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	dbSNP_AF	Algorithm
TTLL10	254173	hgsc.bcm.edu	hg19	1	1119315	1119315	+	Silent	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TTLL10	NM_001130045	exon12	c.G1104A	p.P368P	GAACCCGCTGCTG	.	60.0	20.0	82.0	0.0	.	66	.	.	Atlas-SNP
ARID1A	8289	hgsc.bcm.edu	hg19	1	27089690	27089690	+	Silent	SNP	G	G	C	rs149901342		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ARID1A	NM_006015	exon8	c.G2646C	p.G882G	GTCAGGGATGTGT	.	146.0	52.0	201.0	0.0	.	842	.	G|1.000;C|0.000	Atlas-SNP
RCC1	1104	hgsc.bcm.edu	hg19	1	28863259	28863259	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	RCC1	NM_001048194	exon10	c.G1031A	p.G344E	CCATAGGAAAAGC	.	51.0	19.0	49.0	0.0	.	61	.	.	Atlas-SNP
EPHA10	284656	hgsc.bcm.edu	hg19	1	38227675	38227675	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	EPHA10	NM_001099439	exon3	c.G252A	p.Q84Q	GTTGTCCTGGTTG	.	72.0	32.0	89.0	0.0	.	120	.	.	Atlas-SNP
C8A	731	hgsc.bcm.edu	hg19	1	57320606	57320606	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	C8A	NM_000562	exon1	c.T32A	p.L11X	TGTCTTTGATGAC	.	115.0	36.0	145.0	0.0	.	103	.	.	Atlas-SNP
JAK1	3716	hgsc.bcm.edu	hg19	1	65310503	65310503	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	JAK1,NS,carcinoma,0,2	JAK1	NM_002227	exon16	c.A2185T	p.S729C	ACTCACTGTCGAT	.	135.0	59.0	158.0	0.0	.	209	.	.	Atlas-SNP
CLCA1	1179	hgsc.bcm.edu	hg19	1	86948018	86948018	+	Missense_Mutation	SNP	C	C	A	rs149585400	alternate_allele	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CLCA1	NM_001285	exon5	c.C688A	p.R230S	CAATCCCGCCAGA	.	119.0	45.0	165.0	0.0	.	109	.	C|1.000;T|0.000	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	hg19	1	94522310	94522310	+	Silent	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ABCA4	NM_000350	exon15	c.C2229T	p.A743A	GATGGTGGCAGTG	.	135.0	30.0	208.0	0.0	.	275	.	.	Atlas-SNP
STXBP3	6814	hgsc.bcm.edu	hg19	1	109351498	109351498	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	STXBP3	NM_007269	exon19	c.A1778G	p.X593W	ATGAATAGCATTT	.	88.0	37.0	103.0	0.0	.	44	.	.	Atlas-SNP
KCNA10	3744	hgsc.bcm.edu	hg19	1	111059915	111059915	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	KCNA10	NM_005549	exon1	c.A1495G	p.K499E	TGGTCTTATTAAG	.	74.0	15.0	112.0	0.0	.	92	.	.	Atlas-SNP
GJA8	2703	hgsc.bcm.edu	hg19	1	147380358	147380358	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	GJA8	NM_005267	exon2	c.C276A	p.Y92X	GATGTACGTGGGG	.	79.0	56.0	70.0	0.0	.	108	.	.	Atlas-SNP
RIIAD1	284485	hgsc.bcm.edu	hg19	1	151701300	151701300	+	Silent	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	RIIAD1	NM_001144956	exon4	c.G267A	p.K89K	AGACAAGAAAGCG	.	73.0	47.0	55.0	0.0	.	6	.	.	Atlas-SNP
TCHH	7062	hgsc.bcm.edu	hg19	1	152080637	152080637	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TCHH	NM_007113	exon3	c.C5056T	p.R1686C	CTTGGCGGCGCAG	.	144.0	105.0	118.0	0.0	.	275	.	.	Atlas-SNP
CEP350	9857	hgsc.bcm.edu	hg19	1	179993651	179993651	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CEP350	NM_014810	exon14	c.T3484A	p.S1162T	GCCCAGTCTGCTG	.	105.0	13.0	85.0	0.0	.	418	.	.	Atlas-SNP
PIGR	5284	hgsc.bcm.edu	hg19	1	207106368	207106368	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PIGR	NM_002644	exon7	c.C1849T	p.Q617X	CGGCTTGATCTCT	.	76.0	6.0	56.0	0.0	.	98	.	.	Atlas-SNP
C1orf65	164127	hgsc.bcm.edu	hg19	1	223568318	223568318	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	C1orf65	NM_152610	exon1	c.A1501T	p.M501L	AGGAAGATGCGCA	.	184.0	18.0	122.0	0.0	.	71	.	.	Atlas-SNP
OBSCN	84033	hgsc.bcm.edu	hg19	1	228467638	228467638	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	OBSCN	NM_001271223	exon33	c.G8800A	p.D2934N	AAGGATGACACGC	.	150.0	10.0	148.0	0.0	.	2142	.	.	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	hg19	1	237608813	237608813	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	RYR2	NM_001035	exon14	c.G1283T	p.R428I	TCAATAGATTTAT	.	167.0	8.0	133.0	0.0	.	1273	.	.	Atlas-SNP
APOB	338	hgsc.bcm.edu	hg19	2	21236085	21236085	+	Missense_Mutation	SNP	C	C	G	rs13306187	bycluster;byfrequency;byhapmap;by1000genomes;alternate_allele	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	APOB,NS,malignant_melanoma,-1,1	APOB	NM_000384	exon25	c.G4163C	p.R1388P	TGGTAACGAGCCC	.	121.0	44.0	128.0	0.0	.	761	.	C|0.997;T|0.003	Atlas-SNP
