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	18.0	10.0	46.0	0.0	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	60.0	21.0	61.0	0.0	0.35	0	.	.	none	.	KRT2	94	.	NM_000423	exon1	c.324_325insTGGAGGTGGCAGCGGCTT	p.F108delinsFGGGSGF	.	.	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	77.0	25.0	69.0	0.0	0.325	.	.	.	none	.	NOTCH2	348	.	NM_024408	exon5	c.823_826del	p.275_276del	.	.	PASS	Pindel,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	113.0	64.0	162.0	0.0	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	73.0	23.0	55.0	0.0	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	200.0	37.0	277.0	0.0	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	70.0	24.0	81.0	0.0	0.343	.	.	.	none	.	GPR26	47	.	NM_153442	exon1	c.76_78del	p.26_26del	.	.	PASS	Pindel,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	95.0	35.0	85.0	0.0	0.368	.	.	.	none	HIST1H3B,NS,lymphoid_neoplasm,-1,3	HIST1H3B	59	3	NM_003537	exon1	c.407delC	p.A136fs	.	.	PASS	Pindel,Atlas-Indel
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	140.0	62.0	133.0	0.0	0.442857	0	.	.	none	.	TUBA3D	60	.	NM_080386	exon4	c.T749A	p.V250E	TGAATGTGGACTT	.	PASS	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	71.0	35.0	76.0	0.0	0.492958	0	.	.	none	.	.	.	.	NM_020893	exon3	c.G307A	p.E103K	ACTCCTGAAGGGG	.	PASS	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	54.0	34.0	75.0	0.0	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	28.0	12.0	33.0	0.0	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	111.0	91.0	157.0	1.0	0.81982	0.00636943	.	.	none	.	SLC6A14	56	.	NM_007231	exon9	c.T1161A	p.G387G	CGTAGGTTTTGAT	.	PASS	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	46.0	21.0	42.0	0.0	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	160.0	151.0	173.0	0.0	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	33.0	17.0	52.0	0.0	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	24.0	6.0	32.0	0.0	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	72.0	68.0	78.0	0.0	0.944444	0	.	.	none	.	COL4A1	372	.	NM_001845	exon30	c.G2272A	p.G758R	TGCTCCCCTTCTC	.	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	70.0	34.0	65.0	0.0	0.485714	0	.	.	none	.	TYRO3	169	.	NM_006293	exon7	c.C872T	p.A291V	TGCCTGCCACCAA	.	PASS	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	84.0	41.0	85.0	0.0	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	160.0	71.0	176.0	0.0	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	227.0	54.0	200.0	1.0	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	414.0	40.0	346.0	0.0	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	42.0	13.0	37.0	0.0	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	70.0	28.0	83.0	0.0	0.4	0	.	.	none	.	KLF2	10	.	NM_016270	exon2	c.76-1G>A	.	CCCGCAGCGCTGG	.	PASS	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	84.0	11.0	90.0	0.0	0.130952	0	.	.	none	.	GABBR1	95	.	NM_001470	exon14	c.C1689A	p.S563S	TGTTTTGGACCAG	.	PASS	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	81.0	25.0	108.0	0.0	0.308642	0	.	.	weak	.	C19orf80	8	.	NM_018687	exon1	c.C62T	p.A21V	CCTCAGCGGCCCC	.	PASS	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	57.0	26.0	90.0	0.0	0.45614	0	.	.	none	.	CEP104	79	.	NM_014704	exon18	c.A2354G	p.H785R	TTGCAGTGGTCAC	.	PASS	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	112.0	61.0	130.0	0.0	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	59.0	5.0	73.0	0.0	0.0847458	0	.	.	none	.	DAB1	129	.	NM_021080	exon14	c.G913A	p.A305T	GGACAGCGCCCAT	.	PASS	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	45.0	5.0	30.0	1.0	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	101.0	44.0	97.0	0.0	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	248.0	105.0	247.0	1.0	0.423387	0.00404858	.	.	none	.	DOCK7	184	.	NM_001271999	exon38	c.C4791A	p.G1597G	AGATGTGCCCACC	.	PASS	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	22.0	14.0	19.0	0.0	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	14.0	12.0	21.0	0.0	0.857143	0	.	.	none	.	.	.	.	ENST00000361567	exon1	c.G1195A	p.A399T	GAAACCGCAAACA	.	PASS	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	58.0	23.0	89.0	0.0	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	55.0	25.0	59.0	0.0	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
