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
TEKT2	27285	hgsc.bcm.edu	hg19	1	36553152	36553152	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	TEKT2	NM_014466	exon8	c.A968T	p.Y323F	GAACCTACCGGCC	.	213.0	85.0	275.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
RIMKLA	284716	hgsc.bcm.edu	hg19	1	42875853	42875853	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	RIMKLA	NM_173642	exon4	c.C680T	p.S227F	ACTGCTCTCTCGG	.	63.0	19.0	83.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
MAST2	23139	hgsc.bcm.edu	hg19	1	46501468	46501468	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	MAST2	NM_015112	exon29	c.T5127A	p.S1709R	ACCTAGTGCCCCC	.	156.0	62.0	207.0	0.0	.	136	.	.	.	none	.	.	PASS	Atlas-SNP
L1TD1	54596	hgsc.bcm.edu	hg19	1	62675664	62675664	+	Missense_Mutation	SNP	G	G	T	rs200931139	alternate_allele	TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.,1	L1TD1	NM_001164835	exon5	c.G1218T	p.E406D	GGAGGAGGAGGAA	.	169.0	38.0	132.0	0.0	.	114	.	.	.	alt	.	.	PASS	Atlas-SNP
APH1A	51107	hgsc.bcm.edu	hg19	1	150239509	150239509	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	APH1A	NM_016022	exon5	c.T575A	p.L192Q	ACCACCAGGCCCA	.	189.0	67.0	188.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM79	84283	hgsc.bcm.edu	hg19	1	156261269	156261269	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	TMEM79	NM_032323	exon4	c.G1065C	p.W355C	GATGTGGAACCTC	.	50.0	19.0	70.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
POU2F1	5451	hgsc.bcm.edu	hg19	1	167343522	167343522	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	POU2F1	NM_002697	exon6	c.C580T	p.Q194X	CCCATACAGATCG	.	199.0	82.0	201.0	0.0	.	120	.	.	.	none	.	.	PASS	Atlas-SNP
QSOX1	5768	hgsc.bcm.edu	hg19	1	180148011	180148011	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	QSOX1	NM_002826	exon5	c.G598C	p.G200R	TACCTGGGTAGAG	.	57.0	19.0	74.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
M1AP	130951	hgsc.bcm.edu	hg19	2	74802619	74802619	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	.	NM_138804	exon7	c.G1020A	p.W340X	CTCATCCCAGTCC	.	80.0	30.0	86.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ACVR2A	92	hgsc.bcm.edu	hg19	2	148677844	148677844	+	Silent	SNP	T	T	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ACVR2A	NM_001616	exon8	c.T1008A	p.A336A	GACAGCTTGCATT	.	95.0	30.0	149.0	0.0	.	125	.	.	.	none	.	.	PASS	Atlas-SNP
CRYGD	1421	hgsc.bcm.edu	hg19	2	208988981	208988981	+	Missense_Mutation	SNP	G	G	A	rs200234608		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	CRYGD,NS,neuroblastoma,0,1	CRYGD	NM_006891	exon2	c.C107T	p.A36V	ACGCGCGCCGAGT	.	125.0	5.0	146.0	0.0	.	18	.	.	.	weak	G|0.998;A|0.002	0.002	PASS	Atlas-SNP
CTDSP1	58190	hgsc.bcm.edu	hg19	2	219268024	219268024	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	CTDSP1	NM_021198	exon6	c.T541A	p.C181S	GAGTCCTGCGTCT	.	68.0	30.0	94.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
NBEAL2	23218	hgsc.bcm.edu	hg19	3	47038846	47038846	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	NBEAL2	NM_015175	exon19	c.C2747T	p.T916M	CTGAAACGCATGA	.	15.0	7.0	22.0	0.0	.	267	.	.	.	none	.	.	PASS	Atlas-SNP
BOD1L1	259282	hgsc.bcm.edu	hg19	4	13616300	13616300	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	.	NM_148894	exon4	c.A694G	p.R232G	ACGCTCTCTCACT	.	62.0	4.0	89.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COL25A1	84570	hgsc.bcm.edu	hg19	4	109861784	109861784	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	COL25A1	NM_198721	exon9	c.G583C	p.G195R	GAGGCCCTGCCTG	.	42.0	17.0	63.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
