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
ZMPSTE24	10269	hgsc.bcm.edu	hg19	1	40724033	40724033	+	Silent	SNP	G	G	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	ZMPSTE24	NM_005857	exon1	c.G90C	p.V30V	GACAGTGTATCTT	.	99.0	32.0	83.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
GSTM4	2948	hgsc.bcm.edu	hg19	1	110201466	110201466	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	GSTM4	NM_000850	exon6	c.C391A	p.L131I	GAGGAACTTCCTA	.	303.0	97.0	327.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
IGSF3	3321	hgsc.bcm.edu	hg19	1	117120184	117120184	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	IGSF3	NM_001542	exon12	c.G3395C	p.S1132T	GTGGGACCTGAAA	.	88.0	30.0	57.0	0.0	.	294	.	.	.	none	.	.	PASS	Atlas-SNP
DENND4B	9909	hgsc.bcm.edu	hg19	1	153907305	153907305	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	DENND4B_ENST00000361217,bladder,carcinoma,+2,2	DENND4B	NM_014856	exon18	c.C2704G	p.Q902E	GCTGCTGTTGCTG	.	102.0	24.0	49.0	1.0	.	210	.	.	.	none	.	.	PASS	Atlas-SNP
INSRR	3645	hgsc.bcm.edu	hg19	1	156824054	156824054	+	Missense_Mutation	SNP	G	G	A	rs140386495	bycluster	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	INSRR	NM_014215	exon2	c.C127T	p.R43C	GCTGACGAAGCTC	.	59.0	14.0	57.0	0.0	.	309	.	.	.	weak	G|1.000;A|0.000	0.000	PASS	Atlas-SNP
KLHDC9	126823	hgsc.bcm.edu	hg19	1	161069269	161069269	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	KLHDC9	NM_001007255	exon2	c.G661A	p.G221R	GTAGCTGGGCATT	.	230.0	70.0	193.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
IARS2	55699	hgsc.bcm.edu	hg19	1	220311360	220311360	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	IARS2	NM_018060	exon17	c.A2150G	p.N717S	TGCTCAATGCTGC	.	142.0	11.0	141.0	0.0	.	106	.	.	.	none	.	.	PASS	Atlas-SNP
URB2	9816	hgsc.bcm.edu	hg19	1	229771821	229771821	+	Silent	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	URB2	NM_014777	exon4	c.G1461A	p.Q487Q	GAGGCAGCCTGTG	.	117.0	55.0	114.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
HNRNPU	3192	hgsc.bcm.edu	hg19	1	245018785	245018785	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	HNRNPU	NM_031844	exon12	c.T2293C	p.Y765H	TTGAGTAACTACC	.	119.0	45.0	138.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
OSR1	130497	hgsc.bcm.edu	hg19	2	19552164	19552164	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	OSR1	NM_145260	exon3	c.C673T	p.H225Y	TGGAGTGAATATA	.	101.0	9.0	107.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
UNC80	285175	hgsc.bcm.edu	hg19	2	210714187	210714187	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	UNC80	NM_032504	exon22	c.T3473G	p.F1158C	ACAGTTTTGATGA	.	171.0	59.0	168.0	0.0	.	280	.	.	.	none	.	.	PASS	Atlas-SNP
IP6K2	51447	hgsc.bcm.edu	hg19	3	48728866	48728866	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	IP6K2	NM_016291	exon4	c.T478C	p.Y160H	TGTAGTACAAGAC	.	146.0	51.0	171.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
OR5H2	79310	hgsc.bcm.edu	hg19	3	98001882	98001882	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	OR5H2	NM_001005482	exon1	c.A151C	p.I51L	GGTCTGATTGCTC	.	275.0	97.0	252.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
TPRA1	131601	hgsc.bcm.edu	hg19	3	127292425	127292425	+	Missense_Mutation	SNP	G	G	C	rs201165800	by1000genomes;alternate_allele	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	TPRA1	NM_001136053	exon11	c.C1061G	p.P354R	TGGCAGGGCATGG	.	74.0	24.0	66.0	0.0	.	21	.	.	.	alt	G|0.999;A|0.001	.	PASS	Atlas-SNP
ADD1	118	hgsc.bcm.edu	hg19	4	2883755	2883755	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	ADD1	NM_014190	exon3	c.C326A	p.A109D	CAGCAGCTCCGCA	.	220.0	91.0	161.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
SLC34A2	10568	hgsc.bcm.edu	hg19	4	25676246	25676246	+	Missense_Mutation	SNP	C	C	G	rs375377923	alternate_allele	TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SLC34A2	NM_006424	exon12	c.C1453G	p.L485V	AGTTCACTCCAGG	.	206.0	80.0	174.0	0.0	.	93	.	.	.	alt	.	.	PASS	Atlas-SNP
