGGA	.	PASS	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	37	3	13612936	13612936	+	Missense_Mutation	SNP	A	A	G	rs3732666	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	38	87	0	0.447059	0	A|0.603;G|0.397	0.397	strong	.	FBLN2	137	.	NM_001998	exon2	c.A1081G	p.S361G	GCACCGAGCCTGG	.	PASS	Atlas-SNP
KLC3	147700	hgsc.bcm.edu	37	19	45849909	45849909	+	Silent	SNP	A	A	G	rs9749618	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	19	21	0	0.633333	0	A|0.790;G|0.210	0.210	strong	KLC3,colon,carcinoma,0,1	KLC3	37	1	NM_177417	exon3	c.A366G	p.E122E	GGAGGAACTGGAG	.	PASS	Atlas-SNP
KIF26B	55083	hgsc.bcm.edu	37	1	245850095	245850095	+	Silent	SNP	C	C	T	rs871840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	42	85	0	0.545455	0	C|0.808;T|0.192	0.192	strong	.	KIF26B	343	.	NM_018012	exon12	c.C3810T	p.D1270D	CCAGGACGCAGGG	.	PASS	Atlas-SNP
TAB2	23118	hgsc.bcm.edu	37	6	149730846	149730846	+	Silent	SNP	G	G	A	rs652921	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	66	107	0	0.825	0	G|0.850;A|0.150	0.150	strong	.	TAB2	55	.	NM_015093	exon9	c.G2073A	p.R691R	GCCAAGGCATTTC	.	PASS	Atlas-SNP
FAM22A	728118	hgsc.bcm.edu	37	10	88988115	88988115	+	Missense_Mutation	SNP	G	G	A	rs78157191	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	327	79	330	0	0.24159	0	G|0.375;A|0.625	0.625	strong	FAM22D,NS,haematopoietic_neoplasm,0,2	FAM22A	20	2	NM_001099338	exon2	c.G478A	p.A160T	GGCCCAGCACACG	.	scavenged	Atlas-SNP
TNFRSF14	8764	hgsc.bcm.edu	37	1	2493168	2493168	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	47	67	0	0.652778	0	.	.	none	.	TNFRSF14	89	.	NM_003820	exon6	c.G608A	p.W203X	GGGTATGGTGGTT	.	PASS	Atlas-SNP
HDHD3	81932	hgsc.bcm.edu	37	9	116136198	116136198	+	Missense_Mutation	SNP	C	C	T	rs1043836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	63	76	0	0.583333	0	C|0.419;T|0.581	0.581	strong	.	HDHD3	10	.	NM_031219	exon2	c.G437A	p.G146E	AGGCCCCCCAGGA	.	PASS	Atlas-SNP
PCDHGA9	56107	hgsc.bcm.edu	37	5	140783596	140783596	+	Silent	SNP	C	C	T	rs1363448	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	195	194	0	1	0	C|0.540;T|0.460	0.460	strong	.	PCDHGA9	110	.	NM_032089	exon1	c.C1077T	p.D359D	AGAAGACGCACCT	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	rs117943885	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	33	66	0	0.423077	0	C|0.984;T|0.016	0.016	strong	.	RADIL	110	.	NM_018059	exon12	c.G2512A	p.V838M	GGACCACGTGGTG	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144944225	144944225	+	Missense_Mutation	SNP	C	C	T	rs118079568	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	90	154	0	0.538922	0	C|0.990;T|0.010	0.010	strong	.	EPPK1	199	.	NM_031308	exon1	c.G3197A	p.R1066H	TAGCCACGCTGAA	.	PASS	Atlas-SNP
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362179	105362179	+	Silent	SNP	G	G	A	rs3740473	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	43	115	0	0.467391	0	G|0.894;A|0.106	0.106	strong	.	SH3PXD2A	90	.	NM_014631	exon14	c.C2712T	p.R904R	TTGGACGCGCCTC	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209796329	209796329	+	Missense_Mutation	SNP	T	T	A	rs12748250	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	37	78	0	0.445783	0	T|0.890;A|0.110	0.110	strong	.	LAMB3	136	.	NM_000228	exon17	c.A2554T	p.M852L	TTACCATCTGCCT	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43383680	43383680	+	Silent	SNP	G	G	T	rs1141653	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	5	34	0	0.333333	0	G|0.775;T|0.225	0.225	strong	.	PSG1	196	.	NM_001184826	exon1	c.C54A	p.L18L	GAGCAGGAGCCCC	.	PASS	Atlas-SNP
UBD	10537	hgsc.bcm.edu	37	6	29523952	29523952	+	Missense_Mutation	SNP	A	A	G	rs2076485	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	173	218	0	1	0	G|0.183;N|0.000	0.183	strong	UBD,caecum,carcinoma,0,1	UBD	13	1	NM_006398	exon2	c.T203C	p.I68T	TTGTCAATGCCAT	.	PASS	Atlas-SNP
MYRIP	25924	hgsc.bcm.edu	37	3	40231810	40231810	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	86	146	0	0.462366	0	.	.	none	.	MYRIP	98	.	NM_015460	exon10	c.C1521T	p.T507T	GGAGACCTCGGAC	.	PASS	Atlas-SNP
PRPF4B	8899	hgsc.bcm.edu	37	6	4031998	4031998	+	Missense_Mutation	SNP	A	A	G	rs9503893	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	187	222	0	1	0	A|0.296;G|0.704	0.704	strong	.	PRPF4B	140	.	NM_003913	exon2	c.A247G	p.I83V	AAAGAGATTATTG	.	PASS	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204237416	204237416	+	Missense_Mutation	SNP	C	C	T	rs10900571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	56	52	0	1	0	C|0.359;T|0.641	0.641	strong	PLEKHA6,NS,adenoma,0,1	PLEKHA6	115	1	NM_014935	exon4	c.G127A	p.V43I	AGGCGACGGCTTT	.	PASS	Atlas-SNP
OR10Z1	128368	hgsc.bcm.edu	37	1	158577167	158577167	+	Silent	SNP	A	A	T	rs2427808	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	39	86	0	0.534247	0	A|0.898;T|0.102	0.102	strong	.	OR10Z1	99	.	NM_001004478	exon1	c.A939T	p.G313G	TAAAGGATGAAGG	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34725047	34725047	+	Silent	SNP	C	C	T	rs78716275	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	360	126	369	0	0.35	0	T|1.000;|0.000	1.000	weak	.	FAM205A	45	.	NM_001141917	exon4	c.G2190A	p.P730P	CAGGTCCGGGTCA	.	PASS	Atlas-SNP
ZNF416	55659	hgsc.bcm.edu	37	19	58084930	58084930	+	Silent	SNP	G	G	A	rs3746222	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	91	130	0	0.575949	0	G|0.828;A|0.172	0.172	strong	.	ZNF416	50	.	NM_017879	exon4	c.C342T	p.T114T	AATGTCGGTCAGG	.	PASS	Atlas-SNP
TM4SF20	79853	hgsc.bcm.edu	37	2	228243905	228243905	+	Missense_Mutation	SNP	G	G	A	rs7574414	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	52	91	1	0.525253	0.010989	G|0.889;A|0.111	0.111	strong	TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	NM_024795	exon1	c.C80T	p.A27V	GGTATCGCATTGA	.	scavenged	Atlas-SNP
VEPH1	79674	hgsc.bcm.edu	37	3	157034921	157034921	+	Missense_Mutation	SNP	C	C	T	rs145883418	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	62	127	0	0.442857	0	C|0.999;T|0.001	0.001	strong	.	VEPH1	129	.	NM_001167911	exon10	c.G1805A	p.S602N	GACTTACTGTATA	.	PASS	Atlas-SNP
VCX2	51480	hgsc.bcm.edu	37	X	8138165	8138165	+	Missense_Mutation	SNP	C	C	G	rs1058237	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	82	118	0	0.911111	0	C|0.349;G|0.651	0.651	strong	.	VCX2	16	.	NM_016378	exon3	c.G328C	p.V110L	CTTCCACCTCGCT	.	PASS	Atlas-SNP
CLEC11A	6320	hgsc.bcm.edu	37	19	51228634	51228634	+	Silent	SNP	G	G	A	rs11084024	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	25	27	0	0.409836	0	G|0.808;A|0.192	0.192	strong	.	CLEC11A	23	.	NM_002975	exon4	c.G882A	p.E294E	GCTCGAGAACTGC	.	PASS	Atlas-SNP
ASTE1	28990	hgsc.bcm.edu	37	3	130743812	130743812	+	Silent	SNP	G	G	A	rs35558913	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	53	118	0	0.449153	0	G|0.817;A|0.183	0.183	strong	.	ASTE1	67	.	NM_014065	exon3	c.C339T	p.Y113Y	ACATACGTACCCA	.	PASS	Atlas-SNP
KRT25	147183	hgsc.bcm.edu	37	17	38911327	38911327	+	Missense_Mutation	SNP	C	C	G	rs35076248	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	60	125	0	0.508475	0	C|0.849;G|0.151	0.151	strong	.	KRT25	63	.	NM_181534	exon1	c.G197C	p.G66A	GTGAAGCCAGCAC	.	PASS	Atlas-SNP
CLDN8	9073	hgsc.bcm.edu	37	21	31587793	31587793	+	Missense_Mutation	SNP	A	A	G	rs686364	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	70	121	0	0.518519	0	T|0.003;G|0.402	0.402	strong	.	CLDN8	40	.	NM_199328	exon1	c.T451C	p.S151P	CTATTGAGTTATA	.	PASS	Atlas-SNP
ADCY1	107	hgsc.bcm.edu	37	7	45753324	45753324	+	Silent	SNP	G	G	A	rs2293106	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	45	87	0	0.529412	0	G|0.797;A|0.203	0.203	strong	.	ADCY1	187	.	NM_021116	exon20	c.G3090A	p.R1030R	GAGAAGGTGCCCC	.	PASS	Atlas-SNP
FAIM	55179	hgsc.bcm.edu	37	3	138329862	138329862	+	Silent	SNP	G	G	A	rs811322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	96	142	0	0.432432	0	A|0.616;C|0.002	0.616	strong	.	FAIM	27	.	NM_001033030	exon2	c.G63A	p.P21P	ATCTCCGGACTCT	.	PASS	Atlas-SNP
POLR1D	51082	hgsc.bcm.edu	37	13	28239838	28239838	+	Silent	SNP	T	T	C	rs41291678	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	80	152	0	0.5	0	T|0.965;C|0.035	0.035	strong	.	POLR1D	31	.	NM_152705	exon3	c.T117C	p.L39L	TCCTCTTGCTAGC	.	PASS	Atlas-SNP
DPYD	1806	hgsc.bcm.edu	37	1	97981395	97981395	+	Missense_Mutation	SNP	T	T	C	rs1801159	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	36	80	0	0.439024	0	T|0.802;C|0.198	0.198	strong	.	DPYD	219	.	NM_000110	exon13	c.A1627G	p.I543V	GATTTATAAACTT	.	PASS	Atlas-SNP
ABCC12	94160	hgsc.bcm.edu	37	16	48139232	48139232	+	Nonsense_Mutation	SNP	G	G	A	rs151150316	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	25	42	0	0.641026	0	G|0.998;A|0.002	0.002	strong	.	ABCC12	190	.	NM_033226	exon19	c.C2491T	p.Q831X	TGCCCTGGGGCCC	.	PASS	Atlas-SNP
DGCR2	9993	hgsc.bcm.edu	37	22	19026613	19026613	+	Missense_Mutation	SNP	A	A	G	rs2072123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	52	128	0	0.477064	0	T|0.004;G|0.408	0.408	strong	.	DGCR2	45	.	NM_005137	exon10	c.T1418C	p.V473A	ACCTCCACAGGCT	.	PASS	Atlas-SNP
FASN	2194	hgsc.bcm.edu	37	17	80044211	80044211	+	Silent	SNP	G	G	A	rs41283365	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	56	116	0	0.509091	0	G|0.885;A|0.115	0.115	strong	.	FASN	154	.	NM_004104	exon22	c.C3651T	p.G1217G	CAGGAGGCCGCTG	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23811800	23811800	+	Missense_Mutation	SNP	G	G	T	rs10247878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	122	123	0	1	0	G|0.876;T|0.124	0.124	strong	.	STK31	175	.	NM_031414	exon15	c.G1868T	p.S623I	ATAAGAGTCCCAG	.	PASS	Atlas-SNP
TMEM244	253582	hgsc.bcm.edu	37	6	130152520	130152520	+	Missense_Mutation	SNP	A	A	C	rs7776426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	13	224	0	0.0878378	0	A|0.663;C|0.337	0.337	strong	.	.	.	.	NM_001010876	exon5	c.T331G	p.F111V	AGGGGAATTCCAA	.	PASS	Atlas-SNP
ZNF70	7621	hgsc.bcm.edu	37	22	24086107	24086107	+	Silent	SNP	A	A	G	rs5759985	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	98	182	0	0.510417	0	A|0.481;G|0.519	0.519	strong	ZNF70,NS,carcinoma,-1,1	ZNF70	49	1	NM_021916	exon2	c.T1221C	p.I407I	GTGCTCAATGAGG	.	PASS	Atlas-SNP
DNAH17	8632	hgsc.bcm.edu	37	17	76421443	76421443	+	Silent	SNP	G	G	A	rs1134541	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	41	77	0	0.482353	0	G|0.885;A|0.115	0.115	strong	.	DNAH17	347	.	NM_173628	exon80	c.C13125T	p.Y4375Y	GAGTCCGTACACG	.	PASS	Atlas-SNP
SLC5A12	159963	hgsc.bcm.edu	37	11	26705310	26705310	+	Silent	SNP	A	A	G	rs3924551	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	41	53	0	1	0	A|0.542;G|0.458	0.458	strong	SLC5A12,NS,carcinoma,0,1	SLC5A12	134	1	NM_178498	exon11	c.T1302C	p.N434N	CTTCCAATTCACA	.	PASS	Atlas-SNP
MYO16	23026	hgsc.bcm.edu	37	13	109707827	109707827	+	Silent	SNP	T	T	C	rs9521141	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	64	211	0	0.5	0	T|0.910;C|0.090	0.090	strong	MYO16,NS,carcinoma,0,1	MYO16	285	1	NM_001198950	exon27	c.T3219C	p.D1073D	GCCAGATACTTTT	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25052393	25052393	+	Missense_Mutation	SNP	G	G	T	rs79107024	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	44	98	0	0.252874	0	G|0.874;T|0.126	0.126	strong	.	PARP4	142	.	NM_006437	exon13	c.C1470A	p.H490Q	TCCCGGGTGTGAG	.	PASS	Atlas-SNP
PSME2	5721	hgsc.bcm.edu	37	14	24615435	24615435	+	Silent	SNP	T	T	C	rs4575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	29	57	0	0.517857	0	T|0.531;C|0.469	0.469	strong	.	PSME2	21	.	NM_002818	exon2	c.A63G	p.R21R	ATTCTGTCTGAAG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632714	32632714	+	Silent	SNP	G	G	C	rs3210148	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	33	0	0	1	.	G|0.427;C|0.573	0.573	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.C240G	p.R80R	CACCGCGCGGTAC	.	PASS	Atlas-SNP
OR1N1	138883	hgsc.bcm.edu	37	9	125289521	125289521	+	Missense_Mutation	SNP	G	G	A	rs13287449	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	57	104	0	0.542857	0	.	.	alt	.	OR1N1	38	.	NM_012363	exon1	c.C52T	p.P18S	CTGGAGGCGCTGA	.	PASS	Atlas-SNP
GUCY1B3	2983	hgsc.bcm.edu	37	4	156721198	156721198	+	Silent	SNP	C	C	T	rs2229202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	66	61	0	1	0	C|0.851;T|0.149	0.149	strong	GUCY1B3,NS,carcinoma,0,1	GUCY1B3	65	1	NM_000857	exon9	c.C1147T	p.L383L	AGAGCCCTGGAAG	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39261784	39261784	+	Silent	SNP	C	C	A	rs8002488	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	38	36	0	0.575758	0	C|0.944;A|0.056	0.056	strong	.	FREM2	385	.	NM_207361	exon1	c.C303A	p.P101P	GCAGCCCGGGGAC	.	PASS	Atlas-SNP
SYTL1	84958	hgsc.bcm.edu	37	1	27680292	27680292	+	Silent	SNP	A	A	G	rs8533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	223	205	0	1	0	A|0.367;G|0.633	0.633	strong	.	SYTL1	57	.	NM_001193308	exon15	c.A1638G	p.E546E	GTGCGAATGGGTG	.	PASS	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	37	17	32953258	32953258	+	Silent	SNP	G	G	A	rs4795954	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	35	38	0	0.492958	0	G|0.870;A|0.130	0.130	strong	.	TMEM132E	122	.	NM_207313	exon2	c.G180A	p.E60E	GCGGGAGGCGCGG	.	PASS	Atlas-SNP
CLCN3	1182	hgsc.bcm.edu	37	4	170634390	170634390	+	Silent	SNP	C	C	T	rs1058868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	82	153	1	0.532468	0.00653595	C|0.879;T|0.121	0.121	strong	CLCN3,NS,carcinoma,+1,2	CLCN3	85	2	NM_001829	exon12	c.C2310T	p.I770I	GGAGATCGTGGTG	.	scavenged	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	37	3	73433369	73433369	+	Missense_Mutation	SNP	G	G	A	rs3205537	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	35	66	0	0.583333	0	G|0.729;A|0.271	0.271	strong	.	PDZRN3	196	.	NM_015009	exon10	c.C2348T	p.A783V	CCCTCCGCCGCTC	.	PASS	Atlas-SNP
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	30	73	0	0.357143	0	G|0.466;A|0.534	0.534	strong	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	NM_017617	exon27	c.C5094T	p.D1698D	GGCCACGTCGGTG	.	PASS	Atlas-SNP
SLC39A12	221074	hgsc.bcm.edu	37	10	18254606	18254606	+	Silent	SNP	C	C	A	rs691513	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	67	70	0	0.971014	0	C|0.672;A|0.328	0.328	strong	.	SLC39A12	181	.	NM_152725	exon4	c.C738A	p.T246T	GAATACCCTCCGC	.	PASS	Atlas-SNP
ZDHHC11	79844	hgsc.bcm.edu	37	5	843723	843723	+	Missense_Mutation	SNP	C	C	A	rs71273553		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	502	132	372	0	0.262948	0	C|0.500;A|0.500	0.500	weak	ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	NM_024786	exon4	c.G620T	p.R207M	TCATACCTGGGGT	.	PASS	Atlas-SNP
OR51F1	256892	hgsc.bcm.edu	37	11	4790575	4790575	+	Silent	SNP	A	A	G	rs12788102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	118	200	0	0.578431	0	A|0.911;G|0.089	0.089	strong	.	OR51F1	60	.	NM_001004752	exon1	c.T573C	p.C191C	GTCTGAACATGCT	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130124989	130124989	+	Silent	SNP	C	C	T	rs4688761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	158	164	0	0.981366	0	C|0.577;T|0.423	0.423	strong	.	COL6A5	205	.	NM_153264	exon16	c.C4395T	p.D1465D	TGGAGACGATGGG	.	PASS	Atlas-SNP
CPB1	1360	hgsc.bcm.edu	37	3	148575250	148575250	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	56	130	0	0.444444	0	.	.	none	.	CPB1	74	.	NM_001871	exon10	c.C988T	p.L330L	AATGCCCTGGCTA	.	PASS	Atlas-SNP
FAAH2	158584	hgsc.bcm.edu	37	X	57313357	57313357	+	Silent	SNP	T	T	C	rs2516023	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	110	113	1	1	0.00884956	0|0.003;C|0.507	0.507	strong	.	FAAH2	66	.	NM_174912	exon1	c.T99C	p.G33G	AGGGGGTCCAAAG	.	PASS	Atlas-SNP
RBL2	5934	hgsc.bcm.edu	37	16	53503934	53503934	+	Silent	SNP	G	G	A	rs1131220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	149	134	0	0.980263	0	G|0.461;A|0.539	0.539	strong	.	RBL2	115	.	NM_005611	exon15	c.G2082A	p.T694T	AGGGACGCCTGGG	.	PASS	Atlas-SNP
YAE1D1	57002	hgsc.bcm.edu	37	7	39606107	39606107	+	Silent	SNP	G	G	A	rs1051162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	28	50	1	0.424242	0.02	G|0.842;A|0.158	0.158	strong	C7orf36,NS,carcinoma,0,1	YAE1D1	2	1	NM_020192	exon1	c.G90A	p.A30A	CCTGGCGCAGCGG	.	scavenged	Atlas-SNP
PLA2G5	5322	hgsc.bcm.edu	37	1	20417066	20417066	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	65	134	0	0.373563	0	.	.	none	.	PLA2G5	21	.	NM_000929	exon5	c.G298A	p.G100R	GAGCCCGGGCCCT	.	PASS	Atlas-SNP
NAT6	24142	hgsc.bcm.edu	37	3	50334568	50334568	+	Silent	SNP	G	G	A	rs199554290	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	66	91	0	0.584071	0	G|0.997;A|0.003	0.003	weak	.	NAT6	14	.	NM_012191	exon2	c.C393T	p.S131S	GTGGGGGCTTAGC	.	PASS	Atlas-SNP
APBA3	9546	hgsc.bcm.edu	37	19	3753874	3753874	+	Silent	SNP	G	G	A	rs34868972	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	18	20	0	0.461538	0	G|0.908;A|0.092	0.092	strong	.	APBA3	28	.	NM_004886	exon6	c.C900T	p.I300I	GCAGCCGATGTCG	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27197368	27197368	+	Silent	SNP	T	T	C	rs35357088	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	47	84	0	0.447619	0	T|0.951;C|0.049	0.049	strong	.	TEK	250	.	NM_000459	exon12	c.T1680C	p.N560N	TCTAAATTTGACC	.	PASS	Atlas-SNP
TFAP2D	83741	hgsc.bcm.edu	37	6	50682935	50682935	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	10	196	0	0.0485437	0	.	.	none	.	TFAP2D	144	.	NM_172238	exon2	c.C146G	p.S49C	CTTACTCCACCAC	.	PASS	Atlas-SNP
RNH1	6050	hgsc.bcm.edu	37	11	494942	494942	+	Silent	SNP	G	G	C	rs7983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	77	137	0	0.401042	0	G|0.627;C|0.373	0.373	strong	.	RNH1	24	.	NM_203384	exon9	c.C1239G	p.A413A	GATGCCGGCGTCC	.	PASS	Atlas-SNP
GABBR1	2550	hgsc.bcm.edu	37	6	29581041	29581041	+	Silent	SNP	A	A	G	rs29225	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	35	109	0	0.321101	0	A|0.902;G|0.098	0.098	strong	.	GABBR1	95	.	NM_001470	exon12	c.T1545C	p.S515S	GGACGAAGAGTTC	.	PASS	Atlas-SNP
PCDHB6	56130	hgsc.bcm.edu	37	5	140531746	140531746	+	Missense_Mutation	SNP	C	C	G	rs246703	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	38	28	0	1	0	C|0.397;G|0.603	0.603	strong	.	PCDHB6	161	.	NM_018939	exon1	c.C1908G	p.H636Q	CAAGCACAGGCTG	.	PASS	Atlas-SNP
DEK	7913	hgsc.bcm.edu	37	6	18264210	18264210	+	Silent	SNP	G	G	A	rs11544757	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	21	39	0	0.512195	0	G|0.838;C|0.000;A|0.162	0.162	strong	.	DEK	31	.	NM_003472	exon2	c.C9T	p.A3A	GGCCGAGGCGGAC	.	PASS	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100991430	100991430	+	Missense_Mutation	SNP	C	C	A	rs1573025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	51	144	0	0.451327	0	C|0.837;A|0.163	0.163	strong	TBC1D2,mouth,carcinoma,+1,1	TBC1D2	70	1	NM_001267571	exon5	c.G782T	p.G261V	TCTCTCCCTGCTC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228437757	228437757	+	Silent	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	258	95	290	1	0.368217	0.00344828	.	.	none	.	OBSCN	2142	.	NM_001271223	exon15	c.C4401A	p.A1467A	GGTGGCCCAGGCC	.	PASS	Atlas-SNP
CCDC154	645811	hgsc.bcm.edu	37	16	1484791	1484791	+	Silent	SNP	C	C	T	rs7192233	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	49	61	0	0.515789	0	C|0.911;T|0.089	0.089	strong	.	CCDC154	27	.	NM_001143980	exon16	c.G1755A	p.P585P	CGTCCGCGGGCCC	.	PASS	Atlas-SNP
BTN3A1	11119	hgsc.bcm.edu	37	6	26405835	26405835	+	Missense_Mutation	SNP	G	G	A	rs56161420	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	225	116	234	0	0.515556	0	G|0.835;A|0.165	0.165	strong	BTN3A1_ENST00000476549,NS,carcinoma,0,4	BTN3A1	80	4	NM_007048	exon2	c.G44A	p.R15H	ACTTTCGTGTCTG	.	PASS	Atlas-SNP
CNDP2	55748	hgsc.bcm.edu	37	18	72176083	72176083	+	Missense_Mutation	SNP	T	T	C	rs2278161	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	42	93	0	0.428571	0	T|0.801;C|0.198	0.198	strong	CNDP2,NS,carcinoma,0,1	CNDP2	55	1	NM_018235	exon5	c.T376C	p.Y126H	AAGCTGTATGGGA	.	PASS	Atlas-SNP
AZGP1	563	hgsc.bcm.edu	37	7	99569394	99569394	+	Silent	SNP	G	G	A	rs17295356	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	61	115	0	0.458647	0	G|0.657;A|0.343	0.343	strong	.	AZGP1	41	.	NM_001185	exon2	c.C312T	p.I104I	CTCCACGATGTCT	.	PASS	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	44983567	44983567	+	Missense_Mutation	SNP	C	C	G	rs2253563	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	50	105	0	0.49505	0	C|0.508;G|0.492	0.492	strong	.	ZNF180	103	.	NM_013256	exon4	c.G267C	p.W89C	AGGGTTCCAAGTA	.	PASS	Atlas-SNP
LARS2	23395	hgsc.bcm.edu	37	3	45557707	45557707	+	Silent	SNP	G	G	A	rs11549809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	49	110	0	0.49	0	G|0.727;A|0.273	0.273	strong	.	LARS2	48	.	NM_015340	exon17	c.G1983A	p.T661T	CGACACGATTCGG	.	PASS	Atlas-SNP
KCNJ16	3773	hgsc.bcm.edu	37	17	68128417	68128417	+	Silent	SNP	C	C	T	rs34408089	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	69	149	0	0.50365	0	C|0.976;T|0.024	0.024	strong	.	KCNJ16	72	.	NM_001270422	exon6	c.C189T	p.T63T	CTTCACCACTCTT	.	PASS	Atlas-SNP
DDX60L	91351	hgsc.bcm.edu	37	4	169299528	169299528	+	Missense_Mutation	SNP	T	T	C	rs13110927	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	88	181	0	0.475676	0	T|0.533;C|0.467	0.467	strong	.	DDX60L	116	.	NM_001012967	exon33	c.A4462G	p.N1488D	TTAAATTAGCATT	.	PASS	Atlas-SNP
PLCB1	23236	hgsc.bcm.edu	37	20	8737734	8737734	+	Silent	SNP	G	G	A	rs2076413	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	42	81	0	0.42	0	G|0.773;A|0.227	0.227	strong	.	PLCB1	394	.	NM_015192	exon24	c.T2565A	p.P855P	TGAAGCGAGAACG	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362703	32362703	+	Missense_Mutation	SNP	G	G	T	rs41521946	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	37	151	0	0.349057	0	G|0.871;T|0.129	0.129	strong	.	BTNL2	50	.	NM_019602	exon6	c.C1178A	p.P393Q	CTCCATGGCACGT	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33717877	33717877	+	Silent	SNP	G	G	A	rs2833779	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	29	64	0	0.508772	0	G|0.822;A|0.178	0.178	strong	.	URB1	176	.	NM_014825	exon23	c.C3876T	p.S1292S	GACAGCGGAAGAC	.	PASS	Atlas-SNP
ZNF683	257101	hgsc.bcm.edu	37	1	26691174	26691174	+	Missense_Mutation	SNP	C	C	A	rs11247933	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	85	105	0	0.913979	0	C|0.728;A|0.272	0.272	strong	.	ZNF683	51	.	NM_173574	exon4	c.G863T	p.R288L	CCACCACGCTCCA	.	PASS	Atlas-SNP
TLR6	10333	hgsc.bcm.edu	37	4	38830012	38830012	+	Silent	SNP	G	G	C	rs3821985	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	47	91	0	0.580247	0	G|0.583;C|0.417	0.417	strong	.	TLR6	67	.	NM_006068	exon2	c.C1083G	p.T361T	GTTCTGGGTAAAG	.	PASS	Atlas-SNP
KRT6B	3854	hgsc.bcm.edu	37	12	52844265	52844265	+	Missense_Mutation	SNP	T	T	C	rs652423	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	360	129	277	0	0.358333	0	T|0.604;C|0.396	0.396	strong	.	KRT6B	90	.	NM_005555	exon2	c.A680G	p.N227S	ACGATGTTGTCCA	.	PASS	Atlas-SNP
POU5F1B	5462	hgsc.bcm.edu	37	8	128428751	128428751	+	Missense_Mutation	SNP	A	A	G	rs71520669	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	100	150	0	0.549451	0	A|0.856;G|0.144	0.144	strong	.	POU5F1B	32	.	NM_001159542	exon1	c.A640G	p.N214D	GACAACAATGAAA	.	PASS	Atlas-SNP
OGG1	4968	hgsc.bcm.edu	37	3	9798773	9798773	+	Missense_Mutation	SNP	C	C	G	rs1052134	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	46	81	0	0.494624	0	C|1.000;|0.000	.	weak	.	OGG1	57	.	NM_016820	exon7	c.C994G	p.P332A	GCCAATCCCGCCA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1896059	1896059	+	Missense_Mutation	SNP	G	G	A	rs115287948	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	32	362	0	0.151659	0	G|0.679;A|0.321	0.321	strong	SIRPA,caecum,carcinoma,0,2	SIRPA	83	2	NM_001040022	exon3	c.G394A	p.V132M	GATGACGTGGAGT	.	PASS	Atlas-SNP
RHCE	6006	hgsc.bcm.edu	37	1	25717365	25717365	+	Missense_Mutation	SNP	C	C	G	rs609320	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	179	184	0	0.913265	0	C|0.855;G|0.145	0.145	strong	.	RHCE	36	.	NM_138618	exon5	c.G676C	p.A226P	GCAGAGCAGAGTT	.	PASS	Atlas-SNP
GPR116	221395	hgsc.bcm.edu	37	6	46826979	46826979	+	Silent	SNP	A	A	G	rs9381487	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	67	145	0	0.475177	0	A|0.733;G|0.267	0.267	strong	.	GPR116	133	.	NM_015234	exon17	c.T2661C	p.Y887Y	TTCTAGATAGCTC	.	PASS	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31476458	31476458	+	Missense_Mutation	SNP	C	C	T	rs11150624	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	33	84	1	0.458333	0.0119048	C|0.636;T|0.364	0.364	strong	ARMC5_ENST00000457010,brain,glioma,0,1	ARMC5	94	1	NM_024742	exon4	c.C2114T	p.A705V	GCCCCGCGCCCAG	.	scavenged	Atlas-SNP
SYNE1	23345	hgsc.bcm.edu	37	6	152443744	152443744	+	Missense_Mutation	SNP	G	G	T	rs2295190	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	7	81	0	0.132075	0	G|0.898;T|0.102	0.102	strong	.	SYNE1	3227	.	NM_182961	exon146	c.C26221A	p.L8741M	TGAACAGGAAGCC	.	PASS	Atlas-SNP
TOMM40	10452	hgsc.bcm.edu	37	19	45395714	45395714	+	Silent	SNP	T	T	C	rs157581	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	40	79	0	0.430108	0	T|0.698;C|0.302	0.302	strong	.	TOMM40	13	.	NM_001128917	exon2	c.T339C	p.F113F	CCATTTTCAGGTG	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	37	11	76924066	76924066	+	Missense_Mutation	SNP	G	G	A	rs1132036	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	23	86	1	0.343284	0.0116279	G|0.966;A|0.034	0.034	strong	MYO7A,rectum,carcinoma,0,1	MYO7A	164	1	NM_000260	exon47	c.G6424A	p.D2142N	CTCATCGATCCCA	.	scavenged	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301787	65301787	+	Missense_Mutation	SNP	G	G	C	rs12663622	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	49	106	0	1	0	G|0.905;C|0.095	0.095	strong	EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	1	NM_001142800	exon26	c.C3973G	p.Q1325E	GTTCTTGGAGTAA	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	37	19	38991516	38991516	+	Silent	SNP	G	G	A	rs2228072	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	58	127	0	0.4	0	A|0.101;G|0.899	0.101	strong	.	RYR1	708	.	NM_001042723	exon47	c.G7500A	p.A2500A	CAAGGCGTCCATG	.	PASS	Atlas-SNP
LIPN	643418	hgsc.bcm.edu	37	10	90524237	90524237	+	Silent	SNP	T	T	C	rs430517	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	31	89	0	0.418919	0	T|0.738;C|0.262	0.262	strong	.	LIPN	28	.	NM_001102469	exon3	c.T297C	p.A99A	TTATGCTAATGGA	.	PASS	Atlas-SNP
F11	2160	hgsc.bcm.edu	37	4	187195373	187195373	+	Silent	SNP	C	C	T	rs5973	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	94	169	0	0.474747	0	C|0.938;T|0.062	0.062	strong	.	F11	65	.	NM_000128	exon5	c.C429T	p.D143D	GGATGACGTCCAC	.	PASS	Atlas-SNP
KANSL1	284058	hgsc.bcm.edu	37	17	44109474	44109474	+	Missense_Mutation	SNP	G	G	A	rs7220988	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	38	75	0	0.481013	0	G|0.694;A|0.306	0.306	strong	.	.	.	.	NM_001193466	exon14	c.C3029T	p.P1010L	TGTCGCGGAGTGT	.	PASS	Atlas-SNP
MICAL2	9645	hgsc.bcm.edu	37	11	12248590	12248590	+	Missense_Mutation	SNP	A	A	G	rs35228638	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	51	130	0	0.41129	0	A|0.992;G|0.008	0.008	strong	.	MICAL2	114	.	NM_014632	exon15	c.A1907G	p.Y636C	AAAACTATGGAGA	.	PASS	Atlas-SNP
NDST1	3340	hgsc.bcm.edu	37	5	149919739	149919739	+	Silent	SNP	G	G	C	rs1290147	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	125	132	0	0.992063	0	G|0.238;C|0.762	0.762	strong	NDST1,NS,carcinoma,+1,1	NDST1	79	1	NM_001543	exon8	c.G1662C	p.T554T	CTGGACGAACCTC	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921110	12921110	+	Missense_Mutation	SNP	A	A	G	rs12139546	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	6	156	0	0.0451128	0	A|0.887;G|0.113	0.113	strong	PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	NM_023014	exon4	c.A901G	p.T301A	GAATTAACTTGTG	.	PASS	Atlas-SNP
AKAP12	9590	hgsc.bcm.edu	37	6	151674270	151674270	+	Missense_Mutation	SNP	G	G	A	rs34713284	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	8	61	0	0.145455	0	G|0.924;A|0.076	0.076	strong	.	AKAP12	170	.	NM_005100	exon4	c.G4744A	p.V1582M	GCTCACGTGATAA	.	PASS	Atlas-SNP
COL3A1	1281	hgsc.bcm.edu	37	2	189864582	189864582	+	Silent	SNP	T	T	C	rs1801184	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	169	222	0	0.994118	0	T|0.738;C|0.262	0.262	strong	.	COL3A1	292	.	NM_000090	exon32	c.T2244C	p.G748G	AGGCGGTCCAGGT	.	PASS	Atlas-SNP
NPBWR1	2831	hgsc.bcm.edu	37	8	53852871	53852871	+	Missense_Mutation	SNP	A	A	T	rs33977775	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	24	31	0	0.421053	0	A|0.907;T|0.093	0.093	strong	.	NPBWR1	38	.	NM_005285	exon1	c.A404T	p.Y135F	ACCGCTACCTGGT	.	PASS	Atlas-SNP
WDR52	55779	hgsc.bcm.edu	37	3	113145006	113145006	+	Silent	SNP	C	C	T	rs73239107	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	93	180	0	0.484375	0	C|0.832;T|0.168	0.168	strong	.	WDR52	151	.	NM_001164496	exon4	c.G372A	p.L124L	TGAATCCAGAGTC	.	PASS	Atlas-SNP
VWA3A	146177	hgsc.bcm.edu	37	16	22137603	22137603	+	Missense_Mutation	SNP	G	G	A	rs55732851	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	71	114	0	0.493056	0	G|0.908;A|0.092	0.092	strong	.	VWA3A	115	.	NM_173615	exon17	c.G1637A	p.C546Y	AGGACTGTTTCAA	.	PASS	Atlas-SNP
SCN1B	6324	hgsc.bcm.edu	37	19	35524944	35524944	+	Missense_Mutation	SNP	G	G	C	rs67486287	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	238	115	216	0	0.483193	0	G|0.870;C|0.130	0.130	strong	.	SCN1B	32	.	NM_199037	exon3	c.G749C	p.R250T	GCCAAAGGGTTGT	.	PASS	Atlas-SNP
ALDH1A1	216	hgsc.bcm.edu	37	9	75545882	75545882	+	Silent	SNP	G	G	A	rs13959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	37	101	0	0.445783	0	G|0.598;A|0.402	0.402	strong	.	ALDH1A1	98	.	NM_000689	exon3	c.C225T	p.S75S	CCACGGGGATCCA	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	37	5	140605078	140605078	+	Silent	SNP	C	C	T	rs2907322	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	12	18	0	0.8	0	C|0.835;T|0.165	0.165	strong	.	PCDHB14	132	.	NM_018934	exon1	c.C2001T	p.S667S	CTTCTCCCAGCCC	.	PASS	Atlas-SNP
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821467	100821467	+	Silent	SNP	G	G	A	rs7496640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	15	11	0	0.517241	0	G|0.576;A|0.424	0.424	strong	ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	NM_139057	exon4	c.C756T	p.A252A	CTGGGCGGCCTCG	.	PASS	Atlas-SNP
LRRC16A	55604	hgsc.bcm.edu	37	6	25426768	25426768	+	Missense_Mutation	SNP	G	G	A	rs9358856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	241	117	169	0	0.485477	0	G|0.846;A|0.154	0.154	strong	.	LRRC16A	168	.	NM_001173977	exon4	c.G229A	p.V77I	GGCGTCGTTTGCA	.	PASS	Atlas-SNP
PLA2G7	7941	hgsc.bcm.edu	37	6	46679303	46679303	+	Missense_Mutation	SNP	A	A	G	rs1805018	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	60	150	0	0.405405	0	A|0.878;G|0.122	0.122	strong	.	PLA2G7	49	.	NM_005084	exon7	c.T593C	p.I198T	TCCCCTATTTCTG	.	PASS	Atlas-SNP
FAM221B	392307	hgsc.bcm.edu	37	9	35826058	35826058	+	Missense_Mutation	SNP	T	T	C	rs13294256	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	29	80	0	0.39726	0	T|0.764;C|0.236	0.236	strong	.	FAM221B	38	.	NM_001012446	exon2	c.A101G	p.H34R	GAGATATGGTTCT	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121616250	121616250	+	Silent	SNP	G	G	A	rs4629793	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	45	82	0	0.918367	0	G|0.681;A|0.319	0.319	strong	.	PTPRZ1	605	.	NM_001206838	exon5	c.G480A	p.A160A	TGATGCGGACCGA	.	PASS	Atlas-SNP
ACOX2	8309	hgsc.bcm.edu	37	3	58517520	58517520	+	Silent	SNP	A	A	G	rs57216393	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	28	57	0	0.528302	0	A|0.923;G|0.077	0.077	strong	.	ACOX2	53	.	NM_003500	exon6	c.T603C	p.H201H	CAGGGCATGGGTG	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	143534	143534	+	Missense_Mutation	SNP	G	G	A	rs13436090	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	33	70	1	0.37931	0.0142857	G|0.819;A|0.181	0.181	strong	PLEKHG4B_ENST00000283426,NS,carcinoma,0,1	PLEKHG4B	167	1	NM_052909	exon3	c.G659A	p.R220H	AGGTCCGCACCAG	.	scavenged	Atlas-SNP
CLCA2	9635	hgsc.bcm.edu	37	1	86909493	86909493	+	Silent	SNP	C	C	T	rs2390059	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	36	89	0	0.473684	0	T|0.113;G|0.000;C|0.887	0.113	strong	.	CLCA2	102	.	NM_006536	exon10	c.C1512T	p.V504V	AAATGTCAAACCT	.	PASS	Atlas-SNP
INADL	10207	hgsc.bcm.edu	37	1	62232130	62232130	+	Silent	SNP	T	T	C	rs11207827	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	27	82	0	0.36	0	T|0.727;C|0.273	0.273	strong	.	INADL	179	.	NM_176877	exon4	c.T369C	p.I123I	AGTCATTCAACAG	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227872182	227872182	+	Silent	SNP	G	G	A	rs2228557	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	52	123	0	0.416	0	G|0.540;A|0.460	0.460	strong	.	COL4A4	215	.	NM_000092	exon48	c.C4932T	p.F1644F	ATTTGCGAAAAAG	.	PASS	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	37	3	38674712	38674712	+	Silent	SNP	T	T	C	rs6599230	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	80	61	0	1	0	T|0.233;C|0.767	0.767	strong	.	SCN5A	634	.	NM_001160160	exon2	c.A87G	p.A29A	CTTCTCTGCCATG	.	PASS	Atlas-SNP
NOM1	64434	hgsc.bcm.edu	37	7	156762248	156762248	+	Missense_Mutation	SNP	G	G	A	rs12919	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	8	8	16	0	1	0	G|0.474;A|0.526	0.526	strong	NOM1,rectum,carcinoma,0,1	NOM1	73	1	NM_138400	exon11	c.G2434A	p.V812M	CTGGGGGTGTTAC	.	PASS	Atlas-SNP
PHLDA2	7262	hgsc.bcm.edu	37	11	2950558	2950558	+	Silent	SNP	A	A	G	rs13390	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	19	30	0	0.475	0	A|0.893;G|0.107	0.107	strong	PHLDA2,NS,carcinoma,0,1	PHLDA2	10	1	NM_003311	exon1	c.T37C	p.L13L	TCTCCAACTCGCC	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	37	2	51254901	51254901	+	Silent	SNP	G	G	A	rs1045874	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	76	84	0	0.466258	0	G|0.853;A|0.147	0.147	strong	NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	3	NM_004801	exon2	c.C511T	p.L171L	AGGCCAGGGTGAG	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592265	1592265	+	Silent	SNP	A	A	G	rs45471597	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	39	267	1	0.951219	0.00374532	A|0.417;G|0.583	0.583	strong	.	SIRPB1	83	.	NM_001135844	exon2	c.T171C	p.T57T	CAGGGAAGTCACA	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5042715	5042715	+	Missense_Mutation	SNP	G	G	A	rs61740308	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	34	75	0	0.425	0	G|0.881;A|0.119	0.119	strong	.	USP6	213	.	NM_004505	exon14	c.G1244A	p.C415Y	CGCCCTGTCCTGG	.	PASS	Atlas-SNP
DGKQ	1609	hgsc.bcm.edu	37	4	961397	961397	+	Silent	SNP	C	C	T	rs2305487	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	66	118	0	0.428571	0	T|0.037;G|0.000;C|0.963	0.037	strong	.	DGKQ	29	.	NM_001347	exon8	c.G927A	p.V309V	TCTTCTCACCGCG	.	PASS	Atlas-SNP
SVOPL	136306	hgsc.bcm.edu	37	7	138312122	138312122	+	Missense_Mutation	SNP	A	A	C	rs2305816	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	51	60	0	0.980769	0	A|0.433;C|0.567	0.567	strong	.	SVOPL	111	.	NM_001139456	exon11	c.T1154G	p.F385C	AGAAGGAAGAATA	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	37	7	103155864	103155864	+	Silent	SNP	A	A	G	rs56345626	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	74	68	0	1	0	A|0.829;G|0.171	0.171	strong	.	RELN	593	.	NM_173054	exon50	c.T7887C	p.P2629P	AGCATCAGGAGGG	.	PASS	Atlas-SNP
IQGAP3	128239	hgsc.bcm.edu	37	1	156526387	156526387	+	Missense_Mutation	SNP	C	C	G	rs11264498	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	133	103	0	0.977941	0	C|0.513;G|0.487	0.487	strong	.	IQGAP3	146	.	NM_178229	exon12	c.G1228C	p.V410L	GGTACACTGGAGG	.	PASS	Atlas-SNP
OR5AK2	390181	hgsc.bcm.edu	37	11	56757056	56757056	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	313	118	290	0	0.376997	0	.	.	none	.	OR5AK2	45	.	NM_001005323	exon1	c.C668T	p.A223V	TCATGGCCACCAT	.	PASS	Atlas-SNP
RNF43	54894	hgsc.bcm.edu	37	17	56435080	56435080	+	Missense_Mutation	SNP	G	G	C	rs9652855	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	64	87	0	0.576577	0	G|0.886;C|0.114	0.114	strong	RNF43,lower_third,carcinoma,+1,1	RNF43	157	1	NM_017763	exon9	c.C2057G	p.P686R	ACACTGGGGGTGT	.	PASS	Atlas-SNP
SPOCD1	90853	hgsc.bcm.edu	37	1	32280610	32280610	+	Missense_Mutation	SNP	T	T	C	rs6664445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	79	85	0	0.9875	0	C|0.680;N|0.001	0.680	strong	.	SPOCD1	109	.	NM_144569	exon2	c.A325G	p.T109A	CCTGAGTAGGCAC	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17250836	17250836	+	Silent	SNP	A	A	G	rs57174186	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	52	63	0	0.416	0	A|0.638;G|0.362	0.362	strong	CROCC,NS,carcinoma,0,3	CROCC	185	3	NM_014675	exon3	c.A213G	p.T71T	GGCCACAGAGATG	.	PASS	Atlas-SNP
ARMS2	387715	hgsc.bcm.edu	37	10	124214448	124214448	+	Missense_Mutation	SNP	G	G	T	rs10490924	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	74	163	0	0.448485	0	G|0.712;T|0.288	0.288	strong	.	ARMS2	7	.	NM_001099667	exon1	c.G205T	p.A69S	CCAGCTGCTAAAA	.	PASS	Atlas-SNP
OR10S1	219873	hgsc.bcm.edu	37	11	123848212	123848212	+	Missense_Mutation	SNP	C	C	T	rs17759513	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	29	55	0	0.557692	0	C|0.792;N|0.000	.	strong	.	OR10S1	78	.	NM_001004474	exon1	c.G187A	p.G63S	CAGAGCCCACAGT	.	PASS	Atlas-SNP
MAOA	4128	hgsc.bcm.edu	37	X	43603391	43603391	+	Silent	SNP	T	T	C	rs1137070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	96	84	0	0.989691	0	0|0.014;C|0.615	0.615	strong	.	MAOA	48	.	NM_000240	exon14	c.T1410C	p.D470D	GAAAGATATCTGG	.	PASS	Atlas-SNP
AGMAT	79814	hgsc.bcm.edu	37	1	15904318	15904318	+	Silent	SNP	C	C	T	rs11544523	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	87	106	0	0.915789	0	C|0.729;T|0.271	0.271	strong	.	AGMAT	25	.	NM_024758	exon5	c.G762A	p.S254S	AACCAGCGACTTC	.	PASS	Atlas-SNP
NASP	4678	hgsc.bcm.edu	37	1	46073361	46073361	+	Nonsense_Mutation	SNP	C	C	T	rs78094239	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	4	161	1	0.028169	0.00621118	C|0.980;T|0.020	0.020	strong	NASP,colon,carcinoma,-1,1	NASP	77	1	NM_002482	exon6	c.C778T	p.Q260X	GGAGGTCAGGAGA	.	scavenged	Atlas-SNP
TGM7	116179	hgsc.bcm.edu	37	15	43571390	43571390	+	Silent	SNP	C	C	G	rs567357	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	46	95	0	0.442308	0	C|0.491;G|0.509	0.509	strong	.	TGM7	86	.	NM_052955	exon11	c.G1764C	p.A588A	AACCTCCGCGATG	.	PASS	Atlas-SNP
CHIA	27159	hgsc.bcm.edu	37	1	111857208	111857208	+	Missense_Mutation	SNP	G	G	A	rs3818822	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	36	65	0	0.537313	0	G|0.888;A|0.112	0.112	strong	.	CHIA	115	.	NM_201653	exon5	c.G304A	p.G102R	AACTTCGGGACTG	.	PASS	Atlas-SNP
ZNF862	643641	hgsc.bcm.edu	37	7	149556518	149556518	+	Silent	SNP	C	C	T	rs4725833	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	34	56	0	1	0	C|0.427;T|0.573	0.573	strong	.	ZNF862	97	.	NM_001099220	exon6	c.C1125T	p.A375A	ACCTGCCGCTGCC	.	PASS	Atlas-SNP
SZT2	23334	hgsc.bcm.edu	37	1	43906896	43906896	+	Silent	SNP	A	A	G	rs2027130	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	83	90	0	1	0	A|0.698;G|0.302	0.302	strong	.	SZT2	383	.	NM_015284	exon52	c.A7185G	p.E2395E	AACAGAATGTGGG	.	PASS	Atlas-SNP
ACOX2	8309	hgsc.bcm.edu	37	3	58512237	58512237	+	Silent	SNP	A	A	G	rs1127745	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	55	139	0	0.387324	0	A|0.718;G|0.282	0.282	strong	.	ACOX2	53	.	NM_003500	exon10	c.T1302C	p.C434C	GTAGGTACAGGAG	.	PASS	Atlas-SNP
SBNO1	55206	hgsc.bcm.edu	37	12	123806219	123806219	+	Missense_Mutation	SNP	C	C	T	rs1060105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	290	152	265	1	0.524138	0.00377358	C|0.855;T|0.145	0.145	strong	.	SBNO1	138	.	NM_001167856	exon16	c.G2186A	p.S729N	TCAGAACTGCTAC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9088772	9088772	+	Missense_Mutation	SNP	T	T	C	rs17000950	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	84	162	0	0.528302	0	T|0.797;C|0.203	0.203	strong	.	MUC16	4315	.	NM_024690	exon1	c.A3043G	p.R1015G	GTTCCCTGATAGA	.	PASS	Atlas-SNP
ARHGAP9	64333	hgsc.bcm.edu	37	12	57873042	57873042	+	Missense_Mutation	SNP	T	T	C	rs33927108	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	43	96	0	0.467391	0	T|0.941;C|0.059	0.059	strong	.	ARHGAP9	79	.	NM_001080157	exon1	c.A148G	p.R50G	GGAACCTATCCCC	.	PASS	Atlas-SNP
SELPLG	6404	hgsc.bcm.edu	37	12	109017680	109017680	+	Missense_Mutation	SNP	T	T	G	rs200527674	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	22	175	1	0.136646	0.00571429	T|0.986;G|0.014	0.014	strong	SELPLG_ENST00000550948,NS,haematopoietic_neoplasm,0,1	SELPLG	138	1	NM_001206609	exon2	c.A452C	p.Q151P	ACTGGTTGAGTGG	.	scavenged	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36845738	36845738	+	Missense_Mutation	SNP	C	C	T	rs760998	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	73	103	1	0.565891	0.00970874	C|0.680;T|0.320	0.320	strong	KIAA1755,NS,carcinoma,0,1	KIAA1755	145	1	NM_001029864	exon13	c.G2818A	p.E940K	TCAGCTCAGCCTG	.	scavenged	Atlas-SNP
PLEKHA6	22874	hgsc.bcm.edu	37	1	204198209	204198209	+	Silent	SNP	A	A	G	rs3795571	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	89	95	0	1	0	A|0.469;G|0.531	0.531	strong	.	PLEKHA6	115	.	NM_014935	exon19	c.T2607C	p.H869H	TACCTCATGGATG	.	PASS	Atlas-SNP
AMACR	23600	hgsc.bcm.edu	37	5	34004707	34004707	+	Missense_Mutation	SNP	C	C	T	rs10941112	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	314	130	284	0	0.414013	0	C|0.655;T|0.345	0.345	strong	.	AMACR	38	.	NM_014324	exon3	c.G524A	p.G175D	CCCTTGCCAGTGC	.	PASS	Atlas-SNP
CHPF	79586	hgsc.bcm.edu	37	2	220404726	220404726	+	Silent	SNP	G	G	A	rs1043832	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	82	122	0	0.479532	0	G|0.620;C|0.000;A|0.380	0.380	strong	.	CHPF	56	.	NM_024536	exon4	c.C1707T	p.H569H	TGCCACGTGGGCC	.	PASS	Atlas-SNP
IFI30	10437	hgsc.bcm.edu	37	19	18288069	18288069	+	Silent	SNP	A	A	G	rs7125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	163	194	0	0.993902	0	A|0.525;C|0.003	.	strong	IFI30,NS,carcinoma,0,1	IFI30	12	1	NM_006332	exon5	c.A603G	p.P201P	GCCACCACACGAG	.	PASS	Atlas-SNP
BAG4	9530	hgsc.bcm.edu	37	8	38034402	38034402	+	Silent	SNP	G	G	A	rs61731143	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	36	39	0	0.5	0	G|0.995;A|0.005	0.005	strong	.	BAG4	32	.	NM_001204878	exon1	c.G15A	p.R5R	CCTGAGGCGCTCG	.	PASS	Atlas-SNP
FAM53B	9679	hgsc.bcm.edu	37	10	126370638	126370638	+	Silent	SNP	G	G	A	rs148943049	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	29	90	0	0.47541	0	G|0.999;A|0.001	0.001	strong	.	FAM53B	22	.	NM_014661	exon4	c.C444T	p.S148S	GCCCCCGCTGTAG	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34723744	34723744	+	Missense_Mutation	SNP	C	C	A	rs4878588	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	31	98	0	0.3875	0	C|0.575;A|0.425	0.425	strong	.	FAM205A	45	.	NM_001141917	exon4	c.G3493T	p.A1165S	GTGAAGCCTGGGG	.	PASS	Atlas-SNP
COG5	10466	hgsc.bcm.edu	37	7	106897237	106897237	+	Silent	SNP	A	A	C	rs17349904	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	33	61	0	0.532258	0	A|0.851;C|0.149	0.149	strong	.	COG5	78	.	NM_006348	exon16	c.T1782G	p.V594V	GGAAACAACCTAG	.	PASS	Atlas-SNP
ASB8	140461	hgsc.bcm.edu	37	12	48543584	48543584	+	Silent	SNP	G	G	C	rs3936179	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	84	162	0	0.545455	0	G|0.946;C|0.054	0.054	strong	.	ASB8	25	.	NM_024095	exon4	c.C432G	p.V144V	GGCATTGACAGAG	.	PASS	Atlas-SNP
DNAH6	1768	hgsc.bcm.edu	37	2	84880695	84880695	+	Silent	SNP	G	G	A	rs12992282	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	46	97	0	0.489362	0	G|0.925;A|0.075	0.075	strong	.	DNAH6	194	.	NM_001370	exon34	c.G5331A	p.G1777G	ACTTGGGATAGAA	.	PASS	Atlas-SNP
PARP9	83666	hgsc.bcm.edu	37	3	122274757	122274757	+	Silent	SNP	G	G	C	rs73192127	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	44	106	0	0.427184	0	G|0.793;C|0.207	0.207	strong	PARP9,caecum,carcinoma,+2,1	PARP9	72	1	NM_031458	exon4	c.C366G	p.V122V	TTTCCAGACTGAT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54724458	54724458	+	Missense_Mutation	SNP	A	A	G	rs1052993	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	39	111	0	0.428571	0	A|1.000;|0.000	.	strong	.	LILRB3	67	.	NM_006864	exon6	c.T1198C	p.Y400H	AGCTGTATGAGCC	.	PASS	Atlas-SNP
DCTD	1635	hgsc.bcm.edu	37	4	183815688	183815688	+	Silent	SNP	A	A	G	rs4742	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	73	171	0	0.470968	0	T|0.125;G|0.280;C|0.062;A|0.534	0.280	strong	.	DCTD	30	.	NM_001012732	exon4	c.T348C	p.V116V	CAAGGCAACATAC	.	PASS	Atlas-SNP
INPP5J	27124	hgsc.bcm.edu	37	22	31529463	31529463	+	Silent	SNP	C	C	A	rs35342535	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	35	78	0	0.466667	0	C|0.726;A|0.274	0.274	strong	.	INPP5J	94	.	NM_001002837	exon11	c.C1299A	p.T433T	GAATACCTACCAG	.	PASS	Atlas-SNP
FRRS1	391059	hgsc.bcm.edu	37	1	100174670	100174670	+	Missense_Mutation	SNP	C	C	T	rs12145706	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	34	97	0	0.465753	0	C|0.857;T|0.143	0.143	strong	.	FRRS1	50	.	NM_001013660	exon17	c.G1665A	p.M555I	TAAAAGCATGACC	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165667781	165667781	+	Silent	SNP	T	T	G	rs12408101	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	22	19	0	0.5	0	T|0.850;G|0.150	0.150	strong	ALDH9A1_ENST00000354775,NS,carcinoma,0,1	ALDH9A1	75	1	NM_000696	exon1	c.A15C	p.A5A	CAGGCCTGCTCGG	.	PASS	Atlas-SNP
FMN1	342184	hgsc.bcm.edu	37	15	33261232	33261232	+	Silent	SNP	G	G	A	rs2930131	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	74	78	0	0.986667	0	G|0.489;A|0.511	0.511	strong	.	FMN1	174	.	NM_001103184	exon4	c.C2001T	p.P667P	AGGTGCGGGAGAC	.	PASS	Atlas-SNP
KIAA0226	9711	hgsc.bcm.edu	37	3	197432036	197432036	+	Missense_Mutation	SNP	C	C	T	rs61743568	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	29	58	0	0.47541	0	C|0.929;T|0.071	0.071	strong	.	KIAA0226	136	.	NM_014687	exon3	c.G230A	p.R77H	GTCTGGCGGCGGC	.	PASS	Atlas-SNP
KANK2	25959	hgsc.bcm.edu	37	19	11303943	11303943	+	Silent	SNP	A	A	G	rs3745681	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	12	29	0	0.444444	0	A|0.544;G|0.456	0.456	strong	KANK2,NS,carcinoma,0,1	KANK2	47	1	NM_015493	exon2	c.T813C	p.V271V	TTCTCGAACCCAG	.	PASS	Atlas-SNP
REPIN1	29803	hgsc.bcm.edu	37	7	150068605	150068605	+	Missense_Mutation	SNP	G	G	A	rs17173702	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	58	48	0	1	0	G|0.761;C|0.000;A|0.238	0.238	strong	.	REPIN1	74	.	NM_001099695	exon3	c.G446A	p.R149H	GTGGCCGTCGCTT	.	PASS	Atlas-SNP
OR51B5	282763	hgsc.bcm.edu	37	11	5364276	5364276	+	Missense_Mutation	SNP	G	G	A	rs4910551	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	27	52	0	0.442623	0	G|0.650;A|0.350	0.350	strong	.	OR51B5	60	.	NM_001005567	exon5	c.C479T	p.P160L	TAGAGGGGCCTGA	.	PASS	Atlas-SNP
IL7R	3575	hgsc.bcm.edu	37	5	35876274	35876274	+	Missense_Mutation	SNP	A	A	G	rs3194051	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	98	94	0	0.989899	0	A|0.740;G|0.260	0.260	strong	.	IL7R	200	.	NM_002185	exon8	c.A1066G	p.I356V	GTAGTCATCACTC	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	37	3	121414061	121414061	+	Missense_Mutation	SNP	C	C	T	rs1127412	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	252	121	230	1	0.480159	0.00434783	C|0.760;T|0.240	0.240	strong	.	GOLGB1	319	.	NM_001256486	exon13	c.G5309A	p.G1770D	ACATTACCTTCTA	.	PASS	Atlas-SNP
ARHGAP31	57514	hgsc.bcm.edu	37	3	119133554	119133554	+	Silent	SNP	G	G	A	rs61740281	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	29	51	0	0.557692	0	G|0.878;A|0.122	0.122	strong	ARHGAP31,NS,carcinoma,+1,2	ARHGAP31	175	2	NM_020754	exon12	c.G2778A	p.A926A	AGACGCGCACAAG	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	37	8	144992900	144992900	+	Silent	SNP	G	G	A	rs17062686	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	47	74	0	0.456311	0	G|0.970;A|0.030	0.030	strong	.	PLEC	1144	.	NM_201380	exon32	c.C11500T	p.L3834L	CGGGCAGGTAGAC	.	PASS	Atlas-SNP
BTN3A3	10384	hgsc.bcm.edu	37	6	26443853	26443853	+	Silent	SNP	C	C	A	rs56036950	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	342	160	358	0	0.467836	0	C|0.836;A|0.164	0.164	strong	.	BTN3A3	56	.	NM_006994	exon3	c.C51A	p.S17S	TGTCTCCCTCTTC	.	PASS	Atlas-SNP
GAL3ST2	64090	hgsc.bcm.edu	37	2	242716380	242716380	+	Missense_Mutation	SNP	A	A	T	rs12469459	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	151	98	0	1	0	A|0.631;T|0.369	0.369	strong	.	GAL3ST2	34	.	NM_022134	exon1	c.A10T	p.M4L	ATGTCCATGCTGG	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1916890	1916890	+	Silent	SNP	C	C	T	rs3795280	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	123	111	0	0.904412	0	C|0.606;T|0.394	0.394	strong	.	KIAA1751	92	.	NM_001080484	exon6	c.G435A	p.L145L	TGCAAACAGGCGT	.	PASS	Atlas-SNP
KLHL30	377007	hgsc.bcm.edu	37	2	239059484	239059484	+	Silent	SNP	T	T	C	rs7605194	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	149	117	0	0.980263	0	T|0.149;C|0.851	0.851	strong	.	KLHL30	79	.	NM_198582	exon8	c.T1515C	p.N505N	TGAGAATGGCGCG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608879	26608879	+	Missense_Mutation	SNP	C	C	T	rs1134581	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	32	34	7	0.761905	0.205882	C|1.000;|0.000	.	weak	UBXN11,NS,carcinoma,+2,2	UBXN11	54	2	NM_183008	exon16	c.G1474A	p.G492S	TGGGGCCGGGACC	.	scavenged	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57069568	57069568	+	Missense_Mutation	SNP	T	T	C	rs35272228	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	23	55	0	0.396552	0	T|0.969;C|0.031	0.031	strong	.	TNKS1BP1	148	.	NM_033396	exon8	c.A4814G	p.H1605R	AACAGGTGTGCAT	.	PASS	Atlas-SNP
HCLS1	3059	hgsc.bcm.edu	37	3	121354583	121354583	+	Silent	SNP	G	G	A	rs3772126	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	41	102	0	0.450549	0	G|0.788;A|0.212	0.212	strong	.	HCLS1	78	.	NM_005335	exon9	c.C690T	p.A230A	CTCACCGGCTTCT	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194944	18194944	+	Silent	SNP	T	T	A	rs11024531	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	181	134	0	0.994505	0	T|0.760;A|0.240	0.240	strong	.	MRGPRX4	68	.	NM_054032	exon1	c.T141A	p.V47V	CGCGGTTGTGCTC	.	PASS	Atlas-SNP
SLC35G5	83650	hgsc.bcm.edu	37	8	11188752	11188752	+	Missense_Mutation	SNP	G	G	A	rs77960126		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	141	90	0	0.992958	0	.	.	weak	.	.	.	.	NM_054028	exon1	c.G137A	p.G46D	TGCTGGGTGGGGG	.	PASS	Atlas-SNP
FRA10AC1	118924	hgsc.bcm.edu	37	10	95441272	95441272	+	Missense_Mutation	SNP	G	G	A	rs11187583	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	76	144	0	0.571429	0	G|0.902;A|0.098	0.098	strong	FRA10AC1_ENST00000371426,colon,carcinoma,-1,2	FRA10AC1	68	2	NM_145246	exon11	c.C752T	p.S251F	GCAGAAGATAATC	.	PASS	Atlas-SNP
OR51B4	79339	hgsc.bcm.edu	37	11	5322737	5322737	+	Missense_Mutation	SNP	A	A	G	rs10837771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	176	199	0	0.98324	0	A|0.589;G|0.411	0.411	strong	.	OR51B4	64	.	NM_033179	exon1	c.T440C	p.M147T	CCTCTCATCAGTA	.	PASS	Atlas-SNP
MS4A4A	51338	hgsc.bcm.edu	37	11	60059810	60059810	+	Missense_Mutation	SNP	A	A	G	rs10750931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	76	161	0	0.503311	0	A|0.845;G|0.155	0.155	strong	.	MS4A4A	76	.	NM_148975	exon2	c.A154G	p.K52E	CTGTGGAAAGGAT	.	PASS	Atlas-SNP
RBM6	10180	hgsc.bcm.edu	37	3	50114515	50114515	+	Silent	SNP	C	C	T	rs7061	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	45	87	0	0.401786	0	C|0.329;T|0.671	0.671	strong	.	RBM6	85	.	NM_005777	exon21	c.C3321T	p.Y1107Y	GACTTACCGAGAT	.	PASS	Atlas-SNP
PCDHB5	26167	hgsc.bcm.edu	37	5	140517069	140517069	+	Missense_Mutation	SNP	C	C	T	rs139772435	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	27	34	0	0.415385	0	C|0.997;T|0.003	0.003	strong	.	PCDHB5	184	.	NM_015669	exon1	c.C2053T	p.L685F	GACTCGCTCACTG	.	PASS	Atlas-SNP
TMEM244	253582	hgsc.bcm.edu	37	6	130154667	130154667	+	Missense_Mutation	SNP	T	T	C	rs9492393	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	53	61	0	0.929825	0	T|0.633;C|0.367	0.367	strong	.	.	.	.	NM_001010876	exon4	c.A257G	p.E86G	CATTCTTCCACAA	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512613	4512613	+	Silent	SNP	T	T	G	rs74327986	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	79	180	1	0.975309	0.00555556	T|0.916;G|0.084	0.084	strong	.	PLIN4	191	.	NM_001080400	exon3	c.A1317C	p.T439T	CACGCCTGTCTGG	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	37	6	31604010	31604010	+	Silent	SNP	C	C	G	rs13716	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	54	121	0	0.453782	0	C|0.731;G|0.269	0.269	strong	.	PRRC2A	152	.	NM_004638	exon26	c.C5649G	p.P1883P	ACCCCCCGGCCCA	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55330019	55330019	+	Missense_Mutation	SNP	C	C	T	rs143159382	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	17	22	0	0.53125	0	C|0.884;T|0.116	0.116	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.C320T	p.S107L	GGTGGTCGGCACC	.	PASS	Atlas-SNP
ZNF326	284695	hgsc.bcm.edu	37	1	90484253	90484253	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	66	131	0	0.445946	0	.	.	none	.	ZNF326	60	.	NM_182976	exon9	c.G1084A	p.V362M	TGTATGGTGAATA	.	PASS	Atlas-SNP
FER1L6	654463	hgsc.bcm.edu	37	8	125107201	125107201	+	Silent	SNP	G	G	A	rs6470219	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	134	124	0	1	0	G|0.248;A|0.752	0.752	strong	.	FER1L6	268	.	NM_001039112	exon35	c.G4617A	p.P1539P	TATCCCGGAAGTC	.	PASS	Atlas-SNP
ZNF862	643641	hgsc.bcm.edu	37	7	149558409	149558409	+	Silent	SNP	G	G	C	rs2240361	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	54	71	0	1	0	G|0.536;C|0.464	0.464	strong	.	ZNF862	97	.	NM_001099220	exon7	c.G2160C	p.L720L	GCTGCTGCCTGTC	.	PASS	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55722882	55722882	+	Nonsense_Mutation	SNP	C	C	A	rs57809907	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	41	82	0	0.455556	0	C|0.819;A|0.181	0.181	strong	DYX1C1,NS,carcinoma,+2,1	DYX1C1	54	1	NM_130810	exon10	c.G1249T	p.E417X	TTAGTTCTGTTCC	.	PASS	Atlas-SNP
ABHD12	26090	hgsc.bcm.edu	37	20	25282967	25282967	+	Missense_Mutation	SNP	C	C	T	rs746748	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	28	44	0	0.651163	0	C|0.958;A|0.000	.	strong	.	ABHD12	46	.	NM_001042472	exon12	c.G1045A	p.A349T	CTGGTGCGGCGAT	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51361472	51361472	+	Missense_Mutation	SNP	C	C	A	rs2003783	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	54	82	0	0.482143	0	C|0.896;A|0.104	0.104	strong	.	KLK3	76	.	NM_001030047	exon3	c.C394A	p.L132I	GCCGAGCTCACGG	.	PASS	Atlas-SNP
ARHGAP4	393	hgsc.bcm.edu	37	X	153176254	153176254	+	Silent	SNP	A	A	G	rs2070097	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	22	53	0	1	0	A|0.354;G|0.646	0.646	strong	.	ARHGAP4	103	.	NM_001164741	exon16	c.T1836C	p.H612H	CAGGTCATGGGCA	.	PASS	Atlas-SNP
HSPA9	3313	hgsc.bcm.edu	37	5	137902339	137902339	+	Silent	SNP	T	T	C	rs1042665	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	35	65	0	0.448718	0	T|0.686;C|0.314	0.314	strong	.	HSPA9	49	.	NM_004134	exon9	c.A948G	p.K316K	TTCACATTTAGCC	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497917	32497917	+	Missense_Mutation	SNP	C	C	A	rs71549220	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	88	265	1	0.505747	0.00377358	C|0.956;A|0.044	0.044	strong	HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	NM_002125	exon1	c.G85T	p.A29S	CCCCAGCCAAAGC	.	PASS	Atlas-SNP
HFM1	164045	hgsc.bcm.edu	37	1	91781413	91781413	+	Silent	SNP	T	T	G	rs281992	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	270	123	222	0	0.455556	0	T|0.278;G|0.722	0.722	strong	.	HFM1	188	.	NM_001017975	exon28	c.A3099C	p.I1033I	GTCACCTATGATT	.	PASS	Atlas-SNP
SH3RF2	153769	hgsc.bcm.edu	37	5	145393364	145393364	+	Missense_Mutation	SNP	C	C	T	rs758037	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	62	137	0	0.496	0	C|0.411;T|0.589	0.589	strong	.	SH3RF2	58	.	NM_152550	exon5	c.C799T	p.R267C	TCATCCCGCACAA	.	PASS	Atlas-SNP
AGPAT3	56894	hgsc.bcm.edu	37	21	45389034	45389034	+	Silent	SNP	C	C	T	rs61737069	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	93	145	0	0.556886	0	C|0.986;T|0.014	0.014	strong	.	AGPAT3	37	.	NM_001037553	exon4	c.C384T	p.Y128Y	GCTCTACGTGCCC	.	PASS	Atlas-SNP
KAT2B	8850	hgsc.bcm.edu	37	3	20141356	20141356	+	Silent	SNP	C	C	T	rs35424474	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	37	87	0	0.406593	0	C|0.893;T|0.107	0.107	strong	.	KAT2B	73	.	NM_003884	exon4	c.C579T	p.L193L	GCAGCTCTTGAGA	.	PASS	Atlas-SNP
XYLT1	64131	hgsc.bcm.edu	37	16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	rs113276942	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	78	169	0	0.541667	0	G|0.950;C|0.050	0.050	strong	XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	NM_022166	exon3	c.C668G	p.A223G	GCTGCGGCTCTGT	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2152388	2152388	+	Silent	SNP	C	C	G	rs9935834	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	36	87	0	0.378947	0	C|0.824;G|0.177	0.177	strong	.	PKD1	184	.	NM_000296	exon25	c.G9195C	p.V3065V	AGGAAACACAAAG	.	PASS	Atlas-SNP
UGT2B15	7366	hgsc.bcm.edu	37	4	69512847	69512847	+	Missense_Mutation	SNP	T	T	G	rs4148269	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	264	263	134	0	0.996212	0	T|0.588;G|0.412	0.412	strong	.	UGT2B15	48	.	NM_001076	exon6	c.A1568C	p.K523T	TTTCCTTTTTTGG	.	PASS	Atlas-SNP
DHX35	60625	hgsc.bcm.edu	37	20	37667182	37667182	+	Missense_Mutation	SNP	C	C	T	rs3752302	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	36	63	0	0.486486	0	C|0.855;T|0.145	0.145	strong	.	DHX35	82	.	NM_021931	exon22	c.C2108T	p.P703L	AGGACCCGTGAGA	.	PASS	Atlas-SNP
SULT1C3	442038	hgsc.bcm.edu	37	2	108863767	108863767	+	Silent	SNP	A	A	C	rs9308806	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	174	90	0	0.994286	0	A|0.190;C|0.810	0.810	strong	.	SULT1C3	53	.	NM_001008743	exon1	c.A117C	p.V39V	AAAAGTATGTAAT	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104385711	104385711	+	Missense_Mutation	SNP	C	C	T	rs35768024	bycluster;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	125	154	1	0.976562	0.00649351	CA|0.500;TG|0.500	.	alt	.	GRIN3A	186	.	NM_133445	exon5	c.G2503A	p.D835N	CTGGATCATTCCT	.	PASS	Atlas-SNP
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974405	22974405	+	Missense_Mutation	SNP	C	C	T	rs61736406	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	35	126	0	0.230263	0	A|0.000;C|0.990;T|0.009	0.009	strong	TNFRSF10C,NS,carcinoma,0,5	TNFRSF10C	30	5	NM_003841	exon5	c.C641T	p.T214I	CAATGACCACCAG	.	PASS	Atlas-SNP
SLC22A1	6580	hgsc.bcm.edu	37	6	160543123	160543123	+	Silent	SNP	T	T	C	rs1867351	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	48	110	0	0.872727	0	T|0.754;C|0.246	0.246	strong	.	SLC22A1	69	.	NM_153187	exon1	c.T156C	p.S52S	CCAGAGTCCTGGG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067055	79067055	+	Missense_Mutation	SNP	C	C	T	rs2277549	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	51	81	0	0.894737	0	C|0.727;T|0.273	0.273	strong	ADAMTS7,NS,carcinoma,-1,1	ADAMTS7	142	1	NM_014272	exon12	c.G1787A	p.R596H	GAGGGGCGGCCAG	.	PASS	Atlas-SNP
SPATA31A3	727830	hgsc.bcm.edu	37	9	40702846	40702846	+	Missense_Mutation	SNP	C	C	T	rs273319		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	330	184	263	0	0.557576	0	.	.	weak	FAM75A3_ENST00000356699,NS,carcinoma,-1,6	.	.	6	NM_001083124	exon4	c.C503T	p.T168I	CCTCCACCCCATC	.	scavenged	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220420785	220420785	+	Silent	SNP	G	G	A	rs3087971	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	319	164	281	1	0.514107	0.00355872	G|0.730;A|0.270	0.270	strong	.	OBSL1	120	.	NM_001173431	exon14	c.C4566T	p.C1522C	GCTCTCGCAGCCG	.	PASS	Atlas-SNP
SLC9C1	285335	hgsc.bcm.edu	37	3	111887792	111887792	+	Missense_Mutation	SNP	C	C	A	rs76007436	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	65	107	0	0.52	0	C|0.941;A|0.059	0.059	strong	SLC9A10,NS,carcinoma,0,1	.	.	1	NM_183061	exon25	c.G3169T	p.A1057S	CTACAGCTCCATG	.	PASS	Atlas-SNP
NLRP4	147945	hgsc.bcm.edu	37	19	56373462	56373462	+	Missense_Mutation	SNP	G	G	A	rs12462372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	73	94	0	0.532847	0	G|0.927;A|0.073	0.073	strong	NLRP4_ENST00000301295,colon,carcinoma,+1,7	NLRP4	331	7	NM_134444	exon5	c.G2123A	p.R708H	TCTCTCGTGATGA	.	PASS	Atlas-SNP
OR13C5	138799	hgsc.bcm.edu	37	9	107361439	107361439	+	Missense_Mutation	SNP	G	G	C	rs60573979	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	429	74	579	0	0.172494	0	G|0.308;C|0.692	0.692	strong	.	OR13C5	60	.	NM_001004482	exon1	c.C256G	p.L86V	CTGAAAGGAAGCT	.	PASS	Atlas-SNP
TMEM9B	56674	hgsc.bcm.edu	37	11	8977830	8977830	+	Silent	SNP	A	A	G	rs2568068	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	19	48	0	0.413043	0	T|0.006;G|0.283	0.283	strong	.	TMEM9B	6	.	NM_020644	exon3	c.T213C	p.V71V	CTCCACAACATGA	.	PASS	Atlas-SNP
PTGIS	5740	hgsc.bcm.edu	37	20	48156236	48156236	+	Missense_Mutation	SNP	C	C	T	rs148768155	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	18	37	0	0.409091	0	C|0.999;T|0.001	0.001	strong	PTGIS,scalp,carcinoma,0,1	PTGIS	60	1	NM_000961	exon5	c.G544A	p.G182R	CAATTCCGTAAAG	.	PASS	Atlas-SNP
PTPRD	5789	hgsc.bcm.edu	37	9	8389364	8389364	+	Silent	SNP	C	C	G	rs2279776	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	141	143	0	0.979167	0	C|0.506;G|0.494	0.494	strong	.	PTPRD	1348	.	NM_002839	exon37	c.G4254C	p.G1418G	CCTATACCCATCT	.	PASS	Atlas-SNP
TPST2	8459	hgsc.bcm.edu	37	22	26937087	26937087	+	Silent	SNP	C	C	A	rs5761587	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	24	46	0	0.444444	0	C|0.935;A|0.065	0.065	strong	.	TPST2	23	.	NM_001008566	exon3	c.G510T	p.S170S	CAGGCGCGACAGG	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124369744	124369744	+	Silent	SNP	C	C	T	rs12106716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	29	56	0	0.491525	0	C|0.888;T|0.112	0.112	strong	.	KALRN	556	.	NM_001024660	exon38	c.C5751T	p.N1917N	TAAAAACCCAGAA	.	PASS	Atlas-SNP
PDLIM2	64236	hgsc.bcm.edu	37	8	22442908	22442908	+	Missense_Mutation	SNP	G	G	A	rs11989168	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	46	77	0	0.469388	0	G|0.993;A|0.007	0.007	strong	PDLIM2_ENST00000308354,colon,carcinoma,+1,2	PDLIM2	42	2	NM_021630	exon6	c.G1286A	p.R429Q	GAAGCCGACAGGT	.	PASS	Atlas-SNP
CADPS2	93664	hgsc.bcm.edu	37	7	122303321	122303321	+	Silent	SNP	C	C	T	rs2251761	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	106	108	0	1	0	C|0.261;T|0.739	0.739	strong	.	CADPS2	116	.	NM_001167940	exon3	c.G756A	p.L252L	GTGTTCCAGTTTT	.	PASS	Atlas-SNP
PSG1	5669	hgsc.bcm.edu	37	19	43372941	43372941	+	Missense_Mutation	SNP	T	T	C	rs28374299	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	66	0	0.43662	0	T|0.830;C|0.170	0.170	strong	.	PSG1	196	.	NM_001184826	exon4	c.A955G	p.I319V	TGCGGATGCCACC	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	251541	251541	+	Silent	SNP	A	A	G	rs77210621	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	88	253	0	0.376068	0	A|0.757;G|0.243	0.243	strong	SDHA,NS,carcinoma,+2,1	SDHA	80	1	NM_004168	exon13	c.A1752G	p.A584A	AGAGGCACGGAAG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9070873	9070873	+	Missense_Mutation	SNP	A	A	G	rs79202331	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	248	115	236	1	0.46371	0.00423729	A|0.993;G|0.007	0.007	strong	.	MUC16	4315	.	NM_024690	exon3	c.T16573C	p.S5525P	TAGAGGAGATTTC	.	PASS	Atlas-SNP
SP110	3431	hgsc.bcm.edu	37	2	231036866	231036866	+	Silent	SNP	G	G	A	rs13018234	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	59	83	0	0.495798	0	G|0.906;A|0.094	0.094	strong	.	SP110	105	.	NM_080424	exon16	c.C1731T	p.C577C	CATCCTGCAGAAG	.	PASS	Atlas-SNP
FANCM	57697	hgsc.bcm.edu	37	14	45665468	45665468	+	Missense_Mutation	SNP	C	C	G	rs3736772	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	70	130	0	0.534351	0	C|0.917;G|0.083	0.083	strong	.	FANCM	225	.	NM_020937	exon21	c.C5434G	p.P1812A	AGACTTCCGCAGG	.	PASS	Atlas-SNP
CP	1356	hgsc.bcm.edu	37	3	148917570	148917570	+	Missense_Mutation	SNP	G	G	A	rs35331711	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	270	133	252	0	0.492593	0	G|0.998;A|0.002	0.002	strong	CP,NS,carcinoma,-1,1	CP	112	1	NM_000096	exon8	c.C1430T	p.P477L	CCAATCGGCTCAA	.	PASS	Atlas-SNP
SAMD10	140700	hgsc.bcm.edu	37	20	62607160	62607160	+	Silent	SNP	C	C	T	rs817343	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	21	51	0	0.4375	0	C|0.770;T|0.230	0.230	strong	SAMD10,rectum,carcinoma,0,2	SAMD10	16	2	NM_080621	exon4	c.G471A	p.A157A	CTTCTCCGCATTC	.	PASS	Atlas-SNP
NR4A3	8013	hgsc.bcm.edu	37	9	102595685	102595685	+	Silent	SNP	C	C	T	rs10988904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	195	237	0	0.989848	0	C|0.649;T|0.351	0.351	strong	.	NR4A3	80	.	NM_173200	exon6	c.C1236T	p.A412A	GAATGCCCTTGTC	.	PASS	Atlas-SNP
CABLES2	81928	hgsc.bcm.edu	37	20	60968596	60968596	+	Silent	SNP	A	A	G	rs1570027	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	121	121	0	1	0	A|0.785;G|0.215	0.215	strong	.	CABLES2	30	.	NM_031215	exon6	c.T780C	p.H260H	CAGGCCATGGCTG	.	PASS	Atlas-SNP
CHST12	55501	hgsc.bcm.edu	37	7	2472455	2472455	+	Missense_Mutation	SNP	A	A	T	rs3735100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	36	26	0	0.631579	0	A|0.956;T|0.044	0.044	strong	.	CHST12	39	.	NM_018641	exon2	c.A181T	p.T61S	GAGCTCACGGCCG	.	PASS	Atlas-SNP
PRKD3	23683	hgsc.bcm.edu	37	2	37494591	37494591	+	Silent	SNP	A	A	G	rs2302650	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	44	81	0	0.586667	0	A|0.838;G|0.162	0.162	strong	.	PRKD3	170	.	NM_005813	exon13	c.T1866C	p.N622N	CACTTCATTACGG	.	PASS	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	37	14	65263300	65263300	+	Missense_Mutation	SNP	C	C	T	rs229587	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	42	100	0	0.424242	0	C|0.569;N|0.000	.	strong	.	SPTB	378	.	NM_001024858	exon10	c.G1316A	p.S439N	TTTTCACTGAGCC	.	PASS	Atlas-SNP
ATXN3	4287	hgsc.bcm.edu	37	14	92549586	92549586	+	Silent	SNP	G	G	A	rs16999141	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	57	45	2	1	0.0444444	G|0.463;A|0.537	0.537	strong	ATXN3,NS,carcinoma,0,1	ATXN3	46	1	NM_004993	exon7	c.C492T	p.V164V	CTTAACGACAAAT	.	scavenged	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	37	18	21112206	21112206	+	Missense_Mutation	SNP	C	C	T	rs1805084	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	273	144	246	0	0.527473	0	C|0.886;T|0.114	0.114	strong	NPC1,NS,carcinoma,0,1	NPC1	114	1	NM_000271	exon25	c.G3797A	p.R1266Q	TTGTATCGCTCTT	.	PASS	Atlas-SNP
XPC	7508	hgsc.bcm.edu	37	3	14199887	14199887	+	Missense_Mutation	SNP	G	G	A	rs2228000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	33	79	0	0.402439	0	G|0.772;A|0.228	0.228	strong	XPC,caecum,carcinoma,+1,1	XPC	60	1	NM_004628	exon9	c.C1496T	p.A499V	GATGCCGCTGGCA	.	PASS	Atlas-SNP
PIGT	51604	hgsc.bcm.edu	37	20	44052992	44052992	+	Silent	SNP	G	G	A	rs13217	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	48	104	1	0.5	0.00961538	G|0.654;A|0.346	0.346	strong	PIGT_ENST00000279036,caecum,carcinoma,0,3	PIGT	85	3	NM_015937	exon10	c.G1371A	p.T457T	GTACACGCCAGAT	.	scavenged	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84213434	84213434	+	Missense_Mutation	SNP	A	A	T	rs2230129	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	117	126	0	0.991525	0	A|0.640;T|0.360	0.360	strong	.	TAF1C	60	.	NM_005679	exon14	c.T1723A	p.L575M	AGGGCAAGGGCGG	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38763863	38763863	+	Silent	SNP	G	G	C	rs6771157	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	52	88	0	0.472727	0	G|0.767;C|0.233	0.233	strong	.	SCN10A	359	.	NM_006514	exon19	c.C3393G	p.T1131T	ACTCTTGGTGGTA	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6592951	6592951	+	Missense_Mutation	SNP	T	T	C	rs11604362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	75	94	0	0.590551	0	T|0.994;C|0.006	0.006	strong	.	DNHD1	198	.	NM_144666	exon43	c.T13997C	p.I4666T	ACCCAATAGCTGG	.	PASS	Atlas-SNP
PEX6	5190	hgsc.bcm.edu	37	6	42932200	42932200	+	Missense_Mutation	SNP	G	G	T	rs1129187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	54	102	0	0.442623	0	G|0.617;T|0.383	0.383	strong	PEX6,colon,carcinoma,0,1	PEX6	44	1	NM_000287	exon17	c.C2816A	p.P939Q	CTACCTGGCTCCA	.	PASS	Atlas-SNP
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152390	151152390	+	Missense_Mutation	SNP	G	G	A	rs79596384	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	51	115	0	0.927273	0	G|0.989;A|0.011	0.011	strong	.	PLEKHG1	97	.	NM_001029884	exon16	c.G2143A	p.A715T	CTTTACGCACAAA	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52323908	52323908	+	Missense_Mutation	SNP	A	A	G	rs117864200	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	108	221	0	0.471616	0	A|0.986;G|0.014	0.014	strong	.	PXDNL	414	.	NM_144651	exon16	c.T1964C	p.I655T	TCCACAATCAGTG	.	PASS	Atlas-SNP
SYCE1L	100130958	hgsc.bcm.edu	37	16	77243330	77243330	+	Silent	SNP	C	C	T	rs61740088	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	26	76	0	0.490566	0	C|0.979;T|0.021	0.021	strong	.	SYCE1L	10	.	NM_001129979	exon6	c.C321T	p.L107L	GATCCTCCAGATG	.	PASS	Atlas-SNP
NINL	22981	hgsc.bcm.edu	37	20	25456888	25456888	+	Silent	SNP	A	A	G	rs437635	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	42	99	0	0.466667	0	A|0.506;G|0.494	0.494	strong	.	NINL	148	.	NM_025176	exon17	c.T3039C	p.S1013S	CTCCACACTGTGC	.	PASS	Atlas-SNP
ND2	0	hgsc.bcm.edu	37	MT	4917	4917	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	9	0	0	1	.	.	.	none	.	.	.	.	ENST00000361453	exon1	c.A448G	p.N150D	TCACTAAACGTAA	.	PASS	Atlas-SNP
MYO1D	4642	hgsc.bcm.edu	37	17	30980871	30980871	+	Missense_Mutation	SNP	T	T	A	rs138039699	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	22	58	0	0.488889	0	T|0.998;A|0.002	0.002	strong	.	MYO1D	93	.	NM_015194	exon19	c.A2585T	p.H862L	CGGACGTGACAGG	.	PASS	Atlas-SNP
HLTF	6596	hgsc.bcm.edu	37	3	148786085	148786085	+	Missense_Mutation	SNP	T	T	C	rs2305868	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	37	60	0	0.536232	0	T|0.977;C|0.023	0.023	strong	.	HLTF	87	.	NM_139048	exon8	c.A932G	p.N311S	TGGAAGTTGGTAA	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296466	39296466	+	Missense_Mutation	SNP	G	G	A	rs35985080	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	36	71	0	0.507042	0	G|0.952;A|0.048	0.048	strong	.	KRTAP4-6	46	.	NM_030976	exon1	c.C274T	p.P92S	ACTGGGGTCTGCA	.	PASS	Atlas-SNP
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964299	37964299	+	Silent	SNP	C	C	G	rs2281098	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	18	77	0	0.243243	0	C|0.541;G|0.459	0.459	strong	.	CDC42EP1	53	.	NM_152243	exon3	c.C648G	p.L216L	GAGCCTCCCAGAA	.	PASS	Atlas-SNP
SOX30	11063	hgsc.bcm.edu	37	5	157078402	157078402	+	Missense_Mutation	SNP	C	C	T	rs41275269	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	132	122	0	1	0	C|0.988;T|0.012	0.012	strong	.	SOX30	67	.	NM_178424	exon1	c.G685A	p.E229K	CGGGCTCCGCGCC	.	PASS	Atlas-SNP
CDH24	64403	hgsc.bcm.edu	37	14	23518918	23518918	+	Silent	SNP	T	T	C	rs11623976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	24	50	0	0.413793	0	T|0.841;C|0.159	0.159	strong	.	CDH24	129	.	NM_022478	exon11	c.A1629G	p.R543R	TTCATCTCTGTCC	.	PASS	Atlas-SNP
SYMPK	8189	hgsc.bcm.edu	37	19	46319415	46319415	+	Silent	SNP	G	G	C	rs1132645	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	26	50	0	0.541667	0	G|0.613;C|0.387	0.387	strong	.	SYMPK	104	.	NM_004819	exon26	c.C3381G	p.A1127A	GGCCGGGGCCAAG	.	PASS	Atlas-SNP
NR5A2	2494	hgsc.bcm.edu	37	1	200143281	200143281	+	Silent	SNP	C	C	T	rs1060060	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	81	85	0	1	0	T|0.348;G|0.007	0.348	strong	NR5A2,NS,carcinoma,+1,1	NR5A2	83	1	NM_205860	exon8	c.C1569T	p.C523C	CCTGAACGGGGAT	.	PASS	Atlas-SNP
C10orf90	118611	hgsc.bcm.edu	37	10	128193368	128193368	+	Missense_Mutation	SNP	C	C	T	rs11245008	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	24	86	0	0.342857	0	C|0.781;T|0.219	0.219	strong	.	C10orf90	121	.	NM_001004298	exon3	c.G401A	p.R134H	CCTCTGCGGGGGC	.	PASS	Atlas-SNP
SP140L	93349	hgsc.bcm.edu	37	2	231222675	231222675	+	Missense_Mutation	SNP	T	T	C	rs4973318	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	39	94	0	0.453488	0	T|0.905;C|0.095	0.095	strong	.	SP140L	68	.	NM_138402	exon3	c.T263C	p.M88T	ATAAAATGTTTGA	.	PASS	Atlas-SNP
