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
FAM132A	388581	hgsc.bcm.edu	hg19	1	1179848	1179848	+	Silent	SNP	G	G	C	rs200735866	by1000genomes;alternate_allele	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	FAM132A	NM_001014980	exon2	c.C207G	p.S69S	GGCGTCGGAGAAC	.	90.0	18.0	104.0	0.0	.	12	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
KCNAB2	8514	hgsc.bcm.edu	hg19	1	6142274	6142274	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	KCNAB2	NM_001199862	exon5	c.C320A	p.T107N	TCATGACCTTGGC	.	80.0	29.0	97.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
SPEN	23013	hgsc.bcm.edu	hg19	1	16258337	16258337	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SPEN	NM_015001	exon11	c.T5602G	p.L1868V	TTGGAATTGAAGA	.	67.0	48.0	81.0	0.0	.	374	.	.	.	none	.	.	PASS	Atlas-SNP
SLC44A3	126969	hgsc.bcm.edu	hg19	1	95360468	95360468	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SLC44A3	NM_001114106	exon15	c.T1952C	p.I651T	AGGCCATTGTGAG	.	294.0	58.0	295.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
ATXN7L2	127002	hgsc.bcm.edu	hg19	1	110029635	110029635	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ATXN7L2	NM_153340	exon4	c.G305C	p.R102T	AAAGAAGACATGG	.	130.0	17.0	124.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
AXDND1	126859	hgsc.bcm.edu	hg19	1	179460842	179460842	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	AXDND1	NM_144696	exon19	c.A2261C	p.K754T	CAAGGAAGTTGTA	.	309.0	52.0	309.0	0.0	.	142	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF281	23528	hgsc.bcm.edu	hg19	1	200376815	200376815	+	Silent	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ZNF281	NM_012482	exon2	c.A2019G	p.Q673Q	AGCCTGTTGGAGG	.	66.0	13.0	53.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
HS1BP3	64342	hgsc.bcm.edu	hg19	2	20818857	20818857	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	HS1BP3	NM_022460	exon7	c.G1069C	p.A357P	GCCCAGCCACAGC	.	210.0	93.0	153.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC121	79635	hgsc.bcm.edu	hg19	2	27850548	27850548	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CCDC121	NM_001142683	exon2	c.T605C	p.L202P	TATTCCAGAAAGA	.	129.0	39.0	125.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
ALK	238	hgsc.bcm.edu	hg19	2	29420473	29420473	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ALK	NM_004304	exon27	c.G4008T	p.Q1336H	AACTTCCTGGTTG	.	82.0	37.0	74.0	0.0	.	533	.	.	.	none	.	.	PASS	Atlas-SNP
RGPD3	653489	hgsc.bcm.edu	hg19	2	107073432	107073432	+	Silent	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	RGPD3	NM_001144013	exon4	c.C400T	p.L134L	CCTTTAGTTTATA	.	384.0	132.0	342.0	0.0	.	316	.	.	.	none	.	.	PASS	Atlas-SNP
SCN2A	6326	hgsc.bcm.edu	hg19	2	166153545	166153545	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SCN2A	NM_001040143	exon2	c.A286T	p.K96X	TTGAATAAAGGGA	.	200.0	105.0	174.0	0.0	.	589	.	.	.	none	.	.	PASS	Atlas-SNP
LRP2	4036	hgsc.bcm.edu	hg19	2	170055306	170055306	+	Silent	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	LRP2	NM_004525	exon45	c.T8568C	p.P2856P	ATAAGTAGGGTTT	.	149.0	49.0	119.0	0.0	.	751	.	.	.	none	.	.	PASS	Atlas-SNP
PGAP1	80055	hgsc.bcm.edu	hg19	2	197784853	197784853	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PGAP1	NM_024989	exon2	c.C169A	p.L57M	TTGCCAGTTTCTT	.	56.0	28.0	43.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
FARP2	9855	hgsc.bcm.edu	hg19	2	242407764	242407764	+	Silent	SNP	C	C	G	rs138469271	alternate_allele	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	FARP2	NM_014808	exon18	c.C2103G	p.P701P	CAGCCCCGGGCAC	.	93.0	36.0	89.0	0.0	.	92	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
MKRN2	23609	hgsc.bcm.edu	hg19	3	12611673	12611673	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MKRN2	NM_014160	exon3	c.G259A	p.V87I	TCCGAGGTCACTG	.	83.0	77.0	76.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
