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	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
PLCH2	9651	hgsc.bcm.edu	hg19	1	2436173	2436173	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PLCH2	NM_014638	exon22	c.G3772A	p.G1258S	AGCCTGGGCGACC	.	48.0	19.0	46.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	hg19	1	22214014	22214014	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	HSPG2	NM_005529	exon8	c.G857T	p.G286V	TGGGGCCCACAGG	.	80.0	37.0	70.0	0.0	.	311	.	.	.	none	.	.	PASS	Atlas-SNP
HIVEP3	59269	hgsc.bcm.edu	hg19	1	42048585	42048585	+	Silent	SNP	A	A	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	HIVEP3	NM_024503	exon4	c.T1884A	p.L628L	TTTGGTAAGCTCG	.	152.0	61.0	183.0	0.0	.	235	.	.	.	none	.	.	PASS	Atlas-SNP
CYP4A11	1579	hgsc.bcm.edu	hg19	1	47402352	47402352	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	CYP4A11,NS,carcinoma,0,1	CYP4A11	NM_000778	exon4	c.C494G	p.S165C	CGTACAGAGTCTG	.	62.0	23.0	79.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
ZCCHC11	23318	hgsc.bcm.edu	hg19	1	52902541	52902541	+	Silent	SNP	G	G	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ZCCHC11	NM_001009881	exon26	c.C4048A	p.R1350R	AGTCTCGAGTATC	.	160.0	72.0	178.0	0.0	.	151	.	.	.	none	.	.	PASS	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	hg19	1	180000535	180000535	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	CEP350	NM_014810	exon15	c.A3631C	p.K1211Q	GGAAAGAAATCTG	.	38.0	16.0	36.0	0.0	.	418	.	.	.	none	.	.	PASS	Atlas-SNP
PTPN14	5784	hgsc.bcm.edu	hg19	1	214556993	214556993	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PTPN14	NM_005401	exon13	c.C2205T	p.A735A	CAGCTGGGCACTG	.	67.0	30.0	78.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
SULT1C4	27233	hgsc.bcm.edu	hg19	2	109002781	109002781	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SULT1C4	NM_006588	exon6	c.T749C	p.I250T	CATCGATTCCTGC	.	119.0	59.0	111.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
NFE2L2	4780	hgsc.bcm.edu	hg19	2	178098803	178098803	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	NFE2L2,NS,carcinoma,-1,11	NFE2L2	NM_006164	exon2	c.G242T	p.G81V	AATTCACCTGTCT	.	98.0	51.0	68.0	0.0	.	225	.	.	.	none	.	.	PASS	Atlas-SNP
SLC22A13	9390	hgsc.bcm.edu	hg19	3	38317429	38317429	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SLC22A13	NM_004256	exon7	c.T1079C	p.L360P	TCGGCCTGGACGT	.	77.0	29.0	77.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
SACM1L	22908	hgsc.bcm.edu	hg19	3	45773632	45773632	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SACM1L	NM_014016	exon13	c.A1089T	p.Q363H	AATGCAAGATGAA	.	146.0	69.0	151.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
SLC38A3	10991	hgsc.bcm.edu	hg19	3	50252997	50252997	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SLC38A3	NM_006841	exon6	c.T395C	p.L132P	AGCAGCTGGGCTA	.	65.0	29.0	85.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
PPM1M	132160	hgsc.bcm.edu	hg19	3	52282683	52282683	+	Silent	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PPM1M	NM_144641	exon7	c.C945T	p.L315L	GGATCTCAAGTAC	.	150.0	70.0	140.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
SLMAP	7871	hgsc.bcm.edu	hg19	3	57827089	57827089	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SLMAP	NM_007159	exon3	c.T410C	p.L137P	CCCGGCTCCGCTC	.	81.0	39.0	73.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1524	57650	hgsc.bcm.edu	hg19	3	108282018	108282018	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	KIAA1524,colon,carcinoma,+1,1	KIAA1524	NM_020890	exon13	c.G1589T	p.R530I	AATATTCTCAGTC	.	204.0	74.0	252.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF721	170960	hgsc.bcm.edu	hg19	4	436019	436019	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ZNF721	NM_133474	exon3	c.C2237G	p.T746R	GTATGAATTTTCT	.	33.0	12.0	29.0	0.0	.	205	.	.	.	none	.	.	PASS	Atlas-SNP
