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	dbSNP_AF	Algorithm
VPS13D	55187	hgsc.bcm.edu	hg19	1	12422877	12422877	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	VPS13D	NM_015378	exon51	c.T10243C	p.F3415L	CTTGCATTTGCAC	.	199.0	103.0	110.0	0.0	.	316	.	.	Atlas-SNP
HSPG2	3339	hgsc.bcm.edu	hg19	1	22182073	22182073	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	HSPG2	NM_005529	exon46	c.T5797C	p.C1933R	CTCGGCACAAGTA	.	16.0	4.0	8.0	0.0	.	311	.	.	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	hg19	1	144879542	144879542	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	PDE4DIP,NS,carcinoma,0,2	PDE4DIP	NM_014644	exon27	c.T3908G	p.L1303R	TCCTTGAGGCTGT	.	45.0	7.0	27.0	1.0	.	817	.	.	Atlas-SNP
PDE4DIP	9659	hgsc.bcm.edu	hg19	1	144879561	144879561	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	PDE4DIP_ENST00000369356,NS,carcinoma,0,7	PDE4DIP	NM_014644	exon27	c.T3889C	p.C1297R	CCTCACACTCTGA	.	35.0	8.0	22.0	0.0	.	817	.	.	Atlas-SNP
NOTCH2NL	388677	hgsc.bcm.edu	hg19	1	145281614	145281614	+	Silent	SNP	C	C	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	NOTCH2NL	NM_203458	exon4	c.C544T	p.L182L	GACAGCCTGTATG	.	2183.0	249.0	1284.0	1.0	.	100	.	.	Atlas-SNP
TPO	7173	hgsc.bcm.edu	hg19	2	1520727	1520727	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	TPO	NM_001206744	exon15	c.G2591T	p.G864V	TCGCAGGTCTCAC	.	116.0	36.0	70.0	0.0	.	224	.	.	Atlas-SNP
CLIP4	79745	hgsc.bcm.edu	hg19	2	29386810	29386810	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	CLIP4	NM_024692	exon13	c.A1648G	p.R550G	CCATCCAGGGTGC	.	83.0	4.0	67.0	0.0	.	69	.	.	Atlas-SNP
CEBPZ	10153	hgsc.bcm.edu	hg19	2	37454714	37454714	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	CEBPZ,NS,carcinoma,0,3	CEBPZ	NM_005760	exon2	c.C1622T	p.S541L	CGATCCGATATTG	.	69.0	3.0	44.0	0.0	.	68	.	.	Atlas-SNP
FSIP2	401024	hgsc.bcm.edu	hg19	2	186673528	186673528	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	FSIP2	NM_173651	exon17	c.G19762A	p.V6588M	TTTAATGTGATTC	.	67.0	20.0	90.0	0.0	.	251	.	.	Atlas-SNP
BARD1	580	hgsc.bcm.edu	hg19	2	215617259	215617259	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	BARD1	NM_000465	exon7	c.C1589T	p.P530L	TCGACAGGCCGCA	.	80.0	36.0	51.0	0.0	.	138	.	.	Atlas-SNP
FGD5	152273	hgsc.bcm.edu	hg19	3	14861791	14861791	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	FGD5	NM_152536	exon1	c.G1213T	p.A405S	GGAGCGGCCGAGG	.	84.0	37.0	74.0	0.0	.	248	.	.	Atlas-SNP
KAT2B	8850	hgsc.bcm.edu	hg19	3	20113881	20113881	+	Silent	SNP	C	C	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	KAT2B	NM_003884	exon2	c.C360G	p.P120P	CACTCCCCCCAGA	.	87.0	31.0	71.0	0.0	.	73	.	.	Atlas-SNP
CACNA2D3	55799	hgsc.bcm.edu	hg19	3	54905638	54905638	+	Silent	SNP	C	C	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	CACNA2D3	NM_018398	exon18	c.C1699A	p.R567R	GAAGACCGAGATG	.	198.0	69.0	141.0	0.0	.	159	.	.	Atlas-SNP
CASR	846	hgsc.bcm.edu	hg19	3	121994752	121994752	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	CASR	NM_001178065	exon5	c.A1471G	p.I491V	TATTCCATCATCA	.	241.0	96.0	168.0	0.0	.	190	.	.	Atlas-SNP
