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
SNIP1	79753	hgsc.bcm.edu	hg19	1	38005993	38005993	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	SNIP1	NM_024700	exon3	c.G691C	p.A231P	GAAGTGCCCCAGA	.	118.0	63.0	113.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
CRTC2	200186	hgsc.bcm.edu	hg19	1	153926765	153926765	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	CRTC2	NM_181715	exon4	c.T400C	p.Y134H	ATAAGTAGGCAGG	.	46.0	16.0	70.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
C1orf27	54953	hgsc.bcm.edu	hg19	1	186355194	186355194	+	Silent	SNP	T	T	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	C1orf27	NM_001164245	exon4	c.T309C	p.D103D	AAATGATTTTCAA	.	84.0	37.0	117.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
ERCC3	2071	hgsc.bcm.edu	hg19	2	128051097	128051097	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	ERCC3	NM_000122	exon2	c.C226A	p.L76I	CCCAGAGGGGCCT	.	51.0	18.0	59.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
CHL1	10752	hgsc.bcm.edu	hg19	3	383612	383612	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	CHL1	NM_001253388	exon5	c.C526A	p.Q176K	ATCGAACAAGATG	.	190.0	89.0	199.0	0.0	.	242	.	.	.	none	.	.	PASS	Atlas-SNP
FYCO1	79443	hgsc.bcm.edu	hg19	3	46000087	46000087	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	FYCO1	NM_024513	exon13	c.C3612G	p.Y1204X	GCAGTAGTAACAG	.	117.0	62.0	146.0	0.0	.	115	.	.	.	none	.	.	PASS	Atlas-SNP
CELSR3	1951	hgsc.bcm.edu	hg19	3	48699894	48699894	+	Silent	SNP	G	G	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	CELSR3	NM_001407	exon1	c.C174T	p.G58G	GGCTCCGCCACCG	.	36.0	17.0	61.0	0.0	.	237	.	.	.	none	.	.	PASS	Atlas-SNP
FRMD4B	23150	hgsc.bcm.edu	hg19	3	69230503	69230503	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	FRMD4B	NM_015123	exon21	c.C2398T	p.P800S	AAGACGGTGGCTC	.	102.0	6.0	72.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	hg19	4	7783233	7783233	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	AFAP1	NM_001134647	exon13	c.C1652A	p.P551H	TCAGCAGGAGAGT	.	106.0	40.0	121.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
CTNND2	1501	hgsc.bcm.edu	hg19	5	10992734	10992734	+	Missense_Mutation	SNP	C	C	T	rs367931998		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	CTNND2,mucosal,malignant_melanoma,0,1	CTNND2	NM_001332	exon19	c.G3140A	p.R1047Q	CTTTGCCGGTCCC	.	49.0	25.0	47.0	0.0	.	289	.	.	.	weak	.	.	PASS	Atlas-SNP
HGC6.3	0	hgsc.bcm.edu	hg19	6	168377288	168377288	+	Silent	SNP	T	T	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	.	NM_001129895	exon1	c.A45G	p.G15G	GGTCATTCCCCCT	.	129.0	34.0	164.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MEOX2	4223	hgsc.bcm.edu	hg19	7	15725797	15725797	+	Silent	SNP	A	A	G	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	MEOX2,rectum,carcinoma,0,2	MEOX2	NM_005924	exon1	c.T231C	p.H77H	GTGGTGATGGTGG	.	69.0	7.0	41.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
MEOX2	4223	hgsc.bcm.edu	hg19	7	15725800	15725800	+	Silent	SNP	G	G	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	MEOX2	NM_005924	exon1	c.C228T	p.H76H	GTGATGGTGGTGG	.	35.0	9.0	11.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
DFNA5	1687	hgsc.bcm.edu	hg19	7	24784199	24784199	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	DFNA5	NM_001127453	exon3	c.T386A	p.I129N	TCTCTGATGAGCT	.	66.0	12.0	70.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
POR	5447	hgsc.bcm.edu	hg19	7	75615290	75615290	+	Silent	SNP	T	T	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	POR	NM_000941	exon14	c.T1719C	p.D573D	CTCGGATGAGGAC	.	81.0	18.0	58.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
ATP5J2-PTCD1	100526740	hgsc.bcm.edu	hg19	7	99022430	99022430	+	Silent	SNP	G	G	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	.	NM_001198879	exon7	c.C1872T	p.L624L	GTCTGTGAGAAGC	.	30.0	9.0	35.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CTSB	1508	hgsc.bcm.edu	hg19	8	11705226	11705226	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	CTSB	NM_147780	exon9	c.C638A	p.P213H	TAGCCAGGCTCAC	.	53.0	24.0	62.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
