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
CD1E	913	hgsc.bcm.edu	hg19	1	158325802	158325802	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	CD1E	NM_030893	exon4	c.G811A	p.A271T	CTCCGAGCAACCC	.	128.0	41.0	92.0	0.0	.	129	.	.	Atlas-SNP
NPHP1	4867	hgsc.bcm.edu	hg19	2	110959033	110959033	+	Silent	SNP	A	A	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	NPHP1	NM_207181	exon2	c.T108C	p.A36A	TTCTAGAGCTTCT	.	93.0	42.0	68.0	0.0	.	68	.	.	Atlas-SNP
ERBB4	2066	hgsc.bcm.edu	hg19	2	212615384	212615384	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	ERBB4,NS,carcinoma,0,1	ERBB4	NM_001042599	exon5	c.C602A	p.T201K	TTTTCTGTGGGTC	.	51.0	24.0	32.0	0.0	.	480	.	.	Atlas-SNP
SATB1	6304	hgsc.bcm.edu	hg19	3	18456693	18456693	+	Silent	SNP	T	T	C	rs61733671		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	SATB1	NM_002971	exon5	c.A549G	p.Q183Q	CGACCATTGTTCG	.	105.0	41.0	104.0	0.0	.	96	.	T|0.987;C|0.013	Atlas-SNP
NISCH	11188	hgsc.bcm.edu	hg19	3	52513791	52513791	+	Silent	SNP	A	A	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	NISCH	NM_001276293	exon12	c.A1329G	p.T443T	GACCACAGAGAAG	.	91.0	42.0	74.0	0.0	.	97	.	.	Atlas-SNP
PTPRG	5793	hgsc.bcm.edu	hg19	3	61975392	61975392	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	PTPRG	NM_002841	exon3	c.T284C	p.V95A	CGCGTGTTGGGGA	.	88.0	37.0	81.0	0.0	.	153	.	.	Atlas-SNP
CEP70	80321	hgsc.bcm.edu	hg19	3	138219253	138219253	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	CEP70	NM_024491	exon15	c.C1525T	p.L509F	CTAAGAGTTCTTG	.	196.0	76.0	120.0	0.0	.	51	.	.	Atlas-SNP
TFDP2	7029	hgsc.bcm.edu	hg19	3	141678612	141678612	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	TFDP2	NM_001178139	exon11	c.G955T	p.G319X	ACATTCCCATCCG	.	60.0	26.0	68.0	0.0	.	44	.	.	Atlas-SNP
TFDP2	7029	hgsc.bcm.edu	hg19	3	141678613	141678613	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	TFDP2	NM_001178139	exon11	c.G954T	p.M318I	CATTCCCATCCGC	.	60.0	28.0	71.0	0.0	.	44	.	.	Atlas-SNP
SUCNR1	56670	hgsc.bcm.edu	hg19	3	151598552	151598552	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	SUCNR1	NM_033050	exon3	c.G221T	p.C74F	TTCTGTGCACCCT	.	162.0	59.0	142.0	0.0	.	31	.	.	Atlas-SNP
PIK3CA	5290	hgsc.bcm.edu	hg19	3	178916692	178916692	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	PIK3CA	NM_006218	exon2	c.C79A	p.P27T	TTACTACCAAATG	.	80.0	38.0	74.0	0.0	.	8460	.	.	Atlas-SNP
SHROOM3	57619	hgsc.bcm.edu	hg19	4	77357245	77357245	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	SHROOM3	NM_020859	exon1	c.A40G	p.T14A	AGTGCCACATTAA	.	88.0	42.0	109.0	0.0	.	134	.	.	Atlas-SNP
SDHA	6389	hgsc.bcm.edu	hg19	5	240575	240575	+	Missense_Mutation	SNP	G	G	T	rs192818312	by1000genomes;alternate_allele	TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	SDHA	NM_004168	exon11	c.G1535T	p.R512L	AACTGCGACTCAG	.	157.0	67.0	176.0	0.0	.	80	.	G|0.999;A|0.001	Atlas-SNP
GABRB2	2561	hgsc.bcm.edu	hg19	5	160972296	160972296	+	Silent	SNP	G	G	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	GABRB2	NM_021911	exon4	c.C174T	p.P58P	CACGGGGGGACCT	.	60.0	26.0	53.0	0.0	.	161	.	.	Atlas-SNP
