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
TMEM201	199953	hgsc.bcm.edu	hg19	1	9658629	9658629	+	Silent	SNP	C	C	G	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	TMEM201	NM_001010866	exon4	c.C552G	p.A184A	GCGCGCCCTGTTG	.	241.0	82.0	241.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
KIF1B	23095	hgsc.bcm.edu	hg19	1	10420986	10420986	+	Splice_Site	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	KIF1B	NM_015074	exon37	c.3918-1G>A	.	ACCTTAGGACCTT	.	126.0	7.0	104.0	0.0	.	242	.	.	.	none	.	.	PASS	Atlas-SNP
TMEM39B	55116	hgsc.bcm.edu	hg19	1	32560492	32560492	+	Silent	SNP	C	C	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	TMEM39B	NM_018056	exon7	c.C1035T	p.D345D	CTGTGACCTGCTG	.	46.0	17.0	46.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
ALX3	257	hgsc.bcm.edu	hg19	1	110607426	110607426	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ALX3	NM_006492	exon2	c.G377T	p.G126V	CAGGGGCCTGGGG	.	135.0	49.0	165.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
ASH1L	55870	hgsc.bcm.edu	hg19	1	155308132	155308132	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ASH1L	NM_018489	exon27	c.C8551T	p.Q2851X	CCTCCTGGCCCAA	.	124.0	15.0	97.0	0.0	.	279	.	.	.	none	.	.	PASS	Atlas-SNP
CFHR4	10877	hgsc.bcm.edu	hg19	1	196879470	196879470	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	CFHR4	NM_001201550	exon6	c.C859T	p.R287C	AATACGCGTAGAC	.	220.0	90.0	227.0	0.0	.	141	.	.	.	none	.	.	PASS	Atlas-SNP
CTSE	1510	hgsc.bcm.edu	hg19	1	206318340	206318340	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	CTSE	NM_001910	exon2	c.A98T	p.K33M	CCCTCAAGAAGAA	.	53.0	21.0	99.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	hg19	2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ALMS1	NM_015120	exon1	c.G40C	p.E14Q	CTGGAGGAGGAGG	.	237.0	13.0	202.0	0.0	.	384	.	.	.	none	.	.	PASS	Atlas-SNP
ALMS1	7840	hgsc.bcm.edu	hg19	2	73613037	73613037	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ALMS1	NM_015120	exon1	c.A41T	p.E14V	TGGAGGAGGAGGA	.	239.0	19.0	200.0	0.0	.	384	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC142	84865	hgsc.bcm.edu	hg19	2	74707970	74707970	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	CCDC142	NM_032779	exon5	c.T1408G	p.S470A	CCTCTGAGGCCAG	.	112.0	40.0	114.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
TGOLN2	10618	hgsc.bcm.edu	hg19	2	85554322	85554322	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	TGOLN2	NM_001206841	exon2	c.T533A	p.V178D	TTAGGGACATCTT	.	85.0	38.0	92.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
ACTR3	10096	hgsc.bcm.edu	hg19	2	114670788	114670788	+	Silent	SNP	G	G	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ACTR3	NM_005721	exon2	c.T84T	p.Y28Y	ACCACAGTTTATC	.	288.0	99.0	315.0	1.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
OLA1	29789	hgsc.bcm.edu	hg19	2	174987981	174987981	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	OLA1	NM_013341	exon7	c.T655G	p.F219V	TCAAAAATAAGTG	.	33.0	8.0	46.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
MYO1B	4430	hgsc.bcm.edu	hg19	2	192227007	192227007	+	Silent	SNP	T	T	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	MYO1B	NM_012223	exon9	c.T675C	p.L225L	TAAGCTTGAGAGG	.	126.0	47.0	143.0	0.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
WNT7A	7476	hgsc.bcm.edu	hg19	3	13860792	13860792	+	Silent	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	WNT7A	NM_004625	exon4	c.C699T	p.N233N	GGCCTCGTTGTAC	.	120.0	47.0	73.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
