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
TPRX1	284355	hgsc.bcm.edu	37	19	48305613	48305624	+	In_Frame_Del	DEL	TTGGGCCTGAGA	TTGGGCCTGAGA	-	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	TTGGGCCTGAGA	TTGGGCCTGAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	39.0	11.0	32.0	0.0	0.282051	0	.	.	none	TPRX1,NS,carcinoma,0,1	TPRX1	46	1	NM_198479	exon2	c.645_656del	p.215_219del	.	.	PASS	Atlas-Indel
DSPP	1834	hgsc.bcm.edu	37	4	88537205	88537213	+	In_Frame_Del	DEL	GACAGCAGT	GACAGCAGT	-	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	GACAGCAGT	GACAGCAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	57.0	30.0	107.0	0.0	0.526316	0	.	.	none	.	DSPP	174	.	NM_014208	exon5	c.3390_3398del	p.1130_1133del	.	.	PASS	Atlas-Indel
DUSP27	92235	hgsc.bcm.edu	37	1	167095865	167095865	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	186.0	48.0	155.0	0.0	0.258	.	.	.	none	.	DUSP27	235	.	NM_001080426	exon5	c.1496delG	p.S499fs	.	.	PASS	Pindel,Atlas-Indel
BTG1	694	hgsc.bcm.edu	37	12	92539174	92539180	+	Frame_Shift_Del	DEL	CTCCTGC	CTCCTGC	-	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	CTCCTGC	CTCCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	110.0	25.0	110.0	0.0	0.227	.	.	.	none	.	BTG1	30	.	NM_001731	exon1	c.133_139del	p.45_47del	.	.	PASS	Pindel,Atlas-Indel
MLL2	8085	hgsc.bcm.edu	37	12	49445046	49445047	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	286.0	172.0	125.0	0.0	0.601399	0	.	.	none	.	MLL2	1173	.	NM_003482	exon10	c.2420_2421insT	p.S807fs	.	.	PASS	Atlas-Indel
KIAA0125	9834	hgsc.bcm.edu	37	14	106388019	106388094	+	RNA	DEL	CCAGACCATCAGATGGCCTCCTCACCTACCCCTCTTCAGACAGGGCCTCAGACCTAAGGCAGGAGCACCCCCTATG	CCAGACCATCAGATGGCCTCCTCACCTACCCCTCTTCAGACAGGGCCTCAGACCTAAGGCAGGAGCACCCCCTATG	-	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	CCAGACCATCAGATGGCCTCCTCACCTACCCCTCTTCAGACAGGGCCTCAGACCTAAGGCAGGAGCACCCCCTATG	CCAGACCATCAGATGGCCTCCTCACCTACCCCTCTTCAGACAGGGCCTCAGACCTAAGGCAGGAGCACCCCCTATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	28.0	17.0	109.0	0.0	0.607	.	.	.	none	.	.	.	.	.	.	.	.	.	.	PASS	Pindel
MLL2	8085	hgsc.bcm.edu	37	12	49445040	49445041	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	286.0	80.0	126.0	0.0	0.280	.	.	.	none	.	MLL2	1173	.	NM_003482	exon10	c.2426_2427insC	p.Q809fs	.	.	PASS	Pindel
ELFN1	392617	hgsc.bcm.edu	37	7	1785563	1785563	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	48.0	19.0	31.0	0.0	0.395833	0	.	.	none	.	ELFN1	22	.	NM_001128636	exon2	c.G1331A	p.R444Q	GGCGGCGGCGCCA	.	PASS	Atlas-SNP
ATPBD4	89978	hgsc.bcm.edu	37	15	35830516	35830516	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	163.0	127.0	283.0	0.0	0.779141	0	.	.	none	.	ATPBD4	30	.	NM_001141972	exon3	c.G271A	p.D91N	CCTCATCACCTTC	.	PASS	Atlas-SNP
CCP110	9738	hgsc.bcm.edu	37	16	19556216	19556216	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	405.0	159.0	195.0	0.0	0.392593	0	.	.	none	.	CCP110	57	.	NM_001199022	exon9	c.C2582T	p.A861V	TGTTAGCTCAGGT	.	PASS	Atlas-SNP
MLXIP	22877	hgsc.bcm.edu	37	12	122516989	122516989	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	38.0	17.0	32.0	0.0	0.447368	0	.	.	none	.	MLXIP	46	.	NM_014938	exon1	c.T230C	p.I77T	AGATCATCCACAG	.	PASS	Atlas-SNP
DTX1	1840	hgsc.bcm.edu	37	12	113496135	113496135	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	93.0	38.0	111.0	0.0	0.408602	0	.	.	none	.	DTX1	83	.	NM_004416	exon1	c.C138T	p.H46H	GTGCCACCACATT	.	PASS	Atlas-SNP
NLRP6	171389	hgsc.bcm.edu	37	11	279844	279844	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	42.0	7.0	38.0	0.0	0.166667	0	.	.	none	.	NLRP6	4	.	NM_138329	exon3	c.C321T	p.L107L	CGGGCTCGGCTCC	.	PASS	Atlas-SNP
PMEPA1	56937	hgsc.bcm.edu	37	20	56227142	56227142	+	Silent	SNP	T	T	C	rs138355480		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	115.0	6.0	95.0	0.0	0.0521739	0	T|1.000;C|0.000	0.000	weak	.	PMEPA1	29	.	NM_020182	exon4	c.A831G	p.K277K	CTTCTCTTTGCTC	.	PASS	Atlas-SNP
