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	39	229	.	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	20	104	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	10	23	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	11	83	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	17	98	.	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	47	250	0	0.159864	0	.	.	none	.	OR5AK2	45	.	NM_001005323	exon1	c.528delC	p.H176fs	.	.	PASS	Atlas-Indel
TBP	6908	hgsc.bcm.edu	37	6	170871013	170871014	+	In_Frame_Ins	INS	-	-	CAG	rs201732168	by1000genomes	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	73	46	59	0	0.630137	0	-|0.138;CAG|0.862	0.862	strong	TBP,NS,carcinoma,0,5	TBP	58	5	NM_003194	exon3	c.189_190insCAG	p.Q63delinsQQ	.	.	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	12	80	.	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	23	86	.	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	39	189	.	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	68	279	.	0.185	.	.	.	none	.	BTBD7	112	.	NM_001002860	exon11	c.2798_2799insA	p.T933fs	.	.	PASS	Pindel,Atlas-Indel
ZNF516	9658	hgsc.bcm.edu	37	18	74090958	74090958	+	Frame_Shift_Del	DEL	G	G	-	rs56087742	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	26	12	32	.	0.462	.	G|0.016;-|0.984	0.984	strong	.	ZNF516	102	.	NM_014643	exon5	c.3112delG	p.V1038fs	.	.	PASS	Pindel
HMGN2P46	283651	hgsc.bcm.edu	37	15	45848231	45848231	+	RNA	DEL	T	T	-	rs368577527		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	38	10	24	.	0.263	.	.	.	weak	.	.	.	.	.	.	.	.	.	.	PASS	Pindel
VSIG10	54621	hgsc.bcm.edu	37	12	118506328	118506333	+	In_Frame_Del	DEL	TCCTCC	TCCTCC	-	rs72125532	bycluster;by1000genomes	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	TCCTCC	TCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	209	65	221	0	0.311	0.000	.	.	strong	.	VSIG10	41	.	NM_019086	exon8	c.1417_1422del	p.473_474del	.	.	PASS	Pindel
OR13C2	392376	hgsc.bcm.edu	37	9	107367665	107367666	+	Frame_Shift_Del	DEL	GC	GC	-	rs143760725	bycluster;by1000genomes	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	447	89	396	.	0.199	.	.	.	strong	.	OR13C2	46	.	NM_001004481	exon1	c.244_245del	p.82_82del	.	.	PASS	Pindel
KRT3	3850	hgsc.bcm.edu	37	12	53189414	53189431	+	In_Frame_Del	DEL	CCAAAGCCACCAGCCCCT	CCAAAGCCACCAGCCCCT	-	novel		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	CCAAAGCCACCAGCCCCT	CCAAAGCCACCAGCCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	133	22	131	.	0.165	.	.	.	none	.	KRT3	65	.	NM_057088	exon1	c.397_414del	p.133_138del	.	.	PASS	Pindel
SMARCA2	6595	hgsc.bcm.edu	37	9	2039777	2039779	+	In_Frame_Del	DEL	CAG	CAG	-	rs376509101		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	102	26	64	.	0.255	.	.	.	weak	SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	NM_139045	exon4	c.666_668del	p.222_223del	.	.	PASS	Pindel
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	4	73	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	4	99	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	30	71	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	55	269	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	24	100	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	46	79	0	0.455446	0	.	.	none	.	COL11A1	972	.	NM_080629	exon55	c.G4138T	p.A1380S	CACCTGCAGCTCC	.	PASS	Atlas-SNP
ADAM32	203102	hgsc.bcm.edu	37	8	39091507	39091507	+	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	4	90	0	0.0296296	0	.	.	none	ADAM32,colon,carcinoma,0,1	ADAM32	70	1	NM_145004	exon16	c.G1724A	p.R575Q	TCGTACGAGATTC	.	scavenged	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	17	88	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	15	96	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	14	80	0	0.162791	0	.	.	none	.	.	.	.	NM_001163278	exon4	c.T729C	p.H243H	ATGCAGATGGACT	.	PASS	Atlas-SNP
PRKRA	8575	hgsc.bcm.edu	37	2	179300871	179300871	+	Splice_Site	SNP	C	C	T	rs200649428		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	46	7	46	3	0.152174	0.0652174	.	.	weak	PRKRA,caecum,carcinoma,0,1	PRKRA	56	1	NM_001139518	exon8	c.709+1G>A	.	ATCATACCTATAT	.	scavenged	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	34	146	0	0.255639	0	.	.	none	.	MSMP	15	.	NM_001044264	exon2	c.T174C	p.S58S	GAGCCAAGACTCA	.	PASS	Atlas-SNP
C10orf76	79591	hgsc.bcm.edu	37	10	103771512	103771512	+	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	181	3	132	0	0.0165746	0	.	.	none	C10orf76,NS,carcinoma,0,2	C10orf76	48	2	NM_024541	exon11	c.C799T	p.Q267X	CACTTTGGTGTTC	.	scavenged	Atlas-SNP
LOXHD1	125336	hgsc.bcm.edu	37	18	44109205	44109205	+	Missense_Mutation	SNP	C	C	T	rs199695409	bycluster	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	287	6	286	0	0.0209059	0	.	.	weak	LOXHD1_ENST00000398722,NS,malignant_melanoma,+1,2	LOXHD1	367	2	NM_144612	exon29	c.G4465A	p.G1489R	TGTCCCCGAGGTC	.	scavenged	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134054582	134054582	+	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	4	128	0	0.0307692	0	.	.	none	NCAPD3,caecum,carcinoma,0,1	NCAPD3	141	1	NM_015261	exon19	c.G2401A	p.A801T	GCAAGGCGTCAAC	.	scavenged	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145296403	145296403	+	Silent	SNP	C	C	T	rs4996269	bycluster;byfrequency;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	72	3	82	2	0.0416667	0.0243902	T|0.001;G|0.956	0.001	strong	NBPF10,NS,carcinoma,0,1	NBPF10	221	1	NM_001039703	exon3	c.C325T	p.L109L	ACCCAGCTAAGGG	.	scavenged	Atlas-SNP
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	11	43	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	5	77	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
DYSF	8291	hgsc.bcm.edu	37	2	71909727	71909727	+	Missense_Mutation	SNP	C	C	T	rs121908955		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	199	4	215	0	0.0201005	0	.	.	weak	DYSF_ENST00000410020,NS,carcinoma,-1,2	DYSF	536	2	NM_001130987	exon55	c.C6241T	p.R2081C	TGGCGGCGTTTCC	.	scavenged	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	52	249	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	53	192	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	39	144	0	0.239264	0	.	.	none	LACTB,NS,carcinoma,-1,1	LACTB	29	1	NM_032857	exon6	c.C1424T	p.S475L	ATGGTTCGTGTAG	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	37	11	1093245	1093245	+	Silent	SNP	A	A	T	rs200003195		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	42	8	53	5	0.190476	0.0943396	.	.	weak	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	NM_002457	exon30	c.A5064T	p.P1688P	AACCCCAACACCC	.	scavenged	Atlas-SNP
CSDE1	7812	hgsc.bcm.edu	37	1	115275286	115275286	+	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	234	3	192	0	0.0128205	0	.	.	none	CSDE1_ENST00000369530,NS,carcinoma,-1,2	CSDE1	145	2	NM_001242891	exon11	c.G1127A	p.R376Q	GTTGCTCGCTCTA	.	scavenged	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	18	175	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
HECW2	57520	hgsc.bcm.edu	37	2	197090577	197090577	+	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	158	2	158	0	0.0126582	0	.	.	none	HECW2,colon,carcinoma,0,1	HECW2	239	1	NM_020760	exon23	c.G3935A	p.R1312K	AGGATCCTACCAC	.	scavenged	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	3	67	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	37	126	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