ARGFX	503582	hgsc.bcm.edu	hg19	3	121289566	121289566	+	Silent	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ARGFX	NM_001012659	exon2	c.G6A	p.R2R	CATGAGGAACAGA	.	404.0	240.0	302.0	1.0	.	36	.	.	.	none	.	.	PASS	Atlas-SNP
SI	6476	hgsc.bcm.edu	hg19	3	164783068	164783068	+	Missense_Mutation	SNP	C	C	T	rs143135955		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	SI	NM_001041	exon7	c.G788A	p.R263Q	TGGTCTCGAGTAA	.	257.0	139.0	221.0	0.0	.	500	.	.	.	weak	C|1.000;T|0.000	0.000	PASS	Atlas-SNP
SEC24D	9871	hgsc.bcm.edu	hg19	4	119674015	119674015	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	SEC24D	NM_014822	exon12	c.C1450G	p.R484G	CCACTCGAATTGC	.	119.0	49.0	117.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
UFSP2	55325	hgsc.bcm.edu	hg19	4	186324652	186324652	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	UFSP2	NM_018359	exon11	c.A1319G	p.E440G	ACCTTTTCCAAAA	.	65.0	31.0	88.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRA2	57763	hgsc.bcm.edu	hg19	5	72857114	72857114	+	Splice_Site	SNP	C	C	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ANKRA2	NM_023039	exon4	c.290-1G>A	.	ATTCAGCTAAGTG	.	80.0	29.0	85.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD34B	340120	hgsc.bcm.edu	hg19	5	79854309	79854309	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ANKRD34B	NM_001004441	exon5	c.A1530C	p.Q510H	TACTAATTGCTTA	.	89.0	35.0	58.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
PARK2	5071	hgsc.bcm.edu	hg19	6	162864397	162864397	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PARK2	NM_004562	exon2	c.A116T	p.D39V	AACTGGTCAGCCG	.	65.0	28.0	79.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
PARK2	5071	hgsc.bcm.edu	hg19	6	162864398	162864398	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PARK2	NM_004562	exon2	c.G115A	p.D39N	ACTGGTCAGCCGG	.	66.0	27.0	79.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
DBNL	28988	hgsc.bcm.edu	hg19	7	44091488	44091488	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	DBNL	NM_001122956	exon3	c.T199A	p.C67S	GCCTTCTGCAGAG	.	80.0	47.0	95.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
TNS3	64759	hgsc.bcm.edu	hg19	7	47342974	47342974	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	TNS3	NM_022748	exon22	c.C3031G	p.L1011V	GCGCCAGGGAGTC	.	102.0	49.0	136.0	0.0	.	140	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA13	154664	hgsc.bcm.edu	hg19	7	48390271	48390271	+	Silent	SNP	A	A	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ABCA13	NM_152701	exon30	c.A10236T	p.A3412A	CCATGCAGGCGCT	.	80.0	36.0	107.0	0.0	.	1192	.	.	.	none	.	.	PASS	Atlas-SNP
PPP2CB	5516	hgsc.bcm.edu	hg19	8	30651547	30651547	+	Silent	SNP	T	T	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PPP2CB	NM_001009552	exon5	c.A624T	p.G208G	ACCCCATCCACCA	.	333.0	32.0	323.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
PLEKHF2	79666	hgsc.bcm.edu	hg19	8	96167020	96167020	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PLEKHF2	NM_024613	exon2	c.T748A	p.X250K	AGTGACTAAGGAC	.	83.0	12.0	93.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
PLEC	5339	hgsc.bcm.edu	hg19	8	144997632	144997632	+	Silent	SNP	C	C	G	rs376957701	alternate_allele	TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PLEC	NM_201380	exon31	c.G6876C	p.A2292A	CAGGGCCGCCTGC	.	182.0	76.0	234.0	0.0	.	1144	.	.	.	alt	.	.	PASS	Atlas-SNP
FGD3	89846	hgsc.bcm.edu	hg19	9	95784642	95784642	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	FGD3	NM_001083536	exon14	c.A1528G	p.T510A	GTGGTGACCACCG	.	32.0	13.0	44.0	0.0	.	116	.	.	.	none	.	.	PASS	Atlas-SNP
