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
TNFAIP3	7128	hgsc.bcm.edu	37	6	138192658	138192659	+	Frame_Shift_Ins	INS	-	-	GG	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	18	10	46	.	0.556	.	.	.	none	.	TNFAIP3	340	.	NM_001270507	exon2	c.294_295insGG	p.N98fs	.	.	PASS	Pindel,Atlas-Indel
KRT2	3849	hgsc.bcm.edu	37	12	53045603	53045604	+	In_Frame_Ins	INS	-	-	AAGCCGCTGCCACCTCCA	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	60	21	61	0	0.35	0	.	.	none	.	KRT2	94	.	NM_000423	exon1	c.324_325insTGGAGGTGGCAGCGGCTT	p.F108delinsFGGGSGF	.	.	PASS	Atlas-Indel
NEFH	4744	hgsc.bcm.edu	37	22	29885581	29885604	+	In_Frame_Del	DEL	AGGCCAAGTCCCCAGAGAAGGAAG	AGGCCAAGTCCCCAGAGAAGGAAG	-	rs200984527		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	AGGCCAAGTCCCCAGAGAAGGAAG	AGGCCAAGTCCCCAGAGAAGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	71	37	49	0	0.521127	0	.	.	weak	.	NEFH	178	.	NM_021076	exon4	c.1951_1974del	p.651_658del	.	.	PASS	Atlas-Indel
NOTCH2	4853	hgsc.bcm.edu	37	1	120529632	120529635	+	Frame_Shift_Del	DEL	ACAA	ACAA	-	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	ACAA	ACAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	77	25	69	.	0.325	.	.	.	none	.	NOTCH2	348	.	NM_024408	exon5	c.823_826del	p.275_276del	.	.	PASS	Pindel,Atlas-Indel
ATXN1	6310	hgsc.bcm.edu	37	6	16327915	16327916	+	In_Frame_Ins	INS	-	-	TGC	rs71806515		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	54	16	42	0	0.296296	0	.	.	weak	ATXN1,colon,carcinoma,0,1	ATXN1	117	1	NM_000332	exon8	c.627_628insGCA	p.H209delinsQH	.	.	PASS	Atlas-Indel
SLC6A14	11254	hgsc.bcm.edu	37	X	115584299	115584299	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	113	64	162	.	0.566	.	.	.	none	.	SLC6A14	56	.	NM_007231	exon9	c.1276delG	p.A426fs	.	.	PASS	Pindel,Atlas-Indel
NCAPD2	9918	hgsc.bcm.edu	37	12	6635472	6635473	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	73	23	55	.	0.315	.	.	.	none	.	NCAPD2	99	.	NM_014865	exon20	c.2501_2502insC	p.H834fs	.	.	PASS	Pindel,Atlas-Indel
VEZF1	7716	hgsc.bcm.edu	37	17	56058015	56058016	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	200	37	277	0	0.185	0	.	.	none	.	VEZF1	50	.	NM_007146	exon4	c.925_926insA	p.G309fs	.	.	PASS	Atlas-Indel
GPR26	2849	hgsc.bcm.edu	37	10	125426000	125426002	+	In_Frame_Del	DEL	TGC	TGC	-	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	70	24	81	.	0.343	.	.	.	none	.	GPR26	47	.	NM_153442	exon1	c.76_78del	p.26_26del	.	.	PASS	Pindel,Atlas-Indel
LINC00174	285908	hgsc.bcm.edu	37	7	65842543	65842544	+	RNA	INS	-	-	AT	rs112115083	bycluster;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	28	12	23	0	0.428571	0	-|0.566;AT|0.434	0.434	strong	.	.	.	.	.	.	.	.	.	.	PASS	Atlas-Indel
HIST1H3B	8358	hgsc.bcm.edu	37	6	26031883	26031883	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	95	35	85	.	0.368	.	.	.	none	HIST1H3B,NS,lymphoid_neoplasm,-1,3	HIST1H3B	59	3	NM_003537	exon1	c.407delC	p.A136fs	.	.	PASS	Pindel,Atlas-Indel
BDNF	627	hgsc.bcm.edu	37	11	27681176	27681177	+	RNA	INS	-	-	TGTGTG	rs149254890	bycluster;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	262	44	297	0	0.168	0.000	.	.	strong	.	BDNF	63	.	.	.	.	.	.	.	PASS	Pindel
SOX2	6657	hgsc.bcm.edu	37	3	181431226	181431227	+	RNA	INS	-	-	A	rs201617684	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	80	19	74	0	0.237	0.000	.	.	weak	.	SOX2	28	.	.	.	.	.	.	.	PASS	Pindel
FGD5	152273	hgsc.bcm.edu	37	3	14861747	14861748	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	102	30	109	.	0.294	.	.	.	none	.	FGD5	248	.	NM_152536	exon1	c.1169_1170insG	p.V390fs	.	.	PASS	Pindel
NBPF10	100132406	hgsc.bcm.edu	37	1	145299805	145299805	+	Missense_Mutation	SNP	A	A	C	rs61814629	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	117	7	103	3	0.0598291	0.0291262	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
TUBA3D	113457	hgsc.bcm.edu	37	2	132238015	132238015	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	140	62	133	0	0.442857	0	.	.	none	.	TUBA3D	60	.	NM_080386	exon4	c.T749A	p.V250E	TGAATGTGGACTT	.	PASS	Atlas-SNP
RGPD4	285190	hgsc.bcm.edu	37	2	108487901	108487901	+	Silent	SNP	A	A	G	rs7563250	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	17	3	14	3	0.176471	0.214286	G|1.000;|0.000	1.000	weak	RGPD4,NS,carcinoma,0,1	RGPD4	112	1	NM_182588	exon20	c.A3441G	p.L1147L	GCGGTTAGCAGCA	.	scavenged	Atlas-SNP
RNF145	153830	hgsc.bcm.edu	37	5	158603839	158603839	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	256	7	241	3	0.0273438	0.0124481	.	.	none	RNF145,NS,carcinoma,0,4	RNF145	110	4	NM_001199380	exon5	c.T512C	p.M171T	GTTTTCATGACAC	.	scavenged	Atlas-SNP
CCDC180	0	hgsc.bcm.edu	37	9	100071801	100071801	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	71	35	76	0	0.492958	0	.	.	none	.	.	.	.	NM_020893	exon3	c.G307A	p.E103K	ACTCCTGAAGGGG	.	PASS	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240781	39240781	+	Missense_Mutation	SNP	C	C	G	rs372960430	alternate_allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	37	3	32	0	0.0810811	0	.	.	alt	KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-7	49	2	NM_033061	exon1	c.C323G	p.T108S	AGCCCACCTGCTG	.	scavenged	Atlas-SNP
KRT19	3880	hgsc.bcm.edu	37	17	39681516	39681516	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	54	34	75	0	0.62963	0	.	.	none	.	KRT19	41	.	NM_002276	exon2	c.G430A	p.A144T	TGGTGGCACCAAG	.	PASS	Atlas-SNP
CDH22	64405	hgsc.bcm.edu	37	20	44845551	44845551	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	28	12	33	0	0.428571	0	.	.	none	.	CDH22	112	.	NM_021248	exon5	c.C752T	p.A251V	TGACCCGCCATGT	.	PASS	Atlas-SNP
SLC6A14	11254	hgsc.bcm.edu	37	X	115584183	115584183	+	Silent	SNP	T	T	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	111	91	157	1	0.81982	0.00636943	.	.	none	.	SLC6A14	56	.	NM_007231	exon9	c.T1161A	p.G387G	CGTAGGTTTTGAT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416254	105416254	+	Missense_Mutation	SNP	G	G	A	rs201136817	bycluster;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	160	12	139	2	0.075	0.0143885	G|0.992;A|0.008	0.008	strong	AHNAK2_ENST00000333244,colon,carcinoma,+1,1	AHNAK2	719	1	NM_138420	exon7	c.C5534T	p.S1845L	TCCACCGAGGCCT	.	scavenged	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274150	39274150	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	57	4	47	3	0.0701754	0.0638298	.	.	none	KRTAP4-11,NS,carcinoma,0,5	KRTAP4-11	94	5	NM_033059	exon1	c.A418T	p.S140C	AGATGCTGCAGCT	.	scavenged	Atlas-SNP
