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
TET2	54790	hgsc.bcm.edu	37	4	106182925	106182925	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	251.0	39.0	229.0	0.0	0.155	.	.	.	none	.	TET2	1762	.	NM_001127208	exon8	c.3963delA	p.K1321fs	.	.	PASS	Pindel,Atlas-Indel
PRRC2C	23215	hgsc.bcm.edu	37	1	171557627	171557628	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	118.0	20.0	104.0	0.0	0.169492	0	.	.	none	BAT2D1_ENST00000392078,NS,carcinoma,+2,2	.	.	2	NM_015172	exon33	c.8175_8176del	p.2725_2726del	.	.	PASS	Atlas-Indel
ARHGEF26	26084	hgsc.bcm.edu	37	3	153842198	153842199	+	Splice_Site	INS	-	-	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	31.0	10.0	23.0	0.0	0.322581	0	.	.	none	.	ARHGEF26	158	.	NM_001251962	exon3	c.1084-1->A	.	.	.	PASS	Atlas-Indel
EPB41L4A	64097	hgsc.bcm.edu	37	5	111500817	111500818	+	Splice_Site	INS	-	-	AAAAT	rs369027426	alternate_allele	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	130.0	11.0	83.0	0.0	0.0846154	0	.	.	alt	.	EPB41L4A	130	.	NM_022140	exon24	c.1933-2->ATTTT	.	.	.	PASS	Atlas-Indel
MUSK	4593	hgsc.bcm.edu	37	9	113496632	113496632	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	105.0	17.0	98.0	0.0	0.162	.	.	.	none	.	MUSK	112	.	NM_001166280	exon7	c.759delC	p.I253fs	.	.	PASS	Pindel,Atlas-Indel
OR5AK2	390181	hgsc.bcm.edu	37	11	56756917	56756917	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	294.0	47.0	250.0	0.0	0.159864	0	.	.	none	.	OR5AK2	45	.	NM_001005323	exon1	c.528delC	p.H176fs	.	.	PASS	Atlas-Indel
RBM14	10432	hgsc.bcm.edu	37	11	66392639	66392640	+	In_Frame_Ins	INS	-	-	CTA	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	70.0	12.0	80.0	0.0	0.171	.	.	.	none	.	RBM14	59	.	NM_006328	exon2	c.1292_1293insCTA	p.A431delinsAY	.	.	PASS	Pindel,Atlas-Indel
TET2	54790	hgsc.bcm.edu	37	4	106158250	106158259	+	Frame_Shift_Del	DEL	CAGAAGCAAG	CAGAAGCAAG	-	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	CAGAAGCAAG	CAGAAGCAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	133.0	23.0	86.0	0.0	0.173	.	.	.	none	.	TET2	1762	.	NM_017628	exon3	c.3150_3159del	p.1050_1053del	.	.	PASS	Pindel,Atlas-Indel
PCLO	27445	hgsc.bcm.edu	37	7	82595469	82595469	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	259.0	39.0	189.0	0.0	0.151	.	.	.	none	.	PCLO	1506	.	NM_014510	exon4	c.3636delG	p.K1212fs	.	.	PASS	Pindel,Atlas-Indel
BTBD7	55727	hgsc.bcm.edu	37	14	93709220	93709221	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	367.0	68.0	279.0	0.0	0.185	.	.	.	none	.	BTBD7	112	.	NM_001002860	exon11	c.2798_2799insA	p.T933fs	.	.	PASS	Pindel,Atlas-Indel
SYTL2	54843	hgsc.bcm.edu	37	11	85447546	85447546	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	88.0	4.0	73.0	0.0	0.0454545	0	.	.	none	.	SYTL2	231	.	NM_001162953	exon5	c.A584G	p.E195G	TTACCCTCTTTTG	.	PASS	Atlas-SNP
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246178	47246178	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	95.0	4.0	99.0	0.0	0.0421053	0	.	.	none	B4GALNT2,colon,carcinoma,-2,1	B4GALNT2	67	1	NM_153446	exon10	c.G1411T	p.G471C	ACCAGTGGCGTGG	.	PASS	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76415865	76415865	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	93.0	30.0	71.0	0.0	0.322581	0	.	.	none	.	LMO7	334	.	NM_015842	exon21	c.C3078A	p.D1026E	TTCAGACAGAGAA	.	PASS	Atlas-SNP
ARHGAP22	58504	hgsc.bcm.edu	37	10	49654625	49654625	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	231.0	55.0	269.0	0.0	0.238095	0	.	.	none	.	ARHGAP22	94	.	NM_001256024	exon10	c.T1954C	p.S652P	ACCGGGACATTCG	.	PASS	Atlas-SNP
TNF	7124	hgsc.bcm.edu	37	6	31543674	31543674	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	78.0	24.0	100.0	0.0	0.307692	0	.	.	none	.	TNF	15	.	NM_000594	exon1	c.C156G	p.H52Q	GCTGCACTTTGGA	.	PASS	Atlas-SNP
COL11A1	1301	hgsc.bcm.edu	37	1	103364535	103364535	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	101.0	46.0	79.0	0.0	0.455446	0	.	.	none	.	COL11A1	972	.	NM_080629	exon55	c.G4138T	p.A1380S	CACCTGCAGCTCC	.	PASS	Atlas-SNP
ALAS2	212	hgsc.bcm.edu	37	X	55041425	55041425	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	109.0	17.0	88.0	0.0	0.155963	0	.	.	none	.	ALAS2	163	.	NM_000032	exon9	c.G1192A	p.G398S	TGTAGCCGCCCAC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134493825	134493825	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	108.0	15.0	96.0	0.0	0.138889	0	.	.	none	SGK1_ENST00000528577,NS,carcinoma,0,5	SGK1	387	5	NM_001143676	exon9	c.C922T	p.L308L	AATGCAGGTAGCC	.	PASS	Atlas-SNP
TENM1	10178	hgsc.bcm.edu	37	X	123870854	123870854	+	Silent	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	86.0	14.0	80.0	0.0	0.162791	0	.	.	none	.	.	.	.	NM_001163278	exon4	c.T729C	p.H243H	ATGCAGATGGACT	.	PASS	Atlas-SNP
MSMP	692094	hgsc.bcm.edu	37	9	35753722	35753722	+	Silent	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	133.0	34.0	146.0	0.0	0.255639	0	.	.	none	.	MSMP	15	.	NM_001044264	exon2	c.T174C	p.S58S	GAGCCAAGACTCA	.	PASS	Atlas-SNP
