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
HMGCL	3155	hgsc.bcm.edu	hg19	1	24151846	24151846	+	Silent	SNP	A	A	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	HMGCL	NM_000191	exon1	c.T60C	p.A20A	ACTTACAGCCCGG	.	87.0	27.0	8.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
SYNC	81493	hgsc.bcm.edu	hg19	1	33161106	33161106	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SYNC	NM_001161708	exon2	c.A593C	p.H198P	AGCTCATGGATGA	.	88.0	24.0	131.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
ZC3H12A	80149	hgsc.bcm.edu	hg19	1	37949045	37949045	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ZC3H12A	NM_025079	exon6	c.A1633T	p.R545W	TGGGGCAGGGCAG	.	196.0	53.0	135.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
KTI12	112970	hgsc.bcm.edu	hg19	1	52499078	52499078	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	KTI12	NM_138417	exon1	c.T356C	p.V119A	CCCGCCACCTGAG	.	43.0	13.0	1.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
DHCR24	1718	hgsc.bcm.edu	hg19	1	55317995	55317995	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	DHCR24	NM_014762	exon9	c.T1462G	p.S488A	ACAAGGAGCCATC	.	90.0	4.0	94.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
NRAS	4893	hgsc.bcm.edu	hg19	1	115256491	115256491	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	NRAS	NM_002524	exon3	c.A220T	p.T74S	CGCCTGTCCTCAT	.	74.0	28.0	102.0	0.0	.	3766	.	.	.	none	.	.	PASS	Atlas-SNP
DDR2	4921	hgsc.bcm.edu	hg19	1	162729664	162729664	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	DDR2	NM_001014796	exon9	c.G750A	p.V250V	CCACGTGTGGCCC	.	172.0	52.0	198.0	0.0	.	228	.	.	.	none	.	.	PASS	Atlas-SNP
FAM98A	25940	hgsc.bcm.edu	hg19	2	33813426	33813426	+	Silent	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	FAM98A	NM_015475	exon4	c.A498G	p.Q166Q	GAAGAATTGGAAC	.	75.0	32.0	79.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
TTC31	64427	hgsc.bcm.edu	hg19	2	74718487	74718487	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	TTC31	NM_022492	exon7	c.G669A	p.Q223Q	GGGACAGTGTGGT	.	84.0	22.0	99.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
SUCLG1	8802	hgsc.bcm.edu	hg19	2	84652539	84652539	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SUCLG1	NM_003849	exon8	c.G1014A	p.K338K	GCTCACCTTGTAG	.	119.0	36.0	98.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
KCNIP3	30818	hgsc.bcm.edu	hg19	2	95976175	95976175	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	KCNIP3	NM_013434	exon2	c.A88G	p.I30V	GAGGGTATCAAGT	.	364.0	110.0	356.0	1.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
KCNIP3	30818	hgsc.bcm.edu	hg19	2	95976177	95976177	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	KCNIP3	NM_013434	exon2	c.C90T	p.I30I	GGGTATCAAGTGG	.	361.0	109.0	352.0	1.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
SLC5A7	60482	hgsc.bcm.edu	hg19	2	108604763	108604763	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SLC5A7	NM_021815	exon2	c.T152A	p.L51X	TTGGTTTATTGGT	.	142.0	41.0	133.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
ZRANB3	84083	hgsc.bcm.edu	hg19	2	135988115	135988115	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ZRANB3	NM_032143	exon13	c.G1922A	p.C641Y	ATTTCACAATAAG	.	96.0	5.0	94.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
SSB	6741	hgsc.bcm.edu	hg19	2	170667495	170667495	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SSB	NM_003142	exon10	c.A938C	p.E313A	AAAAAGAAGCACT	.	133.0	42.0	139.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	hg19	2	218678511	218678511	+	Silent	SNP	C	C	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	TNS1,colon,carcinoma,0,1	TNS1	NM_022648	exon26	c.G4446C	p.P1482P	GGCCCCCGGCTCC	.	110.0	34.0	124.0	0.0	.	251	.	.	.	none	.	.	PASS	Atlas-SNP
