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
TRIT1	54802	hgsc.bcm.edu	hg19	1	40307511	40307511	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	TRIT1	NM_017646	exon11	c.A1309G	p.I437V	TTTCTATGGTGTT	.	249.0	99.0	259.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
MIER1	57708	hgsc.bcm.edu	hg19	1	67423741	67423741	+	Splice_Site	SNP	G	G	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	MIER1	NM_001146111	exon6	c.232-1G>C	.	TATTTAGGAAGGC	.	53.0	15.0	88.0	0.0	.	86	.	.	.	none	.	.	PASS	Atlas-SNP
ARHGAP29	9411	hgsc.bcm.edu	hg19	1	94668261	94668261	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	ARHGAP29	NM_004815	exon11	c.G982T	p.A328S	ATTTTGCCTTTTT	.	77.0	26.0	100.0	0.0	.	132	.	.	.	none	.	.	PASS	Atlas-SNP
BCL9	607	hgsc.bcm.edu	hg19	1	147086309	147086309	+	Silent	SNP	A	A	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	BCL9	NM_004326	exon6	c.A454C	p.R152R	GCCCCCAGGTCTT	.	76.0	30.0	98.0	0.0	.	150	.	.	.	none	.	.	PASS	Atlas-SNP
BCL9	607	hgsc.bcm.edu	hg19	1	147086367	147086367	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	BCL9	NM_004326	exon6	c.A512G	p.K171R	CTCAGAAGACTCC	.	63.0	34.0	72.0	0.0	.	150	.	.	.	none	.	.	PASS	Atlas-SNP
KPRP	448834	hgsc.bcm.edu	hg19	1	152733695	152733695	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	KPRP	NM_001025231	exon2	c.G1631A	p.G544D	GTGCTGGCTGTGG	.	117.0	52.0	98.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
NLRP3	114548	hgsc.bcm.edu	hg19	1	247597496	247597496	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	NLRP3	NM_004895	exon5	c.G2419T	p.D807Y	CTGAGTGACAACG	.	121.0	38.0	116.0	0.0	.	286	.	.	.	none	.	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	hg19	2	37280725	37280725	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	HEATR5B	NM_019024	exon17	c.G2425T	p.E809X	CACATTCAGCAAA	.	28.0	8.0	46.0	0.0	.	185	.	.	.	none	.	.	PASS	Atlas-SNP
RANBP2	5903	hgsc.bcm.edu	hg19	2	109379713	109379713	+	Silent	SNP	T	T	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	RANBP2	NM_006267	exon20	c.T2718C	p.N906N	CATGAATAGGCTT	.	93.0	29.0	92.0	0.0	.	488	.	.	.	none	.	.	PASS	Atlas-SNP
SLC40A1	30061	hgsc.bcm.edu	hg19	2	190428774	190428774	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	SLC40A1	NM_014585	exon7	c.G938C	p.G313A	GCAAGACCCATGC	.	68.0	28.0	53.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
VPRBP	9730	hgsc.bcm.edu	hg19	3	51456171	51456171	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	VPRBP	NM_014703	exon15	c.C3237A	p.N1079K	GTGACAGTTATAG	.	208.0	171.0	198.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
PBRM1	55193	hgsc.bcm.edu	hg19	3	52584609	52584609	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PBRM1	NM_018313	exon29	c.T4404A	p.Y1468X	GCCGGGATATGGA	.	95.0	68.0	87.0	0.0	.	1252	.	.	.	none	.	.	PASS	Atlas-SNP
COL8A1	1295	hgsc.bcm.edu	hg19	3	99513269	99513269	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	COL8A1	NM_001850	exon5	c.C524T	p.P175L	GCATGCCTGGGGC	.	52.0	44.0	49.0	0.0	.	68	.	.	.	none	.	.	PASS	Atlas-SNP