POC1A	25886	hgsc.bcm.edu	hg19	3	52181040	52181040	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	POC1A	NM_015426	exon5	c.G527T	p.S176I	TCCCGGCTGCTCT	.	127.0	32.0	150.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	hg19	3	52637647	52637647	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PBRM1	NM_018313	exon18	c.C2669A	p.A890E	CTGAGTGCCGGTG	.	32.0	28.0	23.0	0.0	.	1252	.	.	.	none	.	.	PASS	Atlas-SNP
SLMAP	7871	hgsc.bcm.edu	hg19	3	57743531	57743531	+	Silent	SNP	A	A	G	rs147270008		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SLMAP	NM_007159	exon1	c.A153G	p.L51L	AGTGCTATCAAGG	.	282.0	236.0	317.0	2.0	.	46	.	.	.	weak	A|1.000;G|0.000	0.000	PASS	Atlas-SNP
THPO	7066	hgsc.bcm.edu	hg19	3	184090635	184090635	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	THPO	NM_000460	exon6	c.T728G	p.I243S	CCGGGGATTTGGT	.	150.0	49.0	126.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
EIF4A2	1974	hgsc.bcm.edu	hg19	3	186503770	186503770	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	EIF4A2	NM_001967	exon5	c.G447T	p.Q149H	ACTGCAGGCTGAA	.	149.0	34.0	121.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF622	90441	hgsc.bcm.edu	hg19	5	16465479	16465479	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ZNF622	NM_033414	exon1	c.T296C	p.V99A	GCCTGCACGGCCT	.	155.0	31.0	148.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
MYO10	4651	hgsc.bcm.edu	hg19	5	16685914	16685914	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MYO10	NM_012334	exon29	c.T3923G	p.V1308G	GCGTGGACCTGAC	.	56.0	24.0	60.0	0.0	.	198	.	.	.	none	.	.	PASS	Atlas-SNP
CDH9	1007	hgsc.bcm.edu	hg19	5	26915851	26915851	+	Missense_Mutation	SNP	C	C	T	rs150604531		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	CDH9,NS,carcinoma,-1,1	CDH9	NM_016279	exon3	c.G410A	p.R137Q	ACCTGCCGCCCAG	.	112.0	37.0	112.0	1.0	.	305	.	.	.	weak	C|1.000;T|0.000	0.000	PASS	Atlas-SNP
GDNF	2668	hgsc.bcm.edu	hg19	5	37834925	37834925	+	Splice_Site	SNP	C	C	A	rs13169425	byhapmap	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	GDNF	NM_001190469	exon3	c.26-1G>T	.	CGGCACCTGCGCG	.	48.0	19.0	82.0	0.0	.	56	.	.	.	weak	C|1.000;|0.000	.	PASS	Atlas-SNP
PRRC1	133619	hgsc.bcm.edu	hg19	5	126860514	126860514	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PRRC1	NM_130809	exon3	c.G395C	p.G132A	TATCAGGATTTTC	.	182.0	83.0	145.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
MATR3	9782	hgsc.bcm.edu	hg19	5	138643239	138643239	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MATR3	NM_018834	exon2	c.G135A	p.M45I	AAGGATGAACCAG	.	198.0	84.0	210.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
GRPEL2	134266	hgsc.bcm.edu	hg19	5	148730494	148730494	+	Silent	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	GRPEL2	NM_152407	exon4	c.C327T	p.F109F	GAGTTTCTGTAAG	.	81.0	20.0	69.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
MDC1	9656	hgsc.bcm.edu	hg19	6	30681013	30681013	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MDC1	NM_014641	exon5	c.G706T	p.A236S	TGGCAGCTGAGGA	.	126.0	7.0	126.0	0.0	.	218	.	.	.	none	.	.	PASS	Atlas-SNP
TCP11	6954	hgsc.bcm.edu	hg19	6	35086064	35086064	+	Silent	SNP	T	T	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	TCP11	NM_001093728	exon10	c.A1533C	p.T511T	CACTTTTGTTTCC	.	202.0	87.0	179.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
KLC4	89953	hgsc.bcm.edu	hg19	6	43041648	43041648	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	KLC4	NM_201523	exon15	c.T1808C	p.M603T	GCAACATGAAGCG	.	128.0	40.0	149.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
YIPF3	25844	hgsc.bcm.edu	hg19	6	43480515	43480515	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	YIPF3	NM_015388	exon7	c.T764C	p.L255P	GTGGACAGTCCAC	.	189.0	75.0	165.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
SNAP91	9892	hgsc.bcm.edu	hg19	6	84371294	84371294	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SNAP91	NM_001242794	exon5	c.T379A	p.Y127N	TACTATAGCGCCT	.	100.0	59.0	95.0	0.0	.	199	.	.	.	none	.	.	PASS	Atlas-SNP
