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
IPO13	9670	hgsc.bcm.edu	hg19	1	44423086	44423086	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	IPO13	NM_014652	exon7	c.C1405A	p.L469I	GAGGCCCTCCTCT	.	69.0	54.0	153.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
RRP15	51018	hgsc.bcm.edu	hg19	1	218480910	218480910	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	RRP15	NM_016052	exon4	c.T641G	p.L214W	GTGTTTTGAGAGG	.	28.0	24.0	59.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
GALNT2	2590	hgsc.bcm.edu	hg19	1	230385000	230385000	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	GALNT2	NM_004481	exon9	c.C888A	p.N296K	GGGGAACCCAGTC	.	29.0	18.0	74.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
RGS7	6000	hgsc.bcm.edu	hg19	1	241094065	241094065	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	RGS7	NM_002924	exon6	c.C337G	p.P113A	AATAGGGGGTCTG	.	81.0	68.0	173.0	0.0	.	308	.	.	.	none	.	.	PASS	Atlas-SNP
SLC40A1	30061	hgsc.bcm.edu	hg19	2	190428363	190428363	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SLC40A1	NM_014585	exon7	c.T1349A	p.V450E	ATGGGCACAGATT	.	95.0	40.0	118.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
HECW2	57520	hgsc.bcm.edu	hg19	2	197187250	197187250	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	HECW2	NM_020760	exon7	c.G836A	p.G279E	AGTTTCCCCAGAA	.	194.0	77.0	223.0	0.0	.	239	.	.	.	none	.	.	PASS	Atlas-SNP
ABCB6	10058	hgsc.bcm.edu	hg19	2	220075814	220075814	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ABCB6	NM_005689	exon15	c.T1985C	p.L662P	GACCGGAGAGAGG	.	142.0	55.0	183.0	0.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
SEC13	6396	hgsc.bcm.edu	hg19	3	10342967	10342967	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SEC13	NM_183352	exon9	c.A947G	p.E316G	TGGCCCTCTGTCA	.	98.0	40.0	130.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
MLH1	4292	hgsc.bcm.edu	hg19	3	37042512	37042512	+	Missense_Mutation	SNP	G	G	A	rs63750133	alternate_allele	TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	MLH1	NM_000249	exon3	c.G274A	p.A92T	GATTTAGCCAGTA	.	82.0	41.0	111.0	0.0	.	226	.	.	.	alt	.	.	PASS	Atlas-SNP
XYLB	9942	hgsc.bcm.edu	hg19	3	38404484	38404484	+	Silent	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	XYLB	NM_005108	exon4	c.C267G	p.V89V	TCAAGTCCTAGCC	.	109.0	48.0	116.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
SMARCC1	6599	hgsc.bcm.edu	hg19	3	47716999	47716999	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	SMARCC1,NS,carcinoma,0,1	SMARCC1	NM_003074	exon18	c.G1805C	p.R602P	TCAGTACGGAGAC	.	49.0	2.0	49.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
SLC38A3	10991	hgsc.bcm.edu	hg19	3	50257565	50257565	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SLC38A3	NM_006841	exon16	c.A1471G	p.I491V	ATCATCATTGACT	.	13.0	10.0	14.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
ABHD10	55347	hgsc.bcm.edu	hg19	3	111700691	111700691	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ABHD10	NM_001272069	exon2	c.A203G	p.Y68C	TGGCTTATAAGAA	.	140.0	62.0	136.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
ZMAT3	64393	hgsc.bcm.edu	hg19	3	178785387	178785387	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	ZMAT3,NS,carcinoma,0,1	ZMAT3	NM_022470	exon2	c.G154T	p.E52X	ATAACTCTTCTTC	.	123.0	45.0	161.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
SPOCK3	50859	hgsc.bcm.edu	hg19	4	167713322	167713322	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SPOCK3	NM_016950	exon8	c.C717A	p.S239R	CTTACTGCTTCTC	.	60.0	4.0	75.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGEF28	64283	hgsc.bcm.edu	hg19	5	73205322	73205322	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	.	NM_001080479	exon34	c.T4247A	p.I1416N	ACTCTATCCTCCG	.	20.0	10.0	30.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
