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	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	c_position_WU	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	transcript_error_WU
PKHD1	5314	genome.wustl.edu	36	6	51727649	51727649	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	51727649	51727649	C	T	SNP	PKHD1	NM_138694	human	genbank	54_36p	-1	reviewed	missense	c.8689	p.V2897I	0.252	NULL	HMMPfam_TIG,HMMSmart_SM00429,HMMSmart_SM00710,superfamily_Pectin lyase-like,superfamily_E set domains,HMMPfam_G8	-	no_errors
LOC647954	647954	genome.wustl.edu	36	5	122765339	122765339	+	RNA	DEL	A	A	-			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	122765339	122765339	A	-	DEL	LOC647954	XR_038441	human	genbank	54_36p	-1	model	rna	NULL	NULL	1.000	-	-	-	pseudogene
RCC2	55920	genome.wustl.edu	36	1	17612620	17612620	+	Missense_Mutation	SNP	C	C	T	rs115444207	by1000genomes	TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	17612620	17612620	C	T	SNP	RCC2	NM_018715	human	genbank	54_36p	-1	validated	missense	c.1207	p.G403S	1.000	superfamily_RCC1/BLIP-II	PatternScan_RCC1_1,superfamily_RCC1/BLIP-II,HMMPfam_RCC1,PatternScan_RCC1_2	-	no_errors
DNMT3B	1789	genome.wustl.edu	36	20	30850048	30850048	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	20	30850048	30850048	C	T	SNP	DNMT3B	NM_006892	human	genbank	54_36p	+1	reviewed	missense	c.1612	p.R538C	1.000	superfamily_FYVE/PHD zinc finger	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	-	no_errors
BCHE	590	genome.wustl.edu	36	3	167031170	167031170	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	167031170	167031170	G	-	DEL	BCHE	NM_000055	human	genbank	54_36p	-1	reviewed	frame_shift_del	c.346	p.L116fs	0.974	HMMPfam_COesterase,superfamily_SSF53474	HMMPfam_COesterase,superfamily_SSF53474,PatternScan_CARBOXYLESTERASE_B_2,PatternScan_CARBOXYLESTERASE_B_1,HMMPfam_AChE_tetra	-	no_errors
SMG1	23049	genome.wustl.edu	36	16	18757451	18757451	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	16	18757451	18757451	C	T	SNP	SMG1	NM_015092	human	genbank	54_36p	-1	reviewed	missense	c.7007	p.R2336K	1.000	superfamily_Protein kinase-like (PK-like),HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,PatternScan_PI3_4_KINASE_2	superfamily_ARM repeat,HMMPfam_HEAT,superfamily_Protein kinase-like (PK-like),HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,PatternScan_PI3_4_KINASE_2,HMMPfam_FATC	-	no_errors
CRELD2	79174	genome.wustl.edu	36	22	48704065	48704065	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	22	48704065	48704065	G	C	SNP	CRELD2	NM_024324	human	genbank	54_36p	+1	validated	missense	c.826	p.E276Q	0.076	superfamily_Growth factor receptor domain,HMMSmart_SM00261	superfamily_Growth factor receptor domain,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,PatternScan_EGF_LAM_1,HMMSmart_SM00261,PatternScan_EGF_CA,HMMSmart_SM00179,HMMPfam_EGF_CA,PatternScan_ASX_HYDROXYL	-	no_errors
TMCO5A	145942	genome.wustl.edu	36	15	36030657	36030657	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	15	36030657	36030657	C	T	SNP	TMCO5A	NM_152453	human	genbank	54_36p	+1	provisional	missense	c.797	p.T266I	0.332	NULL	NULL	-	no_errors
DYSF	8291	genome.wustl.edu	36	2	71763170	71763170	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	71763170	71763170	G	A	SNP	DYSF	NM_003494	human	genbank	54_36p	+1	reviewed	missense	c.6059	p.R2020H	1.000	NULL	HMMPfam_C2,HMMSmart_SM00239,HMMSmart_SM00693,HMMSmart_SM00694,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_FerA,HMMPfam_FerB,HMMPfam_FerI	-	no_errors