ANKMY1	51281	hgsc.bcm.edu	hg19	2	241465102	241465102	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ANKMY1	NM_016552	exon6	c.G1068A	p.Q356Q	GCTTACCTGGGGC	.	121.0	45.0	118.0	0.0	.	112	.	.	.	none	.	.	PASS	Atlas-SNP
FAM212A	389119	hgsc.bcm.edu	hg19	3	49842183	49842183	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	.	NM_203370	exon2	c.A627C	p.E209D	GAGTGAAGGGGGT	.	305.0	151.0	93.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
GOLGB1	2804	hgsc.bcm.edu	hg19	3	121415217	121415217	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	GOLGB1	NM_001256486	exon13	c.C4153T	p.Q1385X	CAATTTGTAGTTG	.	59.0	12.0	40.0	0.0	.	319	.	.	.	none	.	.	PASS	Atlas-SNP
ARMC8	25852	hgsc.bcm.edu	hg19	3	137982982	137982982	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ARMC8	NM_015396	exon15	c.C1185T	p.H395H	TTTGCACAGTTTA	.	83.0	24.0	55.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
RBP1	5947	hgsc.bcm.edu	hg19	3	139237296	139237296	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	RBP1	NM_002899	exon3	c.G507T	p.W169C	CTGGGTCCAGCCA	.	86.0	25.0	69.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
EXOC1	55763	hgsc.bcm.edu	hg19	4	56738102	56738102	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	EXOC1	NM_018261	exon8	c.T1052C	p.L351P	GTCACCTCAACAA	.	73.0	4.0	129.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
REST	5978	hgsc.bcm.edu	hg19	4	57797826	57797826	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	REST	NM_001193508	exon4	c.A2802C	p.L934F	AACTTTAAATGGT	.	110.0	43.0	153.0	0.0	.	104	.	.	.	none	.	.	PASS	Atlas-SNP
SPATA24	202051	hgsc.bcm.edu	hg19	5	138739683	138739683	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	.	NM_194296	exon1	c.C67T	p.R23W	CGTCCCGCAGTTG	.	99.0	4.0	89.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
NQO2	4835	hgsc.bcm.edu	hg19	6	3010268	3010268	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	NQO2	NM_000904	exon3	c.T17C	p.V6A	AGAAAGTACTCAT	.	104.0	30.0	123.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
GABBR1	2550	hgsc.bcm.edu	hg19	6	29595420	29595420	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	GABBR1	NM_001470	exon6	c.G500A	p.R167Q	GCGCGCCGTTCTG	.	34.0	14.0	5.0	0.0	.	95	.	.	.	none	.	.	PASS	Atlas-SNP
NFKBIL1	4795	hgsc.bcm.edu	hg19	6	31526116	31526116	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	NFKBIL1	NM_005007	exon4	c.G874A	p.G292S	GGGAGGGGCAGCC	.	69.0	23.0	24.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
HCRTR2	3062	hgsc.bcm.edu	hg19	6	55039411	55039411	+	Missense_Mutation	SNP	C	C	G	rs76774128	alternate_allele	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.,3	HCRTR2	NM_001526	exon1	c.C26G	p.S9C	AGGACTCCCCCCC	.	130.0	47.0	91.0	0.0	.	112	.	.	.	alt	.	.	PASS	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	hg19	6	75848659	75848659	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	COL12A1	NM_004370	exon28	c.C4976A	p.T1659K	AAGTTTGTTGGGG	.	63.0	16.0	64.0	0.0	.	385	.	.	.	none	.	.	PASS	Atlas-SNP
AHR	196	hgsc.bcm.edu	hg19	7	17375399	17375399	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	AHR,NS,carcinoma,0,1	AHR	NM_001621	exon9	c.G1149C	p.Q383H	AACTCAGAGACCA	.	71.0	40.0	57.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
AUTS2	26053	hgsc.bcm.edu	hg19	7	69364300	69364300	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	AUTS2,caecum,carcinoma,+1,1	AUTS2	NM_001127231	exon2	c.G338A	p.R113H	AGGAACGTGTGGA	.	130.0	22.0	73.0	0.0	.	173	.	.	.	none	.	.	PASS	Atlas-SNP