DCAF4L2	138009	hgsc.bcm.edu	hg19	8	88885869	88885869	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	DCAF4L2	NM_152418	exon1	c.G331C	p.E111Q	GGAGCTCAGGGGT	.	85.0	32.0	88.0	0.0	.	187	.	.	.	none	.	.	PASS	Atlas-SNP
PHYHIPL	84457	hgsc.bcm.edu	hg19	10	60936661	60936661	+	Silent	SNP	C	C	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	PHYHIPL	NM_032439	exon1	c.C48A	p.P16P	CAGCCCCTGTGAG	.	46.0	17.0	40.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
MRPL11	65003	hgsc.bcm.edu	hg19	11	66204727	66204727	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	MRPL11	NM_170739	exon4	c.G321C	p.E107D	TGCCACCTCTTTC	.	41.0	22.0	38.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
MTL5	9633	hgsc.bcm.edu	hg19	11	68518126	68518126	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	MTL5	NM_001039656	exon2	c.G3T	p.M1I	CTCCTCCATGGCG	.	33.0	18.0	33.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
SRGAP1	57522	hgsc.bcm.edu	hg19	12	64377795	64377795	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	SRGAP1	NM_020762	exon2	c.C136T	p.L46F	CAGCTTCTCCAGG	.	59.0	24.0	84.0	0.0	.	146	.	.	.	none	.	.	PASS	Atlas-SNP
ARL1	400	hgsc.bcm.edu	hg19	12	101799660	101799660	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	ARL1	NM_001177	exon2	c.A104G	p.Y35C	AATCTGTACAAAA	.	83.0	39.0	123.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
USP30	84749	hgsc.bcm.edu	hg19	12	109490532	109490532	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	USP30	NM_032663	exon1	c.A49T	p.I17F	AGGGCCATCCAGC	.	55.0	26.0	72.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	hg19	13	32972588	32972588	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	BRCA2	NM_000059	exon27	c.A9938C	p.K3313T	CCATAAAGAAAAA	.	125.0	51.0	104.0	0.0	.	812	.	.	.	none	.	.	PASS	Atlas-SNP
SPRY2	10253	hgsc.bcm.edu	hg19	13	80911824	80911824	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	SPRY2	NM_005842	exon2	c.A17G	p.Q6R	CCACTCTGAGCTC	.	32.0	17.0	13.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
ITPK1	3705	hgsc.bcm.edu	hg19	14	93408247	93408247	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	ITPK1	NM_001142593	exon11	c.T904A	p.Y302N	CCTCGTAGCCTGG	.	31.0	18.0	42.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
WDR20	91833	hgsc.bcm.edu	hg19	14	102675840	102675840	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	WDR20	NM_001242417	exon4	c.A1426G	p.S476G	GCTGGCAGCAAAA	.	73.0	31.0	78.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
GLCE	26035	hgsc.bcm.edu	hg19	15	69548696	69548696	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	GLCE	NM_015554	exon3	c.T551C	p.V184A	TGGAAGTCCGAGA	.	46.0	16.0	58.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
MYO9A	4649	hgsc.bcm.edu	hg19	15	72190184	72190184	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	MYO9A	NM_006901	exon25	c.G4660C	p.V1554L	TCTCTACTCTTTG	.	93.0	42.0	76.0	0.0	.	203	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM202	338949	hgsc.bcm.edu	hg19	15	72698982	72698982	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	TMEM202	NM_001080462	exon3	c.T377A	p.V126D	TCTCTGTCTTTAC	.	115.0	55.0	124.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
SCAMP5	192683	hgsc.bcm.edu	hg19	15	75309011	75309011	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	SCAMP5	NM_001178111	exon5	c.G214T	p.G72C	AACTTTGGCCTCG	.	39.0	17.0	47.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
LCAT	3931	hgsc.bcm.edu	hg19	16	67976796	67976796	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	LCAT	NM_000229	exon3	c.C395A	p.S132Y	TCCACAGAGTAGG	.	29.0	12.0	40.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM104	54868	hgsc.bcm.edu	hg19	17	72781730	72781730	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	TMEM104	NM_017728	exon3	c.T155A	p.L52Q	TGTTCCTGGGCTT	.	60.0	34.0	52.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