MLPH	79083	hgsc.bcm.edu	37	2	238427251	238427251	+	Missense_Mutation	SNP	G	G	A	rs3751107	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	87	154	0	0.514793	0	G|0.795;A|0.205	0.205	strong	.	MLPH	41	.	NM_001042467	exon5	c.G515A	p.G172D	AACCTGGCTCAGA	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48375568	48375568	+	Silent	SNP	A	A	G	rs1635553	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	127	128	0	0.992188	0	A|0.519;G|0.481	0.481	strong	COL2A1_ENST00000380518,NS,carcinoma,0,2	COL2A1	368	2	NM_001844	exon36	c.T2400C	p.N800N	CTCGCCATTAGCA	.	PASS	Atlas-SNP
CR1L	1379	hgsc.bcm.edu	37	1	207850879	207850879	+	Silent	SNP	C	C	T	rs34509370	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	88	174	0	0.483516	0	C|0.836;T|0.164	0.164	strong	.	CR1L	97	.	NM_175710	exon2	c.C243T	p.N81N	AAAAAACTCAGTC	.	PASS	Atlas-SNP
ATF3	467	hgsc.bcm.edu	37	1	212788567	212788567	+	Silent	SNP	C	C	T	rs2229346	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	38	86	0	0.44186	0	C|0.951;G|0.000;T|0.049	0.049	strong	.	ATF3	22	.	NM_001674	exon2	c.C204T	p.S68S	TGTCAGCGACAGA	.	PASS	Atlas-SNP
AFF4	27125	hgsc.bcm.edu	37	5	132232315	132232315	+	Silent	SNP	G	G	A	rs739863	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	49	115	0	0.411765	0	G|0.892;A|0.108	0.108	strong	.	AFF4	120	.	NM_014423	exon11	c.C2007T	p.P669P	GCTCTCGGGGTAC	.	PASS	Atlas-SNP
ZNF227	7770	hgsc.bcm.edu	37	19	44739399	44739399	+	Silent	SNP	T	T	C	rs2279072	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	112	139	0	1	0	T|0.393;C|0.607	0.607	strong	.	ZNF227	62	.	NM_182490	exon6	c.T816C	p.H272H	TGTTCATACAGGA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40366374	40366374	+	Silent	SNP	G	G	C	rs2053089	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	62	90	0	0.446043	0	G|0.828;C|0.172	0.172	strong	FCGBP,NS,carcinoma,-1,1	FCGBP	416	1	NM_003890	exon30	c.C13860G	p.P4620P	GTCTGCGGGGTCC	.	PASS	Atlas-SNP
CDH18	1016	hgsc.bcm.edu	37	5	19591174	19591174	+	Silent	SNP	A	A	G	rs17285716	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	41	104	0	0.445652	0	A|0.879;G|0.121	0.121	strong	CDH18_ENST00000507958,NS,adenoma,0,4	CDH18	561	4	NM_001167667	exon7	c.T991C	p.L331L	TCTTTAAAGAAAG	.	PASS	Atlas-SNP
ISYNA1	51477	hgsc.bcm.edu	37	19	18545786	18545786	+	Silent	SNP	G	G	T	rs1045631	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	83	164	0	0.522013	0	G|0.788;T|0.212	0.212	strong	.	ISYNA1	31	.	NM_016368	exon11	c.C1614A	p.T538T	GCCATTGGTGGCA	.	PASS	Atlas-SNP
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	49	161	0	0.347518	0	G|0.710;A|0.290	0.290	strong	.	AKR1C3	21	.	NM_001253908	exon2	c.G90A	p.P30P	GGTTCCGAGAAGT	.	PASS	Atlas-SNP
PLAC8L1	153770	hgsc.bcm.edu	37	5	145464130	145464130	+	Silent	SNP	T	T	C	rs1859897	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	42	64	0	0.6	0	T|0.967;C|0.033	0.033	strong	.	PLAC8L1	17	.	NM_001029869	exon4	c.A399G	p.T133T	ACACAGTGTGCCC	.	PASS	Atlas-SNP
TAAR1	134864	hgsc.bcm.edu	37	6	132966348	132966348	+	Silent	SNP	G	G	A	rs8192619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	89	185	0	0.978022	0	G|0.935;A|0.065	0.065	strong	.	TAAR1	41	.	NM_138327	exon1	c.C795T	p.C265C	GAAAGGGCACCAG	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101761753	101761753	+	Missense_Mutation	SNP	A	A	G	rs117476305	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	58	136	0	0.464	0	A|0.991;G|0.009	0.009	strong	.	UTP20	222	.	NM_014503	exon48	c.A6383G	p.K2128R	ATGTGAAGGTAAG	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	37	22	18300775	18300775	+	Missense_Mutation	SNP	G	G	A	rs61744842	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	38	54	0	0.506667	0	G|0.944;A|0.056	0.056	strong	.	MICAL3	53	.	NM_015241	exon26	c.C4652T	p.P1551L	GGGCGCGGCCAGC	.	PASS	Atlas-SNP
RAET1G	353091	hgsc.bcm.edu	37	6	150240829	150240829	+	Missense_Mutation	SNP	G	G	C	rs9397449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	352	262	677	0	0.744318	0	G|0.807;C|0.193	0.193	strong	.	RAET1G	31	.	NM_001001788	exon2	c.C209G	p.T70R	GTGACTGTCTTGC	.	PASS	Atlas-SNP
TMEM14E	645843	hgsc.bcm.edu	37	3	152058449	152058449	+	Missense_Mutation	SNP	A	A	G	rs13077912	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	96	149	0	0.516129	0	A|0.902;G|0.098	0.098	strong	.	TMEM14E	6	.	NM_001123228	exon1	c.T245C	p.L82P	AGTGTTAGAATCT	.	PASS	Atlas-SNP
SEMA3F	6405	hgsc.bcm.edu	37	3	50197097	50197097	+	Silent	SNP	C	C	T	rs1046953	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	32	62	0	0.551724	0	C|0.626;T|0.374	0.374	strong	.	SEMA3F	62	.	NM_004186	exon2	c.C42T	p.T14T	ACTGACCGGGGCC	.	PASS	Atlas-SNP
TTI1	9675	hgsc.bcm.edu	37	20	36642101	36642101	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	47	106	0	0.460784	0	.	.	none	.	TTI1	104	.	NM_014657	exon3	c.G118A	p.V40M	CACTCACAGCTTG	.	PASS	Atlas-SNP
ALAS2	212	hgsc.bcm.edu	37	X	55039959	55039959	+	Silent	SNP	G	G	T	rs150055592	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	64	65	0	0.969697	0	G|0.997;T|0.003	0.003	strong	.	ALAS2	163	.	NM_000032	exon10	c.C1560A	p.P520P	GGGGGAGGGTGCC	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	109	118	0	1	0	A|0.690;G|0.310	0.310	strong	NUP133,NS,carcinoma,0,1	NUP133	111	1	NM_018230	exon11	c.T1456C	p.L486L	CTTCCAAGTCTTC	.	PASS	Atlas-SNP
TEX26	122046	hgsc.bcm.edu	37	13	31531009	31531009	+	Splice_Site	SNP	G	G	A	rs12857479	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	27	77	0	0.415385	0	G|0.732;A|0.268	0.268	strong	.	.	.	.	NM_152325	exon4	c.313-1G>A	.	TTGATAGGACATT	.	PASS	Atlas-SNP
OR51G1	79324	hgsc.bcm.edu	37	11	4945196	4945196	+	Missense_Mutation	SNP	T	T	G	rs1378739	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	58	0	1	0	T|0.355;G|0.645	0.645	strong	.	OR51G1	74	.	NM_001005237	exon1	c.A374C	p.Y125S	GCCACGTAGCGGT	.	PASS	Atlas-SNP
OR51B4	79339	hgsc.bcm.edu	37	11	5323071	5323071	+	Missense_Mutation	SNP	C	C	T	rs7118113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	162	186	0	0.993865	0	C|0.342;T|0.658	0.658	strong	.	OR51B4	64	.	NM_033179	exon1	c.G106A	p.V36I	AAAGGACGGAGAA	.	PASS	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16356501	16356501	+	Missense_Mutation	SNP	G	G	A	rs1805152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	103	109	0	0.990385	0	G|0.379;A|0.621	0.621	strong	.	CLCNKA	56	.	NM_004070	exon14	c.G1339A	p.A447T	GCCGTCGCCTTCC	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155219662	155219662	+	Missense_Mutation	SNP	G	G	C	rs17031394	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	62	150	0	0.430556	0	G|0.830;C|0.170	0.170	strong	DCHS2,NS,carcinoma,0,1	DCHS2	594	1	NM_017639	exon18	c.C4439G	p.T1480R	TAAAGTGTGGGAA	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140572475	140572475	+	Missense_Mutation	SNP	A	A	C	rs143882112	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	383	192	384	0	0.501305	0	A|0.996;C|0.004	0.004	strong	.	PCDHB10	177	.	NM_018930	exon1	c.A350C	p.Y117S	AGATTTACCGGGC	.	PASS	Atlas-SNP
SUCNR1	56670	hgsc.bcm.edu	37	3	151599267	151599267	+	Silent	SNP	C	C	T	rs139804843		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	49	101	0	0.475728	0	C|1.000;T|0.000	0.000	weak	.	SUCNR1	31	.	NM_033050	exon3	c.C936T	p.H312H	GAGACACAACTTC	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	37	6	160517481	160517481	+	Silent	SNP	C	C	T	rs1803989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	59	112	0	0.797297	0	C|0.839;T|0.161	0.161	strong	.	IGF2R	251	.	NM_000876	exon45	c.C6666T	p.L2222L	CGATCTCGATGTC	.	PASS	Atlas-SNP
DNAJB8	165721	hgsc.bcm.edu	37	3	128181964	128181964	+	Missense_Mutation	SNP	G	G	A	rs142768827		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	75	185	0	0.369458	0	G|1.000;A|0.000	0.000	weak	.	DNAJB8	34	.	NM_153330	exon3	c.C125T	p.A42V	TTCTCCGCCTCCT	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234714	8234714	+	Missense_Mutation	SNP	C	C	T	rs3896980	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	43	72	0	0.551282	0	C|0.612;T|0.388	0.388	strong	.	.	.	.	NM_001080826	exon2	c.G1205A	p.R402Q	GCCTCCCGGGGGT	.	PASS	Atlas-SNP
C18orf8	29919	hgsc.bcm.edu	37	18	21100240	21100240	+	Silent	SNP	C	C	T	rs1367083	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	57	125	0	0.452381	0	T|0.538;G|0.000;C|0.462;A|0.000	0.538	strong	.	C18orf8	58	.	NM_013326	exon10	c.C924T	p.P308P	GCTTCCCGCTCGA	.	PASS	Atlas-SNP
REPIN1	29803	hgsc.bcm.edu	37	7	150068620	150068620	+	Missense_Mutation	SNP	C	C	T	rs17173703	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	51	52	0	0.980769	0	C|0.765;T|0.235	0.235	strong	.	REPIN1	74	.	NM_001099695	exon3	c.C461T	p.A154V	GCCATGCCCCCTT	.	PASS	Atlas-SNP
IGSF8	93185	hgsc.bcm.edu	37	1	160062472	160062472	+	Silent	SNP	C	C	T	rs2295622	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	26	13	0	1	0	T|0.156;G|0.000;C|0.844	0.156	strong	.	IGSF8	59	.	NM_052868	exon5	c.G1326A	p.E442E	CACAGCCTCCAGC	.	PASS	Atlas-SNP
NOL10	79954	hgsc.bcm.edu	37	2	10717806	10717806	+	Missense_Mutation	SNP	C	C	T	rs2287059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	102	192	0	0.481132	0	C|0.810;T|0.190	0.190	strong	.	NOL10	22	.	NM_024894	exon20	c.G1903A	p.D635N	TGGTGTCGGATAC	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	37	20	62195087	62195087	+	Silent	SNP	A	A	G	rs310630	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	11	21	0	0.55	0	A|0.512;G|0.488	0.488	strong	PRIC285,NS,carcinoma,0,3	.	.	3	NM_001037335	exon9	c.T5088C	p.S1696S	GTAGGCAGAGCCC	.	PASS	Atlas-SNP
ONECUT1	3175	hgsc.bcm.edu	37	15	53081800	53081800	+	Silent	SNP	G	G	C	rs61735385	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	38	96	0	0.395833	0	G|0.928;C|0.072	0.072	strong	.	ONECUT1	48	.	NM_004498	exon1	c.C282G	p.P94P	ACCTGGGGGAGTC	.	PASS	Atlas-SNP
ZNF835	90485	hgsc.bcm.edu	37	19	57175484	57175484	+	Silent	SNP	A	A	G	rs7250003	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	34	37	1	0.566667	0.027027	A|0.575;G|0.425	0.425	strong	ZNF835,NS,carcinoma,0,2	ZNF835	106	2	NM_001005850	exon2	c.T1083C	p.P361P	GGGGTAAGGCCGC	.	scavenged	Atlas-SNP
OR8D2	283160	hgsc.bcm.edu	37	11	124189306	124189306	+	Missense_Mutation	SNP	G	G	A	rs2466620	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	40	88	0	0.481928	0	G|0.761;A|0.239	0.239	strong	.	OR8D2	65	.	NM_001002918	exon1	c.C788T	p.P263L	CTGGAAGGGGGCT	.	PASS	Atlas-SNP
TYK2	7297	hgsc.bcm.edu	37	19	10472452	10472452	+	Silent	SNP	G	G	A	rs12720355	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	34	69	0	0.5	0	G|0.992;A|0.008	0.008	strong	.	TYK2	126	.	NM_003331	exon13	c.C1953T	p.I651I	CAGGGCGATGTCA	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	rs6004901	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	37	76	0	0.425287	0	G|0.912;C|0.088	0.088	strong	.	MYO18B	322	.	NM_032608	exon43	c.G7184C	p.G2395A	ATGCGGGCTGTCC	.	PASS	Atlas-SNP
QSOX1	5768	hgsc.bcm.edu	37	1	180165582	180165582	+	Missense_Mutation	SNP	C	C	T	rs140386908	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	81	129	0	0.460227	0	C|0.997;T|0.003	0.003	strong	QSOX1,NS,carcinoma,-2,1	QSOX1	79	1	NM_002826	exon12	c.C1654T	p.R552W	GCTGCCCGGAGGG	.	PASS	Atlas-SNP
GNAT3	346562	hgsc.bcm.edu	37	7	80088041	80088041	+	Silent	SNP	G	G	A	rs2074674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	35	69	0	0.583333	0	G|0.553;A|0.447	0.447	strong	GNAT3_ENST00000398291,NS,carcinoma,0,2	GNAT3	65	2	NM_001102386	exon8	c.C1011T	p.D337D	AACTGCGTCAAAC	.	PASS	Atlas-SNP
UFSP1	402682	hgsc.bcm.edu	37	7	100486754	100486754	+	Missense_Mutation	SNP	G	G	C	rs12666989	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	32	72	0	0.507937	0	G|0.879;C|0.121	0.121	strong	.	UFSP1	8	.	NM_001015072	exon1	c.C139G	p.L47V	TCTCCAGCTCCCC	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	263592	263592	+	Missense_Mutation	SNP	G	G	A	rs199562017	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	5	287	0	0.0290698	0	G|0.020;A|0.980	0.980	strong	C17orf97_ENST00000360127,NS,haematopoietic_neoplasm,0,1	C17orf97	76	1	NM_001013672	exon2	c.G958A	p.E320K	GACCCCGAGGCCC	.	scavenged	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4512890	4512890	+	Missense_Mutation	SNP	G	G	A	rs199944112	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	65	285	1	0.970149	0.00350877	G|0.996;A|0.004	0.004	weak	.	PLIN4	191	.	NM_001080400	exon3	c.C1040T	p.T347I	AGGACAGTCTTGG	.	PASS	Atlas-SNP
CLCNKA	1187	hgsc.bcm.edu	37	1	16351275	16351275	+	Missense_Mutation	SNP	A	A	G	rs10927887	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	132	112	0	0.992481	0	A|0.397;G|0.603	0.603	strong	.	CLCNKA	56	.	NM_004070	exon4	c.A247G	p.R83G	CTGTACAGGGAGA	.	PASS	Atlas-SNP
EPHB4	2050	hgsc.bcm.edu	37	7	100410597	100410597	+	Silent	SNP	G	G	A	rs2230585	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	46	92	0	0.464646	0	G|0.683;A|0.317	0.317	strong	.	EPHB4	106	.	NM_004444	exon12	c.C1890T	p.C630C	CCCCCGGCACACC	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128477472	128477472	+	Silent	SNP	T	T	C	rs2291560	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	24	59	0	0.489796	0	T|0.879;C|0.121	0.121	strong	.	FLNC	339	.	NM_001127487	exon4	c.T720C	p.I240I	GGAGATTGTGGAC	.	PASS	Atlas-SNP
TIMM50	92609	hgsc.bcm.edu	37	19	39980412	39980412	+	Silent	SNP	C	C	T	rs114194716	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	38	57	0	0.408602	0	C|0.991;T|0.009	0.009	strong	.	TIMM50	37	.	NM_001001563	exon11	c.C1323T	p.F441F	CCTCTTCCTTGGC	.	PASS	Atlas-SNP
MMP24	10893	hgsc.bcm.edu	37	20	33834708	33834708	+	Silent	SNP	G	G	A	rs3764733	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	100	151	0	0.507614	0	G|0.841;A|0.159	0.159	strong	.	MMP24	35	.	NM_006690	exon2	c.G312A	p.A104A	CTCAGCGAAGGCC	.	PASS	Atlas-SNP
ALPPL2	251	hgsc.bcm.edu	37	2	233271669	233271669	+	Missense_Mutation	SNP	C	C	T	rs41415150		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	19	121	0	0.0935961	0	C|1.000;|0.000	.	weak	.	ALPPL2	36	.	NM_031313	exon1	c.C65T	p.P22L	TCATCCCAGGTAA	.	PASS	Atlas-SNP
HAP1	9001	hgsc.bcm.edu	37	17	39883350	39883350	+	Missense_Mutation	SNP	G	G	A	rs4523977	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	21	35	0	0.525	0	G|0.825;A|0.175	0.175	strong	.	HAP1	48	.	NM_177977	exon9	c.C1322T	p.T441M	AGAGACGTTCTGA	.	PASS	Atlas-SNP
KIF26A	26153	hgsc.bcm.edu	37	14	104642422	104642422	+	Silent	SNP	A	A	G	rs3742947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	12	19	0	0.521739	0	A|0.697;G|0.303	0.303	strong	.	KIF26A	84	.	NM_015656	exon12	c.A3297G	p.A1099A	GGGGGCAGCCTGG	.	PASS	Atlas-SNP
KIAA1614	57710	hgsc.bcm.edu	37	1	180905263	180905263	+	Missense_Mutation	SNP	C	C	T	rs17302207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	36	54	0	0.590164	0	C|0.975;T|0.025	0.025	strong	.	KIAA1614	75	.	NM_020950	exon5	c.C2218T	p.R740W	GATTCCCGGACTC	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55524172	55524172	+	Missense_Mutation	SNP	G	G	A	rs7306491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	72	152	0	0.458599	0	G|0.681;A|0.319	0.319	strong	.	OR9K2	63	.	NM_001005243	exon1	c.G620A	p.R207H	ATTCTCGCCCACT	.	PASS	Atlas-SNP
TRPC1	7220	hgsc.bcm.edu	37	3	142503605	142503605	+	Silent	SNP	G	G	A	rs7621642	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	63	118	1	0.533898	0.00847458	G|0.616;A|0.384	0.384	strong	TRPC1,NS,carcinoma,0,1	TRPC1	82	1	NM_001251845	exon7	c.G1020A	p.S340S	GATGTCGGGTTAC	.	scavenged	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65303100	65303100	+	Missense_Mutation	SNP	T	T	C	rs17404123	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	42	117	0	0.954545	0	C|0.104;N|0.001	0.104	strong	Q5T669_HUMAN,NS,carcinoma,0,2	EYS	527	2	NM_001142800	exon25	c.A3787G	p.I1263V	GGGGAATTGTATA	.	PASS	Atlas-SNP
FYTTD1	84248	hgsc.bcm.edu	37	3	197495334	197495334	+	Missense_Mutation	SNP	G	G	A	rs3205525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	30	45	0	0.535714	0	G|0.268;A|0.732	0.732	strong	.	FYTTD1	34	.	NM_032288	exon3	c.G260A	p.R87H	TGAATCGTAGAGG	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55542540	55542540	+	Missense_Mutation	SNP	G	G	A	rs61739567	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	53	129	0	0.481818	0	A|0.295;G|0.705	0.295	strong	.	RP1	429	.	NM_006269	exon4	c.G6098A	p.C2033Y	GGTTTTGTATGAA	.	PASS	Atlas-SNP
NES	10763	hgsc.bcm.edu	37	1	156641537	156641537	+	Missense_Mutation	SNP	C	C	T	rs951781	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	161	218	0	0.993827	0	C|0.783;T|0.217	0.217	strong	NES,NS,carcinoma,0,1	NES	196	1	NM_006617	exon4	c.G2443A	p.V815I	CCTCTACGCTCTC	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	37	7	149479935	149479935	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	38	118	0	0.351852	0	.	.	none	.	.	.	.	NM_198455	exon15	c.G1901A	p.G634E	TTCCAGGAGCTGT	.	PASS	Atlas-SNP
NPPA	4878	hgsc.bcm.edu	37	1	11906068	11906068	+	Missense_Mutation	SNP	A	A	G	rs5065	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	10	103	0	0.0826446	0	A|0.796;G|0.204	0.204	strong	.	NPPA	14	.	NM_006172	exon3	c.T454C	p.X152R	ATCTTCAGTACTG	.	PASS	Atlas-SNP
GRWD1	83743	hgsc.bcm.edu	37	19	48954421	48954421	+	Missense_Mutation	SNP	G	G	A	rs2302951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	37	94	0	0.41573	0	G|0.830;A|0.170	0.170	strong	.	GRWD1	41	.	NM_031485	exon6	c.G956A	p.R319Q	GCCGCCGGGAGCC	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13864728	13864728	+	Silent	SNP	C	C	A	rs6554827	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	55	133	1	0.504587	0.0075188	C|0.626;A|0.374	0.374	strong	DNAH5,NS,carcinoma,0,1	DNAH5	868	1	NM_001369	exon28	c.G4374T	p.R1458R	CAAGGCCCGGGGA	.	scavenged	Atlas-SNP
RIN3	79890	hgsc.bcm.edu	37	14	93118198	93118198	+	Silent	SNP	C	C	T	rs3814830	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	34	49	0	0.492754	0	C|0.764;T|0.236	0.236	strong	.	RIN3	81	.	NM_024832	exon6	c.C804T	p.A268A	TGATGCCACCTCA	.	PASS	Atlas-SNP
SYP	6855	hgsc.bcm.edu	37	X	49047924	49047924	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	30	28	0	0.967742	0	.	.	none	.	SYP	71	.	NM_003179	exon6	c.T912C	p.G304G	GGGTGCACCCTGC	.	PASS	Atlas-SNP
CHD7	55636	hgsc.bcm.edu	37	8	61765419	61765419	+	Silent	SNP	G	G	A	rs6999971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	36	59	0	0.5625	0	G|0.976;A|0.024	0.024	strong	.	CHD7	534	.	NM_017780	exon31	c.G6135A	p.P2045P	TGAGCCGATCACA	.	PASS	Atlas-SNP
MAP4K5	11183	hgsc.bcm.edu	37	14	50910675	50910675	+	Missense_Mutation	SNP	C	C	G	rs35768475	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	78	142	0	0.472727	0	C|0.994;G|0.006	0.006	strong	.	MAP4K5	48	.	NM_006575	exon19	c.G1419C	p.K473N	TTTGTCCTTTTTT	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11521542	11521542	+	Silent	SNP	T	T	C	rs3735502	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	102	229	1	0.5	0.00436681	T|0.800;C|0.200	0.200	strong	.	THSD7A	219	.	NM_015204	exon7	c.A1890G	p.P630P	CGGGCATGGGGCA	.	PASS	Atlas-SNP
SLC2A1	6513	hgsc.bcm.edu	37	1	43395635	43395635	+	Silent	SNP	C	C	T	rs2229682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	266	137	289	1	0.515038	0.00346021	T|0.144;G|0.000;C|0.856	0.144	strong	SLC2A1,NS,meningioma,-2,1	SLC2A1	36	1	NM_006516	exon5	c.G588A	p.P196P	CAGGGCCGGGATG	.	PASS	Atlas-SNP
MADCAM1	8174	hgsc.bcm.edu	37	19	501900	501900	+	Missense_Mutation	SNP	C	C	A	rs3745925	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	37	57	0	0.627119	0	C|0.760;A|0.240	0.240	strong	.	MADCAM1	29	.	NM_130760	exon4	c.C899A	p.P300H	CTGGGCCCACGCA	.	PASS	Atlas-SNP
HIF3A	64344	hgsc.bcm.edu	37	19	46812451	46812451	+	Missense_Mutation	SNP	C	C	T	rs61750957	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	74	100	0	0.513889	0	C|0.920;T|0.080	0.080	strong	.	HIF3A	154	.	NM_152795	exon6	c.C605T	p.A202V	CACCTGCGCAGAC	.	PASS	Atlas-SNP
TSSC4	10078	hgsc.bcm.edu	37	11	2424541	2424541	+	Missense_Mutation	SNP	C	C	G	rs2234279	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	64	148	0	0.463768	0	C|0.883;G|0.117	0.117	strong	.	TSSC4	19	.	NM_005706	exon2	c.C678G	p.H226Q	CAGACACGAGAGG	.	PASS	Atlas-SNP
SLC12A7	10723	hgsc.bcm.edu	37	5	1081702	1081702	+	Silent	SNP	A	A	G	rs6865765	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	45	110	0	0.505618	0	A|0.538;G|0.462	0.462	strong	.	SLC12A7	97	.	NM_006598	exon9	c.T1287C	p.P429P	CACGGAAGGGAAG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017575	1017575	+	Silent	SNP	C	C	T	rs76222533	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	592	55	465	31	0.0929054	0.0666667	C|0.500;T|0.500	0.500	strong	MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G5226A	p.T1742T	TTTGGCCGTGCTA	.	scavenged	Atlas-SNP
PRMT7	54496	hgsc.bcm.edu	37	16	68390697	68390697	+	Silent	SNP	C	C	T	rs61733486	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	52	116	0	0.40625	0	C|0.941;T|0.059	0.059	strong	.	PRMT7	51	.	NM_019023	exon18	c.C1905T	p.P635P	AGACCCCGAGGTA	.	PASS	Atlas-SNP
ACSS3	79611	hgsc.bcm.edu	37	12	81627215	81627215	+	Missense_Mutation	SNP	G	G	T	rs145641313	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	63	144	0	0.409091	0	G|0.999;T|0.001	0.001	strong	.	ACSS3	118	.	NM_024560	exon13	c.G1684T	p.A562S	AATGTTGCAGGTC	.	PASS	Atlas-SNP
DENND3	22898	hgsc.bcm.edu	37	8	142170884	142170884	+	Silent	SNP	C	C	T	rs2289001	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	199	216	0	0.99005	0	C|0.724;T|0.276	0.276	strong	DENND3,NS,carcinoma,0,1	DENND3	127	1	NM_014957	exon9	c.C1110T	p.F370F	CATCTTCAGGTAC	.	PASS	Atlas-SNP
OR11H6	122748	hgsc.bcm.edu	37	14	20692574	20692574	+	Missense_Mutation	SNP	T	T	C	rs17277221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	293	116	300	0	0.395904	0	C|0.445;N|0.000	0.445	strong	OR11H6,NS,carcinoma,-2,1	OR11H6	60	1	NM_001004480	exon1	c.T706C	p.Y236H	GGATCTTACACTC	.	PASS	Atlas-SNP
POC5	134359	hgsc.bcm.edu	37	5	74998598	74998598	+	Silent	SNP	G	G	A	rs35130836	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	59	114	0	0.375796	0	G|0.931;A|0.069	0.069	strong	.	POC5	82	.	NM_001099271	exon5	c.C345T	p.H115H	GACTGGGTGAGAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911957	29911957	+	Silent	SNP	G	G	A	rs77380700		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	113	386	1	0.588542	0.00259067	.	.	weak	.	HLA-A	89	.	NM_001242758	exon4	c.G678A	p.R226R	CCTGAGGTGCTGG	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55539395	55539395	+	Missense_Mutation	SNP	A	A	T	rs2293869	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	36	58	0	0.529412	0	A|0.687;T|0.313	0.313	strong	.	RP1	429	.	NM_006269	exon4	c.A2953T	p.N985Y	GGAGATAATCTAT	.	PASS	Atlas-SNP
NFKB2	4791	hgsc.bcm.edu	37	10	104160959	104160959	+	Silent	SNP	C	C	T	rs11574851	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	47	100	0	0.47	0	C|0.963;T|0.037	0.037	strong	.	NFKB2	48	.	NM_001077494	exon19	c.C2094T	p.N698N	TGAAAACGAGGAG	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123970530	123970530	+	Missense_Mutation	SNP	T	T	C	rs2295873	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	22	50	0	0.431373	0	T|0.693;C|0.307	0.307	strong	.	TACC2	271	.	NM_206862	exon9	c.T6590C	p.V2197A	CCGCTGTGGGGCC	.	PASS	Atlas-SNP
SYT1	6857	hgsc.bcm.edu	37	12	79611374	79611374	+	Silent	SNP	C	C	T	rs2037743	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	11	29	0	0.289474	0	C|0.312;T|0.688	0.688	strong	.	SYT1	70	.	NM_001135805	exon5	c.C75T	p.N25N	AAGCAACGCCACA	.	PASS	Atlas-SNP
TMEM214	54867	hgsc.bcm.edu	37	2	27260469	27260469	+	Missense_Mutation	SNP	G	G	A	rs1124649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	93	144	0	0.516667	0	G|0.713;A|0.287	0.287	strong	.	TMEM214	41	.	NM_017727	exon9	c.G1051A	p.V351M	CTGAAAGTGCTGG	.	PASS	Atlas-SNP
IGSF9B	22997	hgsc.bcm.edu	37	11	133807819	133807819	+	Silent	SNP	G	G	A	rs329635	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	89	144	0	0.473404	0	G|0.918;A|0.082	0.082	strong	.	IGSF9B	290	.	NM_014987	exon4	c.C447T	p.I149I	GGCCTCGATGTAC	.	PASS	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56420538	56420538	+	Missense_Mutation	SNP	C	C	T	rs11756977	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	89	215	1	0.497207	0.00465116	C|0.677;N|0.002	.	strong	.	DST	1427	.	NM_015548	exon41	c.G6872A	p.R2291H	ATCCCACGTAAAG	.	PASS	Atlas-SNP
AIM1	202	hgsc.bcm.edu	37	6	106960447	106960447	+	Silent	SNP	G	G	A	rs11152999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	7	61	0	0.155556	0	G|0.804;A|0.196	0.196	strong	.	AIM1	161	.	NM_001624	exon1	c.G231A	p.E77E	CCCAGAGTCCAAG	.	PASS	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	37	3	38592406	38592406	+	Silent	SNP	A	A	G	rs1805126	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	34	77	0	0.5	0	A|0.498;G|0.502	0.502	strong	.	SCN5A	634	.	NM_198056	exon28	c.T5457C	p.D1819D	CAGGGCATCGGCA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919064	12919064	+	Missense_Mutation	SNP	T	T	G	rs3204790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	19	269	4	0.0833333	0.0148699	T|0.824;G|0.176	0.176	strong	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon2	c.T200G	p.V67G	CTCTGGTATCGCT	.	scavenged	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62863518	62863518	+	Missense_Mutation	SNP	A	A	G	rs7113279	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	50	98	0	0.46729	0	A|0.492;G|0.508	0.508	strong	.	SLC22A24	31	.	NM_001136506	exon6	c.T1015C	p.S339P	ACAGGGAAAAAAT	.	PASS	Atlas-SNP
FCGR3A	2214	hgsc.bcm.edu	37	1	161514542	161514542	+	Missense_Mutation	SNP	A	A	C	rs396991	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	241	238	268	1	0.987552	0.00373134	A|0.681;C|0.319	0.319	strong	.	FCGR3A	38	.	NM_000569	exon4	c.T634G	p.F212V	TCCCAAAAAGCCC	.	PASS	Atlas-SNP
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42824907	42824907	+	Silent	SNP	G	G	A	rs9471932	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	43	71	0	0.472527	0	G|0.933;A|0.067	0.067	strong	KIAA0240,NS,carcinoma,0,1	.	.	1	NM_015349	exon9	c.G2187A	p.A729A	TGATGCGGTACAG	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193031926	193031926	+	Missense_Mutation	SNP	C	C	T	rs2280268	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	110	107	0	1	0	C|0.467;T|0.533	0.533	strong	ATP13A5,NS,adenoma,0,1	ATP13A5	171	1	NM_198505	exon19	c.G2215A	p.G739S	GGCTGCCTGGAGG	.	PASS	Atlas-SNP
NFIL3	4783	hgsc.bcm.edu	37	9	94172975	94172975	+	Silent	SNP	C	C	T	rs33973463	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	191	214	1	0.994792	0.0046729	C|0.941;T|0.059	0.059	strong	.	NFIL3	43	.	NM_005384	exon2	c.G42A	p.A14A	AAGAGACGCCTGC	.	PASS	Atlas-SNP
LSM6	11157	hgsc.bcm.edu	37	4	147110790	147110790	+	Silent	SNP	A	A	T	rs41280529	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	49	118	0	0.411765	0	A|0.991;T|0.009	0.009	strong	.	LSM6	5	.	NM_007080	exon4	c.A225T	p.T75T	CAGTACACAGAAG	.	PASS	Atlas-SNP
FGFRL1	53834	hgsc.bcm.edu	37	4	1019011	1019011	+	Missense_Mutation	SNP	C	C	T	rs4647932	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	57	105	0	0.527778	0	C|0.955;T|0.045	0.045	strong	FGFRL1,NS,carcinoma,0,1	FGFRL1	77	1	NM_001004356	exon7	c.C1391T	p.P464L	CAGGCCCAGTTGC	.	PASS	Atlas-SNP
CLUAP1	23059	hgsc.bcm.edu	37	16	3586230	3586230	+	Missense_Mutation	SNP	C	C	T	rs9790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	39	103	0	0.364486	0	C|0.851;N|0.000	.	strong	.	CLUAP1	32	.	NM_015041	exon12	c.C1201T	p.R401W	AGGGTCCGGAAAT	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36260858	36260858	+	Silent	SNP	C	C	T	rs2239795	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	32	62	0	0.477612	0	C|0.568;T|0.432	0.432	strong	PNPLA1_ENST00000394571,NS,carcinoma,+2,2	PNPLA1	92	2	NM_001145717	exon3	c.C459T	p.F153F	CTGCTTCGTCCCG	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243319611	243319611	+	Missense_Mutation	SNP	T	T	C	rs148125417	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	72	138	0	0.48	0	T|0.982;C|0.018	0.018	strong	.	CEP170	153	.	NM_014812	exon14	c.A3823G	p.M1275V	TAGGCATTGCTGA	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40374034	40374034	+	Missense_Mutation	SNP	A	A	G	rs3746009	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1233	756	372	1	0.613139	0.00268817	A|0.200;G|0.800	0.800	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon26	c.T12044C	p.V4015A	TTACCCACATGGC	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2162887	2162887	+	Silent	SNP	A	A	G	rs2369068	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	22	30	0	0.511628	0	A|0.796;G|0.204	0.204	strong	.	PKD1	184	.	NM_000296	exon13	c.T3063C	p.G1021G	CTGCAGACCCTGC	.	PASS	Atlas-SNP
KCNH6	81033	hgsc.bcm.edu	37	17	61623052	61623052	+	Missense_Mutation	SNP	C	C	T	rs35819807	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	50	64	0	0.510204	0	C|0.804;T|0.196	0.196	strong	.	KCNH6	122	.	NM_030779	exon14	c.C2774T	p.T925M	TGGCAACGGACAA	.	PASS	Atlas-SNP
BYSL	705	hgsc.bcm.edu	37	6	41895153	41895153	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	52	144	0	0.385185	0	.	.	none	.	BYSL	17	.	NM_004053	exon2	c.G310A	p.E104K	GACGAGGAGTGGC	.	PASS	Atlas-SNP
NPR2	4882	hgsc.bcm.edu	37	9	35802583	35802583	+	Silent	SNP	C	C	T	rs5812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	216	107	186	0	0.49537	0	C|0.695;T|0.305	0.305	strong	.	NPR2	162	.	NM_003995	exon11	c.C1794T	p.Y598Y	TGAATACTGTCCT	.	PASS	Atlas-SNP
ALDH1A3	220	hgsc.bcm.edu	37	15	101432798	101432798	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	70	136	0	0.551181	0	.	.	none	.	ALDH1A3	61	.	NM_000693	exon4	c.C429G	p.Y143X	CAGATACTTTGCA	.	PASS	Atlas-SNP
CLN5	1203	hgsc.bcm.edu	37	13	77566090	77566090	+	Missense_Mutation	SNP	C	C	T	rs77416795	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	6	4	4	0	0.666667	0	C|0.873;T|0.127	0.127	strong	CLN5,NS,carcinoma,-1,1	CLN5	32	1	NM_006493	exon1	c.C4T	p.R2C	GTCATGCGCCGGA	.	PASS	Atlas-SNP
ADAM2	2515	hgsc.bcm.edu	37	8	39695677	39695677	+	Missense_Mutation	SNP	C	C	A	rs34800519	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	49	113	0	0.395161	0	C|0.977;A|0.023	0.023	strong	ADAM2,NS,carcinoma,+1,1	ADAM2	124	1	NM_001464	exon1	c.G28T	p.G10W	CGAGCCCGCTGAG	.	PASS	Atlas-SNP
MRPL39	54148	hgsc.bcm.edu	37	21	26969703	26969703	+	Silent	SNP	T	T	C	rs1135618	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	73	121	0	0.493243	0	T|0.220;C|0.780	0.780	strong	.	MRPL39	61	.	NM_017446	exon6	c.A612G	p.K204K	AGCATCTTTTGTG	.	PASS	Atlas-SNP
SALL4	57167	hgsc.bcm.edu	37	20	50406871	50406871	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	2	126	0	0.0152672	0	.	.	none	SALL4,NS,carcinoma,-1,1	SALL4	168	1	NM_020436	exon2	c.G2151A	p.S717S	TGATGCCGAGTGG	.	scavenged	Atlas-SNP
ADAM30	11085	hgsc.bcm.edu	37	1	120437718	120437718	+	Silent	SNP	G	G	A	rs2793823	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	29	104	0	0.446154	0	G|0.719;A|0.280	0.280	strong	.	ADAM30	88	.	NM_021794	exon1	c.C1242T	p.D414D	ACCACAGTCACAT	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	37	3	45996761	45996761	+	Silent	SNP	G	G	A	rs1463680	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	66	127	0	0.47482	0	G|0.186;A|0.814	0.814	strong	.	FYCO1	115	.	NM_024513	exon14	c.C3924T	p.L1308L	TGGGTCGAGAGAA	.	PASS	Atlas-SNP
PHACTR4	65979	hgsc.bcm.edu	37	1	28793149	28793149	+	Silent	SNP	C	C	G	rs61748637	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	114	116	0	0.942149	0	C|0.945;G|0.055	0.055	strong	.	PHACTR4	64	.	NM_023923	exon5	c.C723G	p.P241P	AGCACCCAGGACT	.	PASS	Atlas-SNP
CDH3	1001	hgsc.bcm.edu	37	16	68721533	68721533	+	Missense_Mutation	SNP	G	G	C	rs1126933	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	57	118	0	0.53271	0	G|0.672;C|0.328	0.328	strong	.	CDH3	68	.	NM_001793	exon12	c.G1689C	p.Q563H	GCGCCAGGTGCTG	.	PASS	Atlas-SNP
TJP2	9414	hgsc.bcm.edu	37	9	71863235	71863235	+	Missense_Mutation	SNP	A	A	G	rs77236826	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	64	138	0	0.435374	0	A|0.944;G|0.056	0.056	strong	TJP2_ENST00000265384,NS,haematopoietic_neoplasm,0,1	TJP2	120	1	NM_001170630	exon19	c.A2975G	p.H992R	GAAGGCATTCCTA	.	PASS	Atlas-SNP
KIAA1109	84162	hgsc.bcm.edu	37	4	123280860	123280860	+	Silent	SNP	T	T	C	rs1127348	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	34	97	0	0.507463	0	T|0.843;C|0.157	0.157	strong	KIAA1109,colon,carcinoma,0,1	KIAA1109	424	1	NM_015312	exon83	c.T14784C	p.H4928H	ATGGCATCTAGAA	.	PASS	Atlas-SNP
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086407	46086407	+	Missense_Mutation	SNP	C	C	T	rs12481809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	253	127	228	0	0.501976	0	C|0.844;T|0.156	0.156	strong	.	KRTAP12-2	10	.	NM_181684	exon1	c.G397A	p.V133I	AGAGGACGCTGGT	.	PASS	Atlas-SNP
PRKCZ	5590	hgsc.bcm.edu	37	1	1987993	1987993	+	Silent	SNP	T	T	C	rs12184	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	172	176	0	0.914894	0	T|0.462;C|0.538	0.538	strong	.	PRKCZ	84	.	NM_002744	exon3	c.T264C	p.D88D	CAGGGATGAAGGC	.	PASS	Atlas-SNP
CSF2RA	1438	hgsc.bcm.edu	37	X	1401646	1401646	+	Missense_Mutation	SNP	C	C	G	rs67006588	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	454	185	350	0	0.407489	0	C|0.794;G|0.206	0.206	strong	.	CSF2RA	153	.	NM_172247	exon1	c.C50G	p.A17G	ACCCAGCATTCCT	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26774149	26774149	+	Silent	SNP	T	T	C	rs61754418	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	351	179	274	1	0.509971	0.00364964	T|0.987;C|0.013	0.013	strong	.	ITPR2	270	.	NM_002223	exon26	c.A3369G	p.V1123V	CTTTTCTACTGTC	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36485753	36485753	+	Silent	SNP	G	G	C	rs35803744	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	119	146	0	1	0	G|0.772;C|0.228	0.228	strong	.	GPR179	170	.	NM_001004334	exon11	c.C3699G	p.L1233L	GCTGCCGAGGGAC	.	PASS	Atlas-SNP
MRPL40	64976	hgsc.bcm.edu	37	22	19423250	19423250	+	Missense_Mutation	SNP	G	G	A	rs7575	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	49	117	0	0.4375	0	G|0.776;A|0.224	0.224	strong	.	MRPL40	13	.	NM_003776	exon4	c.G386A	p.R129H	AAGAGCGTAAGAT	.	PASS	Atlas-SNP
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56704399	56704399	+	Missense_Mutation	SNP	G	G	A	rs61745809	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	46	111	0	0.469388	0	G|0.915;A|0.085	0.085	strong	ZSCAN5B_ENST00000358992,NS,carcinoma,0,1	ZSCAN5B	160	1	NM_001080456	exon1	c.C23T	p.S8L	CCCCATGAGAGTG	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558317	140558317	+	Silent	SNP	C	C	G	rs17844489	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	51	970	0	0.241706	0	C|0.981;G|0.019	0.019	strong	.	PCDHB8	199	.	NM_019120	exon1	c.C702G	p.V234V	AGTTGTCGATGTC	.	PASS	Atlas-SNP
PCDHGC3	5098	hgsc.bcm.edu	37	5	140857798	140857798	+	Silent	SNP	T	T	C	rs1423148	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	57	94	0	0.548077	0	A|0.002;C|0.545	0.545	strong	.	PCDHGC3	173	.	NM_032402	exon1	c.T2115C	p.F705F	GGGGTTTGTGGTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195515100	195515100	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	5	137	0	0.0510204	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	NM_018406	exon2	c.C3351T	p.H1117H	GGTGGTGTGACCT	.	scavenged	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	256509	256509	+	Missense_Mutation	SNP	G	G	A	rs6962	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	59	133	0	0.483607	0	G|0.823;A|0.177	0.177	strong	SDHA,adrenal_gland,pheochromocytoma,0,1	SDHA	80	1	NM_004168	exon15	c.G1969A	p.V657I	GCCACCGTCCCGC	.	PASS	Atlas-SNP
KIF11	3832	hgsc.bcm.edu	37	10	94369247	94369247	+	Silent	SNP	C	C	T	rs145656661		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	20	49	0	0.37037	0	C|1.000;T|0.000	0.000	weak	.	KIF11	58	.	NM_004523	exon6	c.C679T	p.L227L	GCTACTCTGATGA	.	PASS	Atlas-SNP
ZWILCH	55055	hgsc.bcm.edu	37	15	66832466	66832466	+	Missense_Mutation	SNP	A	A	G	rs75532475	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	81	123	0	0.5	0	A|0.924;G|0.076	0.076	strong	.	ZWILCH	46	.	NM_017975	exon17	c.A1605G	p.I535M	GGAAATATATAGT	.	PASS	Atlas-SNP
GPATCH8	23131	hgsc.bcm.edu	37	17	42475670	42475670	+	Missense_Mutation	SNP	T	T	C	rs760339	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	24	49	0	0.510638	0	T|0.997;C|0.003	0.003	strong	.	GPATCH8	114	.	NM_001002909	exon8	c.A3775G	p.S1259G	GACTGCTGCTATC	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	37	12	133219831	133219831	+	Silent	SNP	T	T	C	rs5744944	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	24	61	0	0.4	0	T|0.448;C|0.552	0.552	strong	.	POLE	416	.	NM_006231	exon35	c.A4530G	p.A1510A	GACGGATGCCCTG	.	PASS	Atlas-SNP
ARID4A	5926	hgsc.bcm.edu	37	14	58831142	58831142	+	Missense_Mutation	SNP	A	A	G	rs1051858	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	60	110	0	0.495868	0	A|0.645;G|0.354	0.354	strong	.	ARID4A	222	.	NM_002892	exon20	c.A2335G	p.T779A	GAAAAAACAGAAG	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612745	53612745	+	Missense_Mutation	SNP	T	T	C	rs1133327	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	131	117	0	0.992424	0	T|0.490;C|0.510	0.510	strong	.	ZNF415	68	.	NM_018355	exon4	c.A553G	p.I185V	TTTTGATGGTAGA	.	PASS	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125848261	125848261	+	Silent	SNP	C	C	T	rs3740904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	63	49	0	1	0	C|0.626;T|0.374	0.374	strong	CDON,NS,carcinoma,0,1	CDON	137	1	NM_016952	exon18	c.G3294A	p.T1098T	CACGGCCGTGTAC	.	PASS	Atlas-SNP
PTK7	5754	hgsc.bcm.edu	37	6	43109751	43109751	+	Silent	SNP	G	G	A	rs6905948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	48	35	0	0.979592	0	G|0.619;A|0.381	0.381	strong	PTK7,NS,carcinoma,+2,1	PTK7	101	1	NM_001270398	exon12	c.G1875A	p.G625G	CCAGGGGGACCCC	.	PASS	Atlas-SNP
ZNF283	284349	hgsc.bcm.edu	37	19	44352639	44352639	+	Missense_Mutation	SNP	G	G	A	rs1061768	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	51	93	0	0.6	0	G|0.832;A|0.168	0.168	strong	.	ZNF283	83	.	NM_181845	exon7	c.G1886A	p.R629H	ATCAACGTAAGGA	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140625429	140625429	+	Missense_Mutation	SNP	C	C	A	rs142267472	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	51	79	0	0.614458	0	C|0.997;A|0.003	0.003	strong	.	PCDHB15	138	.	NM_018935	exon1	c.C283A	p.L95M	GAGAAGCTGTGTG	.	PASS	Atlas-SNP
NT5DC3	51559	hgsc.bcm.edu	37	12	104186946	104186946	+	Silent	SNP	G	G	T	rs1866295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	91	122	0	0.541667	0	G|0.708;T|0.292	0.292	strong	.	NT5DC3	113	.	NM_001031701	exon9	c.C1015A	p.R339R	ACCTCCGCTTATC	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135669810	135669810	+	Missense_Mutation	SNP	C	C	T	rs17778003	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	79	129	0	0.603053	0	C|0.919;T|0.081	0.081	strong	.	ZFAT	265	.	NM_001174157	exon2	c.G190A	p.G64R	CATCTCCGGTTTT	.	PASS	Atlas-SNP
SUPT3H	8464	hgsc.bcm.edu	37	6	45290634	45290634	+	Missense_Mutation	SNP	G	G	A	rs9472463	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	79	156	0	0.451429	0	G|0.989;A|0.011	0.011	strong	.	SUPT3H	75	.	NM_181356	exon3	c.C20T	p.T7M	AAGAACGTTGTTC	.	PASS	Atlas-SNP
CNRIP1	25927	hgsc.bcm.edu	37	2	68511584	68511584	+	Silent	SNP	A	A	G	rs735815	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	36	57	0	0.553846	0	A|0.599;G|0.401	0.401	strong	CNRIP1_ENST00000409559,NS,carcinoma,0,1	CNRIP1	45	1	NM_001111101	exon3	c.T363C	p.S121S	TGTAAGAGAGATC	.	PASS	Atlas-SNP
EDC4	23644	hgsc.bcm.edu	37	16	67911517	67911517	+	Silent	SNP	T	T	C	rs8060686	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	57	115	0	0.6	0	T|0.669;C|0.331	0.331	strong	.	EDC4	101	.	NM_014329	exon6	c.T747C	p.C249C	CTGCTGTGAGGAG	.	PASS	Atlas-SNP
XRN2	22803	hgsc.bcm.edu	37	20	21349188	21349188	+	Silent	SNP	G	G	A	rs149896399	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	26	57	0	0.329114	0	G|0.999;A|0.001	0.001	strong	.	XRN2	90	.	NM_012255	exon27	c.G2544A	p.P848P	CAGGCCGCTTTTG	.	PASS	Atlas-SNP
HYDIN	54768	hgsc.bcm.edu	37	16	71163693	71163693	+	Silent	SNP	A	A	G	rs4788770	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	46	145	0	0.294872	0	A|0.625;G|0.375	0.375	strong	.	HYDIN	788	.	NM_001198542	exon9	c.T1158C	p.D386D	AGTCTCATCCTTC	.	PASS	Atlas-SNP
CLCNKB	1188	hgsc.bcm.edu	37	1	16380252	16380252	+	Silent	SNP	C	C	T	rs45512797	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	153	169	0	0.884393	0	C|0.383;T|0.617	0.617	strong	.	CLCNKB	50	.	NM_000085	exon16	c.C1741T	p.L581L	TATCCCCTGGTGG	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626571	140626571	+	Silent	SNP	C	C	A	rs652104	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	70	150	1	0.510949	0.00666667	C|0.766;A|0.234	0.234	strong	PCDHB15,NS,carcinoma,0,1	PCDHB15	138	1	NM_018935	exon1	c.C1425A	p.A475A	CAGCGCCACAGAC	.	scavenged	Atlas-SNP
CEACAM16	388551	hgsc.bcm.edu	37	19	45211407	45211407	+	Silent	SNP	C	C	T	rs61744497	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	99	169	0	0.614907	0	C|0.867;T|0.133	0.133	strong	.	CEACAM16	56	.	NM_001039213	exon6	c.C1215T	p.T405T	CAAGACCGTCACA	.	PASS	Atlas-SNP
SLC12A8	84561	hgsc.bcm.edu	37	3	124826408	124826408	+	Missense_Mutation	SNP	T	T	C	rs6773138	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	100	191	0	0.555556	0	T|0.903;C|0.097	0.097	strong	.	SLC12A8	81	.	NM_024628	exon10	c.A1622G	p.K541R	TCGCTCTTGGAAG	.	PASS	Atlas-SNP
NME8	51314	hgsc.bcm.edu	37	7	37934147	37934147	+	Silent	SNP	A	A	T	rs41276027	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	225	225	176	0	1	0	A|0.761;T|0.239	0.239	strong	.	.	.	.	NM_016616	exon16	c.A1479T	p.I493I	GCAAATAGAGAAA	.	PASS	Atlas-SNP
TPTE2	93492	hgsc.bcm.edu	37	13	20006620	20006620	+	Silent	SNP	C	C	T	rs76525011		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	57	205	0	0.248908	0	.	.	weak	TPTE2_ENST00000400230,NS,carcinoma,0,6	TPTE2	225	6	NM_199254	exon17	c.G1215A	p.S405S	ACGAATCGAATAA	.	scavenged	Atlas-SNP
TGM6	343641	hgsc.bcm.edu	37	20	2377204	2377204	+	Silent	SNP	C	C	T	rs16984872	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	250	115	217	0	0.46	0	C|0.960;T|0.040	0.040	strong	TGM6,NS,carcinoma,0,1	TGM6	126	1	NM_198994	exon4	c.C477T	p.S159S	GCTCAGCGACAGC	.	PASS	Atlas-SNP
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	58	121	0	0.43609	0	G|0.861;A|0.139	0.139	strong	MDS1,NS,carcinoma,0,1	MECOM	216	1	NM_004991	exon2	c.C358T	p.P120S	AACTGGGGTCTTT	.	PASS	Atlas-SNP
RADIL	55698	hgsc.bcm.edu	37	7	4876064	4876064	+	Silent	SNP	G	G	A	rs150209652	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	34	34	0	0.618182	0	G|0.987;A|0.013	0.013	strong	.	RADIL	110	.	NM_018059	exon3	c.C708T	p.P236P	GGGGCCGGGCTCC	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39091526	39091526	+	Silent	SNP	T	T	C	rs4515515	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	85	87	0	1	0	T|0.781;C|0.219	0.219	strong	ADAM32,NS,carcinoma,0,1	ADAM32	70	1	NM_145004	exon16	c.T1743C	p.T581T	CATAACTGTAGAC	.	PASS	Atlas-SNP
ZDHHC14	79683	hgsc.bcm.edu	37	6	157963743	157963743	+	Silent	SNP	G	G	A	rs2365611	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	10	80	0	0.243902	0	G|0.627;A|0.373	0.373	strong	.	ZDHHC14	39	.	NM_024630	exon2	c.G372A	p.T124T	AGCCACGCCTGAT	.	PASS	Atlas-SNP
GOLGA4	2803	hgsc.bcm.edu	37	3	37368600	37368600	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	50	146	0	0.396825	0	.	.	none	.	GOLGA4	173	.	NM_001172713	exon15	c.A5289T	p.L1763F	TGTTTTACAAAGA	.	PASS	Atlas-SNP
GPR50	9248	hgsc.bcm.edu	37	X	150349533	150349533	+	Missense_Mutation	SNP	G	G	A	rs62620754	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	59	55	0	0.983333	0	G|0.903;A|0.097	0.097	strong	.	GPR50	195	.	NM_004224	exon2	c.G1478A	p.S493N	CCTTCAGTGCTGC	.	PASS	Atlas-SNP
PTPRJ	5795	hgsc.bcm.edu	37	11	48157625	48157625	+	Silent	SNP	C	C	T	rs148782546	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	127	212	0	0.51626	0	C|0.998;T|0.002	0.002	strong	PTPRJ_ENST00000418331,caecum,carcinoma,0,2	PTPRJ	225	2	NM_002843	exon9	c.C1650T	p.Y550Y	GGTCTACGTCACC	.	PASS	Atlas-SNP
ZNF221	7638	hgsc.bcm.edu	37	19	44471252	44471252	+	Missense_Mutation	SNP	T	T	C	rs61734609	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	30	51	0	0.508475	0	T|0.910;C|0.090	0.090	strong	.	ZNF221	59	.	NM_013359	exon6	c.T1598C	p.L533P	AAAAGCTATACAA	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3416449	3416449	+	Missense_Mutation	SNP	C	C	A	rs7553399	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	52	31	0	1	0	C|0.437;A|0.563	0.563	strong	.	MEGF6	91	.	NM_001409	exon22	c.G2747T	p.R916L	TGGCACCGCTGCT	.	PASS	Atlas-SNP
KIR3DL2	3812	hgsc.bcm.edu	37	19	55367311	55367311	+	Missense_Mutation	SNP	G	G	A	rs201726108	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	31	78	0	0.449275	0	G|0.910;A|0.091	0.091	strong	KIR3DL2,NS,carcinoma,0,1	KIR3DL2	55	1	NM_001242867	exon5	c.G893A	p.R298H	CTTTCCGTGCCCT	.	scavenged	Atlas-SNP
RIMBP3	85376	hgsc.bcm.edu	37	22	20457107	20457107	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	640	9	706	3	0.0140625	0.00424929	.	.	none	RIMBP3,NS,carcinoma,+1,1	RIMBP3	42	1	NM_015672	exon1	c.A4195G	p.R1399G	CCCTCCTCTCCTC	.	scavenged	Atlas-SNP
KRT75	9119	hgsc.bcm.edu	37	12	52825363	52825363	+	Silent	SNP	G	G	A	rs1798640	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	49	122	0	0.398374	0	G|0.370;A|0.630	0.630	strong	.	KRT75	75	.	NM_004693	exon4	c.C834T	p.P278P	CTCCTCGGGCAGA	.	PASS	Atlas-SNP
LPPR2	0	hgsc.bcm.edu	37	19	11473358	11473358	+	Missense_Mutation	SNP	C	C	G	rs11540666	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	26	69	0	0.42623	0	C|0.954;G|0.046	0.046	strong	LPPR2,lymph_node,lymphoid_neoplasm,0,1	LPPR2	21	1	NM_022737	exon7	c.C833G	p.T278S	TCGCCACCTTTTT	.	PASS	Atlas-SNP
ZNF69	7620	hgsc.bcm.edu	37	19	11998777	11998777	+	Silent	SNP	C	C	T	rs3810314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	40	73	0	0.487805	0	C|0.897;T|0.103	0.103	strong	.	ZNF69	27	.	NM_021915	exon1	c.C39T	p.P13P	GGACCCCGGGACA	.	PASS	Atlas-SNP
MUC1	4582	hgsc.bcm.edu	37	1	155161833	155161833	+	Silent	SNP	C	C	G	rs147687610	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	19	38	0	0.463415	0	C|0.995;G|0.005	0.005	strong	.	MUC1	94	.	NM_001204286	exon2	c.G327C	p.S109S	TGGGACCGAGGTG	.	PASS	Atlas-SNP
PAX7	5081	hgsc.bcm.edu	37	1	19018432	19018432	+	Silent	SNP	A	A	C	rs2076019	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	57	64	0	0.919355	0	A|0.915;C|0.085	0.085	strong	.	PAX7	127	.	NM_002584	exon5	c.A771C	p.T257T	GCTGACAGAGGCG	.	PASS	Atlas-SNP
SH2D4B	387694	hgsc.bcm.edu	37	10	82369219	82369219	+	Missense_Mutation	SNP	T	T	A	rs17107368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	42	92	1	0.47191	0.0108696	T|0.847;A|0.153	0.153	strong	SH2D4B,colon,carcinoma,+2,1	SH2D4B	44	1	NM_207372	exon6	c.T897A	p.D299E	CAGAGATGTCATC	.	scavenged	Atlas-SNP
MTMR9	66036	hgsc.bcm.edu	37	8	11162496	11162496	+	Silent	SNP	A	A	C	rs2164272	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	101	110	0	1	0	A|0.640;C|0.360	0.360	strong	.	MTMR9	58	.	NM_015458	exon4	c.A564C	p.L188L	AGTACTAAGCTAT	.	PASS	Atlas-SNP
PPA2	27068	hgsc.bcm.edu	37	4	106345379	106345379	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	31	43	0	0.413333	0	.	.	none	.	PPA2	23	.	NM_176869	exon7	c.A629G	p.N210S	GGATCATTCGCAT	.	PASS	Atlas-SNP
LMNA	4000	hgsc.bcm.edu	37	1	156107534	156107534	+	Silent	SNP	C	C	T	rs4641	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	16	27	0	0.432432	0	C|0.808;T|0.192	0.192	strong	.	LMNA	31	.	NM_170707	exon10	c.C1698T	p.H566H	CCACCACGTGAGT	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43822171	43822171	+	Missense_Mutation	SNP	G	G	A	rs7310011	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	80	168	0	0.512821	0	G|0.974;A|0.026	0.026	strong	.	ADAMTS20	635	.	NM_025003	exon26	c.C3818T	p.S1273F	ACAGGGGAACTAG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	48	98	0	0.432432	0	T|0.764;A|0.236	0.236	strong	.	RP1L1	453	.	NM_178857	exon4	c.A5666T	p.D1889V	TCTACATCTTCTG	.	PASS	Atlas-SNP
GJA9	81025	hgsc.bcm.edu	37	1	39340607	39340607	+	Silent	SNP	A	A	G	rs16825625	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	186	214	0	0.916256	0	A|0.929;G|0.071	0.071	strong	GJA9,NS,carcinoma,-1,1	GJA9	55	1	NM_030772	exon2	c.T1164C	p.R388R	AATAGAACGGTGA	.	PASS	Atlas-SNP
C1orf64	149563	hgsc.bcm.edu	37	1	16330816	16330816	+	Silent	SNP	C	C	T	rs1763617	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	10	154	0	0.0561798	0	C|0.835;T|0.165	0.165	strong	.	C1orf64	16	.	NM_178840	exon1	c.C18T	p.D6D	AGAAGACCCCAGG	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362702	32362702	+	Silent	SNP	T	T	C	rs41342846	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	38	152	0	0.35514	0	T|0.871;C|0.129	0.129	strong	.	BTNL2	50	.	NM_019602	exon6	c.A1179G	p.P393P	CCTCCATGGCACG	.	PASS	Atlas-SNP
BAI3	577	hgsc.bcm.edu	37	6	70064187	70064187	+	Silent	SNP	G	G	A	rs2296974	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	62	120	0	0.984127	0	G|0.792;A|0.208	0.208	strong	BAI3,NS,carcinoma,0,1	BAI3	451	1	NM_001704	exon27	c.G3522A	p.S1174S	TTCTTCGAGTTCG	.	PASS	Atlas-SNP
ARSG	22901	hgsc.bcm.edu	37	17	66391276	66391276	+	Missense_Mutation	SNP	G	G	A	rs9972951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	79	137	0	0.49375	0	G|0.931;A|0.069	0.069	strong	.	ARSG	55	.	NM_001267727	exon10	c.G1154A	p.R385H	GACGGCGCTTTGA	.	PASS	Atlas-SNP
ACPP	55	hgsc.bcm.edu	37	3	132075707	132075707	+	Silent	SNP	A	A	G	rs2071505	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	50	116	0	0.471698	0	A|0.554;G|0.446	0.446	strong	.	ACPP	118	.	NM_001099	exon10	c.A1146G	p.E382E	TACTGAAGACAGT	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151962289	151962289	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	11	177	0	0.0639535	0	.	.	none	MLL3_ENST00000355193,NS,carcinoma,+2,2	MLL3	1564	2	NM_170606	exon8	c.G1018A	p.E340K	CATCTTCCTTCGC	.	scavenged	Atlas-SNP
EIF2AK3	9451	hgsc.bcm.edu	37	2	88913273	88913273	+	Missense_Mutation	SNP	G	G	C	rs867529	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	27	47	0	0.45	0	G|0.764;C|0.236	0.236	strong	.	EIF2AK3	160	.	NM_004836	exon2	c.C407G	p.S136C	ACCAAGGAACCGG	.	PASS	Atlas-SNP
RBM47	54502	hgsc.bcm.edu	37	4	40427990	40427990	+	Silent	SNP	G	G	C	rs2292039	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	47	65	0	0.522222	0	G|0.959;C|0.041	0.041	strong	.	RBM47	146	.	NM_001098634	exon7	c.C1713G	p.G571G	TATGTAGCCTGCG	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144854564	144854564	+	Silent	SNP	G	G	A	rs147331822	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	230	28	285	2	0.121739	0.00701754	G|0.935;A|0.065	0.065	strong	PDE4DIP_ENST00000369356,colon,carcinoma,0,2	PDE4DIP	817	2	NM_014644	exon42	c.C6906T	p.N2302N	GTTGGCGTTCTTC	.	scavenged	Atlas-SNP
SLC35G2	80723	hgsc.bcm.edu	37	3	136574521	136574521	+	Silent	SNP	C	C	T	rs1052620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	56	172	0	0.397163	0	C|0.857;T|0.143	0.143	strong	.	.	.	.	NM_025246	exon2	c.C1219T	p.L407L	GAAATACTAGACT	.	PASS	Atlas-SNP
MYH7	4625	hgsc.bcm.edu	37	14	23902753	23902753	+	Silent	SNP	G	G	A	rs2069540	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	51	47	0	0.980769	0	G|0.488;A|0.512	0.512	strong	.	MYH7	349	.	NM_000257	exon3	c.C189T	p.T63T	ATACTCGGTCTCG	.	PASS	Atlas-SNP
CGB7	94027	hgsc.bcm.edu	37	19	49557572	49557572	+	Silent	SNP	T	T	C	rs62127880	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	44	205	4	0.268293	0.0195122	T|0.962;C|0.038	0.038	strong	CGB7,NS,carcinoma,-1,1	CGB7	10	1	NM_033142	exon3	c.A474G	p.S158S	GGTGTCTGAGGGC	.	scavenged	Atlas-SNP
OR8H3	390152	hgsc.bcm.edu	37	11	55889895	55889895	+	Missense_Mutation	SNP	C	C	T	rs61751933	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	90	206	0	0.5	0	C|0.900;T|0.100	0.100	strong	OR8H3,NS,carcinoma,0,1	OR8H3	92	1	NM_001005201	exon1	c.C47T	p.T16M	TCCTTACGGGACT	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340841	55340841	+	Silent	SNP	G	G	C	rs150471749	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	10	23	0	0.30303	0	G|0.905;C|0.096	0.096	strong	.	KIR3DL1	174	.	NM_013289	exon7	c.G1026C	p.L342L	CATTCTGATTGGG	.	PASS	Atlas-SNP
CHRM1	1128	hgsc.bcm.edu	37	11	62677529	62677529	+	Silent	SNP	C	C	T	rs2067478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	25	48	0	0.446429	0	C|0.938;T|0.062	0.062	strong	.	CHRM1	29	.	NM_000738	exon2	c.G1044A	p.Q348Q	GGCCAGCTGCTCC	.	PASS	Atlas-SNP
ABCG4	64137	hgsc.bcm.edu	37	11	119025270	119025270	+	Silent	SNP	G	G	A	rs200058802	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	20	66	0	0.384615	0	G|0.999;A|0.001	0.001	weak	.	ABCG4	77	.	NM_022169	exon5	c.G525A	p.E175E	GCAGGAGGTGAAG	.	PASS	Atlas-SNP
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58350631	58350631	+	Silent	SNP	C	C	T	rs10122	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	34	93	0	0.382022	0	C|0.485;T|0.515	0.515	strong	.	XRCC6BP1	22	.	NM_033276	exon6	c.C699T	p.H233H	TGCTCACAGAGAC	.	PASS	Atlas-SNP
DNAJC13	23317	hgsc.bcm.edu	37	3	132166302	132166302	+	Silent	SNP	T	T	G	rs116489157	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	76	130	0	0.554745	0	T|0.990;G|0.010	0.010	strong	.	DNAJC13	253	.	NM_015268	exon4	c.T282G	p.L94L	ACTTCTTACAGAA	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3173964	3173964	+	Silent	SNP	G	G	A	rs2230163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	64	55	0	1	0	T|0.130;G|0.427;C|0.268;A|0.175	0.175	strong	.	MYOM1	192	.	NM_003803	exon8	c.C1146T	p.H382H	CCCAGCGTGGAAG	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30888169	30888169	+	Silent	SNP	G	G	A	rs2517468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	35	89	0	0.376344	0	G|0.731;A|0.269	0.269	strong	VARS2,NS,carcinoma,0,1	VARS2	60	1	NM_001167734	exon14	c.G1443A	p.L481L	GGGCCTGTTCCGG	.	PASS	Atlas-SNP
TLR6	10333	hgsc.bcm.edu	37	4	38829832	38829832	+	Silent	SNP	T	T	C	rs3775073	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	78	138	0	0.557143	0	T|0.564;C|0.436	0.436	strong	.	TLR6	67	.	NM_006068	exon2	c.A1263G	p.K421K	GTTTTCTTTATGT	.	PASS	Atlas-SNP
TMCO3	55002	hgsc.bcm.edu	37	13	114164578	114164578	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	4	201	0	0.0199005	0	.	.	none	TMCO3,NS,carcinoma,-1,1	TMCO3	77	1	NM_017905	exon7	c.C1064T	p.P355L	AAGGGCCGTGTTA	.	scavenged	Atlas-SNP
PALLD	23022	hgsc.bcm.edu	37	4	169433326	169433326	+	Missense_Mutation	SNP	T	T	C	rs7655494	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	24	77	0	0.436364	0	T|0.732;C|0.268	0.268	strong	.	PALLD	179	.	NM_001166108	exon2	c.T671C	p.M224T	GCCCTATGGAAGA	.	PASS	Atlas-SNP
ITSN1	6453	hgsc.bcm.edu	37	21	35201947	35201947	+	Silent	SNP	C	C	T	rs1108000	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	27	43	0	0.482143	0	C|0.872;T|0.128	0.128	strong	.	ITSN1	166	.	NM_001001132	exon27	c.C3249T	p.A1083A	TATTGCCTCATAC	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248834	48248834	+	Silent	SNP	T	T	C	rs10404034	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	70	96	0	0.588235	0	A|0.000;C|0.097;T|0.903	0.097	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.T18C	p.S6S	AGGCAGTGGCGTT	.	PASS	Atlas-SNP
CDH8	1006	hgsc.bcm.edu	37	16	61935330	61935330	+	Silent	SNP	T	T	C	rs368241476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	44	117	0	0.40367	0	.	.	weak	.	CDH8	273	.	NM_001796	exon3	c.A300G	p.L100L	ACCTGATAGGATA	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218695102	218695102	+	Missense_Mutation	SNP	G	G	A	rs3796028	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	63	66	0	0.984375	0	G|0.646;A|0.354	0.354	strong	.	TNS1	251	.	NM_022648	exon21	c.C3010T	p.R1004W	GGATCCGTCTTCT	.	PASS	Atlas-SNP
CMYA5	202333	hgsc.bcm.edu	37	5	79032562	79032562	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	3	149	1	0.0194805	0.00671141	.	.	none	CMYA5_ENST00000446378,lower_third,carcinoma,0,2	CMYA5	643	2	NM_153610	exon2	c.A7974G	p.V2658V	TCTAGTATTAGAA	.	scavenged	Atlas-SNP
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	63	100	0	0.954545	0	A|0.692;G|0.308	0.308	strong	.	HBS1L	75	.	NM_006620	exon17	c.T1977C	p.F659F	CTCTTTAAAGTCT	.	PASS	Atlas-SNP
KRIT1	889	hgsc.bcm.edu	37	7	91842554	91842554	+	Silent	SNP	T	T	C	rs11542682	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	51	69	0	0.504951	0	T|0.867;C|0.133	0.133	strong	KRIT1,NS,carcinoma,0,1	KRIT1	66	1	NM_194456	exon18	c.A1980G	p.V660V	CACTCCTACATAC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134691424	134691424	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	301	16	315	0	0.0531561	0	.	.	none	.	TTC40	100	.	NM_001200049	exon30	c.G4173T	p.K1391N	CTTCTCCTTGTCC	.	PASS	Atlas-SNP
GLUL	2752	hgsc.bcm.edu	37	1	182356399	182356399	+	Silent	SNP	A	A	G	rs1058111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	66	139	0	0.5	0	T|0.000;G|0.662;C|0.000;A|0.338	0.662	strong	.	GLUL	38	.	NM_001033056	exon3	c.T195C	p.S65S	AGTACTAGAGCCA	.	PASS	Atlas-SNP
SULT2B1	6820	hgsc.bcm.edu	37	19	49096065	49096065	+	Silent	SNP	C	C	T	rs2302948	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	24	34	0	0.545455	0	C|0.814;T|0.186	0.186	strong	.	SULT2B1	72	.	NM_177973	exon5	c.C637T	p.L213L	GAGGAGCTGCAGC	.	PASS	Atlas-SNP
DCAF12L2	340578	hgsc.bcm.edu	37	X	125298690	125298690	+	Silent	SNP	G	G	A	rs3761552	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	133	127	0	0.985185	0	G|0.437;A|0.563	0.563	strong	.	DCAF12L2	157	.	NM_001013628	exon1	c.C1218T	p.C406C	TCTGCCGCAGGCA	.	PASS	Atlas-SNP
CDRT15	146822	hgsc.bcm.edu	37	17	14140081	14140081	+	Nonsense_Mutation	SNP	G	G	A	rs11651890	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	35	220	0	0.144628	0	G|0.908;A|0.092	0.092	strong	.	CDRT15	20	.	NM_001007530	exon1	c.C70T	p.R24X	ATCGTCGGAAAAG	.	PASS	Atlas-SNP
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248907	48248907	+	Missense_Mutation	SNP	G	G	C	rs78530808	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	81	98	0	0.55102	0	G|0.987;C|0.013	0.013	strong	.	GLTSCR2	45	.	NM_015710	exon1	c.G91C	p.D31H	TCGGTGGACCCAG	.	PASS	Atlas-SNP
MBL2	4153	hgsc.bcm.edu	37	10	54531242	54531242	+	Missense_Mutation	SNP	G	G	A	rs5030737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	63	136	0	0.954545	0	G|0.957;A|0.043	0.043	strong	.	MBL2	55	.	NM_000242	exon1	c.C154T	p.R52C	CATCACGCCCATC	.	PASS	Atlas-SNP
OR1F1	4992	hgsc.bcm.edu	37	16	3254470	3254470	+	Missense_Mutation	SNP	T	T	C	rs1834026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	271	136	214	0	0.501845	0	T|0.581;G|0.003	.	strong	.	OR1F1	36	.	NM_012360	exon1	c.T224C	p.F75S	TCTCCTTCACCAC	.	PASS	Atlas-SNP
KRT80	144501	hgsc.bcm.edu	37	12	52579315	52579315	+	Silent	SNP	C	C	T	rs151324530	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	19	33	0	0.575758	0	C|0.999;T|0.001	0.001	strong	.	KRT80	68	.	NM_182507	exon2	c.G357A	p.Q119Q	CTGGCCCTGCAGG	.	PASS	Atlas-SNP
TGM5	9333	hgsc.bcm.edu	37	15	43545728	43545728	+	Silent	SNP	G	G	A	rs555001	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	23	49	0	0.534884	0	G|0.539;A|0.461	0.461	strong	.	TGM5	88	.	NM_201631	exon5	c.C660T	p.Y220Y	GCTGACGTAGACG	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608855	26608855	+	Missense_Mutation	SNP	C	C	T	rs201756933		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	15	26	0	0.375	0	.	.	weak	.	UBXN11	54	.	NM_183008	exon16	c.G1498A	p.G500S	TGGGGCCGGGACC	.	PASS	Atlas-SNP
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847050	100847050	+	Silent	SNP	A	A	G	rs569270	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	124	189	0	0.992	0	A|0.479;G|0.521	0.521	strong	.	ARHGAP42	32	.	NM_152432	exon20	c.A2118G	p.S706S	TGCTTCAGTCACT	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45123937	45123937	+	Silent	SNP	T	T	C	rs112035890	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	10	59	0	0.2	0	T|0.946;C|0.054	0.054	strong	.	NACAD	44	.	NM_001146334	exon2	c.A1842G	p.S614S	GGCTGATGAGAGA	.	PASS	Atlas-SNP
ODF2	4957	hgsc.bcm.edu	37	9	131262512	131262512	+	Missense_Mutation	SNP	G	G	A	rs142129915	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	58	105	0	0.522523	0	G|0.996;A|0.004	0.004	strong	ODF2,NS,carcinoma,+1,1	ODF2	227	1	NM_153435	exon21	c.G2660A	p.R887H	CCATCCGCTCCCG	.	PASS	Atlas-SNP
ITGA6	3655	hgsc.bcm.edu	37	2	173339808	173339808	+	Missense_Mutation	SNP	G	G	A	rs11895564	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	44	87	0	0.488889	0	G|0.714;A|0.286	0.286	strong	ITGA6,NS,NS,-1,1	ITGA6	171	1	NM_001079818	exon7	c.G1138A	p.A380T	GGCATTGCAGTAA	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33875284	33875284	+	Missense_Mutation	SNP	G	G	A	rs9907259	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	48	91	0	0.571429	0	G|0.939;A|0.061	0.061	strong	.	SLFN14	43	.	NM_001129820	exon4	c.C2713T	p.L905F	CATAAAGCAGGTA	.	PASS	Atlas-SNP
TTLL2	83887	hgsc.bcm.edu	37	6	167754360	167754360	+	Silent	SNP	C	C	T	rs77767783	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	80	174	0	0.888889	0	C|0.998;T|0.002	0.002	strong	.	TTLL2	82	.	NM_031949	exon3	c.C972T	p.L324L	GACGCTCAGCAGA	.	PASS	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	96039597	96039597	+	Missense_Mutation	SNP	G	G	C	rs2274224	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	94	109	1	1	0.00917431	G|0.526;C|0.474	0.474	strong	.	PLCE1	543	.	NM_016341	exon20	c.G4724C	p.R1575P	ACCCCCGACCTGC	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129722389	129722389	+	Silent	SNP	A	A	G	rs3749877	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	13	29	0	0.8125	0	A|0.460;G|0.540	0.540	strong	.	LAMA2	481	.	NM_000426	exon38	c.A5466G	p.E1822E	TGTTGAAAGCGGC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1061804	1061804	+	Silent	SNP	T	T	C	rs78320196	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	87	156	0	0.47541	0	T|0.960;C|0.040	0.040	strong	.	ABCA7	174	.	NM_019112	exon41	c.T5487C	p.N1829N	TGTGAATGGAGCA	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	37	17	36491083	36491083	+	Missense_Mutation	SNP	C	C	T	rs4550493	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	48	46	0	0.545455	0	C|0.962;T|0.038	0.038	strong	GPR179,NS,carcinoma,0,1	GPR179	170	1	NM_001004334	exon7	c.G1478A	p.R493H	CCCAGGCGCCGCA	.	PASS	Atlas-SNP
SS18L1	26039	hgsc.bcm.edu	37	20	60737908	60737908	+	Silent	SNP	G	G	A	rs61744430	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	55	111	0	0.458333	0	G|0.922;A|0.078	0.078	strong	.	SS18L1	37	.	NM_198935	exon5	c.G477A	p.S159S	CGCCTCGCAGGGC	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305586	48305586	+	Missense_Mutation	SNP	G	G	A	rs145255760	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	13	30	0	0.295455	0	G|0.957;A|0.043	0.043	strong	.	TPRX1	46	.	NM_198479	exon2	c.C682T	p.P228S	GGCCTGGGATTGG	.	PASS	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50753334	50753334	+	Silent	SNP	G	G	A	rs73439311	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	118	150	0	0.504274	0	G|0.651;A|0.349	0.349	strong	.	.	.	.	NM_001001794	exon10	c.C775T	p.L259L	GAGTCAGCACAGG	.	PASS	Atlas-SNP
CTCFL	140690	hgsc.bcm.edu	37	20	56099114	56099114	+	Missense_Mutation	SNP	C	C	G	rs6070128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	149	133	0	1	0	C|0.675;G|0.325	0.325	strong	CTCFL,caecum,carcinoma,0,1	CTCFL	97	1	NM_001269044	exon1	c.G148C	p.E50Q	TACGCTCGGCCTC	.	PASS	Atlas-SNP
DTX3L	151636	hgsc.bcm.edu	37	3	122290579	122290579	+	Silent	SNP	C	C	T	rs2036342	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	94	118	0	0.989474	0	C|0.681;T|0.319	0.319	strong	.	DTX3L	59	.	NM_138287	exon5	c.C2208T	p.A736A	GAAAGCCAAAGGA	.	PASS	Atlas-SNP
FAM19A3	284467	hgsc.bcm.edu	37	1	113264930	113264930	+	Silent	SNP	C	C	G	rs35995150	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	49	99	0	0.475728	0	C|0.909;G|0.091	0.091	strong	.	FAM19A3	10	.	NM_001004440	exon2	c.C75G	p.T25T	GTGGACCCACCTG	.	PASS	Atlas-SNP
OTOGL	283310	hgsc.bcm.edu	37	12	80665473	80665473	+	Missense_Mutation	SNP	C	C	T	rs183159689	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	74	133	0	0.474359	0	C|0.998;T|0.002	0.002	strong	.	OTOGL	235	.	NM_173591	exon23	c.C2537T	p.P846L	GGTTTCCTGACCC	.	PASS	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151155620	151155620	+	Silent	SNP	G	G	A	rs6781302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	64	64	0	1	0	G|0.352;A|0.648	0.648	strong	.	IGSF10	279	.	NM_178822	exon6	c.C6729T	p.N2243N	AGTTCTGTTTGTA	.	PASS	Atlas-SNP
PROL1	58503	hgsc.bcm.edu	37	4	71275387	71275387	+	Silent	SNP	A	A	G	rs61336549	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	72	194	0	0.458599	0	A|0.903;G|0.097	0.097	strong	.	PROL1	46	.	NM_021225	exon3	c.A342G	p.V114V	CTATGTAGGACCT	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891010	44891010	+	Missense_Mutation	SNP	G	G	C	rs150792548	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	11	127	2	0.0797101	0.015748	A|0.002;C|0.002;G|0.995	0.002	strong	ZNF285,NS,carcinoma,+1,2	ZNF285	86	2	NM_152354	exon4	c.C1397G	p.A466G	CTATACGCAAAAT	.	scavenged	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135956391	135956391	+	Silent	SNP	A	A	G	rs34606958	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	358	150	225	0	0.418994	0	A|0.500;G|0.500	0.500	weak	.	RBMX	149	.	NM_002139	exon9	c.T1086C	p.D362D	GTAGGAATCACGT	.	PASS	Atlas-SNP
TOP1MT	116447	hgsc.bcm.edu	37	8	144399993	144399993	+	Silent	SNP	G	G	A	rs146827342	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	43	83	0	0.438776	0	G|0.997;A|0.003	0.003	strong	.	TOP1MT	63	.	NM_052963	exon10	c.C1230T	p.N410N	GTGCTTGTTCAGG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8176945	8176945	+	Missense_Mutation	SNP	T	T	C	rs4804063	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	71	122	0	0.5	0	C|0.236;N|0.000	0.236	strong	.	FBN3	300	.	NM_032447	exon30	c.A3877G	p.S1293G	CGTGACTGTCACA	.	PASS	Atlas-SNP
STOX1	219736	hgsc.bcm.edu	37	10	70645376	70645376	+	Missense_Mutation	SNP	A	A	C	rs10509305	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	49	78	0	0.510417	0	A|0.858;C|0.142	0.142	strong	.	STOX1	75	.	NM_152709	exon3	c.A1824C	p.E608D	ATATGAAGTGTAT	.	PASS	Atlas-SNP
ANKRD35	148741	hgsc.bcm.edu	37	1	145562881	145562881	+	Silent	SNP	T	T	C	rs10910824	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	10	23	0	0.434783	0	A|0.133;C|0.355	0.355	strong	.	ANKRD35	96	.	NM_144698	exon10	c.T2569C	p.L857L	GCTCTGTTGGAAA	.	PASS	Atlas-SNP
PPP5C	5536	hgsc.bcm.edu	37	19	46878989	46878989	+	Silent	SNP	G	G	A	rs61747094	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	67	131	0	0.36413	0	G|0.628;A|0.372	0.372	strong	.	PPP5C	44	.	NM_006247	exon3	c.G492A	p.S164S	GGACTCGCTGGAC	.	PASS	Atlas-SNP
SLC6A5	9152	hgsc.bcm.edu	37	11	20673867	20673867	+	Silent	SNP	G	G	A	rs2276433	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	133	108	1	0.985185	0.00925926	G|0.601;T|0.003	.	strong	.	SLC6A5	151	.	NM_004211	exon15	c.G2103A	p.E701E	GTGGGAGCCCATG	.	PASS	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	37	9	137779026	137779026	+	Missense_Mutation	SNP	C	C	T	rs17549193	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	54	125	0	0.421875	0	C|0.716;T|0.284	0.284	strong	.	FCN2	55	.	NM_004108	exon8	c.C707T	p.T236M	CCCTGACGTTCCA	.	PASS	Atlas-SNP
SMTN	6525	hgsc.bcm.edu	37	22	31491332	31491332	+	Missense_Mutation	SNP	C	C	T	rs5997872	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	46	72	0	0.534884	0	C|0.847;T|0.153	0.153	strong	.	SMTN	219	.	NM_001207017	exon13	c.C1931T	p.A644V	TGGAAGCGGCCAA	.	PASS	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56137834	56137834	+	Silent	SNP	A	A	G	rs1062601	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	103	109	1	1	0.00917431	A|0.609;G|0.391	0.391	strong	.	PCK1	95	.	NM_002591	exon4	c.A489G	p.S163S	GGATTCACCCTAC	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746701	143746701	+	Silent	SNP	A	A	G	rs3802232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	23	83	0	0.298701	0	A|0.479;G|0.521	0.521	strong	.	.	.	.	NM_003724	exon2	c.T777C	p.N259N	CCAGGCATTCCCC	.	PASS	Atlas-SNP
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956210	18956210	+	Missense_Mutation	SNP	C	C	G	rs139433266	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	73	112	0	0.574803	0	C|1.000;G|0.000	0.000	weak	MRGPRX1,NS,carcinoma,-1,1	MRGPRX1	84	1	NM_147199	exon1	c.G122C	p.G41A	GTCAGCCCGACAA	.	PASS	Atlas-SNP
SAPCD1	401251	hgsc.bcm.edu	37	6	31731881	31731881	+	Missense_Mutation	SNP	C	C	T	rs6905572	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	54	98	0	0.504673	0	C|0.879;T|0.121	0.121	strong	.	.	.	.	NM_001039651	exon3	c.C296T	p.P99L	GCCCCCCGTTAGC	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238244923	238244923	+	Silent	SNP	C	C	T	rs11683438	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	64	61	0	0.984615	0	C|0.933;G|0.000;T|0.067	0.067	strong	.	COL6A3	608	.	NM_004369	exon40	c.G8820A	p.T2940T	CGCTGCCGTTGCT	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56467281	56467281	+	Silent	SNP	A	A	G	rs61750024	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	62	119	0	0.433566	0	A|0.939;G|0.061	0.061	strong	.	NLRP8	225	.	NM_176811	exon3	c.A1857G	p.E619E	GGAGGAAGCCTTT	.	PASS	Atlas-SNP
BDH2	56898	hgsc.bcm.edu	37	4	104013796	104013796	+	Missense_Mutation	SNP	T	T	C	rs1054707	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	238	110	293	0	0.462185	0	T|0.878;C|0.122	0.122	strong	.	BDH2	18	.	NM_020139	exon4	c.A209G	p.N70S	ACTTCATTGGCAA	.	PASS	Atlas-SNP
EHMT1	79813	hgsc.bcm.edu	37	9	140638461	140638461	+	Silent	SNP	T	T	C	rs1129768	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	19	54	0	0.431818	0	A|0.000;C|0.484;G|0.000;T|0.516	0.484	strong	.	EHMT1	196	.	NM_001145527	exon6	c.T1089C	p.G363G	CCATGGTGCAGAG	.	PASS	Atlas-SNP
IGSF22	283284	hgsc.bcm.edu	37	11	18743180	18743180	+	Missense_Mutation	SNP	C	C	G	rs10832975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	46	124	0	0.425926	0	C|0.636;G|0.364	0.364	strong	IGSF22_ENST00000513874,NS,carcinoma,0,2	IGSF22	211	2	NM_173588	exon4	c.G280C	p.A94P	GTTTGGCGTTCCC	.	PASS	Atlas-SNP
MYH4	4622	hgsc.bcm.edu	37	17	10360854	10360854	+	Missense_Mutation	SNP	C	C	T	rs12949680	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	72	146	0	0.458599	0	C|0.945;T|0.055	0.055	strong	.	MYH4	349	.	NM_017533	exon16	c.G1780A	p.A594T	AGCCGGCGATGTT	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139371405	139371405	+	Silent	SNP	G	G	C	rs11999532	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	26	69	0	0.433333	0	G|0.846;C|0.154	0.154	strong	.	SEC16A	249	.	NM_014866	exon3	c.C663G	p.G221G	CTGTGGGCCTCCC	.	PASS	Atlas-SNP
ZNF385B	151126	hgsc.bcm.edu	37	2	180309622	180309622	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	3	162	0	0.0204082	0	.	.	none	ZNF385B,NS,carcinoma,-1,2	ZNF385B	68	2	NM_152520	exon9	c.G1178A	p.R393Q	GGGCTCCGCTGGA	.	scavenged	Atlas-SNP
SEC61A2	55176	hgsc.bcm.edu	37	10	12191933	12191933	+	Silent	SNP	C	C	T	rs10466280	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	39	78	0	0.46988	0	C|0.580;T|0.420	0.420	strong	.	SEC61A2	48	.	NM_001142627	exon6	c.C435T	p.A145A	GGGTGCCGGAATC	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39141120	39141120	+	Missense_Mutation	SNP	C	C	A	rs28705715	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	116	202	0	0.594872	0	C|0.914;A|0.086	0.086	strong	.	ADAM32	70	.	NM_145004	exon24	c.C2334A	p.D778E	ACAGGACAGTACC	.	PASS	Atlas-SNP
ZNF585B	92285	hgsc.bcm.edu	37	19	37677748	37677748	+	Missense_Mutation	SNP	T	T	A	rs45626541	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	91	197	0	0.452736	0	T|0.676;A|0.324	0.324	strong	.	ZNF585B	91	.	NM_152279	exon5	c.A691T	p.I231L	CATGTATACTGAG	.	PASS	Atlas-SNP
PDGFRL	5157	hgsc.bcm.edu	37	8	17447018	17447018	+	Missense_Mutation	SNP	C	C	A	rs374832042		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	21	37	0	0.677419	0	.	.	weak	.	PDGFRL	27	.	NM_006207	exon3	c.C97A	p.P33T	AAAGAACCAGGAG	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	37	17	8455419	8455419	+	Silent	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	6	107	0	0.0458015	0	.	.	none	.	MYH10	148	.	NM_001256012	exon9	c.A864G	p.E288E	AGTACGTTCATCT	.	PASS	Atlas-SNP
IFT81	28981	hgsc.bcm.edu	37	12	110600841	110600841	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	29	77	0	0.391892	0	.	.	none	.	IFT81	86	.	NM_014055	exon11	c.G1159C	p.D387H	GAATTTGATGGTA	.	PASS	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294236	124294236	+	Missense_Mutation	SNP	A	A	G	rs4057749	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	111	112	0	1	0	A|0.720;G|0.280	0.280	strong	.	OR8B4	60	.	NM_001005196	exon1	c.T532C	p.C178R	CGTCACACAGATA	.	PASS	Atlas-SNP
