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
GLIS1	148979	hgsc.bcm.edu	hg19	1	53974802	53974802	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	GLIS1	NM_147193	exon9	c.C1696T	p.P566S	TGGCAGGCAAGGG	.	56.0	9.0	39.0	0.0	.	52	.	.	Atlas-SNP
PALMD	54873	hgsc.bcm.edu	hg19	1	100154970	100154970	+	Nonsense_Mutation	SNP	C	C	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	PALMD	NM_017734	exon7	c.C1154G	p.S385X	ATTCTTCACCCAC	.	77.0	19.0	88.0	0.0	.	64	.	.	Atlas-SNP
PLA2G4A	5321	hgsc.bcm.edu	hg19	1	186880477	186880477	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	PLA2G4A	NM_024420	exon7	c.C514T	p.L172F	AAGAAACTCTTGG	.	133.0	24.0	124.0	0.0	.	125	.	.	Atlas-SNP
ASPM	259266	hgsc.bcm.edu	hg19	1	197094016	197094016	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ASPM	NM_001206846	exon12	c.T3152C	p.I1051T	AACGCTATTTTCC	.	201.0	15.0	127.0	0.0	.	444	.	.	Atlas-SNP
GREB1	9687	hgsc.bcm.edu	hg19	2	11738862	11738862	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	GREB1	NM_014668	exon15	c.C2209G	p.Q737E	GTGGAACAGTATG	.	87.0	25.0	85.0	0.0	.	308	.	.	Atlas-SNP
ATAD2B	54454	hgsc.bcm.edu	hg19	2	23980355	23980355	+	Silent	SNP	A	A	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ATAD2B	NM_017552	exon25	c.T4011C	p.C1337C	ATTGCTACATTCC	.	160.0	39.0	167.0	0.0	.	110	.	.	Atlas-SNP
DGUOK	1716	hgsc.bcm.edu	hg19	2	74185303	74185303	+	Silent	SNP	A	A	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	DGUOK	NM_080916	exon6	c.A738G	p.P246P	CATTCCAGTGCTG	.	174.0	36.0	147.0	0.0	.	16	.	.	Atlas-SNP
IL18RAP	8807	hgsc.bcm.edu	hg19	2	103039738	103039738	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	IL18RAP	NM_003853	exon3	c.A1T	p.M1L	AGAACAATGCTCT	.	185.0	44.0	195.0	0.0	.	102	.	.	Atlas-SNP
SPEG	10290	hgsc.bcm.edu	hg19	2	220326612	220326612	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	SPEG	NM_005876	exon7	c.A2449G	p.T817A	GGGTCTACATCCC	.	75.0	15.0	76.0	0.0	.	272	.	.	Atlas-SNP
PER2	8864	hgsc.bcm.edu	hg19	2	239161713	239161713	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	PER2,NS,carcinoma,0,1	PER2	NM_022817	exon19	c.G2951T	p.R984L	CTGCTGCGGGACT	.	56.0	14.0	61.0	0.0	.	85	.	.	Atlas-SNP
BRPF1	7862	hgsc.bcm.edu	hg19	3	9776140	9776140	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	BRPF1	NM_001003694	exon2	c.C316T	p.R106C	CATGGCCGCGTCC	.	68.0	7.0	59.0	0.0	.	104	.	.	Atlas-SNP
SCN5A	6331	hgsc.bcm.edu	hg19	3	38597244	38597244	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	SCN5A	NM_198056	exon26	c.G4445T	p.G1482V	TCCTGGCCCCCTA	.	116.0	14.0	122.0	0.0	.	634	.	.	Atlas-SNP
CTNNB1	1499	hgsc.bcm.edu	hg19	3	41266104	41266104	+	Missense_Mutation	SNP	G	G	A	rs28931589	bycluster	TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	CTNNB1,gallbladder,other,0,161	CTNNB1	NM_001098209	exon3	c.G101A	p.G34E	ACTCTGGAATCCA	.	174.0	30.0	192.0	0.0	.	4904	.	.	Atlas-SNP
TBCCD1	55171	hgsc.bcm.edu	hg19	3	186269064	186269064	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	TBCCD1	NM_001134415	exon7	c.C1549A	p.Q517K	TCCTTTGATCCCT	.	108.0	19.0	94.0	0.0	.	42	.	.	Atlas-SNP
ARAP2	116984	hgsc.bcm.edu	hg19	4	36230363	36230363	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ARAP2	NM_015230	exon2	c.A746G	p.Q249R	TCTCCTTGAAACT	.	193.0	39.0	170.0	0.0	.	210	.	.	Atlas-SNP
TMED7-TICAM2	100302736	hgsc.bcm.edu	hg19	5	114952130	114952130	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	.	NM_001164468	exon3	c.T451C	p.C151R	AAACACAGGCAGA	.	121.0	25.0	87.0	0.0	.	.	.	.	Atlas-SNP
