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
CLCA2	9635	hgsc.bcm.edu	hg19	1	86890015	86890015	+	Silent	SNP	C	C	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	CLCA2	NM_006536	exon1	c.C85T	p.L29L	CCATTCCTGGGAG	.	55.0	35.0	47.0	0.0	.	102	.	.	.	none	.	.	PASS	Atlas-SNP
ADAR	103	hgsc.bcm.edu	hg19	1	154574741	154574741	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ADAR	NM_015840	exon2	c.T377C	p.L126P	GAGGAAAGGCAAT	.	41.0	24.0	94.0	0.0	.	113	.	.	.	none	.	.	PASS	Atlas-SNP
MIA3	375056	hgsc.bcm.edu	hg19	1	222838735	222838735	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	MIA3	NM_198551	exon28	c.G5498T	p.R1833L	ACCCTCGGGGATT	.	185.0	9.0	315.0	0.0	.	167	.	.	.	none	.	.	PASS	Atlas-SNP
CCT7	10574	hgsc.bcm.edu	hg19	2	73471795	73471795	+	Silent	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	CCT7	NM_006429	exon6	c.G570T	p.L190L	TTTGCTGCAGCTT	.	38.0	12.0	39.0	0.0	.	60	.	.	.	none	.	.	PASS	Atlas-SNP
GORASP2	26003	hgsc.bcm.edu	hg19	2	171806790	171806790	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	GORASP2	NM_015530	exon4	c.T425C	p.V142A	ATACAGTCATGAA	.	76.0	32.0	29.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
TTN	7273	hgsc.bcm.edu	hg19	2	179411556	179411556	+	Silent	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	TTN	NM_001267550	exon341	c.T94599C	p.D31533D	GCCTCCATCATAC	.	44.0	22.0	17.0	0.0	.	18412	.	.	.	none	.	.	PASS	Atlas-SNP
SF3B1	23451	hgsc.bcm.edu	hg19	2	198269882	198269882	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SF3B1	NM_012433	exon11	c.C1457G	p.T486R	CTAAGTGTTGATT	.	42.0	4.0	29.0	0.0	.	1038	.	.	.	none	.	.	PASS	Atlas-SNP
SATB2	23314	hgsc.bcm.edu	hg19	2	200193570	200193570	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SATB2	NM_015265	exon9	c.G1237T	p.V413L	GGTTTACTAGAAG	.	46.0	11.0	16.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
NOP58	51602	hgsc.bcm.edu	hg19	2	203155146	203155146	+	Silent	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	NOP58	NM_015934	exon7	c.T600C	p.D200D	TTCAGATAATTTA	.	76.0	31.0	58.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
CYP27A1	1593	hgsc.bcm.edu	hg19	2	219677361	219677361	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	CYP27A1,NS,malignant_melanoma,-1,1	CYP27A1	NM_000784	exon4	c.G733T	p.G245W	TCCATCGGGTTAA	.	328.0	15.0	528.0	1.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
MLH1	4292	hgsc.bcm.edu	hg19	3	37067255	37067255	+	Missense_Mutation	SNP	G	G	T	rs63750361	bycluster;byfrequency;alternate_allele	TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	MLH1	NM_000249	exon12	c.G1166T	p.R389L	ATTCCCGGGAACA	.	186.0	12.0	206.0	0.0	.	226	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	hg19	3	52588791	52588791	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PBRM1	NM_018313	exon27	c.C4237A	p.P1413T	GGTGGGGTGGAGG	.	39.0	19.0	47.0	0.0	.	1252	.	.	.	none	.	.	PASS	Atlas-SNP
CLDN18	51208	hgsc.bcm.edu	hg19	3	137742626	137742626	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	CLDN18	NM_016369	exon2	c.A347T	p.N116I	AAGCCAACATGAC	.	68.0	22.0	89.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
FNDC3B	64778	hgsc.bcm.edu	hg19	3	171965496	171965496	+	Silent	SNP	C	C	A	rs139712731	bycluster;byfrequency;alternate_allele	TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	FNDC3B	NM_001135095	exon5	c.C438A	p.T146T	TGTTACCGGACCT	.	145.0	8.0	168.0	0.0	.	118	.	.	.	alt	C|0.999;T|0.001	.	PASS	Atlas-SNP
TMEM41A	90407	hgsc.bcm.edu	hg19	3	185209397	185209397	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.,1	TMEM41A	NM_080652	exon5	c.A723T	p.K241N	ACTAAATTTTTTA	.	95.0	41.0	75.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
