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
SDC3	9672	hgsc.bcm.edu	hg19	1	31347253	31347253	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SDC3	NM_014654	exon4	c.C1053A	p.P351P	ACCCTTGGGCAGT	.	96.0	31.0	85.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
PPIE	10450	hgsc.bcm.edu	hg19	1	40211152	40211152	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PPIE	NM_006112	exon7	c.G490A	p.V164I	TCTGATGTCGTGC	.	36.0	20.0	49.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
CAP1	10487	hgsc.bcm.edu	hg19	1	40536545	40536545	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CAP1	NM_006367	exon12	c.C1238T	p.T413I	ACAAAACAGATGG	.	128.0	48.0	126.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
ZFP69	339559	hgsc.bcm.edu	hg19	1	40961061	40961061	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_198494	exon6	c.G911T	p.C304F	AGGAATGTGGAAG	.	66.0	22.0	62.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
NRD1	4898	hgsc.bcm.edu	hg19	1	52256297	52256297	+	Nonsense_Mutation	SNP	C	C	A	rs147279713	bycluster;by1000genomes;alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NRD1	NM_002525	exon31	c.G3280T	p.E1094X	CACACTCCTTCAG	.	58.0	26.0	58.0	0.0	.	89	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
AHCYL1	10768	hgsc.bcm.edu	hg19	1	110561173	110561173	+	Splice_Site	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	AHCYL1	NM_006621	exon13	c.1219-1G>A	.	CTTTCAGACCAGC	.	39.0	16.0	35.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
COPA	1314	hgsc.bcm.edu	hg19	1	160305059	160305059	+	Silent	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	COPA	NM_001098398	exon4	c.T282C	p.D94D	AATATAATCTAAG	.	28.0	14.0	35.0	0.0	.	181	.	.	.	none	.	.	PASS	Atlas-SNP
ASAP2	8853	hgsc.bcm.edu	hg19	2	9515054	9515054	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ASAP2	NM_001135191	exon17	c.T1727C	p.I576T	AAAAAATCCCACT	.	126.0	51.0	107.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
TCF23	150921	hgsc.bcm.edu	hg19	2	27373231	27373231	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	TCF23	NM_175769	exon2	c.A463T	p.K155X	CCTCTCAAGGTAA	.	260.0	107.0	391.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
SPTBN1	6711	hgsc.bcm.edu	hg19	2	54852000	54852000	+	Silent	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SPTBN1	NM_003128	exon11	c.C1242T	p.L414L	TGAGCTCATAAGA	.	58.0	10.0	65.0	0.0	.	378	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	hg19	2	109380509	109380509	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RANBP2	NM_006267	exon20	c.T3514G	p.F1172V	CCTCACTTTGAGC	.	148.0	58.0	132.0	0.0	.	488	.	.	.	none	.	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	hg19	2	141816463	141816463	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	LRP1B	NM_018557	exon9	c.C1397G	p.T466S	GGTTGAGTTCTTT	.	31.0	14.0	28.0	0.0	.	1315	.	.	.	none	.	.	PASS	Atlas-SNP
LRP1B	53353	hgsc.bcm.edu	hg19	2	141816476	141816476	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	LRP1B	NM_018557	exon9	c.T1384A	p.Y462N	TTTGATAAATTCG	.	30.0	10.0	28.0	0.0	.	1315	.	.	.	none	.	.	PASS	Atlas-SNP
HYAL2	8692	hgsc.bcm.edu	hg19	3	50357591	50357591	+	Silent	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	HYAL2	NM_033158	exon3	c.G330A	p.R110R	CATCTTCCGGTGT	.	87.0	30.0	105.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
MFN1	55669	hgsc.bcm.edu	hg19	3	179076735	179076735	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MFN1	NM_033540	exon4	c.A356C	p.D119A	GAACTGATGGAGA	.	81.0	27.0	64.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
USP13	8975	hgsc.bcm.edu	hg19	3	179426711	179426711	+	Silent	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	USP13,NS,malignant_melanoma,+1,1	USP13	NM_003940	exon6	c.C771A	p.A257A	ACTAGCCGTGAAA	.	73.0	33.0	92.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