KCNA10	3744	hgsc.bcm.edu	37	1	111060343	111060343	+	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	166	2	154	0	0.0120482	0	.	.	none	KCNA10,NS,carcinoma,-1,2	KCNA10	92	2	NM_005549	exon1	c.G1067A	p.R356H	GAGTGGCGCGAGA	.	scavenged	Atlas-SNP
ZNF585B	92285	hgsc.bcm.edu	37	19	37677388	37677388	+	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	133	2	127	0	0.0150376	0	.	.	none	ZNF585B,NS,carcinoma,+2,2	ZNF585B	91	2	NM_152279	exon5	c.G1051A	p.E351K	ATTTCTCTCTACT	.	scavenged	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	8	51	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	15	47	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	23	87	0	0.247312	0	.	.	none	.	DOCK3	397	.	NM_004947	exon44	c.G4669A	p.A1557T	GGCATTGCACGCT	.	PASS	Atlas-SNP
UGT1A9	54600	hgsc.bcm.edu	37	2	234580967	234580967	+	Silent	SNP	A	A	G	rs76359435	bycluster;alternate_allele	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	119	8	88	1	0.0672269	0.0113636	.	.	alt	UGT1A9,colon,carcinoma,0,1	UGT1A9	79	1	NM_021027	exon1	c.A387G	p.K129K	GTTTAAAGACAAA	.	scavenged	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	4	89	0	0.0412371	0	.	.	none	.	SLC16A7	82	.	NM_001270622	exon6	c.C1400T	p.A467V	CAAATGCACAGAG	.	PASS	Atlas-SNP
HDLBP	3069	hgsc.bcm.edu	37	2	242192901	242192901	+	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	140	4	118	0	0.0285714	0	.	.	none	HDLBP,caecum,carcinoma,-2,1	HDLBP	118	1	NM_005336	exon10	c.G1200A	p.E400E	TGTGAACTCGATG	.	scavenged	Atlas-SNP
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907708	12907708	+	Silent	SNP	A	A	G	rs4026149	bycluster;byfrequency;by2hit2allele;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	330	19	267	14	0.0575758	0.0524345	A|0.667;G|0.333	0.333	strong	HNRNPCL1,NS,carcinoma,-1,1	HNRNPCL1	68	1	NM_001013631	exon2	c.T435C	p.R145R	ACGTTGACGTTTC	.	scavenged	Atlas-SNP
POM121C	100101267	hgsc.bcm.edu	37	7	75050842	75050842	+	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	294	3	318	0	0.0102041	0	.	.	none	POM121C,NS,carcinoma,0,1	POM121C	46	1	NM_001099415	exon13	c.C2693T	p.P898L	GCAAACGGTGTGC	.	scavenged	Atlas-SNP
KATNBL1	79768	hgsc.bcm.edu	37	15	34445143	34445143	+	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	193	3	173	1	0.015544	0.00578035	.	.	none	C15orf29,NS,carcinoma,0,1	.	.	1	NM_024713	exon4	c.G286A	p.D96N	CCATGTCACAGCC	.	scavenged	Atlas-SNP
MME	4311	hgsc.bcm.edu	37	3	154858001	154858001	+	Nonsense_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	149	3	116	2	0.0201342	0.0172414	.	.	none	MME,colon,carcinoma,-1,2	MME	133	2	NM_007287	exon10	c.C877T	p.R293X	GAAGATCGAAATG	.	scavenged	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	37	6	29910335	29910335	+	Missense_Mutation	SNP	C	C	T	rs200058378		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	140	5	172	0	0.0357143	0	C|0.999;T|0.001	0.001	weak	HLA-A,NS,carcinoma,-1,1	HLA-A	89	1	NM_001242758	exon1	c.C5T	p.A2V	GGATGGCCGTCAT	.	scavenged	Atlas-SNP
INPP4A	3631	hgsc.bcm.edu	37	2	99193602	99193602	+	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	61	2	68	0	0.0327869	0	.	.	none	INPP4A_ENST00000409540,NS,carcinoma,0,3	INPP4A	205	3	NM_001134224	exon25	c.C2797T	p.R933C	TGCATGCGCAGGT	.	scavenged	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279827	46279827	+	Silent	SNP	G	G	A	rs6018623	bycluster;byfrequency;by2hit2allele;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	78	24	75	0	0.307692	0	G|0.861;A|0.139	0.139	strong	.	NCOA3	156	.	NM_181659	exon20	c.G3753A	p.Q1251Q	GCAGCAGCAGCAG	.	PASS	Atlas-SNP
RHPN2	85415	hgsc.bcm.edu	37	19	33493200	33493200	+	Missense_Mutation	SNP	G	G	A	rs200623446	bycluster;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	127	6	131	3	0.0472441	0.0229008	G|0.935;A|0.065	0.065	strong	RHPN2,caecum,carcinoma,-1,17	RHPN2	107	17	NM_033103	exon9	c.C1058T	p.A353V	AGGGCCGCGTAGT	.	scavenged	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	37	13	36167546	36167546	+	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	90	3	74	0	0.0333333	0	.	.	none	NBEA,NS,carcinoma,-1,1	NBEA	340	1	NM_015678	exon47	c.T7258A	p.S2420T	GCAAGGTCTTGGA	.	scavenged	Atlas-SNP
MTOR	2475	hgsc.bcm.edu	37	1	11174434	11174434	+	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	149	5	134	0	0.033557	0	.	.	none	MTOR,NS,lymphoid_neoplasm,-1,1	MTOR	327	1	NM_004958	exon53	c.T7241C	p.V2414A	GCCATGACACTGT	.	scavenged	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	36	145	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	39	146	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	25	131	0	0.171233	0	.	.	none	.	PRRC2B	266	.	NM_013318	exon7	c.G867A	p.P289P	TTCGCCGAAGTCA	.	PASS	Atlas-SNP
BCLAF1	9774	hgsc.bcm.edu	37	6	136582487	136582487	+	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	354	4	347	0	0.0112994	0	.	.	none	BCLAF1_ENST00000531224,lower_third,carcinoma,-2,1	BCLAF1	203	1	NM_014739	exon12	c.A2673G	p.K891K	TTGGTATTTGTCA	.	scavenged	Atlas-SNP
ADAMTS18	170692	hgsc.bcm.edu	37	16	77387748	77387748	+	Missense_Mutation	SNP	T	T	C	rs149505308	bycluster;byfrequency	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	277	5	221	0	0.0180505	0	T|0.999;C|0.001	0.001	strong	ADAMTS18,NS,carcinoma,+1,1	ADAMTS18	270	1	NM_199355	exon10	c.A1496G	p.K499R	GCTTGCTTGGGCT	.	scavenged	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	40	159	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	15	145	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	35	198	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	6	79	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	10	92	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	4	62	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	16	54	0	0.290909	0	.	.	none	.	CPXM1	107	.	NM_019609	exon13	c.T1907A	p.L636H	ATCCCAAGCTCCG	.	PASS	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	37	9	101765754	101765754	+	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	278	4	269	0	0.0143885	0	.	.	none	COL15A1,colon,carcinoma,0,1	COL15A1	211	1	NM_001855	exon8	c.C1085T	p.A362V	CAGCAGCGGGGCT	.	scavenged	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	60	144	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	44	145	0	0.411215	0	.	.	none	.	PIGQ	43	.	NM_004204	exon10	c.G1580A	p.R527H	CCCTCCGCCTCCT	.	PASS	Atlas-SNP
OR51A2	401667	hgsc.bcm.edu	37	11	4976659	4976659	+	Silent	SNP	A	A	T	rs3986369	bycluster;by1000genomes	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	276	4	231	1	0.0144928	0.004329	A|0.689;T|0.311	0.311	strong	OR51A2,NS,carcinoma,0,1	OR51A2	40	1	NM_001004748	exon1	c.T285A	p.S95S	ACTAGAAGAAGTT	.	scavenged	Atlas-SNP
SYTL1	84958	hgsc.bcm.edu	37	1	27674316	27674316	+	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	126	3	110	0	0.0238095	0	.	.	none	SYTL1,NS,carcinoma,-1,1	SYTL1	57	1	NM_032872	exon4	c.C358T	p.H120Y	CCAGGCCACGACA	.	scavenged	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	8	127	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	10	155	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	30	145	0	0.212766	0	.	.	none	.	CAMK4	77	.	NM_001744	exon1	c.A95T	p.Y32F	CGGATTACTGGAT	.	PASS	Atlas-SNP
NCOA3	8202	hgsc.bcm.edu	37	20	46279836	46279836	+	Silent	SNP	A	A	G	rs2664522		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	71	12	74	2	0.169014	0.027027	.	.	weak	NCOA3,NS,carcinoma,0,1	NCOA3	156	1	NM_181659	exon20	c.A3762G	p.Q1254Q	GCAGCAACAGCAG	.	scavenged	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	5	93	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	7	21	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	66	418	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	38	194	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	27	153	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	14	70	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