OR10G7	390265	hgsc.bcm.edu	37	11	123909644	123909644	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	341.0	68.0	236.0	0.0	0.199413	0	.	.	none	OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	NM_001004463	exon1	c.A65G	p.D22G	GGGGCGTCCAGCC	.	PASS	Atlas-SNP
RTBDN	83546	hgsc.bcm.edu	37	19	12936596	12936596	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	131.0	53.0	123.0	0.0	0.40458	0	.	.	none	.	RTBDN	26	.	NM_031429	exon7	c.G710A	p.R237H	CGGGAACGCCGGG	.	PASS	Atlas-SNP
TFG	10342	hgsc.bcm.edu	37	3	100467168	100467168	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	165.0	62.0	143.0	0.0	0.375758	0	.	.	none	.	TFG	42	.	NM_006070	exon8	c.A996T	p.Q332H	TGCCCAAACTTCT	.	PASS	Atlas-SNP
ABCC1	4363	hgsc.bcm.edu	37	16	16162160	16162160	+	Splice_Site	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	159.0	102.0	108.0	0.0	0.641509	0	.	.	none	.	ABCC1	156	.	NM_004996	exon13	c.1824+1G>A	.	GTGCAGGTACAGG	.	PASS	Atlas-SNP
HOXC13	3229	hgsc.bcm.edu	37	12	54333307	54333307	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	57.0	11.0	43.0	0.0	0.192982	0	.	.	none	.	HOXC13	24	.	NM_017410	exon1	c.A617G	p.D206G	GTCACGACGCCCT	.	PASS	Atlas-SNP
WNT5A	7474	hgsc.bcm.edu	37	3	55508445	55508445	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	172.0	86.0	149.0	2.0	0.5	0.0134228	.	.	none	WNT5A,NS,carcinoma,+1,1	WNT5A	43	1	NM_003392	exon4	c.C604T	p.R202W	GCTCCCGCTCGCG	.	scavenged	Atlas-SNP
EXOG	9941	hgsc.bcm.edu	37	3	38537954	38537954	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	98.0	50.0	61.0	0.0	0.510204	0	.	.	none	.	EXOG	29	.	NM_005107	exon1	c.G96A	p.G32G	AGCTGGGCTCGCG	.	PASS	Atlas-SNP
KRTAP2-4	85294	hgsc.bcm.edu	37	17	39221736	39221736	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	53.0	22.0	61.0	0.0	0.415094	0	.	.	none	.	KRTAP2-4	2	.	NM_033184	exon1	c.C362T	p.T121I	CAGGTGGTGCTGC	.	PASS	Atlas-SNP
BCAP29	55973	hgsc.bcm.edu	37	7	107221236	107221236	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	123.0	42.0	113.0	0.0	0.341463	0	.	.	none	.	BCAP29	46	.	NM_018844	exon2	c.G19A	p.A7T	TGGGCTGCAGTGG	.	PASS	Atlas-SNP
AADAC	13	hgsc.bcm.edu	37	3	151542519	151542519	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	123.0	5.0	103.0	0.0	0.0406504	0	.	.	none	.	AADAC	49	.	NM_001086	exon4	c.T500C	p.F167S	GGTGGTTCTTACG	.	PASS	Atlas-SNP
NAV1	89796	hgsc.bcm.edu	37	1	201779198	201779198	+	Missense_Mutation	SNP	G	G	A	rs201416032	bycluster	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	164.0	10.0	122.0	0.0	0.0609756	0	G|0.999;A|0.001	0.001	weak	NAV1,right_upper_lobe,carcinoma,0,2	NAV1	143	2	NM_020443	exon23	c.G4526A	p.R1509H	CTTGCCGTCGAGG	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66423409	66423409	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	82.0	5.0	129.0	0.0	0.0609756	0	.	.	none	.	CDH5	111	.	NM_001795	exon5	c.C765T	p.F255F	CAACTTCCCCTTC	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891202	44891202	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	52.0	4.0	53.0	1.0	0.0769231	0.0188679	.	.	none	ZNF285,NS,carcinoma,0,2	ZNF285	86	2	NM_152354	exon4	c.G1205C	p.C402S	TCACTGCATTTGT	.	scavenged	Atlas-SNP
KCNQ3	3786	hgsc.bcm.edu	37	8	133186530	133186530	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	150.0	45.0	94.0	0.0	0.3	0	.	.	none	.	KCNQ3	164	.	NM_004519	exon6	c.G1000A	p.A334T	AGGTGGCGGCAAT	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	37	8	3141793	3141793	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	64.0	22.0	51.0	0.0	0.34375	0	.	.	none	.	CSMD1	1469	.	NM_033225	exon26	c.C4026T	p.D1342D	CAGGATGTCACTG	.	PASS	Atlas-SNP
ALDH9A1	223	hgsc.bcm.edu	37	1	165652258	165652258	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	92.0	4.0	64.0	0.0	0.0434783	0	.	.	none	.	ALDH9A1	75	.	NM_000696	exon3	c.G417A	p.Q139Q	CAGGCACTGCCAG	.	PASS	Atlas-SNP