CPN2	1370	hgsc.bcm.edu	hg19	3	194062198	194062198	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CPN2	NM_001080513	exon2	c.C1234A	p.Q412K	TGTACTGCTGCAG	.	76.0	28.0	84.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
ODAM	54959	hgsc.bcm.edu	hg19	4	71064324	71064324	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ODAM	NM_017855	exon5	c.T404A	p.M135K	TCAAAATGCCTCA	.	91.0	6.0	73.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
SLC4A4	8671	hgsc.bcm.edu	hg19	4	72429564	72429564	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	SLC4A4,rectum,carcinoma,0,1	SLC4A4	NM_001098484	exon24	c.A3154G	p.M1052V	GACATCATGGAAC	.	122.0	45.0	112.0	0.0	.	269	.	.	.	none	.	.	PASS	Atlas-SNP
EXOSC9	5393	hgsc.bcm.edu	hg19	4	122724130	122724130	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	EXOSC9	NM_001034194	exon4	c.G342A	p.K114K	TTCGAAGTGTATA	.	69.0	32.0	74.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
BDP1	55814	hgsc.bcm.edu	hg19	5	70813231	70813231	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	BDP1	NM_018429	exon22	c.T4943A	p.V1648E	GTCAGGTGGTTCT	.	76.0	32.0	43.0	0.0	.	204	.	.	.	none	.	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	hg19	5	82836395	82836395	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	VCAN	NM_004385	exon8	c.A7573T	p.R2525W	CGTTTCAGGGAAT	.	56.0	21.0	56.0	0.0	.	498	.	.	.	none	.	.	PASS	Atlas-SNP
PCDHGA3	56112	hgsc.bcm.edu	hg19	5	140724920	140724920	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PCDHGA3	NM_032011	exon1	c.G1320T	p.L440L	CACCCTGCATGTG	.	205.0	36.0	176.0	0.0	.	246	.	.	.	none	.	.	PASS	Atlas-SNP
TNIP1	10318	hgsc.bcm.edu	hg19	5	150444534	150444534	+	Silent	SNP	C	C	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	TNIP1	NM_001252385	exon2	c.G123C	p.G41G	CTTTATCCCTTGC	.	128.0	45.0	151.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
WWC1	23286	hgsc.bcm.edu	hg19	5	167833322	167833322	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	WWC1	NM_015238	exon6	c.A710C	p.D237A	AGCAAGATCTCAT	.	165.0	70.0	184.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
DDR1	780	hgsc.bcm.edu	hg19	6	30865203	30865203	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	DDR1	NM_013994	exon14	c.C2063A	p.P688Q	AGGACCCAAACAT	.	70.0	25.0	83.0	0.0	.	213	.	.	.	none	.	.	PASS	Atlas-SNP
KIFC1	3833	hgsc.bcm.edu	hg19	6	33365943	33365943	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KIFC1	NM_002263	exon2	c.G150T	p.K50N	TGAGAAGGTGAGC	.	49.0	15.0	60.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	hg19	6	43153712	43153712	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CUL9	NM_015089	exon4	c.T770C	p.F257S	TGCTTTTCTCCTT	.	69.0	28.0	66.0	0.0	.	248	.	.	.	none	.	.	PASS	Atlas-SNP
CUL9	23113	hgsc.bcm.edu	hg19	6	43153713	43153713	+	Silent	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CUL9	NM_015089	exon4	c.C771T	p.F257F	GCTTTTCTCCTTG	.	71.0	30.0	67.0	0.0	.	248	.	.	.	none	.	.	PASS	Atlas-SNP
PLEKHG1	57480	hgsc.bcm.edu	hg19	6	151117019	151117019	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PLEKHG1	NM_001029884	exon6	c.T610G	p.Y204D	ACCCAGTATTGCA	.	114.0	48.0	127.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
MLLT4	4301	hgsc.bcm.edu	hg19	6	168349109	168349109	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.,2	MLLT4	NM_001040000	exon28	c.A3761T	p.E1254V	ATGAGGAAAAGCC	.	53.0	24.0	55.0	0.0	.	351	.	.	.	none	.	.	PASS	Atlas-SNP
OGDH	4967	hgsc.bcm.edu	hg19	7	44747234	44747234	+	Silent	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	OGDH	NM_002541	exon22	c.T2850C	p.N950N	CCCCAATGCTGAG	.	239.0	66.0	186.0	0.0	.	145	.	.	.	none	.	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	hg19	7	149502569	149502569	+	Silent	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_198455	exon57	c.C8382A	p.G2794G	AGGGGGCCCTGGC	.	85.0	16.0	69.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