SPACA1	81833	hgsc.bcm.edu	hg19	6	88775941	88775941	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SPACA1	NM_030960	exon7	c.C773A	p.P258H	CTACACCTGAGGT	.	39.0	14.0	67.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
HACE1	57531	hgsc.bcm.edu	hg19	6	105298839	105298839	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	HACE1	NM_020771	exon3	c.T164A	p.F55Y	ACATCAAATTTTG	.	105.0	61.0	128.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
SOBP	55084	hgsc.bcm.edu	hg19	6	107827527	107827527	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SOBP	NM_018013	exon3	c.C317A	p.A106D	GGCTTGCCACTGG	.	89.0	16.0	96.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
NUS1	116150	hgsc.bcm.edu	hg19	6	118015319	118015319	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	NUS1	NM_138459	exon3	c.G667A	p.V223I	TTGGATGTAGATA	.	87.0	50.0	125.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
GPR126	57211	hgsc.bcm.edu	hg19	6	142691578	142691578	+	Silent	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	GPR126	NM_198569	exon4	c.C717T	p.V239V	ACCTGTCAAAGAA	.	38.0	8.0	65.0	0.0	.	192	.	.	.	none	.	.	PASS	Atlas-SNP
IGF2R	3482	hgsc.bcm.edu	hg19	6	160445676	160445676	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	IGF2R	NM_000876	exon5	c.T586C	p.Y196H	GGTGCCTACTTGG	.	172.0	47.0	198.0	0.0	.	251	.	.	.	none	.	.	PASS	Atlas-SNP
NEUROD6	63974	hgsc.bcm.edu	hg19	7	31378439	31378439	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	NEUROD6	NM_022728	exon2	c.A444T	p.E148D	CAGAATTTCAGAA	.	96.0	36.0	81.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC129	223075	hgsc.bcm.edu	hg19	7	31682718	31682718	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CCDC129	NM_001257968	exon11	c.C1812A	p.D604E	GCAGGACAGTTTT	.	138.0	61.0	136.0	0.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
HERPUD2	64224	hgsc.bcm.edu	hg19	7	35733937	35733937	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	HERPUD2	NM_022373	exon2	c.G4A	p.D2N	TTTGGTCCATGGT	.	166.0	62.0	156.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
PKD1L1	168507	hgsc.bcm.edu	hg19	7	47853600	47853600	+	Missense_Mutation	SNP	C	C	T	rs147316882		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PKD1L1	NM_138295	exon48	c.G7102A	p.G2368R	TTCCTCCAAGAGC	.	51.0	26.0	39.0	0.0	.	328	.	.	.	weak	C|1.000;T|0.000	0.000	PASS	Atlas-SNP
VWC2	375567	hgsc.bcm.edu	hg19	7	49815193	49815193	+	Silent	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	VWC2	NM_198570	exon2	c.C162T	p.D54D	TCGGGACGGCCCG	.	8.0	7.0	5.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
POMZP3	22932	hgsc.bcm.edu	hg19	7	76240801	76240801	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	POMZP3	NM_012230	exon6	c.C545A	p.S182Y	GACGTGGACCACT	.	382.0	118.0	373.0	1.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	hg19	7	82585266	82585266	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PCLO	NM_014510	exon5	c.A5003G	p.K1668R	ATTGTTTTAAATC	.	99.0	44.0	92.0	0.0	.	1506	.	.	.	none	.	.	PASS	Atlas-SNP
PRKAR2B	5577	hgsc.bcm.edu	hg19	7	106799967	106799967	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PRKAR2B	NM_002736	exon11	c.T1197A	p.Y399X	TACCTATGAAGAA	.	114.0	42.0	111.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
ADCK2	90956	hgsc.bcm.edu	hg19	7	140380887	140380887	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ADCK2	NM_052853	exon4	c.G1255T	p.D419Y	CCCGTGGACTTGA	.	287.0	122.0	278.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
RNF19A	25897	hgsc.bcm.edu	hg19	8	101276971	101276971	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	RNF19A,NS,carcinoma,0,1	RNF19A	NM_015435	exon7	c.C1234T	p.R412W	AATTCCGTTTGTG	.	98.0	23.0	100.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
RSPO2	340419	hgsc.bcm.edu	hg19	8	108970372	108970372	+	Silent	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	RSPO2	NM_178565	exon5	c.A552G	p.T184T	CAGTATTGTGTCT	.	239.0	112.0	217.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