NUP210	23225	hgsc.bcm.edu	37	3	13368892	13368892	+	Silent	SNP	G	G	A	rs2271509	bycluster;byfrequency;byhapmap;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	121	2	134	0	0.0165289	0	G|0.541;A|0.459	0.459	strong	NUP210,NS,carcinoma,0,2	NUP210	182	2	NM_024923	exon32	c.C4332T	p.C1444C	GACAACGCAGGTG	.	scavenged	Atlas-SNP
PAPSS1	9061	hgsc.bcm.edu	37	4	108578129	108578129	+	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	264	3	214	0	0.0113636	0	.	.	none	PAPSS1,NS,carcinoma,0,1	PAPSS1	57	1	NM_005443	exon7	c.G818A	p.G273D	GCCCAACCTTCTG	.	scavenged	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	17	78	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	39	357	1	0.345133	0.00280112	.	.	none	.	TNFRSF14	89	.	NM_003820	exon4	c.T379C	p.C127R	CACTTCTGCATCG	.	PASS	Atlas-SNP
DDX41	51428	hgsc.bcm.edu	37	5	176942194	176942194	+	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	191	2	185	1	0.0104712	0.00540541	.	.	none	DDX41_ENST00000507955,NS,carcinoma,0,1	DDX41	49	1	NM_016222	exon7	c.C637T	p.P213S	TGGTGGGGATGCC	.	scavenged	Atlas-SNP
PRDM16	63976	hgsc.bcm.edu	37	1	3301766	3301766	+	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	195	2	202	0	0.0102564	0	.	.	none	PRDM16,NS,carcinoma,+1,1	PRDM16	147	1	NM_022114	exon4	c.G489A	p.A163A	TCAGGCGGGGGCT	.	scavenged	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	53	205	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	21	148	0	0.133758	0	.	.	none	.	SGK1	387	.	NM_001143676	exon7	c.G682C	p.A228P	GGATTGCTTTCTT	.	PASS	Atlas-SNP
PPP2R5A	5525	hgsc.bcm.edu	37	1	212506921	212506921	+	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	141	2	132	0	0.0141844	0	.	.	none	PPP2R5A,NS,carcinoma,+1,1	PPP2R5A	48	1	NM_006243	exon3	c.C461T	p.A154V	TTGAGGCCTCTTG	.	scavenged	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	14	127	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	4	112	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	22	151	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	9	26	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	17	119	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	5	98	0	0.0462963	0	.	.	none	.	PARP1	100	.	NM_001618	exon7	c.A891G	p.E297E	CGAGCATTCCTCG	.	PASS	Atlas-SNP
RAB11A	8766	hgsc.bcm.edu	37	15	66170250	66170250	+	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	126	5	114	0	0.0396825	0	.	.	none	RAB11A,NS,carcinoma,+1,1	RAB11A	14	1	NM_004663	exon3	c.T387C	p.R129R	TCTACGTCATCTC	.	scavenged	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140476395	140476395	+	Missense_Mutation	SNP	T	T	C	rs71574501	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	19	5	32	4	0.263158	0.125	CT|0.500;TG|0.500	.	alt	PCDHB2,NS,carcinoma,0,1	PCDHB2	163	1	NM_018936	exon1	c.T2021C	p.L674P	ACCTGCTGCTCCC	.	scavenged	Atlas-SNP
NBPF10	100132406	hgsc.bcm.edu	37	1	145323656	145323656	+	Missense_Mutation	SNP	A	A	T	rs75252120	bycluster;byfrequency	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	28	5	31	1	0.178571	0.0322581	A|0.625;T|0.375	0.375	strong	NBPF10,NS,carcinoma,0,7	NBPF10	221	7	NM_001039703	exon27	c.A3493T	p.I1165F	GCAGGAATTAAAA	.	scavenged	Atlas-SNP
OLFML2B	25903	hgsc.bcm.edu	37	1	161953800	161953800	+	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	106	3	85	0	0.0283019	0	.	.	none	OLFML2B,NS,carcinoma,+2,1	OLFML2B	114	1	NM_015441	exon8	c.G1918A	p.G640S	TGAAGCCCTCATC	.	scavenged	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	25	143	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	38	240	0	0.164502	0	.	.	none	.	PRDM9	344	.	NM_020227	exon11	c.C1233T	p.H411H	CAATCACTCCTCT	.	PASS	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105412770	105412770	+	Silent	SNP	C	C	T	rs372139093	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	256	3	287	0	0.0117188	0	.	.	alt	AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	NM_138420	exon7	c.G9018A	p.P3006P	CACCTTCGGCGCA	.	scavenged	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	13	128	0	0.220339	0	.	.	none	.	MAPK7	72	.	NM_002749	exon5	c.C1901T	p.P634L	CCTGCCCACCCCC	.	PASS	Atlas-SNP
NCAPD3	23310	hgsc.bcm.edu	37	11	134055332	134055332	+	Missense_Mutation	SNP	G	G	A	rs143833204	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	107	2	124	0	0.0186916	0	G|0.999;A|0.001	0.001	strong	NCAPD3,NS,carcinoma,0,1	NCAPD3	141	1	NM_015261	exon17	c.C2135T	p.T712M	TGTTCCGTGCCAG	.	scavenged	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	15	48	0	0.258621	0	.	.	none	.	DSCR4	20	.	NM_005867	exon1	c.T4C	p.S2P	TTAACGACATGGA	.	PASS	Atlas-SNP
PLK4	10733	hgsc.bcm.edu	37	4	128807324	128807324	+	Nonsense_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	217	3	174	0	0.0138249	0	.	.	none	PLK4,NS,carcinoma,-1,1	PLK4	65	1	NM_014264	exon5	c.C799T	p.R267X	ATGTCCCGAAATT	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506569	195506569	+	Missense_Mutation	SNP	A	A	G	rs201891747	bycluster	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	37	16	35	9	0.432432	0.257143	.	.	weak	MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	NM_018406	exon2	c.T11882C	p.V3961A	GTGGATACTGAGG	.	scavenged	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	25	78	0	0.25	0	.	.	none	.	LAMA4	227	.	NM_001105206	exon3	c.C227T	p.S76L	TCTCCCGACAGGG	.	PASS	Atlas-SNP
ZNF141	7700	hgsc.bcm.edu	37	4	367267	367267	+	Silent	SNP	T	T	C	rs201021508		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	42	4	32	1	0.0952381	0.03125	T|0.999;C|0.001	0.001	weak	ZNF141,rectum,carcinoma,0,1	ZNF141	48	1	NM_003441	exon4	c.T1041C	p.A347A	CAAAGCTTTTAGA	.	scavenged	Atlas-SNP
OR10H1	26539	hgsc.bcm.edu	37	19	15918678	15918678	+	Missense_Mutation	SNP	G	G	A	rs201182090	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	237	7	308	2	0.0295359	0.00649351	G|0.980;A|0.020	0.020	strong	OR10H1,NS,carcinoma,+1,4	OR10H1	59	4	NM_013940	exon1	c.C170T	p.T57M	ATGGGCGTGTGGA	.	scavenged	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	4	145	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
FAM175B	23172	hgsc.bcm.edu	37	10	126508012	126508012	+	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	130	4	153	0	0.0307692	0	.	.	none	FAM175B_ENST00000298492,NS,carcinoma,+1,1	FAM175B	39	1	NM_032182	exon4	c.G260A	p.R87Q	AAGATCGGAGAAA	.	scavenged	Atlas-SNP
KLRC2	3822	hgsc.bcm.edu	37	12	10588444	10588444	+	Missense_Mutation	SNP	G	G	C	rs34194304		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	292	28	231	19	0.0958904	0.0822511	.	.	weak	KLRC2,NS,carcinoma,+1,1	KLRC2	29	1	NM_002260	exon1	c.C142G	p.P48A	GGGAAGGATTTTG	.	scavenged	Atlas-SNP
LRRC37A2	474170	hgsc.bcm.edu	37	17	44630768	44630768	+	Missense_Mutation	SNP	A	A	G	rs76911105	alternate_allele	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	1189	17	1038	9	0.0142977	0.00867052	.	.	alt	LRRC37A2,NS,carcinoma,0,2	LRRC37A2	37	2	NM_001006607	exon11	c.A4812G	p.I1604M	ACAGATATGTTGT	.	scavenged	Atlas-SNP
KIF24	347240	hgsc.bcm.edu	37	9	34311190	34311190	+	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	174	2	183	0	0.0114943	0	.	.	none	KIF24,NS,carcinoma,+1,2	KIF24	64	2	NM_194313	exon2	c.A155G	p.K52R	AGACGTTTGCGGT	.	scavenged	Atlas-SNP
