Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	TVarRat	NVarRat	dbSNP_Strength	dbSNP_AF	dbSNP_PopFreq	Confidence	Algorithm
TEKT2	27285	hgsc.bcm.edu	hg19	1	36552574	36552574	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	TEKT2	NM_014466	exon6	c.C675T	p.N225N	GTTCAACAAGGAC	.	47.0	17.0	65.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
SLC35D1	23169	hgsc.bcm.edu	hg19	1	67519574	67519574	+	Silent	SNP	C	C	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	SLC35D1	NM_015139	exon1	c.G123T	p.L41L	CAGCTTCAGAAAC	.	115.0	35.0	194.0	0.0	.	22	.	.	.	none	.	.	PASS	Atlas-SNP
C1orf173	127254	hgsc.bcm.edu	hg19	1	75037280	75037280	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	C1orf173	NM_001002912	exon14	c.G4114T	p.A1372S	TATTTGCTATTGT	.	97.0	37.0	149.0	0.0	.	380	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA4	24	hgsc.bcm.edu	hg19	1	94546179	94546179	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	ABCA4	NM_000350	exon8	c.C954T	p.I318I	AGACAGGATGCCC	.	97.0	30.0	138.0	0.0	.	275	.	.	.	none	.	.	PASS	Atlas-SNP
SLC30A7	148867	hgsc.bcm.edu	hg19	1	101387350	101387350	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	SLC30A7	NM_133496	exon8	c.A795G	p.I265M	GATGATAGCAGAT	.	31.0	11.0	59.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	hg19	1	186043967	186043967	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	HMCN1	NM_031935	exon53	c.G8234T	p.C2745F	ATACTTGTGTAGC	.	97.0	4.0	104.0	0.0	.	797	.	.	.	none	.	.	PASS	Atlas-SNP
IRF2BP2	359948	hgsc.bcm.edu	hg19	1	234743060	234743060	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	IRF2BP2	NM_182972	exon2	c.C1587T	p.F529F	GAAGCAGAACTTG	.	99.0	38.0	99.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
GRB14	2888	hgsc.bcm.edu	hg19	2	165477654	165477654	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	GRB14	NM_004490	exon1	c.G166C	p.G56R	GGGTCCCGTCCGG	.	53.0	30.0	2.0	0.0	.	73	.	.	.	none	.	.	PASS	Atlas-SNP
ATG9A	79065	hgsc.bcm.edu	hg19	2	220085516	220085516	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	ATG9A	NM_001077198	exon15	c.G2467A	p.V823M	CGGGCACGGGCTC	.	73.0	4.0	42.0	0.0	.	50	.	.	.	none	.	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	hg19	2	220283244	220283244	+	Silent	SNP	G	G	A	rs1058253	alternate_allele	TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	DES	NM_001927	exon1	c.G60A	p.G20G	CGGCGGGGCCCCG	.	29.0	21.0	3.0	0.0	.	53	.	.	.	alt	G|1.000;|0.000	.	PASS	Atlas-SNP
DES	1674	hgsc.bcm.edu	hg19	2	220283245	220283245	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	DES	NM_001927	exon1	c.G61T	p.A21S	GGCGGGGCCCCGG	.	31.0	24.0	3.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
KIF1A	547	hgsc.bcm.edu	hg19	2	241696843	241696843	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	KIF1A	NM_001244008	exon27	c.G2751T	p.E917D	CTCATCCTCCTCC	.	189.0	11.0	97.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
SETD2	29072	hgsc.bcm.edu	hg19	3	47164505	47164505	+	Silent	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	SETD2	NM_014159	exon3	c.C1621A	p.R541R	ACCCTCGTCGGAA	.	77.0	4.0	42.0	0.0	.	721	.	.	.	none	.	.	PASS	Atlas-SNP
GMPPB	29925	hgsc.bcm.edu	hg19	3	49759370	49759370	+	Missense_Mutation	SNP	C	C	T	rs71324991		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	GMPPB	NM_013334	exon8	c.G979A	p.E327K	CCCTCTCCCCACC	.	113.0	67.0	81.0	0.0	.	14	.	.	.	weak	C|0.500;T|0.500	0.500	PASS	Atlas-SNP
UBA7	7318	hgsc.bcm.edu	hg19	3	49847782	49847782	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	UBA7	NM_003335	exon13	c.T1547A	p.L516Q	GGATCCAGTGGGT	.	254.0	148.0	270.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