NQO1	1728	hgsc.bcm.edu	37	16	69745172	69745172	+	Missense_Mutation	SNP	G	G	A	rs148539025	bycluster	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	86.0	4.0	76.0	0.0	0.0465116	0	G|1.000;A|0.000	0.000	weak	.	NQO1	21	.	NM_000903	exon6	c.C532T	p.H178Y	AGAAATGCAGAAT	.	PASS	Atlas-SNP
RAPGEF3	10411	hgsc.bcm.edu	37	12	48144895	48144895	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	184.0	42.0	91.0	0.0	0.228261	0	.	.	none	.	RAPGEF3	98	.	NM_001098531	exon6	c.G607A	p.E203K	CAGCTTCGGCCAA	.	PASS	Atlas-SNP
C6	729	hgsc.bcm.edu	37	5	41199992	41199992	+	Missense_Mutation	SNP	C	C	T	rs200213547	bycluster	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	144.0	64.0	95.0	0.0	0.444444	0	.	.	weak	.	C6	197	.	NM_001115131	exon4	c.G323A	p.R108H	CTGGGACGCAAGA	.	PASS	Atlas-SNP
WFDC9	259240	hgsc.bcm.edu	37	20	44238795	44238795	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	120.0	54.0	131.0	0.0	0.45	0	.	.	none	.	WFDC9	10	.	NM_147198	exon3	c.T26C	p.V9A	AACATGACGAGTA	.	PASS	Atlas-SNP
SUPT6H	6830	hgsc.bcm.edu	37	17	27010108	27010108	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	70.0	31.0	56.0	0.0	0.442857	0	.	.	none	.	SUPT6H	165	.	NM_003170	exon15	c.A1876G	p.K626E	GGTAGAAAGGTGA	.	PASS	Atlas-SNP
GPRIN3	285513	hgsc.bcm.edu	37	4	90170368	90170368	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	115.0	5.0	141.0	0.0	0.0434783	0	.	.	none	.	GPRIN3	90	.	NM_198281	exon2	c.C894T	p.A298A	CGTACTGGCTTCT	.	PASS	Atlas-SNP
H2AFY2	55506	hgsc.bcm.edu	37	10	71835546	71835546	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	162.0	73.0	136.0	0.0	0.450617	0	.	.	none	.	H2AFY2	30	.	NM_018649	exon2	c.C132T	p.G44G	CGTGGGCGCCCCT	.	PASS	Atlas-SNP
ORC1	4998	hgsc.bcm.edu	37	1	52838903	52838903	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	148.0	61.0	146.0	0.0	0.412162	0	.	.	none	.	ORC1	79	.	NM_004153	exon17	c.C2536T	p.R846W	TGAGCCGCACCCG	.	PASS	Atlas-SNP
ACIN1	22985	hgsc.bcm.edu	37	14	23548793	23548793	+	Missense_Mutation	SNP	C	C	T	rs80007670	bycluster;byfrequency;by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	204.0	11.0	160.0	0.0	0.0539216	0	C|0.994;T|0.006	0.006	strong	.	ACIN1	147	.	NM_001164814	exon6	c.G1925A	p.R642H	CGTGAACGTGACC	.	PASS	Atlas-SNP
ZNF224	7767	hgsc.bcm.edu	37	19	44605366	44605366	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	43.0	21.0	87.0	0.0	0.488372	0	.	.	none	.	ZNF224	70	.	NM_013398	exon5	c.G223T	p.E75X	CAAAGGGAAGGGA	.	PASS	Atlas-SNP
MAGI2	9863	hgsc.bcm.edu	37	7	77885700	77885700	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	278.0	124.0	267.0	0.0	0.446043	0	.	.	none	.	MAGI2	246	.	NM_012301	exon10	c.T1607C	p.V536A	ACCATCACTGGAG	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	37	17	78332155	78332155	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	123.0	6.0	121.0	0.0	0.0487805	0	.	.	none	.	RNF213	766	.	NM_001256071	exon37	c.G10930A	p.D3644N	TTCATCGACAGAG	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	37	16	66423379	66423379	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	91.0	57.0	144.0	0.0	0.626374	0	.	.	none	.	CDH5	111	.	NM_001795	exon5	c.G735A	p.L245L	CGTGCTGGTCACT	.	PASS	Atlas-SNP
ATF7IP	55729	hgsc.bcm.edu	37	12	14578150	14578150	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	126.0	49.0	118.0	0.0	0.388889	0	.	.	none	.	ATF7IP	136	.	NM_018179	exon2	c.A1301G	p.E434G	CAGATGAAATCAT	.	PASS	Atlas-SNP
SSR1	6745	hgsc.bcm.edu	37	6	7313275	7313275	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	80.0	42.0	69.0	0.0	0.525	0	.	.	none	.	SSR1	21	.	NM_003144	exon1	c.G79A	p.G27S	CCTCACCTCTGGG	.	PASS	Atlas-SNP
POMT2	29954	hgsc.bcm.edu	37	14	77746416	77746416	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	116.0	54.0	114.0	0.0	0.465517	0	.	.	none	POMT2,colon,carcinoma,-1,2	POMT2	47	2	NM_013382	exon17	c.G1733A	p.R578H	GAGAAGCGTAGGC	.	PASS	Atlas-SNP
LITAF	9516	hgsc.bcm.edu	37	16	11650529	11650529	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	309.0	40.0	177.0	0.0	0.12945	0	.	.	none	.	LITAF	16	.	NM_001136473	exon2	c.C58T	p.P20S	ATGGAGGTGCGGA	.	PASS	Atlas-SNP