FUBP1	8880	hgsc.bcm.edu	37	1	78429757	78429757	+	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	190	4	162	0	0.0210526	0	.	.	none	FUBP1_ENST00000370768,colon,carcinoma,-1,1	FUBP1	112	1	NM_003902	exon12	c.G1031A	p.R344Q	ACACTTCGAAGAA	.	scavenged	Atlas-SNP
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346595	39346595	+	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	71	10	38	0	0.140845	0	.	.	none	KRTAP9-1_ENST00000398470,rectum,carcinoma,0,2	KRTAP9-1	34	2	NM_001190460	exon1	c.T457A	p.C153S	CCCACCTGCTGTG	.	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	28	157	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	74	261	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	28	147	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	4	127	0	0.04	0	.	.	none	.	KRTCAP3	12	.	NM_173853	exon4	c.T341C	p.L114P	GCCTCCTTCTTGC	.	PASS	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733102	52733102	+	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	310	6	275	2	0.0193548	0.00727273	.	.	none	PCMTD1,extremity,malignant_melanoma,0,3	PCMTD1	73	3	NM_052937	exon6	c.C883T	p.L295F	GAATAAGCTGATT	.	scavenged	Atlas-SNP
AKR7A2	8574	hgsc.bcm.edu	37	1	19632532	19632532	+	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	104	3	107	0	0.0288462	0	.	.	none	AKR7A2,NS,carcinoma,+2,1	AKR7A2	19	1	NM_003689	exon6	c.T898C	p.Y300H	GGTGGTACATCCA	.	scavenged	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	46	154	0	0.227723	0	.	.	none	.	LIMS1	38	.	NM_001193483	exon10	c.900-1G>A	.	TCTTTAGGAATAA	.	PASS	Atlas-SNP
PITPNM2	57605	hgsc.bcm.edu	37	12	123471235	123471235	+	Silent	SNP	C	C	T	rs147680163	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	178	3	172	1	0.0168539	0.00581395	C|0.998;T|0.002	0.002	strong	PITPNM2,bladder,carcinoma,0,1	PITPNM2	105	1	NM_020845	exon23	c.G3555A	p.P1185P	CCGCAGCGGGTCA	.	scavenged	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	16	86	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	4	72	0	0.0487805	0	.	.	none	.	SCN11A	296	.	NM_014139	exon19	c.3219+1G>A	.	GATTTACCAGTGC	.	PASS	Atlas-SNP
CCRL1	51554	hgsc.bcm.edu	37	3	132319326	132319326	+	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	538	10	408	3	0.0185874	0.00735294	.	.	none	CCRL1,NS,carcinoma,0,2	CCRL1	30	2	NM_178445	exon1	c.C85T	p.L29L	TATGAACTGATCT	.	scavenged	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	10	65	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	20	69	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	14	77	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	48	204	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	5	151	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	4	98	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
PCDH12	51294	hgsc.bcm.edu	37	5	141325355	141325355	+	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	204	3	206	0	0.0147059	0	.	.	none	PCDH12,NS,carcinoma,+1,1	PCDH12	133	1	NM_016580	exon4	c.G3146A	p.R1049Q	CTCAGCCGGTCCA	.	scavenged	Atlas-SNP
SERPINC1	462	hgsc.bcm.edu	37	1	173878965	173878965	+	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	125	2	115	2	0.016	0.0173913	.	.	none	SERPINC1,NS,carcinoma,-1,1	SERPINC1	57	1	NM_000488	exon5	c.G878A	p.R293Q	ACGCGCCGATAAC	.	scavenged	Atlas-SNP
ABCB11	8647	hgsc.bcm.edu	37	2	169830315	169830315	+	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	166	3	127	0	0.0180723	0	.	.	none	ABCB11,NS,carcinoma,-1,1	ABCB11	136	1	NM_003742	exon13	c.G1344A	p.G448G	CATTTCCCCTGGT	.	scavenged	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	25	75	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	4	92	2	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
ADCY4	196883	hgsc.bcm.edu	37	14	24788543	24788543	+	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	328	4	302	0	0.0121951	0	.	.	none	ADCY4,NS,carcinoma,+1,1	ADCY4	86	1	NM_001198592	exon23	c.G2833A	p.A945T	GTTGTGCATCCTG	.	scavenged	Atlas-SNP
NTNG2	84628	hgsc.bcm.edu	37	9	135042392	135042392	+	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	161	3	181	0	0.0186335	0	.	.	none	NTNG2,colon,carcinoma,+2,1	NTNG2	66	1	NM_032536	exon2	c.C174T	p.G58G	CTCAGGCATCACA	.	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	4	86	0	0.057971	0	.	.	none	.	PRKD2	94	.	NM_016457	exon7	c.G1106A	p.G369E	TTGCCTCCCTCGC	.	PASS	Atlas-SNP
IFNA4	3441	hgsc.bcm.edu	37	9	21187146	21187146	+	Missense_Mutation	SNP	C	C	T	rs201186279		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	487	7	402	4	0.0143737	0.00995025	.	.	weak	IFNA4,NS,carcinoma,0,1	IFNA4	34	1	NM_021068	exon1	c.G385A	p.V129M	CTTCCACCCCAAC	.	scavenged	Atlas-SNP
HSPD1	3329	hgsc.bcm.edu	37	2	198363534	198363534	+	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	283	5	221	0	0.0176678	0	.	.	none	HSPD1_ENST00000426480,NS,haematopoietic_neoplasm,0,3	HSPD1	68	3	NM_002156	exon2	c.G39A	p.P13P	GGACACCGGTCTC	.	scavenged	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	37	154	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	46	103	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	2	6	0	0.666667	0	.	.	none	CTBS,NS,carcinoma,0,1	CTBS	24	1	NM_004388	exon1	c.G75A	p.L25L	CAGCGCCAGCAGC	.	scavenged	Atlas-SNP
LCE1F	353137	hgsc.bcm.edu	37	1	152749039	152749039	+	Silent	SNP	T	T	C	rs202038292	byfrequency	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	93	5	75	0	0.0537634	0	T|0.954;C|0.046	0.046	strong	LCE1F,NS,carcinoma,+2,1	LCE1F	42	1	NM_178354	exon1	c.T192C	p.G64G	TGGGGGTGGTGGC	.	scavenged	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305785	39305785	+	Missense_Mutation	SNP	A	A	T	rs411367	bycluster;byhapmap;by1000genomes	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	56	11	44	0	0.196429	0	A|0.646;T|0.354	0.354	strong	KRTAP4-5,colon,carcinoma,0,3	KRTAP4-5	34	3	NM_033188	exon1	c.T235A	p.C79S	AGCAGCAGGGGCG	.	PASS	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	93	189	0	0.447115	0	.	.	none	.	DDX39B	38	.	NM_004640	exon7	c.A797G	p.Y266C	TTCACGTAGTACT	.	PASS	Atlas-SNP
USP34	9736	hgsc.bcm.edu	37	2	61454211	61454211	+	Missense_Mutation	SNP	C	C	T	rs371000877		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	203	3	186	0	0.0147783	0	.	.	weak	USP34,rectum,carcinoma,0,1	USP34	334	1	NM_014709	exon62	c.G7586A	p.R2529Q	TCTGATCGAGACT	.	scavenged	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	37	141	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	31	100	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	67	177	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	20	94	0	0.178571	0	.	.	none	.	PCDH9	252	.	NM_203487	exon5	c.T3442G	p.L1148V	GACCCAAGCCAGG	.	PASS	Atlas-SNP
ADAM29	11086	hgsc.bcm.edu	37	4	175897508	175897508	+	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	179	6	117	0	0.0335196	0	.	.	none	ADAM29,rectum,carcinoma,-1,1	ADAM29	262	1	NM_001130703	exon4	c.A832G	p.T278A	AACATTACGCCCC	.	scavenged	Atlas-SNP
SIRPA	140885	hgsc.bcm.edu	37	20	1902270	1902270	+	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	424	4	488	0	0.00943396	0	.	.	none	SIRPA,NS,carcinoma,+2,1	SIRPA	83	1	NM_001040022	exon4	c.T666C	p.V222V	GGACGTTCACTCT	.	scavenged	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	5	24	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