SMAD7	4092	hgsc.bcm.edu	37	18	46448230	46448230	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	46	21	42	0	0.456522	0	.	.	none	.	SMAD7	22	.	NM_005904	exon4	c.G793A	p.A265T	AGTATGCCACCAC	.	PASS	Atlas-SNP
ZNF454	285676	hgsc.bcm.edu	37	5	178391738	178391738	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	160	151	173	0	0.94375	0	.	.	none	.	ZNF454	99	.	NM_001178089	exon5	c.G333T	p.K111N	AATAAAGGAAAGA	.	PASS	Atlas-SNP
SUPT5H	6829	hgsc.bcm.edu	37	19	39950582	39950582	+	Silent	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	33	17	52	0	0.515152	0	.	.	none	.	SUPT5H	119	.	NM_003169	exon9	c.C606A	p.A202A	CATTGCCTACCAG	.	PASS	Atlas-SNP
KRI1	65095	hgsc.bcm.edu	37	19	10671051	10671051	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	24	6	32	0	0.25	0	.	.	none	.	KRI1	65	.	NM_023008	exon9	c.A755G	p.N252S	CGTTTGTTGAGGA	.	PASS	Atlas-SNP
COL4A1	1282	hgsc.bcm.edu	37	13	110831690	110831690	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	72	68	78	0	0.944444	0	.	.	none	.	COL4A1	372	.	NM_001845	exon30	c.G2272A	p.G758R	TGCTCCCCTTCTC	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29885564	29885564	+	Silent	SNP	A	A	G	rs202065964	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	58	13	33	0	0.224138	0	.	.	weak	NEFH,rectum,carcinoma,0,1	NEFH	178	1	NM_021076	exon4	c.A1935G	p.E645E	GGAGGAAGCAAAG	.	PASS	Atlas-SNP
TYRO3	7301	hgsc.bcm.edu	37	15	41859646	41859646	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	70	34	65	0	0.485714	0	.	.	none	.	TYRO3	169	.	NM_006293	exon7	c.C872T	p.A291V	TGCCTGCCACCAA	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	37	5	101724427	101724427	+	Missense_Mutation	SNP	T	T	A	rs199624995	by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	350	4	372	0	0.0114286	0	T|1.000;A|0.000	0.000	strong	SLCO6A1,NS,carcinoma,0,1	SLCO6A1	153	1	NM_173488	exon12	c.A1982T	p.N661I	GTCTTGTTATATA	.	scavenged	Atlas-SNP
GHSR	2693	hgsc.bcm.edu	37	3	172163205	172163205	+	Nonsense_Mutation	SNP	G	G	A	rs148371213	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	84	41	85	0	0.488095	0	G|1.000;A|0.000	0.000	weak	.	GHSR	104	.	NM_198407	exon2	c.C847T	p.R283X	AATATCGCCCTAC	.	PASS	Atlas-SNP
PXDN	7837	hgsc.bcm.edu	37	2	1680761	1680761	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	160	71	176	0	0.44375	0	.	.	none	.	PXDN	255	.	NM_012293	exon8	c.C786T	p.T262T	GTACACGGTGTTC	.	PASS	Atlas-SNP
CARD11	84433	hgsc.bcm.edu	37	7	2987283	2987283	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	227	54	200	1	0.237885	0.005	.	.	none	CARD11,colon,carcinoma,+1,2	CARD11	339	2	NM_032415	exon3	c.G146A	p.C49Y	ACCTTACACTGAC	.	scavenged	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	37	1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	rs62648104	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	414	40	346	0	0.0966184	0	T|0.024;A|0.976	0.976	weak	.	NRD1	89	.	NM_001101662	exon2	c.A449T	p.E150V	TCTTCCTCCACCT	.	PASS	Atlas-SNP
SSTR1	6751	hgsc.bcm.edu	37	14	38679760	38679760	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	42	13	37	0	0.309524	0	.	.	none	.	SSTR1	66	.	NM_001049	exon3	c.C1166T	p.T389M	GGATCACGACGCT	.	PASS	Atlas-SNP
KLF2	10365	hgsc.bcm.edu	37	19	16436026	16436026	+	Splice_Site	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	70	28	83	0	0.4	0	.	.	none	.	KLF2	10	.	NM_016270	exon2	c.76-1G>A	.	CCCGCAGCGCTGG	.	PASS	Atlas-SNP
LINGO1	84894	hgsc.bcm.edu	37	15	77906995	77906995	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	128	3	124	0	0.0234375	0	.	.	none	LINGO1,right_upper_lobe,carcinoma,-1,1	LINGO1	76	1	NM_032808	exon2	c.C1254A	p.Y418X	GGTGAAGTAGTTG	.	scavenged	Atlas-SNP
GABBR1	2550	hgsc.bcm.edu	37	6	29578720	29578720	+	Silent	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	84	11	90	0	0.130952	0	.	.	none	.	GABBR1	95	.	NM_001470	exon14	c.C1689A	p.S563S	TGTTTTGGACCAG	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416255	105416255	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	160	12	139	2	0.075	0.0143885	.	.	none	AHNAK2_ENST00000333244,colon,carcinoma,+2,1	AHNAK2	719	1	NM_138420	exon7	c.T5533A	p.S1845T	CCACCGAGGCCTC	.	scavenged	Atlas-SNP
C19orf80	55908	hgsc.bcm.edu	37	19	11350375	11350375	+	Missense_Mutation	SNP	C	C	T	rs368909299		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	81	25	108	0	0.308642	0	.	.	weak	.	C19orf80	8	.	NM_018687	exon1	c.C62T	p.A21V	CCTCAGCGGCCCC	.	PASS	Atlas-SNP
AQP7	364	hgsc.bcm.edu	37	9	33395103	33395103	+	Silent	SNP	G	G	A	rs148012859	bycluster;byfrequency;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	138	4	133	1	0.0289855	0.0075188	A|0.002;G|0.998;T|0.000	0.002	strong	AQP7,NS,carcinoma,0,1	AQP7	58	1	NM_001170	exon3	c.C117T	p.A39A	GAACTCGGCCAGG	.	scavenged	Atlas-SNP
CEP104	9731	hgsc.bcm.edu	37	1	3742332	3742332	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	57	26	90	0	0.45614	0	.	.	none	.	CEP104	79	.	NM_014704	exon18	c.A2354G	p.H785R	TTGCAGTGGTCAC	.	PASS	Atlas-SNP
MAPKAPK5	8550	hgsc.bcm.edu	37	12	112321487	112321487	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	158	3	149	0	0.0189873	0	.	.	none	MAPKAPK5_ENST00000202788,lymph_node,lymphoid_neoplasm,-1,1	MAPKAPK5	56	1	NM_139078	exon9	c.C763T	p.R255X	GATATGCGAAGAA	.	scavenged	Atlas-SNP
ID3	3399	hgsc.bcm.edu	37	1	23885712	23885712	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	112	61	130	0	0.544643	0	.	.	none	.	ID3	29	.	NM_002167	exon1	c.T206C	p.I69T	TGTAGGATTTCCA	.	PASS	Atlas-SNP
DAB1	1600	hgsc.bcm.edu	37	1	57481087	57481087	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	59	5	73	0	0.0847458	0	.	.	none	.	DAB1	129	.	NM_021080	exon14	c.G913A	p.A305T	GGACAGCGCCCAT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195507817	195507817	+	Missense_Mutation	SNP	A	A	G	rs200993341	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	369	20	393	14	0.0542005	0.0356234	G|0.994;T|0.006	0.994	weak	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.T10634C	p.V3545A	GTGGATACTGAGG	.	scavenged	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954870	30954870	+	Silent	SNP	T	T	C	rs9262377	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	45	5	30	1	0.111111	0.0333333	.	.	weak	MUC21,rectum,carcinoma,0,1	MUC21	98	1	NM_001010909	exon2	c.T918C	p.S306S	GTCCAGTACGACC	.	scavenged	Atlas-SNP
