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
PHF13	148479	hgsc.bcm.edu	hg19	1	6681657	6681657	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PHF13	NM_153812	exon4	c.A863G	p.N288S	GTTCCAACCGCTC	.	110.0	6.0	156.0	0.0	.	24	.	.	Atlas-SNP
FBXO2	26232	hgsc.bcm.edu	hg19	1	11710798	11710798	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	FBXO2,NS,carcinoma,0,1	FBXO2	NM_012168	exon2	c.A116C	p.E39A	GCCGCCTCCTCCT	.	16.0	2.0	25.0	0.0	.	25	.	.	Atlas-SNP
TNFRSF8	943	hgsc.bcm.edu	hg19	1	12169683	12169683	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	TNFRSF8	NM_001243	exon5	c.C482T	p.A161V	CCTGTGCCAGCCC	.	68.0	4.0	85.0	0.0	.	70	.	.	Atlas-SNP
PADI2	11240	hgsc.bcm.edu	hg19	1	17410314	17410314	+	Silent	SNP	C	C	T	rs141844952		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PADI2	NM_007365	exon9	c.G957A	p.L319L	CAGGAACAGGTAA	.	67.0	30.0	93.0	0.0	.	72	.	C|1.000;T|0.000	Atlas-SNP
FAM110D	79927	hgsc.bcm.edu	hg19	1	26487902	26487902	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	.	NM_024869	exon2	c.G120T	p.E40D	ACAGGAGCCAGCC	.	92.0	33.0	149.0	0.0	.	.	.	.	Atlas-SNP
IPP	3652	hgsc.bcm.edu	hg19	1	46195357	46195357	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	IPP	NM_001145349	exon4	c.A809C	p.K270T	CAAAACTTGTTCT	.	247.0	52.0	294.0	0.0	.	66	.	.	Atlas-SNP
CA14	23632	hgsc.bcm.edu	hg19	1	150235583	150235583	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	CA14	NM_012113	exon7	c.G705T	p.Q235H	GTCCCAGATTTCA	.	211.0	11.0	165.0	0.0	.	37	.	.	Atlas-SNP
TADA1	117143	hgsc.bcm.edu	hg19	1	166826920	166826920	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	TADA1	NM_053053	exon8	c.G892C	p.A298P	TAAGAGCATAGAC	.	172.0	59.0	152.0	0.0	.	32	.	.	Atlas-SNP
HMCN1	83872	hgsc.bcm.edu	hg19	1	186047303	186047303	+	Silent	SNP	T	T	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	HMCN1	NM_031935	exon55	c.T8550A	p.A2850A	TGTGGCTGTGAAT	.	214.0	32.0	179.0	0.0	.	797	.	.	Atlas-SNP
PGBD5	79605	hgsc.bcm.edu	hg19	1	230492809	230492809	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	PGBD5,rectum,carcinoma,-1,1	PGBD5	NM_001258311	exon2	c.G590A	p.R197H	AGGCTGCGGTTGC	.	134.0	6.0	134.0	0.0	.	73	.	.	Atlas-SNP
LRPPRC	10128	hgsc.bcm.edu	hg19	2	44152227	44152227	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	LRPPRC	NM_133259	exon27	c.T2875C	p.Y959H	GATTGTAGTACAT	.	63.0	13.0	95.0	0.0	.	105	.	.	Atlas-SNP
ANTXR1	84168	hgsc.bcm.edu	hg19	2	69408989	69408989	+	Silent	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ANTXR1	NM_032208	exon15	c.C1161T	p.G387G	GAGAGGCGTTGGA	.	96.0	23.0	154.0	0.0	.	128	.	.	Atlas-SNP
DPP4	1803	hgsc.bcm.edu	hg19	2	162894911	162894911	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	DPP4	NM_001935	exon8	c.A514G	p.I172V	CATAAATGTCATT	.	186.0	19.0	271.0	0.0	.	90	.	.	Atlas-SNP
ANKRD44	91526	hgsc.bcm.edu	hg19	2	197948233	197948233	+	Silent	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ANKRD44	NM_001195144	exon14	c.G1317A	p.R439R	AGGGGTCCTGAAA	.	74.0	11.0	88.0	0.0	.	281	.	.	Atlas-SNP
