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
SKI	6497	hgsc.bcm.edu	hg19	1	2238153	2238153	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	SKI	NM_003036	exon7	c.G2136A	p.R712R	GCCGCGGGCCCGC	.	26.0	21.0	0.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
ARID1A	8289	hgsc.bcm.edu	hg19	1	27101241	27101241	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ARID1A	NM_006015	exon18	c.A4523G	p.Y1508C	ATAATTATGCCAA	.	70.0	20.0	92.0	0.0	.	842	.	.	.	none	.	.	PASS	Atlas-SNP
DLGAP3	58512	hgsc.bcm.edu	hg19	1	35331687	35331687	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	DLGAP3	NM_001080418	exon10	c.G2937A	p.L979L	CGGTCACAGCCTG	.	45.0	13.0	1.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD35	148741	hgsc.bcm.edu	hg19	1	145567075	145567075	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ANKRD35	NM_144698	exon12	c.C2923T	p.H975Y	AGGAATCATCTAC	.	142.0	38.0	165.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
PKP1	5317	hgsc.bcm.edu	hg19	1	201285751	201285751	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	PKP1,NS,carcinoma,0,1	PKP1	NM_001005337	exon4	c.G772A	p.D258N	TCCCAGGATGAGA	.	207.0	54.0	250.0	1.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
TAF5L	27097	hgsc.bcm.edu	hg19	1	229730727	229730727	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	TAF5L	NM_014409	exon5	c.G1087A	p.D363N	ACATGTCTTCAGA	.	85.0	5.0	110.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
GKN1	56287	hgsc.bcm.edu	hg19	2	69207170	69207170	+	Silent	SNP	A	A	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	GKN1	NM_019617	exon5	c.A483G	p.T161T	TCCAACATACATG	.	207.0	41.0	248.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
DCAF17	80067	hgsc.bcm.edu	hg19	2	172333421	172333421	+	Silent	SNP	T	T	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	DCAF17	NM_025000	exon11	c.T1143A	p.S381S	GATCTCTGAAGAT	.	144.0	29.0	150.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
SLC40A1	30061	hgsc.bcm.edu	hg19	2	190437577	190437577	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	SLC40A1	NM_014585	exon4	c.G382T	p.V128F	CGAGAACCCATCC	.	215.0	42.0	196.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
GLS	2744	hgsc.bcm.edu	hg19	2	191795284	191795284	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	GLS	NM_014905	exon13	c.A1547G	p.H516R	GAATTCACTTTTG	.	119.0	31.0	120.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
PGAP1	80055	hgsc.bcm.edu	hg19	2	197791195	197791195	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	PGAP1	NM_024989	exon1	c.A146T	p.Q49L	CTTACCTGATACT	.	220.0	40.0	197.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
SGOL2	151246	hgsc.bcm.edu	hg19	2	201438489	201438489	+	Silent	SNP	T	T	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	SGOL2	NM_001160046	exon7	c.T3420G	p.S1140S	TTTGTCTGAGATA	.	74.0	13.0	80.0	0.0	.	126	.	.	.	none	.	.	PASS	Atlas-SNP
COPG1	22820	hgsc.bcm.edu	hg19	3	128993744	128993744	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	.	NM_016128	exon22	c.G2320T	p.A774S	TTCGAAGCAGCCT	.	313.0	63.0	279.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COPG1	22820	hgsc.bcm.edu	hg19	3	128993745	128993745	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	.	NM_016128	exon22	c.C2321A	p.A774E	TCGAAGCAGCCTG	.	313.0	64.0	283.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1239	57495	hgsc.bcm.edu	hg19	4	37447184	37447184	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	KIAA1239	NM_001144990	exon7	c.G3574A	p.V1192M	AGTGAGGTGGTCA	.	88.0	25.0	77.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
HPSE	10855	hgsc.bcm.edu	hg19	4	84240579	84240579	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	HPSE	NM_001199830	exon3	c.G417C	p.K139N	CCGTAACTTCTCC	.	113.0	17.0	104.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