ACER1	125981	hgsc.bcm.edu	hg19	19	6312214	6312214	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	ACER1	NM_133492	exon3	c.G296A	p.G99D	CTATAGCCACTGC	.	68.0	24.0	87.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
C21orf2	755	hgsc.bcm.edu	hg19	21	45750162	45750162	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	C21orf2	NM_001271441	exon7	c.G1047T	p.E349D	CAGCCCCTCTGCA	.	55.0	23.0	46.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
MN1	4330	hgsc.bcm.edu	hg19	22	28192976	28192976	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	MN1	NM_002430	exon1	c.G3556A	p.A1186T	CGACGGCGCACTC	.	35.0	16.0	26.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
MID1IP1	58526	hgsc.bcm.edu	hg19	X	38664368	38664368	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	MID1IP1	NM_021242	exon2	c.G169T	p.G57C	GAGGTAGGCGGCA	.	151.0	74.0	151.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
RPA4	29935	hgsc.bcm.edu	hg19	X	96139635	96139635	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	RPA4	NM_013347	exon1	c.G326A	p.G109D	GGTTTGGTAGAGA	.	61.0	33.0	70.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
RBMX2	51634	hgsc.bcm.edu	hg19	X	129546641	129546641	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	RBMX2	NM_016024	exon6	c.A788T	p.K263M	AAGAAAAGACCAG	.	201.0	91.0	233.0	1.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
FCGR1B	2210	hgsc.bcm.edu	hg19	1	120927211	120927212	+	Frame_Shift_Del	DEL	GC	GC	-	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	FCGR1B	NM_001017986	exon5	c.769_770del	p.257_257del	.	.	508.0	66.0	611.0	0.0	.	14	.	0.129921	0	none	.	.	PASS	Atlas-INDEL
SERPINI2	5276	hgsc.bcm.edu	hg19	3	167189524	167189526	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	SERPINI2	NM_001012303	exon3	c.128_130del	p.43_44del	.	.	75.0	35.0	89.0	0.0	.	85	.	0.466667	0	none	.	.	PASS	Atlas-INDEL
ADD1	118	hgsc.bcm.edu	hg19	4	2930230	2930232	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	ADD1	NM_014189	exon15	c.2286_2288del	p.762_763del	.	.	117.0	50.0	157.0	0.0	.	56	.	0.42735	0	none	.	.	PASS	Atlas-Indel,Pindel
RPS2	6187	hgsc.bcm.edu	hg19	16	2014483	2014484	+	In_Frame_Ins	INS	-	-	CGGCCT	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	RPS2	NM_002952	exon2	c.144_145insAGGCCG	p.R48delinsRGR	.	.	59.0	19.0	55.0	0.0	.	18	.	0.322034	0	none	.	.	PASS	Atlas-INDEL
LARS	51520	hgsc.bcm.edu	hg19	5	145547749	145547751	+	In_Frame_Del	DEL	TCC	TCC	-	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	LARS	NM_020117	exon5	c.373_375del	p.125_125del	.	.	88.0	28.0	105.0	0.0	.	100	.	0.318182	0	none	.	.	PASS	Atlas-Indel,Pindel
PCDHGC5	56097	hgsc.bcm.edu	hg19	5	140870632	140870633	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	PCDHGC5	NM_018929	exon1	c.1825_1826insT	p.L609fs	.	.	38.0	19.0	40.0	0.0	.	199	.	0.5	0	none	.	.	PASS	Atlas-Indel,Pindel
FCGR1A	2209	hgsc.bcm.edu	hg19	1	149762998	149762999	+	Frame_Shift_Del	DEL	GC	GC	-	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	FCGR1A	NM_000566	exon6	c.1049_1050del	p.350_350del	.	.	416.0	26.0	431.0	0.0	.	27	.	0.0625	0	none	.	.	PASS	Atlas-INDEL
ACSBG2	81616	hgsc.bcm.edu	hg19	19	6165945	6165945	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	ACSBG2	NM_030924	exon7	c.656delA	p.Q219fs	.	.	56.0	18.0	70.0	0.0	.	83	.	0.321429	0	none	.	.	PASS	Atlas-Indel,Pindel
SERPINI2	5276	hgsc.bcm.edu	hg19	3	167189524	167189527	+	Frame_Shift_Del	DEL	AAGA	AAGA	-	novel		TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	AAGA	AAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.	SERPINI2	NM_001012303	exon3	c.127_130del	p.43_44del	.	.	79.0	30.0	87.0	0.0	.	85	.	0.380	.	none	.	.	PASS	Pindel
BCL6B	255877	hgsc.bcm.edu	hg19	17	6928020	6928031	+	In_Frame_Del	DEL	CAGCAGCAGCAG	CAGCAGCAGCAG	-	rs146207245	bycluster;by1000genomes;alternate_allele	TCGA-B1-A654-01A-11D-A31X-10	TCGA-B1-A654-10A-01D-A31X-10	CAGCAGCAGCAG	CAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	de661caf-c510-4b30-860a-a6b90ce03bdb	d5f5011d-91bc-4ca2-b4ff-2b456e1e1cbb	.,22	BCL6B	NM_181844	exon4	c.701_712del	p.234_238del	.	.	67.0	23.0	64.0	0.0	.	85	.	0.343	.	alt	.	.	PASS	Pindel