SORCS2	57537	hgsc.bcm.edu	hg19	4	7714544	7714544	+	Silent	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	SORCS2	NM_020777	exon15	c.G1953A	p.E651E	CGGCGAGGAGGAC	.	170.0	70.0	87.0	0.0	.	98	.	.	Atlas-SNP
NME5	8382	hgsc.bcm.edu	hg19	5	137465065	137465065	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	NME5	NM_003551	exon3	c.G222A	p.M74I	AGAACTCATGTAA	.	135.0	41.0	144.0	0.0	.	15	.	.	Atlas-SNP
KLHL32	114792	hgsc.bcm.edu	hg19	6	97561726	97561726	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	KLHL32	NM_052904	exon7	c.G695A	p.R232H	ACATCCGCTTTGG	.	180.0	95.0	183.0	0.0	.	85	.	.	Atlas-SNP
RFX6	222546	hgsc.bcm.edu	hg19	6	117237178	117237178	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	RFX6	NM_173560	exon8	c.C788T	p.T263M	TTGATACGCTCAT	.	143.0	53.0	104.0	0.0	.	141	.	.	Atlas-SNP
ZBTB2	57621	hgsc.bcm.edu	hg19	6	151694605	151694605	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	ZBTB2	NM_020861	exon2	c.G168C	p.Q56H	CCTGGTCTGATGG	.	256.0	86.0	154.0	0.0	.	30	.	.	Atlas-SNP
ZNF3	7551	hgsc.bcm.edu	hg19	7	99662525	99662525	+	Silent	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	ZNF3	NM_017715	exon6	c.C282T	p.H94H	ACAGACGTGTATC	.	214.0	64.0	100.0	0.0	.	54	.	.	Atlas-SNP
SSPO	23145	hgsc.bcm.edu	hg19	7	149523815	149523815	+	Silent	SNP	C	C	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	.	NM_198455	exon103	c.C14625G	p.T4875T	CTGCACCCAGCAT	.	37.0	11.0	24.0	0.0	.	.	.	.	Atlas-SNP
EN2	2020	hgsc.bcm.edu	hg19	7	155251239	155251239	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	EN2	NM_001427	exon1	c.C167A	p.A56E	TGCAGGCGCCCGG	.	12.0	6.0	13.0	0.0	.	14	.	.	Atlas-SNP
TTPA	7274	hgsc.bcm.edu	hg19	8	63973814	63973814	+	Silent	SNP	T	T	C	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	TTPA	NM_000370	exon5	c.A834G	p.Q278Q	TTCTCATTGAATG	.	45.0	17.0	31.0	0.0	.	29	.	.	Atlas-SNP
RMDN1	51115	hgsc.bcm.edu	hg19	8	87520767	87520767	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	.	NM_016033	exon1	c.C83A	p.S28X	CTGCCCGAAGTCC	.	9.0	5.0	20.0	0.0	.	.	.	.	Atlas-SNP
COL14A1	7373	hgsc.bcm.edu	hg19	8	121381587	121381587	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	COL14A1,colon,carcinoma,0,1	COL14A1	NM_021110	exon47	c.G5174A	p.R1725Q	AGAGTCGGCCTGG	.	40.0	13.0	22.0	0.0	.	292	.	.	Atlas-SNP
MLLT10	8028	hgsc.bcm.edu	hg19	10	21901356	21901356	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	MLLT10	NM_001195626	exon5	c.G485T	p.C162F	ATGGATGTCGACA	.	48.0	20.0	50.0	0.0	.	183	.	.	Atlas-SNP
OR51B6	390058	hgsc.bcm.edu	hg19	11	5372775	5372775	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	OR51B6	NM_001004750	exon1	c.C38T	p.T13I	AGCTTACTGGCTT	.	229.0	87.0	148.0	0.0	.	53	.	.	Atlas-SNP
IL10RA	3587	hgsc.bcm.edu	hg19	11	117860190	117860190	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	IL10RA	NM_001558	exon3	c.C222A	p.N74K	CTCCAACTGTAGC	.	308.0	100.0	231.0	0.0	.	46	.	.	Atlas-SNP