TRPM2	7226	hgsc.bcm.edu	37	21	45826486	45826486	+	Missense_Mutation	SNP	G	G	A	rs56379273	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	14	16	0	0.482759	0	G|0.988;A|0.012	0.012	strong	.	TRPM2	196	.	NM_003307	exon19	c.G2800A	p.V934I	AAGGACGTCTTCT	.	PASS	Atlas-SNP
MYOM1	8736	hgsc.bcm.edu	37	18	3164385	3164385	+	Silent	SNP	C	C	T	rs11659820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	51	108	0	0.481132	0	C|0.820;T|0.180	0.180	strong	.	MYOM1	192	.	NM_003803	exon10	c.G1392A	p.R464R	CGTTGCCCGCTCT	.	PASS	Atlas-SNP
GSPT1	2935	hgsc.bcm.edu	37	16	11981487	11981487	+	Silent	SNP	G	G	A	rs3752426	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	188	199	0	1	0	G|0.830;A|0.170	0.170	strong	.	GSPT1	71	.	NM_002094	exon7	c.C897T	p.G299G	CTTGTGGCCAGGG	.	PASS	Atlas-SNP
TRIM16	10626	hgsc.bcm.edu	37	17	15532147	15532147	+	Missense_Mutation	SNP	G	G	A	rs3174720	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	76	187	0	0.431818	0	G|0.971;A|0.029	0.029	strong	.	TRIM16	45	.	NM_006470	exon9	c.C1477T	p.R493W	GCCTCCGGAAAGG	.	PASS	Atlas-SNP
SCAMP3	10067	hgsc.bcm.edu	37	1	155230131	155230131	+	Silent	SNP	C	C	T	rs1142287	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	36	55	0	0.62069	0	C|0.584;T|0.416	0.416	strong	.	SCAMP3	33	.	NM_005698	exon4	c.G378A	p.G126G	TGTGCCCCCCAGG	.	PASS	Atlas-SNP
CCDC108	255101	hgsc.bcm.edu	37	2	219900300	219900300	+	Silent	SNP	A	A	C	rs77746575	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	310	150	277	1	0.483871	0.00361011	A|0.999;C|0.001	0.001	strong	CCDC108_ENST00000295729,colon,carcinoma,-2,2	CCDC108	208	2	NM_194302	exon5	c.T444G	p.A148A	CTCCTCAGCCACC	.	PASS	Atlas-SNP
TARSL2	123283	hgsc.bcm.edu	37	15	102264476	102264476	+	Missense_Mutation	SNP	C	C	A	rs1143136	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	10	4	0	0.416667	0	C|0.794;A|0.206	0.206	strong	.	TARSL2	63	.	NM_152334	exon1	c.G115T	p.A39S	AGGGCGCGTTCAG	.	PASS	Atlas-SNP
SETD6	79918	hgsc.bcm.edu	37	16	58550386	58550386	+	Missense_Mutation	SNP	G	G	A	rs147467868	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	30	53	0	0.428571	0	G|0.999;A|0.001	0.001	strong	.	SETD6	27	.	NM_001160305	exon4	c.G481A	p.E161K	AGGCCAGAGGAGG	.	PASS	Atlas-SNP
DSE	29940	hgsc.bcm.edu	37	6	116720514	116720514	+	Missense_Mutation	SNP	C	C	T	rs35548455	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	40	82	0	0.784314	0	C|0.955;T|0.045	0.045	strong	.	DSE	98	.	NM_001080976	exon2	c.C101T	p.P34L	TGATTCCCTTCAC	.	PASS	Atlas-SNP
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	3	91	0	0.0337079	0	.	.	none	ZNF880,colon,carcinoma,-1,1	ZNF880	45	1	NM_001145434	exon4	c.A313T	p.K105X	TCTCTTAAAAATC	.	scavenged	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57069375	57069375	+	Missense_Mutation	SNP	A	A	G	rs34069781	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	18	55	0	0.3	0	A|0.968;G|0.032;T|0.000	0.032	strong	.	TNKS1BP1	148	.	NM_033396	exon9	c.T4877C	p.V1626A	TCCTCCACTACCT	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449399	89449399	+	Silent	SNP	T	T	C	rs77567101	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	424	79	275	0	0.186321	0	T|0.500;C|0.500	0.500	strong	.	.	.	.	NM_001162536	exon3	c.A111G	p.V37V	CAAGAGTACTTCC	.	PASS	Atlas-SNP
AP2B1	163	hgsc.bcm.edu	37	17	33998904	33998904	+	Silent	SNP	T	T	C	rs17670584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	102	105	0	0.980769	0	T|0.929;C|0.071	0.071	strong	AP2B1,NS,chondrosarcoma,+1,1	AP2B1	70	1	NM_001030006	exon16	c.T2163C	p.Y721Y	TGGATATGTGGCT	.	PASS	Atlas-SNP
LRRC15	131578	hgsc.bcm.edu	37	3	194080696	194080696	+	Silent	SNP	G	G	A	rs9682541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	80	143	0	0.536913	0	G|0.844;A|0.156	0.156	strong	.	LRRC15	137	.	NM_001135057	exon3	c.C1095T	p.N365N	GAAGACGTTCCCG	.	PASS	Atlas-SNP
ZRANB3	84083	hgsc.bcm.edu	37	2	135988186	135988186	+	Silent	SNP	G	G	A	rs58917764	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	299	154	280	0	0.51505	0	G|0.871;A|0.129	0.129	strong	.	ZRANB3	109	.	NM_032143	exon13	c.C1851T	p.T617T	GGCTGGGGTGGTT	.	PASS	Atlas-SNP
WRN	7486	hgsc.bcm.edu	37	8	31024654	31024654	+	Missense_Mutation	SNP	T	T	C	rs1346044	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	156	134	1	0.993631	0.00746269	T|0.798;C|0.202	0.202	strong	.	WRN	116	.	NM_000553	exon34	c.T4099C	p.C1367R	CCTTCATGTGATG	.	PASS	Atlas-SNP
VPS41	27072	hgsc.bcm.edu	37	7	38829465	38829465	+	Silent	SNP	C	C	T	rs1001476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	55	131	0	0.44	0	T|0.138;G|0.005	0.138	strong	.	VPS41	102	.	NM_014396	exon10	c.G720A	p.V240V	TGAGCACACCTGG	.	PASS	Atlas-SNP
GPRIN1	114787	hgsc.bcm.edu	37	5	176026129	176026129	+	Missense_Mutation	SNP	C	C	A	rs199714570	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	20	157	0	0.20202	0	C|0.851;A|0.149	0.149	strong	.	GPRIN1	77	.	NM_052899	exon2	c.G707T	p.G236V	AAAGACCCAGGAT	.	PASS	Atlas-SNP
PCDHB13	56123	hgsc.bcm.edu	37	5	140595375	140595375	+	Silent	SNP	C	C	T	rs77651135		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	16	45	0	0.470588	0	.	.	weak	PCDHB13,NS,carcinoma,0,1	PCDHB13	142	1	NM_018933	exon1	c.C1680T	p.F560F	GCCCTTCGTGCTG	.	PASS	Atlas-SNP
DDX42	11325	hgsc.bcm.edu	37	17	61888461	61888461	+	Silent	SNP	G	G	A	rs56197520	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	107	112	0	0.990741	0	G|0.940;A|0.060	0.060	strong	.	DDX42	86	.	NM_203499	exon13	c.G1326A	p.R442R	TTTTCGGAAGAAG	.	PASS	Atlas-SNP
WDR35	57539	hgsc.bcm.edu	37	2	20131079	20131079	+	Missense_Mutation	SNP	T	T	C	rs1191778	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	78	135	1	0.516556	0.00740741	T|0.710;C|0.290	0.290	strong	WDR35,NS,carcinoma,-1,1	WDR35	92	1	NM_001006657	exon25	c.A2948G	p.E983G	ATCTGTTCATGGT	.	scavenged	Atlas-SNP
CLDN1	9076	hgsc.bcm.edu	37	3	190039888	190039888	+	Silent	SNP	G	G	A	rs72466472	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	90	141	0	0.497238	0	G|0.971;A|0.029	0.029	strong	.	CLDN1	23	.	NM_021101	exon1	c.C108T	p.A36A	GTCGCCGGCATAG	.	PASS	Atlas-SNP
SETD9	133383	hgsc.bcm.edu	37	5	56209735	56209735	+	Missense_Mutation	SNP	A	A	G	rs40497	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	32	83	0	0.516129	0	A|0.788;G|0.212	0.212	strong	.	.	.	.	NM_153706	exon4	c.A625G	p.K209E	CCTTTAAAAATGA	.	PASS	Atlas-SNP
PRDM11	56981	hgsc.bcm.edu	37	11	45245778	45245778	+	Missense_Mutation	SNP	G	G	T	rs35090414	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	26	62	0	0.45614	0	G|0.940;T|0.060	0.060	strong	PRDM11,caecum,carcinoma,0,2	PRDM11	53	2	NM_001256695	exon7	c.G753T	p.R251S	GAAGAGGTTGCAG	.	PASS	Atlas-SNP
RFPL4B	442247	hgsc.bcm.edu	37	6	112671611	112671611	+	Missense_Mutation	SNP	G	G	A	rs11153361	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	74	188	0	0.787234	0	G|0.808;A|0.192	0.192	strong	.	RFPL4B	36	.	NM_001013734	exon3	c.G701A	p.G234D	ATGATGGTTTCTT	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392360	40392360	+	Missense_Mutation	SNP	G	G	A	rs200977347		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	30	536	1	0.177515	0.00186567	.	.	weak	FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	NM_003890	exon16	c.C8144T	p.A2715V	CCAGCTGCCTGGC	.	scavenged	Atlas-SNP
ALOX15	246	hgsc.bcm.edu	37	17	4536241	4536241	+	Silent	SNP	T	T	C	rs743646	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	52	102	0	0.536082	0	T|0.920;C|0.080	0.080	strong	.	ALOX15	70	.	NM_001140	exon11	c.A1455G	p.T485T	CACGTCTGTCTTA	.	PASS	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	95931111	95931111	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	4	216	0	0.0207254	0	.	.	none	PLCE1_ENST00000371375,caecum,carcinoma,+1,3	PLCE1	543	3	NM_016341	exon4	c.T1667C	p.L556P	ACTACCTTTGCTT	.	scavenged	Atlas-SNP
OR5D14	219436	hgsc.bcm.edu	37	11	55563900	55563900	+	Missense_Mutation	SNP	T	T	C	rs297055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	31	82	0	0.382716	0	T|0.746;C|0.254	0.254	strong	OR5D14,NS,carcinoma,-1,3	OR5D14	116	3	NM_001004735	exon1	c.T869C	p.L290P	ACCCTCTGATCTA	.	PASS	Atlas-SNP
OCA2	4948	hgsc.bcm.edu	37	15	28260053	28260053	+	Missense_Mutation	SNP	G	G	A	rs1800401	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	35	49	0	0.555556	0	G|0.922;A|0.078	0.078	strong	.	OCA2	173	.	NM_000275	exon9	c.C913T	p.R305W	AGGCCCGGATGCT	.	PASS	Atlas-SNP
ZAR1L	646799	hgsc.bcm.edu	37	13	32885654	32885654	+	Missense_Mutation	SNP	T	T	C	rs445909	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	18	9	4	0	0.5	0	T|0.596;C|0.404	0.404	strong	ZAR1L,NS,meningioma,0,1	ZAR1L	17	1	NM_001136571	exon1	c.A409G	p.T137A	GGCCGGTGGCGGG	.	PASS	Atlas-SNP
FOXK1	221937	hgsc.bcm.edu	37	7	4780514	4780514	+	Silent	SNP	G	G	T	rs3087749	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	57	107	0	0.542857	0	G|0.511;T|0.489	0.489	strong	.	FOXK1	64	.	NM_001037165	exon2	c.G606T	p.T202T	GTTCACGTCGCTC	.	PASS	Atlas-SNP
SEPT4	5414	hgsc.bcm.edu	37	17	56598655	56598655	+	Silent	SNP	C	C	T	rs1057065	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	35	78	0	0.538462	0	C|0.961;T|0.039	0.039	strong	SEPT4,colon,carcinoma,-2,1	SEPT4	48	1	NM_001256782	exon10	c.G1119A	p.R373R	AACTCGCCGCCCT	.	PASS	Atlas-SNP
ZNF543	125919	hgsc.bcm.edu	37	19	57840547	57840547	+	Missense_Mutation	SNP	A	A	G	rs10410649	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	58	109	0	0.527273	0	A|0.737;G|0.263	0.263	strong	.	ZNF543	61	.	NM_213598	exon4	c.A1717G	p.M573V	CCTTTTATGACTG	.	PASS	Atlas-SNP
CLRN3	119467	hgsc.bcm.edu	37	10	129690990	129690990	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	20	63	0	0.434783	0	.	.	none	.	CLRN3	27	.	NM_152311	exon1	c.C59A	p.S20Y	ATGAAGGACCCAA	.	PASS	Atlas-SNP
LRRC28	123355	hgsc.bcm.edu	37	15	99892589	99892589	+	Missense_Mutation	SNP	G	G	A	rs139516247		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	16	39	0	0.484848	0	G|1.000;A|0.000	0.000	weak	LRRC28,NS,malignant_melanoma,+1,1	LRRC28	38	1	NM_144598	exon7	c.G608A	p.R203Q	GATCTCGAGAACT	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36549690	36549690	+	Silent	SNP	C	C	T	rs11538454	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	38	56	0	0.542857	0	C|0.854;G|0.000;T|0.146	0.146	strong	WDR62,NS,carcinoma,0,1	WDR62	102	1	NM_173636	exon2	c.C186T	p.L62L	GTCACTCGAGAAG	.	PASS	Atlas-SNP
ADAMTS20	80070	hgsc.bcm.edu	37	12	43828141	43828141	+	Missense_Mutation	SNP	T	T	A	rs7302446	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	69	120	0	0.518797	0	T|0.974;A|0.026	0.026	strong	.	ADAMTS20	635	.	NM_025003	exon19	c.A2627T	p.K876M	TCACTCTTATGTA	.	PASS	Atlas-SNP
CEP78	84131	hgsc.bcm.edu	37	9	80879149	80879149	+	Silent	SNP	C	C	T	rs1057650	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	50	141	0	0.357143	0	C|0.921;T|0.079	0.079	strong	CEP78,NS,carcinoma,0,1	CEP78	79	1	NM_001098802	exon13	c.C1545T	p.I515I	TATGATCCTGGAT	.	PASS	Atlas-SNP
WDR62	284403	hgsc.bcm.edu	37	19	36575645	36575645	+	Silent	SNP	G	G	A	rs2301734	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	21	32	0	0.4375	0	G|0.854;A|0.146	0.146	strong	WDR62,NS,carcinoma,0,1	WDR62	102	1	NM_173636	exon12	c.G1641A	p.T547T	AGAGACGGGTGAG	.	PASS	Atlas-SNP
KDM3A	55818	hgsc.bcm.edu	37	2	86718360	86718360	+	Silent	SNP	C	C	T	rs61750310	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	87	146	0	0.508772	0	C|0.998;T|0.002	0.002	strong	.	KDM3A	179	.	NM_001146688	exon25	c.C3847T	p.L1283L	CGATATCTGTCAC	.	PASS	Atlas-SNP
FRG2B	441581	hgsc.bcm.edu	37	10	135438933	135438933	+	Silent	SNP	C	C	T	rs200793608		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	469	5	435	4	0.010661	0.0091954	C|0.996;T|0.004	0.004	weak	FRG2B,colon,carcinoma,-1,1	FRG2B	47	1	NM_001080998	exon4	c.G507A	p.P169P	AATTGACGGTGTT	.	scavenged	Atlas-SNP
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651352	1651352	+	Silent	SNP	C	C	T	rs75391124	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	73	121	0	0.462025	0	C|0.929;T|0.071	0.071	strong	KRTAP5-5,NS,haematopoietic_neoplasm,0,1	KRTAP5-5	86	1	NM_001001480	exon1	c.C282T	p.G94G	CGGGGGCTCCAAG	.	PASS	Atlas-SNP
ZNF76	7629	hgsc.bcm.edu	37	6	35253974	35253974	+	Missense_Mutation	SNP	C	C	T	rs2228265	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	47	89	0	0.427273	0	C|0.910;T|0.090	0.090	strong	.	ZNF76	37	.	NM_003427	exon3	c.C143T	p.T48M	AGGTGACGGTACA	.	PASS	Atlas-SNP
CYSLTR2	57105	hgsc.bcm.edu	37	13	49281414	49281414	+	Missense_Mutation	SNP	G	G	A	rs143735193	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	37	74	0	0.513889	0	G|0.998;A|0.002	0.002	strong	.	CYSLTR2	55	.	NM_020377	exon1	c.G461A	p.S154N	TCAGGAGTGCCTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511116	195511116	+	Silent	SNP	A	A	G	rs200940092	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	442	60	452	12	0.135747	0.0265487	A|0.965;G|0.034	0.034	strong	MUC4_ENST00000463781,caecum,carcinoma,-2,1	MUC4	1505	1	NM_018406	exon2	c.T7335C	p.H2445H	GGTGGCATGACCT	.	scavenged	Atlas-SNP
OR8B4	283162	hgsc.bcm.edu	37	11	124294349	124294349	+	Missense_Mutation	SNP	C	C	A	rs7116575	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	62	140	1	0.508197	0.00714286	C|0.845;A|0.155	0.155	strong	OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	NM_001005196	exon1	c.G419T	p.C140F	AGAAAGCAGACCC	.	scavenged	Atlas-SNP
KIAA1324L	222223	hgsc.bcm.edu	37	7	86542455	86542455	+	Silent	SNP	C	C	T	rs35895874	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	84	96	0	1	0	C|0.907;T|0.093	0.093	strong	.	KIAA1324L	225	.	NM_001142749	exon14	c.G1797A	p.G599G	CGCCACCCCATCA	.	PASS	Atlas-SNP
ZNF587B	100293516	hgsc.bcm.edu	37	19	58352806	58352806	+	Missense_Mutation	SNP	T	T	C	rs35313547	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	50	89	0	0.485437	0	T|0.866;C|0.134	0.134	strong	.	.	.	.	NM_001204818	exon3	c.T764C	p.V255A	AATATGTTAGCTT	.	PASS	Atlas-SNP
OR51G2	81282	hgsc.bcm.edu	37	11	4936608	4936608	+	Missense_Mutation	SNP	C	C	G	rs12419598	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	30	77	0	0.508475	0	C|0.921;G|0.079	0.079	strong	.	OR51G2	70	.	NM_001005238	exon1	c.G286C	p.E96Q	TAATTTCTCGTGC	.	PASS	Atlas-SNP
DNMT1	1786	hgsc.bcm.edu	37	19	10265593	10265593	+	Silent	SNP	G	G	T	rs2228613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	88	81	0	1	0	T|0.063;G|0.937;C|0.000	0.063	strong	.	DNMT1	148	.	NM_001130823	exon20	c.C1632A	p.I544I	CTTGTTGATCAGG	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75981300	75981300	+	Silent	SNP	G	G	A	rs144158910	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	42	71	0	0.545455	0	G|0.992;A|0.008	0.008	strong	.	CSPG4	175	.	NM_001897	exon3	c.C2106T	p.R702R	AGTGACGCGGAAC	.	PASS	Atlas-SNP
VPS4A	27183	hgsc.bcm.edu	37	16	69354963	69354963	+	Silent	SNP	A	A	G	rs1127231	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	46	97	0	0.469388	0	A|0.722;G|0.278	0.278	strong	.	VPS4A	18	.	NM_013245	exon9	c.A861G	p.K287K	TGAAAAACGAATT	.	PASS	Atlas-SNP
KRT27	342574	hgsc.bcm.edu	37	17	38938557	38938557	+	Silent	SNP	G	G	A	rs67771170	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	33	56	0	0.507692	0	G|0.899;A|0.101	0.101	strong	.	KRT27	41	.	NM_181537	exon1	c.C189T	p.G63G	TCCCCCGCCCAGA	.	PASS	Atlas-SNP
TOP1MT	116447	hgsc.bcm.edu	37	8	144403485	144403485	+	Silent	SNP	G	G	C	rs11544482	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	71	77	0	1	0	G|0.684;C|0.316	0.316	strong	TOP1MT,NS,carcinoma,0,1	TOP1MT	63	1	NM_052963	exon8	c.C1032G	p.R344R	CTCCACGCGGAGG	.	PASS	Atlas-SNP
KRT28	162605	hgsc.bcm.edu	37	17	38955991	38955991	+	Missense_Mutation	SNP	C	C	T	rs7209228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	31	68	0	0.508197	0	C|0.859;T|0.141	0.141	strong	.	KRT28	65	.	NM_181535	exon1	c.G155A	p.G52D	CCCAAGCCCCCTC	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	37	2	220286142	220286142	+	Silent	SNP	G	G	A	rs1058284	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	40	98	0	0.38835	0	G|0.640;A|0.360	0.360	strong	DES,right_upper_lobe,carcinoma,+1,1	DES	53	1	NM_001927	exon6	c.G1104A	p.A368A	CATTGCGCGCCTG	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48349647	48349647	+	Missense_Mutation	SNP	C	C	T	rs3931814	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	102	188	0	0.481132	0	C|0.896;T|0.104	0.104	strong	.	ABCA13	1192	.	NM_152701	exon24	c.C9425T	p.A3142V	TCGCAGCGGAGGA	.	PASS	Atlas-SNP
AZIN1	51582	hgsc.bcm.edu	37	8	103851052	103851052	+	Silent	SNP	T	T	C	rs1062048	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	98	157	0	0.451613	0	T|0.804;C|0.196	0.196	strong	.	AZIN1	26	.	NM_015878	exon6	c.A369G	p.A123A	TTTTGCTGCATAC	.	PASS	Atlas-SNP
NKX2-6	137814	hgsc.bcm.edu	37	8	23563908	23563908	+	Silent	SNP	A	A	G	rs61732911	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	32	44	0	0.561404	0	A|0.816;G|0.184	0.184	strong	.	NKX2-6	6	.	NM_001136271	exon1	c.T204C	p.D68D	CGAACCATCCAGC	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1047161	1047161	+	Silent	SNP	A	A	G	rs3752237	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	50	40	0	1	0	A|0.347;G|0.653	0.653	strong	.	ABCA7	174	.	NM_019112	exon15	c.A1851G	p.G617G	GCTGGGAGACATC	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720540	135720540	+	Missense_Mutation	SNP	A	A	G	rs9814557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	73	148	0	0.496599	0	A|0.801;G|0.199	0.199	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.A200G	p.D67G	ATGCAGATCTGAA	.	PASS	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58421128	58421128	+	Missense_Mutation	SNP	C	C	T	rs3826671	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	678	558	407	0	0.823009	0	C|0.500;T|0.500	0.500	weak	ZNF417,NS,carcinoma,+1,1	ZNF417	44	1	NM_152475	exon3	c.G518A	p.R173H	AACTCGCGGAAGA	.	PASS	Atlas-SNP
PRKAR2B	5577	hgsc.bcm.edu	37	7	106799997	106799997	+	Silent	SNP	G	G	A	rs257376	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	47	61	0	1	0	G|0.497;A|0.503	0.503	strong	.	PRKAR2B	34	.	NM_002736	exon11	c.G1227A	p.T409T	TGGAACGAACATG	.	PASS	Atlas-SNP
CIDEA	1149	hgsc.bcm.edu	37	18	12274104	12274104	+	Missense_Mutation	SNP	G	G	T	rs11545881	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	36	41	0	0.972973	0	C|0.000;G|0.668;T|0.332	0.332	strong	.	CIDEA	32	.	NM_001279	exon4	c.G343T	p.V115F	CAGCACGTCCCCA	.	PASS	Atlas-SNP
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73944185	73944185	+	Silent	SNP	T	T	C	rs2240357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	29	67	1	0.426471	0.0149254	T|0.735;C|0.265	0.265	strong	GTF2IRD1,caecum,carcinoma,+1,1	GTF2IRD1	91	1	NM_001199207	exon9	c.T1308C	p.Y436Y	CACTTATGGAGTC	.	scavenged	Atlas-SNP
OR8J3	81168	hgsc.bcm.edu	37	11	55905078	55905078	+	Missense_Mutation	SNP	C	C	T	rs61742348	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	78	165	0	0.478528	0	C|0.901;T|0.099	0.099	strong	OR8J3,NS,carcinoma,0,2	OR8J3	112	2	NM_001004064	exon1	c.G117A	p.M39I	CCCTGCCATGGTC	.	PASS	Atlas-SNP
NARFL	64428	hgsc.bcm.edu	37	16	784765	784765	+	Silent	SNP	C	C	T	rs9928077	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	61	163	0	0.42069	0	C|0.740;T|0.260	0.260	strong	NARFL,NS,carcinoma,0,1	NARFL	31	1	NM_022493	exon5	c.G546A	p.A182A	GGGCAGCGCCTGT	.	PASS	Atlas-SNP
NLRP2	55655	hgsc.bcm.edu	37	19	55494188	55494188	+	Silent	SNP	C	C	T	rs61730066	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	75	111	0	0.543478	0	C|0.833;T|0.167	0.167	strong	.	NLRP2	161	.	NM_017852	exon6	c.C1122T	p.D374D	TGGAGACGAGGAC	.	PASS	Atlas-SNP
TRERF1	55809	hgsc.bcm.edu	37	6	42224546	42224546	+	Missense_Mutation	SNP	A	A	T	rs2295275	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	78	121	0	0.461538	0	A|0.937;T|0.063	0.063	strong	.	TRERF1	124	.	NM_033502	exon12	c.T2500A	p.C834S	TGGAACAGCACAA	.	PASS	Atlas-SNP
ZNF48	197407	hgsc.bcm.edu	37	16	30409699	30409699	+	Silent	SNP	C	C	T	rs9936065	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	56	77	0	0.509091	0	C|0.886;T|0.114	0.114	strong	ZNF48,NS,carcinoma,+2,1	ZNF48	34	1	NM_001214906	exon3	c.C1128T	p.R376R	TCTTCGCCACCGC	.	PASS	Atlas-SNP
EVC2	132884	hgsc.bcm.edu	37	4	5642274	5642274	+	Silent	SNP	T	T	C	rs13131655	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	87	215	0	0.446154	0	T|0.716;C|0.284	0.284	strong	.	EVC2	202	.	NM_147127	exon10	c.A1437G	p.E479E	TTCTGCTTCCTCC	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17469026	17469026	+	Silent	SNP	G	G	A	rs5992604	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	55	82	0	0.474138	0	G|0.617;A|0.383	0.383	strong	.	GAB4	95	.	NM_001037814	exon3	c.C510T	p.H170H	GAGGCCGTGACTG	.	PASS	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	37	8	95541302	95541302	+	Silent	SNP	A	A	G	rs957448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	82	148	0	0.491018	0	A|0.691;G|0.309	0.309	strong	.	KIAA1429	176	.	NM_015496	exon7	c.T876C	p.G292G	ACCTTCACCTTCT	.	PASS	Atlas-SNP
LCT	3938	hgsc.bcm.edu	37	2	136594158	136594158	+	Silent	SNP	G	G	A	rs2236783	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	103	182	0	0.502439	0	G|0.584;A|0.416	0.416	strong	.	LCT	309	.	NM_002299	exon1	c.C582T	p.T194T	ACTGAGGGTCTGG	.	PASS	Atlas-SNP
LMF1	64788	hgsc.bcm.edu	37	16	961051	961051	+	Silent	SNP	C	C	T	rs2277893	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	35	58	0	0.522388	0	C|0.748;T|0.252	0.252	strong	LMF1,NS,carcinoma,0,1	LMF1	42	1	NM_022773	exon4	c.G543A	p.G181G	CAGGAACCCCGTC	.	PASS	Atlas-SNP
PPA1	5464	hgsc.bcm.edu	37	10	71969338	71969338	+	Silent	SNP	C	C	A	rs79719906	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	5	133	0	0.0299401	0	C|0.987;A|0.013	0.013	strong	PPA1,NS,carcinoma,-1,2	PPA1	24	2	NM_021129	exon7	c.G615T	p.A205A	ATTAAACGCAAAC	.	scavenged	Atlas-SNP
CYP2A7	1549	hgsc.bcm.edu	37	19	41383134	41383134	+	Silent	SNP	A	A	G	rs147847954	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	91	190	0	0.441748	0	A|0.978;G|0.022	0.022	strong	.	CYP2A7	71	.	NM_000764	exon7	c.T1122C	p.V374V	CTTTTTAACCCTG	.	PASS	Atlas-SNP
KRT36	8689	hgsc.bcm.edu	37	17	39643646	39643646	+	Missense_Mutation	SNP	G	G	A	rs2301354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	28	62	0	0.466667	0	G|0.523;A|0.477	0.477	strong	.	KRT36	52	.	NM_003771	exon5	c.C944T	p.T315M	TTGACCGTACGTC	.	PASS	Atlas-SNP
GALNT13	114805	hgsc.bcm.edu	37	2	155102403	155102403	+	Silent	SNP	T	T	C	rs375635744		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	23	77	0	0.479167	0	.	.	weak	.	GALNT13	170	.	NM_052917	exon7	c.T765C	p.Y255Y	GACTTATGGGGGT	.	PASS	Atlas-SNP
OR2T8	343172	hgsc.bcm.edu	37	1	248085124	248085124	+	Missense_Mutation	SNP	G	G	A	rs4590708	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	304	191	302	1	0.628289	0.00331126	G|0.755;A|0.245	0.245	strong	.	OR2T8	67	.	NM_001005522	exon1	c.G805A	p.D269N	AACCACGACAAGG	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56515334	56515334	+	Silent	SNP	C	C	T	rs1560691	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	60	93	0	0.521739	0	C|0.797;T|0.203	0.203	strong	.	NLRP5	217	.	NM_153447	exon2	c.C315T	p.N105N	TGCCAACGTGGAA	.	PASS	Atlas-SNP
C9orf40	55071	hgsc.bcm.edu	37	9	77563087	77563087	+	Silent	SNP	C	C	T	rs2769058	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	44	130	0	0.488889	0	C|0.688;T|0.312	0.312	strong	C9orf40,NS,carcinoma,0,1	C9orf40	5	1	NM_017998	exon2	c.G462A	p.Q154Q	CCAGTACTGGAAG	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	37	15	75980159	75980159	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	92	123	0	0.5	0	.	.	none	.	CSPG4	175	.	NM_001897	exon3	c.C3247A	p.Q1083K	CCTCCTGGGTGAA	.	PASS	Atlas-SNP
DIRC1	116093	hgsc.bcm.edu	37	2	189599497	189599497	+	Missense_Mutation	SNP	A	A	C	rs72902678	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	87	209	0	0.524096	0	A|0.985;C|0.015	0.015	strong	.	DIRC1	13	.	NM_052952	exon2	c.T151G	p.S51A	CAGCAGAAGAACA	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629868	32629868	+	Silent	SNP	A	A	G	rs1049088	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	59	99	0	0.541284	0	G|0.171;A|0.829	0.171	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.T537C	p.L179L	CCTAATAAGGGGG	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19751694	19751694	+	Silent	SNP	A	A	G	rs9507567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	308	149	302	1	0.483766	0.00331126	A|0.959;G|0.041	0.041	strong	.	TUBA3C	166	.	NM_006001	exon4	c.T429C	p.G143G	AGTGCCACCCCCA	.	PASS	Atlas-SNP
FAIM	55179	hgsc.bcm.edu	37	3	138347988	138347988	+	Missense_Mutation	SNP	T	T	C	rs13043	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	77	95	0	0.516779	0	T|0.810;C|0.190	0.190	strong	.	FAIM	27	.	NM_001033030	exon5	c.T482C	p.L161S	AAAAATTGGAGAC	.	PASS	Atlas-SNP
TMEM132D	121256	hgsc.bcm.edu	37	12	130184947	130184947	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	34	82	0	0.386364	0	.	.	none	.	TMEM132D	299	.	NM_133448	exon2	c.A376T	p.N126Y	TCCAGTTAAGAGA	.	PASS	Atlas-SNP
FAM160B2	64760	hgsc.bcm.edu	37	8	21956108	21956108	+	Missense_Mutation	SNP	A	A	G	rs35497596	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	39	57	0	0.590909	0	A|0.627;G|0.373	0.373	strong	RAI16,NS,carcinoma,0,2	FAM160B2	35	2	NM_022749	exon7	c.A943G	p.T315A	ATTGCCACCTTAG	.	PASS	Atlas-SNP
AGPHD1	123688	hgsc.bcm.edu	37	15	78825562	78825562	+	Silent	SNP	C	C	T	rs12906951	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	34	124	0	0.350515	0	C|0.733;T|0.267	0.267	strong	AGPHD1,NS,carcinoma,0,1	AGPHD1	22	1	NM_001013619	exon5	c.C672T	p.H224H	CAATCACGGAGAT	.	PASS	Atlas-SNP
LRRC18	474354	hgsc.bcm.edu	37	10	50122109	50122109	+	Missense_Mutation	SNP	C	C	T	rs17772611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	47	82	0	0.494737	0	C|0.869;T|0.131	0.131	strong	LRRC18,caecum,carcinoma,0,2	LRRC18	52	2	NM_001006939	exon1	c.G92A	p.R31H	TCAAGGCGCTTTT	.	PASS	Atlas-SNP
SLC7A4	6545	hgsc.bcm.edu	37	22	21385985	21385985	+	Silent	SNP	C	C	T	rs402931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	50	99	0	0.480769	0	C|0.795;T|0.205	0.205	strong	.	SLC7A4	50	.	NM_004173	exon2	c.G117A	p.T39T	GTCCAGCGTGGAC	.	PASS	Atlas-SNP
STRADB	55437	hgsc.bcm.edu	37	2	202342402	202342402	+	Silent	SNP	G	G	T	rs3175787	byfrequency;bysubmitter	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	105	227	1	0.454545	0.00440529	G|0.513;T|0.487	0.487	strong	.	STRADB	33	.	NM_001206864	exon8	c.G609T	p.L203L	TGGCCTGTCCCAT	.	PASS	Atlas-SNP
PPARGC1B	133522	hgsc.bcm.edu	37	5	149216095	149216095	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	34	97	0	0.539683	0	.	.	none	.	PPARGC1B	74	.	NM_133263	exon8	c.G2077A	p.D693N	GACCATGACTACT	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23545004	23545004	+	Silent	SNP	G	G	A	rs296092	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	40	95	0	0.430108	0	G|0.682;A|0.318	0.318	strong	.	ZNF91	349	.	NM_003430	exon4	c.C777T	p.I259I	AGCACAGATTATT	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55238874	55238874	+	Silent	SNP	T	T	A	rs2227984	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	54	65	0	1	0	T|0.645;A|0.355	0.355	strong	.	EGFR	20426	.	NM_005228	exon16	c.T1887A	p.T629T	ATGCACTGGGCCA	.	PASS	Atlas-SNP
WNK2	65268	hgsc.bcm.edu	37	9	96021312	96021312	+	Missense_Mutation	SNP	G	G	A	rs10761203	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	256	117	164	0	0.457031	0	G|0.644;A|0.356	0.356	strong	WNK2_ENST00000297954,NS,carcinoma,0,2	WNK2	277	2	NM_006648	exon11	c.G2482A	p.V828M	CCTCCCGTGCCAC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9085643	9085643	+	Missense_Mutation	SNP	A	A	G	rs1574479	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	15	62	0	0.294118	0	A|0.810;G|0.190	0.190	strong	.	MUC16	4315	.	NM_024690	exon1	c.T6172C	p.S2058P	GGAGAGATGTAGT	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982116	240982116	+	Missense_Mutation	SNP	C	C	A	rs72993513	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	109	16	0	0.851562	0	C|0.741;A|0.259	0.259	strong	.	PRR21	53	.	NM_001080835	exon1	c.G284T	p.R95L	AAGGGCCGTGGGT	.	PASS	Atlas-SNP
CHD9	80205	hgsc.bcm.edu	37	16	53358439	53358439	+	Missense_Mutation	SNP	A	A	G	rs3743771	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	23	43	0	0.534884	0	A|0.774;G|0.225	0.225	strong	CHD9,NS,carcinoma,0,1	CHD9	203	1	NM_025134	exon39	c.A8278G	p.T2760A	CCTTCCACATCCT	.	PASS	Atlas-SNP
ADGB	79747	hgsc.bcm.edu	37	6	147045358	147045358	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	55	133	0	0.753425	0	.	.	none	.	ADGB	93	.	NM_024694	exon18	c.T2132G	p.L711R	CTGGACTTCTCAC	.	PASS	Atlas-SNP
DIAPH3	81624	hgsc.bcm.edu	37	13	60240961	60240961	+	Silent	SNP	C	C	T	rs9538494	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	267	127	225	0	0.475655	0	C|0.820;T|0.180	0.180	strong	.	DIAPH3	139	.	NM_001042517	exon28	c.G3339A	p.L1113L	TTCTGTCAACTGC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9061559	9061559	+	Silent	SNP	C	C	G	rs1423052	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	392	159	319	0	0.405612	0	C|0.616;G|0.384	0.384	strong	.	MUC16	4315	.	NM_024690	exon3	c.G25887C	p.T8629T	TTCAGACGTGGCT	.	PASS	Atlas-SNP
PI3	5266	hgsc.bcm.edu	37	20	43803606	43803606	+	Missense_Mutation	SNP	G	G	A	rs41282752	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	83	95	0	0.601449	0	G|0.973;A|0.027	0.027	strong	.	PI3	21	.	NM_002638	exon1	c.G43A	p.A15T	CTCATCGCTGGGA	.	PASS	Atlas-SNP
OPA1	4976	hgsc.bcm.edu	37	3	193334991	193334991	+	Missense_Mutation	SNP	G	G	A	rs7624750	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	110	239	0	0.454545	0	G|0.517;A|0.483	0.483	strong	OPA1,NS,carcinoma,0,1	OPA1	79	1	NM_130836	exon4	c.G473A	p.S158N	TTCCTAGTTCAGA	.	PASS	Atlas-SNP
SENP7	57337	hgsc.bcm.edu	37	3	101066717	101066717	+	Missense_Mutation	SNP	T	T	A	rs2433031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	87	98	0	1	0	T|0.679;A|0.321	0.321	strong	SENP7,NS,carcinoma,0,1	SENP7	170	1	NM_020654	exon13	c.A1836T	p.Q612H	CTCACATTGCTGG	.	PASS	Atlas-SNP
ABRA	137735	hgsc.bcm.edu	37	8	107782335	107782335	+	Silent	SNP	G	G	A	rs11996457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	37	129	0	0.373737	0	G|0.710;A|0.290	0.290	strong	ABRA,NS,adenoma,0,1	ABRA	57	1	NM_139166	exon1	c.C84T	p.S28S	GGCCAAGCTGATG	.	PASS	Atlas-SNP
MNS1	55329	hgsc.bcm.edu	37	15	56756285	56756285	+	Missense_Mutation	SNP	T	T	G	rs1715919	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	93	143	0	0.540698	0	G|0.074;N|0.000	0.074	strong	.	MNS1	39	.	NM_018365	exon2	c.A164C	p.Q55P	AGAAATTGCTTGC	.	PASS	Atlas-SNP
CLEC4M	10332	hgsc.bcm.edu	37	19	7831047	7831047	+	Silent	SNP	G	G	A	rs868878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	39	52	0	0.590909	0	A|0.087;C|0.000;G|0.913	0.087	strong	.	CLEC4M	58	.	NM_014257	exon4	c.G738A	p.K246K	GTCCAAGCAGCAG	.	PASS	Atlas-SNP
ITFG3	83986	hgsc.bcm.edu	37	16	304514	304514	+	Silent	SNP	C	C	T	rs3213508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	43	75	0	0.518072	0	C|0.801;T|0.199	0.199	strong	.	ITFG3	42	.	NM_032039	exon3	c.C102T	p.N34N	GGATAACGTGAAA	.	PASS	Atlas-SNP
ARHGEF18	23370	hgsc.bcm.edu	37	19	7505146	7505146	+	Missense_Mutation	SNP	A	A	C	rs200643326		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	53	74	0	0.449153	0	A|0.999;C|0.001	0.001	weak	.	ARHGEF18	129	.	NM_001130955	exon1	c.A320C	p.Q107P	GGCCGCAGTCGGA	.	PASS	Atlas-SNP
C16orf93	90835	hgsc.bcm.edu	37	16	30768895	30768895	+	Missense_Mutation	SNP	G	G	A	rs182267845	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	77	105	0	0.583333	0	A|0.001;G|0.999	0.001	strong	.	C16orf93	33	.	NM_001014979	exon9	c.C898T	p.R300W	TGAGCCGCTCCTC	.	PASS	Atlas-SNP
SMPD1	6609	hgsc.bcm.edu	37	11	6413108	6413108	+	Silent	SNP	T	T	C	rs61876771	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	43	68	0	0.605634	0	A|0.000;C|0.006;T|0.993	0.006	strong	.	SMPD1	108	.	NM_000543	exon2	c.T813C	p.P271P	CGGCCCTTTTGAT	.	PASS	Atlas-SNP
KLHL35	283212	hgsc.bcm.edu	37	11	75133765	75133765	+	Silent	SNP	G	G	A	rs11539810	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	28	54	0	0.54902	0	G|0.910;A|0.090	0.090	strong	KLHL35,NS,carcinoma,0,1	KLHL35	15	1	NM_001039548	exon6	c.C1611T	p.G537G	CCGCCCGCCAAGG	.	PASS	Atlas-SNP
DDR1	780	hgsc.bcm.edu	37	6	30860313	30860313	+	Missense_Mutation	SNP	A	A	T	rs143367160	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	23	42	0	0.365079	0	A|0.997;T|0.003	0.003	strong	.	DDR1	213	.	NM_001202523	exon8	c.A1147T	p.I383F	TCCTTCATCTCTG	.	PASS	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145299805	145299805	+	Missense_Mutation	SNP	A	A	C	rs61814629	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	8	116	7	0.0720721	0.0603448	A|0.999;G|0.001	.	weak	NBPF10_ENST00000369338,extremity,malignant_melanoma,0,2	NBPF10	221	2	NM_001039703	exon6	c.A854C	p.E285A	AGGCAGAGATGAA	.	scavenged	Atlas-SNP
OR52M1	119772	hgsc.bcm.edu	37	11	4566870	4566870	+	Silent	SNP	T	T	C	rs61747520	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	387	188	379	1	0.485788	0.00263852	T|0.968;C|0.032	0.032	strong	OR52M1,right_upper_lobe,carcinoma,+1,1	OR52M1	53	1	NM_001004137	exon1	c.T450C	p.S150S	TGTTTCTCTCCTC	.	PASS	Atlas-SNP
OR52K2	119774	hgsc.bcm.edu	37	11	4471276	4471276	+	Missense_Mutation	SNP	G	G	A	rs331537	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	206	104	207	1	0.504854	0.00483092	G|0.792;A|0.208	0.208	strong	.	OR52K2	61	.	NM_001005172	exon1	c.G707A	p.R236H	AGGCCCGCTACAA	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	19	94	0	0.223529	0	.	.	none	SPRR3,colon,carcinoma,0,3	SPRR3	45	3	NM_001097589	exon2	c.C219T	p.G73G	GCCAGGCTGTACC	.	PASS	Atlas-SNP
ANKRD18A	253650	hgsc.bcm.edu	37	9	38595886	38595886	+	Missense_Mutation	SNP	T	T	C	rs2996347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	56	175	0	0.408759	0	T|0.680;C|0.320	0.320	strong	ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	NM_147195	exon9	c.A1451G	p.N484S	AAGGTATTGAACT	.	PASS	Atlas-SNP
ESPN	83715	hgsc.bcm.edu	37	1	6501044	6501044	+	Silent	SNP	C	C	G	rs2311045	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	13	67	0	0.139785	0	C|0.828;G|0.172	0.172	strong	.	ESPN	32	.	NM_031475	exon5	c.C909G	p.R303R	CGACCGCGACGGG	.	PASS	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28504183	28504183	+	Silent	SNP	G	G	A	rs9625408	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	67	122	0	0.57265	0	G|0.949;A|0.051	0.051	strong	.	TTC28	84	.	NM_001145418	exon7	c.C1650T	p.R550R	TGAGGCGCGGTCA	.	PASS	Atlas-SNP
EXOC3	11336	hgsc.bcm.edu	37	5	465838	465838	+	Silent	SNP	C	C	T	rs13162508	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	62	105	0	0.652632	0	C|0.986;T|0.014	0.014	strong	.	EXOC3	54	.	NM_007277	exon12	c.C1944T	p.F648F	GGGTTTCGGGGAA	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3594296	3594296	+	Silent	SNP	C	C	T	rs35402060	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	45	60	0	0.46875	0	C|0.947;T|0.053	0.053	strong	.	NLRC3	103	.	NM_178844	exon17	c.G2805A	p.A935A	CGCACACGCTCCG	.	PASS	Atlas-SNP
SPRR1A	6698	hgsc.bcm.edu	37	1	152957887	152957887	+	Missense_Mutation	SNP	G	G	A	rs1611764	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	45	118	0	0.432692	0	G|0.417;A|0.583	0.583	strong	.	SPRR1A	17	.	NM_001199828	exon2	c.G181A	p.V61I	CCCAAGGTTCCAG	.	PASS	Atlas-SNP
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	37	62	0	0.521127	0	G|0.572;A|0.428	0.428	strong	WWP2,NS,carcinoma,0,1	WWP2	88	1	NM_001270454	exon24	c.G2595A	p.E865E	GACCGAGGGCTTT	.	PASS	Atlas-SNP
C19orf55	148137	hgsc.bcm.edu	37	19	36259415	36259415	+	Missense_Mutation	SNP	G	G	A	rs35178229	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	4	4	0	0	1	.	G|0.872;A|0.128	0.128	strong	.	C19orf55	39	.	NM_001039887	exon12	c.G1411A	p.E471K	AGAAGGGAAGGAG	.	PASS	Atlas-SNP
ACSBG2	81616	hgsc.bcm.edu	37	19	6156483	6156483	+	Missense_Mutation	SNP	T	T	C	rs4807840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	101	173	2	0.502488	0.0115607	T|0.289;C|0.711	0.711	strong	ACSBG2,NS,carcinoma,+1,1	ACSBG2	83	1	NM_030924	exon5	c.T428C	p.V143A	CCGAGGTTTGTCA	.	scavenged	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2957005	2957005	+	Silent	SNP	T	T	C	rs3735124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	30	38	0	0.5	0	T|0.633;C|0.367	0.367	strong	.	CARD11	339	.	NM_032415	exon20	c.A2622G	p.P874P	TTCTTCTGGCTGC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301679	65301679	+	Missense_Mutation	SNP	T	T	C	rs17403955	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	77	171	0	1	0	T|0.900;C|0.100	0.100	strong	.	EYS	527	.	NM_001142800	exon26	c.A4081G	p.I1361V	GGACAATTTGTGC	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39263772	39263772	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	50	132	0	0.50505	0	.	.	none	.	FREM2	385	.	NM_207361	exon1	c.C2291T	p.T764I	TCTTGACTGACAA	.	PASS	Atlas-SNP
ABT1	29777	hgsc.bcm.edu	37	6	26598188	26598188	+	Silent	SNP	A	A	G	rs3800303	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	131	142	0	1	0	A|0.536;G|0.464	0.464	strong	.	ABT1	39	.	NM_013375	exon2	c.A288G	p.G96G	CGGAGGAAAAAAG	.	PASS	Atlas-SNP
ABI3BP	25890	hgsc.bcm.edu	37	3	100473505	100473505	+	Silent	SNP	C	C	T	rs10936352	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	67	136	0	0.465278	0	C|0.725;T|0.275	0.275	strong	.	ABI3BP	305	.	NM_015429	exon31	c.G2748A	p.P916P	ACCAAGCGGGTTT	.	PASS	Atlas-SNP
PPAN-P2RY11	692312	hgsc.bcm.edu	37	19	10224548	10224548	+	Missense_Mutation	SNP	G	G	A	rs3745601	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	31	57	0	0.449275	0	G|0.855;A|0.145	0.145	strong	.	PPAN-P2RY11	81	.	NM_001040664	exon13	c.G1519A	p.A507T	CTGGCCGCCTACC	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99150237	99150237	+	Silent	SNP	G	G	A	rs41300219	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	19	42	0	0.395833	0	G|0.949;A|0.051	0.051	strong	.	RRP12	97	.	NM_015179	exon6	c.C696T	p.P232P	GGTCACGGGGTAG	.	PASS	Atlas-SNP
SCFD1	23256	hgsc.bcm.edu	37	14	31164033	31164033	+	Missense_Mutation	SNP	A	A	G	rs61754285	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	54	151	0	0.380282	0	A|0.987;G|0.013	0.013	strong	SCFD1,NS,carcinoma,-2,1	SCFD1	43	1	NM_016106	exon15	c.A1297G	p.T433A	AAAACTACTCTGG	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	37	18	21124945	21124945	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	32	144	0	0.307692	0	.	.	none	.	NPC1	114	.	NM_000271	exon12	c.G1926C	p.M642I	GCTTTTCATGTGC	.	PASS	Atlas-SNP
ACAN	176	hgsc.bcm.edu	37	15	89386652	89386652	+	Missense_Mutation	SNP	G	G	A	rs34949187	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	37	81	0	0.451219	0	G|0.889;A|0.111	0.111	strong	.	ACAN	220	.	NM_001135	exon6	c.G824A	p.R275Q	GCCGGCGGCTGGG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9084299	9084299	+	Missense_Mutation	SNP	T	T	C	rs1609458	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	62	134	1	0.466165	0.00746269	T|0.562;C|0.438	0.438	strong	MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	NM_024690	exon1	c.A7516G	p.T2506A	CACTGGTCCATGT	.	scavenged	Atlas-SNP
C2orf71	388939	hgsc.bcm.edu	37	2	29293837	29293837	+	Silent	SNP	C	C	T	rs183536545	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	48	117	0	0.421053	0	C|0.990;T|0.010	0.010	strong	.	C2orf71	146	.	NM_001029883	exon1	c.G3291A	p.Q1097Q	GTGCTCCTGAGAA	.	PASS	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74899134	74899134	+	Missense_Mutation	SNP	C	C	G	rs3736518	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	47	104	0	0.443396	0	C|0.823;G|0.177	0.177	strong	.	ECD	50	.	NM_001135752	exon12	c.G1453C	p.E485Q	AGACTTCAGTTAA	.	PASS	Atlas-SNP
EBF2	64641	hgsc.bcm.edu	37	8	25708267	25708267	+	Silent	SNP	T	T	C	rs10866845	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	106	110	0	0.990654	0	T|0.539;C|0.461	0.461	strong	.	EBF2	138	.	NM_022659	exon15	c.A1539G	p.S513S	GGGACTTGATGAC	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31091209	31091209	+	Silent	SNP	T	T	C	rs3751855	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	66	96	0	0.511628	0	A|0.000;C|0.415;T|0.584	0.415	strong	.	ZNF646	133	.	NM_014699	exon2	c.T3564C	p.T1188T	GGAGACTGCCGAG	.	PASS	Atlas-SNP
MAP3K15	389840	hgsc.bcm.edu	37	X	19387318	19387318	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	36	24	0	1	0	.	.	none	.	MAP3K15	108	.	NM_001001671	exon25	c.G3420T	p.E1140D	GGTAGGCTCAAAG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388379	1388379	+	Missense_Mutation	SNP	G	G	A	rs56109734	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	22	151	1	0.133333	0.00662252	G|0.996;A|0.004	0.004	strong	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.G80A	p.C27Y	GCTCATGTGCCCA	.	scavenged	Atlas-SNP
CCDC141	285025	hgsc.bcm.edu	37	2	179839833	179839833	+	Silent	SNP	A	A	G	rs10930846	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	34	63	0	0.414634	0	A|0.651;G|0.348	0.348	strong	.	CCDC141	362	.	NM_173648	exon4	c.T477C	p.S159S	CTCAGCACTCTCA	.	PASS	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56137798	56137798	+	Silent	SNP	G	G	A	rs1062600	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	91	95	0	1	0	G|0.633;A|0.367	0.367	strong	.	PCK1	95	.	NM_002591	exon4	c.G453A	p.S151S	GGGCTCGCCTCTG	.	PASS	Atlas-SNP
OR2C1	4993	hgsc.bcm.edu	37	16	3406626	3406626	+	Missense_Mutation	SNP	G	G	A	rs11648783	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	39	86	0	0.453488	0	G|0.723;A|0.277	0.277	strong	.	OR2C1	38	.	NM_012368	exon1	c.G686A	p.R229H	AAATCCGCTCTGC	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139369062	139369062	+	Silent	SNP	C	C	T	rs3812595	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	28	68	0	0.430769	0	C|0.837;T|0.163	0.163	strong	.	SEC16A	249	.	NM_014866	exon3	c.G3006A	p.L1002L	ATTTTCCAAAGTC	.	PASS	Atlas-SNP
CCDC62	84660	hgsc.bcm.edu	37	12	123262043	123262043	+	Silent	SNP	C	C	T	rs61956960	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	27	57	0	0.442623	0	C|0.990;T|0.010	0.010	strong	.	CCDC62	119	.	NM_201435	exon2	c.C42T	p.I14I	GAACATCGGGTCA	.	PASS	Atlas-SNP
ARHGAP26	23092	hgsc.bcm.edu	37	5	142254679	142254679	+	Silent	SNP	A	A	G	rs185200	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	57	145	0	0.504425	0	A|0.466;G|0.534	0.534	strong	.	ARHGAP26	57	.	NM_015071	exon3	c.A255G	p.R85R	AGCAAGATCTTTG	.	PASS	Atlas-SNP
ETV7	51513	hgsc.bcm.edu	37	6	36343721	36343721	+	Missense_Mutation	SNP	G	G	A	rs2234075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	22	43	0	0.488889	0	G|0.968;A|0.032	0.032	strong	.	ETV7	31	.	NM_001207037	exon3	c.C16T	p.R6W	GAACCCGTGCTCC	.	PASS	Atlas-SNP
ZNF844	284391	hgsc.bcm.edu	37	19	12187907	12187907	+	Missense_Mutation	SNP	G	G	A	rs55703333	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	28	43	0	0.4375	0	G|0.980;A|0.020	0.020	strong	.	ZNF844	69	.	NM_001136501	exon4	c.G1972A	p.V658I	CCTTTCGTAGACA	.	PASS	Atlas-SNP
KRT83	3889	hgsc.bcm.edu	37	12	52711549	52711549	+	Silent	SNP	G	G	A	rs2857667	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	41	121	0	0.372727	0	T|0.002;G|0.586;A|0.413	0.413	strong	KRT83,NS,carcinoma,-1,3	KRT83	64	3	NM_002282	exon4	c.C666T	p.C222C	GTAGGCGCAGTCC	.	PASS	Atlas-SNP
RALGDS	5900	hgsc.bcm.edu	37	9	135982493	135982493	+	Silent	SNP	C	C	T	rs45487303	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	132	151	0	1	0	C|0.985;T|0.015	0.015	strong	.	RALGDS	75	.	NM_006266	exon7	c.G1392A	p.E464E	CCAGTGCTCCACC	.	PASS	Atlas-SNP
SEC24C	9632	hgsc.bcm.edu	37	10	75523634	75523634	+	Missense_Mutation	SNP	A	A	G	rs35528438	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	76	143	0	0.481013	0	A|0.983;G|0.017	0.017	strong	.	SEC24C	86	.	NM_198597	exon8	c.A1120G	p.I374V	CGATACATCCGAT	.	PASS	Atlas-SNP
SPRR3	6707	hgsc.bcm.edu	37	1	152975739	152975739	+	Silent	SNP	T	T	A	rs17851565	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	3	93	0	0.0348837	0	A|0.010;C|0.001;T|0.988	0.010	strong	SPRR3,colon,carcinoma,0,4	SPRR3	45	4	NM_001097589	exon2	c.T243A	p.G81G	GCCAGGTTGTACC	.	scavenged	Atlas-SNP
PIP4K2B	8396	hgsc.bcm.edu	37	17	36926731	36926731	+	Silent	SNP	T	T	G	rs228289	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	82	198	0	0.476744	0	T|0.663;G|0.337	0.337	strong	.	PIP4K2B	35	.	NM_003559	exon9	c.A1128C	p.T376T	CTTCTTTGTATCG	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79637367	79637367	+	Missense_Mutation	SNP	C	C	G	rs7226091	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	100	98	0	1	0	C|0.754;G|0.245	0.245	strong	CCDC137,NS,carcinoma,0,2	CCDC137	27	2	NM_199287	exon3	c.C381G	p.H127Q	TATCCACCGCATG	.	PASS	Atlas-SNP
TRRAP	8295	hgsc.bcm.edu	37	7	98592335	98592335	+	Silent	SNP	G	G	A	rs56282945	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	76	152	0	0.444444	0	G|1.000;A|0.000	0.000	strong	.	TRRAP	863	.	NM_001244580	exon66	c.G10131A	p.T3377T	GAGCACGTTTGGG	.	PASS	Atlas-SNP
HELB	92797	hgsc.bcm.edu	37	12	66731864	66731864	+	Silent	SNP	C	C	A	rs1168329	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	18	38	0	0.439024	0	C|0.503;A|0.497	0.497	strong	.	HELB	90	.	NM_033647	exon13	c.C3246A	p.T1082T	GCCCACCGATAAT	.	PASS	Atlas-SNP
OR5K4	403278	hgsc.bcm.edu	37	3	98073313	98073313	+	Missense_Mutation	SNP	A	A	G	rs9822460	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	46	136	0	0.446602	0	A|0.782;G|0.218	0.218	strong	.	OR5K4	75	.	NM_001005517	exon1	c.A616G	p.I206V	ATACCAATTCAAA	.	PASS	Atlas-SNP
NFATC1	4772	hgsc.bcm.edu	37	18	77170505	77170505	+	Missense_Mutation	SNP	C	C	T	rs143045693	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	44	49	0	0.54321	0	C|1.000;T|0.000	0.000	strong	.	NFATC1	105	.	NM_172390	exon2	c.C230T	p.P77L	CCACACCGGGCAT	.	PASS	Atlas-SNP
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	39	74	0	0.541667	0	A|0.817;G|0.183	0.183	strong	.	MET	412	.	NM_000245	exon7	c.A1944G	p.Q648Q	AACACAATACAGT	.	PASS	Atlas-SNP
ARHGAP22	58504	hgsc.bcm.edu	37	10	49658842	49658842	+	Missense_Mutation	SNP	C	C	G	rs34940331	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	39	84	0	0.433333	0	C|0.991;G|0.009	0.009	strong	.	ARHGAP22	94	.	NM_001256024	exon9	c.G1378C	p.G460R	CGCCCCCCTTCGG	.	PASS	Atlas-SNP
STEAP1B	256227	hgsc.bcm.edu	37	7	22532260	22532260	+	Missense_Mutation	SNP	A	A	G	rs62447564	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	110	234	0	0.447154	0	A|0.702;G|0.298	0.298	strong	STEAP1B,NS,carcinoma,0,4	STEAP1B	22	4	NM_001164460	exon4	c.T686C	p.I229T	GCCAGTATTGCCA	.	PASS	Atlas-SNP
SLC34A1	6569	hgsc.bcm.edu	37	5	176815124	176815124	+	Silent	SNP	T	T	C	rs5030873	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	57	112	0	0.491379	0	T|0.759;C|0.241	0.241	strong	.	SLC34A1	73	.	NM_003052	exon7	c.T774C	p.H258H	CATCCATGGTGGC	.	PASS	Atlas-SNP
NACAD	23148	hgsc.bcm.edu	37	7	45124008	45124008	+	Missense_Mutation	SNP	T	T	C	rs7777835	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	154	127	0	0.993548	0	T|0.384;C|0.616	0.616	strong	.	NACAD	44	.	NM_001146334	exon2	c.A1771G	p.K591E	CCTCTTTAGCCTG	.	PASS	Atlas-SNP
SLC22A8	9376	hgsc.bcm.edu	37	11	62763226	62763226	+	Silent	SNP	C	C	T	rs57743826	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	63	117	0	0.577982	0	C|0.989;T|0.011	0.011	strong	.	SLC22A8	60	.	NM_001184732	exon7	c.G951A	p.L317L	CCGGAACAGGTCA	.	PASS	Atlas-SNP
WDR25	79446	hgsc.bcm.edu	37	14	100847930	100847930	+	Silent	SNP	A	A	G	rs3742387	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	31	69	0	0.455882	0	A|0.337;G|0.663	0.663	strong	.	WDR25	37	.	NM_001161476	exon2	c.A669G	p.P223P	TCAGCCATATTTG	.	PASS	Atlas-SNP
CASP9	842	hgsc.bcm.edu	37	1	15850613	15850613	+	Missense_Mutation	SNP	G	G	A	rs1052571	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	23	18	0	0.766667	0	G|0.387;A|0.613	0.613	strong	.	CASP9	40	.	NM_001229	exon1	c.C83T	p.A28V	AGCAGGGCGTCCC	.	PASS	Atlas-SNP
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	62	98	0	0.96875	0	G|0.744;A|0.256	0.256	strong	ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	NM_001007231	exon6	c.G756A	p.Q252Q	GAGCCAGTACGAA	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1255773	1255773	+	Silent	SNP	C	C	T	rs7116614	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	65	156	0	0.451389	0	C|0.647;T|0.353	0.353	strong	MUC5B,NS,carcinoma,0,2	MUC5B	473	2	NM_002458	exon21	c.C2493T	p.C831C	ACACTGCGTGTCC	.	PASS	Atlas-SNP
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	88	248	0	0.451282	0	G|0.712;A|0.288	0.288	strong	.	FKBP15	128	.	NM_015258	exon26	c.C3286T	p.L1096L	GGGACAGTCTTGT	.	PASS	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31349647	31349647	+	Missense_Mutation	SNP	C	C	T	rs2491132	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	9	58	0	0.109756	0	C|0.879;G|0.000;T|0.121	0.121	strong	.	SDC3	45	.	NM_014654	exon3	c.G622A	p.V208I	TCCGTACGCCAGT	.	PASS	Atlas-SNP
KLK4	9622	hgsc.bcm.edu	37	19	51412666	51412666	+	Silent	SNP	C	C	A	rs1654552	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	61	92	0	0.564815	0	C|0.685;A|0.315	0.315	strong	KLK4,colon,carcinoma,0,2	KLK4	46	2	NM_004917	exon2	c.G66T	p.S22S	GACGAGCGATCCT	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	37	16	51172786	51172786	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	46	119	0	0.403509	0	.	.	none	.	SALL1	301	.	NM_002968	exon2	c.C3347T	p.S1116F	GTGGCAGAGGAAG	.	PASS	Atlas-SNP
EPHB4	2050	hgsc.bcm.edu	37	7	100403131	100403131	+	Missense_Mutation	SNP	C	C	A	rs35638378	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	46	79	0	0.46	0	C|0.993;A|0.007	0.007	strong	.	EPHB4	106	.	NM_004444	exon15	c.G2670T	p.E890D	GCCATTCTCCCGG	.	PASS	Atlas-SNP
CHGB	1114	hgsc.bcm.edu	37	20	5903067	5903067	+	Missense_Mutation	SNP	T	T	A	rs6085324	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	41	83	0	0.482353	0	T|0.776;A|0.224	0.224	strong	CHGB,colon,carcinoma,0,2	CHGB	112	2	NM_001819	exon4	c.T277A	p.S93T	GATGCCTCGGAAG	.	PASS	Atlas-SNP
PCDHAC1	56135	hgsc.bcm.edu	37	5	140306903	140306903	+	Silent	SNP	C	C	T	rs149532133	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	66	109	0	0.6	0	C|0.992;T|0.008	0.008	strong	.	PCDHAC1	141	.	NM_031882	exon1	c.C426T	p.R142R	AGCCCGCTTTACT	.	PASS	Atlas-SNP
DAXX	1616	hgsc.bcm.edu	37	6	33288271	33288271	+	Silent	SNP	A	A	G	rs1059231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	16	38	0	0.340426	0	A|0.778;G|0.222	0.222	strong	.	DAXX	111	.	NM_001141970	exon4	c.T1173C	p.Y391Y	CATTGCATATTTG	.	PASS	Atlas-SNP
GRXCR1	389207	hgsc.bcm.edu	37	4	42895308	42895308	+	Missense_Mutation	SNP	G	G	A	rs78136490	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	66	132	0	0.452055	0	G|0.906;A|0.094	0.094	strong	.	GRXCR1	78	.	NM_001080476	exon1	c.G25A	p.E9K	AAGCCAGAAAGTG	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24527220	24527220	+	Silent	SNP	C	C	T	rs4982853	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	38	97	0	0.506667	0	C|0.898;T|0.102	0.102	strong	.	LRRC16B	120	.	NM_138360	exon16	c.C1269T	p.Y423Y	CGCCTACACACTG	.	PASS	Atlas-SNP
AHSG	197	hgsc.bcm.edu	37	3	186338382	186338382	+	Missense_Mutation	SNP	G	G	C	rs4918	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	76	75	0	1	0	G|0.337;C|0.663	0.663	strong	.	AHSG	40	.	NM_001622	exon7	c.G767C	p.S256T	CCGTGAGCTCACA	.	PASS	Atlas-SNP
NBPF15	284565	hgsc.bcm.edu	37	1	148594563	148594563	+	Missense_Mutation	SNP	G	G	T	rs146229961	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	486	36	457	41	0.0740741	0.0897155	G|0.996;T|0.005	0.005	strong	NBPF15,brain,glioma,0,1	NBPF15	20	1	NM_173638	exon19	c.G1936T	p.V646L	CTTTACGTGGACA	.	scavenged	Atlas-SNP
PRRG4	79056	hgsc.bcm.edu	37	11	32852167	32852167	+	Missense_Mutation	SNP	C	C	T	rs61889489	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	21	51	0	0.396226	0	C|0.945;T|0.055	0.055	strong	.	PRRG4	15	.	NM_024081	exon2	c.C92T	p.A31V	AGCATGCGGGAGA	.	PASS	Atlas-SNP
C2orf69	205327	hgsc.bcm.edu	37	2	200776353	200776353	+	Missense_Mutation	SNP	T	T	G	rs62178345	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	10	14	0	0.416667	0	T|0.898;G|0.102	0.102	strong	.	C2orf69	17	.	NM_153689	exon1	c.T192G	p.D64E	AGCCGATCCGCAG	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	37	19	6468907	6468907	+	Missense_Mutation	SNP	G	G	A	rs35001260	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	28	40	0	0.466667	0	G|0.983;A|0.017	0.017	strong	.	DENND1C	93	.	NM_024898	exon20	c.C1465T	p.R489C	CTGAGCGGCTGGG	.	PASS	Atlas-SNP
FAM205A	259308	hgsc.bcm.edu	37	9	34724241	34724241	+	Missense_Mutation	SNP	C	C	A	rs3739881	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	193	100	167	0	0.518135	0	C|0.579;A|0.421	0.421	strong	.	FAM205A	45	.	NM_001141917	exon4	c.G2996T	p.S999I	TCCCCACTGGGCT	.	PASS	Atlas-SNP
ZNF584	201514	hgsc.bcm.edu	37	19	58928309	58928309	+	Missense_Mutation	SNP	C	C	T	rs11668789	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	45	112	0	0.5	0	C|0.831;T|0.169	0.169	strong	.	ZNF584	31	.	NM_173548	exon4	c.C424T	p.P142S	TTCCCACCTGGTT	.	PASS	Atlas-SNP
TTC29	83894	hgsc.bcm.edu	37	4	147824864	147824864	+	Missense_Mutation	SNP	G	G	A	rs17610219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	108	134	0	0.981818	0	G|0.507;A|0.493	0.493	strong	.	TTC29	63	.	NM_031956	exon6	c.C418T	p.H140Y	TATTATGTACATC	.	PASS	Atlas-SNP
ZEB2	9839	hgsc.bcm.edu	37	2	145157593	145157593	+	Silent	SNP	T	T	C	rs146673563	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	48	105	0	0.475248	0	T|0.999;C|0.001	0.001	strong	ZEB2,NS,carcinoma,0,1	ZEB2	218	1	NM_014795	exon8	c.A1161G	p.L387L	TTTAAGTAAGCCT	.	PASS	Atlas-SNP
BSPRY	54836	hgsc.bcm.edu	37	9	116132275	116132275	+	Silent	SNP	G	G	A	rs3750529	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	34	57	0	0.566667	0	G|0.919;A|0.081	0.081	strong	.	BSPRY	21	.	NM_017688	exon6	c.G1062A	p.L354L	CCAGCTGGGTGTA	.	PASS	Atlas-SNP
NOX3	50508	hgsc.bcm.edu	37	6	155750035	155750035	+	Silent	SNP	C	C	T	rs231954	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	19	148	0	0.204301	0	C|0.349;T|0.651	0.651	strong	.	NOX3	93	.	NM_015718	exon9	c.G1038A	p.E346E	AAAGTCCTCCTGG	.	PASS	Atlas-SNP
FNDC3A	22862	hgsc.bcm.edu	37	13	49776080	49776080	+	Silent	SNP	A	A	G	rs9316430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	75	142	0	0.493421	0	A|0.949;G|0.051	0.051	strong	.	FNDC3A	93	.	NM_001079673	exon24	c.A3132G	p.K1044K	TCCAAAATCTGTC	.	PASS	Atlas-SNP
DROSHA	29102	hgsc.bcm.edu	37	5	31423007	31423007	+	Silent	SNP	T	T	C	rs2287584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	22	50	0	0.431373	0	T|0.554;C|0.446	0.446	strong	.	DROSHA	130	.	NM_013235	exon28	c.A3306G	p.P1102P	TAGAACTGGAGAA	.	PASS	Atlas-SNP
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609207	32609207	+	Missense_Mutation	SNP	C	C	T	rs1142324	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	19	20	20	0.195876	1	C|0.523;T|0.477	0.477	strong	HLA-DQA1,colon,carcinoma,0,1	HLA-DQA1	52	1	NM_002122	exon2	c.C203T	p.A68V	AGACTGCCTGGCG	.	scavenged	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144852379	144852379	+	Missense_Mutation	SNP	G	G	T	rs113954821	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	30	97	0	0.315789	0	G|0.500;T|0.500	0.500	weak	.	PDE4DIP	817	.	NM_001198834	exon44	c.C7064A	p.P2355H	ACAAAAGGGGGAC	.	PASS	Atlas-SNP
MYH6	4624	hgsc.bcm.edu	37	14	23852443	23852443	+	Silent	SNP	G	G	A	rs200662317	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	47	113	0	0.484536	0	G|0.997;A|0.003	0.003	strong	.	MYH6	274	.	NM_002471	exon37	c.C5652T	p.A1884A	CTCCTCGGCCTGG	.	PASS	Atlas-SNP
ZNF646	9726	hgsc.bcm.edu	37	16	31090407	31090407	+	Missense_Mutation	SNP	G	G	C	rs35713203	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	18	45	0	0.409091	0	G|0.716;C|0.284	0.284	strong	.	ZNF646	133	.	NM_014699	exon2	c.G2762C	p.G921A	AGGAAGGAGTGGC	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8176554	8176554	+	Missense_Mutation	SNP	C	C	T	rs12549973	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	10	16	0	0.4	0	C|0.701;T|0.299	0.299	strong	.	.	.	.	NM_001080826	exon5	c.G3331A	p.A1111T	GCTCCGCCTGGTG	.	PASS	Atlas-SNP
OR2T3	343173	hgsc.bcm.edu	37	1	248637543	248637543	+	Missense_Mutation	SNP	C	C	T	rs74984555	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1103	273	964	2	0.247507	0.00207469	C|0.500;T|0.500	0.500	strong	OR2T3,NS,carcinoma,-2,1	OR2T3	79	1	NM_001005495	exon1	c.C892T	p.R298C	AGTCTCCGCAACA	.	scavenged	Atlas-SNP
COL25A1	84570	hgsc.bcm.edu	37	4	109841743	109841743	+	Silent	SNP	C	C	T	rs17596705	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	30	71	0	0.428571	0	C|0.843;T|0.157	0.157	strong	.	COL25A1	178	.	NM_198721	exon11	c.G726A	p.P242P	TTGTCCCGGAGGC	.	PASS	Atlas-SNP
SPATA17	128153	hgsc.bcm.edu	37	1	217856626	217856626	+	Silent	SNP	G	G	A	rs12068167	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	70	192	0	0.469799	0	G|0.826;A|0.174	0.174	strong	.	SPATA17	59	.	NM_138796	exon5	c.G318A	p.R106R	CTATAGGGTTCGG	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19753575	19753575	+	Silent	SNP	A	A	G	rs36215075	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	268	118	231	0	0.440298	0	A|0.958;G|0.042	0.042	strong	.	TUBA3C	166	.	NM_006001	exon2	c.T132C	p.G44G	GTCCCCACCACCA	.	PASS	Atlas-SNP
AZI1	22994	hgsc.bcm.edu	37	17	79166384	79166384	+	Silent	SNP	C	C	T	rs3744150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	31	93	0	0.484375	0	C|0.876;T|0.124	0.124	strong	.	AZI1	145	.	NM_014984	exon20	c.G2439A	p.A813A	CAGCTCCGCCCGC	.	PASS	Atlas-SNP
KIAA1549L	25758	hgsc.bcm.edu	37	11	33581306	33581306	+	Silent	SNP	G	G	A	rs2281380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	139	132	0	1	0	G|0.613;A|0.387	0.387	strong	.	.	.	.	NM_012194	exon6	c.G2976A	p.T992T	GAGCACGTCCAAT	.	PASS	Atlas-SNP
GAR1	54433	hgsc.bcm.edu	37	4	110737389	110737389	+	Silent	SNP	T	T	C	rs2276326	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	44	54	0	0.956522	0	T|0.264;C|0.736	0.736	strong	GAR1,NS,carcinoma,0,1	GAR1	16	1	NM_018983	exon2	c.T69C	p.G23G	CCGAGGTGGCAGC	.	PASS	Atlas-SNP
BPIFA2	140683	hgsc.bcm.edu	37	20	31760763	31760763	+	Silent	SNP	C	C	T	rs150791330	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	2	135	0	0.0141844	0	C|1.000;A|0.000	.	alt	C20orf70,face,carcinoma,+2,1	.	.	1	NM_080574	exon3	c.C183T	p.D61D	GGTCGACCTAGGA	.	scavenged	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54725744	54725744	+	Nonsense_Mutation	SNP	C	C	T	rs59533602	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	16	42	0	0.666667	0	C|0.500;T|0.500	0.500	strong	LILRB3,NS,neuroblastoma,-1,1	LILRB3	67	1	NM_006864	exon4	c.G614A	p.W205X	CACACCCAGGGGG	.	scavenged	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	37	18	14848821	14848821	+	Silent	SNP	G	G	A	rs71323607		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	189	233	0	0.921951	0	G|0.500;A|0.500	0.500	weak	ANKRD30B_ENST00000358984,NS,carcinoma,+1,1	ANKRD30B	237	1	NM_001145029	exon34	c.G2931A	p.T977T	ACAAACGAAAAAT	.	PASS	Atlas-SNP
RBL2	5934	hgsc.bcm.edu	37	16	53504721	53504721	+	Silent	SNP	T	T	C	rs10748	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	105	101	0	0.990566	0	T|0.470;C|0.530	0.530	strong	.	RBL2	115	.	NM_005611	exon17	c.T2590C	p.L864L	GATGAATTGAGGA	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46900410	46900410	+	Silent	SNP	C	C	T	rs2236467	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	73	137	0	0.45625	0	C|0.881;T|0.119	0.119	strong	.	COL18A1	129	.	NM_030582	exon11	c.C1968T	p.F656F	TGGCTTCGGGGGC	.	PASS	Atlas-SNP
BZRAP1	9256	hgsc.bcm.edu	37	17	56386289	56386289	+	Silent	SNP	C	C	T	rs145131712	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	32	56	0	0.5	0	C|0.991;T|0.009	0.009	strong	.	BZRAP1	287	.	NM_004758	exon22	c.G4344A	p.E1448E	ACCCCTCTCCCGT	.	PASS	Atlas-SNP
TTC7B	145567	hgsc.bcm.edu	37	14	91252545	91252545	+	Silent	SNP	G	G	A	rs17794971	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	44	89	0	0.444444	0	G|0.976;A|0.024	0.024	strong	.	TTC7B	93	.	NM_001010854	exon2	c.C249T	p.T83T	GGCGGCGGTCAGA	.	PASS	Atlas-SNP
CSTL1	128817	hgsc.bcm.edu	37	20	23424613	23424613	+	Missense_Mutation	SNP	T	T	C	rs3746736	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	40	86	0	0.470588	0	C|0.629;N|0.000	0.629	strong	.	CSTL1	30	.	NM_138283	exon3	c.T262C	p.W88R	ATTGGCTGGACCA	.	PASS	Atlas-SNP
OR7A5	26659	hgsc.bcm.edu	37	19	14938190	14938190	+	Silent	SNP	A	A	G	rs2240561	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	9	69	0	0.0782609	0	A|0.999;G|0.001	0.001	strong	.	OR7A5	43	.	NM_017506	exon1	c.T864C	p.F288F	ATAGATAAAGGGG	.	PASS	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227216775	227216775	+	Missense_Mutation	SNP	C	C	T	rs1929860	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	28	38	0	0.518519	0	T|0.301;C|0.699	0.301	strong	.	CDC42BPA	528	.	NM_003607	exon29	c.G3910A	p.V1304I	AAGTTACGGTTTG	.	PASS	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32756407	32756407	+	Missense_Mutation	SNP	A	A	G	rs61747109	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	106	231	1	0.484018	0.004329	A|0.959;G|0.041	0.041	strong	RFPL3_ENST00000249007,NS,carcinoma,0,2	RFPL3	91	2	NM_001098535	exon2	c.A542G	p.Y181C	GCCACTACTGGGA	.	PASS	Atlas-SNP
CEP170	9859	hgsc.bcm.edu	37	1	243329049	243329049	+	Missense_Mutation	SNP	G	G	A	rs71627763	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	59	209	0	0.246862	0	G|0.167;A|0.833	0.833	weak	.	CEP170	153	.	NM_014812	exon13	c.C2213T	p.T738I	AAAGAAGTTTCCT	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305550	48305550	+	Missense_Mutation	SNP	G	G	A	rs75909117	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	4	29	0	0.105263	0	G|0.971;A|0.029	0.029	strong	TPRX1,colon,carcinoma,0,1	TPRX1	46	1	NM_198479	exon2	c.C718T	p.P240S	GGCCTGGGATCGG	.	PASS	Atlas-SNP
USP53	54532	hgsc.bcm.edu	37	4	120214030	120214030	+	Missense_Mutation	SNP	T	T	G	rs3749591	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	42	75	0	0.5	0	T|0.725;G|0.275	0.275	strong	USP53,NS,carcinoma,0,1	USP53	69	1	NM_019050	exon18	c.T2886G	p.S962R	GCACAGTTTAAGT	.	PASS	Atlas-SNP
SLC37A2	219855	hgsc.bcm.edu	37	11	124947149	124947149	+	Silent	SNP	G	G	A	rs12276567	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	65	115	0	0.515873	0	G|0.679;A|0.321	0.321	strong	SLC37A2_ENST00000403796,NS,adenoma,0,3	SLC37A2	105	3	NM_001145290	exon3	c.G165A	p.S55S	CTGCTCGGAGCAG	.	PASS	Atlas-SNP
ZNF215	7762	hgsc.bcm.edu	37	11	6977175	6977175	+	Missense_Mutation	SNP	G	G	C	rs2239730	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	37	55	0	0.528571	0	G|0.761;C|0.239	0.239	strong	ZNF215,colon,carcinoma,0,1	ZNF215	72	1	NM_013250	exon7	c.G967C	p.V323L	ATACAAGTGGGAA	.	PASS	Atlas-SNP
BTN3A3	10384	hgsc.bcm.edu	37	6	26446209	26446209	+	Silent	SNP	C	C	T	rs3846848	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	78	170	0	0.516556	0	C|0.838;T|0.162	0.162	strong	.	BTN3A3	56	.	NM_006994	exon5	c.C711T	p.I237I	ATCCATCGCAGGT	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	37	16	51175658	51175658	+	Missense_Mutation	SNP	T	T	C	rs13336129	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	95	93	1	0.95	0.0107527	T|0.933;C|0.067	0.067	strong	SALL1,NS,carcinoma,0,1	SALL1	301	1	NM_002968	exon2	c.A475G	p.S159G	CGCCGCTGCTGCT	.	scavenged	Atlas-SNP
ZFP36L1	677	hgsc.bcm.edu	37	14	69259661	69259661	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	51	79	0	0.447368	0	.	.	none	.	ZFP36L1	47	.	NM_001244701	exon2	c.C202T	p.H68Y	TCCTGTGCGTTCG	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	37	15	86800209	86800209	+	Silent	SNP	C	C	T	rs1353578	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	45	103	0	0.420561	0	C|0.471;T|0.529	0.529	strong	.	AGBL1	151	.	NM_152336	exon7	c.C723T	p.P241P	GGTCCCCGGGTGC	.	PASS	Atlas-SNP
OR5T2	219464	hgsc.bcm.edu	37	11	55999950	55999950	+	Missense_Mutation	SNP	G	G	C	rs12221615	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	78	227	0	0.5	0	G|0.901;C|0.099	0.099	strong	OR5T2,right_upper_lobe,carcinoma,+2,3	OR5T2	107	3	NM_001004746	exon1	c.C712G	p.L238V	AGAAGAGTAGAAG	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26422980	26422980	+	Missense_Mutation	SNP	A	A	G	rs2236005	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	19	43	0	0.463415	0	A|0.618;G|0.382	0.382	strong	MYO18B,NS,carcinoma,-1,1	MYO18B	322	1	NM_032608	exon43	c.A7040G	p.Q2347R	AAACCCAATTCAG	.	PASS	Atlas-SNP
MRPL28	10573	hgsc.bcm.edu	37	16	419092	419092	+	Silent	SNP	A	A	G	rs3830160	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	48	119	0	0.48	0	A|0.346;G|0.654	0.654	strong	.	MRPL28	15	.	NM_006428	exon3	c.T417C	p.Y139Y	GAGCCCATAAGCC	.	PASS	Atlas-SNP
RBM46	166863	hgsc.bcm.edu	37	4	155720274	155720274	+	Silent	SNP	T	T	C	rs156502	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	156	126	0	0.987342	0	T|0.395;C|0.605	0.605	strong	.	RBM46	76	.	NM_144979	exon4	c.T960C	p.N320N	TCTTAATGGTCAG	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38768300	38768300	+	Missense_Mutation	SNP	T	T	C	rs57326399	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	139	149	2	1	0.0134228	T|0.779;C|0.221	0.221	strong	SCN10A,NS,carcinoma,0,1	SCN10A	359	1	NM_006514	exon16	c.A2884G	p.I962V	CAGCAATGTGGTT	.	scavenged	Atlas-SNP
IDNK	414328	hgsc.bcm.edu	37	9	86258685	86258685	+	Missense_Mutation	SNP	A	A	C	rs1052690	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	12	28	0	0.631579	0	A|0.889;C|0.111	0.111	strong	.	.	.	.	NM_001001551	exon5	c.A554C	p.K185T	CCCTAAAAATGAA	.	PASS	Atlas-SNP
C19orf57	79173	hgsc.bcm.edu	37	19	14003969	14003969	+	Missense_Mutation	SNP	G	G	C	rs62622787	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	36	82	0	0.418605	0	G|0.955;C|0.045	0.045	strong	.	C19orf57	34	.	NM_024323	exon4	c.C274G	p.L92V	GAGGAAGGGGAGC	.	PASS	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77709405	77709405	+	Silent	SNP	C	C	T	rs78553282	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	33	63	0	0.407407	0	C|0.963;T|0.037	0.037	strong	.	ENPP7	63	.	NM_178543	exon3	c.C963T	p.Y321Y	CCACTACGCCAAC	.	PASS	Atlas-SNP
DTX2	113878	hgsc.bcm.edu	37	7	76126737	76126737	+	Missense_Mutation	SNP	C	C	T	rs145964625		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	356	118	419	0	0.331461	0	.	.	weak	DTX2,NS,haematopoietic_neoplasm,0,3	DTX2	64	3	NM_001102594	exon6	c.C1093T	p.R365C	GCCTCCCGTCTGG	.	scavenged	Atlas-SNP
OR1B1	347169	hgsc.bcm.edu	37	9	125391241	125391241	+	Nonsense_Mutation	SNP	G	G	A	rs1476860	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	37	74	0	0.345794	0	G|0.725;A|0.275	0.275	strong	.	OR1B1	48	.	NM_001004450	exon1	c.C574T	p.R192X	AGGCTCGCAGAAG	.	PASS	Atlas-SNP
TULP4	56995	hgsc.bcm.edu	37	6	158870081	158870081	+	Silent	SNP	A	A	G	rs705956	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	48	57	1	1	0.0175439	A|0.374;G|0.626	0.626	strong	TULP4,NS,carcinoma,+1,1	TULP4	137	1	NM_020245	exon4	c.A597G	p.R199R	CGGCAGAATGCTG	.	scavenged	Atlas-SNP
RNF183	138065	hgsc.bcm.edu	37	9	116060221	116060221	+	Missense_Mutation	SNP	C	C	T	rs3750533	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	89	122	0	0.523529	0	C|0.613;T|0.386	0.386	strong	.	RNF183	11	.	NM_145051	exon2	c.G244A	p.A82T	GCAGGGCGAGCAT	.	PASS	Atlas-SNP
HRNR	388697	hgsc.bcm.edu	37	1	152191033	152191033	+	Silent	SNP	A	A	G	rs148722408	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	96	158	0	0.52459	0	A|0.991;G|0.009	0.009	strong	HRNR,NS,carcinoma,0,2	HRNR	403	2	NM_001009931	exon3	c.T3072C	p.Y1024Y	TGGGCCATAGCTG	.	PASS	Atlas-SNP
CSTF2T	23283	hgsc.bcm.edu	37	10	53458047	53458047	+	Silent	SNP	A	A	G	rs3740228	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	196	102	204	1	0.520408	0.00490196	A|0.755;G|0.245	0.245	strong	CSTF2T,NS,carcinoma,0,1	CSTF2T	64	1	NM_015235	exon1	c.T1263C	p.R421R	CATGGCACGAGTC	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8191184	8191184	+	Missense_Mutation	SNP	C	C	T	rs35025963	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	100	90	0	1	0	C|0.760;T|0.240	0.240	strong	.	FBN3	300	.	NM_032447	exon20	c.G2602A	p.D868N	TACCATCGCAGGT	.	PASS	Atlas-SNP
PDLIM5	10611	hgsc.bcm.edu	37	4	95496882	95496882	+	Missense_Mutation	SNP	C	C	T	rs2452600	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	232	126	171	0	0.543103	0	C|0.737;T|0.263	0.263	strong	.	PDLIM5	76	.	NM_006457	exon5	c.C407T	p.S136F	CTGTGTCTTCACC	.	PASS	Atlas-SNP
FAM178B	51252	hgsc.bcm.edu	37	2	97559759	97559759	+	Silent	SNP	G	G	A	rs11677797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	59	67	0	1	0	G|0.745;A|0.255	0.255	strong	.	FAM178B	35	.	NM_001122646	exon14	c.C1680T	p.L560L	CCTCATGAGGCCC	.	PASS	Atlas-SNP
TCP11L1	55346	hgsc.bcm.edu	37	11	33065394	33065394	+	Silent	SNP	C	C	T	rs1064005	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	31	54	0	0.43662	0	C|0.583;T|0.417	0.417	strong	.	TCP11L1	40	.	NM_001145541	exon2	c.C75T	p.L25L	AGGCCTCGAAGAT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9083457	9083457	+	Missense_Mutation	SNP	C	C	T	rs17000886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	35	87	0	0.421687	0	C|0.797;T|0.203	0.203	strong	.	MUC16	4315	.	NM_024690	exon1	c.G8358A	p.M2786I	TAGTGGCATCACA	.	PASS	Atlas-SNP
CRYZ	1429	hgsc.bcm.edu	37	1	75175886	75175886	+	Missense_Mutation	SNP	T	T	C	rs3819946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	112	201	0	0.523364	0	C|0.339;N|0.000	0.339	strong	.	CRYZ	28	.	NM_001130043	exon6	c.A526G	p.I176V	CCAAAATCTTTAA	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373251	5373251	+	Missense_Mutation	SNP	C	C	T	rs5006884	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	80	217	0	0.441989	0	C|0.767;T|0.233	0.233	strong	.	OR51B6	53	.	NM_001004750	exon1	c.C514T	p.L172F	CATGTACTCTCCC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	145075775	145075775	+	Missense_Mutation	SNP	G	G	A	rs76199660	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	22	82	0	0.23913	0	A|0.016;G|0.984	0.016	strong	PDE4DIP_ENST00000369348,NS,carcinoma,0,3	PDE4DIP	817	3	NM_022359	exon1	c.C88T	p.P30S	GGTAAGGCGTGTA	.	PASS	Atlas-SNP
RIPK4	54101	hgsc.bcm.edu	37	21	43187167	43187167	+	Missense_Mutation	SNP	G	G	C	rs6586239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	25	23	0	0.675676	0	G|0.846;C|0.154	0.154	strong	RIPK4_ENST00000352483,colon,carcinoma,0,2	RIPK4	151	2	NM_020639	exon1	c.C35G	p.A12G	AGCAGCGCCAGGG	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46268493	46268493	+	Silent	SNP	A	A	G	rs2076546	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	34	82	0	0.43038	0	A|0.863;G|0.137	0.137	strong	.	NCOA3	156	.	NM_181659	exon15	c.A2880G	p.T960T	TCCCACATTGCCT	.	PASS	Atlas-SNP
GLYATL3	389396	hgsc.bcm.edu	37	6	49479775	49479775	+	Silent	SNP	A	A	T	rs1480615	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	43	43	0	1	0	T|0.431;N|0.000	0.431	strong	GLYATL3,trunk,malignant_melanoma,+1,1	GLYATL3	19	1	NM_001010904	exon2	c.A72T	p.S24S	TGAATCACTCAAG	.	PASS	Atlas-SNP
FNDC7	163479	hgsc.bcm.edu	37	1	109273456	109273456	+	Silent	SNP	A	A	G	rs4970809	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	50	89	0	0.510204	0	A|0.477;G|0.523;T|0.000	0.523	strong	.	FNDC7	113	.	NM_001144937	exon9	c.A1785G	p.G595G	CCTAGGATGCATC	.	PASS	Atlas-SNP
TBC1D2	55357	hgsc.bcm.edu	37	9	100995758	100995758	+	Missense_Mutation	SNP	G	G	T	rs879368	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	43	100	0	0.5375	0	G|0.769;T|0.231	0.231	strong	.	TBC1D2	70	.	NM_001267571	exon4	c.C721A	p.P241T	TCTGTGGAGAATC	.	PASS	Atlas-SNP
MYEOV	26579	hgsc.bcm.edu	37	11	69063767	69063767	+	Missense_Mutation	SNP	C	C	A	rs12274095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	51	77	0	0.525773	0	C|0.952;A|0.048	0.048	strong	.	MYEOV	42	.	NM_138768	exon3	c.C850A	p.P284T	GTGGGGCCCACTA	.	PASS	Atlas-SNP
FAM160B2	64760	hgsc.bcm.edu	37	8	21955116	21955116	+	Silent	SNP	C	C	T	rs11352	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	183	78	202	0	0.42623	0	C|0.639;T|0.361	0.361	strong	.	FAM160B2	35	.	NM_022749	exon4	c.C387T	p.V129V	CAGCGTCCACAGG	.	PASS	Atlas-SNP
CD200	4345	hgsc.bcm.edu	37	3	112063850	112063850	+	Missense_Mutation	SNP	C	C	A	rs2272022	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	40	91	0	0.5	0	C|0.748;A|0.252	0.252	strong	.	CD200	33	.	NM_001004196	exon4	c.C211A	p.P71T	TACACACCTGCTT	.	PASS	Atlas-SNP
TUBAL3	79861	hgsc.bcm.edu	37	10	5436260	5436260	+	Silent	SNP	A	A	G	rs7910290	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	62	132	0	0.455882	0	A|0.257;G|0.743	0.743	strong	.	TUBAL3	54	.	NM_024803	exon4	c.T561C	p.A187A	TACCACAGCAGTG	.	PASS	Atlas-SNP
HGS	9146	hgsc.bcm.edu	37	17	79658569	79658569	+	Silent	SNP	C	C	T	rs148002494	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	58	110	0	0.483333	0	C|0.999;T|0.001	0.001	strong	.	HGS	54	.	NM_004712	exon8	c.C630T	p.R210R	GGTGCGCGTGTGT	.	PASS	Atlas-SNP