EEF1D	1936	hgsc.bcm.edu	hg19	8	144661995	144661995	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	EEF1D	NM_001130053	exon10	c.G1911C	p.Q637H	GACACTCTGCACC	.	112.0	42.0	99.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
MELK	9833	hgsc.bcm.edu	hg19	9	36583634	36583634	+	Silent	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MELK	NM_001256688	exon3	c.A69G	p.A23A	CTTTGCAAAGGTC	.	31.0	13.0	34.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
MSS51	118490	hgsc.bcm.edu	hg19	10	75187422	75187422	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	.	NM_001024593	exon3	c.G326T	p.R109I	AGTGCTCTACAGT	.	83.0	43.0	110.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
FUT11	170384	hgsc.bcm.edu	hg19	10	75533456	75533456	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	FUT11	NM_173540	exon2	c.C1217T	p.A406V	CCCACGCGGCCTC	.	98.0	50.0	128.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
FBXO3	26273	hgsc.bcm.edu	hg19	11	33770331	33770331	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	FBXO3	NM_012175	exon9	c.G1040A	p.G347E	ACTACTCCAGGTC	.	51.0	14.0	50.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
PPP2R5B	5526	hgsc.bcm.edu	hg19	11	64694184	64694184	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PPP2R5B	NM_006244	exon3	c.A200G	p.D67G	CCCCAGATGTGCC	.	35.0	6.0	44.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
MYO7A	4647	hgsc.bcm.edu	hg19	11	76925728	76925728	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MYO7A	NM_000260	exon49	c.G6635T	p.R2212M	GCTCCAGGAGCGG	.	84.0	8.0	107.0	0.0	.	164	.	.	.	none	.	.	PASS	Atlas-SNP
C11orf93	120376	hgsc.bcm.edu	hg19	11	111179020	111179020	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	C11orf93	NM_001271458	exon5	c.C614G	p.S205W	GCGCATCGTGTGA	.	62.0	5.0	125.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
PHLDB1	23187	hgsc.bcm.edu	hg19	11	118509935	118509935	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PHLDB1	NM_001144758	exon12	c.G2702A	p.R901K	GGGGCAGGCCTTT	.	95.0	77.0	169.0	1.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
C2CD5	9847	hgsc.bcm.edu	hg19	12	22670928	22670928	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	.	NM_014802	exon8	c.C944A	p.P315H	GTTTTGGGTGTCA	.	85.0	36.0	70.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PRPH	5630	hgsc.bcm.edu	hg19	12	49690229	49690229	+	Silent	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PRPH	NM_006262	exon3	c.C621T	p.A207A	CGATGCCACTCTG	.	151.0	9.0	168.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
KRT85	3891	hgsc.bcm.edu	hg19	12	52754642	52754642	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	KRT85	NM_002283	exon9	c.G1519A	p.A507T	ACTAGGCAAAGCG	.	68.0	29.0	77.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
LRP1	4035	hgsc.bcm.edu	hg19	12	57587701	57587701	+	Silent	SNP	C	C	T	rs367824154		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	LRP1	NM_002332	exon48	c.C7824T	p.G2608G	TGTGGGCGAGTTC	.	140.0	6.0	127.0	0.0	.	428	.	.	.	weak	.	.	PASS	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	hg19	12	70932007	70932007	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PTPRB	NM_001109754	exon28	c.T5874A	p.D1958E	CGTGGCATCATCT	.	184.0	74.0	145.0	0.0	.	676	.	.	.	none	.	.	PASS	Atlas-SNP
TMCC3	57458	hgsc.bcm.edu	hg19	12	94965249	94965249	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	TMCC3	NM_020698	exon4	c.A1396G	p.I466V	ACAGGATATGGTC	.	139.0	66.0	176.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
PABPC3	5042	hgsc.bcm.edu	hg19	13	25671122	25671122	+	Silent	SNP	C	C	T	rs79072440	bycluster	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PABPC3	NM_030979	exon1	c.C786T	p.Y262Y	AATTTACGTTGGT	.	153.0	13.0	159.0	0.0	.	129	.	.	.	weak	C|0.500;T|0.500	0.500	PASS	Atlas-SNP
ABCC4	10257	hgsc.bcm.edu	hg19	13	95840715	95840715	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ABCC4	NM_005845	exon10	c.G1345T	p.A449S	TCCCTGCTCCCAC	.	112.0	23.0	140.0	0.0	.	248	.	.	.	none	.	.	PASS	Atlas-SNP