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	41.0	21.0	30.0	0.0	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	134.0	61.0	136.0	0.0	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	87.0	35.0	71.0	0.0	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	72.0	31.0	81.0	0.0	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	95.0	45.0	77.0	1.0	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	54.0	14.0	60.0	0.0	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	100.0	79.0	252.0	0.0	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	130.0	51.0	138.0	0.0	0.392308	0	.	.	none	.	MBD5	164	.	NM_018328	exon9	c.C1279T	p.Q427X	AGAGTTCAGCATT	.	PASS	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	160.0	66.0	192.0	0.0	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	64.0	21.0	81.0	0.0	0.328125	0	.	.	none	.	PSAPL1	51	.	NM_001085382	exon1	c.A530T	p.Q177L	GGCGCCTGGCGGG	.	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	127.0	52.0	124.0	0.0	0.409449	0	.	.	none	.	ABCC1	156	.	NM_004996	exon11	c.T1385C	p.L462P	AGAATCTGGGCCC	.	PASS	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	85.0	4.0	68.0	0.0	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
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	128.0	64.0	126.0	0.0	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	446.0	195.0	437.0	0.0	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	141.0	43.0	191.0	0.0	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	74.0	22.0	64.0	0.0	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	81.0	30.0	36.0	0.0	0.37037	0	.	.	none	.	PDE4A	236	.	NM_001111307	exon11	c.T1428A	p.D476E	TGTGGATCACCCT	.	PASS	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	46.0	6.0	55.0	0.0	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	209.0	111.0	262.0	0.0	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	105.0	52.0	131.0	0.0	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	152.0	12.0	155.0	0.0	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	32.0	13.0	37.0	0.0	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	176.0	81.0	198.0	0.0	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	139.0	11.0	114.0	0.0	0.0791367	0	.	.	none	.	DCHS1	277	.	NM_003737	exon8	c.C3756T	p.I1252I	GTACAAGATGGTC	.	PASS	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	158.0	75.0	184.0	0.0	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	58.0	21.0	61.0	0.0	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	221.0	99.0	189.0	0.0	0.447964	0	.	.	none	.	MYO5C	162	.	NM_018728	exon40	c.C5024T	p.P1675L	TCTATAGGTGTGT	.	PASS	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	47.0	26.0	37.0	0.0	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	118.0	40.0	108.0	0.0	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	180.0	66.0	184.0	0.0	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	139.0	10.0	123.0	0.0	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	102.0	57.0	108.0	0.0	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	32.0	14.0	44.0	0.0	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	21.0	17.0	20.0	0.0	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	37.0	17.0	30.0	0.0	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	142.0	67.0	152.0	0.0	0.471831	0	.	.	none	ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	NM_015245	exon9	c.G1242A	p.P414P	GCCACCGCCCGAT	.	PASS	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	188.0	90.0	196.0	0.0	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	132.0	68.0	124.0	0.0	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	225.0	95.0	207.0	0.0	0.422222	0	.	.	none	THAP6,NS,carcinoma,0,1	THAP6	14	1	NM_144721	exon5	c.C480T	p.G160G	GATCGGCGAGCTA	.	PASS	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	95.0	5.0	90.0	0.0	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	72.0	34.0	80.0	0.0	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	33.0	22.0	37.0	0.0	0.666667	0	.	.	none	.	TFR2	53	.	NM_003227	exon10	c.C1287T	p.I429I	GGCCCCGATGACA	.	PASS	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	102.0	13.0	82.0	2.0	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	142.0	63.0	132.0	0.0	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	278.0	96.0	289.0	0.0	0.345324	0	.	.	none	.	LRP1B	1315	.	NM_018557	exon32	c.T5300C	p.L1767S	ACTTCTAAATTAC	.	PASS	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	71.0	64.0	90.0	0.0	0.901408	0	.	.	none	.	ASB12	102	.	NM_130388	exon2	c.G548A	p.G183D	AGGGGGCCAGAAC	.	PASS	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	121.0	56.0	160.0	0.0	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	40.0	34.0	84.0	0.0	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	45.0	20.0	52.0	0.0	0.444444	0	.	.	none	.	DLGAP3	107	.	NM_001080418	exon5	c.C1633T	p.P545S	CCGGCGGGATGGG	.	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	49.0	43.0	38.0	0.0	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	209.0	84.0	210.0	0.0	0.401914	0	.	.	none	NDUFS1,NS,carcinoma,-1,3	NDUFS1	82	3	NM_001199984	exon3	c.G107A	p.R36Q	GTTGTTCGAACTG	.	PASS	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	58.0	30.0	78.0	0.0	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	86.0	11.0	82.0	0.0	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