CAP2	10486	hgsc.bcm.edu	hg19	6	17463259	17463259	+	Silent	SNP	G	G	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	CAP2	NM_006366	exon4	c.G255A	p.Q85Q	GGCCCAGCGGGCT	.	64.0	34.0	49.0	0.0	.	61	.	.	Atlas-SNP
ZNF804B	219578	hgsc.bcm.edu	hg19	7	88963115	88963115	+	Silent	SNP	A	A	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	ZNF804B	NM_181646	exon4	c.A819G	p.T273T	AGATACACACCTT	.	109.0	54.0	119.0	0.0	.	322	.	.	Atlas-SNP
ARHGEF39	84904	hgsc.bcm.edu	hg19	9	35662720	35662720	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	.	NM_032818	exon7	c.A692T	p.Q231L	CAGCCCTGGCGTA	.	94.0	34.0	57.0	0.0	.	.	.	.	Atlas-SNP
COL15A1	1306	hgsc.bcm.edu	hg19	9	101778304	101778304	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	COL15A1	NM_001855	exon11	c.C1550T	p.P517L	AGGAGCCCCTCAT	.	51.0	30.0	34.0	0.0	.	211	.	.	Atlas-SNP
HK1	3098	hgsc.bcm.edu	hg19	10	71148962	71148962	+	Silent	SNP	C	C	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	HK1	NM_033498	exon17	c.C1957T	p.L653L	TTTGACCTGGACG	.	57.0	46.0	162.0	0.0	.	170	.	.	Atlas-SNP
HIPK3	10114	hgsc.bcm.edu	hg19	11	33358704	33358704	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	HIPK3	NM_001048200	exon4	c.A1305T	p.K435N	TTGCAAAGAAACA	.	72.0	33.0	57.0	0.0	.	92	.	.	Atlas-SNP
HIPK3	10114	hgsc.bcm.edu	hg19	11	33358706	33358706	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	HIPK3	NM_001048200	exon4	c.A1307C	p.E436A	GCAAAGAAACAGA	.	71.0	32.0	56.0	0.0	.	92	.	.	Atlas-SNP
AHNAK	79026	hgsc.bcm.edu	hg19	11	62290411	62290411	+	Silent	SNP	C	C	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	AHNAK	NM_001620	exon5	c.G11478T	p.V3826V	CAGGTTCACATCC	.	81.0	34.0	71.0	0.0	.	532	.	.	Atlas-SNP
VPS51	738	hgsc.bcm.edu	hg19	11	64878964	64878964	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	.	NM_013265	exon10	c.C2254G	p.L752V	CACTTGCTGCTGG	.	73.0	28.0	83.0	0.0	.	.	.	.	Atlas-SNP
TMEM218	219854	hgsc.bcm.edu	hg19	11	124972140	124972140	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	TMEM218	NM_001258243	exon4	c.G103A	p.G35R	CCATCCCGCGGGG	.	11.0	11.0	25.0	0.0	.	14	.	.	Atlas-SNP
TULP3	7289	hgsc.bcm.edu	hg19	12	3048495	3048495	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	TULP3	NM_003324	exon11	c.A1214T	p.Q405L	TCATGCAGTTTGG	.	124.0	51.0	150.0	0.0	.	45	.	.	Atlas-SNP
APAF1	317	hgsc.bcm.edu	hg19	12	99117014	99117014	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	APAF1	NM_181861	exon23	c.A3128G	p.H1043R	GAGGCCATCAGGA	.	123.0	48.0	113.0	0.0	.	111	.	.	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	hg19	13	35731313	35731313	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	NBEA	NM_015678	exon21	c.A2750G	p.Y917C	TGGTCTACAATAT	.	116.0	109.0	111.0	1.0	.	340	.	.	Atlas-SNP
PPP2R5C	5527	hgsc.bcm.edu	hg19	14	102391540	102391540	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	PPP2R5C	NM_001161725	exon16	c.C1599A	p.D533E	TCAGGACCCCCAC	.	80.0	36.0	61.0	0.0	.	74	.	.	Atlas-SNP
IL16	3603	hgsc.bcm.edu	hg19	15	81589305	81589305	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	IL16	NM_001172128	exon13	c.G1939A	p.E647K	CCACAGGAAGACA	.	46.0	22.0	65.0	0.0	.	254	.	.	Atlas-SNP