SLC19A3	80704	hgsc.bcm.edu	37	2	228564154	228564154	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	101	44	97	0	0.435644	0	.	.	none	.	SLC19A3	62	.	NM_025243	exon3	c.A277C	p.T93P	GCCAGGTAATGAT	.	PASS	Atlas-SNP
DOCK7	85440	hgsc.bcm.edu	37	1	62962115	62962115	+	Silent	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	248	105	247	1	0.423387	0.00404858	.	.	none	.	DOCK7	184	.	NM_001271999	exon38	c.C4791A	p.G1597G	AGATGTGCCCACC	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327915	16327915	+	Missense_Mutation	SNP	A	A	C	rs11969612	bycluster;byfrequency;by2hit2allele;byhapmap	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	52	12	22	1	0.230769	0.0454545	A|0.571;C|0.429	0.429	strong	ATXN1,colon,carcinoma,0,1	ATXN1	117	1	NM_001128164	exon7	c.T627G	p.H209Q	ATGCTGATGCTGC	.	scavenged	Atlas-SNP
CYTB	0	hgsc.bcm.edu	37	MT	15873	15873	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	22	14	19	0	0.636364	0	.	.	none	.	.	.	.	ENST00000361789	exon1	c.T1127C	p.M376T	ACAAAATACTCAA	.	PASS	Atlas-SNP
ND5	0	hgsc.bcm.edu	37	MT	13531	13531	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	14	12	21	0	0.857143	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.G1195A	p.A399T	GAAACCGCAAACA	.	PASS	Atlas-SNP
PRR21	643905	hgsc.bcm.edu	37	2	240982131	240982131	+	Missense_Mutation	SNP	A	A	G	rs79839275	bycluster;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	54	9	58	10	0.166667	0.172414	A|0.737;G|0.263	0.263	strong	PRR21,NS,carcinoma,0,2	PRR21	53	2	NM_001080835	exon1	c.T269C	p.M90T	AGAGGCATGGATG	.	scavenged	Atlas-SNP
SLC29A2	3177	hgsc.bcm.edu	37	11	66133453	66133453	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	58	23	89	0	0.396552	0	.	.	none	.	SLC29A2	24	.	NM_001532	exon10	c.A1013G	p.N338S	ATGATGTTGAAGA	.	PASS	Atlas-SNP
TMEM132C	92293	hgsc.bcm.edu	37	12	129189698	129189698	+	Missense_Mutation	SNP	G	G	A	rs116496800	bycluster;byfrequency;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	55	25	59	0	0.454545	0	G|0.997;A|0.003	0.003	strong	.	TMEM132C	142	.	NM_001136103	exon9	c.G2185A	p.D729N	ATCTACGACACCA	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77765319	77765319	+	Silent	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	54	32	69	37	0.592593	0.536232	.	.	none	ZFHX4,rectum,carcinoma,0,1	ZFHX4	878	1	NM_024721	exon10	c.T6162C	p.P2054P	TCCTCCTCCCCCC	.	scavenged	Atlas-SNP
EP400	57634	hgsc.bcm.edu	37	12	132547087	132547087	+	Silent	SNP	G	G	A	rs12366766		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	70	5	61	1	0.0714286	0.0163934	.	.	weak	EP400,NS,carcinoma,0,20	EP400	370	20	NM_015409	exon47	c.G8175A	p.Q2725Q	GCAGCAGCAACAA	.	scavenged	Atlas-SNP
EPHA2	1969	hgsc.bcm.edu	37	1	16475116	16475116	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	41	21	30	0	0.512195	0	.	.	none	.	EPHA2	102	.	NM_004431	exon3	c.G580A	p.V194I	CACGGACGGAGAG	.	PASS	Atlas-SNP
EML1	2009	hgsc.bcm.edu	37	14	100402447	100402447	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	134	61	136	0	0.455224	0	.	.	none	.	EML1	97	.	NM_001008707	exon19	c.G2048A	p.R683Q	ACACGCGAGTGGG	.	PASS	Atlas-SNP
HVCN1	84329	hgsc.bcm.edu	37	12	111089042	111089042	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	87	35	71	0	0.402299	0	.	.	none	HVCN1,caecum,carcinoma,-1,2	HVCN1	38	2	NM_032369	exon6	c.G623A	p.R208Q	GCCACCCGCCACA	.	PASS	Atlas-SNP
COL4A3	1285	hgsc.bcm.edu	37	2	228125811	228125811	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	72	31	81	0	0.430556	0	.	.	none	.	COL4A3	293	.	NM_000091	exon20	c.C1128T	p.P376P	TGGTCCCCCCGGA	.	PASS	Atlas-SNP
ABCC11	85320	hgsc.bcm.edu	37	16	48209258	48209258	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	95	45	77	1	0.473684	0.012987	.	.	none	ABCC11,right_upper_lobe,carcinoma,-2,1	ABCC11	177	1	NM_033151	exon25	c.C3609T	p.G1203G	GTCCACGCCGTCA	.	scavenged	Atlas-SNP
ZIC1	7545	hgsc.bcm.edu	37	3	147128137	147128137	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	54	14	60	0	0.259259	0	.	.	none	.	ZIC1	141	.	NM_003412	exon1	c.C238A	p.H80N	GGCCATCACCATC	.	PASS	Atlas-SNP
THOC1	9984	hgsc.bcm.edu	37	18	216549	216549	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	100	79	252	0	0.79	0	.	.	none	.	THOC1	43	.	NM_005131	exon19	c.G1539A	p.Q513Q	AAACTGCTGGTTG	.	PASS	Atlas-SNP
MBD5	55777	hgsc.bcm.edu	37	2	149226791	149226791	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	130	51	138	0	0.392308	0	.	.	none	.	MBD5	164	.	NM_018328	exon9	c.C1279T	p.Q427X	AGAGTTCAGCATT	.	PASS	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	37	1	52306066	52306066	+	Missense_Mutation	SNP	T	T	A	rs72663147	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	196	65	62	1	0.331633	0.016129	.	.	weak	NRD1,NS,other,0,1	NRD1	89	1	NM_001101662	exon2	c.A462T	p.E154D	ATCATCTTCTTCT	.	scavenged	Atlas-SNP
APOBEC3D	140564	hgsc.bcm.edu	37	22	39421643	39421643	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	160	66	192	0	0.4125	0	.	.	none	.	APOBEC3D	61	.	NM_152426	exon4	c.C572T	p.A191V	ATTATGCATCCCT	.	PASS	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7436077	7436077	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	64	21	81	0	0.328125	0	.	.	none	.	PSAPL1	51	.	NM_001085382	exon1	c.A530T	p.Q177L	GGCGCCTGGCGGG	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249152	71249152	+	Silent	SNP	C	C	T	rs112809261	bycluster;byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	140	22	124	0	0.157143	0	C|0.896;T|0.104	0.104	strong	KRTAP5-8,NS,carcinoma,+1,1	KRTAP5-8	28	1	NM_021046	exon1	c.C51T	p.C17C	GGGCTGCGGCTCT	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16146585	16146585	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	127	52	124	0	0.409449	0	.	.	none	.	ABCC1	156	.	NM_004996	exon11	c.T1385C	p.L462P	AGAATCTGGGCCC	.	PASS	Atlas-SNP
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	277	10	447	5	0.0361011	0.0111857	.	.	none	POTEC,NS,carcinoma,-1,5	POTEC	129	5	NM_001137671	exon1	c.G492T	p.T164T	CATGTCCGTGTCC	.	scavenged	Atlas-SNP