KLF10	7071	hgsc.bcm.edu	37	8	103663912	103663912	+	Silent	SNP	T	T	G	rs11552577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	60	102	0	0.5	0	T|0.865;G|0.135	0.135	strong	.	KLF10	44	.	NM_005655	exon3	c.A648C	p.T216T	TGCCACTGTGTTT	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227892720	227892720	+	Missense_Mutation	SNP	C	C	T	rs2229813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	16	33	0	0.592593	0	C|0.549;T|0.451	0.451	strong	.	COL4A4	215	.	NM_000092	exon42	c.G3979A	p.V1327M	ATCCCACTGGTCC	.	PASS	Atlas-SNP
KCNB2	9312	hgsc.bcm.edu	37	8	73849768	73849768	+	Silent	SNP	A	A	C	rs142525254	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	23	63	0	0.410714	0	A|0.989;C|0.011	0.011	strong	.	KCNB2	228	.	NM_004770	exon3	c.A2178C	p.A726A	CAGTGCACCACAG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467160	10467160	+	Missense_Mutation	SNP	G	G	A	rs62490855	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	34	44	0	0.586207	0	G|0.853;A|0.147	0.147	strong	.	RP1L1	453	.	NM_178857	exon4	c.C4448T	p.A1483V	ATGGTGGCTCCGG	.	PASS	Atlas-SNP
KIAA1211	57482	hgsc.bcm.edu	37	4	57182758	57182758	+	Silent	SNP	C	C	T	rs28559894	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	15	30	0	0.5	0	C|0.728;T|0.272	0.272	strong	KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	NM_020722	exon8	c.C3090T	p.D1030D	GAGGGACGAGGAG	.	PASS	Atlas-SNP
PNMAL1	55228	hgsc.bcm.edu	37	19	46974077	46974077	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	31	66	0	0.402597	0	.	.	none	.	PNMAL1	87	.	NM_018215	exon2	c.G216A	p.E72E	ACCAACCTCAATG	.	PASS	Atlas-SNP
CPT2	1376	hgsc.bcm.edu	37	1	53676448	53676448	+	Missense_Mutation	SNP	G	G	A	rs1799821	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	52	128	0	0.5	0	G|0.523;A|0.477	0.477	strong	.	CPT2	34	.	NM_000098	exon4	c.G1102A	p.V368I	ACTGCCGTCCACT	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	108013936	108013936	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	3	174	0	0.0179641	0	.	.	none	BTBD11,caecum,carcinoma,-2,1	BTBD11	122	1	NM_001018072	exon11	c.A2626G	p.S876G	AAAGCGAGCAAGG	.	scavenged	Atlas-SNP
CYP2D6	1565	hgsc.bcm.edu	37	22	42526763	42526763	+	Missense_Mutation	SNP	C	C	T	rs769258	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	259	121	230	0	0.467181	0	C|0.971;T|0.029	0.029	strong	.	CYP2D6	104	.	NM_000106	exon1	c.G31A	p.V11M	CTATCACGGCCAG	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33688865	33688865	+	Silent	SNP	A	A	G	rs7279896	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	52	59	0	0.712329	0	A|0.758;G|0.242	0.242	strong	.	URB1	176	.	NM_014825	exon38	c.T6546C	p.A2182A	CTGGGCAGCCACC	.	PASS	Atlas-SNP
KLRG1	10219	hgsc.bcm.edu	37	12	9161648	9161648	+	Silent	SNP	T	T	C	rs3026251	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	84	197	0	0.48	0	T|0.754;C|0.246	0.246	strong	.	KLRG1	16	.	NM_005810	exon4	c.T435C	p.D145D	GGAAGATGGATCA	.	PASS	Atlas-SNP
AMOTL1	154810	hgsc.bcm.edu	37	11	94533373	94533373	+	Silent	SNP	C	C	T	rs2303960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	74	77	0	1	0	C|0.744;T|0.256	0.256	strong	AMOTL1,colon,carcinoma,+2,1	AMOTL1	95	1	NM_130847	exon3	c.C1017T	p.P339P	GCACCCCGGGATG	.	PASS	Atlas-SNP
FAM21C	253725	hgsc.bcm.edu	37	10	46254783	46254783	+	Silent	SNP	A	A	G	rs61856727	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	326	27	436	0	0.0828221	0	A|0.375;G|0.625	0.625	strong	FAM21C,caecum,carcinoma,0,1	FAM21C	68	1	NM_015262	exon17	c.A1569G	p.K523K	CAGCAAAAATCTC	.	scavenged	Atlas-SNP
NPR1	4881	hgsc.bcm.edu	37	1	153662423	153662423	+	Missense_Mutation	SNP	G	G	A	rs35479618	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	33	79	0	0.388235	0	G|0.993;A|0.007	0.007	strong	.	NPR1	104	.	NM_000906	exon19	c.G2899A	p.E967K	CCCCAGGAGCAGC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47831309	47831309	+	Silent	SNP	G	G	A	rs58559714	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	29	58	0	0.491525	0	G|0.830;A|0.170	0.170	strong	.	PCNT	283	.	NM_006031	exon28	c.G5322A	p.E1774E	GAGCGAGCTGCTC	.	PASS	Atlas-SNP
COL6A3	1293	hgsc.bcm.edu	37	2	238244781	238244781	+	Missense_Mutation	SNP	T	T	C	rs11690358	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	59	64	0	0.983333	0	T|0.934;C|0.066	0.066	strong	.	COL6A3	608	.	NM_004369	exon40	c.A8962G	p.M2988V	TACCCATGGGCTT	.	PASS	Atlas-SNP
FCGR2A	2212	hgsc.bcm.edu	37	1	161487863	161487863	+	Silent	SNP	C	C	T	rs143182858	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	355	279	329	0	0.785915	0	C|0.901;T|0.099	0.099	strong	.	FCGR2A	38	.	NM_001136219	exon7	c.C879T	p.P293P	GAACCCCAGGGCA	.	PASS	Atlas-SNP
COL6A1	1291	hgsc.bcm.edu	37	21	47422174	47422174	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	20	36	0	0.5	0	.	.	none	.	COL6A1	101	.	NM_001848	exon32	c.G2109A	p.T703T	CTTCACGGGGGAG	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113537773	113537773	+	Silent	SNP	C	C	T	rs12422659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	69	117	0	0.565574	0	C|0.897;T|0.103	0.103	strong	.	RASAL1	89	.	NM_001193520	exon22	c.G2382A	p.Q794Q	TCGCTCCTGCTGC	.	PASS	Atlas-SNP
NKTR	4820	hgsc.bcm.edu	37	3	42662976	42662976	+	Silent	SNP	A	A	C	rs35419602	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	30	109	0	0.379747	0	A|0.988;C|0.012	0.012	strong	.	NKTR	116	.	NM_005385	exon6	c.A342C	p.R114R	AAATCGAGGGAAA	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30919701	30919701	+	Silent	SNP	T	T	C	rs2517449	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	27	57	0	0.529412	0	T|0.723;C|0.277	0.277	strong	.	DPCR1	99	.	NM_080870	exon2	c.T3460C	p.L1154L	ACCACATTGGCCC	.	PASS	Atlas-SNP
SENP5	205564	hgsc.bcm.edu	37	3	196613075	196613075	+	Silent	SNP	C	C	T	rs34533379	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	47	72	0	0.580247	0	C|0.751;T|0.249	0.249	strong	.	SENP5	68	.	NM_152699	exon2	c.C1023T	p.D341D	TTTAGACGAAGCA	.	PASS	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	37	21	43896143	43896143	+	Missense_Mutation	SNP	C	C	T	rs117385282	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	46	71	0	0.528736	0	C|0.869;T|0.131	0.131	strong	RSPH1,NS,carcinoma,0,1	RSPH1	36	1	NM_080860	exon8	c.G742A	p.G248R	CCTCCCCGGGTTC	.	PASS	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	224633	224633	+	Silent	SNP	A	A	G	rs34930948	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	56	194	0	0.391608	0	A|0.882;G|0.118	0.118	strong	.	SDHA	80	.	NM_004168	exon3	c.A309G	p.A103A	TGCAGCACAGGTA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29912281	29912281	+	Silent	SNP	G	G	A	rs1136917	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	116	335	0	0.53211	0	G|0.872;A|0.128	0.128	strong	.	HLA-A	89	.	NM_001242758	exon5	c.G900A	p.L300L	AGAGCTGTCTTCC	.	PASS	Atlas-SNP
DTHD1	401124	hgsc.bcm.edu	37	4	36317970	36317970	+	Silent	SNP	T	T	C	rs9995922	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	42	67	0	0.456522	0	T|0.642;C|0.358	0.358	strong	.	DTHD1	63	.	NM_001170700	exon7	c.T1827C	p.S609S	CTATAGTTGCCCT	.	PASS	Atlas-SNP
DCBLD2	131566	hgsc.bcm.edu	37	3	98519481	98519481	+	Silent	SNP	G	G	A	rs1822017	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	72	152	0	0.476821	0	G|0.846;A|0.154	0.154	strong	.	DCBLD2	62	.	NM_080927	exon15	c.C1800T	p.S600S	AACTTCGCTGCTG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467605	10467605	+	Missense_Mutation	SNP	C	C	T	rs61503212	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	53	258	14	0.299435	0.0542636	C|0.500;T|0.500	0.500	weak	RP1L1,NS,carcinoma,+1,1	RP1L1	453	1	NM_178857	exon4	c.G4003A	p.G1335R	GCACCCCCTCTTC	.	scavenged	Atlas-SNP
ZNF862	643641	hgsc.bcm.edu	37	7	149559465	149559465	+	Silent	SNP	C	C	T	rs2074701	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	69	56	0	1	0	C|0.500;T|0.500	0.500	strong	ZNF862,NS,carcinoma,0,1	ZNF862	97	1	NM_001099220	exon7	c.C3216T	p.G1072G	GAACGGCGTGGCC	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3240343	3240343	+	Missense_Mutation	SNP	G	G	A	rs1635246	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	138	178	1	0.978723	0.00561798	G|0.441;A|0.559	0.559	strong	.	MXRA5	815	.	NM_015419	exon5	c.C3383T	p.A1128V	GTTGTTGCTGTTG	.	PASS	Atlas-SNP
GNL3	26354	hgsc.bcm.edu	37	3	52721305	52721305	+	Missense_Mutation	SNP	G	G	A	rs11177	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	62	163	0	0.534483	0	G|0.658;A|0.342	0.342	strong	.	GNL3	37	.	NM_014366	exon3	c.G116A	p.R39Q	AAAAGCGGGGTCA	.	PASS	Atlas-SNP
CACNA1C	775	hgsc.bcm.edu	37	12	2721137	2721137	+	Silent	SNP	C	C	T	rs216008	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	50	110	1	0.390625	0.00909091	C|0.730;T|0.270	0.270	strong	Q6YL47_HUMAN,NS,carcinoma,+2,4	CACNA1C	1023	4	NM_199460	exon30	c.C3846T	p.F1282F	CCTCTTCACCGTG	.	scavenged	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144880832	144880832	+	Missense_Mutation	SNP	T	T	C	rs12568796	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	216	48	190	0	0.222222	0	T|0.794;C|0.206	0.206	strong	.	PDE4DIP	817	.	NM_014644	exon26	c.A3796G	p.K1266E	TCTGCTTGCTGTC	.	PASS	Atlas-SNP
PCNXL3	399909	hgsc.bcm.edu	37	11	65403651	65403651	+	Missense_Mutation	SNP	C	C	A	rs7114037	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	56	148	0	0.455285	0	C|0.980;A|0.020	0.020	strong	.	PCNXL3	140	.	NM_032223	exon33	c.C5466A	p.H1822Q	GCTTCACAAGGGC	.	PASS	Atlas-SNP
KIAA1751	85452	hgsc.bcm.edu	37	1	1888193	1888193	+	Missense_Mutation	SNP	C	C	A	rs3820011	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	97	85	0	0.932692	0	C|0.775;A|0.225	0.225	strong	.	KIAA1751	92	.	NM_001080484	exon17	c.G1882T	p.G628C	AGCTGCCGAAGTC	.	PASS	Atlas-SNP
RXRG	6258	hgsc.bcm.edu	37	1	165398115	165398115	+	Silent	SNP	T	T	C	rs113471	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	68	126	1	0.5	0.00793651	T|0.776;G|0.003	.	strong	RXRG,NS,carcinoma,-2,1	RXRG	91	1	NM_006917	exon2	c.A138G	p.T46T	GGTATCTGTGTAG	.	scavenged	Atlas-SNP
SLC15A1	6564	hgsc.bcm.edu	37	13	99340578	99340578	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	38	107	0	0.391753	0	.	.	none	.	SLC15A1	92	.	NM_005073	exon20	c.C1607T	p.P536L	TGTGGCGGAATCT	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8234077	8234077	+	Silent	SNP	G	G	C	rs4840952	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	46	91	0	0.455446	0	G|0.632;C|0.368	0.368	strong	.	.	.	.	NM_001080826	exon2	c.C1842G	p.A614A	CGAGGCGGCAGGC	.	PASS	Atlas-SNP
HAUS6	54801	hgsc.bcm.edu	37	9	19058921	19058921	+	Missense_Mutation	SNP	G	G	A	rs62622380	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	391	171	332	1	0.43734	0.00301205	G|0.889;A|0.111	0.111	strong	.	HAUS6	66	.	NM_017645	exon16	c.C1844T	p.A615V	TGTTCAGCATCCA	.	PASS	Atlas-SNP
LRRC19	64922	hgsc.bcm.edu	37	9	26998122	26998122	+	Silent	SNP	T	T	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	38	95	0	0.475	0	.	.	none	.	LRRC19	24	.	NM_022901	exon3	c.A199C	p.R67R	GAACTCTTGTGTC	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15111218	15111218	+	Missense_Mutation	SNP	C	C	T	rs75456399		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	102	118	0	0.539683	0	.	.	weak	.	PDXDC1	59	.	NM_015027	exon11	c.C902T	p.P301L	CTGGCCCGTGGCT	.	PASS	Atlas-SNP
COBLL1	22837	hgsc.bcm.edu	37	2	165551404	165551404	+	Missense_Mutation	SNP	G	G	A	rs17244632	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	38	108	0	0.387755	0	G|0.913;A|0.087	0.087	strong	COBLL1,NS,carcinoma,0,1	COBLL1	122	1	NM_014900	exon12	c.C2612T	p.T871I	GTGCCAGTGTCTC	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449434	89449434	+	Missense_Mutation	SNP	T	T	C	rs2893084	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	486	89	318	2	0.183128	0.00628931	T|0.500;C|0.500	0.500	strong	CCBL2,NS,neuroblastoma,+1,2	.	.	2	NM_001162536	exon3	c.A76G	p.T26A	ATACTGTTTCAAG	.	scavenged	Atlas-SNP
ARSA	410	hgsc.bcm.edu	37	22	51064416	51064416	+	Missense_Mutation	SNP	T	T	C	rs2071421	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	46	114	0	0.418182	0	T|0.784;C|0.216	0.216	strong	.	ARSA	19	.	NM_001085426	exon7	c.A1055G	p.N352S	GTGACATTGGGCA	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227892619	227892619	+	Silent	SNP	C	C	T	rs2228556	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	23	40	0	0.522727	0	C|0.556;T|0.444	0.444	strong	.	COL4A4	215	.	NM_000092	exon42	c.G4080A	p.P1360P	CTCACCCGGAAGA	.	PASS	Atlas-SNP
SMCR8	140775	hgsc.bcm.edu	37	17	18221010	18221010	+	Missense_Mutation	SNP	A	A	G	rs12449313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	72	96	0	0.986301	0	A|0.770;G|0.229	0.229	strong	.	SMCR8	62	.	NM_144775	exon1	c.A1907G	p.N636S	ATGCCAACCCTTC	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50678717	50678717	+	Missense_Mutation	SNP	T	T	C	rs2228526	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	102	106	0	1	0	T|0.824;C|0.176	0.176	strong	.	ERCC6	162	.	NM_000124	exon18	c.A3289G	p.M1097V	TACTCATGTGAGG	.	PASS	Atlas-SNP
NUP214	8021	hgsc.bcm.edu	37	9	134020092	134020092	+	Missense_Mutation	SNP	C	C	T	rs103612	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	91	100	0	0.978495	0	C|0.333;N|0.001	.	strong	.	NUP214	166	.	NM_005085	exon12	c.C1720T	p.P574S	ATGAAGCCCTCCT	.	PASS	Atlas-SNP
FBXO32	114907	hgsc.bcm.edu	37	8	124525483	124525483	+	Silent	SNP	C	C	T	rs3739287	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	67	108	0	0.362162	0	C|0.843;T|0.157	0.157	strong	.	FBXO32	39	.	NM_058229	exon6	c.G606A	p.T202T	GAGAATCGTCTCC	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81211548	81211548	+	Silent	SNP	G	G	A	rs9934605	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	16	35	0	0.444444	0	G|0.813;A|0.187	0.187	strong	.	PKD1L2	361	.	NM_001076780	exon14	c.C2301T	p.I767I	AGTGCTGATCACA	.	PASS	Atlas-SNP
C17orf53	78995	hgsc.bcm.edu	37	17	42225547	42225547	+	Missense_Mutation	SNP	A	A	C	rs227584	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	70	132	0	0.510949	0	T|0.004;G|0.002	.	strong	.	C17orf53	59	.	NM_001171251	exon3	c.A376C	p.T126P	AGAGAGACAGCAA	.	PASS	Atlas-SNP
FAM104B	90736	hgsc.bcm.edu	37	X	55172630	55172630	+	Nonsense_Mutation	SNP	G	G	A	rs113263757	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	4	33	0	0.0869565	0	.	.	weak	.	FAM104B	28	.	NM_001166699	exon3	c.C238T	p.Q80X	AGAACTGGGGAAA	.	PASS	Atlas-SNP
COIL	8161	hgsc.bcm.edu	37	17	55028170	55028170	+	Missense_Mutation	SNP	C	C	T	rs61731978	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	153	194	0	0.968354	0	C|0.911;T|0.089	0.089	strong	.	COIL	49	.	NM_004645	exon2	c.G433A	p.V145I	CCAAGACCTTCTC	.	PASS	Atlas-SNP
C22orf28	51493	hgsc.bcm.edu	37	22	32795641	32795641	+	Silent	SNP	C	C	T	rs5749426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	111	111	0	0.982301	0	C|0.552;T|0.448	0.448	strong	.	C22orf28	43	.	NM_014306	exon6	c.G603A	p.Q201Q	GTCAGCCTGCAGC	.	PASS	Atlas-SNP
RIF1	55183	hgsc.bcm.edu	37	2	152314385	152314385	+	Silent	SNP	G	G	A	rs16830047	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	63	126	0	0.512195	0	G|0.749;A|0.251	0.251	strong	.	RIF1	244	.	NM_018151	exon24	c.G2763A	p.L921L	ATTTCTGCACAAG	.	PASS	Atlas-SNP
GATA5	140628	hgsc.bcm.edu	37	20	61040951	61040951	+	Silent	SNP	C	C	T	rs6587239	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	28	50	0	0.430769	0	C|0.469;T|0.531	0.531	strong	GATA5,NS,haematopoietic_neoplasm,-2,4	GATA5	22	4	NM_080473	exon5	c.G852A	p.K284K	GCTTTCCTTCTTC	.	PASS	Atlas-SNP
CCDC154	645811	hgsc.bcm.edu	37	16	1484455	1484455	+	Missense_Mutation	SNP	T	T	C	rs61743495	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	50	93	0	0.47619	0	T|0.943;C|0.057	0.057	strong	.	CCDC154	27	.	NM_001143980	exon17	c.A1958G	p.Q653R	TGCTCCTGGCTGT	.	PASS	Atlas-SNP
ABCA1	19	hgsc.bcm.edu	37	9	107624029	107624029	+	Silent	SNP	C	C	T	rs2230805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	40	141	0	0.380952	0	C|0.656;T|0.344	0.344	strong	ABCA1,NS,carcinoma,0,1	ABCA1	244	1	NM_005502	exon6	c.G474A	p.L158L	GTGATACAGGAAC	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737595	248737595	+	Missense_Mutation	SNP	A	A	G	rs79056151	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	564	119	512	1	0.210993	0.00195312	A|0.500;G|0.500	0.500	weak	OR2T34,NS,carcinoma,0,2	OR2T34	72	2	NM_001001821	exon1	c.T464C	p.V155A	CCCAAAACCCAGC	.	scavenged	Atlas-SNP
SRFBP1	153443	hgsc.bcm.edu	37	5	121355961	121355961	+	Silent	SNP	G	G	A	rs55708726	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	41	84	0	0.518987	0	G|0.890;A|0.110	0.110	strong	.	SRFBP1	47	.	NM_152546	exon6	c.G531A	p.A177A	ATTGGCGAAGAAA	.	PASS	Atlas-SNP
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766776	27766776	+	Silent	SNP	G	G	A	rs45553337	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	133	140	1	0.985185	0.00714286	G|0.816;A|0.184	0.184	strong	.	DCAF8L2	79	.	NM_001136533	exon1	c.G1764A	p.T588T	CGTGACGCAGAGA	.	PASS	Atlas-SNP
ADAMTS16	170690	hgsc.bcm.edu	37	5	5146335	5146335	+	Missense_Mutation	SNP	C	C	G	rs2086310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	70	65	0	0.985915	0	C|0.294;G|0.706	0.706	strong	.	ADAMTS16	543	.	NM_139056	exon3	c.C268G	p.P90A	GCAGTGCCCGTGT	.	PASS	Atlas-SNP
DHFRL1	200895	hgsc.bcm.edu	37	3	93780109	93780109	+	Missense_Mutation	SNP	G	G	C	rs61739170	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	100	232	0	0.440529	0	G|0.833;C|0.167	0.167	strong	DHFRL1,NS,carcinoma,0,1	DHFRL1	25	1	NM_001195643	exon2	c.C247G	p.P83A	GTGGAGGTTCCTT	.	PASS	Atlas-SNP
GRAMD1A	57655	hgsc.bcm.edu	37	19	35506729	35506729	+	Silent	SNP	G	G	A	rs2290647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	61	91	0	0.559633	0	G|0.711;A|0.289	0.289	strong	.	GRAMD1A	39	.	NM_020895	exon11	c.G1071A	p.A357A	TCCAGCGGACTTG	.	PASS	Atlas-SNP
TMEM43	79188	hgsc.bcm.edu	37	3	14175262	14175262	+	Missense_Mutation	SNP	T	T	C	rs2340917	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	134	158	0	1	0	T|0.607;C|0.393	0.393	strong	.	TMEM43	33	.	NM_024334	exon7	c.T536C	p.M179T	CATTCATGGCAAC	.	PASS	Atlas-SNP
C19orf80	55908	hgsc.bcm.edu	37	19	11350340	11350340	+	Silent	SNP	C	C	G	rs892066	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	141	123	1	0.992958	0.00813008	C|0.688;G|0.312	0.312	strong	.	C19orf80	8	.	NM_018687	exon1	c.C27G	p.L9L	CCTGCTCTGGGCC	.	PASS	Atlas-SNP
NME4	4833	hgsc.bcm.edu	37	16	450309	450309	+	Silent	SNP	C	C	T	rs5841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	26	45	0	0.481481	0	C|0.595;T|0.405	0.405	strong	.	NME4	9	.	NM_005009	exon5	c.C531T	p.D177D	GGCAGACGGGGGC	.	PASS	Atlas-SNP
OR9K2	441639	hgsc.bcm.edu	37	12	55523685	55523685	+	Missense_Mutation	SNP	C	C	T	rs12303066	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	76	173	0	0.410811	0	C|0.679;T|0.321	0.321	strong	OR9K2,NS,carcinoma,0,2	OR9K2	63	2	NM_001005243	exon1	c.C133T	p.R45C	AGGGTACGCCCAG	.	PASS	Atlas-SNP
SAMD4A	23034	hgsc.bcm.edu	37	14	55227152	55227152	+	Missense_Mutation	SNP	G	G	T	rs149416017	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	6	4	0	0	0.666667	.	G|0.987;T|0.013	0.013	strong	.	SAMD4A	68	.	NM_015589	exon6	c.G1450T	p.A484S	GAGCTGGCCGTCG	.	PASS	Atlas-SNP
ZZEF1	23140	hgsc.bcm.edu	37	17	3947644	3947644	+	Missense_Mutation	SNP	T	T	C	rs781831	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	92	161	0	0.440191	0	T|0.465;G|0.001	.	strong	.	ZZEF1	195	.	NM_015113	exon38	c.A6040G	p.I2014V	GTCTGATTTCCTC	.	PASS	Atlas-SNP
GZMH	2999	hgsc.bcm.edu	37	14	25076906	25076906	+	Missense_Mutation	SNP	C	C	G	rs52812266	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	460	60	333	3	0.130435	0.00900901	.	.	alt	GZMH,colon,carcinoma,-1,1	GZMH	24	1	NM_033423	exon3	c.G251C	p.R84P	TGGGTCCGCTCCT	.	scavenged	Atlas-SNP
CPA3	1359	hgsc.bcm.edu	37	3	148614447	148614447	+	Silent	SNP	C	C	T	rs61733454	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	60	109	0	0.674157	0	C|0.971;T|0.029	0.029	strong	.	CPA3	75	.	NM_001870	exon11	c.C1207T	p.L403L	ACCATGCTAGCTG	.	PASS	Atlas-SNP
MEGF6	1953	hgsc.bcm.edu	37	1	3413868	3413868	+	Missense_Mutation	SNP	C	C	G	rs4648506	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	23	13	0	1	0	C|0.736;G|0.264	0.264	strong	.	MEGF6	91	.	NM_001409	exon27	c.G3410C	p.G1137A	GCAGCGCCAGGCG	.	PASS	Atlas-SNP
ZNF302	55900	hgsc.bcm.edu	37	19	35175775	35175775	+	Missense_Mutation	SNP	C	C	T	rs11543232	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	45	91	0	0.517241	0	C|0.704;T|0.296	0.296	strong	.	ZNF302	27	.	NM_018443	exon5	c.C833T	p.T278I	AGAGCACTCACAC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301824	65301824	+	Silent	SNP	T	T	C	rs12662610	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	34	72	0	0.971429	0	T|0.906;C|0.094	0.094	strong	.	EYS	527	.	NM_001142800	exon26	c.A3936G	p.T1312T	TCTTAATGTTGCC	.	PASS	Atlas-SNP
SPTB	6710	hgsc.bcm.edu	37	14	65260227	65260227	+	Silent	SNP	T	T	G	rs229591	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	100	118	1	1	0.00847458	T|0.558;G|0.442	0.442	strong	.	SPTB	378	.	NM_001024858	exon13	c.A2154C	p.I718I	CTCCTTTATGCGG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634341	32634341	+	Missense_Mutation	SNP	A	A	G	rs3189152	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	6	4	3	0.230769	0.75	A|0.710;G|0.290	0.290	strong	HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	NM_002123	exon1	c.T44C	p.V15A	GTTGCTACCCGAA	.	scavenged	Atlas-SNP
NID1	4811	hgsc.bcm.edu	37	1	236144951	236144951	+	Silent	SNP	A	A	G	rs3738525	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	35	74	0	0.448718	0	A|0.729;G|0.271	0.271	strong	.	NID1	196	.	NM_002508	exon16	c.T3187C	p.L1063L	TCACCAAGTCAGT	.	PASS	Atlas-SNP
BTNL2	56244	hgsc.bcm.edu	37	6	32362741	32362741	+	Missense_Mutation	SNP	C	C	T	rs28362677	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	44	132	0	0.385965	0	C|0.859;T|0.141	0.141	strong	.	BTNL2	50	.	NM_019602	exon6	c.G1140A	p.M380I	AGAGCACATCGGC	.	PASS	Atlas-SNP
C20orf166	128826	hgsc.bcm.edu	37	20	61167883	61167883	+	Silent	SNP	G	G	A	rs6143064	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	59	68	0	1	0	G|0.722;A|0.278	0.278	strong	.	C20orf166	17	.	NM_178463	exon4	c.G353A	p.X118X	ACTGCTGAAGGGA	.	PASS	Atlas-SNP
ZNF813	126017	hgsc.bcm.edu	37	19	53993670	53993670	+	Missense_Mutation	SNP	G	G	A	rs2617667	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	61	135	0	0.458647	0	G|0.745;A|0.255	0.255	strong	.	ZNF813	81	.	NM_001004301	exon4	c.G184A	p.A62T	TCAACAGCACAAG	.	PASS	Atlas-SNP
PYCRL	65263	hgsc.bcm.edu	37	8	144689146	144689146	+	Missense_Mutation	SNP	C	C	T	rs2242089	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	67	134	0	0.39645	0	C|0.785;T|0.215	0.215	strong	PYCRL,NS,carcinoma,0,1	PYCRL	14	1	NM_023078	exon3	c.G349A	p.V117M	GAGACACCCCAGC	.	PASS	Atlas-SNP
C9orf171	389799	hgsc.bcm.edu	37	9	135374764	135374764	+	Missense_Mutation	SNP	G	G	A	rs7047726	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	8	42	0	0.380952	0	G|0.865;A|0.135	0.135	strong	.	C9orf171	53	.	NM_207417	exon4	c.G409A	p.G137R	GCCATCGGACGCT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27804432	27804432	+	Missense_Mutation	SNP	T	T	C	rs28381983	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	52	88	0	0.514852	0	T|0.364;C|0.636	0.636	strong	.	C2orf16	357	.	NM_032266	exon1	c.T4993C	p.S1665P	CGCAGTTCCTCTG	.	PASS	Atlas-SNP
TRPV3	162514	hgsc.bcm.edu	37	17	3436080	3436080	+	Silent	SNP	C	C	T	rs395357	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	238	182	0	0.995816	0	C|0.601;T|0.399	0.399	strong	.	TRPV3	85	.	NM_001258205	exon8	c.G936A	p.T312T	ATTCTGCGTCTTG	.	PASS	Atlas-SNP
IQCF1	132141	hgsc.bcm.edu	37	3	51930850	51930850	+	Missense_Mutation	SNP	T	T	C	rs57859638	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	74	151	0	0.528571	0	T|0.851;C|0.149	0.149	strong	IQCF1,tonsil,carcinoma,0,1	IQCF1	26	1	NM_152397	exon3	c.A169G	p.K57E	ATACTTTTTCTGA	.	PASS	Atlas-SNP
GDPGP1	390637	hgsc.bcm.edu	37	15	90784930	90784930	+	Missense_Mutation	SNP	C	C	A	rs10152994	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	47	107	0	0.460784	0	C|0.833;A|0.167	0.167	strong	.	.	.	.	NM_001013657	exon4	c.C790A	p.P264T	CCAGGGCCTGACT	.	PASS	Atlas-SNP
WDR18	57418	hgsc.bcm.edu	37	19	991968	991968	+	Silent	SNP	T	T	C	rs1127043	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	4	9	0	0.444444	0	T|0.651;C|0.349	0.349	strong	.	WDR18	20	.	NM_024100	exon8	c.T945C	p.N315N	CACCAATGCCGCC	.	PASS	Atlas-SNP
CSHL1	1444	hgsc.bcm.edu	37	17	61987570	61987570	+	Missense_Mutation	SNP	G	G	T	rs2727307	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	312	310	455	0	0.99359	0	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	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274319	39274319	+	Missense_Mutation	SNP	G	G	C	rs199712484		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	8	48	1	0.109589	0.0208333	.	.	weak	KRTAP4-11,NS,carcinoma,0,2	KRTAP4-11	94	2	NM_033059	exon1	c.C249G	p.S83R	GCAGCAGCTGGAC	.	scavenged	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25016092	25016092	+	Silent	SNP	C	C	T	rs55888616	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	27	48	0	1	0	C|0.673;T|0.327	0.327	strong	.	PARP4	142	.	NM_006437	exon30	c.G3558A	p.S1186S	AAAAGGCGACTCA	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	164	185	1	0.993939	0.00540541	A|0.536;G|0.464	0.464	strong	FMO2,NS,carcinoma,0,2	FMO2	66	2	NM_001460	exon5	c.A585G	p.S195S	AAACTCAGGCTCA	.	PASS	Atlas-SNP
ALPI	248	hgsc.bcm.edu	37	2	233322958	233322958	+	Silent	SNP	T	T	C	rs41265121	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	89	192	0	0.508571	0	T|0.910;C|0.090	0.090	strong	.	ALPI	64	.	NM_001631	exon9	c.T1023C	p.G341G	TGAGGGTGTGGCT	.	PASS	Atlas-SNP
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487229	32487229	+	Silent	SNP	C	C	T	rs148633289	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	67	179	0	0.51938	0	C|0.781;T|0.219	0.219	strong	HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	NM_002125	exon3	c.G570A	p.L190L	TGTTTCCAGCATC	.	scavenged	Atlas-SNP
ZNF502	91392	hgsc.bcm.edu	37	3	44762830	44762830	+	Missense_Mutation	SNP	A	A	G	rs56084453	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	55	89	1	0.544554	0.011236	A|0.848;G|0.152	0.152	strong	ZNF502,NS,carcinoma,-1,1	ZNF502	58	1	NM_001134440	exon4	c.A521G	p.Q174R	AACATCAGAGAAC	.	scavenged	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629764	32629764	+	Missense_Mutation	SNP	C	C	T	rs1130398	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	36	77	0	0.418605	0	T|0.416;C|0.584	0.416	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.G641A	p.S214N	ATGGGGCTCTGGA	.	PASS	Atlas-SNP
ATR	545	hgsc.bcm.edu	37	3	142178144	142178144	+	Missense_Mutation	SNP	C	C	T	rs2229032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	55	126	0	0.533981	0	C|0.883;T|0.117	0.117	strong	ATR,NS,carcinoma,0,1	ATR	285	1	NM_001184	exon43	c.G7274A	p.R2425Q	AATTCTCGGAATA	.	PASS	Atlas-SNP
BCL9L	283149	hgsc.bcm.edu	37	11	118769442	118769442	+	Silent	SNP	A	A	G	rs7104819	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	36	94	0	0.413793	0	A|0.524;G|0.476	0.476	strong	.	BCL9L	254	.	NM_182557	exon8	c.T4182C	p.P1394P	CTGTCCAGGGTGG	.	PASS	Atlas-SNP
SLC25A51	92014	hgsc.bcm.edu	37	9	37888101	37888101	+	Silent	SNP	C	C	T	rs2296204	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	104	239	1	0.492891	0.0041841	C|0.847;T|0.153	0.153	strong	.	.	.	.	NM_033412	exon3	c.G447A	p.K149K	ATGATGCTTGTGG	.	PASS	Atlas-SNP
TMEM108	66000	hgsc.bcm.edu	37	3	133099245	133099245	+	Silent	SNP	G	G	A	rs1197314	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	74	130	0	0.578125	0	G|0.616;A|0.384	0.384	strong	.	TMEM108	67	.	NM_023943	exon4	c.G690A	p.P230P	GGAACCGGAGCCC	.	PASS	Atlas-SNP
PCYOX1	51449	hgsc.bcm.edu	37	2	70488470	70488470	+	Missense_Mutation	SNP	C	C	T	rs2706762	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	84	113	0	0.552632	0	C|0.912;T|0.088	0.088	strong	.	PCYOX1	34	.	NM_016297	exon3	c.C446T	p.S149F	TTCAATCCCTCCG	.	PASS	Atlas-SNP
BTN3A1	11119	hgsc.bcm.edu	37	6	26413744	26413744	+	Missense_Mutation	SNP	C	C	A	rs4712990	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	45	117	0	0.436893	0	C|0.883;A|0.117	0.117	strong	.	BTN3A1	80	.	NM_007048	exon10	c.C1366A	p.P456T	CCTAAGCCCCCTA	.	PASS	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29205072	29205072	+	Missense_Mutation	SNP	T	T	C	rs61745366	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	83	156	0	0.494048	0	T|0.943;C|0.057	0.057	strong	.	ATAD5	150	.	NM_024857	exon17	c.T3970C	p.F1324L	AAAACATTCATGG	.	PASS	Atlas-SNP
PADI4	23569	hgsc.bcm.edu	37	1	17668609	17668609	+	Missense_Mutation	SNP	C	C	T	rs1748020	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	105	112	0	0.905172	0	C|0.939;T|0.061	0.061	strong	.	PADI4	70	.	NM_012387	exon7	c.C824T	p.S275F	ACACGTCCAACCT	.	PASS	Atlas-SNP
C19orf40	91442	hgsc.bcm.edu	37	19	33467515	33467515	+	Missense_Mutation	SNP	T	T	C	rs3816032	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	67	101	0	0.507576	0	C|0.146;N|0.000	0.146	strong	.	C19orf40	21	.	NM_152266	exon5	c.T575C	p.I192T	CTTCCATTGGGGA	.	PASS	Atlas-SNP
MYRF	745	hgsc.bcm.edu	37	11	61539020	61539020	+	Silent	SNP	C	C	G	rs149803	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	45	97	0	0.424528	0	C|0.825;G|0.175	0.175	strong	.	.	.	.	NM_001127392	exon6	c.C789G	p.P263P	CCCCCCCAGCACC	.	PASS	Atlas-SNP
C7orf63	79846	hgsc.bcm.edu	37	7	89938680	89938680	+	Missense_Mutation	SNP	C	C	T	rs1134956	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	181	180	168	0	0.994475	0	C|0.596;N|0.000;T|0.404	0.404	strong	C7orf63_ENST00000389297,NS,carcinoma,+1,2	C7orf63	158	2	NM_001039706	exon22	c.C2654T	p.T885M	ACACAACGGTAAG	.	PASS	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596484	48596484	+	Missense_Mutation	SNP	A	A	T	rs75413005	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	50	80	0	0.5	0	A|0.934;T|0.066	0.066	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.T592A	p.W198R	TTGCCCACAGACT	.	PASS	Atlas-SNP
PDGFD	80310	hgsc.bcm.edu	37	11	103780455	103780455	+	Silent	SNP	A	A	G	rs10791649	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	48	122	0	0.410256	0	A|0.527;G|0.473	0.473	strong	.	PDGFD	125	.	NM_025208	exon7	c.T1080C	p.C360C	ACAATCACATCGT	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491840	110491840	+	Missense_Mutation	SNP	C	C	G	rs1783147	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	28	127	0	0.474576	0	C|0.626;G|0.374	0.374	strong	.	PKHD1L1	522	.	NM_177531	exon54	c.C9150G	p.H3050Q	ACCTCACCCAGGG	.	PASS	Atlas-SNP
ZNF273	10793	hgsc.bcm.edu	37	7	64389067	64389067	+	Missense_Mutation	SNP	G	G	A	rs1830080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	9	27	0	0.45	0	G|0.953;A|0.047	0.047	strong	.	ZNF273	45	.	NM_021148	exon4	c.G1361A	p.G454E	ATACTGGAGCAAA	.	PASS	Atlas-SNP
ALG8	79053	hgsc.bcm.edu	37	11	77815059	77815059	+	Missense_Mutation	SNP	A	A	G	rs17825668	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	44	56	0	0.556962	0	A|0.977;G|0.023	0.023	strong	.	ALG8	54	.	NM_024079	exon12	c.T1316C	p.I439T	CTATATATGGTGA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130952718	130952718	+	Silent	SNP	G	G	A	rs3853852	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	267	82	306	0	0.307116	0	G|0.637;A|0.363	0.363	strong	.	TUBA3E	73	.	NM_207312	exon3	c.C309T	p.Y103Y	CCTGGCGTAATTA	.	PASS	Atlas-SNP
RHBDL2	54933	hgsc.bcm.edu	37	1	39352271	39352271	+	Missense_Mutation	SNP	G	G	T	rs2147914	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	6	90	1	0.0731707	0.0111111	G|0.652;T|0.348	0.348	strong	RHBDL2,bladder,carcinoma,+2,1	RHBDL2	28	1	NM_017821	exon8	c.C817A	p.L273M	CTTTCAGCAGTGC	.	scavenged	Atlas-SNP
HBP1	26959	hgsc.bcm.edu	37	7	106826381	106826381	+	Silent	SNP	C	C	T	rs7794598	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	43	93	0	0.483146	0	C|0.818;T|0.182	0.182	strong	.	HBP1	31	.	NM_001244262	exon4	c.C564T	p.H188H	AAGACACGAAAGG	.	PASS	Atlas-SNP
ZNF415	55786	hgsc.bcm.edu	37	19	53612311	53612311	+	Silent	SNP	T	T	C	rs4803051	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	47	44	0	1	0	T|0.561;C|0.439	0.439	strong	.	ZNF415	68	.	NM_018355	exon4	c.A987G	p.T329T	TTTACATGTGTAA	.	PASS	Atlas-SNP
BRWD1	54014	hgsc.bcm.edu	37	21	40641858	40641858	+	Silent	SNP	T	T	G	rs61740760	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	97	152	0	0.489899	0	T|0.978;G|0.022	0.022	strong	.	BRWD1	325	.	NM_018963	exon15	c.A1497C	p.T499T	ACCTTTTGTAATA	.	PASS	Atlas-SNP
KAZN	23254	hgsc.bcm.edu	37	1	15438990	15438990	+	Missense_Mutation	SNP	G	G	A	rs10803354	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	228	198	0	1	0	G|0.601;A|0.399	0.399	strong	.	KAZN	57	.	NM_201628	exon14	c.G2116A	p.A706T	ACGCGGGCAGGAA	.	PASS	Atlas-SNP
SLC16A4	9122	hgsc.bcm.edu	37	1	110924353	110924353	+	Silent	SNP	G	G	A	rs3738750	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	253	119	275	2	0.470356	0.00727273	G|0.839;A|0.161	0.161	strong	SLC16A4,NS,carcinoma,0,2	SLC16A4	47	2	NM_004696	exon4	c.C285T	p.F95F	AACAACGAAAGCC	.	scavenged	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	37	4	47570876	47570876	+	Missense_Mutation	SNP	G	G	A	rs17462252	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	70	123	0	0.44586	0	G|0.961;A|0.039	0.039	strong	.	ATP10D	168	.	NM_020453	exon16	c.G2876A	p.S959N	TGATGAGCACAAT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	94	242	1	0.606452	0.00413223	C|0.931;T|0.069	0.069	strong	.	LILRB3	67	.	NM_006864	exon4	c.G445A	p.G149R	GATATCCCTTCTG	.	PASS	Atlas-SNP
SH3RF1	57630	hgsc.bcm.edu	37	4	170037572	170037572	+	Missense_Mutation	SNP	G	G	A	rs3811813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	50	118	0	0.485437	0	G|0.906;A|0.094	0.094	strong	SH3RF1,NS,carcinoma,+2,1	SH3RF1	60	1	NM_020870	exon10	c.C1987T	p.P663S	TCAGTGGAGCAGC	.	PASS	Atlas-SNP
CHD2	1106	hgsc.bcm.edu	37	15	93567864	93567864	+	Silent	SNP	A	A	C	rs12906163	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	62	147	0	0.433566	0	A|0.767;C|0.233	0.233	strong	.	CHD2	280	.	NM_001271	exon39	c.A5416C	p.R1806R	GATCATAGGTCTC	.	PASS	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121878659	121878659	+	Silent	SNP	C	C	T	rs1064951	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	56	71	0	0.583333	0	C|0.667;T|0.333	0.333	strong	.	KDM2B	218	.	NM_032590	exon21	c.G3570A	p.Q1190Q	CCGCATCTGGGCA	.	PASS	Atlas-SNP
RAD54B	25788	hgsc.bcm.edu	37	8	95419698	95419698	+	Silent	SNP	A	A	G	rs2291439	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	247	116	253	1	0.469636	0.00395257	A|0.610;C|0.003	.	strong	.	RAD54B	88	.	NM_012415	exon5	c.T750C	p.N250N	TTTGCAATTTTGG	.	PASS	Atlas-SNP
PLG	5340	hgsc.bcm.edu	37	6	161159619	161159619	+	Silent	SNP	T	T	C	rs4252195	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	81	175	0	0.870968	0	T|0.996;C|0.004	0.004	strong	.	PLG	150	.	NM_000301	exon15	c.T1852C	p.L618L	TGGGTGTTGACTG	.	PASS	Atlas-SNP
LEPR	3953	hgsc.bcm.edu	37	1	66075952	66075952	+	Missense_Mutation	SNP	G	G	C	rs1805094	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	157	155	0	0.993671	0	G|0.841;C|0.159	0.159	strong	.	LEPR	284	.	NM_001003680	exon14	c.G1968C	p.K656N	GAAAAAGGAGAAA	.	PASS	Atlas-SNP
TMC1	117531	hgsc.bcm.edu	37	9	75315438	75315438	+	Missense_Mutation	SNP	G	G	A	rs1796993	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	30	39	0	0.483871	0	G|0.761;A|0.239	0.239	strong	.	TMC1	87	.	NM_138691	exon8	c.G241A	p.E81K	AGAGAAGAAGAAG	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46490456	46490456	+	Silent	SNP	G	G	A	rs61737000	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	54	136	0	0.509434	0	G|0.929;A|0.071	0.071	strong	.	LTF	98	.	NM_002343	exon9	c.C1110T	p.G370G	CTGCTCGCCCACC	.	PASS	Atlas-SNP
ABCB11	8647	hgsc.bcm.edu	37	2	169789016	169789016	+	Silent	SNP	T	T	C	rs497692	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	87	129	0	0.54375	0	T|0.519;C|0.481	0.481	strong	ABCB11,colon,carcinoma,-1,2	ABCB11	136	2	NM_003742	exon24	c.A3084G	p.A1028A	AGCTGTTGCACTC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1267562	1267562	+	Missense_Mutation	SNP	C	C	T	rs61737593	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	253	123	316	3	0.486166	0.00949367	C|0.929;T|0.071	0.071	strong	MUC5AC,NS,carcinoma,-1,1	MUC5B	473	1	NM_002458	exon31	c.C9452T	p.T3151M	GCCCCACGGCCAC	.	scavenged	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	37	22	28389453	28389453	+	Silent	SNP	T	T	C	rs470101	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	61	64	0	0.491935	0	T|0.926;C|0.074	0.074	strong	.	TTC28	84	.	NM_001145418	exon18	c.A5298G	p.T1766T	CTGGGATGTGTAC	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	37	1	186031041	186031041	+	Silent	SNP	C	C	T	rs7522627	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	41	89	0	0.455556	0	C|0.372;T|0.628	0.628	strong	.	HMCN1	797	.	NM_031935	exon47	c.C7371T	p.C2457C	TACTTGCGTTGTA	.	PASS	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	37	12	107712880	107712880	+	Silent	SNP	C	C	T	rs10082935	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	17	46	0	0.369565	0	C|0.868;T|0.132	0.132	strong	.	BTBD11	122	.	NM_001018072	exon1	c.C163T	p.L55L	CCGCCTCTAGCTG	.	PASS	Atlas-SNP
GNB1L	54584	hgsc.bcm.edu	37	22	19808769	19808769	+	Missense_Mutation	SNP	C	C	T	rs5748449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	25	76	0	0.384615	0	C|0.860;T|0.140	0.140	strong	.	GNB1L	34	.	NM_053004	exon3	c.G110A	p.R37H	AGCGGGCGCCCCT	.	PASS	Atlas-SNP
BYSL	705	hgsc.bcm.edu	37	6	41895150	41895150	+	Missense_Mutation	SNP	G	G	A	rs2296916	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	73	144	0	0.55303	0	G|0.919;A|0.081	0.081	strong	.	BYSL	17	.	NM_004053	exon2	c.G307A	p.E103K	GAGGACGAGGAGT	.	PASS	Atlas-SNP
RECQL4	9401	hgsc.bcm.edu	37	8	145742879	145742879	+	Silent	SNP	T	T	C	rs2306386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	9	0	0	1	.	T|0.468;C|0.532	0.532	strong	.	RECQL4	75	.	NM_004260	exon3	c.A132G	p.E44E	GCGGTATTCCCGG	.	PASS	Atlas-SNP
GLYATL3	389396	hgsc.bcm.edu	37	6	49489397	49489397	+	Missense_Mutation	SNP	C	C	A	rs9369905	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	43	94	0	0.488636	0	C|0.805;A|0.195	0.195	strong	GLYATL3,NS,carcinoma,0,3	GLYATL3	19	3	NM_001010904	exon5	c.C353A	p.A118D	CGGTTGCCAATTC	.	PASS	Atlas-SNP
TPR	7175	hgsc.bcm.edu	37	1	186330768	186330768	+	Missense_Mutation	SNP	T	T	C	rs201760745	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	97	239	0	0.480198	0	.	.	weak	.	TPR	441	.	NM_003292	exon9	c.A944G	p.K315R	GCTTCTTTCAAAA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910730	29910730	+	Missense_Mutation	SNP	T	T	A	rs199474436	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	85	138	1	0.904255	0.00724638	A|0.321;T|0.679	0.321	strong	HLA-A,NS,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon2	c.T270A	p.N90K	ACGGAATGTGAAG	.	PASS	Atlas-SNP
ABCC12	94160	hgsc.bcm.edu	37	16	48122582	48122582	+	Missense_Mutation	SNP	G	G	A	rs7193955	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	104	77	0	0.990476	0	G|0.395;A|0.605	0.605	strong	ABCC12,colon,carcinoma,0,1	ABCC12	190	1	NM_033226	exon24	c.C3349T	p.R1117C	CCCCACGGCTGGG	.	PASS	Atlas-SNP
MEN1	4221	hgsc.bcm.edu	37	11	64572602	64572602	+	Silent	SNP	G	G	A	rs2071313	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	45	85	0	0.494505	0	G|0.698;A|0.302	0.302	strong	MEN1,NS,adenoma,-2,1	MEN1	442	1	NM_130800	exon9	c.C1269T	p.D423D	GATGCCGTCGTAG	.	PASS	Atlas-SNP
CERCAM	51148	hgsc.bcm.edu	37	9	131196695	131196695	+	Silent	SNP	C	C	T	rs7258	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	73	56	0	1	0	C|0.738;T|0.262	0.262	strong	.	CERCAM	104	.	NM_016174	exon11	c.C1338T	p.L446L	CTACCTCGGACGG	.	PASS	Atlas-SNP
PLEKHN1	84069	hgsc.bcm.edu	37	1	906122	906122	+	Silent	SNP	C	C	T	rs41285812	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	99	118	1	0.933962	0.00847458	C|0.995;T|0.005	0.005	strong	.	PLEKHN1	49	.	NM_001160184	exon5	c.C468T	p.H156H	AGAGCACGCCTTC	.	PASS	Atlas-SNP
NLRP8	126205	hgsc.bcm.edu	37	19	56459458	56459458	+	Missense_Mutation	SNP	C	C	T	rs61195059	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	43	72	0	0.614286	0	C|0.925;T|0.075	0.075	strong	.	NLRP8	225	.	NM_176811	exon1	c.C190T	p.L64F	ACTGAGCTCAGTA	.	PASS	Atlas-SNP
DNAH9	1770	hgsc.bcm.edu	37	17	11833287	11833287	+	Silent	SNP	A	A	G	rs2286303	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	64	90	0	0.507937	0	A|0.755;G|0.245	0.245	strong	.	DNAH9	695	.	NM_001372	exon63	c.A11982G	p.P3994P	AGAGCCAGCACCC	.	PASS	Atlas-SNP
KCNJ4	3761	hgsc.bcm.edu	37	22	38823676	38823676	+	Silent	SNP	C	C	G	rs77032485	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	36	54	0	0.404494	0	C|0.995;G|0.005	0.005	strong	.	KCNJ4	74	.	NM_004981	exon2	c.G462C	p.V154V	CTGGACCACCACA	.	PASS	Atlas-SNP
CLCNKB	1188	hgsc.bcm.edu	37	1	16380243	16380243	+	Missense_Mutation	SNP	A	A	G	rs2275166	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	161	173	0	0.860963	0	A|0.294;G|0.706	0.706	strong	.	CLCNKB	50	.	NM_000085	exon16	c.A1732G	p.K578E	GTGGCCAAGTATC	.	PASS	Atlas-SNP
HLCS	3141	hgsc.bcm.edu	37	21	38308911	38308911	+	Silent	SNP	G	G	A	rs1065758	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	50	103	0	0.434783	0	G|0.893;A|0.107	0.107	strong	.	HLCS	64	.	NM_000411	exon5	c.C834T	p.S278S	CACCTCGCTCTGG	.	PASS	Atlas-SNP
UBE2S	27338	hgsc.bcm.edu	37	19	55913038	55913038	+	Silent	SNP	C	C	T	rs7608	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	47	52	0	0.886792	0	C|0.427;T|0.573	0.573	strong	.	UBE2S	8	.	NM_014501	exon4	c.G435A	p.A145A	CCGAGCCGCATAC	.	PASS	Atlas-SNP
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458772	39458772	+	Missense_Mutation	SNP	G	G	A	rs117847625	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	23	61	0	0.38983	0	G|0.969;A|0.031	0.031	strong	.	KRTAP29-1	2	.	NM_001257309	exon1	c.C332T	p.S111L	GATTCCGAGCAGG	.	PASS	Atlas-SNP
SLFN14	342618	hgsc.bcm.edu	37	17	33876083	33876083	+	Silent	SNP	G	G	A	rs1001441	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	56	119	0	0.504505	0	G|0.790;A|0.210	0.210	strong	.	SLFN14	43	.	NM_001129820	exon4	c.C1914T	p.T638T	GCAGGTGGTTTGT	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	48	71	0	0.484848	0	T|0.601;G|0.399	0.399	strong	CPAMD8,NS,carcinoma,-1,1	CPAMD8	192	1	NM_015692	exon14	c.A1665C	p.R555R	CTTGCTTCGCTGC	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4451570	4451570	+	Missense_Mutation	SNP	G	G	A	rs142700966	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	34	62	0	0.523077	0	G|0.998;A|0.002	0.002	strong	.	MYBBP1A	69	.	NM_014520	exon12	c.C1592T	p.A531V	CCCGGTGCCTGCT	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99118716	99118716	+	Missense_Mutation	SNP	G	G	T	rs143870774	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	27	44	0	0.6	0	G|0.998;A|0.002	.	alt	.	RRP12	97	.	NM_015179	exon32	c.C3692A	p.A1231D	TATTCAGCCCCAG	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140573754	140573754	+	Missense_Mutation	SNP	A	A	C	rs77697313		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	22	132	0	1	0	.	.	weak	PCDHB10,colon,carcinoma,0,1	PCDHB10	177	1	NM_018930	exon1	c.A1629C	p.R543S	GAGCAGAGAGGCG	.	PASS	Atlas-SNP
ZNF860	344787	hgsc.bcm.edu	37	3	32031962	32031962	+	Missense_Mutation	SNP	A	A	G	rs1808125	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	33	78	0	0.452055	0	A|0.545;G|0.455	0.455	strong	ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	NM_001137674	exon2	c.A1391G	p.H464R	CCTTCCATCACAA	.	PASS	Atlas-SNP
TDP2	51567	hgsc.bcm.edu	37	6	24667074	24667074	+	Missense_Mutation	SNP	C	C	A	rs61760186	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	29	43	0	0.604167	0	C|0.997;A|0.003	0.003	strong	.	TDP2	29	.	NM_016614	exon1	c.G17T	p.C6F	TCCAGGCAACTCC	.	PASS	Atlas-SNP
DHX35	60625	hgsc.bcm.edu	37	20	37601243	37601243	+	Silent	SNP	A	A	G	rs16987712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	24	52	0	0.436364	0	A|0.815;G|0.185	0.185	strong	.	DHX35	82	.	NM_021931	exon3	c.A216G	p.T72T	TCAGACAGTGGTG	.	PASS	Atlas-SNP
MYT1L	23040	hgsc.bcm.edu	37	2	1842968	1842968	+	Silent	SNP	T	T	C	rs6728368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	36	99	0	0.363636	0	T|0.535;C|0.455;A|0.010	0.455	strong	.	MYT1L	241	.	NM_015025	exon21	c.A3027G	p.G1009G	GTCGCATCCTGGC	.	PASS	Atlas-SNP
PUS7L	83448	hgsc.bcm.edu	37	12	44148259	44148259	+	Missense_Mutation	SNP	T	T	C	rs1057190	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	256	132	280	0	0.515625	0	T|0.749;C|0.251	0.251	strong	.	PUS7L	73	.	NM_001098614	exon2	c.A790G	p.K264E	TCATTTTAGAAAA	.	PASS	Atlas-SNP
MPHOSPH8	54737	hgsc.bcm.edu	37	13	20224387	20224387	+	Silent	SNP	A	A	G	rs9578176	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	30	84	0	0.410959	0	A|0.886;G|0.114	0.114	strong	.	MPHOSPH8	58	.	NM_017520	exon5	c.A1563G	p.A521A	CCAAGCAGATGAG	.	PASS	Atlas-SNP
FAM83D	81610	hgsc.bcm.edu	37	20	37555116	37555116	+	Missense_Mutation	SNP	G	G	C	rs3752290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	14	13	0	0.933333	0	G|0.618;C|0.382	0.382	strong	FAM83D,NS,carcinoma,0,2	FAM83D	60	2	NM_030919	exon1	c.G121C	p.V41L	GACGAGGTGCCCG	.	PASS	Atlas-SNP
AAK1	22848	hgsc.bcm.edu	37	2	69709919	69709919	+	Silent	SNP	A	A	G	rs6721259	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	46	84	0	0.560976	0	A|0.862;G|0.138	0.138	strong	.	AAK1	121	.	NM_014911	exon18	c.T2391C	p.S797S	GTCAGGAGATTTG	.	PASS	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	37	21	43258138	43258138	+	Silent	SNP	C	C	T	rs76107411	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	56	75	0	0.543689	0	C|0.958;T|0.042	0.042	strong	.	PRDM15	110	.	NM_022115	exon15	c.G2004A	p.P668P	CTCATCCGGAGGG	.	PASS	Atlas-SNP
IFT80	57560	hgsc.bcm.edu	37	3	159997061	159997061	+	Missense_Mutation	SNP	T	T	A	rs6778728	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	106	153	0	0.524752	0	T|0.699;A|0.301	0.301	strong	.	IFT80	68	.	NM_020800	exon16	c.A1756T	p.T586S	ATGGTGTTATGCT	.	PASS	Atlas-SNP
ATP11A	23250	hgsc.bcm.edu	37	13	113508839	113508839	+	Silent	SNP	G	G	C	rs9549573	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	38	48	0	1	0	G|0.292;C|0.708	0.708	strong	.	ATP11A	225	.	NM_032189	exon19	c.G2238C	p.L746L	CAACCTGTCCGGG	.	PASS	Atlas-SNP
BOD1L1	259282	hgsc.bcm.edu	37	4	13603591	13603591	+	Missense_Mutation	SNP	C	C	T	rs17807493	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	75	145	0	0.559702	0	C|0.979;T|0.021	0.021	strong	.	.	.	.	NM_148894	exon10	c.G4933A	p.V1645I	TCACAACGCTATT	.	PASS	Atlas-SNP
OR2T29	343563	hgsc.bcm.edu	37	1	248722777	248722777	+	Missense_Mutation	SNP	T	T	A	rs77589892	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	687	218	892	0	0.317322	0	T|0.770;A|0.230	0.230	strong	.	OR2T29	8	.	NM_001004694	exon1	c.A16T	p.R6W	CCATCCTGGTGAT	.	PASS	Atlas-SNP
SEMA6D	80031	hgsc.bcm.edu	37	15	48056958	48056958	+	Silent	SNP	C	C	T	rs3743281	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	59	109	0	0.517544	0	C|0.814;T|0.186	0.186	strong	.	SEMA6D	322	.	NM_153617	exon12	c.C1221T	p.A407A	CATTGCCGATGAG	.	PASS	Atlas-SNP
RBM27	54439	hgsc.bcm.edu	37	5	145650597	145650597	+	Silent	SNP	A	A	G	rs17104362	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	180	88	142	0	0.488889	0	A|0.836;G|0.164	0.164	strong	.	RBM27	119	.	NM_018989	exon18	c.A2772G	p.K924K	ACGGAAAAAACTC	.	PASS	Atlas-SNP
PCDHB15	56121	hgsc.bcm.edu	37	5	140626778	140626778	+	Silent	SNP	G	G	A	rs112457389	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	80	116	0	0.481928	0	G|0.990;A|0.010	0.010	strong	PCDHB15,NS,carcinoma,+2,1	PCDHB15	138	1	NM_018935	exon1	c.G1632A	p.E544E	CAGCGAGGCGCTG	.	PASS	Atlas-SNP
SPESP1	246777	hgsc.bcm.edu	37	15	69238272	69238272	+	Missense_Mutation	SNP	G	G	T	rs3743091	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	39	58	1	0.513158	0.0172414	G|0.921;T|0.079	0.079	strong	SPESP1,NS,carcinoma,0,1	SPESP1	39	1	NM_145658	exon2	c.G399T	p.L133F	TGTTTTGCATGCA	.	scavenged	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909627	123909627	+	Missense_Mutation	SNP	T	T	C	rs11219420	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	256	100	276	0	0.390625	0	T|0.681;C|0.319	0.319	strong	OR10G7,NS,carcinoma,0,1	OR10G7	103	1	NM_001004463	exon1	c.A82G	p.I28V	GGAAGATTCCAAA	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49116359	49116359	+	Missense_Mutation	SNP	T	T	C	rs447802	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	47	102	0	0.47	0	T|0.521;C|0.479	0.479	strong	FAM83E,NS,carcinoma,0,2	FAM83E	34	2	NM_017708	exon1	c.A271G	p.T91A	CATCGGTGGTGGT	.	PASS	Atlas-SNP
TIMM10B	26515	hgsc.bcm.edu	37	11	6502780	6502780	+	Silent	SNP	C	C	A	rs11555935	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	21	47	0	0.456522	0	A|0.180;C|0.820;G|0.000;T|0.000	0.180	strong	.	.	.	.	NM_012192	exon1	c.C34A	p.R12R	CAACTGCGAAACG	.	PASS	Atlas-SNP
TMEM8A	58986	hgsc.bcm.edu	37	16	427784	427784	+	Silent	SNP	G	G	A	rs11641742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	53	93	0	0.486239	0	G|0.455;A|0.545	0.545	strong	.	TMEM8A	49	.	NM_021259	exon2	c.C186T	p.Y62Y	ACTGCCGTACCAG	.	PASS	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs78337605	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	306	30	220	0	0.0980392	0	C|0.500;T|0.500	0.500	strong	.	CYP2A6	69	.	NM_000762	exon7	c.G1039A	p.A347T	TCTTGGCCCGGTC	.	PASS	Atlas-SNP
POLR1E	64425	hgsc.bcm.edu	37	9	37489378	37489378	+	Silent	SNP	C	C	T	rs11542231	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	50	65	0	0.555556	0	C|0.888;T|0.112	0.112	strong	.	POLR1E	28	.	NM_022490	exon4	c.C324T	p.N108N	GTTCAACATGCAG	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135956462	135956462	+	Missense_Mutation	SNP	G	G	C	rs74667874		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	438	195	224	0	0.445205	0	.	.	weak	.	RBMX	149	.	NM_002139	exon9	c.C1015G	p.R339G	GATCACGACCACT	.	PASS	Atlas-SNP
RLF	6018	hgsc.bcm.edu	37	1	40705726	40705726	+	Missense_Mutation	SNP	A	A	T	rs10889205	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	115	128	0	0.942623	0	A|0.804;T|0.196	0.196	strong	RLF,NS,carcinoma,0,1	RLF	152	1	NM_012421	exon8	c.A5352T	p.E1784D	GAAAGAAGATGAT	.	PASS	Atlas-SNP
CWF19L2	143884	hgsc.bcm.edu	37	11	107299631	107299631	+	Missense_Mutation	SNP	G	G	A	rs659040	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	77	161	0	0.469512	0	G|0.822;A|0.178	0.178	strong	.	CWF19L2	135	.	NM_152434	exon8	c.C1327T	p.H443Y	GTTGGTGTTCATC	.	PASS	Atlas-SNP
GPR1	2825	hgsc.bcm.edu	37	2	207041441	207041441	+	Silent	SNP	G	G	A	rs3732082	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	37	74	0	0.430233	0	G|0.626;A|0.374	0.374	strong	.	GPR1	38	.	NM_001098199	exon3	c.C531T	p.D177D	CACAGTGTCCCGG	.	PASS	Atlas-SNP
KIRREL	55243	hgsc.bcm.edu	37	1	158057633	158057633	+	Silent	SNP	C	C	G	rs36008419	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	55	77	0	0.518868	0	C|0.762;G|0.238	0.238	strong	KIRREL_ENST00000368173,NS,carcinoma,0,2	KIRREL	346	2	NM_018240	exon6	c.C750G	p.P250P	CAACCCCGAGATC	.	PASS	Atlas-SNP
GRXCR2	643226	hgsc.bcm.edu	37	5	145252239	145252239	+	Missense_Mutation	SNP	C	C	T	rs71594518	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	157	174	1	0.987421	0.00574713	C|0.949;T|0.051	0.051	strong	.	GRXCR2	32	.	NM_001080516	exon1	c.G293A	p.G98D	TGGCCGCCTGCCA	.	PASS	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140475665	140475665	+	Missense_Mutation	SNP	C	C	A	rs116177548	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	113	153	0	0.472803	0	C|0.996;A|0.004	0.004	strong	PCDHB2,NS,carcinoma,-2,1	PCDHB2	163	1	NM_018936	exon1	c.C1291A	p.P431T	GGGACACCCAGGC	.	PASS	Atlas-SNP
FBXO24	26261	hgsc.bcm.edu	37	7	100198386	100198386	+	Missense_Mutation	SNP	C	C	T	rs11768465	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	56	134	0	0.5	0	C|0.761;T|0.239	0.239	strong	.	FBXO24	125	.	NM_012172	exon10	c.C1721T	p.T574M	ACCGCACGGAGAA	.	PASS	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1895950	1895950	+	Missense_Mutation	SNP	C	C	G	rs138283486	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	262	25	494	0	0.0954198	0	C|0.693;G|0.307	0.307	strong	.	SIRPA	83	.	NM_001040022	exon3	c.C285G	p.D95E	TTCAGACCTCACA	.	PASS	Atlas-SNP
GZMH	2999	hgsc.bcm.edu	37	14	25076836	25076836	+	Silent	SNP	G	G	A	rs41469548	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	437	63	308	0	0.144165	0	G|0.721;A|0.279	0.279	strong	.	GZMH	24	.	NM_033423	exon3	c.C321T	p.N107N	GATGTCGTTGGAG	.	PASS	Atlas-SNP
C18orf8	29919	hgsc.bcm.edu	37	18	21109250	21109250	+	Silent	SNP	T	T	C	rs1788825	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	26	57	0	0.5	0	T|0.236;G|0.000;C|0.764	0.764	strong	.	C18orf8	58	.	NM_013326	exon15	c.T1404C	p.F468F	AGCCTTTGTGGAA	.	PASS	Atlas-SNP
PKD1L2	114780	hgsc.bcm.edu	37	16	81219187	81219187	+	Missense_Mutation	SNP	C	C	T	rs13339342	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	35	47	0	0.5	0	C|0.865;T|0.135	0.135	strong	PKD1L2_ENST00000525539,NS,carcinoma,-1,2	PKD1L2	361	2	NM_001076780	exon11	c.G1907A	p.R636H	GCCAGGCGCAGGG	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179650408	179650408	+	Missense_Mutation	SNP	G	G	A	rs35813871	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	63	129	0	0.496063	0	G|0.827;A|0.173	0.173	strong	.	TTN	18412	.	NM_001267550	exon15	c.C2432T	p.T811I	CTAGCTGTGCGGG	.	PASS	Atlas-SNP
NMUR2	56923	hgsc.bcm.edu	37	5	151784183	151784183	+	Silent	SNP	G	G	A	rs3749787	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	46	81	0	0.554217	0	G|0.781;A|0.219	0.219	strong	NMUR2,NS,carcinoma,-2,1	NMUR2	111	1	NM_020167	exon1	c.C492T	p.L164L	GATCCTGAGGGCC	.	PASS	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1690752	1690752	+	Missense_Mutation	SNP	G	G	A	rs11549830	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	67	152	0	0.482014	0	G|0.609;A|0.391	0.391	strong	.	SMYD4	50	.	NM_052928	exon6	c.C1684T	p.R562W	TAATCCGCTGTGA	.	PASS	Atlas-SNP
HHAT	55733	hgsc.bcm.edu	37	1	210577831	210577831	+	Silent	SNP	C	C	T	rs34772809	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	70	87	0	0.985915	0	C|0.875;T|0.125	0.125	strong	.	HHAT	66	.	NM_001170587	exon5	c.C495T	p.N165N	AGAAAACGAGTAC	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910602	29910602	+	Missense_Mutation	SNP	G	G	T	rs41552219	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	14	105	0	0.162791	0	A|0.043;G|0.955;T|0.002	0.002	strong	HLA-A,NS,carcinoma,-2,4	HLA-A	89	4	NM_001242758	exon2	c.G142T	p.A48S	TTCATCGCCGTGG	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88964000	88964000	+	Silent	SNP	C	C	T	rs801839	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	29	92	0	0.508772	0	C|0.493;T|0.507	0.507	strong	.	ZNF804B	322	.	NM_181646	exon4	c.C1704T	p.F568F	TACTTTCAGTGCA	.	PASS	Atlas-SNP
GPR18	2841	hgsc.bcm.edu	37	13	99907341	99907341	+	Silent	SNP	G	G	A	rs3742130	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	48	143	0	0.372093	0	G|0.849;A|0.151	0.151	strong	.	GPR18	23	.	NM_001098200	exon2	c.C786T	p.N262N	GTAACTGTTCTCC	.	PASS	Atlas-SNP
TLE2	7089	hgsc.bcm.edu	37	19	2997897	2997897	+	Silent	SNP	G	G	A	rs11150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	59	104	0	0.522124	0	G|0.801;A|0.199	0.199	strong	.	TLE2	35	.	NM_003260	exon20	c.C2181T	p.I727I	TGTCACGATGTAT	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89422353	89422353	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	26	23	0	0.481481	0	.	.	none	.	HAPLN3	43	.	NM_178232	exon4	c.C641T	p.A214V	CAGCCCGCGTTGC	.	PASS	Atlas-SNP
BET1L	51272	hgsc.bcm.edu	37	11	205398	205398	+	Silent	SNP	G	G	A	rs190584141	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	90	118	0	0.559006	0	G|0.998;A|0.002	0.002	strong	.	BET1L	7	.	NM_001098787	exon4	c.C240T	p.S80S	TTGTCCGGACCTT	.	PASS	Atlas-SNP
MROH9	80133	hgsc.bcm.edu	37	1	170934394	170934394	+	Missense_Mutation	SNP	T	T	C	rs16863872	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	44	93	0	0.415094	0	T|0.955;C|0.045	0.045	strong	C1orf129_ENST00000367759,NS,carcinoma,-2,2	.	.	2	NM_025063	exon7	c.T478C	p.Y160H	AGAAAATACGTAA	.	PASS	Atlas-SNP
ACTN4	81	hgsc.bcm.edu	37	19	39215172	39215172	+	Silent	SNP	T	T	C	rs12986337	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	66	127	0	0.492537	0	T|0.942;C|0.058	0.058	strong	.	ACTN4	69	.	NM_004924	exon16	c.T1977C	p.N659N	GGCCAATGTTGTG	.	PASS	Atlas-SNP
EBP	10682	hgsc.bcm.edu	37	X	48382174	48382174	+	Silent	SNP	G	G	T	rs3048	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	39	50	0	0.951219	0	G|0.693;T|0.307	0.307	strong	.	EBP	30	.	NM_006579	exon2	c.G15T	p.A5A	CAACGCGGGCCCC	.	PASS	Atlas-SNP
C14orf37	145407	hgsc.bcm.edu	37	14	58598357	58598357	+	Silent	SNP	C	C	T	rs45465593	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	44	103	0	0.483516	0	C|0.979;T|0.021	0.021	strong	.	C14orf37	87	.	NM_001001872	exon4	c.G1704A	p.V568V	TTCCCCCACCATT	.	PASS	Atlas-SNP
ANKRD35	148741	hgsc.bcm.edu	37	1	145562087	145562087	+	Missense_Mutation	SNP	G	G	A	rs41315701	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	32	59	0	0.5	0	G|0.837;A|0.163	0.163	strong	.	ANKRD35	96	.	NM_144698	exon10	c.G1775A	p.R592Q	GGGCTCGAGGAGA	.	PASS	Atlas-SNP
CLDN6	9074	hgsc.bcm.edu	37	16	3065596	3065596	+	Missense_Mutation	SNP	T	T	C	rs2257295	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	41	140	0	0.37963	0	T|0.645;C|0.355	0.355	strong	CLDN6,rectum,carcinoma,0,3	CLDN6	31	3	NM_021195	exon2	c.A427G	p.I143V	GGATGATGGCATG	.	PASS	Atlas-SNP
EGFR	1956	hgsc.bcm.edu	37	7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	rs2227983	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	65	69	0	1	0	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong	.	EGFR	20426	.	NM_005228	exon13	c.G1562A	p.R521K	AGCCCAGGGACTG	.	PASS	Atlas-SNP
BCAR1	9564	hgsc.bcm.edu	37	16	75263816	75263816	+	Silent	SNP	G	G	A	rs145141523	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	39	38	0	0.52	0	G|0.993;A|0.007	0.007	strong	BCAR1_ENST00000393420,NS,carcinoma,0,2	BCAR1	184	2	NM_001170714	exon8	c.C2344T	p.L782L	GCCCCAGGCCGCC	.	PASS	Atlas-SNP
SCAF4	57466	hgsc.bcm.edu	37	21	33074633	33074633	+	Silent	SNP	A	A	G	rs2202128	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	119	189	0	0.636364	0	A|0.977;G|0.023	0.023	strong	.	SCAF4	142	.	NM_020706	exon5	c.T381C	p.I127I	TTGAATAATTTCA	.	PASS	Atlas-SNP
OTUD6B	51633	hgsc.bcm.edu	37	8	92083424	92083424	+	Silent	SNP	A	A	G	rs11557571	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	39	112	0	0.52	0	A|0.518;G|0.482	0.482	strong	.	OTUD6B	28	.	NM_016023	exon2	c.A231G	p.Q77Q	GAAGCAACTCACC	.	PASS	Atlas-SNP
CCDC114	93233	hgsc.bcm.edu	37	19	48821757	48821757	+	Missense_Mutation	SNP	G	G	A	rs16981988	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	42	79	0	0.531646	0	G|0.970;A|0.030	0.030	strong	.	CCDC114	100	.	NM_144577	exon3	c.C136T	p.R46W	GAAGCCGCTTGAC	.	PASS	Atlas-SNP
C1orf116	79098	hgsc.bcm.edu	37	1	207195561	207195561	+	Silent	SNP	G	G	A	rs34185174	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	30	41	0	0.526316	0	G|0.991;A|0.009	0.009	strong	.	C1orf116	64	.	NM_023938	exon4	c.C1548T	p.D516D	GATCTTGTCCAAG	.	PASS	Atlas-SNP
SAPCD1	401251	hgsc.bcm.edu	37	6	31731301	31731301	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	54	0	0.5	0	.	.	none	.	.	.	.	NM_001039651	exon2	c.G224A	p.R75Q	CACAGCGACAGCA	.	PASS	Atlas-SNP
WBP4	11193	hgsc.bcm.edu	37	13	41639377	41639377	+	Silent	SNP	C	C	T	rs61740513	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	39	54	0	0.549296	0	C|0.967;T|0.033	0.033	strong	.	WBP4	40	.	NM_007187	exon4	c.C216T	p.A72A	AGCTGCCCTGAAA	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220432957	220432957	+	Missense_Mutation	SNP	G	G	A	rs35009641	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	62	119	0	0.462687	0	G|0.968;A|0.032	0.032	strong	.	OBSL1	120	.	NM_001173431	exon2	c.C1102T	p.R368C	GGATGCGGGAGTT	.	PASS	Atlas-SNP
CDC20B	166979	hgsc.bcm.edu	37	5	54439466	54439466	+	Missense_Mutation	SNP	G	G	A	rs1021580	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	183	217	0	0.994565	0	G|0.261;A|0.739	0.739	strong	.	CDC20B	61	.	NM_001170402	exon4	c.C361T	p.R121C	CTTTGCGGGATCC	.	PASS	Atlas-SNP
C5orf49	134121	hgsc.bcm.edu	37	5	7835555	7835555	+	Missense_Mutation	SNP	C	C	G	rs6883562	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	29	60	0	0.453125	0	C|0.808;G|0.192	0.192	strong	.	C5orf49	27	.	NM_001089584	exon2	c.G204C	p.Q68H	CAACTTCTGATCA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151873853	151873853	+	Silent	SNP	C	C	T	rs6464211	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	80	161	0	0.536913	0	C|0.643;T|0.357	0.357	strong	.	MLL3	1564	.	NM_170606	exon38	c.G8685A	p.Q2895Q	GGATGCCTGAATG	.	PASS	Atlas-SNP
SH3GL1	6455	hgsc.bcm.edu	37	19	4362691	4362691	+	Silent	SNP	G	G	C	rs243261	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	29	55	0	0.557692	0	G|0.684;C|0.316	0.316	strong	.	SH3GL1	52	.	NM_003025	exon8	c.C771G	p.P257P	GGGCTTGGGCTTA	.	PASS	Atlas-SNP
TRAP1	10131	hgsc.bcm.edu	37	16	3724352	3724352	+	Silent	SNP	G	G	A	rs11541712	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	51	89	0	0.490385	0	T|0.006;G|0.845;C|0.107;A|0.041	0.041	strong	.	TRAP1	53	.	NM_016292	exon9	c.C1032T	p.Y344Y	GGGCACGTAGAAG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	612	33	470	11	0.0539216	0.0234043	.	.	none	MUC6_ENST00000421673,NS,carcinoma,-2,2	MUC6	408	2	NM_005961	exon31	c.C5235T	p.T1745T	TGTAGAGGTTTTG	.	scavenged	Atlas-SNP
ZSCAN29	146050	hgsc.bcm.edu	37	15	43653322	43653322	+	Silent	SNP	G	G	A	rs35278805	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	73	179	0	0.496599	0	G|0.822;A|0.178	0.178	strong	.	ZSCAN29	57	.	NM_152455	exon5	c.C2508T	p.H836H	TTCTCCGTGCTTA	.	PASS	Atlas-SNP
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32917735	32917735	+	Missense_Mutation	SNP	A	A	G	rs71462813	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	252	128	255	0	0.507937	0	A|0.250;G|0.750	0.750	weak	.	ARHGAP11A	84	.	NM_199357	exon6	c.A763G	p.I255V	TTGGGTATTGATG	.	PASS	Atlas-SNP
CCDC137	339230	hgsc.bcm.edu	37	17	79639550	79639550	+	Missense_Mutation	SNP	G	G	A	rs11546630	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	60	101	0	0.517241	0	G|0.854;A|0.146	0.146	strong	CCDC137,colon,carcinoma,+1,2	CCDC137	27	2	NM_199287	exon6	c.G686A	p.R229Q	TGCTGCGGATGCT	.	PASS	Atlas-SNP
UBR3	130507	hgsc.bcm.edu	37	2	170762566	170762566	+	Silent	SNP	A	A	T	rs10194785	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	34	69	0	0.43038	0	A|0.748;T|0.252	0.252	strong	.	UBR3	182	.	NM_172070	exon10	c.A1671T	p.L557L	AGAACTAAACGAG	.	PASS	Atlas-SNP
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs56376819		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	15	43	0	0.428571	0	.	.	weak	.	CPAMD8	192	.	NM_015692	exon15	c.A1778G	p.H593R	GCCAGATGAAGAG	.	PASS	Atlas-SNP
FAM179A	165186	hgsc.bcm.edu	37	2	29274704	29274704	+	Silent	SNP	C	C	T	rs61749512	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	74	143	0	0.48366	0	C|0.785;T|0.215	0.215	strong	.	FAM179A	106	.	NM_199280	exon20	c.C2805T	p.T935T	GAACACCGCCACC	.	PASS	Atlas-SNP
WDR93	56964	hgsc.bcm.edu	37	15	90255284	90255284	+	Missense_Mutation	SNP	A	A	G	rs112224433	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	19	60	0	0.358491	0	A|0.981;G|0.019	0.019	strong	.	WDR93	63	.	NM_020212	exon5	c.A589G	p.I197V	ACCTGTATAAAGA	.	PASS	Atlas-SNP
OR4C15	81309	hgsc.bcm.edu	37	11	55322211	55322211	+	Silent	SNP	A	A	G	rs9804659	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	36	99	0	0.45	0	A|0.760;G|0.240	0.240	strong	.	OR4C15	145	.	NM_001001920	exon1	c.A429G	p.K143K	GACAAAAACCATC	.	PASS	Atlas-SNP
HDAC4	9759	hgsc.bcm.edu	37	2	240003870	240003870	+	Silent	SNP	G	G	A	rs1063639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	230	111	258	0	0.482609	0	G|0.456;A|0.544	0.544	strong	.	HDAC4	127	.	NM_006037	exon21	c.C2565T	p.P855P	GACGCTGGGGTCG	.	PASS	Atlas-SNP
OR2T27	403239	hgsc.bcm.edu	37	1	248813785	248813785	+	Missense_Mutation	SNP	A	A	T	rs200036975	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	445	67	265	4	0.150562	0.0150943	A|0.863;T|0.137	0.137	strong	OR2T27,bladder,carcinoma,0,1	OR2T27	52	1	NM_001001824	exon1	c.T401A	p.V134D	ATGAGGACAGGAT	.	scavenged	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38129332	38129332	+	Silent	SNP	G	G	A	rs7284476	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	188	178	0	0.994709	0	G|0.639;A|0.361	0.361	strong	.	TRIOBP	262	.	NM_001039141	exon8	c.G3975A	p.Q1325Q	CTTCCAGGCCCAG	.	PASS	Atlas-SNP
HELT	391723	hgsc.bcm.edu	37	4	185940952	185940952	+	Missense_Mutation	SNP	C	C	G	rs1078461	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	83	105	0	0.509202	0	C|0.898;G|0.102	0.102	strong	.	HELT	34	.	NM_001029887	exon3	c.C439G	p.L147V	CAGTACCTGAGAG	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228557755	228557755	+	Missense_Mutation	SNP	G	G	A	rs145597580	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	45	80	0	0.608108	0	G|0.998;A|0.002	0.002	strong	.	OBSCN	2142	.	NM_001271223	exon102	c.G22951A	p.A7651T	GAAGACGCCAAAG	.	PASS	Atlas-SNP
ARHGAP9	64333	hgsc.bcm.edu	37	12	57871437	57871437	+	Silent	SNP	C	C	T	rs34160414	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	40	95	0	0.384615	0	C|0.920;T|0.080	0.080	strong	.	ARHGAP9	79	.	NM_001080157	exon3	c.G561A	p.E187E	AGGGGGCTCTGAC	.	PASS	Atlas-SNP
ADORA3	140	hgsc.bcm.edu	37	1	112042732	112042732	+	Missense_Mutation	SNP	A	A	T	rs2800889	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	47	170	0	0.367188	0	A|0.980;T|0.020	0.020	strong	.	ADORA3	104	.	NM_000677	exon2	c.T797A	p.M266K	ATGCCCATGTACA	.	PASS	Atlas-SNP
SV2B	9899	hgsc.bcm.edu	37	15	91825027	91825027	+	Silent	SNP	C	C	T	rs1117388	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	44	92	0	0.431373	0	C|0.652;T|0.348	0.348	strong	.	SV2B	98	.	NM_014848	exon11	c.C1443T	p.D481D	TGAAGACGTAACA	.	PASS	Atlas-SNP
RTP4	64108	hgsc.bcm.edu	37	3	187088656	187088656	+	Missense_Mutation	SNP	C	C	T	rs1047584	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	95	174	0	0.470297	0	C|0.802;T|0.198	0.198	strong	.	RTP4	20	.	NM_022147	exon2	c.C236T	p.T79I	ACTGGACATCCCA	.	PASS	Atlas-SNP
POR	5447	hgsc.bcm.edu	37	7	75615287	75615287	+	Silent	SNP	G	G	A	rs1057870	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	32	62	0	0.52459	0	G|0.826;A|0.174	0.174	strong	.	POR	46	.	NM_000941	exon14	c.G1716A	p.S572S	CCGCTCGGATGAG	.	PASS	Atlas-SNP
ILK	3611	hgsc.bcm.edu	37	11	6631016	6631016	+	Silent	SNP	C	C	T	rs2292195	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	84	154	0	0.571429	0	C|0.793;T|0.207	0.207	strong	.	ILK	41	.	NM_001014794	exon10	c.C918T	p.A306A	CATGGCCTTCCTA	.	PASS	Atlas-SNP
SIM2	6493	hgsc.bcm.edu	37	21	38117505	38117505	+	Silent	SNP	C	C	T	rs2073602	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	267	142	210	1	0.531835	0.0047619	C|0.739;T|0.261	0.261	strong	.	SIM2	55	.	NM_009586	exon10	c.C1644T	p.G548G	CCATGGCGGTGGG	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90402482	90402482	+	Missense_Mutation	SNP	G	G	A	rs9294445	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	53	122	0	0.981481	0	G|0.429;A|0.571	0.571	strong	.	MDN1	478	.	NM_014611	exon63	c.C10267T	p.H3423Y	TGCTGTGGAGTGA	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121622563	121622563	+	Silent	SNP	G	G	A	rs1621388	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	106	80	1	1	0.0125	G|0.649;A|0.351	0.351	strong	P2RX7,NS,carcinoma,0,1	P2RX7	53	1	NM_002562	exon13	c.G1746A	p.P582P	GTTTCCGAAGAGT	.	scavenged	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	rs78575608	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	85	214	0	0.425	0	G|0.974;C|0.026	0.026	strong	.	ABCA13	1192	.	NM_152701	exon17	c.G2821C	p.V941L	CAAGAAGTTGATA	.	PASS	Atlas-SNP
SCN10A	6336	hgsc.bcm.edu	37	3	38793989	38793989	+	Silent	SNP	G	G	A	rs7617919	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	80	77	0	0.97561	0	G|0.780;A|0.220	0.220	strong	.	SCN10A	359	.	NM_006514	exon11	c.C1476T	p.L492L	AGAGGCGAGGCCT	.	PASS	Atlas-SNP
HRCT1	646962	hgsc.bcm.edu	37	9	35906583	35906583	+	Missense_Mutation	SNP	T	T	A	rs112821450	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	3	20	0	0.0882353	0	T|0.500;A|0.500	0.500	weak	HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	NM_001039792	exon1	c.T299A	p.L100H	ACCACCTCCACCA	.	scavenged	Atlas-SNP
DPP6	1804	hgsc.bcm.edu	37	7	154667628	154667628	+	Silent	SNP	A	A	G	rs2293353	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	29	90	0	0.54717	0	G|0.584;N|0.001	0.584	strong	.	DPP6	383	.	NM_130797	exon20	c.A1896G	p.P632P	CACCCCAGGCAGC	.	PASS	Atlas-SNP
RNF40	9810	hgsc.bcm.edu	37	16	30780861	30780861	+	Silent	SNP	C	C	T	rs142343572	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	25	71	0	0.431034	0	C|0.997;T|0.003	0.003	strong	.	RNF40	83	.	NM_014771	exon17	c.C2526T	p.L842L	CAGCCTCGGGGGT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228412228	228412228	+	Missense_Mutation	SNP	G	G	A	rs1757153	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	101	202	1	0.5	0.00495049	G|0.756;A|0.244	0.244	strong	.	OBSCN	2142	.	NM_001271223	exon10	c.G2998A	p.A1000T	GCCAGTGCCACAC	.	PASS	Atlas-SNP
UVSSA	57654	hgsc.bcm.edu	37	4	1377615	1377615	+	Silent	SNP	A	A	G	rs9996817	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	21	70	0	0.428571	0	A|0.277;G|0.723	0.723	strong	KIAA1530,NS,carcinoma,0,1	.	.	1	NM_020894	exon13	c.A1923G	p.S641S	CGGCTCATCCAGG	.	PASS	Atlas-SNP
KIAA1429	25962	hgsc.bcm.edu	37	8	95538468	95538468	+	Silent	SNP	T	T	C	rs2890827	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	99	255	1	0.507692	0.00392157	T|0.651;C|0.349	0.349	strong	.	KIAA1429	176	.	NM_015496	exon8	c.A2004G	p.P668P	AGGGTATGGATCA	.	PASS	Atlas-SNP
AMACR	23600	hgsc.bcm.edu	37	5	34008100	34008100	+	Missense_Mutation	SNP	C	C	T	rs3195676	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	60	46	0	0.560748	0	C|0.609;T|0.391	0.391	strong	AMACR,NS,carcinoma,0,3	AMACR	38	3	NM_014324	exon1	c.G25A	p.V9M	GCTCCACGACCGA	.	PASS	Atlas-SNP
APOBEC3G	60489	hgsc.bcm.edu	37	22	39482557	39482557	+	Missense_Mutation	SNP	A	A	G	rs139265278		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	37	96	0	0.513889	0	A|1.000;G|0.000	0.000	weak	.	APOBEC3G	69	.	NM_021822	exon6	c.A1009G	p.I337V	ATTTCAATAATGA	.	PASS	Atlas-SNP
PIK3C2B	5287	hgsc.bcm.edu	37	1	204396830	204396830	+	Silent	SNP	G	G	A	rs17334387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	43	101	0	0.398148	0	G|0.857;A|0.143	0.143	strong	.	PIK3C2B	142	.	NM_002646	exon32	c.C4533T	p.S1511S	GGAGATGGACAGC	.	PASS	Atlas-SNP
ZNF469	84627	hgsc.bcm.edu	37	16	88504204	88504204	+	Missense_Mutation	SNP	G	G	C	rs56236932	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	9	22	0	0.529412	0	G|0.994;C|0.006	0.006	strong	ZNF469,NS,carcinoma,+1,1	ZNF469	121	1	NM_001127464	exon2	c.G10242C	p.R3414S	CCTCAGGGGGGGG	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31324711	31324711	+	Missense_Mutation	SNP	A	A	G	rs2596492	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	68	31	0	1	0	G|0.148;C|0.008;A|0.845	0.148	strong	.	HLA-B	54	.	NM_005514	exon2	c.T97C	p.Y33H	AGGTGTAGAAATA	.	PASS	Atlas-SNP
PDZRN4	29951	hgsc.bcm.edu	37	12	41966306	41966306	+	Silent	SNP	G	G	A	rs12298745	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	154	161	0	0.987179	0	G|0.858;A|0.142	0.142	strong	.	PDZRN4	346	.	NM_001164595	exon10	c.G1725A	p.E575E	AGCCGAGGACCCC	.	PASS	Atlas-SNP
DCDC2	51473	hgsc.bcm.edu	37	6	24205236	24205236	+	Silent	SNP	G	G	A	rs9467075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	88	138	0	0.470588	0	G|0.867;A|0.133	0.133	strong	.	DCDC2	53	.	NM_001195610	exon9	c.C1017T	p.V339V	CTGATCGACTGGA	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127231774	127231774	+	Missense_Mutation	SNP	C	C	G	rs1570580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	134	100	0	1	0	C|0.408;G|0.592	0.592	strong	.	GPR144	33	.	NM_001161808	exon16	c.C2506G	p.R836G	CGTGCCCGCATGT	.	PASS	Atlas-SNP
EXOC3L4	91828	hgsc.bcm.edu	37	14	103566904	103566904	+	Silent	SNP	G	G	A	rs1057640	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	91	167	0	0.511236	0	G|0.830;A|0.170	0.170	strong	.	EXOC3L4	35	.	NM_001077594	exon1	c.G348A	p.Q116Q	CAGCCAGCAGGCA	.	PASS	Atlas-SNP
AKAP5	9495	hgsc.bcm.edu	37	14	64935411	64935411	+	Missense_Mutation	SNP	C	C	T	rs2230491	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	38	98	0	0.457831	0	C|0.906;T|0.094	0.094	strong	.	AKAP5	23	.	NM_004857	exon2	c.C299T	p.P100L	AAAAGCCATTGGA	.	PASS	Atlas-SNP