GPR113	165082	hgsc.bcm.edu	hg19	2	26536264	26536264	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	GPR113	NM_001145168	exon9	c.C1454A	p.A485D	AACAAGGCCAGGA	.	98.0	37.0	142.0	0.0	.	134	.	.	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	hg19	2	51255333	51255333	+	Silent	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	NRXN1	NM_004801	exon2	c.C79T	p.L27L	TGCCCAGCTCCGC	.	54.0	21.0	40.0	0.0	.	1118	.	.	Atlas-SNP
EHBP1	23301	hgsc.bcm.edu	hg19	2	63206420	63206420	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	EHBP1	NM_015252	exon16	c.A2663G	p.Y888C	CCAGCTATGGTGA	.	114.0	42.0	130.0	0.0	.	127	.	.	Atlas-SNP
SNRNP27	11017	hgsc.bcm.edu	hg19	2	70123665	70123665	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SNRNP27	NM_006857	exon3	c.G253C	p.E85Q	AGCAAAGAACGGC	.	64.0	14.0	77.0	0.0	.	18	.	.	Atlas-SNP
ZNF638	27332	hgsc.bcm.edu	hg19	2	71591128	71591128	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF638	NM_014497	exon5	c.C1463G	p.S488C	GACGTTCTCATTC	.	132.0	51.0	141.0	0.0	.	179	.	.	Atlas-SNP
C2orf15	150590	hgsc.bcm.edu	hg19	2	99767195	99767195	+	Silent	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	C2orf15	NM_144706	exon4	c.A276G	p.T92T	CTTTACAAGGATT	.	418.0	120.0	477.0	0.0	.	11	.	.	Atlas-SNP
EIF5B	9669	hgsc.bcm.edu	hg19	2	99976706	99976706	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	EIF5B	NM_015904	exon2	c.G43A	p.D15N	ACCAAGGATGACA	.	462.0	146.0	506.0	0.0	.	95	.	.	Atlas-SNP
SEPT10	151011	hgsc.bcm.edu	hg19	2	110332246	110332246	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	SEPT10_ENST00000397712,NS,carcinoma,0,4	SEPT10	NM_144710	exon5	c.G512T	p.R171L	TGGATGCGAGAAT	.	95.0	31.0	109.0	1.0	.	58	.	.	Atlas-SNP
FZD5	7855	hgsc.bcm.edu	hg19	2	208633107	208633107	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	FZD5	NM_003468	exon2	c.G357A	p.L119L	GCGCATCAGCGGC	.	24.0	12.0	27.0	0.0	.	22	.	.	Atlas-SNP
AGFG1	3267	hgsc.bcm.edu	hg19	2	228401645	228401645	+	Silent	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	AGFG1	NM_001135187	exon11	c.T1386A	p.A462A	TGTTGCTGCTGCT	.	92.0	23.0	205.0	0.0	.	80	.	.	Atlas-SNP
AGFG1	3267	hgsc.bcm.edu	hg19	2	228401648	228401648	+	Silent	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	AGFG1	NM_001135187	exon11	c.T1389A	p.A463A	TGCTGCTGCTGGT	.	94.0	24.0	208.0	0.0	.	80	.	.	Atlas-SNP
OXSM	54995	hgsc.bcm.edu	hg19	3	25835810	25835810	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	OXSM	NM_017897	exon3	c.G1205C	p.C402S	TAGCTTGTTATTA	.	172.0	62.0	176.0	0.0	.	54	.	.	Atlas-SNP
PLCD1	5333	hgsc.bcm.edu	hg19	3	38049272	38049272	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PLCD1	NM_001130964	exon15	c.C2326T	p.Q776X	AGTCCTGGAGGGA	.	88.0	36.0	95.0	0.0	.	87	.	.	Atlas-SNP
WDR5B	54554	hgsc.bcm.edu	hg19	3	122133743	122133743	+	Silent	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	WDR5B	NM_019069	exon1	c.T633C	p.P211P	GACAGGAGGGTTA	.	96.0	35.0	97.0	0.0	.	36	.	.	Atlas-SNP
SNX4	8723	hgsc.bcm.edu	hg19	3	125195601	125195601	+	Splice_Site	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SNX4	NM_003794	exon9	c.727-1G>T	.	TACTCTCTGAAAT	.	445.0	136.0	483.0	0.0	.	29	.	.	Atlas-SNP
PLXNA1	5361	hgsc.bcm.edu	hg19	3	126736619	126736619	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PLXNA1	NM_032242	exon18	c.G3544T	p.G1182C	GCACCCGGCAACT	.	93.0	37.0	94.0	0.0	.	185	.	.	Atlas-SNP
CEP63	80254	hgsc.bcm.edu	hg19	3	134278032	134278032	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	CEP63,bladder,carcinoma,0,1	CEP63	NM_025180	exon15	c.G1714A	p.E572K	AAGACTGAGCACT	.	159.0	39.0	135.0	0.0	.	56	.	.	Atlas-SNP
ESYT3	83850	hgsc.bcm.edu	hg19	3	138153695	138153695	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ESYT3	NM_031913	exon1	c.C55G	p.R19G	GCCCAGCGCACGC	.	43.0	15.0	45.0	0.0	.	64	.	.	Atlas-SNP
TRIM42	287015	hgsc.bcm.edu	hg19	3	140409822	140409822	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TRIM42	NM_152616	exon4	c.T1873C	p.C625R	TGGACATGTCCAG	.	109.0	30.0	112.0	0.0	.	143	.	.	Atlas-SNP