SIAH2	6478	hgsc.bcm.edu	hg19	3	150480232	150480232	+	Silent	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	SIAH2	NM_005067	exon1	c.G405A	p.L135L	GGGAAACAGGACT	.	52.0	23.0	94.0	0.0	.	33	.	.	Atlas-SNP
ATP13A3	79572	hgsc.bcm.edu	hg19	3	194140666	194140666	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ATP13A3	NM_024524	exon30	c.A3344G	p.Y1115C	AAAATATATAAAA	.	620.0	30.0	717.0	0.0	.	94	.	.	Atlas-SNP
ALB	213	hgsc.bcm.edu	hg19	4	74280793	74280793	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ALB	NM_000477	exon9	c.T1100C	p.V367A	ACTCTGTCGTGCT	.	80.0	34.0	132.0	0.0	.	132	.	.	Atlas-SNP
PDHA2	5161	hgsc.bcm.edu	hg19	4	96761441	96761441	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PDHA2	NM_005390	exon1	c.G140T	p.G47V	AAGAGGGTCCCCC	.	137.0	25.0	183.0	0.0	.	118	.	.	Atlas-SNP
CDKN2AIP	55602	hgsc.bcm.edu	hg19	4	184367702	184367702	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	CDKN2AIP	NM_017632	exon3	c.G865T	p.E289X	GAGATCGAGGTGC	.	159.0	39.0	172.0	0.0	.	31	.	.	Atlas-SNP
ANKRD55	79722	hgsc.bcm.edu	hg19	5	55422893	55422893	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ANKRD55	NM_024669	exon8	c.A653C	p.H218P	CCCTGGTGATGGC	.	187.0	57.0	150.0	0.0	.	70	.	.	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	hg19	5	169507279	169507279	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	DOCK2	NM_004946	exon50	c.C5279A	p.T1760N	TGCCTACCATCCC	.	91.0	26.0	78.0	0.0	.	389	.	.	Atlas-SNP
DOCK2	1794	hgsc.bcm.edu	hg19	5	169507280	169507280	+	Silent	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	DOCK2	NM_004946	exon50	c.C5280A	p.T1760T	GCCTACCATCCCA	.	90.0	27.0	77.0	0.0	.	389	.	.	Atlas-SNP
PKHD1	5314	hgsc.bcm.edu	hg19	6	51910977	51910977	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PKHD1	NM_170724	exon24	c.T2417C	p.V806A	ATTTGTACAGGGA	.	105.0	11.0	151.0	0.0	.	927	.	.	Atlas-SNP
COL12A1	1303	hgsc.bcm.edu	hg19	6	75847218	75847218	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	COL12A1	NM_004370	exon31	c.A5329G	p.S1777G	GACCACTAGCAGG	.	99.0	33.0	125.0	0.0	.	385	.	.	Atlas-SNP
PRDM13	59336	hgsc.bcm.edu	hg19	6	100057092	100057092	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PRDM13	NM_021620	exon3	c.G306T	p.Q102H	CGTCCAGCCAGGG	.	99.0	37.0	114.0	0.0	.	65	.	.	Atlas-SNP
PCLO	27445	hgsc.bcm.edu	hg19	7	82545902	82545902	+	Silent	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	PCLO_ENST00000333891,right_upper_lobe,carcinoma,0,2	PCLO	NM_014510	exon7	c.C11400T	p.Y3800Y	TTCCAGGTATCGT	.	129.0	9.0	144.0	0.0	.	1506	.	.	Atlas-SNP
DPP6	1804	hgsc.bcm.edu	hg19	7	154667719	154667719	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	DPP6	NM_130797	exon20	c.C1987T	p.R663C	GACGGCCGTGGCA	.	94.0	16.0	106.0	0.0	.	383	.	.	Atlas-SNP
ANGPT1	284	hgsc.bcm.edu	hg19	8	108315574	108315574	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ANGPT1	NM_001146	exon5	c.G830T	p.R277I	TCCTCTCTTTTTC	.	141.0	8.0	99.0	0.0	.	111	.	.	Atlas-SNP