NUP93	9688	hgsc.bcm.edu	37	16	56873495	56873495	+	Silent	SNP	C	C	T	rs1138295	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	129	229	0	0.539749	0	C|0.811;T|0.189	0.189	strong	.	NUP93	75	.	NM_014669	exon20	c.C2199T	p.A733A	GGCTGCCTTCAGA	.	PASS	Atlas-SNP
CCDC154	645811	hgsc.bcm.edu	37	16	1488141	1488141	+	Silent	SNP	C	C	T	rs12925639	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	39	64	0	0.493671	0	C|0.791;T|0.209	0.209	strong	.	CCDC154	27	.	NM_001143980	exon10	c.G1062A	p.G354G	CAGCTCCCCAGCC	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525071	248525071	+	Silent	SNP	T	T	C	rs28499298	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	732	21	702	0	0.0286885	0	T|0.769;C|0.231	0.231	strong	OR2T4,NS,carcinoma,0,1	OR2T4	126	1	NM_001004696	exon1	c.T189C	p.I63I	GGTCATTTTTGTG	.	scavenged	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786753	75786753	+	Missense_Mutation	SNP	C	C	T	rs74213916		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	22	41	0	0.564103	0	.	.	weak	.	ZNF717	160	.	NM_001128223	exon5	c.G2021A	p.R674H	TCCATACGGTTTT	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301408	65301408	+	Missense_Mutation	SNP	A	A	G	rs62415828	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	100	0	1	0	A|0.900;G|0.100	0.100	strong	.	EYS	527	.	NM_001142800	exon26	c.T4352C	p.I1451T	GCAGCTATAAGCA	.	PASS	Atlas-SNP
ABCC5	10057	hgsc.bcm.edu	37	3	183660585	183660585	+	Silent	SNP	G	G	A	rs3749442	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	45	99	0	0.436893	0	G|0.765;A|0.235	0.235	strong	.	ABCC5	142	.	NM_005688	exon25	c.C3624T	p.L1208L	TAGGACGAGAGGG	.	PASS	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	37	20	56137807	56137807	+	Silent	SNP	A	A	G	rs1042523	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	92	101	0	1	0	A|0.601;G|0.399	0.399	strong	.	PCK1	95	.	NM_002591	exon4	c.A462G	p.S154S	TCTGTCAAAGATC	.	PASS	Atlas-SNP
RANGAP1	5905	hgsc.bcm.edu	37	22	41652733	41652733	+	Silent	SNP	G	G	A	rs139509	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	47	65	0	0.460784	0	G|0.769;A|0.231	0.231	strong	.	RANGAP1	47	.	NM_002883	exon8	c.C870T	p.G290G	CAGGCCGCCGCGG	.	PASS	Atlas-SNP
ACHE	43	hgsc.bcm.edu	37	7	100488658	100488658	+	Missense_Mutation	SNP	G	G	C	rs1799806	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	95	159	0	0.489691	0	G|0.724;C|0.276	0.276	strong	ACHE,NS,carcinoma,0,1	ACHE	80	1	NM_015831	exon5	c.C1775G	p.P592R	GGCCTCGGAGCAG	.	PASS	Atlas-SNP
CNTN2	6900	hgsc.bcm.edu	37	1	205031116	205031116	+	Missense_Mutation	SNP	C	C	T	rs2229866	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	48	47	0	0.623377	0	C|0.586;T|0.414	0.414	strong	.	CNTN2	116	.	NM_005076	exon9	c.C1097T	p.P366L	GGGAGCCTCTGGC	.	PASS	Atlas-SNP
PRKCQ	5588	hgsc.bcm.edu	37	10	6472891	6472891	+	Silent	SNP	G	G	T	rs11258747	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	8	49	0	0.307692	0	G|0.847;T|0.153	0.153	strong	.	PRKCQ	113	.	NM_006257	exon17	c.C1846A	p.R616R	GTTCTCGCACGAA	.	PASS	Atlas-SNP
ITGA3	3675	hgsc.bcm.edu	37	17	48151296	48151296	+	Silent	SNP	T	T	C	rs117783166	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	20	78	0	0.322581	0	T|0.997;C|0.003	0.003	strong	.	ITGA3	128	.	NM_005501	exon8	c.T1173C	p.A391A	GGGAGCTCCGTTT	.	PASS	Atlas-SNP
DSC1	1823	hgsc.bcm.edu	37	18	28722133	28722133	+	Silent	SNP	T	T	C	rs36081634	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	60	144	0	0.441176	0	T|0.970;C|0.030	0.030	strong	.	DSC1	240	.	NM_004948	exon9	c.A1089G	p.V363V	TTCTTCTACTTCT	.	PASS	Atlas-SNP
RFPL3	10738	hgsc.bcm.edu	37	22	32754103	32754103	+	Missense_Mutation	SNP	A	A	C	rs58637580	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	126	233	0	0.531646	0	A|0.883;C|0.108;T|0.009	0.108	strong	.	RFPL3	91	.	NM_001098535	exon1	c.A45C	p.Q15H	ACCTCAAGGAAAT	.	PASS	Atlas-SNP
STARD13	90627	hgsc.bcm.edu	37	13	33704154	33704154	+	Silent	SNP	C	C	T	rs596742	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	26	59	0	0.490566	0	C|0.894;T|0.106	0.106	strong	.	STARD13	100	.	NM_178006	exon5	c.G660A	p.P220P	CATGACCGGGTTG	.	PASS	Atlas-SNP
ZNF259	8882	hgsc.bcm.edu	37	11	116652892	116652892	+	Missense_Mutation	SNP	A	A	T	rs11550892	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	47	115	0	0.474747	0	A|0.996;T|0.004	0.004	strong	.	ZNF259	27	.	NM_003904	exon12	c.T1161A	p.F387L	CTGGCTAAACTCC	.	PASS	Atlas-SNP
SEC14L4	284904	hgsc.bcm.edu	37	22	30901592	30901592	+	Missense_Mutation	SNP	T	T	C	rs9608956	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	15	33	0	0.357143	0	T|0.801;C|0.199	0.199	strong	.	SEC14L4	43	.	NM_001161368	exon1	c.A7G	p.S3G	CTCGGCTGCTCAT	.	PASS	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34827085	34827085	+	Missense_Mutation	SNP	A	A	T	rs9469913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	36	75	0	0.5	0	A|0.822;T|0.178	0.178	strong	.	UHRF1BP1	102	.	NM_017754	exon14	c.A2952T	p.Q984H	AACCCAAGCCTCC	.	PASS	Atlas-SNP
TPTE	7179	hgsc.bcm.edu	37	21	10920086	10920086	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	30	99	0	0.23622	0	.	.	none	TPTE_ENST00000361285,NS,carcinoma,0,3	TPTE	513	3	NM_199261	exon19	c.C1168A	p.Q390K	TTACCTGAGAAGG	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	37	7	141752154	141752154	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	30	52	0	0.576923	0	.	.	none	.	MGAM	767	.	NM_004668	exon25	c.A2866T	p.I956L	TGGAGCATAAAGA	.	PASS	Atlas-SNP
CORO1A	11151	hgsc.bcm.edu	37	16	30198151	30198151	+	Silent	SNP	A	A	G	rs1132812	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	45	86	0	0.511364	0	A|0.292;G|0.708	0.708	strong	.	CORO1A	36	.	NM_007074	exon4	c.A336G	p.P112P	GATCCCAGATGGG	.	PASS	Atlas-SNP
ACLY	47	hgsc.bcm.edu	37	17	40065774	40065774	+	Missense_Mutation	SNP	T	T	G	rs2304497	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	73	149	0	0.421965	0	T|0.896;G|0.104	0.104	strong	.	ACLY	85	.	NM_001096	exon5	c.A525C	p.E175D	CTTGTCTTCAGGG	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513635	72513635	+	Missense_Mutation	SNP	C	C	A	rs12774070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	36	49	0	0.571429	0	A|0.174;C|0.826;G|0.000	0.174	strong	ADAMTS14,NS,carcinoma,0,2	ADAMTS14	148	2	NM_139155	exon19	c.C2818A	p.L940M	TGCCTGCTGCCCC	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	37001761	37001761	+	Missense_Mutation	SNP	T	T	C	rs2232618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	31	83	0	0.449275	0	T|0.884;C|0.116	0.116	strong	.	LBP	60	.	NM_004139	exon13	c.T1306C	p.F436L	AACACCTTCTACC	.	PASS	Atlas-SNP
P2RX7	5027	hgsc.bcm.edu	37	12	121622196	121622196	+	Missense_Mutation	SNP	A	A	G	rs2230912	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	13	28	0	0.433333	0	A|0.889;G|0.111	0.111	strong	.	P2RX7	53	.	NM_002562	exon13	c.A1379G	p.Q460R	AGATACAGCTGCT	.	PASS	Atlas-SNP
ARNT	405	hgsc.bcm.edu	37	1	150808889	150808889	+	Silent	SNP	C	C	G	rs2228099	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	63	106	0	0.588785	0	C|0.562;G|0.438	0.438	strong	ARNT,NS,carcinoma,0,1	ARNT	68	1	NM_001668	exon7	c.G567C	p.V189V	GTCAGACACATAC	.	PASS	Atlas-SNP
ZNF180	7733	hgsc.bcm.edu	37	19	45001346	45001346	+	Missense_Mutation	SNP	G	G	A	rs2571108	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	17	22	0	0.414634	0	G|0.703;A|0.297	0.297	strong	ZNF180,colon,carcinoma,0,1	ZNF180	103	1	NM_013256	exon2	c.C122T	p.A41V	GCACAGGCCTTCG	.	PASS	Atlas-SNP
LRRIQ4	344657	hgsc.bcm.edu	37	3	169540397	169540397	+	Silent	SNP	T	T	C	rs1920119	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	215	214	193	1	0.995349	0.00518135	T|0.444;C|0.556	0.556	strong	.	LRRIQ4	68	.	NM_001080460	exon1	c.T688C	p.L230L	GCGTCCTTGTGCC	.	PASS	Atlas-SNP
MYCBP2	23077	hgsc.bcm.edu	37	13	77632470	77632470	+	Silent	SNP	C	C	T	rs2285386	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	211	108	194	0	0.511848	0	C|0.903;T|0.097	0.097	strong	.	MYCBP2	1029	.	NM_015057	exon78	c.G13212A	p.E4404E	ACAGTGCTCTTCG	.	PASS	Atlas-SNP
ELMOD3	84173	hgsc.bcm.edu	37	2	85590286	85590286	+	Missense_Mutation	SNP	C	C	T	rs7564372	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	41	76	0	0.471264	0	C|0.935;T|0.065	0.065	strong	.	ELMOD3	53	.	NM_001135022	exon6	c.C196T	p.R66C	GAGCCACGTGGTA	.	PASS	Atlas-SNP
FCER2	2208	hgsc.bcm.edu	37	19	7755056	7755056	+	Silent	SNP	G	G	A	rs2228138	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	31	55	1	0.584906	0.0181818	G|0.634;A|0.366	0.366	strong	FCER2,colon,carcinoma,0,1	FCER2	19	1	NM_002002	exon10	c.C717T	p.H239H	GTCCACGTGGCTC	.	scavenged	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1251357	1251357	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	71	34	66	0	0.478873	0	.	.	none	.	MUC5B	473	.	NM_002458	exon11	c.G1343C	p.S448T	ACTGCAGCTACGT	.	PASS	Atlas-SNP
TMEM60	85025	hgsc.bcm.edu	37	7	77423574	77423574	+	Silent	SNP	G	G	A	rs7953	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	89	106	1	1	0.00943396	G|0.424;A|0.576	0.576	strong	.	TMEM60	24	.	NM_032936	exon2	c.C117T	p.F39F	TGGAATGAATATG	.	PASS	Atlas-SNP
DYX1C1	161582	hgsc.bcm.edu	37	15	55722872	55722872	+	Missense_Mutation	SNP	G	G	C	rs77641439	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	44	76	0	0.536585	0	G|0.908;C|0.092	0.092	strong	DYX1C1,colon,carcinoma,0,2	DYX1C1	54	2	NM_130810	exon10	c.C1259G	p.S420C	CATTAAGATTTTA	.	PASS	Atlas-SNP
LCE3D	84648	hgsc.bcm.edu	37	1	152552285	152552285	+	Missense_Mutation	SNP	C	C	A	rs61745411		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	219	156	1	0.960526	0.00641026	C|0.986;A|0.014	0.014	weak	LCE3D,NS,carcinoma,0,1	LCE3D	28	1	NM_032563	exon2	c.G128T	p.G43V	CCACAGCCCCCAG	.	PASS	Atlas-SNP
UBR4	23352	hgsc.bcm.edu	37	1	19499954	19499954	+	Silent	SNP	G	G	A	rs952790	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	108	103	0	0.923077	0	G|0.937;A|0.063	0.063	strong	.	UBR4	415	.	NM_020765	exon23	c.C3144T	p.S1048S	ATAGGAGCTGATC	.	PASS	Atlas-SNP
FAM65A	79567	hgsc.bcm.edu	37	16	67578257	67578257	+	Missense_Mutation	SNP	C	C	T	rs61744916	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	26	67	0	0.412698	0	C|0.926;T|0.074	0.074	strong	.	FAM65A	104	.	NM_001193523	exon15	c.C2716T	p.R906C	AGTGCCCGCCCCC	.	PASS	Atlas-SNP
CORO2A	7464	hgsc.bcm.edu	37	9	100895443	100895443	+	Silent	SNP	C	C	T	rs735111	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	66	159	0	0.404908	0	T|0.076;G|0.006	0.076	strong	.	CORO2A	54	.	NM_003389	exon5	c.G525A	p.T175T	GCTAATCGTACTC	.	PASS	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79443850	79443850	+	Missense_Mutation	SNP	G	G	A	rs931606	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	40	83	0	0.5	0	G|0.491;A|0.509	0.509	strong	.	FRAS1	779	.	NM_025074	exon69	c.G10696A	p.V3566I	TCTTTCGTATTGA	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301734	65301734	+	Silent	SNP	G	G	A	rs12663619	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	125	0	1	0	G|0.903;A|0.097	0.097	strong	.	EYS	527	.	NM_001142800	exon26	c.C4026T	p.S1342S	ATCTGCGGAAGAA	.	PASS	Atlas-SNP
TDG	6996	hgsc.bcm.edu	37	12	104380734	104380734	+	Missense_Mutation	SNP	G	G	A	rs2888805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	35	82	0	0.443038	0	G|0.908;A|0.092	0.092	strong	.	TDG	43	.	NM_003211	exon10	c.G1099A	p.V367M	GAGAGCGTGGAGT	.	PASS	Atlas-SNP
COL2A1	1280	hgsc.bcm.edu	37	12	48376291	48376291	+	Silent	SNP	G	G	A	rs2276454	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	117	92	0	0.975	0	G|0.590;A|0.410	0.410	strong	.	COL2A1	368	.	NM_001844	exon34	c.C2295T	p.G765G	CCTGTCGCCTTTG	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	37	10	135012652	135012652	+	Silent	SNP	T	T	C	rs3008388	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	36	38	1	1	0.0263158	T|0.587;C|0.413	0.413	strong	KNDC1,rectum,carcinoma,0,2	KNDC1	155	2	NM_152643	exon14	c.T2640C	p.D880D	CGTGGATGCCTCG	.	scavenged	Atlas-SNP
PPAN	56342	hgsc.bcm.edu	37	19	10221227	10221227	+	Missense_Mutation	SNP	C	C	T	rs139737427	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	43	89	0	0.52439	0	C|0.999;T|0.001	0.001	strong	.	PPAN	43	.	NM_020230	exon10	c.C968T	p.A323V	TGAAGGCGCAGAG	.	PASS	Atlas-SNP
PCDHGB6	56100	hgsc.bcm.edu	37	5	140789933	140789933	+	Missense_Mutation	SNP	G	G	A	rs3749767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	229	223	246	0	0.973799	0	G|0.702;A|0.298	0.298	strong	.	PCDHGB6	120	.	NM_032100	exon1	c.G2164A	p.A722T	AGCCCTGCTACTT	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9066874	9066874	+	Missense_Mutation	SNP	G	G	T	rs12609150	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	321	148	327	0	0.461059	0	G|0.786;T|0.214	0.214	strong	.	MUC16	4315	.	NM_024690	exon3	c.C20572A	p.P6858T	AATTTGGAGGTGA	.	PASS	Atlas-SNP
LAG3	3902	hgsc.bcm.edu	37	12	6887020	6887020	+	Missense_Mutation	SNP	T	T	C	rs870849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	40	111	0	0.377358	0	T|0.375;C|0.625	0.625	strong	.	LAG3	35	.	NM_002286	exon7	c.T1364C	p.I455T	TTCTCATCCTTGG	.	PASS	Atlas-SNP
GBP1	2633	hgsc.bcm.edu	37	1	89525966	89525966	+	Missense_Mutation	SNP	T	T	C	rs1048401	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	61	130	0	0.451852	0	T|0.960;C|0.040	0.040	strong	.	GBP1	68	.	NM_002053	exon3	c.A232G	p.I78V	TCCAGATTCCTTT	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1817367	1817367	+	Silent	SNP	G	G	A	rs7003969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	164	206	0	0.987952	0	G|0.777;A|0.223	0.223	strong	.	ARHGEF10	255	.	NM_014629	exon7	c.G630A	p.E210E	TCCAGAGGAAGCA	.	PASS	Atlas-SNP
VTN	7448	hgsc.bcm.edu	37	17	26694483	26694483	+	Silent	SNP	A	A	G	rs2227728	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	52	143	0	0.409449	0	A|0.881;G|0.119	0.119	strong	.	VTN	45	.	NM_000638	exon8	c.T1344C	p.N448N	GCGAAGATTGACT	.	PASS	Atlas-SNP
ANKRD35	148741	hgsc.bcm.edu	37	1	145561594	145561594	+	Missense_Mutation	SNP	C	C	T	rs6670984	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	52	119	0	0.464286	0	C|0.526;T|0.474	0.474	strong	.	ANKRD35	96	.	NM_144698	exon10	c.C1282T	p.P428S	GGGCCACCCCAGA	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25924539	25924539	+	Silent	SNP	T	T	C	rs1047700	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	13	51	0	0.371429	0	T|0.749;C|0.251	0.251	strong	.	ATP10A	270	.	NM_024490	exon21	c.A4449G	p.Q1483Q	TGGCCCTTGAAGT	.	PASS	Atlas-SNP
ZHX2	22882	hgsc.bcm.edu	37	8	123964431	123964431	+	Silent	SNP	G	G	A	rs3204141	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	74	115	1	0.573643	0.00869565	G|0.767;A|0.233	0.233	strong	ZHX2,NS,carcinoma,0,1	ZHX2	106	1	NM_014943	exon3	c.G681A	p.S227S	CCTCTCGAGACTC	.	scavenged	Atlas-SNP
C9orf163	158055	hgsc.bcm.edu	37	9	139378914	139378914	+	Missense_Mutation	SNP	T	T	C	rs34376913	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	20	52	0	0.465116	0	T|0.830;C|0.170	0.170	strong	.	C9orf163	9	.	NM_152571	exon1	c.T14C	p.L5P	GCCCACTCACCTG	.	PASS	Atlas-SNP
GALNT15	117248	hgsc.bcm.edu	37	3	16268974	16268974	+	Silent	SNP	T	T	A	rs15767	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	75	73	0	1	0	T|0.600;A|0.400	0.400	strong	GALNTL2,colon,carcinoma,0,4	.	.	4	NM_054110	exon10	c.T1887A	p.R629R	GTGGCGTTTTGAC	.	PASS	Atlas-SNP
UBAP2	55833	hgsc.bcm.edu	37	9	33971740	33971740	+	Silent	SNP	A	A	G	rs3739690	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	48	67	0	0.527473	0	A|0.762;G|0.238	0.238	strong	.	UBAP2	82	.	NM_018449	exon8	c.T588C	p.P196P	GTCTGCAGGATTA	.	PASS	Atlas-SNP
INPP5A	3632	hgsc.bcm.edu	37	10	134540400	134540400	+	Silent	SNP	C	C	T	rs945943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	29	87	0	0.367089	0	C|0.917;T|0.083	0.083	strong	.	INPP5A	77	.	NM_005539	exon9	c.C723T	p.S241S	CAAGTCCGTCGTG	.	PASS	Atlas-SNP
HPSE	10855	hgsc.bcm.edu	37	4	84222208	84222208	+	Silent	SNP	A	A	G	rs11031	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	47	143	0	0.5	0	A|0.911;G|0.089	0.089	strong	.	HPSE	55	.	NM_001098540	exon11	c.T1377C	p.N459N	GGTGACATTATGG	.	PASS	Atlas-SNP
RFT1	91869	hgsc.bcm.edu	37	3	53159970	53159970	+	Missense_Mutation	SNP	A	A	G	rs146354877	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	35	143	0	0.380435	0	A|0.999;G|0.001	0.001	strong	.	RFT1	34	.	NM_052859	exon2	c.T104C	p.I35T	CGAAGAATAAATG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9046876	9046876	+	Missense_Mutation	SNP	G	G	T	rs4804378	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	65	123	0	0.507812	0	G|0.807;T|0.193	0.193	strong	.	MUC16	4315	.	NM_024690	exon5	c.C34755A	p.S11585R	CGTTGTGCTGGTT	.	PASS	Atlas-SNP
MLNR	2862	hgsc.bcm.edu	37	13	49794650	49794650	+	Silent	SNP	C	C	A	rs9568169	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	25	34	0	0.5	0	C|0.676;A|0.324	0.324	strong	MLNR,NS,carcinoma,0,1	MLNR	26	1	NM_001507	exon1	c.C177A	p.T59T	GGTGACCGTGATG	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919963	12919963	+	Missense_Mutation	SNP	T	T	G	rs72472699	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	133	11	142	1	0.0827068	0.00704225	T|0.756;G|0.244	0.244	strong	PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	NM_023014	exon3	c.T703G	p.C235G	ACTCTTTGCAAAC	.	scavenged	Atlas-SNP
ZBTB1	22890	hgsc.bcm.edu	37	14	64988924	64988924	+	Silent	SNP	T	T	C	rs10133411	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	46	84	0	0.541176	0	T|0.831;C|0.169	0.169	strong	ZBTB1_ENST00000394712,adrenal_gland,adrenal_cortical_adenoma,0,2	ZBTB1	93	2	NM_014950	exon2	c.T702C	p.H234H	TGAGCATGTGCTA	.	PASS	Atlas-SNP
CD40LG	959	hgsc.bcm.edu	37	X	135730555	135730555	+	Silent	SNP	T	T	C	rs1126535	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	57	61	0	0.982759	0	0|0.032;C|0.165	0.165	strong	.	CD40LG	46	.	NM_000074	exon1	c.T148C	p.L50L	AGAAGGTTGGACA	.	PASS	Atlas-SNP
SLC19A1	6573	hgsc.bcm.edu	37	21	46957794	46957794	+	Missense_Mutation	SNP	T	T	C	rs1051266	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	19	13	23	0	0.684211	0	T|0.518;C|0.482	0.482	strong	.	SLC19A1	53	.	NM_001205206	exon2	c.A80G	p.H27R	ACGAGGTGCCGCC	.	PASS	Atlas-SNP
GPN1	11321	hgsc.bcm.edu	37	2	27851918	27851918	+	Missense_Mutation	SNP	G	G	A	rs3749147	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	52	88	0	0.464286	0	G|0.772;A|0.228	0.228	strong	.	GPN1	28	.	NM_007266	exon1	c.G35A	p.R12K	GGGCCAGGAGGAA	.	PASS	Atlas-SNP
SMURF2	64750	hgsc.bcm.edu	37	17	62587204	62587204	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	5	120	0	0.049505	0	.	.	none	.	SMURF2	63	.	NM_022739	exon5	c.T398C	p.V133A	TTACCTACTATCT	.	PASS	Atlas-SNP
ZNF454	285676	hgsc.bcm.edu	37	5	178391860	178391860	+	Missense_Mutation	SNP	G	G	A	rs6867221	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	125	118	0	1	0	G|0.733;A|0.267	0.267	strong	.	ZNF454	99	.	NM_001178089	exon5	c.G455A	p.C152Y	AGGAATGTGATGA	.	PASS	Atlas-SNP
SGSH	6448	hgsc.bcm.edu	37	17	78184679	78184679	+	Missense_Mutation	SNP	C	C	T	rs9894254	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	20	61	0	0.487805	0	C|0.918;T|0.082	0.082	strong	.	SGSH	27	.	NM_000199	exon8	c.G1081A	p.V361I	CAAAGACGGTGGC	.	PASS	Atlas-SNP
KIAA1984	84960	hgsc.bcm.edu	37	9	139693596	139693596	+	Missense_Mutation	SNP	T	T	C	rs945386	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	43	78	0	0.43	0	T|0.759;C|0.241	0.241	strong	.	KIAA1984	39	.	NM_001039374	exon2	c.T113C	p.M38T	AGAATATGGACCA	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	37	3	52610651	52610651	+	Silent	SNP	T	T	A	rs17264436	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	35	61	0	0.448718	0	T|0.652;A|0.348	0.348	strong	.	PBRM1	1252	.	NM_018313	exon23	c.A3522T	p.P1174P	TTCTTCTGGGTGA	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90402840	90402840	+	Silent	SNP	C	C	G	rs9351212	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	52	84	0	1	0	A|0.032;C|0.170;G|0.798	0.798	strong	.	MDN1	478	.	NM_014611	exon63	c.G9909C	p.L3303L	ATTATCCAGCCGA	.	PASS	Atlas-SNP
ARMC5	79798	hgsc.bcm.edu	37	16	31471283	31471283	+	Silent	SNP	G	G	A	rs201280100	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	12	24	0	0.571429	0	G|0.993;A|0.007	0.007	strong	.	ARMC5	94	.	NM_024742	exon1	c.G438A	p.R146R	GTGCCGGACCGAA	.	PASS	Atlas-SNP
SLC22A10	387775	hgsc.bcm.edu	37	11	63072310	63072310	+	Missense_Mutation	SNP	C	C	T	rs1201559	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	79	145	0	0.519737	0	C|0.537;T|0.463	0.463	strong	.	SLC22A10	79	.	NM_001039752	exon9	c.C1547T	p.P516L	TCCTACCAGAAAC	.	PASS	Atlas-SNP
ALPK3	57538	hgsc.bcm.edu	37	15	85400564	85400564	+	Silent	SNP	C	C	T	rs114957070	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	42	54	0	0.646154	0	C|0.996;T|0.004	0.004	strong	.	ALPK3	289	.	NM_020778	exon6	c.C3201T	p.P1067P	GGTACCCACGATG	.	PASS	Atlas-SNP
ICA1	3382	hgsc.bcm.edu	37	7	8198226	8198226	+	Missense_Mutation	SNP	A	A	C	rs7798010	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	55	101	0	0.5	0	A|0.880;C|0.120	0.120	strong	.	ICA1	65	.	NM_001136020	exon7	c.T636G	p.F212L	TTGACAAACATCC	.	PASS	Atlas-SNP
NRXN2	9379	hgsc.bcm.edu	37	11	64415767	64415767	+	Silent	SNP	G	G	A	rs3825074	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	34	96	0	0.586207	0	G|0.897;A|0.103	0.103	strong	.	NRXN2	247	.	NM_015080	exon17	c.C3327T	p.G1109G	GCAGACGCCCTGG	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276876	71276876	+	Silent	SNP	A	A	G	rs12788123	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	14	111	8	0.14433	0.0720721	A|0.998;G|0.002	0.002	weak	KRTAP5-10,NS,carcinoma,0,1	KRTAP5-10	37	1	NM_001012710	exon1	c.A243G	p.K81K	CTCCAAAGGGGGC	.	scavenged	Atlas-SNP
ZNF80	7634	hgsc.bcm.edu	37	3	113955820	113955820	+	Silent	SNP	G	G	C	rs3732780	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	67	126	0	0.577586	0	G|0.703;C|0.297	0.297	strong	.	ZNF80	75	.	NM_007136	exon1	c.C102G	p.S34S	TCCCTGGGAGTCA	.	PASS	Atlas-SNP
MANSC4	100287284	hgsc.bcm.edu	37	12	27915718	27915718	+	Missense_Mutation	SNP	A	A	T	rs10842975	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	103	236	1	0.445887	0.00423729	A|0.494;T|0.506	0.506	strong	.	MANSC4	9	.	NM_001146221	exon3	c.T976A	p.S326T	GCAAGGATCCTGA	.	PASS	Atlas-SNP
MESDC1	59274	hgsc.bcm.edu	37	15	81294774	81294774	+	Silent	SNP	G	G	C	rs11541231	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	12	10	5	0	0.833333	0	G|0.972;C|0.028	0.028	strong	.	MESDC1	7	.	NM_022566	exon1	c.G162C	p.S54S	GCTGTCGAGCGAG	.	PASS	Atlas-SNP
SMG6	23293	hgsc.bcm.edu	37	17	2202943	2202943	+	Silent	SNP	T	T	C	rs216196	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	225	124	205	0	0.551111	0	T|0.712;C|0.288	0.288	strong	.	SMG6	97	.	NM_017575	exon2	c.A1104G	p.S368S	CCTGGCTGACCTC	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40392588	40392588	+	Missense_Mutation	SNP	C	C	T	rs62108885	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	438	181	367	0	0.413242	0	C|0.895;T|0.105	0.105	strong	.	FCGBP	416	.	NM_003890	exon16	c.G7916A	p.S2639N	CCCTCGCTCCCCG	.	PASS	Atlas-SNP
CPXCR1	53336	hgsc.bcm.edu	37	X	88008807	88008807	+	Missense_Mutation	SNP	G	G	A	rs5984611	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	51	84	0	1	0	0|0.003;A|0.269	0.269	strong	.	CPXCR1	83	.	NM_001184771	exon3	c.G392A	p.R131H	AAACTCGTTTTCG	.	PASS	Atlas-SNP
PPP1R16B	26051	hgsc.bcm.edu	37	20	37534665	37534665	+	Silent	SNP	C	C	T	rs4812332	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	81	71	0	1	0	C|0.671;T|0.329	0.329	strong	.	PPP1R16B	103	.	NM_015568	exon7	c.C750T	p.D250D	CCTGGACCATGGA	.	PASS	Atlas-SNP
TMEM132A	54972	hgsc.bcm.edu	37	11	60701136	60701136	+	Silent	SNP	C	C	G	rs9513	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	20	20	11	0	1	0	C|0.581;G|0.419	0.419	strong	.	TMEM132A	135	.	NM_017870	exon8	c.C1482G	p.P494P	GGCCCCCCTGCTA	.	PASS	Atlas-SNP
TMEM26	219623	hgsc.bcm.edu	37	10	63170292	63170292	+	Silent	SNP	A	A	G	rs7083475	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	73	173	0	0.480263	0	A|0.802;G|0.198	0.198	strong	.	TMEM26	47	.	NM_178505	exon6	c.T895C	p.L299L	GTTGCAACACCAC	.	PASS	Atlas-SNP
IVL	3713	hgsc.bcm.edu	37	1	152882979	152882979	+	Missense_Mutation	SNP	C	C	T	rs17855670	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	21	81	0	0.265823	0	C|0.943;T|0.057	0.057	strong	IVL,colon,carcinoma,0,2	IVL	100	2	NM_005547	exon2	c.C706T	p.P236S	GAGCTCCCACAGC	.	PASS	Atlas-SNP
MT1M	4499	hgsc.bcm.edu	37	16	56667282	56667282	+	Missense_Mutation	SNP	C	C	A	rs1827210	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	66	186	0	0.385965	0	C|0.207;A|0.793	0.793	strong	.	MT1M	13	.	NM_176870	exon2	c.C59A	p.T20K	CCTGCACGTGCAA	.	PASS	Atlas-SNP
LRRC8E	80131	hgsc.bcm.edu	37	19	7964727	7964727	+	Silent	SNP	G	G	A	rs3745382	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	12	37	0	0.315789	0	G|0.802;A|0.198	0.198	strong	.	LRRC8E	67	.	NM_001268284	exon4	c.G1320A	p.E440E	GGTGGAGTCACTC	.	PASS	Atlas-SNP
LTF	4057	hgsc.bcm.edu	37	3	46480958	46480958	+	Missense_Mutation	SNP	C	C	G	rs2073495	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	57	104	0	0.478992	0	C|0.739;G|0.261	0.261	strong	LTF,NS,carcinoma,0,1	LTF	98	1	NM_002343	exon15	c.G1737C	p.E579D	CCATGCCTCATTG	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	37	19	14991643	14991643	+	Silent	SNP	G	G	A	rs10401818	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	90	123	0	0.523256	0	G|0.709;A|0.291	0.291	strong	.	OR7A17	37	.	NM_030901	exon1	c.C525T	p.P175P	AAAGTGGGGGATT	.	PASS	Atlas-SNP
TAS2R30	259293	hgsc.bcm.edu	37	12	11286736	11286736	+	Silent	SNP	G	G	C	rs112605675		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	282	10	251	1	0.035461	0.00398406	G|0.500;C|0.500	0.500	weak	TAS2R30,NS,carcinoma,0,1	TAS2R30	28	1	NM_001097643	exon1	c.C108G	p.V36V	TCTCTTGACCCAC	.	scavenged	Atlas-SNP
NEK4	6787	hgsc.bcm.edu	37	3	52800284	52800284	+	Silent	SNP	T	T	C	rs2230535	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	299	137	246	1	0.458194	0.00406504	T|0.652;C|0.348	0.348	strong	.	NEK4	51	.	NM_003157	exon3	c.A468G	p.L156L	GTTCTCTAACACT	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	37	7	47874630	47874630	+	Missense_Mutation	SNP	G	G	A	rs66755489	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	55	63	0	0.632184	0	G|0.831;A|0.169	0.169	strong	PKD1L1,caecum,carcinoma,+1,1	PKD1L1	328	1	NM_138295	exon39	c.C6062T	p.P2021L	GACCCCGGGGCTT	.	PASS	Atlas-SNP
DBH	1621	hgsc.bcm.edu	37	9	136509370	136509370	+	Missense_Mutation	SNP	G	G	T	rs4531	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	29	47	0	0.460317	0	G|0.913;T|0.087	0.087	strong	.	DBH	86	.	NM_000787	exon5	c.G952T	p.A318S	GGCCTTGCCTTCG	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9060572	9060572	+	Silent	SNP	G	G	A	rs56405542	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	90	238	0	0.384615	0	G|0.788;A|0.212	0.212	strong	.	MUC16	4315	.	NM_024690	exon3	c.C26874T	p.G8958G	TGGGAGGCCTGGA	.	PASS	Atlas-SNP
TM6SF2	53345	hgsc.bcm.edu	37	19	19380996	19380996	+	Silent	SNP	G	G	T	rs2074300	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	45	116	0	0.46875	0	G|0.794;T|0.206	0.206	strong	.	TM6SF2	39	.	NM_001001524	exon4	c.C387A	p.G129G	GATGGCGCCGGCC	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171168584	171168584	+	Missense_Mutation	SNP	C	C	T	rs2020862	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	165	185	1	1	0.00540541	C|0.606;T|0.394	0.394	strong	FMO2,NS,carcinoma,-1,2	FMO2	66	2	NM_001460	exon5	c.C584T	p.S195L	GAAACTCAGGCTC	.	PASS	Atlas-SNP
FCHSD1	89848	hgsc.bcm.edu	37	5	141021294	141021294	+	Missense_Mutation	SNP	T	T	G	rs116772138	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	25	53	0	0.409836	0	T|0.986;G|0.014	0.014	strong	.	FCHSD1	51	.	NM_033449	exon19	c.A1982C	p.D661A	ATCATGTCCAGGA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910378	29910378	+	Silent	SNP	C	C	T	rs41546314	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	52	153	0	0.464286	0	C|0.769;T|0.231	0.231	strong	HLA-A,NS,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon1	c.C48T	p.A16A	GGGGGCCCTGGCC	.	PASS	Atlas-SNP
C11orf63	79864	hgsc.bcm.edu	37	11	122795688	122795688	+	Silent	SNP	T	T	C	rs11218891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	71	95	0	0.663551	0	T|0.780;C|0.220	0.220	strong	.	C11orf63	116	.	NM_024806	exon4	c.T948C	p.D316D	TGAAGATAAATGG	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100122291	100122291	+	Missense_Mutation	SNP	T	T	C	rs3747495	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	79	165	0	0.523179	0	T|0.807;C|0.193	0.193	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon26	c.T3523C	p.F1175L	CTCAGCTTCGTCC	.	PASS	Atlas-SNP
TMEM132A	54972	hgsc.bcm.edu	37	11	60703882	60703882	+	Missense_Mutation	SNP	G	G	A	rs61755079	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	58	134	0	0.439394	0	G|0.963;A|0.037	0.037	strong	.	TMEM132A	135	.	NM_017870	exon11	c.G2578A	p.V860M	TTCTGCGTGGCCA	.	PASS	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	37	16	15131962	15131962	+	Missense_Mutation	SNP	A	A	G	rs1135999	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	133	120	0	0.992537	0	A|0.707;G|0.293	0.293	strong	.	NTAN1	21	.	NM_173474	exon10	c.T859C	p.S287P	TTCCAGAAAACAG	.	PASS	Atlas-SNP
LPCAT1	79888	hgsc.bcm.edu	37	5	1501695	1501695	+	Silent	SNP	G	G	A	rs17588991	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	176	85	213	1	0.482955	0.00469484	G|0.956;A|0.044	0.044	strong	.	LPCAT1	70	.	NM_024830	exon2	c.C159T	p.L53L	CGGGAAGAGCGTC	.	PASS	Atlas-SNP
KRT35	3886	hgsc.bcm.edu	37	17	39634625	39634625	+	Silent	SNP	A	A	G	rs7216017	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	45	71	0	0.535714	0	A|0.455;G|0.545	0.545	strong	.	KRT35	58	.	NM_002280	exon5	c.T987C	p.A329A	GTGCTGAGCCTGC	.	PASS	Atlas-SNP
AP5Z1	9907	hgsc.bcm.edu	37	7	4827330	4827330	+	Silent	SNP	C	C	T	rs17135128	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	52	80	0	0.452174	0	C|0.943;T|0.057	0.057	strong	KIAA0415_ENST00000450194,rectum,carcinoma,0,2	.	.	2	NM_014855	exon11	c.C1377T	p.D459D	GGTGGACGCTGGC	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50534599	50534599	+	Missense_Mutation	SNP	G	G	A	rs10857472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	9	20	0	0.36	0	G|0.683;A|0.317	0.317	strong	.	C10orf71	179	.	NM_001135196	exon3	c.G4009A	p.G1337S	TACCCCGGCTTCC	.	PASS	Atlas-SNP
ZNF608	57507	hgsc.bcm.edu	37	5	123983915	123983915	+	Missense_Mutation	SNP	G	G	T	rs6862252	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	70	124	0	0.514706	0	G|0.405;N|0.001	.	strong	.	ZNF608	117	.	NM_020747	exon4	c.C2162A	p.T721N	CAGTTGGTAGCTT	.	PASS	Atlas-SNP
ZCWPW1	55063	hgsc.bcm.edu	37	7	99998750	99998750	+	Silent	SNP	G	G	A	rs145308367	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	49	82	0	0.441441	0	G|0.994;A|0.006	0.006	strong	.	ZCWPW1	41	.	NM_017984	exon18	c.C1834T	p.L612L	GGTCCAGGTCACT	.	PASS	Atlas-SNP
C4orf27	54969	hgsc.bcm.edu	37	4	170678993	170678993	+	Silent	SNP	T	T	C	rs11540095	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	9	10	0	0.333333	0	T|0.200;C|0.800	0.800	strong	.	C4orf27	32	.	NM_017867	exon1	c.A36G	p.G12G	CCCCTCTCCGCCG	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951581	130951581	+	Silent	SNP	A	A	G	rs16848443	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	373	104	336	0	0.27882	0	A|0.790;G|0.210	0.210	strong	.	TUBA3E	73	.	NM_207312	exon4	c.T834C	p.A278A	CTTCTCAGCTGAG	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1389156	1389156	+	Missense_Mutation	SNP	T	T	C	rs71614972	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	26	101	0	0.285714	0	C|1.000;|0.000	1.000	strong	CRIPAK,rectum,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.T857C	p.M286T	TGCCGATGTGGAG	.	PASS	Atlas-SNP
SH2D1B	117157	hgsc.bcm.edu	37	1	162367071	162367071	+	Silent	SNP	C	C	T	rs17852003	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	37	99	0	0.411111	0	C|0.671;T|0.329	0.329	strong	.	SH2D1B	19	.	NM_053282	exon4	c.G398A	p.X133X	TATCTTCAAGGCA	.	PASS	Atlas-SNP
SLC9A5	6553	hgsc.bcm.edu	37	16	67286590	67286590	+	Silent	SNP	G	G	C	rs61740454	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	61	127	0	0.472868	0	G|0.970;C|0.030	0.030	strong	.	SLC9A5	82	.	NM_004594	exon2	c.G333C	p.L111L	CTTCCTGCTGCCT	.	PASS	Atlas-SNP
NDRG4	65009	hgsc.bcm.edu	37	16	58545426	58545426	+	Silent	SNP	A	A	G	rs42945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	75	156	0	0.477707	0	A|0.274;G|0.726	0.726	strong	.	NDRG4	29	.	NM_001130487	exon16	c.A1122G	p.S374S	CCACTCAGAGAGC	.	PASS	Atlas-SNP
F2	2147	hgsc.bcm.edu	37	11	46745003	46745003	+	Missense_Mutation	SNP	C	C	T	rs5896	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	49	107	1	0.418803	0.00934579	C|0.835;T|0.165	0.165	strong	F2,colon,carcinoma,-1,2	F2	75	2	NM_000506	exon6	c.C494T	p.T165M	GCACCACGGGACC	.	scavenged	Atlas-SNP
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919244	51919244	+	Missense_Mutation	SNP	G	G	C	rs200798488	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	39	176	0	0.361111	0	G|0.993;C|0.007	0.007	strong	.	SIGLEC10	112	.	NM_001171157	exon5	c.C932G	p.P311R	ACCCCGGGCAGCT	.	PASS	Atlas-SNP
EFCAB4A	283229	hgsc.bcm.edu	37	11	828916	828916	+	Missense_Mutation	SNP	G	G	A	rs7126805	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	42	55	0	1	0	G|0.368;A|0.632	0.632	strong	.	EFCAB4A	16	.	NM_173584	exon3	c.G230A	p.R77Q	TGGACCGGGCTCA	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449298	89449298	+	Missense_Mutation	SNP	C	C	G	rs78052473		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	352	52	238	0	0.147727	0	.	.	weak	CCBL2,NS,neuroblastoma,0,1	.	.	1	NM_001162536	exon3	c.G212C	p.G71A	GACTTTCCATTCA	.	PASS	Atlas-SNP
LMO2	4005	hgsc.bcm.edu	37	11	33886294	33886294	+	Silent	SNP	A	A	G	rs2038602	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	49	88	0	0.544444	0	A|0.546;G|0.454	0.454	strong	.	LMO2	21	.	NM_005574	exon5	c.T318C	p.I106I	GTCCCCAATGTTC	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	37	12	57571249	57571249	+	Silent	SNP	C	C	T	rs2228187	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	94	149	0	0.537143	0	C|0.994;T|0.006	0.006	strong	.	LRP1	428	.	NM_002332	exon26	c.C4236T	p.R1412R	GCCCCGCATTGAG	.	PASS	Atlas-SNP
SOLH	6650	hgsc.bcm.edu	37	16	601632	601632	+	Silent	SNP	T	T	C	rs3213574	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	58	53	1	0.983051	0.0188679	T|0.359;C|0.641	0.641	strong	SOLH,NS,carcinoma,+1,1	SOLH	47	1	NM_005632	exon9	c.T2313C	p.G771G	TGAGGGTGTCTTC	.	scavenged	Atlas-SNP
ZNF417	147687	hgsc.bcm.edu	37	19	58420167	58420167	+	Silent	SNP	T	T	C	rs17852300	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	141	238	0	1	0	T|0.773;C|0.227	0.227	strong	ZNF417,NS,carcinoma,0,1	ZNF417	44	1	NM_152475	exon3	c.A1479G	p.E493E	ATTGCATTCATAC	.	PASS	Atlas-SNP
PCDHB4	56131	hgsc.bcm.edu	37	5	140502433	140502433	+	Missense_Mutation	SNP	G	G	C	rs149340599	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	53	112	0	0.46087	0	G|0.996;C|0.004	0.004	strong	.	PCDHB4	177	.	NM_018938	exon1	c.G853C	p.D285H	GCATCAGATGAAA	.	PASS	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	37	2	149799216	149799216	+	Silent	SNP	T	T	C	rs61734995	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	69	127	0	0.511111	0	T|0.860;C|0.140	0.140	strong	.	KIF5C	166	.	NM_004522	exon7	c.T531C	p.P177P	GAGCCCTGAGGAA	.	PASS	Atlas-SNP
TACC3	10460	hgsc.bcm.edu	37	4	1729988	1729988	+	Missense_Mutation	SNP	G	G	A	rs1063743	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	28	54	0	0.491228	0	G|0.806;A|0.194	0.194	strong	.	TACC3	69	.	NM_006342	exon4	c.G859A	p.G287S	GCAGATGGCACTC	.	PASS	Atlas-SNP
E2F7	144455	hgsc.bcm.edu	37	12	77419341	77419341	+	Missense_Mutation	SNP	A	A	T	rs310831	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	48	104	0	0.521739	0	A|0.918;T|0.082	0.082	strong	.	E2F7	201	.	NM_203394	exon12	c.T2562A	p.H854Q	CACCTGATGTAAT	.	PASS	Atlas-SNP
MYO3A	53904	hgsc.bcm.edu	37	10	26434455	26434455	+	Missense_Mutation	SNP	G	G	T	rs33947968	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	61	103	1	0.429577	0.00970874	G|0.941;T|0.059	0.059	strong	MYO3A,NS,carcinoma,0,1	MYO3A	371	1	NM_017433	exon22	c.G2497T	p.A833S	CATTATGCAGGAA	.	scavenged	Atlas-SNP
C1orf68	100129271	hgsc.bcm.edu	37	1	152692588	152692588	+	Silent	SNP	A	A	G	rs944682	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	179	224	0	0.983516	0	A|0.651;G|0.349	0.349	strong	C1orf68,NS,carcinoma,+1,2	C1orf68	19	2	NM_001024679	exon1	c.A591G	p.S197S	AGGATCATCTGGC	.	PASS	Atlas-SNP
TAS2R1	50834	hgsc.bcm.edu	37	5	9629529	9629529	+	Missense_Mutation	SNP	G	G	A	rs2234233	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	30	56	0	0.566038	0	G|0.878;A|0.122	0.122	strong	TAS2R1,NS,carcinoma,0,1	TAS2R1	84	1	NM_019599	exon1	c.C616T	p.R206W	TTTGCCGGGTGTG	.	PASS	Atlas-SNP
ANKRD65	441869	hgsc.bcm.edu	37	1	1354515	1354515	+	Missense_Mutation	SNP	C	C	G	rs904589	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	7	116	0	0.0406977	0	C|0.714;G|0.286	0.286	strong	.	ANKRD65	4	.	NM_001145210	exon4	c.G1165C	p.E389Q	CCTTCTCCCCCCC	.	PASS	Atlas-SNP
ADCYAP1	116	hgsc.bcm.edu	37	18	907675	907675	+	Silent	SNP	G	G	A	rs8192597	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	16	12	1	1	0.75	1	G|0.306;A|0.694	0.694	strong	ADCYAP1,NS,carcinoma,0,1	ADCYAP1	24	1	NM_001099733	exon3	c.G126A	p.A42A	AGAGGCGTACGGC	.	scavenged	Atlas-SNP
BPIFA3	128861	hgsc.bcm.edu	37	20	31812923	31812923	+	Missense_Mutation	SNP	G	G	A	rs3818222	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	63	100	0	0.470149	0	G|0.380;A|0.620	0.620	strong	.	.	.	.	NM_178466	exon4	c.G406A	p.V136I	AACATCGTAAAGA	.	PASS	Atlas-SNP
GALC	2581	hgsc.bcm.edu	37	14	88459448	88459448	+	Missense_Mutation	SNP	C	C	G	rs111887056	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	23	9	0	1	0	C|0.908;G|0.092	0.092	strong	.	GALC	48	.	NM_000153	exon1	c.G61C	p.A21P	AACCCGCGGCCGC	.	PASS	Atlas-SNP
BCL2	596	hgsc.bcm.edu	37	18	60985833	60985833	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	17	28	0	0.515152	0	.	.	none	.	BCL2	272	.	NM_000633	exon2	c.C67T	p.L23L	GCGACAGCTTATA	.	PASS	Atlas-SNP
IL12RB1	3594	hgsc.bcm.edu	37	19	18186575	18186575	+	Silent	SNP	G	G	A	rs17852635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	30	58	0	0.434783	0	G|0.748;A|0.252	0.252	strong	.	IL12RB1	92	.	NM_153701	exon7	c.C684T	p.P228P	GCACACGGGGCTG	.	PASS	Atlas-SNP
TRAPPC11	60684	hgsc.bcm.edu	37	4	184615117	184615117	+	Missense_Mutation	SNP	A	A	C	rs62358032	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	63	146	0	0.466667	0	A|0.924;C|0.076	0.076	strong	.	.	.	.	NM_021942	exon22	c.A2434C	p.T812P	CATGGAACAGAAC	.	PASS	Atlas-SNP
MYO3B	140469	hgsc.bcm.edu	37	2	171260797	171260797	+	Missense_Mutation	SNP	A	A	G	rs33962844	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	51	102	0	0.490385	0	A|0.726;G|0.274	0.274	strong	MYO3B,neck,malignant_melanoma,+1,1	MYO3B	320	1	NM_001083615	exon20	c.A2318G	p.E773G	CCGTGGAATATGA	.	PASS	Atlas-SNP
SCN3B	55800	hgsc.bcm.edu	37	11	123513161	123513161	+	Silent	SNP	G	G	A	rs1275085	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	36	84	0	0.455696	0	G|0.914;A|0.086	0.086	strong	.	SCN3B	53	.	NM_018400	exon3	c.C438T	p.T146T	CTCCTCGGTGACT	.	PASS	Atlas-SNP
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299188	125299188	+	Silent	SNP	T	T	G	rs12014937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	69	51	0	0.985714	0	T|0.485;G|0.515	0.515	strong	.	DCAF12L2	157	.	NM_001013628	exon1	c.A720C	p.P240P	ATATACTGGGAGA	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5072333	5072333	+	Missense_Mutation	SNP	T	T	G	rs3816913	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	92	189	0	0.442308	0	T|0.884;G|0.116	0.116	strong	.	USP6	213	.	NM_004505	exon27	c.T3500G	p.I1167S	CTAACATCAGCAG	.	PASS	Atlas-SNP
PAX2	5076	hgsc.bcm.edu	37	10	102568983	102568983	+	Silent	SNP	A	A	C	rs1800898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	17	39	0	0.447368	0	A|0.594;C|0.406	0.406	strong	.	PAX2	83	.	NM_003987	exon8	c.A978C	p.P326P	ATACCCAGTTGTG	.	PASS	Atlas-SNP
C9orf173	441476	hgsc.bcm.edu	37	9	140147273	140147273	+	Missense_Mutation	SNP	C	C	T	rs61759822	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	19	66	0	0.387755	0	C|0.847;T|0.153	0.153	strong	.	C9orf173	19	.	NM_001004353	exon5	c.C652T	p.L218F	TCCCTGCTTCAGG	.	PASS	Atlas-SNP
LAMA2	3908	hgsc.bcm.edu	37	6	129722425	129722425	+	Silent	SNP	G	G	A	rs3749878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	25	31	0	0.892857	0	G|0.461;A|0.539	0.539	strong	.	LAMA2	481	.	NM_000426	exon38	c.G5502A	p.E1834E	AAAAGAGGGCAAT	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911951	29911951	+	Silent	SNP	C	C	T	rs74658171	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	200	116	417	2	0.58	0.00479616	.	.	weak	.	HLA-A	89	.	NM_001242758	exon4	c.C672T	p.T224T	GGCCACCCTGAGG	.	PASS	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525290	248525290	+	Silent	SNP	C	C	T	rs202028348	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	877	23	781	0	0.0262258	0	C|0.840;T|0.160	0.160	strong	OR2T4,NS,carcinoma,0,1	OR2T4	126	1	NM_001004696	exon1	c.C408T	p.Y136Y	CTTCTACGTGACA	.	scavenged	Atlas-SNP
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081048	57081048	+	Missense_Mutation	SNP	G	G	C	rs79638626	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	23	40	0	0.522727	0	G|0.970;C|0.030	0.030	strong	TNKS1BP1,NS,haematopoietic_neoplasm,0,1	TNKS1BP1	148	1	NM_033396	exon5	c.C1114G	p.P372A	CCTCAGGGGGTGG	.	PASS	Atlas-SNP
PLEKHG4B	153478	hgsc.bcm.edu	37	5	140532	140532	+	Missense_Mutation	SNP	T	T	C	rs12516846	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	73	148	0	0.486667	0	T|0.846;C|0.154	0.154	strong	.	PLEKHG4B	167	.	NM_052909	exon1	c.T110C	p.V37A	GGGCAGTAGCCAG	.	PASS	Atlas-SNP
UPK3A	7380	hgsc.bcm.edu	37	22	45685002	45685002	+	Silent	SNP	A	A	G	rs1135360	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	46	0	1	0	A|0.413;G|0.587	0.587	strong	.	UPK3A	14	.	NM_006953	exon4	c.A549G	p.S183S	GTGGTCAGACCCC	.	PASS	Atlas-SNP
C20orf26	26074	hgsc.bcm.edu	37	20	20079360	20079360	+	Missense_Mutation	SNP	A	A	G	rs6075614	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	101	228	0	0.422594	0	A|0.909;G|0.091	0.091	strong	.	C20orf26	188	.	NM_015585	exon8	c.A761G	p.H254R	TGCTGCATGAGTG	.	PASS	Atlas-SNP
OR13C9	286362	hgsc.bcm.edu	37	9	107380215	107380215	+	Missense_Mutation	SNP	T	T	A	rs993658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	453	226	504	1	0.498896	0.00198413	T|0.743;A|0.257	0.257	strong	OR13C9,colon,carcinoma,+2,1	OR13C9	42	1	NM_001001956	exon1	c.A271T	p.T91S	AAATGGTCTTTCT	.	PASS	Atlas-SNP
SLC26A1	10861	hgsc.bcm.edu	37	4	982852	982852	+	Silent	SNP	G	G	A	rs3796621	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	82	55	0	1	0	G|0.565;A|0.435	0.435	strong	.	SLC26A1	44	.	NM_022042	exon3	c.C1875T	p.A625A	CACACCGGCTGCG	.	PASS	Atlas-SNP
MAP4	4134	hgsc.bcm.edu	37	3	47956424	47956424	+	Missense_Mutation	SNP	C	C	T	rs1137524	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	51	82	0	0.490385	0	T|0.303;G|0.116;C|0.511;N|0.000;A|0.069	0.303	strong	.	MAP4	176	.	NM_001134364	exon8	c.G1882A	p.V628I	CTGTGACGGTTTC	.	PASS	Atlas-SNP
ARSH	347527	hgsc.bcm.edu	37	X	2942109	2942109	+	Silent	SNP	T	T	C	rs5939407	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	132	125	1	1	0.008	T|0.346;C|0.654	0.654	strong	.	ARSH	72	.	NM_001011719	exon6	c.T949C	p.L317L	CACACCTTGGTGT	.	PASS	Atlas-SNP
AMPH	273	hgsc.bcm.edu	37	7	38433726	38433726	+	Missense_Mutation	SNP	T	T	G	rs35024632	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	33	83	0	0.383721	0	T|0.934;G|0.066	0.066	strong	.	AMPH	157	.	NM_001635	exon18	c.A1487C	p.K496T	GTGGCCTTCTCCG	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88537123	88537123	+	Silent	SNP	C	C	T	rs372453629		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	12	17	4	0.857143	0.235294	.	.	weak	DSPP,NS,carcinoma,0,2	DSPP	174	2	NM_014208	exon5	c.C3309T	p.S1103S	CAGCAGCGACAGC	.	scavenged	Atlas-SNP
ATP2A2	488	hgsc.bcm.edu	37	12	110765378	110765378	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	45	134	0	0.354331	0	.	.	none	.	ATP2A2	78	.	NM_001681	exon8	c.G651A	p.G217G	TGCTGGGAAAGCT	.	PASS	Atlas-SNP
XXYLT1	152002	hgsc.bcm.edu	37	3	194790782	194790782	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	14	2	5	0	0.142857	0	.	.	none	C3orf21,bladder,carcinoma,+2,1	.	.	1	NM_152531	exon4	c.C844T	p.P282S	CCTCGGGGGGCGG	.	scavenged	Atlas-SNP
SUCO	51430	hgsc.bcm.edu	37	1	172547465	172547465	+	Silent	SNP	A	A	G	rs2285664	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	98	140	0	0.576471	0	A|0.770;G|0.230	0.230	strong	.	.	.	.	NM_014283	exon14	c.A1368G	p.E456E	GGAAGAATATGAA	.	PASS	Atlas-SNP
P2RX2	22953	hgsc.bcm.edu	37	12	133196596	133196596	+	Silent	SNP	T	T	C	rs7964634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	25	73	0	0.396825	0	T|0.323;C|0.677	0.677	strong	P2RX2,NS,carcinoma,0,1	P2RX2	49	1	NM_170683	exon5	c.T468C	p.T156T	GAGGACTGGGCGC	.	PASS	Atlas-SNP
ZNF677	342926	hgsc.bcm.edu	37	19	53741188	53741188	+	Silent	SNP	C	C	T	rs12984473	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	20	46	0	0.526316	0	C|0.591;T|0.409	0.409	strong	.	ZNF677	94	.	NM_182609	exon5	c.G792A	p.K264K	ATTACACTTGTAT	.	PASS	Atlas-SNP
CXCR5	643	hgsc.bcm.edu	37	11	118765267	118765267	+	Silent	SNP	G	G	C	rs598207	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	26	9	42	0	0.346154	0	G|0.684;C|0.316	0.316	strong	.	CXCR5	34	.	NM_001716	exon2	c.G1014C	p.T338T	CCTGACGAAGCTG	.	PASS	Atlas-SNP
CRIM1	51232	hgsc.bcm.edu	37	2	36704144	36704144	+	Silent	SNP	C	C	T	rs848547	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	68	111	0	0.566667	0	C|0.450;T|0.550	0.550	strong	.	CRIM1	88	.	NM_016441	exon6	c.C1104T	p.T368T	CTTCACCGCCCAG	.	PASS	Atlas-SNP
OR5D16	390144	hgsc.bcm.edu	37	11	55606818	55606818	+	Silent	SNP	C	C	T	rs11231253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	90	268	0	0.412844	0	C|0.619;T|0.381	0.381	strong	OR5D16,NS,adenoma,0,1	OR5D16	94	1	NM_001005496	exon1	c.C591T	p.S197S	TCTCAGCCAGTTG	.	PASS	Atlas-SNP
ITPKC	80271	hgsc.bcm.edu	37	19	41235167	41235167	+	Missense_Mutation	SNP	G	G	A	rs112628847	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	31	76	0	0.492063	0	G|0.967;A|0.033	0.033	strong	.	ITPKC	36	.	NM_025194	exon3	c.G1316A	p.R439H	AGCAGCGCAGCCT	.	PASS	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	37	5	169454941	169454941	+	Silent	SNP	C	C	G	rs9791113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	75	130	0	0.547445	0	C|0.563;G|0.437	0.437	strong	.	DOCK2	389	.	NM_004946	exon34	c.C3456G	p.L1152L	GCAGCTCCTGGAG	.	PASS	Atlas-SNP
UNC13D	201294	hgsc.bcm.edu	37	17	73839137	73839137	+	Silent	SNP	G	G	A	rs3744007	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	42	68	0	0.5	0	G|0.926;A|0.074	0.074	strong	.	UNC13D	68	.	NM_199242	exon4	c.C279T	p.P93P	CTCCTCGGGCTCC	.	PASS	Atlas-SNP
FNDC8	54752	hgsc.bcm.edu	37	17	33454415	33454415	+	Silent	SNP	C	C	A	rs2306508	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	57	47	0	0.966102	0	C|0.608;A|0.392	0.392	strong	.	FNDC8	28	.	NM_017559	exon2	c.C564A	p.T188T	GCACACCGTCAAC	.	PASS	Atlas-SNP
RNF168	165918	hgsc.bcm.edu	37	3	196229836	196229836	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	57	124	0	0.518182	0	.	.	none	RNF168,colon,carcinoma,0,1	RNF168	49	1	NM_152617	exon1	c.C209G	p.S70C	ACGAGAGAATTTC	.	PASS	Atlas-SNP
HPSE2	60495	hgsc.bcm.edu	37	10	100219374	100219374	+	Missense_Mutation	SNP	T	T	A	rs10883100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	94	0	1	0	A|0.539;N|0.000	0.539	strong	HPSE2,NS,carcinoma,0,1	HPSE2	203	1	NM_021828	exon12	c.A1736T	p.Y579F	ACCACATAAAAGC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144879339	144879339	+	Missense_Mutation	SNP	C	C	T	rs145959230	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	43	188	0	0.206731	0	C|0.940;T|0.060	0.060	strong	PDE4DIP_ENST00000369356,NS,carcinoma,+2,3	PDE4DIP	817	3	NM_014644	exon27	c.G4111A	p.V1371I	GAATGACCTTGTT	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279860	46279860	+	Silent	SNP	G	G	A	rs151060280	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	4	93	0	0.05	0	G|0.997;A|0.003	0.003	strong	NCOA3,bladder,carcinoma,0,6	NCOA3	156	6	NM_181659	exon20	c.G3786A	p.Q1262Q	GCAGCAGCAGCAA	.	PASS	Atlas-SNP
TUBA3E	112714	hgsc.bcm.edu	37	2	130951949	130951949	+	Missense_Mutation	SNP	G	G	A	rs76125467	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	356	159	370	1	0.446629	0.0027027	G|0.500;A|0.500	0.500	weak	TUBA3E,NS,carcinoma,+2,1	TUBA3E	73	1	NM_207312	exon4	c.C466T	p.R156W	AGAGCCGCTCCAT	.	PASS	Atlas-SNP
OR8H1	219469	hgsc.bcm.edu	37	11	56058535	56058535	+	Missense_Mutation	SNP	C	C	T	rs11600896	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	14	32	0	0.388889	0	C|0.902;T|0.098	0.098	strong	.	OR8H1	89	.	NM_001005199	exon1	c.G4A	p.G2S	TTCTACCCATGAT	.	PASS	Atlas-SNP
NID2	22795	hgsc.bcm.edu	37	14	52481917	52481917	+	Silent	SNP	C	C	T	rs946615	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	46	88	0	0.484211	0	C|0.604;T|0.396	0.396	strong	NID2,NS,carcinoma,0,1	NID2	201	1	NM_007361	exon15	c.G3105A	p.R1035R	GTCATCCCGGGGG	.	PASS	Atlas-SNP
LRRC16A	55604	hgsc.bcm.edu	37	6	25435758	25435758	+	Silent	SNP	A	A	G	rs9467515	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	33	53	1	0.55	0.0188679	A|0.568;G|0.432	0.432	strong	LRRC16A_ENST00000329474,colon,carcinoma,0,2	LRRC16A	168	2	NM_001173977	exon5	c.A297G	p.S99S	GGCGTCACCCGAG	.	scavenged	Atlas-SNP
ENTHD2	146705	hgsc.bcm.edu	37	17	79205421	79205421	+	Missense_Mutation	SNP	G	G	A	rs61745945	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	75	106	0	0.572519	0	G|0.990;A|0.010	0.010	strong	C17orf56,NS,carcinoma,+1,1	.	.	1	NM_144679	exon9	c.C772T	p.R258C	AGGCGCGTGGTCC	.	PASS	Atlas-SNP
TMC7	79905	hgsc.bcm.edu	37	16	19041595	19041595	+	Missense_Mutation	SNP	G	G	A	rs4072393	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	59	120	0	0.464567	0	G|0.443;A|0.557	0.557	strong	.	TMC7	75	.	NM_024847	exon6	c.G761A	p.G254E	TTGATGGGGTGAA	.	PASS	Atlas-SNP
VSTM1	284415	hgsc.bcm.edu	37	19	54545531	54545531	+	Missense_Mutation	SNP	T	T	C	rs2433724	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	73	106	0	0.55303	0	T|0.619;C|0.381	0.381	strong	.	VSTM1	30	.	NM_198481	exon5	c.A487G	p.S163G	GCTCACTGTGCTG	.	PASS	Atlas-SNP
GRM7	2917	hgsc.bcm.edu	37	3	7620382	7620382	+	Silent	SNP	C	C	T	rs7614915	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	72	121	0	0.580645	0	C|0.804;T|0.196	0.196	strong	.	GRM7	223	.	NM_000844	exon8	c.C1789T	p.L597L	GTCTTCCTGGCAA	.	PASS	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12920067	12920067	+	Silent	SNP	C	C	G	rs17038709	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	15	195	0	0.078534	0	C|0.887;G|0.113	0.113	strong	PRAMEF2,NS,carcinoma,+2,1	PRAMEF2	85	1	NM_023014	exon3	c.C807G	p.L269L	ACACCTCCAGTTG	.	PASS	Atlas-SNP
MEGF10	84466	hgsc.bcm.edu	37	5	126746147	126746147	+	Silent	SNP	C	C	T	rs35550094	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	68	132	0	0.468966	0	C|0.983;T|0.017	0.017	strong	.	MEGF10	152	.	NM_032446	exon10	c.C984T	p.N328N	TGTCAACGGAGGG	.	PASS	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	37	2	186672897	186672897	+	Silent	SNP	A	A	G	rs4666690	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	221	105	219	1	0.475113	0.00456621	A|0.658;G|0.342	0.342	strong	FSIP2_ENST00000343098,caecum,carcinoma,+2,2	FSIP2	251	2	NM_173651	exon17	c.A19131G	p.L6377L	CTTTTTAATGGTG	.	PASS	Atlas-SNP
GFAP	2670	hgsc.bcm.edu	37	17	42987524	42987524	+	Missense_Mutation	SNP	T	T	C	rs9916491	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	312	312	314	3	1	0.00955414	T|0.759;C|0.241	0.241	strong	.	GFAP	88	.	NM_001131019	exon8	c.A1276G	p.T426A	GCGGCGTTCCATT	.	PASS	Atlas-SNP
MDN1	23195	hgsc.bcm.edu	37	6	90390443	90390443	+	Missense_Mutation	SNP	C	C	A	rs9353689	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	28	51	0	0.965517	0	C|0.413;A|0.587	0.587	strong	.	MDN1	478	.	NM_014611	exon74	c.G12130T	p.A4044S	GAGCAGCGCCCTG	.	PASS	Atlas-SNP
KL	9365	hgsc.bcm.edu	37	13	33628193	33628193	+	Missense_Mutation	SNP	G	G	C	rs9527025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	44	120	0	0.37931	0	G|0.848;C|0.152	0.152	strong	.	KL	106	.	NM_004795	exon2	c.G1109C	p.C370S	CTCTTTGCTTTGG	.	PASS	Atlas-SNP
SLC15A4	121260	hgsc.bcm.edu	37	12	129278864	129278864	+	Silent	SNP	A	A	G	rs1059312	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	44	90	0	0.5	0	A|0.574;G|0.426	0.426	strong	.	SLC15A4	41	.	NM_145648	exon8	c.T1611C	p.F537F	CAGAAGAAAAAAG	.	PASS	Atlas-SNP
SERPINB8	5271	hgsc.bcm.edu	37	18	61647069	61647069	+	Missense_Mutation	SNP	G	G	A	rs1944270	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	35	73	0	0.460526	0	G|0.632;T|0.004	.	strong	.	SERPINB8	42	.	NM_001031848	exon3	c.G203A	p.R68Q	TTCACCGAGGTTT	.	PASS	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	37	5	167891830	167891830	+	Silent	SNP	T	T	C	rs3203960	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	35	82	0	0.360825	0	T|0.625;C|0.375	0.375	strong	.	WWC1	98	.	NM_001161662	exon21	c.T3031C	p.L1011L	AGCCAATTGACCC	.	PASS	Atlas-SNP
C4A	720	hgsc.bcm.edu	37	6	31964228	31964228	+	Silent	SNP	A	A	G	rs17874654	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	326	121	328	0	0.371166	0	A|0.017;G|0.983	0.983	strong	.	C4A	15	.	NM_007293	exon28	c.G3527G	p.S1176S	AGGCAAACTCATT	.	PASS	Atlas-SNP
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156067	39156067	+	Silent	SNP	A	A	G	rs9890989	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	43	162	0	0.394495	0	A|0.750;G|0.250	0.250	strong	.	KRTAP3-2	11	.	NM_031959	exon1	c.T39C	p.T13T	AGGCCCAGTGGGG	.	PASS	Atlas-SNP
TCTN3	26123	hgsc.bcm.edu	37	10	97453464	97453464	+	Missense_Mutation	SNP	T	T	G	rs11553577	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	52	81	0	0.547368	0	T|0.905;G|0.095	0.095	strong	.	TCTN3	66	.	NM_015631	exon1	c.A193C	p.T65P	CCACTGTAGGGAG	.	PASS	Atlas-SNP
SLX4	84464	hgsc.bcm.edu	37	16	3650987	3650987	+	Missense_Mutation	SNP	T	T	C	rs113490934	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	63	178	0	0.362069	0	T|0.945;C|0.055	0.055	strong	.	SLX4	173	.	NM_032444	exon5	c.A1156G	p.M386V	TGAACATGGGTGG	.	PASS	Atlas-SNP
C17orf97	400566	hgsc.bcm.edu	37	17	260299	260299	+	Missense_Mutation	SNP	G	G	A	rs4581766	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	10	8	3	2	0.8	0.666667	G|0.798;A|0.202	0.202	strong	C17orf97_ENST00000360127,NS,carcinoma,0,4	C17orf97	76	4	NM_001013672	exon1	c.G166A	p.E56K	GAGGAGGAGGAGC	.	scavenged	Atlas-SNP
PMEL	6490	hgsc.bcm.edu	37	12	56351346	56351346	+	Silent	SNP	G	G	A	rs1052165	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	42	83	0	0.531646	0	G|0.799;N|0.000	.	strong	.	PMEL	60	.	NM_001200054	exon6	c.C741T	p.P247P	GCCACTGGGGTCA	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9088330	9088330	+	Missense_Mutation	SNP	G	G	A	rs17000947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	68	150	0	0.475524	0	G|0.811;A|0.189	0.189	strong	.	MUC16	4315	.	NM_024690	exon1	c.C3485T	p.T1162I	TTGGGAGTAGGAG	.	PASS	Atlas-SNP
CDCA2	157313	hgsc.bcm.edu	37	8	25364331	25364331	+	Missense_Mutation	SNP	G	G	A	rs4872318	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	23	55	0	0.5	0	G|0.761;A|0.239	0.239	strong	.	CDCA2	78	.	NM_152562	exon15	c.G2149A	p.V717I	GCTTCTGTAACTG	.	PASS	Atlas-SNP
TNRC6A	27327	hgsc.bcm.edu	37	16	24802331	24802331	+	Silent	SNP	C	C	T	rs72770409	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	13	40	0	0.371429	0	C|0.966;T|0.034	0.034	strong	.	TNRC6A	171	.	NM_014494	exon6	c.C2368T	p.L790L	CCTGCTCTGAGGT	.	PASS	Atlas-SNP
COL4A3BP	10087	hgsc.bcm.edu	37	5	74681773	74681773	+	Silent	SNP	T	T	C	rs698912	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	83	85	0	0.988095	0	T|0.743;C|0.257	0.257	strong	COL4A3BP,NS,carcinoma,0,1	COL4A3BP	72	1	NM_001130105	exon14	c.A1755G	p.E585E	GCAGACTTCATGT	.	PASS	Atlas-SNP
CD226	10666	hgsc.bcm.edu	37	18	67534642	67534642	+	Missense_Mutation	SNP	C	C	T	rs72481820	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	36	84	0	0.521739	0	C|0.926;T|0.074	0.074	strong	.	CD226	51	.	NM_006566	exon6	c.G836A	p.R279K	CTCCTTCTCCTTC	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	37	10	73434888	73434888	+	Missense_Mutation	SNP	G	G	C	rs1227049	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	38	60	0	0.612903	0	G|0.821;C|0.179	0.179	strong	.	CDH23	365	.	NM_022124	exon14	c.G1469C	p.G490A	ATGCAGGCACCTT	.	PASS	Atlas-SNP
NFASC	23114	hgsc.bcm.edu	37	1	204978704	204978704	+	Silent	SNP	G	G	A	rs55678495	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	18	62	0	0.375	0	G|0.891;A|0.109	0.109	strong	.	NFASC	396	.	NM_001005388	exon28	c.G3309A	p.A1103A	CCAAGCGGACATC	.	PASS	Atlas-SNP
SERPINF1	5176	hgsc.bcm.edu	37	17	1674429	1674429	+	Silent	SNP	T	T	C	rs8074840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	45	88	0	0.56962	0	T|0.735;C|0.265	0.265	strong	SERPINF1,NS,carcinoma,0,1	SERPINF1	31	1	NM_002615	exon4	c.T390C	p.T130T	GGTCACTGCCCCC	.	PASS	Atlas-SNP
PLA2G2D	26279	hgsc.bcm.edu	37	1	20442054	20442054	+	Missense_Mutation	SNP	T	T	C	rs584367	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	103	127	0	0.903509	0	C|0.710;N|0.000	0.710	strong	.	PLA2G2D	7	.	NM_012400	exon3	c.A238G	p.S80G	AGATGCTGCACCC	.	PASS	Atlas-SNP
SEC14L4	284904	hgsc.bcm.edu	37	22	30891250	30891250	+	Silent	SNP	T	T	C	rs9606738	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	31	49	0	0.476923	0	T|0.824;C|0.176	0.176	strong	.	SEC14L4	43	.	NM_001161368	exon5	c.A414G	p.Q138Q	CTGAGTTTGCAGC	.	PASS	Atlas-SNP
DYNC2H1	79659	hgsc.bcm.edu	37	11	103124135	103124135	+	Silent	SNP	T	T	G	rs11225634	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	93	270	1	0.467337	0.0037037	T|0.824;G|0.176	0.176	strong	.	DYNC2H1	246	.	NM_001080463	exon67	c.T10185G	p.T3395T	TGTTACTGAGGTT	.	PASS	Atlas-SNP
URB1	9875	hgsc.bcm.edu	37	21	33719400	33719400	+	Silent	SNP	A	A	G	rs9981151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	20	37	0	0.540541	0	A|0.788;G|0.212	0.212	strong	.	URB1	176	.	NM_014825	exon22	c.T3733C	p.L1245L	ACAGCAAGTGGGT	.	PASS	Atlas-SNP
WDR11	55717	hgsc.bcm.edu	37	10	122649482	122649482	+	Silent	SNP	A	A	G	rs2289337	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	35	50	0	0.530303	0	T|0.005;G|0.229	0.229	strong	WDR11,NS,carcinoma,0,1	WDR11	95	1	NM_018117	exon18	c.A2304G	p.A768A	AATAGCAATGTAC	.	PASS	Atlas-SNP
SLC16A2	6567	hgsc.bcm.edu	37	X	73641569	73641569	+	Missense_Mutation	SNP	T	T	C	rs6647476	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	14	12	0	0.933333	0	T|0.366;C|0.634	0.634	strong	.	SLC16A2	54	.	NM_006517	exon1	c.T97C	p.S33P	CCGGAGTCTGAGC	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	37	16	27373980	27373980	+	Missense_Mutation	SNP	C	C	T	rs1805013	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	41	82	0	0.42268	0	C|0.958;T|0.042	0.042	strong	.	IL4R	70	.	NM_000418	exon11	c.C1307T	p.S436L	CACCTTCGGGAAG	.	PASS	Atlas-SNP
ZNF138	7697	hgsc.bcm.edu	37	7	64291976	64291976	+	Missense_Mutation	SNP	G	G	A	rs10949946	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	29	71	0	0.453125	0	G|0.629;A|0.371	0.371	strong	ZNF138_ENST00000440155,NS,carcinoma,-1,3	ZNF138	43	3	NM_001271639	exon4	c.G356A	p.G119E	GTAAGGGACACCA	.	PASS	Atlas-SNP
PLEKHA4	57664	hgsc.bcm.edu	37	19	49340661	49340661	+	Missense_Mutation	SNP	C	C	A	rs35965411	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	39	98	0	0.493671	0	C|0.932;A|0.068	0.068	strong	.	PLEKHA4	70	.	NM_020904	exon20	c.G2225T	p.G742V	CCTCCTCCACGCC	.	PASS	Atlas-SNP
SETBP1	26040	hgsc.bcm.edu	37	18	42530295	42530295	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	35	59	0	0.583333	0	.	.	none	.	SETBP1	577	.	NM_015559	exon4	c.G990A	p.T330T	ACCTACGGTGGGC	.	PASS	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	37	2	227896976	227896976	+	Silent	SNP	C	C	T	rs10203363	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	22	78	0	0.314286	0	C|0.544;T|0.456	0.456	strong	.	COL4A4	215	.	NM_000092	exon39	c.G3594A	p.G1198G	AGGTGGCCCCACA	.	PASS	Atlas-SNP
OVCH1	341350	hgsc.bcm.edu	37	12	29642573	29642573	+	Missense_Mutation	SNP	A	A	C	rs967181	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	49	84	0	0.550562	0	A|0.579;C|0.421	0.421	strong	OVCH1,colon,carcinoma,0,1	OVCH1	195	1	NM_183378	exon6	c.T682G	p.W228G	TTCCCCAATCAGG	.	PASS	Atlas-SNP
TAF1C	9013	hgsc.bcm.edu	37	16	84215390	84215390	+	Silent	SNP	T	T	C	rs2230127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	208	208	191	1	1	0.0052356	T|0.654;C|0.346	0.346	strong	TAF1C,NS,carcinoma,0,1	TAF1C	60	1	NM_005679	exon8	c.A996G	p.A332A	CTGCATTGCCTGC	.	PASS	Atlas-SNP
OR10H2	26538	hgsc.bcm.edu	37	19	15838967	15838967	+	Silent	SNP	G	G	A	rs45442392	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	100	195	1	0.4329	0.00512821	G|0.611;A|0.389	0.389	strong	OR10H2,NS,carcinoma,+1,1	OR10H2	59	1	NM_013939	exon1	c.G114A	p.T38T	GTTCACGCTGCTG	.	scavenged	Atlas-SNP
CRTC1	23373	hgsc.bcm.edu	37	19	18876258	18876258	+	Missense_Mutation	SNP	G	G	A	rs36070283	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	48	69	0	0.648649	0	G|0.935;A|0.065	0.065	strong	.	CRTC1	88	.	NM_001098482	exon10	c.G979A	p.V327I	GCTGGCGTCAGCC	.	PASS	Atlas-SNP
SERGEF	26297	hgsc.bcm.edu	37	11	17809724	17809724	+	Missense_Mutation	SNP	T	T	C	rs1528	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	360	164	329	0	0.455556	0	T|0.878;C|0.122	0.122	strong	.	SERGEF	38	.	NM_012139	exon11	c.A1285G	p.K429E	TGGCTTTCTGAGA	.	PASS	Atlas-SNP
PLA2G15	23659	hgsc.bcm.edu	37	16	68293320	68293320	+	Silent	SNP	T	T	C	rs3743739	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	26	53	0	0.464286	0	T|0.778;C|0.222	0.222	strong	PLA2G15,NS,carcinoma,0,1	PLA2G15	30	1	NM_012320	exon6	c.T999C	p.G333G	CTATGGTACTGGC	.	PASS	Atlas-SNP
ZNF33A	7581	hgsc.bcm.edu	37	10	38344700	38344700	+	Missense_Mutation	SNP	C	C	G	rs2505232	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	70	98	0	0.958904	0	C|0.507;G|0.493	0.493	strong	.	ZNF33A	103	.	NM_006954	exon5	c.C1648G	p.Q550E	ACAGGGCAGAAAC	.	PASS	Atlas-SNP
SOS2	6655	hgsc.bcm.edu	37	14	50585109	50585109	+	Missense_Mutation	SNP	G	G	A	rs140995728	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	73	206	0	0.442424	0	G|0.999;A|0.001	0.001	strong	.	SOS2	195	.	NM_006939	exon23	c.C3952T	p.P1318S	ACAATGGGGGGTG	.	PASS	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76370887	76370887	+	Splice_Site	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	26	60	0	0.26	0	.	.	none	.	LMO7	334	.	NM_005358	exon7	c.618+2T>C	.	CGAAGGTAAGTAA	.	PASS	Atlas-SNP
SOD3	6649	hgsc.bcm.edu	37	4	24801315	24801315	+	Missense_Mutation	SNP	G	G	A	rs2536512	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	7	1	0	0.777778	0	G|0.600;A|0.400	0.400	strong	.	SOD3	4	.	NM_003102	exon2	c.G172A	p.A58T	GACGGCGCGCTCC	.	PASS	Atlas-SNP
SPP1	6696	hgsc.bcm.edu	37	4	88903853	88903853	+	Silent	SNP	C	C	T	rs1126616	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	82	166	0	0.5	0	C|0.733;G|0.000;T|0.267	0.267	strong	SPP1,NS,carcinoma,0,1	SPP1	35	1	NM_001251830	exon8	c.C789T	p.A263A	GAAAGCCAATGAT	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643066	1643066	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	10	130	5	0.0746269	0.0384615	.	.	none	KRTAP5-4,NS,carcinoma,0,3	KRTAP5-4	78	3	NM_001012709	exon1	c.T258C	p.G86G	CTTGGAACCCCCA	.	scavenged	Atlas-SNP
NHLRC3	387921	hgsc.bcm.edu	37	13	39613322	39613322	+	Missense_Mutation	SNP	T	T	G	rs115821169	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	51	82	1	0.53125	0.0121951	T|0.983;G|0.017	0.017	strong	NHLRC3,NS,carcinoma,+1,1	NHLRC3	35	1	NM_001012754	exon2	c.T134G	p.L45R	AAATTCTTTACCG	.	scavenged	Atlas-SNP
KIF13B	23303	hgsc.bcm.edu	37	8	29033654	29033654	+	Silent	SNP	A	A	G	rs148531473	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	30	96	0	0.37037	0	A|0.997;G|0.003	0.003	strong	.	KIF13B	192	.	NM_015254	exon10	c.T876C	p.D292D	ACTCTGATCTGCA	.	PASS	Atlas-SNP
ACTR5	79913	hgsc.bcm.edu	37	20	37396120	37396120	+	Missense_Mutation	SNP	A	A	G	rs2245231	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	94	74	0	1	0	A|0.563;G|0.437	0.437	strong	.	ACTR5	44	.	NM_024855	exon8	c.A1447G	p.I483V	AAGGACATTCAGG	.	PASS	Atlas-SNP
GPD1L	23171	hgsc.bcm.edu	37	3	32181761	32181761	+	Silent	SNP	C	C	T	rs9835387	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	62	90	0	0.574074	0	C|0.828;T|0.172	0.172	strong	.	GPD1L	25	.	NM_015141	exon4	c.C408T	p.D136D	TTCTGACATCATC	.	PASS	Atlas-SNP
OR1Q1	158131	hgsc.bcm.edu	37	9	125377734	125377734	+	Missense_Mutation	SNP	A	A	G	rs727913	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	70	159	0	0.39548	0	A|0.881;G|0.119	0.119	strong	.	OR1Q1	46	.	NM_012364	exon1	c.A718G	p.T240A	TTTTCTACCTGCG	.	PASS	Atlas-SNP
CSTL1	128817	hgsc.bcm.edu	37	20	23424638	23424638	+	Missense_Mutation	SNP	C	C	T	rs3746737	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	43	77	0	0.438776	0	C|0.903;T|0.097	0.097	strong	CSTL1,NS,carcinoma,0,1	CSTL1	30	1	NM_138283	exon3	c.C287T	p.T96M	ATGACACGAGCAA	.	PASS	Atlas-SNP
PLEKHA4	57664	hgsc.bcm.edu	37	19	49340746	49340746	+	Missense_Mutation	SNP	T	T	C	rs34460869	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	76	146	0	0.531469	0	T|0.929;C|0.071	0.071	strong	.	PLEKHA4	70	.	NM_020904	exon20	c.A2140G	p.T714A	GGCGCGTGGGGTC	.	PASS	Atlas-SNP
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	82	75	0	0.987952	0	C|0.647;T|0.353	0.353	strong	.	JAK2	35466	.	NM_004972	exon6	c.C489T	p.H163H	TGTGCACGGATGG	.	PASS	Atlas-SNP
ZBTB46	140685	hgsc.bcm.edu	37	20	62407104	62407104	+	Silent	SNP	C	C	T	rs3827026	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	67	128	0	0.523438	0	C|0.909;T|0.091	0.091	strong	.	ZBTB46	72	.	NM_025224	exon3	c.G1149A	p.L383L	GGCCTTCAGCGAC	.	PASS	Atlas-SNP
KPTN	11133	hgsc.bcm.edu	37	19	47983623	47983623	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	2	127	0	0.0115607	0	.	.	none	KPTN,NS,carcinoma,-1,1	KPTN	34	1	NM_007059	exon7	c.G641T	p.R214L	AGGCGCCGGGACG	.	scavenged	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136037742	136037742	+	Missense_Mutation	SNP	G	G	A	rs2073924	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	69	115	0	0.507353	0	G|0.741;A|0.259	0.259	strong	GBGT1,NS,carcinoma,0,1	GBGT1	25	1	NM_021996	exon2	c.C58T	p.L20F	CACTGAGGCTTGT	.	PASS	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	37	1	154842250	154842250	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	5	31	5	0.113636	0.16129	.	.	none	KCNN3,colon,carcinoma,0,1	KCNN3	141	1	NM_001204087	exon1	c.C191A	p.P64Q	AGCTGCGGAGGCT	.	scavenged	Atlas-SNP
PRKCQ	5588	hgsc.bcm.edu	37	10	6498723	6498723	+	Silent	SNP	G	G	A	rs11258943	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	53	105	0	0.434426	0	G|0.837;A|0.163	0.163	strong	.	PRKCQ	113	.	NM_006257	exon15	c.C1560T	p.I520I	ATCCGCGATCTTG	.	PASS	Atlas-SNP
GAS8	2622	hgsc.bcm.edu	37	16	90102835	90102835	+	Silent	SNP	A	A	G	rs868045	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	119	103	1	0.983471	0.00970874	A|0.644;G|0.356	0.356	strong	.	GAS8	29	.	NM_001481	exon6	c.A597G	p.E199E	GGACGAACTCGAC	.	PASS	Atlas-SNP
DDX60	55601	hgsc.bcm.edu	37	4	169197297	169197297	+	Missense_Mutation	SNP	C	C	T	rs550625	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	65	156	1	0.515873	0.00641026	C|0.882;T|0.118	0.118	strong	DDX60_ENST00000393743,NS,carcinoma,+2,2	DDX60	304	2	NM_017631	exon15	c.G2014A	p.V672M	TCATCACCTGAAC	.	scavenged	Atlas-SNP
SERPINA11	256394	hgsc.bcm.edu	37	14	94912799	94912799	+	Silent	SNP	G	G	A	rs12888805	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	160	166	0	0.987654	0	G|0.707;A|0.293	0.293	strong	SERPINA11,right_lower_lobe,carcinoma,-1,1	SERPINA11	53	1	NM_001080451	exon3	c.C786T	p.T262T	GAGGACGGTGCAA	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	rs75209396	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	185	81	188	0	0.437838	0	C|0.950;G|0.050	0.050	strong	.	DMBT1	677	.	NM_007329	exon4	c.C155G	p.S52W	TTCCCTCGGAGTC	.	PASS	Atlas-SNP
BTN2A1	11120	hgsc.bcm.edu	37	6	26458871	26458871	+	Missense_Mutation	SNP	T	T	C	rs146399224	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	6	101	0	0.0540541	0	T|0.999;C|0.001	0.001	weak	.	BTN2A1	118	.	NM_001197234	exon2	c.T7C	p.S3P	ATGGAATCAGCTG	.	PASS	Atlas-SNP
SIM1	6492	hgsc.bcm.edu	37	6	100868779	100868779	+	Missense_Mutation	SNP	G	G	T	rs3734354	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	17	127	1	0.193182	0.00787402	T|0.145;G|0.854;A|0.000	0.145	strong	SIM1,NS,carcinoma,+2,2	SIM1	173	2	NM_005068	exon9	c.C1054A	p.P352T	AGGCTGGTTTGGA	.	scavenged	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155219318	155219318	+	Missense_Mutation	SNP	C	C	T	rs28561984	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	77	187	0	0.461078	0	C|0.867;G|0.027;T|0.106	0.106	strong	.	DCHS2	594	.	NM_017639	exon18	c.G4783A	p.E1595K	GCGACTCGGGGGA	.	PASS	Atlas-SNP
GLE1	2733	hgsc.bcm.edu	37	9	131285955	131285955	+	Missense_Mutation	SNP	A	A	G	rs2275260	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	130	120	0	1	0	A|0.707;G|0.293	0.293	strong	.	GLE1	42	.	NM_001499	exon6	c.A727G	p.I243V	GGCCAGATCCGCC	.	PASS	Atlas-SNP
MGAT5B	146664	hgsc.bcm.edu	37	17	74942478	74942478	+	Silent	SNP	C	C	T	rs8067984	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	25	56	0	0.438596	0	C|0.639;T|0.361	0.361	strong	.	MGAT5B	98	.	NM_198955	exon14	c.C1896T	p.Y632Y	ACCCTACGAGTAC	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720851	135720851	+	Missense_Mutation	SNP	G	G	T	rs6779903	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	46	84	0	0.541176	0	G|0.660;T|0.340	0.340	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.G511T	p.A171S	GGGAACGCCCCAT	.	PASS	Atlas-SNP
TYSND1	219743	hgsc.bcm.edu	37	10	71905569	71905569	+	Silent	SNP	C	C	A	rs3750774	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	5	0	0	1	.	C|0.608;A|0.392	0.392	strong	.	TYSND1	20	.	NM_173555	exon1	c.G774T	p.L258L	GCCGGGCAGGCAG	.	PASS	Atlas-SNP
GGT1	2678	hgsc.bcm.edu	37	22	25023459	25023459	+	Missense_Mutation	SNP	G	G	C	rs138813205	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	266	29	203	3	0.109023	0.0147783	C|0.014;G|0.986	0.014	strong	GGT1,NS,carcinoma,0,1	GGT1	68	1	NM_013430	exon12	c.G1081C	p.D361H	TCTGACGACACCA	.	scavenged	Atlas-SNP
HOXA6	3203	hgsc.bcm.edu	37	7	27185520	27185520	+	Silent	SNP	G	G	A	rs17500863	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	28	77	0	0.4375	0	G|0.926;A|0.074	0.074	strong	.	HOXA6	25	.	NM_024014	exon2	c.C459T	p.S153S	CCCATGGCTCCCA	.	PASS	Atlas-SNP
GOT2	2806	hgsc.bcm.edu	37	16	58750604	58750604	+	Silent	SNP	G	G	A	rs1058192	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	42	66	0	0.976744	0	G|0.286;A|0.714	0.714	strong	GOT2,NS,carcinoma,0,1	GOT2	42	1	NM_002080	exon7	c.C816T	p.C272C	GCAGAGGCAAACA	.	PASS	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	37	17	48701800	48701800	+	Silent	SNP	C	C	T	rs2301835	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	268	132	267	1	0.492537	0.00374532	C|0.878;T|0.122	0.122	strong	.	CACNA1G	659	.	NM_018896	exon37	c.C6309T	p.L2103L	TCTGCTCCAGCCC	.	PASS	Atlas-SNP
ADNP2	22850	hgsc.bcm.edu	37	18	77895192	77895192	+	Silent	SNP	G	G	A	rs3744878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	32	64	0	0.426667	0	G|0.871;A|0.129	0.129	strong	.	ADNP2	102	.	NM_014913	exon4	c.G1896A	p.A632A	CCTTGCGACTGTC	.	PASS	Atlas-SNP
MYO1C	4641	hgsc.bcm.edu	37	17	1370542	1370542	+	Silent	SNP	C	C	A	rs2302458	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	31	48	0	0.469697	0	C|0.904;A|0.096	0.096	strong	.	MYO1C	57	.	NM_001080779	exon31	c.G3159T	p.L1053L	CACAGCCAGGTGC	.	PASS	Atlas-SNP
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10912719	10912719	+	Silent	SNP	G	G	A	rs72777388	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	41	75	0	0.383178	0	G|0.830;A|0.170	0.170	strong	.	ATP6V1C2	73	.	NM_001039362	exon8	c.G621A	p.V207V	CATGGTGGTCCCT	.	PASS	Atlas-SNP