ACOX1	51	hgsc.bcm.edu	37	17	73945836	73945836	+	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	165	2	167	0	0.0121212	0	.	.	none	ACOX1_ENST00000301608,NS,carcinoma,0,4	ACOX1	85	4	NM_007292	exon10	c.G1441A	p.E481K	GGCTTTCGGGGCT	.	scavenged	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	37	5	256470	256470	+	Missense_Mutation	SNP	G	G	A	rs3211483		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	4	135	1	0.0296296	0.00740741	G|1.000;|0.000	.	weak	SDHA,NS,adenocarcinoma,0,2	SDHA	80	2	NM_004168	exon15	c.G1930A	p.V644M	AGACCCGTGATCG	.	scavenged	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	23	124	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	68	252	0	0.247273	0	.	.	none	.	KCNK10	273	.	NM_138318	exon7	c.G1462A	p.E488K	TCTCCTCGTCCAG	.	PASS	Atlas-SNP
C16orf46	123775	hgsc.bcm.edu	37	16	81097482	81097482	+	Missense_Mutation	SNP	G	G	A	rs367739815	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	141	2	155	0	0.0141844	0	.	.	alt	C16orf46_ENST00000378611,NS,malignant_melanoma,0,2	C16orf46	57	2	NM_001100873	exon2	c.C79T	p.P27S	AGGTTGGTTCTGT	.	scavenged	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	6	20	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	18	102	0	0.189474	0	.	.	none	.	RHBDF1	54	.	NM_022450	exon6	c.G771T	p.E257D	GTCCAGCTCATCG	.	PASS	Atlas-SNP
FER	2241	hgsc.bcm.edu	37	5	108207168	108207168	+	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	303	5	249	0	0.0165017	0	.	.	none	FER,NS,carcinoma,+1,1	FER	100	1	NM_005246	exon7	c.T768C	p.P256P	AGATCCTAGTACA	.	scavenged	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	4	74	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	13	78	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	12	76	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	15	248	0	0.0622407	0	.	.	none	.	DDX3X	138	.	NM_001193416	exon15	c.C1702T	p.P568S	GAAGTGCCGTCTT	.	PASS	Atlas-SNP
CHCHD4	131474	hgsc.bcm.edu	37	3	14154566	14154566	+	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	128	2	126	0	0.015625	0	.	.	none	CHCHD4,NS,carcinoma,0,1	CHCHD4	8	1	NM_144636	exon4	c.G289A	p.G97R	CTGACCCCTTGAT	.	scavenged	Atlas-SNP
SI	6476	hgsc.bcm.edu	37	3	164704969	164704969	+	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	248	4	216	0	0.016129	0	.	.	none	SI,NS,carcinoma,0,1	SI	500	1	NM_001041	exon45	c.G5154A	p.Q1718Q	TGCCATCTGATTA	.	scavenged	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	5	66	0	0.0609756	0	.	.	none	.	LOXHD1	367	.	NM_144612	exon22	c.G3514T	p.D1172Y	GAAAACCTTTCTG	.	PASS	Atlas-SNP
KCNJ18	100134444	hgsc.bcm.edu	37	17	21318951	21318951	+	Silent	SNP	C	C	T	rs75757803		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	169	41	189	48	0.242604	0.253968	C|0.500;T|0.500	0.500	weak	KCNJ12,NS,carcinoma,+2,1	.	.	1	NM_001194958	exon3	c.C297T	p.G99G	GTTCGGCATCATC	.	scavenged	Atlas-SNP
EID2B	126272	hgsc.bcm.edu	37	19	40023308	40023308	+	Silent	SNP	A	A	G	rs1123301	bycluster;byfrequency;by1000genomes	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	6	5	6	1	0.833333	0.166667	A|0.234;G|0.766	0.766	strong	EID2B,NS,carcinoma,0,1	EID2B	9	1	NM_152361	exon1	c.T135C	p.A45A	TTCCCGAGCCTCC	.	scavenged	Atlas-SNP
LILRA6	79168	hgsc.bcm.edu	37	19	54744358	54744358	+	Nonsense_Mutation	SNP	A	A	C	rs1052992	bycluster	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	25	24	28	24	0.96	0.857143	A|1.000;|0.000	.	weak	LILRA6,NS,carcinoma,0,1	LILRA6	75	1	NM_024318	exon6	c.T1050G	p.Y350X	GTCAAAATAACCC	.	scavenged	Atlas-SNP
C1QTNF9	338872	hgsc.bcm.edu	37	13	24895902	24895902	+	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	154	4	119	3	0.025974	0.0252101	.	.	none	C1QTNF9,bladder,carcinoma,0,1	C1QTNF9	22	1	NM_178540	exon4	c.C998A	p.P333Q	GCAGCCCGTGACA	.	scavenged	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	59	109	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
NOTCH3	4854	hgsc.bcm.edu	37	19	15290007	15290007	+	Missense_Mutation	SNP	C	C	T	rs10408676	bycluster;byfrequency;byhapmap;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	48	14	42	0	0.291667	0	C|0.924;T|0.076	0.076	strong	.	NOTCH3	340	.	NM_000435	exon22	c.G3547A	p.V1183M	GGTCCACGCAGGT	.	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	45	124	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
BCL7B	9275	hgsc.bcm.edu	37	7	72952324	72952324	+	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	149	2	184	0	0.0134228	0	.	.	none	BCL7B,NS,carcinoma,-1,1	BCL7B	16	1	NM_001707	exon5	c.G456A	p.S152S	AACTTCCGAGGAG	.	scavenged	Atlas-SNP
CMTM7	112616	hgsc.bcm.edu	37	3	32491043	32491043	+	Missense_Mutation	SNP	C	C	T	rs375912380		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	191	4	175	0	0.0209424	0	.	.	weak	CMTM7,NS,carcinoma,-1,1	CMTM7	14	1	NM_138410	exon3	c.C431T	p.A144V	CCGGAGCGGTGAG	.	scavenged	Atlas-SNP
ACTN2	88	hgsc.bcm.edu	37	1	236923039	236923039	+	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	125	2	120	0	0.016	0	.	.	none	ACTN2,rectum,carcinoma,-2,1	ACTN2	191	1	NM_001103	exon19	c.A2317T	p.M773L	GGCCTGATGGATC	.	scavenged	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	13	99	0	0.19403	0	.	.	none	.	PLXNA1	185	.	NM_032242	exon13	c.G2803A	p.A935T	CATGACGCCCTGG	.	PASS	Atlas-SNP
UPP1	7378	hgsc.bcm.edu	37	7	48142960	48142960	+	Missense_Mutation	SNP	C	C	T	rs140206015	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	215	4	186	0	0.0186047	0	C|1.000;G|0.000	.	alt	UPP1,NS,carcinoma,-1,1	UPP1	35	1	NM_003364	exon6	c.C388T	p.R130W	TATGCCCGGTGCT	.	scavenged	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	22	89	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	13	78	0	0.180556	0	.	.	none	.	DSEL	196	.	NM_032160	exon2	c.G1009T	p.V337L	TACCCACAGTTCT	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	37	6	30954754	30954754	+	Missense_Mutation	SNP	G	G	A	rs9262365	bycluster;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	145	4	161	0	0.0275862	0	G|0.901;A|0.099	0.099	strong	MUC21,NS,carcinoma,0,1	MUC21	98	1	NM_001010909	exon2	c.G802A	p.G268S	GGGGCCGGCACAG	.	scavenged	Atlas-SNP
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238705	71238705	+	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	3	139	1	0.0222222	0.00719424	.	.	none	KRTAP5-7,NS,carcinoma,0,3	KRTAP5-7	23	3	NM_001012503	exon1	c.G359A	p.C120Y	AGCCCTGCTGCTG	.	scavenged	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	6	34	0	0.206897	0	.	.	none	.	FAM83D	60	.	NM_030919	exon1	c.C100G	p.L34V	GCTCTGCTGTCCG	.	PASS	Atlas-SNP
ZNF563	147837	hgsc.bcm.edu	37	19	12430265	12430265	+	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	162	2	150	0	0.0123457	0	.	.	none	ZNF563,NS,carcinoma,0,1	ZNF563	77	1	NM_145276	exon4	c.G574A	p.G192S	TTCCACCTTGCAC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152284305	152284305	+	Silent	SNP	C	C	T	rs145495264	bycluster	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	316	6	270	1	0.0189873	0.0037037	C|0.999;T|0.001	0.001	weak	FLG,NS,carcinoma,-1,3	FLG	900	3	NM_002016	exon3	c.G3057A	p.A1019A	GGATGACGCAGCC	.	scavenged	Atlas-SNP
DDX11	1663	hgsc.bcm.edu	37	12	31250830	31250830	+	Missense_Mutation	SNP	C	C	G	rs2911826	bycluster	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	11	203	6	0.05	0.0295567	.	.	weak	DDX11,extremity,malignant_melanoma,0,1	DDX11	188	1	NM_030653	exon18	c.C1774G	p.Q592E	CTCAGTCAGAGCA	.	scavenged	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	6	85	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	4	142	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