COL22A1	169044	hgsc.bcm.edu	hg19	8	139601631	139601631	+	Silent	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	COL22A1	NM_152888	exon65	c.C4746T	p.G1582G	TTGAGGGCCAGGG	.	338.0	33.0	233.0	0.0	.	390	.	.	Atlas-SNP
TOPORS	10210	hgsc.bcm.edu	hg19	9	32543499	32543499	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	TOPORS	NM_005802	exon3	c.C1024T	p.P342S	AAAATGGTCTTAA	.	69.0	15.0	68.0	0.0	.	127	.	.	Atlas-SNP
TRPM3	80036	hgsc.bcm.edu	hg19	9	73213415	73213415	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	TRPM3	NM_001007471	exon20	c.A2932T	p.I978F	AGTAAATGATGTT	.	183.0	29.0	179.0	0.0	.	700	.	.	Atlas-SNP
TRIM32	22954	hgsc.bcm.edu	hg19	9	119460448	119460448	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	TRIM32	NM_012210	exon2	c.G427A	p.E143K	GCAGCTGAGGAGC	.	106.0	50.0	110.0	0.0	.	67	.	.	Atlas-SNP
ATRNL1	26033	hgsc.bcm.edu	hg19	10	117278802	117278802	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ATRNL1	NM_207303	exon25	c.G3684A	p.M1228I	AATCATGGACCTT	.	96.0	42.0	102.0	0.0	.	219	.	.	Atlas-SNP
FOXI2	399823	hgsc.bcm.edu	hg19	10	129537185	129537185	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	FOXI2_ENST00000388920,NS,carcinoma,0,2	FOXI2	NM_207426	exon2	c.C913T	p.R305C	GGCTTCCGCCTCA	.	72.0	6.0	63.0	0.0	.	35	.	.	Atlas-SNP
MUC6	4588	hgsc.bcm.edu	hg19	11	1031883	1031883	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	MUC6	NM_005961	exon3	c.C286T	p.R96W	TGATCCGCGAGAT	.	73.0	9.0	63.0	0.0	.	408	.	.	Atlas-SNP
MUC5B	727897	hgsc.bcm.edu	hg19	11	1251007	1251007	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	MUC5B	NM_002458	exon10	c.G1190A	p.G397D	GCCCGGGCACCTC	.	45.0	14.0	41.0	0.0	.	473	.	.	Atlas-SNP
TCIRG1	10312	hgsc.bcm.edu	hg19	11	67815394	67815394	+	Silent	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	TCIRG1	NM_006019	exon13	c.C1509T	p.N503N	TCCCAACGTCACC	.	118.0	36.0	140.0	0.0	.	40	.	.	Atlas-SNP
CCDC60	160777	hgsc.bcm.edu	hg19	12	119978493	119978493	+	Silent	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	CCDC60	NM_178499	exon14	c.C1626T	p.P542P	CATACCCATTGGG	.	57.0	18.0	72.0	0.0	.	84	.	.	Atlas-SNP
COG3	83548	hgsc.bcm.edu	hg19	13	46085912	46085912	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	COG3	NM_031431	exon16	c.C1732A	p.Q578K	GTGTTCCAAGGAT	.	83.0	9.0	82.0	0.0	.	52	.	.	Atlas-SNP
FAM179B	23116	hgsc.bcm.edu	hg19	14	45496671	45496671	+	Silent	SNP	A	A	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	FAM179B	NM_015091	exon9	c.A3498G	p.E1166E	GAATGAAAAAGAT	.	167.0	39.0	210.0	0.0	.	115	.	.	Atlas-SNP
ZFP36L1	677	hgsc.bcm.edu	hg19	14	69256295	69256295	+	Silent	SNP	T	T	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ZFP36L1	NM_001244701	exon3	c.A1179C	p.S393S	GCGTCTTGAGTTG	.	73.0	11.0	105.0	0.0	.	47	.	.	Atlas-SNP
GABRA5	2558	hgsc.bcm.edu	hg19	15	27193200	27193200	+	Silent	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	GABRA5	NM_001165037	exon11	c.C1209A	p.V403V	CTCAGTCTCAGTA	.	427.0	180.0	395.0	0.0	.	127	.	.	Atlas-SNP
