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
H6PD	9563	hgsc.bcm.edu	hg19	1	9305536	9305536	+	Silent	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	H6PD	NM_004285	exon2	c.C543T	p.F181F	CCACTTCTCAGCC	.	101.0	39.0	108.0	0.0	.	71	.	.	.	none	.	.	PASS	Atlas-SNP
RABGGTB	5876	hgsc.bcm.edu	hg19	1	76253203	76253203	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	RABGGTB	NM_004582	exon2	c.A25G	p.I9V	GATGTTATTATCA	.	162.0	72.0	127.0	0.0	.	37	.	.	.	none	.	.	PASS	Atlas-SNP
OVGP1	5016	hgsc.bcm.edu	hg19	1	111957940	111957940	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	OVGP1	NM_002557	exon11	c.T1183G	p.F395V	GCCAAAATTGTGG	.	98.0	38.0	91.0	0.0	.	177	.	.	.	none	.	.	PASS	Atlas-SNP
CCT3	7203	hgsc.bcm.edu	hg19	1	156294858	156294858	+	Silent	SNP	A	A	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	CCT3	NM_005998	exon6	c.T327C	p.A109A	GTGCTCAGCTACA	.	36.0	17.0	30.0	0.0	.	61	.	.	.	none	.	.	PASS	Atlas-SNP
HHIPL2	79802	hgsc.bcm.edu	hg19	1	222705394	222705394	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	HHIPL2	NM_024746	exon6	c.G1637A	p.C546Y	CCCAGGCAAAGAT	.	65.0	31.0	56.0	0.0	.	122	.	.	.	none	.	.	PASS	Atlas-SNP
C1orf95	375057	hgsc.bcm.edu	hg19	1	226784625	226784625	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	C1orf95	NM_001003665	exon2	c.G325A	p.V109I	GCCATCGTCATGG	.	91.0	38.0	84.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
CTNNA2	1496	hgsc.bcm.edu	hg19	2	80136916	80136916	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	CTNNA2	NM_001164883	exon7	c.T1049C	p.M350T	AGTACATGAATAA	.	169.0	70.0	156.0	0.0	.	462	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	hg19	2	185802210	185802210	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ZNF804A	NM_194250	exon4	c.A2087C	p.N696T	AAAAGAACACAAT	.	570.0	24.0	135.0	0.0	.	322	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	hg19	2	185802211	185802211	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	ZNF804A,NS,carcinoma,0,1	ZNF804A	NM_194250	exon4	c.C2088A	p.N696K	AAAGAACACAATA	.	570.0	32.0	137.0	0.0	.	322	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF804A	91752	hgsc.bcm.edu	hg19	2	185802216	185802216	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ZNF804A	NM_194250	exon4	c.T2093C	p.I698T	ACACAATACTTTT	.	569.0	30.0	137.0	0.0	.	322	.	.	.	none	.	.	PASS	Atlas-SNP
CUL3	8452	hgsc.bcm.edu	hg19	2	225362540	225362540	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	CUL3,NS,adenocarcinoma,0,1	CUL3	NM_001257198	exon12	c.G1655C	p.R552P	AGCTGTCGACCAC	.	52.0	48.0	122.0	0.0	.	96	.	.	.	none	.	.	PASS	Atlas-SNP
CISH	1154	hgsc.bcm.edu	hg19	3	50645901	50645901	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	CISH	NM_013324	exon3	c.G195T	p.E65D	GGTACCCTCTGCC	.	49.0	28.0	64.0	0.0	.	27	.	.	.	none	.	.	PASS	Atlas-SNP
DNAH1	25981	hgsc.bcm.edu	hg19	3	52380547	52380547	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	DNAH1	NM_015512	exon11	c.C1716A	p.S572R	CAGCAGCCTGCGC	.	42.0	11.0	36.0	0.0	.	534	.	.	.	none	.	.	PASS	Atlas-SNP
A4GNT	51146	hgsc.bcm.edu	hg19	3	137849689	137849689	+	Splice_Site	SNP	A	A	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	A4GNT	NM_016161	exon3	c.408+2T>G	.	ACACTTACTTGAT	.	195.0	96.0	136.0	0.0	.	42	.	.	.	none	.	.	PASS	Atlas-SNP