U2AF1	7307	genome.wustl.edu	36	21	43397525	43397525	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	21	43397525	43397525	G	T	SNP	U2AF1	NM_001025203	human	genbank	54_36p	-1	reviewed	missense	c.101	p.S34Y	1.000	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	-	no_errors
ZNF626	199777	genome.wustl.edu	36	19	20599017	20599018	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	20599017	20599018	-	A	INS	ZNF626	NM_001076675	human	genbank	54_36p	-1	validated	frame_shift_ins	c.1506_1505	p.I503fs	0.835:0.747	superfamily_C2H2 and C2HC zinc fingers	HMMPfam_KRAB,HMMSmart_SM00349,superfamily_KRAB domain (Kruppel-associated box Pfam 01352),HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_C2H2 and C2HC zinc fingers	-	no_errors
MAP3K4	4216	genome.wustl.edu	36	6	161439341	161439343	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	CTG	CTG			CTG	CTG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	161439341	161439343	CTG	-	DEL	MAP3K4	NM_005922	human	genbank	54_36p	+1	reviewed	in_frame_del	c.3566_3568	p.A1193in_frame_del	0.981:0.960:0.963	NULL	HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	-	no_errors
TRPM3	80036	genome.wustl.edu	36	9	72408167	72408167	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	72408167	72408167	C	T	SNP	TRPM3	NM_001007471	human	genbank	54_36p	-1	reviewed	missense	c.2671	p.V891M	1.000	NULL	HMMPfam_Ion_trans	-	no_errors
KLHDC3	116138	genome.wustl.edu	36	6	43092952	43092952	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	43092952	43092952	T	C	SNP	KLHDC3	NM_057161	human	genbank	54_36p	+1	reviewed	missense	c.44	p.V15A	1.000	superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2	superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2,HMMPfam_Kelch_1	-	no_errors
ALG6	29929	genome.wustl.edu	36	1	63649475	63649475	+	Missense_Mutation	SNP	G	G	A	rs6449710	byCluster;byFrequency;by2Hit2Allele;byHapMap;by1000genomes	TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	63649475	63649475	G	A	SNP	ALG6	NM_013339	human	genbank	54_36p	+1	reviewed	missense	c.565	p.G189R	1.000	HMMPfam_Alg6_Alg8	HMMPfam_Alg6_Alg8	-	no_errors
SDK1	221935	genome.wustl.edu	36	7	3980582	3980582	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	3980582	3980582	G	A	SNP	SDK1	NM_152744	human	genbank	54_36p	+1	validated	missense	c.1873	p.V625M	0.004	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin	-	no_errors
SNORD37	26812	genome.wustl.edu	36	19	3933568	3933568	+	RNA	SNP	A	A	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	3933568	3933568	A	T	SNP	SNORD37	NR_002602	human	genbank	54_36p	-1	provisional	rna	NULL	NULL	0.000	-	-	-	no_errors
MT-ND2	0	genome.wustl.edu	36	MT	4854	4854	+	Silent	SNP	G	G	A			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	MT	4854	4854	G	A	SNP	MT-ND2	ENST00000361453	human	ensembl	54_36p	+1	known	silent	c.384	p.L128	NULL	HMMPfam_Oxidored_q1	HMMPfam_Oxidored_q1,HMMPfam_NADH_dehy_S2_C	-	no_stop_codon:bad_bp_length_for_coding_region
DYNC2H1	79659	genome.wustl.edu	36	11	102485613	102485613	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	11	102485613	102485613	T	G	SNP	DYNC2H1	NM_001080463	human	genbank	54_36p	+1	provisional	missense	c.100	p.C34G	0.000	NULL	HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMSmart_SM00382,HMMPfam_AAA_5,HMMPfam_Dynein_heavy	-	no_errors