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057634	46057634	+	Silent	SNP	T	T	C	rs61029972		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	84	142	0	0.57931	0	C|1.000;|0.000	1.000	weak	.	KRTAP10-10	37	.	NM_181688	exon1	c.T300C	p.C100C	CTGCTGTGTGCCC	.	PASS	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124138855	124138855	+	Silent	SNP	G	G	A	rs16898012	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	89	144	0	0.536145	0	G|0.705;A|0.295	0.295	strong	.	WDR67	97	.	NM_001145088	exon13	c.G1812A	p.L604L	CCTTCTGATGACT	.	PASS	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43338328	43338328	+	Silent	SNP	C	C	A	rs2839422	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	16	35	0	0.296296	0	C|0.943;A|0.057	0.057	strong	.	C2CD2	47	.	NM_015500	exon5	c.G606T	p.V202V	CTCAGCCACCTGG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8176569	8176569	+	Silent	SNP	G	G	A	rs35306870	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	63	107	0	0.422819	0	G|0.761;A|0.239	0.239	strong	FBN3,colon,carcinoma,0,1	FBN3	300	1	NM_032447	exon31	c.C4047T	p.C1349C	CTGGCGGCAGGTG	.	PASS	Atlas-SNP
DPCR1	135656	hgsc.bcm.edu	37	6	30919878	30919878	+	Missense_Mutation	SNP	G	G	C	rs11970154	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	37	64	0	0.5	0	G|0.816;C|0.184	0.184	strong	.	DPCR1	99	.	NM_080870	exon2	c.G3637C	p.G1213R	AACCTGGGGAACA	.	PASS	Atlas-SNP
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	44	118	0	0.435644	0	A|0.799;G|0.201	0.201	strong	MLH1,NS,carcinoma,0,1	MLH1	226	1	NM_000249	exon8	c.A655G	p.I219V	CGCTCCATCTTTG	.	PASS	Atlas-SNP
MSLN	10232	hgsc.bcm.edu	37	16	813650	813650	+	Silent	SNP	G	G	A	rs3765319	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	31	55	0	0.563636	0	A|0.146;G|0.854;T|0.000	0.146	strong	.	MSLN	109	.	NM_005823	exon5	c.G138A	p.A46A	GGCTGCGCCCCTG	.	PASS	Atlas-SNP
SERPINB13	5275	hgsc.bcm.edu	37	18	61264468	61264468	+	Silent	SNP	C	C	T	rs1020693	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	73	89	0	0.986486	0	C|0.229;T|0.771	0.771	strong	.	SERPINB13	51	.	NM_012397	exon8	c.C1047T	p.T349T	TGCCACCGGCATA	.	PASS	Atlas-SNP
PDGFRB	5159	hgsc.bcm.edu	37	5	149504348	149504348	+	Silent	SNP	C	C	T	rs56072663	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	24	42	0	0.436364	0	C|0.971;T|0.029	0.029	strong	PDGFRB,NS,carcinoma,0,2	PDGFRB	142	2	NM_002609	exon13	c.G1854A	p.T618T	ATGAGCCGTGGCC	.	PASS	Atlas-SNP
INHBC	3626	hgsc.bcm.edu	37	12	57843711	57843711	+	Missense_Mutation	SNP	G	G	A	rs2229357	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	30	43	0	0.576923	0	G|0.838;A|0.162	0.162	strong	.	INHBC	28	.	NM_005538	exon2	c.G965A	p.R322Q	CGGCCCGGCGCCC	.	PASS	Atlas-SNP
TNRC18	84629	hgsc.bcm.edu	37	7	5399044	5399044	+	Silent	SNP	C	C	G	rs12531309	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	64	123	0	0.48855	0	C|0.729;G|0.271	0.271	strong	.	TNRC18	311	.	NM_001080495	exon15	c.G4818C	p.S1606S	GAAGTCCGACGAG	.	PASS	Atlas-SNP
PHLDB3	653583	hgsc.bcm.edu	37	19	44001345	44001345	+	Silent	SNP	C	C	T	rs7257767	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	26	50	0	0.419355	0	C|0.843;T|0.157	0.157	strong	.	PHLDB3	30	.	NM_198850	exon6	c.G750A	p.E250E	CCGATCCTCCTCC	.	PASS	Atlas-SNP
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67243024	67243024	+	Missense_Mutation	SNP	C	C	A	rs2133173	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	142	54	136	0	0.380282	0	C|0.762;N|0.000	.	strong	.	TCTEX1D1	27	.	NM_152665	exon5	c.C427A	p.L143I	AGCATACTTATTG	.	PASS	Atlas-SNP
SBF1	6305	hgsc.bcm.edu	37	22	50898026	50898026	+	Silent	SNP	G	G	A	rs58335489	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	42	55	0	0.545455	0	G|0.848;A|0.152	0.152	strong	.	SBF1	211	.	NM_002972	exon27	c.C3561T	p.Y1187Y	CTGGCGGTAGCAG	.	PASS	Atlas-SNP
TRDMT1	1787	hgsc.bcm.edu	37	10	17210881	17210881	+	Silent	SNP	A	A	G	rs7096233	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	34	64	0	0.523077	0	A|0.879;G|0.121	0.121	strong	.	TRDMT1	46	.	NM_004412	exon3	c.T210C	p.F70F	CATATCAAAAGAT	.	PASS	Atlas-SNP
HSPA1B	3304	hgsc.bcm.edu	37	6	31797587	31797587	+	Silent	SNP	C	C	G	rs61730067	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	259	111	287	1	0.428571	0.00348432	C|0.554;G|0.446	0.446	strong	.	HSPA1B	5	.	NM_005346	exon1	c.C1860G	p.G620G	GCCTGGCGGCTTC	.	PASS	Atlas-SNP
HOXB1	3211	hgsc.bcm.edu	37	17	46607817	46607817	+	Silent	SNP	C	C	T	rs7207109	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	60	116	0	0.517241	0	C|0.838;T|0.162	0.162	strong	.	HOXB1	67	.	NM_002144	exon1	c.G450A	p.A150A	AAAGCTCGCGGTC	.	PASS	Atlas-SNP
TEK	7010	hgsc.bcm.edu	37	9	27202870	27202870	+	Silent	SNP	A	A	G	rs639225	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	80	205	0	0.40201	0	A|0.569;G|0.431	0.431	strong	TEK_ENST00000380036,colon,carcinoma,+1,1	TEK	250	1	NM_000459	exon13	c.A1962G	p.S654S	CTCCTCAGCTGTG	.	PASS	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62848568	62848568	+	Silent	SNP	C	C	G	rs11231342	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	41	90	0	0.44086	0	C|0.539;G|0.461	0.461	strong	.	SLC22A24	31	.	NM_001136506	exon9	c.G1422C	p.V474V	ACCGGACACTGCA	.	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-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	37	124	0	0.33945	0	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	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107671407	107671407	+	Missense_Mutation	SNP	C	C	G	rs2528693	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	66	100	0	0.485294	0	C|0.892;G|0.108	0.108	strong	.	LAMB4	253	.	NM_007356	exon32	c.G4836C	p.R1612S	CATTTCCCTGGTT	.	PASS	Atlas-SNP
IL18R1	8809	hgsc.bcm.edu	37	2	103001402	103001402	+	Silent	SNP	C	C	T	rs1035130	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	49	97	0	0.449541	0	C|0.765;T|0.235	0.235	strong	.	IL18R1	72	.	NM_003855	exon6	c.C753T	p.F251F	GATGTTCGGGGAA	.	PASS	Atlas-SNP
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520417	72520417	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	38	70	0	0.506667	0	.	.	none	ADAMTS14,rectum,carcinoma,+2,2	ADAMTS14	148	2	NM_139155	exon22	c.A3489G	p.P1163P	CTCCCCAGGGACC	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25009485	25009485	+	Missense_Mutation	SNP	C	C	G	rs41506549		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	106	104	0	0.990654	0	.	.	weak	.	PARP4	142	.	NM_006437	exon31	c.G3794C	p.G1265A	CCTAAGCCATCCT	.	PASS	Atlas-SNP
OXTR	5021	hgsc.bcm.edu	37	3	8809222	8809222	+	Missense_Mutation	SNP	C	C	T	rs4686302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	56	76	0	0.538462	0	C|0.878;T|0.122	0.122	strong	.	OXTR	31	.	NM_000916	exon3	c.G652A	p.A218T	AGCAGGCAGCGAG	.	PASS	Atlas-SNP
NEU4	129807	hgsc.bcm.edu	37	2	242757820	242757820	+	Missense_Mutation	SNP	G	G	A	rs11545301	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	41	0	1	0	G|0.725;A|0.275	0.275	strong	.	NEU4	39	.	NM_001167599	exon4	c.G940A	p.G314R	GGCCCCGGGAGTC	.	PASS	Atlas-SNP
BSPRY	54836	hgsc.bcm.edu	37	9	116122954	116122954	+	Silent	SNP	A	A	G	rs752757	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	72	85	0	1	0	G|0.353;C|0.000;N|0.000;A|0.647	0.353	strong	BSPRY,NS,carcinoma,0,2	BSPRY	21	2	NM_017688	exon3	c.A468G	p.K156K	GCAGAAACTTGAC	.	PASS	Atlas-SNP
METTL21C	196541	hgsc.bcm.edu	37	13	103346806	103346806	+	Missense_Mutation	SNP	C	C	G	rs2390760	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	17	22	0	1	0	C|0.324;G|0.676	0.676	strong	METTL21C,NS,adenoma,+1,1	METTL21C	23	1	NM_001010977	exon1	c.G43C	p.G15R	CTTCCCCCCGGCG	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	37	5	16769273	16769273	+	Missense_Mutation	SNP	G	G	A	rs11750538	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	44	65	0	0.53012	0	G|0.492;A|0.507	0.507	strong	.	MYO10	198	.	NM_012334	exon10	c.C970T	p.R324W	CTTCCCGAACTTC	.	PASS	Atlas-SNP
RNF19B	127544	hgsc.bcm.edu	37	1	33409693	33409693	+	Silent	SNP	G	G	A	rs194645	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	12	109	0	0.0827586	0	G|0.818;A|0.182	0.182	strong	.	RNF19B	43	.	NM_153341	exon6	c.C1332T	p.G444G	ACAGCCGCCTCCA	.	PASS	Atlas-SNP
LAMB4	22798	hgsc.bcm.edu	37	7	107720162	107720162	+	Missense_Mutation	SNP	C	C	A	rs9690688	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	33	47	0	0.515625	0	C|0.819;A|0.181	0.181	strong	LAMB4,NS,carcinoma,0,1	LAMB4	253	1	NM_007356	exon15	c.G1771T	p.V591F	ATGTAACAGGGTT	.	PASS	Atlas-SNP
SLC25A42	284439	hgsc.bcm.edu	37	19	19212658	19212658	+	Silent	SNP	G	G	A	rs56144126	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	35	44	0	0.625	0	G|0.937;A|0.063	0.063	strong	.	SLC25A42	18	.	NM_178526	exon3	c.G150A	p.A50A	AACAGCGGTAGCT	.	PASS	Atlas-SNP
SLC52A1	55065	hgsc.bcm.edu	37	17	4937575	4937575	+	Missense_Mutation	SNP	T	T	C	rs346822	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	54	39	0	1	0	T|0.058;C|0.942	0.942	strong	.	.	.	.	NM_017986	exon3	c.A209G	p.Q70R	GCCAGCTGCCTCC	.	PASS	Atlas-SNP
NME4	4833	hgsc.bcm.edu	37	16	449659	449659	+	Silent	SNP	G	G	A	rs14293	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	61	127	0	0.455224	0	G|0.557;A|0.443	0.443	strong	NME4,NS,carcinoma,0,1	NME4	9	1	NM_005009	exon4	c.G360A	p.S120S	CGCCTCGAGGGCC	.	PASS	Atlas-SNP
DYSF	8291	hgsc.bcm.edu	37	2	71780248	71780248	+	Silent	SNP	C	C	T	rs35721373	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	70	165	0	0.486111	0	C|0.967;T|0.033	0.033	strong	.	DYSF	536	.	NM_001130982	exon21	c.C1956T	p.Y652Y	GAACTACGGGAAC	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134682802	134682802	+	Missense_Mutation	SNP	C	C	T	rs7084629	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	40	34	0	0.606061	0	C|0.878;T|0.122	0.122	strong	.	TTC40	100	.	NM_001200049	exon33	c.G4586A	p.C1529Y	CTGACGCACACCT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155295076	155295076	+	Missense_Mutation	SNP	A	A	G	rs11721758	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	38	80	0	0.463415	0	A|0.641;G|0.359	0.359	strong	.	DCHS2	594	.	NM_017639	exon4	c.T458C	p.V153A	ACCTTCACCAGGG	.	PASS	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	37	3	38645420	38645420	+	Missense_Mutation	SNP	T	T	C	rs1805124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	156	161	0	1	0	T|0.790;C|0.210	0.210	strong	SCN5A_ENST00000413689,colon,carcinoma,0,3	SCN5A	634	3	NM_001160160	exon12	c.A1673G	p.H558R	GATGTGTGGTGGC	.	PASS	Atlas-SNP
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346712	140346712	+	Silent	SNP	T	T	C	rs155808	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	26	46	0	0.464286	0	T|0.675;C|0.325	0.325	strong	.	PCDHAC2	142	.	NM_031883	exon1	c.T361C	p.L121L	CTCAGCTTGGAAG	.	PASS	Atlas-SNP
IDH3A	3419	hgsc.bcm.edu	37	15	78441769	78441769	+	Silent	SNP	T	T	C	rs11555541	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	6	11	0	0.4	0	T|0.494;C|0.506	0.506	strong	.	IDH3A	24	.	NM_005530	exon1	c.T24C	p.S8S	GATCTCTAAGGTG	.	PASS	Atlas-SNP
WDR87	83889	hgsc.bcm.edu	37	19	38382328	38382328	+	Silent	SNP	C	C	T	rs953370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	94	88	0	1	0	C|0.366;T|0.634	0.634	strong	.	WDR87	191	.	NM_031951	exon5	c.G3141A	p.P1047P	AAAAGCCGGCTTT	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77765398	77765398	+	Missense_Mutation	SNP	A	A	G	rs16919452	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	74	155	0	0.506849	0	A|0.927;G|0.073	0.073	strong	.	ZFHX4	878	.	NM_024721	exon10	c.A6241G	p.I2081V	CCTTCCATTATGA	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629155	32629155	+	Silent	SNP	C	C	A	rs1130431	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	55	38	0	0.901639	0	C|0.805;A|0.195	0.195	strong	.	HLA-DQB1	15	.	NM_002123	exon4	c.G741T	p.L247L	AAGGCCCAGCCCA	.	PASS	Atlas-SNP
C11orf24	53838	hgsc.bcm.edu	37	11	68029738	68029738	+	Missense_Mutation	SNP	G	G	A	rs143548724	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	475	238	452	0	0.501053	0	G|0.998;A|0.002	0.002	strong	.	C11orf24	35	.	NM_022338	exon4	c.C725T	p.A242V	CTTGCCGCGGTGT	.	PASS	Atlas-SNP
LILRB1	10859	hgsc.bcm.edu	37	19	55143157	55143157	+	Missense_Mutation	SNP	G	G	A	rs12460501	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	231	115	240	0	0.497835	0	G|0.855;A|0.145	0.145	strong	.	LILRB1	140	.	NM_001081637	exon4	c.G277A	p.A93T	GAACATGCAGGGC	.	PASS	Atlas-SNP
HAPLN3	145864	hgsc.bcm.edu	37	15	89422286	89422286	+	Silent	SNP	C	C	T	rs3809574	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	17	16	0	0.68	0	C|0.791;T|0.209	0.209	strong	HAPLN3,NS,lymphoid_neoplasm,0,1	HAPLN3	43	1	NM_178232	exon4	c.G708A	p.P236P	CAGGCCCGGGCCA	.	PASS	Atlas-SNP
CHMP4A	29082	hgsc.bcm.edu	37	14	24679877	24679877	+	Missense_Mutation	SNP	C	C	T	rs2295322	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	135	138	0	0.985401	0	C|0.594;T|0.406	0.406	strong	.	CHMP4A	20	.	NM_014169	exon4	c.G586A	p.G196R	CATCTCCAAAGCC	.	PASS	Atlas-SNP
FBXO41	150726	hgsc.bcm.edu	37	2	73491514	73491514	+	Silent	SNP	C	C	T	rs61735876	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	76	196	0	0.439306	0	C|0.950;T|0.050	0.050	strong	.	FBXO41	82	.	NM_001080410	exon5	c.G1698A	p.T566T	TGTGCGCGTGTCC	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113191533	113191533	+	Silent	SNP	C	C	T	rs75212846	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	24	48	0	0.533333	0	C|0.963;T|0.037	0.037	strong	.	SVEP1	326	.	NM_153366	exon35	c.G5697A	p.V1899V	TTCACACACAGGA	.	PASS	Atlas-SNP
FMO2	2327	hgsc.bcm.edu	37	1	171174531	171174531	+	Missense_Mutation	SNP	A	A	G	rs2020863	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	39	93	0	0.428571	0	A|0.884;G|0.116	0.116	strong	FMO2,NS,carcinoma,0,1	FMO2	66	1	NM_001460	exon7	c.A941G	p.E314G	TCTTTGAGGATGG	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	13368	13368	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	9	2	0	1	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.G1032A	p.G344G	CTCCGGGTCCATC	.	PASS	Atlas-SNP
ATP2C2	9914	hgsc.bcm.edu	37	16	84476200	84476200	+	Missense_Mutation	SNP	A	A	T	rs247897	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	67	113	0	0.598214	0	A|0.597;T|0.403	0.403	strong	.	ATP2C2	75	.	NM_014861	exon15	c.A1396T	p.M466L	CTGGCGATGAAGG	.	PASS	Atlas-SNP
ZNF517	340385	hgsc.bcm.edu	37	8	146032842	146032842	+	Missense_Mutation	SNP	G	G	A	rs62531506	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	18	44	0	0.339623	0	G|0.922;A|0.078	0.078	strong	.	ZNF517	30	.	NM_213605	exon5	c.G541A	p.V181M	AGGTGCGTGTGCG	.	PASS	Atlas-SNP
OR2J2	26707	hgsc.bcm.edu	37	6	29141849	29141849	+	Missense_Mutation	SNP	T	T	C	rs3116856	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	367	180	334	1	0.490463	0.00299401	T|0.566;C|0.434	0.434	strong	.	OR2J2	51	.	NM_030905	exon1	c.T437C	p.V146A	TGTTGGTTGCGGC	.	PASS	Atlas-SNP
IFITM5	387733	hgsc.bcm.edu	37	11	299411	299411	+	Missense_Mutation	SNP	C	C	G	rs57285449	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	50	72	0	0.471698	0	C|0.546;G|0.454	0.454	strong	.	IFITM5	12	.	NM_001025295	exon1	c.G80C	p.G27A	GGGGCCCCCAGTG	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	131817850	131817850	+	Silent	SNP	T	T	C	rs75848889	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	60	140	0	0.444444	0	T|0.898;C|0.102	0.102	strong	.	PLXNA4	873	.	NM_020911	exon31	c.A5547G	p.A1849A	TGAGAGTGCACTC	.	PASS	Atlas-SNP
ANKRD18A	253650	hgsc.bcm.edu	37	9	38588602	38588602	+	Missense_Mutation	SNP	T	T	C	rs2799163	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	201	93	200	0	0.462687	0	T|0.588;C|0.412	0.412	strong	ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	NM_147195	exon11	c.A2063G	p.Y688C	GCAGTATAGTTCA	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168106246	168106246	+	Missense_Mutation	SNP	G	G	A	rs16853330	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	64	133	0	0.484848	0	G|0.774;A|0.225	0.225	strong	XIRP2,NS,carcinoma,-1,1	XIRP2	914	1	NM_152381	exon9	c.G8344A	p.V2782I	GTGACAGTACAAT	.	PASS	Atlas-SNP
MICB	4277	hgsc.bcm.edu	37	6	31474000	31474000	+	Missense_Mutation	SNP	G	G	A	rs1051788	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	82	145	0	0.43617	0	A|0.285;G|0.715	0.285	strong	.	MICB	26	.	NM_005931	exon3	c.G406A	p.D136N	TACTACGATGGGG	.	PASS	Atlas-SNP
FBN3	84467	hgsc.bcm.edu	37	19	8138054	8138054	+	Missense_Mutation	SNP	C	C	A	rs7257948	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	157	128	0	0.993671	0	C|0.380;A|0.620	0.620	strong	FBN3,colon,carcinoma,0,1	FBN3	300	1	NM_032447	exon61	c.G7830T	p.E2610D	ATCCACCTCCTGG	.	PASS	Atlas-SNP
F13A1	2162	hgsc.bcm.edu	37	6	6174856	6174856	+	Silent	SNP	T	T	C	rs5986	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	289	118	270	0	0.408305	0	T|0.924;C|0.076	0.076	strong	F13A1,NS,NS,0,1	F13A1	135	1	NM_000129	exon12	c.A1704G	p.E568E	CTTGAATTCTGCC	.	PASS	Atlas-SNP
CARS2	79587	hgsc.bcm.edu	37	13	111335406	111335406	+	Missense_Mutation	SNP	C	C	T	rs146773721	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	6	47	0	0.285714	0	C|0.987;T|0.013	0.013	strong	.	CARS2	37	.	NM_024537	exon6	c.G647A	p.G216E	GGCTCTCCGACTG	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195505822	195505822	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	8	165	1	0.0522876	0.00606061	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C12629A	p.P4210H	GTGACAGGAAGAG	.	scavenged	Atlas-SNP
TUBAL3	79861	hgsc.bcm.edu	37	10	5437365	5437365	+	Silent	SNP	A	A	G	rs11253156	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	36	67	0	0.455696	0	A|0.247;G|0.753	0.753	strong	.	TUBAL3	54	.	NM_024803	exon3	c.T321C	p.A107A	ATTGTTAGCAGCA	.	PASS	Atlas-SNP
DSG3	1830	hgsc.bcm.edu	37	18	29046606	29046606	+	Missense_Mutation	SNP	G	G	A	rs16961975	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	46	84	0	0.613333	0	G|0.975;A|0.025	0.025	strong	.	DSG3	172	.	NM_001944	exon11	c.G1525A	p.V509M	CCTTCCGTGGTTG	.	PASS	Atlas-SNP
ZP2	7783	hgsc.bcm.edu	37	16	21215672	21215672	+	Silent	SNP	A	A	G	rs2075526	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	59	115	0	0.433824	0	A|0.721;G|0.279	0.279	strong	.	ZP2	92	.	NM_003460	exon8	c.T747C	p.P249P	CTGTCCAGGAGAT	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856852	144856852	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	57	237	2	0.313187	0.00843882	.	.	none	PDE4DIP_ENST00000369356,NS,carcinoma,-1,3	PDE4DIP	817	3	NM_014644	exon40	c.G6633A	p.A2211A	GCTGCACGCTGAT	.	scavenged	Atlas-SNP
SDC3	9672	hgsc.bcm.edu	37	1	31351513	31351513	+	Silent	SNP	G	G	A	rs1891419	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	125	101	0	1	0	G|0.818;A|0.182	0.182	strong	.	SDC3	45	.	NM_014654	exon2	c.C213T	p.P71P	ATCATCGGGAAAG	.	PASS	Atlas-SNP
PLRG1	5356	hgsc.bcm.edu	37	4	155461113	155461113	+	Silent	SNP	T	T	C	rs7671792	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	41	99	0	0.418367	0	T|0.738;C|0.262	0.262	strong	.	PLRG1	43	.	NM_002669	exon11	c.A1032G	p.Q344Q	AATAATTTGTGGT	.	PASS	Atlas-SNP
KIF13A	63971	hgsc.bcm.edu	37	6	17764731	17764731	+	Silent	SNP	G	G	C	rs6459569	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	78	132	0	0.461538	0	G|0.857;C|0.143	0.143	strong	.	KIF13A	276	.	NM_022113	exon39	c.C5028G	p.A1676A	CCCTTTGGCTAAG	.	PASS	Atlas-SNP
CMAS	55907	hgsc.bcm.edu	37	12	22213786	22213786	+	Silent	SNP	C	C	T	rs10841930	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	13	51	0	0.433333	0	C|0.831;G|0.000;T|0.169	0.169	strong	.	CMAS	45	.	NM_018686	exon5	c.C714T	p.Y238Y	ATACTACGAAATG	.	PASS	Atlas-SNP
ETHE1	23474	hgsc.bcm.edu	37	19	44031324	44031324	+	Silent	SNP	C	C	T	rs3810381	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	6	6	0	0	1	.	C|0.835;T|0.165	0.165	strong	.	ETHE1	7	.	NM_014297	exon1	c.G6A	p.A2A	AGCCTCCGCCATC	.	PASS	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	37	1	201286771	201286771	+	Silent	SNP	C	C	T	rs1722779	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	102	190	0	0.534031	0	T|0.178;C|0.822;A|0.000	0.178	strong	.	PKP1	127	.	NM_001005337	exon5	c.C918T	p.A306A	GCAGGCCGCGGCA	.	PASS	Atlas-SNP
MARCH4	57574	hgsc.bcm.edu	37	2	217148417	217148417	+	Silent	SNP	C	C	A	rs876771	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	40	106	0	0.47619	0	C|0.576;A|0.424	0.424	strong	.	MARCH4	50	.	NM_020814	exon2	c.G552T	p.S184S	CTTGACCGAGCCA	.	PASS	Atlas-SNP
ASB18	401036	hgsc.bcm.edu	37	2	237103548	237103548	+	Silent	SNP	G	G	A	rs10177825	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	52	102	0	0.42623	0	G|0.807;A|0.193	0.193	strong	.	ASB18	34	.	NM_212556	exon6	c.C1368T	p.Y456Y	AAGTAGGTAATTC	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	37	19	9086318	9086318	+	Missense_Mutation	SNP	G	G	A	rs4520945	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	76	162	0	0.520548	0	G|0.812;A|0.188	0.188	strong	.	MUC16	4315	.	NM_024690	exon1	c.C5497T	p.L1833F	GAGTGAGAGAAAT	.	PASS	Atlas-SNP
SP100	6672	hgsc.bcm.edu	37	2	231379967	231379967	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	36	81	0	0.461538	0	.	.	none	.	SP100	167	.	NM_003113	exon25	c.C2252T	p.T751I	TGAAAACCTATAT	.	PASS	Atlas-SNP
NCR1	9437	hgsc.bcm.edu	37	19	55420801	55420801	+	Silent	SNP	C	C	A	rs3765013	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	31	33	0	0.96875	0	C|0.604;A|0.396	0.396	strong	.	NCR1	60	.	NM_001145458	exon4	c.C553A	p.R185R	GCCCACCGAGGGA	.	PASS	Atlas-SNP
IP6K3	117283	hgsc.bcm.edu	37	6	33703089	33703089	+	Silent	SNP	C	C	T	rs623813	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	27	83	0	0.287234	0	C|0.889;T|0.111	0.111	strong	.	IP6K3	52	.	NM_001142883	exon3	c.G165A	p.P55P	GGCCAGCGGCAGG	.	PASS	Atlas-SNP
KIAA1755	85449	hgsc.bcm.edu	37	20	36841914	36841914	+	Missense_Mutation	SNP	G	G	A	rs3746471	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	54	0	1	0	G|0.644;A|0.356	0.356	strong	.	KIAA1755	145	.	NM_001029864	exon14	c.C3133T	p.R1045W	GCATCCGGATCTC	.	PASS	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100087345	100087345	+	Silent	SNP	A	A	G	rs3747496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	30	78	0	0.434783	0	A|0.437;G|0.563	0.563	strong	KIAA1529,NS,carcinoma,0,1	.	.	1	NM_020893	exon14	c.A1548G	p.S516S	GAGTTCACACCTC	.	PASS	Atlas-SNP
TTC29	83894	hgsc.bcm.edu	37	4	147830297	147830297	+	Missense_Mutation	SNP	A	A	G	rs35123039	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	39	90	0	0.46988	0	A|0.972;G|0.028	0.028	strong	.	TTC29	63	.	NM_031956	exon5	c.T281C	p.L94P	TCCCTCAGGGCAT	.	PASS	Atlas-SNP
RNF31	55072	hgsc.bcm.edu	37	14	24620710	24620710	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	37	88	0	0.45679	0	.	.	none	RNF31,NS,carcinoma,0,1	RNF31	95	1	NM_017999	exon10	c.C1754G	p.S585C	TCCAGTCTCTAGG	.	PASS	Atlas-SNP
PIGK	10026	hgsc.bcm.edu	37	1	77685042	77685042	+	Missense_Mutation	SNP	T	T	C	rs12723684	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	53	114	0	0.417323	0	T|0.821;C|0.179	0.179	strong	.	PIGK	46	.	NM_005482	exon1	c.A46G	p.T16A	ACACAGTTGCCAA	.	PASS	Atlas-SNP
PDE11A	50940	hgsc.bcm.edu	37	2	178682603	178682603	+	Silent	SNP	T	T	C	rs6720891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	26	100	0	0.40625	0	T|0.578;C|0.422	0.422	strong	.	PDE11A	283	.	NM_016953	exon8	c.A1626G	p.A542A	TTGATCTGCATCA	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737454	248737454	+	Missense_Mutation	SNP	A	A	G	rs79750523	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	460	132	350	0	0.286957	0	A|0.848;G|0.152	0.152	strong	.	OR2T34	72	.	NM_001001821	exon1	c.T605C	p.M202T	GTGAGCATCTTAT	.	PASS	Atlas-SNP
OTUD7B	56957	hgsc.bcm.edu	37	1	149916118	149916118	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	34	38	0	0.523077	0	.	.	none	.	OTUD7B	76	.	NM_020205	exon12	c.C2170G	p.L724V	GTGGTAGGCCCCC	.	PASS	Atlas-SNP
LIPH	200879	hgsc.bcm.edu	37	3	185236964	185236964	+	Silent	SNP	G	G	A	rs144288709	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	38	93	0	0.431818	0	G|0.971;A|0.029	0.029	strong	.	LIPH	56	.	NM_139248	exon6	c.C852T	p.C284C	CGTGCCGCAGCTG	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158528254	158528254	+	Silent	SNP	G	G	A	rs34974906	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	32	92	0	0.438356	0	G|0.884;A|0.116	0.116	strong	ESYT2,NS,malignant_melanoma,0,3	ESYT2	70	3	NM_020728	exon20	c.C2526T	p.L842L	AACGTCGAGCGTT	.	PASS	Atlas-SNP
MYT1L	23040	hgsc.bcm.edu	37	2	1926617	1926617	+	Silent	SNP	G	G	A	rs2241686	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	236	113	256	0	0.478814	0	G|0.979;A|0.021	0.021	strong	.	MYT1L	241	.	NM_015025	exon10	c.C924T	p.N308N	GAGTCCGTTGTTC	.	PASS	Atlas-SNP
AKAP11	11215	hgsc.bcm.edu	37	13	42876103	42876103	+	Missense_Mutation	SNP	C	C	T	rs61756566	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	40	86	0	0.512821	0	C|0.988;T|0.012	0.012	strong	AKAP11,NS,carcinoma,0,1	AKAP11	146	1	NM_016248	exon8	c.C3221T	p.S1074F	TCTCATCTACAGC	.	PASS	Atlas-SNP
MRC1	4360	hgsc.bcm.edu	37	10	17875762	17875762	+	Silent	SNP	G	G	A	rs2985837	bycluster;bysubmitter	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	4	185	1	0.05	0.00540541	G|0.750;A|0.250	0.250	weak	MRC1L1,rectum,carcinoma,0,2	MRC1	13	2	NM_002438	exon4	c.G726A	p.Q242Q	GCACCAGGCGAGG	.	scavenged	Atlas-SNP
FGFRL1	53834	hgsc.bcm.edu	37	4	1006333	1006333	+	Silent	SNP	G	G	A	rs4647942	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	7	7	1	0	1	0	G|0.475;A|0.525	0.525	strong	.	FGFRL1	77	.	NM_001004356	exon2	c.G60A	p.P20P	CTTCCCGCCGGCC	.	PASS	Atlas-SNP
CLIP2	7461	hgsc.bcm.edu	37	7	73731906	73731906	+	Silent	SNP	C	C	T	rs148561130	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	34	63	0	0.43038	0	C|0.968;T|0.032	0.032	strong	.	CLIP2	134	.	NM_032421	exon2	c.C30T	p.P10P	GCCCCCCGGCCGT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228471379	228471379	+	Silent	SNP	G	G	C	rs56168609	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	69	155	0	0.448052	0	G|0.721;C|0.279	0.279	strong	OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	NM_001271223	exon38	c.G10200C	p.R3400R	CCTGCGGCTCACC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509212	195509212	+	Missense_Mutation	SNP	G	G	A	rs200749420	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	38	217	0	0.277372	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.C9239T	p.S3080L	GATGCTGAGGAAG	.	PASS	Atlas-SNP
FERMT1	55612	hgsc.bcm.edu	37	20	6069723	6069723	+	Silent	SNP	G	G	A	rs35413391	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	20	52	0	0.333333	0	G|0.949;A|0.051	0.051	strong	.	FERMT1	106	.	NM_017671	exon10	c.C1153T	p.L385L	TTGGTAGTAACTT	.	PASS	Atlas-SNP
MAST2	23139	hgsc.bcm.edu	37	1	46500613	46500613	+	Silent	SNP	T	T	C	rs17855317	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	82	139	1	0.493976	0.00719424	A|0.000;C|0.179;T|0.821	0.179	strong	MAST2_ENST00000361297,NS,carcinoma,0,1	MAST2	136	1	NM_015112	exon29	c.T4272C	p.T1424T	AGCCACTTCTCGC	.	scavenged	Atlas-SNP
ANKRD30B	374860	hgsc.bcm.edu	37	18	14779969	14779969	+	Missense_Mutation	SNP	C	C	G	rs9675365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	100	98	0	0.934579	0	C|0.546;G|0.454	0.454	strong	ANKRD30B_ENST00000358984,NS,carcinoma,0,2	ANKRD30B	237	2	NM_001145029	exon11	c.C1431G	p.F477L	GATGTTCCCATCA	.	PASS	Atlas-SNP
CPNE6	9362	hgsc.bcm.edu	37	14	24543808	24543808	+	Silent	SNP	G	G	C	rs2070343	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	82	0	1	0	G|0.789;C|0.211	0.211	strong	.	CPNE6	40	.	NM_006032	exon6	c.G567C	p.L189L	TCAGCTGGTCTGG	.	PASS	Atlas-SNP
UGGT1	56886	hgsc.bcm.edu	37	2	128939817	128939817	+	Silent	SNP	G	G	A	rs1699	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	151	140	1	1	0.00714286	G|0.589;A|0.411	0.411	strong	.	UGGT1	126	.	NM_020120	exon37	c.G4197A	p.K1399K	CTGGAAGTCAGGG	.	PASS	Atlas-SNP
SMCR9	140776	hgsc.bcm.edu	37	17	17326605	17326605	+	Silent	SNP	A	A	G	rs7225831	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	21	18	0	1	0	A|0.600;G|0.400	0.400	strong	.	.	.	.	NM_001243312	exon3	c.A420G	p.A140A	TGGGGCAAATGCC	.	PASS	Atlas-SNP
MMRN1	22915	hgsc.bcm.edu	37	4	90816294	90816294	+	Missense_Mutation	SNP	A	A	G	rs1442138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	19	57	0	0.463415	0	A|0.914;G|0.086	0.086	strong	.	MMRN1	174	.	NM_007351	exon1	c.A172G	p.T58A	CCAACCACTCGGG	.	PASS	Atlas-SNP
TCEB2	6923	hgsc.bcm.edu	37	16	2821525	2821525	+	Missense_Mutation	SNP	G	G	A	rs4036	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	75	135	0	0.496689	0	G|0.812;A|0.188	0.188	strong	.	TCEB2	6	.	NM_207013	exon5	c.C434T	p.T145M	TCCCTCGTTGAAC	.	PASS	Atlas-SNP
COMP	1311	hgsc.bcm.edu	37	19	18895865	18895865	+	Silent	SNP	C	C	T	rs34467947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	58	83	0	0.5	0	C|0.952;T|0.048	0.048	strong	.	COMP	62	.	NM_000095	exon16	c.G1755A	p.T585T	ATGGAACGTGCCC	.	PASS	Atlas-SNP
CLUAP1	23059	hgsc.bcm.edu	37	16	3554799	3554799	+	Silent	SNP	T	T	C	rs34672214	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	203	91	218	0	0.448276	0	T|0.955;C|0.045	0.045	strong	.	CLUAP1	32	.	NM_015041	exon2	c.T102C	p.L34L	TGGACTTGTATCT	.	PASS	Atlas-SNP
KIF25	3834	hgsc.bcm.edu	37	6	168442687	168442687	+	Missense_Mutation	SNP	A	A	C	rs12197062	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	23	264	0	0.154362	0	A|0.910;C|0.090	0.090	strong	.	KIF25	75	.	NM_030615	exon7	c.A685C	p.T229P	GAGCAAACAGAGG	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558315	140558315	+	Missense_Mutation	SNP	G	G	C	rs17844488		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	205	48	977	1	0.234146	0.00102354	.	.	weak	.	PCDHB8	199	.	NM_019120	exon1	c.G700C	p.V234L	GAAGTTGTCGATG	.	PASS	Atlas-SNP
APOB	338	hgsc.bcm.edu	37	2	21232195	21232195	+	Silent	SNP	G	G	A	rs693	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	153	162	1	1	0.00617284	G|0.665;N|0.000	.	strong	.	APOB	761	.	NM_000384	exon26	c.C7545T	p.T2515T	TTCTAGGGTCTCT	.	PASS	Atlas-SNP
SALL2	6297	hgsc.bcm.edu	37	14	21991626	21991626	+	Missense_Mutation	SNP	C	C	G	rs1263810	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	41	72	0	0.460674	0	C|0.711;G|0.289	0.289	strong	.	SALL2	95	.	NM_005407	exon2	c.G2236C	p.G746R	AACTCCCTGCCCC	.	PASS	Atlas-SNP
ZFYVE26	23503	hgsc.bcm.edu	37	14	68229051	68229051	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	45	89	0	0.428571	0	.	.	none	.	ZFYVE26	223	.	NM_015346	exon34	c.A6238G	p.T2080A	CAGCAGTGAGGTT	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47773103	47773103	+	Silent	SNP	C	C	A	rs2249057	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	34	87	0	0.472222	0	C|0.694;A|0.306	0.306	strong	PCNT,NS,carcinoma,0,1	PCNT	283	1	NM_006031	exon10	c.C1542A	p.S514S	TGAGTCCGAACTG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118629599	118629599	+	Silent	SNP	G	G	A	rs12142616	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	46	95	0	0.469388	0	G|0.923;A|0.077	0.077	strong	.	SPAG17	263	.	NM_206996	exon11	c.C1392T	p.P464P	CAGACTGGGTGGG	.	PASS	Atlas-SNP
PIK3AP1	118788	hgsc.bcm.edu	37	10	98369563	98369563	+	Silent	SNP	T	T	C	rs141067860	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	59	119	0	0.409722	0	T|0.999;C|0.001	0.001	strong	.	PIK3AP1	111	.	NM_152309	exon14	c.A2076G	p.G692G	ATAGACTCCAAAC	.	PASS	Atlas-SNP
OR11H6	122748	hgsc.bcm.edu	37	14	20692291	20692291	+	Silent	SNP	C	C	T	rs34693535	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	49	135	0	0.462264	0	C|0.533;T|0.467	0.467	strong	.	OR11H6	60	.	NM_001004480	exon1	c.C423T	p.Y141Y	TCGGTACCTGGCC	.	PASS	Atlas-SNP
CRIP3	401262	hgsc.bcm.edu	37	6	43273604	43273604	+	Missense_Mutation	SNP	A	A	G	rs2242416	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	43	121	0	0.40566	0	G|0.469;N|0.000	0.469	strong	.	CRIP3	30	.	NM_206922	exon8	c.T563C	p.I188T	TCGCCAATGTTCA	.	PASS	Atlas-SNP
NPR3	4883	hgsc.bcm.edu	37	5	32786389	32786389	+	Missense_Mutation	SNP	A	A	G	rs2270915	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	100	174	0	0.50505	0	A|0.833;G|0.167	0.167	strong	.	NPR3	65	.	NM_001204375	exon8	c.A1564G	p.N522D	GAAAGTAACCTTG	.	PASS	Atlas-SNP
HCFC1R1	54985	hgsc.bcm.edu	37	16	3073240	3073240	+	Missense_Mutation	SNP	G	G	T	rs10508	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	33	89	0	0.55	0	G|0.817;T|0.183	0.183	strong	HCFC1R1_ENST00000248089,NS,carcinoma,0,2	HCFC1R1	17	2	NM_017885	exon3	c.C275A	p.P92Q	CTGAGTGGGGGCA	.	PASS	Atlas-SNP
OR5AP2	338675	hgsc.bcm.edu	37	11	56409010	56409010	+	Missense_Mutation	SNP	A	A	T	rs61747872	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	94	0	0.5	0	A|0.960;T|0.040	0.040	strong	.	OR5AP2	69	.	NM_001002925	exon1	c.T906A	p.D302E	TTTTACATCCTTA	.	PASS	Atlas-SNP
C18orf54	162681	hgsc.bcm.edu	37	18	51888169	51888169	+	Missense_Mutation	SNP	G	G	C	rs1657907	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	184	77	181	0	0.418478	0	A|0.000;C|0.067;G|0.933	0.067	strong	.	C18orf54	40	.	NM_173529	exon3	c.G440C	p.R147P	GTCACCGAACGAG	.	PASS	Atlas-SNP
UEVLD	55293	hgsc.bcm.edu	37	11	18555901	18555901	+	Silent	SNP	C	C	G	rs56151250	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	12	46	0	0.387097	0	C|0.794;G|0.206	0.206	strong	.	UEVLD	58	.	NM_001040697	exon11	c.G1224C	p.V408V	AGAATGCACTTTC	.	PASS	Atlas-SNP
S1PR5	53637	hgsc.bcm.edu	37	19	10624863	10624863	+	Silent	SNP	C	C	T	rs75861469	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	56	31	46	0	0.553571	0	C|0.981;T|0.019	0.019	strong	.	S1PR5	33	.	NM_030760	exon2	c.G825A	p.V275V	GCACGCCACGTCG	.	PASS	Atlas-SNP
DAGLB	221955	hgsc.bcm.edu	37	7	6456302	6456302	+	Silent	SNP	C	C	T	rs2288152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	53	53	0	0.602273	0	C|0.922;T|0.078	0.078	strong	.	DAGLB	74	.	NM_139179	exon11	c.G1383A	p.P461P	GACCTGCGGGTAG	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73677833	73677833	+	Silent	SNP	A	A	G	rs6546836	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	68	110	0	0.503704	0	A|0.737;G|0.263	0.263	strong	ALMS1,colon,carcinoma,0,1	ALMS1	384	1	NM_015120	exon8	c.A4176G	p.Q1392Q	CTACCAACAGTCG	.	PASS	Atlas-SNP
IGHMBP2	3508	hgsc.bcm.edu	37	11	68703959	68703959	+	Missense_Mutation	SNP	A	A	G	rs622082	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	32	71	0	0.52459	0	A|0.767;G|0.233	0.233	strong	.	IGHMBP2	83	.	NM_002180	exon13	c.A2011G	p.T671A	CCTGCTACGTCCA	.	PASS	Atlas-SNP
PCDHB8	56128	hgsc.bcm.edu	37	5	140558308	140558308	+	Silent	SNP	T	T	C	rs2910316	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	46	1000	1	0.214953	0.001	T|0.831;C|0.169	0.169	strong	.	PCDHB8	199	.	NM_019120	exon1	c.T693C	p.I231I	CTACATTGAAGTT	.	PASS	Atlas-SNP
IFNL2	282616	hgsc.bcm.edu	37	19	39760191	39760191	+	Missense_Mutation	SNP	A	A	G	rs8103362	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	69	160	0	0.479167	0	A|0.795;G|0.205	0.205	strong	.	.	.	.	NM_172138	exon4	c.A334G	p.T112A	GAGGCCACCGCTG	.	PASS	Atlas-SNP
TAF7L	54457	hgsc.bcm.edu	37	X	100547806	100547806	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	44	53	0	0.956522	0	.	.	none	.	TAF7L	64	.	NM_024885	exon1	c.G228T	p.Q76H	TGGGGCCTGGGCA	.	PASS	Atlas-SNP
NME8	51314	hgsc.bcm.edu	37	7	37934146	37934146	+	Missense_Mutation	SNP	T	T	C	rs56128139	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	226	226	182	0	1	0	T|0.761;C|0.239	0.239	strong	.	.	.	.	NM_016616	exon16	c.T1478C	p.I493T	AGCAAATAGAGAA	.	PASS	Atlas-SNP
RBMX	27316	hgsc.bcm.edu	37	X	135958696	135958696	+	Silent	SNP	T	T	C	rs112800567	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	340	41	259	0	0.120588	0	.	.	weak	.	RBMX	149	.	NM_002139	exon5	c.A507G	p.G169G	AACTGGTCCTGAA	.	PASS	Atlas-SNP
MEFV	4210	hgsc.bcm.edu	37	16	3297073	3297073	+	Silent	SNP	A	A	G	rs224206	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	61	139	0	0.488	0	A|0.391;G|0.609	0.609	strong	.	MEFV	170	.	NM_000243	exon5	c.T1530C	p.D510D	CAGCGCATCGAGC	.	PASS	Atlas-SNP
CCDC157	550631	hgsc.bcm.edu	37	22	30765502	30765502	+	Silent	SNP	G	G	A	rs5749080	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	80	64	0	0.987654	0	A|0.198;C|0.000;G|0.802	0.198	strong	.	CCDC157	86	.	NM_001017437	exon4	c.G330A	p.A110A	GGCTGCGGGGCCC	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15095675	15095675	+	Silent	SNP	C	C	A	rs9921162	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	91	141	1	0.514124	0.0070922	C|0.773;A|0.227	0.227	strong	PDXDC1,NS,carcinoma,0,1	PDXDC1	59	1	NM_015027	exon4	c.C204A	p.L68L	GAATCTCATGCAT	.	scavenged	Atlas-SNP
SCN1A	6323	hgsc.bcm.edu	37	2	166897864	166897864	+	Silent	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	109	116	0	0.981982	0	.	.	none	SCN1A,rectum,carcinoma,-1,1	SCN1A	641	1	NM_001165963	exon13	c.T2292C	p.V764V	CATCACAACCAGG	.	PASS	Atlas-SNP
WSB2	55884	hgsc.bcm.edu	37	12	118481134	118481134	+	Silent	SNP	C	C	T	rs199804263	by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	2	94	0	0.0188679	0	C|1.000;T|0.000	0.000	strong	WSB2,colon,carcinoma,0,1	WSB2	32	1	NM_018639	exon3	c.G231A	p.T77T	CCCTTTCGTCTCA	.	scavenged	Atlas-SNP
MRPL45	84311	hgsc.bcm.edu	37	17	36453208	36453208	+	Missense_Mutation	SNP	T	T	C	rs149988943	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	89	67	3	0.988889	0.0447761	T|0.781;C|0.219	0.219	strong	MRPL45,NS,carcinoma,0,1	MRPL45	27	1	NM_032351	exon1	c.T59C	p.F20S	GGTGGTTTCGGCA	.	scavenged	Atlas-SNP
LRRN1	57633	hgsc.bcm.edu	37	3	3886721	3886721	+	Silent	SNP	C	C	A	rs3749350	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	47	131	0	0.435185	0	C|0.758;A|0.242	0.242	strong	.	LRRN1	82	.	NM_020873	exon2	c.C396A	p.T132T	GATTACCGAGATG	.	PASS	Atlas-SNP
TP73	7161	hgsc.bcm.edu	37	1	3645894	3645894	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	3	83	0	0.027027	0	.	.	none	TP73,NS,carcinoma,0,1	TP73	54	1	NM_005427	exon10	c.C1078T	p.R360X	CAGGTGCGAGGCC	.	scavenged	Atlas-SNP
ICK	22858	hgsc.bcm.edu	37	6	52878637	52878637	+	Silent	SNP	T	T	C	rs2297211	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	188	184	2	0.930693	0.0108696	T|0.711;C|0.289	0.289	strong	ICK,NS,carcinoma,0,1	ICK	62	1	NM_016513	exon10	c.A975G	p.P325P	GGCTGGTGGCTGG	.	scavenged	Atlas-SNP
SEC16B	89866	hgsc.bcm.edu	37	1	177902388	177902388	+	Silent	SNP	G	G	A	rs3813647	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	34	61	0	0.330097	0	G|0.878;A|0.122	0.122	strong	.	SEC16B	92	.	NM_033127	exon22	c.C2784T	p.P928P	TCCAGCGGGGGAT	.	PASS	Atlas-SNP
HSPB8	26353	hgsc.bcm.edu	37	12	119617350	119617350	+	Missense_Mutation	SNP	G	G	T	rs55826713	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	22	25	0	0.52381	0	G|0.999;T|0.001	0.001	strong	.	HSPB8	45	.	NM_014365	exon1	c.G233T	p.R78M	CCGCCAGGTTTGG	.	PASS	Atlas-SNP
ABCC6	368	hgsc.bcm.edu	37	16	16263662	16263662	+	Missense_Mutation	SNP	G	G	T	rs61340537	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	41	113	0	0.41	0	G|0.989;T|0.011	0.011	strong	.	ABCC6	110	.	NM_001171	exon22	c.C2836A	p.L946I	GGCAGAGGGGGGT	.	PASS	Atlas-SNP
UST	10090	hgsc.bcm.edu	37	6	149395197	149395197	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	14	126	0	0.162791	0	.	.	none	UST,right_upper_lobe,carcinoma,0,2	UST	42	2	NM_005715	exon8	c.T1166A	p.I389N	AGCCAATCGACGA	.	PASS	Atlas-SNP
OR2G2	81470	hgsc.bcm.edu	37	1	247752367	247752367	+	Missense_Mutation	SNP	A	A	G	rs869111	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	104	254	0	0.495238	0	A|0.573;G|0.426	0.426	strong	.	OR2G2	88	.	NM_001001915	exon1	c.A706G	p.R236G	GCTACCAGGAGAC	.	PASS	Atlas-SNP
LRRC18	474354	hgsc.bcm.edu	37	10	50121721	50121721	+	Silent	SNP	G	G	A	rs35986885	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	54	152	0	0.519231	0	G|0.859;A|0.141	0.141	strong	LRRC18,scalp,malignant_melanoma,-2,1	LRRC18	52	1	NM_001006939	exon1	c.C480T	p.P160P	GCTCACGGGGATG	.	PASS	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	37	16	1389196	1389196	+	Missense_Mutation	SNP	C	C	T	rs61749061	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	22	43	0	0.52381	0	C|0.970;T|0.030	0.030	strong	.	BAIAP3	88	.	NM_003933	exon4	c.C356T	p.P119L	CACCCCCGGAGCC	.	PASS	Atlas-SNP
HCFC1	3054	hgsc.bcm.edu	37	X	153219665	153219665	+	Silent	SNP	C	C	T	rs2071133	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	41	41	57	0	1	0	C|0.603;T|0.397	0.397	strong	.	HCFC1	284	.	NM_005334	exon17	c.G4185A	p.A1395A	GGGTGCCGCCGCC	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1272858	1272858	+	Silent	SNP	C	C	T	rs4963059	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	35	101	0	0.432099	0	C|0.663;T|0.337	0.337	strong	.	MUC5B	473	.	NM_002458	exon31	c.C14748T	p.F4916F	AACCTTCAGCGTG	.	PASS	Atlas-SNP
LMTK3	114783	hgsc.bcm.edu	37	19	49004551	49004551	+	Silent	SNP	C	C	T	rs55953841	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	46	81	0	0.484211	0	C|0.988;T|0.012	0.012	strong	.	LMTK3	125	.	NM_001080434	exon10	c.G1077A	p.E359E	GTTGCTCTCGCGG	.	PASS	Atlas-SNP
GAB4	128954	hgsc.bcm.edu	37	22	17468918	17468918	+	Missense_Mutation	SNP	C	C	A	rs144427521	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	59	89	0	0.536364	0	C|0.983;A|0.017	0.017	strong	.	GAB4	95	.	NM_001037814	exon3	c.G618T	p.W206C	GATGGGCCAGGTG	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629936	32629936	+	Missense_Mutation	SNP	C	C	T	rs1049107	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	71	62	0	0.739583	0	C|0.812;T|0.188	0.188	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.G469A	p.G157S	TCTGGCCTGGATA	.	PASS	Atlas-SNP
TMEM86A	144110	hgsc.bcm.edu	37	11	18723210	18723210	+	Missense_Mutation	SNP	C	C	T	rs144559255	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	52	131	0	0.464286	0	C|0.987;T|0.013	0.013	strong	TMEM86A,caecum,carcinoma,-1,1	TMEM86A	29	1	NM_153347	exon3	c.C377T	p.A126V	TGGCAGCGCTGTC	.	PASS	Atlas-SNP
IDO2	169355	hgsc.bcm.edu	37	8	39873053	39873053	+	Missense_Mutation	SNP	G	G	A	rs72632016	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	53	101	0	0.452991	0	G|0.929;A|0.071	0.071	strong	.	IDO2	78	.	NM_194294	exon11	c.G1195A	p.A399T	GGAACCGCAGTTA	.	PASS	Atlas-SNP
ERCC2	2068	hgsc.bcm.edu	37	19	45855524	45855524	+	Silent	SNP	G	G	A	rs1052555	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	62	79	0	0.455882	0	G|0.767;N|0.002	.	strong	ERCC2_ENST00000391945,trunk,malignant_melanoma,-2,1	ERCC2	78	1	NM_000400	exon22	c.C2133T	p.D711D	ACCCTCGTCCACG	.	PASS	Atlas-SNP
C10orf10	11067	hgsc.bcm.edu	37	10	45473432	45473432	+	Missense_Mutation	SNP	C	C	T	rs149255069	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	36	101	0	0.395604	0	C|0.999;T|0.001	0.001	strong	.	C10orf10	6	.	NM_007021	exon2	c.G47A	p.R16Q	GTCTCCCGAATTG	.	PASS	Atlas-SNP
ODF3	113746	hgsc.bcm.edu	37	11	199492	199492	+	Missense_Mutation	SNP	G	G	A	rs72878024	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	18	37	0	0.514286	0	G|0.940;A|0.060	0.060	strong	.	ODF3	27	.	NM_053280	exon6	c.G658A	p.A220T	CCAGGCGCCCACA	.	PASS	Atlas-SNP
OR5T1	390155	hgsc.bcm.edu	37	11	56043604	56043604	+	Missense_Mutation	SNP	A	A	G	rs12360890	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	348	189	317	0	0.543103	0	A|0.653;G|0.347	0.347	strong	.	OR5T1	95	.	NM_001004745	exon1	c.A490G	p.S164G	GTTGCTAGCATTT	.	PASS	Atlas-SNP
IL9R	3581	hgsc.bcm.edu	37	X	155239827	155239827	+	Missense_Mutation	SNP	A	A	G	rs3865220		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	124	69	0	0.885714	0	.	.	weak	.	IL9R	73	.	NM_002186	exon9	c.A1319G	p.N440S	GCAACAACAACAA	.	PASS	Atlas-SNP
PDE3A	5139	hgsc.bcm.edu	37	12	20522252	20522252	+	Missense_Mutation	SNP	G	G	A	rs12305038	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	13	13	14	0	1	0	G|0.663;A|0.337	0.337	strong	PDE3A,NS,carcinoma,0,1	PDE3A	184	1	NM_000921	exon1	c.G34A	p.D12N	GTCAGGGACAAGC	.	PASS	Atlas-SNP
IBA57	200205	hgsc.bcm.edu	37	1	228362682	228362682	+	Missense_Mutation	SNP	G	G	A	rs2298014	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	18	44	0	0.62069	0	G|0.783;A|0.217	0.217	strong	.	IBA57	22	.	NM_001010867	exon2	c.G631A	p.G211S	CCCGGGGGCCGGC	.	PASS	Atlas-SNP
SLC12A5	57468	hgsc.bcm.edu	37	20	44680424	44680424	+	Silent	SNP	G	G	T	rs79522550	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	36	82	0	0.5	0	G|0.989;T|0.011	0.011	strong	.	SLC12A5	181	.	NM_001134771	exon18	c.G2361T	p.G787G	CCTCGGGGGGCTG	.	PASS	Atlas-SNP
WDR18	57418	hgsc.bcm.edu	37	19	991129	991129	+	Missense_Mutation	SNP	G	G	A	rs11538683	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	18	57	0	0.473684	0	G|0.891;A|0.109	0.109	strong	.	WDR18	20	.	NM_024100	exon6	c.G790A	p.V264I	GGGAAGGTCTTCA	.	PASS	Atlas-SNP
SEC23A	10484	hgsc.bcm.edu	37	14	39545199	39545199	+	Silent	SNP	A	A	G	rs17108797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	78	93	0	0.52349	0	A|0.959;G|0.041	0.041	strong	.	SEC23A	73	.	NM_006364	exon8	c.T927C	p.P309P	TCTTATAGGTGTC	.	PASS	Atlas-SNP
FOXK1	221937	hgsc.bcm.edu	37	7	4800907	4800907	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	22	26	0	0.647059	0	.	.	none	.	FOXK1	64	.	NM_001037165	exon8	c.G1909A	p.G637S	TTAGCCGGCAACG	.	PASS	Atlas-SNP
PXDNL	137902	hgsc.bcm.edu	37	8	52321966	52321966	+	Missense_Mutation	SNP	G	G	A	rs201280324	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	14	28	0	0.411765	0	G|0.998;A|0.002	0.002	strong	PXDNL_ENST00000356297,NS,carcinoma,+2,1	PXDNL	414	1	NM_144651	exon17	c.C2218T	p.P740S	ACGTGGGCTGCTG	.	scavenged	Atlas-SNP
KRT26	353288	hgsc.bcm.edu	37	17	38928014	38928014	+	Missense_Mutation	SNP	A	A	G	rs9898164	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	78	150	0	0.448276	0	A|0.854;G|0.146	0.146	strong	.	KRT26	49	.	NM_181539	exon1	c.T352C	p.W118R	CGTACCAGCCCTT	.	PASS	Atlas-SNP
TRIP11	9321	hgsc.bcm.edu	37	14	92460176	92460176	+	Missense_Mutation	SNP	C	C	G	rs137974620	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	86	136	0	0.544304	0	C|0.998;G|0.002	0.002	strong	.	TRIP11	184	.	NM_004239	exon15	c.G5137C	p.E1713Q	TTCCTTCCAGATT	.	PASS	Atlas-SNP
TMEM245	23731	hgsc.bcm.edu	37	9	111881856	111881856	+	Missense_Mutation	SNP	T	T	C	rs1051474	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	5	3	0	1	0	T|0.646;C|0.354	0.354	strong	.	.	.	.	NM_032012	exon1	c.A338G	p.H113R	GCGCGGTGCAGGC	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535832	+	Missense_Mutation	SNP	A	A	G	rs201553143	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	38	166	0	0.202128	0	.	.	weak	.	DSPP	174	.	NM_014208	exon5	c.A2018G	p.D673G	GCAGTGATAGCAG	.	PASS	Atlas-SNP
CDSN	1041	hgsc.bcm.edu	37	6	31084170	31084170	+	Missense_Mutation	SNP	A	A	C	rs1042127	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	46	42	0	1	0	A|0.846;C|0.154	0.154	strong	.	CDSN	48	.	NM_001264	exon2	c.T1222G	p.S408A	AACCGGAGCTGCT	.	PASS	Atlas-SNP
L3MBTL2	83746	hgsc.bcm.edu	37	22	41613188	41613188	+	Silent	SNP	C	C	T	rs9611519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	11	36	0	0.354839	0	C|0.775;T|0.225	0.225	strong	L3MBTL2,NS,carcinoma,0,1	L3MBTL2	61	1	NM_031488	exon5	c.C582T	p.P194P	TGCTCCCGTCAGC	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	37	13	39452993	39452993	+	Missense_Mutation	SNP	C	C	T	rs7996253	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	66	158	0	0.425806	0	C|0.978;T|0.022	0.022	strong	.	FREM2	385	.	NM_207361	exon23	c.C8885T	p.A2962V	CACAAGCGACCAG	.	PASS	Atlas-SNP
NKAIN4	128414	hgsc.bcm.edu	37	20	61879074	61879074	+	Silent	SNP	C	C	T	rs11906010	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	122	191	0	0.559633	0	C|0.922;T|0.078	0.078	strong	.	NKAIN4	23	.	NM_152864	exon4	c.G327A	p.E109E	CCAGCGCTCACGC	.	PASS	Atlas-SNP
NPAS2	4862	hgsc.bcm.edu	37	2	101594191	101594191	+	Missense_Mutation	SNP	C	C	T	rs11541353	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	22	42	0	0.44898	0	C|0.870;T|0.130	0.130	strong	.	NPAS2	88	.	NM_002518	exon15	c.C1412T	p.S471L	CCCCATCGTCCTG	.	PASS	Atlas-SNP
TMEM132E	124842	hgsc.bcm.edu	37	17	32962004	32962004	+	Silent	SNP	C	C	T	rs73988752	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	26	48	0	0.412698	0	C|0.929;T|0.071	0.071	strong	.	TMEM132E	122	.	NM_207313	exon8	c.C1605T	p.T535T	GGTCACCGACCTA	.	PASS	Atlas-SNP
MANEA	79694	hgsc.bcm.edu	37	6	96053922	96053922	+	Missense_Mutation	SNP	T	T	A	rs35772543	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	5	59	0	0.151515	0	T|0.936;A|0.064	0.064	strong	.	MANEA	58	.	NM_024641	exon5	c.T1030A	p.F344I	AAATTATTTTGTG	.	PASS	Atlas-SNP
OXER1	165140	hgsc.bcm.edu	37	2	42991200	42991200	+	Missense_Mutation	SNP	C	C	G	rs34142793	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	110	101	0	0.973451	0	C|0.981;G|0.019	0.019	strong	.	OXER1	33	.	NM_148962	exon1	c.G120C	p.M40I	AAGTTCCATGGGC	.	PASS	Atlas-SNP
CUBN	8029	hgsc.bcm.edu	37	10	17147521	17147521	+	Missense_Mutation	SNP	G	G	T	rs1801224	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	81	173	0	0.455056	0	T|0.469;G|0.343;C|0.092;A|0.097	0.469	strong	.	CUBN	515	.	NM_001081	exon11	c.C1165A	p.P389T	CATTTGGCCCATA	.	PASS	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983265	97983265	+	Missense_Mutation	SNP	C	C	A	rs4241472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	312	158	302	0	0.50641	0	C|0.873;A|0.127	0.127	strong	.	OR5H6	89	.	NM_001005479	exon1	c.C137A	p.A46E	TCCTGGCATTCTT	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017773	1017773	+	Silent	SNP	G	G	A	rs57384288	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	878	65	776	38	0.0740319	0.0489691	G|0.500;A|0.500	0.500	strong	MUC6,NS,carcinoma,0,1	MUC6	408	1	NM_005961	exon31	c.C5028T	p.S1676S	GGTCCCGCTGGTG	.	scavenged	Atlas-SNP
ULK4	54986	hgsc.bcm.edu	37	3	41877410	41877410	+	Missense_Mutation	SNP	T	T	G	rs192218045	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	118	215	0	0.462745	0	T|0.997;G|0.003	0.003	strong	.	ULK4	150	.	NM_017886	exon18	c.A1710C	p.L570F	CTGTTTTAATTTG	.	PASS	Atlas-SNP
IL2	3558	hgsc.bcm.edu	37	4	123377482	123377482	+	Silent	SNP	C	C	A	rs2069763	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	71	129	0	0.486301	0	C|0.718;A|0.282	0.282	strong	.	IL2	23	.	NM_000586	exon1	c.G114T	p.L38L	ATCCAGCAGTAAA	.	PASS	Atlas-SNP
NBN	4683	hgsc.bcm.edu	37	8	90958422	90958422	+	Silent	SNP	T	T	C	rs1061302	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	48	107	0	0.369231	0	T|0.690;C|0.310	0.310	strong	.	NBN	86	.	NM_002485	exon13	c.A2016G	p.P672P	GCCAGATGGATTT	.	PASS	Atlas-SNP
DUSP23	54935	hgsc.bcm.edu	37	1	159752066	159752066	+	Missense_Mutation	SNP	G	G	A	rs1129923	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	74	115	0	0.532374	0	G|0.938;A|0.062	0.062	strong	.	DUSP23	9	.	NM_017823	exon3	c.G391A	p.G131S	CGACCCGGCTCCA	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629891	32629891	+	Missense_Mutation	SNP	C	C	T	rs1063323	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	44	90	0	0.427184	0	C|0.587;T|0.413	0.413	strong	HLA-DQB1,colon,carcinoma,+1,1	HLA-DQB1	15	1	NM_002123	exon3	c.G514A	p.A172T	CGCCGGCTGTCTC	.	PASS	Atlas-SNP
IFIT5	24138	hgsc.bcm.edu	37	10	91178000	91178000	+	Silent	SNP	C	C	T	rs304448	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	68	124	0	0.5	0	C|0.376;T|0.624	0.624	strong	.	IFIT5	32	.	NM_012420	exon2	c.C1044T	p.Y348Y	CATGTACGCTGAA	.	PASS	Atlas-SNP
SAAL1	113174	hgsc.bcm.edu	37	11	18127464	18127464	+	Missense_Mutation	SNP	C	C	T	rs77233279	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	20	22	0	0.512821	0	C|0.981;T|0.019	0.019	strong	SAAL1,NS,carcinoma,0,1	SAAL1	34	1	NM_138421	exon1	c.G125A	p.G42E	ATGAGTCCGCTGA	.	PASS	Atlas-SNP
LIPG	9388	hgsc.bcm.edu	37	18	47093864	47093864	+	Missense_Mutation	SNP	C	C	T	rs2000813	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	49	85	0	0.583333	0	C|0.760;T|0.240	0.240	strong	.	LIPG	47	.	NM_006033	exon3	c.C332T	p.T111I	TGCACACAAGAGA	.	PASS	Atlas-SNP
FBN2	2201	hgsc.bcm.edu	37	5	127595153	127595153	+	Silent	SNP	G	G	C	rs34383505	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	220	111	197	0	0.504545	0	G|0.973;C|0.027	0.027	strong	.	FBN2	858	.	NM_001999	exon65	c.C8733G	p.L2911L	TTAATAGAGCTGA	.	PASS	Atlas-SNP
MLN	4295	hgsc.bcm.edu	37	6	33768897	33768897	+	Missense_Mutation	SNP	A	A	G	rs2281820	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	69	123	0	0.448052	0	A|0.403;G|0.597	0.597	strong	.	MLN	16	.	NM_002418	exon2	c.T44C	p.V15A	GCAGCTACATGCA	.	PASS	Atlas-SNP
TMEM63B	55362	hgsc.bcm.edu	37	6	44121579	44121579	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	2	121	0	0.015625	0	.	.	none	TMEM63B,NS,carcinoma,+1,1	TMEM63B	77	1	NM_018426	exon21	c.G2109A	p.T703T	GCGCACGGGTGAG	.	scavenged	Atlas-SNP
IQSEC3	440073	hgsc.bcm.edu	37	12	274647	274647	+	Silent	SNP	T	T	C	rs4980859	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	117	115	0	1	0	T|0.740;C|0.260	0.260	strong	.	IQSEC3	154	.	NM_001170738	exon10	c.T2757C	p.F919F	CACCTTTTGCAAG	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	37	19	40368619	40368619	+	Silent	SNP	G	G	A	rs61732292	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	436	45	335	1	0.103211	0.00298507	G|0.932;A|0.068	0.068	strong	FCGBP,NS,carcinoma,0,1	FCGBP	416	1	NM_003890	exon28	c.C12729T	p.G4243G	GCTGCCGCCCCAG	.	scavenged	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	37	12	114377885	114377885	+	Silent	SNP	G	G	C	rs2290790	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	36	60	0	0.473684	0	G|0.761;C|0.239	0.239	strong	.	RBM19	117	.	NM_001146699	exon15	c.C1818G	p.T606T	GCCGAAGGTCTCC	.	PASS	Atlas-SNP
APOBEC4	403314	hgsc.bcm.edu	37	1	183617266	183617266	+	Silent	SNP	C	C	G	rs17436878	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	140	140	200	0	1	0	C|0.811;G|0.189	0.189	strong	.	APOBEC4	45	.	NM_203454	exon2	c.G651C	p.G217G	TGCTCTCCCAGTT	.	PASS	Atlas-SNP
SMG1	23049	hgsc.bcm.edu	37	16	18882775	18882775	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	295	118	282	0	0.4	0	.	.	none	.	SMG1	401	.	NM_015092	exon16	c.C2213T	p.A738V	ACAGCTGCTTCCA	.	PASS	Atlas-SNP
DCAF6	55827	hgsc.bcm.edu	37	1	168013850	168013850	+	Missense_Mutation	SNP	T	T	C	rs11558511	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	70	113	0	0.542636	0	C|0.196;N|0.000	0.196	strong	.	DCAF6	99	.	NM_001198956	exon15	c.T1871C	p.V624A	AGGATGTGACAAA	.	PASS	Atlas-SNP
SERPINI2	5276	hgsc.bcm.edu	37	3	167189607	167189607	+	Missense_Mutation	SNP	A	A	C	rs17246389	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	41	81	0	0.518987	0	A|0.830;C|0.170	0.170	strong	.	SERPINI2	85	.	NM_001012303	exon3	c.T46G	p.L16V	TCCACAAGAAGAT	.	PASS	Atlas-SNP
TMEM72	643236	hgsc.bcm.edu	37	10	45430153	45430153	+	Silent	SNP	G	G	A	rs17157262	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	38	67	0	0.475	0	G|0.990;A|0.010	0.010	strong	.	TMEM72	25	.	NM_001123376	exon5	c.G399A	p.R133R	CAAGCGGAAGAAG	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155411065	155411065	+	Silent	SNP	T	T	C	rs7656522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	40	60	0	0.430108	0	T|0.235;C|0.765	0.765	strong	.	DCHS2	594	.	NM_001142552	exon1	c.A1443G	p.L481L	GCCGGGTAGCAAC	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65301854	65301854	+	Silent	SNP	G	G	A	rs12663916	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	24	23	53	0	0.958333	0	G|0.904;A|0.096	0.096	strong	.	EYS	527	.	NM_001142800	exon26	c.C3906T	p.H1302H	AATGTCGTGCTTG	.	PASS	Atlas-SNP
MICAL2	9645	hgsc.bcm.edu	37	11	12281414	12281414	+	Missense_Mutation	SNP	G	G	A	rs148517207		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	53	108	0	0.375887	0	G|1.000;A|0.000	0.000	weak	.	MICAL2	114	.	NM_014632	exon26	c.G3304A	p.A1102T	GTGGCCGCCATTG	.	PASS	Atlas-SNP
TRPC4AP	26133	hgsc.bcm.edu	37	20	33665969	33665969	+	Silent	SNP	C	C	T	rs139800499	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	32	83	0	0.415584	0	C|0.995;T|0.005	0.005	strong	.	TRPC4AP	64	.	NM_199368	exon2	c.G177A	p.E59E	AAAAGTCTCAGTG	.	PASS	Atlas-SNP
ZNF154	7710	hgsc.bcm.edu	37	19	58213952	58213952	+	Missense_Mutation	SNP	C	C	A	rs2074078	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	96	162	0	0.536313	0	C|0.818;A|0.182	0.182	strong	.	ZNF154	34	.	NM_001085384	exon3	c.G365T	p.G122V	GCCCCACCGTCGC	.	PASS	Atlas-SNP
SLC2A2	6514	hgsc.bcm.edu	37	3	170715830	170715830	+	Silent	SNP	G	G	A	rs5398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	35	104	0	0.406977	0	G|0.622;A|0.378	0.378	strong	.	SLC2A2	71	.	NM_000340	exon11	c.C1437T	p.F479F	AAATGTGAACAGG	.	PASS	Atlas-SNP
SPAG17	200162	hgsc.bcm.edu	37	1	118624123	118624123	+	Silent	SNP	C	C	T	rs2298176	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	67	94	0	0.558333	0	C|0.922;T|0.078	0.078	strong	.	SPAG17	263	.	NM_206996	exon14	c.G1905A	p.P635P	GTCCCACGGTATG	.	PASS	Atlas-SNP
DENND5B	160518	hgsc.bcm.edu	37	12	31600503	31600503	+	Missense_Mutation	SNP	T	T	C	rs34129725	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	69	109	0	0.453947	0	T|0.995;C|0.005	0.005	strong	.	DENND5B	114	.	NM_144973	exon6	c.A1830G	p.I610M	CTGATATATAGAT	.	PASS	Atlas-SNP
KIAA0141	9812	hgsc.bcm.edu	37	5	141309824	141309824	+	Missense_Mutation	SNP	G	G	A	rs351260	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	68	126	0	0.544	0	G|0.771;T|0.005	.	strong	.	KIAA0141	44	.	NM_001142603	exon7	c.G739A	p.A247T	TCCATCGCTTTCA	.	PASS	Atlas-SNP
IFIT3	3437	hgsc.bcm.edu	37	10	91098877	91098877	+	Silent	SNP	G	G	A	rs34847428	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	17	54	0	0.459459	0	G|0.987;A|0.013	0.013	strong	IFIT3,colon,carcinoma,0,2	IFIT3	36	2	NM_001549	exon2	c.G465A	p.A155A	AAGGGCGAAGGTG	.	PASS	Atlas-SNP
SH3TC1	54436	hgsc.bcm.edu	37	4	8228943	8228943	+	Missense_Mutation	SNP	G	G	A	rs34994651	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	49	112	0	0.453704	0	G|0.948;A|0.052	0.052	strong	.	SH3TC1	105	.	NM_018986	exon12	c.G1522A	p.A508T	CTGAACGCCCCTG	.	PASS	Atlas-SNP
GPR144	347088	hgsc.bcm.edu	37	9	127230891	127230891	+	Missense_Mutation	SNP	G	G	A	rs10760365	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	105	87	0	0.972222	0	G|0.465;A|0.535	0.535	strong	.	GPR144	33	.	NM_001161808	exon14	c.G2248A	p.V750M	AGGAAGGTGGTAG	.	PASS	Atlas-SNP
GRXCR2	643226	hgsc.bcm.edu	37	5	145252377	145252377	+	Missense_Mutation	SNP	C	C	T	rs34892428	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	171	197	1	0.994186	0.00507614	C|0.949;T|0.051	0.051	strong	.	GRXCR2	32	.	NM_001080516	exon1	c.G155A	p.S52N	AGAAAACTGTGAG	.	PASS	Atlas-SNP
HSD17B7	51478	hgsc.bcm.edu	37	1	162775267	162775267	+	Silent	SNP	C	C	T	rs79689427	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	182	90	192	0	0.494505	0	T|1.000;|0.000	1.000	weak	.	HSD17B7	25	.	NM_016371	exon8	c.C888T	p.Y296Y	AAATTACATTATG	.	PASS	Atlas-SNP
TRPC1	7220	hgsc.bcm.edu	37	3	142443441	142443441	+	Missense_Mutation	SNP	G	G	A	rs78975236	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	17	23	0	0.53125	0	G|0.977;A|0.023	0.023	strong	.	TRPC1	82	.	NM_001251845	exon1	c.G40A	p.A14T	TCGGGCGCCTCCT	.	PASS	Atlas-SNP
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53671754	53671754	+	Missense_Mutation	SNP	C	C	T	rs2111119	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	47	100	0	0.5	0	C|0.869;T|0.131	0.131	strong	RPGRIP1L,NS,carcinoma,0,1	RPGRIP1L	118	1	NM_015272	exon21	c.G3073A	p.G1025S	CACTGCCTTCTTG	.	PASS	Atlas-SNP
NUP50	10762	hgsc.bcm.edu	37	22	45574145	45574145	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	254	24	243	13	0.0944882	0.0534979	.	.	none	NUP50,hand,carcinoma,0,2	NUP50	24	2	NM_007172	exon5	c.A367G	p.T123A	CCTACCACCTTGG	.	scavenged	Atlas-SNP
C20orf26	26074	hgsc.bcm.edu	37	20	20150027	20150027	+	Silent	SNP	C	C	T	rs6075630	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	61	76	0	0.530435	0	C|0.834;T|0.166	0.166	strong	.	C20orf26	188	.	NM_015585	exon13	c.C1308T	p.N436N	CCAGAACTTCGTG	.	PASS	Atlas-SNP
ATE1	11101	hgsc.bcm.edu	37	10	123549691	123549691	+	Silent	SNP	T	T	G	rs35350755	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	50	63	0	0.510204	0	T|0.544;G|0.456	0.456	strong	.	ATE1	67	.	NM_001001976	exon11	c.A1371C	p.P457P	TGCTTCTGGGTCC	.	PASS	Atlas-SNP
KRT6A	3853	hgsc.bcm.edu	37	12	52886478	52886478	+	Silent	SNP	T	T	C	rs376545	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	303	134	343	0	0.442244	0	T|0.615;C|0.385	0.385	strong	.	KRT6A	89	.	NM_005554	exon1	c.A495G	p.E165E	GATCTGTTCACGC	.	PASS	Atlas-SNP
NUP133	55746	hgsc.bcm.edu	37	1	229623338	229623338	+	Missense_Mutation	SNP	T	T	C	rs1065674	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	44	54	0	1	0	T|0.691;C|0.309	0.309	strong	.	NUP133	111	.	NM_018230	exon10	c.A1217G	p.Q406R	GTCAACTGACACA	.	PASS	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	37	21	43221826	43221826	+	Silent	SNP	T	T	C	rs2236696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	122	129	0	1	0	T|0.226;C|0.774	0.774	strong	.	PRDM15	110	.	NM_022115	exon31	c.A4098G	p.L1366L	GTTGGTTAAGCCG	.	PASS	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31571786	31571786	+	Silent	SNP	A	A	G	rs1884725	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	69	117	0	0.479167	0	A|0.214;G|0.786	0.786	strong	.	XDH	191	.	NM_000379	exon27	c.T3030C	p.F1010F	AACTGTAAAGCTT	.	PASS	Atlas-SNP
CROCC	9696	hgsc.bcm.edu	37	1	17272037	17272037	+	Missense_Mutation	SNP	G	G	A	rs142404824	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	326	18	156	0	0.0552147	0	G|0.972;A|0.028	0.028	strong	CROCC,colon,carcinoma,-1,1	CROCC	185	1	NM_014675	exon15	c.G2072A	p.R691H	TGAGCCGCGCCAC	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179605725	179605725	+	Missense_Mutation	SNP	T	T	C	rs34070843	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	46	110	0	0.442308	0	T|0.989;C|0.011	0.011	strong	.	TTN	18412	.	NM_001267550	exon48	c.A12235G	p.I4079V	TCAAAATGGTGTC	.	PASS	Atlas-SNP
TMPRSS11BNL	401136	hgsc.bcm.edu	37	4	69056974	69056974	+	Silent	SNP	T	T	G	rs114552880	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	46	99	0	0.474227	0	T|0.973;G|0.027	0.027	strong	TMPRSS11BNL,caecum,carcinoma,0,1	TMPRSS11BNL	4	1	NM_001129907	exon4	c.A303C	p.S101S	CCAGTGTGATGAC	.	PASS	Atlas-SNP
FAM21C	253725	hgsc.bcm.edu	37	10	46254776	46254776	+	Missense_Mutation	SNP	A	A	C	rs2596979	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	285	41	398	1	0.14386	0.00251256	A|0.300;C|0.700	0.700	strong	FAM21C,NS,carcinoma,0,6	FAM21C	68	6	NM_015262	exon17	c.A1562C	p.Y521S	TATCTTACAGCAA	.	scavenged	Atlas-SNP
CDON	50937	hgsc.bcm.edu	37	11	125830906	125830906	+	Silent	SNP	T	T	G	rs139588649		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	96	186	0	0.484848	0	T|1.000;G|0.000	0.000	weak	.	CDON	137	.	NM_001243597	exon20	c.A3795C	p.T1265T	CCACATTGTCTTC	.	PASS	Atlas-SNP
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276888	71276888	+	Silent	SNP	T	T	C	rs12793134	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	6	109	1	0.0645161	0.00917431	T|0.998;C|0.002	0.002	weak	KRTAP5-10,NS,neuroblastoma,0,1	KRTAP5-10	37	1	NM_001012710	exon1	c.T255C	p.G85G	CTGTGGTTCCTGT	.	scavenged	Atlas-SNP
MOG	4340	hgsc.bcm.edu	37	6	29627313	29627313	+	Silent	SNP	A	A	G	rs34758289	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	69	153	0	0.46	0	A|0.992;G|0.008	0.008	strong	.	MOG	47	.	NM_001008229	exon2	c.A306G	p.K102K	GCTGAAAGATGCT	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25259006	25259006	+	Missense_Mutation	SNP	G	G	T	rs2228976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	46	87	0	0.455446	0	G|0.833;T|0.167	0.167	strong	PYGB,NS,carcinoma,0,2	PYGB	84	2	NM_002862	exon8	c.G907T	p.A303S	GTGGCCGCCACGC	.	PASS	Atlas-SNP
ZNF596	169270	hgsc.bcm.edu	37	8	194695	194695	+	Missense_Mutation	SNP	C	C	A	rs148383942	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	117	212	1	0.534247	0.00471698	C|0.997;A|0.003	0.003	strong	.	ZNF596	34	.	NM_173539	exon5	c.C300A	p.S100R	CATCAGCACAATG	.	PASS	Atlas-SNP
ZNF664	144348	hgsc.bcm.edu	37	12	124496864	124496864	+	Missense_Mutation	SNP	T	T	G	rs80197353	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	48	127	0	0.275862	0	T|0.928;G|0.072	0.072	strong	.	ZNF664	27	.	NM_152437	exon5	c.T173G	p.V58G	AGAAGGTCTATAA	.	PASS	Atlas-SNP
TMEM230	29058	hgsc.bcm.edu	37	20	5086918	5086918	+	Silent	SNP	G	G	A	rs147693982	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	53	93	0	0.56383	0	G|0.990;A|0.010	0.010	strong	.	.	.	.	NM_001009923	exon4	c.C327T	p.I109I	AAGTGCGATGGCC	.	PASS	Atlas-SNP
MYO18B	84700	hgsc.bcm.edu	37	22	26422651	26422651	+	Silent	SNP	G	G	A	rs199593757	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	48	66	0	0.55814	0	G|0.993;A|0.007	0.007	strong	.	MYO18B	322	.	NM_032608	exon43	c.G6711A	p.P2237P	ATCCCCGCTGTCG	.	PASS	Atlas-SNP
ZNF652	22834	hgsc.bcm.edu	37	17	47394516	47394516	+	Missense_Mutation	SNP	C	C	T	rs368716483		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	188	93	162	0	0.494681	0	.	.	weak	.	ZNF652	54	.	NM_001145365	exon2	c.G572A	p.R191K	CTGGTTCTCCTTT	.	PASS	Atlas-SNP
STK36	27148	hgsc.bcm.edu	37	2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	rs1863704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	83	157	0	0.432292	0	G|0.767;A|0.233	0.233	strong	STK36,rectum,carcinoma,0,1	STK36	111	1	NM_015690	exon25	c.G3008A	p.G1003D	TTATAGGTGTCTT	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	37	16	15098047	15098047	+	Missense_Mutation	SNP	C	C	G	rs11549900	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	254	118	196	0	0.464567	0	C|0.742;G|0.258	0.258	strong	.	PDXDC1	59	.	NM_015027	exon5	c.C246G	p.I82M	CAGAATCCAAAAT	.	PASS	Atlas-SNP
HIGD1C	613227	hgsc.bcm.edu	37	12	51354803	51354803	+	Silent	SNP	C	C	T	rs12306808	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	175	82	133	0	0.468571	0	C|0.758;T|0.242	0.242	strong	.	HIGD1C	4	.	NM_001109619	exon2	c.C147T	p.Y49Y	AAAGTACAGAAGA	.	PASS	Atlas-SNP
CLEC18A	348174	hgsc.bcm.edu	37	16	69985383	69985383	+	Silent	SNP	G	G	A	rs79631099		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	414	84	269	0	0.202899	0	G|0.500;A|0.500	0.500	weak	CLEC18A,NS,carcinoma,0,1	CLEC18A	9	1	NM_001271197	exon2	c.G114A	p.P38P	GGCTCCGATGGCC	.	scavenged	Atlas-SNP
OR13C2	392376	hgsc.bcm.edu	37	9	107367841	107367841	+	Missense_Mutation	SNP	A	A	T	rs61745782	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	413	137	428	0	0.331719	0	A|0.026;T|0.974	0.974	strong	OR13C2,NS,carcinoma,-1,1	OR13C2	46	1	NM_001004481	exon1	c.T68A	p.L23H	AACTCAAGTCTTG	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911198	29911198	+	Missense_Mutation	SNP	T	T	C	rs1059516	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	173	80	191	0	0.462428	0	T|0.717;C|0.283	0.283	strong	.	HLA-A	89	.	NM_001242758	exon3	c.T497C	p.I166T	CTCAGATCACCAA	.	PASS	Atlas-SNP
PDZRN3	23024	hgsc.bcm.edu	37	3	73433494	73433494	+	Silent	SNP	T	T	C	rs13091636	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	27	47	0	0.519231	0	A|0.000;C|0.372;T|0.627	0.372	strong	.	PDZRN3	196	.	NM_015009	exon10	c.A2223G	p.S741S	GATATCTGAGAGC	.	PASS	Atlas-SNP
EPS8L1	54869	hgsc.bcm.edu	37	19	55587822	55587822	+	Missense_Mutation	SNP	G	G	A	rs12609976	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	160	87	105	0	0.54375	0	G|0.878;A|0.122	0.122	strong	EPS8L1,NS,carcinoma,0,1	EPS8L1	122	1	NM_133180	exon2	c.G10A	p.A4T	AGCACCGCCACAG	.	PASS	Atlas-SNP
INPP4B	8821	hgsc.bcm.edu	37	4	143324094	143324094	+	Silent	SNP	G	G	A	rs1982966	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	22	54	0	0.372881	0	G|0.743;A|0.257	0.257	strong	INPP4B,NS,carcinoma,0,1	INPP4B	132	1	NM_003866	exon8	c.C369T	p.D123D	TACGGTGTCATGA	.	PASS	Atlas-SNP
ESPNL	339768	hgsc.bcm.edu	37	2	239039057	239039057	+	Missense_Mutation	SNP	A	A	G	rs13033248	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	25	38	0	0.520833	0	A|0.615;G|0.385	0.385	strong	.	ESPNL	63	.	NM_194312	exon9	c.A1702G	p.I568V	GCCTCAATCCCAG	.	PASS	Atlas-SNP
TMPRSS12	283471	hgsc.bcm.edu	37	12	51236802	51236802	+	Missense_Mutation	SNP	T	T	C	rs10876100	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	48	71	0	0.521739	0	T|0.715;C|0.285	0.285	strong	.	TMPRSS12	33	.	NM_182559	exon1	c.T55C	p.Y19H	CACTTATACTCAG	.	PASS	Atlas-SNP
AGPHD1	123688	hgsc.bcm.edu	37	15	78807407	78807407	+	Nonsense_Mutation	SNP	T	T	A	rs183603441	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	34	56	0	0.539683	0	T|0.993;A|0.007	0.007	strong	.	AGPHD1	22	.	NM_001013619	exon3	c.T435A	p.Y145X	ATTGTATGAAATT	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	37	6	100964147	100964147	+	Missense_Mutation	SNP	G	G	C	rs240780	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	53	87	1	0.898305	0.0114943	G|0.308;C|0.692	0.692	strong	ASCC3,NS,carcinoma,0,1	ASCC3	205	1	NM_006828	exon39	c.C5984G	p.S1995C	GGAAGGGACTCGA	.	scavenged	Atlas-SNP
OR5B12	390191	hgsc.bcm.edu	37	11	58207203	58207203	+	Missense_Mutation	SNP	C	C	T	rs11229457	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	41	94	0	0.450549	0	C|0.782;T|0.218	0.218	strong	.	OR5B12	80	.	NM_001004733	exon1	c.G422A	p.C141Y	GCCAGGCAAGCAC	.	PASS	Atlas-SNP
TARBP1	6894	hgsc.bcm.edu	37	1	234541801	234541801	+	Silent	SNP	A	A	G	rs12073170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	79	176	0	0.417989	0	A|0.897;G|0.103	0.103	strong	.	TARBP1	111	.	NM_005646	exon24	c.T3837C	p.C1279C	ATTGAAACACCAC	.	PASS	Atlas-SNP
OR2D2	120776	hgsc.bcm.edu	37	11	6913243	6913243	+	Missense_Mutation	SNP	T	T	C	rs1965207	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	85	191	0	0.508982	0	T|0.866;C|0.134	0.134	strong	.	OR2D2	52	.	NM_003700	exon1	c.A489G	p.I163M	CCTCAGTATGAAG	.	PASS	Atlas-SNP
PIK3C2B	5287	hgsc.bcm.edu	37	1	204403659	204403659	+	Silent	SNP	A	A	G	rs3747636	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	82	138	0	0.438503	0	A|0.650;G|0.350	0.350	strong	.	PIK3C2B	142	.	NM_002646	exon25	c.T3594C	p.N1198N	GTTGTCATTATGT	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168103925	168103925	+	Missense_Mutation	SNP	A	A	G	rs7607246	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	74	151	0	0.477419	0	A|0.837;G|0.163	0.163	strong	.	XIRP2	914	.	NM_152381	exon9	c.A6023G	p.N2008S	ATGGCAATTTAGT	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2140010	2140010	+	Silent	SNP	A	A	G	rs7203729	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	42	55	0	0.477273	0	A|0.688;G|0.312	0.312	strong	.	PKD1	184	.	NM_001009944	exon46	c.T12630C	p.P4210P	GGGCTCAGGCTCA	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	37	15	43707808	43707808	+	Silent	SNP	A	A	T	rs2230451	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	55	105	0	0.491071	0	A|0.828;T|0.172	0.172	strong	.	TP53BP1	157	.	NM_001141980	exon23	c.T5073A	p.S1691S	TGTGGCAGACTTG	.	PASS	Atlas-SNP
OR51Q1	390061	hgsc.bcm.edu	37	11	5444150	5444150	+	Silent	SNP	C	C	T	rs118011081	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	66	153	0	0.452055	0	C|0.985;T|0.015	0.015	strong	.	OR51Q1	79	.	NM_001004757	exon1	c.C720T	p.L240L	TGCCCTCAATAAC	.	PASS	Atlas-SNP
SAMD9L	219285	hgsc.bcm.edu	37	7	92762681	92762681	+	Silent	SNP	A	A	G	rs1029357	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	51	125	0	0.395349	0	A|0.774;G|0.226	0.226	strong	SAMD9L,NS,carcinoma,0,1	SAMD9L	227	1	NM_152703	exon5	c.T2604C	p.A868A	ACCAAAAGCTCTT	.	PASS	Atlas-SNP
ZNF761	388561	hgsc.bcm.edu	37	19	53959343	53959343	+	Missense_Mutation	SNP	G	G	A	rs2708742	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	31	46	0	0.492063	0	G|0.635;A|0.365	0.365	strong	.	ZNF761	104	.	NM_001008401	exon7	c.G1582A	p.G528S	GAGTGCGGCAAGA	.	PASS	Atlas-SNP
ASPHD2	57168	hgsc.bcm.edu	37	22	26830316	26830316	+	Silent	SNP	G	G	A	rs11705277	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	60	109	0	0.447761	0	G|0.880;A|0.120	0.120	strong	.	ASPHD2	42	.	NM_020437	exon2	c.G735A	p.R245R	CTGTAGGAAGTGC	.	PASS	Atlas-SNP
NDST1	3340	hgsc.bcm.edu	37	5	149907602	149907602	+	Silent	SNP	A	A	G	rs2273234	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	20	61	0	0.434783	0	A|0.687;G|0.313	0.313	strong	.	NDST1	79	.	NM_001543	exon3	c.A750G	p.P250P	CATCCCACACCTG	.	PASS	Atlas-SNP
DNASE1	1773	hgsc.bcm.edu	37	16	3707747	3707747	+	Missense_Mutation	SNP	G	G	A	rs1053874	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	51	67	0	0.515152	0	G|0.520;A|0.480	0.480	strong	.	DNASE1	16	.	NM_005223	exon8	c.G731A	p.R244Q	TGCTCCGAGGCGC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28459095	28459095	+	Silent	SNP	G	G	A	rs191942261	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	191	15	214	0	0.078534	0	G|0.993;A|0.007	0.007	strong	.	HERC2	501	.	NM_004667	exon42	c.C6579T	p.P2193P	GGAGTCGGGGAAG	.	PASS	Atlas-SNP
CLSTN1	22883	hgsc.bcm.edu	37	1	9811541	9811541	+	Silent	SNP	A	A	G	rs11674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	150	13	78	0	0.0866667	0	A|0.749;G|0.251	0.251	strong	.	CLSTN1	88	.	NM_001009566	exon5	c.T639C	p.V213V	TTTGTCAACAGTA	.	PASS	Atlas-SNP