PDIA5	10954	hgsc.bcm.edu	hg19	3	122821610	122821610	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PDIA5	NM_006810	exon5	c.T354A	p.F118L	TGCATTTCATACT	.	27.0	24.0	37.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
AFM	173	hgsc.bcm.edu	hg19	4	74364944	74364944	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	AFM	NM_001133	exon11	c.T1403C	p.F468S	AAGAGTTTGCCTG	.	49.0	18.0	66.0	0.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
LEF1	51176	hgsc.bcm.edu	hg19	4	109084775	109084775	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	LEF1	NM_001130714	exon3	c.T363G	p.N121K	GTCGTTATTCATA	.	103.0	40.0	169.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
FAM105A	54491	hgsc.bcm.edu	hg19	5	14609077	14609077	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	FAM105A	NM_019018	exon7	c.T848C	p.F283S	TGAGCTTCATGAT	.	222.0	83.0	217.0	0.0	.	32	.	.	.	none	.	.	PASS	Atlas-SNP
TXNDC5	81567	hgsc.bcm.edu	hg19	6	7889004	7889004	+	Silent	SNP	A	A	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	TXNDC5	NM_030810	exon7	c.T897G	p.T299T	CGCTCCAGTCTCT	.	275.0	114.0	250.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
UNC5D	137970	hgsc.bcm.edu	hg19	8	35541184	35541184	+	Silent	SNP	C	C	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	UNC5D	NM_080872	exon5	c.C690T	p.T230T	TTACACCTGCATG	.	58.0	22.0	55.0	0.0	.	393	.	.	.	none	.	.	PASS	Atlas-SNP
NOV	4856	hgsc.bcm.edu	hg19	8	120429171	120429171	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	NOV	NM_002514	exon2	c.G272C	p.R91P	GTGATCGCAGCGC	.	49.0	23.0	44.0	0.0	.	51	.	.	.	none	.	.	PASS	Atlas-SNP
RASEF	158158	hgsc.bcm.edu	hg19	9	85597649	85597649	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	RASEF	NM_152573	exon17	c.T2166G	p.N722K	GGTTAGATTGGTA	.	273.0	87.0	252.0	0.0	.	69	.	.	.	none	.	.	PASS	Atlas-SNP
SPATA31C2	645961	hgsc.bcm.edu	hg19	9	90747533	90747533	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	.	NM_001166137	exon4	c.C419A	p.A140D	CGGGAGGCTCCAT	.	230.0	25.0	201.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
PAPPA	5069	hgsc.bcm.edu	hg19	9	118969850	118969850	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PAPPA	NM_002581	exon3	c.C1594T	p.P532S	ACTTGGCCATGGG	.	74.0	23.0	96.0	0.0	.	243	.	.	.	none	.	.	PASS	Atlas-SNP
ASTN2	23245	hgsc.bcm.edu	hg19	9	119495750	119495750	+	Missense_Mutation	SNP	T	T	A	rs150944935	bycluster;byfrequency;alternate_allele	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	ASTN2	NM_014010	exon13	c.A2296T	p.I766F	GCGGGATCACCAA	.	165.0	16.0	115.0	0.0	.	307	.	.	.	alt	T|1.000;C|0.000	.	PASS	Atlas-SNP
ECD	11319	hgsc.bcm.edu	hg19	10	74906091	74906091	+	Missense_Mutation	SNP	C	C	G	rs147908494	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	ECD	NM_001135752	exon9	c.G1070C	p.R357P	CTTTCCCGGTACT	.	40.0	7.0	37.0	0.0	.	50	.	.	.	alt	C|0.999;T|0.001	.	PASS	Atlas-SNP
ADK	132	hgsc.bcm.edu	hg19	10	76468112	76468112	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	ADK	NM_006721	exon11	c.T998C	p.L333P	AGCCTCTGACTGA	.	184.0	67.0	201.0	0.0	.	28	.	.	.	none	.	.	PASS	Atlas-SNP
OR1S1	219959	hgsc.bcm.edu	hg19	11	57982376	57982376	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	OR1S1	NM_001004458	exon1	c.G160A	p.G54R	GTGATTGGGAACG	.	229.0	90.0	322.0	0.0	.	139	.	.	.	none	.	.	PASS	Atlas-SNP