BAZ1B	9031	hgsc.bcm.edu	hg19	7	72873963	72873963	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	BAZ1B	NM_032408	exon13	c.T3335C	p.F1112S	GCCATGAAGCCTT	.	70.0	43.0	60.0	0.0	.	147	.	.	.	none	.	.	PASS	Atlas-SNP
CUX1	1523	hgsc.bcm.edu	hg19	7	101882763	101882763	+	Silent	SNP	G	G	A	rs140169027		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	CUX1,colon,carcinoma,0,1	CUX1	NM_001202543	exon23	c.G3819A	p.A1273A	ACGAGCGTATCAG	.	158.0	98.0	57.0	0.0	.	253	.	.	.	weak	G|1.000;A|0.000	0.000	PASS	Atlas-SNP
MLL3	58508	hgsc.bcm.edu	hg19	7	151845991	151845991	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	MLL3	NM_170606	exon52	c.G13021T	p.G4341W	CAAACCCACCATG	.	97.0	23.0	62.0	0.0	.	1564	.	.	.	none	.	.	PASS	Atlas-SNP
VDAC3	7419	hgsc.bcm.edu	hg19	8	42259309	42259309	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	VDAC3	NM_001135694	exon7	c.G330C	p.K110N	CAGAAAGAAGAGT	.	72.0	22.0	64.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
SFMBT2	57713	hgsc.bcm.edu	hg19	10	7214001	7214001	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SFMBT2	NM_001029880	exon19	c.C2271T	p.P757P	CCTCCGGGGCCGG	.	8.0	6.0	1.0	0.0	.	209	.	.	.	none	.	.	PASS	Atlas-SNP
PLXDC2	84898	hgsc.bcm.edu	hg19	10	20335920	20335920	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PLXDC2	NM_032812	exon3	c.G447T	p.L149F	AATATTGTCCAAT	.	58.0	5.0	56.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	hg19	10	70332130	70332130	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	TET1	NM_030625	exon2	c.T35C	p.L12S	CCAGATTAGTCAG	.	85.0	28.0	93.0	0.0	.	255	.	.	.	none	.	.	PASS	Atlas-SNP
PTEN	5728	hgsc.bcm.edu	hg19	10	89717690	89717690	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PTEN	NM_000314	exon7	c.A715G	p.M239V	AAGTTCATGTACT	.	171.0	49.0	163.0	0.0	.	3652	.	.	.	none	.	.	PASS	Atlas-SNP
PDZD8	118987	hgsc.bcm.edu	hg19	10	119043959	119043959	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PDZD8	NM_173791	exon5	c.C2285A	p.P762H	GCCTTAGGTGAGG	.	68.0	23.0	70.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
PWWP2B	170394	hgsc.bcm.edu	hg19	10	134218416	134218416	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PWWP2B	NM_001098637	exon2	c.C412T	p.L138L	TACAAGCTGTGGG	.	5.0	4.0	0.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	hg19	11	1018068	1018068	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	MUC6	NM_005961	exon31	c.C4733T	p.P1578L	GTAGGTGGGGAGT	.	411.0	70.0	394.0	0.0	.	408	.	.	.	none	.	.	PASS	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	hg19	11	1643254	1643254	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	KRTAP5-4	NM_001012709	exon1	c.T70C	p.C24R	AGCCACAGCCCCC	.	133.0	6.0	57.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
EEF1G	1937	hgsc.bcm.edu	hg19	11	62334912	62334912	+	Missense_Mutation	SNP	A	A	C	rs11549626		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	EEF1G	NM_001404	exon6	c.T611G	p.L204W	TCGCCCAAGACAG	.	99.0	32.0	70.0	0.0	.	33	.	.	.	weak	.	.	PASS	Atlas-SNP
DGAT2	84649	hgsc.bcm.edu	hg19	11	75509414	75509414	+	Missense_Mutation	SNP	G	G	C	rs145750206	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	DGAT2	NM_032564	exon7	c.G952C	p.G318R	GGTCGAGGCCTCT	.	97.0	33.0	77.0	0.0	.	37	.	.	.	alt	G|0.999;A|0.001	.	PASS	Atlas-SNP
DENND5B	160518	hgsc.bcm.edu	hg19	12	31551284	31551284	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	DENND5B	NM_144973	exon17	c.G3081A	p.G1027G	CCACCGCCCACAT	.	24.0	9.0	44.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
PRPH	5630	hgsc.bcm.edu	hg19	12	49689459	49689459	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PRPH	NM_006262	exon1	c.G476A	p.G159D	TGTTGGGCCGCGA	.	7.0	4.0	0.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