IGSF10	285313	hgsc.bcm.edu	hg19	3	151160830	151160830	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	IGSF10	NM_178822	exon5	c.C5905T	p.P1969S	GTTTGGGCTCCCC	.	73.0	16.0	94.0	0.0	.	279	.	.	Atlas-SNP
GFM1	85476	hgsc.bcm.edu	hg19	3	158407956	158407956	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	GFM1	NM_024996	exon16	c.G1914C	p.L638F	AGCCTTGGCAAAT	.	63.0	18.0	91.0	0.0	.	83	.	.	Atlas-SNP
HS3ST1	9957	hgsc.bcm.edu	hg19	4	11401299	11401299	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	HS3ST1	NM_005114	exon2	c.T331A	p.W111R	GTGGCCAGGAGAA	.	48.0	25.0	110.0	0.0	.	41	.	.	Atlas-SNP
PCDH7	5099	hgsc.bcm.edu	hg19	4	30723995	30723995	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PCDH7	NM_032457	exon1	c.G951T	p.L317F	CGACTTGGCTGAG	.	123.0	52.0	197.0	0.0	.	215	.	.	Atlas-SNP
NUDT6	11162	hgsc.bcm.edu	hg19	4	123818824	123818824	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	NUDT6	NM_007083	exon4	c.A508G	p.M170V	TCCACATATTTTT	.	542.0	215.0	652.0	1.0	.	50	.	.	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	hg19	4	187541512	187541512	+	Silent	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	FAT1	NM_005245	exon10	c.T6228C	p.D2076D	CGCATTATCATTT	.	90.0	45.0	131.0	0.0	.	500	.	.	Atlas-SNP
HAPLN1	1404	hgsc.bcm.edu	hg19	5	82940201	82940201	+	Silent	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	HAPLN1	NM_001884	exon4	c.T756C	p.C252C	TGTAAAACAGAAA	.	146.0	18.0	198.0	0.0	.	79	.	.	Atlas-SNP
GPR98	84059	hgsc.bcm.edu	hg19	5	90002212	90002212	+	Splice_Site	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	GPR98	NM_032119	exon38	c.8730+1G>A	.	CTTGAGGTAAAAC	.	226.0	43.0	239.0	0.0	.	605	.	.	Atlas-SNP
EGR1	1958	hgsc.bcm.edu	hg19	5	137801456	137801456	+	Silent	SNP	C	C	G	rs200905400	alternate_allele	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	EGR1	NM_001964	exon1	c.C6G	p.A2A	GATGGCCGCGGCC	.	113.0	16.0	118.0	0.0	.	52	.	.	Atlas-SNP
PCDHA13	56136	hgsc.bcm.edu	hg19	5	140262072	140262072	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PCDHA13	NM_031865	exon1	c.C219A	p.D73E	CGGGGACCTTCTG	.	111.0	54.0	142.0	0.0	.	213	.	.	Atlas-SNP
STK10	6793	hgsc.bcm.edu	hg19	5	171533682	171533682	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	STK10	NM_005990	exon6	c.C730T	p.R244W	GGACCCGCATGGG	.	109.0	20.0	106.0	0.0	.	100	.	.	Atlas-SNP
RNF44	22838	hgsc.bcm.edu	hg19	5	175959156	175959156	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	RNF44	NM_014901	exon3	c.G146T	p.R49L	TCATCCCGGGCAG	.	206.0	27.0	243.0	0.0	.	33	.	.	Atlas-SNP
SQSTM1	8878	hgsc.bcm.edu	hg19	5	179260608	179260608	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SQSTM1	NM_003900	exon7	c.T991A	p.C331S	GATAACTGTTCAG	.	104.0	12.0	131.0	0.0	.	30	.	.	Atlas-SNP
FOXC1	2296	hgsc.bcm.edu	hg19	6	1611582	1611582	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	FOXC1	NM_001453	exon1	c.C902G	p.P301R	CCCCGCCGCCGCA	.	62.0	34.0	89.0	0.0	.	19	.	.	Atlas-SNP
SLC22A23	63027	hgsc.bcm.edu	hg19	6	3273355	3273355	+	Silent	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SLC22A23	NM_015482	exon10	c.C1995T	p.H665H	GGCATCGTGGAGG	.	27.0	8.0	34.0	0.0	.	89	.	.	Atlas-SNP
SLC22A23	63027	hgsc.bcm.edu	hg19	6	3273357	3273357	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SLC22A23	NM_015482	exon10	c.C1993A	p.H665N	CATCGTGGAGGCC	.	27.0	8.0	33.0	0.0	.	89	.	.	Atlas-SNP
F13A1	2162	hgsc.bcm.edu	hg19	6	6145859	6145859	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	F13A1	NM_000129	exon15	c.C2192T	p.S731F	CACATGGAAGGTC	.	97.0	24.0	114.0	0.0	.	135	.	.	Atlas-SNP
ZNF318	24149	hgsc.bcm.edu	hg19	6	43307288	43307288	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF318	NM_014345	exon10	c.C4448T	p.S1483F	GTCTGAGATACAA	.	92.0	31.0	97.0	0.0	.	175	.	.	Atlas-SNP
POLR1C	9533	hgsc.bcm.edu	hg19	6	43487179	43487179	+	Splice_Site	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	POLR1C	NM_203290	exon3	c.249+1G>T	.	GCTGAGGTATTGG	.	117.0	39.0	144.0	0.0	.	52	.	.	Atlas-SNP
ADCYAP1R1	117	hgsc.bcm.edu	hg19	7	31139807	31139807	+	Silent	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ADCYAP1R1	NM_001199635	exon14	c.A1113G	p.E371E	GTCAGAACTGTCC	.	58.0	14.0	57.0	0.0	.	78	.	.	Atlas-SNP
