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
DVL1	1855	hgsc.bcm.edu	hg19	1	1277480	1277480	+	Missense_Mutation	SNP	A	A	G	rs147424815		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	DVL1	NM_004421	exon4	c.T419C	p.M140T	CTGACCATGGACT	.	150.0	27.0	153.0	0.0	.	36	.	A|1.000;G|0.000	Atlas-SNP
CAMTA1	23261	hgsc.bcm.edu	hg19	1	7700465	7700465	+	Silent	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	CAMTA1	NM_015215	exon7	c.C516T	p.P172P	GAACCCCGACATC	.	130.0	27.0	137.0	0.0	.	226	.	.	Atlas-SNP
MFAP2	4237	hgsc.bcm.edu	hg19	1	17301519	17301519	+	Splice_Site	SNP	C	C	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	MFAP2	NM_001135248	exon10	c.446-1G>C	.	GGTCAGCTATTGG	.	114.0	19.0	125.0	0.0	.	8	.	.	Atlas-SNP
FGR	2268	hgsc.bcm.edu	hg19	1	27941376	27941376	+	Silent	SNP	C	C	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	FGR	NM_001042729	exon10	c.G1080T	p.V360V	CATGTCCACCAAT	.	147.0	19.0	204.0	0.0	.	39	.	.	Atlas-SNP
IPP	3652	hgsc.bcm.edu	hg19	1	46165836	46165836	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	IPP	NM_001145349	exon9	c.G1557T	p.M519I	CACTTTCATTGAG	.	34.0	6.0	38.0	0.0	.	66	.	.	Atlas-SNP
PTPN22	26191	hgsc.bcm.edu	hg19	1	114380848	114380848	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	PTPN22	NM_015967	exon13	c.G1174A	p.D392N	TTGTGTCAGCATT	.	52.0	8.0	53.0	0.0	.	90	.	.	Atlas-SNP
OR10J5	127385	hgsc.bcm.edu	hg19	1	159504893	159504893	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	OR10J5	NM_001004469	exon1	c.G905C	p.R302T	ACAACTCTGCATA	.	52.0	7.0	46.0	0.0	.	68	.	.	Atlas-SNP
FCRLB	127943	hgsc.bcm.edu	hg19	1	161697408	161697408	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	FCRLB	NM_001002901	exon6	c.G1237A	p.A413T	CACTTTGCTGTGA	.	123.0	8.0	115.0	0.0	.	35	.	.	Atlas-SNP
CACNA1E	777	hgsc.bcm.edu	hg19	1	181767462	181767462	+	Missense_Mutation	SNP	C	C	G	rs189356042	by1000genomes;alternate_allele	TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	CACNA1E	NM_001205293	exon48	c.C6434G	p.S2145C	TCCCCTCTGTCTC	.	36.0	9.0	33.0	0.0	.	778	.	C|1.000;T|0.000	Atlas-SNP
LYST	1130	hgsc.bcm.edu	hg19	1	235973623	235973623	+	Silent	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	LYST	NM_000081	exon5	c.C495A	p.T165T	ATCTGAGGTGGAG	.	92.0	20.0	83.0	0.0	.	370	.	.	Atlas-SNP
RYR2	6262	hgsc.bcm.edu	hg19	1	237778097	237778097	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	RYR2	NM_001035	exon37	c.A5669C	p.K1890T	GGCCCAAGGAAGG	.	156.0	31.0	185.0	0.0	.	1273	.	.	Atlas-SNP
GRHL1	29841	hgsc.bcm.edu	hg19	2	10095217	10095217	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	GRHL1	NM_198182	exon2	c.A194G	p.Y65C	TGCTCTATGACTA	.	110.0	16.0	132.0	0.0	.	95	.	.	Atlas-SNP
DQX1	165545	hgsc.bcm.edu	hg19	2	74745708	74745708	+	Silent	SNP	T	T	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	DQX1	NM_133637	exon12	c.A2019T	p.P673P	GAAGTATGGAGGG	.	139.0	24.0	147.0	0.0	.	95	.	.	Atlas-SNP
LMAN2L	81562	hgsc.bcm.edu	hg19	2	97405772	97405772	+	Silent	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	LMAN2L	NM_030805	exon1	c.G6A	p.A2A	AGTCGCCGCCATC	.	37.0	9.0	22.0	0.0	.	27	.	.	Atlas-SNP
