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
CSMD2	114784	hgsc.bcm.edu	hg19	1	34180229	34180229	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	CSMD2	NM_052896	exon21	c.G3244A	p.G1082S	GTCTGCCCCCCAG	.	106.0	71.0	302.0	0.0	.	946	.	.	.	none	.	.	PASS	Atlas-SNP
ENSA	2029	hgsc.bcm.edu	hg19	1	150601936	150601936	+	Missense_Mutation	SNP	T	T	G	rs148754482	byfrequency;alternate_allele	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	ENSA	NM_004436	exon1	c.A11C	p.K4T	TCTTGTTTCTGGG	.	76.0	35.0	108.0	0.0	.	41	.	.	.	alt	T|1.000;C|0.000	.	PASS	Atlas-SNP
C2orf16	84226	hgsc.bcm.edu	hg19	2	27802751	27802751	+	Silent	SNP	C	C	A	rs375978019	alternate_allele	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	C2orf16_ENST00000408964,NS,carcinoma,0,2	C2orf16	NM_032266	exon1	c.C3312A	p.P1104P	ACCCCCCGATGTG	.	155.0	9.0	159.0	2.0	.	357	.	.	.	alt	.	.	PASS	Atlas-SNP
HEATR5B	54497	hgsc.bcm.edu	hg19	2	37235951	37235951	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	HEATR5B	NM_019024	exon28	c.C4325T	p.S1442L	GGTTTTGACTCTG	.	196.0	83.0	243.0	0.0	.	185	.	.	.	none	.	.	PASS	Atlas-SNP
CLASP1	23332	hgsc.bcm.edu	hg19	2	122122716	122122716	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	CLASP1	NM_015282	exon35	c.T4031G	p.F1344C	GTCTTGAAGTGCT	.	39.0	20.0	40.0	0.0	.	135	.	.	.	none	.	.	PASS	Atlas-SNP
NFE2L2	4780	hgsc.bcm.edu	hg19	2	178098800	178098800	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	NFE2L2,NS,carcinoma,+1,7	NFE2L2	NM_006164	exon2	c.A245G	p.E82G	AGAAATTCACCTG	.	99.0	41.0	118.0	0.0	.	225	.	.	.	none	.	.	PASS	Atlas-SNP
ATIC	471	hgsc.bcm.edu	hg19	2	216211585	216211585	+	Nonsense_Mutation	SNP	C	C	A	rs139340343	bycluster;byfrequency;alternate_allele	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	ATIC_ENST00000236959,NS,carcinoma,-1,1	ATIC	NM_004044	exon14	c.C1424A	p.S475X	TGCTTTCGATGAA	.	121.0	5.0	147.0	1.0	.	84	.	.	.	alt	C|1.000;T|0.000	.	PASS	Atlas-SNP
FN1	2335	hgsc.bcm.edu	hg19	2	216289927	216289927	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	FN1	NM_212476	exon7	c.T926G	p.V309G	TCTGTGACACAGT	.	224.0	90.0	267.0	1.0	.	521	.	.	.	none	.	.	PASS	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	hg19	3	38645417	38645417	+	Missense_Mutation	SNP	G	G	A	rs199473575		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	SCN5A	NM_001160160	exon12	c.C1676T	p.T559I	AGTGATGTGTGGT	.	67.0	35.0	77.0	0.0	.	634	.	.	.	weak	.	.	PASS	Atlas-SNP
AFAP1	60312	hgsc.bcm.edu	hg19	4	7857226	7857226	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	AFAP1	NM_001134647	exon4	c.A301C	p.S101R	CGGGGCTCAGCGG	.	60.0	26.0	88.0	0.0	.	93	.	.	.	none	.	.	PASS	Atlas-SNP
SMARCAD1	56916	hgsc.bcm.edu	hg19	4	95191935	95191935	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	SMARCAD1	NM_001128429	exon11	c.A1538G	p.K513R	TACATAAACATGG	.	123.0	47.0	164.0	0.0	.	97	.	.	.	none	.	.	PASS	Atlas-SNP
PDZD2	23037	hgsc.bcm.edu	hg19	5	32108145	32108145	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PDZD2	NM_178140	exon24	c.G8424A	p.L2808L	ACCTCTGGTTGGG	.	125.0	54.0	125.0	0.0	.	306	.	.	.	none	.	.	PASS	Atlas-SNP