KRT2	3849	hgsc.bcm.edu	hg19	12	53045499	53045499	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	KRT2	NM_000423	exon1	c.C428G	p.P143R	CCTCCAGGCCCAA	.	117.0	39.0	120.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
MDM1	56890	hgsc.bcm.edu	hg19	12	68696605	68696605	+	Silent	SNP	T	T	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	MDM1	NM_017440	exon12	c.A1767T	p.I589I	TGTTTTTATACCA	.	27.0	6.0	37.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
SRRM4	84530	hgsc.bcm.edu	hg19	12	119583229	119583229	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SRRM4	NM_194286	exon9	c.C815A	p.A272D	AAACAGCCAGCCC	.	106.0	28.0	81.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
RABGGTA	5875	hgsc.bcm.edu	hg19	14	24734893	24734893	+	Silent	SNP	C	C	T	rs369935041		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	RABGGTA,NS,lymphoid_neoplasm,0,1	RABGGTA	NM_004581	exon16	c.G1632A	p.P544P	GCACAGCGGGTTA	.	116.0	40.0	119.0	0.0	.	43	.	.	.	weak	.	.	PASS	Atlas-SNP
RALGAPA1	253959	hgsc.bcm.edu	hg19	14	36143779	36143779	+	Silent	SNP	A	A	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	RALGAPA1	NM_194301	exon22	c.T3243G	p.P1081P	TATTTCAGGATCC	.	243.0	72.0	246.0	0.0	.	289	.	.	.	none	.	.	PASS	Atlas-SNP
NPAP1	23742	hgsc.bcm.edu	hg19	15	24923342	24923342	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	C15orf2,NS,carcinoma,0,1	.	NM_018958	exon1	c.C2328T	p.A776A	TGGGGCCCCTGAT	.	34.0	14.0	20.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF75A	7627	hgsc.bcm.edu	hg19	16	3363138	3363138	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ZNF75A	NM_153028	exon4	c.T63A	p.D21E	CAATGATGTAATG	.	170.0	84.0	112.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
ACADVL	37	hgsc.bcm.edu	hg19	17	7127679	7127679	+	Silent	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ACADVL	NM_001270447	exon17	c.T1641C	p.L547L	CGGACTTGTCCAC	.	106.0	49.0	73.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
POLR2A	5430	hgsc.bcm.edu	hg19	17	7405000	7405000	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	POLR2A	NM_000937	exon14	c.G2301A	p.K767K	CTTCAAGTCTATG	.	140.0	34.0	88.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
GPR179	440435	hgsc.bcm.edu	hg19	17	36492994	36492994	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	GPR179	NM_001004334	exon4	c.G1094A	p.S365N	ATGCAGCTGGTGC	.	78.0	14.0	25.0	0.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
OTOP3	347741	hgsc.bcm.edu	hg19	17	72942796	72942796	+	Silent	SNP	G	G	A	rs200903740	bycluster	TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	OTOP3	NM_178233	exon6	c.G846A	p.A282A	CACCGCGTGTGAA	.	90.0	4.0	60.0	0.0	.	64	.	.	.	weak	G|0.999;A|0.001	0.001	PASS	Atlas-SNP
CBX4	8535	hgsc.bcm.edu	hg19	17	77807927	77807927	+	Missense_Mutation	SNP	A	A	G	rs200965379		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	CBX4,uveal_tract,malignant_melanoma,0,1	CBX4	NM_003655	exon5	c.T1514C	p.V505A	GCCGCCACCGCCA	.	27.0	6.0	4.0	1.0	.	40	.	.	.	weak	.	.	PASS	Atlas-SNP
HMHA1	23526	hgsc.bcm.edu	hg19	19	1081736	1081736	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	HMHA1	NM_001258328	exon18	c.A2426C	p.K809T	GCACCAAGGTGAG	.	31.0	10.0	2.0	0.0	.	78	.	.	.	none	.	.	PASS	Atlas-SNP
EVI5L	115704	hgsc.bcm.edu	hg19	19	7917990	7917990	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	EVI5L	NM_001159944	exon8	c.C1006G	p.P336A	GTGATCCCCCACC	.	112.0	43.0	79.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