WDFY3	23001	hgsc.bcm.edu	hg19	4	85722839	85722839	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	WDFY3	NM_014991	exon17	c.G2786T	p.R929L	GCTAATCGTTCAA	.	36.0	16.0	24.0	0.0	.	314	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS12	81792	hgsc.bcm.edu	hg19	5	33534943	33534943	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ADAMTS12	NM_030955	exon23	c.G4601T	p.S1534I	CCGGCACTTTTCT	.	91.0	44.0	65.0	0.0	.	464	.	.	.	none	.	.	PASS	Atlas-SNP
PCDHB14	56122	hgsc.bcm.edu	hg19	5	140605127	140605127	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	PCDHB14	NM_018934	exon1	c.G2050A	p.D684N	CAGGCCGACTCCC	.	73.0	5.0	85.0	0.0	.	132	.	.	.	none	.	.	PASS	Atlas-SNP
E2F3	1871	hgsc.bcm.edu	hg19	6	20490451	20490451	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	E2F3	NM_001949	exon7	c.C1188G	p.N396K	GGGAAACCTTTCT	.	101.0	52.0	83.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
HLA-A	3105	hgsc.bcm.edu	hg19	6	29910554	29910554	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	HLA-A	NM_001242758	exon2	c.T94G	p.F32V	AGGTATTTCTTCA	.	134.0	38.0	109.0	0.0	.	89	.	.	.	none	.	.	PASS	Atlas-SNP
BRD2	6046	hgsc.bcm.edu	hg19	6	32944714	32944714	+	Splice_Site	SNP	G	G	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	BRD2_ENST00000395289,mouth,carcinoma,0,1	BRD2	NM_005104	exon7	c.1200+1G>A	.	GTCAAGGTACCCA	.	42.0	21.0	29.0	0.0	.	70	.	.	.	none	.	.	PASS	Atlas-SNP
ASCC3	10973	hgsc.bcm.edu	hg19	6	101075824	101075824	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ASCC3	NM_006828	exon28	c.G4415T	p.R1472L	TTTGTTCGAGATA	.	69.0	30.0	74.0	0.0	.	205	.	.	.	none	.	.	PASS	Atlas-SNP
NRCAM	4897	hgsc.bcm.edu	hg19	7	107807453	107807453	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	NRCAM	NM_001037132	exon27	c.A3379G	p.M1127V	CTGGCATTAGACC	.	133.0	50.0	123.0	0.0	.	267	.	.	.	none	.	.	PASS	Atlas-SNP
OR6V1	346517	hgsc.bcm.edu	hg19	7	142750247	142750247	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	OR6V1	NM_001001667	exon1	c.G810C	p.K270N	CAGGAAGGTCGTG	.	80.0	41.0	72.0	0.0	.	77	.	.	.	none	.	.	PASS	Atlas-SNP
SNAI2	6591	hgsc.bcm.edu	hg19	8	49833817	49833817	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	SNAI2,NS,carcinoma,0,1	SNAI2	NM_003068	exon1	c.G8C	p.R3P	AAGGAGCGCGGCA	.	38.0	22.0	36.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
RFX3	5991	hgsc.bcm.edu	hg19	9	3301560	3301560	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	RFX3	NM_134428	exon6	c.C535T	p.L179F	TGAGAAGAGAGCT	.	87.0	44.0	75.0	0.0	.	156	.	.	.	none	.	.	PASS	Atlas-SNP
ZSWIM8	23053	hgsc.bcm.edu	hg19	10	75561460	75561460	+	Silent	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	.	NM_001242488	exon26	c.C5605T	p.L1869L	CTAGGGCTGGGGG	.	14.0	7.0	5.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	hg19	11	1276776	1276776	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	MUC5B	NM_002458	exon37	c.G16054T	p.G5352C	GCAACCGGTGGCC	.	62.0	4.0	53.0	0.0	.	473	.	.	.	none	.	.	PASS	Atlas-SNP
SF3B2	10992	hgsc.bcm.edu	hg19	11	65826742	65826742	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	SF3B2	NM_006842	exon11	c.C1253T	p.A418V	CTGCAGCCCCCAA	.	141.0	6.0	132.0	0.0	.	85	.	.	.	none	.	.	PASS	Atlas-SNP
TMTC2	160335	hgsc.bcm.edu	hg19	12	83251132	83251132	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	TMTC2,NS,carcinoma,0,1	TMTC2	NM_152588	exon2	c.G427T	p.G143W	GATGTCGGGGCCA	.	84.0	37.0	82.0	0.0	.	100	.	.	.	none	.	.	PASS	Atlas-SNP
FOXA1	3169	hgsc.bcm.edu	hg19	14	38060788	38060788	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	FOXA1	NM_004496	exon2	c.T1201A	p.S401T	TGATGGAGAACGG	.	116.0	63.0	98.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