ACIN1	22985	hgsc.bcm.edu	hg19	14	23549484	23549484	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ACIN1	NM_001164814	exon6	c.G1234C	p.E412Q	TCTCCTCCTCGCT	.	239.0	111.0	222.0	0.0	.	147	.	.	.	none	.	.	PASS	Atlas-SNP
SAMD4A	23034	hgsc.bcm.edu	hg19	14	55203876	55203876	+	Missense_Mutation	SNP	C	C	T	rs138744574	bycluster;byfrequency;alternate_allele	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SAMD4A	NM_015589	exon3	c.C850T	p.L284F	CAGTGCCTCCCAT	.	130.0	52.0	140.0	0.0	.	68	.	.	.	alt	C|0.999;A|0.001	.	PASS	Atlas-SNP
SYNE2	23224	hgsc.bcm.edu	hg19	14	64610587	64610587	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SYNE2	NM_182914	exon83	c.A15404G	p.Y5135C	AGCGCTATGAAAG	.	169.0	88.0	216.0	1.0	.	577	.	.	.	none	.	.	PASS	Atlas-SNP
MTHFD1	4522	hgsc.bcm.edu	hg19	14	64924942	64924942	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MTHFD1	NM_005956	exon27	c.T2729C	p.M910T	GCACAATGCCTGG	.	57.0	24.0	67.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
RDH11	51109	hgsc.bcm.edu	hg19	14	68159767	68159767	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	RDH11	NM_001252650	exon2	c.A77C	p.K26T	AGCATTTTCCTGC	.	93.0	35.0	96.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
NUSAP1	51203	hgsc.bcm.edu	hg19	15	41657726	41657726	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	NUSAP1	NM_016359	exon7	c.A787G	p.T263A	CAGAGTACCTTGG	.	88.0	32.0	72.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
TP53BP1	7158	hgsc.bcm.edu	hg19	15	43771711	43771711	+	Silent	SNP	T	T	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	TP53BP1	NM_001141980	exon7	c.A672G	p.E224E	CTGTTCTTCATGC	.	287.0	103.0	270.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
CATSPER2	117155	hgsc.bcm.edu	hg19	15	43940128	43940128	+	Silent	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	CATSPER2,right_upper_lobe,carcinoma,0,1	CATSPER2	NM_172097	exon2	c.C132T	p.I44I	CTCCCTGATAGTG	.	454.0	184.0	486.0	2.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
DAPK2	23604	hgsc.bcm.edu	hg19	15	64204316	64204316	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	DAPK2	NM_014326	exon10	c.G939C	p.R313S	CCACCGCCTGCGG	.	64.0	38.0	47.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
SENP8	123228	hgsc.bcm.edu	hg19	15	72432461	72432461	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SENP8	NM_001166340	exon2	c.A497T	p.Y166F	GGATGTACGTGAT	.	33.0	10.0	33.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
PARP6	56965	hgsc.bcm.edu	hg19	15	72543559	72543559	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PARP6	NM_020214	exon16	c.C1297T	p.P433S	TGAGAGGTAGTTT	.	100.0	48.0	90.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
OR4F6	390648	hgsc.bcm.edu	hg19	15	102346642	102346642	+	Silent	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	OR4F6	NM_001005326	exon1	c.G720T	p.L240L	TATGCTGTCAGCT	.	124.0	42.0	180.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
PLK1	5347	hgsc.bcm.edu	hg19	16	23690422	23690422	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PLK1	NM_005030	exon1	c.C169A	p.R57S	CGGGGCCGCTTTT	.	157.0	60.0	98.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
LONP2	83752	hgsc.bcm.edu	hg19	16	48311386	48311386	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	LONP2	NM_031490	exon8	c.T1379G	p.L460R	CTCTGCTTGAGGT	.	188.0	63.0	123.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
GUCY2D	3000	hgsc.bcm.edu	hg19	17	7910749	7910749	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	GUCY2D_ENST00000254854,NS,carcinoma,0,1	GUCY2D	NM_000180	exon6	c.G1469A	p.R490Q	GGCACCGGCTACT	.	88.0	6.0	90.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
SGK494	0	hgsc.bcm.edu	hg19	17	26938587	26938587	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	.	NM_001174103	exon9	c.T809C	p.M270T	TCACCCATGTACT	.	116.0	39.0	89.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