PTPN12	5782	hgsc.bcm.edu	hg19	7	77256222	77256222	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PTPN12	NM_002835	exon13	c.A1226G	p.Y409C	GAAACTATAGTAA	.	132.0	39.0	140.0	0.0	.	83	.	.	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	hg19	7	131849014	131849014	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PLXNA4	NM_020911	exon24	c.T4387G	p.C1463G	TGGCACAGAACAG	.	66.0	22.0	84.0	0.0	.	873	.	.	Atlas-SNP
ADAM9	8754	hgsc.bcm.edu	hg19	8	38947598	38947598	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ADAM9	NM_003816	exon19	c.G2101A	p.V701I	CTTCTGGTCTTCT	.	67.0	35.0	143.0	0.0	.	66	.	.	Atlas-SNP
VCPIP1	80124	hgsc.bcm.edu	hg19	8	67578049	67578049	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	VCPIP1	NM_025054	exon1	c.A1145G	p.Q382R	AGGTCCTGAGGCA	.	105.0	35.0	105.0	0.0	.	110	.	.	Atlas-SNP
C8orf34	116328	hgsc.bcm.edu	hg19	8	69552726	69552726	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	C8orf34	NM_052958	exon8	c.C1221T	p.N407N	ACTGAACATCTGT	.	144.0	72.0	138.0	0.0	.	170	.	.	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	hg19	8	77768445	77768445	+	Silent	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZFHX4	NM_024721	exon10	c.A9288T	p.T3096T	GCCAACAGCCTAC	.	135.0	51.0	97.0	0.0	.	878	.	.	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	hg19	8	100123343	100123343	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	VPS13B	NM_152564	exon6	c.A598T	p.R200X	GTGCTGAGAAAGG	.	399.0	98.0	176.0	0.0	.	811	.	.	Atlas-SNP
ZFPM2	23414	hgsc.bcm.edu	hg19	8	106811123	106811123	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZFPM2	NM_012082	exon7	c.C911G	p.T304S	AGTGCACCAAGAG	.	193.0	8.0	74.0	0.0	.	219	.	.	Atlas-SNP
ZNF250	58500	hgsc.bcm.edu	hg19	8	146107094	146107094	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF250	NM_021061	exon6	c.C1489A	p.H497N	TCAGGTGCACAAT	.	61.0	36.0	85.0	0.0	.	37	.	.	Atlas-SNP
CDKN2A	1029	hgsc.bcm.edu	hg19	9	21994138	21994138	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	CDKN2A_ENST00000361570,NS,carcinoma,0,1	CDKN2A	NM_058195	exon1	c.G193C	p.G65R	TCCTACCTGGTCT	.	56.0	16.0	47.0	0.0	.	4810	.	.	Atlas-SNP
TMC1	117531	hgsc.bcm.edu	hg19	9	75406907	75406907	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TMC1	NM_138691	exon16	c.G1330C	p.G444R	CTACTGGGACGCA	.	142.0	49.0	188.0	0.0	.	87	.	.	Atlas-SNP
RASEF	158158	hgsc.bcm.edu	hg19	9	85640772	85640772	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	RASEF	NM_152573	exon2	c.T496C	p.Y166H	GTTCATATGGCTG	.	94.0	4.0	146.0	0.0	.	69	.	.	Atlas-SNP
DIRAS2	54769	hgsc.bcm.edu	hg19	9	93375592	93375592	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	DIRAS2	NM_017594	exon2	c.C518A	p.T173N	CTCACGGTCCTGC	.	89.0	4.0	102.0	0.0	.	21	.	.	Atlas-SNP
LHX6	26468	hgsc.bcm.edu	hg19	9	124989224	124989224	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	LHX6	NM_014368	exon3	c.T242C	p.V81A	GAGCAGACAGATG	.	27.0	11.0	49.0	0.0	.	73	.	.	Atlas-SNP
AKR1C4	1109	hgsc.bcm.edu	hg19	10	5238850	5238850	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	AKR1C4	NM_001818	exon1	c.G20A	p.R7H	ATCAGCGTGTAGA	.	190.0	116.0	129.0	0.0	.	57	.	.	Atlas-SNP
FAM171A1	221061	hgsc.bcm.edu	hg19	10	15256432	15256432	+	Silent	SNP	G	G	C	rs143895945	alternate_allele	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	FAM171A1	NM_001010924	exon8	c.C1155G	p.P385P	GGCCTCGGGGCGG	.	151.0	31.0	94.0	0.0	.	252	.	G|1.000;A|0.000	Atlas-SNP
ZNF485	220992	hgsc.bcm.edu	hg19	10	44111881	44111881	+	Silent	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF485	NM_145312	exon5	c.T390C	p.Y130Y	GAACTATAAGTGC	.	203.0	101.0	243.0	0.0	.	102	.	.	Atlas-SNP
STOX1	219736	hgsc.bcm.edu	hg19	10	70646233	70646233	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	STOX1	NM_152709	exon3	c.G2681C	p.R894T	AAATGAGAAAACA	.	103.0	21.0	115.0	0.0	.	75	.	.	Atlas-SNP
SLC35G1	159371	hgsc.bcm.edu	hg19	10	95660950	95660950	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	.	NM_001134658	exon3	c.C801T	p.V267V	AAGTGTCATCATC	.	161.0	28.0	168.0	0.0	.	.	.	.	Atlas-SNP
SEC23IP	11196	hgsc.bcm.edu	hg19	10	121678006	121678006	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SEC23IP	NM_007190	exon10	c.C1855G	p.H619D	CAGCTACATTTTC	.	66.0	26.0	122.0	0.0	.	100	.	.	Atlas-SNP
