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
RERE	473	hgsc.bcm.edu	hg19	1	8419867	8419867	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	RERE,NS,carcinoma,-1,1	RERE	NM_012102	exon20	c.G3575A	p.R1192Q	CGCTCCCGCTCCT	.	46.0	4.0	15.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
RERE	473	hgsc.bcm.edu	hg19	1	8419868	8419868	+	Silent	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	RERE,NS,carcinoma,0,1	RERE	NM_012102	exon20	c.C3574A	p.R1192R	GCTCCCGCTCCTT	.	45.0	4.0	15.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
NSUN4	387338	hgsc.bcm.edu	hg19	1	46818626	46818626	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	NSUN4	NM_199044	exon4	c.G679T	p.D227Y	ATCAGGGATGGAA	.	95.0	4.0	53.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
CLCA1	1179	hgsc.bcm.edu	hg19	1	86934706	86934706	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	CLCA1	NM_001285	exon1	c.G52A	p.G18R	CTAGAAGGGGCCC	.	87.0	41.0	68.0	0.0	.	109	.	.	.	none	.	.	PASS	Atlas-SNP
LCE1C	353133	hgsc.bcm.edu	hg19	1	152777877	152777877	+	Silent	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	LCE1C	NM_178351	exon2	c.C78T	p.T26T	CTTTGGGGTGGGG	.	198.0	18.0	50.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
SPRR2D	6703	hgsc.bcm.edu	hg19	1	153012642	153012642	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	SPRR2D	NM_006945	exon2	c.C181A	p.P61T	AGGGTGGGGAAGG	.	342.0	16.0	93.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
DUSP23	54935	hgsc.bcm.edu	hg19	1	159751066	159751066	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	DUSP23	NM_017823	exon2	c.A176T	p.H59L	CCCTGCACCGCCT	.	183.0	78.0	3.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
NFASC	23114	hgsc.bcm.edu	hg19	1	204985554	204985554	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	NFASC	NM_001005388	exon30	c.G3610T	p.E1204X	TTCAATGAAGACG	.	310.0	34.0	89.0	0.0	.	396	.	.	.	none	.	.	PASS	Atlas-SNP
NRXN1	9378	hgsc.bcm.edu	hg19	2	50850682	50850682	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	NRXN1	NM_001135659	exon7	c.C1003A	p.Q335K	TGCTTTGAATGGG	.	79.0	34.0	66.0	0.0	.	1118	.	.	.	none	.	.	PASS	Atlas-SNP
C2orf81	388963	hgsc.bcm.edu	hg19	2	74642235	74642235	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	C2orf81	NM_001145054	exon4	c.G988A	p.D330N	GCACATCCGAGTG	.	95.0	50.0	2.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
SPOPL	339745	hgsc.bcm.edu	hg19	2	139322375	139322375	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	SPOPL	NM_001001664	exon9	c.A935G	p.H312R	ATTTGCACAGTGC	.	176.0	29.0	80.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
SCN9A	6335	hgsc.bcm.edu	hg19	2	167055820	167055820	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	SCN9A	NM_002977	exon27	c.G5296A	p.D1766N	AGTCATCCTCACT	.	189.0	10.0	142.0	0.0	.	296	.	.	.	none	.	.	PASS	Atlas-SNP
GIGYF2	26058	hgsc.bcm.edu	hg19	2	233671361	233671361	+	Silent	SNP	T	T	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	GIGYF2	NM_001103147	exon17	c.T1863A	p.P621P	CCCTCCTCATATG	.	54.0	35.0	39.0	0.0	.	288	.	.	.	none	.	.	PASS	Atlas-SNP