POLK	51426	hgsc.bcm.edu	hg19	5	74872636	74872636	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	POLK	NM_016218	exon6	c.A572C	p.N191T	ATCCCAATTTTAT	.	54.0	24.0	79.0	0.0	.	123	.	.	.	none	.	.	PASS	Atlas-SNP
MAML1	9794	hgsc.bcm.edu	hg19	5	179192887	179192887	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	MAML1	NM_014757	exon2	c.G876A	p.L292L	CCCCTTGGCACAG	.	146.0	68.0	164.0	0.0	.	118	.	.	.	none	.	.	PASS	Atlas-SNP
PRRC2A	7916	hgsc.bcm.edu	hg19	6	31595867	31595867	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PRRC2A	NM_004638	exon12	c.C1616T	p.A539V	CATCAGCCCCAAC	.	136.0	55.0	159.0	0.0	.	152	.	.	.	none	.	.	PASS	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	hg19	6	51917922	51917922	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PKHD1	NM_170724	exon21	c.G2092A	p.G698S	ACAGGCCCGTCTC	.	62.0	25.0	85.0	0.0	.	927	.	.	.	none	.	.	PASS	Atlas-SNP
CLIP2	7461	hgsc.bcm.edu	hg19	7	73752800	73752800	+	Silent	SNP	A	A	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	CLIP2	NM_032421	exon3	c.A144T	p.S48S	ACAGTCATCTGGA	.	29.0	18.0	19.0	0.0	.	134	.	.	.	none	.	.	PASS	Atlas-SNP
CHCHD3	54927	hgsc.bcm.edu	hg19	7	132754922	132754922	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	CHCHD3	NM_017812	exon2	c.C149T	p.S50F	GCACCAGAATACC	.	82.0	17.0	71.0	0.0	.	21	.	.	.	none	.	.	PASS	Atlas-SNP
EXOC4	60412	hgsc.bcm.edu	hg19	7	133692515	133692515	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	EXOC4	NM_021807	exon17	c.A2614G	p.R872G	ATGTGTAGGAACA	.	83.0	36.0	63.0	0.0	.	118	.	.	.	none	.	.	PASS	Atlas-SNP
MGAM	8972	hgsc.bcm.edu	hg19	7	141750617	141750617	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	MGAM	NM_004668	exon24	c.G2758T	p.V920F	AATGGTGTCCCAA	.	196.0	41.0	147.0	0.0	.	767	.	.	.	none	.	.	PASS	Atlas-SNP
LZTS1	11178	hgsc.bcm.edu	hg19	8	20107305	20107305	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	LZTS1	NM_021020	exon3	c.C1719T	p.A573A	CTCCCCGGCGCTG	.	124.0	56.0	132.0	0.0	.	72	.	.	.	none	.	.	PASS	Atlas-SNP
PKHD1L1	93035	hgsc.bcm.edu	hg19	8	110451259	110451259	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PKHD1L1	NM_177531	exon32	c.G3894A	p.K1298K	GCCCAAGTTGTCT	.	212.0	81.0	249.0	0.0	.	522	.	.	.	none	.	.	PASS	Atlas-SNP
NMT2	9397	hgsc.bcm.edu	hg19	10	15154953	15154953	+	Missense_Mutation	SNP	C	C	A	rs201047504	alternate_allele	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	NMT2,NS,carcinoma,0,1	NMT2	NM_004808	exon10	c.G1180T	p.G394C	GTTTACCGTTGGG	.	121.0	8.0	144.0	2.0	.	44	.	.	.	alt	.	.	PASS	Atlas-SNP
SLC16A9	220963	hgsc.bcm.edu	hg19	10	61413807	61413807	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	SLC16A9	NM_194298	exon5	c.T977C	p.L326P	TCCATAAGTAATG	.	77.0	29.0	55.0	0.0	.	58	.	.	.	none	.	.	PASS	Atlas-SNP
PDLIM1	9124	hgsc.bcm.edu	hg19	10	96998413	96998413	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PDLIM1	NM_020992	exon6	c.A715C	p.S239R	TAACACTTCTGAA	.	66.0	26.0	64.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