SMC5	23137	hgsc.bcm.edu	37	9	72897468	72897468	+	Missense_Mutation	SNP	G	G	A	rs115131883	bycluster;by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	247.0	103.0	257.0	0.0	0.417004	0	G|1.000;A|0.000	0.000	strong	.	SMC5	96	.	NM_015110	exon7	c.G950A	p.R317H	ACGAGCGTCACAA	.	PASS	Atlas-SNP
RRAS2	22800	hgsc.bcm.edu	37	11	14300971	14300971	+	Splice_Site	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	107.0	5.0	124.0	0.0	0.046729	0	.	.	none	.	RRAS2	29	.	NM_012250	exon7	c.528-1G>A	.	AATTTCCTGTAAG	.	PASS	Atlas-SNP
KCNT1	57582	hgsc.bcm.edu	37	9	138671231	138671231	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	101.0	46.0	92.0	0.0	0.455446	0	.	.	none	.	KCNT1	139	.	NM_020822	exon24	c.C2756T	p.T919M	TCACCACGGAGCT	.	PASS	Atlas-SNP
SFXN5	94097	hgsc.bcm.edu	37	2	73215387	73215387	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	91.0	4.0	61.0	0.0	0.043956	0	.	.	none	.	SFXN5	31	.	NM_144579	exon10	c.G625A	p.A209T	TCTTACCTACAGC	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608867	26608867	+	Missense_Mutation	SNP	C	C	A	rs193142354	bycluster;by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	26.0	7.0	26.0	2.0	0.269231	0.0769231	C|0.880;A|0.120	0.120	strong	UBXN11,colon,carcinoma,0,2	UBXN11	54	2	NM_183008	exon16	c.G1486T	p.G496C	CGGGACCGGGACT	.	scavenged	Atlas-SNP
DST	667	hgsc.bcm.edu	37	6	56374517	56374517	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	239.0	94.0	219.0	0.0	0.393305	0	.	.	none	.	DST	1427	.	NM_015548	exon55	c.T11066C	p.L3689S	TCATACAACGGCT	.	PASS	Atlas-SNP
TBC1D3F	84218	hgsc.bcm.edu	37	17	36339597	36339597	+	Missense_Mutation	SNP	G	G	T	rs373252714		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	9.0	5.0	5.0	0.0	0.555556	0	.	.	weak	TBC1D3_ENST00000537432,NS,carcinoma,0,4	TBC1D3F	14	4	NM_032258	exon13	c.C1060A	p.Q354K	CCCCCTGCTTTCT	.	scavenged	Atlas-SNP
FAM47C	442444	hgsc.bcm.edu	37	X	37028314	37028314	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	227.0	94.0	178.0	0.0	0.414097	0	.	.	none	.	FAM47C	267	.	NM_001013736	exon1	c.C1831T	p.P611S	GAGCCTCCAGAGA	.	PASS	Atlas-SNP
GAD2	2572	hgsc.bcm.edu	37	10	26508109	26508109	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	87.0	4.0	81.0	0.0	0.045977	0	.	.	none	.	GAD2	116	.	NM_000818	exon4	c.C424T	p.L142F	GAGCTTCTCCAAG	.	PASS	Atlas-SNP
PRAMEF11	440560	hgsc.bcm.edu	37	1	12887686	12887686	+	Silent	SNP	T	T	C	rs59802947	bycluster;byfrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	53.0	5.0	41.0	0.0	0.0943396	0	T|0.986;C|0.014	0.014	strong	PRAMEF11,NS,carcinoma,0,1	PRAMEF11	72	1	NM_001146344	exon3	c.A171G	p.R57R	TTTCCATCTCCTG	.	scavenged	Atlas-SNP
CYP2J2	1573	hgsc.bcm.edu	37	1	60381646	60381646	+	Missense_Mutation	SNP	C	C	T	rs11572242	bycluster;byfrequency;byhapmap;by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	128.0	44.0	88.0	0.0	0.34375	0	C|0.998;T|0.002	0.002	strong	CYP2J2,colon,carcinoma,0,1	CYP2J2	34	1	NM_000775	exon2	c.G337A	p.V113M	GGGTCACGGGGCG	.	PASS	Atlas-SNP
MICU1	10367	hgsc.bcm.edu	37	10	74183072	74183072	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	149.0	54.0	136.0	0.0	0.362416	0	.	.	none	.	.	.	.	NM_001195518	exon9	c.C991T	p.L331L	CAAGTAGCATGCC	.	PASS	Atlas-SNP
ZNF285	26974	hgsc.bcm.edu	37	19	44891217	44891217	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	57.0	4.0	53.0	0.0	0.0701754	0	.	.	none	ZNF285,NS,carcinoma,0,2	ZNF285	86	2	NM_152354	exon4	c.A1190G	p.E397G	GGCTTCTCTCCAG	.	scavenged	Atlas-SNP
BRSK2	9024	hgsc.bcm.edu	37	11	1467077	1467077	+	Missense_Mutation	SNP	C	C	T	rs368418167		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	61.0	32.0	43.0	0.0	0.52459	0	.	.	weak	.	BRSK2	97	.	NM_001256630	exon12	c.C1304T	p.T435M	GCGTGACGGACGG	.	PASS	Atlas-SNP
DOCK1	1793	hgsc.bcm.edu	37	10	129209114	129209114	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	60.0	23.0	70.0	0.0	0.383333	0	.	.	none	.	DOCK1	188	.	NM_001380	exon43	c.G4291T	p.V1431L	TACAGGGTGAACG	.	PASS	Atlas-SNP