PTPN5	84867	hgsc.bcm.edu	hg19	11	18787389	18787389	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PTPN5	NM_032781	exon3	c.G62A	p.G21E	AGGGCCCCTCCCT	.	94.0	27.0	98.0	0.0	.	163	.	.	Atlas-SNP
CCDC88B	283234	hgsc.bcm.edu	hg19	11	64110657	64110657	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CCDC88B	NM_032251	exon11	c.C1069T	p.R357W	GAGGAGCGGGTGC	.	29.0	12.0	36.0	0.0	.	89	.	.	Atlas-SNP
B3GNT1	11041	hgsc.bcm.edu	hg19	11	66114190	66114190	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	B3GNT1	NM_006876	exon1	c.T827A	p.V276E	AGCTGCACCAGCT	.	45.0	15.0	74.0	0.0	.	28	.	.	Atlas-SNP
NUMA1	4926	hgsc.bcm.edu	hg19	11	71725431	71725431	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	NUMA1	NM_006185	exon15	c.G3118A	p.E1040K	GCTGCTCGTTGAG	.	23.0	9.0	56.0	0.0	.	142	.	.	Atlas-SNP
PGM2L1	283209	hgsc.bcm.edu	hg19	11	74058249	74058249	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PGM2L1	NM_173582	exon7	c.G883A	p.D295N	CTGGATCAGGATC	.	97.0	23.0	148.0	0.0	.	59	.	.	Atlas-SNP
KCNE3	10008	hgsc.bcm.edu	hg19	11	74168597	74168597	+	Silent	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	KCNE3	NM_005472	exon3	c.C12T	p.T4T	TCCATTGGTAGTC	.	88.0	26.0	138.0	0.0	.	7	.	.	Atlas-SNP
TRPC6	7225	hgsc.bcm.edu	hg19	11	101344488	101344488	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TRPC6	NM_004621	exon7	c.C1761A	p.D587E	AGAGGGGTCCCAC	.	66.0	23.0	137.0	0.0	.	132	.	.	Atlas-SNP
NEUROD4	58158	hgsc.bcm.edu	hg19	12	55420588	55420588	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	NEUROD4	NM_021191	exon2	c.A365G	p.K122R	CCCAAAAACTTTC	.	129.0	34.0	119.0	0.0	.	87	.	.	Atlas-SNP
PTPRB	5787	hgsc.bcm.edu	hg19	12	71016198	71016198	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PTPRB	NM_001109754	exon3	c.C680G	p.T227S	GGCTGAGTAGTCG	.	78.0	19.0	88.0	0.0	.	676	.	.	Atlas-SNP
HAL	3034	hgsc.bcm.edu	hg19	12	96384225	96384225	+	Silent	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	HAL	NM_001258334	exon10	c.A801G	p.L267L	TCCAACTAGCCCA	.	112.0	36.0	125.0	0.0	.	73	.	.	Atlas-SNP
SETD1B	23067	hgsc.bcm.edu	hg19	12	122260499	122260499	+	Silent	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SETD1B	NM_015048	exon12	c.G3885T	p.P1295P	ACCGCCGGAGCCT	.	73.0	22.0	86.0	0.0	.	105	.	.	Atlas-SNP
KL	9365	hgsc.bcm.edu	hg19	13	33629230	33629230	+	Silent	SNP	C	C	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	KL,trunk,malignant_melanoma,0,1	KL	NM_004795	exon3	c.C1377G	p.S459S	ATGGTCCCTCATG	.	147.0	31.0	162.0	0.0	.	106	.	.	Atlas-SNP
PCID2	55795	hgsc.bcm.edu	hg19	13	113835450	113835450	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PCID2	NM_001258212	exon10	c.G942A	p.M314I	CAATAGCATTTTT	.	122.0	47.0	116.0	0.0	.	30	.	.	Atlas-SNP
LAMP1	3916	hgsc.bcm.edu	hg19	13	113975881	113975881	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	LAMP1	NM_005561	exon8	c.T953G	p.F318C	CTGCCTTTAAAGC	.	161.0	16.0	127.0	0.0	.	41	.	.	Atlas-SNP
MDGA2	161357	hgsc.bcm.edu	hg19	14	48143777	48143777	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	MDGA2	NM_001113498	exon1	c.G223T	p.G75C	CGAGACCGTACAG	.	102.0	26.0	159.0	0.0	.	470	.	.	Atlas-SNP
ATL1	51062	hgsc.bcm.edu	hg19	14	51079994	51079994	+	Silent	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ATL1	NM_015915	exon7	c.T648C	p.V216V	TCTTGTTCGAGAC	.	109.0	16.0	112.0	0.0	.	46	.	.	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	hg19	14	71479802	71479802	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PCNX	NM_014982	exon11	c.A2879G	p.Y960C	CTACTTACGGCCC	.	70.0	29.0	108.0	0.0	.	198	.	.	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	hg19	14	71479827	71479827	+	Silent	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PCNX	NM_014982	exon11	c.A2904G	p.Q968Q	TGCCCAAAAGGTT	.	71.0	30.0	100.0	0.0	.	198	.	.	Atlas-SNP
C14orf166B	145497	hgsc.bcm.edu	hg19	14	77297607	77297607	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	C14orf166B	NM_194287	exon3	c.G279A	p.M93I	GCTGATGGGTGTA	.	99.0	47.0	144.0	0.0	.	52	.	.	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	hg19	14	105417141	105417141	+	Missense_Mutation	SNP	G	G	T	rs372521162	alternate_allele	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	AHNAK2	NM_138420	exon7	c.C4647A	p.D1549E	CTCCAGGTCAGCA	.	175.0	7.0	217.0	0.0	.	719	.	.	Atlas-SNP