GTF3C3	9330	hgsc.bcm.edu	37	2	197657782	197657782	+	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	269	8	212	0	0.0297398	0	.	.	none	GTF3C3,NS,carcinoma,0,3	GTF3C3	96	3	NM_001206774	exon3	c.G309A	p.E103E	CTCCTCCTCTTCT	.	scavenged	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	5	92	0	0.0485437	0	.	.	none	.	MCMDC2	84	.	NM_173518	exon9	c.A993G	p.V331V	TCTAGTACAGACA	.	PASS	Atlas-SNP
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261693	39261693	+	Missense_Mutation	SNP	A	A	T	rs113059833	bycluster	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	75	8	51	1	0.106667	0.0196078	T|1.000;|0.000	1.000	weak	KRTAP4-9,NS,carcinoma,0,6	KRTAP4-9	110	6	NM_001146041	exon1	c.A53T	p.D18V	GCCAAGACCTCTG	.	scavenged	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	22	98	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	58	195	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	4	110	0	0.0449438	0	.	.	none	.	NTPCR	15	.	NM_032324	exon5	c.C552T	p.C184C	GACGTGCGTGCAG	.	PASS	Atlas-SNP
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240781	39240781	+	Missense_Mutation	SNP	C	C	G	rs372960430	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	36	4	42	1	0.111111	0.0238095	.	.	alt	KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-7	49	2	NM_033061	exon1	c.C323G	p.T108S	AGCCCACCTGCTG	.	scavenged	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	41	143	0	0.231638	0	.	.	none	.	RBMS3	62	.	NM_001177712	exon10	c.927+1G>T	.	TACCAGGTATGTC	.	PASS	Atlas-SNP
ASXL3	80816	hgsc.bcm.edu	37	18	31319710	31319710	+	Missense_Mutation	SNP	C	C	T	rs201776257	bycluster	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	66	2	83	0	0.030303	0	.	.	weak	ASXL3_ENST00000269197,right_lower_lobe,carcinoma,+1,2	ASXL3	405	2	NM_030632	exon11	c.C2342T	p.P781L	TCTCCCCGCAGAA	.	scavenged	Atlas-SNP
FAM8A1	51439	hgsc.bcm.edu	37	6	17602826	17602826	+	Nonsense_Mutation	SNP	G	G	T	rs74444948	bycluster;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	53	9	58	5	0.169811	0.0862069	G|0.992;T|0.008	0.008	strong	FAM8A1,NS,carcinoma,-1,2	FAM8A1	26	2	NM_016255	exon2	c.G718T	p.E240X	GGCAGAGAATATG	.	scavenged	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	51	181	0	0.221739	0	.	.	none	.	SP140	121	.	NM_007237	exon3	c.T300G	p.S100R	ACTCAGTGAACTG	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	37	19	54721049	54721049	+	Silent	SNP	A	A	G	rs60566950	bycluster;byfrequency;by1000genomes	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	336	4	354	0	0.0119048	0	A|0.980;G|0.020	0.020	strong	LILRB3,NS,carcinoma,0,1	LILRB3	67	1	NM_001081450	exon13	c.T1812C	p.L604L	CCGTCTAAGGGTC	.	scavenged	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	13	57	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	11	155	0	0.139241	0	.	.	none	.	SOX15	10	.	NM_006942	exon1	c.G309A	p.K103K	GAGCCGCTTGGCC	.	PASS	Atlas-SNP
FAM8A1	51439	hgsc.bcm.edu	37	6	17606159	17606159	+	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	215	3	218	1	0.0139535	0.00458716	.	.	none	FAM8A1,colon,carcinoma,-1,1	FAM8A1	26	1	NM_016255	exon4	c.C1012A	p.L338I	CTGGGGCTTCGAG	.	scavenged	Atlas-SNP
ASPN	54829	hgsc.bcm.edu	37	9	95237027	95237027	+	Missense_Mutation	SNP	A	A	C	rs200538582	bycluster	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	5	38	0	0.0769231	0	.	.	weak	ASPN,caecum,carcinoma,0,1	ASPN	52	1	NM_001193335	exon2	c.T153G	p.D51E	GTCCTCATCATCA	.	scavenged	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733214	52733214	+	Missense_Mutation	SNP	A	A	C	rs200377849		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	235	6	266	2	0.0255319	0.0075188	.	.	weak	PCMTD1,trunk,malignant_melanoma,0,1	PCMTD1	73	1	NM_052937	exon6	c.T771G	p.N257K	TATGAAATTTCTA	.	scavenged	Atlas-SNP
MTR	4548	hgsc.bcm.edu	37	1	237057789	237057789	+	Missense_Mutation	SNP	G	G	A	rs146071220	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	81	3	93	0	0.037037	0	G|0.997;A|0.003	0.003	strong	MTR,NS,carcinoma,-1,1	MTR	127	1	NM_000254	exon30	c.G3337A	p.A1113T	AGCAAGGCCTATG	.	scavenged	Atlas-SNP
OR2L2	26246	hgsc.bcm.edu	37	1	248201941	248201941	+	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	218	3	188	0	0.0137615	0	.	.	none	OR2L2,NS,carcinoma,+1,1	OR2L2	115	1	NM_001004686	exon1	c.C372T	p.A124A	TGTGGCCATTTGC	.	scavenged	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	15	52	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	5	94	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	18	130	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	3	99	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
DIDO1	11083	hgsc.bcm.edu	37	20	61511760	61511760	+	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	95	2	96	0	0.0210526	0	.	.	none	DIDO1,NS,carcinoma,0,2	DIDO1	321	2	NM_001193369	exon16	c.G5548A	p.G1850R	TCTCCCCATGGGG	.	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	31	130	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	27	174	0	0.177632	0	.	.	none	.	KLHL6	100	.	NM_130446	exon7	c.G1639C	p.E547Q	CCCGCTCGTGGCT	.	PASS	Atlas-SNP
PRAMEF1	65121	hgsc.bcm.edu	37	1	12854401	12854401	+	Nonsense_Mutation	SNP	G	G	T	rs78584260	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	458	37	501	29	0.080786	0.0578842	G|0.500;C|0.500	.	alt	PRAMEF1,NS,carcinoma,0,2	PRAMEF1	78	2	NM_023013	exon3	c.G625T	p.E209X	ATTCAAGAGCTGG	.	scavenged	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	31	142	0	0.15736	0	.	.	none	.	CHD8	339	.	NM_001170629	exon19	c.G3977A	p.C1326Y	TCTTCACAAAACT	.	PASS	Atlas-SNP
NBPF15	284565	hgsc.bcm.edu	37	1	148594563	148594563	+	Missense_Mutation	SNP	G	G	T	rs146229961	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	538	44	472	45	0.0817844	0.095339	G|0.996;T|0.005	0.005	strong	NBPF15,brain,glioma,0,1	NBPF15	20	1	NM_173638	exon19	c.G1936T	p.V646L	CTTTACGTGGACA	.	scavenged	Atlas-SNP
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	4	57	0	0.0615385	0	.	.	none	ZNF572,colon,carcinoma,+1,1	ZNF572	82	1	NM_152412	exon3	c.A1212G	p.R404R	TCAGAGAACACAT	.	PASS	Atlas-SNP
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324333	39324333	+	Missense_Mutation	SNP	T	T	A	rs12953139	bycluster;byfrequency	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	197	41	142	1	0.208122	0.00704225	A|0.046;T|0.954	0.046	strong	KRTAP4-3,NS,carcinoma,0,1	KRTAP4-3	40	1	NM_033187	exon1	c.A92T	p.Q31L	GTGGTCTGGCAGC	.	scavenged	Atlas-SNP
SP140	11262	hgsc.bcm.edu	37	2	231157487	231157487	+	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	117	19	113	20	0.162393	0.176991	.	.	none	SP140_ENST00000392045,NS,carcinoma,+1,1	SP140	121	1	NM_007237	exon20	c.T1952C	p.L651P	GGCCCCTACGATG	.	scavenged	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	22	89	0	0.207547	0	.	.	none	.	SULF1	153	.	NM_001128205	exon9	c.G868A	p.D290N	TCAGTGGATGATT	.	PASS	Atlas-SNP
VMP1	81671	hgsc.bcm.edu	37	17	57915717	57915717	+	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	226	3	228	0	0.0132743	0	.	.	none	VMP1,caecum,carcinoma,0,1	VMP1	49	1	NM_030938	exon11	c.C1036T	p.R346W	GCTCAACGGCAGA	.	scavenged	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	95	460	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	20	73	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	41	187	0	0.267974	0	.	.	alt	.	COASY	45	.	NM_001042532	exon4	c.G965A	p.R322H	CCTATCGTGGGGG	.	PASS	Atlas-SNP
SEMG1	6406	hgsc.bcm.edu	37	20	43837052	43837052	+	Missense_Mutation	SNP	C	C	A	rs199672858	by1000genomes;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	158	3	111	0	0.0189873	0	C|1.000;T|0.000	.	alt	SEMG1,bladder,carcinoma,0,3	SEMG1	71	3	NM_003007	exon2	c.C1114A	p.R372S	TCCCAACGCAGTA	.	scavenged	Atlas-SNP