MOK	5891	hgsc.bcm.edu	hg19	14	102718326	102718326	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	.	NM_014226	exon5	c.G290T	p.R97I	GGGTATCTTCTCC	.	130.0	60.0	124.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
C15orf56	644809	hgsc.bcm.edu	hg19	15	40544920	40544920	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	C15orf56	NM_001039905	exon1	c.G170A	p.R57Q	GAGGTTCGCGGCG	.	137.0	59.0	121.0	0.0	.	3	.	.	.	none	.	.	PASS	Atlas-SNP
EME2	197342	hgsc.bcm.edu	hg19	16	1826070	1826070	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	EME2	NM_001257370	exon8	c.C971T	p.A324V	CCTAGGCGCTGGA	.	62.0	22.0	39.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
ABCA3	21	hgsc.bcm.edu	hg19	16	2369834	2369834	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ABCA3	NM_001089	exon8	c.C621G	p.I207M	TTCCCGGATGTAC	.	33.0	10.0	34.0	0.0	.	176	.	.	.	none	.	.	PASS	Atlas-SNP
PRM3	58531	hgsc.bcm.edu	hg19	16	11367405	11367405	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	PRM3	NM_021247	exon1	c.C48G	p.H16Q	TGGGCTGTGGCCT	.	21.0	7.0	15.0	0.0	.	8	.	.	.	none	.	.	PASS	Atlas-SNP
DCTPP1	79077	hgsc.bcm.edu	hg19	16	30435583	30435583	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	DCTPP1	NM_024096	exon3	c.T484A	p.C162S	AGTCACAGGGAAT	.	80.0	43.0	54.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
DHX38	9785	hgsc.bcm.edu	hg19	16	72142801	72142801	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	DHX38	NM_014003	exon24	c.C3358T	p.H1120Y	GTGTATCACGAGT	.	62.0	23.0	80.0	0.0	.	91	.	.	.	none	.	.	PASS	Atlas-SNP
NCOR1	9611	hgsc.bcm.edu	hg19	17	15971431	15971431	+	Silent	SNP	T	T	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	NCOR1	NM_001190440	exon31	c.A4566C	p.T1522T	AGAAATTGTAACT	.	117.0	32.0	90.0	0.0	.	240	.	.	.	none	.	.	PASS	Atlas-SNP
CCR7	1236	hgsc.bcm.edu	hg19	17	38711306	38711306	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	CCR7	NM_001838	exon3	c.C825A	p.F275L	CAGCTGGAAGACT	.	129.0	41.0	72.0	0.0	.	31	.	.	.	none	.	.	PASS	Atlas-SNP
KIF2B	84643	hgsc.bcm.edu	hg19	17	51901648	51901648	+	Silent	SNP	C	C	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	KIF2B	NM_032559	exon1	c.C1254T	p.V418V	ACCTGTCAACGCT	.	221.0	68.0	137.0	0.0	.	254	.	.	.	none	.	.	PASS	Atlas-SNP
ANKRD12	23253	hgsc.bcm.edu	hg19	18	9257703	9257703	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ANKRD12	NM_015208	exon9	c.C4438G	p.Q1480E	TGTGCTCAGGATC	.	104.0	40.0	118.0	0.0	.	167	.	.	.	none	.	.	PASS	Atlas-SNP
MBP	4155	hgsc.bcm.edu	hg19	18	74700845	74700845	+	Silent	SNP	C	C	T	rs112511603		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	MBP	NM_001025101	exon6	c.G705A	p.P235P	CTGCGACGGGGGT	.	65.0	28.0	80.0	0.0	.	45	.	.	.	weak	C|0.500;T|0.500	0.500	PASS	Atlas-SNP
XAB2	56949	hgsc.bcm.edu	hg19	19	7691039	7691039	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	XAB2,NS,carcinoma,0,1	XAB2	NM_020196	exon5	c.G640T	p.G214C	ACTTGCCGGCCTT	.	40.0	2.0	37.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF43	7594	hgsc.bcm.edu	hg19	19	21990696	21990696	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ZNF43	NM_001256653	exon4	c.T2170A	p.F724I	GGTTAAAAGCTTT	.	37.0	20.0	27.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
FBXO46	23403	hgsc.bcm.edu	hg19	19	46215847	46215847	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	FBXO46	NM_001080469	exon2	c.A907G	p.K303E	TGATCTTGTCCTT	.	101.0	47.0	75.0	0.0	.	34	.	.	.	none	.	.	PASS	Atlas-SNP