UBE3C	9690	hgsc.bcm.edu	hg19	7	156963038	156963038	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	UBE3C	NM_014671	exon4	c.T236A	p.L79X	CTACCTTGTCACA	.	158.0	43.0	97.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
KIF13B	23303	hgsc.bcm.edu	hg19	8	28991587	28991587	+	Silent	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KIF13B	NM_015254	exon22	c.G2754A	p.P918P	GCAGTGCGGCTCC	.	52.0	19.0	37.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
SPTLC1	10558	hgsc.bcm.edu	hg19	9	94821490	94821490	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SPTLC1	NM_006415	exon7	c.C661T	p.L221L	CTTTTAGTAGTCG	.	25.0	10.0	20.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
OR1L8	138881	hgsc.bcm.edu	hg19	9	125330116	125330116	+	Missense_Mutation	SNP	C	C	T	rs377120372	alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	OR1L8	NM_001004454	exon1	c.G641A	p.C214Y	GCAATGCAGAGAA	.	48.0	23.0	33.0	0.0	.	90	.	.	.	alt	.	.	PASS	Atlas-SNP
NUDT5	11164	hgsc.bcm.edu	hg19	10	12226925	12226925	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NUDT5	NM_014142	exon3	c.G94C	p.E32Q	TTTTTTCAAGCTT	.	35.0	16.0	26.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
HSPA14	51182	hgsc.bcm.edu	hg19	10	14896200	14896200	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	HSPA14	NM_016299	exon9	c.T811A	p.S271T	AAACATTCTTTGT	.	91.0	12.0	98.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
FAM13C	220965	hgsc.bcm.edu	hg19	10	61112192	61112192	+	Silent	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	FAM13C	NM_198215	exon3	c.G162T	p.L54L	TTCTACCAGAGCC	.	37.0	13.0	26.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
CPEB3	22849	hgsc.bcm.edu	hg19	10	93999658	93999658	+	Silent	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CPEB3	NM_014912	exon2	c.T450G	p.T150T	GGAGAAAGTGCCT	.	30.0	9.0	38.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
TLL2	7093	hgsc.bcm.edu	hg19	10	98145849	98145849	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	TLL2	NM_012465	exon15	c.C1976G	p.S659C	TGAAGGGAGATCC	.	71.0	14.0	82.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
GBF1	8729	hgsc.bcm.edu	hg19	10	104139057	104139057	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	GBF1	NM_004193	exon34	c.A4508G	p.H1503R	TGATGCACACCCT	.	107.0	13.0	128.0	0.0	.	142	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC55	219527	hgsc.bcm.edu	hg19	11	56949791	56949791	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	LRRC55	NM_001005210	exon1	c.A424T	p.N142Y	CACAACAACTCCT	.	42.0	16.0	51.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC55	219527	hgsc.bcm.edu	hg19	11	56949792	56949792	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	LRRC55	NM_001005210	exon1	c.A425C	p.N142T	ACAACAACTCCTT	.	41.0	16.0	50.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
RAB38	23682	hgsc.bcm.edu	hg19	11	87908439	87908439	+	Silent	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	RAB38	NM_022337	exon1	c.C114T	p.Y38Y	GGCCCGGTAGTGC	.	53.0	20.0	71.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
NXPE4	54827	hgsc.bcm.edu	hg19	11	114450961	114450961	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	.	NM_001077639	exon5	c.G992A	p.S331N	GCCAAACTACAGG	.	134.0	54.0	123.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
DSCAML1	57453	hgsc.bcm.edu	hg19	11	117308640	117308640	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	DSCAML1	NM_020693	exon25	c.A4583G	p.E1528G	ATGATCTCGCTGA	.	28.0	12.0	39.0	0.0	.	286	.	.	.	none	.	.	PASS	Atlas-SNP
ARF3	377	hgsc.bcm.edu	hg19	12	49334777	49334777	+	Silent	SNP	T	T	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ARF3	NM_001659	exon2	c.A102G	p.L34L	CTTGTATAGGATG	.	295.0	98.0	228.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	hg19	14	64633956	64633956	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SYNE2	NM_182914	exon91	c.T16611A	p.H5537Q	GAATCATGTGCTG	.	51.0	14.0	29.0	0.0	.	577	.	.	.	none	.	.	PASS	Atlas-SNP