FGFR3	2261	hgsc.bcm.edu	hg19	4	1806088	1806088	+	Silent	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	FGFR3,bladder,carcinoma,0,6	FGFR3	NM_001163213	exon9	c.G1113T	p.A371A	CGAGGCGGGCAGT	.	166.0	8.0	289.0	0.0	.	3320	.	.	.	none	.	.	PASS	Atlas-SNP
SLC10A6	345274	hgsc.bcm.edu	hg19	4	87749228	87749228	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SLC10A6	NM_197965	exon4	c.C679G	p.L227V	TGGTCAGAAGGGT	.	45.0	16.0	55.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
CAMK2D	817	hgsc.bcm.edu	hg19	4	114434488	114434488	+	Silent	SNP	G	G	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	CAMK2D	NM_172128	exon12	c.C942T	p.F314F	ACCTGAGAAATTC	.	113.0	42.0	84.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
NPY1R	4886	hgsc.bcm.edu	hg19	4	164246582	164246582	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	NPY1R	NM_000909	exon3	c.G1028T	p.R343L	TCATCCCGAGACC	.	188.0	8.0	113.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
TLR3	7098	hgsc.bcm.edu	hg19	4	187004092	187004092	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	TLR3	NM_003265	exon4	c.A1252C	p.K418Q	AAGAATAAAATCT	.	79.0	26.0	62.0	0.0	.	83	.	.	.	none	.	.	PASS	Atlas-SNP
ZFR	51663	hgsc.bcm.edu	hg19	5	32403408	32403408	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ZFR	NM_016107	exon8	c.C1319T	p.S440L	GGCTTTGAAGCAG	.	160.0	70.0	102.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
PIK3R1	5295	hgsc.bcm.edu	hg19	5	67576767	67576767	+	Silent	SNP	T	T	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PIK3R1	NM_181523	exon7	c.T849G	p.T283T	TAATACTGAAAAC	.	61.0	18.0	41.0	0.0	.	869	.	.	.	none	.	.	PASS	Atlas-SNP
PAPD4	167153	hgsc.bcm.edu	hg19	5	78975410	78975410	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PAPD4	NM_173797	exon14	c.G1217C	p.S406T	GGAATAGTCAAAT	.	73.0	33.0	57.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
NELFE	7936	hgsc.bcm.edu	hg19	6	31922209	31922209	+	Silent	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	.	NM_002904	exon8	c.A753G	p.S251S	AGGGAATGAATCC	.	88.0	30.0	109.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
EYS	346007	hgsc.bcm.edu	hg19	6	66204808	66204808	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	EYS	NM_001142801	exon4	c.A496C	p.N166H	TCACATTTAGTCG	.	97.0	32.0	54.0	0.0	.	527	.	.	.	none	.	.	PASS	Atlas-SNP
ETV1	2115	hgsc.bcm.edu	hg19	7	13971323	13971323	+	Silent	SNP	C	C	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ETV1	NM_004956	exon9	c.G606C	p.T202T	TGGCATCGTCGGC	.	45.0	17.0	46.0	0.0	.	138	.	.	.	none	.	.	PASS	Atlas-SNP
SUN3	256979	hgsc.bcm.edu	hg19	7	48035693	48035693	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SUN3	NM_152782	exon8	c.G628A	p.A210T	ATTTTGCTTTATT	.	126.0	40.0	115.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
PEX1	5189	hgsc.bcm.edu	hg19	7	92151473	92151473	+	Silent	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PEX1	NM_000466	exon2	c.T216C	p.N72N	AGCCACATTTTCA	.	130.0	55.0	90.0	0.0	.	102	.	.	.	none	.	.	PASS	Atlas-SNP
TUSC3	7991	hgsc.bcm.edu	hg19	8	15508312	15508312	+	Missense_Mutation	SNP	G	G	A	rs371225890		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	TUSC3	NM_178234	exon3	c.G415A	p.V139I	ACAGACGTTTTTC	.	222.0	96.0	163.0	0.0	.	98	.	.	.	weak	.	.	PASS	Atlas-SNP
PSD3	23362	hgsc.bcm.edu	hg19	8	18430149	18430149	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PSD3	NM_015310	exon14	c.A2673T	p.K891N	ATTGATTTTGTTT	.	225.0	73.0	115.0	0.0	.	142	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF395	55893	hgsc.bcm.edu	hg19	8	28206721	28206721	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ZNF395	NM_018660	exon9	c.A1351G	p.S451G	GCTCGCTGAAGCT	.	70.0	22.0	110.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
ARID3C	138715	hgsc.bcm.edu	hg19	9	34622092	34622092	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ARID3C	NM_001017363	exon6	c.G1063A	p.G355R	GAGGCCCATCCAG	.	130.0	44.0	184.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