GLI2	2736	hgsc.bcm.edu	hg19	2	121554929	121554929	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	GLI2,NS,carcinoma,0,1	GLI2	NM_005270	exon1	c.G33T	p.E11D	CTCCGAGAAGCAA	.	68.0	15.0	73.0	0.0	.	187	.	.	Atlas-SNP
BAZ2B	29994	hgsc.bcm.edu	hg19	2	160242941	160242941	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	BAZ2B	NM_013450	exon22	c.A3394T	p.M1132L	CACCCATGCTGTC	.	61.0	10.0	98.0	0.0	.	196	.	.	Atlas-SNP
HOXD9	3235	hgsc.bcm.edu	hg19	2	176988265	176988265	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	HOXD9	NM_014213	exon1	c.G769C	p.E257Q	CTGAAGGAGGAGG	.	70.0	12.0	91.0	0.0	.	49	.	.	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	hg19	2	186673299	186673299	+	Silent	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	FSIP2	NM_173651	exon17	c.C19533T	p.V6511V	GGTTGTCGATTCC	.	98.0	16.0	127.0	0.0	.	251	.	.	Atlas-SNP
ITGAV	3685	hgsc.bcm.edu	hg19	2	187465066	187465066	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	ITGAV	NM_001144999	exon1	c.T5C	p.L2P	AAATGCTCCTAGG	.	49.0	7.0	71.0	0.0	.	124	.	.	Atlas-SNP
COL4A4	1286	hgsc.bcm.edu	hg19	2	227906897	227906897	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	COL4A4	NM_000092	exon37	c.G3472T	p.D1158Y	CTGGATCCCCCTG	.	45.0	7.0	56.0	0.0	.	215	.	.	Atlas-SNP
FBLN2	2199	hgsc.bcm.edu	hg19	3	13612210	13612210	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	FBLN2	NM_001998	exon2	c.C355T	p.P119S	CTGCCGCCCAACT	.	108.0	21.0	75.0	0.0	.	137	.	.	Atlas-SNP
LTF	4057	hgsc.bcm.edu	hg19	3	46492064	46492064	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	LTF	NM_002343	exon7	c.G803T	p.R268L	GGGACCCGGGCCA	.	150.0	25.0	178.0	0.0	.	98	.	.	Atlas-SNP
C3orf67	200844	hgsc.bcm.edu	hg19	3	58849427	58849427	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	C3orf67	NM_198463	exon12	c.C1075T	p.P359S	ATCGTGGTCTTGA	.	77.0	13.0	94.0	0.0	.	45	.	.	Atlas-SNP
OR5H14	403273	hgsc.bcm.edu	hg19	3	97868812	97868812	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	OR5H14	NM_001005514	exon1	c.A583T	p.N195Y	TCTATTAACTTTC	.	52.0	15.0	62.0	0.0	.	56	.	.	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	hg19	4	7787959	7787959	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	AFAP1	NM_001134647	exon12	c.G1492A	p.A498T	GAAGTGCCGTCCC	.	98.0	19.0	137.0	0.0	.	93	.	.	Atlas-SNP
TRPC3	7222	hgsc.bcm.edu	hg19	4	122853884	122853884	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TRPC3	NM_001130698	exon2	c.G529A	p.D177N	GGGCGTCGCCAAT	.	132.0	28.0	152.0	0.0	.	201	.	.	Atlas-SNP
FAM160A1	729830	hgsc.bcm.edu	hg19	4	152507926	152507926	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	FAM160A1	NM_001109977	exon6	c.T866C	p.L289P	ACTCCCTGGAGTT	.	82.0	11.0	103.0	0.0	.	60	.	.	Atlas-SNP
SPEF2	79925	hgsc.bcm.edu	hg19	5	35704679	35704679	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	SPEF2	NM_024867	exon17	c.G2422A	p.A808T	AAAACTGCTCACG	.	40.0	7.0	63.0	0.0	.	324	.	.	Atlas-SNP
PCDHA3	56145	hgsc.bcm.edu	hg19	5	140182464	140182464	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	PCDHA3	NM_031497	exon1	c.A1682G	p.N561S	ACGACAACGCGCC	.	133.0	14.0	41.0	0.0	.	396	.	.	Atlas-SNP