FBLN5	10516	hgsc.bcm.edu	hg19	14	92349359	92349359	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	FBLN5	NM_006329	exon8	c.C801A	p.G267G	GTATGTGCCGGGC	.	93.0	39.0	97.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
VPS39	23339	hgsc.bcm.edu	hg19	15	42462024	42462024	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	VPS39	NM_015289	exon12	c.C1131A	p.P377P	GTCTGTGGGCAGC	.	73.0	33.0	89.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
NOL3	8996	hgsc.bcm.edu	hg19	16	67208730	67208730	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NOL3	NM_001276319	exon5	c.G688A	p.E230K	GAACCGGAGCCGG	.	36.0	5.0	32.0	0.0	.	6	.	.	.	none	.	.	PASS	Atlas-SNP
ADAD2	161931	hgsc.bcm.edu	hg19	16	84228709	84228709	+	Silent	SNP	G	G	A	rs369199969		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ADAD2	NM_139174	exon5	c.G858A	p.A286A	CGCAGCGTTGGTG	.	86.0	21.0	77.0	0.0	.	46	.	.	.	weak	.	.	PASS	Atlas-SNP
ZNF709	163051	hgsc.bcm.edu	hg19	19	12576137	12576137	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ZNF709	NM_152601	exon4	c.A599C	p.E200A	CCACATTCCTTAC	.	81.0	30.0	92.0	0.0	.	80	.	.	.	none	.	.	PASS	Atlas-SNP
NOTCH3	4854	hgsc.bcm.edu	hg19	19	15303027	15303027	+	Silent	SNP	G	G	T	rs116044239	by1000genomes;alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NOTCH3	NM_000435	exon4	c.C423A	p.R141R	GAGGAAGCGTCCA	.	28.0	10.0	34.0	0.0	.	340	.	.	.	alt	G|0.995;A|0.005	.	PASS	Atlas-SNP
CLIP3	25999	hgsc.bcm.edu	hg19	19	36515358	36515358	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CLIP3	NM_001199570	exon6	c.T858G	p.N286K	CATGAGATTGCCT	.	70.0	30.0	122.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	hg19	20	25271238	25271238	+	Missense_Mutation	SNP	G	G	A	rs139162483		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PYGB	NM_002862	exon16	c.G1949A	p.R650H	ACTACCGTGTGTC	.	272.0	161.0	231.0	0.0	.	84	.	.	.	weak	G|1.000;A|0.000	0.000	PASS	Atlas-SNP
KIF3B	9371	hgsc.bcm.edu	hg19	20	30897803	30897803	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KIF3B	NM_004798	exon2	c.G223A	p.E75K	TACGATGAGACGT	.	149.0	84.0	100.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
SDC4	6385	hgsc.bcm.edu	hg19	20	43959164	43959164	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	SDC4,NS,carcinoma,0,1	SDC4	NM_002999	exon4	c.G287T	p.G96V	TGGCTCCCAGACC	.	66.0	17.0	52.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
ARFGEF2	10564	hgsc.bcm.edu	hg19	20	47628619	47628619	+	Silent	SNP	C	C	A	rs371146257	alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	ARFGEF2	NM_006420	exon28	c.C3916A	p.R1306R	AGGCCTCGGGTTC	.	109.0	61.0	97.0	0.0	.	160	.	.	.	alt	.	.	PASS	Atlas-SNP
CDH26	60437	hgsc.bcm.edu	hg19	20	58569544	58569544	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CDH26	NM_177980	exon11	c.G1666C	p.G556R	AATTGGGGTGAGT	.	74.0	24.0	62.0	0.0	.	229	.	.	.	none	.	.	PASS	Atlas-SNP
NCAM2	4685	hgsc.bcm.edu	hg19	21	22849618	22849618	+	Missense_Mutation	SNP	A	A	G	rs201923816		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	NCAM2	NM_004540	exon15	c.A1903G	p.K635E	AAAGATAAGGAAG	.	36.0	12.0	45.0	0.0	.	220	.	.	.	weak	A|0.999;G|0.001	0.001	PASS	Atlas-SNP
MRPL40	64976	hgsc.bcm.edu	hg19	22	19423455	19423455	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MRPL40	NM_003776	exon4	c.G591T	p.K197N	CACCAAGGTGTAC	.	63.0	23.0	80.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
KLHL22	84861	hgsc.bcm.edu	hg19	22	20796432	20796432	+	Silent	SNP	G	G	C	rs149300605	alternate_allele	TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	KLHL22	NM_032775	exon7	c.C1833G	p.A611A	CGGGTCGGCCTGG	.	67.0	26.0	65.0	0.0	.	52	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