IGF2BP2	10644	hgsc.bcm.edu	hg19	3	185542743	185542743	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	IGF2BP2	NM_001007225	exon1	c.G6C	p.M2I	CTTGTTCATCATC	.	169.0	34.0	88.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
NKX3-2	579	hgsc.bcm.edu	hg19	4	13545664	13545664	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	NKX3-2	NM_001189	exon1	c.C375T	p.L125L	CTGGCCGAGGCTC	.	29.0	18.0	3.0	0.0	.	15	.	.	.	none	.	.	PASS	Atlas-SNP
NIPAL1	152519	hgsc.bcm.edu	hg19	4	48037862	48037862	+	Silent	SNP	T	T	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	NIPAL1	NM_207330	exon6	c.T906C	p.N302N	CTTTAATACCTCT	.	145.0	58.0	201.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
MAP3K1	4214	hgsc.bcm.edu	hg19	5	56170960	56170960	+	Silent	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	MAP3K1	NM_005921	exon10	c.G1788T	p.L596L	CCTGCTGTTGGCA	.	72.0	4.0	96.0	0.0	.	355	.	.	.	none	.	.	PASS	Atlas-SNP
MSH3	4437	hgsc.bcm.edu	hg19	5	79970928	79970928	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	MSH3	NM_002439	exon7	c.A1154T	p.N385I	AGGGCAACATTTT	.	98.0	41.0	148.0	0.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
KDM3B	51780	hgsc.bcm.edu	hg19	5	137717257	137717257	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	KDM3B	NM_016604	exon6	c.A758C	p.D253A	TGATGGATAATTC	.	72.0	25.0	87.0	0.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
CASP8AP2	9994	hgsc.bcm.edu	hg19	6	90573643	90573643	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	CASP8AP2	NM_001137667	exon7	c.T2215C	p.Y739H	TCAGATTATTGTG	.	68.0	5.0	113.0	0.0	.	108	.	.	.	none	.	.	PASS	Atlas-SNP
REPS1	85021	hgsc.bcm.edu	hg19	6	139262487	139262487	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	REPS1	NM_001128617	exon8	c.T1120A	p.L374M	CTTCCAAATCAAT	.	64.0	12.0	76.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
PDE1C	5137	hgsc.bcm.edu	hg19	7	31862809	31862809	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	PDE1C	NM_001191058	exon15	c.G1640T	p.G547V	TCTGAACCAGAGG	.	117.0	38.0	100.0	0.0	.	465	.	.	.	none	.	.	PASS	Atlas-SNP
CSMD1	64478	hgsc.bcm.edu	hg19	8	2824167	2824167	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	CSMD1	NM_033225	exon58	c.T9025C	p.Y3009H	TCTTGTAGCCTTC	.	122.0	50.0	211.0	0.0	.	1469	.	.	.	none	.	.	PASS	Atlas-SNP
NEFL	4747	hgsc.bcm.edu	hg19	8	24813800	24813800	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	NEFL	NM_006158	exon1	c.C230T	p.A77V	ATGGCGGCTACCT	.	173.0	13.0	174.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
MATN2	4147	hgsc.bcm.edu	hg19	8	99039960	99039960	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	MATN2	NM_002380	exon14	c.G2259T	p.R753S	GGCCAGGCCCCTT	.	137.0	52.0	124.0	0.0	.	165	.	.	.	none	.	.	PASS	Atlas-SNP
FOCAD	54914	hgsc.bcm.edu	hg19	9	20988333	20988333	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	.	NM_017794	exon43	c.G4909A	p.V1637I	TCAGGCGTTTTGA	.	91.0	8.0	103.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
TOPORS	10210	hgsc.bcm.edu	hg19	9	32541932	32541932	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	TOPORS	NM_005802	exon3	c.G2591A	p.S864N	CTTAGGCTCCGGG	.	38.0	11.0	72.0	0.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
FCN2	2220	hgsc.bcm.edu	hg19	9	137777085	137777085	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	FCN2	NM_004108	exon5	c.G302T	p.G101V	TCCCAGGCCCGCG	.	45.0	16.0	54.0	0.0	.	55	.	.	.	none	.	.	PASS	Atlas-SNP
KCNT1	57582	hgsc.bcm.edu	hg19	9	138594140	138594140	+	Silent	SNP	C	C	G	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	KCNT1	NM_001272003	exon1	c.C36G	p.G12G	GGGGGGCGTCTGC	.	23.0	14.0	1.0	0.0	.	139	.	.	.	none	.	.	PASS	Atlas-SNP