CWH43	80157	hgsc.bcm.edu	hg19	4	49032879	49032879	+	Silent	SNP	T	T	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	CWH43	NM_025087	exon11	c.T1410G	p.S470S	TGCTTCTAAGCCC	.	115.0	41.0	142.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
PRKG2	5593	hgsc.bcm.edu	hg19	4	82061797	82061797	+	Silent	SNP	A	A	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	PRKG2	NM_006259	exon11	c.T1434A	p.A478A	AGCAAAAGCAACA	.	156.0	37.0	139.0	0.0	.	195	.	.	.	none	.	.	PASS	Atlas-SNP
FAT1	2195	hgsc.bcm.edu	hg19	4	187627969	187627969	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	FAT1	NM_005245	exon2	c.G3013A	p.D1005N	CCTTGTCTTTGGC	.	262.0	91.0	219.0	0.0	.	500	.	.	.	none	.	.	PASS	Atlas-SNP
SKIV2L2	23517	hgsc.bcm.edu	hg19	5	54635905	54635905	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SKIV2L2	NM_015360	exon6	c.A583G	p.S195G	GCTCTGAGTAACC	.	80.0	24.0	102.0	0.0	.	104	.	.	.	none	.	.	PASS	Atlas-SNP
VCAN	1462	hgsc.bcm.edu	hg19	5	82815685	82815685	+	Silent	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	VCAN	NM_004385	exon7	c.G1560A	p.L520L	ACCATTGGTAACT	.	134.0	43.0	148.0	0.0	.	498	.	.	.	none	.	.	PASS	Atlas-SNP
PHACTR1	221692	hgsc.bcm.edu	hg19	6	13283687	13283687	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	PHACTR1	NM_030948	exon13	c.G1543C	p.E515Q	CTTCGGGAAAGAA	.	124.0	43.0	78.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
ZFP57	346171	hgsc.bcm.edu	hg19	6	29643249	29643249	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	ZFP57	NM_001109809	exon3	c.A266G	p.H89R	GGCTTATGCAGAA	.	218.0	91.0	223.0	0.0	.	80	.	.	.	none	.	.	PASS	Atlas-SNP
ABHD16A	7920	hgsc.bcm.edu	hg19	6	31657863	31657863	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	ABHD16A	NM_021160	exon11	c.G949A	p.G317R	TGCTTCCAGCAAA	.	76.0	25.0	91.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
GRB10	2887	hgsc.bcm.edu	hg19	7	50742288	50742288	+	Silent	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	GRB10	NM_005311	exon3	c.C207T	p.A69A	GCTGCAGGCCGAG	.	91.0	8.0	51.0	0.0	.	155	.	.	.	none	.	.	PASS	Atlas-SNP
WDR91	29062	hgsc.bcm.edu	hg19	7	134893687	134893687	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	WDR91	NM_014149	exon3	c.G367T	p.A123S	ACTCAGCCTGGTT	.	521.0	195.0	290.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	hg19	8	77616434	77616434	+	Silent	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	ZFHX4	NM_024721	exon2	c.G111A	p.G37G	TGCAGGGATGGAG	.	274.0	84.0	238.0	0.0	.	878	.	.	.	none	.	.	PASS	Atlas-SNP
TONSL	4796	hgsc.bcm.edu	hg19	8	145654714	145654714	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	TONSL	NM_013432	exon26	c.G3949A	p.A1317T	GGACGGCGCAGCC	.	7.0	5.0	0.0	0.0	.	128	.	.	.	none	.	.	PASS	Atlas-SNP
OPN4	94233	hgsc.bcm.edu	hg19	10	88419072	88419072	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	OPN4,NS,carcinoma,0,2	OPN4	NM_001030015	exon6	c.G680A	p.G227E	CCGAGGGGTTGCT	.	77.0	29.0	56.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	hg19	11	1093204	1093204	+	Missense_Mutation	SNP	C	C	A	rs56299570		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	MUC2_ENST00000441003,caecum,carcinoma,0,4	MUC2	NM_002457	exon30	c.C5023A	p.P1675T	CCAACCCCAACAG	.	144.0	8.0	130.0	2.0	.	614	.	.	.	weak	.	.	PASS	Atlas-SNP
KCNA4	3739	hgsc.bcm.edu	hg19	11	30034138	30034138	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	KCNA4	NM_002233	exon2	c.C88T	p.R30W	TCTCCCGCTCCCG	.	12.0	5.0	14.0	0.0	.	158	.	.	.	none	.	.	PASS	Atlas-SNP
API5	8539	hgsc.bcm.edu	hg19	11	43350300	43350300	+	Silent	SNP	A	A	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	API5	NM_006595	exon9	c.A984T	p.G328G	AAATGGAGAGAAT	.	234.0	73.0	244.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
MCAM	4162	hgsc.bcm.edu	hg19	11	119185945	119185945	+	Silent	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	MCAM	NM_006500	exon2	c.G96A	p.A32A	CTCAGGCGCAGGC	.	48.0	5.0	42.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