NLRC3	197358	hgsc.bcm.edu	37	16	3614077	3614077	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	28.0	11.0	43.0	0.0	0.392857	0	.	.	none	NLRC3,NS,carcinoma,-2,1	NLRC3	103	1	NM_178844	exon5	c.G861A	p.R287R	AAAGCCCCGGATC	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279860	46279860	+	Silent	SNP	G	G	A	rs151060280	byfrequency	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	82.0	5.0	77.0	0.0	0.0609756	0	G|0.997;A|0.003	0.003	strong	NCOA3,bladder,carcinoma,0,6	NCOA3	156	6	NM_181659	exon20	c.G3786A	p.Q1262Q	GCAGCAGCAGCAA	.	PASS	Atlas-SNP
HECW1	23072	hgsc.bcm.edu	37	7	43283515	43283515	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	222.0	52.0	249.0	0.0	0.234234	0	.	.	none	.	HECW1	540	.	NM_015052	exon3	c.A11G	p.H4R	TGCTGCACCTGTG	.	PASS	Atlas-SNP
GAREM	64762	hgsc.bcm.edu	37	18	29850212	29850212	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	185.0	53.0	192.0	0.0	0.286486	0	.	.	none	.	.	.	.	NM_022751	exon5	c.C1701T	p.T567T	GGACAAGGTGGGG	.	PASS	Atlas-SNP
LACTB	114294	hgsc.bcm.edu	37	15	63433784	63433784	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	163.0	39.0	144.0	0.0	0.239264	0	.	.	none	LACTB,NS,carcinoma,-1,1	LACTB	29	1	NM_032857	exon6	c.C1424T	p.S475L	ATGGTTCGTGTAG	.	PASS	Atlas-SNP
PRR5-ARHGAP8	553158	hgsc.bcm.edu	37	22	45221390	45221390	+	Silent	SNP	C	C	T	rs368897846		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	99.0	18.0	175.0	0.0	0.181818	0	.	.	weak	PRR5-ARHGAP8,NS,carcinoma,0,2	PRR5-ARHGAP8	53	2	NM_181334	exon10	c.C879T	p.H293H	CCTGCACGAGGGC	.	PASS	Atlas-SNP
PIK3CA	5290	hgsc.bcm.edu	37	3	178916936	178916936	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	59.0	3.0	67.0	0.0	0.0508475	0	.	.	none	PIK3CA_ENST00000263967,colon,carcinoma,0,39	PIK3CA	8460	39	NM_006218	exon2	c.G323T	p.R108L	GCAACCGTGAAGA	.	scavenged	Atlas-SNP
RAF1	5894	hgsc.bcm.edu	37	3	12645694	12645694	+	Missense_Mutation	SNP	A	A	G	rs3730271	bycluster;byhapmap	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	165.0	37.0	126.0	0.0	0.224242	0	A|1.000;|0.000	.	weak	RAF1,caecum,carcinoma,0,3	RAF1	66	3	NM_002880	exon7	c.T775C	p.S259P	GTGTGGATGTCGA	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	37	8	77776035	77776035	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	48.0	8.0	51.0	0.0	0.166667	0	.	.	none	.	ZFHX4	878	.	NM_024721	exon11	c.A10085T	p.D3362V	CCAACGATGCTTC	.	PASS	Atlas-SNP
FBXL7	23194	hgsc.bcm.edu	37	5	15928178	15928178	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	54.0	15.0	47.0	0.0	0.277778	0	.	.	none	FBXL7,NS,carcinoma,-2,1	FBXL7	138	1	NM_012304	exon3	c.C307A	p.L103I	ATCCGGCTCGCCT	.	PASS	Atlas-SNP
DOCK3	1795	hgsc.bcm.edu	37	3	51394558	51394558	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	93.0	23.0	87.0	0.0	0.247312	0	.	.	none	.	DOCK3	397	.	NM_004947	exon44	c.G4669A	p.A1557T	GGCATTGCACGCT	.	PASS	Atlas-SNP
SLC16A7	9194	hgsc.bcm.edu	37	12	60173423	60173423	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	97.0	4.0	89.0	0.0	0.0412371	0	.	.	none	.	SLC16A7	82	.	NM_001270622	exon6	c.C1400T	p.A467V	CAAATGCACAGAG	.	PASS	Atlas-SNP
CDH10	1008	hgsc.bcm.edu	37	5	24593514	24593514	+	Missense_Mutation	SNP	G	G	A	rs140810299	bycluster;by1000genomes	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	185.0	36.0	145.0	0.0	0.194595	0	G|1.000;A|0.000	0.000	strong	.	CDH10	391	.	NM_006727	exon2	c.C86T	p.T29M	ACAGGCGTCCTTC	.	PASS	Atlas-SNP
RBMS3	27303	hgsc.bcm.edu	37	3	29938966	29938966	+	Missense_Mutation	SNP	G	G	T	rs13060292	bycluster;alternate_allele	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	175.0	39.0	146.0	0.0	0.222857	0	.	.	alt	.	RBMS3	62	.	NM_001177712	exon10	c.G927T	p.Q309H	ATACCAGGTATGT	.	PASS	Atlas-SNP
PRRC2B	84726	hgsc.bcm.edu	37	9	134322483	134322483	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	146.0	25.0	131.0	0.0	0.171233	0	.	.	none	.	PRRC2B	266	.	NM_013318	exon7	c.G867A	p.P289P	TTCGCCGAAGTCA	.	PASS	Atlas-SNP
DDX52	11056	hgsc.bcm.edu	37	17	35979827	35979827	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	179.0	40.0	159.0	0.0	0.223464	0	.	.	none	.	DDX52	40	.	NM_007010	exon13	c.T1635G	p.F545L	TTTCTGAAAACCT	.	PASS	Atlas-SNP
TMEM255B	348013	hgsc.bcm.edu	37	13	114514733	114514733	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	110.0	15.0	145.0	0.0	0.136364	0	.	.	none	.	.	.	.	NM_182614	exon9	c.C838G	p.P280A	GTTGCGCCCTCCT	.	PASS	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	37	X	63411917	63411917	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	190.0	35.0	198.0	0.0	0.184211	0	.	.	none	.	.	.	.	NM_152424	exon2	c.C1250T	p.P417L	GGCCGTGGATACA	.	PASS	Atlas-SNP
TTC9	23508	hgsc.bcm.edu	37	14	71109098	71109098	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	64.0	6.0	79.0	0.0	0.09375	0	.	.	none	.	TTC9	11	.	NM_015351	exon1	c.G252A	p.L84L	GGCGTTGCTGGAG	.	PASS	Atlas-SNP