IQCA1	79781	hgsc.bcm.edu	hg19	2	237272540	237272540	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	IQCA1_ENST00000409907,NS,carcinoma,0,2	IQCA1	NM_001270585	exon15	c.G1776A	p.L592L	ATGGACCAGCATT	.	187.0	100.0	94.0	1.0	.	170	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRG	5793	hgsc.bcm.edu	hg19	3	62189090	62189090	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PTPRG	NM_002841	exon12	c.G1621C	p.A541P	CCGACGGCCGCCT	.	99.0	67.0	32.0	0.0	.	153	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	hg19	3	113376122	113376122	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	KIAA2018	NM_001009899	exon7	c.G4407A	p.Q1469Q	CTGCTGCTGCTGC	.	98.0	17.0	24.0	0.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA2018	205717	hgsc.bcm.edu	hg19	3	113376128	113376128	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	KIAA2018	NM_001009899	exon7	c.G4401A	p.Q1467Q	CTGCTGCTGCTGC	.	93.0	22.0	21.0	0.0	.	180	.	.	.	none	.	.	PASS	Atlas-SNP
ROPN1B	152015	hgsc.bcm.edu	hg19	3	125690910	125690910	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ROPN1B	NM_001012337	exon2	c.G13T	p.D5Y	CAGACAGATAAGC	.	86.0	26.0	30.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
PPP2R3A	5523	hgsc.bcm.edu	hg19	3	135825108	135825108	+	Silent	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PPP2R3A	NM_002718	exon13	c.T3273C	p.A1091A	TGCCGCTGAGGAG	.	126.0	41.0	69.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
MFSD1	64747	hgsc.bcm.edu	hg19	3	158519842	158519842	+	Silent	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	MFSD1	NM_022736	exon1	c.G48A	p.R16R	CTCCCGGAGTCAT	.	15.0	9.0	0.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
YEATS2	55689	hgsc.bcm.edu	hg19	3	183525842	183525842	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	YEATS2	NM_018023	exon29	c.G4036T	p.A1346S	CCCGTGGCACTCC	.	140.0	6.0	42.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
DGKG	1608	hgsc.bcm.edu	hg19	3	185960324	185960324	+	Nonsense_Mutation	SNP	T	T	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	DGKG	NM_001346	exon20	c.A1795T	p.R599X	TCTCTCTCATCAC	.	111.0	31.0	27.0	0.0	.	98	.	.	.	none	.	.	PASS	Atlas-SNP
PPP2R2C	5522	hgsc.bcm.edu	hg19	4	6335365	6335365	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PPP2R2C	NM_181876	exon7	c.A884G	p.Y295C	AGCATGTAGCGGC	.	128.0	77.0	59.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
ATP10D	57205	hgsc.bcm.edu	hg19	4	47593174	47593174	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ATP10D	NM_020453	exon23	c.G4057T	p.A1353S	AGAGGGGCTGGAA	.	90.0	4.0	77.0	0.0	.	168	.	.	.	none	.	.	PASS	Atlas-SNP
DSPP	1834	hgsc.bcm.edu	hg19	4	88536436	88536436	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	DSPP	NM_014208	exon5	c.C2622T	p.S874S	CAGCAGCAACAGC	.	371.0	30.0	131.0	0.0	.	174	.	.	.	none	.	.	PASS	Atlas-SNP
TLX3	30012	hgsc.bcm.edu	hg19	5	170736390	170736390	+	Silent	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	TLX3	NM_021025	exon1	c.G21A	p.A7A	CAGCGCGCAGACC	.	45.0	21.0	0.0	0.0	.	23	.	.	.	none	.	.	PASS	Atlas-SNP
OR10C1	442194	hgsc.bcm.edu	hg19	6	29408232	29408232	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	OR10C1	NM_013941	exon1	c.C440T	p.A147V	GGTCGGCGTGGGC	.	61.0	4.0	26.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
HLA-C	3107	hgsc.bcm.edu	hg19	6	31239552	31239552	+	Missense_Mutation	SNP	T	T	A	rs41545521	alternate_allele	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	NM_002117	exon2	c.A167T	p.Q56L	ACGAACTGCGTGT	.	174.0	11.0	14.0	1.0	.	92	.	.	.	alt	.	.	PASS	Atlas-SNP
CD2AP	23607	hgsc.bcm.edu	hg19	6	47471115	47471115	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	CD2AP,NS,carcinoma,0,1	CD2AP	NM_012120	exon2	c.A104T	p.E35V	AGGAGGAAGGGTG	.	384.0	30.0	51.0	0.0	.	43	.	.	.	none	.	.	PASS	Atlas-SNP