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970774	45970774	+	Missense_Mutation	SNP	G	G	A	rs76536096	bycluster;byfrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	201.0	12.0	95.0	0.0	0.0597015	0	G|0.917;A|0.083	0.083	strong	.	KRTAP10-2	21	.	NM_198693	exon1	c.C568T	p.P190S	AGACAGGCTTGCA	.	PASS	Atlas-SNP
DGKB	1607	hgsc.bcm.edu	37	7	14378196	14378196	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	180.0	64.0	156.0	0.0	0.355556	0	.	.	none	DGKB,NS,carcinoma,0,1	DGKB	166	1	NM_145695	exon22	c.G2069T	p.G690V	TCAGACCCTTTTT	.	PASS	Atlas-SNP
SUMO2	6613	hgsc.bcm.edu	37	17	73177275	73177275	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	115.0	60.0	131.0	0.0	0.521739	0	.	.	none	.	SUMO2	4	.	NM_006937	exon2	c.C30T	p.V10V	AGTCTTGACTCCT	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	37	7	132174144	132174144	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	132.0	57.0	109.0	0.0	0.431818	0	.	.	none	.	PLXNA4	873	.	NM_001105543	exon3	c.G1278A	p.T426T	GTCCTCCGTGAAG	.	PASS	Atlas-SNP
SFSWAP	6433	hgsc.bcm.edu	37	12	132198771	132198771	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	92.0	4.0	59.0	0.0	0.0434783	0	.	.	none	.	SFSWAP	69	.	NM_001261411	exon2	c.A374G	p.E125G	TTGAGGAGGAGGC	.	PASS	Atlas-SNP
MLF1	4291	hgsc.bcm.edu	37	3	158289125	158289125	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	276.0	120.0	223.0	0.0	0.434783	0	.	.	none	.	MLF1	62	.	NM_022443	exon1	c.C36T	p.D12D	GGATGACCCCTTC	.	PASS	Atlas-SNP
DGKB	1607	hgsc.bcm.edu	37	7	14217692	14217692	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	48.0	17.0	62.0	0.0	0.354167	0	.	.	none	DGKB,NS,carcinoma,0,1	DGKB	166	1	NM_145695	exon23	c.G2210T	p.G737V	CGCCGGCCAGCAC	.	PASS	Atlas-SNP
RP1L1	94137	hgsc.bcm.edu	37	8	10470003	10470003	+	Silent	SNP	C	C	T	rs200772091	bycluster	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	38.0	13.0	42.0	0.0	0.342105	0	C|0.999;T|0.001	0.001	weak	.	RP1L1	453	.	NM_178857	exon4	c.G1605A	p.S535S	GGCTGACGAGTCC	.	PASS	Atlas-SNP
TESK1	7016	hgsc.bcm.edu	37	9	35608460	35608460	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	68.0	30.0	60.0	0.0	0.441176	0	.	.	none	TESK1,NS,neuroblastoma,0,1	TESK1	46	1	NM_006285	exon9	c.G954A	p.L318L	GCAGCTGCCTGAG	.	PASS	Atlas-SNP
SULT1A1	6817	hgsc.bcm.edu	37	16	28618318	28618318	+	Missense_Mutation	SNP	C	C	G	rs1042014	bycluster;byfrequency;byhapmap	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	393.0	248.0	239.0	0.0	0.631043	0	C|0.970;G|0.030	0.030	strong	.	SULT1A1	53	.	NM_177534	exon4	c.G453C	p.E151D	CCCAGGCTCAGGG	.	PASS	Atlas-SNP
RPUSD4	84881	hgsc.bcm.edu	37	11	126075445	126075445	+	Silent	SNP	C	C	T	rs201545291	bycluster;alternate_allele	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	226.0	63.0	111.0	0.0	0.278761	0	C|0.999;A|0.001	.	alt	.	RPUSD4	36	.	NM_032795	exon5	c.G714A	p.R238R	CGCATTCCGGCTG	.	PASS	Atlas-SNP
HIAT1	64645	hgsc.bcm.edu	37	1	100547630	100547630	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	257.0	112.0	214.0	0.0	0.435798	0	.	.	none	.	HIAT1	46	.	NM_033055	exon12	c.G1338A	p.L446L	TGCCTTGTTTATT	.	PASS	Atlas-SNP
MUC4	4585	hgsc.bcm.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	44.0	8.0	35.0	2.0	0.181818	0.0571429	.	.	weak	MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	NM_018406	exon2	c.G11896A	p.A3966T	AGGTGGCGTGACC	.	scavenged	Atlas-SNP
P2RY8	286530	hgsc.bcm.edu	37	X	1585400	1585400	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	52.0	44.0	32.0	0.0	0.846154	0	.	.	none	.	P2RY8	53	.	NM_178129	exon2	c.C52T	p.R18W	GGTTCCGCAGCAT	.	PASS	Atlas-SNP
NPLOC4	55666	hgsc.bcm.edu	37	17	79532602	79532602	+	Missense_Mutation	SNP	C	C	T	rs371370139		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	32.0	4.0	34.0	0.0	0.125	0	.	.	weak	.	NPLOC4	27	.	NM_017921	exon16	c.G1598A	p.R533Q	CTGGTCCGCACGG	.	PASS	Atlas-SNP