ANK3	288	hgsc.bcm.edu	hg19	10	61829169	61829169	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	ANK3	NM_020987	exon37	c.G11470A	p.V3824M	CTTTCACTGGGTT	.	57.0	23.0	76.0	0.0	.	703	.	.	.	none	.	.	PASS	Atlas-SNP
MMRN2	79812	hgsc.bcm.edu	hg19	10	88703695	88703695	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	MMRN2	NM_024756	exon6	c.C846T	p.A282A	AGCCCTGGCCACG	.	89.0	41.0	109.0	0.0	.	49	.	.	.	none	.	.	PASS	Atlas-SNP
RRP12	23223	hgsc.bcm.edu	hg19	10	99160073	99160073	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	RRP12	NM_001145114	exon2	c.G358A	p.A120T	TGTGGGCAGCCGA	.	75.0	22.0	112.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
STK32C	282974	hgsc.bcm.edu	hg19	10	134036392	134036392	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	STK32C	NM_173575	exon9	c.G1092A	p.K364K	CACCCTCTTCTCG	.	51.0	19.0	2.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
SLC22A18	5002	hgsc.bcm.edu	hg19	11	2937874	2937874	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	SLC22A18	NM_002555	exon6	c.G559T	p.A187S	ATCCTGGCTGCCC	.	124.0	50.0	57.0	0.0	.	20	.	.	.	none	.	.	PASS	Atlas-SNP
MARS	4141	hgsc.bcm.edu	hg19	12	57894254	57894254	+	Silent	SNP	G	G	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	MARS	NM_004990	exon10	c.G1242C	p.R414R	GGCTCGGGGTGAC	.	187.0	44.0	213.0	0.0	.	84	.	.	.	none	.	.	PASS	Atlas-SNP
NBEA	26960	hgsc.bcm.edu	hg19	13	35770159	35770159	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	NBEA	NM_015678	exon31	c.G5086T	p.G1696C	AGTACAGGCCCTG	.	111.0	57.0	100.0	0.0	.	340	.	.	.	none	.	.	PASS	Atlas-SNP
FSIP1	161835	hgsc.bcm.edu	hg19	15	40056080	40056080	+	Silent	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	FSIP1	NM_152597	exon5	c.G501A	p.E167E	CATCTCCTCTTTA	.	121.0	49.0	155.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
NDUFAF1	51103	hgsc.bcm.edu	hg19	15	41689069	41689069	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	NDUFAF1	NM_016013	exon2	c.C189T	p.H63H	TTTCTGGTGATCT	.	60.0	24.0	77.0	0.0	.	39	.	.	.	none	.	.	PASS	Atlas-SNP
TICRR	90381	hgsc.bcm.edu	hg19	15	90167321	90167321	+	Silent	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	.	NM_152259	exon20	c.G3780A	p.T1260T	GGGCACGCCTCAG	.	39.0	17.0	49.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
ANKS3	124401	hgsc.bcm.edu	hg19	16	4748510	4748510	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	ANKS3	NM_133450	exon14	c.C1642A	p.R548S	GGGCGCGGTCCTG	.	25.0	17.0	1.0	0.0	.	44	.	.	.	none	.	.	PASS	Atlas-SNP
GRIN2A	2903	hgsc.bcm.edu	hg19	16	10273887	10273887	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	GRIN2A	NM_000833	exon3	c.C382G	p.H128D	CCCCATGAATGCC	.	158.0	42.0	145.0	0.0	.	366	.	.	.	none	.	.	PASS	Atlas-SNP
DBNDD1	79007	hgsc.bcm.edu	hg19	16	90072805	90072805	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	DBNDD1	NM_024043	exon4	c.C475A	p.P159T	GCTCGGGGTCGCC	.	62.0	16.0	38.0	0.0	.	9	.	.	.	none	.	.	PASS	Atlas-SNP
DNAH2	146754	hgsc.bcm.edu	hg19	17	7727530	7727530	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	DNAH2	NM_020877	exon75	c.A11570T	p.H3857L	CAGAGCACATGGG	.	100.0	56.0	27.0	0.0	.	498	.	.	.	none	.	.	PASS	Atlas-SNP
SPAG5	10615	hgsc.bcm.edu	hg19	17	26912886	26912886	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	SPAG5	NM_006461	exon7	c.A1736G	p.D579G	ACCGCATCCTTGC	.	79.0	48.0	74.0	0.0	.	92	.	.	.	none	.	.	PASS	Atlas-SNP
KRT13	3860	hgsc.bcm.edu	hg19	17	39658844	39658844	+	Silent	SNP	T	T	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	KRT13	NM_002274	exon6	c.A1026G	p.K342K	CCCCGCTTTCTGG	.	63.0	19.0	67.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