FMN1	342184	hgsc.bcm.edu	37	15	33261127	33261127	+	Silent	SNP	T	T	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	28	18	28	11	0.642857	0.392857	.	.	none	FMN1_ENST00000334528,NS,carcinoma,0,4	FMN1	174	4	NM_001103184	exon4	c.A2106C	p.P702P	TGGGGGTGGGGGT	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506460	195506460	+	Missense_Mutation	SNP	G	G	C	rs113130007	bycluster;byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	19	4	22	3	0.210526	0.136364	C|0.994;G|0.006	0.994	strong	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11991G	p.H3997Q	GGTGGCGTGACCT	.	scavenged	Atlas-SNP
TBC1D29	26083	hgsc.bcm.edu	37	17	28887667	28887667	+	Silent	SNP	T	T	C	rs78888987	bycluster;byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	63	8	47	2	0.126984	0.0425532	T|0.806;C|0.194	0.194	strong	TBC1D29,NS,carcinoma,0,1	TBC1D29	19	1	NM_015594	exon3	c.T111C	p.D37D	GTGGGATATGTAT	.	scavenged	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	37	2	107049681	107049681	+	Missense_Mutation	SNP	T	T	C	rs369310197		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	703	8	681	4	0.0113798	0.00587372	.	.	weak	RGPD3_ENST00000304514,NS,carcinoma,0,6	RGPD3	316	6	NM_001144013	exon16	c.A2266G	p.N756D	TATAGTTTTCGAG	.	scavenged	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274360	39274360	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	85	4	68	0	0.0470588	0	.	.	none	KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	NM_033059	exon1	c.T208A	p.C70S	AGATGCAGCATCT	.	scavenged	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386176	7386176	+	Silent	SNP	G	G	C	rs76776066	alternate_allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	185	21	203	1	0.113514	0.00492611	.	.	alt	POLR2A_ENST00000412468,NS,haematopoietic_neoplasm,0,1	.	.	1	NM_001102614	exon2	c.G873C	p.V291V	GGTGGTGGTGGCC	.	scavenged	Atlas-SNP
KIAA1549L	25758	hgsc.bcm.edu	37	11	33667420	33667420	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	128	64	126	0	0.5	0	.	.	none	.	.	.	.	NM_012194	exon16	c.C4707T	p.H1569H	GGGCCACGCAGGC	.	PASS	Atlas-SNP
HELZ	9931	hgsc.bcm.edu	37	17	65116527	65116527	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	446	195	437	0	0.43722	0	.	.	none	.	HELZ	160	.	NM_014877	exon27	c.C3832T	p.R1278X	CATTTCGATTTTG	.	PASS	Atlas-SNP
LRRTM4	80059	hgsc.bcm.edu	37	2	77745577	77745577	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	141	43	191	0	0.304965	0	.	.	none	.	LRRTM4	334	.	NM_024993	exon3	c.C1418A	p.S473Y	CTTTCAGACTCTC	.	PASS	Atlas-SNP
RGS3	5998	hgsc.bcm.edu	37	9	116346320	116346320	+	Silent	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	74	22	64	0	0.297297	0	.	.	none	.	RGS3	251	.	NM_144488	exon21	c.G2628T	p.S876S	CTGCTCGGGAGAT	.	PASS	Atlas-SNP
PDE4A	5141	hgsc.bcm.edu	37	19	10571742	10571742	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	81	30	36	0	0.37037	0	.	.	none	.	PDE4A	236	.	NM_001111307	exon11	c.T1428A	p.D476E	TGTGGATCACCCT	.	PASS	Atlas-SNP
PCDHA8	56140	hgsc.bcm.edu	37	5	140221065	140221065	+	Silent	SNP	G	G	A	rs62384462	bycluster;byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	128	10	110	2	0.078125	0.0181818	G|0.903;A|0.097	0.097	strong	PCDHA8_ENST00000531613,caecum,carcinoma,0,2	PCDHA8	366	2	NM_031856	exon1	c.G159A	p.G53G	CCTGGGGCTGGAG	.	scavenged	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240795	39240795	+	Missense_Mutation	SNP	A	A	T	rs9894966	bycluster;by2hit2allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	39	6	37	0	0.153846	0	.	.	weak	KRTAP4-7,NS,carcinoma,0,1	KRTAP4-7	49	1	NM_033061	exon1	c.A337T	p.S113C	CGCCCCAGCTGCT	.	scavenged	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	37	10	81932570	81932570	+	Silent	SNP	A	A	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	46	6	55	0	0.130435	0	.	.	none	.	ANXA11	32	.	NM_145868	exon3	c.T48A	p.A16A	TGGTGCAGCTGGT	.	PASS	Atlas-SNP
DNER	92737	hgsc.bcm.edu	37	2	230312065	230312065	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	209	111	262	0	0.5311	0	.	.	none	.	DNER	129	.	NM_139072	exon8	c.G1453A	p.V485M	TGCCCACGCTGCG	.	PASS	Atlas-SNP
SYNDIG1	79953	hgsc.bcm.edu	37	20	24565617	24565617	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	105	52	131	0	0.495238	0	.	.	none	.	SYNDIG1	58	.	NM_024893	exon3	c.C606T	p.Y202Y	CTTCTACTTGTCC	.	PASS	Atlas-SNP
CDH2	1000	hgsc.bcm.edu	37	18	25572711	25572711	+	Missense_Mutation	SNP	C	C	T	rs200263846	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	152	12	155	0	0.0789474	0	.	.	weak	.	CDH2	194	.	NM_001792	exon9	c.G1252A	p.A418T	ACACTGCGTTCCA	.	PASS	Atlas-SNP
IZUMO2	126123	hgsc.bcm.edu	37	19	50657864	50657864	+	Missense_Mutation	SNP	C	C	T	rs189762069	bycluster;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	32	13	37	0	0.40625	0	C|0.999;T|0.001	0.001	strong	.	IZUMO2	26	.	NM_152358	exon6	c.G616A	p.V206M	AGACCACGATGAC	.	PASS	Atlas-SNP
PTPRF	5792	hgsc.bcm.edu	37	1	44085859	44085859	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	176	81	198	0	0.460227	0	.	.	none	.	PTPRF	172	.	NM_002840	exon30	c.C5205T	p.I1735I	CATCATCGTCATG	.	PASS	Atlas-SNP
DCHS1	8642	hgsc.bcm.edu	37	11	6652558	6652558	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	139	11	114	0	0.0791367	0	.	.	none	.	DCHS1	277	.	NM_003737	exon8	c.C3756T	p.I1252I	GTACAAGATGGTC	.	PASS	Atlas-SNP
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249125	71249125	+	Silent	SNP	A	A	G	rs113379698	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	166	19	159	2	0.114458	0.0125786	A|0.500;G|0.500	0.500	weak	KRTAP5-8,rectum,carcinoma,0,2	KRTAP5-8	28	2	NM_021046	exon1	c.A24G	p.G8G	CTCTGGAGGCTGT	.	scavenged	Atlas-SNP
OSBPL6	114880	hgsc.bcm.edu	37	2	179255816	179255816	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	158	75	184	0	0.474684	0	.	.	none	OSBPL6,NS,carcinoma,-1,1	OSBPL6	178	1	NM_001201480	exon23	c.C2393A	p.S798Y	GGAATTCTAACAT	.	PASS	Atlas-SNP
HOXA9	3205	hgsc.bcm.edu	37	7	27204938	27204938	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	58	21	61	0	0.362069	0	.	.	none	.	HOXA9	20	.	NM_152739	exon1	c.G139A	p.E47K	GGTGCTCGGCCAG	.	PASS	Atlas-SNP
MYO5C	55930	hgsc.bcm.edu	37	15	52487626	52487626	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	221	99	189	0	0.447964	0	.	.	none	.	MYO5C	162	.	NM_018728	exon40	c.C5024T	p.P1675L	TCTATAGGTGTGT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100680438	100680438	+	Missense_Mutation	SNP	G	G	C	rs112926140	bycluster;byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	57	3	69	4	0.0526316	0.057971	A|0.001;G|0.999	.	strong	MUC17,right_upper_lobe,carcinoma,+1,1	MUC17	804	1	NM_001040105	exon3	c.G5741C	p.S1914T	ACGGTAGCAGCAT	.	scavenged	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100684573	100684573	+	Silent	SNP	G	G	A	rs144023476	bycluster;byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	87	5	75	1	0.0574713	0.0133333	G|0.984;A|0.016	0.016	strong	MUC17,NS,haematopoietic_neoplasm,0,1	MUC17	804	1	NM_001040105	exon3	c.G9876A	p.T3292T	CACAACGGTGGCC	.	scavenged	Atlas-SNP