ANKS6	203286	hgsc.bcm.edu	hg19	9	101546300	101546300	+	Silent	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ANKS6	NM_173551	exon4	c.C1047T	p.H349H	ATCCGCGTGCCTC	.	37.0	15.0	26.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
ANKS6	203286	hgsc.bcm.edu	hg19	9	101552742	101552742	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ANKS6	NM_173551	exon2	c.T506C	p.F169S	TCCACAAAGGCAC	.	167.0	65.0	160.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC8A	56262	hgsc.bcm.edu	hg19	9	131669737	131669737	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	LRRC8A	NM_001127244	exon3	c.G294C	p.K98N	CATCAAGTATGAC	.	44.0	22.0	50.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
LRRC8A	56262	hgsc.bcm.edu	hg19	9	131669746	131669746	+	Silent	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	LRRC8A	NM_001127244	exon3	c.G303A	p.L101L	TGACCTGGACCGG	.	42.0	20.0	53.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
LCN15	389812	hgsc.bcm.edu	hg19	9	139656704	139656704	+	Silent	SNP	G	G	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	LCN15	NM_203347	exon5	c.C456G	p.S152S	CTGGAAGGACTTC	.	234.0	105.0	243.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
LCN15	389812	hgsc.bcm.edu	hg19	9	139656705	139656705	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	LCN15	NM_203347	exon5	c.C455G	p.S152C	TGGAAGGACTTCA	.	231.0	103.0	242.0	0.0	.	11	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF195	7748	hgsc.bcm.edu	hg19	11	3380399	3380399	+	Silent	SNP	T	T	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ZNF195	NM_001130520	exon6	c.A1839G	p.K613K	GAAGGCTTTGCCA	.	68.0	34.0	87.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
SMPD1	6609	hgsc.bcm.edu	hg19	11	6411960	6411960	+	Silent	SNP	G	G	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	SMPD1	NM_000543	exon1	c.G132T	p.A44A	GCTGGCGCTGGCG	.	87.0	6.0	125.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
NDUFS8	4728	hgsc.bcm.edu	hg19	11	67800585	67800585	+	Silent	SNP	C	C	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	NDUFS8	NM_002496	exon5	c.C207A	p.G69G	CCTGGGCATGACC	.	144.0	55.0	152.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
CCDC81	60494	hgsc.bcm.edu	hg19	11	86125892	86125892	+	Silent	SNP	A	A	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	CCDC81	NM_001156474	exon12	c.A1453C	p.R485R	TACAAGAGAGCTT	.	181.0	67.0	123.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
PRICKLE1	144165	hgsc.bcm.edu	hg19	12	42854000	42854000	+	Silent	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PRICKLE1	NM_001144882	exon8	c.C2107T	p.L703L	TGTACAGCCGCAG	.	111.0	49.0	113.0	0.0	.	105	.	.	.	none	.	.	PASS	Atlas-SNP
HOXC8	3224	hgsc.bcm.edu	hg19	12	54403214	54403214	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	HOXC8	NM_022658	exon1	c.T146A	p.F49Y	CCGGCTTCCAGCA	.	78.0	30.0	111.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
BRCA2	675	hgsc.bcm.edu	hg19	13	32907282	32907282	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	BRCA2	NM_000059	exon10	c.A1667G	p.N556S	GTCCAAATTTAAT	.	251.0	104.0	317.0	0.0	.	812	.	.	.	none	.	.	PASS	Atlas-SNP
SNW1	22938	hgsc.bcm.edu	hg19	14	78184510	78184510	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	SNW1	NM_012245	exon14	c.A1532G	p.H511R	CCACCATGCTGTT	.	88.0	34.0	113.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
PML	5371	hgsc.bcm.edu	hg19	15	74315345	74315345	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PML	NM_033250	exon3	c.A779C	p.Q260P	ACGCGCAGATGCA	.	48.0	14.0	37.0	0.0	.	169	.	.	.	none	.	.	PASS	Atlas-SNP