NIPA1	123606	hgsc.bcm.edu	hg19	15	23086388	23086388	+	Silent	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	NIPA1,NS,carcinoma,0,1	NIPA1	NM_144599	exon1	c.G24T	p.A8A	CGCCGCCGCTGCC	.	42.0	2.0	130.0	0.0	.	26	.	.	Atlas-SNP
HS3ST6	64711	hgsc.bcm.edu	hg19	16	1961878	1961878	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	HS3ST6	NM_001009606	exon2	c.A649G	p.S217G	CCCCGCTGACGAA	.	105.0	44.0	115.0	0.0	.	26	.	.	Atlas-SNP
LAT	27040	hgsc.bcm.edu	hg19	16	29001280	29001280	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	LAT	NM_001014989	exon12	c.G757T	p.E253X	GCAGAGGAAGTGG	.	65.0	14.0	78.0	0.0	.	22	.	.	Atlas-SNP
TAOK2	9344	hgsc.bcm.edu	hg19	16	29998697	29998697	+	Missense_Mutation	SNP	G	G	T	rs144609126	alternate_allele	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TAOK2	NM_016151	exon16	c.G3104T	p.R1035L	GCTGGCGCCGAGG	.	71.0	24.0	75.0	0.0	.	142	.	G|1.000;A|0.000	Atlas-SNP
BRD7	29117	hgsc.bcm.edu	hg19	16	50357578	50357578	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	BRD7	NM_013263	exon12	c.T1363A	p.Y455N	ACGGATAATCTTG	.	80.0	25.0	92.0	0.0	.	61	.	.	Atlas-SNP
CHD9	80205	hgsc.bcm.edu	hg19	16	53307551	53307551	+	Silent	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CHD9	NM_025134	exon23	c.T4731A	p.P1577P	AGCTCCTGTACCC	.	362.0	120.0	405.0	0.0	.	203	.	.	Atlas-SNP
TCF25	22980	hgsc.bcm.edu	hg19	16	89977033	89977033	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TCF25	NM_014972	exon17	c.C1834T	p.L612F	ATTGCTCTCTTCT	.	51.0	12.0	64.0	0.0	.	61	.	.	Atlas-SNP
TP53	7157	hgsc.bcm.edu	hg19	17	7574006	7574006	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	TP53_ENST00000269305,colon,carcinoma,0,2	TP53	NM_000546	exon10	c.T1021G	p.F341V	CTCGGAACATCTC	.	109.0	74.0	147.0	0.0	.	33396	.	.	Atlas-SNP
SLFN11	91607	hgsc.bcm.edu	hg19	17	33679852	33679852	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SLFN11	NM_152270	exon5	c.A2229T	p.K743N	CATTTCTTTTTGT	.	130.0	35.0	91.0	0.0	.	112	.	.	Atlas-SNP
SPATA20	64847	hgsc.bcm.edu	hg19	17	48632950	48632950	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SPATA20	NM_022827	exon17	c.A2336G	p.Y779C	CTGCATATGTGTG	.	77.0	15.0	79.0	0.0	.	59	.	.	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	hg19	17	48653617	48653617	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CACNA1G	NM_001256360	exon8	c.C1854T	p.T618T	CCCAACCCTCACC	.	351.0	105.0	306.0	0.0	.	659	.	.	Atlas-SNP
CACNA1G	8913	hgsc.bcm.edu	hg19	17	48696133	48696133	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CACNA1G	NM_001256325	exon33	c.G5566A	p.V1856M	ATCGCCGTGCTGA	.	133.0	25.0	151.0	0.0	.	659	.	.	Atlas-SNP
PGS1	9489	hgsc.bcm.edu	hg19	17	76411090	76411090	+	Silent	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PGS1	NM_024419	exon8	c.G1533A	p.L511L	GGCCCTGCAGCAG	.	104.0	46.0	99.0	0.0	.	30	.	.	Atlas-SNP
CDH2	1000	hgsc.bcm.edu	hg19	18	25589824	25589824	+	Silent	SNP	T	T	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CDH2	NM_001792	exon5	c.A559C	p.R187R	TATCTCTATCAGA	.	62.0	19.0	47.0	0.0	.	194	.	.	Atlas-SNP
ZNF430	80264	hgsc.bcm.edu	hg19	19	21216318	21216318	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF430	NM_025189	exon3	c.C153T	p.C51C	GCAATGCCTGGAC	.	126.0	48.0	166.0	0.0	.	59	.	.	Atlas-SNP
ZNF568	374900	hgsc.bcm.edu	hg19	19	37440949	37440949	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF568	NM_198539	exon7	c.A894T	p.R298S	CCACAGAATTCAT	.	115.0	15.0	122.0	0.0	.	106	.	.	Atlas-SNP
CYP2A6	1548	hgsc.bcm.edu	hg19	19	41355743	41355743	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CYP2A6	NM_000762	exon2	c.A323G	p.D108G	ACCCAGTCGAAGG	.	200.0	46.0	228.0	0.0	.	69	.	.	Atlas-SNP
ZNF845	91664	hgsc.bcm.edu	hg19	19	53856625	53856625	+	Silent	SNP	A	A	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF845	NM_138374	exon4	c.A2697G	p.Q899Q	TCAACAAGCACAC	.	160.0	55.0	149.0	0.0	.	101	.	.	Atlas-SNP