RUSC2	9853	hgsc.bcm.edu	hg19	9	35547391	35547391	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	RUSC2	NM_014806	exon2	c.G873C	p.M291I	CAAGATGCATGGC	.	93.0	31.0	150.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
NANS	54187	hgsc.bcm.edu	hg19	9	100840514	100840514	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	NANS	NM_018946	exon4	c.A488G	p.D163G	CAATGGACACCAT	.	127.0	47.0	167.0	0.0	.	24	.	.	.	none	.	.	PASS	Atlas-SNP
NR6A1	2649	hgsc.bcm.edu	hg19	9	127316717	127316717	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	NR6A1	NM_033334	exon3	c.G275T	p.R92L	TATACCCGTTTGT	.	135.0	7.0	107.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
USP6NL	9712	hgsc.bcm.edu	hg19	10	11523768	11523768	+	Splice_Site	SNP	C	C	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	USP6NL,NS,carcinoma,0,1	USP6NL	NM_014688	exon15	c.1078+1G>C	.	TTCTTACCAGGTT	.	50.0	2.0	41.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
THNSL1	79896	hgsc.bcm.edu	hg19	10	25312238	25312238	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	THNSL1	NM_024838	exon3	c.C86T	p.A29V	AACATGCACAGCG	.	118.0	48.0	80.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
TULP3	7289	hgsc.bcm.edu	hg19	12	3048537	3048537	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.,1	TULP3	NM_003324	exon11	c.A1256C	p.N419T	ATTACAACTACCC	.	165.0	48.0	170.0	0.0	.	45	.	.	.	none	.	.	PASS	Atlas-SNP
HEBP1	50865	hgsc.bcm.edu	hg19	12	13142261	13142261	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	HEBP1	NM_015987	exon2	c.G167T	p.R56L	GCTTCCCGTAGAG	.	138.0	7.0	118.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
HOXC11	3227	hgsc.bcm.edu	hg19	12	54367330	54367330	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	HOXC11_ENST00000546378,bladder,carcinoma,0,1	HOXC11	NM_014212	exon1	c.G305T	p.R102L	TGCACCGGGAGTG	.	192.0	9.0	258.0	1.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
ACAD10	80724	hgsc.bcm.edu	hg19	12	112183962	112183962	+	Silent	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ACAD10	NM_001136538	exon15	c.T2223C	p.A741A	CAAAGCTGAAGGA	.	101.0	34.0	132.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
GAS6	2621	hgsc.bcm.edu	hg19	13	114523928	114523928	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	GAS6	NM_000820	exon15	c.A1946G	p.N649S	CTCCGGTTGACCT	.	52.0	23.0	69.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
RBM23	55147	hgsc.bcm.edu	hg19	14	23374814	23374814	+	Splice_Site	SNP	C	C	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	RBM23	NM_018107	exon6	c.407+1G>C	.	AACCCACCTGACT	.	40.0	26.0	99.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
SMG1	23049	hgsc.bcm.edu	hg19	16	18840922	18840922	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SMG1	NM_015092	exon54	c.C9289A	p.L3097I	TGGGTAGCCCTAT	.	70.0	40.0	38.0	0.0	.	401	.	.	.	none	.	.	PASS	Atlas-SNP
FTSJD1	55783	hgsc.bcm.edu	hg19	16	71317552	71317552	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	FTSJD1	NM_018348	exon3	c.G2272A	p.E758K	CTCTCTCTCTTTG	.	67.0	17.0	31.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	hg19	16	81990321	81990321	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PLCG2	NM_002661	exon32	c.T3592G	p.S1198A	CTTTACTCCTCCT	.	77.0	28.0	67.0	0.0	.	276	.	.	.	none	.	.	PASS	Atlas-SNP
CRLF3	51379	hgsc.bcm.edu	hg19	17	29119514	29119514	+	Silent	SNP	C	C	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	CRLF3	NM_015986	exon6	c.G903T	p.S301S	AACACCCGATGAT	.	189.0	11.0	205.0	0.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
ZNHIT3	9326	hgsc.bcm.edu	hg19	17	34849806	34849806	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ZNHIT3	NM_004773	exon4	c.A242G	p.D81G	ATAGTGATGAGGA	.	162.0	65.0	128.0	0.0	.	14	.	.	.	none	.	.	PASS	Atlas-SNP