FYN	2534	hgsc.bcm.edu	hg19	6	112035597	112035597	+	Silent	SNP	A	A	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	FYN	NM_153047	exon2	c.T297C	p.D99D	CAGGTCATCTTCT	.	40.0	5.0	60.0	0.0	.	108	.	.	Atlas-SNP
TUBE1	51175	hgsc.bcm.edu	hg19	6	112408489	112408489	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TUBE1	NM_016262	exon2	c.A46T	p.I16F	AGCCGATCTGGTT	.	280.0	31.0	336.0	0.0	.	49	.	.	Atlas-SNP
LAMA4	3910	hgsc.bcm.edu	hg19	6	112435307	112435307	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	LAMA4	NM_001105206	exon38	c.G5298C	p.R1766S	AGGCTCCCTGTGA	.	54.0	8.0	55.0	0.0	.	227	.	.	Atlas-SNP
AMZ1	155185	hgsc.bcm.edu	hg19	7	2740124	2740124	+	Silent	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	AMZ1	NM_133463	exon2	c.G39A	p.G13G	CTTCGGGCCCCGG	.	62.0	13.0	55.0	0.0	.	41	.	.	Atlas-SNP
SDK1	221935	hgsc.bcm.edu	hg19	7	4285345	4285345	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	SDK1	NM_152744	exon44	c.T6289C	p.S2097P	CACTACTCAGACG	.	140.0	17.0	157.0	0.0	.	361	.	.	Atlas-SNP
HOXA3	3200	hgsc.bcm.edu	hg19	7	27148273	27148273	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	HOXA3	NM_030661	exon3	c.A593G	p.Y198C	CTCGTGTAGGCCG	.	55.0	8.0	39.0	0.0	.	62	.	.	Atlas-SNP
CCDC129	223075	hgsc.bcm.edu	hg19	7	31683502	31683502	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	CCDC129	NM_001257968	exon11	c.C2596A	p.Q866K	GGTCACCAGGAAG	.	75.0	11.0	57.0	0.0	.	127	.	.	Atlas-SNP
GIGYF1	64599	hgsc.bcm.edu	hg19	7	100284048	100284048	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	GIGYF1	NM_022574	exon8	c.C703A	p.P235T	AGCGGGGACCACC	.	60.0	5.0	50.0	0.0	.	113	.	.	Atlas-SNP
MUC12	10071	hgsc.bcm.edu	hg19	7	100646199	100646199	+	Missense_Mutation	SNP	T	T	C	rs4632981		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	MUC12,NS,carcinoma,0,1	MUC12	NM_001164462	exon2	c.T12355C	p.F4119L	ACACACTTTTCTG	.	13.0	6.0	2.0	1.0	.	140	.	C|1.000;|0.000	Atlas-SNP
EPHA1	2041	hgsc.bcm.edu	hg19	7	143096483	143096483	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	EPHA1	NM_005232	exon5	c.A859T	p.M287L	TGTCCATCCGGTA	.	144.0	44.0	144.0	0.0	.	193	.	.	Atlas-SNP
OR2A2	442361	hgsc.bcm.edu	hg19	7	143807041	143807041	+	Nonsense_Mutation	SNP	T	T	A	rs201869620	by1000genomes;alternate_allele	TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	OR2A2	NM_001005480	exon1	c.T366A	p.Y122X	TAGGTATGTGGCC	.	159.0	21.0	143.0	0.0	.	48	.	T|0.999;C|0.001	Atlas-SNP
BLK	640	hgsc.bcm.edu	hg19	8	11420535	11420535	+	Missense_Mutation	SNP	G	G	A	rs376140772		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	BLK	NM_001715	exon12	c.G1228A	p.G410R	CACTTCGGGGTCT	.	172.0	32.0	152.0	0.0	.	78	.	.	Atlas-SNP
SLC39A14	23516	hgsc.bcm.edu	hg19	8	22273745	22273745	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	SLC39A14	NM_001135153	exon7	c.A1099G	p.I367V	CAAGGCATCAGCA	.	147.0	23.0	140.0	0.0	.	59	.	.	Atlas-SNP
FNTA	2339	hgsc.bcm.edu	hg19	8	42911627	42911627	+	Silent	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	FNTA	NM_002027	exon1	c.C138T	p.A46A	GGAAGCCGTGGCG	.	52.0	14.0	33.0	0.0	.	34	.	.	Atlas-SNP