PTCHD4	442213	hgsc.bcm.edu	hg19	6	48036108	48036108	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	.	NM_001013732	exon1	c.A284G	p.D95G	GACTGGTCCAGGG	.	377.0	19.0	41.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF451	26036	hgsc.bcm.edu	hg19	6	56989656	56989656	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ZNF451	NM_001031623	exon4	c.G311A	p.R104K	CATTCAGAGTATG	.	253.0	16.0	102.0	0.0	.	181	.	.	.	none	.	.	PASS	Atlas-SNP
PHF3	23469	hgsc.bcm.edu	hg19	6	64394128	64394128	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PHF3	NM_015153	exon3	c.G505A	p.A169T	TCTACTGCTAAAG	.	233.0	92.0	139.0	0.0	.	191	.	.	.	none	.	.	PASS	Atlas-SNP
UNC93A	54346	hgsc.bcm.edu	hg19	6	167709627	167709627	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	UNC93A	NM_018974	exon3	c.C377T	p.A126V	AGAAGGCGGGAAA	.	270.0	109.0	105.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
TRA2A	29896	hgsc.bcm.edu	hg19	7	23547073	23547073	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	TRA2A	NM_013293	exon5	c.C607T	p.P203S	GTGTTGGTGTGTG	.	102.0	37.0	40.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
ARPC1B	10095	hgsc.bcm.edu	hg19	7	98990335	98990335	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ARPC1B	NM_005720	exon8	c.C825T	p.A275A	CGCCGCCGCGGGG	.	147.0	84.0	5.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
OPN1SW	611	hgsc.bcm.edu	hg19	7	128415147	128415147	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	OPN1SW	NM_001708	exon2	c.G414A	p.K138K	GAAGGGCTTACAG	.	197.0	54.0	62.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
AGAP3	116988	hgsc.bcm.edu	hg19	7	150839014	150839014	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	AGAP3	NM_031946	exon14	c.G1834A	p.V612M	GTGGTGGTGTCCC	.	327.0	124.0	88.0	0.0	.	121	.	.	.	none	.	.	PASS	Atlas-SNP
RHEB	6009	hgsc.bcm.edu	hg19	7	151188050	151188050	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	RHEB,NS,carcinoma,0,3	RHEB	NM_005614	exon2	c.T103A	p.Y35N	GATCGTAGGAGTC	.	87.0	5.0	48.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
TRAPPC9	83696	hgsc.bcm.edu	hg19	8	140744445	140744445	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	TRAPPC9	NM_031466	exon22	c.A3350C	p.D1117A	AGCACATCTGTAA	.	27.0	12.0	0.0	0.0	.	114	.	.	.	none	.	.	PASS	Atlas-SNP
FRMPD1	22844	hgsc.bcm.edu	hg19	9	37745145	37745145	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	FRMPD1	NM_014907	exon16	c.G3116A	p.G1039E	CTCAAGGAGACAC	.	47.0	18.0	33.0	0.0	.	237	.	.	.	none	.	.	PASS	Atlas-SNP
PRKACG	5568	hgsc.bcm.edu	hg19	9	71628295	71628295	+	Silent	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PRKACG	NM_002732	exon1	c.C714T	p.P238P	GTAGAAGGGTGGG	.	96.0	34.0	35.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
NIPSNAP3A	25934	hgsc.bcm.edu	hg19	9	107521616	107521616	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	NIPSNAP3A	NM_015469	exon6	c.A741C	p.K247N	ACTGAAATAGTTT	.	85.0	24.0	63.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
SVEP1	79987	hgsc.bcm.edu	hg19	9	113233740	113233740	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	SVEP1	NM_153366	exon16	c.G2902T	p.A968S	CTGATGCAAGCTG	.	152.0	16.0	88.0	0.0	.	326	.	.	.	none	.	.	PASS	Atlas-SNP
SDCCAG3	10807	hgsc.bcm.edu	hg19	9	139302279	139302279	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	SDCCAG3	NM_001039707	exon4	c.A401C	p.K134T	TTTACCTTTGCAT	.	43.0	11.0	28.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
CUL2	8453	hgsc.bcm.edu	hg19	10	35360197	35360197	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	CUL2	NM_001198778	exon2	c.C106G	p.L36V	TCAAAAGTTTGTT	.	173.0	41.0	116.0	0.0	.	63	.	.	.	none	.	.	PASS	Atlas-SNP