DLX3	1747	hgsc.bcm.edu	hg19	17	48072053	48072053	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	DLX3	NM_005220	exon1	c.C310G	p.P104A	GGGCTGGCAGCGG	.	51.0	25.0	69.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
TBCD	6904	hgsc.bcm.edu	hg19	17	80885835	80885835	+	Silent	SNP	G	G	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	TBCD	NM_005993	exon30	c.G2664C	p.R888R	GGCTCGGAGCCAG	.	97.0	33.0	108.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
NPC1	4864	hgsc.bcm.edu	hg19	18	21128030	21128030	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	NPC1	NM_000271	exon11	c.C1697A	p.P566H	TTGACAGGGAAGG	.	184.0	72.0	207.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
RNF165	494470	hgsc.bcm.edu	hg19	18	44013357	44013357	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	RNF165	NM_152470	exon2	c.A266G	p.Q89R	CCCTGCAGTTCCA	.	58.0	16.0	58.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA7	10347	hgsc.bcm.edu	hg19	19	1062293	1062293	+	Missense_Mutation	SNP	C	C	A	rs144378856	alternate_allele	TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ABCA7	NM_019112	exon42	c.C5693A	p.P1898Q	GTGTCCCGGAGGC	.	128.0	8.0	244.0	0.0	.	174	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
MUC16	94025	hgsc.bcm.edu	hg19	19	9061598	9061598	+	Silent	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	MUC16	NM_024690	exon3	c.T25848C	p.P8616P	ATTTGGAGGTGAA	.	100.0	4.0	66.0	0.0	.	4315	.	.	.	none	.	.	PASS	Atlas-SNP
LDLR	3949	hgsc.bcm.edu	hg19	19	11216253	11216253	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	LDLR	NM_001195798	exon4	c.A671C	p.D224A	GCAAGGACAAATC	.	66.0	28.0	74.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
AP1M1	8907	hgsc.bcm.edu	hg19	19	16339616	16339616	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	AP1M1	NM_001130524	exon10	c.C960G	p.N320K	AGCCAACAACGTG	.	56.0	19.0	78.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF737	100129842	hgsc.bcm.edu	hg19	19	20728254	20728254	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	ZNF737,NS,carcinoma,0,1	ZNF737	NM_001159293	exon4	c.G755C	p.S252T	TCTCCACTATGAA	.	33.0	2.0	22.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF430	80264	hgsc.bcm.edu	hg19	19	21240182	21240182	+	Silent	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	ZNF430,NS,carcinoma,0,1	ZNF430	NM_025189	exon5	c.A1068G	p.Q356Q	TAACCAATCCTCA	.	94.0	4.0	69.0	1.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
FCGBP	8857	hgsc.bcm.edu	hg19	19	40362919	40362919	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	FCGBP	NM_003890	exon32	c.G15151T	p.G5051W	GCTGCCCGCAGGC	.	82.0	8.0	148.0	0.0	.	416	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF577	84765	hgsc.bcm.edu	hg19	19	52376753	52376753	+	Missense_Mutation	SNP	C	C	A	rs200063901	by1000genomes;alternate_allele	TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	ZNF577	NM_032679	exon7	c.G490T	p.G164W	CTCTCCCGCACAC	.	159.0	7.0	158.0	0.0	.	63	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
UBOX5	22888	hgsc.bcm.edu	hg19	20	3102965	3102965	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	UBOX5	NM_014948	exon3	c.C320T	p.P107L	ACAGATGGCTCAG	.	73.0	23.0	116.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
PLAGL2	5326	hgsc.bcm.edu	hg19	20	30784822	30784822	+	Silent	SNP	C	C	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	PLAGL2,NS,carcinoma,-1,1	PLAGL2	NM_002657	exon3	c.G924T	p.T308T	CACGCCCGTGCTG	.	146.0	8.0	177.0	1.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
SETD4	54093	hgsc.bcm.edu	hg19	21	37418117	37418117	+	Silent	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SETD4	NM_001007259	exon6	c.A489G	p.R163R	GTGGGCTCTCTGC	.	204.0	90.0	200.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