HNRNPH1	3187	hgsc.bcm.edu	37	5	179044053	179044053	+	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	399	7	383	3	0.0175439	0.0078329	.	.	none	HNRPH1,NS,carcinoma,-2,3	HNRNPH1	62	3	NM_001257293	exon10	c.C1116T	p.Y372Y	GCTACCGTAAGCA	.	scavenged	Atlas-SNP
RBBP8NL	140893	hgsc.bcm.edu	37	20	60992303	60992303	+	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	99	3	174	0	0.030303	0	.	.	none	C20orf151,NS,carcinoma,0,1	.	.	1	NM_080833	exon4	c.G177A	p.E59E	CAGGTTCTCCTTC	.	scavenged	Atlas-SNP
ASNSD1	54529	hgsc.bcm.edu	37	2	190532027	190532027	+	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	105	3	70	0	0.0285714	0	.	.	none	ASNSD1,rectum,carcinoma,+1,1	ASNSD1	63	1	NM_019048	exon4	c.C1169T	p.A390V	ATGTTGCTGCTGC	.	scavenged	Atlas-SNP
OR51A2	401667	hgsc.bcm.edu	37	11	4976656	4976656	+	Silent	SNP	A	A	G	rs3986370		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	278	4	234	1	0.0143885	0.0042735	.	.	weak	OR51A2,NS,carcinoma,-1,1	OR51A2	40	1	NM_001004748	exon1	c.T288C	p.S96S	GGCACTAGAAGAA	.	scavenged	Atlas-SNP
CNTNAP5	129684	hgsc.bcm.edu	37	2	125555738	125555738	+	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	179	3	194	0	0.0167598	0	.	.	none	CNTNAP5,NS,carcinoma,-2,1	CNTNAP5	405	1	NM_130773	exon19	c.A3055G	p.T1019A	CCTGTGACCAAGA	.	scavenged	Atlas-SNP
ALDH3B2	222	hgsc.bcm.edu	37	11	67432799	67432799	+	Silent	SNP	G	G	A	rs80147122	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	243	3	277	2	0.0123457	0.00722022	.	.	strong	ALDH3B2,NS,haematopoietic_neoplasm,0,2	ALDH3B2	46	2	NM_001031615	exon7	c.C663T	p.R221R	GGCCACGCGGCTG	.	scavenged	Atlas-SNP
PCMTD1	115294	hgsc.bcm.edu	37	8	52733209	52733209	+	Missense_Mutation	SNP	A	A	G	rs202074278		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	245	8	274	2	0.0326531	0.00729927	.	.	weak	PCMTD1,NS,carcinoma,0,2	PCMTD1	73	2	NM_052937	exon6	c.T776C	p.I259T	TCATTTATGAAAT	.	scavenged	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	4	101	0	0.0434783	0	.	.	none	.	TOR1AIP1	58	.	NM_001267578	exon1	c.C385T	p.R129C	ACTACCCGCCTTC	.	PASS	Atlas-SNP
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519094	113519094	+	Missense_Mutation	SNP	C	C	T	rs199968105		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	347	4	285	1	0.0115274	0.00350877	C|0.999;T|0.001	0.001	weak	PPP1R3A,right_upper_lobe,carcinoma,+2,1	PPP1R3A	317	1	NM_002711	exon4	c.G2053A	p.V685M	CCCACACGTCTTC	.	scavenged	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	68	344	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	27	115	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	51	205	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	27	96	1	0.221311	0.0104167	.	.	none	EPHA6,NS,carcinoma,+1,1	EPHA6	439	1	NM_001080448	exon11	c.G2297A	p.R766Q	TGGATCGGCAAAG	.	scavenged	Atlas-SNP
DNER	92737	hgsc.bcm.edu	37	2	230253013	230253013	+	Missense_Mutation	SNP	G	G	A	rs368405241	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	81	3	80	0	0.037037	0	.	.	alt	DNER,NS,carcinoma,0,1	DNER	129	1	NM_139072	exon11	c.C1823T	p.P608L	CCATGCGGGCAGT	.	scavenged	Atlas-SNP
FRAS1	80144	hgsc.bcm.edu	37	4	79188493	79188493	+	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	320	4	255	0	0.0125	0	.	.	none	FRAS1_ENST00000325942,pharynx,carcinoma,+2,2	FRAS1	779	2	NM_001166133	exon9	c.A888G	p.E296E	GGACGAAATGTGG	.	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	28	113	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	48	136	0	0.324324	0	.	.	none	.	LTBP1	317	.	NM_206943	exon32	c.G4743C	p.V1581V	CCCCGTGACGGGA	.	PASS	Atlas-SNP
RPLP2	6181	hgsc.bcm.edu	37	11	812762	812762	+	Nonsense_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	100	2	150	1	0.02	0.00666667	.	.	none	RPLP2,NS,carcinoma,0,1	RPLP2	2	1	NM_001004	exon5	c.G274T	p.E92X	ACAGCAGAGGAGA	.	scavenged	Atlas-SNP
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921277	12921277	+	Silent	SNP	A	A	G	rs3204826	bycluster;byfrequency	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	440	8	416	4	0.0181818	0.00961538	A|0.996;G|0.004	0.004	strong	PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	NM_023014	exon4	c.A1068G	p.L356L	CGTGTTAGAGGGC	.	scavenged	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195509606	195509606	+	Missense_Mutation	SNP	C	C	T	rs79543693	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	215	7	289	14	0.0325581	0.0484429	C|0.625;T|0.375	0.375	strong	MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	NM_018406	exon2	c.G8845A	p.D2949N	AAGTGTCGGTGAC	.	scavenged	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	11	92	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	24	118	1	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
GPRIN2	9721	hgsc.bcm.edu	37	10	46999601	46999601	+	Missense_Mutation	SNP	G	G	A	rs9422022	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	88	10	91	0	0.113636	0	G|0.638;A|0.362	0.362	strong	GPRIN2,caecum,adenoma,0,1	GPRIN2	94	1	NM_014696	exon3	c.G721A	p.V241M	AGGGAGGTGAGGG	.	PASS	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	14	354	0	0.042042	0	.	.	none	.	ZBTB2	30	.	NM_020861	exon3	c.G1109A	p.R370H	AATTTGCGTCCAC	.	PASS	Atlas-SNP
APMAP	57136	hgsc.bcm.edu	37	20	24954343	24954343	+	Missense_Mutation	SNP	C	C	T	rs115779992	bycluster;byfrequency;by1000genomes;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	103	2	94	0	0.0194175	0	C|0.997;A|0.003	.	alt	C20orf3,trunk,malignant_melanoma,-1,1	APMAP	3	1	NM_020531	exon4	c.G359A	p.R120Q	ACGACCCGGCCAT	.	scavenged	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44892153	44892153	+	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	199	6	205	4	0.0301508	0.0195122	.	.	none	ZNF285,NS,carcinoma,0,1	ZNF285	86	1	NM_152354	exon4	c.C254G	p.T85S	CTCACAGTTAAAT	.	scavenged	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	27	167	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
CSMD3	114788	hgsc.bcm.edu	37	8	113316986	113316986	+	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	161	2	126	0	0.0124224	0	.	.	none	CSMD3_ENST00000343508,right_lower_lobe,carcinoma,+2,2	CSMD3	2325	2	NM_198123	exon52	c.A8230G	p.T2744A	TCCAAGTACCATT	.	scavenged	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	37	162	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	25	85	0	0.168919	0	.	.	none	.	ANK2	576	.	NM_001148	exon45	c.T11719G	p.Y3907D	AGGCGGTATGTAT	.	PASS	Atlas-SNP
FAM209B	388799	hgsc.bcm.edu	37	20	55108530	55108530	+	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	223	3	287	0	0.0134529	0	.	.	none	C20orf107,NS,carcinoma,-1,1	.	.	1	NM_001013646	exon1	c.C133T	p.R45W	CGGATTCGGCAGA	.	scavenged	Atlas-SNP
ALKBH1	8846	hgsc.bcm.edu	37	14	78140406	78140406	+	Missense_Mutation	SNP	C	C	T	rs370329463		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	2	114	0	0.0169492	0	.	.	weak	ALKBH1,NS,carcinoma,0,1	ALKBH1	30	1	NM_006020	exon6	c.G919A	p.A307T	GAGGTGCCTCTAG	.	scavenged	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	10	47	0	0.277778	0	.	.	none	ADM2,rectum,carcinoma,0,2	ADM2	15	2	NM_024866	exon2	c.A279C	p.R93R	CCCCCGAAGACAC	.	PASS	Atlas-SNP
SLC35G6	643664	hgsc.bcm.edu	37	17	7386272	7386272	+	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	141	3	151	1	0.0212766	0.00662252	.	.	none	POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	NM_001102614	exon2	c.C969T	p.I323I	CATCATCACAGCC	.	scavenged	Atlas-SNP