DDX46	9879	hgsc.bcm.edu	hg19	5	134152221	134152221	+	Silent	SNP	T	T	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	DDX46	NM_014829	exon19	c.T2538A	p.A846A	AAATGCTGAGAAA	.	67.0	12.0	69.0	0.0	.	77	.	.	Atlas-SNP
PDE6A	5145	hgsc.bcm.edu	hg19	5	149324082	149324082	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	PDE6A	NM_000440	exon1	c.C155T	p.P52L	CTGCTCGGGGAGT	.	48.0	9.0	59.0	0.0	.	98	.	.	Atlas-SNP
UBR2	23304	hgsc.bcm.edu	hg19	6	42612241	42612241	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	UBR2	NM_015255	exon20	c.G2251A	p.E751K	CTAATAGAAGAAA	.	96.0	22.0	64.0	0.0	.	134	.	.	Atlas-SNP
L3MBTL3	84456	hgsc.bcm.edu	hg19	6	130455007	130455007	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	L3MBTL3	NM_032438	exon22	c.G2156C	p.S719T	TACAGAGCTTACC	.	30.0	6.0	62.0	0.0	.	99	.	.	Atlas-SNP
MRPS24	64951	hgsc.bcm.edu	hg19	7	43906467	43906467	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	MRPS24	NM_032014	exon4	c.G335A	p.R112H	CCCCGGCGCTTTA	.	52.0	11.0	41.0	0.0	.	9	.	.	Atlas-SNP
COBL	23242	hgsc.bcm.edu	hg19	7	51287547	51287547	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	COBL	NM_015198	exon2	c.G136A	p.G46R	GCGACCCGAGGGC	.	62.0	10.0	74.0	0.0	.	167	.	.	Atlas-SNP
SEMA3A	10371	hgsc.bcm.edu	hg19	7	83592651	83592651	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	SEMA3A,NS,carcinoma,0,1	SEMA3A	NM_006080	exon16	c.G1730A	p.G577D	CTGTGGCCATGGT	.	62.0	10.0	75.0	0.0	.	121	.	.	Atlas-SNP
RB1CC1	9821	hgsc.bcm.edu	hg19	8	53536345	53536345	+	Silent	SNP	T	T	C	rs145350535		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	RB1CC1	NM_014781	exon24	c.A4782G	p.V1594V	AAGTTATACTTTC	.	99.0	19.0	72.0	0.0	.	163	.	T|1.000;C|0.000	Atlas-SNP
HEY1	23462	hgsc.bcm.edu	hg19	8	80679323	80679323	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	HEY1	NM_012258	exon3	c.T170G	p.I57S	TTCTCAATTATCT	.	79.0	16.0	74.0	0.0	.	51	.	.	Atlas-SNP
C9orf64	84267	hgsc.bcm.edu	hg19	9	86571248	86571248	+	Silent	SNP	G	G	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	C9orf64	NM_032307	exon1	c.C168T	p.N56N	CCTGGGGTTCAGC	.	55.0	8.0	54.0	0.0	.	28	.	.	Atlas-SNP
ATRNL1	26033	hgsc.bcm.edu	hg19	10	117075032	117075032	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ATRNL1	NM_207303	exon18	c.A2823T	p.Q941H	AGCTCAAAATTGT	.	71.0	14.0	63.0	0.0	.	219	.	.	Atlas-SNP
BSCL2	26580	hgsc.bcm.edu	hg19	11	62458597	62458597	+	Missense_Mutation	SNP	C	C	T	rs144725547		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	BSCL2	NM_001122955	exon8	c.G1022A	p.R341K	TTGTCTCTTTTTC	.	76.0	16.0	100.0	0.0	.	35	.	C|1.000;T|0.000	Atlas-SNP
PYGM	5837	hgsc.bcm.edu	hg19	11	64522286	64522286	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	PYGM	NM_005609	exon8	c.G878A	p.R293Q	TTCAGCCGCAGCT	.	29.0	8.0	38.0	0.0	.	77	.	.	Atlas-SNP
BATF2	116071	hgsc.bcm.edu	hg19	11	64757247	64757247	+	Missense_Mutation	SNP	C	C	A	rs374070737	alternate_allele	TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	BATF2	NM_138456	exon3	c.G179T	p.R60L	TCCTTCCGCAGGG	.	59.0	10.0	61.0	0.0	.	20	.	.	Atlas-SNP
NLRX1	79671	hgsc.bcm.edu	hg19	11	119044251	119044251	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	NLRX1_ENST00000409265,NS,carcinoma,0,2	NLRX1	NM_024618	exon5	c.G293A	p.R98H	AGGAGCGCCAGTT	.	40.0	9.0	41.0	0.0	.	128	.	.	Atlas-SNP
SPATA13	221178	hgsc.bcm.edu	hg19	13	24798144	24798144	+	Silent	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	SPATA13	NM_001166271	exon2	c.C1077T	p.D359D	GCATGACGACTAC	.	34.0	11.0	29.0	0.0	.	92	.	.	Atlas-SNP