EFCAB5	374786	hgsc.bcm.edu	hg19	17	28296149	28296149	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	EFCAB5	NM_198529	exon4	c.A531T	p.K177N	TGACAAACTTCTA	.	118.0	52.0	162.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
PTRF	284119	hgsc.bcm.edu	hg19	17	40557359	40557359	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PTRF	NM_012232	exon2	c.A519T	p.K173N	CGACTCTTTCAGC	.	20.0	4.0	16.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
MBTD1	54799	hgsc.bcm.edu	hg19	17	49302371	49302371	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MBTD1	NM_017643	exon3	c.T152G	p.M51R	TCACCCATGCCAG	.	86.0	26.0	100.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
NAT9	26151	hgsc.bcm.edu	hg19	17	72768142	72768142	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	NAT9	NM_015654	exon6	c.A446C	p.N149T	GGTTCATTTCCTT	.	126.0	54.0	108.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
CARD14	79092	hgsc.bcm.edu	hg19	17	78166392	78166392	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CARD14	NM_024110	exon9	c.G1330A	p.D444N	GACAGCGACTGCA	.	203.0	43.0	210.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
DSG3	1830	hgsc.bcm.edu	hg19	18	29038453	29038453	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	DSG3	NM_001944	exon4	c.T262G	p.S88A	CGAATCTCTGGAG	.	108.0	56.0	102.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	hg19	19	1059069	1059069	+	Silent	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ABCA7	NM_019112	exon40	c.G5448T	p.G1816G	CCTGGGGATTCCC	.	118.0	28.0	116.0	0.0	.	174	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF799	90576	hgsc.bcm.edu	hg19	19	12502558	12502558	+	Silent	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	NM_001080821	exon4	c.G654A	p.T218T	AGTGTGCGTTCTC	.	99.0	39.0	160.0	1.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
CD97	976	hgsc.bcm.edu	hg19	19	14517156	14517156	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CD97	NM_078481	exon15	c.G1835T	p.C612F	TGCGCTGCCGCCT	.	28.0	15.0	18.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
IFI30	10437	hgsc.bcm.edu	hg19	19	18288015	18288015	+	Silent	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	IFI30	NM_006332	exon5	c.C549T	p.R183R	GGACCGCGGCATG	.	160.0	34.0	215.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	hg19	19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T	rs111727691	bycluster	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ZNF814	NM_001144989	exon3	c.C968A	p.P323H	TCATAAGGTCTTT	.	131.0	13.0	108.0	0.0	.	93	.	.	.	weak	G|0.500;T|0.500	0.500	PASS	Atlas-SNP
ZNF814	730051	hgsc.bcm.edu	hg19	19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T	rs113623532	bycluster	TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ZNF814	NM_001144989	exon3	c.G965A	p.R322K	TAAGGTCTTTTCC	.	122.0	12.0	103.0	0.0	.	93	.	.	.	weak	C|0.500;T|0.500	0.500	PASS	Atlas-SNP
CHD6	84181	hgsc.bcm.edu	hg19	20	40143495	40143495	+	Silent	SNP	C	C	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CHD6	NM_032221	exon4	c.G651T	p.T217T	TGGGTTCGTCAGG	.	99.0	38.0	92.0	0.0	.	312	.	.	.	none	.	.	PASS	Atlas-SNP
MYBL2	4605	hgsc.bcm.edu	hg19	20	42328636	42328636	+	Silent	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	MYBL2	NM_002466	exon7	c.C903T	p.I301I	CCTCATCCCTGCT	.	82.0	34.0	92.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
WFDC8	90199	hgsc.bcm.edu	hg19	20	44181865	44181865	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	WFDC8	NM_181510	exon5	c.C496A	p.P166T	AAGGTGGACACTC	.	131.0	51.0	147.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
BCAS4	55653	hgsc.bcm.edu	hg19	20	49458324	49458324	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	BCAS4	NM_198799	exon4	c.C376T	p.H126Y	GTTGGACACCACG	.	250.0	109.0	333.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
ZDHHC8	29801	hgsc.bcm.edu	hg19	22	20128194	20128194	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ZDHHC8	NM_001185024	exon6	c.A715T	p.N239Y	TGTGGGAATGTGG	.	32.0	16.0	40.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