GRID2	2895	hgsc.bcm.edu	hg19	4	94436380	94436380	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	GRID2,NS,carcinoma,0,1	GRID2	NM_001510	exon13	c.C2011T	p.L671F	CAGGACCTTTCCA	.	81.0	16.0	83.0	0.0	.	233	.	.	.	none	.	.	PASS	Atlas-SNP
ADH6	130	hgsc.bcm.edu	hg19	4	100129912	100129912	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ADH6	NM_000672	exon6	c.A741T	p.L247F	TTTCTTTAAGTCC	.	148.0	39.0	123.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
LARP7	51574	hgsc.bcm.edu	hg19	4	113568519	113568519	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	LARP7	NM_001267039	exon9	c.C832A	p.Q278K	CAAAAGCAGTGCT	.	147.0	16.0	126.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
IQGAP2	10788	hgsc.bcm.edu	hg19	5	75902074	75902074	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	IQGAP2	NM_006633	exon12	c.G1303A	p.E435K	TGGAATGAAATTC	.	122.0	27.0	109.0	0.0	.	186	.	.	.	none	.	.	PASS	Atlas-SNP
DDX41	51428	hgsc.bcm.edu	hg19	5	176940458	176940458	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	DDX41	NM_016222	exon11	c.G1126C	p.A376P	TGGTGGCACTGAA	.	135.0	27.0	146.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
HECW1	23072	hgsc.bcm.edu	hg19	7	43484075	43484075	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	HECW1	NM_015052	exon11	c.C1304A	p.P435H	TGGGACCTGAAGG	.	118.0	23.0	131.0	0.0	.	540	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	hg19	7	48563956	48563956	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ABCA13	NM_152701	exon54	c.A14164C	p.N4722H	TTATACAACCTTA	.	138.0	30.0	167.0	0.0	.	1192	.	.	.	none	.	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	hg19	7	149518182	149518182	+	Silent	SNP	C	C	T	rs199773714		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	.	NM_198455	exon87	c.C12525T	p.C4175C	CTCATGCGGGCCC	.	37.0	6.0	13.0	0.0	.	.	.	.	.	weak	.	.	PASS	Atlas-SNP
EFR3A	23167	hgsc.bcm.edu	hg19	8	132996502	132996502	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	EFR3A	NM_015137	exon15	c.T1692G	p.N564K	GGCTAATGAAGAA	.	82.0	15.0	86.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
OC90	729330	hgsc.bcm.edu	hg19	8	133041425	133041425	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	OC90	NM_001080399	exon13	c.T1033A	p.C345S	AGCAGCACCTAAG	.	95.0	15.0	107.0	0.0	.	163	.	.	.	none	.	.	PASS	Atlas-SNP
OC90	729330	hgsc.bcm.edu	hg19	8	133041426	133041426	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	OC90	NM_001080399	exon13	c.G1032A	p.R344R	GCAGCACCTAAGA	.	94.0	14.0	105.0	0.0	.	163	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA2	20	hgsc.bcm.edu	hg19	9	139907277	139907277	+	Silent	SNP	C	C	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ABCA2	NM_212533	exon31	c.G5058C	p.V1686V	CCCGCCCACACTG	.	157.0	23.0	59.0	0.0	.	113	.	.	.	none	.	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	hg19	10	61833342	61833342	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ANK3	NM_020987	exon37	c.G7297T	p.D2433Y	AAGAGTCATCAGA	.	111.0	18.0	102.0	0.0	.	703	.	.	.	none	.	.	PASS	Atlas-SNP
ENTPD7	57089	hgsc.bcm.edu	hg19	10	101421214	101421214	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ENTPD7	NM_020354	exon3	c.C20A	p.S7Y	GTTTTTCCTACCT	.	61.0	16.0	71.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	hg19	10	101715503	101715503	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	DNMBP	NM_015221	exon4	c.C1728A	p.H576Q	TGAAAAGTGGCGT	.	55.0	8.0	67.0	0.0	.	173	.	.	.	none	.	.	PASS	Atlas-SNP
CYP17A1	1586	hgsc.bcm.edu	hg19	10	104590667	104590667	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	CYP17A1	NM_000102	exon8	c.G1319A	p.R440H	CAGGAGCGAGGTC	.	151.0	31.0	177.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