GLI1	2735	hgsc.bcm.edu	hg19	12	57861257	57861257	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	GLI1	NM_005269	exon9	c.C1054A	p.Q352K	AAGCACCAGAATC	.	368.0	92.0	214.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
PAWR	5074	hgsc.bcm.edu	hg19	12	80083606	80083606	+	Missense_Mutation	SNP	G	G	A	rs369162125		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	PAWR	NM_002583	exon2	c.C419T	p.S140L	GGGCCCGAGCTCT	.	100.0	5.0	40.0	0.0	.	14	.	.	.	weak	.	.	PASS	Atlas-SNP
P2RX2	22953	hgsc.bcm.edu	hg19	12	133197702	133197702	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	P2RX2	NM_170683	exon8	c.C890T	p.S297L	CCTCGTCAGGCTA	.	182.0	11.0	124.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
POU4F1	5457	hgsc.bcm.edu	hg19	13	79175599	79175599	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	POU4F1	NM_006237	exon2	c.G1211T	p.C404F	TGGTTGCAAAACC	.	43.0	12.0	48.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
DCAF5	8816	hgsc.bcm.edu	hg19	14	69521317	69521317	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	DCAF5	NM_003861	exon9	c.A2086G	p.T696A	GGCTGGTTCCTGC	.	68.0	21.0	60.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
IGDCC4	57722	hgsc.bcm.edu	hg19	15	65684246	65684246	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	IGDCC4	NM_020962	exon12	c.G2196C	p.K732N	CTTGCCCTTCCAC	.	112.0	40.0	92.0	0.0	.	95	.	.	.	none	.	.	PASS	Atlas-SNP
PEAK1	0	hgsc.bcm.edu	hg19	15	77472613	77472613	+	Silent	SNP	A	A	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	.	NM_024776	exon5	c.T1656A	p.T552T	TCCACTAGTAATT	.	110.0	35.0	140.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CARHSP1	23589	hgsc.bcm.edu	hg19	16	8953055	8953055	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	CARHSP1,NS,carcinoma,0,2	CARHSP1	NM_001042476	exon2	c.C131T	p.P44L	CGAGTGGGCAGTG	.	112.0	42.0	110.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
IL4R	3566	hgsc.bcm.edu	hg19	16	27374134	27374134	+	Silent	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	IL4R	NM_000418	exon11	c.G1461A	p.T487T	AGAGACGCCCCTC	.	117.0	40.0	86.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
SETD1A	9739	hgsc.bcm.edu	hg19	16	30970101	30970101	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SETD1A	NM_014712	exon2	c.T49C	p.W17R	TTCCAGTGGCGGA	.	152.0	46.0	136.0	0.0	.	143	.	.	.	none	.	.	PASS	Atlas-SNP
SALL1	6299	hgsc.bcm.edu	hg19	16	51171349	51171349	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SALL1	NM_002968	exon3	c.T3649G	p.F1217V	TCTGGAACATTTC	.	116.0	29.0	133.0	0.0	.	301	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP10	57610	hgsc.bcm.edu	hg19	16	67761787	67761787	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	RANBP10	NM_020850	exon12	c.C1487A	p.P496H	CGCCGAGGATGCC	.	108.0	32.0	118.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
CDK10	8558	hgsc.bcm.edu	hg19	16	89760632	89760632	+	Silent	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	CDK10	NM_052988	exon9	c.C660T	p.I220I	CAGCATCGACATG	.	158.0	65.0	169.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
CAMTA2	23125	hgsc.bcm.edu	hg19	17	4877742	4877742	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	CAMTA2	NM_001171167	exon12	c.A2023C	p.M675L	CTGCCATCCGCTT	.	193.0	89.0	153.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
SCRN2	90507	hgsc.bcm.edu	hg19	17	45916860	45916860	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SCRN2	NM_138355	exon4	c.C506T	p.A169V	ACCCACGCCTCAG	.	220.0	108.0	170.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
NXPH3	11248	hgsc.bcm.edu	hg19	17	47656051	47656051	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	NXPH3	NM_007225	exon2	c.C148T	p.R50W	CGGAAGCGGGGCC	.	169.0	101.0	72.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	hg19	17	62045582	62045582	+	Silent	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SCN4A	NM_000334	exon6	c.G837A	p.K279K	CACACACTTCTGC	.	518.0	129.0	365.0	0.0	.	205	.	.	.	none	.	.	PASS	Atlas-SNP