POLA1	5422	hgsc.bcm.edu	hg19	X	24744126	24744126	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	POLA1	NM_016937	exon13	c.T1328A	p.I443K	TTGAGATACCTGA	.	34.0	26.0	99.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
SLC25A53	401612	hgsc.bcm.edu	hg19	X	103349337	103349337	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	.	NM_001012755	exon2	c.G604A	p.G202S	CCAGGCCATCCTG	.	84.0	12.0	66.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COL4A5	1287	hgsc.bcm.edu	hg19	X	107938134	107938134	+	Missense_Mutation	SNP	G	G	A	rs104886424		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	COL4A5	NM_000495	exon49	c.G4786A	p.G1596S	TGGATTGGTTATT	.	219.0	9.0	184.0	0.0	.	262	.	.	.	weak	.	.	PASS	Atlas-SNP
FUT10	84750	hgsc.bcm.edu	hg19	8	33246682	33246683	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	FUT10	NM_032664	exon4	c.1011_1012insT	p.I337fs	.	.	311.0	126.0	301.0	0.0	.	62	.	0.405145	0	none	.	.	PASS	Atlas-Indel,Pindel
NPTX1	4884	hgsc.bcm.edu	hg19	17	78449367	78449367	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	NPTX1	NM_002522	exon2	c.597delC	p.V199fs	.	.	130.0	55.0	98.0	0.0	.	28	.	0.423077	0	none	.	.	PASS	Atlas-Indel,Pindel
RBM33	155435	hgsc.bcm.edu	hg19	7	155534581	155534582	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	RBM33	NM_053043	exon13	c.2118_2119insA	p.S706fs	.	.	165.0	69.0	190.0	0.0	.	157	.	0.418182	0	none	.	.	PASS	Atlas-Indel,Pindel
RPSA	3921	hgsc.bcm.edu	hg19	3	39453553	39453556	+	Frame_Shift_Del	DEL	GTAT	GTAT	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	GTAT	GTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	RPSA	NM_001012321	exon5	c.793_793del	p.265_265del	.	.	23.0	17.0	39.0	0.0	.	15	.	0.73913	0	none	.	.	PASS	Atlas-Indel,Pindel
CD6	923	hgsc.bcm.edu	hg19	11	60778597	60778605	+	In_Frame_Del	DEL	AGTCACTAT	AGTCACTAT	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AGTCACTAT	AGTCACTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CD6	NM_006725	exon6	c.1139_1147del	p.380_383del	.	.	171.0	38.0	230.0	0.0	.	122	.	0.222222	0	none	.	.	PASS	Atlas-Indel,Pindel
HEPHL1	341208	hgsc.bcm.edu	hg19	11	93797512	93797529	+	In_Frame_Del	DEL	ATTCAGGGACACGGAATG	ATTCAGGGACACGGAATG	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	ATTCAGGGACACGGAATG	ATTCAGGGACACGGAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	HEPHL1	NM_001098672	exon4	c.643_660del	p.215_220del	.	.	68.0	15.0	130.0	0.0	.	144	.	0.220588	0	none	.	.	PASS	Atlas-Indel,Pindel
KCNH3	23416	hgsc.bcm.edu	hg19	12	49951017	49951018	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	KCNH3	NM_012284	exon14	c.2626_2627del	p.876_876del	.	.	126.0	51.0	131.0	0.0	.	88	.	0.404762	0	none	.	.	PASS	Atlas-Indel,Pindel
HNRNPUL2	221092	hgsc.bcm.edu	hg19	11	62491416	62491416	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	HNRNPUL2	NM_001079559	exon3	c.722delA	p.E241fs	.	.	157.0	95.0	215.0	0.0	.	41	.	0.605096	0	none	.	.	PASS	Atlas-Indel,Pindel
CCDC42B	387885	hgsc.bcm.edu	hg19	12	113593105	113593106	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CCDC42B	NM_001144872	exon6	c.730_731del	p.244_244del	.	.	80.0	35.0	62.0	0.0	.	3	.	0.4375	0	none	.	.	PASS	Atlas-Indel,Pindel
DNALI1	7802	hgsc.bcm.edu	hg19	1	38027791	38027793	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	DNALI1	NM_003462	exon5	c.751_753del	p.251_251del	.	.	110.0	56.0	119.0	0.0	.	25	.	0.509091	0	none	.	.	PASS	Atlas-Indel,Pindel
TMPRSS11A	339967	hgsc.bcm.edu	hg19	4	68777111	68777111	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	TMPRSS11A	NM_182606	exon10	c.1216delA	p.T406fs	.	.	163.0	70.0	206.0	0.0	.	74	.	0.429448	0	none	.	.	PASS	Atlas-INDEL
EPS15L1	58513	hgsc.bcm.edu	hg19	19	16548668	16548669	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	EPS15L1	NM_021235	exon5	c.222_223del	p.74_75del	.	.	113.0	34.0	103.0	0.0	.	81	.	0.300885	0	none	.	.	PASS	Atlas-Indel,Pindel