NSUN7	79730	hgsc.bcm.edu	hg19	4	40778094	40778094	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	NSUN7	NM_024677	exon7	c.C854A	p.S285Y	TCCATTCTGTAAA	.	41.0	19.0	52.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
POLR2B	5431	hgsc.bcm.edu	hg19	4	57891054	57891054	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	POLR2B	NM_000938	exon22	c.A2967G	p.V989V	AAAGGTATCGGCT	.	86.0	38.0	91.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
DHX29	54505	hgsc.bcm.edu	hg19	5	54591351	54591351	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	DHX29	NM_019030	exon5	c.T507C	p.D169D	AAGTGCATCTTAA	.	58.0	24.0	67.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
CTNNA1	1495	hgsc.bcm.edu	hg19	5	138268291	138268291	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	CTNNA1	NM_001903	exon17	c.G2323A	p.D775N	AAGCAGGACCTGC	.	34.0	19.0	43.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
ANKHD1	54882	hgsc.bcm.edu	hg19	5	139864824	139864824	+	Silent	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ANKHD1	NM_017747	exon12	c.T1989C	p.H663H	TACTCATCGACTC	.	46.0	18.0	49.0	0.0	.	233	.	.	.	none	.	.	PASS	Atlas-SNP
TMCO6	55374	hgsc.bcm.edu	hg19	5	140021512	140021512	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	TMCO6	NM_018502	exon4	c.G372A	p.L124L	CCTGCTGCAGCTT	.	89.0	37.0	88.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
C6orf47	57827	hgsc.bcm.edu	hg19	6	31627425	31627425	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	C6orf47	NM_021184	exon1	c.T300C	p.T100T	CTCTTGAGTGCTA	.	86.0	35.0	83.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
PHF1	5252	hgsc.bcm.edu	hg19	6	33380325	33380325	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PHF1	NM_024165	exon3	c.A200T	p.D67V	TTGAGGATGATTC	.	114.0	45.0	146.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
GUCA1B	2979	hgsc.bcm.edu	hg19	6	42152609	42152609	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	GUCA1B	NM_002098	exon4	c.G547T	p.D183Y	TCATGTCCATCTG	.	89.0	46.0	112.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
SYNJ2	8871	hgsc.bcm.edu	hg19	6	158450005	158450005	+	Silent	SNP	C	C	T	rs372960799		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SYNJ2	NM_003898	exon3	c.C432T	p.V144V	GACTGTCCGCACG	.	89.0	34.0	76.0	0.0	.	111	.	.	.	weak	.	.	PASS	Atlas-SNP
ARMC10	83787	hgsc.bcm.edu	hg19	7	102724230	102724230	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ARMC10	NM_031905	exon3	c.A346G	p.R116G	ATTGAAAGAGCTT	.	98.0	32.0	76.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
RP1	6101	hgsc.bcm.edu	hg19	8	55534829	55534829	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	RP1	NM_006269	exon3	c.A768G	p.A256A	AAATGCAAAGTCA	.	51.0	18.0	51.0	0.0	.	429	.	.	.	none	.	.	PASS	Atlas-SNP
SLC45A4	57210	hgsc.bcm.edu	hg19	8	142238284	142238284	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SLC45A4	NM_001080431	exon1	c.C82T	p.Q28X	CTTTCTGAAGACT	.	187.0	83.0	217.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
PITRM1	10531	hgsc.bcm.edu	hg19	10	3206029	3206029	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PITRM1	NM_014889	exon7	c.C679T	p.P227S	GGTCAGGAAGAAG	.	63.0	28.0	79.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
NCOA4	8031	hgsc.bcm.edu	hg19	10	51586276	51586276	+	Silent	SNP	A	A	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	NCOA4	NM_001145261	exon10	c.A1752T	p.V584V	GGAAGTATTACTT	.	127.0	48.0	137.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
PTEN	5728	hgsc.bcm.edu	hg19	10	89717669	89717669	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.,1	PTEN	NM_000314	exon7	c.A694G	p.T232A	GGACCCACACGAC	.	91.0	30.0	116.0	1.0	.	3652	.	.	.	none	.	.	PASS	Atlas-SNP
