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
ACAP3	116983	hgsc.bcm.edu	hg19	1	1235981	1235981	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ACAP3	NM_030649	exon6	c.A430G	p.R144G	GGTGCCTCGGGGC	.	156.0	53.0	162.0	0.0	.	87	.	.	.	none	.	.	PASS	Atlas-SNP
GJB3	2707	hgsc.bcm.edu	hg19	1	35250656	35250656	+	Missense_Mutation	SNP	G	G	A	rs201314683		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	GJB3,NS,carcinoma,0,1	GJB3	NM_001005752	exon2	c.G293A	p.R98H	CCTACCGTGAGGA	.	63.0	26.0	49.0	0.0	.	40	.	.	.	weak	G|0.999;A|0.001	0.001	PASS	Atlas-SNP
MUTYH	4595	hgsc.bcm.edu	hg19	1	45797447	45797447	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	MUTYH	NM_001128425	exon12	c.T1072C	p.F358L	TGGGGAAGTTGAC	.	46.0	17.0	46.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC17	149483	hgsc.bcm.edu	hg19	1	46088725	46088725	+	Silent	SNP	C	C	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	CCDC17	NM_001114938	exon4	c.G558T	p.L186L	CTGCTCCAGGCCG	.	79.0	41.0	58.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
ABCD3	5825	hgsc.bcm.edu	hg19	1	94939389	94939389	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ABCD3	NM_002858	exon5	c.C403A	p.L135I	ATGCCTCTTGTAA	.	65.0	23.0	66.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
CSDE1	7812	hgsc.bcm.edu	hg19	1	115280171	115280171	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	CSDE1	NM_001242891	exon6	c.T461A	p.V154D	TGAGGAACAGCGC	.	368.0	148.0	351.0	1.0	.	145	.	.	.	none	.	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	hg19	1	152732843	152732843	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	KPRP	NM_001025231	exon2	c.G779A	p.R260Q	CTCCTCGGCGGCT	.	80.0	4.0	62.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
FCRL4	83417	hgsc.bcm.edu	hg19	1	157548316	157548316	+	Silent	SNP	T	T	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	FCRL4	NM_031282	exon10	c.A1377T	p.G459G	CAAATCTCCCTTT	.	70.0	32.0	108.0	0.0	.	95	.	.	.	none	.	.	PASS	Atlas-SNP
MYO7B	4648	hgsc.bcm.edu	hg19	2	128389949	128389949	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	MYO7B	NM_001080527	exon38	c.G5300C	p.C1767S	CCGACTGCAGCCG	.	251.0	112.0	212.0	0.0	.	359	.	.	.	none	.	.	PASS	Atlas-SNP
LRTM1	57408	hgsc.bcm.edu	hg19	3	54958819	54958819	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	LRTM1	NM_020678	exon2	c.C431T	p.T144I	TCCCAAGTCTCTC	.	88.0	42.0	107.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
KALRN	8997	hgsc.bcm.edu	hg19	3	124210171	124210171	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	KALRN	NM_003947	exon31	c.C4583T	p.T1528I	TACAGACCTCAGA	.	97.0	51.0	83.0	0.0	.	556	.	.	.	none	.	.	PASS	Atlas-SNP
IFT122	55764	hgsc.bcm.edu	hg19	3	129185869	129185869	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	IFT122	NM_052985	exon9	c.G853A	p.E285K	GAGGAAGAACCAG	.	119.0	28.0	95.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
SEL1L3	23231	hgsc.bcm.edu	hg19	4	25759396	25759396	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	SEL1L3	NM_015187	exon22	c.A3100T	p.N1034Y	CCTCGTTACTGTG	.	256.0	92.0	260.0	0.0	.	62	.	.	.	none	.	.	PASS	Atlas-SNP