TROAP	10024	hgsc.bcm.edu	37	12	49724403	49724403	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	321.0	16.0	157.0	1.0	0.0498442	0.00636943	.	.	none	TROAP,bladder,carcinoma,0,3	TROAP	80	3	NM_005480	exon13	c.A1775G	p.Y592C	AGTCCTACTGTAG	.	scavenged	Atlas-SNP
RABL3	285282	hgsc.bcm.edu	37	3	120409318	120409318	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	237.0	102.0	199.0	0.0	0.43038	0	.	.	none	.	RABL3	23	.	NM_173825	exon7	c.A623G	p.Y208C	AAAAAGTATCTCT	.	PASS	Atlas-SNP
BMP2	650	hgsc.bcm.edu	37	20	6750880	6750880	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	43.0	14.0	27.0	0.0	0.325581	0	.	.	none	.	BMP2	45	.	NM_001200	exon2	c.C107T	p.A36V	CGGCGGCGTCGTC	.	PASS	Atlas-SNP
AMOTL1	154810	hgsc.bcm.edu	37	11	94583290	94583290	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	89.0	22.0	34.0	0.0	0.247191	0	.	.	none	.	AMOTL1	95	.	NM_130847	exon7	c.T1660G	p.L554V	GAATTCTTGAAGG	.	PASS	Atlas-SNP
EBF3	253738	hgsc.bcm.edu	37	10	131761680	131761680	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	142.0	65.0	127.0	1.0	0.457746	0.00787402	.	.	none	EBF3_ENST00000355311,NS,carcinoma,+1,2	EBF3	193	2	NM_001005463	exon2	c.C242T	p.P81L	TCCACCGGCTGCC	.	scavenged	Atlas-SNP
WT1	7490	hgsc.bcm.edu	37	11	32456397	32456397	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	109.0	41.0	90.0	0.0	0.376147	0	.	.	none	.	WT1	744	.	NM_024424	exon1	c.C495T	p.S165S	CTGGCCGGAAAAG	.	PASS	Atlas-SNP
ARAP3	64411	hgsc.bcm.edu	37	5	141033945	141033945	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	78.0	36.0	69.0	0.0	0.461538	0	.	.	none	.	ARAP3	139	.	NM_022481	exon33	c.T4207C	p.Y1403H	CCTCGTACACAGG	.	PASS	Atlas-SNP
NCAM2	4685	hgsc.bcm.edu	37	21	22656612	22656612	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	130.0	31.0	83.0	0.0	0.238462	0	.	.	none	NCAM2,colon,carcinoma,0,2	NCAM2	220	2	NM_004540	exon3	c.C229T	p.R77W	AGGTCACGGTTAA	.	PASS	Atlas-SNP
IRF4	3662	hgsc.bcm.edu	37	6	393224	393224	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	124.0	46.0	84.0	0.0	0.370968	0	.	.	none	.	IRF4	65	.	NM_001195286	exon2	c.C72T	p.L24L	GAAGCTCCGCCAG	.	PASS	Atlas-SNP
ADAMTS7	11173	hgsc.bcm.edu	37	15	79066981	79066981	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	51.0	25.0	75.0	0.0	0.490196	0	.	.	none	.	ADAMTS7	142	.	NM_014272	exon12	c.C1861G	p.P621A	CCACGGGCACCCA	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	37	8	55534023	55534023	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	212.0	91.0	163.0	0.0	0.429245	0	.	.	none	RP1,NS,carcinoma,0,1	RP1	429	1	NM_006269	exon2	c.C497T	p.T166M	CGAAGACGAGGCG	.	PASS	Atlas-SNP
SMCR8	140775	hgsc.bcm.edu	37	17	18220270	18220270	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	137.0	6.0	115.0	0.0	0.0437956	0	.	.	none	.	SMCR8	62	.	NM_144775	exon1	c.A1167G	p.I389M	AAGCATACCCTCT	.	PASS	Atlas-SNP
FAM43A	131583	hgsc.bcm.edu	37	3	194408350	194408350	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	183.0	88.0	121.0	0.0	0.480874	0	.	.	none	.	FAM43A	24	.	NM_153690	exon1	c.G795A	p.E265E	GCAGGAGCTGCAG	.	PASS	Atlas-SNP
COL11A1	1301	hgsc.bcm.edu	37	1	103484376	103484376	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	130.0	53.0	94.0	0.0	0.407692	0	.	.	none	.	COL11A1	972	.	NM_080629	exon10	c.G1384A	p.A462T	ATACTGCAGGTCC	.	PASS	Atlas-SNP
JSRP1	126306	hgsc.bcm.edu	37	19	2254194	2254194	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	62.0	24.0	60.0	0.0	0.387097	0	.	.	none	.	JSRP1	18	.	NM_144616	exon4	c.C254A	p.A85D	GCTCCGGCTTTCA	.	PASS	Atlas-SNP
UBXN11	91544	hgsc.bcm.edu	37	1	26608866	26608866	+	Missense_Mutation	SNP	C	C	G	rs188535926	bycluster;by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	25.0	7.0	25.0	2.0	0.28	0.08	C|0.991;G|0.009	0.009	strong	UBXN11,colon,carcinoma,-1,2	UBXN11	54	2	NM_183008	exon16	c.G1487C	p.G496A	CCGGGACCGGGAC	.	scavenged	Atlas-SNP
ZNF20	7568	hgsc.bcm.edu	37	19	12243529	12243529	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	78.0	38.0	85.0	0.0	0.487179	0	.	.	none	.	ZNF20	86	.	NM_021143	exon4	c.A1472G	p.N491S	ATGTAATTGGAAA	.	PASS	Atlas-SNP