TET1	80312	hgsc.bcm.edu	hg19	10	70404893	70404893	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	TET1_ENST00000373644,NS,carcinoma,0,1	TET1	NM_030625	exon4	c.G2407T	p.A803S	AAAAACGCTATGA	.	84.0	10.0	102.0	0.0	.	255	.	.	.	none	.	.	PASS	Atlas-SNP
C10orf129	142827	hgsc.bcm.edu	hg19	10	96967018	96967018	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	C10orf129_ENST00000341686,NS,carcinoma,0,1	C10orf129	NM_207321	exon4	c.C457A	p.Q153K	CGCTATCAATTAC	.	94.0	20.0	53.0	0.0	.	52	.	.	.	none	.	.	PASS	Atlas-SNP
PDZD7	79955	hgsc.bcm.edu	hg19	10	102783355	102783355	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PDZD7	NM_001195263	exon4	c.T380C	p.L127P	ACGCACAGGCCAG	.	31.0	13.0	13.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
MUC2	4583	hgsc.bcm.edu	hg19	11	1078339	1078339	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	MUC2	NM_002457	exon5	c.C626T	p.P209L	AGGATCCCGAGGA	.	224.0	60.0	73.0	0.0	.	614	.	.	.	none	.	.	PASS	Atlas-SNP
OR10A2	341276	hgsc.bcm.edu	hg19	11	6891503	6891503	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	OR10A2,right_upper_lobe,carcinoma,0,1	OR10A2	NM_001004460	exon1	c.G518A	p.R173K	TGCTGAGGCTGGT	.	248.0	12.0	87.0	1.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
PDE3B	5140	hgsc.bcm.edu	hg19	11	14666027	14666027	+	Missense_Mutation	SNP	C	C	G	rs373522381	alternate_allele	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PDE3B	NM_000922	exon1	c.C406G	p.L136V	TGCTTCCTCACCC	.	146.0	52.0	10.0	0.0	.	98	.	.	.	alt	.	.	PASS	Atlas-SNP
OR4X1	390113	hgsc.bcm.edu	hg19	11	48285602	48285602	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	OR4X1	NM_001004726	exon1	c.T190G	p.L64V	AGCTACTTATCCT	.	156.0	18.0	66.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
MLL	4297	hgsc.bcm.edu	hg19	11	118373932	118373932	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	MLL	NM_001197104	exon27	c.A7325C	p.E2442A	TCAAAGAAAAGCA	.	87.0	34.0	96.0	0.0	.	548	.	.	.	none	.	.	PASS	Atlas-SNP
SCNN1A	6337	hgsc.bcm.edu	hg19	12	6457064	6457064	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	SCNN1A	NM_001159576	exon12	c.C2162T	p.S721F	CAGGTGGAGGAAC	.	95.0	31.0	34.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
KLRC4-KLRK1	0	hgsc.bcm.edu	hg19	12	10539523	10539523	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	.	NM_001199805	exon8	c.A127G	p.K43E	TGCTTTTGACTAC	.	85.0	32.0	47.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PTPRO	5800	hgsc.bcm.edu	hg19	12	15673198	15673198	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PTPRO	NM_002848	exon10	c.G1843A	p.D615N	TGGGGAGATCCAG	.	262.0	78.0	96.0	0.0	.	148	.	.	.	none	.	.	PASS	Atlas-SNP
DDN	23109	hgsc.bcm.edu	hg19	12	49391677	49391677	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	DDN	NM_015086	exon2	c.G982A	p.G328S	CGCTACCACTGTT	.	53.0	11.0	20.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
FAM216A	29902	hgsc.bcm.edu	hg19	12	110906786	110906786	+	Missense_Mutation	SNP	C	C	T	rs202079205	bycluster	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	.	NM_013300	exon1	c.C106T	p.P36S	GCAGAGCCGCCCG	.	25.0	12.0	1.0	0.0	.	.	.	.	.	weak	.	.	PASS	Atlas-SNP
RAD9B	144715	hgsc.bcm.edu	hg19	12	110969392	110969392	+	Silent	SNP	A	A	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	RAD9B	NM_152442	exon12	c.A1248G	p.K416K	CAGGAAAGAATTT	.	27.0	9.0	12.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