CSRP2BP	57325	hgsc.bcm.edu	hg19	20	18143146	18143146	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CSRP2BP	NM_020536	exon6	c.A1228T	p.I410L	GAACAGATAAAGC	.	152.0	8.0	190.0	0.0	.	80	.	.	Atlas-SNP
CSE1L	1434	hgsc.bcm.edu	hg19	20	47682737	47682737	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CSE1L	NM_001256135	exon4	c.T237G	p.D79E	TGAAGATGAACCA	.	114.0	37.0	135.0	0.0	.	83	.	.	Atlas-SNP
ZFP64	55734	hgsc.bcm.edu	hg19	20	50803417	50803417	+	Silent	SNP	A	A	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZFP64	NM_018197	exon2	c.T240G	p.T80T	GGTCTGAGTCTGG	.	119.0	39.0	150.0	0.0	.	240	.	.	Atlas-SNP
PCK1	5105	hgsc.bcm.edu	hg19	20	56138179	56138179	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PCK1	NM_002591	exon5	c.G706A	p.G236S	GGGTACGGCGGGA	.	85.0	33.0	92.0	0.0	.	95	.	.	Atlas-SNP
ZNF831	128611	hgsc.bcm.edu	hg19	20	57766466	57766466	+	Missense_Mutation	SNP	C	C	A	rs143620250	bycluster;by1000genomes;alternate_allele	TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZNF831	NM_178457	exon1	c.C392A	p.T131K	GCCCCACGCTGGG	.	134.0	43.0	116.0	0.0	.	287	.	C|0.999;T|0.001	Atlas-SNP
IFNGR2	3460	hgsc.bcm.edu	hg19	21	34805131	34805131	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	IFNGR2	NM_005534	exon6	c.A832C	p.K278Q	CTGATTAAATACT	.	106.0	19.0	102.0	0.0	.	30	.	.	Atlas-SNP
DOPEY2	9980	hgsc.bcm.edu	hg19	21	37617605	37617605	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	DOPEY2	NM_005128	exon19	c.C3327T	p.H1109H	CGAGCACACCGAG	.	76.0	15.0	85.0	0.0	.	184	.	.	Atlas-SNP
MICAL3	57553	hgsc.bcm.edu	hg19	22	18324653	18324653	+	Silent	SNP	C	C	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	MICAL3	NM_015241	exon20	c.G2736A	p.E912E	CTGAGTCTCCTCC	.	27.0	12.0	56.0	0.0	.	53	.	.	Atlas-SNP
ATF4	468	hgsc.bcm.edu	hg19	22	39918368	39918368	+	Missense_Mutation	SNP	G	G	A	rs372679887		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ATF4	NM_001675	exon2	c.G817A	p.V273I	GCAAAAGTAAAGG	.	359.0	104.0	388.0	0.0	.	27	.	.	Atlas-SNP
CENPM	79019	hgsc.bcm.edu	hg19	22	42341233	42341233	+	Silent	SNP	T	T	C	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CENPM	NM_024053	exon4	c.A306G	p.T102T	ACCACCTGTGGCG	.	167.0	37.0	161.0	0.0	.	8	.	.	Atlas-SNP
ZBED1	9189	hgsc.bcm.edu	hg19	X	2408700	2408700	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ZBED1	NM_001171135	exon2	c.G61T	p.A21S	TCTTGGCGCGGGG	.	114.0	25.0	111.0	0.0	.	64	.	.	Atlas-SNP
MED12	9968	hgsc.bcm.edu	hg19	X	70346907	70346907	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	MED12	NM_005120	exon20	c.G2774T	p.C925F	GCCTGTGCATCGT	.	45.0	30.0	52.0	0.0	.	984	.	.	Atlas-SNP
PPFIBP2	8495	hgsc.bcm.edu	hg19	11	7647047	7647070	+	In_Frame_Del	DEL	GATGCAGAAATTGAGCGTCTGCAC	GATGCAGAAATTGAGCGTCTGCAC	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	GATGCAGAAATTGAGCGTCTGCAC	GATGCAGAAATTGAGCGTCTGCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PPFIBP2	NM_003621	exon8	c.750_773del	p.250_258del	.	.	115.0	23.0	200.0	0.0	.	87	.	.	Atlas-INDEL
LAMP1	3916	hgsc.bcm.edu	hg19	13	113975888	113975888	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	LAMP1	NM_005561	exon8	c.959delC	p.A320fs	.	.	158.0	15.0	120.0	0.0	.	41	.	.	Atlas-INDEL
TTC28	23331	hgsc.bcm.edu	hg19	22	28693650	28693654	+	Frame_Shift_Del	DEL	CAGGG	CAGGG	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CAGGG	CAGGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TTC28	NM_001145418	exon4	c.717_721del	p.239_241del	.	.	34.0	15.0	76.0	0.0	.	84	.	.	Atlas-INDEL
KDM3A	55818	hgsc.bcm.edu	hg19	2	86718396	86718408	+	Frame_Shift_Del	DEL	CAGGTAAAAATAG	CAGGTAAAAATAG	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CAGGTAAAAATAG	CAGGTAAAAATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	KDM3A	NM_018433	exon25	c.3882_3885del	p.1294_1295del	.	.	96.0	16.0	90.0	0.0	.	179	.	.	Atlas-INDEL
POP1	10940	hgsc.bcm.edu	hg19	8	99142204	99142214	+	Splice_Site	DEL	TGAAACTATAG	TGAAACTATAG	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	TGAAACTATAG	TGAAACTATAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	POP1	.	.	.	.	.	.	219.0	20.0	132.0	0.0	.	85	.	.	Atlas-INDEL