TMPRSS11F	389208	hgsc.bcm.edu	hg19	4	68934461	68934461	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	TMPRSS11F	NM_207407	exon7	c.G630T	p.R210S	TGTTTCCCTTCCT	.	82.0	36.0	104.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
FNIP2	57600	hgsc.bcm.edu	hg19	4	159812743	159812743	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	FNIP2	NM_020840	exon15	c.C3095G	p.S1032C	AGGTGTCCAGTTT	.	61.0	27.0	80.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
RAPGEF6	51735	hgsc.bcm.edu	hg19	5	130791652	130791652	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	RAPGEF6	NM_001164387	exon21	c.C2933G	p.P978R	TTGCTTGGTAACT	.	100.0	43.0	110.0	0.0	.	361	.	.	.	none	.	.	PASS	Atlas-SNP
PCDHB3	56132	hgsc.bcm.edu	hg19	5	140482079	140482079	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PCDHB3	NM_018937	exon1	c.G1846C	p.G616R	CTGTTCGGCGTGT	.	30.0	16.0	31.0	0.0	.	208	.	.	.	none	.	.	PASS	Atlas-SNP
KIFC1	3833	hgsc.bcm.edu	hg19	6	33365934	33365934	+	Silent	SNP	G	G	A	rs368144446		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	KIFC1	NM_002263	exon2	c.G141A	p.E47E	CCTGGAGCCTGAG	.	123.0	57.0	119.0	0.0	.	47	.	.	.	weak	.	.	PASS	Atlas-SNP
POP7	10248	hgsc.bcm.edu	hg19	7	100304640	100304640	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	POP7	NM_005837	exon2	c.C187T	p.Q63X	CGGGGTCAGAACG	.	230.0	78.0	86.0	0.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
RELN	5649	hgsc.bcm.edu	hg19	7	103474054	103474054	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	RELN	NM_173054	exon3	c.C403G	p.H135D	GCAGGTGACTCAC	.	228.0	39.0	140.0	0.0	.	593	.	.	.	none	.	.	PASS	Atlas-SNP
SND1	27044	hgsc.bcm.edu	hg19	7	127725765	127725765	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	SND1	NM_014390	exon20	c.A2237G	p.Y746C	GCAGGTACCGTGC	.	83.0	10.0	53.0	0.0	.	104	.	.	.	none	.	.	PASS	Atlas-SNP
PLXNA4	91584	hgsc.bcm.edu	hg19	7	131864511	131864511	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PLXNA4	NM_020911	exon20	c.C3809T	p.T1270M	TTCAGCGTGAGGT	.	130.0	25.0	70.0	0.0	.	873	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF425	155054	hgsc.bcm.edu	hg19	7	148801369	148801369	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	ZNF425,colon,carcinoma,0,1	ZNF425	NM_001001661	exon4	c.G1594A	p.G532S	TGCGGCCGCACTC	.	145.0	31.0	51.0	0.0	.	99	.	.	.	none	.	.	PASS	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	hg19	7	149518600	149518600	+	Silent	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	.	NM_198455	exon88	c.C12669T	p.T4223T	CCGCACCCTGGGG	.	76.0	31.0	55.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
GPR124	25960	hgsc.bcm.edu	hg19	8	37693093	37693093	+	Missense_Mutation	SNP	A	A	G	rs377757244		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	GPR124	NM_032777	exon13	c.A1855G	p.I619V	GCCTCCATCCAGC	.	40.0	15.0	56.0	0.0	.	85	.	.	.	weak	.	.	PASS	Atlas-SNP
NOL6	65083	hgsc.bcm.edu	hg19	9	33467705	33467705	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	NOL6	NM_022917	exon12	c.G1586A	p.R529Q	GGGGGTCGAGAGT	.	76.0	39.0	60.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