DNMBP	23268	hgsc.bcm.edu	hg19	10	101646325	101646325	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	DNMBP	NM_015221	exon13	c.C3350G	p.P1117R	TTATGGGGCCCTG	.	236.0	80.0	256.0	0.0	.	173	.	.	.	none	.	.	PASS	Atlas-SNP
SLK	9748	hgsc.bcm.edu	hg19	10	105750528	105750528	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	SLK	NM_014720	exon2	c.A246G	p.I82M	TGACATATTAGCA	.	69.0	29.0	75.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	hg19	11	1247945	1247945	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	MUC5B	NM_002458	exon4	c.C300G	p.N100K	TTGCAACTACGTG	.	36.0	7.0	37.0	0.0	.	473	.	.	.	none	.	.	PASS	Atlas-SNP
PRKRIR	5612	hgsc.bcm.edu	hg19	11	76063689	76063689	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PRKRIR	NM_004705	exon5	c.C505G	p.L169V	CAAATAGAGATTT	.	29.0	21.0	54.0	0.0	.	65	.	.	.	none	.	.	PASS	Atlas-SNP
DIP2B	57609	hgsc.bcm.edu	hg19	12	51019819	51019819	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	DIP2B,NS,carcinoma,0,1	DIP2B	NM_173602	exon2	c.C161A	p.P54Q	ACAGCCCGCAGAC	.	142.0	10.0	128.0	2.0	.	167	.	.	.	none	.	.	PASS	Atlas-SNP
MON2	23041	hgsc.bcm.edu	hg19	12	62959064	62959064	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	MON2	NM_015026	exon27	c.A4080G	p.I1360M	AGCTATATTTGAC	.	199.0	91.0	227.0	1.0	.	160	.	.	.	none	.	.	PASS	Atlas-SNP
DOCK9	23348	hgsc.bcm.edu	hg19	13	99540613	99540613	+	Splice_Site	SNP	C	C	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	DOCK9	NM_015296	exon18	c.1980+1G>A	.	CACTCACCTTGGC	.	224.0	24.0	227.0	0.0	.	311	.	.	.	none	.	.	PASS	Atlas-SNP
FAM71D	161142	hgsc.bcm.edu	hg19	14	67688507	67688507	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	FAM71D	NM_173526	exon7	c.C1172A	p.T391N	TGAGAACTGAATC	.	54.0	11.0	63.0	0.0	.	33	.	.	.	none	.	.	PASS	Atlas-SNP
DPF3	8110	hgsc.bcm.edu	hg19	14	73238479	73238479	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	DPF3_ENST00000541685,NS,carcinoma,0,3	DPF3	NM_012074	exon2	c.A155C	p.N52T	TAGCAGTTGTTCT	.	90.0	38.0	158.0	1.0	.	117	.	.	.	none	.	.	PASS	Atlas-SNP
PPP4R4	57718	hgsc.bcm.edu	hg19	14	94741788	94741788	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PPP4R4	NM_058237	exon24	c.C2527A	p.R843S	ACTTCCCGTGGGA	.	186.0	9.0	204.0	0.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
ZNF609	23060	hgsc.bcm.edu	hg19	15	64966235	64966235	+	Silent	SNP	G	G	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	ZNF609	NM_015042	exon4	c.G1182T	p.G394G	CAAAGGGACCAGT	.	150.0	55.0	191.0	0.0	.	106	.	.	.	none	.	.	PASS	Atlas-SNP
THSD4	79875	hgsc.bcm.edu	hg19	15	72063439	72063439	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	THSD4	NM_024817	exon16	c.G2806C	p.E936Q	GTCCGGGAAGTGC	.	143.0	63.0	172.0	0.0	.	75	.	.	.	none	.	.	PASS	Atlas-SNP
BNC1	646	hgsc.bcm.edu	hg19	15	83932666	83932666	+	Missense_Mutation	SNP	G	G	A	rs377611889		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	BNC1	NM_001717	exon4	c.C1337T	p.T446M	GGGGACGTCACTG	.	71.0	27.0	92.0	0.0	.	149	.	.	.	weak	.	.	PASS	Atlas-SNP
AKAP13	11214	hgsc.bcm.edu	hg19	15	86125257	86125257	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	AKAP13	NM_007200	exon7	c.G3958C	p.G1320R	GCCACGGGGAGCC	.	89.0	4.0	115.0	0.0	.	394	.	.	.	none	.	.	PASS	Atlas-SNP