PGLYRP2	114770	hgsc.bcm.edu	hg19	19	15582776	15582776	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PGLYRP2	NM_052890	exon3	c.C1268T	p.T423M	CAGCGCGTGAAGT	.	88.0	5.0	59.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM38A	79041	hgsc.bcm.edu	hg19	19	16793291	16793291	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	TMEM38A	NM_024074	exon4	c.G526C	p.E176Q	AAGCCAGAGACCA	.	133.0	42.0	92.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
BABAM1	29086	hgsc.bcm.edu	hg19	19	17384931	17384931	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	BABAM1	NM_014173	exon5	c.T481C	p.S161P	CTGACCTCCGACC	.	51.0	23.0	40.0	0.0	.	14	.	.	.	none	.	.	PASS	Atlas-SNP
SUGP2	10147	hgsc.bcm.edu	hg19	19	19106027	19106027	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SUGP2	NM_014884	exon9	c.G3054A	p.M1018I	CTGCAGCATCTGG	.	57.0	19.0	61.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
VSTM2B	342865	hgsc.bcm.edu	hg19	19	30018151	30018151	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	VSTM2B	NM_001146339	exon2	c.T116C	p.V39A	TGACAGTACGGGA	.	69.0	13.0	52.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
ETHE1	23474	hgsc.bcm.edu	hg19	19	44030497	44030497	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ETHE1	NM_014297	exon3	c.T231A	p.N77K	GTGGGTATTCACT	.	131.0	43.0	143.0	0.0	.	7	.	.	.	none	.	.	PASS	Atlas-SNP
JAG1	182	hgsc.bcm.edu	hg19	20	10653490	10653490	+	Nonsense_Mutation	SNP	A	A	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	JAG1	NM_000214	exon2	c.T246G	p.Y82X	GGACTGATACTCC	.	94.0	25.0	49.0	0.0	.	213	.	.	.	none	.	.	PASS	Atlas-SNP
DZANK1	55184	hgsc.bcm.edu	hg19	20	18414380	18414380	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	DZANK1	NM_001099407	exon9	c.G777A	p.L259L	GGGTACCAAGCTT	.	61.0	14.0	68.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
SS18L1	26039	hgsc.bcm.edu	hg19	20	60738629	60738629	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SS18L1	NM_198935	exon6	c.C672A	p.S224R	GGGGAGCAGCATG	.	98.0	43.0	2.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
PWP2	5822	hgsc.bcm.edu	hg19	21	45534138	45534138	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PWP2	NM_005049	exon4	c.T305C	p.V102A	ACAGTGTGTCCTT	.	85.0	17.0	89.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
C22orf15	150248	hgsc.bcm.edu	hg19	22	24106287	24106287	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	C22orf15	NM_182520	exon2	c.G39A	p.V13V	CTCGGTGCTGGTG	.	65.0	25.0	95.0	0.0	.	5	.	.	.	none	.	.	PASS	Atlas-SNP
GATSL3	652968	hgsc.bcm.edu	hg19	22	30685454	30685454	+	Silent	SNP	C	C	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	GATSL3	NM_001037666	exon1	c.G33A	p.R11R	CAGCACCCGCACC	.	56.0	20.0	8.0	0.0	.	14	.	.	.	none	.	.	PASS	Atlas-SNP
CBY1	25776	hgsc.bcm.edu	hg19	22	39066951	39066951	+	Silent	SNP	G	G	A	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	CBY1	NM_001002880	exon4	c.G270A	p.L90L	GAACCTGGCAGGG	.	67.0	14.0	64.0	0.0	.	10	.	.	.	none	.	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	hg19	MT	14808	14808	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	.	ENST00000361789	exon1	c.T62C	p.L21P	TCGACCTCCCCAC	.	21.0	11.0	188.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
HOOK2	29911	hgsc.bcm.edu	hg19	19	12874398	12874398	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	HOOK2	NM_013312	exon22	c.1955delG	p.S652fs	.	.	118.0	40.0	121.0	0.0	.	73	.	0.338983	0	none	.	.	PASS	Atlas-Indel,Pindel
TTLL5	23093	hgsc.bcm.edu	hg19	14	76243163	76243163	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	TTLL5	NM_015072	exon23	c.2356delG	p.E786fs	.	.	97.0	21.0	92.0	0.0	.	102	.	0.216495	0	none	.	.	PASS	Atlas-Indel,Pindel
RSPH3	83861	hgsc.bcm.edu	hg19	6	159398820	159398821	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	RSPH3	NM_031924	exon8	c.1433_1434del	p.478_478del	.	.	77.0	23.0	72.0	0.0	.	48	.	0.298701	0	none	.	.	PASS	Atlas-Indel,Pindel