NLRP6	171389	hgsc.bcm.edu	hg19	11	284253	284253	+	Missense_Mutation	SNP	A	A	G	rs150530901		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	NLRP6	NM_138329	exon6	c.A2225G	p.D742G	TCCCTGACGCGGT	.	87.0	25.0	60.0	0.0	.	4	.	.	.	weak	A|1.000;G|0.000	0.000	PASS	Atlas-SNP
CTSD	1509	hgsc.bcm.edu	hg19	11	1785082	1785082	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	CTSD	NM_001909	exon1	c.C8T	p.P3L	CTGGAGGGCTGCA	.	23.0	13.0	0.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
MRGPRX4	117196	hgsc.bcm.edu	hg19	11	18195097	18195097	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	MRGPRX4,NS,carcinoma,0,1	MRGPRX4	NM_054032	exon1	c.C294T	p.L98L	AATCCTCGTTTCT	.	187.0	33.0	235.0	1.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
LRP5	4041	hgsc.bcm.edu	hg19	11	68181318	68181318	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	LRP5,NS,carcinoma,0,1	LRP5	NM_002335	exon12	c.G2665T	p.V889L	GACTTCGTGATGG	.	67.0	23.0	59.0	1.0	.	136	.	.	.	none	.	.	PASS	Atlas-SNP
DNAJC14	85406	hgsc.bcm.edu	hg19	12	56217194	56217194	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	DNAJC14	NM_032364	exon3	c.G1506C	p.E502D	CTCATACTCCTTT	.	86.0	15.0	76.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
DDX54	79039	hgsc.bcm.edu	hg19	12	113610195	113610195	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	DDX54	NM_024072	exon11	c.C1242T	p.S414S	GGGGAAGCTGTAG	.	215.0	72.0	175.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
MIS18BP1	55320	hgsc.bcm.edu	hg19	14	45693181	45693181	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	MIS18BP1	NM_018353	exon11	c.G2609A	p.C870Y	GGTAAGCATTCTA	.	50.0	14.0	57.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
STOML1	9399	hgsc.bcm.edu	hg19	15	74281093	74281093	+	Silent	SNP	A	A	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	STOML1	NM_001256672	exon4	c.T441C	p.F147F	GATGCGAAACTGG	.	71.0	15.0	89.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
LMAN1L	79748	hgsc.bcm.edu	hg19	15	75111060	75111060	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	LMAN1L	NM_021819	exon5	c.G499T	p.D167Y	CACAGGGATGGAG	.	68.0	24.0	56.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
ST8SIA2	8128	hgsc.bcm.edu	hg19	15	93007416	93007416	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ST8SIA2	NM_006011	exon6	c.T929A	p.I310N	AACAAATCTACCT	.	74.0	18.0	119.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
ST8SIA2	8128	hgsc.bcm.edu	hg19	15	93007417	93007417	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ST8SIA2	NM_006011	exon6	c.C930T	p.I310I	ACAAATCTACCTC	.	76.0	19.0	119.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
MMP15	4324	hgsc.bcm.edu	hg19	16	58079023	58079023	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	MMP15	NM_002428	exon10	c.G1683C	p.E561D	CCAGGAGCACGTG	.	90.0	28.0	50.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
CLEC18B	497190	hgsc.bcm.edu	hg19	16	74447559	74447559	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	CLEC18B	NM_001011880	exon4	c.T472A	p.S158T	GGCTTGAGGTGGC	.	245.0	21.0	270.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
CTDNEP1	23399	hgsc.bcm.edu	hg19	17	7147902	7147902	+	Silent	SNP	A	A	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	CTDNEP1	NM_001143775	exon7	c.T642C	p.L214L	GTTGAGAAGGGCT	.	58.0	18.0	63.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
CHD3	1107	hgsc.bcm.edu	hg19	17	7794342	7794342	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	CHD3	NM_001005271	exon4	c.C646G	p.H216D	GATTACCACACGC	.	196.0	47.0	184.0	0.0	.	169	.	.	.	none	.	.	PASS	Atlas-SNP