EFCAB14	9813	hgsc.bcm.edu	hg19	1	47144193	47144194	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	.	NM_014774	exon11	c.1428_1429del	p.476_477del	.	.	56.0	21.0	89.0	0.0	.	.	.	0.375	0	none	.	.	PASS	Atlas-Indel,Pindel
SETD2	29072	hgsc.bcm.edu	hg19	3	47163966	47163967	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SETD2	NM_014159	exon3	c.2160_2161insG	p.G720fs	.	.	49.0	37.0	71.0	0.0	.	721	.	0.755102	0	none	.	.	PASS	Atlas-Indel,Pindel
CTTNBP2NL	55917	hgsc.bcm.edu	hg19	1	112999419	112999419	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	CTTNBP2NL	NM_018704	exon6	c.1304delA	p.K435fs	.	.	142.0	88.0	120.0	0.0	.	65	.	0.619718	0	none	.	.	PASS	Atlas-Indel,Pindel
ZNF648	127665	hgsc.bcm.edu	hg19	1	182026912	182026918	+	Frame_Shift_Del	DEL	TTCCTCT	TTCCTCT	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TTCCTCT	TTCCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ZNF648	NM_001009992	exon2	c.229_235del	p.77_79del	.	.	160.0	31.0	121.0	0.0	.	111	.	0.19375	0	none	.	.	PASS	Atlas-Indel,Pindel
FANCI	55215	hgsc.bcm.edu	hg19	15	89801970	89801970	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	FANCI	NM_001113378	exon3	c.119delG	p.G40fs	.	.	102.0	46.0	82.0	0.0	.	129	.	0.45098	0	none	.	.	PASS	Atlas-Indel,Pindel
SLC17A3	10786	hgsc.bcm.edu	hg19	6	25850278	25850278	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	SLC17A3	NM_001098486	exon9	c.1122delA	p.L374fs	.	.	99.0	41.0	95.0	0.0	.	95	.	0.414141	0	none	.	.	PASS	Atlas-Indel,Pindel
RCAN3	11123	hgsc.bcm.edu	hg19	1	24840954	24840954	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	RCAN3	NM_001251980	exon1	c.91delG	p.E31fs	.	.	264.0	121.0	325.0	0.0	.	22	.	0.458333	0	none	.	.	PASS	Atlas-Indel,Pindel
PCLO	27445	hgsc.bcm.edu	hg19	7	82579041	82579041	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PCLO	NM_014510	exon6	c.10864delG	p.V3622fs	.	.	111.0	46.0	87.0	0.0	.	1506	.	0.414414	0	none	.	.	PASS	Atlas-Indel,Pindel
PDCD11	22984	hgsc.bcm.edu	hg19	10	105205187	105205189	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PDCD11	NM_014976	exon36	c.5496_5498del	p.1832_1833del	.	.	209.0	56.0	218.0	0.0	.	160	.	0.267943	0	none	.	.	PASS	Atlas-Indel,Pindel
ARID2	196528	hgsc.bcm.edu	hg19	12	46205220	46205221	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	ARID2	NM_152641	exon4	c.303_304del	p.101_102del	.	.	82.0	33.0	85.0	0.0	.	311	.	0.402439	0	none	.	.	PASS	Atlas-Indel,Pindel
KLC4	89953	hgsc.bcm.edu	hg19	6	43041642	43041643	+	Frame_Shift_Ins	INS	-	-	CAACACGA	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	KLC4	NM_201523	exon15	c.1802_1803insCAACACGA	p.S601fs	.	.	123.0	21.0	147.0	0.0	.	89	.	0.170732	0	none	.	.	PASS	Atlas-Indel,Pindel
PXN	5829	hgsc.bcm.edu	hg19	12	120653013	120653013	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	PXN	NM_001243756	exon7	c.1040delA	p.Q347fs	.	.	68.0	28.0	84.0	0.0	.	69	.	0.411765	0	none	.	.	PASS	Atlas-Indel,Pindel
C22orf42	150297	hgsc.bcm.edu	hg19	22	32555017	32555019	+	In_Frame_Del	DEL	CTG	CTG	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	C22orf42	NM_001010859	exon1	c.185_187del	p.62_63del	.	.	274.0	49.0	290.0	0.0	.	37	.	0.178832	0	none	.	.	PASS	Atlas-Indel,Pindel
STAB1	23166	hgsc.bcm.edu	hg19	3	52555670	52555671	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	STAB1	NM_015136	exon57	c.6117_6118insT	p.C2039fs	.	.	92.0	14.0	108.0	0.0	.	178	.	0.152	.	none	.	.	PASS	Pindel
TMPRSS11A	339967	hgsc.bcm.edu	hg19	4	68777111	68777112	+	Frame_Shift_Del	DEL	GT	GT	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	TMPRSS11A	NM_182606	exon10	c.1215_1216del	p.405_406del	.	.	165.0	48.0	207.0	0.0	.	74	.	0.291	.	none	.	.	PASS	Pindel
DSP	1832	hgsc.bcm.edu	hg19	6	7562996	7562996	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-B9-A44B-01A-11D-A25F-10	TCGA-B9-A44B-10A-01D-A25F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	88e35d25-d98d-4576-8ebe-1cd74010ecd8	5d028c99-a58c-419a-b566-610dcba9cd5c	.	DSP	NM_004415	exon5	c.708delC	p.D236fs	.	.	103.0	29.0	113.0	0.0	.	306	.	0.282	.	none	.	.	PASS	Pindel