PRKACG	5568	hgsc.bcm.edu	hg19	9	71628443	71628443	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PRKACG	NM_002732	exon1	c.C566T	p.A189V	CGCTTGGCGAAAC	.	79.0	30.0	67.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
RALGDS	5900	hgsc.bcm.edu	hg19	9	135975749	135975749	+	Silent	SNP	A	A	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	RALGDS	NM_006266	exon17	c.T2475G	p.A825A	AGCCGGAGCCTTA	.	76.0	29.0	62.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
OPTN	10133	hgsc.bcm.edu	hg19	10	13167963	13167963	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	OPTN	NM_001008212	exon11	c.T1166A	p.L389Q	CTGTGCTACAGAT	.	139.0	47.0	157.0	0.0	.	57	.	.	.	none	.	.	PASS	Atlas-SNP
JMJD1C	221037	hgsc.bcm.edu	hg19	10	64957243	64957243	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	JMJD1C	NM_032776	exon13	c.T5572C	p.W1858R	AGACCCAGTGAAT	.	90.0	35.0	110.0	0.0	.	347	.	.	.	none	.	.	PASS	Atlas-SNP
CDH23	64072	hgsc.bcm.edu	hg19	10	73567274	73567274	+	Silent	SNP	C	C	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	CDH23,colon,carcinoma,0,1	CDH23	NM_022124	exon57	c.C8310G	p.A2770A	CTCAGCCGGCAAC	.	78.0	33.0	55.0	0.0	.	365	.	.	.	none	.	.	PASS	Atlas-SNP
ECD	11319	hgsc.bcm.edu	hg19	10	74899240	74899240	+	Silent	SNP	T	T	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ECD	NM_001135752	exon12	c.A1347G	p.L449L	GAGATCTAACCAC	.	47.0	20.0	58.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	hg19	11	1093437	1093437	+	Silent	SNP	G	G	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	NM_002457	exon30	c.G5256C	p.T1752T	CACCACGGTGACC	.	25.0	3.0	25.0	0.0	.	614	.	.	.	none	.	.	PASS	Atlas-SNP
NUP160	23279	hgsc.bcm.edu	hg19	11	47869930	47869930	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	NUP160	NM_015231	exon1	c.G43A	p.V15M	CCGTCACTTCCGG	.	45.0	18.0	49.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
ZBTB3	79842	hgsc.bcm.edu	hg19	11	62520283	62520283	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ZBTB3	NM_024784	exon2	c.T1004A	p.V335D	GCTGAGACAGGGG	.	65.0	24.0	56.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
FAM186A	121006	hgsc.bcm.edu	hg19	12	50744556	50744556	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	FAM186A	NM_001145475	exon4	c.C6059T	p.T2020I	TATTTGGTGAAAT	.	151.0	78.0	111.0	0.0	.	181	.	.	.	none	.	.	PASS	Atlas-SNP
SLC4A8	9498	hgsc.bcm.edu	hg19	12	51853759	51853759	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	SLC4A8	NM_001039960	exon8	c.A880G	p.I294V	AAAAAAATTCCTA	.	138.0	70.0	138.0	0.0	.	292	.	.	.	none	.	.	PASS	Atlas-SNP
ANKS1B	56899	hgsc.bcm.edu	hg19	12	99837527	99837527	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ANKS1B	NM_152788	exon11	c.C1499T	p.T500I	GGGCCTGTTGAGC	.	209.0	139.0	164.0	1.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
POLE	5426	hgsc.bcm.edu	hg19	12	133219525	133219525	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	POLE	NM_006231	exon36	c.C4609T	p.L1537F	CCAGGAGGAGGCC	.	93.0	38.0	72.0	0.0	.	416	.	.	.	none	.	.	PASS	Atlas-SNP