KLRC3	3823	hgsc.bcm.edu	hg19	12	10573086	10573086	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	KLRC3	NM_007333	exon1	c.65delG	p.R22fs	.	.	48.0	13.0	68.0	0.0	.	25	.	0.270833	0	none	.	.	PASS	Atlas-INDEL
LOC81691	0	hgsc.bcm.edu	hg19	16	20851720	20851720	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	LOC81691	NM_001144924	exon15	c.1555delA	p.R519fs	.	.	70.0	34.0	71.0	0.0	.	41	.	0.485714	0	none	.	.	PASS	Atlas-Indel,Pindel
KLRC2	3822	hgsc.bcm.edu	hg19	12	10588522	10588522	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	KLRC2	NM_002260	exon1	c.65delG	p.R22fs	.	.	154.0	34.0	146.0	0.0	.	29	.	0.220779	0	none	.	.	PASS	Atlas-INDEL
C1orf114	57821	hgsc.bcm.edu	hg19	1	169390718	169390718	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	C1orf114	NM_021179	exon3	c.952delA	p.N318fs	.	.	77.0	35.0	73.0	0.0	.	67	.	0.454545	0	none	.	.	PASS	Atlas-Indel,Pindel
GPATCH8	23131	hgsc.bcm.edu	hg19	17	42475173	42475176	+	Frame_Shift_Del	DEL	TGAG	TGAG	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TGAG	TGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	GPATCH8	NM_001002909	exon8	c.4270_4273del	p.1424_1425del	.	.	263.0	112.0	206.0	0.0	.	114	.	0.425856	0	none	.	.	PASS	Atlas-Indel,Pindel
SLC7A13	157724	hgsc.bcm.edu	hg19	8	87235298	87235298	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	SLC7A13	NM_138817	exon2	c.721delT	p.C241fs	.	.	55.0	16.0	47.0	0.0	.	97	.	0.290909	0	none	.	.	PASS	Atlas-Indel,Pindel
MLL3	58508	hgsc.bcm.edu	hg19	7	151873882	151873883	+	Frame_Shift_Del	DEL	TT	TT	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	MLL3	NM_170606	exon38	c.8656_8657del	p.2886_2886del	.	.	164.0	98.0	98.0	0.0	.	1564	.	0.597561	0	none	.	.	PASS	Atlas-Indel,Pindel
THSD7A	221981	hgsc.bcm.edu	hg19	7	11486930	11486931	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	THSD7A	NM_015204	exon12	c.2727_2728insA	p.L909fs	.	.	167.0	84.0	85.0	0.0	.	219	.	0.502994	0	none	.	.	PASS	Atlas-Indel,Pindel
PIK3R1	5295	hgsc.bcm.edu	hg19	5	67588157	67588158	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PIK3R1	NM_181523	exon8	c.987_988insG	p.Q329fs	.	.	55.0	24.0	51.0	0.0	.	869	.	0.436364	0	none	.	.	PASS	Atlas-Indel,Pindel
NUP62	23636	hgsc.bcm.edu	hg19	19	50411616	50411633	+	In_Frame_Del	DEL	GTCCATGTGCGCATTGAG	GTCCATGTGCGCATTGAG	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	GTCCATGTGCGCATTGAG	GTCCATGTGCGCATTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	NUP62	NM_153719	exon3	c.1433_1450del	p.478_484del	.	.	62.0	17.0	47.0	0.0	.	50	.	0.274194	0	none	.	.	PASS	Atlas-INDEL
ROBO1	6091	hgsc.bcm.edu	hg19	3	79639003	79639003	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	ROBO1	NM_002941	exon2	c.60delT	p.N20fs	.	.	165.0	11.0	153.0	0.0	.	833	.	0.0666667	0	none	.	.	PASS	Atlas-INDEL
PRKCG	5582	hgsc.bcm.edu	hg19	19	54401854	54401854	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	PRKCG	NM_002739	exon11	c.1252delA	p.T418fs	.	.	71.0	28.0	52.0	0.0	.	246	.	0.394366	0	none	.	.	PASS	Atlas-Indel,Pindel
BPIFA1	51297	hgsc.bcm.edu	hg19	20	31829269	31829269	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	.	NM_130852	exon6	c.659delA	p.Q220fs	.	.	85.0	20.0	115.0	0.0	.	.	.	0.235294	0	none	.	.	PASS	Atlas-Indel,Pindel
NAIP	4671	hgsc.bcm.edu	hg19	5	70279772	70279772	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-P4-A5E7-01A-31D-A28G-10	TCGA-P4-A5E7-11A-11D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	4b75f116-8565-4b91-8bbe-c053a72fad8c	4106b575-287e-4493-8e74-2a72b1b94591	.	NAIP	NM_004536	exon12	c.3105delC	p.N1035fs	.	.	221.0	17.0	221.0	0.0	.	38	.	0.0769231	0	none	.	.	PASS	Atlas-INDEL