OR10H5	284433	hgsc.bcm.edu	37	19	15905664	15905664	+	Missense_Mutation	SNP	C	C	T	rs144567857	bycluster;by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	173.0	63.0	222.0	1.0	0.364162	0.0045045	C|0.998;T|0.002	0.002	strong	OR10H5,NS,carcinoma,-1,1	OR10H5	49	1	NM_001004466	exon1	c.C806T	p.P269L	AGTCTCCGGAAGG	.	scavenged	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105418008	105418008	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	209.0	86.0	197.0	0.0	0.411483	0	.	.	none	.	AHNAK2	719	.	NM_138420	exon7	c.C3780A	p.D1260E	CTTGAGGTCCACT	.	PASS	Atlas-SNP
NR2C1	7181	hgsc.bcm.edu	37	12	95442844	95442844	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	67.0	24.0	93.0	0.0	0.358209	0	.	.	none	.	NR2C1	56	.	NM_001032287	exon9	c.G1131A	p.R377R	AAATACCCTGAAA	.	PASS	Atlas-SNP
TP53	7157	hgsc.bcm.edu	37	17	7578419	7578419	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	83.0	72.0	137.0	0.0	0.86747	0	.	.	none	TP53_ENST00000545858,bladder,carcinoma,0,47	TP53	33396	47	NM_000546	exon5	c.G511T	p.E171X	CAACCTCCGTCAT	.	PASS	Atlas-SNP
CTSH	1512	hgsc.bcm.edu	37	15	79220112	79220112	+	Missense_Mutation	SNP	G	G	C	rs142506062	alternate_allele	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	44.0	28.0	58.0	0.0	0.636364	0	G|1.000;A|0.000	.	alt	.	CTSH	23	.	NM_004390	exon9	c.C642G	p.C214W	GAACTTGCAATAA	.	PASS	Atlas-SNP
PAK7	57144	hgsc.bcm.edu	37	20	9560944	9560944	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	400.0	125.0	266.0	0.0	0.3125	0	.	.	none	.	PAK7	194	.	NM_177990	exon4	c.C838T	p.P280S	TGGTGGGCTGAGG	.	PASS	Atlas-SNP
PTPRZ1	5803	hgsc.bcm.edu	37	7	121650463	121650463	+	Silent	SNP	A	A	C	rs199595173		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	80.0	38.0	78.0	0.0	0.475	0	A|0.999;C|0.001	0.001	weak	.	PTPRZ1	605	.	NM_001206838	exon12	c.A1363C	p.R455R	CAAATCAGGAAAA	.	PASS	Atlas-SNP
AMN	81693	hgsc.bcm.edu	37	14	103394811	103394811	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	103.0	43.0	84.0	0.0	0.417476	0	.	.	none	.	AMN	13	.	NM_030943	exon4	c.G256A	p.G86S	GGATTCGGCGTCT	.	PASS	Atlas-SNP
ENPP7	339221	hgsc.bcm.edu	37	17	77709108	77709108	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	41.0	17.0	35.0	0.0	0.414634	0	.	.	none	.	ENPP7	63	.	NM_178543	exon3	c.C666T	p.T222T	CCGGACCGTGGGC	.	PASS	Atlas-SNP
PTGER3	5733	hgsc.bcm.edu	37	1	71318536	71318536	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	122.0	45.0	118.0	0.0	0.368852	0	.	.	none	PTGER3_ENST00000460330,NS,carcinoma,0,1	PTGER3	246	1	NM_198716	exon4	c.T1111G	p.F371V	CCCAAAATTCCTC	.	PASS	Atlas-SNP
TUFM	7284	hgsc.bcm.edu	37	16	28854369	28854369	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	98.0	4.0	170.0	0.0	0.0408163	0	.	.	none	TUFM,colon,carcinoma,-1,1	TUFM	33	1	NM_003321	exon10	c.G1295A	p.R432Q	ATAGTCCGGTTGC	.	PASS	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	37	1	228522538	228522538	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	42.0	32.0	62.0	0.0	0.761905	0	.	.	none	.	OBSCN	2142	.	NM_001271223	exon72	c.G18981A	p.P6327P	GGTGCCGCCCCGA	.	PASS	Atlas-SNP
MSRB3	253827	hgsc.bcm.edu	37	12	65857048	65857048	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	190.0	55.0	126.0	0.0	0.289474	0	.	.	none	MSRB3_ENST00000355192,colon,carcinoma,+2,4	MSRB3	80	4	NM_198080	exon6	c.C525T	p.A175A	CACCGCCGAGGGA	.	PASS	Atlas-SNP
NRG2	9542	hgsc.bcm.edu	37	5	139260442	139260442	+	Silent	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	86.0	26.0	67.0	0.0	0.302326	0	.	.	none	NRG2,NS,carcinoma,0,1	NRG2	69	1	NM_013982	exon3	c.C990T	p.S330S	CCTACCGCTGTTG	.	PASS	Atlas-SNP
DMBT1	1755	hgsc.bcm.edu	37	10	124358568	124358568	+	Missense_Mutation	SNP	T	T	A	rs201802690		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	224.0	14.0	184.0	2.0	0.0625	0.0108696	.	.	weak	DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	NM_007329	exon26	c.T3235A	p.S1079T	TGGCTCTCCCACA	.	scavenged	Atlas-SNP