FANCI	55215	hgsc.bcm.edu	hg19	15	89844660	89844660	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	FANCI	NM_001113378	exon27	c.C2993T	p.P998L	TGGAGCCCTCCTC	.	94.0	27.0	88.0	0.0	.	129	.	.	Atlas-SNP
MMP2	4313	hgsc.bcm.edu	hg19	16	55517934	55517934	+	Silent	SNP	T	T	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	MMP2	NM_004530	exon3	c.T387A	p.I129I	GATCATTGGCTAC	.	80.0	21.0	72.0	0.0	.	119	.	.	Atlas-SNP
ANKFY1	51479	hgsc.bcm.edu	hg19	17	4098292	4098292	+	Silent	SNP	G	G	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ANKFY1	NM_001257999	exon10	c.C1479T	p.D493D	AGGTGCGTCTGTG	.	60.0	11.0	51.0	0.0	.	81	.	.	Atlas-SNP
ALPK2	115701	hgsc.bcm.edu	hg19	18	56247067	56247067	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ALPK2	NM_052947	exon4	c.T941C	p.I314T	AGGGTTATCTCTG	.	171.0	28.0	139.0	0.0	.	487	.	.	Atlas-SNP
GMIP	51291	hgsc.bcm.edu	hg19	19	19745495	19745495	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	GMIP	NM_016573	exon18	c.C1905G	p.I635M	GAAGGGGATCACG	.	79.0	8.0	81.0	0.0	.	55	.	.	Atlas-SNP
PPP5C	5536	hgsc.bcm.edu	hg19	19	46890688	46890688	+	Silent	SNP	G	G	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	PPP5C	NM_006247	exon9	c.G1113A	p.R371R	TGAGCGGAATCGA	.	47.0	13.0	44.0	0.0	.	44	.	.	Atlas-SNP
ZNF665	79788	hgsc.bcm.edu	hg19	19	53669326	53669326	+	Silent	SNP	A	A	G	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ZNF665	NM_024733	exon4	c.T417C	p.N139N	AAGCTGATTTTCA	.	162.0	42.0	138.0	0.0	.	136	.	.	Atlas-SNP
ZNF677	342926	hgsc.bcm.edu	hg19	19	53747007	53747007	+	Silent	SNP	A	A	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	ZNF677	NM_182609	exon4	c.T159A	p.P53P	TTCTGGAGGGATG	.	82.0	21.0	71.0	0.0	.	94	.	.	Atlas-SNP
PTPRT	11122	hgsc.bcm.edu	hg19	20	40944364	40944364	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	PTPRT	NM_007050	exon12	c.G2138A	p.G713E	CTTACTCCATTGG	.	86.0	13.0	110.0	0.0	.	372	.	.	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	hg19	20	47307560	47307560	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	PREX1	NM_020820	exon9	c.G1111T	p.V371F	TGCAGACAAACCA	.	132.0	30.0	131.0	0.0	.	441	.	.	Atlas-SNP
BCR	613	hgsc.bcm.edu	hg19	22	23656199	23656199	+	Missense_Mutation	SNP	C	C	G	rs200185744	by1000genomes;alternate_allele	TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	BCR	NM_004327	exon21	c.C3502G	p.L1168V	AACCTGCTGCTGT	.	25.0	7.0	36.0	0.0	.	74	.	C|1.000;T|0.000	Atlas-SNP
CACNG2	10369	hgsc.bcm.edu	hg19	22	37098516	37098516	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	CACNG2	NM_006078	exon1	c.T106A	p.S36T	CTCTGGAGTAGAG	.	162.0	32.0	174.0	0.0	.	43	.	.	Atlas-SNP
IL2RB	3560	hgsc.bcm.edu	hg19	22	37524431	37524431	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	IL2RB	NM_000878	exon10	c.G1361A	p.R454K	GGCATCCTCTCTT	.	32.0	8.0	25.0	0.0	.	44	.	.	Atlas-SNP
ND2	0	hgsc.bcm.edu	hg19	MT	5478	5478	+	Silent	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	.	ENST00000361453	exon1	c.C1009T	p.L337L	CTACTCCTACCTA	.	65.0	6.0	25.0	0.0	.	.	.	.	Atlas-SNP
ND5	0	hgsc.bcm.edu	hg19	MT	13323	13323	+	Silent	SNP	C	C	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	.	ENST00000361567	exon1	c.C987T	p.I329I	GCACATCTGTACC	.	11.0	11.0	0.0	0.0	.	.	.	.	Atlas-SNP
SDS	10993	hgsc.bcm.edu	hg19	12	113834987	113834988	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-EP-A3RK-01A-11D-A22F-10	TCGA-EP-A3RK-10A-01D-A22F-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	0d259ac2-03d1-4814-9b0b-d05e3a6029b7	f4ebcdb4-5fcb-4fbc-bb8c-d961ef98312b	.	SDS	NM_006843	exon6	c.636_637insA	p.S212fs	.	.	69.0	13.0	84.0	0.0	.	35	.	.	Atlas-INDEL