SACS	26278	hgsc.bcm.edu	hg19	13	23909168	23909168	+	Silent	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	SACS	NM_014363	exon10	c.T8847C	p.I2949I	AACATGAATAGGG	.	81.0	37.0	72.0	0.0	.	871	.	.	.	none	.	.	PASS	Atlas-SNP
CDK8	1024	hgsc.bcm.edu	hg19	13	26975672	26975672	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	CDK8	NM_001260	exon12	c.A1180T	p.S394C	GACAGCAGTCACA	.	118.0	47.0	115.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGEF40	55701	hgsc.bcm.edu	hg19	14	21543510	21543510	+	Silent	SNP	C	C	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ARHGEF40	NM_018071	exon4	c.C1470G	p.G490G	AGAAGGCCCCCTG	.	129.0	51.0	116.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
PPP2R3C	55012	hgsc.bcm.edu	hg19	14	35579746	35579746	+	Silent	SNP	A	A	G	rs201403377	bycluster;alternate_allele	TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PPP2R3C	NM_017917	exon3	c.T276C	p.D92D	TTCATTATCTAAC	.	43.0	14.0	38.0	0.0	.	44	.	.	.	alt	.	.	PASS	Atlas-SNP
DUT	1854	hgsc.bcm.edu	hg19	15	48623926	48623926	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	DUT	NM_001025248	exon1	c.A214G	p.T72A	GCCAGTACAGTCG	.	29.0	6.0	27.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF280D	54816	hgsc.bcm.edu	hg19	15	56935189	56935189	+	Silent	SNP	T	T	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ZNF280D	NM_017661	exon20	c.A2220G	p.K740K	TTCTTTTTTTAAT	.	419.0	167.0	405.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
MRPL46	26589	hgsc.bcm.edu	hg19	15	89010546	89010546	+	Silent	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	MRPL46	NM_022163	exon1	c.G63A	p.R21R	CCAGAGCCTCTCG	.	107.0	50.0	114.0	0.0	.	13	.	.	.	none	.	.	PASS	Atlas-SNP
LRRK1	79705	hgsc.bcm.edu	hg19	15	101602839	101602839	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	LRRK1	NM_024652	exon31	c.G4858T	p.A1620S	CAACAGGCCTTGG	.	88.0	34.0	119.0	0.0	.	310	.	.	.	none	.	.	PASS	Atlas-SNP
PPL	5493	hgsc.bcm.edu	hg19	16	4933991	4933991	+	Silent	SNP	G	G	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PPL	NM_002705	exon22	c.C4665G	p.S1555S	TTCCTTGGATGAC	.	33.0	16.0	51.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
C16orf72	29035	hgsc.bcm.edu	hg19	16	9186850	9186850	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	C16orf72	NM_014117	exon2	c.T299A	p.L100H	CCAATCTCTACAA	.	124.0	48.0	131.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
SLC6A2	6530	hgsc.bcm.edu	hg19	16	55719085	55719085	+	Silent	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	SLC6A2	NM_001172501	exon5	c.C675T	p.S225S	GAGCAGCGGGATT	.	60.0	26.0	46.0	0.0	.	189	.	.	.	none	.	.	PASS	Atlas-SNP
DPEP1	1800	hgsc.bcm.edu	hg19	16	89704613	89704613	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	DPEP1	NM_001128141	exon11	c.T1219C	p.C407R	GTCCTCTGTCTGT	.	33.0	10.0	27.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
SCARF1	8578	hgsc.bcm.edu	hg19	17	1540075	1540075	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	SCARF1	NM_003693	exon10	c.G1561A	p.D521N	AGGAGTCATCAGT	.	68.0	31.0	67.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