TENM3	55714	hgsc.bcm.edu	hg19	4	183674665	183674665	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	.	NM_001080477	exon20	c.G3925A	p.D1309N	AAAGTTGACCAAA	.	120.0	43.0	183.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
FRG1	2483	hgsc.bcm.edu	hg19	4	190878551	190878551	+	Splice_Site	SNP	A	A	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	FRG1,NS,malignant_melanoma,0,1	FRG1	NM_004477	exon6	c.433-2A>G	.	TCACTTAGGGGAA	.	92.0	6.0	91.0	1.0	.	76	.	.	.	none	.	.	PASS	Atlas-SNP
CHD1	1105	hgsc.bcm.edu	hg19	5	98235232	98235232	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	CHD1	NM_001270	exon7	c.T1037A	p.M346K	TTTTTCATTCCTC	.	46.0	15.0	59.0	0.0	.	137	.	.	.	none	.	.	PASS	Atlas-SNP
SHROOM1	134549	hgsc.bcm.edu	hg19	5	132160915	132160915	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	SHROOM1	NM_133456	exon1	c.C918A	p.S306R	TGAAGCGCTCCGA	.	71.0	20.0	89.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM173	340061	hgsc.bcm.edu	hg19	5	138856029	138856029	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	TMEM173	NM_198282	exon8	c.T957G	p.D319E	GCTGTCATCTGCA	.	49.0	10.0	58.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
FGFR4	2264	hgsc.bcm.edu	hg19	5	176523128	176523128	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	FGFR4	NM_002011	exon14	c.T1892C	p.F631S	CTGACTTTGGGCT	.	77.0	35.0	96.0	0.0	.	174	.	.	.	none	.	.	PASS	Atlas-SNP
GFPT2	9945	hgsc.bcm.edu	hg19	5	179743359	179743359	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	GFPT2	NM_005110	exon13	c.T1255C	p.F419L	TGAAAAAGCAAAC	.	122.0	38.0	151.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
ATXN1	6310	hgsc.bcm.edu	hg19	6	16327864	16327864	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.,1	ATXN1	NM_001128164	exon7	c.C678G	p.H226Q	GCTGAGGTGCTGC	.	64.0	3.0	67.0	2.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
HIST1H2AH	85235	hgsc.bcm.edu	hg19	6	27115069	27115069	+	Silent	SNP	G	G	A	rs7756481	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes;alternate_allele	TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	HIST1H2AH	NM_080596	exon1	c.G162A	p.A54A	GGCTGCGGTGCTG	.	142.0	8.0	131.0	0.0	.	26	.	.	.	alt	G|0.936;C|0.064	.	PASS	Atlas-SNP
BEND3	57673	hgsc.bcm.edu	hg19	6	107390745	107390745	+	Silent	SNP	A	A	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	BEND3	NM_001080450	exon5	c.T1650C	p.G550G	GTCGGCACCGGGC	.	34.0	12.0	40.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
ZSCAN21	7589	hgsc.bcm.edu	hg19	7	99661446	99661446	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ZSCAN21	NM_145914	exon4	c.G628T	p.D210Y	TCAGCAGATGAGC	.	176.0	113.0	103.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
UPK3BL	100134938	hgsc.bcm.edu	hg19	7	102279605	102279605	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	UPK3BL	NM_001114403	exon4	c.A527C	p.E176A	TTGGTTTCAGCCA	.	625.0	41.0	452.0	0.0	.	6	.	.	.	none	.	.	PASS	Atlas-SNP
BRAF	673	hgsc.bcm.edu	hg19	7	140507811	140507811	+	Silent	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	BRAF	NM_004333	exon5	c.A660G	p.E220E	CAATTCTTCTCCA	.	126.0	29.0	80.0	0.0	.	36346	.	.	.	none	.	.	PASS	Atlas-SNP
DUSP4	1846	hgsc.bcm.edu	hg19	8	29197704	29197704	+	Silent	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	DUSP4	NM_001394	exon2	c.C490T	p.L164L	CTGCCAGGGCCTT	.	55.0	22.0	56.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
VPS13B	157680	hgsc.bcm.edu	hg19	8	100836128	100836128	+	Silent	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	VPS13B	NM_017890	exon51	c.T9327C	p.T3109T	CAAGACTACAATA	.	80.0	35.0	66.0	0.0	.	811	.	.	.	none	.	.	PASS	Atlas-SNP