UXS1	80146	hgsc.bcm.edu	37	2	106729179	106729179	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	65.0	10.0	92.0	0.0	0.153846	0	.	.	none	.	UXS1	75	.	NM_001253875	exon10	c.G802A	p.G268R	GTGGCCCAAAGGT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1258274	1258274	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	59.0	4.0	62.0	0.0	0.0677966	0	.	.	none	.	MUC5B	473	.	NM_002458	exon25	c.C3177T	p.P1059P	CTCCCCCTCCTGC	.	PASS	Atlas-SNP
CPXM1	56265	hgsc.bcm.edu	37	20	2775239	2775239	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	55.0	16.0	54.0	0.0	0.290909	0	.	.	none	.	CPXM1	107	.	NM_019609	exon13	c.T1907A	p.L636H	ATCCCAAGCTCCG	.	PASS	Atlas-SNP
HECW2	57520	hgsc.bcm.edu	37	2	197092929	197092929	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	216.0	60.0	144.0	0.0	0.277778	0	.	.	none	.	HECW2	239	.	NM_020760	exon22	c.G3814T	p.E1272X	AGAGTTCTCTGGA	.	PASS	Atlas-SNP
PIGQ	9091	hgsc.bcm.edu	37	16	632296	632296	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	107.0	44.0	145.0	0.0	0.411215	0	.	.	none	.	PIGQ	43	.	NM_004204	exon10	c.G1580A	p.R527H	CCCTCCGCCTCCT	.	PASS	Atlas-SNP
SSX2IP	117178	hgsc.bcm.edu	37	1	85128001	85128001	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	131.0	8.0	127.0	0.0	0.0610687	0	.	.	none	.	SSX2IP	53	.	NM_001166417	exon9	c.A807C	p.Q269H	TAGGATTTGTTTC	.	PASS	Atlas-SNP
ULK3	25989	hgsc.bcm.edu	37	15	75131687	75131687	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	118.0	10.0	155.0	0.0	0.0847458	0	.	.	none	.	ULK3	30	.	NM_001099436	exon8	c.A880G	p.K294E	GGTCTTTCTTCAC	.	PASS	Atlas-SNP
CAMK4	814	hgsc.bcm.edu	37	5	110560276	110560276	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	141.0	30.0	145.0	0.0	0.212766	0	.	.	none	.	CAMK4	77	.	NM_001744	exon1	c.A95T	p.Y32F	CGGATTACTGGAT	.	PASS	Atlas-SNP
SCAND1	51282	hgsc.bcm.edu	37	20	34542105	34542105	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	69.0	5.0	93.0	0.0	0.0724638	0	.	.	none	.	SCAND1	2	.	NM_033630	exon2	c.C291G	p.N97K	CACACAGTTACGC	.	PASS	Atlas-SNP
IRS4	8471	hgsc.bcm.edu	37	X	107976167	107976167	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	15.0	7.0	21.0	0.0	0.466667	0	.	.	none	.	IRS4	253	.	NM_003604	exon1	c.G3408A	p.A1136A	GGAGGCCGCAGCT	.	PASS	Atlas-SNP
ARHGAP23	57636	hgsc.bcm.edu	37	17	36654042	36654042	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	366.0	66.0	418.0	0.0	0.180328	0	.	.	none	.	ARHGAP23	48	.	NM_001199417	exon21	c.A3292G	p.S1098G	TTCTTCAGTGACG	.	PASS	Atlas-SNP
CKAP5	9793	hgsc.bcm.edu	37	11	46831321	46831321	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	222.0	38.0	194.0	0.0	0.171171	0	.	.	none	.	CKAP5	134	.	NM_001008938	exon6	c.A734T	p.Q245L	GACTGTTGTTGTT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494426	134494426	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	149.0	27.0	153.0	0.0	0.181208	0	.	.	none	.	SGK1	387	.	NM_001143676	exon7	c.C688G	p.L230V	TTTTCAGGATTGC	.	PASS	Atlas-SNP
PI15	51050	hgsc.bcm.edu	37	8	75737657	75737657	+	Missense_Mutation	SNP	G	G	A	rs141788887	bycluster;byfrequency;by1000genomes	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	87.0	14.0	70.0	0.0	0.16092	0	G|0.997;A|0.003	0.003	strong	.	PI15	73	.	NM_015886	exon2	c.G173A	p.R58Q	CCAGGCGGAAGCG	.	PASS	Atlas-SNP
TMC5	79838	hgsc.bcm.edu	37	16	19498605	19498605	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	98.0	17.0	78.0	0.0	0.173469	0	.	.	none	.	TMC5	169	.	NM_001105249	exon17	c.T2530C	p.S844P	TTCCCATCCTTCA	.	PASS	Atlas-SNP
TNFRSF14	8764	hgsc.bcm.edu	37	1	2491336	2491336	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	113.0	39.0	357.0	1.0	0.345133	0.00280112	.	.	none	.	TNFRSF14	89	.	NM_003820	exon4	c.T379C	p.C127R	CACTTCTGCATCG	.	PASS	Atlas-SNP
ZFX	7543	hgsc.bcm.edu	37	X	24229366	24229366	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	240.0	53.0	205.0	0.0	0.220833	0	.	.	none	.	ZFX	61	.	NM_003410	exon10	c.G2291A	p.R764Q	TTAAACGGCACGT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134494432	134494432	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	157.0	21.0	148.0	0.0	0.133758	0	.	.	none	.	SGK1	387	.	NM_001143676	exon7	c.G682C	p.A228P	GGATTGCTTTCTT	.	PASS	Atlas-SNP
SLC6A6	6533	hgsc.bcm.edu	37	3	14523273	14523273	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	85.0	14.0	127.0	0.0	0.164706	0	.	.	none	.	SLC6A6	58	.	NM_003043	exon14	c.T1646C	p.L549P	GGAGCCTGGCCCT	.	PASS	Atlas-SNP
TRIOBP	11078	hgsc.bcm.edu	37	22	38122289	38122289	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	82.0	4.0	112.0	0.0	0.0487805	0	.	.	none	.	TRIOBP	262	.	NM_001039141	exon7	c.C3726T	p.P1242P	GGCACCCTCACCT	.	PASS	Atlas-SNP
NF1	4763	hgsc.bcm.edu	37	17	29667603	29667603	+	Silent	SNP	T	T	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	155.0	22.0	151.0	0.0	0.141935	0	.	.	none	.	NF1	1586	.	NM_001042492	exon47	c.T7002G	p.G2334G	AGCAGGTACCGCA	.	PASS	Atlas-SNP