BRCA1	672	hgsc.bcm.edu	37	17	41244429	41244429	+	Missense_Mutation	SNP	C	C	T	rs4986852	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	214	99	203	1	0.462617	0.00492611	C|0.982;T|0.018	0.018	strong	BRCA1,NS,carcinoma,0,1	BRCA1	304	1	NM_007300	exon10	c.G3119A	p.S1040N	CTTGAGCTGGCTT	.	scavenged	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140222316	140222316	+	Silent	SNP	G	G	A	rs202126810	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	304	152	242	0	0.5	0	G|0.999;T|0.001	.	alt	PCDHA8_ENST00000531613,rectum,carcinoma,0,2	PCDHA8	366	2	NM_031856	exon1	c.G1410A	p.P470P	CCCGCCGGGCTGC	.	PASS	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	37	11	5373170	5373170	+	Missense_Mutation	SNP	C	C	G	rs5006886	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	197	64	247	0	0.324873	0	C|0.755;G|0.245	0.245	strong	OR51B6,caecum,carcinoma,-1,1	OR51B6	53	1	NM_001004750	exon1	c.C433G	p.R145G	GGTGTGCGGGTAT	.	PASS	Atlas-SNP
GALC	2581	hgsc.bcm.edu	37	14	88442712	88442712	+	Missense_Mutation	SNP	C	C	T	rs34362748	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	46	42	0	0.978723	0	C|0.895;T|0.105	0.105	strong	.	GALC	48	.	NM_000153	exon7	c.G742A	p.D248N	TAACATCAACCAC	.	PASS	Atlas-SNP
CARD8	22900	hgsc.bcm.edu	37	19	48737764	48737764	+	Silent	SNP	A	A	G	rs2288876	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	68	76	0	1	0	A|0.758;G|0.242	0.242	strong	.	CARD8	53	.	NM_001184900	exon3	c.T246C	p.L82L	GTCACAAAGGGTC	.	PASS	Atlas-SNP
MFRP	83552	hgsc.bcm.edu	37	11	119216279	119216279	+	Silent	SNP	G	G	A	rs36015759	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	27	36	0	0.54	0	G|0.781;A|0.219	0.219	strong	.	MFRP	63	.	NM_031433	exon5	c.C492T	p.Y164Y	GGGGGGGTAAGGG	.	PASS	Atlas-SNP
LIPJ	142910	hgsc.bcm.edu	37	10	90356598	90356598	+	Missense_Mutation	SNP	A	A	G	rs1409136	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	17	33	0	0.447368	0	A|0.165;G|0.835	0.835	strong	.	LIPJ	32	.	NM_001010939	exon8	c.A628G	p.I210V	AAATTCATTGGTT	.	PASS	Atlas-SNP
GPR1	2825	hgsc.bcm.edu	37	2	207041053	207041053	+	Missense_Mutation	SNP	T	T	C	rs3732083	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	99	93	0	0.980198	0	T|0.502;C|0.498	0.498	strong	.	GPR1	38	.	NM_001098199	exon3	c.A919G	p.I307V	TACTAATTAGGAC	.	PASS	Atlas-SNP
ANKRD18B	441459	hgsc.bcm.edu	37	9	33541216	33541216	+	Missense_Mutation	SNP	G	G	C	rs111814125		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	343	56	276	1	0.163265	0.00362319	G|0.500;C|0.500	0.500	weak	ANKRD18B,NS,carcinoma,0,1	ANKRD18B	46	1	NM_001244752	exon7	c.G880C	p.G294R	AAAGAAGGTGCAA	.	scavenged	Atlas-SNP
ZNF584	201514	hgsc.bcm.edu	37	19	58928302	58928302	+	Silent	SNP	T	T	C	rs10423138	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	48	110	0	0.510638	0	T|0.459;C|0.541	0.541	strong	.	ZNF584	31	.	NM_173548	exon4	c.T417C	p.A139A	GGCAGCTTTCCCA	.	PASS	Atlas-SNP
RHOBTB3	22836	hgsc.bcm.edu	37	5	95091194	95091194	+	Silent	SNP	C	C	T	rs34898	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	208	217	0	0.990476	0	C|0.586;T|0.414	0.414	strong	.	RHOBTB3	43	.	NM_014899	exon6	c.C777T	p.Y259Y	ATTTTACAACCCC	.	PASS	Atlas-SNP
USP6	9098	hgsc.bcm.edu	37	17	5042837	5042837	+	Missense_Mutation	SNP	C	C	T	rs61745111	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	22	51	0	0.458333	0	C|0.881;T|0.119	0.119	strong	USP6,NS,carcinoma,0,1	USP6	213	1	NM_004505	exon14	c.C1366T	p.R456W	ATGCCCCGGCTCC	.	PASS	Atlas-SNP
PRKX	5613	hgsc.bcm.edu	37	X	3592725	3592725	+	Silent	SNP	G	G	A	rs10871864	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	128	126	100	0	0.984375	0	G|0.502;A|0.498	0.498	strong	.	PRKX	29	.	NM_005044	exon2	c.C249T	p.P83P	GACGTCGGGAATG	.	PASS	Atlas-SNP
LRRC52	440699	hgsc.bcm.edu	37	1	165532746	165532746	+	Missense_Mutation	SNP	T	T	A	rs17407838	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	32	48	0	0.542373	0	T|0.917;A|0.083	0.083	strong	.	LRRC52	50	.	NM_001005214	exon2	c.T627A	p.D209E	AGATGATCTAAAT	.	PASS	Atlas-SNP
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035301	110035301	+	Silent	SNP	A	A	G	rs1026607	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	33	68	0	0.471429	0	A|0.729;G|0.271	0.271	strong	.	ZC3H12C	83	.	NM_033390	exon6	c.A1491G	p.T497T	AAGGACACAAGTC	.	PASS	Atlas-SNP
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Silent	SNP	C	C	T	rs371465078	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	22	19	463	1	0.863636	0.00215983	.	.	weak	SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	NM_001135844	exon2	c.G243A	p.Q81Q	TTCTTTCTGATTG	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327897	16327897	+	Missense_Mutation	SNP	C	C	A	rs184327938	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	21	52	0	0.388889	0	C|0.926;A|0.074	0.074	strong	ATXN1,NS,carcinoma,0,3	ATXN1	117	3	NM_001128164	exon7	c.G645T	p.Q215H	CTGCTGCTGCTGC	.	PASS	Atlas-SNP
C1orf86	199990	hgsc.bcm.edu	37	1	2125258	2125258	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	2	83	1	0.0224719	0.0120482	.	.	none	C1orf86,NS,carcinoma,0,1	C1orf86	20	1	NM_001256946	exon3	c.C290A	p.P97Q	CGGCCCGGGCCCC	.	scavenged	Atlas-SNP
CTSS	1520	hgsc.bcm.edu	37	1	150727539	150727539	+	Missense_Mutation	SNP	G	G	A	rs2230061	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	64	137	0	0.477612	0	T|0.068;G|0.534;C|0.117;N|0.000;A|0.281	0.281	strong	CTSS,NS,carcinoma,0,1	CTSS	31	1	NM_004079	exon4	c.C337T	p.R113W	ATATCCGATTAGG	.	PASS	Atlas-SNP
F7	2155	hgsc.bcm.edu	37	13	113770068	113770068	+	Silent	SNP	C	C	T	rs6042	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	26	110	0	0.376812	0	C|0.876;T|0.124	0.124	strong	F7,NS,carcinoma,0,1	F7	49	1	NM_000131	exon6	c.C525T	p.H175H	GTGCCACGAGGGG	.	PASS	Atlas-SNP
ITGA11	22801	hgsc.bcm.edu	37	15	68643659	68643659	+	Silent	SNP	G	G	A	rs61729770	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	72	146	0	0.473684	0	G|0.995;A|0.005	0.005	strong	.	ITGA11	110	.	NM_001004439	exon8	c.C831T	p.S277S	GTCTGGGCTGTCG	.	PASS	Atlas-SNP
UEVLD	55293	hgsc.bcm.edu	37	11	18600322	18600322	+	Silent	SNP	T	T	G	rs10500835	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	26	55	0	0.472727	0	T|0.879;G|0.121	0.121	strong	.	UEVLD	58	.	NM_001040697	exon2	c.A76C	p.R26R	CATTCCTTAGTTC	.	PASS	Atlas-SNP
TRIM3	10612	hgsc.bcm.edu	37	11	6478619	6478619	+	Silent	SNP	G	G	A	rs16913748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	31	59	0	0.455882	0	G|0.791;A|0.209	0.209	strong	.	TRIM3	67	.	NM_001248006	exon5	c.C603T	p.I201I	TGCACTGATCTGG	.	PASS	Atlas-SNP
DDX41	51428	hgsc.bcm.edu	37	5	176943352	176943352	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	59	131	0	0.468254	0	.	.	none	.	DDX41	49	.	NM_016222	exon3	c.C235G	p.L79V	GGCCTAGCGGGAT	.	PASS	Atlas-SNP
MOV10L1	54456	hgsc.bcm.edu	37	22	50589196	50589196	+	Silent	SNP	C	C	A	rs2294396	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	63	114	0	0.552632	0	C|0.878;A|0.122	0.122	strong	.	MOV10L1	238	.	NM_018995	exon21	c.C2760A	p.G920G	GCTCGGCCCAGTC	.	PASS	Atlas-SNP
ARC	23237	hgsc.bcm.edu	37	8	143694520	143694520	+	Silent	SNP	C	C	T	rs371075422		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	23	32	0	0.433962	0	.	.	weak	ARC,colon,carcinoma,-2,1	ARC	34	1	NM_015193	exon1	c.G1113A	p.P371P	CTCCACCGGGAGG	.	PASS	Atlas-SNP
COL6A5	256076	hgsc.bcm.edu	37	3	130124491	130124491	+	Silent	SNP	G	G	A	rs10934940	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	158	168	0	0.993711	0	G|0.508;A|0.492	0.492	strong	COL6A5,colon,carcinoma,0,1	COL6A5	205	1	NM_153264	exon14	c.G4341A	p.A1447A	AGGGGCGTGGGGT	.	PASS	Atlas-SNP
OR6C74	254783	hgsc.bcm.edu	37	12	55641328	55641328	+	Missense_Mutation	SNP	G	G	A	rs6581025	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	74	191	0	0.445783	0	G|0.760;A|0.240	0.240	strong	.	OR6C74	52	.	NM_001005490	exon1	c.G257A	p.G86D	CAACAGGTGATAA	.	PASS	Atlas-SNP
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	40	69	0	0.45977	0	A|0.663;G|0.337	0.337	strong	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	NM_001130442	exon2	c.T81C	p.H27H	CACAAAATGGTTC	.	PASS	Atlas-SNP
APBB2	323	hgsc.bcm.edu	37	4	41015823	41015823	+	Silent	SNP	G	G	A	rs2292234	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	222	115	188	0	0.518018	0	A|0.342;G|0.575;T|0.083	0.342	strong	.	APBB2	61	.	NM_173075	exon6	c.C612T	p.G204G	CAAATCGCCATTC	.	PASS	Atlas-SNP
CLEC10A	10462	hgsc.bcm.edu	37	17	6980273	6980273	+	Missense_Mutation	SNP	C	C	T	rs16956478	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	53	84	0	0.456897	0	C|0.948;T|0.052	0.052	strong	.	CLEC10A	40	.	NM_182906	exon4	c.G218A	p.R73K	TCTGTTCTCAGGG	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155410731	155410731	+	Missense_Mutation	SNP	G	G	C	rs72731016	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	46	80	0	0.582278	0	G|0.836;C|0.164	0.164	strong	.	DCHS2	594	.	NM_001142552	exon1	c.C1777G	p.Q593E	TTGATTGCAGGGA	.	PASS	Atlas-SNP
DDX55	57696	hgsc.bcm.edu	37	12	124104686	124104686	+	Silent	SNP	G	G	A	rs3204541	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	57	114	0	0.504425	0	G|0.707;A|0.293	0.293	strong	.	DDX55	51	.	NM_020936	exon14	c.G1802A	p.X601X	ACTGCTGATTCCA	.	PASS	Atlas-SNP
USP10	9100	hgsc.bcm.edu	37	16	84778690	84778690	+	Silent	SNP	C	C	T	rs1812062	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	55	151	0	0.381944	0	C|0.773;T|0.227	0.227	strong	.	USP10	51	.	NM_001272075	exon5	c.C615T	p.P205P	CATGCCCCCGTCA	.	PASS	Atlas-SNP
AGGF1	55109	hgsc.bcm.edu	37	5	76343999	76343999	+	Silent	SNP	T	T	C	rs13155212	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	46	81	0	0.522727	0	C|0.234;N|0.001	0.234	strong	.	AGGF1	71	.	NM_018046	exon7	c.T1215C	p.I405I	CAAAATTTGGCCC	.	PASS	Atlas-SNP
DPAGT1	1798	hgsc.bcm.edu	37	11	118967758	118967758	+	Missense_Mutation	SNP	T	T	C	rs643788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	66	179	0	0.415094	0	A|0.003;C|0.413	0.413	strong	.	DPAGT1	43	.	NM_001382	exon9	c.A1177G	p.I393V	AGGTGATGGCACT	.	PASS	Atlas-SNP
OR5B2	390190	hgsc.bcm.edu	37	11	58190136	58190136	+	Missense_Mutation	SNP	A	A	G	rs4298923	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	36	55	0	0.413793	0	A|0.507;G|0.493	0.493	strong	.	OR5B2	75	.	NM_001005566	exon1	c.T599C	p.M200T	CTTGACATAAAAA	.	PASS	Atlas-SNP
A2ML1	144568	hgsc.bcm.edu	37	12	9016456	9016456	+	Missense_Mutation	SNP	C	C	T	rs73040625	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	39	116	0	0.458824	0	C|0.949;T|0.051	0.051	strong	.	A2ML1	199	.	NM_144670	exon29	c.C3569T	p.A1190V	AGCCTGCGGCTGT	.	PASS	Atlas-SNP
SEZ6L	23544	hgsc.bcm.edu	37	22	26688388	26688388	+	Silent	SNP	A	A	C	rs35377445	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	28	45	0	0.444444	0	A|0.919;C|0.081	0.081	strong	SEZ6L,NS,carcinoma,+2,1	SEZ6L	174	1	NM_001184777	exon2	c.A111C	p.G37G	CGAGGGAGATGCT	.	PASS	Atlas-SNP
FAM160A2	84067	hgsc.bcm.edu	37	11	6239139	6239139	+	Silent	SNP	A	A	G	rs11040809	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	15	30	0	0.405405	0	A|0.841;G|0.159;N|0.000;T|0.000	0.159	strong	.	FAM160A2	100	.	NM_032127	exon9	c.T1719C	p.R573R	ACCACGACGTGCC	.	PASS	Atlas-SNP
SAMD12	401474	hgsc.bcm.edu	37	8	119391791	119391791	+	Silent	SNP	T	T	C	rs5020517	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	288	139	298	0	0.482639	0	T|0.303;C|0.697	0.697	strong	.	SAMD12	24	.	NM_207506	exon4	c.A471G	p.L157L	AAGCAATAGGGTA	.	PASS	Atlas-SNP
NLRC4	58484	hgsc.bcm.edu	37	2	32463365	32463365	+	Missense_Mutation	SNP	C	C	A	rs149451729	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	37	102	0	0.445783	0	C|0.997;A|0.003	0.003	strong	.	NLRC4	165	.	NM_001199138	exon6	c.G2357T	p.G786V	TTCAGGCCTTCAG	.	PASS	Atlas-SNP
GINS2	51659	hgsc.bcm.edu	37	16	85711860	85711860	+	Silent	SNP	C	C	T	rs1053328	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	86	153	0	0.421569	0	C|0.657;T|0.343	0.343	strong	GINS2,colon,carcinoma,-1,1	GINS2	15	1	NM_016095	exon5	c.G516A	p.T172T	GAGGTTCGTGCGG	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10467604	10467604	+	Missense_Mutation	SNP	C	C	A	rs74366179	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	103	257	1	0.581921	0.00389105	C|0.824;A|0.176	0.176	strong	RP1L1,NS,carcinoma,0,1	RP1L1	453	1	NM_178857	exon4	c.G4004T	p.G1335V	TGCACCCCCTCTT	.	PASS	Atlas-SNP
NALCN	259232	hgsc.bcm.edu	37	13	101828654	101828654	+	Silent	SNP	T	T	C	rs17582557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	14	31	0	0.482759	0	T|0.965;C|0.035	0.035	strong	NALCN,NS,carcinoma,0,1	NALCN	431	1	NM_052867	exon15	c.A1836G	p.K612K	TACTTGTTTAAGC	.	PASS	Atlas-SNP
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329892	55329892	+	Missense_Mutation	SNP	A	A	G	rs149123986	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	25	31	0	0.595238	0	A|0.860;G|0.140	0.140	strong	.	KIR3DL1	174	.	NM_013289	exon3	c.A193G	p.R65G	GAAGACAGAATCC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28459325	28459325	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	5	90	1	0.0480769	0.0111111	.	.	none	HERC2,NS,carcinoma,0,2	HERC2	501	2	NM_004667	exon41	c.G6452A	p.R2151H	AGCGTGCGCAGCA	.	scavenged	Atlas-SNP
PASD1	139135	hgsc.bcm.edu	37	X	150817094	150817094	+	Missense_Mutation	SNP	C	C	G	rs5924658	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	124	115	0	0.992	0	0|0.024;C|0.826;G|0.150	0.150	strong	.	PASD1	286	.	NM_173493	exon9	c.C637G	p.Q213E	AGCTCTCAAGGTC	.	PASS	Atlas-SNP
LRRC16B	90668	hgsc.bcm.edu	37	14	24529209	24529209	+	Silent	SNP	C	C	T	rs61564890	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	57	82	0	0.456	0	C|0.908;T|0.092	0.092	strong	.	LRRC16B	120	.	NM_138360	exon23	c.C1899T	p.P633P	CTTCCCCGTGAGC	.	PASS	Atlas-SNP
OR10G3	26533	hgsc.bcm.edu	37	14	22038450	22038450	+	Silent	SNP	G	G	A	rs11626669	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	55	106	0	0.544554	0	G|0.547;A|0.453	0.453	strong	.	OR10G3	40	.	NM_001005465	exon1	c.C426T	p.S142S	CAAGGCGCTCAGC	.	PASS	Atlas-SNP
MAPK6	5597	hgsc.bcm.edu	37	15	52353498	52353498	+	Missense_Mutation	SNP	C	C	G	rs35697691	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	100	187	0	0.478469	0	C|0.939;G|0.061	0.061	strong	MAPK6,face,carcinoma,0,5	MAPK6	70	5	NM_002748	exon5	c.C868G	p.L290V	GCAGCACTGGATT	.	PASS	Atlas-SNP
PLD2	5338	hgsc.bcm.edu	37	17	4722876	4722876	+	Missense_Mutation	SNP	G	G	A	rs3764897	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	21	55	0	0.552632	0	G|0.804;A|0.196	0.196	strong	.	PLD2	138	.	NM_002663	exon23	c.G2461A	p.G821S	TGCTTCGGGTAGA	.	PASS	Atlas-SNP
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713018	32713018	+	Silent	SNP	C	C	T	rs17213281	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	194	98	144	0	0.505155	0	C|0.824;T|0.176	0.176	strong	.	HLA-DQA2	27	.	NM_020056	exon2	c.C165T	p.D55D	TGGAGACGAGGAG	.	PASS	Atlas-SNP
LAMA1	284217	hgsc.bcm.edu	37	18	7049171	7049171	+	Missense_Mutation	SNP	C	C	T	rs140718292	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	46	109	0	0.442308	0	C|0.993;T|0.007	0.007	strong	LAMA1,scalp,carcinoma,-1,1	LAMA1	458	1	NM_005559	exon5	c.G674A	p.R225H	CGAAGGCGAATAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506693	195506693	+	Missense_Mutation	SNP	G	G	A	rs146525749	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	129	1	0	0.992308	0	G|0.995;A|0.005	0.005	strong	MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	NM_018406	exon2	c.C11758T	p.R3920C	GAAGACGGGTGGT	.	PASS	Atlas-SNP
HLA-B	3106	hgsc.bcm.edu	37	6	31322303	31322303	+	Missense_Mutation	SNP	C	C	G	rs3210072		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	127	124	0	0.984496	0	.	.	weak	.	HLA-B	54	.	NM_005514	exon7	c.G1046C	p.C349S	TCGCTGCCTGGAG	.	PASS	Atlas-SNP
SEC24C	9632	hgsc.bcm.edu	37	10	75506674	75506674	+	Silent	SNP	T	T	C	rs2306325	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	61	114	1	0.438849	0.00877193	T|0.851;C|0.149	0.149	strong	SEC24C,NS,carcinoma,0,1	SEC24C	86	1	NM_198597	exon2	c.T84C	p.Y28Y	CAGCTATGGTGGG	.	scavenged	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643255	1643255	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	8	89	1	0.0519481	0.011236	.	.	none	KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	NM_001012709	exon1	c.C69T	p.G23G	GCCACAGCCCCCA	.	scavenged	Atlas-SNP
STRA8	346673	hgsc.bcm.edu	37	7	134925411	134925411	+	Silent	SNP	G	G	A	rs7805859	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	224	117	189	0	0.522321	0	G|0.591;A|0.409	0.409	strong	.	STRA8	39	.	NM_182489	exon2	c.G201A	p.A67A	GGCAGCGCTCTTC	.	PASS	Atlas-SNP
SPECC1	92521	hgsc.bcm.edu	37	17	20109189	20109189	+	Silent	SNP	C	C	T	rs2703807	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	19	7	0	0.612903	0	C|0.553;T|0.447	0.447	strong	.	SPECC1	100	.	NM_001033553	exon4	c.C1827T	p.N609N	GGCAAACGGTGAA	.	PASS	Atlas-SNP
LAMP2	3920	hgsc.bcm.edu	37	X	119590533	119590533	+	Silent	SNP	T	T	A	rs12097	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	104	111	0	0.981132	0	T|0.602;0|0.012	.	strong	.	LAMP2	101	.	NM_013995	exon2	c.A156T	p.V52V	ATAGCGTACTGTG	.	PASS	Atlas-SNP
TLN2	83660	hgsc.bcm.edu	37	15	63131117	63131117	+	Silent	SNP	T	T	A	rs937418	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	45	81	0	0.535714	0	T|0.656;A|0.344	0.344	strong	.	TLN2	253	.	NM_015059	exon55	c.T7437A	p.A2479A	GGCAGCTTTTGGC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195512235	195512235	+	Silent	SNP	T	T	C	rs78417473		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	39	239	0	0.203125	0	T|0.500;C|0.500	0.500	weak	.	MUC4	1505	.	NM_018406	exon2	c.A6216G	p.S2072S	GGATGCTGAGGAA	.	PASS	Atlas-SNP
STK31	56164	hgsc.bcm.edu	37	7	23775477	23775477	+	Missense_Mutation	SNP	G	G	T	rs10264967	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	36	41	0	0.947368	0	G|0.862;T|0.138	0.138	strong	.	STK31	175	.	NM_031414	exon7	c.G804T	p.K268N	CTTGAAGGATGAA	.	PASS	Atlas-SNP
ARHGEF10	9639	hgsc.bcm.edu	37	8	1808256	1808256	+	Silent	SNP	A	A	G	rs749822	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	74	151	0	0.506849	0	A|0.940;G|0.060	0.060	strong	.	ARHGEF10	255	.	NM_014629	exon4	c.A387G	p.V129V	GCCTGTACCCTGC	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13829799	13829799	+	Silent	SNP	G	G	A	rs1348689	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	88	80	0	1	0	G|0.574;A|0.426	0.426	strong	.	DNAH5	868	.	NM_001369	exon38	c.C6264T	p.A2088A	CCGTCCGGCATAG	.	PASS	Atlas-SNP
CUL4A	8451	hgsc.bcm.edu	37	13	113882307	113882307	+	Missense_Mutation	SNP	T	T	C	rs113697945	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	37	46	0	0.74	0	T|0.995;C|0.005	0.005	strong	.	CUL4A	50	.	NM_001008895	exon4	c.T386C	p.V129A	ATAGTGTTTTATT	.	PASS	Atlas-SNP
PLCH1	23007	hgsc.bcm.edu	37	3	155301264	155301264	+	Silent	SNP	T	T	C	rs9289957	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	55	125	0	0.474138	0	T|0.957;C|0.043	0.043	strong	.	PLCH1	406	.	NM_001130960	exon5	c.A732G	p.Q244Q	TACCTTTTGCTCC	.	PASS	Atlas-SNP
GLIS1	148979	hgsc.bcm.edu	37	1	54060016	54060016	+	Missense_Mutation	SNP	G	G	C	rs35227000	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	15	27	0	0.517241	0	G|0.757;C|0.243	0.243	strong	.	GLIS1	52	.	NM_147193	exon3	c.C560G	p.A187G	CTGCCTGCCAGGC	.	PASS	Atlas-SNP
C12orf43	64897	hgsc.bcm.edu	37	12	121442883	121442883	+	Silent	SNP	G	G	A	rs11537856	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	31	52	0	0.607843	0	G|0.965;A|0.035	0.035	strong	.	C12orf43	30	.	NM_022895	exon5	c.C375T	p.F125F	TGTGAAGAAAAGG	.	PASS	Atlas-SNP
ARHGAP23	57636	hgsc.bcm.edu	37	17	36622482	36622482	+	Silent	SNP	G	G	C	rs8075324	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	42	36	0	1	0	G|0.680;C|0.320	0.320	strong	.	ARHGAP23	48	.	NM_001199417	exon7	c.G558C	p.P186P	GCCACCGCCGATC	.	PASS	Atlas-SNP
APCDD1	147495	hgsc.bcm.edu	37	18	10487918	10487918	+	Silent	SNP	C	C	T	rs3185480	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	37	70	0	0.468354	0	C|0.613;T|0.387	0.387	strong	.	APCDD1	57	.	NM_153000	exon5	c.C1428T	p.L476L	GGACCTCGCAGAA	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1016889	1016889	+	Missense_Mutation	SNP	G	G	A	rs373231068		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	724	40	703	1	0.0552486	0.00142248	.	.	weak	MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	NM_005961	exon31	c.C5912T	p.P1971L	GTAGGTGGGGAGT	.	scavenged	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113191597	113191597	+	Missense_Mutation	SNP	G	G	A	rs76469101	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	13	29	0	0.448276	0	G|0.980;A|0.020	0.020	strong	SVEP1,NS,carcinoma,0,1	SVEP1	326	1	NM_153366	exon35	c.C5633T	p.T1878I	GCCAGAGTATATC	.	PASS	Atlas-SNP
MYO5C	55930	hgsc.bcm.edu	37	15	52527951	52527951	+	Missense_Mutation	SNP	T	T	C	rs55753304	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	60	113	0	0.5	0	T|0.980;C|0.020	0.020	strong	.	MYO5C	162	.	NM_018728	exon23	c.A2878G	p.K960E	GAAGCTTTGCCAA	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	449874	449874	+	Missense_Mutation	SNP	G	G	C	rs34908836	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	41	91	0	0.493976	0	G|0.927;C|0.073	0.073	strong	.	DOCK8	401	.	NM_203447	exon45	c.G5908C	p.A1970P	CCTGATGCAAAGA	.	PASS	Atlas-SNP
PTPRN2	5799	hgsc.bcm.edu	37	7	157931144	157931144	+	Missense_Mutation	SNP	C	C	T	rs1130499	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	38	101	0	0.475	0	C|0.623;T|0.377	0.377	strong	.	PTPRN2	243	.	NM_130843	exon7	c.G974A	p.S325N	AGGCCACTCAGGC	.	PASS	Atlas-SNP
OR56B1	387748	hgsc.bcm.edu	37	11	5758646	5758646	+	Silent	SNP	T	T	C	rs4486660	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	41	105	0	0.405941	0	T|0.941;C|0.059	0.059	strong	.	OR56B1	38	.	NM_001005180	exon1	c.T900C	p.Y300Y	AGTTTATGCACTT	.	PASS	Atlas-SNP
SLC27A5	10998	hgsc.bcm.edu	37	19	59023174	59023174	+	Missense_Mutation	SNP	A	A	G	rs35350976	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	41	35	0	0.546667	0	A|0.840;G|0.160	0.160	strong	.	SLC27A5	58	.	NM_012254	exon1	c.T149C	p.M50T	GCTAACATGGCCA	.	PASS	Atlas-SNP
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803167	43803167	+	Missense_Mutation	SNP	T	T	C	rs2839500	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	59	47	0	0.983333	0	A|0.006;C|0.194	0.194	strong	.	TMPRSS3	40	.	NM_001256317	exon8	c.A757G	p.I253V	CAGTGATGATCCA	.	PASS	Atlas-SNP
SERGEF	26297	hgsc.bcm.edu	37	11	17809639	17809639	+	Missense_Mutation	SNP	C	C	T	rs10788	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	269	120	296	1	0.446097	0.00337838	C|0.875;T|0.125	0.125	strong	.	SERGEF	38	.	NM_012139	exon11	c.G1370A	p.G457E	CACAGTCCCCCAT	.	PASS	Atlas-SNP
AIPL1	23746	hgsc.bcm.edu	37	17	6337247	6337247	+	Missense_Mutation	SNP	C	C	G	rs12449580	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	54	112	0	0.425197	0	C|0.803;G|0.197	0.197	strong	.	AIPL1	34	.	NM_014336	exon2	c.G268C	p.D90H	TGGTGTCGCACCA	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	12	84	0	0.139535	0	.	.	none	MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	2	NM_002457	exon30	c.C4709T	p.T1570I	CGGTGACCCCAAC	.	PASS	Atlas-SNP
GAS2L3	283431	hgsc.bcm.edu	37	12	101018161	101018161	+	Silent	SNP	C	C	T	rs1045603	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	31	49	0	0.584906	0	C|0.901;T|0.099	0.099	strong	.	GAS2L3	76	.	NM_174942	exon10	c.C1578T	p.S526S	CAGTTCCAAAACC	.	PASS	Atlas-SNP
LGR6	59352	hgsc.bcm.edu	37	1	202287754	202287754	+	Missense_Mutation	SNP	G	G	A	rs75658797	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	62	143	0	0.430556	0	G|0.899;A|0.101	0.101	strong	.	LGR6	102	.	NM_001017403	exon18	c.G2323A	p.V775M	AGGCACGTGGCCT	.	PASS	Atlas-SNP
C11orf1	64776	hgsc.bcm.edu	37	11	111754574	111754574	+	Silent	SNP	A	A	C	rs1045282	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	30	51	0	0.454545	0	A|0.734;C|0.266	0.266	strong	.	C11orf1	15	.	NM_022761	exon4	c.A423C	p.S141S	AAAGTCAACTTAC	.	PASS	Atlas-SNP
PLCH2	9651	hgsc.bcm.edu	37	1	2436256	2436256	+	Silent	SNP	G	G	A	rs138038983	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	6	78	0	0.0545455	0	G|0.983;A|0.017	0.017	strong	.	PLCH2	131	.	NM_014638	exon22	c.G3855A	p.G1285G	GGGAGGGACACGG	.	PASS	Atlas-SNP
OR52E2	119678	hgsc.bcm.edu	37	11	5080234	5080234	+	Silent	SNP	T	T	C	rs2445333	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	55	81	0	0.528846	0	T|0.698;C|0.302	0.302	strong	.	OR52E2	63	.	NM_001005164	exon1	c.A624G	p.L208L	AAACACTAGATTA	.	PASS	Atlas-SNP
ZDHHC8	29801	hgsc.bcm.edu	37	22	20131116	20131116	+	Missense_Mutation	SNP	G	G	A	rs80226867	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	14	9	0	0.411765	0	G|0.962;A|0.038	0.038	strong	.	ZDHHC8	77	.	NM_001185024	exon10	c.G1963A	p.A655T	AGCAACGCCCCGG	.	PASS	Atlas-SNP
PARP4	143	hgsc.bcm.edu	37	13	25009441	25009441	+	Missense_Mutation	SNP	C	C	G	rs13428	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	168	143	0	0.994083	0	G|0.405;C|0.595;A|0.000	0.405	strong	PARP4,NS,carcinoma,0,1	PARP4	142	1	NM_006437	exon31	c.G3838C	p.G1280R	CCACACCTCCACG	.	PASS	Atlas-SNP
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458598	4458598	+	Missense_Mutation	SNP	G	G	C	rs3809849	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	46	41	0	0.534884	0	G|0.795;C|0.205	0.205	strong	.	MYBBP1A	69	.	NM_014520	exon1	c.C22G	p.Q8E	TCGGCTGGGCGGG	.	PASS	Atlas-SNP
JRK	8629	hgsc.bcm.edu	37	8	143746416	143746416	+	Silent	SNP	A	A	G	rs754957	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	40	103	0	0.430108	0	A|0.478;G|0.522	0.522	strong	.	.	.	.	NM_003724	exon2	c.T1062C	p.H354H	GCGGGCATGGGGG	.	PASS	Atlas-SNP
EDARADD	128178	hgsc.bcm.edu	37	1	236645670	236645670	+	Silent	SNP	C	C	T	rs604070	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	111	68	102	0	0.612613	0	C|0.824;T|0.176	0.176	strong	.	EDARADD	31	.	NM_145861	exon6	c.C369T	p.D123D	ACTAGACGTGATC	.	PASS	Atlas-SNP
CASP9	842	hgsc.bcm.edu	37	1	15844615	15844615	+	Silent	SNP	A	A	G	rs1132312	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	121	150	0	0.930769	0	G|0.589;A|0.411	0.589	strong	CASP9,NS,carcinoma,0,1	CASP9	40	1	NM_001229	exon2	c.T408C	p.F136F	ATCACCAAATCCT	.	PASS	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632744	32632744	+	Silent	SNP	C	C	T	rs1049082	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	14	0	0	0.388889	.	C|0.668;T|0.332	0.332	strong	.	HLA-DQB1	15	.	NM_002123	exon2	c.G210A	p.A70A	GAAGCGCGCGTAC	.	PASS	Atlas-SNP
DTX1	1840	hgsc.bcm.edu	37	12	113532617	113532617	+	Silent	SNP	A	A	G	rs12427377	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	70	153	2	0.542636	0.0130719	A|0.898;G|0.102	0.102	strong	DTX1,NS,carcinoma,0,1	DTX1	83	1	NM_004416	exon6	c.A1251G	p.R417R	GGAGCGACTGGTC	.	scavenged	Atlas-SNP
ANO1	55107	hgsc.bcm.edu	37	11	70034065	70034065	+	Silent	SNP	C	C	T	rs61731870	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	28	36	0	0.56	0	C|0.998;T|0.002	0.002	strong	.	ANO1	156	.	NM_018043	exon26	c.C2916T	p.L972L	CAGCCTCGGCAGC	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	37	10	99126513	99126513	+	Silent	SNP	C	C	T	rs45527941	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	36	38	0	0.580645	0	C|0.962;T|0.038	0.038	strong	.	RRP12	97	.	NM_015179	exon27	c.G3201A	p.Q1067Q	TTTGCCCTGGGCG	.	PASS	Atlas-SNP
LIN9	286826	hgsc.bcm.edu	37	1	226474132	226474132	+	Silent	SNP	G	G	A	rs10799347	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	27	55	0	0.509434	0	G|0.296;A|0.704	0.704	strong	.	LIN9	57	.	NM_173083	exon6	c.C474T	p.F158F	TACACAGAAGTCA	.	PASS	Atlas-SNP
SLC2A10	81031	hgsc.bcm.edu	37	20	45354291	45354291	+	Missense_Mutation	SNP	G	G	A	rs2235491	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	30	67	0	0.517241	0	G|0.878;A|0.122	0.122	strong	.	SLC2A10	75	.	NM_030777	exon2	c.G616A	p.A206T	GGTGAGGCCCCCA	.	PASS	Atlas-SNP
OR5M1	390168	hgsc.bcm.edu	37	11	56380134	56380134	+	Missense_Mutation	SNP	C	C	G	rs4939078	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	356	158	385	0	0.44382	0	C|0.621;G|0.379	0.379	strong	.	OR5M1	92	.	NM_001004740	exon1	c.G845C	p.S282T	ATTGGGCTCAAAA	.	PASS	Atlas-SNP
LRRC23	10233	hgsc.bcm.edu	37	12	7022085	7022085	+	Missense_Mutation	SNP	T	T	A	rs1057077	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	45	25	62	0	0.555556	0	T|0.598;A|0.402	0.402	strong	.	LRRC23	46	.	NM_001135217	exon7	c.T950A	p.V317E	CTGATGTGATTCG	.	PASS	Atlas-SNP
NOTCH2	4853	hgsc.bcm.edu	37	1	120458161	120458161	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	51	104	0	0.408	0	.	.	none	.	NOTCH2	348	.	NM_024408	exon34	c.C7184G	p.S2395X	GCATTTGAGGAAG	.	PASS	Atlas-SNP
PLCE1	51196	hgsc.bcm.edu	37	10	95931011	95931011	+	Missense_Mutation	SNP	A	A	G	rs61751494	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	84	130	0	0.571429	0	A|0.996;G|0.004	0.004	strong	.	PLCE1	543	.	NM_016341	exon4	c.A1567G	p.I523V	GAGCTGATCGATC	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	37	12	26784850	26784850	+	Silent	SNP	G	G	A	rs2230372	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	41	137	0	0.390476	0	G|0.527;A|0.473	0.473	strong	.	ITPR2	270	.	NM_002223	exon22	c.C2883T	p.H961H	ATCCTCGTGCTCG	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720673	135720673	+	Silent	SNP	T	T	C	rs9872542	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	31	76	0	0.430556	0	T|0.802;C|0.198	0.198	strong	.	PPP2R3A	114	.	NM_002718	exon2	c.T333C	p.D111D	AAAGGATATTGCA	.	PASS	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50751529	50751529	+	Silent	SNP	G	G	C	rs67248662	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	65	86	0	0.570175	0	G|0.713;C|0.287	0.287	strong	FAM116B,caecum,carcinoma,0,1	.	.	1	NM_001001794	exon17	c.C1356G	p.P452P	GATCTGGGGGGGA	.	PASS	Atlas-SNP
C10orf71	118461	hgsc.bcm.edu	37	10	50534350	50534350	+	Missense_Mutation	SNP	G	G	A	rs11101095	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	19	38	0	0.452381	0	G|0.909;A|0.091	0.091	strong	C10orf71_ENST00000374144,NS,carcinoma,0,1	C10orf71	179	1	NM_001135196	exon3	c.G3760A	p.V1254I	GAGCCTGTCGGGA	.	PASS	Atlas-SNP
FCAR	2204	hgsc.bcm.edu	37	19	55401170	55401170	+	Missense_Mutation	SNP	A	A	G	rs16986050	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	16	35	0	0.551724	0	A|0.795;G|0.205	0.205	strong	FCAR,NS,carcinoma,-2,1	FCAR	110	1	NM_002000	exon5	c.A805G	p.S269G	AGCTGGAGCCAAC	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107049604	107049604	+	Silent	SNP	T	T	C	rs2912839		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	477	116	381	0	0.243187	0	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,-1,2	RGPD3	316	2	NM_001144013	exon16	c.A2343G	p.P781P	AGGAGATGGTGTA	.	scavenged	Atlas-SNP
ZNF70	7621	hgsc.bcm.edu	37	22	24086026	24086026	+	Silent	SNP	C	C	T	rs41277301	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	76	157	0	0.510067	0	C|0.974;T|0.026	0.026	strong	.	ZNF70	49	.	NM_021916	exon2	c.G1302A	p.L434L	GCGAATCAGGTGC	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124339378	124339378	+	Missense_Mutation	SNP	A	A	G	rs1969620	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	141	64	146	0	0.453901	0	A|0.909;G|0.091	0.091	strong	.	DMBT1	677	.	NM_007329	exon10	c.A964G	p.N322D	ACCCACAACTGTG	.	PASS	Atlas-SNP
SLC9A3	6550	hgsc.bcm.edu	37	5	483564	483564	+	Silent	SNP	A	A	G	rs56098739	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	73	129	0	0.429412	0	A|0.839;G|0.161	0.161	strong	SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	NM_004174	exon6	c.T966C	p.Y322Y	CTTCACATACTTC	.	PASS	Atlas-SNP
CIB2	10518	hgsc.bcm.edu	37	15	78398139	78398139	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	63	27	66	0	0.428571	0	.	.	none	.	CIB2	24	.	NM_006383	exon5	c.G484A	p.G162S	GCTTGCCGTCACC	.	PASS	Atlas-SNP
DPF1	8193	hgsc.bcm.edu	37	19	38702950	38702950	+	Silent	SNP	G	G	A	rs11547760	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	38	64	0	0.5	0	G|0.929;A|0.071	0.071	strong	.	DPF1	54	.	NM_001135155	exon11	c.C1144T	p.L382L	GACTCAGGCAGTA	.	PASS	Atlas-SNP
C17orf47	284083	hgsc.bcm.edu	37	17	56620501	56620501	+	Silent	SNP	A	A	G	rs17222523	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	170	95	144	0	0.558824	0	A|0.825;G|0.175	0.175	strong	.	C17orf47	59	.	NM_001038704	exon1	c.T1047C	p.H349H	TGTCACATGGTGA	.	PASS	Atlas-SNP
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035262	110035262	+	Silent	SNP	A	A	G	rs1026608	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	42	76	0	0.545455	0	A|0.746;G|0.254	0.254	strong	.	ZC3H12C	83	.	NM_033390	exon6	c.A1452G	p.R484R	CAAACGAGGTGCT	.	PASS	Atlas-SNP
ZNF598	90850	hgsc.bcm.edu	37	16	2049640	2049640	+	Missense_Mutation	SNP	A	A	G	rs2286469	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	21	41	0	0.446809	0	A|0.429;G|0.571	0.571	strong	ZNF598,NS,carcinoma,0,4	ZNF598	55	4	NM_178167	exon11	c.T1910C	p.M637T	CCCTCCATGTGTC	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	37	8	110534512	110534512	+	Silent	SNP	G	G	A	rs1563578	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	29	74	0	0.446154	0	G|0.740;A|0.260	0.260	strong	PKHD1L1,NS,carcinoma,+1,1	PKHD1L1	522	1	NM_177531	exon74	c.G12129A	p.S4043S	CATTTCGTCCATG	.	PASS	Atlas-SNP
TAF3	83860	hgsc.bcm.edu	37	10	8007260	8007260	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	41	84	0	0.554054	0	.	.	none	.	TAF3	93	.	NM_031923	exon3	c.A1787C	p.E596A	AATTTGAAGATGT	.	PASS	Atlas-SNP
ANKS1A	23294	hgsc.bcm.edu	37	6	35048899	35048899	+	Silent	SNP	T	T	C	rs35455943	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	49	18	48	0	0.367347	0	T|0.970;C|0.030	0.030	strong	.	ANKS1A	123	.	NM_015245	exon17	c.T2673C	p.P891P	TGACCCTGCGGCA	.	PASS	Atlas-SNP
OR5B21	219968	hgsc.bcm.edu	37	11	58275303	58275303	+	Silent	SNP	G	G	A	rs146345059	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	54	134	1	0.457627	0.00746269	G|0.999;A|0.001	0.001	strong	OR5B21,rectum,NS,0,1	OR5B21	59	1	NM_001005218	exon1	c.C276T	p.Y92Y	TCCATCGTAGGAG	.	scavenged	Atlas-SNP
WWC3	55841	hgsc.bcm.edu	37	X	10085674	10085674	+	Silent	SNP	T	T	C	rs6530368	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	17	17	14	0	1	0	T|0.061;C|0.939	0.939	strong	.	WWC3	142	.	NM_015691	exon11	c.T1575C	p.D525D	CGGGGATGGGGAA	.	PASS	Atlas-SNP
KIF1C	10749	hgsc.bcm.edu	37	17	4926882	4926882	+	Silent	SNP	A	A	G	rs346828	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	58	124	0	0.389262	0	A|0.339;G|0.661	0.661	strong	KIF1C,NS,carcinoma,0,1	KIF1C	70	1	NM_006612	exon23	c.A2748G	p.P916P	CTCGCCACCACTG	.	PASS	Atlas-SNP
ZNF717	100131827	hgsc.bcm.edu	37	3	75786440	75786440	+	Silent	SNP	C	C	T	rs6790146	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	30	42	1	0.967742	0.0238095	C|0.603;T|0.397	0.397	strong	ZNF717,NS,carcinoma,0,1	ZNF717	160	1	NM_001128223	exon5	c.G2334A	p.G778G	GTGAGTCCCCTGA	.	scavenged	Atlas-SNP
KRT40	125115	hgsc.bcm.edu	37	17	39140272	39140272	+	Missense_Mutation	SNP	A	A	G	rs17843015	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	78	136	0	0.481481	0	A|0.851;G|0.148	0.148	strong	.	KRT40	27	.	NM_182497	exon3	c.T254C	p.F85S	CTAGTGAACACCC	.	PASS	Atlas-SNP
LRRC37B	114659	hgsc.bcm.edu	37	17	30376271	30376271	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	331	5	307	0	0.0151057	0	.	.	none	LRRC37B,colon,carcinoma,+1,1	LRRC37B	67	1	NM_052888	exon10	c.G2534A	p.R845Q	TGTTGCGAACAGG	.	scavenged	Atlas-SNP
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629963	32629963	+	Missense_Mutation	SNP	C	C	T	rs1049100	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	71	56	0	0.763441	0	C|0.816;T|0.184	0.184	strong	.	HLA-DQB1	15	.	NM_002123	exon3	c.G442A	p.V148I	AGCAGACCAGCAG	.	PASS	Atlas-SNP
WDR78	79819	hgsc.bcm.edu	37	1	67313249	67313249	+	Silent	SNP	G	G	A	rs57010209	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	109	187	0	0.465812	0	G|0.910;A|0.090	0.090	strong	.	WDR78	102	.	NM_207014	exon8	c.C1209T	p.D403D	AAATAAGTCCTGA	.	PASS	Atlas-SNP
HAUS6	54801	hgsc.bcm.edu	37	9	19093287	19093287	+	Silent	SNP	A	A	G	rs41269011	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	250	132	199	0	0.528	0	A|0.878;G|0.122	0.122	strong	HAUS6,NS,carcinoma,0,1	HAUS6	66	1	NM_017645	exon4	c.T318C	p.S106S	AAAGCTACTTCCA	.	PASS	Atlas-SNP
TOPBP1	11073	hgsc.bcm.edu	37	3	133341988	133341988	+	Missense_Mutation	SNP	T	T	C	rs10935070	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	58	87	0	0.537037	0	T|0.819;C|0.181	0.181	strong	.	TOPBP1	218	.	NM_007027	exon19	c.A3125G	p.N1042S	TTATTATTGGTGG	.	PASS	Atlas-SNP
STAB2	55576	hgsc.bcm.edu	37	12	104123911	104123911	+	Silent	SNP	C	C	T	rs10778281	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	17	53	0	0.361702	0	C|0.717;T|0.283	0.283	strong	.	STAB2	370	.	NM_017564	exon49	c.C5100T	p.N1700N	TATAAACAATAAG	.	PASS	Atlas-SNP
TECTA	7007	hgsc.bcm.edu	37	11	120989335	120989335	+	Missense_Mutation	SNP	A	A	G	rs612969	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	50	120	0	0.423729	0	A|0.525;G|0.475	0.475	strong	.	TECTA	329	.	NM_005422	exon6	c.A1111G	p.R371G	CACCGCAGAGGTT	.	PASS	Atlas-SNP
MCTP2	55784	hgsc.bcm.edu	37	15	94884108	94884108	+	Silent	SNP	G	G	C	rs8025851	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	77	96	0	0.974684	0	G|0.505;C|0.495	0.495	strong	MCTP2,NS,carcinoma,0,2	MCTP2	122	2	NM_001159643	exon6	c.G924C	p.V308V	GATCGTGTTAAAT	.	PASS	Atlas-SNP
PNPLA1	285848	hgsc.bcm.edu	37	6	36270130	36270130	+	Missense_Mutation	SNP	C	C	A	rs12199580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	46	102	2	0.516854	0.0196078	C|0.661;A|0.339	0.339	strong	PNPLA1,back,malignant_melanoma,-1,1	PNPLA1	92	1	NM_001145717	exon6	c.C1268A	p.P423H	CTTCACCCAGGCC	.	scavenged	Atlas-SNP
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825662	34825662	+	Silent	SNP	T	T	C	rs16894959	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	106	44	117	0	0.415094	0	T|0.852;C|0.148	0.148	strong	.	UHRF1BP1	102	.	NM_017754	exon13	c.T1735C	p.L579L	GAACACTTGGACA	.	PASS	Atlas-SNP
SERTAD4	56256	hgsc.bcm.edu	37	1	210415626	210415626	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	34	66	0	0.377778	0	.	.	none	.	SERTAD4	53	.	NM_019605	exon4	c.A1015C	p.K339Q	CGGAAAAAGGAGG	.	PASS	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1686410	1686410	+	Missense_Mutation	SNP	T	T	C	rs9902398	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	94	78	0	0.979167	0	T|0.220;C|0.780	0.780	strong	.	SMYD4	50	.	NM_052928	exon10	c.A2180G	p.Y727C	ACCACGTAGAGAC	.	PASS	Atlas-SNP
ZNF592	9640	hgsc.bcm.edu	37	15	85341859	85341859	+	Missense_Mutation	SNP	G	G	A	rs8182086	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	26	57	0	0.448276	0	G|0.705;A|0.295	0.295	strong	ZNF592,colon,carcinoma,0,1	ZNF592	95	1	NM_014630	exon8	c.G2777A	p.S926N	TGTCAAGCCTCCA	.	PASS	Atlas-SNP
DBC1	1620	hgsc.bcm.edu	37	9	121929932	121929932	+	Silent	SNP	C	C	T	rs147029533	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	41	87	0	0.476744	0	C|0.994;T|0.006	0.006	strong	DBC1,NS,carcinoma,-2,1	DBC1	194	1	NM_014618	exon8	c.G1716A	p.S572S	GCCCTCCGAATGG	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	37	15	43748304	43748304	+	Silent	SNP	A	A	G	rs690367	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	114	46	122	0	0.403509	0	A|0.491;G|0.509	0.509	strong	.	TP53BP1	157	.	NM_001141980	exon12	c.T2502C	p.D834D	TGAAGAATCTTGC	.	PASS	Atlas-SNP
IL16	3603	hgsc.bcm.edu	37	15	81598416	81598416	+	Silent	SNP	G	G	A	rs1803275	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	25	63	0	0.480769	0	G|0.855;A|0.145	0.145	strong	.	IL16	254	.	NM_001172128	exon17	c.G3588A	p.R1196R	CACAAGGAAGCTG	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	37	19	13397560	13397560	+	Missense_Mutation	SNP	C	C	T	rs16027	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	35	24	0	0.614035	0	C|0.927;T|0.073	0.073	strong	.	CACNA1A	715	.	NM_001127221	exon20	c.G3313A	p.G1105S	TGGGGCCGGGGTC	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978090	45978090	+	Missense_Mutation	SNP	C	C	T	rs233252	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	98	70	0	0.98	0	C|0.106;T|0.894	0.894	strong	.	KRTAP10-3	17	.	NM_198696	exon1	c.G509A	p.C170Y	ACACAGCAGGTGG	.	PASS	Atlas-SNP
UTP14C	9724	hgsc.bcm.edu	37	13	52603241	52603241	+	Missense_Mutation	SNP	A	A	G	rs3742290	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	210	112	203	0	0.533333	0	A|0.911;G|0.089	0.089	strong	UTP14C,NS,carcinoma,0,1	UTP14C	67	1	NM_021645	exon2	c.A301G	p.T101A	TTGGCCACTGTAA	.	PASS	Atlas-SNP
ALDH3B2	222	hgsc.bcm.edu	37	11	67432799	67432799	+	Silent	SNP	G	G	A	rs80147122	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	233	6	230	1	0.0257511	0.00434783	.	.	strong	ALDH3B2,NS,haematopoietic_neoplasm,0,2	ALDH3B2	46	2	NM_001031615	exon7	c.C663T	p.R221R	GGCCACGCGGCTG	.	scavenged	Atlas-SNP
RPL13A	23521	hgsc.bcm.edu	37	19	49993535	49993535	+	Silent	SNP	C	C	G	rs1064257	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	18	41	0	0.391304	0	C|0.964;G|0.036	0.036	strong	.	RPL13A	13	.	NM_012423	exon3	c.C135G	p.G45G	TTCTGGCAATTTC	.	PASS	Atlas-SNP
SESTD1	91404	hgsc.bcm.edu	37	2	179979930	179979930	+	Silent	SNP	T	T	C	rs2289993	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	41	133	0	0.414141	0	T|0.810;C|0.190	0.190	strong	.	SESTD1	66	.	NM_178123	exon16	c.A1701G	p.Q567Q	CAAAGATTGGCAT	.	PASS	Atlas-SNP
TMEM222	84065	hgsc.bcm.edu	37	1	27660731	27660731	+	Silent	SNP	G	G	C	rs6663062	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	129	114	155	0	0.883721	0	G|0.969;C|0.031	0.031	strong	.	TMEM222	16	.	NM_032125	exon5	c.G498C	p.V166V	TATGGTGACGCTC	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168115797	168115797	+	Missense_Mutation	SNP	G	G	C	rs75758327	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	36	108	0	0.514286	0	G|0.922;C|0.078	0.078	strong	.	XIRP2	914	.	NM_001199143	exon11	c.G2840C	p.R947T	TTCCCAGAGTGGA	.	PASS	Atlas-SNP
DNTTIP2	30836	hgsc.bcm.edu	37	1	94341267	94341267	+	Silent	SNP	A	A	G	rs2273165	bycluster;byfrequency;bysubmitter;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	76	74	0	1	0	A|0.510;G|0.490	0.490	strong	.	DNTTIP2	59	.	NM_014597	exon3	c.T1740C	p.F580F	TGCATTAAAATTA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506747	195506747	+	Missense_Mutation	SNP	C	C	T	rs62282470	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	58	21	0	0.763158	0	C|0.920;T|0.080	0.080	strong	MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	NM_018406	exon2	c.G11704A	p.A3902T	GGGTGGCGTGACG	.	PASS	Atlas-SNP
NDUFB1	4707	hgsc.bcm.edu	37	14	92588002	92588002	+	Silent	SNP	T	T	G	rs3818263	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	39	65	0	0.419355	0	T|0.520;G|0.480	0.480	strong	NDUFB1,rectum,carcinoma,0,1	NDUFB1	5	1	NM_004545	exon1	c.A120C	p.V40V	AGCGCCTACAGCG	.	PASS	Atlas-SNP
GDPGP1	390637	hgsc.bcm.edu	37	15	90785060	90785060	+	Missense_Mutation	SNP	C	C	T	rs10153004	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	67	132	0	0.452703	0	C|0.835;T|0.165	0.165	strong	.	.	.	.	NM_001013657	exon4	c.C920T	p.T307I	CCCTCACAGGGGT	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6580495	6580495	+	Silent	SNP	G	G	A	rs72901756	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	57	110	0	0.487179	0	G|0.957;A|0.043	0.043	strong	.	DNHD1	198	.	NM_144666	exon28	c.G9501A	p.Q3167Q	ACAGCAGCTGAAA	.	PASS	Atlas-SNP
FGD3	89846	hgsc.bcm.edu	37	9	95782667	95782667	+	Silent	SNP	C	C	T	rs11790517	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	47	81	0	0.460784	0	C|0.684;T|0.316	0.316	strong	.	FGD3	116	.	NM_001083536	exon13	c.C1455T	p.F485F	CGCCTTCAGCCAG	.	PASS	Atlas-SNP
C16orf70	80262	hgsc.bcm.edu	37	16	67166731	67166731	+	Missense_Mutation	SNP	G	G	A	rs34017457	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	60	190	0	0.447761	0	G|0.994;A|0.006	0.006	strong	.	C16orf70	38	.	NM_025187	exon6	c.G367A	p.A123T	AACTCCGCTGAGC	.	PASS	Atlas-SNP
MRPL4	51073	hgsc.bcm.edu	37	19	10370310	10370310	+	Missense_Mutation	SNP	A	A	G	rs77884668	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	40	71	0	0.540541	0	A|0.984;G|0.016	0.016	strong	.	MRPL4	22	.	NM_146387	exon10	c.A757G	p.M253V	CACAGCATGCTCA	.	PASS	Atlas-SNP
MMP17	4326	hgsc.bcm.edu	37	12	132335592	132335592	+	Missense_Mutation	SNP	G	G	A	rs11835665	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	94	165	0	0.531073	0	G|0.816;A|0.184	0.184	strong	.	MMP17	77	.	NM_016155	exon10	c.G1585A	p.D529N	CAGGCCGATGGAT	.	PASS	Atlas-SNP
SLC25A10	1468	hgsc.bcm.edu	37	17	79682558	79682558	+	Silent	SNP	T	T	C	rs2072700	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	70	55	0	0.972222	0	T|0.579;C|0.421	0.421	strong	SLC25A10,NS,carcinoma,0,1	SLC25A10	24	1	NM_001270888	exon3	c.T264C	p.R88R	GGACCGTGTGGCC	.	PASS	Atlas-SNP
ANKRD50	57182	hgsc.bcm.edu	37	4	125592065	125592065	+	Silent	SNP	C	C	A	rs10018651	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	161	88	193	0	0.546584	0	C|0.743;A|0.257	0.257	strong	.	ANKRD50	136	.	NM_020337	exon4	c.G2367T	p.A789A	CATAGACGCTGCT	.	PASS	Atlas-SNP
PIK3R1	5295	hgsc.bcm.edu	37	5	67522722	67522722	+	Silent	SNP	C	C	T	rs706713	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	71	172	0	0.514493	0	C|0.633;T|0.367	0.367	strong	.	PIK3R1	869	.	NM_181523	exon2	c.C219T	p.Y73Y	AACTTACGTAGAA	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108133967	108133967	+	Silent	SNP	A	A	G	rs2229085	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	219	101	172	0	0.461187	0	A|0.801;G|0.199	0.199	strong	.	FER	100	.	NM_005246	exon3	c.A84G	p.V28V	AACAGTAAAGAAA	.	PASS	Atlas-SNP
RUFY4	285180	hgsc.bcm.edu	37	2	218940259	218940259	+	Silent	SNP	C	C	T	rs7423696	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	64	101	0	0.547009	0	C|0.769;T|0.231	0.231	strong	.	RUFY4	59	.	NM_198483	exon9	c.C1044T	p.P348P	GATGCCCAGCCCC	.	PASS	Atlas-SNP
PTTG2	10744	hgsc.bcm.edu	37	4	37962133	37962133	+	Silent	SNP	G	G	A	rs2290740	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	186	106	180	0	0.569892	0	G|0.784;A|0.216	0.216	strong	.	PTTG2	15	.	NM_006607	exon1	c.G78A	p.L26L	GAAGCTGGAGTCT	.	PASS	Atlas-SNP
AGPS	8540	hgsc.bcm.edu	37	2	178364363	178364363	+	Silent	SNP	A	A	C	rs148418568	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	6	32	0	0.26087	0	A|1.000;C|0.000	0.000	strong	.	AGPS	56	.	NM_003659	exon14	c.A1380C	p.P460P	TGACCCAAATCAG	.	PASS	Atlas-SNP
CAD	790	hgsc.bcm.edu	37	2	27447310	27447310	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	40	88	0	0.444444	0	.	.	none	CAD,NS,carcinoma,+2,1	CAD	199	1	NM_004341	exon9	c.G1206A	p.G402G	CTCAGGGGGCCTC	.	PASS	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	37	1	144931087	144931087	+	Missense_Mutation	SNP	T	T	C	rs41315684	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	46	150	0	0.294872	0	T|0.845;C|0.155	0.155	strong	.	PDE4DIP	817	.	NM_001002811	exon1	c.A622G	p.T208A	CTTCAGTGCAAAT	.	PASS	Atlas-SNP
MIB2	142678	hgsc.bcm.edu	37	1	1562536	1562536	+	Silent	SNP	G	G	A	rs11544452	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	90	81	0	0.909091	0	G|0.860;A|0.140	0.140	strong	.	MIB2	62	.	NM_080875	exon11	c.G1668A	p.A556A	GGTGGCGCTGGGT	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	37	2	27801418	27801418	+	Missense_Mutation	SNP	C	C	A	rs1919126	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	102	286	0	0.421488	0	C|0.365;A|0.635	0.635	strong	.	C2orf16	357	.	NM_032266	exon1	c.C1979A	p.A660E	AGTCTGCAGAATT	.	PASS	Atlas-SNP
ADAT3	113179	hgsc.bcm.edu	37	19	1912934	1912934	+	Silent	SNP	T	T	C	rs12984675	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	15	15	8	0	1	0	T|0.727;C|0.273	0.273	strong	.	ADAT3	15	.	NM_138422	exon2	c.T888C	p.T296T	GTGCACTGGCTAC	.	PASS	Atlas-SNP
COL13A1	1305	hgsc.bcm.edu	37	10	71562437	71562437	+	Silent	SNP	G	G	A	rs10998973	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	58	120	0	0.391892	0	G|0.444;A|0.556	0.556	strong	COL13A1_ENST00000398978,NS,carcinoma,0,2	COL13A1	133	2	NM_080802	exon1	c.G258A	p.T86T	GGAGACGGCTATT	.	PASS	Atlas-SNP
MON2	23041	hgsc.bcm.edu	37	12	62979216	62979216	+	Silent	SNP	G	G	A	rs11174557	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	69	133	0	0.579832	0	G|0.884;A|0.116	0.116	strong	.	MON2	160	.	NM_015026	exon33	c.G4842A	p.R1614R	AAAGAGGTCCCAA	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	37	2	216298084	216298084	+	Silent	SNP	G	G	A	rs2289202	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	57	117	0	0.508929	0	G|0.783;A|0.217	0.217	strong	FN1,NS,carcinoma,-2,1	FN1	521	1	NM_212476	exon3	c.C378T	p.I126I	AGCCCCGATGCAG	.	PASS	Atlas-SNP
PLA2G5	5322	hgsc.bcm.edu	37	1	20411332	20411332	+	Silent	SNP	C	C	T	rs2020887	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	186	158	0	0.984127	0	C|0.724;T|0.276	0.276	strong	PLA2G5,NS,carcinoma,+2,2	PLA2G5	21	2	NM_000929	exon2	c.C9T	p.G3G	GAAAGGCCTCCTC	.	PASS	Atlas-SNP
NCF2	4688	hgsc.bcm.edu	37	1	183542387	183542387	+	Missense_Mutation	SNP	T	T	C	rs2274064	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	120	63	121	0	0.525	0	T|0.538;C|0.462	0.462	strong	.	NCF2	69	.	NM_001127651	exon6	c.A542G	p.K181R	AACAGCTTGCCCA	.	PASS	Atlas-SNP
PRR22	163154	hgsc.bcm.edu	37	19	5783905	5783905	+	Missense_Mutation	SNP	G	G	A	rs3745640	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	28	30	0	0.56	0	G|0.702;A|0.298	0.298	strong	.	PRR22	25	.	NM_001134316	exon3	c.C353T	p.P118L	GGCTGAGGCTCCA	.	PASS	Atlas-SNP
PCSK1N	27344	hgsc.bcm.edu	37	X	48690749	48690749	+	Silent	SNP	C	C	T	rs11538178	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	10	9	11	0	0.9	0	C|0.763;T|0.237	0.237	strong	.	PCSK1N	6	.	NM_013271	exon2	c.G117A	p.E39E	GCGGGGCTCCTGC	.	PASS	Atlas-SNP
SLITRK2	84631	hgsc.bcm.edu	37	X	144904252	144904252	+	Silent	SNP	G	G	A	rs3810704	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	82	74	0	0.97619	0	G|0.836;A|0.164	0.164	strong	.	SLITRK2	221	.	NM_001144005	exon5	c.G309A	p.T103T	CCGAACGGGGGCA	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	37	11	117391966	117391966	+	Silent	SNP	G	G	A	rs2276340	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	44	77	0	0.478261	0	G|0.848;A|0.152	0.152	strong	DSCAML1,colon,carcinoma,-1,1	DSCAML1	286	1	NM_020693	exon6	c.C1272T	p.R424R	GAGCCCGCGGATG	.	PASS	Atlas-SNP
ZDHHC8	29801	hgsc.bcm.edu	37	22	20126741	20126741	+	Silent	SNP	G	G	T	rs61737216	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	58	98	0	0.517857	0	G|0.959;T|0.041	0.041	strong	.	ZDHHC8	77	.	NM_001185024	exon2	c.G129T	p.V43V	AGCTGTGTCCCCA	.	PASS	Atlas-SNP
CHL1	10752	hgsc.bcm.edu	37	3	361508	361508	+	Missense_Mutation	SNP	C	C	T	rs2272522	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	23	47	0	0.5	0	C|0.678;T|0.322	0.322	strong	CHL1,caecum,carcinoma,0,2	CHL1	242	2	NM_001253388	exon1	c.C49T	p.L17F	ATGTTCCTCCTGT	.	PASS	Atlas-SNP
ESYT2	57488	hgsc.bcm.edu	37	7	158528233	158528233	+	Silent	SNP	A	A	G	rs3816462	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	34	91	0	0.453333	0	A|0.703;G|0.297	0.297	strong	.	ESYT2	70	.	NM_020728	exon20	c.T2547C	p.S849S	GCCGCCACTGTTC	.	PASS	Atlas-SNP
LRP4	4038	hgsc.bcm.edu	37	11	46897446	46897446	+	Missense_Mutation	SNP	G	G	A	rs2306033	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	204	112	175	0	0.54902	0	G|0.848;A|0.152	0.152	strong	.	LRP4	160	.	NM_002334	exon26	c.C3608T	p.A1203V	AGCACCGCGCGGT	.	PASS	Atlas-SNP
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24381387	24381387	+	Silent	SNP	G	G	C	rs1207577	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	467	466	406	1	0.997859	0.00246305	G|0.535;C|0.465	0.465	strong	.	.	.	.	NM_001136234	exon1	c.G510C	p.T170T	TCCAACGATGCAG	.	PASS	Atlas-SNP
FAM83E	54854	hgsc.bcm.edu	37	19	49106995	49106995	+	Missense_Mutation	SNP	G	G	A	rs3745728	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	4	8	0	0.8	0	G|0.814;A|0.186	0.186	strong	FAM83E,NS,NS,0,1	FAM83E	34	1	NM_017708	exon4	c.C932T	p.P311L	CGGTGCGGGCTGC	.	scavenged	Atlas-SNP
KIF5C	3800	hgsc.bcm.edu	37	2	149806388	149806388	+	Silent	SNP	C	C	T	rs60169973	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	54	115	0	0.5	0	C|0.884;T|0.116	0.116	strong	.	KIF5C	166	.	NM_004522	exon9	c.C750T	p.D250D	TCTTGACGAAGCT	.	PASS	Atlas-SNP
RNASE9	390443	hgsc.bcm.edu	37	14	21026773	21026773	+	Splice_Site	SNP	C	C	T	rs891297	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	56	94	0	0.538462	0	C|0.689;T|0.311	0.311	strong	.	RNASE9	30	.	NM_001110361	exon5	c.1+1G>A	.	AACATACTCTCAC	.	PASS	Atlas-SNP
PRR5-ARHGAP8	553158	hgsc.bcm.edu	37	22	45258333	45258333	+	Missense_Mutation	SNP	C	C	G	rs9614957	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	85	80	0	1	0	C|0.911;G|0.089	0.089	strong	.	PRR5-ARHGAP8	53	.	NM_181334	exon15	c.C1526G	p.P509R	AGGCACCTGGGGA	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31379773	31379773	+	Silent	SNP	C	C	T	rs56319010		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	64	138	1	0.984615	0.00724638	.	.	weak	.	MICA	21	.	NM_001177519	exon4	c.C663T	p.I221I	CAACATCACCGTG	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557489	32557489	+	Missense_Mutation	SNP	A	A	T	rs199514452	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	246	22	275	2	0.0894309	0.00727273	A|0.864;T|0.136	0.136	strong	HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon1	c.T31A	p.C11S	TCATGCAGGAGCC	.	scavenged	Atlas-SNP
ATG9A	79065	hgsc.bcm.edu	37	2	220087088	220087088	+	Silent	SNP	T	T	G	rs146429396	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	41	105	0	0.43617	0	T|0.990;G|0.010	0.010	strong	ATG9A,NS,carcinoma,+1,1	ATG9A	50	1	NM_001077198	exon12	c.A1933C	p.R645R	CAGCCCTGTGCCT	.	PASS	Atlas-SNP
OR2T34	127068	hgsc.bcm.edu	37	1	248737348	248737348	+	Silent	SNP	G	G	A	rs61833442	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	365	48	353	0	0.131507	0	G|0.787;A|0.213	0.213	strong	OR2T34,NS,carcinoma,-2,1	OR2T34	72	1	NM_001001821	exon1	c.C711T	p.A237A	GCGGCCGGCGGCA	.	scavenged	Atlas-SNP
PEG3	5178	hgsc.bcm.edu	37	19	57327503	57327503	+	Silent	SNP	A	A	G	rs33931963	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	116	260	0	0.454902	0	A|0.767;G|0.233	0.233	strong	ZIM2_ENST00000326441,NS,carcinoma,-1,2	PEG3	414	2	NM_001146184	exon9	c.T2307C	p.Y769Y	TGCCTCATAGACA	.	PASS	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	37	8	139824057	139824057	+	Silent	SNP	G	G	A	rs10101430	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	87	215	0	0.453125	0	G|0.507;A|0.493	0.493	strong	.	COL22A1	390	.	NM_152888	exon9	c.C1434T	p.C478C	AGCTGGGCAGGAG	.	PASS	Atlas-SNP
CASQ2	845	hgsc.bcm.edu	37	1	116310967	116310967	+	Missense_Mutation	SNP	T	T	C	rs4074536	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	62	146	0	0.459259	0	T|0.631;C|0.369	0.369	strong	CASQ2,colon,carcinoma,0,1	CASQ2	54	1	NM_001232	exon1	c.A196G	p.T66A	TTTGCGTGACCTT	.	PASS	Atlas-SNP
ATP4A	495	hgsc.bcm.edu	37	19	36051333	36051333	+	Missense_Mutation	SNP	G	G	T	rs139075511	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	31	41	0	0.508197	0	G|0.993;T|0.007	0.007	strong	.	ATP4A	123	.	NM_000704	exon6	c.C719A	p.P240H	CACTCGGGTGAGC	.	PASS	Atlas-SNP
HERC2	8924	hgsc.bcm.edu	37	15	28474686	28474686	+	Missense_Mutation	SNP	G	G	C	rs118112076	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	348	151	347	0	0.433908	0	G|0.990;C|0.010	0.010	strong	.	HERC2	501	.	NM_004667	exon33	c.C5040G	p.S1680R	ATTCTTGCTCGCC	.	PASS	Atlas-SNP
NCOR2	9612	hgsc.bcm.edu	37	12	124826462	124826462	+	Missense_Mutation	SNP	C	C	T	rs2229840	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	62	111	0	0.563636	0	C|0.859;T|0.141	0.141	strong	.	NCOR2	475	.	NM_006312	exon36	c.G5095A	p.A1699T	TGGCCGCGTTGTG	.	PASS	Atlas-SNP
ZNF850	342892	hgsc.bcm.edu	37	19	37239278	37239278	+	Silent	SNP	C	C	A	rs11672680	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	9	7	0	0	0.777778	.	C|0.777;A|0.223	0.223	strong	.	ZNF850	14	.	NM_001193552	exon5	c.G2664T	p.R888R	AATTCGCCGATGT	.	PASS	Atlas-SNP
OR10G9	219870	hgsc.bcm.edu	37	11	123893801	123893801	+	Missense_Mutation	SNP	A	A	G	rs74791330	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	309	46	402	1	0.148867	0.00248756	A|0.814;G|0.186	0.186	strong	OR10G9,NS,haematopoietic_neoplasm,0,3	OR10G9	80	3	NM_001001953	exon1	c.A82G	p.I28V	TTTGGAATCTTCC	.	scavenged	Atlas-SNP
ATAD5	79915	hgsc.bcm.edu	37	17	29159404	29159404	+	Silent	SNP	G	G	C	rs999796	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	29	72	1	0.439394	0.0138889	G|0.765;C|0.235	0.235	strong	ATAD5,NS,carcinoma,0,1	ATAD5	150	1	NM_024857	exon1	c.G39C	p.P13P	TGCTCCGCCTCCC	.	scavenged	Atlas-SNP
AHRR	57491	hgsc.bcm.edu	37	5	434722	434722	+	Missense_Mutation	SNP	G	G	C	rs34453673	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	58	82	0	0.53211	0	G|0.808;C|0.192	0.192	strong	AHRR,colon,carcinoma,0,1	AHRR	67	1	NM_020731	exon12	c.G1933C	p.D645H	CCCACAGACGGCC	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	377111	377111	+	Silent	SNP	G	G	C	rs10814431	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	23	13	22	0	0.565217	0	G|0.749;C|0.251	0.251	strong	.	DOCK8	401	.	NM_203447	exon20	c.G2340C	p.L780L	CTGCCTGAACTCC	.	PASS	Atlas-SNP
OR5V1	81696	hgsc.bcm.edu	37	6	29323905	29323905	+	Missense_Mutation	SNP	A	A	C	rs6930033	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	105	47	85	0	0.447619	0	A|0.805;C|0.195	0.195	strong	.	OR5V1	63	.	NM_030876	exon1	c.T68G	p.L23W	AACTGCAATTCAT	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54724443	54724443	+	Missense_Mutation	SNP	G	G	A	rs201735825	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	62	38	74	0	0.612903	0	G|0.860;A|0.140	0.140	strong	.	LILRB3	67	.	NM_006864	exon6	c.C1213T	p.H405Y	GCAGGTGGGGGTT	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134682833	134682833	+	Missense_Mutation	SNP	C	C	T	rs149742494	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	34	34	0	0.596491	0	C|0.994;T|0.006	0.006	strong	.	TTC40	100	.	NM_001200049	exon33	c.G4555A	p.A1519T	GGCGCGCGGCTGC	.	PASS	Atlas-SNP
LGALS14	56891	hgsc.bcm.edu	37	19	40196627	40196627	+	Missense_Mutation	SNP	G	G	A	rs72480733	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	186	166	1	0.994652	0.0060241	G|0.919;A|0.081	0.081	strong	LGALS14,colon,carcinoma,+1,1	LGALS14	38	1	NM_203471	exon2	c.G80A	p.R27H	AAGGACGTCCATT	.	PASS	Atlas-SNP
FAH	2184	hgsc.bcm.edu	37	15	80472561	80472561	+	Silent	SNP	C	C	T	rs1801374	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	10	26	0	0.37037	0	C|0.952;T|0.048	0.048	strong	.	FAH	36	.	NM_000137	exon12	c.C1056T	p.S352S	CATCAGCGGGCCG	.	PASS	Atlas-SNP
GAK	2580	hgsc.bcm.edu	37	4	844781	844781	+	Silent	SNP	G	G	A	rs75072999	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	198	78	239	0	0.393939	0	G|0.939;A|0.061	0.061	strong	GAK,rectum,carcinoma,0,1	GAK	104	1	NM_005255	exon26	c.C3600T	p.T1200T	TGCAATGGTCTTT	.	PASS	Atlas-SNP
SPATC1L	84221	hgsc.bcm.edu	37	21	47588465	47588465	+	Missense_Mutation	SNP	C	C	T	rs77889636	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	31	45	0	0.476923	0	C|0.967;T|0.033	0.033	strong	.	.	.	.	NM_001142854	exon3	c.G301A	p.D101N	AGGTGTCGTCCTC	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	37	7	48311563	48311563	+	Missense_Mutation	SNP	T	T	G	rs17712293	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	121	59	133	0	0.487603	0	T|0.817;G|0.183	0.183	strong	.	ABCA13	1192	.	NM_152701	exon17	c.T2300G	p.I767S	AGGATATTCTGAA	.	PASS	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41865525	41865525	+	Missense_Mutation	SNP	G	G	T	rs62001448	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	14	74	0	0.142857	0	G|0.915;T|0.085	0.085	strong	.	TYRO3	169	.	NM_006293	exon17	c.G2005T	p.V669L	ATGACAGTGTGTG	.	PASS	Atlas-SNP
KRT27	342574	hgsc.bcm.edu	37	17	38938316	38938316	+	Missense_Mutation	SNP	C	C	T	rs12453124	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	16	27	0	0.533333	0	C|0.859;T|0.141	0.141	strong	.	KRT27	41	.	NM_181537	exon1	c.G430A	p.E144K	TAAGTTCGTCAAT	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	T	G	rs7863519	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	58	118	1	0.460317	0.00847458	T|0.684;G|0.316	0.316	strong	SVEP1,NS,carcinoma,0,2	SVEP1	326	2	NM_153366	exon26	c.A4330C	p.M1444L	GGAGCATGCCATC	.	scavenged	Atlas-SNP
CDT1	81620	hgsc.bcm.edu	37	16	88870967	88870967	+	Silent	SNP	T	T	C	rs475667	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	36	125	0	0.310345	0	T|0.874;C|0.126	0.126	strong	.	CDT1	30	.	NM_030928	exon2	c.T243C	p.S81S	CCCCAGTACCCCC	.	PASS	Atlas-SNP
PHC1	1911	hgsc.bcm.edu	37	12	9070366	9070366	+	Silent	SNP	T	T	A	rs4883198	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	199	197	211	0	0.98995	0	T|0.310;A|0.690	0.690	strong	.	PHC1	67	.	NM_004426	exon2	c.T93A	p.L31L	GTCACTTTATGAA	.	PASS	Atlas-SNP
DBNL	28988	hgsc.bcm.edu	37	7	44099664	44099664	+	Silent	SNP	T	T	C	rs11552797	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	192	97	201	1	0.505208	0.00497512	T|0.715;C|0.285	0.285	strong	DBNL,NS,carcinoma,0,1	DBNL	26	1	NM_001122956	exon12	c.T1092C	p.A364A	AGGTGCTGGCTCT	.	PASS	Atlas-SNP
DOCK8	81704	hgsc.bcm.edu	37	9	390512	390512	+	Silent	SNP	C	C	T	rs2297075	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	264	138	259	1	0.522727	0.003861	C|0.729;T|0.271	0.271	strong	DOCK8_ENST00000453981,NS,adenoma,0,2	DOCK8	401	2	NM_203447	exon24	c.C2916T	p.T972T	CAGCACCGGAATG	.	PASS	Atlas-SNP
NUCB2	4925	hgsc.bcm.edu	37	11	17351683	17351683	+	Missense_Mutation	SNP	C	C	G	rs757081	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	34	58	0	0.596491	0	C|0.738;G|0.262	0.262	strong	.	NUCB2	31	.	NM_005013	exon12	c.C1012G	p.Q338E	TTAGATCAGCAAC	.	PASS	Atlas-SNP
SAMD9	54809	hgsc.bcm.edu	37	7	92730687	92730687	+	Missense_Mutation	SNP	C	C	T	rs148724199	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	28	66	0	0.4375	0	C|0.999;T|0.001	0.001	strong	.	SAMD9	239	.	NM_001193307	exon2	c.G4724A	p.G1575E	GAAAATCCCAGGT	.	PASS	Atlas-SNP
KRT14	3861	hgsc.bcm.edu	37	17	39742856	39742856	+	Silent	SNP	G	G	A	rs6503639	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	42	23	51	0	0.547619	0	G|0.774;A|0.226	0.226	strong	.	KRT14	65	.	NM_000526	exon1	c.C231T	p.S77S	GCTGCTGCTGCTG	.	PASS	Atlas-SNP
SPHK2	56848	hgsc.bcm.edu	37	19	49132634	49132634	+	Silent	SNP	G	G	A	rs3745733	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	34	25	0	0.653846	0	G|0.907;A|0.093	0.093	strong	SPHK2,NS,carcinoma,0,1	SPHK2	62	1	NM_020126	exon7	c.G1569A	p.L523L	TCCGCTGGGCACC	.	PASS	Atlas-SNP
IDI2	91734	hgsc.bcm.edu	37	10	1068639	1068639	+	Silent	SNP	C	C	T	rs13377037	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	48	22	59	0	0.458333	0	C|0.900;N|0.000	.	strong	.	IDI2	20	.	NM_033261	exon3	c.G219A	p.T73T	GACTTTCGTGTCC	.	PASS	Atlas-SNP
OR4D2	124538	hgsc.bcm.edu	37	17	56247101	56247101	+	Missense_Mutation	SNP	C	C	A	rs60994383	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	60	141	0	0.444444	0	C|0.745;A|0.255	0.255	strong	.	OR4D2	48	.	NM_001004707	exon1	c.C85A	p.L29I	CTGTTTCTAATGT	.	PASS	Atlas-SNP
SLC52A1	55065	hgsc.bcm.edu	37	17	4936336	4936336	+	Silent	SNP	A	A	T	rs72822610	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	31	42	0	0.525424	0	A|0.868;T|0.132	0.132	strong	.	.	.	.	NM_017986	exon5	c.T1263A	p.L421L	GGCACCAAGCAGG	.	PASS	Atlas-SNP
TRMU	55687	hgsc.bcm.edu	37	22	46733831	46733831	+	Missense_Mutation	SNP	G	G	A	rs55952751	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	32	124	0	0.347826	0	G|0.999;A|0.001	0.001	strong	.	TRMU	23	.	NM_018006	exon2	c.G238A	p.D80N	TGGAATGATGTGT	.	PASS	Atlas-SNP
PRSS53	339105	hgsc.bcm.edu	37	16	31096164	31096164	+	Missense_Mutation	SNP	G	G	C	rs7199949	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	242	121	250	0	0.5	0	G|0.648;C|0.352	0.352	strong	PRSS53,NS,carcinoma,0,2	PRSS53	29	2	NM_001039503	exon8	c.C1216G	p.P406A	GGTCAGGATAGGG	.	PASS	Atlas-SNP
PLRG1	5356	hgsc.bcm.edu	37	4	155459194	155459194	+	Silent	SNP	A	A	T	rs7668818	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	212	112	209	0	0.528302	0	A|0.748;T|0.252	0.252	strong	.	PLRG1	43	.	NM_002669	exon13	c.T1218A	p.I406I	ATTTTGAATGAAA	.	PASS	Atlas-SNP
STRN3	29966	hgsc.bcm.edu	37	14	31425437	31425437	+	Silent	SNP	T	T	C	rs12886419	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	48	89	0	0.489796	0	T|0.773;C|0.227	0.227	strong	.	STRN3	117	.	NM_001083893	exon2	c.A294G	p.A98A	TAGAAATGCAATC	.	PASS	Atlas-SNP
UNC93A	54346	hgsc.bcm.edu	37	6	167719436	167719436	+	Missense_Mutation	SNP	G	G	A	rs2072767	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	66	99	0	0.985075	0	G|0.732;A|0.268	0.268	strong	.	UNC93A	66	.	NM_018974	exon6	c.G874A	p.V292I	CAGTTCGTCGGCT	.	PASS	Atlas-SNP
CDH7	1005	hgsc.bcm.edu	37	18	63530016	63530016	+	Missense_Mutation	SNP	A	A	G	rs2291343	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	94	165	0	0.497355	0	A|0.380;G|0.620	0.620	strong	.	CDH7	362	.	NM_004361	exon11	c.A1727G	p.N576S	GCACCAACACCCT	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139369212	139369212	+	Silent	SNP	G	G	A	rs17567909	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	24	62	0	0.48	0	G|0.926;A|0.074	0.074	strong	.	SEC16A	249	.	NM_014866	exon3	c.C2856T	p.P952P	AAATCCGGGAAGA	.	PASS	Atlas-SNP
KCTD2	23510	hgsc.bcm.edu	37	17	73058249	73058249	+	Missense_Mutation	SNP	A	A	G	rs61750318	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	239	95	195	0	0.39749	0	A|0.999;G|0.001	0.001	strong	.	KCTD2	15	.	NM_015353	exon5	c.A671G	p.N224S	ACGGCAATGAGGA	.	PASS	Atlas-SNP
ADPRH	141	hgsc.bcm.edu	37	3	119301139	119301139	+	Silent	SNP	C	C	T	rs20568	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	84	127	0	0.506024	0	C|0.915;T|0.085	0.085	strong	.	ADPRH	33	.	NM_001125	exon3	c.C123T	p.G41G	GCTGGGCGGCTTG	.	PASS	Atlas-SNP
KBTBD2	25948	hgsc.bcm.edu	37	7	32909182	32909182	+	Silent	SNP	G	G	A	rs752730	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	47	112	0	0.419643	0	G|0.819;A|0.181	0.181	strong	.	KBTBD2	37	.	NM_015483	exon4	c.C1647T	p.Y549Y	GGTGACGTATTTA	.	PASS	Atlas-SNP
KDM4C	23081	hgsc.bcm.edu	37	9	7103816	7103816	+	Silent	SNP	C	C	T	rs3763651	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	164	126	0	1	0	C|0.456;T|0.544	0.544	strong	.	KDM4C	186	.	NM_001146694	exon18	c.C2556T	p.D852D	TGATGACTGGCCT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1264581	1264581	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	505	5	579	2	0.00990099	0.00345423	.	.	none	MUC5B,NS,carcinoma,+1,2	MUC5B	473	2	NM_002458	exon31	c.C6471T	p.P2157P	AACTCCCATCCCC	.	scavenged	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2161793	2161793	+	Silent	SNP	G	G	A	rs74331768	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	33	16	0	0.55	0	G|0.856;A|0.144	0.144	strong	.	PKD1	184	.	NM_000296	exon15	c.C3375T	p.S1125S	GGGCAGGGAGGCG	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219617523	219617523	+	Missense_Mutation	SNP	A	A	G	rs116116034	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	262	140	227	0	0.534351	0	A|0.996;G|0.004	0.004	strong	.	TTLL4	96	.	NM_014640	exon17	c.A3014G	p.D1005G	CACCAGATGATGT	.	PASS	Atlas-SNP
STEAP2	261729	hgsc.bcm.edu	37	7	89856608	89856608	+	Silent	SNP	C	C	T	rs110360	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	176	169	0	0.99435	0	C|0.523;T|0.477	0.477	strong	STEAP2_ENST00000394626,NS,carcinoma,0,2	STEAP2	78	2	NM_001244946	exon4	c.C816T	p.L272L	ATACCTCGCAGGT	.	PASS	Atlas-SNP
SIL1	64374	hgsc.bcm.edu	37	5	138456815	138456815	+	Silent	SNP	T	T	C	rs3088052	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	109	111	1	0.990909	0.00900901	T|0.513;C|0.487	0.487	strong	.	SIL1	31	.	NM_001037633	exon4	c.A153G	p.T51T	TCTCTCTGTTTCT	.	PASS	Atlas-SNP
SLC12A8	84561	hgsc.bcm.edu	37	3	124829057	124829057	+	Silent	SNP	A	A	G	rs11714448	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	24	67	0	0.333333	0	A|0.986;G|0.013	0.013	strong	.	SLC12A8	81	.	NM_024628	exon9	c.T1035C	p.P345P	AAGTGCAGGGATC	.	PASS	Atlas-SNP
DHX34	9704	hgsc.bcm.edu	37	19	47879279	47879279	+	Silent	SNP	G	G	A	rs2694558	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	36	50	0	0.514286	0	G|0.887;A|0.113	0.113	strong	.	DHX34	98	.	NM_014681	exon11	c.G2406A	p.L802L	GAAGCTGGTGCTG	.	PASS	Atlas-SNP
SOCS6	9306	hgsc.bcm.edu	37	18	67992684	67992684	+	Silent	SNP	C	C	T	rs1047657	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	234	101	215	0	0.431624	0	C|0.900;T|0.100	0.100	strong	SOCS6,NS,carcinoma,+2,2	SOCS6	54	2	NM_004232	exon2	c.C780T	p.R260R	AGGGCGCGCTTTC	.	PASS	Atlas-SNP
HSPA6	3310	hgsc.bcm.edu	37	1	161495040	161495040	+	Missense_Mutation	SNP	C	C	T	rs63749092	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	281	264	320	1	0.939502	0.003125	C|0.897;T|0.103	0.103	strong	.	HSPA6	53	.	NM_002155	exon1	c.C592T	p.L198F	AACGTGCTCATTT	.	PASS	Atlas-SNP
ANAPC16	119504	hgsc.bcm.edu	37	10	73992862	73992862	+	Silent	SNP	C	C	G	rs9275	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	24	39	0	0.6	0	G|0.064;C|0.936	0.064	strong	.	ANAPC16	10	.	NM_001242546	exon5	c.C321G	p.P107P	CACCCCCTCTTCA	.	PASS	Atlas-SNP
OR5B2	390190	hgsc.bcm.edu	37	11	58190112	58190112	+	Missense_Mutation	SNP	A	A	G	rs10466659	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	47	65	0	0.439252	0	A|0.781;G|0.219	0.219	strong	OR5B2,NS,carcinoma,0,1	OR5B2	75	1	NM_001005566	exon1	c.T623C	p.V208A	AGAAGAACAAAAA	.	PASS	Atlas-SNP
MAML2	84441	hgsc.bcm.edu	37	11	95825404	95825404	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	4	108	2	0.0296296	0.0185185	.	.	none	MAML2,caecum,carcinoma,0,1	MAML2	94	1	NM_032427	exon2	c.G1791A	p.Q597Q	CTGCTGCTGCTGC	.	scavenged	Atlas-SNP
MPDZ	8777	hgsc.bcm.edu	37	9	13190162	13190162	+	Missense_Mutation	SNP	T	T	A	rs4740548	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	39	74	0	0.4875	0	T|0.988;A|0.012	0.012	strong	.	MPDZ	324	.	NM_003829	exon16	c.A2105T	p.E702V	TCCAGCTCTATGT	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228412308	228412308	+	Silent	SNP	G	G	A	rs1757152	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	143	244	0	0.560784	0	G|0.567;A|0.433	0.433	strong	.	OBSCN	2142	.	NM_001271223	exon10	c.G3078A	p.S1026S	CAGCTCGAAAGTG	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65612302	65612302	+	Silent	SNP	A	A	G	rs75634595	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	59	108	0	0.842857	0	A|0.981;G|0.019	0.019	strong	.	EYS	527	.	NM_001142800	exon17	c.T2733C	p.N911N	CCTGAAATTGTTG	.	PASS	Atlas-SNP
SCN8A	6334	hgsc.bcm.edu	37	12	52200499	52200499	+	Silent	SNP	C	C	A	rs370268493		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	96	177	0	0.588957	0	.	.	weak	.	SCN8A	331	.	NM_014191	exon27	c.C5229A	p.I1743I	GGGCATCTTCTTC	.	PASS	Atlas-SNP
ECD	11319	hgsc.bcm.edu	37	10	74894375	74894375	+	Missense_Mutation	SNP	T	T	C	rs2271904	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	163	63	200	0	0.386503	0	T|0.869;C|0.131	0.131	strong	ECD,NS,carcinoma,-1,2	ECD	50	2	NM_001135752	exon15	c.A2000G	p.D667G	CTGTGATCGGTGT	.	PASS	Atlas-SNP
RASAL1	8437	hgsc.bcm.edu	37	12	113573237	113573237	+	Missense_Mutation	SNP	C	C	G	rs7960087	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	86	126	0	0.52439	0	C|0.974;G|0.026	0.026	strong	RASAL1,NS,carcinoma,0,2	RASAL1	89	2	NM_004658	exon2	c.G31C	p.V11L	CCACCACGCGAAC	.	PASS	Atlas-SNP
FAM21B	55747	hgsc.bcm.edu	37	10	47915898	47915898	+	Silent	SNP	A	A	G	rs61856727	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	321	92	443	0	0.286604	0	A|0.375;G|0.625	0.625	strong	FAM21B_ENST00000358474,NS,carcinoma,0,1	FAM21B	31	1	NM_018232	exon15	c.A1305G	p.K435K	CAGCAAAAATCTC	.	scavenged	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978591	45978591	+	Missense_Mutation	SNP	G	G	A	rs79221051	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	126	64	95	1	0.507937	0.0105263	G|0.850;A|0.150	0.150	strong	KRTAP10-3,rectum,carcinoma,-1,1	KRTAP10-3	17	1	NM_198696	exon1	c.C8T	p.T3M	GTAGACGTGGCCA	.	scavenged	Atlas-SNP
GALNT4	8693	hgsc.bcm.edu	37	12	89917349	89917349	+	Silent	SNP	C	C	T	rs200228838	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	290	141	275	0	0.486207	0	C|0.996;T|0.004	0.004	strong	.	GALNT4	38	.	NM_003774	exon1	c.G978A	p.T326T	GTCATACGTTCCA	.	PASS	Atlas-SNP
PCDHB10	56126	hgsc.bcm.edu	37	5	140572668	140572668	+	Silent	SNP	C	C	T	rs597064	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	144	199	1	1	0.00502513	C|0.561;T|0.439	0.439	strong	.	PCDHB10	177	.	NM_018930	exon1	c.C543T	p.N181N	TATTAACATTAGT	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47836426	47836426	+	Silent	SNP	T	T	C	rs57108405	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	45	108	0	0.473684	0	T|0.876;C|0.124	0.124	strong	.	PCNT	283	.	NM_006031	exon30	c.T6594C	p.G2198G	ACTTGGTGGCTCC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506364	195506364	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	4	23	0	0.0571429	0	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.C12087G	p.H4029Q	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