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779		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	406	39	358	30	0.0960591	0.0837989	.	.	weak	FLG,NS,malignant_melanoma,+1,1	FLG	900	1	NM_002016	exon3	c.T6671A	p.L2224Q	CCCACCAGTGAGT	.	scavenged	Atlas-SNP
MADCAM1	8174	hgsc.bcm.edu	37	19	501802	501802	+	Missense_Mutation	SNP	G	G	C	rs75905809	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	81	30	146	39	0.37037	0.267123	G|0.500;C|0.500	0.500	weak	MADCAM1,rectum,carcinoma,+1,1	MADCAM1	29	1	NM_130760	exon4	c.G801C	p.K267N	CGACAAGACCTCC	.	scavenged	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891043	44891043	+	Missense_Mutation	SNP	G	G	T	rs77661661	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	132	4	103	2	0.030303	0.0194175	.	.	weak	ZNF285,trunk,malignant_melanoma,0,1	ZNF285	86	1	NM_152354	exon4	c.C1364A	p.P455Q	TTGTATGGTTTCT	.	scavenged	Atlas-SNP
PCDHB2	56133	hgsc.bcm.edu	37	5	140476396	140476396	+	Silent	SNP	G	G	T	rs429198	bycluster;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	19	5	31	4	0.263158	0.129032	G|0.895;T|0.105	0.105	strong	PCDHB2,NS,carcinoma,+1,1	PCDHB2	163	1	NM_018936	exon1	c.G2022T	p.L674L	CCTGCTGCTCCCG	.	scavenged	Atlas-SNP
SEMG2	6407	hgsc.bcm.edu	37	20	43851631	43851631	+	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	131	2	92	1	0.0152672	0.0108696	.	.	none	SEMG2,NS,carcinoma,0,1	SEMG2	92	1	NM_003008	exon2	c.C1358A	p.P453H	CAATTCCTAGTCA	.	scavenged	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	5	131	0	0.045045	0	.	.	none	.	ZFAT	265	.	NM_020863	exon6	c.C2057T	p.P686L	ACTGGAGGGAGGA	.	PASS	Atlas-SNP
MKI67	4288	hgsc.bcm.edu	37	10	129906293	129906293	+	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	274	4	218	1	0.0145985	0.00458716	.	.	none	MKI67,NS,carcinoma,+1,1	MKI67	363	1	NM_002417	exon13	c.A3811G	p.R1271G	TACTTCTCTTGGG	.	scavenged	Atlas-SNP
KLF10	7071	hgsc.bcm.edu	37	8	103664424	103664424	+	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	89	2	78	0	0.0224719	0	.	.	none	KLF10,NS,carcinoma,+2,1	KLF10	44	1	NM_005655	exon2	c.G238A	p.G80R	GTGTTCCCGGAAG	.	scavenged	Atlas-SNP
FAM98B	283742	hgsc.bcm.edu	37	15	38776833	38776833	+	Silent	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	74	2	61	1	0.027027	0.0163934	.	.	none	FAM98B_ENST00000397609,NS,carcinoma,0,2	FAM98B	53	2	NM_173611	exon8	c.T1275A	p.G425G	TGGTGGTGGAGGA	.	scavenged	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	47	160	0	0.264045	0	.	.	none	.	MYH11	520	.	NM_001040114	exon5	c.C534T	p.G178G	AGACTCGCCTCTG	.	PASS	Atlas-SNP
GBA2	57704	hgsc.bcm.edu	37	9	35739047	35739047	+	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	148	2	132	0	0.0135135	0	.	.	none	GBA2,colon,carcinoma,0,1	GBA2	77	1	NM_020944	exon11	c.G1747A	p.A583T	CAGGTGCCATCAC	.	scavenged	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	7	61	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	26	88	1	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	51	127	0	0.504951	0	.	.	none	.	ZBTB12	25	.	NM_181842	exon2	c.C385T	p.P129S	TTTTGGGCTCAAT	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	37	11	1258241	1258241	+	Silent	SNP	A	A	G	rs79773885	bycluster	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	7	53	2	0.145833	0.0377358	A|0.500;G|0.500	0.500	weak	MUC5B,NS,carcinoma,+2,2	MUC5B	473	2	NM_002458	exon25	c.A3144G	p.A1048A	GGACGCACTGGAG	.	scavenged	Atlas-SNP
SSFA2	6744	hgsc.bcm.edu	37	2	182792918	182792918	+	Missense_Mutation	SNP	C	C	T	rs201351475	bycluster	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	258	3	224	0	0.0116279	0	.	.	weak	SSFA2_ENST00000431877,colon,carcinoma,-1,1	SSFA2	130	1	NM_001130445	exon17	c.C3706T	p.R1236W	ATCAGACGGGAAA	.	scavenged	Atlas-SNP
CRIPAK	285464	hgsc.bcm.edu	37	4	1388697	1388697	+	Missense_Mutation	SNP	C	C	T	rs113316888	bycluster	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	32	10	59	8	0.3125	0.135593	C|0.500;T|0.500	0.500	weak	CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	NM_175918	exon1	c.C398T	p.A133V	CCCATGCGGAGTG	.	scavenged	Atlas-SNP
JAKMIP2	9832	hgsc.bcm.edu	37	5	146997574	146997574	+	Missense_Mutation	SNP	G	G	A	rs181696687	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	229	5	228	0	0.0218341	0	G|1.000;A|0.000	0.000	strong	JAKMIP2,colon,carcinoma,0,1	JAKMIP2	154	1	NM_001270941	exon19	c.C2246T	p.T749M	ACTGCCGTCCTCA	.	scavenged	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	26	169	0	0.154762	0	.	.	none	.	MTUS2	279	.	NM_001033602	exon8	c.C3387T	p.H1129H	GGAGCACGGTGAC	.	PASS	Atlas-SNP
SUV420H1	51111	hgsc.bcm.edu	37	11	67925541	67925541	+	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	186	2	186	0	0.0107527	0	.	.	none	SUV420H1,NS,carcinoma,0,1	SUV420H1	125	1	NM_017635	exon11	c.T2272C	p.Y758H	CTACATAGAGATT	.	scavenged	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	104	252	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	61	138	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	15	58	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	7	25	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	26	121	0	0.172185	0	.	.	none	.	SYT14	89	.	NM_001146261	exon10	c.G1740C	p.M580I	AGAGATGATAGGC	.	PASS	Atlas-SNP
CDC37	11140	hgsc.bcm.edu	37	19	10506866	10506866	+	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	286	3	360	2	0.0104895	0.00555556	.	.	none	CDC37,NS,carcinoma,-1,1	CDC37	32	1	NM_007065	exon2	c.G116A	p.R39H	TCCATGCGTTCCA	.	scavenged	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	16	61	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	10	31	0	0.243902	0	.	.	none	.	.	.	.	NM_001029870	exon1	c.G63A	p.V21V	GTTGGTCACGCGG	.	PASS	Atlas-SNP
PEX6	5190	hgsc.bcm.edu	37	6	42946490	42946490	+	Silent	SNP	C	C	A	rs9462858	bycluster;byfrequency;by2hit2allele;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	4	4	0	0	1	.	C|0.673;A|0.327	0.327	strong	.	PEX6	44	.	NM_000287	exon1	c.G399T	p.V133V	TCCGGGCACTGGG	.	PASS	Atlas-SNP
FAM111B	374393	hgsc.bcm.edu	37	11	58891900	58891900	+	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	52	2	30	0	0.0384615	0	.	.	none	FAM111B,colon,carcinoma,+2,1	FAM111B	84	1	NM_198947	exon4	c.C330T	p.A110A	CTCAGCCCTGAGT	.	scavenged	Atlas-SNP
IZUMO3	100129669	hgsc.bcm.edu	37	9	24545513	24545513	+	Silent	SNP	G	G	A	rs6475797	bycluster;byfrequency;by2hit2allele;byhapmap;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	8	8	0	0	1	.	G|0.259;A|0.740	0.740	strong	.	.	.	.	NM_001271706	exon1	c.C135T	p.P45P	TCGGCCGGGGACT	.	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	35	144	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	12	101	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	4	83	0	0.0430108	0	.	.	none	.	EPHA3	501	.	NM_005233	exon5	c.C1017T	p.T339T	CGAGACCTCAGTT	.	PASS	Atlas-SNP
PSPH	5723	hgsc.bcm.edu	37	7	56085002	56085002	+	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	488	6	464	2	0.0122951	0.00431034	.	.	none	PSPH,NS,carcinoma,0,2	PSPH	23	2	NM_004577	exon6	c.G346A	p.V116I	GCTCTACAATACT	.	scavenged	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	4	67	0	0.0434783	0	.	.	none	.	LMO7	334	.	NM_015842	exon7	c.G649A	p.E217K	GACCTCGAGATGG	.	PASS	Atlas-SNP
MTERFD2	130916	hgsc.bcm.edu	37	2	242035741	242035741	+	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	149	2	157	0	0.0134228	0	.	.	none	MTERFD2,NS,carcinoma,-1,1	MTERFD2	33	1	NM_182501	exon4	c.G818A	p.R273Q	TGGTACCGTCCCA	.	scavenged	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	15	71	0	0.185185	0	.	.	none	.	TMSB4X	3	.	NM_021109	exon3	c.G117C	p.K39N	GGAGAAGCAAGCA	.	PASS	Atlas-SNP