ALOX15B	247	hgsc.bcm.edu	hg19	17	7948885	7948885	+	Missense_Mutation	SNP	C	C	T	rs370434436		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	ALOX15B,NS,carcinoma,0,1	ALOX15B	NM_001141	exon8	c.C1081T	p.R361C	TGGGTGCGCAATG	.	41.0	3.0	50.0	0.0	.	66	.	.	.	weak	.	.	PASS	Atlas-SNP
MYH10	4628	hgsc.bcm.edu	hg19	17	8448780	8448780	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	MYH10	NM_001256012	exon13	c.T1417C	p.F473L	TTTCAAATCCAGC	.	69.0	27.0	74.0	0.0	.	148	.	.	.	none	.	.	PASS	Atlas-SNP
KRT10	3858	hgsc.bcm.edu	hg19	17	38975316	38975316	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	KRT10	NM_000421	exon7	c.C1471T	p.H491Y	CGCCGTGGCCGCC	.	125.0	8.0	44.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
PLEKHH3	79990	hgsc.bcm.edu	hg19	17	40823573	40823573	+	Silent	SNP	G	G	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PLEKHH3	NM_024927	exon8	c.C1080A	p.T360T	CTGCTCGGTCCTG	.	152.0	40.0	112.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
DHX8	1659	hgsc.bcm.edu	hg19	17	41597598	41597598	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	DHX8	NM_004941	exon19	c.T2900A	p.L967Q	GGGCCCTGGATGA	.	84.0	22.0	77.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
DSG4	147409	hgsc.bcm.edu	hg19	18	28968923	28968923	+	Silent	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	DSG4	NM_001134453	exon5	c.C459T	p.N153N	TGATAACGCTCCA	.	100.0	46.0	77.0	0.0	.	343	.	.	.	none	.	.	PASS	Atlas-SNP
FZR1	51343	hgsc.bcm.edu	hg19	19	3527661	3527661	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	FZR1	NM_001136198	exon6	c.C503G	p.T168S	AACCCACCCGCAA	.	40.0	15.0	41.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
PLIN4	729359	hgsc.bcm.edu	hg19	19	4512405	4512405	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PLIN4	NM_001080400	exon3	c.A1525C	p.T509P	TGGTGGTGTCTAC	.	92.0	32.0	81.0	0.0	.	191	.	.	.	none	.	.	PASS	Atlas-SNP
CLEC4M	10332	hgsc.bcm.edu	hg19	19	7830731	7830731	+	Missense_Mutation	SNP	G	G	A	rs76899402	bycluster	TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	CLEC4M,colon,carcinoma,0,1	CLEC4M	NM_001144908	exon4	c.G422A	p.R141Q	TGACCCGGCTGAA	.	30.0	2.0	28.0	0.0	.	58	.	.	.	weak	G|0.250;A|0.750	0.750	PASS	Atlas-SNP
TNPO2	30000	hgsc.bcm.edu	hg19	19	12816127	12816127	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	TNPO2	NM_013433	exon17	c.A1949G	p.E650G	AGGCCCTCGGCCA	.	58.0	23.0	58.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF536	9745	hgsc.bcm.edu	hg19	19	30934626	30934626	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ZNF536	NM_014717	exon2	c.C157T	p.R53W	CATCCCCGGCCCA	.	80.0	42.0	89.0	0.0	.	424	.	.	.	none	.	.	PASS	Atlas-SNP
MKKS	8195	hgsc.bcm.edu	hg19	20	10393727	10393727	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	MKKS	NM_170784	exon3	c.A436C	p.S146R	GAGTACTACTAAA	.	53.0	24.0	62.0	0.0	.	35	.	.	.	none	.	.	PASS	Atlas-SNP
ISM1	140862	hgsc.bcm.edu	hg19	20	13273028	13273028	+	Silent	SNP	A	A	G	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ISM1	NM_080826	exon5	c.A795G	p.E265E	AATTGAAGACACT	.	67.0	27.0	91.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