ZFHX4	79776	hgsc.bcm.edu	hg19	8	77767616	77767616	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	ZFHX4	NM_024721	exon10	c.A8459C	p.N2820T	AGGGAAACACTGA	.	43.0	11.0	82.0	0.0	.	878	.	.	Atlas-SNP
REXO1L1	254958	hgsc.bcm.edu	hg19	8	86573858	86573858	+	Silent	SNP	G	G	A	rs145542023		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	REXO1L1_ENST00000379010,NS,carcinoma,0,2	REXO1L1	NM_172239	exon1	c.C1869T	p.A623A	GTAGTCGGCCGCG	.	50.0	9.0	11.0	1.0	.	28	.	.	Atlas-SNP
LRRC69	100130742	hgsc.bcm.edu	hg19	8	92114903	92114903	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	LRRC69	NM_001129890	exon1	c.T14C	p.L5S	AGAGATTGTTAAT	.	58.0	9.0	48.0	0.0	.	24	.	.	Atlas-SNP
CISD1	55847	hgsc.bcm.edu	hg19	10	60037077	60037077	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	CISD1	NM_018464	exon2	c.A232T	p.K78X	AGGTCCAAAAAGG	.	181.0	28.0	217.0	0.0	.	7	.	.	Atlas-SNP
TNKS2	80351	hgsc.bcm.edu	hg19	10	93558647	93558647	+	Splice_Site	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TNKS2	NM_025235	exon1	c.199+1G>T	.	CCGCAGGTAACCG	.	75.0	12.0	67.0	0.0	.	103	.	.	Atlas-SNP
KRTAP5-4	387267	hgsc.bcm.edu	hg19	11	1643105	1643105	+	Silent	SNP	G	G	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	NM_001012709	exon1	c.C219G	p.S73S	CCCACAGGAGCCA	.	121.0	7.0	96.0	1.0	.	78	.	.	Atlas-SNP
OR51D1	390038	hgsc.bcm.edu	hg19	11	4661048	4661048	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	OR51D1	NM_001004751	exon1	c.A28G	p.I10V	GTCCCTATCATAG	.	50.0	8.0	79.0	0.0	.	49	.	.	Atlas-SNP
OR51T1	401665	hgsc.bcm.edu	hg19	11	4903313	4903313	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	OR51T1	NM_001004759	exon1	c.T265A	p.Y89N	CCCATGTATTATT	.	79.0	16.0	97.0	0.0	.	92	.	.	Atlas-SNP
NAALADL1	10004	hgsc.bcm.edu	hg19	11	64820704	64820704	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	NAALADL1	NM_005468	exon8	c.C1184T	p.T395I	AGCAGGGTCCCCA	.	206.0	31.0	191.0	0.0	.	58	.	.	Atlas-SNP
GRAMD1B	57476	hgsc.bcm.edu	hg19	11	123489506	123489506	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	GRAMD1B	NM_020716	exon18	c.A2007T	p.E669D	CCAAGAAAGGTAA	.	98.0	16.0	102.0	0.0	.	122	.	.	Atlas-SNP
SPATS2	65244	hgsc.bcm.edu	hg19	12	49919817	49919817	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	SPATS2	NM_023071	exon14	c.A1417G	p.M473V	GACAGTATGGGTC	.	231.0	49.0	309.0	0.0	.	43	.	.	Atlas-SNP
ASIC1	41	hgsc.bcm.edu	hg19	12	50473752	50473752	+	Silent	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	.	NM_001256830	exon6	c.C1221T	p.G407G	CTATGGCAAAGAG	.	324.0	53.0	325.0	0.0	.	.	.	.	Atlas-SNP
RAB3IP	117177	hgsc.bcm.edu	hg19	12	70206599	70206599	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	RAB3IP	NM_175623	exon9	c.G1220A	p.R407K	AACACAGAATTAA	.	75.0	13.0	116.0	0.0	.	48	.	.	Atlas-SNP
GLT8D2	83468	hgsc.bcm.edu	hg19	12	104388181	104388181	+	Silent	SNP	G	G	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	GLT8D2	NM_031302	exon9	c.C699G	p.A233A	CATGTTGGCAACA	.	130.0	18.0	132.0	0.0	.	40	.	.	Atlas-SNP
BTBD11	121551	hgsc.bcm.edu	hg19	12	108012091	108012091	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	BTBD11	NM_001018072	exon10	c.G2388T	p.R796S	CCTGAGGGAGGCC	.	83.0	12.0	86.0	0.0	.	122	.	.	Atlas-SNP