FBXO5	26271	hgsc.bcm.edu	37	6	153296370	153296370	+	Missense_Mutation	SNP	G	G	A	rs7763565	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	11	192	0	0.108911	0	G|0.911;A|0.089	0.089	strong	.	FBXO5	40	.	NM_012177	exon2	c.C490T	p.L164F	CCAGGAGGCTACC	.	PASS	Atlas-SNP
OR2W1	26692	hgsc.bcm.edu	37	6	29012067	29012067	+	Missense_Mutation	SNP	C	C	T	rs35771565	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	90	179	0	0.481283	0	C|0.806;T|0.194	0.194	strong	.	OR2W1	36	.	NM_030903	exon1	c.G886A	p.D296N	TCATGTCCTTATT	.	PASS	Atlas-SNP
BRAF	673	hgsc.bcm.edu	37	7	140477811	140477811	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	26	54	0	0.371429	0	.	.	none	.	BRAF	36346	.	NM_004333	exon12	c.A1497T	p.K499N	TTCATTTTTGAAG	.	PASS	Atlas-SNP
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73969541	73969541	+	Missense_Mutation	SNP	A	A	G	rs2301895	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	30	56	0	0.508475	0	A|0.616;G|0.384	0.384	strong	.	GTF2IRD1	91	.	NM_001199207	exon18	c.A2050G	p.M684V	CCCATCATGGATA	.	PASS	Atlas-SNP
FAM126B	285172	hgsc.bcm.edu	37	2	201846180	201846180	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	63	127	0	0.477273	0	.	.	none	FAM126B,NS,carcinoma,-1,1	FAM126B	34	1	NM_173822	exon12	c.T1406C	p.I469T	ACCCCAATGCTGG	.	PASS	Atlas-SNP
FREM1	158326	hgsc.bcm.edu	37	9	14801710	14801710	+	Missense_Mutation	SNP	C	C	A	rs35870000	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	250	245	244	0	0.98	0	C|0.719;A|0.281	0.281	strong	.	FREM1	261	.	NM_144966	exon21	c.G3634T	p.A1212S	GGTTGGCTGGCTG	.	PASS	Atlas-SNP
NTAN1	123803	hgsc.bcm.edu	37	16	15133889	15133889	+	Silent	SNP	T	T	G	rs14347	bycluster;byfrequency;bysubmitter;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	55	57	0	0.964912	0	T|0.710;G|0.290	0.290	strong	.	NTAN1	21	.	NM_173474	exon8	c.A576C	p.A192A	AAAGGATGCTCTG	.	PASS	Atlas-SNP
PITPNM2	57605	hgsc.bcm.edu	37	12	123471094	123471094	+	Silent	SNP	G	G	A	rs12811109	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	116	70	117	0	0.603448	0	G|0.860;A|0.140	0.140	strong	PITPNM2,colon,carcinoma,0,1	PITPNM2	105	1	NM_020845	exon24	c.C3615T	p.H1205H	GGCCGCGTGCACG	.	PASS	Atlas-SNP
ZMYM5	9205	hgsc.bcm.edu	37	13	20425948	20425948	+	Missense_Mutation	SNP	T	T	C	rs9579718	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	131	55	146	0	0.419847	0	T|0.901;C|0.099	0.099	strong	.	ZMYM5	73	.	NM_001039650	exon3	c.A373G	p.I125V	TTTCTATGTCCTC	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509941	195509941	+	Missense_Mutation	SNP	A	A	C	rs199849290	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	164	13	253	3	0.0792683	0.0118577	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.T8510G	p.I2837S	GAAGGGATGGTGA	.	scavenged	Atlas-SNP
CHFR	55743	hgsc.bcm.edu	37	12	133423695	133423695	+	Silent	SNP	A	A	G	rs2306537	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	40	14	42	0	0.35	0	A|0.803;G|0.197	0.197	strong	.	CHFR	83	.	NM_001161344	exon15	c.T1705C	p.L569L	ATGTCAAACCTCT	.	PASS	Atlas-SNP
IL37	27178	hgsc.bcm.edu	37	2	113676219	113676219	+	Missense_Mutation	SNP	T	T	C	rs2708947	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	137	65	116	0	0.474453	0	T|0.902;C|0.098	0.098	strong	.	IL37	56	.	NM_014439	exon5	c.T490C	p.W164R	GGCTCCTGGAACA	.	PASS	Atlas-SNP
FGL1	2267	hgsc.bcm.edu	37	8	17739639	17739639	+	Missense_Mutation	SNP	C	C	A	rs78484373	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	101	43	119	1	0.425743	0.00840336	C|0.981;A|0.019	0.019	strong	FGL1,colon,carcinoma,-1,3	FGL1	31	3	NM_201553	exon4	c.G113T	p.R38L	AGCAGGCGCACCT	.	scavenged	Atlas-SNP
TENM2	57451	hgsc.bcm.edu	37	5	167553880	167553880	+	Silent	SNP	C	C	T	rs10055910	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	78	167	0	0.45614	0	C|0.828;T|0.172	0.172	strong	.	.	.	.	NM_001122679	exon12	c.C2331T	p.H777H	TGAGCACGGGACC	.	PASS	Atlas-SNP
ATPAF2	91647	hgsc.bcm.edu	37	17	17921995	17921995	+	Silent	SNP	C	C	T	rs33997182	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	29	79	0	0.391892	0	C|0.978;T|0.022	0.022	strong	.	ATPAF2	15	.	NM_145691	exon8	c.G738A	p.Q246Q	CCACTTCTGGATC	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	37	2	73717567	73717567	+	Missense_Mutation	SNP	G	G	T	rs2056486	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	35	83	0	0.466667	0	G|0.663;T|0.337	0.337	strong	.	ALMS1	384	.	NM_015120	exon10	c.G8478T	p.R2826S	TACCAGGGCAAAT	.	PASS	Atlas-SNP
C22orf28	51493	hgsc.bcm.edu	37	22	32784051	32784051	+	Silent	SNP	T	T	C	rs11635	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	147	76	129	0	0.517007	0	T|0.883;C|0.117	0.117	strong	.	C22orf28	43	.	NM_014306	exon12	c.A1446G	p.V482V	GGTATTTACCACA	.	PASS	Atlas-SNP
PDE8B	8622	hgsc.bcm.edu	37	5	76708987	76708987	+	Silent	SNP	A	A	G	rs335614	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	207	94	194	0	0.454106	0	A|0.284;G|0.716	0.716	strong	.	PDE8B	103	.	NM_003719	exon17	c.A1764G	p.E588E	ATGTGAATTTTTA	.	PASS	Atlas-SNP
NSUN2	54888	hgsc.bcm.edu	37	5	6600150	6600150	+	Silent	SNP	G	G	A	rs3822434	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	67	105	1	0.536	0.00952381	G|0.862;C|0.000;A|0.138	0.138	strong	NSUN2,colon,carcinoma,0,1	NSUN2	82	1	NM_017755	exon19	c.C2193T	p.D731D	AGTCACGTCATTG	.	scavenged	Atlas-SNP
OR5K3	403277	hgsc.bcm.edu	37	3	98109640	98109640	+	Missense_Mutation	SNP	G	G	A	rs13068323	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	369	173	327	1	0.468835	0.0030581	G|0.846;A|0.154	0.154	strong	OR5K3,rectum,carcinoma,-1,1	OR5K3	60	1	NM_001005516	exon1	c.G131A	p.G44D	ACATTGGTTTGGT	.	PASS	Atlas-SNP
INCA1	388324	hgsc.bcm.edu	37	17	4892176	4892176	+	Missense_Mutation	SNP	C	C	G	rs74744272	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	87	37	94	0	0.425287	0	C|0.915;G|0.085	0.085	strong	.	INCA1	17	.	NM_001167986	exon8	c.G459C	p.E153D	ACAGCCCTCTTCG	.	PASS	Atlas-SNP
ETV1	2115	hgsc.bcm.edu	37	7	14025766	14025766	+	Silent	SNP	T	T	A	rs10215655	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	27	27	45	0	1	0	T|0.412;A|0.588	0.588	strong	.	ETV1	138	.	NM_001163152	exon1	c.A36T	p.P12P	ACAAGGTGGAAAG	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	37	20	25262769	25262769	+	Missense_Mutation	SNP	G	G	A	rs2227891	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	30	39	0	0.566038	0	G|0.839;A|0.161	0.161	strong	.	PYGB	84	.	NM_002862	exon12	c.G1504A	p.D502N	CTGGCCGATACCA	.	PASS	Atlas-SNP
CNTNAP3	79937	hgsc.bcm.edu	37	9	39149904	39149904	+	Silent	SNP	G	G	A	rs200999166	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	1008	254	816	0	0.251984	0	G|0.999;A|0.001	0.001	weak	.	CNTNAP3	82	.	NM_033655	exon10	c.C1548T	p.L516L	GGTGATGAGCCTT	.	PASS	Atlas-SNP
PIGZ	80235	hgsc.bcm.edu	37	3	196674259	196674259	+	Silent	SNP	G	G	A	rs61179255	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	34	21	40	0	0.617647	0	G|0.889;A|0.111	0.111	strong	.	PIGZ	34	.	NM_025163	exon3	c.C1509T	p.T503T	TTGTCTGGTGAAG	.	PASS	Atlas-SNP
FCGR1B	2210	hgsc.bcm.edu	37	1	120934573	120934573	+	Missense_Mutation	SNP	C	C	T	rs7531523		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	576	115	605	0	0.199653	0	.	.	weak	FCGR1B,NS,carcinoma,0,1	FCGR1B	14	1	NM_001017986	exon3	c.G115A	p.V39I	AGGTTACGGTTTC	.	scavenged	Atlas-SNP
DEPDC7	91614	hgsc.bcm.edu	37	11	33053107	33053107	+	Silent	SNP	C	C	T	rs966191	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	85	42	69	0	0.494118	0	C|0.588;T|0.412	0.412	strong	.	DEPDC7	94	.	NM_001077242	exon5	c.C966T	p.D322D	ATCTGACGTTCAT	.	PASS	Atlas-SNP
HIGD2A	192286	hgsc.bcm.edu	37	5	175815874	175815874	+	Silent	SNP	T	T	C	rs1060588	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	30	64	0	0.375	0	T|0.893;C|0.107	0.107	strong	.	HIGD2A	7	.	NM_138820	exon1	c.T54C	p.P18P	GAAGCCTCCAGTC	.	PASS	Atlas-SNP
ZNF256	10172	hgsc.bcm.edu	37	19	58453342	58453342	+	Silent	SNP	T	T	C	rs959231	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	127	123	1	1	0.00813008	T|0.741;C|0.259	0.259	strong	.	ZNF256	117	.	NM_005773	exon3	c.A834G	p.Q278Q	AGAGCTTTGCCTA	.	PASS	Atlas-SNP
VAV3	10451	hgsc.bcm.edu	37	1	108319891	108319891	+	Silent	SNP	A	A	G	rs17020006	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	54	111	0	0.477876	0	A|0.992;G|0.008	0.008	strong	.	VAV3	176	.	NM_006113	exon4	c.T408C	p.N136N	TTCATCATTAATG	.	PASS	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41862356	41862356	+	Splice_Site	SNP	T	T	C	rs149022093		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	8	110	0	0.0672269	0	.	.	weak	TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	NM_006293	exon10	c.1382+2T>C	.	TTTGGGTAAGGGG	.	PASS	Atlas-SNP
ZNF782	158431	hgsc.bcm.edu	37	9	99581882	99581882	+	Silent	SNP	C	C	T	rs35658789	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	174	84	169	0	0.482759	0	C|0.984;T|0.016	0.016	strong	.	ZNF782	64	.	NM_001001662	exon6	c.G423A	p.A141A	AGACCCCGCAATG	.	PASS	Atlas-SNP
DHRS9	10170	hgsc.bcm.edu	37	2	169952233	169952233	+	Silent	SNP	T	T	C	rs1059261	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	168	85	137	0	0.505952	0	T|0.732;C|0.268	0.268	strong	.	DHRS9	29	.	NM_005771	exon8	c.T916C	p.L306L	TTTTTATTGTTGA	.	PASS	Atlas-SNP
FAM177A1	283635	hgsc.bcm.edu	37	14	35546373	35546373	+	Silent	SNP	T	T	C	rs3211139	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	179	68	167	0	0.379888	0	T|0.844;C|0.156	0.156	strong	.	FAM177A1	9	.	NM_173607	exon3	c.T357C	p.G119G	CTGGGGTCCCTAC	.	PASS	Atlas-SNP
TRIM26	7726	hgsc.bcm.edu	37	6	30154049	30154049	+	Silent	SNP	G	G	A	rs16897204	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	122	57	94	0	0.467213	0	G|0.968;A|0.032	0.032	strong	.	TRIM26	74	.	NM_001242783	exon9	c.C1224T	p.D408D	CCAGTCGTCATAT	.	PASS	Atlas-SNP
XRCC2	7516	hgsc.bcm.edu	37	7	152346007	152346007	+	Missense_Mutation	SNP	C	C	T	rs3218536	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	33	78	0	0.392857	0	C|0.949;T|0.051	0.051	strong	.	XRCC2	30	.	NM_005431	exon3	c.G563A	p.R188H	ACCAGGCGATAGT	.	PASS	Atlas-SNP
CNTN3	5067	hgsc.bcm.edu	37	3	74344356	74344356	+	Silent	SNP	T	T	G	rs10490832	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	56	105	0	0.495575	0	T|0.912;G|0.088	0.088	strong	.	CNTN3	174	.	NM_020872	exon18	c.A2433C	p.A811A	GCTATTTGCAGAG	.	PASS	Atlas-SNP
HSPA2	3306	hgsc.bcm.edu	37	14	65008251	65008251	+	Silent	SNP	C	C	T	rs1063391	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	35	73	0	0.507246	0	C|0.368;T|0.632	0.632	strong	HSPA2,right_upper_lobe,carcinoma,+1,1	HSPA2	83	1	NM_021979	exon1	c.C684T	p.D228D	CGGCGACACCCAC	.	PASS	Atlas-SNP
PIK3CD	5293	hgsc.bcm.edu	37	1	9784423	9784423	+	Silent	SNP	C	C	T	rs41476649	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	11	133	0	0.0808824	0	C|0.800;T|0.200	0.200	strong	.	PIK3CD	86	.	NM_005026	exon22	c.C2808T	p.Y936Y	CACCTACGACTTT	.	PASS	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	37	1	201288955	201288955	+	Missense_Mutation	SNP	G	G	A	rs1626370	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	9	38	0	0.36	0	G|0.825;A|0.175	0.175	strong	.	PKP1	127	.	NM_000299	exon7	c.G1244A	p.G415D	GACTGGGCATGCG	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134680995	134680995	+	Missense_Mutation	SNP	C	C	T	rs150661681	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	55	128	0	0.447154	0	C|0.993;T|0.007	0.007	strong	.	TTC40	100	.	NM_001200049	exon34	c.G4627A	p.A1543T	TCAACGCGATCTC	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109693982	109693982	+	Silent	SNP	C	C	T	rs3742023	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	145	69	114	0	0.475862	0	C|0.719;T|0.281	0.281	strong	.	ACACB	330	.	NM_001093	exon44	c.C6204T	p.H2068H	TGACCACGGCAGT	.	PASS	Atlas-SNP
UVSSA	57654	hgsc.bcm.edu	37	4	1374695	1374695	+	Silent	SNP	C	C	A	rs28614045	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	321	151	305	1	0.470405	0.00327869	C|0.306;A|0.694	0.694	strong	KIAA1530,NS,carcinoma,0,1	.	.	1	NM_020894	exon12	c.C1780A	p.R594R	GTTCCACGGGACG	.	PASS	Atlas-SNP
NPR2	4882	hgsc.bcm.edu	37	9	35792423	35792423	+	Silent	SNP	T	T	C	rs2228580	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	38	93	0	0.4	0	T|0.691;C|0.309	0.309	strong	.	NPR2	162	.	NM_003995	exon1	c.T18C	p.L6L	ATCACTTCTGCTG	.	PASS	Atlas-SNP
FCHSD1	89848	hgsc.bcm.edu	37	5	141021108	141021108	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	62	90	0	0.553571	0	.	.	none	.	FCHSD1	51	.	NM_033449	exon20	c.C2030T	p.P677L	TTAGCCGGCGGGG	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	37	3	124181454	124181454	+	Silent	SNP	C	C	T	rs2289839	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	46	60	0	0.560976	0	C|0.950;T|0.050	0.050	strong	.	KALRN	556	.	NM_003947	exon25	c.C3999T	p.I1333I	CAACATCCAAGAG	.	PASS	Atlas-SNP
TSC1	7248	hgsc.bcm.edu	37	9	135786904	135786904	+	Missense_Mutation	SNP	A	A	G	rs1073123	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	109	104	0	0.990909	0	A|0.859;C|0.001	.	strong	.	TSC1	167	.	NM_000368	exon10	c.T965C	p.M322T	CCTGGCATATTTA	.	PASS	Atlas-SNP
GALNT3	2591	hgsc.bcm.edu	37	2	166621413	166621413	+	Silent	SNP	C	C	T	rs13423840	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	269	117	232	1	0.434944	0.00431034	C|0.987;T|0.013	0.013	strong	.	GALNT3	65	.	NM_004482	exon3	c.G669A	p.V223V	ATCATCCACCAAA	.	PASS	Atlas-SNP
CHDH	55349	hgsc.bcm.edu	37	3	53856653	53856653	+	Silent	SNP	C	C	T	rs2241808	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	39	57	0	0.609375	0	C|0.555;T|0.444	0.444	strong	CHDH,colon,carcinoma,-2,1	CHDH	34	1	NM_018397	exon4	c.G720A	p.A240A	ACAGGCCGCGCTC	.	PASS	Atlas-SNP
PVR	5817	hgsc.bcm.edu	37	19	45162189	45162189	+	Missense_Mutation	SNP	C	C	A	rs35385129	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	65	148	0	0.430464	0	C|0.834;A|0.166	0.166	strong	.	PVR	23	.	NM_001135770	exon6	c.C1171A	p.R391S	AGCTGCCGTAATT	.	PASS	Atlas-SNP
GPR112	139378	hgsc.bcm.edu	37	X	135426968	135426968	+	Missense_Mutation	SNP	C	C	A	rs5930931	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	52	56	0	0.981132	0	0|0.025;A|0.455	0.455	strong	.	GPR112	459	.	NM_153834	exon6	c.C1103A	p.P368H	AACCACCTACACC	.	PASS	Atlas-SNP
PCNT	5116	hgsc.bcm.edu	37	21	47841941	47841941	+	Missense_Mutation	SNP	A	A	G	rs7277175	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	68	36	63	0	0.529412	0	A|0.802;G|0.198	0.198	strong	.	PCNT	283	.	NM_006031	exon32	c.A7082G	p.Q2361R	AGGCTCAAACTGC	.	PASS	Atlas-SNP
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993757	96993757	+	Missense_Mutation	SNP	C	C	T	rs2279105	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	58	117	0	0.471545	0	C|0.705;T|0.295	0.295	strong	.	ITPRIPL1	58	.	NM_178495	exon1	c.C1412T	p.T471M	CCCTCACGGACTG	.	PASS	Atlas-SNP
KCNQ4	9132	hgsc.bcm.edu	37	1	41289831	41289831	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	39	45	0	0.886364	0	.	.	none	.	KCNQ4	58	.	NM_004700	exon9	c.A1193G	p.E398G	CCCTGGAGGTGCG	.	PASS	Atlas-SNP
GBGT1	26301	hgsc.bcm.edu	37	9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	rs35898523	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	28	13	20	0	0.464286	0	G|0.941;T|0.059	0.059	strong	GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	NM_021996	exon7	c.C363A	p.Y121X	ATGAGTGTACCTA	.	PASS	Atlas-SNP
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978592	45978592	+	Missense_Mutation	SNP	T	T	C	rs452472	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	62	94	0	0.488189	0	T|0.735;C|0.265	0.265	strong	KRTAP10-3,rectum,carcinoma,0,1	KRTAP10-3	17	1	NM_198696	exon1	c.A7G	p.T3A	TAGACGTGGCCAT	.	PASS	Atlas-SNP
ARSE	415	hgsc.bcm.edu	37	X	2852957	2852957	+	Silent	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	144	143	138	0	0.993056	0	.	.	none	.	ARSE	43	.	NM_000047	exon11	c.G1686C	p.L562L	GTTGCCCAGCCTG	.	PASS	Atlas-SNP
TMEM187	8269	hgsc.bcm.edu	37	X	153247745	153247745	+	Missense_Mutation	SNP	A	A	G	rs7350355	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	75	74	0	0.986842	0	A|0.587;0|0.003	.	strong	.	TMEM187	21	.	NM_003492	exon2	c.A232G	p.M78V	GGCGCGATGGGGC	.	PASS	Atlas-SNP
SLC2A6	11182	hgsc.bcm.edu	37	9	136341407	136341407	+	Missense_Mutation	SNP	T	T	C	rs147872568	bycluster;byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	69	30	50	0	0.434783	0	T|1.000;C|0.000	0.000	strong	.	SLC2A6	31	.	NM_017585	exon4	c.A514G	p.T172A	GGGGTGTGGCCCC	.	PASS	Atlas-SNP
EPB41	2035	hgsc.bcm.edu	37	1	29320013	29320013	+	Missense_Mutation	SNP	G	G	A	rs111642750	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	136	122	135	0	0.897059	0	G|0.968;A|0.032	0.032	strong	.	EPB41	118	.	NM_203343	exon3	c.G640A	p.V214I	TGCAAGGTTTCTT	.	PASS	Atlas-SNP
UBE2I	7329	hgsc.bcm.edu	37	16	1364365	1364365	+	Silent	SNP	A	A	G	rs4610	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	38	86	0	0.457831	0	A|0.870;G|0.130	0.130	strong	.	UBE2I	15	.	NM_003345	exon3	c.A138G	p.P46P	CATTCCAGGAAAG	.	PASS	Atlas-SNP
PGC	5225	hgsc.bcm.edu	37	6	41704716	41704716	+	Silent	SNP	G	G	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	53	118	0	0.509615	0	.	.	none	.	PGC	56	.	NM_002630	exon9	c.C1041A	p.V347V	GGGCTCGACTCCC	.	PASS	Atlas-SNP
ERCC6	2074	hgsc.bcm.edu	37	10	50678544	50678544	+	Silent	SNP	A	A	C	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	156	58	142	1	0.371795	0.00704225	.	.	none	ERCC6,NS,haematopoietic_neoplasm,-1,1	ERCC6	162	1	NM_000124	exon18	c.C3462G	p.A1154A	TTTGTAAGAAAGA	.	scavenged	Atlas-SNP
DCAF13	25879	hgsc.bcm.edu	37	8	104427541	104427541	+	Missense_Mutation	SNP	C	C	T	rs3134296	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	75	40	65	0	0.533333	0	C|0.817;T|0.183	0.183	strong	DCAF13,NS,carcinoma,-1,1	DCAF13	66	1	NM_015420	exon1	c.C323T	p.P108L	TTGAGCCAGCAGG	.	PASS	Atlas-SNP
PLA2G1B	5319	hgsc.bcm.edu	37	12	120762837	120762837	+	Silent	SNP	A	A	G	rs5634	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	189	103	194	0	0.544974	0	A|0.934;G|0.066	0.066	strong	.	PLA2G1B	8	.	NM_000928	exon3	c.T222C	p.Y74Y	CTGGTCATAGCAG	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	14905	14905	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	21	21	8	0	1	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.G159A	p.M53M	AGCCATGCACTAC	.	PASS	Atlas-SNP
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246163	47246163	+	Missense_Mutation	SNP	T	T	C	rs7224888	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	44	98	0	0.453608	0	T|0.874;C|0.126	0.126	strong	.	B4GALNT2	67	.	NM_153446	exon10	c.T1396C	p.C466R	CCCAGCTGCGTGG	.	PASS	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	37	19	23543834	23543834	+	Silent	SNP	C	C	T	rs7255296	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	26	81	0	0.356164	0	C|0.854;T|0.146	0.146	strong	.	ZNF91	349	.	NM_003430	exon4	c.G1947A	p.K649K	AATTCTCTTATGT	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	37	21	46899842	46899842	+	Silent	SNP	C	C	T	rs1131100	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	44	26	79	0	0.590909	0	C|0.882;T|0.118	0.118	strong	COL18A1_ENST00000359759,NS,carcinoma,0,2	COL18A1	129	2	NM_030582	exon9	c.C1815T	p.P605P	CTTCCCCGGGACT	.	PASS	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	37	7	88965021	88965021	+	Missense_Mutation	SNP	G	G	A	rs10487075	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	125	61	126	0	0.488	0	G|0.916;A|0.084	0.084	strong	.	ZNF804B	322	.	NM_181646	exon4	c.G2725A	p.E909K	CCTTCAGAAACCA	.	PASS	Atlas-SNP
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs56451138		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	29	27	293	0	0.931035	0	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
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84611805	84611805	+	Missense_Mutation	SNP	C	C	T	rs61752778	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	33	91	0	0.507692	0	C|0.988;T|0.012	0.012	strong	.	ADAMTSL3	290	.	NM_207517	exon19	c.C2461T	p.P821S	TGTCCTCCACATT	.	PASS	Atlas-SNP
USP21	27005	hgsc.bcm.edu	37	1	161132777	161132777	+	Missense_Mutation	SNP	G	G	A	rs17356051	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	132	64	145	0	0.484848	0	G|0.960;A|0.040	0.040	strong	.	USP21	63	.	NM_012475	exon6	c.G962A	p.G321D	GCCGAGGCCGCCG	.	PASS	Atlas-SNP
ADRA2C	152	hgsc.bcm.edu	37	4	3769573	3769573	+	Missense_Mutation	SNP	G	G	C	rs370580020	alternate_allele	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	77	35	72	0	0.454545	0	.	.	alt	.	ADRA2C	24	.	NM_000683	exon1	c.G1240C	p.V414L	TGCCAGGTGCCCG	.	PASS	Atlas-SNP
ASTN1	460	hgsc.bcm.edu	37	1	176992676	176992676	+	Silent	SNP	C	C	T	rs10798496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	53	134	0	0.430894	0	C|0.677;T|0.323	0.323	strong	.	ASTN1	314	.	NM_004319	exon7	c.G1302A	p.Q434Q	ATCCAGCTGGCTC	.	PASS	Atlas-SNP
THBS3	7059	hgsc.bcm.edu	37	1	155172725	155172725	+	Missense_Mutation	SNP	T	T	C	rs35154152	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	62	119	0	0.563636	0	T|0.857;C|0.143	0.143	strong	.	THBS3	70	.	NM_007112	exon8	c.A835G	p.S279G	TGGGGCTGCAGTG	.	PASS	Atlas-SNP
OR4N4	283694	hgsc.bcm.edu	37	15	22383064	22383064	+	Missense_Mutation	SNP	C	C	A	rs12441468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	409	125	411	2	0.305623	0.00486618	C|0.770;A|0.230	0.230	strong	OR4N4,colon,carcinoma,0,1	OR4N4	108	1	NM_001005241	exon1	c.C592A	p.L198I	GAGCTTCTAATGG	.	scavenged	Atlas-SNP
KDM2B	84678	hgsc.bcm.edu	37	12	121881848	121881848	+	Silent	SNP	G	G	A	rs10849885	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	54	79	0	0.580645	0	G|0.666;A|0.334	0.334	strong	KDM2B_ENST00000377071,NS,carcinoma,0,2	KDM2B	218	2	NM_032590	exon16	c.C2418T	p.Y806Y	CTTCTCGTATTTC	.	PASS	Atlas-SNP
DPPA4	55211	hgsc.bcm.edu	37	3	109049384	109049384	+	Silent	SNP	T	T	C	rs13059848	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	61	125	0	0.469231	0	T|0.879;C|0.121	0.121	strong	.	DPPA4	56	.	NM_018189	exon5	c.A666G	p.P222P	CTCTTGTGGAGAT	.	PASS	Atlas-SNP
CYP11B2	1585	hgsc.bcm.edu	37	8	143994041	143994041	+	Missense_Mutation	SNP	C	C	T	rs4545	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	51	99	0	0.428571	0	C|0.914;T|0.086	0.086	strong	CYP11B2,NS,carcinoma,+2,1	CYP11B2	107	1	NM_000498	exon8	c.G1303A	p.G435S	TCCTGCCGGAGCC	.	PASS	Atlas-SNP
DLC1	10395	hgsc.bcm.edu	37	8	12957475	12957475	+	Missense_Mutation	SNP	C	C	T	rs532841	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	31	19	40	0	0.612903	0	C|0.490;T|0.510	0.510	strong	DLC1,NS,carcinoma,0,1	DLC1	411	1	NM_182643	exon9	c.G2371A	p.V791M	GCTCCACCACGTT	.	PASS	Atlas-SNP
LBP	3929	hgsc.bcm.edu	37	20	36989381	36989381	+	Silent	SNP	G	G	A	rs2232596	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	44	125	0	0.444444	0	G|0.400;A|0.599	0.599	strong	.	LBP	60	.	NM_004139	exon6	c.G612A	p.S204S	GAAATCGGTGTCC	.	PASS	Atlas-SNP
WBSCR28	135886	hgsc.bcm.edu	37	7	73279361	73279361	+	Silent	SNP	C	C	T	rs61742124	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	169	78	150	0	0.461538	0	C|0.789;T|0.211	0.211	strong	.	WBSCR28	24	.	NM_182504	exon2	c.C111T	p.L37L	CCTGCTCCTCAAG	.	PASS	Atlas-SNP
NFASC	23114	hgsc.bcm.edu	37	1	204970302	204970302	+	Silent	SNP	T	T	C	rs4951151	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	118	60	110	0	0.508475	0	T|0.790;C|0.210	0.210	strong	NFASC_ENST00000339876,NS,carcinoma,0,1	NFASC	396	1	NM_001005388	exon26	c.T3024C	p.P1008P	AGCCCCTGATGAG	.	PASS	Atlas-SNP
CCDC135	84229	hgsc.bcm.edu	37	16	57738810	57738810	+	Missense_Mutation	SNP	T	T	A	rs58373934	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	31	85	0	0.516667	0	T|0.897;A|0.103	0.103	strong	.	CCDC135	97	.	NM_032269	exon6	c.T722A	p.V241E	AAAAGGTGCTGCC	.	PASS	Atlas-SNP
PRPF18	8559	hgsc.bcm.edu	37	10	13642257	13642257	+	Missense_Mutation	SNP	A	A	G	rs142307573	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	22	65	0	0.415094	0	A|0.998;G|0.002	0.002	strong	.	PRPF18	32	.	NM_003675	exon3	c.A158G	p.E53G	CAAAAGAGGAGGA	.	PASS	Atlas-SNP
HERC4	26091	hgsc.bcm.edu	37	10	69773841	69773841	+	Silent	SNP	G	G	A	rs866255	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	56	151	0	0.370861	0	G|0.595;A|0.405	0.405	strong	.	HERC4	78	.	NM_022079	exon9	c.C1011T	p.S337S	AAAGGGGCTTTTC	.	PASS	Atlas-SNP
PHC2	1912	hgsc.bcm.edu	37	1	33820515	33820515	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	98	93	72	0	0.94898	0	.	.	none	.	PHC2	78	.	NM_198040	exon7	c.G1316C	p.G439A	GGCACGCCCTCGG	.	PASS	Atlas-SNP
WDR67	93594	hgsc.bcm.edu	37	8	124142489	124142489	+	Silent	SNP	T	T	C	rs2272724	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	209	108	180	0	0.516746	0	T|0.650;C|0.350	0.350	strong	.	WDR67	97	.	NM_001145088	exon16	c.T2322C	p.D774D	ACAAGATGCTGCA	.	PASS	Atlas-SNP
USP10	9100	hgsc.bcm.edu	37	16	84778697	84778697	+	Missense_Mutation	SNP	G	G	C	rs1812061	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	53	153	0	0.363014	0	G|0.896;C|0.104	0.104	strong	.	USP10	51	.	NM_001272075	exon5	c.G622C	p.V208L	CCGTCAGTTACGC	.	PASS	Atlas-SNP
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56704260	56704260	+	Silent	SNP	C	C	T	rs61742908	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	428	198	361	0	0.462617	0	C|0.913;T|0.087	0.087	strong	ZSCAN5B_ENST00000358992,NS,carcinoma,0,1	ZSCAN5B	160	1	NM_001080456	exon1	c.G162A	p.E54E	CGACTCCTCTGGG	.	PASS	Atlas-SNP
POLR3D	661	hgsc.bcm.edu	37	8	22105502	22105502	+	Silent	SNP	T	T	C	rs1126677	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	80	35	63	0	0.4375	0	A|0.000;C|0.657;G|0.000;T|0.342	0.657	strong	.	POLR3D	26	.	NM_001722	exon4	c.T342C	p.A114A	CCCAGCTGAAATG	.	PASS	Atlas-SNP
OR10R2	343406	hgsc.bcm.edu	37	1	158450314	158450314	+	Missense_Mutation	SNP	A	A	G	rs6679056	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	223	101	201	0	0.452915	0	A|0.467;G|0.533	0.533	strong	OR10R2,colon,carcinoma,+1,1	OR10R2	81	1	NM_001004472	exon1	c.A647G	p.E216G	TTAACGAATTTGT	.	PASS	Atlas-SNP
UBASH3B	84959	hgsc.bcm.edu	37	11	122646967	122646967	+	Missense_Mutation	SNP	G	G	A	rs12790613	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	43	17	42	0	0.395349	0	G|0.779;A|0.221	0.221	strong	UBASH3B,NS,carcinoma,0,1	UBASH3B	73	1	NM_032873	exon2	c.G202A	p.A68T	GTTCAGGCAGCAT	.	PASS	Atlas-SNP
CNN2	1265	hgsc.bcm.edu	37	19	1036444	1036444	+	Silent	SNP	G	G	A	rs930231	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	140	155	0	0.979021	0	G|0.770;C|0.000;A|0.230	0.230	strong	.	CNN2	26	.	NM_004368	exon6	c.G537A	p.S179S	CCAGTCGGGCATG	.	PASS	Atlas-SNP
MDM1	56890	hgsc.bcm.edu	37	12	68707287	68707287	+	Missense_Mutation	SNP	G	G	A	rs2306392	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	40	125	0	0.4	0	G|0.764;A|0.236	0.236	strong	.	MDM1	74	.	NM_017440	exon11	c.C1655T	p.P552L	TGTTCTGGGGCTG	.	PASS	Atlas-SNP
DSG1	1828	hgsc.bcm.edu	37	18	28898294	28898294	+	Missense_Mutation	SNP	A	A	G	rs1426310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	29	69	0	0.527273	0	A|0.579;G|0.421	0.421	strong	.	DSG1	176	.	NM_001942	exon1	c.A31G	p.M11V	GTTGCAATGCTGT	.	PASS	Atlas-SNP
EPS8L1	54869	hgsc.bcm.edu	37	19	55594996	55594996	+	Missense_Mutation	SNP	C	C	G	rs1628576	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	65	37	52	0	0.569231	0	C|0.859;G|0.141	0.141	strong	.	EPS8L1	122	.	NM_133180	exon14	c.C1369G	p.Q457E	GCCCCCCAGGTCG	.	PASS	Atlas-SNP
COL19A1	1310	hgsc.bcm.edu	37	6	70733547	70733547	+	Missense_Mutation	SNP	C	C	G	rs2273426	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	9	68	0	0.173077	0	C|0.761;G|0.239	0.239	strong	.	COL19A1	232	.	NM_001858	exon12	c.C1055G	p.A352G	ATCCAGCTCTGGC	.	PASS	Atlas-SNP
SLC22A24	283238	hgsc.bcm.edu	37	11	62886800	62886800	+	Missense_Mutation	SNP	G	G	C	rs4963245	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	67	34	63	0	0.507463	0	G|0.827;C|0.173	0.173	strong	.	SLC22A24	31	.	NM_001136506	exon3	c.C514G	p.R172G	TCTTCCGTCCAAC	.	PASS	Atlas-SNP
CXorf21	80231	hgsc.bcm.edu	37	X	30577846	30577846	+	Silent	SNP	A	A	C	rs887369	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	91	106	0	0.98913	0	A|0.160;0|0.002	.	strong	.	CXorf21	42	.	NM_025159	exon3	c.T627G	p.V209V	ATTCAGAACTGCA	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151882672	151882672	+	Missense_Mutation	SNP	C	C	A	rs145848316	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	178	35	100	0	0.196629	0	C|0.983;A|0.017	0.017	strong	MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	2	NM_170606	exon34	c.G5053T	p.A1685S	AGCTTGCTTTTCT	.	PASS	Atlas-SNP
DCHS2	54798	hgsc.bcm.edu	37	4	155156412	155156412	+	Missense_Mutation	SNP	G	G	A	rs61746132	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	64	148	0	0.421053	0	G|0.943;A|0.057	0.057	strong	DCHS2,NS,carcinoma,0,1	DCHS2	594	1	NM_017639	exon25	c.C8027T	p.P2676L	GAGTCTGGCACCC	.	PASS	Atlas-SNP
DENND6B	414918	hgsc.bcm.edu	37	22	50754648	50754648	+	Silent	SNP	T	T	C	rs11553141	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	13	44	0	0.351351	0	T|0.547;C|0.453	0.453	strong	FAM116B,NS,carcinoma,0,2	.	.	2	NM_001001794	exon7	c.A594G	p.A198A	CCCAGGTGCAGGC	.	PASS	Atlas-SNP
KRT6A	3853	hgsc.bcm.edu	37	12	52886490	52886490	+	Silent	SNP	A	A	G	rs711317	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	317	130	358	1	0.410095	0.0027933	A|0.452;G|0.547	0.547	strong	KRT6A,NS,carcinoma,0,1	KRT6A	89	1	NM_005554	exon1	c.T483C	p.A161A	CTCCTCAGCCCGC	.	PASS	Atlas-SNP
MIOX	55586	hgsc.bcm.edu	37	22	50926768	50926768	+	Silent	SNP	C	C	T	rs2232883	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	56	95	0	0.602151	0	C|0.878;T|0.122	0.122	strong	.	MIOX	21	.	NM_017584	exon5	c.C405T	p.P135P	GGAGCCCCAGGTA	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29911296	29911296	+	Missense_Mutation	SNP	G	G	A	rs41559916	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	138	23	189	0	0.166667	0	A|0.146;G|0.854	0.146	strong	HLA-A,NS,carcinoma,0,1	HLA-A	89	1	NM_001242758	exon3	c.G595A	p.G199R	GAGAACGGGAAGG	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	497	18	404	7	0.0362173	0.0173267	.	.	weak	MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	NM_005961	exon31	c.G4827C	p.Q1609H	TGTGGTCTGAGGG	.	scavenged	Atlas-SNP
OR10AD1	121275	hgsc.bcm.edu	37	12	48596579	48596579	+	Missense_Mutation	SNP	C	C	T	rs17224674	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	143	65	113	0	0.454545	0	C|0.954;T|0.046	0.046	strong	.	OR10AD1	24	.	NM_001004134	exon1	c.G497A	p.R166Q	GGCTCTCGGAATG	.	PASS	Atlas-SNP
TMEM99	147184	hgsc.bcm.edu	37	17	38991003	38991003	+	Missense_Mutation	SNP	T	T	C	rs10558	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	227	117	214	0	0.515419	0	T|0.704;C|0.296	0.296	strong	.	TMEM99	21	.	NM_001195386	exon3	c.T235C	p.Y79H	CTTCGCTATCTTG	.	PASS	Atlas-SNP
RAPGEF3	10411	hgsc.bcm.edu	37	12	48142636	48142636	+	Missense_Mutation	SNP	C	C	T	rs12422983	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	152	77	152	0	0.506579	0	C|0.880;T|0.120	0.120	strong	RAPGEF3,colon,carcinoma,+1,1	RAPGEF3	98	1	NM_001098531	exon11	c.G1120A	p.G374S	AAGGGCCGGCGCC	.	PASS	Atlas-SNP
DNHD1	144132	hgsc.bcm.edu	37	11	6549779	6549779	+	Missense_Mutation	SNP	A	A	C	rs4633449	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	93	72	0	1	0	A|0.272;C|0.728	0.728	strong	.	DNHD1	198	.	NM_144666	exon11	c.A1865C	p.D622A	CAAAAGACGAATT	.	PASS	Atlas-SNP
C6orf57	135154	hgsc.bcm.edu	37	6	71289189	71289189	+	Missense_Mutation	SNP	A	A	G	rs1048886	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	35	7	95	0	0.2	0	A|0.787;G|0.213	0.213	strong	.	C6orf57	13	.	NM_145267	exon2	c.A137G	p.Q46R	TCAAACAGTCCCT	.	PASS	Atlas-SNP
SPINK5	11005	hgsc.bcm.edu	37	5	147480112	147480112	+	Silent	SNP	T	T	C	rs2303065	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	60	70	1	1	0.0142857	T|0.546;C|0.454	0.454	strong	SPINK5,NS,carcinoma,0,1	SPINK5	245	1	NM_001127699	exon13	c.T1188C	p.H396H	AGTGCATGGCAAC	.	scavenged	Atlas-SNP
FSCB	84075	hgsc.bcm.edu	37	14	44975511	44975511	+	Missense_Mutation	SNP	G	G	A	rs45478391	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	154	71	142	0	0.461039	0	G|0.852;A|0.148	0.148	strong	.	FSCB	173	.	NM_032135	exon1	c.C680T	p.P227L	AGTACCGGGGGAC	.	PASS	Atlas-SNP
L3MBTL2	83746	hgsc.bcm.edu	37	22	41610024	41610024	+	Silent	SNP	G	G	A	rs139451	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	47	73	0	0.489583	0	G|0.598;A|0.402	0.402	strong	.	L3MBTL2	61	.	NM_031488	exon3	c.G390A	p.R130R	GGCTAGGTTACAG	.	PASS	Atlas-SNP
OR13D1	286365	hgsc.bcm.edu	37	9	107457725	107457725	+	Silent	SNP	G	G	A	rs12338899	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	92	39	65	0	0.423913	0	G|0.786;A|0.214	0.214	strong	.	OR13D1	42	.	NM_001004484	exon1	c.G1023A	p.L341L	ACATCTGCATTTA	.	PASS	Atlas-SNP
SIGLEC1	6614	hgsc.bcm.edu	37	20	3682126	3682126	+	Missense_Mutation	SNP	C	C	T	rs34924243	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	151	76	129	0	0.503311	0	C|0.952;T|0.048	0.048	strong	.	SIGLEC1	210	.	NM_023068	exon6	c.G1391A	p.R464H	CTGAAGCGTGGGC	.	PASS	Atlas-SNP
ATP13A5	344905	hgsc.bcm.edu	37	3	193036794	193036794	+	Silent	SNP	G	G	C	rs6788770	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	50	79	0	1	0	G|0.140;C|0.860	0.860	strong	.	ATP13A5	171	.	NM_198505	exon17	c.C2019G	p.V673V	GTGCTCGACTTCT	.	PASS	Atlas-SNP
TAS2R4	50832	hgsc.bcm.edu	37	7	141478574	141478574	+	Missense_Mutation	SNP	G	G	C	rs2234001	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	213	104	257	0	0.488263	0	G|0.508;C|0.492	0.492	strong	.	TAS2R4	25	.	NM_016944	exon1	c.G286C	p.V96L	AGCAGTGTCTGGT	.	PASS	Atlas-SNP
UTP20	27340	hgsc.bcm.edu	37	12	101693534	101693534	+	Missense_Mutation	SNP	C	C	G	rs4764643	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	48	133	0	0.417391	0	C|0.865;G|0.135	0.135	strong	.	UTP20	222	.	NM_014503	exon13	c.C1505G	p.S502C	TTTTATCTATAAT	.	PASS	Atlas-SNP
PHC1	1911	hgsc.bcm.edu	37	12	9086898	9086898	+	Missense_Mutation	SNP	A	A	G	rs1049925	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	74	70	0	0.891566	0	A|0.630;G|0.370	0.370	strong	.	PHC1	67	.	NM_004426	exon10	c.A2077G	p.T693A	GCTAATACTCCAA	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195511102	195511102	+	Missense_Mutation	SNP	G	G	A	rs200212097		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	395	37	425	0	0.0936709	0	.	.	weak	.	MUC4	1505	.	NM_018406	exon2	c.C7349T	p.P2450L	GTGACAGGAAGAG	.	PASS	Atlas-SNP
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	348	125	371	0	0.359195	0	G|0.751;A|0.249	0.249	strong	.	SLC12A6	205	.	NM_133647	exon4	c.C475T	p.L159L	GAGTCAGATTAGT	.	PASS	Atlas-SNP
MIS18BP1	55320	hgsc.bcm.edu	37	14	45696037	45696037	+	Missense_Mutation	SNP	T	T	G	rs34101857	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	52	114	0	0.5	0	T|0.910;G|0.090	0.090	strong	.	MIS18BP1	92	.	NM_018353	exon10	c.A1749C	p.E583D	AATTAATTCCTTC	.	PASS	Atlas-SNP
GZF1	64412	hgsc.bcm.edu	37	20	23345844	23345844	+	Missense_Mutation	SNP	A	A	C	rs6048760	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	44	83	0	0.494382	0	A|0.371;C|0.627;G|0.002;T|0.000	0.627	strong	.	GZF1	61	.	NM_022482	exon1	c.A824C	p.Q275P	TGGAGCAGGTTTC	.	PASS	Atlas-SNP
ZNF260	339324	hgsc.bcm.edu	37	19	37004938	37004938	+	Silent	SNP	T	T	C	rs2967505	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	35	91	0	0.353535	0	T|0.648;C|0.352	0.352	strong	.	ZNF260	34	.	NM_001166038	exon3	c.A1203G	p.S401S	GTGATGTGACTTT	.	PASS	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	37	2	160289863	160289863	+	Silent	SNP	T	T	C	rs61733380	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	45	81	0	0.436893	0	T|0.956;C|0.044	0.044	strong	.	BAZ2B	196	.	NM_013450	exon9	c.A1305G	p.K435K	TGCCTGTTTATAT	.	PASS	Atlas-SNP
MCM10	55388	hgsc.bcm.edu	37	10	13239651	13239651	+	Missense_Mutation	SNP	A	A	G	rs2274110	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	89	43	64	0	0.483146	0	A|0.880;G|0.120	0.120	strong	MCM10,NS,carcinoma,0,1	MCM10	76	1	NM_182751	exon15	c.A2006G	p.K669R	GGGCAAAAGGCCA	.	PASS	Atlas-SNP
PLEKHM3	389072	hgsc.bcm.edu	37	2	208841407	208841407	+	Missense_Mutation	SNP	C	C	T	rs192125155	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	139	2	117	0	0.0143885	0	C|1.000;T|0.000	0.000	strong	PLEKHM3_ENST00000427836,NS,carcinoma,-1,4	PLEKHM3	101	4	NM_001080475	exon3	c.G1514A	p.R505Q	AGTCCTCGTTCCA	.	scavenged	Atlas-SNP
NPR2	4882	hgsc.bcm.edu	37	9	35806500	35806500	+	Silent	SNP	C	C	T	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	54	99	0	0.529412	0	.	.	none	.	NPR2	162	.	NM_003995	exon16	c.C2484T	p.R828R	AAAACGCAAGGCT	.	PASS	Atlas-SNP
SEC16A	9919	hgsc.bcm.edu	37	9	139368953	139368953	+	Missense_Mutation	SNP	G	G	A	rs3812594	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	31	72	0	0.469697	0	G|0.852;A|0.148	0.148	strong	.	SEC16A	249	.	NM_014866	exon3	c.C3115T	p.R1039C	AAAAACGGTCAAG	.	PASS	Atlas-SNP
VENTX	27287	hgsc.bcm.edu	37	10	135051562	135051562	+	Silent	SNP	A	A	G	rs2998143	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	36	43	0	1	0	A|0.248;G|0.752	0.752	strong	VENTX,NS,carcinoma,0,1	VENTX	24	1	NM_014468	exon1	c.A144G	p.P48P	TGGCCCAGGCCAG	.	PASS	Atlas-SNP
DNAH5	1767	hgsc.bcm.edu	37	5	13845045	13845045	+	Silent	SNP	G	G	A	rs10041113	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	104	88	0	1	0	G|0.574;A|0.426	0.426	strong	.	DNAH5	868	.	NM_001369	exon32	c.C5172T	p.A1724A	TAGAAGGGCAGGA	.	PASS	Atlas-SNP
SLC24A3	57419	hgsc.bcm.edu	37	20	19565671	19565671	+	Silent	SNP	G	G	A	rs17293432	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	54	62	0	0.710526	0	G|0.931;A|0.069	0.069	strong	.	SLC24A3	92	.	NM_020689	exon5	c.G480A	p.S160S	AAGTTCGGCCCCA	.	PASS	Atlas-SNP
ABHD12	26090	hgsc.bcm.edu	37	20	25282944	25282944	+	Silent	SNP	A	A	G	rs10966	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	50	19	50	0	0.38	0	A|0.530;G|0.470	0.470	strong	.	ABHD12	46	.	NM_001042472	exon12	c.T1068C	p.D356D	TTTGAAATCTCGG	.	PASS	Atlas-SNP
KRT35	3886	hgsc.bcm.edu	37	17	39633349	39633349	+	Missense_Mutation	SNP	G	G	C	rs2071601	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	38	83	0	0.463415	0	G|0.489;C|0.511	0.511	strong	.	KRT35	58	.	NM_002280	exon7	c.C1327G	p.P443A	GGCGGGGGCTGCA	.	PASS	Atlas-SNP
SERPINF2	5345	hgsc.bcm.edu	37	17	1648294	1648294	+	Missense_Mutation	SNP	C	C	T	rs2070862	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	84	41	71	0	0.488095	0	C|0.780;T|0.220	0.220	strong	SERPINF2,NS,carcinoma,-1,1	SERPINF2	33	1	NM_000934	exon2	c.C5T	p.A2V	ACATGGCGCTGCT	.	PASS	Atlas-SNP
TACC2	10579	hgsc.bcm.edu	37	10	123970569	123970569	+	Missense_Mutation	SNP	C	C	T	rs2295874	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	52	20	52	0	0.384615	0	C|0.900;T|0.100	0.100	strong	.	TACC2	271	.	NM_206862	exon9	c.C6629T	p.A2210V	AGAGTGCAGAAGG	.	PASS	Atlas-SNP
SFXN5	94097	hgsc.bcm.edu	37	2	73226090	73226090	+	Silent	SNP	G	G	A	rs12233055	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	36	77	0	0.418605	0	G|0.682;A|0.318	0.318	strong	SFXN5,NS,carcinoma,-2,1	SFXN5	31	1	NM_144579	exon9	c.C522T	p.A174A	GGAGACGGCGCTG	.	PASS	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	37	10	64945364	64945364	+	Silent	SNP	G	G	A	rs3211105	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	60	80	0	0.983607	0	G|0.356;A|0.644	0.644	strong	.	JMJD1C	347	.	NM_032776	exon20	c.C6789T	p.D2263D	AGGCCAGTCTTTC	.	PASS	Atlas-SNP
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552029	32552029	+	Missense_Mutation	SNP	A	A	T	rs17884945	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	16	18	0	0.347826	0	A|0.523;T|0.477	0.477	strong	HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	NM_002124	exon2	c.T227A	p.F76Y	GCCCGGAACTCCC	.	PASS	Atlas-SNP
CEP85	64793	hgsc.bcm.edu	37	1	26596080	26596080	+	Missense_Mutation	SNP	G	G	A	rs7550997	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	53	87	0	0.898305	0	G|0.849;A|0.151	0.151	strong	.	CEP85	61	.	NM_022778	exon9	c.G1624A	p.A542T	AGAGAAGCAGAAT	.	PASS	Atlas-SNP
OR4K15	81127	hgsc.bcm.edu	37	14	20444441	20444441	+	Missense_Mutation	SNP	C	C	A	rs10135246	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	148	67	185	0	0.452703	0	C|0.776;A|0.224	0.224	strong	.	OR4K15	82	.	NM_001005486	exon1	c.C764A	p.A255E	CCTCTGCAAGCAT	.	PASS	Atlas-SNP
ELFN2	114794	hgsc.bcm.edu	37	22	37770357	37770357	+	Silent	SNP	A	A	G	rs7292751	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	83	34	108	0	0.409639	0	A|0.542;G|0.458	0.458	strong	.	ELFN2	89	.	NM_052906	exon3	c.T1218C	p.F406F	CATGCCAAAGAGG	.	PASS	Atlas-SNP
RBMXL1	494115	hgsc.bcm.edu	37	1	89449390	89449390	+	Missense_Mutation	SNP	T	T	C	rs78952987		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	386	67	255	0	0.173575	0	.	.	weak	.	.	.	.	NM_001162536	exon3	c.A120G	p.I40M	GTCTTTTATCAAG	.	PASS	Atlas-SNP
IL37	27178	hgsc.bcm.edu	37	2	113675269	113675269	+	Missense_Mutation	SNP	C	C	T	rs2723187	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	32	52	0	0.533333	0	C|0.903;T|0.097	0.097	strong	.	IL37	56	.	NM_014439	exon4	c.C323T	p.P108L	GAAGTCCGATTCT	.	PASS	Atlas-SNP
MXRA5	25878	hgsc.bcm.edu	37	X	3239545	3239545	+	Missense_Mutation	SNP	C	C	T	rs1726199	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	61	88	0	1	0	0|0.013;T|0.704	0.704	strong	.	MXRA5	815	.	NM_015419	exon5	c.G4181A	p.G1394D	GGTATGCCTGTCT	.	PASS	Atlas-SNP
ANKRD20A2	441430	hgsc.bcm.edu	37	9	42368549	42368549	+	Silent	SNP	C	C	T	rs77881930		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	228	65	347	0	0.285088	0	.	.	weak	ANKRD20A2,bladder,carcinoma,+2,2	ANKRD20A2	9	2	NM_001012421	exon1	c.C135T	p.D45D	AGGCGACGCCGCG	.	scavenged	Atlas-SNP
RAB11B	9230	hgsc.bcm.edu	37	19	8468337	8468337	+	Silent	SNP	C	C	T	rs2230876	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	115	48	85	0	0.417391	0	C|0.701;A|0.004	.	strong	.	RAB11B	15	.	NM_004218	exon5	c.C552T	p.R184R	AGACCGCGCTGCC	.	PASS	Atlas-SNP
VEPH1	79674	hgsc.bcm.edu	37	3	156983414	156983414	+	Silent	SNP	T	T	C	rs7652298	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	124	52	95	0	0.419355	0	T|0.781;C|0.219	0.219	strong	VEPH1,NS,carcinoma,0,1	VEPH1	129	1	NM_001167912	exon13	c.A2166G	p.K722K	TTTAAGTTTTCCT	.	PASS	Atlas-SNP
ZHX2	22882	hgsc.bcm.edu	37	8	123964819	123964819	+	Missense_Mutation	SNP	G	G	A	rs9649951	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	56	121	0	0.430769	0	G|0.974;A|0.026	0.026	strong	.	ZHX2	106	.	NM_014943	exon3	c.G1069A	p.V357M	ACAAAGGTGACGC	.	PASS	Atlas-SNP
NLN	57486	hgsc.bcm.edu	37	5	65118738	65118738	+	Missense_Mutation	SNP	C	C	T	rs6860508	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	47	95	0	0.534091	0	C|0.918;T|0.082	0.082	strong	.	NLN	51	.	NM_020726	exon13	c.C2110T	p.P704S	CATGCTCCGTGAA	.	PASS	Atlas-SNP
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504794	227504794	+	Silent	SNP	T	T	C	rs11804613	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	217	103	175	0	0.474654	0	T|0.768;C|0.232	0.232	strong	.	CDC42BPA	528	.	NM_003607	exon1	c.A90G	p.T30T	CAGTAATGTCTCC	.	PASS	Atlas-SNP
BOC	91653	hgsc.bcm.edu	37	3	112998265	112998265	+	Silent	SNP	A	A	G	rs2649878	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	55	60	0	1	0	A|0.504;G|0.496	0.496	strong	.	BOC	139	.	NM_033254	exon12	c.A1983G	p.P661P	CCCCCCATCGCGG	.	PASS	Atlas-SNP
ZNF512	84450	hgsc.bcm.edu	37	2	27838058	27838058	+	Silent	SNP	C	C	A	rs11127071	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	135	63	129	0	0.466667	0	C|0.399;A|0.601	0.601	strong	.	ZNF512	54	.	NM_032434	exon11	c.C1155A	p.L385L	AGGGCTCCCTACC	.	PASS	Atlas-SNP
ZNF169	169841	hgsc.bcm.edu	37	9	97062981	97062981	+	Missense_Mutation	SNP	C	C	T	rs12236219	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	38	69	0	0.513514	0	C|0.894;T|0.106	0.106	strong	ZNF169,NS,carcinoma,-1,1	ZNF169	60	1	NM_194320	exon5	c.C1141T	p.R381C	TGTGGGCGTAGCT	.	PASS	Atlas-SNP
TRAPPC12	51112	hgsc.bcm.edu	37	2	3392021	3392021	+	Silent	SNP	C	C	T	rs140551015	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	24	11	0	0.413793	0	C|0.991;T|0.009	0.009	strong	.	.	.	.	NM_016030	exon2	c.C627T	p.F209F	CACGTTCTTCGGA	.	PASS	Atlas-SNP
TPRX1	284355	hgsc.bcm.edu	37	19	48305555	48305555	+	Missense_Mutation	SNP	G	G	A	rs147380237	bycluster;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	38	7	29	0	0.184211	0	G|0.989;A|0.011	0.011	strong	TPRX1,colon,carcinoma,+1,1	TPRX1	46	1	NM_198479	exon2	c.C713T	p.P238L	GGGATCGGGCCTG	.	PASS	Atlas-SNP
JMJD4	65094	hgsc.bcm.edu	37	1	227920665	227920665	+	Missense_Mutation	SNP	A	A	G	rs41270159	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	64	32	64	0	0.5	0	A|0.967;G|0.033	0.033	strong	.	JMJD4	28	.	NM_023007	exon5	c.T1024C	p.F342L	GCAAGAAGCGCCA	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	37	19	1054267	1054267	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	25	13	26	0	0.52	0	.	.	none	.	ABCA7	174	.	NM_019112	exon27	c.G3653A	p.R1218H	TGACCCGCCAGCA	.	PASS	Atlas-SNP
RPS6KL1	83694	hgsc.bcm.edu	37	14	75386576	75386576	+	Missense_Mutation	SNP	G	G	A	rs2286913	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	65	87	0	0.546219	0	G|0.708;A|0.292	0.292	strong	RPS6KL1,colon,carcinoma,0,1	RPS6KL1	35	1	NM_031464	exon3	c.C362T	p.P121L	CTCAGCGGCCGCT	.	PASS	Atlas-SNP
LETM1	3954	hgsc.bcm.edu	37	4	1824020	1824020	+	Missense_Mutation	SNP	C	C	T	rs28681468	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	110	53	129	0	0.481818	0	C|0.980;T|0.020	0.020	strong	.	LETM1	48	.	NM_012318	exon10	c.G1496A	p.R499H	ACCACACGTTCGG	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	37	19	4510530	4510530	+	Missense_Mutation	SNP	G	G	A	rs7250947	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	103	54	92	0	0.524272	0	G|0.909;A|0.091	0.091	strong	.	PLIN4	191	.	NM_001080400	exon3	c.C3400T	p.R1134C	CCAAGCGTGGGGC	.	PASS	Atlas-SNP
TUBA3C	7278	hgsc.bcm.edu	37	13	19753554	19753554	+	Silent	SNP	C	C	T	rs36215076	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	265	113	240	0	0.426415	0	C|0.958;T|0.042	0.042	strong	.	TUBA3C	166	.	NM_006001	exon2	c.G153A	p.T51T	GAAGAACGTGTTG	.	PASS	Atlas-SNP
MPV17L2	84769	hgsc.bcm.edu	37	19	18305824	18305824	+	Silent	SNP	C	C	T	rs2271881	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	86	86	74	0	1	0	C|0.706;T|0.294	0.294	strong	.	MPV17L2	12	.	NM_032683	exon4	c.C492T	p.P164P	GCCCCCCCAATTT	.	PASS	Atlas-SNP
ITPR3	3710	hgsc.bcm.edu	37	6	33654857	33654857	+	Silent	SNP	C	C	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	96	2	81	0	0.0208333	0	.	.	none	ITPR3_ENST00000374316,right_lower_lobe,carcinoma,0,2	ITPR3	409	2	NM_002224	exon44	c.C6051A	p.L2017L	AATCCTCATCAGC	.	scavenged	Atlas-SNP
JPH3	57338	hgsc.bcm.edu	37	16	87723838	87723838	+	Silent	SNP	T	T	C	rs34767155	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	48	70	0	0.516129	0	T|0.583;C|0.417	0.417	strong	JPH3,NS,carcinoma,0,1	JPH3	95	1	NM_020655	exon4	c.T1872C	p.H624H	GACGCATCCCCAG	.	PASS	Atlas-SNP
TBCK	93627	hgsc.bcm.edu	37	4	107157623	107157623	+	Missense_Mutation	SNP	G	G	A	rs34307452	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	26	59	0	0.433333	0	G|0.974;A|0.026	0.026	strong	TBCK,NS,carcinoma,+1,1	TBCK	89	1	NM_001163436	exon14	c.C1274T	p.T425M	GGGAGCGTGGCAG	.	PASS	Atlas-SNP
COL5A1	1289	hgsc.bcm.edu	37	9	137686951	137686951	+	Silent	SNP	G	G	A	rs41310207	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	29	51	0	0.47541	0	G|0.975;A|0.025	0.025	strong	COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	NM_000093	exon33	c.G2724A	p.P908P	AGGACCGCGGGGG	.	PASS	Atlas-SNP
CER1	9350	hgsc.bcm.edu	37	9	14720193	14720193	+	Silent	SNP	C	C	T	rs61759465	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	70	127	0	0.522388	0	C|0.989;T|0.011	0.011	strong	.	CER1	41	.	NM_005454	exon2	c.G699A	p.V233V	CAGCATCACCACC	.	PASS	Atlas-SNP
UFL1	23376	hgsc.bcm.edu	37	6	96997651	96997651	+	Silent	SNP	C	C	T	rs149844923	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	61	4	127	0	0.0655738	0	C|0.991;T|0.009	0.009	strong	.	.	.	.	NM_015323	exon15	c.C1794T	p.D598D	AGTAGACGATCCT	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	37	5	82833391	82833391	+	Silent	SNP	A	A	G	rs16900528	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	42	78	0	0.6	0	A|0.942;G|0.058	0.058	strong	.	VCAN	498	.	NM_004385	exon8	c.A4569G	p.T1523T	AGTCACAGAGAGA	.	PASS	Atlas-SNP
ASPHD2	57168	hgsc.bcm.edu	37	22	26829914	26829914	+	Silent	SNP	T	T	C	rs3747128	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	39	21	38	0	0.538462	0	T|0.890;C|0.110	0.110	strong	.	ASPHD2	42	.	NM_020437	exon2	c.T333C	p.P111P	GTCCCCTGAGTGC	.	PASS	Atlas-SNP
SLC23A2	9962	hgsc.bcm.edu	37	20	4854682	4854682	+	Silent	SNP	A	A	G	rs1110277	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	95	53	76	0	0.557895	0	A|0.562;C|0.001	.	strong	SLC23A2,NS,carcinoma,0,2	SLC23A2	62	2	NM_203327	exon11	c.T1002C	p.D334D	GAAGACATCTGTC	.	PASS	Atlas-SNP
OBSL1	23363	hgsc.bcm.edu	37	2	220427395	220427395	+	Silent	SNP	G	G	A	rs3183099	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	31	58	0	0.469697	0	G|0.802;A|0.198	0.198	strong	.	OBSL1	120	.	NM_001173431	exon8	c.C2682T	p.D894D	GGAGACGTCTGGA	.	PASS	Atlas-SNP
GAS2L3	283431	hgsc.bcm.edu	37	12	101018014	101018014	+	Silent	SNP	T	T	C	rs1045602	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	40	78	0	0.547945	0	T|0.585;C|0.415	0.415	strong	GAS2L3,NS,carcinoma,0,1	GAS2L3	76	1	NM_174942	exon10	c.T1431C	p.N477N	ACATAATCATATT	.	PASS	Atlas-SNP
IL34	146433	hgsc.bcm.edu	37	16	70690989	70690989	+	Missense_Mutation	SNP	G	G	C	rs8046424	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	108	60	77	0	0.555556	0	G|0.354;C|0.646	0.646	strong	.	IL34	26	.	NM_152456	exon5	c.G367C	p.E123Q	GAGGTGGAGACGC	.	PASS	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388378	1388378	+	Missense_Mutation	SNP	T	T	C	rs55884223	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	27	149	4	0.161677	0.0268456	T|0.993;C|0.007	0.007	strong	CRIPAK,NS,carcinoma,-1,1	CRIPAK	185	1	NM_175918	exon1	c.T79C	p.C27R	TGCTCATGTGCCC	.	scavenged	Atlas-SNP
C2CD2	25966	hgsc.bcm.edu	37	21	43338302	43338302	+	Missense_Mutation	SNP	A	A	G	rs2839421	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	21	41	0	0.318182	0	A|0.929;G|0.071	0.071	strong	.	C2CD2	47	.	NM_015500	exon5	c.T632C	p.V211A	TTGAGAACGTCAG	.	PASS	Atlas-SNP
SGK223	0	hgsc.bcm.edu	37	8	8176221	8176221	+	Missense_Mutation	SNP	C	C	T	rs13269488	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	54	18	54	0	0.333333	0	C|0.478;T|0.522	0.522	strong	.	.	.	.	NM_001080826	exon5	c.G3664A	p.G1222S	GGGTGCCGCCCGG	.	PASS	Atlas-SNP
LETMD1	25875	hgsc.bcm.edu	37	12	51442944	51442944	+	Missense_Mutation	SNP	G	G	A	rs12379	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	158	62	149	0	0.392405	0	G|0.509;A|0.491	0.491	strong	.	LETMD1	33	.	NM_001243689	exon2	c.G250A	p.V84I	TTCTATGTCCTGT	.	PASS	Atlas-SNP
AK5	26289	hgsc.bcm.edu	37	1	77759578	77759578	+	Silent	SNP	A	A	G	rs2815311	bycluster;byfrequency;by2hit2allele;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	172	70	139	0	0.406977	0	A|0.843;G|0.157	0.157	strong	.	AK5	86	.	NM_174858	exon3	c.A348G	p.A116A	GACTGCAGAGTTG	.	PASS	Atlas-SNP
UVSSA	57654	hgsc.bcm.edu	37	4	1343405	1343405	+	Silent	SNP	T	T	C	rs2276903	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	149	75	150	0	0.503356	0	T|0.371;C|0.629	0.629	strong	.	.	.	.	NM_020894	exon3	c.T192C	p.I64I	CCAGATTGTGGAG	.	PASS	Atlas-SNP
SLC45A1	50651	hgsc.bcm.edu	37	1	8390384	8390384	+	Silent	SNP	G	G	C	rs56125713	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	88	10	99	0	0.113636	0	G|0.867;C|0.133	0.133	strong	.	SLC45A1	85	.	NM_001080397	exon4	c.G831C	p.L277L	CACCCTGAGCGTC	.	PASS	Atlas-SNP
LAMB3	3914	hgsc.bcm.edu	37	1	209788703	209788703	+	Silent	SNP	T	T	C	rs1049607	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	24	44	0	0.510638	0	T|0.560;C|0.440	0.440	strong	.	LAMB3	136	.	NM_000228	exon23	c.A3432G	p.S1144S	GTCCGCTGAGCGC	.	PASS	Atlas-SNP
PSORS1C1	170679	hgsc.bcm.edu	37	6	31107648	31107648	+	Missense_Mutation	SNP	C	C	T	rs1063646	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	270	269	253	1	0.996296	0.00395257	C|0.847;N|0.000	.	strong	.	PSORS1C1	11	.	NM_014068	exon6	c.C398T	p.P133L	TGGCTCCAACTCT	.	PASS	Atlas-SNP
OR1B1	347169	hgsc.bcm.edu	37	9	125391677	125391677	+	Silent	SNP	T	T	C	rs12347681	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	87	148	0	0.520958	0	T|0.778;C|0.222	0.222	strong	OR1B1,NS,carcinoma,0,1	OR1B1	48	1	NM_001004450	exon1	c.A138G	p.T46T	CACCAGTGTCACA	.	PASS	Atlas-SNP
MAGEB3	4114	hgsc.bcm.edu	37	X	30254530	30254530	+	Silent	SNP	A	A	G	rs2071310	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	162	161	158	1	0.993827	0.00632911	A|0.567;0|0.003	.	strong	.	MAGEB3	54	.	NM_002365	exon5	c.A489G	p.V163V	GGTGGTATTTGGT	.	PASS	Atlas-SNP
ESR1	2099	hgsc.bcm.edu	37	6	152420095	152420095	+	Silent	SNP	G	G	A	rs2228480	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	36	36	66	0	1	0	G|0.822;A|0.178	0.178	strong	.	ESR1	94	.	NM_000125	exon8	c.G1782A	p.T594T	TGCCACGGTCTGA	.	PASS	Atlas-SNP
FAM200B	285550	hgsc.bcm.edu	37	4	15689928	15689928	+	Missense_Mutation	SNP	G	G	A	rs4235380	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	165	77	181	0	0.466667	0	G|0.679;A|0.321	0.321	strong	.	FAM200B	56	.	NM_001145191	exon2	c.G1328A	p.S443N	AACTGAGTTTAAA	.	PASS	Atlas-SNP
SRRM5	100170229	hgsc.bcm.edu	37	19	44116956	44116956	+	Missense_Mutation	SNP	A	A	G	rs13343696	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	58	58	55	0	1	0	A|0.784;G|0.216	0.216	strong	.	SRRM5	38	.	NM_001145641	exon1	c.A683G	p.K228R	CCTCCAAGGAGAA	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44157764	44157764	+	Missense_Mutation	SNP	C	C	A	rs34589386	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	73	39	76	0	0.534247	0	C|0.983;A|0.017	0.017	strong	.	LOXHD1	367	.	NM_144612	exon14	c.G1876T	p.G626C	CTTTGCCATCGTG	.	PASS	Atlas-SNP
CCHCR1	54535	hgsc.bcm.edu	37	6	31116220	31116220	+	Silent	SNP	G	G	A	rs130070	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	130	128	133	1	0.984615	0.0075188	G|0.871;A|0.129	0.129	strong	.	CCHCR1	68	.	NM_001105564	exon10	c.C1542T	p.A514A	CTCCTCGGCTGAG	.	PASS	Atlas-SNP
C17orf47	284083	hgsc.bcm.edu	37	17	56620167	56620167	+	Missense_Mutation	SNP	C	C	T	rs17822735	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	39	126	0	0.402062	0	C|0.828;N|0.000	.	strong	.	C17orf47	59	.	NM_001038704	exon1	c.G1381A	p.G461S	TAAAACCGGACAA	.	PASS	Atlas-SNP
GPR114	221188	hgsc.bcm.edu	37	16	57601792	57601792	+	Silent	SNP	C	C	T	rs9937918	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	47	63	0	1	0	C|0.625;T|0.375	0.375	strong	.	GPR114	52	.	NM_153837	exon9	c.C846T	p.R282R	AACACGCATCCAC	.	PASS	Atlas-SNP
SLIT2	9353	hgsc.bcm.edu	37	4	20544184	20544184	+	Silent	SNP	C	C	T	rs7690492	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	167	85	222	1	0.508982	0.0045045	C|0.682;T|0.318	0.318	strong	.	SLIT2	290	.	NM_004787	exon21	c.C2211T	p.V737V	TACAGTCGTCCGA	.	PASS	Atlas-SNP
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835055	27835055	+	Silent	SNP	G	G	A	rs116008322	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	157	82	152	0	0.522293	0	G|0.982;A|0.018	0.018	strong	.	HIST1H1B	54	.	NM_005322	exon1	c.C253T	p.L85L	GGCCCAGCTTAAT	.	PASS	Atlas-SNP
TTC40	54777	hgsc.bcm.edu	37	10	134671148	134671148	+	Missense_Mutation	SNP	C	C	T	rs144154094	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	123	55	127	0	0.447154	0	C|0.988;T|0.012	0.012	strong	.	TTC40	100	.	NM_001200049	exon39	c.G5520A	p.M1840I	CTCAGCCATGGCG	.	PASS	Atlas-SNP
MSX2	4488	hgsc.bcm.edu	37	5	174156168	174156168	+	Missense_Mutation	SNP	T	T	C	rs4242182	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	76	31	60	0	0.407895	0	T|0.240;C|0.760	0.760	strong	MSX2,NS,carcinoma,-1,1	MSX2	24	1	NM_002449	exon2	c.T386C	p.M129T	GACATATGAGCCC	.	PASS	Atlas-SNP
GRIN3A	116443	hgsc.bcm.edu	37	9	104433235	104433235	+	Missense_Mutation	SNP	C	C	T	rs10989589	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	245	241	253	0	0.983673	0	C|0.670;T|0.330	0.330	strong	GRIN3A,caecum,carcinoma,+1,1	GRIN3A	186	1	NM_133445	exon3	c.G1459A	p.G487R	TCTTTCCCCCCTG	.	PASS	Atlas-SNP
SNX25	83891	hgsc.bcm.edu	37	4	186283092	186283092	+	Missense_Mutation	SNP	C	C	T	rs34120554	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	30	13	47	0	0.433333	0	C|0.993;T|0.007	0.007	strong	.	SNX25	100	.	NM_031953	exon17	c.C2174T	p.T725I	GGGACACAGTCAG	.	PASS	Atlas-SNP
ACAD11	84129	hgsc.bcm.edu	37	3	132337477	132337477	+	Splice_Site	SNP	C	C	A	rs41272317	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	153	66	136	2	0.431373	0.0147059	A|0.027;C|0.973;T|0.000	0.027	strong	ACAD11,NS,carcinoma,0,1	ACAD11	78	1	NM_032169	exon12	c.1414+1G>T	.	TAGTAACCTGGTG	.	scavenged	Atlas-SNP
CCDC79	283847	hgsc.bcm.edu	37	16	66812797	66812797	+	Silent	SNP	C	C	T	rs363162	bycluster;byfrequency;bysubmitter;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	97	95	84	0	0.979381	0	C|0.441;T|0.559	0.559	strong	.	CCDC79	32	.	NM_001136505	exon10	c.G822A	p.T274T	AGTCTTCGTCACA	.	PASS	Atlas-SNP
KCNJ11	3767	hgsc.bcm.edu	37	11	17409069	17409069	+	Silent	SNP	G	G	A	rs5218	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	60	26	65	0	0.433333	0	G|0.773;A|0.227	0.227	strong	.	KCNJ11	39	.	NM_000525	exon1	c.C570T	p.A190A	GCGCAGGGCGATC	.	PASS	Atlas-SNP
ERAP1	51752	hgsc.bcm.edu	37	5	96130836	96130836	+	Missense_Mutation	SNP	T	T	C	rs26618	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	70	70	44	0	1	0	T|0.783;C|0.217	0.217	strong	.	ERAP1	59	.	NM_001198541	exon5	c.A828G	p.I276M	TTGATTTATCTTG	.	PASS	Atlas-SNP
NDUFV3	4731	hgsc.bcm.edu	37	21	44323720	44323720	+	Nonsense_Mutation	SNP	C	C	T	rs4148974	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	32	14	45	0	0.4375	0	C|0.950;T|0.050	0.050	strong	NDUFV3,caecum,carcinoma,-1,1	NDUFV3	23	1	NM_021075	exon3	c.C598T	p.R200X	GCCCCCCGAGTTA	.	PASS	Atlas-SNP
ACACB	32	hgsc.bcm.edu	37	12	109605730	109605730	+	Silent	SNP	C	C	T	rs4766516	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	127	48	88	0	0.377953	0	C|0.805;T|0.195	0.195	strong	.	ACACB	330	.	NM_001093	exon3	c.C816T	p.A272A	TGCCGCCGTGAAG	.	PASS	Atlas-SNP
WIPI2	26100	hgsc.bcm.edu	37	7	5257639	5257639	+	Silent	SNP	G	G	A	rs147063855	byfrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	171	84	130	0	0.491228	0	G|0.999;A|0.001	0.001	strong	WIPI2,NS,carcinoma,+1,1	WIPI2	41	1	NM_015610	exon7	c.G663A	p.S221S	GGCTTCGGAGAAG	.	PASS	Atlas-SNP
MICA	100507436	hgsc.bcm.edu	37	6	31378425	31378425	+	Missense_Mutation	SNP	A	A	G	rs1051786	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	195	191	157	0	0.979487	0	A|0.641;G|0.359	0.359	strong	.	MICA	21	.	NM_001177519	exon2	c.A176G	p.Y59C	TGCGCTATGACAG	.	PASS	Atlas-SNP
CGB2	114336	hgsc.bcm.edu	37	19	49536390	49536390	+	Missense_Mutation	SNP	C	C	A	rs78219294		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	237	5	209	1	0.021097	0.00478469	A|1.000;|0.000	1.000	weak	CGB2,NS,carcinoma,0,1	CGB2	6	1	NM_033378	exon3	c.C404A	p.A135D	TCCAGGCCTCCTC	.	scavenged	Atlas-SNP
ZNF175	7728	hgsc.bcm.edu	37	19	52090100	52090100	+	Silent	SNP	T	T	C	rs45541134	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	117	52	124	0	0.444444	0	T|0.795;C|0.205	0.205	strong	.	ZNF175	65	.	NM_007147	exon5	c.T516C	p.N172N	AAGCAATTGTGAA	.	PASS	Atlas-SNP
PLCB3	5331	hgsc.bcm.edu	37	11	64026685	64026685	+	Silent	SNP	C	C	T	rs28395882	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	5	3	2	0	0.6	0	C|0.817;T|0.183	0.183	strong	PLCB3,NS,carcinoma,0,1	PLCB3	103	1	NM_000932	exon13	c.C1494T	p.S498S	GAGCTCCGCGGCC	.	scavenged	Atlas-SNP
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605971	84605971	+	Missense_Mutation	SNP	C	C	A	rs111857392	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	202	88	193	0	0.435644	0	C|0.989;A|0.011	0.011	strong	.	.	.	.	NM_001001670	exon4	c.C586A	p.P196T	CCACCACCCCCCT	.	PASS	Atlas-SNP
UBC	7316	hgsc.bcm.edu	37	12	125397435	125397435	+	Silent	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	262	4	281	2	0.0152672	0.00711744	.	.	none	UBC,NS,carcinoma,0,1	UBC	79	1	NM_021009	exon2	c.C883T	p.L295L	GGTGCAGGGTAGA	.	scavenged	Atlas-SNP
BANP	54971	hgsc.bcm.edu	37	16	88066717	88066717	+	Missense_Mutation	SNP	C	C	T	rs74992447	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	279	136	243	0	0.487455	0	C|0.875;T|0.125	0.125	strong	BANP,rectum,carcinoma,-1,1	BANP	67	1	NM_001173542	exon9	c.C1066T	p.P356S	ACAGAGCCGATGA	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279836	46279836	+	Silent	SNP	A	A	G	rs2664522		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	72	9	88	0	0.125	0	.	.	weak	NCOA3,NS,carcinoma,0,1	NCOA3	156	1	NM_181659	exon20	c.A3762G	p.Q1254Q	GCAGCAACAGCAG	.	PASS	Atlas-SNP
SMYD4	114826	hgsc.bcm.edu	37	17	1704296	1704296	+	Missense_Mutation	SNP	C	C	A	rs7224496	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	94	45	107	0	0.478723	0	C|0.642;A|0.358	0.358	strong	.	SMYD4	50	.	NM_052928	exon5	c.G392T	p.R131I	TGTGCTCTGTTAA	.	PASS	Atlas-SNP
SEMA5A	9037	hgsc.bcm.edu	37	5	9136646	9136646	+	Silent	SNP	C	C	G	rs17238609	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	57	26	63	0	0.45614	0	C|0.930;G|0.070	0.070	strong	SEMA5A,NS,carcinoma,0,1	SEMA5A	236	1	NM_003966	exon13	c.G1569C	p.T523T	CCACTGCGTCATG	.	PASS	Atlas-SNP
ADCY7	113	hgsc.bcm.edu	37	16	50342658	50342658	+	Silent	SNP	C	C	T	rs17289102	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	55	23	56	0	0.418182	0	C|0.842;T|0.158	0.158	strong	ADCY7,NS,carcinoma,0,1	ADCY7	90	1	NM_001114	exon16	c.C2016T	p.A672A	CCTGGCCGTCCTG	.	PASS	Atlas-SNP
PODXL	5420	hgsc.bcm.edu	37	7	131195959	131195959	+	Missense_Mutation	SNP	C	C	T	rs3735035	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	258	138	259	1	0.534884	0.003861	C|0.627;T|0.373	0.373	strong	.	PODXL	53	.	NM_001018111	exon2	c.G334A	p.G112S	CTGAGCCGCCTCC	.	PASS	Atlas-SNP
CD97	976	hgsc.bcm.edu	37	19	14512489	14512489	+	Missense_Mutation	SNP	G	G	A	rs2230748	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	93	44	75	0	0.473118	0	G|0.848;A|0.152	0.152	strong	.	CD97	86	.	NM_078481	exon11	c.G1100A	p.R367Q	AGGAGCGGGGGGA	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110864225	110864225	+	Silent	SNP	A	A	T	rs532625	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	113	70	117	0	0.619469	0	A|0.550;N|0.000	.	strong	.	COL4A1	372	.	NM_001845	exon7	c.T432A	p.A144A	ATTTCCAGCGAAA	.	PASS	Atlas-SNP
THSD7A	221981	hgsc.bcm.edu	37	7	11509561	11509561	+	Missense_Mutation	SNP	G	G	C	rs2285744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	100	50	104	0	0.5	0	G|0.719;C|0.281	0.281	strong	.	THSD7A	219	.	NM_015204	exon9	c.C2313G	p.D771E	AATACAGTCCTTC	.	PASS	Atlas-SNP
CSMD3	114788	hgsc.bcm.edu	37	8	113237045	113237045	+	Silent	SNP	C	C	T	rs4876458	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	271	140	298	0	0.516605	0	C|0.918;T|0.082	0.082	strong	CSMD3_ENST00000343508,NS,carcinoma,-1,6	CSMD3	2325	6	NM_198123	exon71	c.G11079A	p.A3693A	TCGTACCGCCTTC	.	PASS	Atlas-SNP
DHX37	57647	hgsc.bcm.edu	37	12	125448960	125448960	+	Silent	SNP	C	C	T	rs4076777	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	53	32	40	0	0.603774	0	C|0.671;T|0.329	0.329	strong	.	DHX37	114	.	NM_032656	exon15	c.G2025A	p.T675T	GGGCTCCGTCCGT	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	37	2	179447755	179447755	+	Silent	SNP	G	G	A	rs72646867	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	187	84	159	0	0.449198	0	G|0.999;A|0.001	0.001	weak	.	TTN	18412	.	NM_001267550	exon313	c.C65775T	p.S21925S	GTTCACGCTGAAT	.	PASS	Atlas-SNP
ATAD3C	219293	hgsc.bcm.edu	37	1	1390875	1390875	+	Silent	SNP	C	C	T	rs1781147	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	159	158	100	0	0.993711	0	C|0.608;T|0.392	0.392	strong	ATAD3C,NS,carcinoma,+2,1	ATAD3C	23	1	NM_001039211	exon5	c.C414T	p.D138D	CCAGGACGTGCTG	.	PASS	Atlas-SNP
SERPINA6	866	hgsc.bcm.edu	37	14	94776221	94776221	+	Missense_Mutation	SNP	A	A	C	rs2228541	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	102	52	0	0.980769	0	T|0.003;G|0.002	.	strong	SERPINA6_ENST00000341584,NS,adenoma,+2,1	SERPINA6	102	1	NM_001756	exon3	c.T736G	p.S246A	GCTCCGAGTCATG	.	PASS	Atlas-SNP
KLK3	354	hgsc.bcm.edu	37	19	51362803	51362803	+	Silent	SNP	C	C	T	rs35192866	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	91	48	81	0	0.527473	0	C|0.912;T|0.088	0.088	strong	.	KLK3	76	.	NM_001030047	exon5	c.C648T	p.T216T	GATCACCGAACTG	.	PASS	Atlas-SNP
DOCK6	57572	hgsc.bcm.edu	37	19	11348911	11348911	+	Silent	SNP	A	A	G	rs7252937	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	82	36	102	0	0.439024	0	A|0.830;G|0.170	0.170	strong	.	DOCK6	104	.	NM_020812	exon15	c.T1713C	p.A571A	TCGCACAGCAAGG	.	PASS	Atlas-SNP
SPATA19	219938	hgsc.bcm.edu	37	11	133714522	133714522	+	Missense_Mutation	SNP	G	G	A	rs2282602	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	99	42	88	0	0.424242	0	G|0.673;A|0.327	0.327	strong	.	SPATA19	36	.	NM_174927	exon3	c.C149T	p.A50V	CGAGAAGCCTCTT	.	PASS	Atlas-SNP
SPATC1	375686	hgsc.bcm.edu	37	8	145095328	145095328	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	90	53	69	0	0.588889	0	.	.	none	.	SPATC1	77	.	NM_001134374	exon2	c.T730A	p.S244T	CCCCAGTCCCCAG	.	PASS	Atlas-SNP
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071115	6071115	+	Missense_Mutation	SNP	A	A	G	rs12334093	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	155	83	129	0	0.535484	0	A|0.885;G|0.115	0.115	strong	.	.	.	.	NM_001271700	exon1	c.A109G	p.M37V	GCCATCATGAGAG	.	PASS	Atlas-SNP
TMEM255B	348013	hgsc.bcm.edu	37	13	114498154	114498154	+	Missense_Mutation	SNP	G	G	C	rs150323609	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	47	18	45	0	0.382979	0	G|0.996;C|0.004	0.004	strong	.	.	.	.	NM_182614	exon4	c.G286C	p.V96L	TTTGGCGTGGTGG	.	PASS	Atlas-SNP
HSD17B14	51171	hgsc.bcm.edu	37	19	49339098	49339098	+	Missense_Mutation	SNP	T	T	C	rs8110220	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	33	17	42	0	0.515152	0	C|0.335;N|0.001	0.335	strong	.	HSD17B14	25	.	NM_016246	exon2	c.A91G	p.N31D	CGCTGTTCACTGA	.	PASS	Atlas-SNP
POU4F3	5459	hgsc.bcm.edu	37	5	145719368	145719368	+	Silent	SNP	G	G	A	rs113137300	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	59	29	44	0	0.491525	0	G|0.997;A|0.003	0.003	strong	.	POU4F3	47	.	NM_002700	exon2	c.G378A	p.T126T	GCCCACGCTGAGT	.	PASS	Atlas-SNP
FCN1	2219	hgsc.bcm.edu	37	9	137801800	137801800	+	Silent	SNP	T	T	C	rs1071583	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	177	173	160	0	0.977401	0	T|0.300;C|0.700	0.700	strong	.	FCN1	62	.	NM_002003	exon9	c.A825G	p.Q275Q	GGCTCCTTGGAAC	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	37	6	30680916	30680916	+	Missense_Mutation	SNP	C	C	T	rs9262152	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	218	99	219	0	0.454128	0	C|0.897;T|0.103	0.103	strong	.	MDC1	218	.	NM_014641	exon5	c.G803A	p.R268K	TTGTCCCTCTCCT	.	PASS	Atlas-SNP
IRX4	50805	hgsc.bcm.edu	37	5	1878325	1878325	+	Missense_Mutation	SNP	C	C	T	rs201914951	bycluster	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	37	18	25	0	0.486486	0	C|0.993;T|0.007	0.007	weak	.	IRX4	45	.	NM_016358	exon5	c.G1318A	p.D440N	CCCCGTCCACCCA	.	PASS	Atlas-SNP
CCDC74A	90557	hgsc.bcm.edu	37	2	132290912	132290912	+	Missense_Mutation	SNP	G	G	A	rs140033985	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	255	118	272	1	0.462745	0.00367647	G|0.991;A|0.009	0.009	strong	.	CCDC74A	44	.	NM_138770	exon8	c.G1078A	p.E360K	TTTGCCGAGAGGC	.	PASS	Atlas-SNP
FMN1	342184	hgsc.bcm.edu	37	15	33261185	33261185	+	Missense_Mutation	SNP	G	G	A	rs117804335	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	46	22	52	0	0.478261	0	G|0.966;A|0.034	0.034	strong	.	FMN1	174	.	NM_001103184	exon4	c.C2048T	p.P683L	GGAGGCGGAGGTG	.	PASS	Atlas-SNP
PFKP	5214	hgsc.bcm.edu	37	10	3155353	3155353	+	Silent	SNP	C	C	T	rs3816699	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	20	58	0	0.392157	0	C|0.848;T|0.152	0.152	strong	.	PFKP	182	.	NM_002627	exon12	c.C1197T	p.I399I	TGCCATCAAGCTG	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129902368	129902368	+	Missense_Mutation	SNP	T	T	A	rs79661992	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	81	80	106	0	0.987654	0	T|0.949;A|0.051	0.051	strong	MKI67,NS,carcinoma,0,1	MKI67	363	1	NM_002417	exon13	c.A7736T	p.D2579V	TTTTTGTCAATAG	.	PASS	Atlas-SNP
FBXW8	26259	hgsc.bcm.edu	37	12	117383320	117383320	+	Missense_Mutation	SNP	G	G	A	rs4076700	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	79	38	68	0	0.481013	0	G|0.340;A|0.660	0.660	strong	.	FBXW8	53	.	NM_153348	exon3	c.G575A	p.R192Q	TGTTACGAACCAA	.	PASS	Atlas-SNP
EPHA1	2041	hgsc.bcm.edu	37	7	143093538	143093538	+	Silent	SNP	G	G	A	rs10952549	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	78	42	62	0	0.538462	0	G|0.193;A|0.807	0.807	strong	.	EPHA1	193	.	NM_005232	exon11	c.C1837T	p.L613L	AGTCCAGGGCTCC	.	PASS	Atlas-SNP
CAPS	828	hgsc.bcm.edu	37	19	5914470	5914470	+	Missense_Mutation	SNP	G	G	A	rs143117009	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	104	52	112	0	0.5	0	G|0.988;A|0.012	0.012	strong	.	CAPS	14	.	NM_080590	exon2	c.G53A	p.R18H	TGTCCCGCGGGGC	.	PASS	Atlas-SNP
CCDC127	133957	hgsc.bcm.edu	37	5	205565	205565	+	Silent	SNP	G	G	A	rs10060089	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	107	49	120	0	0.457944	0	G|0.869;A|0.131	0.131	strong	.	CCDC127	27	.	NM_145265	exon3	c.C630T	p.T210T	TATGTCGGTGAGA	.	PASS	Atlas-SNP
ATP10A	57194	hgsc.bcm.edu	37	15	25926179	25926179	+	Missense_Mutation	SNP	C	C	T	rs2076744	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	109	55	103	0	0.504587	0	C|0.734;T|0.266	0.266	strong	ATP10A,colon,carcinoma,0,1	ATP10A	270	1	NM_024490	exon18	c.G3535A	p.A1179T	GGAAGGCGGCGTC	.	PASS	Atlas-SNP
ZC3HC1	51530	hgsc.bcm.edu	37	7	129663533	129663533	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	74	27	63	0	0.364865	0	.	.	none	ZC3HC1,NS,carcinoma,0,1	ZC3HC1	45	1	NM_016478	exon8	c.C1051T	p.R351X	GAGTTCGAGAGAC	.	PASS	Atlas-SNP
NPAS2	4862	hgsc.bcm.edu	37	2	101580575	101580575	+	Silent	SNP	G	G	A	rs41280595	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	119	62	118	0	0.521008	0	G|0.866;A|0.134	0.134	strong	.	NPAS2	88	.	NM_002518	exon8	c.G654A	p.V218V	CCGGGTGCCACTA	.	PASS	Atlas-SNP
TMEM260	0	hgsc.bcm.edu	37	14	57072338	57072338	+	Silent	SNP	C	C	T	rs3737170	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	102	49	91	0	0.480392	0	C|0.874;T|0.126	0.126	strong	.	.	.	.	NM_017799	exon5	c.C573T	p.H191H	CCAGCACACAATA	.	PASS	Atlas-SNP
SH2D3A	10045	hgsc.bcm.edu	37	19	6755007	6755007	+	Silent	SNP	T	T	C	rs2305806	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	66	33	51	0	0.5	0	T|0.656;C|0.344	0.344	strong	.	SH2D3A	53	.	NM_005490	exon5	c.A816G	p.T272T	TGGTCTTGTAAAA	.	PASS	Atlas-SNP
PKD1	5310	hgsc.bcm.edu	37	16	2140680	2140680	+	Missense_Mutation	SNP	T	T	C	rs10960	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	51	24	43	0	0.470588	0	T|0.709;C|0.291	0.291	strong	.	PKD1	184	.	NM_001009944	exon44	c.A12133G	p.I4045V	CCAGGATGGCCAG	.	PASS	Atlas-SNP
PCDHB7	56129	hgsc.bcm.edu	37	5	140554481	140554481	+	Missense_Mutation	SNP	G	G	T	rs1811237	bycluster;byfrequency;bysubmitter;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	112	111	220	1	0.991071	0.00454545	G|0.758;T|0.242	0.242	strong	PCDHB7,NS,carcinoma,0,1	PCDHB7	231	1	NM_018940	exon1	c.G2065T	p.V689L	TACCTGGTGGTGG	.	PASS	Atlas-SNP
NOX4	50507	hgsc.bcm.edu	37	11	89088168	89088168	+	Silent	SNP	G	G	A	rs75735530	bycluster;byfrequency;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	166	59	204	0	0.355422	0	G|0.942;A|0.058	0.058	strong	NOX4,right_upper_lobe,carcinoma,-1,1	NOX4	101	1	NM_001143836	exon13	c.C1179T	p.S393S	AATTTCGGAGTCT	.	PASS	Atlas-SNP
LCLAT1	253558	hgsc.bcm.edu	37	2	30863108	30863108	+	Missense_Mutation	SNP	A	A	G	rs12471868	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	146	145	151	1	0.993151	0.00662252	A|0.870;G|0.130	0.130	strong	.	LCLAT1	51	.	NM_182551	exon7	c.A868G	p.I290V	TATCCAATAGACA	.	PASS	Atlas-SNP
ATF6B	1388	hgsc.bcm.edu	37	6	32088854	32088854	+	Silent	SNP	G	G	C	rs2228628	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	134	72	129	0	0.537313	0	G|0.784;C|0.216	0.216	strong	.	ATF6B	40	.	NM_004381	exon7	c.C612G	p.S204S	TGAAGGGGACAGG	.	PASS	Atlas-SNP