MYO15A	51168	hgsc.bcm.edu	hg19	17	18022452	18022473	+	Frame_Shift_Del	DEL	GCCGCCGTGGCTACGGCCGCCT	GCCGCCGTGGCTACGGCCGCCT	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	GCCGCCGTGGCTACGGCCGCCT	GCCGCCGTGGCTACGGCCGCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	MYO15A	NM_016239	exon2	c.337_358del	p.113_120del	.	.	112.0	55.0	198.0	0.0	.	268	.	.	Atlas-INDEL
GCDH	2639	hgsc.bcm.edu	hg19	19	13006809	13006810	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	GCDH	NM_013976	exon7	c.509_510insG	p.Q170fs	.	.	73.0	20.0	72.0	0.0	.	76	.	.	Atlas-INDEL
SYNJ1	8867	hgsc.bcm.edu	hg19	21	34053835	34053837	+	In_Frame_Del	DEL	CTG	CTG	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SYNJ1	NM_203446	exon11	c.1440_1442del	p.480_481del	.	.	110.0	16.0	128.0	0.0	.	253	.	.	Atlas-INDEL
MAPK9	5601	hgsc.bcm.edu	hg19	5	179696379	179696380	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	MAPK9	NM_139068	exon3	c.153_154del	p.51_52del	.	.	171.0	34.0	149.0	0.0	.	173	.	.	Atlas-INDEL
TTC28	23331	hgsc.bcm.edu	hg19	22	28693694	28693697	+	Frame_Shift_Del	DEL	CAAT	CAAT	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CAAT	CAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TTC28	NM_001145418	exon4	c.674_677del	p.225_226del	.	.	51.0	22.0	78.0	0.0	.	84	.	.	Atlas-INDEL
HCFC2	29915	hgsc.bcm.edu	hg19	12	104474581	104474581	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	HCFC2	NM_013320	exon5	c.739delC	p.L247fs	.	.	124.0	38.0	131.0	0.0	.	94	.	.	Atlas-INDEL
GBA2	57704	hgsc.bcm.edu	hg19	9	35738529	35738530	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	GBA2	NM_020944	exon13	c.2048_2049insC	p.G683fs	.	.	64.0	27.0	81.0	0.0	.	77	.	.	Atlas-INDEL
ANKRD13A	88455	hgsc.bcm.edu	hg19	12	110463610	110463611	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ANKRD13A	NM_033121	exon8	c.865_866insA	p.E289fs	.	.	194.0	64.0	193.0	0.0	.	39	.	.	Atlas-INDEL
KIAA0947	23379	hgsc.bcm.edu	hg19	5	5462837	5462838	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	KIAA0947_ENST00000296564,NS,carcinoma,0,1	KIAA0947	NM_015325	exon13	c.3390_3391insA	p.Q1130fs	.	.	91.0	14.0	71.0	0.0	.	301	.	.	Atlas-INDEL
SYNJ1	8867	hgsc.bcm.edu	hg19	21	34053840	34053864	+	Frame_Shift_Del	DEL	TATATCTTACTGATTGAATCACCAT	TATATCTTACTGATTGAATCACCAT	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	TATATCTTACTGATTGAATCACCAT	TATATCTTACTGATTGAATCACCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	SYNJ1	NM_203446	exon11	c.1413_1437del	p.471_479del	.	.	98.0	16.0	132.0	0.0	.	253	.	.	Atlas-INDEL
PKHD1	5314	hgsc.bcm.edu	hg19	6	51524083	51524087	+	Frame_Shift_Del	DEL	CTGTC	CTGTC	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CTGTC	CTGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	PKHD1	NM_138694	exon61	c.10838_10842del	p.3613_3614del	.	.	87.0	26.0	92.0	0.0	.	927	.	.	Atlas-INDEL
TMEM62	80021	hgsc.bcm.edu	hg19	15	43446911	43446911	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	TMEM62	NM_024956	exon9	c.1063delG	p.V355fs	.	.	73.0	24.0	68.0	0.0	.	47	.	.	Atlas-INDEL
AGFG1	3267	hgsc.bcm.edu	hg19	2	228401650	228401679	+	In_Frame_Del	DEL	CTGGTCCTTCTGTGGCATCTTCTACAAACC	CTGGTCCTTCTGTGGCATCTTCTACAAACC	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	CTGGTCCTTCTGTGGCATCTTCTACAAACC	CTGGTCCTTCTGTGGCATCTTCTACAAACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	AGFG1	NM_001135187	exon11	c.1390_1419del	p.464_473del	.	.	93.0	12.0	205.0	0.0	.	80	.	.	Atlas-INDEL
ECT2	1894	hgsc.bcm.edu	hg19	3	172479465	172479468	+	Frame_Shift_Del	DEL	GAAT	GAAT	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	GAAT	GAAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	ECT2	NM_001258315	exon8	c.749_752del	p.250_251del	.	.	165.0	74.0	130.0	0.0	.	79	.	.	Atlas-INDEL
C2CD4A	145741	hgsc.bcm.edu	hg19	15	62360051	62360051	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	C2CD4A	NM_207322	exon2	c.238delC	p.R80fs	.	.	54.0	34.0	69.0	0.0	.	3	.	.	Atlas-INDEL
CKAP5	9793	hgsc.bcm.edu	hg19	11	46765632	46765633	+	In_Frame_Ins	INS	-	-	GGA	novel		TCGA-DD-AAD5-01A-11D-A40R-10	TCGA-DD-AAD5-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f2984bd1-84c5-4dd0-9156-fec653c55146	a7e8434c-a3c4-4216-a700-809a6c5e6383	.	CKAP5	NM_001008938	exon44	c.6040_6041insTCC	p.T2014delinsST	.	.	96.0	34.0	163.0	0.0	.	134	.	.	Atlas-INDEL