SCN4A	6329	hgsc.bcm.edu	hg19	17	62045585	62045585	+	Silent	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SCN4A	NM_000334	exon6	c.G834A	p.Q278Q	ACACTTCTGCCTC	.	504.0	125.0	359.0	0.0	.	205	.	.	.	none	.	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	hg19	19	6475944	6475944	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	DENND1C	NM_024898	exon11	c.C683T	p.T228I	CACGAGGTCAGCT	.	8.0	6.0	4.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
CYP4F22	126410	hgsc.bcm.edu	hg19	19	15651480	15651480	+	Silent	SNP	C	C	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	CYP4F22	NM_173483	exon8	c.C891T	p.A297A	TAAGGCCAAGCAG	.	102.0	23.0	98.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
CAPN12	147968	hgsc.bcm.edu	hg19	19	39226166	39226166	+	Silent	SNP	G	G	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	CAPN12	NM_144691	exon13	c.C1602A	p.I534I	TGCGCTGATCACG	.	75.0	26.0	89.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
PSG5	5673	hgsc.bcm.edu	hg19	19	43689069	43689069	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	PSG5	NM_002781	exon2	c.G295T	p.E99X	CTGTTTCTCGTCC	.	252.0	79.0	254.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
LILRB3	11025	hgsc.bcm.edu	hg19	19	54721052	54721052	+	Silent	SNP	G	G	T	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	LILRB3	NM_001081450	exon13	c.C1809A	p.T603T	TCTAAGGGTCAAG	.	189.0	101.0	180.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
BCL2L1	598	hgsc.bcm.edu	hg19	20	30253881	30253881	+	Silent	SNP	A	A	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	BCL2L1	NM_138578	exon3	c.T573C	p.F191F	TTCCACAAAAGTA	.	137.0	71.0	84.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	hg19	21	28305272	28305272	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	ADAMTS5	NM_007038	exon5	c.G1781C	p.C594S	TTATTACAGTGAC	.	198.0	57.0	163.0	0.0	.	184	.	.	.	none	.	.	PASS	Atlas-SNP
SEZ6L	23544	hgsc.bcm.edu	hg19	22	26761491	26761491	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	SEZ6L	NM_021115	exon13	c.G2753A	p.G918E	TCCTGGGACAGCC	.	149.0	49.0	174.0	0.0	.	174	.	.	.	none	.	.	PASS	Atlas-SNP
MPHOSPH10	10199	hgsc.bcm.edu	hg19	2	71368372	71368378	+	Frame_Shift_Del	DEL	ATGTAGT	ATGTAGT	-	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	ATGTAGT	ATGTAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	MPHOSPH10	NM_005791	exon7	c.1318_1324del	p.440_442del	.	.	151.0	16.0	186.0	0.0	.	81	.	0.10596	0	none	.	.	PASS	Atlas-Indel,Pindel
TRMT10C	54931	hgsc.bcm.edu	hg19	3	101284160	101284160	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	.	NM_017819	exon2	c.534delA	p.L178fs	.	.	46.0	18.0	30.0	0.0	.	.	.	0.391304	0	none	.	.	PASS	Atlas-Indel,Pindel
PLS3	5358	hgsc.bcm.edu	hg19	X	114880464	114880465	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	PLS3	NM_005032	exon12	c.1335_1336insA	p.V445fs	.	.	141.0	92.0	140.0	0.0	.	60	.	0.652482	0	none	.	.	PASS	Atlas-Indel,Pindel
EZH1	2145	hgsc.bcm.edu	hg19	17	40880917	40880920	+	Frame_Shift_Del	DEL	AGTA	AGTA	-	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	AGTA	AGTA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	EZH1	NM_001991	exon3	c.41_44del	p.14_15del	.	.	93.0	26.0	78.0	0.0	.	62	.	0.27957	0	none	.	.	PASS	Atlas-Indel,Pindel
RAD51AP2	729475	hgsc.bcm.edu	hg19	2	17692220	17692220	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	RAD51AP2	NM_001099218	exon3	c.3332delG	p.S1111fs	.	.	105.0	17.0	87.0	0.0	.	134	.	0.161905	0	none	.	.	PASS	Atlas-Indel,Pindel
CTAGE5	4253	hgsc.bcm.edu	hg19	14	39815176	39815179	+	Frame_Shift_Del	DEL	CTGT	CTGT	-	novel		TCGA-MH-A562-01A-11D-A26P-10	TCGA-MH-A562-10A-01D-A26P-10	CTGT	CTGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	dddea2e4-b8c3-4157-9d92-6de472e8375a	bd8aec5f-0589-436d-9c8e-eaf4e60046e2	.	CTAGE5	NM_001247989	exon21	c.1914_1917del	p.638_639del	.	.	200.0	11.0	219.0	0.0	.	75	.	0.055	.	none	.	.	PASS	Pindel