SHANK1	50944	hgsc.bcm.edu	37	19	51170329	51170329	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	47	26	37	0	0.553191	0	.	.	none	.	SHANK1	210	.	NM_016148	exon22	c.G4888A	p.E1630K	CCACCTCGCTGTC	.	PASS	Atlas-SNP
NEK7	140609	hgsc.bcm.edu	37	1	198288596	198288596	+	Missense_Mutation	SNP	G	G	A	rs114884409	bycluster;byfrequency;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	118	40	108	0	0.338983	0	G|0.999;A|0.001	0.001	strong	NEK7,NS,carcinoma,0,1	NEK7	42	1	NM_133494	exon10	c.G853A	p.V285I	CCAGACGTCACCT	.	PASS	Atlas-SNP
KRT25	147183	hgsc.bcm.edu	37	17	38906791	38906791	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	180	66	184	0	0.366667	0	.	.	none	KRT25,NS,carcinoma,0,4	KRT25	63	4	NM_181534	exon6	c.C1016G	p.A339G	ATCTGCGCCAGCT	.	PASS	Atlas-SNP
MTNR1B	4544	hgsc.bcm.edu	37	11	92714681	92714681	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	139	10	123	0	0.0719424	0	.	.	none	.	MTNR1B	75	.	NM_005959	exon2	c.C292A	p.L98I	CTAATCCTCGTGG	.	PASS	Atlas-SNP
CYYR1	116159	hgsc.bcm.edu	37	21	27938630	27938630	+	Missense_Mutation	SNP	G	G	A	rs79874795	bycluster;byfrequency;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	102	57	108	0	0.558824	0	G|0.994;A|0.006	0.006	strong	.	CYYR1	38	.	NM_052954	exon2	c.C131T	p.T44M	TAGGGCGTGGTTC	.	PASS	Atlas-SNP
GNS	2799	hgsc.bcm.edu	37	12	65153012	65153012	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	32	14	44	0	0.4375	0	.	.	none	.	GNS	41	.	NM_002076	exon1	c.C45T	p.S15S	GCGGGGGCTGCCC	.	PASS	Atlas-SNP
ARC	23237	hgsc.bcm.edu	37	8	143695095	143695095	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	21	17	20	0	0.809524	0	.	.	none	.	ARC	34	.	NM_015193	exon1	c.G538A	p.A180T	CGCCAGCGGCTGG	.	PASS	Atlas-SNP
CPT1B	1375	hgsc.bcm.edu	37	22	51012005	51012005	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	37	17	30	0	0.459459	0	.	.	none	.	CPT1B	61	.	NM_001145135	exon10	c.C1110T	p.D370D	GGAGGGGTCGTCC	.	PASS	Atlas-SNP
ANKS1A	23294	hgsc.bcm.edu	37	6	34957033	34957033	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	142	67	152	0	0.471831	0	.	.	none	ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	NM_015245	exon9	c.G1242A	p.P414P	GCCACCGCCCGAT	.	PASS	Atlas-SNP
MUC17	140453	hgsc.bcm.edu	37	7	100679799	100679799	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	81	3	66	3	0.037037	0.0454545	.	.	none	MUC17,caecum,carcinoma,-1,1	MUC17	804	1	NM_001040105	exon3	c.C5102T	p.P1701L	CAACACCGGTGGC	.	scavenged	Atlas-SNP
TRAPPC8	22878	hgsc.bcm.edu	37	18	29511319	29511319	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	188	90	196	0	0.478723	0	.	.	none	.	TRAPPC8	126	.	NM_014939	exon2	c.G325A	p.A109T	CTCCTGCTGTAAT	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92539174	92539174	+	Missense_Mutation	SNP	C	C	G	rs200623021	by1000genomes;alternate_allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	132	68	124	0	0.515152	0	C|1.000;T|0.000	.	alt	BTG1,NS,lymphoid_neoplasm,0,1	BTG1	30	1	NM_001731	exon1	c.G138C	p.E46D	CAGCAGCTCCTGC	.	PASS	Atlas-SNP
THAP6	152815	hgsc.bcm.edu	37	4	76452235	76452235	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	225	95	207	0	0.422222	0	.	.	none	THAP6,NS,carcinoma,0,1	THAP6	14	1	NM_144721	exon5	c.C480T	p.G160G	GATCGGCGAGCTA	.	PASS	Atlas-SNP
PCDHA6	56142	hgsc.bcm.edu	37	5	140207965	140207965	+	Missense_Mutation	SNP	G	G	C	rs61730626	byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	123	16	104	5	0.130081	0.0480769	G|0.921;C|0.079	0.079	strong	PCDHA6_ENST00000529310,NS,carcinoma,0,2	PCDHA6	442	2	NM_018909	exon1	c.G289C	p.G97R	CTGTGCGGGCGGA	.	scavenged	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525639	248525639	+	Missense_Mutation	SNP	A	A	T	rs76878172	alternate_allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	597	574	613	606	0.961474	0.988581	.	.	alt	OR2T4,brain,glioma,0,1	OR2T4	126	1	NM_001004696	exon1	c.A757T	p.I253F	TTACTCATCCTCC	.	scavenged	Atlas-SNP
CDIPT	10423	hgsc.bcm.edu	37	16	29870830	29870830	+	Silent	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	95	5	90	0	0.0526316	0	.	.	none	.	CDIPT	15	.	NM_006319	exon5	c.C429A	p.T143T	ACACAAGGTGAAC	.	PASS	Atlas-SNP
EPHA8	2046	hgsc.bcm.edu	37	1	22915717	22915717	+	Missense_Mutation	SNP	G	G	A	rs199679973		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	72	34	80	0	0.472222	0	G|0.999;A|0.001	0.001	weak	EPHA8_ENST00000374644,colon,carcinoma,0,1	EPHA8	221	1	NM_001006943	exon5	c.G1333A	p.V445I	AACTCCGTCCCGC	.	PASS	Atlas-SNP
TFR2	7036	hgsc.bcm.edu	37	7	100226979	100226979	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	33	22	37	0	0.666667	0	.	.	none	.	TFR2	53	.	NM_003227	exon10	c.C1287T	p.I429I	GGCCCCGATGACA	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274157	39274157	+	Silent	SNP	G	G	A	rs76095941		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	53	4	47	1	0.0754717	0.0212766	G|0.500;A|0.500	0.500	weak	KRTAP4-11,NS,carcinoma,0,8	KRTAP4-11	94	8	NM_033059	exon1	c.C411T	p.P137P	GCAGCTGGGGTGG	.	scavenged	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240794	39240794	+	Silent	SNP	C	C	A	rs9894106	by2hit2allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	39	5	37	0	0.128205	0	.	.	weak	KRTAP4-7,NS,carcinoma,0,3	KRTAP4-7	49	3	NM_033061	exon1	c.C336A	p.P112P	CCGCCCCAGCTGC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152278049	152278049	+	Missense_Mutation	SNP	A	A	C	rs2065958	bycluster;byfrequency;byhapmap	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	9	6	6	5	0.666667	0.833333	A|0.173;C|0.827	0.827	strong	FLG,NS,carcinoma,+2,1	FLG	900	1	NM_002016	exon3	c.T9313G	p.Y3105D	GACCGTATTGGGA	.	scavenged	Atlas-SNP
PCDHA3	56145	hgsc.bcm.edu	37	5	140180941	140180941	+	Silent	SNP	G	G	A	rs201478898	byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	102	13	82	2	0.127451	0.0243902	G|0.926;A|0.074	0.074	strong	PCDHA3_ENST00000522353,NS,haematopoietic_neoplasm,0,2	PCDHA3	396	2	NM_031497	exon1	c.G159A	p.G53G	CCTGGGGCTGGAG	.	scavenged	Atlas-SNP