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	59.0	26.0	53.0	0.0	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	92.0	83.0	98.0	0.0	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	325.0	145.0	327.0	0.0	0.446154	0	.	.	none	.	MYH8	346	.	NM_002472	exon40	c.G5783A	p.R1928Q	ACCTCTCGGCTCT	.	PASS	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	124.0	53.0	130.0	0.0	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	41.0	17.0	28.0	0.0	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	120.0	55.0	146.0	0.0	0.458333	0	.	.	none	.	EPHA5	315	.	NM_004439	exon5	c.G1085A	p.R362Q	GCATTCCGAGGAG	.	PASS	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	130.0	59.0	117.0	0.0	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	125.0	49.0	121.0	0.0	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	56.0	23.0	36.0	0.0	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	98.0	38.0	126.0	0.0	0.387755	0	.	.	none	.	DAB1	129	.	NM_021080	exon14	c.A1211C	p.D404A	GGCTTGTCGGTCT	.	PASS	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	252.0	102.0	253.0	1.0	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	150.0	68.0	222.0	0.0	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	75.0	30.0	72.0	0.0	0.4	0	.	.	none	.	NLRP5	217	.	NM_153447	exon7	c.G898A	p.V300M	AGGATCGTGCTGT	.	PASS	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	65.0	27.0	52.0	0.0	0.415385	0	.	.	none	.	STRN	71	.	NM_003162	exon1	c.G109A	p.A37T	CAGCCGCCCCGTC	.	PASS	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	98.0	37.0	102.0	0.0	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	81.0	32.0	87.0	0.0	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	198.0	79.0	218.0	0.0	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
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	182.0	78.0	211.0	0.0	0.428571	0	.	.	none	ARID2,lower_third,carcinoma,0,1	ARID2	311	1	NM_152641	exon15	c.C2110T	p.Q704X	GTCATTCAAAGTA	.	PASS	Atlas-SNP
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	64.0	28.0	12.0	2.0	0.4375	0.166667	.	.	none	OR2T4,brain,glioma,+1,1	OR2T4	126	1	NM_001004696	exon1	c.T758C	p.I253T	TACTCATCCTCCT	.	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	85.0	45.0	98.0	0.0	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	177.0	80.0	186.0	0.0	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	210.0	83.0	215.0	2.0	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	97.0	41.0	107.0	0.0	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	163.0	64.0	222.0	1.0	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	71.0	34.0	99.0	0.0	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	60.0	17.0	85.0	0.0	0.283333	0	.	.	alt	.	PCDH1	119	.	NM_032420	exon3	c.C2133G	p.N711K	GGGTGCGTTGTCA	.	PASS	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	74.0	69.0	95.0	0.0	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	202.0	74.0	249.0	0.0	0.366337	0	.	.	weak	.	MRVI1	113	.	NM_001206880	exon3	c.C309T	p.T103T	TTTGTCGGTTTCT	.	PASS	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	63.0	21.0	81.0	0.0	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	85.0	30.0	86.0	0.0	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	197.0	37.0	280.0	1.0	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	83.0	67.0	155.0	0.0	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	125.0	61.0	132.0	0.0	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	91.0	42.0	88.0	0.0	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	67.0	36.0	81.0	0.0	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	283.0	22.0	295.0	0.0	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	80.0	4.0	62.0	2.0	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	358.0	157.0	354.0	0.0	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	95.0	90.0	106.0	0.0	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	108.0	89.0	123.0	0.0	0.824074	0	.	.	none	.	AWAT2	36	.	NM_001002254	exon7	c.C934T	p.R312C	GTTTACGTAGGGC	.	PASS	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	266.0	136.0	272.0	0.0	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	104.0	8.0	102.0	0.0	0.0769231	0	.	.	none	CNNM1_ENST00000356713,NS,carcinoma,-1,1	CNNM1	101	1	NM_020348	exon1	c.G937A	p.G313R	GGCACCGGGGAAG	.	PASS	Atlas-SNP