STK17A	9263	hgsc.bcm.edu	37	7	43664438	43664438	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	23.0	9.0	26.0	0.0	0.391304	0	.	.	none	.	STK17A	31	.	NM_004760	exon7	c.C1242G	p.Y414X	TATCTACTGAGCA	.	PASS	Atlas-SNP
TTLL4	9654	hgsc.bcm.edu	37	2	219602439	219602439	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	120.0	17.0	119.0	0.0	0.141667	0	.	.	none	.	TTLL4	96	.	NM_014640	exon3	c.C40T	p.R14C	GGCCTCCGCCAGA	.	PASS	Atlas-SNP
PARP1	142	hgsc.bcm.edu	37	1	226573325	226573325	+	Silent	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	108.0	5.0	98.0	0.0	0.0462963	0	.	.	none	.	PARP1	100	.	NM_001618	exon7	c.A891G	p.E297E	CGAGCATTCCTCG	.	PASS	Atlas-SNP
CDH16	1014	hgsc.bcm.edu	37	16	66944286	66944286	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	135.0	25.0	143.0	0.0	0.185185	0	.	.	none	.	CDH16	91	.	NM_004062	exon15	c.C2044T	p.H682Y	AGCCATGGTCTTG	.	PASS	Atlas-SNP
PRDM9	56979	hgsc.bcm.edu	37	5	23526430	23526430	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	231.0	38.0	240.0	0.0	0.164502	0	.	.	none	.	PRDM9	344	.	NM_020227	exon11	c.C1233T	p.H411H	CAATCACTCCTCT	.	PASS	Atlas-SNP
MAPK7	5598	hgsc.bcm.edu	37	17	19285517	19285517	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	59.0	13.0	128.0	0.0	0.220339	0	.	.	none	.	MAPK7	72	.	NM_002749	exon5	c.C1901T	p.P634L	CCTGCCCACCCCC	.	PASS	Atlas-SNP
DSCR4	10281	hgsc.bcm.edu	37	21	39493346	39493346	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	58.0	15.0	48.0	0.0	0.258621	0	.	.	none	.	DSCR4	20	.	NM_005867	exon1	c.T4C	p.S2P	TTAACGACATGGA	.	PASS	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	37	6	112537639	112537639	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	100.0	25.0	78.0	0.0	0.25	0	.	.	none	.	LAMA4	227	.	NM_001105206	exon3	c.C227T	p.S76L	TCTCCCGACAGGG	.	PASS	Atlas-SNP
RNF166	115992	hgsc.bcm.edu	37	16	88766062	88766062	+	Missense_Mutation	SNP	C	C	T	rs144508728		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	99.0	4.0	145.0	0.0	0.040404	0	C|1.000;T|0.000	0.000	weak	.	RNF166	3	.	NM_178841	exon3	c.G391A	p.V131I	CGGGGACGAACTT	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230365	23230365	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	114.0	28.0	157.0	0.0	0.245614	0	.	.	none	.	IGLL5	26	.	NM_001256296	exon1	c.A26T	p.H9L	GGTTGCACCGCAA	.	PASS	Atlas-SNP
OR5H6	79295	hgsc.bcm.edu	37	3	97983269	97983269	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	296.0	74.0	261.0	0.0	0.25	0	.	.	none	OR5H6,bladder,carcinoma,0,1	OR5H6	89	1	NM_001005479	exon1	c.C141A	p.F47L	GGCATTCTTGGTA	.	PASS	Atlas-SNP
KLK6	5653	hgsc.bcm.edu	37	19	51466703	51466703	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	133.0	28.0	147.0	0.0	0.210526	0	.	.	none	.	KLK6	35	.	NM_001012964	exon4	c.C300T	p.A100A	GCTGGCGGCATCA	.	PASS	Atlas-SNP
KRTCAP3	200634	hgsc.bcm.edu	37	2	27666008	27666008	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	100.0	4.0	127.0	0.0	0.04	0	.	.	none	.	KRTCAP3	12	.	NM_173853	exon4	c.T341C	p.L114P	GCCTCCTTCTTGC	.	PASS	Atlas-SNP
LIMS1	3987	hgsc.bcm.edu	37	2	109300340	109300340	+	Splice_Site	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	202.0	46.0	154.0	0.0	0.227723	0	.	.	none	.	LIMS1	38	.	NM_001193483	exon10	c.900-1G>A	.	TCTTTAGGAATAA	.	PASS	Atlas-SNP
PDE5A	8654	hgsc.bcm.edu	37	4	120460116	120460116	+	Missense_Mutation	SNP	G	G	A	rs142017762	bycluster	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	127.0	16.0	86.0	0.0	0.125984	0	G|1.000;A|0.000	0.000	weak	.	PDE5A	83	.	NM_001083	exon11	c.C1631T	p.A544V	ATTACCGCTAACG	.	PASS	Atlas-SNP
SCN11A	11280	hgsc.bcm.edu	37	3	38924723	38924723	+	Splice_Site	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	82.0	4.0	72.0	0.0	0.0487805	0	.	.	none	.	SCN11A	296	.	NM_014139	exon19	c.3219+1G>A	.	GATTTACCAGTGC	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	37	22	50728063	50728063	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	42.0	10.0	65.0	0.0	0.238095	0	.	.	none	.	PLXNB2	172	.	NM_012401	exon3	c.C951T	p.D317D	CACCTTGTCCAGC	.	PASS	Atlas-SNP
CYYR1	116159	hgsc.bcm.edu	37	21	27945186	27945186	+	Splice_Site	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	104.0	20.0	69.0	0.0	0.192308	0	.	.	none	.	CYYR1	38	.	NM_052954	exon2	c.73+1G>A	.	CACTGACCTGCGT	.	PASS	Atlas-SNP
SEMA3A	10371	hgsc.bcm.edu	37	7	83610791	83610791	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	90.0	14.0	77.0	0.0	0.155556	0	.	.	none	.	SEMA3A	121	.	NM_006080	exon14	c.C1498T	p.Q500X	ATAGTTGTTGCTG	.	PASS	Atlas-SNP
THRB	7068	hgsc.bcm.edu	37	3	24231681	24231681	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	246.0	48.0	204.0	0.0	0.195122	0	.	.	none	.	THRB	52	.	NM_000461	exon4	c.C167T	p.P56L	AGATGTGGCGACG	.	PASS	Atlas-SNP
IGLL5	100423062	hgsc.bcm.edu	37	22	23230348	23230348	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	118.0	5.0	151.0	0.0	0.0423729	0	.	.	none	.	IGLL5	26	.	NM_001178126	exon1	c.C115T	p.L39L	GGCCTGCTGCGCC	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	37	16	2339491	2339491	+	Missense_Mutation	SNP	C	C	T	rs145565697	bycluster;byfrequency	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	90.0	4.0	98.0	0.0	0.0444444	0	C|0.998;T|0.002	0.002	strong	.	ABCA3	176	.	NM_001089	exon20	c.G2644A	p.D882N	TGCCGTCGGAGGG	.	PASS	Atlas-SNP