PRSS16	10279	hgsc.bcm.edu	37	6	27219672	27219672	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	142	63	132	0	0.443662	0	.	.	none	.	PRSS16	66	.	NM_005865	exon8	c.G861A	p.A287A	GGGGGCGCTGCAG	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	37	2	141571285	141571285	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	278	96	289	0	0.345324	0	.	.	none	.	LRP1B	1315	.	NM_018557	exon32	c.T5300C	p.L1767S	ACTTCTAAATTAC	.	PASS	Atlas-SNP
FAM72A	729533	hgsc.bcm.edu	37	1	206145504	206145504	+	Missense_Mutation	SNP	T	T	C	rs55683315	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	921	14	848	5	0.0152009	0.00589623	.	.	weak	FAM72A,NS,carcinoma,0,1	FAM72A	9	1	NM_001123168	exon3	c.T281C	p.L94P	GTCTTCTTTCCTG	.	scavenged	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	37	6	16327918	16327918	+	Missense_Mutation	SNP	C	C	A	rs28555263		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	54	6	43	1	0.111111	0.0232558	C|0.500;A|0.500	0.500	weak	ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	NM_001128164	exon7	c.G624T	p.Q208H	CTGATGCTGCTGC	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105411852	105411852	+	Silent	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	149	3	158	0	0.0201342	0	.	.	none	AHNAK2_ENST00000333244,NS,carcinoma,-1,1	AHNAK2	719	1	NM_138420	exon7	c.A9936G	p.K3312K	CTTGAATTTGGGC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506982	195506982	+	Silent	SNP	G	G	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	85	9	86	4	0.105882	0.0465116	.	.	none	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.C11469G	p.T3823T	AAGAGGGGTGGTG	.	scavenged	Atlas-SNP
ASB12	142689	hgsc.bcm.edu	37	X	63444983	63444983	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	71	64	90	0	0.901408	0	.	.	none	.	ASB12	102	.	NM_130388	exon2	c.G548A	p.G183D	AGGGGGCCAGAAC	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	37	2	109382170	109382170	+	Silent	SNP	A	A	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	388	6	336	4	0.0154639	0.0119048	.	.	none	RANBP2_ENST00000283195,NS,carcinoma,0,6	RANBP2	488	6	NM_006267	exon20	c.A5175G	p.E1725E	GAAGGAAGGACAG	.	scavenged	Atlas-SNP
TFAP2B	7021	hgsc.bcm.edu	37	6	50791293	50791293	+	Silent	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	121	56	160	0	0.46281	0	.	.	none	.	TFAP2B	91	.	NM_003221	exon2	c.C255A	p.P85P	GGACCCCTACTCC	.	PASS	Atlas-SNP
P2RY8	286530	hgsc.bcm.edu	37	X	1585333	1585333	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	40	34	84	0	0.85	0	.	.	none	.	P2RY8	53	.	NM_178129	exon2	c.G119A	p.G40D	AGGTTGCCCGGGA	.	PASS	Atlas-SNP
DLGAP3	58512	hgsc.bcm.edu	37	1	35351360	35351360	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	45	20	52	0	0.444444	0	.	.	none	.	DLGAP3	107	.	NM_001080418	exon5	c.C1633T	p.P545S	CCGGCGGGATGGG	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	37	16	51175658	51175658	+	Missense_Mutation	SNP	T	T	C	rs13336129	bycluster;byfrequency;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	160	7	151	0	0.04375	0	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	.	PASS	Atlas-SNP
MAF1	84232	hgsc.bcm.edu	37	8	145160665	145160665	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	49	43	38	0	0.877551	0	.	.	none	.	MAF1	16	.	NM_032272	exon2	c.G79T	p.G27C	ATCATTGGCAGGT	.	PASS	Atlas-SNP
NDUFS1	4719	hgsc.bcm.edu	37	2	207017231	207017231	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	209	84	210	0	0.401914	0	.	.	none	NDUFS1,NS,carcinoma,-1,3	NDUFS1	82	3	NM_001199984	exon3	c.G107A	p.R36Q	GTTGTTCGAACTG	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885567	+	Silent	SNP	A	A	C	rs75808076	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	61	18	32	1	0.295082	0.03125	.	.	weak	NEFH,rectum,carcinoma,0,1	NEFH	178	1	NM_021076	exon4	c.A1938C	p.A646A	GGAAGCAAAGTCC	.	scavenged	Atlas-SNP
CPNE2	221184	hgsc.bcm.edu	37	16	57171163	57171163	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	58	30	78	0	0.517241	0	.	.	none	.	CPNE2	48	.	NM_152727	exon14	c.C1271G	p.A424G	GGTTTGCGGCCCA	.	PASS	Atlas-SNP
C2orf81	388963	hgsc.bcm.edu	37	2	74642291	74642291	+	Missense_Mutation	SNP	A	A	G	rs116859876	bycluster;byfrequency;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	86	11	82	0	0.127907	0	A|0.959;G|0.041	0.041	strong	.	C2orf81	23	.	NM_001145054	exon4	c.T932C	p.V311A	CCGCCCACAGAGG	.	PASS	Atlas-SNP
NEFH	4744	hgsc.bcm.edu	37	22	29885562	29885562	+	Missense_Mutation	SNP	G	G	A	rs370929798		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	56	9	33	0	0.160714	0	.	.	weak	NEFH,rectum,carcinoma,-2,1	NEFH	178	1	NM_021076	exon4	c.G1933A	p.E645K	AAGGAGGAAGCAA	.	scavenged	Atlas-SNP
CHURC1-FNTB	100529261	hgsc.bcm.edu	37	14	65520040	65520040	+	Missense_Mutation	SNP	C	C	T	rs374785351		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	59	26	53	0	0.440678	0	.	.	weak	FNTB,rectum,carcinoma,-1,1	.	.	1	NM_001202559	exon12	c.C1223T	p.A408V	GCCCTGCGGGGGG	.	PASS	Atlas-SNP
KRTCAP2	200185	hgsc.bcm.edu	37	1	155145757	155145757	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	92	83	98	0	0.902174	0	.	.	none	.	KRTCAP2	15	.	NM_173852	exon1	c.C22T	p.R8W	TGAACCGGGTGCG	.	PASS	Atlas-SNP
MYH8	4626	hgsc.bcm.edu	37	17	10293802	10293802	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	325	145	327	0	0.446154	0	.	.	none	.	MYH8	346	.	NM_002472	exon40	c.G5783A	p.R1928Q	ACCTCTCGGCTCT	.	PASS	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152276490	152276490	+	Silent	SNP	C	C	T	rs199933055	bycluster	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	326	13	255	3	0.0398773	0.0117647	C|0.999;G|0.001	.	weak	FLG,NS,carcinoma,-2,1	FLG	900	1	NM_002016	exon3	c.G10872A	p.E3624E	ATGTCTCTCTCCT	.	scavenged	Atlas-SNP
MYD88	4615	hgsc.bcm.edu	37	3	38182292	38182292	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	124	53	130	0	0.427419	0	.	.	none	MYD88,NS,lymphoid_neoplasm,0,8	MYD88	900	8	NM_001172567	exon4	c.G752A	p.S251N	TGCAGAGCAAGGA	.	PASS	Atlas-SNP
SH3GLB2	56904	hgsc.bcm.edu	37	9	131790419	131790419	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	41	17	28	0	0.414634	0	.	.	none	.	SH3GLB2	32	.	NM_020145	exon1	c.G15A	p.M5I	CTTCTTCATGTTG	.	PASS	Atlas-SNP
EPHA5	2044	hgsc.bcm.edu	37	4	66356412	66356412	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	120	55	146	0	0.458333	0	.	.	none	.	EPHA5	315	.	NM_004439	exon5	c.G1085A	p.R362Q	GCATTCCGAGGAG	.	PASS	Atlas-SNP