KIAA2018	205717	genome.wustl.edu	36	3	114858801	114858803	+	In_Frame_Del	DEL	TGC	TGC	-			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	TGC	TGC			TGC	TGC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	114858801	114858803	TGC	-	DEL	KIAA2018	NM_001009899	human	genbank	54_36p	-1	validated	in_frame_del	c.4418_4416	p.Q1476in_frame_del	1.000:1.000:0.999	NULL	superfamily_HLH helix-loop-helix DNA-binding domain,HMMPfam_HLH,HMMSmart_SM00353	-	no_errors
NFKBIZ	64332	genome.wustl.edu	36	3	103058719	103058720	+	Splice_Site	INS	-	-	ACTTTTAGAAAGCTTTAATAACC			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	103058719	103058720	-	ACTTTTAGAAAGCTTTAATAACC	INS	NFKBIZ	NM_031419	human	genbank	54_36p	+1	reviewed	splice_site_ins	c.1935+2_1935+1	e10+2	0.997:0.000	-	-	-	no_errors
C12orf33	253128	genome.wustl.edu	36	12	9102638	9102638	+	RNA	DEL	G	G	-			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	9102638	9102638	G	-	DEL	C12orf33	XR_041988	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.000	-	-	-	no_errors
LOC390298	390298	genome.wustl.edu	36	12	17444984	17444984	+	RNA	SNP	G	G	A			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	17444984	17444984	G	A	SNP	LOC390298	XR_016971	human	genbank	54_36p	+1	model	rna	NULL	NULL	0.975	-	-	-	pseudogene
LOC51233	51233	genome.wustl.edu	36	22	22294283	22294285	+	In_Frame_Del	DEL	CAT	CAT	-			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	CAT	CAT			CAT	CAT	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	22	22294283	22294285	CAT	-	DEL	LOC51233	NM_016449	human	genbank	54_36p	-1	predicted	in_frame_del	c.379_377	p.D126in_frame_del	0.001:0.003:0.003	NULL	NULL	-	no_errors
HAO1	54363	genome.wustl.edu	36	20	7814398	7814398	+	Silent	SNP	C	C	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	20	7814398	7814398	C	T	SNP	HAO1	NM_017545	human	genbank	54_36p	-1	reviewed	silent	c.927	p.K309	0.990	superfamily_FMN-linked oxidoreductases,HMMPfam_FMN_dh	superfamily_FMN-linked oxidoreductases,HMMPfam_FMN_dh,PatternScan_FMN_HYDROXY_ACID_DH_1	-	no_errors
LOC285359	285359	genome.wustl.edu	36	3	102914047	102914047	+	RNA	DEL	A	A	-			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	102914047	102914047	A	-	DEL	LOC285359	NR_002941	human	genbank	54_36p	+1	validated	rna	NULL	NULL	0.998	-	-	-	pseudogene
CADPS	8618	genome.wustl.edu	36	3	62459970	62459970	+	Silent	SNP	C	C	G			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	62459970	62459970	C	G	SNP	CADPS	NM_003716	human	genbank	54_36p	-1	reviewed	silent	c.2613	p.R871	0.921	HMMPfam_DUF1041	HMMPfam_C2,superfamily_PH domain-like,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_DUF1041	-	no_errors
NIPSNAP1	8508	genome.wustl.edu	36	22	28296426	28296426	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	22	28296426	28296426	T	C	SNP	NIPSNAP1	NM_003634	human	genbank	54_36p	-1	reviewed	missense	c.194	p.K65R	1.000	NULL	HMMPfam_NIPSNAP	-	no_errors
SCAF8	22828	genome.wustl.edu	36	6	155195736	155195736	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2882-03A-01W-0761-09	TCGA-AB-2882-11A-01W-0732-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	155195736	155195736	G	T	SNP	RBM16	NM_014892	human	genbank	54_36p	+1	validated	missense	c.3331	p.G1111C	0.996	NULL	HMMPfam_RRM_1,HMMSmart_RRM,HMMSmart_RPR,HMMPfam_DUF618,superfamily_ENTH_VHS,superfamily_SSF54928	-	no_errors