TNF	7124	hgsc.bcm.edu	37	6	31543635	31543635	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	69.0	25.0	75.0	0.0	0.362319	0	.	.	none	.	TNF	15	.	NM_000594	exon1	c.G117A	p.L39L	CTTCCTGATCGTG	.	PASS	Atlas-SNP
ZNF181	339318	hgsc.bcm.edu	37	19	35232117	35232117	+	Silent	SNP	C	C	T	rs200927726		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	73.0	4.0	92.0	2.0	0.0547945	0.0217391	C|0.999;T|0.001	0.001	weak	ZNF181,NS,carcinoma,+2,2	ZNF181	65	2	NM_001029997	exon4	c.C831T	p.G277G	CCATGGCTCATCC	.	scavenged	Atlas-SNP
PRKD2	25865	hgsc.bcm.edu	37	19	47204071	47204071	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	69.0	4.0	86.0	0.0	0.057971	0	.	.	none	.	PRKD2	94	.	NM_016457	exon7	c.G1106A	p.G369E	TTGCCTCCCTCGC	.	PASS	Atlas-SNP
FLNC	2318	hgsc.bcm.edu	37	7	128483878	128483878	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	114.0	37.0	154.0	0.0	0.324561	0	.	.	none	.	FLNC	339	.	NM_001127487	exon19	c.G2840A	p.G947D	CTTATGGCGGGGA	.	PASS	Atlas-SNP
SLCO1B7	338821	hgsc.bcm.edu	37	12	21201693	21201693	+	Missense_Mutation	SNP	T	T	A	rs370821380	alternate_allele	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	176.0	46.0	103.0	0.0	0.261364	0	.	.	alt	.	SLCO1B7	85	.	NM_001009562	exon8	c.T1042A	p.Y348N	GGAGGATATATCA	.	PASS	Atlas-SNP
CTBS	1486	hgsc.bcm.edu	37	1	85040024	85040024	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	3.0	2.0	6.0	0.0	0.666667	0	.	.	none	CTBS,NS,carcinoma,0,1	CTBS	24	1	NM_004388	exon1	c.G75A	p.L25L	CAGCGCCAGCAGC	.	scavenged	Atlas-SNP
DDX39B	7919	hgsc.bcm.edu	37	6	31500627	31500627	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	208.0	93.0	189.0	0.0	0.447115	0	.	.	none	.	DDX39B	38	.	NM_004640	exon7	c.A797G	p.Y266C	TTCACGTAGTACT	.	PASS	Atlas-SNP
TENM4	26011	hgsc.bcm.edu	37	11	78380664	78380664	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	143.0	37.0	141.0	0.0	0.258741	0	.	.	none	ODZ4_ENST00000278550,colon,carcinoma,-1,2	.	.	2	NM_001098816	exon32	c.C6726T	p.R2242R	GCGGTCGCGGATG	.	PASS	Atlas-SNP
RBM27	54439	hgsc.bcm.edu	37	5	145613242	145613242	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	106.0	31.0	100.0	0.0	0.292453	0	.	.	none	.	RBM27	119	.	NM_018989	exon7	c.T1080G	p.S360R	CCATAGTATGAGA	.	PASS	Atlas-SNP
VWA7	80737	hgsc.bcm.edu	37	6	31744405	31744405	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	158.0	67.0	177.0	0.0	0.424051	0	.	.	none	.	.	.	.	NM_025258	exon2	c.A152G	p.E51G	GCTGCCTCCTCAG	.	PASS	Atlas-SNP
PCDH9	5101	hgsc.bcm.edu	37	13	66879059	66879059	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	112.0	20.0	94.0	0.0	0.178571	0	.	.	none	.	PCDH9	252	.	NM_203487	exon5	c.T3442G	p.L1148V	GACCCAAGCCAGG	.	PASS	Atlas-SNP
FHOD3	80206	hgsc.bcm.edu	37	18	34340708	34340708	+	Silent	SNP	C	C	T	rs200423151	by1000genomes	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	22.0	5.0	24.0	0.0	0.227273	0	C|1.000;T|0.000	0.000	strong	.	FHOD3	210	.	NM_025135	exon23	c.C4038T	p.P1346P	CACCCCCGCGCTG	.	PASS	Atlas-SNP
ZNF423	23090	hgsc.bcm.edu	37	16	49670344	49670344	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	119.0	23.0	124.0	0.0	0.193277	0	.	.	none	ZNF423_ENST00000262383,NS,carcinoma,+2,2	ZNF423	463	2	NM_015069	exon4	c.C2719T	p.R907W	GGTCCCGCAGCCG	.	PASS	Atlas-SNP
KCNK10	54207	hgsc.bcm.edu	37	14	88652049	88652049	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	275.0	68.0	252.0	0.0	0.247273	0	.	.	none	.	KCNK10	273	.	NM_138318	exon7	c.G1462A	p.E488K	TCTCCTCGTCCAG	.	PASS	Atlas-SNP
TIAM2	26230	hgsc.bcm.edu	37	6	155458711	155458711	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	25.0	6.0	20.0	0.0	0.24	0	.	.	none	TIAM2,NS,malignant_melanoma,0,1	TIAM2	161	1	NM_012454	exon4	c.G1595A	p.R532Q	TGGCACGAAGGAA	.	scavenged	Atlas-SNP
RHBDF1	64285	hgsc.bcm.edu	37	16	112797	112797	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	95.0	18.0	102.0	0.0	0.189474	0	.	.	none	.	RHBDF1	54	.	NM_022450	exon6	c.G771T	p.E257D	GTCCAGCTCATCG	.	PASS	Atlas-SNP
ZFC3H1	196441	hgsc.bcm.edu	37	12	72017233	72017233	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	90.0	4.0	74.0	0.0	0.0444444	0	.	.	none	.	ZFC3H1	172	.	NM_144982	exon24	c.T4651C	p.S1551P	TTCTTGAAGGATT	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495711	134495711	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	47.0	13.0	78.0	0.0	0.276596	0	.	.	none	.	SGK1	387	.	NM_001143676	exon4	c.G375A	p.Q125Q	CCTCCTCTGCTTC	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495706	134495706	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	48.0	12.0	76.0	0.0	0.25	0	.	.	none	SGK1_ENST00000367858,NS,lymphoid_neoplasm,0,2	SGK1	387	2	NM_001143676	exon4	c.G380A	p.R127K	CCCATCCTCCTCT	.	PASS	Atlas-SNP