OR5I1	10798	hgsc.bcm.edu	37	11	55703506	55703506	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	107	2	109	0	0.0186916	0	.	.	none	OR5I1,colon,carcinoma,0,3	OR5I1	110	3	NM_006637	exon1	c.G371T	p.R124L	ACATAGCGATCAT	.	scavenged	Atlas-SNP
DGCR8	54487	hgsc.bcm.edu	37	22	20077332	20077332	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	130	59	117	0	0.453846	0	.	.	none	.	DGCR8	53	.	NM_001190326	exon4	c.C1021T	p.R341W	AGCATACGGGTAG	.	PASS	Atlas-SNP
SLCO6A1	133482	hgsc.bcm.edu	37	5	101834271	101834271	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	125	49	121	0	0.392	0	.	.	none	.	SLCO6A1	153	.	NM_173488	exon1	c.G278A	p.C93Y	ACTAAGCAGCCCA	.	PASS	Atlas-SNP
C12orf52	84934	hgsc.bcm.edu	37	12	113624824	113624824	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	56	23	36	0	0.410714	0	.	.	none	.	C12orf52	19	.	NM_032848	exon3	c.C273T	p.T91T	CCCCACCCTCACA	.	PASS	Atlas-SNP
DAB1	1600	hgsc.bcm.edu	37	1	57480789	57480789	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	98	38	126	0	0.387755	0	.	.	none	.	DAB1	129	.	NM_021080	exon14	c.A1211C	p.D404A	GGCTTGTCGGTCT	.	PASS	Atlas-SNP
ZFP36L2	678	hgsc.bcm.edu	37	2	43452183	43452183	+	Silent	SNP	A	A	G	rs7933	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	9	5	2	1	0.555556	0.5	A|0.568;G|0.432	0.432	strong	ZFP36L2,NS,carcinoma,0,2	ZFP36L2	56	2	NM_006887	exon2	c.T760C	p.L254L	GGTGCAACTTGGG	.	scavenged	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	37	3	151164755	151164755	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	228	3	180	0	0.0131579	0	.	.	none	IGSF10,colon,carcinoma,0,1	IGSF10	279	1	NM_178822	exon4	c.C3014A	p.P1005Q	AACAGCGGGATGT	.	scavenged	Atlas-SNP
MAP4K3	8491	hgsc.bcm.edu	37	2	39552696	39552696	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	252	102	253	1	0.404762	0.00395257	.	.	none	.	MAP4K3	109	.	NM_001270425	exon12	c.A881T	p.H294L	GTGGAATGATCTG	.	PASS	Atlas-SNP
XIRP2	129446	hgsc.bcm.edu	37	2	168100213	168100213	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	150	68	222	0	0.453333	0	.	.	none	XIRP2,colon,carcinoma,0,1	XIRP2	914	1	NM_152381	exon9	c.C2311T	p.R771W	ACAGCACGGTGGA	.	PASS	Atlas-SNP
NLRP5	126206	hgsc.bcm.edu	37	19	56538497	56538497	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	75	30	72	0	0.4	0	.	.	none	.	NLRP5	217	.	NM_153447	exon7	c.G898A	p.V300M	AGGATCGTGCTGT	.	PASS	Atlas-SNP
PRAMEF6	440561	hgsc.bcm.edu	37	1	13365987	13365987	+	Missense_Mutation	SNP	A	A	G	rs78698593		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	9	5	5	1	0.555556	0.2	A|0.250;G|0.750	0.750	weak	PRAMEF5,brain,glioma,0,1	PRAMEF6	21	1	NM_001010889	exon3	c.A431G	p.Q144R	GAGGACAGCAGCC	.	scavenged	Atlas-SNP
STRN	6801	hgsc.bcm.edu	37	2	37193498	37193498	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	65	27	52	0	0.415385	0	.	.	none	.	STRN	71	.	NM_003162	exon1	c.G109A	p.A37T	CAGCCGCCCCGTC	.	PASS	Atlas-SNP
RNASEH2B	79621	hgsc.bcm.edu	37	13	51530597	51530597	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	429	7	334	1	0.016317	0.00299401	.	.	none	RNASEH2B,NS,carcinoma,0,2	RNASEH2B	26	2	NM_024570	exon11	c.T926A	p.I309N	AAAAAATTGGAAA	.	scavenged	Atlas-SNP
MED16	10025	hgsc.bcm.edu	37	19	880103	880103	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	98	37	102	0	0.377551	0	.	.	none	.	MED16	61	.	NM_005481	exon8	c.G1187A	p.R396Q	GAGAGCCGGTGCA	.	PASS	Atlas-SNP
DSEL	92126	hgsc.bcm.edu	37	18	65178778	65178778	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	81	32	87	0	0.395062	0	.	.	none	DSEL,colon,carcinoma,0,2	DSEL	196	2	NM_032160	exon2	c.C3098A	p.S1033X	CTCATCGAAGCTC	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	37	7	151896389	151896389	+	Silent	SNP	C	C	T	rs200269228	by1000genomes	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	198	79	218	0	0.39899	0	C|1.000;T|0.000	0.000	strong	.	MLL3	1564	.	NM_170606	exon27	c.G4248A	p.S1416S	TGGAGCCGAGGAT	.	PASS	Atlas-SNP
CDHR5	53841	hgsc.bcm.edu	37	11	618683	618683	+	Missense_Mutation	SNP	T	T	C	rs200124815		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	284	16	324	11	0.056338	0.0339506	.	.	weak	CDHR5,NS,malignant_melanoma,0,1	CDHR5	77	1	NM_021924	exon13	c.A1876G	p.T626A	GTGTGGTTGGTTG	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195513411	195513411	+	Silent	SNP	A	A	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	388	16	439	6	0.0412371	0.0136674	.	.	none	MUC4_ENST00000463781,trunk,malignant_melanoma,-2,4	MUC4	1505	4	NM_018406	exon2	c.T5040A	p.P1680P	AGGAAGAGGGGTG	.	scavenged	Atlas-SNP
ARID2	196528	hgsc.bcm.edu	37	12	46244016	46244016	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	182	78	211	0	0.428571	0	.	.	none	ARID2,lower_third,carcinoma,0,1	ARID2	311	1	NM_152641	exon15	c.C2110T	p.Q704X	GTCATTCAAAGTA	.	PASS	Atlas-SNP
SLC7A2	6542	hgsc.bcm.edu	37	8	17409423	17409423	+	Missense_Mutation	SNP	C	C	T	rs371734086	alternate_allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	412	13	421	0	0.0315534	0	.	.	alt	SLC7A2,NS,carcinoma,-1,1	SLC7A2	157	1	NM_001164771	exon6	c.C1103T	p.A368V	CTGTAGCGTTTGA	.	scavenged	Atlas-SNP
OR2T4	127074	hgsc.bcm.edu	37	1	248525640	248525640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	64	28	12	2	0.4375	0.166667	.	.	none	OR2T4,brain,glioma,+1,1	OR2T4	126	1	NM_001004696	exon1	c.T758C	p.I253T	TACTCATCCTCCT	.	scavenged	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	37	12	50746166	50746166	+	Silent	SNP	G	G	C	rs368983791		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	274	4	239	2	0.0145985	0.0083682	.	.	weak	FAM186A_ENST00000327337,NS,carcinoma,0,3	FAM186A	181	3	NM_001145475	exon4	c.C4449G	p.L1483L	AGGGATGAGAGGG	.	scavenged	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23526712	23526712	+	Silent	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	85	45	98	0	0.529412	0	.	.	none	.	PRDM9	344	.	NM_020227	exon11	c.T1515C	p.N505N	AGTGAATCCAGGG	.	PASS	Atlas-SNP
DCDC5	100506627	hgsc.bcm.edu	37	11	30915852	30915852	+	Silent	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	177	80	186	0	0.451977	0	.	.	none	.	DCDC5	137	.	NM_020869	exon16	c.C2157A	p.G719G	GGTCCAGCCTCCT	.	PASS	Atlas-SNP
PLXDC2	84898	hgsc.bcm.edu	37	10	20432282	20432282	+	Silent	SNP	A	A	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	210	83	215	2	0.395238	0.00930233	.	.	none	PLXDC2,NS,carcinoma,+1,2	PLXDC2	108	2	NM_032812	exon5	c.A600T	p.A200A	CATAGCACCTTTA	.	scavenged	Atlas-SNP