CELSR1	9620	hgsc.bcm.edu	hg19	22	46765598	46765598	+	Silent	SNP	A	A	G	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CELSR1	NM_014246	exon26	c.T7863C	p.A2621A	TATAACAGCTCCG	.	63.0	24.0	78.0	0.0	.	242	.	.	.	none	.	.	PASS	Atlas-SNP
MIOX	55586	hgsc.bcm.edu	hg19	22	50926723	50926723	+	Silent	SNP	G	G	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	MIOX	NM_017584	exon5	c.G360T	p.G120G	CGTCGGGCTCCTG	.	38.0	16.0	65.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
THOC2	57187	hgsc.bcm.edu	hg19	X	122755201	122755201	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	THOC2	NM_001081550	exon31	c.A4023T	p.K1341N	CTTAAATTTCTCA	.	68.0	56.0	74.0	0.0	.	310	.	.	.	none	.	.	PASS	Atlas-SNP
FBXO36	130888	hgsc.bcm.edu	hg19	2	230861514	230861516	+	In_Frame_Del	DEL	AAT	AAT	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	FBXO36	NM_174899	exon3	c.252_254del	p.84_85del	.	.	115.0	47.0	152.0	0.0	.	22	.	0.408696	0	none	.	.	PASS	Atlas-INDEL
SCAPER	49855	hgsc.bcm.edu	hg19	15	76726602	76726603	+	Frame_Shift_Ins	INS	-	-	TA	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SCAPER	NM_020843	exon25	c.3128_3129insTA	p.K1043fs	.	.	95.0	36.0	91.0	0.0	.	160	.	0.378947	0	none	.	.	PASS	Atlas-INDEL
PIP5K1C	23396	hgsc.bcm.edu	hg19	19	3653310	3653310	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PIP5K1C	NM_012398	exon7	c.900delG	p.K300fs	.	.	67.0	24.0	74.0	0.0	.	63	.	0.358209	0	none	.	.	PASS	Atlas-INDEL
WWC3	55841	hgsc.bcm.edu	hg19	X	10094307	10094307	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	WWC3	NM_015691	exon15	c.2066delA	p.Y689fs	.	.	78.0	11.0	85.0	0.0	.	142	.	0.141026	0	none	.	.	PASS	Atlas-INDEL
CEP63	80254	hgsc.bcm.edu	hg19	3	134267996	134267996	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CEP63	NM_025180	exon11	c.1159delG	p.E387fs	.	.	52.0	16.0	38.0	0.0	.	56	.	0.307692	0	none	.	.	PASS	Atlas-INDEL
POLR3C	10623	hgsc.bcm.edu	hg19	1	145592731	145592731	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	POLR3C	NM_006468	exon15	c.1565delT	p.L522fs	.	.	83.0	30.0	96.0	0.0	.	41	.	0.361446	0	none	.	.	PASS	Atlas-INDEL
SHROOM3	57619	hgsc.bcm.edu	hg19	4	77661360	77661360	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SHROOM3	NM_020859	exon5	c.2033delT	p.L678fs	.	.	165.0	83.0	156.0	0.0	.	134	.	0.50303	0	none	.	.	PASS	Atlas-INDEL
PRMT6	55170	hgsc.bcm.edu	hg19	1	107600260	107600260	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	PRMT6	NM_018137	exon1	c.922delT	p.S308fs	.	.	83.0	37.0	93.0	0.0	.	55	.	0.445783	0	none	.	.	PASS	Atlas-INDEL
GPANK1	7918	hgsc.bcm.edu	hg19	6	31632033	31632035	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	GPANK1	NM_001199238	exon3	c.222_224del	p.74_75del	.	.	92.0	34.0	95.0	0.0	.	19	.	0.369565	0	none	.	.	PASS	Atlas-INDEL
CHMP2A	27243	hgsc.bcm.edu	hg19	19	59063432	59063433	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CHMP2A	NM_198426	exon4	c.469_470insA	p.E157fs	.	.	216.0	80.0	281.0	0.0	.	25	.	0.37037	0	none	.	.	PASS	Atlas-INDEL
DDX58	23586	hgsc.bcm.edu	hg19	9	32467853	32467868	+	Frame_Shift_Del	DEL	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	AGGTGGCAATCAGAAT	AGGTGGCAATCAGAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	DDX58	NM_014314	exon15	c.2078_2093del	p.693_698del	.	.	56.0	17.0	79.0	0.0	.	82	.	0.303571	0	none	.	.	PASS	Atlas-INDEL
CHD8	57680	hgsc.bcm.edu	hg19	14	21870158	21870158	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	CHD8	NM_001170629	exon19	c.4021delA	p.I1341fs	.	.	141.0	63.0	151.0	0.0	.	339	.	0.446809	0	none	.	.	PASS	Atlas-INDEL
SMG1	23049	hgsc.bcm.edu	hg19	16	18856931	18856931	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8517-01A-11D-2396-08	TCGA-A4-8517-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d231371b-1540-4abd-bde7-41846fb8a9a1	4ccb3bcc-4c0f-4047-97fc-0515f0cf05b5	.	SMG1	NM_015092	exon39	c.6040delA	p.M2014X	.	.	140.0	84.0	99.0	0.0	.	401	.	0.6	0	none	.	.	PASS	Atlas-INDEL