DAAM1	23002	hgsc.bcm.edu	hg19	14	59821978	59821978	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	DAAM1	NM_014992	exon20	c.C2482G	p.Q828E	AAAGGTCAAAGAG	.	63.0	12.0	109.0	0.0	.	95	.	.	Atlas-SNP
DHRS7	51635	hgsc.bcm.edu	hg19	14	60631900	60631900	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	DHRS7	NM_016029	exon1	c.G128A	p.R43H	CCTGGGCGTCGTC	.	220.0	27.0	219.0	0.0	.	31	.	.	Atlas-SNP
NLRC5	84166	hgsc.bcm.edu	hg19	16	57060281	57060281	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	NLRC5	NM_032206	exon5	c.T1426A	p.Y476N	ATCTTCTATGCAA	.	66.0	15.0	94.0	0.0	.	186	.	.	Atlas-SNP
SLC2A4	6517	hgsc.bcm.edu	hg19	17	7187403	7187403	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	SLC2A4	NM_001042	exon5	c.G559T	p.A187S	CTGATCGCCCAGG	.	58.0	10.0	86.0	0.0	.	44	.	.	Atlas-SNP
TP53	7157	hgsc.bcm.edu	hg19	17	7576633	7576633	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TP53	NM_001126114	exon10	c.A1018G	p.N340D	AACAATTTTCTTT	.	42.0	16.0	109.0	0.0	.	33396	.	.	Atlas-SNP
GREB1L	80000	hgsc.bcm.edu	hg19	18	19079942	19079942	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	GREB1L	NM_001142966	exon22	c.G3644A	p.G1215E	GGCCGGGACAGCC	.	54.0	11.0	60.0	0.0	.	69	.	.	Atlas-SNP
NCLN	56926	hgsc.bcm.edu	hg19	19	3206308	3206308	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	NCLN	NM_020170	exon12	c.C1384T	p.Q462X	ACCAACCAGCCGC	.	109.0	27.0	105.0	0.0	.	27	.	.	Atlas-SNP
C19orf10	56005	hgsc.bcm.edu	hg19	19	4664897	4664897	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	C19orf10	NM_019107	exon3	c.C278A	p.T93N	CAGATGGTGCAGG	.	94.0	13.0	143.0	0.0	.	9	.	.	Atlas-SNP
JAK3	3718	hgsc.bcm.edu	hg19	19	17943612	17943612	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	JAK3	NM_000215	exon18	c.C2477T	p.S826L	AGCTGTGAGATGT	.	198.0	35.0	263.0	0.0	.	341	.	.	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	hg19	19	39071081	39071081	+	Silent	SNP	C	C	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	RYR1	NM_000540	exon101	c.C14583T	p.R4861R	CTTCCGCAAGTTC	.	264.0	46.0	246.0	0.0	.	708	.	.	Atlas-SNP
CD37	951	hgsc.bcm.edu	hg19	19	49841271	49841271	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	CD37	NM_001774	exon5	c.C432G	p.D144E	CTGGGACTATGTG	.	194.0	62.0	180.0	0.0	.	33	.	.	Atlas-SNP
A1BG	1	hgsc.bcm.edu	hg19	19	58862780	58862780	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	A1BG,NS,carcinoma,0,1	A1BG	NM_130786	exon5	c.C887T	p.P296L	TCGACCGGCGCGC	.	96.0	27.0	68.0	0.0	.	40	.	.	Atlas-SNP
SEC23B	10483	hgsc.bcm.edu	hg19	20	18505223	18505223	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	SEC23B	NM_032985	exon5	c.G513C	p.R171S	TGGAAGGATGGTG	.	99.0	17.0	153.0	0.0	.	70	.	.	Atlas-SNP
PYGB	5834	hgsc.bcm.edu	hg19	20	25261588	25261588	+	Missense_Mutation	SNP	G	G	A	rs201813153		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	PYGB	NM_002862	exon11	c.G1243A	p.V415M	CAGCACGTGGCCG	.	169.0	24.0	173.0	0.0	.	84	.	.	Atlas-SNP
CPNE1	8904	hgsc.bcm.edu	hg19	20	34220601	34220601	+	Silent	SNP	C	C	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	CPNE1	NM_003915	exon3	c.G162T	p.R54R	CCGCACCCGTTCA	.	125.0	10.0	186.0	0.0	.	44	.	.	Atlas-SNP