DDX3X	1654	hgsc.bcm.edu	37	X	41206198	41206198	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	241.0	15.0	248.0	0.0	0.0622407	0	.	.	none	.	DDX3X	138	.	NM_001193416	exon15	c.C1702T	p.P568S	GAAGTGCCGTCTT	.	PASS	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44126858	44126858	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	82.0	5.0	66.0	0.0	0.0609756	0	.	.	none	.	LOXHD1	367	.	NM_144612	exon22	c.G3514T	p.D1172Y	GAAAACCTTTCTG	.	PASS	Atlas-SNP
PIK3CD	5293	hgsc.bcm.edu	37	1	9787030	9787030	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	117.0	59.0	109.0	0.0	0.504274	0	.	.	none	PIK3CD,NS,lymphoid_neoplasm,0,2	PIK3CD	86	2	NM_005026	exon24	c.G3061A	p.E1021K	TTTAACGAAGCCC	.	PASS	Atlas-SNP
MAPK10	5602	hgsc.bcm.edu	37	4	87022299	87022299	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	174.0	45.0	124.0	0.0	0.258621	0	.	.	none	MAPK10_ENST00000449047,NS,carcinoma,0,1	MAPK10	106	1	NM_002753	exon8	c.G636A	p.R212R	TGCTGTCCTGGCC	.	PASS	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	37	3	126733600	126733600	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	67.0	13.0	99.0	0.0	0.19403	0	.	.	none	.	PLXNA1	185	.	NM_032242	exon13	c.G2803A	p.A935T	CATGACGCCCTGG	.	PASS	Atlas-SNP
FAU	2197	hgsc.bcm.edu	37	11	64889279	64889279	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	87.0	22.0	89.0	0.0	0.252874	0	.	.	none	FAU,NS,carcinoma,+2,1	FAU	17	1	NM_001997	exon2	c.C7G	p.L3V	CAAAGAGCTGCAT	.	PASS	Atlas-SNP
DSEL	92126	hgsc.bcm.edu	37	18	65180867	65180867	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	72.0	13.0	78.0	0.0	0.180556	0	.	.	none	.	DSEL	196	.	NM_032160	exon2	c.G1009T	p.V337L	TACCCACAGTTCT	.	PASS	Atlas-SNP
FAM83D	81610	hgsc.bcm.edu	37	20	37555095	37555095	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	29.0	6.0	34.0	0.0	0.206897	0	.	.	none	.	FAM83D	60	.	NM_030919	exon1	c.C100G	p.L34V	GCTCTGCTGTCCG	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495211	134495211	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	73.0	6.0	85.0	0.0	0.0821918	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	NM_001143676	exon5	c.G445C	p.V149L	ACTGAACTTCAGG	.	PASS	Atlas-SNP
INHBB	3625	hgsc.bcm.edu	37	2	121107185	121107185	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	100.0	4.0	142.0	0.0	0.04	0	.	.	none	INHBB,NS,malignant_melanoma,-1,1	INHBB	29	1	NM_002193	exon2	c.G959A	p.W320X	ACGACTGGATCAT	.	PASS	Atlas-SNP
MCMDC2	157777	hgsc.bcm.edu	37	8	67796149	67796149	+	Silent	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	103.0	5.0	92.0	0.0	0.0485437	0	.	.	none	.	MCMDC2	84	.	NM_173518	exon9	c.A993G	p.V331V	TCTAGTACAGACA	.	PASS	Atlas-SNP
SMG1	23049	hgsc.bcm.edu	37	16	18847712	18847712	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	125.0	22.0	98.0	0.0	0.176	0	.	.	none	.	SMG1	401	.	NM_015092	exon47	c.C7747T	p.L2583F	CTTGAAGCAAGCT	.	PASS	Atlas-SNP
TACR3	6870	hgsc.bcm.edu	37	4	104511045	104511045	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	252.0	58.0	195.0	0.0	0.230159	0	.	.	none	.	TACR3	102	.	NM_001059	exon5	c.A1192G	p.S398G	TACTGCTTTGCCG	.	PASS	Atlas-SNP
NTPCR	84284	hgsc.bcm.edu	37	1	233113956	233113956	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	89.0	4.0	110.0	0.0	0.0449438	0	.	.	none	.	NTPCR	15	.	NM_032324	exon5	c.C552T	p.C184C	GACGTGCGTGCAG	.	PASS	Atlas-SNP
RBMS3	27303	hgsc.bcm.edu	37	3	29938967	29938967	+	Splice_Site	SNP	G	G	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	177.0	41.0	143.0	0.0	0.231638	0	.	.	none	.	RBMS3	62	.	NM_001177712	exon10	c.927+1G>T	.	TACCAGGTATGTC	.	PASS	Atlas-SNP
SP140	11262	hgsc.bcm.edu	37	2	231102990	231102990	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	230.0	51.0	181.0	0.0	0.221739	0	.	.	none	.	SP140	121	.	NM_007237	exon3	c.T300G	p.S100R	ACTCAGTGAACTG	.	PASS	Atlas-SNP
RALYL	138046	hgsc.bcm.edu	37	8	85774611	85774611	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	53.0	13.0	57.0	0.0	0.245283	0	.	.	none	.	RALYL	123	.	NM_001100391	exon6	c.C533T	p.T178M	TCACAACGACTCG	.	PASS	Atlas-SNP
SOX15	6665	hgsc.bcm.edu	37	17	7492686	7492686	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	79.0	11.0	155.0	0.0	0.139241	0	.	.	none	.	SOX15	10	.	NM_006942	exon1	c.G309A	p.K103K	GAGCCGCTTGGCC	.	PASS	Atlas-SNP
OR5W2	390148	hgsc.bcm.edu	37	11	55681542	55681542	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	69.0	15.0	52.0	0.0	0.217391	0	.	.	none	OR5W2,colon,carcinoma,+2,1	OR5W2	112	1	NM_001001960	exon1	c.G517T	p.E173X	TAATCTCATTAGA	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495170	134495170	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	71.0	5.0	94.0	0.0	0.0704225	0	.	.	none	.	SGK1	387	.	NM_001143676	exon5	c.G486C	p.E162D	CATAAGCTCAGGC	.	PASS	Atlas-SNP
HECTD4	283450	hgsc.bcm.edu	37	12	112622063	112622063	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	82.0	18.0	130.0	0.0	0.219512	0	.	.	none	.	.	.	.	NM_001109662	exon61	c.C10305T	p.S3435S	GTACATGGAGCCC	.	PASS	Atlas-SNP