SLC47A1	55244	hgsc.bcm.edu	hg19	17	19449787	19449787	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	SLC47A1	NM_018242	exon3	c.T277C	p.S93P	GGCTTATCTTCTG	.	172.0	36.0	156.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
TLK2	11011	hgsc.bcm.edu	hg19	17	60679418	60679418	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	TLK2_ENST00000346027,NS,carcinoma,0,3	TLK2	NM_006852	exon19	c.T1736A	p.V579E	TTTTAGTAAATGG	.	81.0	5.0	52.0	0.0	.	223	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC37A3	374819	hgsc.bcm.edu	hg19	17	62855782	62855782	+	Silent	SNP	A	A	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	LRRC37A3	NM_199340	exon11	c.T4482A	p.I1494I	ATGAGCAATGAGC	.	433.0	90.0	440.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
CBX4	8535	hgsc.bcm.edu	hg19	17	77807927	77807927	+	Missense_Mutation	SNP	A	A	G	rs200965379		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	CBX4,uveal_tract,malignant_melanoma,0,1	CBX4	NM_003655	exon5	c.T1514C	p.V505A	GCCGCCACCGCCA	.	29.0	5.0	4.0	1.0	.	40	.	.	.	weak	.	.	PASS	Atlas-SNP
MC5R	4161	hgsc.bcm.edu	hg19	18	13826448	13826448	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	MC5R,NS,carcinoma,0,1	MC5R	NM_005913	exon1	c.G684A	p.A228A	CTCTGCGCGGCAG	.	125.0	28.0	45.0	1.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF780A	284323	hgsc.bcm.edu	hg19	19	40578806	40578806	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ZNF780A	NM_001142579	exon8	c.T435A	p.F145L	ATAACCAAATGCA	.	59.0	4.0	69.0	0.0	.	156	.	.	.	none	.	.	PASS	Atlas-SNP
PRR19	284338	hgsc.bcm.edu	hg19	19	42814045	42814045	+	Silent	SNP	C	C	A	rs78424339	bycluster;alternate_allele	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	PRR19,NS,carcinoma,0,1	PRR19	NM_199285	exon2	c.C309A	p.P103P	ACTCCCCGCCAAG	.	61.0	3.0	40.0	1.0	.	30	.	.	.	alt	C|0.500;T|0.500	.	PASS	Atlas-SNP
DLGAP4	22839	hgsc.bcm.edu	hg19	20	35064566	35064566	+	Missense_Mutation	SNP	G	G	A	rs199988815	bycluster	TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	DLGAP4	NM_014902	exon3	c.G1054A	p.D352N	GAGACGGATGCCG	.	34.0	21.0	1.0	0.0	.	111	.	.	.	weak	.	.	PASS	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	hg19	21	43241557	43241557	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	PRDM15,NS,carcinoma,0,1	PRDM15	NM_022115	exon23	c.G3024A	p.L1008L	GTGCTTCAGGTAC	.	105.0	24.0	115.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	hg19	22	50716444	50716444	+	Splice_Site	SNP	T	T	C	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	PLXNB2	NM_012401	exon33	c.4888-2A>G	.	GTGCCCTGTGGGG	.	124.0	17.0	97.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	hg19	7	151919708	151919708	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	MLL3	NM_170606	exon21	c.3384delC	p.D1128fs	.	.	336.0	59.0	343.0	0.0	.	1564	.	0.175595	0	none	.	.	PASS	Atlas-Indel,Pindel
MON2	23041	hgsc.bcm.edu	hg19	12	62954348	62954349	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	MON2	NM_015026	exon26	c.3487_3488insT	p.L1163fs	.	.	43.0	11.0	30.0	0.0	.	160	.	0.255814	0	none	.	.	PASS	Atlas-INDEL
NUP98	4928	hgsc.bcm.edu	hg19	11	3789956	3789956	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	NUP98	NM_016320	exon8	c.804delA	p.T268fs	.	.	52.0	12.0	49.0	0.0	.	149	.	0.230769	0	none	.	.	PASS	Atlas-INDEL
MYH3	4621	hgsc.bcm.edu	hg19	17	10558280	10558281	+	Frame_Shift_Del	DEL	GG	GG	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	MYH3	NM_002470	exon3	c.102_103del	p.34_35del	.	.	164.0	38.0	150.0	0.0	.	227	.	0.231707	0	none	.	.	PASS	Atlas-Indel,Pindel
MTA1	9112	hgsc.bcm.edu	hg19	14	105936238	105936239	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	MTA1	NM_004689	exon20	c.1906_1907insG	p.R636fs	.	.	139.0	28.0	153.0	0.0	.	61	.	0.201439	0	none	.	.	PASS	Atlas-Indel,Pindel