DNAJB3	414061	hgsc.bcm.edu	37	2	234652351	234652351	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	97	41	107	0	0.42268	0	.	.	none	.	.	.	.	NM_001001394	exon1	c.C212T	p.A71V	GCCCCCGCCTCGC	.	PASS	Atlas-SNP
WDPCP	51057	hgsc.bcm.edu	37	2	63661025	63661025	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	163	64	222	1	0.392638	0.0045045	.	.	none	WDPCP,colon,carcinoma,+1,3	WDPCP	79	3	NM_015910	exon9	c.C679T	p.R227X	GATGTCGCTCTGT	.	scavenged	Atlas-SNP
GPATCH2L	55668	hgsc.bcm.edu	37	14	76620825	76620825	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	71	34	99	0	0.478873	0	.	.	none	.	.	.	.	NM_017926	exon2	c.G119A	p.R40Q	AGCTTCGGAAACG	.	PASS	Atlas-SNP
PCDH1	5097	hgsc.bcm.edu	37	5	141243763	141243763	+	Missense_Mutation	SNP	G	G	C	rs374090402	alternate_allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	60	17	85	0	0.283333	0	.	.	alt	.	PCDH1	119	.	NM_032420	exon3	c.C2133G	p.N711K	GGGTGCGTTGTCA	.	PASS	Atlas-SNP
MST1L	11223	hgsc.bcm.edu	37	1	17083776	17083776	+	Missense_Mutation	SNP	C	C	A	rs77199961	byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	194	7	209	3	0.0360825	0.0143541	C|0.500;A|0.500	0.500	strong	Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	NM_001271733	exon15	c.G2021T	p.R674L	GAGACACGCGTGA	.	scavenged	Atlas-SNP
THRB	7068	hgsc.bcm.edu	37	3	24231773	24231773	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	221	4	214	1	0.0180995	0.0046729	.	.	none	THRB,NS,lymphoid_neoplasm,0,1	THRB	52	1	NM_000461	exon4	c.C75T	p.H25H	CCAGTCGTGTTCT	.	scavenged	Atlas-SNP
NDP	4693	hgsc.bcm.edu	37	X	43809178	43809178	+	Missense_Mutation	SNP	C	C	T	rs104894867	bycluster;alternate_allele	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	74	69	95	0	0.932432	0	.	.	alt	.	NDP	12	.	NM_000266	exon3	c.G269A	p.R90H	GAGGAACGGAAGG	.	PASS	Atlas-SNP
MRVI1	10335	hgsc.bcm.edu	37	11	10655535	10655535	+	Silent	SNP	G	G	A	rs373779712		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	202	74	249	0	0.366337	0	.	.	weak	.	MRVI1	113	.	NM_001206880	exon3	c.C309T	p.T103T	TTTGTCGGTTTCT	.	PASS	Atlas-SNP
NRP1	8829	hgsc.bcm.edu	37	10	33469014	33469014	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	269	5	257	0	0.0185874	0	.	.	none	NRP1,lower_third,carcinoma,+1,1	NRP1	126	1	NM_003873	exon17	c.C2762A	p.S921X	GCCTCCGAATAAG	.	scavenged	Atlas-SNP
PSAPL1	768239	hgsc.bcm.edu	37	4	7436076	7436076	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	63	21	81	0	0.333333	0	.	.	none	.	PSAPL1	51	.	NM_001085382	exon1	c.G531T	p.Q177H	AGGCGCCTGGCGG	.	PASS	Atlas-SNP
SEC24C	9632	hgsc.bcm.edu	37	10	75526107	75526107	+	Splice_Site	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	85	30	86	0	0.352941	0	.	.	none	.	SEC24C	86	.	NM_004922	exon13	c.1608-1G>A	.	TCTACAGGGAGGG	.	PASS	Atlas-SNP
VEZF1	7716	hgsc.bcm.edu	37	17	56058016	56058016	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	197	37	280	1	0.187817	0.00357143	.	.	none	VEZF1,NS,carcinoma,-2,1	VEZF1	50	1	NM_007146	exon4	c.T924A	p.H308Q	CTGCCCATGAGTC	.	scavenged	Atlas-SNP
CCNC	892	hgsc.bcm.edu	37	6	99998133	99998133	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	83	67	155	0	0.807229	0	.	.	none	.	CCNC	23	.	NM_005190	exon8	c.A491C	p.Q164P	ATGTCCTGCACAT	.	PASS	Atlas-SNP
PHLDB3	653583	hgsc.bcm.edu	37	19	44006279	44006279	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	125	61	132	0	0.488	0	.	.	none	Q96HZ0_HUMAN,rectum,carcinoma,0,4	PHLDB3	30	4	NM_198850	exon3	c.C370T	p.R124C	TCTGGCGCTGTAG	.	PASS	Atlas-SNP
SIX6	4990	hgsc.bcm.edu	37	14	60976600	60976600	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	91	42	88	0	0.461538	0	.	.	none	.	SIX6	27	.	NM_007374	exon1	c.G484A	p.A162T	GAGCTCGCCCAGG	.	PASS	Atlas-SNP
KCTD8	386617	hgsc.bcm.edu	37	4	44450163	44450163	+	Silent	SNP	C	C	T	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	67	36	81	0	0.537313	0	.	.	none	.	KCTD8	96	.	NM_198353	exon1	c.G378A	p.E126E	CTCCTTCTCGGGG	.	PASS	Atlas-SNP
MUC15	143662	hgsc.bcm.edu	37	11	26582712	26582712	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	283	22	295	0	0.0777385	0	.	.	none	.	MUC15	88	.	NM_001135091	exon5	c.A986G	p.Y329C	GGATTGTAGTAGC	.	PASS	Atlas-SNP
EPPK1	83481	hgsc.bcm.edu	37	8	144940706	144940706	+	Missense_Mutation	SNP	C	C	T	rs112377501	bycluster;byfrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	80	4	62	2	0.05	0.0322581	C|0.993;T|0.007	0.007	strong	EPPK1,NS,carcinoma,0,9	EPPK1	199	9	NM_031308	exon1	c.G6716A	p.R2239H	TCCTGGCGGCCGG	.	scavenged	Atlas-SNP
KRT17	3872	hgsc.bcm.edu	37	17	39775873	39775873	+	Silent	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	358	157	354	0	0.438547	0	.	.	none	.	KRT17	57	.	NM_000422	exon8	c.C1272T	p.R424R	CTGCTCGCGGGAG	.	PASS	Atlas-SNP
CSNK1A1	1452	hgsc.bcm.edu	37	5	148930448	148930448	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	95	90	106	0	0.947368	0	.	.	none	.	CSNK1A1	63	.	NM_001025105	exon1	c.C80G	p.S27C	CCGAAGGAGCCAG	.	PASS	Atlas-SNP
AWAT2	158835	hgsc.bcm.edu	37	X	69261726	69261726	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	108	89	123	0	0.824074	0	.	.	none	.	AWAT2	36	.	NM_001002254	exon7	c.C934T	p.R312C	GTTTACGTAGGGC	.	PASS	Atlas-SNP
TPTE2	93492	hgsc.bcm.edu	37	13	20056679	20056679	+	Missense_Mutation	SNP	T	T	G	rs200244531		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	454	10	374	3	0.0220264	0.00802139	.	.	weak	TPTE2_ENST00000400230,NS,carcinoma,0,1	TPTE2	225	1	NM_199254	exon5	c.A128C	p.E43A	AGTCGTTCTAACA	.	scavenged	Atlas-SNP
DNAJC10	54431	hgsc.bcm.edu	37	2	183627529	183627529	+	Splice_Site	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	266	136	272	0	0.511278	0	.	.	none	.	DNAJC10	76	.	NM_018981	exon22	c.2265+1G>A	.	GCAAAGGTATGTC	.	PASS	Atlas-SNP
CNNM1	26507	hgsc.bcm.edu	37	10	101090081	101090081	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	104	8	102	0	0.0769231	0	.	.	none	CNNM1_ENST00000356713,NS,carcinoma,-1,1	CNNM1	101	1	NM_020348	exon1	c.G937A	p.G313R	GGCACCGGGGAAG	.	PASS	Atlas-SNP
FAM120B	84498	hgsc.bcm.edu	37	6	170627667	170627667	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	121	7	229	6	0.0578512	0.0262009	.	.	none	FAM120B,NS,carcinoma,-1,1	FAM120B	108	1	NM_032448	exon2	c.T1189C	p.S397P	CCTGAATCCAGGC	.	scavenged	Atlas-SNP