DRD4	1815	hgsc.bcm.edu	hg19	11	639919	639919	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	DRD4	NM_000797	exon3	c.G670A	p.V224M	TGGGAGGTGGCAC	.	33.0	15.0	39.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
OR4A16	81327	hgsc.bcm.edu	hg19	11	55110978	55110978	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	OR4A16	NM_001005274	exon1	c.T302C	p.I101T	TCTTCATAGAACA	.	268.0	22.0	317.0	0.0	.	120	.	.	.	none	.	.	PASS	Atlas-SNP
UBE4A	9354	hgsc.bcm.edu	hg19	11	118250228	118250228	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	UBE4A	NM_004788	exon11	c.C1660T	p.Q554X	GATGCTCAGCAAA	.	97.0	51.0	144.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	hg19	11	119044337	119044337	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	NLRX1	NM_024618	exon5	c.C379T	p.P127S	CGCCCACCCGCGG	.	46.0	18.0	71.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
TRIM29	23650	hgsc.bcm.edu	hg19	11	119988941	119988941	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	TRIM29	NM_012101	exon7	c.C1617T	p.F539F	CAGGGAGAAGGAG	.	33.0	12.0	37.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
FKBP4	2288	hgsc.bcm.edu	hg19	12	2909052	2909052	+	Silent	SNP	A	A	G	rs201311104		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	FKBP4	NM_002014	exon6	c.A708G	p.Q236Q	GTTCCAAATCCCA	.	33.0	19.0	39.0	0.0	.	29	.	.	.	weak	A|0.999;G|0.001	0.001	PASS	Atlas-SNP
DPPA3	359787	hgsc.bcm.edu	hg19	12	7867786	7867786	+	Silent	SNP	T	T	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	DPPA3	NM_199286	exon2	c.T90A	p.S30S	GGCCTCTCAAATC	.	223.0	102.0	235.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
CNTN1	1272	hgsc.bcm.edu	hg19	12	41323760	41323760	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	CNTN1	NM_001256063	exon7	c.A659G	p.K220R	TTACAAAGAGCGT	.	210.0	85.0	219.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
CCNT1	904	hgsc.bcm.edu	hg19	12	49087909	49087909	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	CCNT1	NM_001240	exon9	c.C1088A	p.S363Y	GGTAAGGAATGAT	.	176.0	78.0	154.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
FREM2	341640	hgsc.bcm.edu	hg19	13	39450406	39450406	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	FREM2	NM_207361	exon20	c.T8431G	p.Y2811D	GGGACCTATACTG	.	82.0	42.0	97.0	0.0	.	385	.	.	.	none	.	.	PASS	Atlas-SNP
TEP1	7011	hgsc.bcm.edu	hg19	14	20845481	20845481	+	Silent	SNP	G	G	A	rs375172392	alternate_allele	TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	TEP1	NM_007110	exon41	c.C6046T	p.L2016L	GTCCTAGCACAGG	.	49.0	22.0	41.0	0.0	.	224	.	.	.	alt	.	.	PASS	Atlas-SNP
PNP	4860	hgsc.bcm.edu	hg19	14	20944608	20944608	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PNP	NM_000270	exon6	c.C718T	p.L240F	TTCTCACTCATCA	.	93.0	43.0	94.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
RNF31	55072	hgsc.bcm.edu	hg19	14	24626550	24626550	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	RNF31	NM_017999	exon15	c.C2545T	p.R849C	TGGAAACGCATGA	.	28.0	16.0	37.0	0.0	.	95	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA0391	9692	hgsc.bcm.edu	hg19	14	35592664	35592664	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	KIAA0391	NM_014672	exon2	c.T213G	p.D71E	GAAAGATGAGGGC	.	52.0	25.0	61.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
VTI1B	10490	hgsc.bcm.edu	hg19	14	68118141	68118141	+	Silent	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	VTI1B	NM_006370	exon6	c.G660A	p.L220L	GCCTCCCAGGATG	.	89.0	48.0	98.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
SIN3A	25942	hgsc.bcm.edu	hg19	15	75664533	75664533	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SIN3A	NM_001145358	exon21	c.C3609T	p.S1203S	ACGCTTGCTTACA	.	135.0	47.0	151.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