SEMA6A	57556	hgsc.bcm.edu	hg19	5	115822558	115822558	+	Silent	SNP	G	G	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SEMA6A	NM_020796	exon10	c.C849T	p.C283C	AACTGAGCAGTTC	.	137.0	59.0	136.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
SLC25A48	153328	hgsc.bcm.edu	hg19	5	135178132	135178132	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SLC25A48	NM_145282	exon2	c.C74A	p.P25H	GCCACCCTCTGGA	.	204.0	69.0	180.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP17	64901	hgsc.bcm.edu	hg19	5	170323085	170323085	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	RANBP17	NM_022897	exon5	c.T455A	p.I152K	GAGTAATAATCCT	.	106.0	43.0	90.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
SLC17A4	10050	hgsc.bcm.edu	hg19	6	25773825	25773825	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SLC17A4	NM_005495	exon8	c.G910A	p.E304K	TTCTGTGAATACT	.	92.0	36.0	89.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
MUC21	394263	hgsc.bcm.edu	hg19	6	30955264	30955264	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	MUC21	NM_001010909	exon2	c.T1312A	p.S438T	ACCAACTCTGGGT	.	179.0	75.0	211.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
MCM3	4172	hgsc.bcm.edu	hg19	6	52141973	52141973	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	MCM3,pharynx,carcinoma,0,1	MCM3	NM_002388	exon8	c.C1192G	p.Q398E	GAAGCTGAGACTT	.	39.0	12.0	65.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1549	57670	hgsc.bcm.edu	hg19	7	138597164	138597164	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	KIAA1549	NM_020910	exon3	c.T2921G	p.I974S	TCTTTGATTGCTG	.	71.0	43.0	71.0	0.0	.	314	.	.	.	none	.	.	PASS	Atlas-SNP
ATP6V0E2	155066	hgsc.bcm.edu	hg19	7	149576654	149576654	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ATP6V0E2	NM_001100592	exon3	c.C530G	p.P177R	AATACCCGCACTG	.	28.0	19.0	25.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
LYN	4067	hgsc.bcm.edu	hg19	8	56922610	56922610	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	LYN	NM_002350	exon13	c.C1480A	p.Q494K	TACTTACAGAGCG	.	103.0	39.0	125.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
GEM	2669	hgsc.bcm.edu	hg19	8	95262646	95262646	+	Silent	SNP	G	G	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	GEM	NM_181702	exon5	c.C783T	p.S261S	GGGCATGCTCTCC	.	67.0	25.0	83.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
BNC2	54796	hgsc.bcm.edu	hg19	9	16552664	16552664	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	BNC2	NM_017637	exon5	c.G533A	p.G178E	TGTGTCCCATAGA	.	97.0	4.0	96.0	0.0	.	166	.	.	.	none	.	.	PASS	Atlas-SNP
OR13J1	392309	hgsc.bcm.edu	hg19	9	35869823	35869823	+	Silent	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	OR13J1	NM_001004487	exon1	c.G576A	p.T192T	GACCGACGTGTTG	.	56.0	18.0	89.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
SECISBP2	79048	hgsc.bcm.edu	hg19	9	91965762	91965762	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SECISBP2	NM_024077	exon14	c.C2108T	p.S703L	TACAGTCAAAAGG	.	67.0	34.0	75.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
RAD23B	5887	hgsc.bcm.edu	hg19	9	110091836	110091836	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	RAD23B,colon,carcinoma,0,1	RAD23B	NM_002874	exon10	c.G1129A	p.G377R	GCATTAGGATTTC	.	102.0	33.0	114.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
RABGAP1	23637	hgsc.bcm.edu	hg19	9	125751642	125751642	+	Silent	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	RABGAP1	NM_012197	exon5	c.C657T	p.V219V	CTGTGTCAGAGGG	.	90.0	44.0	119.0	0.0	.	164	.	.	.	none	.	.	PASS	Atlas-SNP
MLLT10	8028	hgsc.bcm.edu	hg19	10	22022934	22022934	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	MLLT10_ENST00000377072,NS,carcinoma,0,2	MLLT10	NM_004641	exon21	c.A2782T	p.I928F	AATGGCATTGTAG	.	78.0	33.0	86.0	0.0	.	183	.	.	.	none	.	.	PASS	Atlas-SNP