GPSM1	26086	hgsc.bcm.edu	hg19	9	139231429	139231429	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	GPSM1	NM_015597	exon4	c.G478T	p.G160C	GCCAAAGGCAAGC	.	107.0	49.0	142.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD16	54522	hgsc.bcm.edu	hg19	10	5922267	5922267	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	ANKRD16,NS,carcinoma,0,2	ANKRD16	NM_001009941	exon6	c.C922T	p.R308X	CTGATCGATTTTT	.	38.0	19.0	69.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
KNDC1	85442	hgsc.bcm.edu	hg19	10	135012281	135012281	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	KNDC1	NM_152643	exon14	c.G2269A	p.G757S	GCCCAGGGCCGCC	.	74.0	20.0	91.0	0.0	.	155	.	.	.	none	.	.	PASS	Atlas-SNP
GTF2H1	2965	hgsc.bcm.edu	hg19	11	18382179	18382179	+	Silent	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	GTF2H1	NM_001142307	exon15	c.T1485C	p.S495S	GAAAAGTAATTTG	.	44.0	17.0	66.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
DAGLA	747	hgsc.bcm.edu	hg19	11	61490356	61490356	+	Silent	SNP	C	C	T	rs374808753		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	DAGLA	NM_006133	exon4	c.C333T	p.Y111Y	CATCTACGCCATC	.	67.0	27.0	85.0	0.0	.	109	.	.	.	weak	.	.	PASS	Atlas-SNP
INPPL1	3636	hgsc.bcm.edu	hg19	11	71941503	71941503	+	Silent	SNP	C	C	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	INPPL1	NM_001567	exon10	c.C1188A	p.V396V	CTTTGTCAGTGCC	.	87.0	39.0	92.0	0.0	.	120	.	.	.	none	.	.	PASS	Atlas-SNP
FCHSD2	9873	hgsc.bcm.edu	hg19	11	72700036	72700036	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	FCHSD2	NM_014824	exon6	c.T494C	p.V165A	TCTCGTACTGCAT	.	78.0	31.0	94.0	0.0	.	106	.	.	.	none	.	.	PASS	Atlas-SNP
RSF1	51773	hgsc.bcm.edu	hg19	11	77412208	77412208	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	RSF1	NM_016578	exon6	c.C2066A	p.S689Y	ATGCCAGAGGTCT	.	78.0	31.0	81.0	0.0	.	105	.	.	.	none	.	.	PASS	Atlas-SNP
ATM	472	hgsc.bcm.edu	hg19	11	108213973	108213973	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ATM	NM_000051	exon57	c.G8293A	p.G2765S	CGAAGTGGTGTTC	.	136.0	8.0	104.0	0.0	.	1657	.	.	.	none	.	.	PASS	Atlas-SNP
DLAT	1737	hgsc.bcm.edu	hg19	11	111933142	111933142	+	Silent	SNP	T	T	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	DLAT	NM_001931	exon14	c.T1827A	p.A609A	TGTGGCTAGCATG	.	50.0	11.0	56.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
TMPRSS13	84000	hgsc.bcm.edu	hg19	11	117789218	117789218	+	Silent	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	TMPRSS13	NM_001206790	exon2	c.G357A	p.V119V	AAGGTACACTCTG	.	89.0	40.0	112.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
KIF21A	55605	hgsc.bcm.edu	hg19	12	39695383	39695383	+	Silent	SNP	G	G	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	KIF21A	NM_001173464	exon37	c.C4830G	p.V1610V	GTTCCAGACTTTC	.	243.0	123.0	226.0	1.0	.	238	.	.	.	none	.	.	PASS	Atlas-SNP
HDAC7	51564	hgsc.bcm.edu	hg19	12	48181543	48181543	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	HDAC7	NM_015401	exon21	c.G2405C	p.G802A	AGACCTCCAGCCC	.	134.0	68.0	151.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
NAA16	79612	hgsc.bcm.edu	hg19	13	41936177	41936177	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	NAA16	NM_024561	exon13	c.C1421T	p.S474F	GAACATCTGCCAT	.	63.0	22.0	65.0	0.0	.	74	.	.	.	none	.	.	PASS	Atlas-SNP
DCT	1638	hgsc.bcm.edu	hg19	13	95121020	95121020	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	DCT	NM_001129889	exon2	c.C575T	p.S192F	CTAACAGAATAAT	.	44.0	17.0	54.0	0.0	.	186	.	.	.	none	.	.	PASS	Atlas-SNP
COL4A2	1284	hgsc.bcm.edu	hg19	13	111082947	111082947	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	COL4A2	NM_001846	exon10	c.G641A	p.G214E	CTCCAGGGAGACC	.	100.0	45.0	145.0	0.0	.	178	.	.	.	none	.	.	PASS	Atlas-SNP
PELI2	57161	hgsc.bcm.edu	hg19	14	56746403	56746403	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	PELI2	NM_021255	exon3	c.T217C	p.C73R	ATCAGCTGCAAAG	.	44.0	17.0	47.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