ADAMTS17	170691	hgsc.bcm.edu	hg19	15	100871170	100871170	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	ADAMTS17	NM_139057	exon3	c.C540T	p.I180I	GCGCCTGATCAGA	.	87.0	47.0	99.0	0.0	.	127	.	.	.	none	.	.	PASS	Atlas-SNP
PDILT	204474	hgsc.bcm.edu	hg19	16	20410442	20410442	+	Missense_Mutation	SNP	G	G	T	rs368369154	alternate_allele	TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	PDILT,NS,carcinoma,+1,1	PDILT	NM_174924	exon2	c.C181A	p.R61S	GGAAGCGGGTCTG	.	105.0	7.0	68.0	1.0	.	120	.	.	.	alt	.	.	PASS	Atlas-SNP
IRX6	79190	hgsc.bcm.edu	hg19	16	55360382	55360382	+	Silent	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	IRX6	NM_024335	exon2	c.G180A	p.A60A	CAGTGCGCGACCG	.	48.0	28.0	40.0	0.0	.	66	.	.	.	none	.	.	PASS	Atlas-SNP
CDH5	1003	hgsc.bcm.edu	hg19	16	66413245	66413245	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	CDH5	NM_001795	exon2	c.A5C	p.Q2P	AGATGCAGAGGCT	.	268.0	61.0	231.0	0.0	.	111	.	.	.	none	.	.	PASS	Atlas-SNP
ZC3H18	124245	hgsc.bcm.edu	hg19	16	88666335	88666335	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	ZC3H18	NM_144604	exon6	c.C1067A	p.P356Q	GGATCCCGAGAGA	.	184.0	9.0	153.0	0.0	.	90	.	.	.	none	.	.	PASS	Atlas-SNP
SREBF1	6720	hgsc.bcm.edu	hg19	17	17722461	17722461	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	SREBF1	NM_001005291	exon6	c.A1024G	p.S342G	CCTTGCTGCCAGC	.	83.0	34.0	92.0	0.0	.	47	.	.	.	none	.	.	PASS	Atlas-SNP
POLG2	11232	hgsc.bcm.edu	hg19	17	62486981	62486981	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	POLG2	NM_007215	exon4	c.G901C	p.E301Q	GGGTTTCTATTAA	.	81.0	39.0	86.0	0.0	.	29	.	.	.	none	.	.	PASS	Atlas-SNP
RNF213	57674	hgsc.bcm.edu	hg19	17	78293016	78293016	+	Silent	SNP	C	C	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	RNF213	NM_001256071	exon17	c.C2928G	p.A976A	CACTGCCTACTGC	.	218.0	79.0	217.0	0.0	.	766	.	.	.	none	.	.	PASS	Atlas-SNP
LPHN1	22859	hgsc.bcm.edu	hg19	19	14268166	14268166	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	LPHN1,NS,carcinoma,0,1	LPHN1	NM_001008701	exon15	c.G2657T	p.R886L	AGCCCCCGCAGGA	.	135.0	7.0	113.0	1.0	.	107	.	.	.	none	.	.	PASS	Atlas-SNP
EPS15L1	58513	hgsc.bcm.edu	hg19	19	16503123	16503123	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	EPS15L1	NM_021235	exon19	c.C2095T	p.P699S	TCGAAGGTAAGGA	.	80.0	43.0	82.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
EPS15L1	58513	hgsc.bcm.edu	hg19	19	16503124	16503124	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	EPS15L1	NM_021235	exon19	c.A2094T	p.L698F	CGAAGGTAAGGAA	.	79.0	43.0	84.0	0.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
EPS15L1	58513	hgsc.bcm.edu	hg19	19	16551694	16551694	+	Silent	SNP	A	A	G	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	EPS15L1	NM_021235	exon4	c.T192C	p.G64G	CCCTTTACCTTCT	.	503.0	186.0	541.0	1.0	.	81	.	.	.	none	.	.	PASS	Atlas-SNP
BCAM	4059	hgsc.bcm.edu	hg19	19	45322619	45322619	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	BCAM	NM_001013257	exon12	c.C1490T	p.P497L	CAATCCCCGGACG	.	46.0	22.0	84.0	0.0	.	53	.	.	.	none	.	.	PASS	Atlas-SNP