PLXNB2	23654	hgsc.bcm.edu	hg19	22	50721158	50721158	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	PLXNB2,NS,carcinoma,0,1	PLXNB2	NM_012401	exon18	c.C2969T	p.P990L	CGTAGCGGCTCGA	.	121.0	57.0	111.0	0.0	.	172	.	.	.	none	.	.	PASS	Atlas-SNP
MAGIX	79917	hgsc.bcm.edu	hg19	X	49022721	49022721	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	MAGIX	NM_024859	exon6	c.G988A	p.G330R	GCAGCCGGAAGGC	.	57.0	10.0	77.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
GABRQ	55879	hgsc.bcm.edu	hg19	X	151821371	151821371	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	GABRQ	NM_018558	exon9	c.G1526A	p.R509H	ATGAGCGCCATGG	.	97.0	81.0	90.0	0.0	.	131	.	.	.	none	.	.	PASS	Atlas-SNP
USP15	9958	hgsc.bcm.edu	hg19	12	62777661	62777667	+	Frame_Shift_Del	DEL	AGCAGCA	AGCAGCA	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	AGCAGCA	AGCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	USP15	NM_001252078	exon10	c.1129_1135del	p.377_379del	.	.	89.0	28.0	88.0	0.0	.	105	.	0.314607	0	none	.	.	PASS	Atlas-Indel,Pindel
ACN9	57001	hgsc.bcm.edu	hg19	7	96810419	96810420	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ACN9	NM_020186	exon2	c.270_271insA	p.L90fs	.	.	924.0	671.0	410.0	0.0	.	19	.	0.72619	0	none	.	.	PASS	Atlas-Indel,Pindel
GABRB3	2562	hgsc.bcm.edu	hg19	15	26793258	26793258	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	GABRB3	NM_021912	exon9	c.1105delT	p.L369X	.	.	55.0	29.0	65.0	0.0	.	338	.	0.527273	0	none	.	.	PASS	Atlas-Indel,Pindel
CYP2J2	1573	hgsc.bcm.edu	hg19	1	60370654	60370654	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	CYP2J2	NM_000775	exon7	c.1081delT	p.Y361fs	.	.	76.0	26.0	89.0	0.0	.	34	.	0.342105	0	none	.	.	PASS	Atlas-Indel,Pindel
IL12RB2	3595	hgsc.bcm.edu	hg19	1	67816591	67816592	+	Frame_Shift_Ins	INS	-	-	TA	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	IL12RB2	NM_001559	exon9	c.1077_1078insTA	p.H359fs	.	.	381.0	144.0	395.0	0.0	.	94	.	0.377953	0	none	.	.	PASS	Atlas-Indel,Pindel
CHP1	11261	hgsc.bcm.edu	hg19	15	41555021	41555022	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	.	NM_007236	exon4	c.289_290insA	p.E97fs	.	.	236.0	84.0	190.0	0.0	.	.	.	0.355932	0	none	.	.	PASS	Atlas-Indel,Pindel
PSG9	5678	hgsc.bcm.edu	hg19	19	43762353	43762353	+	Splice_Site	DEL	C	C	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	PSG9	NM_002784	exon6	c.1243+2G>-	.	.	.	110.0	48.0	73.0	0.0	.	77	.	0.436364	0	none	.	.	PASS	Atlas-Indel,Pindel
MIRLET7BHG	400931	hgsc.bcm.edu	hg19	22	46501743	46501744	+	RNA	DEL	CA	CA	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	.	.	.	.	.	.	.	39.0	16.0	19.0	0.0	.	.	.	0.410256	0	none	.	.	PASS	Atlas-Indel,Pindel
TULP4	56995	hgsc.bcm.edu	hg19	6	158882608	158882629	+	Frame_Shift_Del	DEL	GTGGTGCACACAGGGGGACTTG	GTGGTGCACACAGGGGGACTTG	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GTGGTGCACACAGGGGGACTTG	GTGGTGCACACAGGGGGACTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	TULP4	NM_001007466	exon6	c.872_893del	p.291_298del	.	.	41.0	15.0	46.0	0.0	.	137	.	0.365854	0	none	.	.	PASS	Atlas-Indel,Pindel