STARD5	80765	hgsc.bcm.edu	hg19	15	81615246	81615246	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	STARD5	NM_181900	exon2	c.G143T	p.G48V	AGGTTCCCTGGAA	.	74.0	43.0	69.0	0.0	.	20	.	.	Atlas-SNP
TP53	7157	hgsc.bcm.edu	hg19	17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	rs28934571	bycluster	TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	NM_000546	exon7	c.G747T	p.R249S	GATGGGCCTCCGG	.	51.0	39.0	83.0	0.0	.	33396	.	.	Atlas-SNP
MYO18A	399687	hgsc.bcm.edu	hg19	17	27442787	27442787	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	MYO18A	NM_078471	exon12	c.G2122A	p.E708K	ACAGCTCCTCCAG	.	34.0	15.0	54.0	0.0	.	217	.	.	Atlas-SNP
PTPN2	5771	hgsc.bcm.edu	hg19	18	12802149	12802149	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	PTPN2	NM_001207013	exon9	c.A929C	p.K310T	CATCGTTTCTAGG	.	98.0	51.0	66.0	0.0	.	37	.	.	Atlas-SNP
PIN1	5300	hgsc.bcm.edu	hg19	19	9949168	9949168	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	PIN1_ENST00000247970,NS,carcinoma,0,1	PIN1	NM_006221	exon2	c.G115T	p.G39C	CCCAGCGGCAACA	.	46.0	17.0	55.0	0.0	.	7	.	.	Atlas-SNP
ARHGAP33	115703	hgsc.bcm.edu	hg19	19	36272086	36272086	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	ARHGAP33	NM_052948	exon12	c.T1017G	p.I339M	GTTCATTGAGGCC	.	42.0	19.0	34.0	0.0	.	102	.	.	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	hg19	X	63410591	63410591	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	.	NM_152424	exon2	c.A2576T	p.Y859F	CCTTGGTAGAATC	.	82.0	36.0	107.0	0.0	.	.	.	.	Atlas-SNP
TNMD	64102	hgsc.bcm.edu	hg19	X	99854571	99854571	+	Silent	SNP	C	C	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	TNMD	NM_022144	exon7	c.C811A	p.R271R	TGCCGTCGAGGCA	.	61.0	18.0	81.0	0.0	.	40	.	.	Atlas-SNP
LONRF3	79836	hgsc.bcm.edu	hg19	X	118148215	118148215	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	LONRF3	NM_001031855	exon10	c.G2020A	p.V674I	AACTGTGTCTATC	.	127.0	60.0	89.0	0.0	.	138	.	.	Atlas-SNP
ND3	0	hgsc.bcm.edu	hg19	MT	10114	10114	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	.	ENST00000361227	exon1	c.T56C	p.I19T	TAATAATTATTAC	.	147.0	136.0	166.0	0.0	.	.	.	.	Atlas-SNP
TEX11	56159	hgsc.bcm.edu	hg19	X	70053381	70053383	+	In_Frame_Del	DEL	CAA	CAA	-	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	TEX11	NM_001003811	exon9	c.632_634del	p.211_212del	.	.	172.0	63.0	178.0	0.0	.	132	.	.	Atlas-Indel,Pindel
CYP3A5	1577	hgsc.bcm.edu	hg19	7	99247719	99247721	+	In_Frame_Del	DEL	AGG	AGG	-	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	CYP3A5	NM_000777	exon12	c.1389_1391del	p.463_464del	.	.	172.0	69.0	192.0	0.0	.	46	.	.	Atlas-Indel,Pindel
RB1	5925	hgsc.bcm.edu	hg19	13	48947605	48947606	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.,1	RB1	NM_000321	exon12	c.1192_1193insA	p.E398fs	.	.	312.0	277.0	228.0	0.0	.	1068	.	.	Atlas-INDEL
TNPO1	3842	hgsc.bcm.edu	hg19	5	72189531	72189532	+	Splice_Site	INS	-	-	T	novel		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	.	TNPO1	NM_002270	exon18	c.2143+1->T	.	.	.	74.0	35.0	81.0	0.0	.	90	.	.	Atlas-INDEL