DPF2	5977	hgsc.bcm.edu	hg19	11	65113439	65113439	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	DPF2	NM_006268	exon8	c.T814C	p.Y272H	AACAACTACTGTG	.	220.0	95.0	176.0	0.0	.	54	.	.	.	none	.	.	PASS	Atlas-SNP
SPTBN2	6712	hgsc.bcm.edu	hg19	11	66488565	66488565	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	SPTBN2	NM_006946	exon2	c.G147C	p.K49N	CAGAGCCTTAATG	.	74.0	37.0	64.0	0.0	.	188	.	.	.	none	.	.	PASS	Atlas-SNP
PCF11	51585	hgsc.bcm.edu	hg19	11	82877707	82877707	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	PCF11_ENST00000298281,NS,carcinoma,0,2	PCF11	NM_015885	exon5	c.A1768C	p.S590R	TGGCAAAGTTCCA	.	151.0	57.0	170.0	0.0	.	220	.	.	.	none	.	.	PASS	Atlas-SNP
B4GALNT3	283358	hgsc.bcm.edu	hg19	12	662534	662534	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	B4GALNT3	NM_173593	exon14	c.C1445A	p.P482H	CTCAGCCCCGGGA	.	132.0	40.0	128.0	0.0	.	64	.	.	.	none	.	.	PASS	Atlas-SNP
TMTC3	160418	hgsc.bcm.edu	hg19	12	88548132	88548132	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	TMTC3	NM_181783	exon4	c.A476G	p.Y159C	TGTCATATACCAG	.	82.0	30.0	103.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
PCNX	22990	hgsc.bcm.edu	hg19	14	71413816	71413816	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PCNX	NM_014982	exon2	c.G338T	p.R113M	CAACCAGGAGAAA	.	24.0	9.0	31.0	0.0	.	198	.	.	.	none	.	.	PASS	Atlas-SNP
HERC1	8925	hgsc.bcm.edu	hg19	15	64005696	64005696	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	HERC1	NM_003922	exon23	c.C4319G	p.A1440G	CATGCAGCAGTGT	.	96.0	33.0	104.0	0.0	.	624	.	.	.	none	.	.	PASS	Atlas-SNP
CILP	8483	hgsc.bcm.edu	hg19	15	65496681	65496681	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	CILP	NM_003613	exon6	c.T844A	p.F282I	GGGCAAACTTGAC	.	128.0	53.0	143.0	0.0	.	124	.	.	.	none	.	.	PASS	Atlas-SNP
SRL	6345	hgsc.bcm.edu	hg19	16	4245669	4245669	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	SRL	NM_001098814	exon5	c.T495G	p.F165L	CTGGCCAAACTTC	.	217.0	154.0	104.0	0.0	.	56	.	.	.	none	.	.	PASS	Atlas-SNP
NLK	51701	hgsc.bcm.edu	hg19	17	26490600	26490600	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	NLK	NM_016231	exon5	c.A783G	p.L261L	CATTTTACATCGA	.	46.0	17.0	59.0	0.0	.	88	.	.	.	none	.	.	PASS	Atlas-SNP
COX11	1353	hgsc.bcm.edu	hg19	17	53045784	53045784	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	COX11	NM_001162861	exon1	c.A224C	p.K75T	GAGCTCTTAGGCC	.	149.0	75.0	108.0	0.0	.	16	.	.	.	none	.	.	PASS	Atlas-SNP
DDX5	1655	hgsc.bcm.edu	hg19	17	62500170	62500170	+	Silent	SNP	T	T	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	DDX5	NM_004396	exon4	c.A372G	p.G124G	TGGCCATCCCTGA	.	172.0	103.0	173.0	1.0	.	101	.	.	.	none	.	.	PASS	Atlas-SNP
SLC9A3R1	9368	hgsc.bcm.edu	hg19	17	72745286	72745286	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	SLC9A3R1	NM_004252	exon1	c.A301T	p.K101X	CTGCAGAAGCTCG	.	28.0	15.0	19.0	0.0	.	12	.	.	.	none	.	.	PASS	Atlas-SNP
FASN	2194	hgsc.bcm.edu	hg19	17	80038618	80038618	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	FASN	NM_004104	exon39	c.G6776A	p.S2259N	GCCAGGCTGTGGA	.	32.0	7.0	28.0	0.0	.	154	.	.	.	none	.	.	PASS	Atlas-SNP