RBM19	9904	hgsc.bcm.edu	hg19	12	114385205	114385205	+	Silent	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	RBM19	NM_001146699	exon11	c.C1341T	p.F447F	GGTGATGAATGCA	.	278.0	64.0	73.0	0.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
BRI3BP	140707	hgsc.bcm.edu	hg19	12	125509640	125509640	+	Silent	SNP	C	C	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	BRI3BP	NM_080626	exon3	c.C420A	p.S140S	CTTGTCCCTGACC	.	85.0	32.0	25.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
N6AMT2	221143	hgsc.bcm.edu	hg19	13	21306119	21306119	+	Silent	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	N6AMT2	NM_174928	exon4	c.A369G	p.P123P	GTCCAATGGATTA	.	82.0	37.0	83.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
FARP1	10160	hgsc.bcm.edu	hg19	13	99092299	99092299	+	Splice_Site	SNP	T	T	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	FARP1	NM_005766	exon22	c.2516+2T>A	.	GCCAGGTAACTCG	.	70.0	13.0	27.0	0.0	.	207	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGEF40	55701	hgsc.bcm.edu	hg19	14	21543565	21543565	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ARHGEF40	NM_018071	exon4	c.G1525C	p.D509H	AAAGGGGACAACA	.	227.0	62.0	108.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
KIAA1737	85457	hgsc.bcm.edu	hg19	14	77580238	77580238	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	KIAA1737,NS,carcinoma,0,1	KIAA1737	NM_033426	exon4	c.C777T	p.F259F	GACCTTCGCTTCC	.	48.0	24.0	26.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
ITPK1	3705	hgsc.bcm.edu	hg19	14	93408017	93408017	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ITPK1	NM_001142593	exon11	c.G1134A	p.A378A	GCCGCCCGCGTCG	.	14.0	12.0	0.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
CASC5	57082	hgsc.bcm.edu	hg19	15	40915310	40915310	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	CASC5	NM_170589	exon11	c.G2926T	p.V976F	AATCATGTTGAAC	.	88.0	21.0	58.0	0.0	.	269	.	.	.	none	.	.	PASS	Atlas-SNP
TGM7	116179	hgsc.bcm.edu	hg19	15	43585144	43585144	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	TGM7	NM_052955	exon3	c.C202A	p.P68T	CTGACGGCTTGGG	.	65.0	14.0	44.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
TGM7	116179	hgsc.bcm.edu	hg19	15	43585145	43585145	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	TGM7	NM_052955	exon3	c.G201A	p.K67K	TGACGGCTTGGGT	.	62.0	14.0	44.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
HDC	3067	hgsc.bcm.edu	hg19	15	50535435	50535435	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	HDC	NM_002112	exon11	c.G1147A	p.E383K	CCATTTCAGTACC	.	155.0	62.0	106.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
MYO5C	55930	hgsc.bcm.edu	hg19	15	52500781	52500781	+	Silent	SNP	G	G	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	MYO5C	NM_018728	exon36	c.C4356A	p.L1452L	GCAATTGAGAAAA	.	108.0	9.0	58.0	0.0	.	162	.	.	.	none	.	.	PASS	Atlas-SNP
CSPG4	1464	hgsc.bcm.edu	hg19	15	75982866	75982866	+	Silent	SNP	G	G	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	CSPG4	NM_001897	exon3	c.C540G	p.L180L	CCGGAGGAGGCTG	.	62.0	20.0	43.0	0.0	.	175	.	.	.	none	.	.	PASS	Atlas-SNP
HMOX2	3163	hgsc.bcm.edu	hg19	16	4557977	4557977	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	HMOX2	NM_001127205	exon4	c.C468T	p.R156R	CACCCGCTACATG	.	216.0	85.0	80.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
LAT	27040	hgsc.bcm.edu	hg19	16	28996234	28996234	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	LAT	NM_001014989	exon1	c.G52A	p.A18T	GGGGGGGCCAGCA	.	91.0	29.0	16.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