OVCH1	341350	hgsc.bcm.edu	hg19	12	29626033	29626033	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	OVCH1	NM_183378	exon15	c.C1604T	p.S535F	TTTAAAGACTCTG	.	51.0	17.0	63.0	0.0	.	195	.	.	Atlas-SNP
EP400	57634	hgsc.bcm.edu	hg19	12	132512744	132512744	+	Silent	SNP	G	G	T	rs34531099	bycluster;byfrequency;by1000genomes;alternate_allele	TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	EP400	NM_015409	exon27	c.G5292T	p.A1764A	GCCAGCGCACAGT	.	329.0	141.0	135.0	0.0	.	370	.	G|0.997;A|0.003	Atlas-SNP
SYNE3	161176	hgsc.bcm.edu	hg19	14	95909555	95909555	+	Silent	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	SYNE3	NM_152592	exon10	c.C1848T	p.P616P	GTGGTTGGGGTTC	.	170.0	58.0	103.0	0.0	.	130	.	.	Atlas-SNP
AP4E1	23431	hgsc.bcm.edu	hg19	15	51223097	51223097	+	Silent	SNP	C	C	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	AP4E1	NM_007347	exon7	c.C798T	p.H266H	TTACCACAGTGTG	.	107.0	40.0	70.0	0.0	.	78	.	.	Atlas-SNP
CORO2B	10391	hgsc.bcm.edu	hg19	15	69011111	69011111	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	CORO2B	NM_006091	exon9	c.G1042T	p.G348C	CTCAAGGGCCTGA	.	175.0	64.0	78.0	0.0	.	68	.	.	Atlas-SNP
SLC47A1	55244	hgsc.bcm.edu	hg19	17	19452981	19452981	+	Silent	SNP	A	A	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	SLC47A1	NM_018242	exon5	c.A489T	p.P163P	CATTCCAGCTCTT	.	102.0	65.0	94.0	0.0	.	55	.	.	Atlas-SNP
PPP1R1B	84152	hgsc.bcm.edu	hg19	17	37792089	37792089	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	PPP1R1B	NM_032192	exon7	c.C586T	p.R196C	CCTCAGCGCCCTT	.	75.0	27.0	29.0	0.0	.	9	.	.	Atlas-SNP
DCC	1630	hgsc.bcm.edu	hg19	18	51025826	51025826	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	DCC	NM_005215	exon27	c.C4057G	p.P1353A	CCTCCACCAATGA	.	290.0	90.0	204.0	0.0	.	360	.	.	Atlas-SNP
HNRNPM	4670	hgsc.bcm.edu	hg19	19	8520429	8520429	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	HNRNPM	NM_031203	exon2	c.A254G	p.Q85R	AATGGCAGTCACT	.	117.0	39.0	70.0	0.0	.	61	.	.	Atlas-SNP
CC2D1A	54862	hgsc.bcm.edu	hg19	19	14020723	14020723	+	Missense_Mutation	SNP	G	G	C	rs368933699	alternate_allele	TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	CC2D1A	NM_017721	exon2	c.G148C	p.A50P	TTCTTGGCTTTGG	.	223.0	22.0	136.0	0.0	.	67	.	.	Atlas-SNP
PLEKHA4	57664	hgsc.bcm.edu	hg19	19	49364729	49364729	+	Missense_Mutation	SNP	C	C	T	rs369244059		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	PLEKHA4	NM_001161354	exon5	c.G295A	p.V99I	GCAGGACGCTGCC	.	36.0	10.0	22.0	0.0	.	70	.	.	Atlas-SNP
ACPT	93650	hgsc.bcm.edu	hg19	19	51298384	51298384	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	ACPT	NM_033068	exon11	c.G1250A	p.G417E	GACCAGGGTGCCT	.	14.0	10.0	8.0	0.0	.	43	.	.	Atlas-SNP
COL20A1	57642	hgsc.bcm.edu	hg19	20	61937235	61937235	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	COL20A1	NM_020882	exon5	c.G340T	p.E114X	GCAGTTGAGGATC	.	125.0	19.0	41.0	0.0	.	137	.	.	Atlas-SNP
POTEH	23784	hgsc.bcm.edu	hg19	22	16287641	16287641	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	POTEH	NM_001136213	exon1	c.C245T	p.T82I	CCAGAAGTGCCCA	.	551.0	154.0	370.0	0.0	.	114	.	.	Atlas-SNP