METTL4	64863	hgsc.bcm.edu	hg19	18	2554953	2554953	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	METTL4	NM_022840	exon4	c.C544G	p.Q182E	TGTCCTGTTTTTC	.	104.0	61.0	219.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
PALM	5064	hgsc.bcm.edu	hg19	19	746543	746543	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PALM	NM_002579	exon9	c.T893G	p.V298G	CCCCGGTCACAAT	.	56.0	19.0	49.0	0.0	.	26	.	.	.	none	.	.	PASS	Atlas-SNP
PIAS4	51588	hgsc.bcm.edu	hg19	19	4013072	4013072	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PIAS4	NM_015897	exon2	c.A179C	p.E60A	TCAAGGAGCTGTA	.	86.0	38.0	55.0	0.0	.	40	.	.	.	none	.	.	PASS	Atlas-SNP
FBXW9	84261	hgsc.bcm.edu	hg19	19	12807385	12807385	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	FBXW9	NM_032301	exon1	c.C11A	p.P4H	CCTAGGGGAAGCT	.	99.0	31.0	75.0	0.0	.	30	.	.	.	none	.	.	PASS	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	hg19	19	38976604	38976604	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	RYR1,lower_third,carcinoma,0,1	RYR1	NM_001042723	exon34	c.C5309T	p.S1770L	CCACTTCGCTGAG	.	87.0	41.0	67.0	0.0	.	708	.	.	.	none	.	.	PASS	Atlas-SNP
PSG3	5671	hgsc.bcm.edu	hg19	19	43237192	43237192	+	Silent	SNP	G	G	T	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PSG3	NM_021016	exon3	c.C453A	p.I151I	GCTGGAGATGGAG	.	310.0	117.0	341.0	1.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
PCBP3	54039	hgsc.bcm.edu	hg19	21	47333926	47333926	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	PCBP3	NM_020528	exon8	c.T662G	p.F221C	TCATTTTTGCAGG	.	100.0	39.0	78.0	0.0	.	82	.	.	.	none	.	.	PASS	Atlas-SNP
AMER1	139285	hgsc.bcm.edu	hg19	X	63412033	63412033	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	.	NM_152424	exon2	c.T1134C	p.D378D	CTCGTCATCATCA	.	85.0	7.0	88.0	0.0	.	.	.	.	.	none	.	.	PASS	Atlas-SNP
CDH17	1015	hgsc.bcm.edu	hg19	8	95158391	95158391	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	CDH17	NM_004063	exon15	c.1933delT	p.S645fs	.	.	76.0	24.0	81.0	0.0	.	119	.	0.315789	0	none	.	.	PASS	Atlas-INDEL
NID2	22795	hgsc.bcm.edu	hg19	14	52474565	52474565	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	NID2	NM_007361	exon19	c.3844delG	p.D1282fs	.	.	61.0	21.0	72.0	0.0	.	201	.	0.344262	0	none	.	.	PASS	Atlas-INDEL
TRMT112	51504	hgsc.bcm.edu	hg19	11	64084953	64084953	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	TRMT112	NM_016404	exon1	c.47delT	p.V16fs	.	.	34.0	11.0	16.0	0.0	.	9	.	0.323529	0	none	.	.	PASS	Atlas-INDEL
LRBA	987	hgsc.bcm.edu	hg19	4	151827549	151827549	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	LRBA	NM_006726	exon12	c.1503delG	p.L501fs	.	.	120.0	36.0	145.0	0.0	.	253	.	0.3	0	none	.	.	PASS	Atlas-INDEL
GPRASP1	9737	hgsc.bcm.edu	hg19	X	101912417	101912418	+	Frame_Shift_Del	DEL	TC	TC	-	novel		TCGA-BQ-7058-01A-11D-1961-08	TCGA-BQ-7058-11A-01D-1961-08	TC	TC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	041f174c-a781-487c-9e56-c867fb4aecfc	bd3d0c3b-1fb5-4164-96a9-7764d25ea84d	.	GPRASP1	NM_001184727	exon6	c.3575_3576del	p.1192_1192del	.	.	69.0	52.0	76.0	0.0	.	140	.	0.753623	0	none	.	.	PASS	Atlas-INDEL