PRRT2	112476	hgsc.bcm.edu	hg19	16	29825753	29825753	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PRRT2	NM_001256442	exon3	c.A979C	p.I327L	GTCCTCATCATCA	.	59.0	18.0	18.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	hg19	16	72141342	72141342	+	Missense_Mutation	SNP	G	G	A	rs374391366		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	DHX38	NM_014003	exon20	c.G2704A	p.G902R	TCCCTCGGGGTGC	.	118.0	5.0	25.0	0.0	.	91	.	.	.	weak	.	.	PASS	Atlas-SNP
MYO1D	4642	hgsc.bcm.edu	hg19	17	31098169	31098169	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	MYO1D	NM_015194	exon6	c.T688C	p.Y230H	GAATATAGTTGTA	.	87.0	4.0	64.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
LYZL6	57151	hgsc.bcm.edu	hg19	17	34263772	34263772	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	LYZL6	NM_020426	exon3	c.G364C	p.G122R	TCATCCCCCGTGC	.	115.0	61.0	20.0	0.0	.	18	.	.	.	none	.	.	PASS	Atlas-SNP
KRTAP4-11	653240	hgsc.bcm.edu	hg19	17	39274238	39274238	+	Silent	SNP	A	A	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	KRTAP4-11	NM_033059	exon1	c.T330C	p.C110C	GGGGCGACAGCAG	.	116.0	14.0	27.0	0.0	.	94	.	.	.	none	.	.	PASS	Atlas-SNP
KRTAP4-12	83755	hgsc.bcm.edu	hg19	17	39280069	39280069	+	Silent	SNP	G	G	A	rs374262239		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	KRTAP4-12	NM_031854	exon1	c.C306T	p.R102R	GCTGGGGCGGCAG	.	197.0	20.0	13.0	0.0	.	32	.	.	.	weak	.	.	PASS	Atlas-SNP
KRTAP4-6	81871	hgsc.bcm.edu	hg19	17	39296467	39296467	+	Silent	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	KRTAP4-6	NM_030976	exon1	c.A273G	p.R91R	CTGGGGTCTGCAG	.	131.0	9.0	15.0	0.0	.	46	.	.	.	none	.	.	PASS	Atlas-SNP
TUBG1	7283	hgsc.bcm.edu	hg19	17	40765685	40765685	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	TUBG1,colon,carcinoma,0,1	TUBG1	NM_001070	exon7	c.C627T	p.A209A	CACAGCCCTGAAC	.	200.0	8.0	65.0	0.0	.	25	.	.	.	none	.	.	PASS	Atlas-SNP
SOST	50964	hgsc.bcm.edu	hg19	17	41835944	41835944	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	SOST	NM_025237	exon1	c.A166G	p.M56V	GGTTCATGGTCTT	.	87.0	26.0	22.0	0.0	.	19	.	.	.	none	.	.	PASS	Atlas-SNP
HDAC5	10014	hgsc.bcm.edu	hg19	17	42171119	42171119	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	HDAC5,NS,carcinoma,0,1	HDAC5	NM_001015053	exon4	c.C181T	p.R61W	CCCCCCGTAGCTC	.	156.0	73.0	26.0	0.0	.	67	.	.	.	none	.	.	PASS	Atlas-SNP
RALBP1	10928	hgsc.bcm.edu	hg19	18	9524725	9524725	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	RALBP1,NS,neuroblastoma,0,1	RALBP1	NM_006788	exon5	c.C1187T	p.A396V	CCCAGGCGGGCAT	.	73.0	6.0	64.0	1.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
OR7E24	26648	hgsc.bcm.edu	hg19	19	9362181	9362181	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	OR7E24	NM_001079935	exon1	c.G462C	p.M154I	CATCATGAACCCA	.	124.0	36.0	51.0	0.0	.	48	.	.	.	none	.	.	PASS	Atlas-SNP
MAN2B1	4125	hgsc.bcm.edu	hg19	19	12760979	12760979	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	MAN2B1	NM_000528	exon17	c.C2104T	p.R702C	ACAGGCGAACCAC	.	166.0	8.0	43.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF571	51276	hgsc.bcm.edu	hg19	19	38056037	38056037	+	Silent	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ZNF571	NM_016536	exon4	c.C1293T	p.G431G	TTGTTTGCCACAA	.	34.0	20.0	66.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
GLTSCR1	29998	hgsc.bcm.edu	hg19	19	48183862	48183862	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	GLTSCR1	NM_015711	exon6	c.G1435C	p.A479P	GCCCCGGCGGTCC	.	44.0	12.0	1.0	0.0	.	79	.	.	.	none	.	.	PASS	Atlas-SNP