ARHGEF40	55701	hgsc.bcm.edu	hg19	14	21543506	21543506	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ARHGEF40	NM_018071	exon4	c.1465delG	p.E489fs	.	.	128.0	52.0	120.0	0.0	.	84	.	0.40625	0	none	.	.	PASS	Atlas-Indel,Pindel
CUBN	8029	hgsc.bcm.edu	hg19	10	17113553	17113554	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	CUBN,NS,carcinoma,0,1	CUBN	NM_001081	exon19	c.2497_2498insT	p.P833fs	.	.	42.0	11.0	62.0	0.0	.	515	.	0.261905	0	none	.	.	PASS	Atlas-Indel,Pindel
CALCR	799	hgsc.bcm.edu	hg19	7	93090259	93090259	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	CALCR	NM_001164737	exon10	c.625delA	p.S209fs	.	.	168.0	26.0	108.0	0.0	.	200	.	0.154762	0	none	.	.	PASS	Atlas-INDEL
ZNF423	23090	hgsc.bcm.edu	hg19	16	49672690	49672690	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ZNF423	NM_015069	exon4	c.374delT	p.L125fs	.	.	60.0	22.0	59.0	0.0	.	463	.	0.366667	0	none	.	.	PASS	Atlas-INDEL
ZNF423	23090	hgsc.bcm.edu	hg19	16	49672693	49672695	+	In_Frame_Del	DEL	CAC	CAC	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ZNF423	NM_015069	exon4	c.369_371del	p.123_124del	.	.	58.0	22.0	56.0	0.0	.	463	.	0.37931	0	none	.	.	PASS	Atlas-INDEL
CALCR	799	hgsc.bcm.edu	hg19	7	93090262	93090267	+	Splice_Site	DEL	GGAAGA	GGAAGA	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GGAAGA	GGAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	CALCR	.	.	.	.	.	.	161.0	25.0	108.0	0.0	.	200	.	0.15528	0	none	.	.	PASS	Atlas-INDEL
TRIM13	10206	hgsc.bcm.edu	hg19	13	50588476	50588477	+	RNA	INS	-	-	T	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	TRIM13	.	.	.	.	.	.	28.0	13.0	26.0	0.0	.	30	.	0.464286	0	none	.	.	PASS	Atlas-INDEL
TNRC18	84629	hgsc.bcm.edu	hg19	7	5352473	5352476	+	Frame_Shift_Del	DEL	ATCG	ATCG	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	ATCG	ATCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	TNRC18	NM_001080495	exon27	c.8047_8050del	p.2683_2684del	.	.	101.0	47.0	83.0	0.0	.	311	.	0.465347	0	none	.	.	PASS	Atlas-Indel,Pindel
CALCR	799	hgsc.bcm.edu	hg19	7	93090260	93090267	+	Frame_Shift_Del	DEL	CTGGAAGA	CTGGAAGA	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CTGGAAGA	CTGGAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.,2	CALCR	NM_001164737	exon10	c.624_624del	p.208_208del	.	.	163.0	23.0	107.0	0.0	.	200	.	0.141	.	none	.	.	PASS	Pindel
NOTCH3	4854	hgsc.bcm.edu	hg19	19	15288556	15288567	+	In_Frame_Del	DEL	TGGCCTGGCAGG	TGGCCTGGCAGG	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	TGGCCTGGCAGG	TGGCCTGGCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	NOTCH3	NM_000435	exon24	c.4173_4184del	p.1391_1395del	.	.	94.0	21.0	97.0	0.0	.	340	.	0.223	.	none	.	.	PASS	Pindel
ZNF423	23090	hgsc.bcm.edu	hg19	16	49672691	49672695	+	Frame_Shift_Del	DEL	GTCAC	GTCAC	-	novel		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GTCAC	GTCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	.	ZNF423	NM_015069	exon4	c.369_373del	p.123_125del	.	.	60.0	20.0	58.0	0.0	.	463	.	0.333	.	none	.	.	PASS	Pindel