EDN3	1908	hgsc.bcm.edu	hg19	20	57876603	57876603	+	Missense_Mutation	SNP	G	G	T	rs457651	alternate_allele	TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	EDN3	NM_207034	exon2	c.G191T	p.G64V	GCGAGGGGACTGT	.	94.0	43.0	77.0	0.0	.	83	.	.	.	alt	G|1.000;A|0.000	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	hg19	X	66765207	66765207	+	Silent	SNP	G	G	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	AR	NM_000044	exon1	c.G219A	p.Q73Q	GCAGCAGCAGCAG	.	102.0	9.0	97.0	0.0	.	249	.	.	.	none	.	.	PASS	Atlas-SNP
AR	367	hgsc.bcm.edu	hg19	X	66765208	66765208	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	AR	NM_000044	exon1	c.C220G	p.Q74E	CAGCAGCAGCAGC	.	104.0	8.0	97.0	0.0	.	249	.	.	.	none	.	.	PASS	Atlas-SNP
CYTB	0	hgsc.bcm.edu	hg19	MT	14889	14889	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	.	ENST00000361789	exon1	c.G143A	p.G48E	CCACAGGACTATT	.	290.0	27.0	175.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
MYH13	8735	hgsc.bcm.edu	hg19	17	10215392	10215392	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	MYH13_ENST00000252172,NS,carcinoma,0,2	MYH13	NM_003802	exon32	c.4368delC	p.V1456fs	.	.	93.0	30.0	63.0	0.0	.	533	.	0.322581	0	none	.	.	PASS	Atlas-Indel,Pindel
CD83	9308	hgsc.bcm.edu	hg19	6	14133946	14133946	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	CD83	NM_004233	exon4	c.448delG	p.A150fs	.	.	107.0	49.0	73.0	0.0	.	23	.	0.457944	0	none	.	.	PASS	Atlas-Indel,Pindel
EXOSC2	23404	hgsc.bcm.edu	hg19	9	133579154	133579154	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	EXOSC2	NM_014285	exon9	c.874delG	p.E292fs	.	.	92.0	46.0	67.0	0.0	.	15	.	0.5	0	none	.	.	PASS	Atlas-Indel,Pindel
PRKCI	5584	hgsc.bcm.edu	hg19	3	170020905	170020905	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	PRKCI	NM_002740	exon18	c.1780delG	p.E594fs	.	.	86.0	36.0	71.0	0.0	.	82	.	0.418605	0	none	.	.	PASS	Atlas-Indel,Pindel
CASC5	57082	hgsc.bcm.edu	hg19	15	40914359	40914359	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	CASC5	NM_170589	exon11	c.1974delC	p.N658fs	.	.	111.0	45.0	103.0	0.0	.	269	.	0.405405	0	none	.	.	PASS	Atlas-Indel,Pindel
IL17RB	55540	hgsc.bcm.edu	hg19	3	53886139	53886147	+	In_Frame_Del	DEL	CCCTCTGGT	CCCTCTGGT	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	CCCTCTGGT	CCCTCTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	IL17RB	NM_018725	exon4	c.339_347del	p.113_116del	.	.	103.0	35.0	126.0	0.0	.	27	.	0.339806	0	none	.	.	PASS	Atlas-Indel,Pindel
ULK4	54986	hgsc.bcm.edu	hg19	3	41795965	41795965	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ULK4	NM_017886	exon22	c.2210delT	p.I737fs	.	.	123.0	42.0	106.0	0.0	.	150	.	0.341	.	none	.	.	PASS	Pindel
MTSS1	9788	hgsc.bcm.edu	hg19	8	125570101	125570101	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	MTSS1	NM_014751	exon11	c.1052delC	p.S351fs	.	.	56.0	17.0	67.0	0.0	.	79	.	0.304	.	none	.	.	PASS	Pindel
KANK4	163782	hgsc.bcm.edu	hg19	1	62740357	62740358	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	KANK4	NM_181712	exon3	c.419_420del	p.140_140del	.	.	62.0	15.0	51.0	0.0	.	135	.	0.242	.	none	.	.	PASS	Pindel
ADCY9	115	hgsc.bcm.edu	hg19	16	4042307	4042307	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-A5Y0-01A-11D-A31X-10	TCGA-A4-A5Y0-11A-11D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	257fa140-0c01-4edc-8247-82c96ecfb384	6022828f-21e4-4e71-8abd-439d01decea4	.	ADCY9	NM_001116	exon5	c.2048delA	p.E683fs	.	.	76.0	26.0	69.0	0.0	.	151	.	0.342	.	none	.	.	PASS	Pindel