ALKBH8	91801	hgsc.bcm.edu	37	11	107423860	107423860	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	74.0	3.0	99.0	0.0	0.0405405	0	.	.	none	ALKBH8_ENST00000428149,colon,carcinoma,0,2	ALKBH8	88	2	NM_138775	exon5	c.T569A	p.V190E	TTATCTACATTGT	.	scavenged	Atlas-SNP
GRIK4	2900	hgsc.bcm.edu	37	11	120831697	120831697	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	130.0	31.0	130.0	0.0	0.238462	0	.	.	none	GRIK4,NS,carcinoma,-1,1	GRIK4	149	1	NM_014619	exon15	c.C1954T	p.P652S	GATGTGCCCATTG	.	PASS	Atlas-SNP
KLHL6	89857	hgsc.bcm.edu	37	3	183209942	183209942	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	152.0	27.0	174.0	0.0	0.177632	0	.	.	none	.	KLHL6	100	.	NM_130446	exon7	c.G1639C	p.E547Q	CCCGCTCGTGGCT	.	PASS	Atlas-SNP
CHD8	57680	hgsc.bcm.edu	37	14	21870201	21870201	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	197.0	31.0	142.0	0.0	0.15736	0	.	.	none	.	CHD8	339	.	NM_001170629	exon19	c.G3977A	p.C1326Y	TCTTCACAAAACT	.	PASS	Atlas-SNP
ZNF572	137209	hgsc.bcm.edu	37	8	125989722	125989722	+	Silent	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	65.0	4.0	57.0	0.0	0.0615385	0	.	.	none	ZNF572,colon,carcinoma,+1,1	ZNF572	82	1	NM_152412	exon3	c.A1212G	p.R404R	TCAGAGAACACAT	.	PASS	Atlas-SNP
SULF1	23213	hgsc.bcm.edu	37	8	70512971	70512971	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	106.0	22.0	89.0	0.0	0.207547	0	.	.	none	.	SULF1	153	.	NM_001128205	exon9	c.G868A	p.D290N	TCAGTGGATGATT	.	PASS	Atlas-SNP
GH2	2689	hgsc.bcm.edu	37	17	61957782	61957782	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	412.0	95.0	460.0	0.0	0.230583	0	.	.	none	.	GH2	73	.	NM_002059	exon5	c.A553T	p.N185Y	CGTAGTTCTTGAG	.	PASS	Atlas-SNP
BRIP1	83990	hgsc.bcm.edu	37	17	59760682	59760682	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	102.0	20.0	73.0	0.0	0.196078	0	.	.	none	.	BRIP1	237	.	NM_032043	exon20	c.A3725C	p.K1242T	ATGCCTTTATTTT	.	PASS	Atlas-SNP
COASY	80347	hgsc.bcm.edu	37	17	40716156	40716156	+	Missense_Mutation	SNP	G	G	A	rs367865615	alternate_allele	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	153.0	41.0	187.0	0.0	0.267974	0	.	.	alt	.	COASY	45	.	NM_001042532	exon4	c.G965A	p.R322H	CCTATCGTGGGGG	.	PASS	Atlas-SNP
TOR1AIP1	26092	hgsc.bcm.edu	37	1	179852022	179852022	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	92.0	4.0	101.0	0.0	0.0434783	0	.	.	none	.	TOR1AIP1	58	.	NM_001267578	exon1	c.C385T	p.R129C	ACTACCCGCCTTC	.	PASS	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	35632915	35632915	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	395.0	68.0	344.0	0.0	0.172152	0	.	.	none	.	NBEA	340	.	NM_015678	exon8	c.G1154A	p.G385D	TCTGTGGTCAACT	.	PASS	Atlas-SNP
CCR6	1235	hgsc.bcm.edu	37	6	167550741	167550741	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	137.0	27.0	115.0	0.0	0.19708	0	.	.	none	.	CCR6	36	.	NM_004367	exon3	c.C1023A	p.Y341X	GAAGTACAAGTCC	.	PASS	Atlas-SNP
TMEM184C	55751	hgsc.bcm.edu	37	4	148539118	148539118	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	220.0	51.0	205.0	0.0	0.231818	0	.	.	none	.	TMEM184C	25	.	NM_018241	exon1	c.C11T	p.T4I	CTTGCACTTGTAC	.	PASS	Atlas-SNP
EPHA6	285220	hgsc.bcm.edu	37	3	97251298	97251298	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	122.0	27.0	96.0	1.0	0.221311	0.0104167	.	.	none	EPHA6,NS,carcinoma,+1,1	EPHA6	439	1	NM_001080448	exon11	c.G2297A	p.R766Q	TGGATCGGCAAAG	.	scavenged	Atlas-SNP
RFTN1	23180	hgsc.bcm.edu	37	3	16419279	16419279	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	82.0	28.0	113.0	0.0	0.341463	0	.	.	none	.	RFTN1	79	.	NM_015150	exon5	c.C772T	p.L258L	CATCCAGTGTCTT	.	PASS	Atlas-SNP
LTBP1	4052	hgsc.bcm.edu	37	2	33614282	33614282	+	Silent	SNP	G	G	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	148.0	48.0	136.0	0.0	0.324324	0	.	.	none	.	LTBP1	317	.	NM_206943	exon32	c.G4743C	p.V1581V	CCCCGTGACGGGA	.	PASS	Atlas-SNP
SGK1	6446	hgsc.bcm.edu	37	6	134495159	134495159	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	64.0	11.0	92.0	0.0	0.171875	0	.	.	none	SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	NM_001143676	exon5	c.C497T	p.A166V	GGGTTGGCATTCA	.	PASS	Atlas-SNP
B2M	567	hgsc.bcm.edu	37	15	45003764	45003764	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	104.0	24.0	118.0	1.0	0.230769	0.00847458	.	.	none	B2M,NS,lymphoid_neoplasm,0,1	B2M	99	1	NM_004048	exon1	c.T20C	p.L7S	TGGCCTTAGCTGT	.	scavenged	Atlas-SNP
ZBTB2	57621	hgsc.bcm.edu	37	6	151687092	151687092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	333.0	14.0	354.0	0.0	0.042042	0	.	.	none	.	ZBTB2	30	.	NM_020861	exon3	c.G1109A	p.R370H	AATTTGCGTCCAC	.	PASS	Atlas-SNP
CD93	22918	hgsc.bcm.edu	37	20	23065878	23065878	+	Missense_Mutation	SNP	C	C	T	rs140540216	bycluster;alternate_allele	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	150.0	27.0	167.0	0.0	0.18	0	C|1.000;A|0.000	.	alt	CD93,colon,carcinoma,0,1	CD93	84	1	NM_012072	exon1	c.G952A	p.V318I	CCAGGACGCACGT	.	PASS	Atlas-SNP