ANXA11	311	hgsc.bcm.edu	hg19	10	81927005	81927005	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ANXA11	NM_145868	exon6	c.T626G	p.L209R	TTCCGCAGGACCT	.	61.0	31.0	70.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
SLC35F2	54733	hgsc.bcm.edu	hg19	11	107677532	107677532	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SLC35F2	NM_017515	exon4	c.T485G	p.V162G	TGGATCACTCTGT	.	81.0	32.0	100.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
SLC6A12	6539	hgsc.bcm.edu	hg19	12	308019	308019	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SLC6A12	NM_001122848	exon8	c.T790A	p.Y264N	CCTGGTAGGCTCC	.	128.0	69.0	104.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
KDM5A	5927	hgsc.bcm.edu	hg19	12	401948	401948	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	KDM5A	NM_001042603	exon27	c.T4843C	p.C1615R	TTTGGCAGTTCTG	.	151.0	48.0	137.0	0.0	.	307	.	.	.	none	.	.	PASS	Atlas-SNP
C12orf5	57103	hgsc.bcm.edu	hg19	12	4461705	4461705	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	C12orf5	NM_020375	exon6	c.C661G	p.L221V	GCCACTCTGAGCA	.	125.0	49.0	136.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
GPR162	27239	hgsc.bcm.edu	hg19	12	6933600	6933600	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	GPR162	NM_019858	exon2	c.T536C	p.F179S	TCGGCTTTGGCGT	.	97.0	39.0	131.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
ITPR2	3709	hgsc.bcm.edu	hg19	12	26809443	26809443	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ITPR2	NM_002223	exon19	c.G2231C	p.R744P	TACTGGCGATCCA	.	85.0	27.0	91.0	0.0	.	270	.	.	.	none	.	.	PASS	Atlas-SNP
DIP2B	57609	hgsc.bcm.edu	hg19	12	51092173	51092173	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	DIP2B	NM_173602	exon18	c.A2111G	p.Y704C	TGAGCTATGGGGT	.	104.0	38.0	117.0	0.0	.	167	.	.	.	none	.	.	PASS	Atlas-SNP
ESPL1	9700	hgsc.bcm.edu	hg19	12	53680427	53680427	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ESPL1	NM_012291	exon18	c.C3907A	p.P1303T	AGTGTCCCTGGCT	.	79.0	40.0	103.0	0.0	.	158	.	.	.	none	.	.	PASS	Atlas-SNP
GLIPR1L2	144321	hgsc.bcm.edu	hg19	12	75785104	75785104	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	GLIPR1L2	NM_152436	exon1	c.C208A	p.P70T	GTCATTCCCCGAG	.	81.0	39.0	92.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
CUL4A	8451	hgsc.bcm.edu	hg19	13	113915023	113915023	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	CUL4A	NM_001008895	exon19	c.C2134G	p.H712D	CTTGGTCATAATC	.	31.0	14.0	43.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
LAMP1	3916	hgsc.bcm.edu	hg19	13	113963979	113963979	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	LAMP1	NM_005561	exon3	c.T205C	p.S69P	CTGCCATCAGATG	.	115.0	45.0	110.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
NEMF	9147	hgsc.bcm.edu	hg19	14	50292672	50292672	+	Missense_Mutation	SNP	G	G	A	rs370101877		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	NEMF	NM_004713	exon16	c.C1490T	p.A497V	TTGAATGCCTATT	.	23.0	17.0	47.0	0.0	.	79	.	.	.	weak	.	.	PASS	Atlas-SNP
PPM1A	5494	hgsc.bcm.edu	hg19	14	60712638	60712638	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	PPM1A	NM_177952	exon1	c.A73G	p.R25G	AAAAGAAGAATGG	.	4.0	4.0	12.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
MYO5A	4644	hgsc.bcm.edu	hg19	15	52606371	52606371	+	Silent	SNP	T	T	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	MYO5A	NM_000259	exon40	c.A5364G	p.P1788P	ATTAACTGGAGTA	.	82.0	29.0	88.0	0.0	.	145	.	.	.	none	.	.	PASS	Atlas-SNP
SRRM2	23524	hgsc.bcm.edu	hg19	16	2812806	2812806	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SRRM2	NM_016333	exon11	c.C2277G	p.S759R	GCGGAGCAGGTCT	.	285.0	170.0	237.0	0.0	.	263	.	.	.	none	.	.	PASS	Atlas-SNP