LAMB1	3912	hgsc.bcm.edu	hg19	7	107592551	107592555	+	Frame_Shift_Del	DEL	TCACA	TCACA	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TCACA	TCACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	LAMB1	NM_002291	exon23	c.3194_3198del	p.1065_1066del	.	.	211.0	19.0	240.0	0.0	.	185	.	0.0900474	0	none	.	.	PASS	Atlas-INDEL
LAMB1	3912	hgsc.bcm.edu	hg19	7	107592557	107592562	+	In_Frame_Del	DEL	TTCTGC	TTCTGC	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TTCTGC	TTCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	LAMB1	NM_002291	exon23	c.3187_3192del	p.1063_1064del	.	.	200.0	19.0	219.0	0.0	.	185	.	0.095	0	none	.	.	PASS	Atlas-INDEL
RDH16	8608	hgsc.bcm.edu	hg19	12	57346721	57346721	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	RDH16	NM_003708	exon3	c.627delC	p.F209fs	.	.	90.0	31.0	55.0	0.0	.	33	.	0.344444	0	none	.	.	PASS	Atlas-Indel,Pindel
OSGIN2	734	hgsc.bcm.edu	hg19	8	90936735	90936736	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	OSGIN2	NM_001126111	exon6	c.625_626insT	p.L209fs	.	.	83.0	16.0	56.0	0.0	.	73	.	0.192771	0	none	.	.	PASS	Atlas-INDEL
KDM1B	221656	hgsc.bcm.edu	hg19	6	18218101	18218101	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	KDM1B	NM_153042	exon17	c.1673delT	p.V558fs	.	.	97.0	22.0	95.0	0.0	.	58	.	0.226804	0	none	.	.	PASS	Atlas-Indel,Pindel
ZBTB1	22890	hgsc.bcm.edu	hg19	14	64989255	64989256	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ZBTB1	NM_001123329	exon2	c.1033_1034insT	p.I345fs	.	.	151.0	36.0	216.0	0.0	.	93	.	0.238411	0	none	.	.	PASS	Atlas-Indel,Pindel
HEATR5B	54497	hgsc.bcm.edu	hg19	2	37286106	37286107	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	HEATR5B	NM_019024	exon13	c.1874_1875insT	p.C625fs	.	.	284.0	57.0	309.0	0.0	.	185	.	0.200704	0	none	.	.	PASS	Atlas-Indel,Pindel
TRPC4AP	26133	hgsc.bcm.edu	hg19	20	33603843	33603844	+	Frame_Shift_Ins	INS	-	-	AA	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	TRPC4AP	NM_015638	exon10	c.1318_1319insTT	p.H440fs	.	.	143.0	32.0	135.0	0.0	.	64	.	0.223776	0	none	.	.	PASS	Atlas-Indel,Pindel
FHL5	9457	hgsc.bcm.edu	hg19	6	97053903	97053904	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	FHL5	NM_020482	exon5	c.459_460del	p.153_154del	.	.	139.0	35.0	146.0	0.0	.	73	.	0.251799	0	none	.	.	PASS	Atlas-Indel,Pindel
CDH12	1010	hgsc.bcm.edu	hg19	5	21751876	21751876	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	CDH12	NM_004061	exon15	c.2356delG	p.E786fs	.	.	121.0	33.0	111.0	0.0	.	238	.	0.272727	0	none	.	.	PASS	Atlas-Indel,Pindel
ATPAF2	91647	hgsc.bcm.edu	hg19	17	17942265	17942266	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	ATPAF2	NM_145691	exon1	c.63_64insG	p.G21fs	.	.	145.0	11.0	44.0	0.0	.	15	.	0.0758621	0	none	.	.	PASS	Atlas-INDEL
LAMA3	3909	hgsc.bcm.edu	hg19	18	21508155	21508158	+	Frame_Shift_Del	DEL	GATT	GATT	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	GATT	GATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	LAMA3	NM_198129	exon63	c.8245_8248del	p.2749_2750del	.	.	208.0	41.0	215.0	0.0	.	397	.	0.197115	0	none	.	.	PASS	Atlas-Indel,Pindel
LAMB1	3912	hgsc.bcm.edu	hg19	7	107592551	107592562	+	In_Frame_Del	DEL	TCACAGTTCTGC	TCACAGTTCTGC	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	TCACAGTTCTGC	TCACAGTTCTGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	LAMB1	NM_002291	exon23	c.3187_3198del	p.1063_1066del	.	.	210.0	23.0	228.0	0.0	.	185	.	0.110	.	none	.	.	PASS	Pindel
POLR1B	84172	hgsc.bcm.edu	hg19	2	113330280	113330285	+	In_Frame_Del	DEL	CCAATG	CCAATG	-	novel		TCGA-PJ-A5Z8-01A-11D-A28G-10	TCGA-PJ-A5Z8-10A-01D-A28G-10	CCAATG	CCAATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8661bd12-fa20-4263-b1ab-034a4b225560	32a7ff68-4d91-4377-bc04-dd8688d15196	.	POLR1B	NM_019014	exon13	c.2215_2220del	p.739_740del	.	.	120.0	10.0	172.0	0.0	.	95	.	0.083	.	none	.	.	PASS	Pindel