SIK1	150094	hgsc.bcm.edu	hg19	21	44841223	44841223	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SIK1	NM_173354	exon6	c.A524G	p.K175R	CCTGACTTGTAGA	.	119.0	46.0	168.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	hg19	21	46911142	46911142	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	COL18A1	NM_030582	exon21	c.G2611A	p.D871N	CAGGGAGATCCAG	.	52.0	19.0	65.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
COL18A1	80781	hgsc.bcm.edu	hg19	21	46911143	46911143	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	COL18A1	NM_030582	exon21	c.A2612T	p.D871V	AGGGAGATCCAGG	.	51.0	18.0	65.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
PHF21B	112885	hgsc.bcm.edu	hg19	22	45312440	45312440	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PHF21B	NM_138415	exon4	c.C284A	p.P95H	GTTGGGGGCTGCT	.	85.0	30.0	134.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
KLHL4	56062	hgsc.bcm.edu	hg19	X	86773063	86773063	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	KLHL4	NM_019117	exon1	c.C167G	p.S56C	GCCACTCTCGGGA	.	31.0	26.0	16.0	0.0	.	263	.	.	.	none	.	.	PASS	Atlas-SNP
GAB3	139716	hgsc.bcm.edu	hg19	X	153928305	153928305	+	Silent	SNP	G	G	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	GAB3	NM_001081573	exon5	c.C1099A	p.R367R	TGTCTCGGTGTCT	.	137.0	7.0	84.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
ND4	0	hgsc.bcm.edu	hg19	MT	10816	10816	+	Silent	SNP	A	A	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	.	ENST00000361381	exon1	c.A57G	p.K19K	TTCCAAAAAACAC	.	5.0	5.0	0.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
HAO1	54363	hgsc.bcm.edu	hg19	20	7886831	7886832	+	In_Frame_Ins	INS	-	-	TTT	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	HAO1	NM_017545	exon4	c.691_692insAAA	p.L231delinsKL	.	.	183.0	51.0	120.0	0.0	.	71	.	0.278689	0	none	.	.	PASS	Atlas-INDEL
PROM1	8842	hgsc.bcm.edu	hg19	4	15989284	15989287	+	Frame_Shift_Del	DEL	ACCA	ACCA	-	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	ACCA	ACCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	PROM1	NM_001145850	exon19	c.2130_2130del	p.710_710del	.	.	233.0	69.0	228.0	0.0	.	91	.	0.296137	0	none	.	.	PASS	Atlas-INDEL
BPIFB2	80341	hgsc.bcm.edu	hg19	20	31604905	31604906	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	.	NM_025227	exon7	c.574_575insT	p.I192fs	.	.	111.0	35.0	143.0	0.0	.	.	.	0.315315	0	none	.	.	PASS	Atlas-INDEL
RNF165	494470	hgsc.bcm.edu	hg19	18	44013351	44013353	+	In_Frame_Del	DEL	CCC	CCC	-	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	RNF165	NM_152470	exon2	c.259_261del	p.87_87del	.	.	49.0	15.0	51.0	0.0	.	34	.	0.306122	0	none	.	.	PASS	Atlas-INDEL
SAMD4B	55095	hgsc.bcm.edu	hg19	19	39868382	39868391	+	Frame_Shift_Del	DEL	TCCCACTGAT	TCCCACTGAT	-	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	TCCCACTGAT	TCCCACTGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	SAMD4B	NM_018028	exon10	c.1361_1370del	p.454_457del	.	.	61.0	10.0	110.0	0.0	.	48	.	0.163934	0	none	.	.	PASS	Atlas-INDEL
DOLK	22845	hgsc.bcm.edu	hg19	9	131708944	131708945	+	Frame_Shift_Ins	INS	-	-	G	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.	DOLK	NM_014908	exon1	c.639_640insC	p.L213fs	.	.	105.0	36.0	146.0	0.0	.	39	.	0.342857	0	none	.	.	PASS	Atlas-INDEL
HDGF	3068	hgsc.bcm.edu	hg19	1	156715103	156715104	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-A4-7583-01A-11D-2136-08	TCGA-A4-7583-10A-01D-2136-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b40c1178-c913-4b63-8863-f631473fffde	0a94c473-a646-42ca-9537-145517302063	.,2	HDGF	NM_001126050	exon2	c.198_199insT	p.F66fs	.	.	21.0	13.0	42.0	0.0	.	60	.	0.619048	0	none	.	.	PASS	Atlas-INDEL