NOXRED1	122945	hgsc.bcm.edu	hg19	14	77872299	77872299	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	NOXRED1	NM_001113475	exon5	c.G862T	p.D288Y	CAAAATCTGTTAA	.	56.0	19.0	67.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
EIF2AK4	440275	hgsc.bcm.edu	hg19	15	40226434	40226434	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	EIF2AK4	NM_001013703	exon1	c.A38G	p.D13G	GCCGGGACGAGCC	.	79.0	16.0	101.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
FBN1	2200	hgsc.bcm.edu	hg19	15	48780565	48780565	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	FBN1	NM_000138	exon26	c.G3208A	p.D1070N	ACTGACCTGTGCA	.	75.0	21.0	79.0	0.0	.	310	.	.	.	none	.	.	PASS	Atlas-SNP
CEP152	22995	hgsc.bcm.edu	hg19	15	49031304	49031304	+	Silent	SNP	G	G	A	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	CEP152	NM_001194998	exon27	c.C4275T	p.N1425N	CTCTGAGTTCTCT	.	74.0	30.0	85.0	0.0	.	145	.	.	.	none	.	.	PASS	Atlas-SNP
AGBL1	123624	hgsc.bcm.edu	hg19	15	86790909	86790909	+	Missense_Mutation	SNP	C	C	A	rs370819428	alternate_allele	TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	AGBL1	NM_152336	exon6	c.C396A	p.N132K	GTCGAACGGCCGC	.	94.0	5.0	102.0	0.0	.	151	.	.	.	alt	.	.	PASS	Atlas-SNP
ZNF689	115509	hgsc.bcm.edu	hg19	16	30616527	30616527	+	Silent	SNP	G	G	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ZNF689	NM_138447	exon3	c.C561A	p.S187S	TGGATAGGAAAAG	.	79.0	26.0	125.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
MYH1	4619	hgsc.bcm.edu	hg19	17	10404987	10404987	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	MYH1	NM_005963	exon26	c.T3272A	p.M1091K	CCGCTCATTTCAA	.	129.0	80.0	151.0	0.0	.	403	.	.	.	none	.	.	PASS	Atlas-SNP
PHF12	57649	hgsc.bcm.edu	hg19	17	27251300	27251300	+	Silent	SNP	C	C	T	rs200428291	alternate_allele	TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	PHF12	NM_020889	exon4	c.G342A	p.E114E	ACCCAGCTCCTTT	.	86.0	22.0	53.0	0.0	.	69	.	.	.	alt	C|0.999;G|0.001	.	PASS	Atlas-SNP
NBR1	4077	hgsc.bcm.edu	hg19	17	41341718	41341718	+	Silent	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	NBR1	NM_031862	exon8	c.T594C	p.P198P	AATGCCTACTTCA	.	123.0	23.0	114.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
SLC4A1	6521	hgsc.bcm.edu	hg19	17	42335164	42335164	+	Missense_Mutation	SNP	G	G	A	rs373768879		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	SLC4A1	NM_000342	exon12	c.C1294T	p.R432W	GGTTCCGGGTCTT	.	105.0	66.0	82.0	0.0	.	104	.	.	.	weak	.	.	PASS	Atlas-SNP
PSMG2	56984	hgsc.bcm.edu	hg19	18	12720515	12720515	+	Silent	SNP	C	C	T	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	PSMG2	NM_020232	exon5	c.C414T	p.P138P	TACTCCCTTCCGG	.	94.0	4.0	118.0	0.0	.	17	.	.	.	none	.	.	PASS	Atlas-SNP
DEFB116	245930	hgsc.bcm.edu	hg19	20	29891079	29891079	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	DEFB116	NM_001037731	exon2	c.A245G	p.K82R	TCCTCCTTCACAT	.	76.0	28.0	124.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
DEFB116	245930	hgsc.bcm.edu	hg19	20	29891080	29891080	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	DEFB116	NM_001037731	exon2	c.A244G	p.K82E	CCTCCTTCACATT	.	77.0	29.0	121.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
CBFA2T2	9139	hgsc.bcm.edu	hg19	20	32199106	32199106	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	CBFA2T2	NM_005093	exon4	c.G412C	p.G138R	GAGATTGGGGAGA	.	80.0	32.0	83.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	hg19	X	63411064	63411064	+	Silent	SNP	C	C	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	.	NM_152424	exon2	c.G2103C	p.L701L	CTTCTCCAGAGGA	.	60.0	49.0	75.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