FCAR	2204	hgsc.bcm.edu	hg19	19	55385758	55385758	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	FCAR	NM_133279	exon1	c.C13T	p.Q5X	CCCAAACAGACCA	.	136.0	59.0	138.0	0.0	.	110	.	.	.	none	.	.	PASS	Atlas-SNP
LNX2	222484	hgsc.bcm.edu	hg19	13	28136573	28136575	+	In_Frame_Del	DEL	CCG	CCG	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	LNX2	NM_153371	exon5	c.1200_1202del	p.400_401del	.	.	143.0	58.0	175.0	0.0	.	70	.	0.405594	0	none	.	.	PASS	Atlas-INDEL
PORCN	64840	hgsc.bcm.edu	hg19	X	48371012	48371012	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PORCN	NM_203475	exon5	c.590delT	p.L197fs	.	.	11.0	11.0	15.0	0.0	.	61	.	1	0	none	.	.	PASS	Atlas-INDEL
C15orf43	145645	hgsc.bcm.edu	hg19	15	45270783	45270783	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	C15orf43	NM_152448	exon7	c.619delG	p.E207fs	.	.	44.0	18.0	52.0	0.0	.	19	.	0.409091	0	none	.	.	PASS	Atlas-INDEL
C19orf45	374877	hgsc.bcm.edu	hg19	19	7570473	7570475	+	In_Frame_Del	DEL	CGG	CGG	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	C19orf45	NM_198534	exon6	c.965_967del	p.322_323del	.	.	71.0	25.0	97.0	0.0	.	36	.	0.352113	0	none	.	.	PASS	Atlas-INDEL
PARD6B	84612	hgsc.bcm.edu	hg19	20	49366983	49366991	+	In_Frame_Del	DEL	TCAAAAACT	TCAAAAACT	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	TCAAAAACT	TCAAAAACT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PARD6B	NM_032521	exon3	c.1076_1084del	p.359_362del	.	.	74.0	22.0	66.0	0.0	.	31	.	0.297297	0	none	.	.	PASS	Atlas-INDEL
NF1	4763	hgsc.bcm.edu	hg19	17	29552188	29552189	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	NF1	NM_001042492	exon17	c.1920_1921del	p.640_641del	.	.	177.0	70.0	171.0	0.0	.	1586	.	0.39548	0	none	.	.	PASS	Atlas-INDEL
ITPKA	3706	hgsc.bcm.edu	hg19	15	41794669	41794670	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	ITPKA	NM_002220	exon5	c.1078_1079insA	p.E360fs	.	.	80.0	29.0	67.0	0.0	.	19	.	0.3625	0	none	.	.	PASS	Atlas-INDEL
NF1	4763	hgsc.bcm.edu	hg19	17	29490388	29490388	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	NF1	NM_001042492	exon4	c.472delT	p.S158fs	.	.	104.0	56.0	110.0	0.0	.	1586	.	0.538462	0	none	.	.	PASS	Atlas-INDEL
SLC10A4	201780	hgsc.bcm.edu	hg19	4	48490947	48490948	+	Frame_Shift_Ins	INS	-	-	TC	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.,1	SLC10A4	NM_152679	exon3	c.1305_1306insTC	p.T435fs	.	.	67.0	16.0	63.0	0.0	.	23	.	0.238806	0	none	.	.	PASS	Atlas-INDEL
UFSP1	402682	hgsc.bcm.edu	hg19	7	100486530	100486530	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	UFSP1	NM_001015072	exon1	c.364delA	p.N122fs	.	.	197.0	106.0	153.0	0.0	.	8	.	0.538071	0	none	.	.	PASS	Atlas-INDEL
PPP2R2A	5520	hgsc.bcm.edu	hg19	8	26227846	26227849	+	Frame_Shift_Del	DEL	CACA	CACA	-	novel		TCGA-BQ-7044-01A-11D-1961-08	TCGA-BQ-7044-11A-01D-1961-08	CACA	CACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f0589e51-4685-4613-8004-44efad45180f	12341a8c-b9d0-445d-b2fd-ed077738ba31	.	PPP2R2A	NM_001177591	exon10	c.1290_1293del	p.430_431del	.	.	45.0	11.0	51.0	0.0	.	44	.	0.244444	0	none	.	.	PASS	Atlas-INDEL