PRR12	57479	hgsc.bcm.edu	hg19	19	50100554	50100554	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PRR12	NM_020719	exon4	c.G2962A	p.D988N	GCTTATGATCCCT	.	36.0	26.0	0.0	0.0	.	157	.	.	.	none	.	.	PASS	Atlas-SNP
GPR32	2854	hgsc.bcm.edu	hg19	19	51274070	51274070	+	Silent	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	GPR32	NM_001506	exon1	c.T213C	p.R71R	CTTCCGTATGGCA	.	158.0	8.0	57.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
GPR32	2854	hgsc.bcm.edu	hg19	19	51274076	51274076	+	Silent	SNP	A	A	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	GPR32	NM_001506	exon1	c.A219C	p.A73A	TATGGCACGCACG	.	164.0	10.0	55.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
GPR32	2854	hgsc.bcm.edu	hg19	19	51274184	51274184	+	Silent	SNP	C	C	T	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	GPR32	NM_001506	exon1	c.C327T	p.L109L	GCTCCTCGGAGAG	.	129.0	6.0	44.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
LRRN4	164312	hgsc.bcm.edu	hg19	20	6033147	6033147	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	LRRN4	NM_152611	exon2	c.A299G	p.Q100R	TGCAGCTGCTCCA	.	31.0	13.0	0.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
ARFGAP1	55738	hgsc.bcm.edu	hg19	20	61918934	61918934	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ARFGAP1	NM_175609	exon14	c.T954G	p.S318R	CCACAGTTATCAG	.	76.0	26.0	35.0	0.0	.	38	.	.	.	none	.	.	PASS	Atlas-SNP
HELZ2	85441	hgsc.bcm.edu	hg19	20	62197379	62197379	+	Silent	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	.	NM_001037335	exon9	c.C2796T	p.I932I	CTCACGGATGAAG	.	78.0	32.0	5.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS5	11096	hgsc.bcm.edu	hg19	21	28338045	28338045	+	Silent	SNP	A	A	T	rs369445782	bycluster	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ADAMTS5	NM_007038	exon1	c.T666A	p.A222A	CGCCGGAGCATGC	.	73.0	33.0	0.0	0.0	.	184	.	.	.	weak	.	.	PASS	Atlas-SNP
TTC3	7267	hgsc.bcm.edu	hg19	21	38519809	38519809	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	TTC3	NM_001001894	exon22	c.G1922A	p.C641Y	AAGAATGCAAGTT	.	56.0	4.0	38.0	0.0	.	182	.	.	.	none	.	.	PASS	Atlas-SNP
PRDM15	63977	hgsc.bcm.edu	hg19	21	43221434	43221434	+	Missense_Mutation	SNP	G	G	A	rs147616045	bycluster	TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PRDM15	NM_022115	exon31	c.C4490T	p.A1497V	TGCTCCGCCTGCA	.	24.0	10.0	0.0	0.0	.	110	.	.	.	weak	G|1.000;A|0.000	0.000	PASS	Atlas-SNP
PRPS2	5634	hgsc.bcm.edu	hg19	X	12840843	12840843	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PRPS2	NM_001039091	exon7	c.C894G	p.I298M	CATGATCTTGGCC	.	232.0	69.0	90.0	0.0	.	41	.	.	.	none	.	.	PASS	Atlas-SNP
PHKA2	5256	hgsc.bcm.edu	hg19	X	18919658	18919658	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PHKA2	NM_000292	exon27	c.G2972T	p.G991V	GTGACTCCGGTAT	.	186.0	65.0	53.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
BRWD3	254065	hgsc.bcm.edu	hg19	X	80001213	80001213	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	BRWD3	NM_153252	exon7	c.C446T	p.A149V	TGCCTGGCAGAGG	.	303.0	98.0	204.0	0.0	.	251	.	.	.	none	.	.	PASS	Atlas-SNP
COX2	5743	hgsc.bcm.edu	hg19	MT	7925	7925	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	.	ENST00000361739	exon1	c.G340A	p.G114S	GACTACGGCGGAC	.	67.0	7.0	8.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
COX3	5742	hgsc.bcm.edu	hg19	MT	9930	9930	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	.	ENST00000362079	exon1	c.T724C	p.W242R	TGATACTGGCATT	.	29.0	29.0	12.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