PRKCB	5579	hgsc.bcm.edu	hg19	16	23848699	23848699	+	Silent	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	PRKCB	NM_212535	exon2	c.C177T	p.G59G	CAGGGGCTTCGGG	.	342.0	202.0	337.0	1.0	.	383	.	.	.	none	.	.	PASS	Atlas-SNP
ZC3H18	124245	hgsc.bcm.edu	hg19	16	88653085	88653085	+	Silent	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ZC3H18	NM_144604	exon3	c.C681T	p.F227F	GTTCTTCATGAAA	.	74.0	18.0	44.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
SAT2	112483	hgsc.bcm.edu	hg19	17	7530935	7530935	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SAT2	NM_133491	exon1	c.C19T	p.R7X	CCTCTCGGATCCG	.	58.0	18.0	77.0	0.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
LINGO3	645191	hgsc.bcm.edu	hg19	19	2290213	2290213	+	Silent	SNP	C	C	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	LINGO3	NM_001101391	exon2	c.G1563A	p.P521P	GTCGAGCGGCGCG	.	59.0	23.0	47.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF557	79230	hgsc.bcm.edu	hg19	19	7075688	7075688	+	Silent	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ZNF557	NM_001044387	exon4	c.C54G	p.A18A	CCCAGCCTCTCAG	.	108.0	52.0	140.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
CACNA1A	773	hgsc.bcm.edu	hg19	19	13346025	13346025	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	CACNA1A	NM_001127221	exon33	c.C5134T	p.Q1712X	TCACCTGCATCCC	.	15.0	5.0	21.0	0.0	.	715	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF461	92283	hgsc.bcm.edu	hg19	19	37147417	37147417	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ZNF461	NM_153257	exon4	c.C165G	p.I55M	TGAGGAGATTACG	.	78.0	32.0	94.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
ERCC2	2068	hgsc.bcm.edu	hg19	19	45868315	45868315	+	Silent	SNP	G	G	A	rs139263710	alternate_allele	TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	ERCC2	NM_000400	exon6	c.C462T	p.H154H	TCGGCAGTGGGGC	.	50.0	23.0	60.0	0.0	.	78	.	.	.	alt	G|1.000;C|0.000	.	PASS	Atlas-SNP
BAX	581	hgsc.bcm.edu	hg19	19	49464330	49464330	+	Silent	SNP	T	T	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	BAX	NM_004324	exon5	c.T633C	p.Y211Y	GGTCTATAATGCG	.	96.0	45.0	83.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF816-ZNF321P	100529240	hgsc.bcm.edu	hg19	19	53432286	53432286	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	.	NM_001202473	exon4	c.T572C	p.L191S	GATGTCAAAATTA	.	200.0	89.0	214.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
NLRP9	338321	hgsc.bcm.edu	hg19	19	56244868	56244868	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	NLRP9	NM_176820	exon2	c.T329A	p.I110K	TCCCATATGAGTT	.	124.0	57.0	149.0	0.0	.	163	.	.	.	none	.	.	PASS	Atlas-SNP
MZF1	7593	hgsc.bcm.edu	hg19	19	59073766	59073766	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	MZF1	NM_198055	exon6	c.C1878A	p.H626Q	ACCGCAGTGGTAG	.	17.0	11.0	16.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
CPXM1	56265	hgsc.bcm.edu	hg19	20	2776796	2776796	+	Silent	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	CPXM1	NM_001184699	exon10	c.G1254C	p.L418L	GCCCACCAGCTCT	.	83.0	32.0	101.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
HUNK	30811	hgsc.bcm.edu	hg19	21	33371363	33371363	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	HUNK	NM_014586	exon11	c.A2011C	p.M671L	GGACAGATGTTAA	.	114.0	36.0	143.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	hg19	22	18293513	18293513	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	MICAL3	NM_015241	exon28	c.A5512G	p.R1838G	CCTGTCTCCGAGC	.	76.0	26.0	68.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
POLR2F	5435	hgsc.bcm.edu	hg19	22	38355418	38355418	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	POLR2F	NM_021974	exon3	c.C156G	p.I52M	GCGAATCACCACA	.	230.0	99.0	294.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