RPL36A-HNRNPH2	0	hgsc.bcm.edu	hg19	X	100650416	100650416	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	.	NM_001199973	exon4	c.T379G	p.F127V	AAGCATTTTGAAC	.	115.0	87.0	118.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ENOX2	10495	hgsc.bcm.edu	hg19	X	129822852	129822852	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ENOX2	NM_182314	exon6	c.T325C	p.F109L	GAGGGAAGAGCGT	.	53.0	38.0	49.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
ACOT11	26027	hgsc.bcm.edu	hg19	1	55060319	55060319	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ACOT11	NM_147161	exon6	c.561delT	p.Y187X	.	.	166.0	59.0	175.0	0.0	.	105	.	0.355422	0	none	.	.	PASS	Atlas-Indel,Pindel
TTYH3	80727	hgsc.bcm.edu	hg19	7	2686778	2686778	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	TTYH3	NM_025250	exon3	c.295delG	p.A99fs	.	.	74.0	40.0	54.0	0.0	.	36	.	0.540541	0	none	.	.	PASS	Atlas-Indel,Pindel
ABCA12	26154	hgsc.bcm.edu	hg19	2	215820066	215820067	+	Frame_Shift_Del	DEL	TC	TC	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ABCA12	NM_173076	exon43	c.6253_6254del	p.2085_2085del	.	.	253.0	95.0	299.0	0.0	.	368	.	0.375494	0	none	.	.	PASS	Atlas-Indel,Pindel
NCOA2	10499	hgsc.bcm.edu	hg19	8	71068654	71068654	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	NCOA2	NM_006540	exon11	c.1947delT	p.S649fs	.	.	54.0	27.0	75.0	0.0	.	147	.	0.5	0	none	.	.	PASS	Atlas-Indel,Pindel
PGM1	5236	hgsc.bcm.edu	hg19	1	64125282	64125282	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	PGM1	NM_001172818	exon11	c.1678delA	p.I560fs	.	.	77.0	22.0	110.0	0.0	.	75	.	0.285714	0	none	.	.	PASS	Atlas-Indel,Pindel
ADAD1	132612	hgsc.bcm.edu	hg19	4	123333812	123333812	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ADAD1	NM_139243	exon10	c.1096delA	p.I366fs	.	.	90.0	41.0	108.0	0.0	.	94	.	0.455556	0	none	.	.	PASS	Atlas-Indel,Pindel
MYL12B	103910	hgsc.bcm.edu	hg19	18	3272961	3272961	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	MYL12B	NM_033546	exon2	c.64delG	p.V22fs	.	.	157.0	58.0	201.0	0.0	.	11	.	0.369427	0	none	.	.	PASS	Atlas-Indel,Pindel
COL6A5	256076	hgsc.bcm.edu	hg19	3	130120011	130120011	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	COL6A5	NM_153264	exon11	c.4127delA	p.Q1376fs	.	.	137.0	49.0	206.0	0.0	.	205	.	0.357664	0	none	.	.	PASS	Atlas-Indel,Pindel
ADAMTS6	11174	hgsc.bcm.edu	hg19	5	64510676	64510682	+	Frame_Shift_Del	DEL	AACTTCA	AACTTCA	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	AACTTCA	AACTTCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ADAMTS6	NM_197941	exon20	c.2515_2521del	p.839_841del	.	.	77.0	17.0	121.0	0.0	.	174	.	0.220779	0	none	.	.	PASS	Atlas-Indel,Pindel
ZBTB8B	728116	hgsc.bcm.edu	hg19	1	32936383	32936393	+	Frame_Shift_Del	DEL	TCATTCACTAT	TCATTCACTAT	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	TCATTCACTAT	TCATTCACTAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	ZBTB8B	NM_001145720	exon2	c.157_167del	p.53_56del	.	.	86.0	23.0	99.0	0.0	.	28	.	0.267442	0	none	.	.	PASS	Atlas-Indel,Pindel
PHF3	23469	hgsc.bcm.edu	hg19	6	64404652	64404653	+	Frame_Shift_Ins	INS	-	-	AGGT	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	PHF3	NM_015153	exon5	c.2678_2679insAGGT	p.P893fs	.	.	199.0	34.0	266.0	0.0	.	191	.	0.171	.	none	.	.	PASS	Pindel
GXYLT1	283464	hgsc.bcm.edu	hg19	12	42538257	42538295	+	In_Frame_Del	DEL	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	-	novel		TCGA-Y8-A8RY-01A-11D-A36X-10	TCGA-Y8-A8RY-10A-01D-A370-10	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	GCCCGCGACGCCGGCGCCTCTCACGGCGCCGCGTCCGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	fbd6df33-90cf-4c79-bf0c-9f5bd762c16f	7a66b4e5-8f59-4d6e-b6dc-58884cf787ff	.	GXYLT1	NM_001099650	exon1	c.155_193del	p.52_65del	.	.	8.0	11.0	7.0	0.0	.	47	.	1.375	.	none	.	.	PASS	Pindel