FAM5B	57795	hgsc.bcm.edu	hg19	1	177242681	177242690	+	Frame_Shift_Del	DEL	GTCAGTTCTG	GTCAGTTCTG	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	GTCAGTTCTG	GTCAGTTCTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	FAM5B	NM_021165	exon5	c.726_735del	p.242_245del	.	.	181.0	18.0	126.0	0.0	.	191	.	0.0994475	0	none	.	.	PASS	Atlas-Indel,Pindel
GABRQ	55879	hgsc.bcm.edu	hg19	X	151808889	151808890	+	Frame_Shift_Del	DEL	TG	TG	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	GABRQ	NM_018558	exon2	c.199_200del	p.67_67del	.	.	159.0	56.0	70.0	0.0	.	131	.	0.352201	0	none	.	.	PASS	Atlas-Indel,Pindel
CUX2	23316	hgsc.bcm.edu	hg19	12	111785758	111785759	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	CUX2	NM_015267	exon22	c.4090_4091insA	p.Q1364fs	.	.	69.0	24.0	40.0	0.0	.	145	.	0.347826	0	none	.	.	PASS	Atlas-Indel,Pindel
PKHD1	5314	hgsc.bcm.edu	hg19	6	51890186	51890186	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PKHD1	NM_170724	exon32	c.4423delA	p.N1475fs	.	.	239.0	53.0	40.0	0.0	.	927	.	0.221757	0	none	.	.	PASS	Atlas-Indel,Pindel
CIZ1	25792	hgsc.bcm.edu	hg19	9	130947865	130947865	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	CIZ1	NM_001257975	exon5	c.640delC	p.Q214fs	.	.	118.0	36.0	45.0	0.0	.	75	.	0.305085	0	none	.	.	PASS	Atlas-Indel,Pindel
GPR112	139378	hgsc.bcm.edu	hg19	X	135475736	135475737	+	Frame_Shift_Ins	INS	-	-	AAAAT	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	GPR112	NM_153834	exon18	c.8077_8078insAAAAT	p.N2693fs	.	.	58.0	16.0	52.0	0.0	.	459	.	0.275862	0	none	.	.	PASS	Atlas-Indel,Pindel
ZFHX3	463	hgsc.bcm.edu	hg19	16	72923790	72923790	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	ZFHX3	NM_006885	exon4	c.3289delA	p.T1097fs	.	.	42.0	14.0	16.0	0.0	.	404	.	0.333333	0	none	.	.	PASS	Atlas-Indel,Pindel
CRIPAK	285464	hgsc.bcm.edu	hg19	4	1388661	1388665	+	Frame_Shift_Del	DEL	CGATG	CGATG	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	CGATG	CGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	CRIPAK	NM_175918	exon1	c.361_365del	p.121_122del	.	.	98.0	11.0	11.0	0.0	.	185	.	0.112245	0	none	.	.	PASS	Atlas-INDEL
MLL3	58508	hgsc.bcm.edu	hg19	7	152012386	152012386	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	MLL3	NM_170606	exon4	c.428delG	p.S143fs	.	.	144.0	52.0	87.0	0.0	.	1564	.	0.361111	0	none	.	.	PASS	Atlas-Indel,Pindel
B9D2	80776	hgsc.bcm.edu	hg19	19	41869392	41869392	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	B9D2	NM_030578	exon2	c.34delG	p.G12fs	.	.	124.0	67.0	72.0	0.0	.	9	.	0.540323	0	none	.	.	PASS	Atlas-Indel,Pindel
PPP4R1L	55370	hgsc.bcm.edu	hg19	20	56813334	56813337	+	RNA	DEL	AAAG	AAAG	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	PPP4R1L	.	.	.	.	.	.	46.0	22.0	28.0	0.0	.	1	.	0.478261	0	none	.	.	PASS	Atlas-Indel,Pindel
KIAA1324L	222223	hgsc.bcm.edu	hg19	7	86577110	86577110	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	KIAA1324L	NM_001142749	exon3	c.440delC	p.S147fs	.	.	178.0	64.0	73.0	0.0	.	225	.	0.359551	0	none	.	.	PASS	Atlas-Indel,Pindel
LRRC1	55227	hgsc.bcm.edu	hg19	6	53764574	53764575	+	Frame_Shift_Del	DEL	TT	TT	-	novel		TCGA-Q2-A5QZ-01A-11D-A28G-10	TCGA-Q2-A5QZ-10A-01D-A28G-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	b249fd0e-a8a3-4d18-b3a2-16901434f261	1b6d1224-f192-4682-9d71-3c30ffcd4589	.	LRRC1	NM_018214	exon8	c.671_672del	p.224_224del	.	.	409.0	32.0	83.0	0.0	.	59	.	0.0782396	0	none	.	.	PASS	Atlas-Indel,Pindel