KDELR3	11015	hgsc.bcm.edu	hg19	22	38875733	38875733	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	KDELR3	NM_016657	exon3	c.A328G	p.N110D	CTTGAAAACTACA	.	386.0	171.0	418.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
ND1	10625	hgsc.bcm.edu	hg19	MT	3316	3316	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	.	ENST00000361390	exon1	c.G10A	p.A4T	CCCATGGCCAACC	.	5.0	5.0	0.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	hg19	21	38568034	38568035	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	TTC3	NM_003316	exon42	c.5276_5277insT	p.S1759fs	.	.	305.0	129.0	340.0	0.0	.	182	.	0.422951	0	none	.	.	PASS	Atlas-INDEL
HSPA9	3313	hgsc.bcm.edu	hg19	5	137904733	137904733	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	HSPA9	NM_004134	exon5	c.417delT	p.N139fs	.	.	103.0	40.0	100.0	0.0	.	49	.	0.38835	0	none	.	.	PASS	Atlas-INDEL
SEMA3D	223117	hgsc.bcm.edu	hg19	7	84636164	84636164	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SEMA3D	NM_152754	exon16	c.1863delT	p.T621fs	.	.	441.0	305.0	276.0	0.0	.	177	.	0.69161	0	none	.	.	PASS	Atlas-INDEL
DISP2	85455	hgsc.bcm.edu	hg19	15	40661086	40661086	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	DISP2	NM_033510	exon8	c.2772delC	p.Y924X	.	.	98.0	40.0	138.0	0.0	.	86	.	0.408163	0	none	.	.	PASS	Atlas-INDEL
KIAA1109	84162	hgsc.bcm.edu	hg19	4	123229112	123229112	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	KIAA1109	NM_015312	exon56	c.9849delG	p.L3283fs	.	.	171.0	65.0	193.0	0.0	.	424	.	0.380117	0	none	.	.	PASS	Atlas-INDEL
SIDT2	51092	hgsc.bcm.edu	hg19	11	117058116	117058118	+	In_Frame_Del	DEL	TTC	TTC	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SIDT2	NM_001040455	exon11	c.1037_1039del	p.346_347del	.	.	153.0	58.0	170.0	0.0	.	82	.	0.379085	0	none	.	.	PASS	Atlas-INDEL
FERD3L	222894	hgsc.bcm.edu	hg19	7	19184646	19184646	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	FERD3L	NM_152898	exon1	c.341delT	p.M114fs	.	.	80.0	26.0	64.0	0.0	.	63	.	0.325	0	none	.	.	PASS	Atlas-INDEL
DLGAP5	9787	hgsc.bcm.edu	hg19	14	55655750	55655751	+	Frame_Shift_Ins	INS	-	-	AT	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	DLGAP5	NM_014750	exon2	c.148_149insAT	p.V50fs	.	.	43.0	28.0	58.0	0.0	.	84	.	0.651163	0	none	.	.	PASS	Atlas-INDEL
MOCS2	4338	hgsc.bcm.edu	hg19	5	52397195	52397196	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	MOCS2	NM_004531	exon5	c.371_372insA	p.R124fs	.	.	175.0	83.0	175.0	0.0	.	28	.	0.474286	0	none	.	.	PASS	Atlas-INDEL
CHMP3	51652	hgsc.bcm.edu	hg19	2	86790455	86790455	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	.	NM_001193517	exon1	c.18delG	p.K6fs	.	.	219.0	93.0	223.0	0.0	.	.	.	0.424658	0	none	.	.	PASS	Atlas-INDEL
RAD54B	25788	hgsc.bcm.edu	hg19	8	95419720	95419720	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	RAD54B	NM_012415	exon5	c.729delT	p.N243fs	.	.	116.0	58.0	99.0	0.0	.	88	.	0.5	0	none	.	.	PASS	Atlas-INDEL
NEIL2	252969	hgsc.bcm.edu	hg19	8	11637150	11637150	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	NEIL2	NM_001135746	exon3	c.181delG	p.E61fs	.	.	190.0	91.0	183.0	0.0	.	14	.	0.478947	0	none	.	.	PASS	Atlas-INDEL
PKD1	5310	hgsc.bcm.edu	hg19	16	2155478	2155488	+	Splice_Site	DEL	GGGGCAGGCAG	GGGGCAGGCAG	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	GGGGCAGGCAG	GGGGCAGGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	PKD1	.	.	.	.	.	.	99.0	18.0	190.0	0.0	.	184	.	0.181818	0	none	.	.	PASS	Atlas-INDEL
SLC30A1	7779	hgsc.bcm.edu	hg19	1	211749303	211749308	+	In_Frame_Del	DEL	ATCTAA	ATCTAA	-	novel		TCGA-GL-8500-01A-11D-2396-08	TCGA-GL-8500-10A-01D-2396-08	ATCTAA	ATCTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	41177191-296c-48e7-945d-6b382e01efef	c4639d70-5aff-4a23-b1bd-33ce71bff272	.	SLC30A1	NM_021194	exon2	c.947_952del	p.316_318del	.	.	95.0	72.0	214.0	0.0	.	27	.	0.757895	0	none	.	.	PASS	Atlas-INDEL