CBX4	8535	hgsc.bcm.edu	hg19	17	77807927	77807927	+	Missense_Mutation	SNP	A	A	G	rs200965379		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	CBX4,uveal_tract,malignant_melanoma,0,1	CBX4	NM_003655	exon5	c.T1514C	p.V505A	GCCGCCACCGCCA	.	34.0	22.0	2.0	1.0	.	40	.	.	.	weak	.	.	PASS	Atlas-SNP
TMC2	117532	hgsc.bcm.edu	hg19	20	2592879	2592879	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	TMC2	NM_080751	exon13	c.C1636G	p.L546V	TGGACTCTGTTTA	.	78.0	10.0	63.0	0.0	.	121	.	.	.	none	.	.	PASS	Atlas-SNP
PANK2	80025	hgsc.bcm.edu	hg19	20	3869791	3869791	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	PANK2	NM_153638	exon1	c.C44T	p.A15V	GGGCGGCGCCGCC	.	113.0	34.0	85.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
KRTAP19-5	337972	hgsc.bcm.edu	hg19	21	31874285	31874285	+	Missense_Mutation	SNP	C	C	T	rs370535457		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	KRTAP19-5	NM_181611	exon1	c.G124A	p.G42R	AGCCTCCGTAGCC	.	48.0	34.0	172.0	0.0	.	32	.	.	.	weak	.	.	PASS	Atlas-SNP
TBL1X	6907	hgsc.bcm.edu	hg19	X	9683003	9683003	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	TBL1X	NM_001139466	exon17	c.C1667T	p.A556V	GGAACGCCCGAGG	.	178.0	81.0	272.0	0.0	.	103	.	.	.	none	.	.	PASS	Atlas-SNP
PHKA1	5255	hgsc.bcm.edu	hg19	X	71802352	71802352	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	PHKA1	NM_002637	exon31	c.C3394T	p.L1132F	GGACAAGGATGGC	.	293.0	86.0	417.0	1.0	.	129	.	.	.	none	.	.	PASS	Atlas-SNP
GPR50	9248	hgsc.bcm.edu	hg19	X	150348665	150348665	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	GPR50	NM_004224	exon2	c.G610A	p.V204M	CTCATCGTGGGTT	.	43.0	12.0	80.0	0.0	.	195	.	.	.	none	.	.	PASS	Atlas-SNP
RENBP	5973	hgsc.bcm.edu	hg19	X	153200791	153200791	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	RENBP	NM_002910	exon11	c.C1232A	p.P411H	GGGGCGGGGCGGC	.	8.0	4.0	0.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
SREBF2	6721	hgsc.bcm.edu	hg19	22	42289217	42289217	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	SREBF2	NM_004599	exon12	c.2304delG	p.K768fs	.	.	70.0	24.0	97.0	0.0	.	99	.	0.342857	0	none	.	.	PASS	Atlas-Indel,Pindel
PLEC	5339	hgsc.bcm.edu	hg19	8	145024821	145024825	+	Frame_Shift_Del	DEL	CACCT	CACCT	-	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CACCT	CACCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	PLEC	NM_201380	exon1	c.51_55del	p.17_19del	.	.	46.0	17.0	3.0	0.0	.	1144	.	0.369565	0	none	.	.	PASS	Atlas-Indel,Pindel
VAPB	9217	hgsc.bcm.edu	hg19	20	57009683	57009684	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	VAPB	NM_004738	exon3	c.237_238insC	p.D79fs	.	.	79.0	21.0	89.0	0.0	.	21	.	0.265823	0	none	.	.	PASS	Atlas-Indel,Pindel
IGFLR1	79713	hgsc.bcm.edu	hg19	19	36230984	36230986	+	In_Frame_Del	DEL	CGG	CGG	-	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	IGFLR1	NM_024660	exon4	c.347_349del	p.116_117del	.	.	34.0	11.0	44.0	0.0	.	28	.	0.323529	0	none	.	.	PASS	Atlas-INDEL
SLC14A1	6563	hgsc.bcm.edu	hg19	18	43316457	43316458	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.	SLC14A1	NM_001146037	exon5	c.675_676insA	p.S225fs	.	.	128.0	51.0	156.0	0.0	.	84	.	0.398438	0	none	.	.	PASS	Atlas-Indel,Pindel
MIA3	375056	hgsc.bcm.edu	hg19	1	222803477	222803477	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-PJ-A5Z9-01A-11D-A28G-10	TCGA-PJ-A5Z9-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0040144d-5bfe-4476-b511-2fa1fed81583	32635493-96c3-4fed-a9f7-85537363c7f0	.,1	MIA3	NM_198551	exon4	c.2914delG	p.E972fs	.	.	73.0	32.0	76.0	0.0	.	167	.	0.438356	0	none	.	.	PASS	Atlas-Indel,Pindel