PARP6	56965	hgsc.bcm.edu	hg19	15	72541642	72541642	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PARP6	NM_020214	exon19	c.C1505T	p.A502V	CCATAGGCTGCTC	.	70.0	31.0	58.0	0.0	.	44	.	.	Atlas-SNP
BAIAP3	8938	hgsc.bcm.edu	hg19	16	1396324	1396324	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	BAIAP3	NM_003933	exon25	c.C2560T	p.R854W	CTGCAACGGGAGG	.	153.0	50.0	171.0	0.0	.	88	.	.	Atlas-SNP
TP53	7157	hgsc.bcm.edu	hg19	17	7577538	7577538	+	Missense_Mutation	SNP	C	C	T	rs11540652	bycluster	TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	TP53_ENST00000545858,NS,adenocarcinoma,0,4	TP53	NM_000546	exon7	c.G743A	p.R248Q	GGCCTCCGGTTCA	.	86.0	18.0	98.0	0.0	.	33396	.	.	Atlas-SNP
SOX9	6662	hgsc.bcm.edu	hg19	17	70120053	70120053	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	SOX9	NM_000346	exon3	c.C1055T	p.A352V	CACAGGCCCCGCC	.	61.0	23.0	135.0	0.0	.	91	.	.	Atlas-SNP
UNK	85451	hgsc.bcm.edu	hg19	17	73805893	73805893	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	UNK	NM_001080419	exon2	c.T157C	p.C53R	CACAAATGCACGC	.	124.0	29.0	154.0	0.0	.	87	.	.	Atlas-SNP
ZNF91	7644	hgsc.bcm.edu	hg19	19	23542679	23542679	+	Silent	SNP	G	G	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ZNF91	NM_003430	exon4	c.C3102T	p.S1034S	CTTTGAGGATCGA	.	50.0	4.0	38.0	0.0	.	349	.	.	Atlas-SNP
KLK10	5655	hgsc.bcm.edu	hg19	19	51520439	51520439	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	KLK10	NM_145888	exon3	c.G196T	p.G66C	AGAGGCCGTTGAA	.	120.0	7.0	125.0	0.0	.	32	.	.	Atlas-SNP
ZNF665	79788	hgsc.bcm.edu	hg19	19	53668097	53668097	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ZNF665	NM_024733	exon4	c.A1646G	p.K549R	AAGACCTTGCCGC	.	96.0	22.0	121.0	0.0	.	136	.	.	Atlas-SNP
VSTM1	284415	hgsc.bcm.edu	hg19	19	54545432	54545432	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	VSTM1,NS,carcinoma,0,1	VSTM1	NM_198481	exon6	c.C506G	p.S169C	TTGGTGGATTCCT	.	101.0	36.0	147.0	0.0	.	30	.	.	Atlas-SNP
LILRA3	11026	hgsc.bcm.edu	hg19	19	54802132	54802132	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	LILRA3	NM_006865	exon6	c.G1056C	p.M352I	AGTGTGCATCCCT	.	88.0	34.0	93.0	0.0	.	65	.	.	Atlas-SNP
LENG8	114823	hgsc.bcm.edu	hg19	19	54967900	54967900	+	Nonsense_Mutation	SNP	A	A	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	LENG8	NM_052925	exon11	c.A1531T	p.K511X	AAGCAGAAGCGGG	.	123.0	5.0	127.0	0.0	.	73	.	.	Atlas-SNP
U2AF2	11338	hgsc.bcm.edu	hg19	19	56180129	56180129	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	U2AF2	NM_001012478	exon9	c.G916C	p.E306Q	TTCTGTGAGTACG	.	73.0	19.0	72.0	0.0	.	62	.	.	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	hg19	20	47267479	47267479	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PREX1	NM_020820	exon23	c.G2770T	p.D924Y	TGGTGTCACAGAT	.	77.0	16.0	63.0	0.0	.	441	.	.	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	hg19	20	47267528	47267528	+	Silent	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PREX1	NM_020820	exon23	c.G2721A	p.L907L	GCTGCTCAGGGCC	.	92.0	17.0	74.0	0.0	.	441	.	.	Atlas-SNP