TICRR	90381	hgsc.bcm.edu	hg19	15	90138745	90138745	+	Silent	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	.	NM_152259	exon7	c.T1803C	p.D601D	TCCGGATGTGGCT	.	88.0	40.0	119.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SPAG5	10615	hgsc.bcm.edu	hg19	17	26911390	26911390	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SPAG5	NM_006461	exon12	c.T2270C	p.L757P	TGGCAGAGTAACT	.	368.0	253.0	291.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
KRT27	342574	hgsc.bcm.edu	hg19	17	38938378	38938378	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	KRT27	NM_181537	exon1	c.T368C	p.F123S	GGTCCAAATTTCT	.	190.0	10.0	129.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
HEXDC	284004	hgsc.bcm.edu	hg19	17	80382347	80382347	+	Silent	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	HEXDC	NM_173620	exon3	c.T162C	p.P54P	GGGCCCTCTGAGG	.	139.0	38.0	115.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
TIMM21	29090	hgsc.bcm.edu	hg19	18	71816322	71816322	+	Silent	SNP	C	C	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	.	NM_014177	exon1	c.C279G	p.T93T	GGGAACCGCCGTC	.	67.0	32.0	72.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
STXBP2	6813	hgsc.bcm.edu	hg19	19	7712265	7712265	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	STXBP2	NM_001272034	exon18	c.A1597T	p.N533Y	CACAAGAACAAGG	.	52.0	21.0	57.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
DOCK6	57572	hgsc.bcm.edu	hg19	19	11312640	11312640	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	DOCK6	NM_020812	exon44	c.G5613T	p.K1871N	CTTACGCTTGTGT	.	20.0	11.0	16.0	0.0	.	104	.	.	.	none	.	.	PASS	Atlas-SNP
DOCK6	57572	hgsc.bcm.edu	hg19	19	11312680	11312680	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	DOCK6	NM_020812	exon44	c.C5573G	p.P1858R	CCATCCGGCGTGA	.	35.0	10.0	42.0	0.0	.	104	.	.	.	none	.	.	PASS	Atlas-SNP
OR7A17	26333	hgsc.bcm.edu	hg19	19	14991895	14991895	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	OR7A17	NM_030901	exon1	c.C273T	p.V91V	GGTGATGACTCTG	.	126.0	59.0	95.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
USHBP1	83878	hgsc.bcm.edu	hg19	19	17362478	17362478	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	USHBP1	NM_031941	exon12	c.G1835C	p.R612P	TCCCTGCGCAGAG	.	104.0	48.0	96.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
CRTC1	23373	hgsc.bcm.edu	hg19	19	18876245	18876245	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	CRTC1	NM_001098482	exon10	c.C966G	p.H322Q	ACAGCACCGCCCA	.	180.0	66.0	199.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF253	56242	hgsc.bcm.edu	hg19	19	20003291	20003291	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ZNF253	NM_021047	exon4	c.C1235T	p.S412F	TCCTCTCCAAACA	.	38.0	19.0	37.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF471	57573	hgsc.bcm.edu	hg19	19	57037192	57037192	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ZNF471	NM_020813	exon5	c.T1756C	p.C586R	TCATCCTGTGCTC	.	76.0	33.0	62.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRT	11122	hgsc.bcm.edu	hg19	20	41100970	41100970	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PTPRT	NM_007050	exon8	c.C1386T	p.L462L	CAGCAAGAGTCGC	.	147.0	51.0	103.0	0.0	.	372	.	.	.	none	.	.	PASS	Atlas-SNP
ZGPAT	84619	hgsc.bcm.edu	hg19	20	62366823	62366823	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ZGPAT	NM_032527	exon6	c.T1364C	p.L455P	GGGCCCTGAGCCT	.	51.0	30.0	32.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
SFI1	9814	hgsc.bcm.edu	hg19	22	32002357	32002357	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SFI1	NM_001007467	exon21	c.G2098C	p.D700H	CGAGTGGATGAAG	.	63.0	25.0	61.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