TMEM200A	114801	hgsc.bcm.edu	37	6	130761752	130761752	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	207.0	37.0	162.0	0.0	0.178744	0	.	.	none	TMEM200A,NS,carcinoma,0,2	TMEM200A	108	2	NM_001258277	exon3	c.G185T	p.G62V	CATCTGGTTTTTT	.	PASS	Atlas-SNP
ANK2	287	hgsc.bcm.edu	37	4	114294465	114294465	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	148.0	25.0	85.0	0.0	0.168919	0	.	.	none	.	ANK2	576	.	NM_001148	exon45	c.T11719G	p.Y3907D	AGGCGGTATGTAT	.	PASS	Atlas-SNP
ADM2	79924	hgsc.bcm.edu	37	22	50921164	50921164	+	Silent	SNP	A	A	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	36.0	10.0	47.0	0.0	0.277778	0	.	.	none	ADM2,rectum,carcinoma,0,2	ADM2	15	2	NM_024866	exon2	c.A279C	p.R93R	CCCCCGAAGACAC	.	PASS	Atlas-SNP
ZFAT	57623	hgsc.bcm.edu	37	8	135613905	135613905	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	111.0	5.0	131.0	0.0	0.045045	0	.	.	none	.	ZFAT	265	.	NM_020863	exon6	c.C2057T	p.P686L	ACTGGAGGGAGGA	.	PASS	Atlas-SNP
MYH11	4629	hgsc.bcm.edu	37	16	15880586	15880586	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	178.0	47.0	160.0	0.0	0.264045	0	.	.	none	.	MYH11	520	.	NM_001040114	exon5	c.C534T	p.G178G	AGACTCGCCTCTG	.	PASS	Atlas-SNP
BCL11B	64919	hgsc.bcm.edu	37	14	99641016	99641016	+	Silent	SNP	C	C	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	28.0	7.0	61.0	0.0	0.25	0	.	.	none	BCL11B,NS,carcinoma,-2,1	BCL11B	108	1	NM_138576	exon4	c.G2157C	p.R719R	GAAGTGCCGCGAC	.	PASS	Atlas-SNP
MAP2K1	5604	hgsc.bcm.edu	37	15	66727441	66727441	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	94.0	26.0	88.0	1.0	0.276596	0.0113636	.	.	none	MAP2K1,rectum,carcinoma,0,3	MAP2K1	115	3	NM_002755	exon2	c.T157C	p.F53L	GAGGCCTTTCTTA	.	scavenged	Atlas-SNP
ZBTB12	221527	hgsc.bcm.edu	37	6	31868698	31868698	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	101.0	51.0	127.0	0.0	0.504951	0	.	.	none	.	ZBTB12	25	.	NM_181842	exon2	c.C385T	p.P129S	TTTTGGGCTCAAT	.	PASS	Atlas-SNP
MTUS2	23281	hgsc.bcm.edu	37	13	30054459	30054459	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	168.0	26.0	169.0	0.0	0.154762	0	.	.	none	.	MTUS2	279	.	NM_001033602	exon8	c.C3387T	p.H1129H	GGAGCACGGTGAC	.	PASS	Atlas-SNP
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017331	26017331	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	245.0	104.0	252.0	0.0	0.42449	0	.	.	none	.	HIST1H1A	25	.	NM_005325	exon1	c.G630A	p.A210A	GGGTGCCGCTTTC	.	PASS	Atlas-SNP
TRIM38	10475	hgsc.bcm.edu	37	6	25983696	25983696	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	170.0	61.0	138.0	0.0	0.358824	0	.	.	none	.	TRIM38	50	.	NM_006355	exon8	c.T1179A	p.Y393X	AGGCTATGTAGCA	.	PASS	Atlas-SNP
RAF1	5894	hgsc.bcm.edu	37	3	12627290	12627290	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	61.0	15.0	58.0	0.0	0.245902	0	.	.	none	.	RAF1	66	.	NM_002880	exon14	c.C1426T	p.L476F	CATGGAGAAATAT	.	PASS	Atlas-SNP
ARL8A	127829	hgsc.bcm.edu	37	1	202113679	202113679	+	Silent	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	29.0	7.0	25.0	0.0	0.241379	0	.	.	none	.	ARL8A	14	.	NM_138795	exon1	c.C22T	p.L8L	CCAGCAGCTTGTT	.	PASS	Atlas-SNP
SYT14	255928	hgsc.bcm.edu	37	1	210334267	210334267	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	151.0	26.0	121.0	0.0	0.172185	0	.	.	none	.	SYT14	89	.	NM_001146261	exon10	c.G1740C	p.M580I	AGAGATGATAGGC	.	PASS	Atlas-SNP
RNGTT	8732	hgsc.bcm.edu	37	6	89554108	89554108	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	67.0	16.0	61.0	0.0	0.238806	0	.	.	none	.	RNGTT	52	.	NM_003800	exon11	c.A1237T	p.K413X	ACGGCTTATTTCT	.	PASS	Atlas-SNP
SOWAHB	345079	hgsc.bcm.edu	37	4	77818940	77818940	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	41.0	10.0	31.0	0.0	0.243902	0	.	.	none	.	.	.	.	NM_001029870	exon1	c.G63A	p.V21V	GTTGGTCACGCGG	.	PASS	Atlas-SNP
ATP2C2	9914	hgsc.bcm.edu	37	16	84473085	84473085	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	161.0	35.0	144.0	0.0	0.217391	0	.	.	none	.	ATP2C2	75	.	NM_014861	exon13	c.A1164T	p.E388D	CAATGAAATGACA	.	PASS	Atlas-SNP
MAGEC1	9947	hgsc.bcm.edu	37	X	140995472	140995472	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	82.0	12.0	101.0	0.0	0.146341	0	.	.	none	.	MAGEC1	317	.	NM_005462	exon4	c.A2282G	p.E761G	TCCCTGAGAGTCC	.	PASS	Atlas-SNP
EPHA3	2042	hgsc.bcm.edu	37	3	89390951	89390951	+	Silent	SNP	C	C	T	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	93.0	4.0	83.0	0.0	0.0430108	0	.	.	none	.	EPHA3	501	.	NM_005233	exon5	c.C1017T	p.T339T	CGAGACCTCAGTT	.	PASS	Atlas-SNP
LMO7	4008	hgsc.bcm.edu	37	13	76381767	76381767	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	92.0	4.0	67.0	0.0	0.0434783	0	.	.	none	.	LMO7	334	.	NM_015842	exon7	c.G649A	p.E217K	GACCTCGAGATGG	.	PASS	Atlas-SNP
TMSB4X	7114	hgsc.bcm.edu	37	X	12994912	12994912	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	81.0	15.0	71.0	0.0	0.185185	0	.	.	none	.	TMSB4X	3	.	NM_021109	exon3	c.G117C	p.K39N	GGAGAAGCAAGCA	.	PASS	Atlas-SNP