LEFTY2	7044	hgsc.bcm.edu	37	1	226127479	226127479	+	Silent	SNP	G	G	A	rs188858500	by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	14.0	12.0	1.0	0.0	0.857143	0	G|0.990;A|0.010	0.010	strong	.	LEFTY2	25	.	NM_003240	exon2	c.C474T	p.N158N	GGTGCGGTTGGAG	.	PASS	Atlas-SNP
ATF7	11016	hgsc.bcm.edu	37	12	53911012	53911012	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	147.0	7.0	74.0	0.0	0.047619	0	.	.	none	.	ATF7	51	.	NM_006856	exon12	c.T1361C	p.L454P	TGAGTGAGGACCG	.	PASS	Atlas-SNP
IFITM3	10410	hgsc.bcm.edu	37	11	320723	320723	+	Missense_Mutation	SNP	C	C	T	rs56227617		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	86.0	4.0	53.0	1.0	0.0465116	0.0188679	.	.	weak	IFITM3,brain,glioma,0,1	IFITM3	132	1	NM_021034	exon1	c.G91A	p.V31M	CCAGCACAGCCAC	.	scavenged	Atlas-SNP
EYS	346007	hgsc.bcm.edu	37	6	65612316	65612316	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	98.0	43.0	119.0	0.0	0.438776	0	.	.	none	EYS_ENST00000370621,NS,carcinoma,+2,1	EYS	527	1	NM_001142800	exon17	c.G2719T	p.D907Y	CCATATCTTCACA	.	PASS	Atlas-SNP
RAPH1	65059	hgsc.bcm.edu	37	2	204304225	204304225	+	Silent	SNP	G	G	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	87.0	4.0	62.0	0.0	0.045977	0	.	.	none	.	RAPH1	118	.	NM_213589	exon14	c.C3688A	p.R1230R	CTCTCCGCAACGT	.	PASS	Atlas-SNP
BTG1	694	hgsc.bcm.edu	37	12	92538187	92538187	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	131.0	39.0	118.0	0.0	0.29771	0	.	.	none	.	BTG1	30	.	NM_001731	exon2	c.G185A	p.C62Y	CCCTTGCATGGCT	.	PASS	Atlas-SNP
VARS2	57176	hgsc.bcm.edu	37	6	30893890	30893890	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	307.0	128.0	263.0	0.0	0.416938	0	.	.	none	.	VARS2	60	.	NM_001167734	exon30	c.C3185T	p.S1062F	AGCTTTCTTCCCT	.	PASS	Atlas-SNP
ZBTB22	9278	hgsc.bcm.edu	37	6	33283277	33283277	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	78.0	35.0	69.0	0.0	0.448718	0	.	.	none	.	ZBTB22	48	.	NM_001145338	exon2	c.G1417C	p.V473L	CAGGGACCCCACC	.	PASS	Atlas-SNP
ACIN1	22985	hgsc.bcm.edu	37	14	23548787	23548787	+	Missense_Mutation	SNP	C	C	T	rs61741619	bycluster;byfrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	198.0	34.0	150.0	0.0	0.171717	0	C|0.985;T|0.015	0.015	strong	.	ACIN1	147	.	NM_001164814	exon6	c.G1931A	p.R644H	CGAGAACGTGAAC	.	PASS	Atlas-SNP
TEX15	56154	hgsc.bcm.edu	37	8	30701914	30701914	+	Silent	SNP	C	C	T	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	196.0	75.0	172.0	0.0	0.382653	0	.	.	none	.	TEX15	350	.	NM_031271	exon1	c.G4620A	p.E1540E	CTTCTTCTCTCTT	.	PASS	Atlas-SNP
TUBB4A	10382	hgsc.bcm.edu	37	19	6495416	6495416	+	Missense_Mutation	SNP	G	G	A	rs1053267		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	108.0	57.0	98.0	1.0	0.527778	0.0102041	G|1.000;|0.000	.	weak	TUBB4,colon,carcinoma,+1,1	.	.	1	NM_006087	exon4	c.C1094T	p.A365V	AAGGTCGCGGCCA	.	scavenged	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	37	1	117158983	117158983	+	Missense_Mutation	SNP	T	T	G	rs75884067		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	139.0	6.0	88.0	2.0	0.0431655	0.0227273	T|0.500;G|0.500	0.500	weak	IGSF3_ENST00000369483,NS,carcinoma,+1,2	IGSF3	294	2	NM_001542	exon3	c.A140C	p.Y47S	CCCTGGTAGCCAC	.	scavenged	Atlas-SNP
CLCN2	1181	hgsc.bcm.edu	37	3	184071474	184071474	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	74.0	30.0	76.0	0.0	0.405405	0	.	.	none	.	CLCN2	74	.	NM_004366	exon16	c.A1831C	p.M611L	CCAGCATTCGGCC	.	PASS	Atlas-SNP
PSME4	23198	hgsc.bcm.edu	37	2	54135501	54135501	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	57.0	43.0	64.0	0.0	0.754386	0	.	.	none	PSME4,rectum,carcinoma,+1,1	PSME4	247	1	NM_014614	exon24	c.C2740T	p.R914X	TCCATCGGGAGTC	.	PASS	Atlas-SNP
TMC5	79838	hgsc.bcm.edu	37	16	19481009	19481009	+	Silent	SNP	C	C	T	rs145726955	bycluster;byfrequency;by1000genomes	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	304.0	94.0	113.0	0.0	0.309211	0	C|0.999;T|0.001	0.001	strong	.	TMC5	169	.	NM_001105249	exon10	c.C1644T	p.A548A	CATGGCCAAGTAT	.	PASS	Atlas-SNP