PDXDC1	23042	hgsc.bcm.edu	hg19	16	15110996	15110996	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PDXDC1	NM_015027	exon10	c.G832A	p.A278T	ACATTGGCTCTGG	.	142.0	40.0	111.0	0.0	.	59	.	.	.	none	.	.	PASS	Atlas-SNP
GLG1	2734	hgsc.bcm.edu	hg19	16	74491772	74491772	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	GLG1	NM_001145667	exon24	c.C3265T	p.Q1089X	ACTTACGACGCCC	.	108.0	66.0	103.0	0.0	.	106	.	.	.	none	.	.	PASS	Atlas-SNP
PLCG2	5336	hgsc.bcm.edu	hg19	16	81965133	81965133	+	Silent	SNP	C	C	G	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PLCG2	NM_002661	exon25	c.C2613G	p.S871S	GAAGTCCTTTGTC	.	118.0	8.0	100.0	0.0	.	276	.	.	.	none	.	.	PASS	Atlas-SNP
GPATCH8	23131	hgsc.bcm.edu	hg19	17	42476063	42476063	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	GPATCH8	NM_001002909	exon8	c.C3382T	p.Q1128X	AACCTTGTGGGGG	.	59.0	28.0	67.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
MYL4	4635	hgsc.bcm.edu	hg19	17	45299172	45299172	+	Silent	SNP	C	C	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	MYL4	NM_001002841	exon5	c.C438T	p.S146S	GGAGAGCAATGGC	.	58.0	18.0	62.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
BPTF	2186	hgsc.bcm.edu	hg19	17	65916183	65916183	+	Silent	SNP	T	T	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	BPTF	NM_004459	exon15	c.T5859C	p.V1953V	AGATGTTGGTCCT	.	75.0	25.0	89.0	0.0	.	415	.	.	.	none	.	.	PASS	Atlas-SNP
UBE2O	63893	hgsc.bcm.edu	hg19	17	74449137	74449137	+	Silent	SNP	G	G	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	UBE2O	NM_022066	exon1	c.C87T	p.A29A	GGCTGCGGCTGGG	.	48.0	23.0	53.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
SH2D3A	10045	hgsc.bcm.edu	hg19	19	6760717	6760717	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	SH2D3A	NM_005490	exon3	c.G351T	p.Q117H	AGGCCCCTGCCAA	.	72.0	28.0	98.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
HSD17B14	51171	hgsc.bcm.edu	hg19	19	49316726	49316726	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	HSD17B14	NM_016246	exon8	c.G626C	p.G209A	AGCATGCCCTCTC	.	67.0	20.0	64.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF836	162962	hgsc.bcm.edu	hg19	19	52663822	52663822	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	ZNF836	NM_001102657	exon4	c.T38A	p.V13E	ATGGCTACATCCC	.	48.0	15.0	71.0	0.0	.	158	.	.	.	none	.	.	PASS	Atlas-SNP
C20orf26	26074	hgsc.bcm.edu	hg19	20	20226857	20226857	+	Silent	SNP	C	C	T	rs114266049	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	C20orf26	NM_015585	exon19	c.C2157T	p.S719S	AGCCAGCGAGTAT	.	215.0	66.0	205.0	0.0	.	188	.	.	.	alt	C|0.994;A|0.006	.	PASS	Atlas-SNP
PPIL2	23759	hgsc.bcm.edu	hg19	22	22024222	22024222	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	PPIL2	NM_014337	exon2	c.A53T	p.Y18F	CTGAATACACTCA	.	76.0	39.0	82.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
DENND1C	79958	hgsc.bcm.edu	hg19	19	6468935	6468936	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	DENND1C	NM_024898	exon20	c.1437_1438insG	p.G479fs	.	.	56.0	20.0	47.0	0.0	.	93	.	0.357143	0	none	.	.	PASS	Atlas-Indel,Pindel
TCHH	7062	hgsc.bcm.edu	hg19	1	152084184	152084185	+	In_Frame_Ins	INS	-	-	CGCCTCTCCTGCTGCTCG	novel		TCGA-P4-AAVM-01A-11D-A42J-10	TCGA-P4-AAVM-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	1c5d3340-513d-4576-8298-848fee2f3edc	2e812561-7f51-41c5-bdb3-4861f646b630	.	TCHH	NM_007113	exon3	c.1509_1510insCGAGCAGCAGGAGAGGCG	p.R503delinsREQQERR	.	.	25.0	10.0	27.0	0.0	.	275	.	0.4	0	none	.	.	PASS	Atlas-INDEL