C1QTNF6	114904	hgsc.bcm.edu	hg19	22	37578251	37578251	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	C1QTNF6	NM_182486	exon3	c.C814G	p.L272V	TGATGAGGTGGCC	.	35.0	18.0	48.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
ARFGAP3	26286	hgsc.bcm.edu	hg19	22	43213794	43213794	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ARFGAP3	NM_014570	exon10	c.T882C	p.I294I	GCCACTAATGTTC	.	139.0	63.0	174.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
SYN1	6853	hgsc.bcm.edu	hg19	X	47432308	47432308	+	Silent	SNP	G	G	C	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SYN1	NM_006950	exon13	c.C2073G	p.T691T	GCGGATGGTCTCA	.	58.0	56.0	74.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
HEPH	9843	hgsc.bcm.edu	hg19	X	65390505	65390505	+	Silent	SNP	C	C	T	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	HEPH	NM_138737	exon2	c.C255T	p.G85G	CCTGGGCATCCGG	.	23.0	19.0	25.0	0.0	.	224	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGAP36	158763	hgsc.bcm.edu	hg19	X	130215818	130215818	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ARHGAP36	NM_144967	exon2	c.G179A	p.R60H	TGGAGCGTCTGAA	.	96.0	87.0	127.0	0.0	.	171	.	.	.	none	.	.	PASS	Atlas-SNP
MFN2	9927	hgsc.bcm.edu	hg19	1	12061548	12061549	+	Frame_Shift_Del	DEL	TT	TT	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	MFN2	NM_014874	exon9	c.906_907del	p.302_303del	.	.	47.0	26.0	48.0	0.0	.	83	.	0.553191	0	none	.	.	PASS	Atlas-INDEL
MLL3	58508	hgsc.bcm.edu	hg19	7	151880116	151880116	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	MLL3	NM_170606	exon35	c.5209delA	p.K1737fs	.	.	463.0	289.0	340.0	0.0	.	1564	.	0.62419	0	none	.	.	PASS	Atlas-INDEL
ADAMTS9	56999	hgsc.bcm.edu	hg19	3	64536694	64536703	+	Frame_Shift_Del	DEL	CACCACCTTG	CACCACCTTG	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CACCACCTTG	CACCACCTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ADAMTS9	NM_182920	exon31	c.4735_4744del	p.1579_1582del	.	.	135.0	26.0	237.0	0.0	.	206	.	0.192593	0	none	.	.	PASS	Atlas-INDEL
SLC46A1	113235	hgsc.bcm.edu	hg19	17	26731859	26731859	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	SLC46A1	NM_001242366	exon2	c.857delA	p.D286fs	.	.	112.0	70.0	88.0	0.0	.	17	.	0.625	0	none	.	.	PASS	Atlas-INDEL
MLL2	8085	hgsc.bcm.edu	hg19	12	49435198	49435199	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.,2	MLL2	NM_003482	exon31	c.6355_6356insC	p.A2119fs	.	.	38.0	19.0	42.0	0.0	.	1173	.	0.5	0	none	.	.	PASS	Atlas-INDEL
MATN2	4147	hgsc.bcm.edu	hg19	8	98943606	98943609	+	Frame_Shift_Del	DEL	CTAA	CTAA	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CTAA	CTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	MATN2	NM_002380	exon3	c.567_570del	p.189_190del	.	.	44.0	19.0	53.0	0.0	.	165	.	0.431818	0	none	.	.	PASS	Atlas-INDEL
ADAMTS20	80070	hgsc.bcm.edu	hg19	12	43823478	43823478	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	ADAMTS20	NM_025003	exon24	c.3432delA	p.L1144fs	.	.	27.0	12.0	19.0	0.0	.	635	.	0.444444	0	none	.	.	PASS	Atlas-INDEL
KBTBD6	89890	hgsc.bcm.edu	hg19	13	41705610	41705612	+	In_Frame_Del	DEL	CAC	CAC	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	KBTBD6	NM_152903	exon1	c.1037_1039del	p.346_347del	.	.	94.0	29.0	152.0	0.0	.	83	.	0.308511	0	none	.	.	PASS	Atlas-INDEL
COX5A	9377	hgsc.bcm.edu	hg19	15	75221461	75221461	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	COX5A	NM_004255	exon2	c.214delA	p.K72fs	.	.	108.0	34.0	174.0	0.0	.	9	.	0.314815	0	none	.	.	PASS	Atlas-INDEL
PAK1	5058	hgsc.bcm.edu	hg19	11	77047284	77047284	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-BQ-7051-01A-12D-1961-08	TCGA-BQ-7051-11A-02D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	9b9c9f82-1e35-4ff6-94dc-0d2af8f0219b	d10a271b-6cf9-4623-a59e-f8cb7afcaca5	.	PAK1	NM_001128620	exon13	c.1261delC	p.R421fs	.	.	104.0	43.0	121.0	0.0	.	89	.	0.413462	0	none	.	.	PASS	Atlas-INDEL