YPEL1	29799	hgsc.bcm.edu	hg19	22	22064931	22064931	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	YPEL1	NM_013313	exon2	c.G103A	p.E35K	TGAGCTCGTCATG	.	398.0	43.0	231.0	0.0	.	6	.	.	Atlas-SNP
CCNB3	85417	hgsc.bcm.edu	hg19	X	50090667	50090667	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	CCNB3	NM_033031	exon10	c.A3853G	p.I1285V	CGCTACATCTGCG	.	183.0	22.0	131.0	0.0	.	367	.	.	Atlas-SNP
ZNF280C	55609	hgsc.bcm.edu	hg19	X	129349844	129349844	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	ZNF280C	NM_017666	exon14	c.T1759A	p.S587T	CTTTGGACTTAGC	.	222.0	89.0	155.0	0.0	.	63	.	.	Atlas-SNP
COX1	5742	hgsc.bcm.edu	hg19	MT	7164	7164	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	.	ENST00000361624	exon1	c.G1261A	p.V421M	ATCGGCGTAAATC	.	59.0	23.0	5.0	0.0	.	.	.	.	Atlas-SNP
ND4	0	hgsc.bcm.edu	hg19	MT	11438	11438	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	.	ENST00000361381	exon1	c.G679A	p.G227X	ATCGCTGGGTCAA	.	34.0	23.0	5.0	0.0	.	.	.	.	Atlas-SNP
ND5	0	hgsc.bcm.edu	hg19	MT	12989	12989	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	.	ENST00000361567	exon1	c.T653C	p.L218P	TCCTCCTAGCAGC	.	67.0	18.0	6.0	0.0	.	.	.	.	Atlas-SNP
QRICH2	84074	hgsc.bcm.edu	hg19	17	74289942	74289954	+	Frame_Shift_Del	DEL	CCAGATCCTGATG	CCAGATCCTGATG	-	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	CCAGATCCTGATG	CCAGATCCTGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	QRICH2	NM_032134	exon4	c.357_369del	p.119_123del	.	.	115.0	22.0	74.0	0.0	.	143	.	.	Atlas-Indel,Pindel
MTERF	7978	hgsc.bcm.edu	hg19	7	91503047	91503053	+	Frame_Shift_Del	DEL	GAATCCA	GAATCCA	-	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	GAATCCA	GAATCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	MTERF	NM_006980	exon3	c.1056_1062del	p.352_354del	.	.	71.0	11.0	73.0	0.0	.	32	.	.	Atlas-INDEL
EED	8726	hgsc.bcm.edu	hg19	11	85975252	85975260	+	In_Frame_Del	DEL	CTGGTGGCA	CTGGTGGCA	-	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	CTGGTGGCA	CTGGTGGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	EED	NM_152991	exon7	c.672_680del	p.224_227del	.	.	110.0	15.0	113.0	0.0	.	50	.	.	Atlas-Indel,Pindel
PIK3R1	5295	hgsc.bcm.edu	hg19	5	67591127	67591129	+	In_Frame_Del	DEL	AGA	AGA	-	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	PIK3R1_ENST00000336483,NS,carcinoma,+1,5	PIK3R1	NM_181523	exon13	c.1719_1721del	p.573_574del	.	.	108.0	65.0	99.0	0.0	.	869	.	.	Atlas-Indel,Pindel
ZSCAN1	284312	hgsc.bcm.edu	hg19	19	58565260	58565260	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	ZSCAN1	NM_182572	exon6	c.1067delG	p.G356fs	.	.	153.0	54.0	99.0	0.0	.	102	.	.	Atlas-Indel,Pindel
PRICKLE2	166336	hgsc.bcm.edu	hg19	3	64148733	64148742	+	Frame_Shift_Del	DEL	TTCGCAGTTT	TTCGCAGTTT	-	novel		TCGA-PD-A5DF-01A-11D-A27I-10	TCGA-PD-A5DF-10A-01D-A27I-10	TTCGCAGTTT	TTCGCAGTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	f1a4f60a-5228-47cd-883f-ff8d2dfe1633	ce137c9c-43df-49e8-82f8-3530d13eecfd	.	PRICKLE2	NM_198859	exon3	c.209_218del	p.70_73del	.	.	155.0	34.0	121.0	0.0	.	88	.	.	Atlas-Indel,Pindel