ATP9A	10079	hgsc.bcm.edu	hg19	20	50287714	50287714	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	ATP9A	NM_006045	exon12	c.C1120T	p.R374C	TGGAGCGAACCAC	.	100.0	7.0	123.0	0.0	.	135	.	.	Atlas-SNP
PHACTR3	116154	hgsc.bcm.edu	hg19	20	58322830	58322830	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	PHACTR3	NM_080672	exon3	c.G298T	p.A100S	AAGATGGCCGGCA	.	103.0	15.0	183.0	0.0	.	104	.	.	Atlas-SNP
CHRNA4	1137	hgsc.bcm.edu	hg19	20	61978125	61978125	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	CHRNA4	NM_000744	exon6	c.C1849T	p.L617F	GGAAGAGGCCCAC	.	130.0	23.0	130.0	0.0	.	98	.	.	Atlas-SNP
RSPH1	89765	hgsc.bcm.edu	hg19	21	43896039	43896039	+	Silent	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	RSPH1	NM_080860	exon8	c.C846T	p.D282D	CTCCTGGTCATAC	.	104.0	24.0	114.0	0.0	.	36	.	.	Atlas-SNP
THAP7	80764	hgsc.bcm.edu	hg19	22	21354333	21354333	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	THAP7	NM_030573	exon4	c.C766T	p.R256C	GCTGGCGCTGGGC	.	122.0	23.0	92.0	0.0	.	15	.	.	Atlas-SNP
TTC28	23331	hgsc.bcm.edu	hg19	22	28494971	28494971	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TTC28	NM_001145418	exon10	c.A3479G	p.Y1160C	AGTTTGTAGTCCG	.	245.0	25.0	204.0	0.0	.	84	.	.	Atlas-SNP
COL4A6	1288	hgsc.bcm.edu	hg19	X	107681209	107681209	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	COL4A6	NM_001847	exon2	c.T29A	p.L10Q	GTAACCAGGAGCA	.	226.0	64.0	268.0	0.0	.	270	.	.	Atlas-SNP
ND2	0	hgsc.bcm.edu	hg19	MT	5374	5374	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	.	ENST00000361453	exon1	c.T905C	p.I302T	CCTCAATCACACT	.	601.0	94.0	5.0	0.0	.	.	.	.	Atlas-SNP
TSC2	7249	hgsc.bcm.edu	hg19	16	2136306	2136311	+	In_Frame_Del	DEL	TGTACC	TGTACC	-	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	TGTACC	TGTACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TSC2	NM_000548	exon37	c.4774_4779del	p.1592_1593del	.	.	156.0	20.0	239.0	0.0	.	364	.	.	Atlas-Indel,Pindel
H1F0	3005	hgsc.bcm.edu	hg19	22	38201683	38201684	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	H1F0	NM_005318	exon1	c.132_133insT	p.G44fs	.	.	111.0	11.0	176.0	0.0	.	12	.	.	Atlas-INDEL
FAM227B	196951	hgsc.bcm.edu	hg19	15	49620847	49620850	+	Frame_Shift_Del	DEL	TCTC	TCTC	-	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	.	NM_152647	exon16	c.1443_1446del	p.481_482del	.	.	66.0	10.0	74.0	0.0	.	.	.	.	Atlas-INDEL
TRIM67	440730	hgsc.bcm.edu	hg19	1	231344856	231344857	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TRIM67	NM_001004342	exon8	c.1983_1984insA	p.D661fs	.	.	275.0	85.0	246.0	0.0	.	160	.	.	Atlas-Indel,Pindel
TUBE1	51175	hgsc.bcm.edu	hg19	6	112408473	112408484	+	In_Frame_Del	DEL	CAGAAGCAGCAG	CAGAAGCAGCAG	-	novel		TCGA-DD-A4NQ-01A-21D-A28X-10	TCGA-DD-A4NQ-10A-01D-A28X-10	CAGAAGCAGCAG	CAGAAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	c2df6b36-605d-46f7-8c66-d9625766c023	7985bd29-3002-4677-91fc-3754d1e3f0a4	.	TUBE1	NM_016262	exon2	c.52_63del	p.18_21del	.	.	258.0	22.0	305.0	0.0	.	49	.	.	Atlas-Indel,Pindel