PREX1	57580	hgsc.bcm.edu	hg19	20	47267976	47267976	+	Silent	SNP	C	C	T	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	PREX1	NM_020820	exon22	c.G2613A	p.E871E	GATCTTCTCCAGC	.	112.0	14.0	85.0	0.0	.	441	.	.	Atlas-SNP
TSHZ2	128553	hgsc.bcm.edu	hg19	20	51870809	51870809	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	TSHZ2,NS,carcinoma,0,1	TSHZ2	NM_173485	exon2	c.C812A	p.A271D	AGGATGCTCAAAA	.	281.0	12.0	207.0	1.0	.	209	.	.	Atlas-SNP
CCT8L2	150160	hgsc.bcm.edu	hg19	22	17071949	17071949	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	CCT8L2	NM_014406	exon1	c.A1492G	p.I498V	TGACTATTAGGGT	.	156.0	68.0	165.0	0.0	.	150	.	.	Atlas-SNP
RYR1	6261	hgsc.bcm.edu	hg19	19	38964339	38964340	+	In_Frame_Ins	INS	-	-	GGG	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	RYR1	NM_001042723	exon28	c.4088_4089insGGG	p.A1363delinsAG	.	.	357.0	32.0	367.0	0.0	.	708	.	.	Atlas-INDEL
ZNF800	168850	hgsc.bcm.edu	hg19	7	127014205	127014205	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	ZNF800	NM_176814	exon5	c.1186delG	p.G396fs	.	.	155.0	24.0	135.0	0.0	.	78	.	.	Atlas-INDEL
NKX2-2	4821	hgsc.bcm.edu	hg19	20	21493051	21493065	+	In_Frame_Del	DEL	GACTCGTCGGCCGAG	GACTCGTCGGCCGAG	-	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	GACTCGTCGGCCGAG	GACTCGTCGGCCGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	NKX2-2	NM_002509	exon2	c.319_333del	p.107_111del	.	.	55.0	25.0	54.0	0.0	.	49	.	.	Atlas-INDEL
NLGN4Y	22829	hgsc.bcm.edu	hg19	Y	16941993	16942000	+	Frame_Shift_Del	DEL	GTGTCCAA	GTGTCCAA	-	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	GTGTCCAA	GTGTCCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	NLGN4Y	NM_014893	exon5	c.1194_1201del	p.398_401del	.	.	223.0	36.0	290.0	0.0	.	44	.	.	Atlas-INDEL
NLGN4Y	22829	hgsc.bcm.edu	hg19	Y	16942005	16942017	+	Frame_Shift_Del	DEL	GTGGACAACCTTT	GTGGACAACCTTT	-	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	GTGGACAACCTTT	GTGGACAACCTTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	NLGN4Y	NM_014893	exon5	c.1206_1218del	p.402_406del	.	.	225.0	36.0	270.0	0.0	.	44	.	.	Atlas-INDEL
UPF3B	65109	hgsc.bcm.edu	hg19	X	118975107	118975108	+	Frame_Shift_Ins	INS	-	-	A	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	UPF3B	NM_023010	exon7	c.739_740insT	p.I247fs	.	.	53.0	33.0	40.0	0.0	.	74	.	.	Atlas-INDEL
ALB	213	hgsc.bcm.edu	hg19	4	74272459	74272459	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.,1	ALB	NM_000477	exon3	c.250delG	p.E84fs	.	.	75.0	12.0	92.0	0.0	.	132	.	.	Atlas-INDEL
TBX18	9096	hgsc.bcm.edu	hg19	6	85446692	85446699	+	Frame_Shift_Del	DEL	TGGTTAGT	TGGTTAGT	-	novel		TCGA-WQ-AB4B-01A-11D-A40P-10	TCGA-WQ-AB4B-10A-01D-A40P-10	TGGTTAGT	TGGTTAGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.	.	Illumina HiSeq	d1df28a1-65e0-4a10-b05b-7e20735cf012	3fa70dca-15c8-4428-978e-0c1403b4f704	.	TBX18	NM_001080508	exon8	c.1529_1536del	p.510_512del	.	.	129.0	28.0	174.0	0.0	.	131	.	.	Atlas-INDEL
