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
CNGA3	1261	genome.wustl.edu	36	2	98378805	98378805	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	98378805	98378805	C	T	SNP	CNGA3	NM_001298	human	genbank	54_36p	+1	reviewed	missense	c.740	p.T247M	0.001	superfamily_SSF81324,HMMPfam_Ion_trans	superfamily_SSF81324,HMMPfam_Ion_trans,superfamily_cNMP_binding,HMMSmart_cNMP,HMMPfam_cNMP_binding,PatternScan_CNMP_BINDING_1,PatternScan_CNMP_BINDING_2	-	no_errors
MUC5B	727897	genome.wustl.edu	36	11	1221954	1221954	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	11	1221954	1221954	C	T	SNP	MUC5B	NM_002458	human	genbank	54_36p	+1	validated	missense	c.7277	p.T2426M	0.027	NULL	HMMSmart_SM00216,HMMPfam_VWD,HMMPfam_C8,superfamily_Serine proterase inhibitors,HMMPfam_TIL,HMMSmart_SM00214,HMMSmart_SM00215,superfamily_PMP inhibitors,PatternScan_VWFC_1,HMMPfam_VWC,HMMSmart_SM00041,HMMPfam_Cys_knot,PatternScan_CTCK_1	-	no_errors
TLR4	7099	genome.wustl.edu	36	9	119515138	119515141	+	Frame_Shift_Del	DEL	TTAA	TTAA	-			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	TTAA	TTAA			TTAA	TTAA	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	119515138	119515141	TTAA	-	DEL	TLR4	NM_138554	human	genbank	54_36p	+1	reviewed	frame_shift_del	c.911_914	p.N305fs	0.040:0.049:0.060:0.352	superfamily_L domain-like	superfamily_L domain-like,HMMSmart_SM00369,HMMPfam_LRR_1,HMMSmart_SM00365,HMMSmart_SM00082,HMMPfam_LRRCT,superfamily_Toll/Interleukin receptor TIR domain,HMMSmart_SM00255,HMMPfam_TIR	-	no_errors
LOC400986	400986	genome.wustl.edu	36	2	95889367	95889367	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	95889367	95889367	G	T	SNP	LOC400986	XM_001717763	human	genbank	54_36p	-1	model	missense	c.3865	p.L1289I	0.998	NULL	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	-	no_errors
SPAM1	6677	genome.wustl.edu	36	7	123386834	123386834	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	123386834	123386834	G	A	SNP	SPAM1	NM_003117	human	genbank	54_36p	+1	reviewed	missense	c.1105	p.V369I	1.000	HMMPfam_Glyco_hydro_56	HMMPfam_Glyco_hydro_56,superfamily_Glyco_hydro_cat	-	no_errors
SLC38A11	151258	genome.wustl.edu	36	2	165504314	165504314	+	Splice_Site	SNP	T	T	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	165504314	165504314	T	A	SNP	SLC38A11	NM_173512	human	genbank	54_36p	-1	provisional	splice_site	c.197-2	e3-2	1.000	-	-	-	no_errors
SPTA1	6708	genome.wustl.edu	36	1	156859471	156859471	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	156859471	156859471	G	A	SNP	SPTA1	NM_003126	human	genbank	54_36p	-1	reviewed	missense	c.6046	p.R2016C	1.000	HMMPfam_Spectrin,superfamily_Spectrin repeat,HMMSmart_SM00150	superfamily_Spectrin repeat,HMMPfam_Spectrin,HMMSmart_SM00150,superfamily_SH3-domain,HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_EF-hand,HMMPfam_efhand_Ca_insen	-	no_errors
ENSG00000204762	0	genome.wustl.edu	36	5	171656349	171656349	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	171656349	171656349	G	A	SNP	ENSG00000204762	ENST00000377334	human	ensembl	54_36p	+1	known	missense	c.25	p.G9S	0.004	NULL	NULL	-	no_start_codon
PLCE1	51196	genome.wustl.edu	36	10	95921184	95921184	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	10	95921184	95921184	C	A	SNP	PLCE1	NM_016341	human	genbank	54_36p	+1	validated	missense	c.1750	p.L584I	0.239	HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF	HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RA,HMMSmart_SM00314,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand	-	no_errors
SYT1	6857	genome.wustl.edu	36	12	78135485	78135485	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	78135485	78135485	G	A	SNP	SYT1	NM_005639	human	genbank	54_36p	+1	validated	missense	c.55	p.A19T	0.964	NULL	superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMSmart_SM00239,HMMPfam_C2	-	no_errors
U2AF1	7307	genome.wustl.edu	36	21	43397525	43397525	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	21	43397525	43397525	G	A	SNP	U2AF1	NM_001025203	human	genbank	54_36p	-1	reviewed	missense	c.101	p.S34F	1.000	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	-	no_errors
PANK4	55229	genome.wustl.edu	36	1	2447870	2447870	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	2447870	2447870	G	C	SNP	PANK4	NM_018216	human	genbank	54_36p	-1	reviewed	missense	c.17	p.A6G	0.714	NULL	HMMPfam_DUF89,superfamily_Hypothetical protein At2g17340,HMMPfam_Fumble	-	no_errors
ENSG00000214627	0	genome.wustl.edu	36	16	31902998	31902998	+	Silent	SNP	T	T	C			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	16	31902998	31902998	T	C	SNP	ENSG00000214627	ENST00000398685	human	ensembl	54_36p	+1	known	silent	c.753	p.P251	0.961	NULL	HMMSmart_PH,superfamily_SSF50729,superfamily_Rho_GAP,HMMSmart_RhoGAP,HMMPfam_RhoGAP	-	no_stop_codon
DDX11	1663	genome.wustl.edu	36	12	31142142	31142142	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	31142142	31142142	G	C	SNP	DDX11	NM_152438	human	genbank	54_36p	+1	reviewed	missense	c.1819	p.A607P	1.000	NULL	HMMSmart_SM00488,HMMSmart_SM00491,HMMPfam_DEAD_2,superfamily_P-loop containing nucleoside triphosphate hydrolases	-	no_errors
CD74	972	genome.wustl.edu	36	5	149772478	149772478	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	149772478	149772478	G	A	SNP	CD74	NM_001025159	human	genbank	54_36p	-1	validated	missense	c.28	p.R10W	0.002	NULL	HMMPfam_Thyroglobulin_1,HMMSmart_SM00211,PatternScan_THYROGLOBULIN_1_1,superfamily_Thyroglobulin type-1 domain,HMMPfam_MHCassoc_trimer,superfamily_Class II MHC-associated invariant chain ectoplasmic trimerization domain,HMMPfam_MHC2-interact	-	no_errors
LOC653657	653657	genome.wustl.edu	36	19	7007571	7007571	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	7007571	7007571	G	T	SNP	LOC653657	XM_928697	human	genbank	54_36p	-1	model	missense	c.389	p.A130D	0.000	NULL	NULL	-	no_errors
KIT	3815	genome.wustl.edu	36	4	55259459	55259459	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	55259459	55259459	C	T	SNP	KIT	NM_000222	human	genbank	54_36p	+1	reviewed	missense	c.590	p.S197L	0.086	NULL	superfamily_SSF48726,HMMSmart_IGc2,HMMPfam_ig,HMMSmart_IG,superfamily_Kinase_like,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_PROTEIN_KINASE_ATP,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR	-	no_errors
LOC399965	399965	genome.wustl.edu	36	11	124489839	124489839	+	RNA	SNP	G	G	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	11	124489839	124489839	G	T	SNP	LOC399965	XR_016979	human	genbank	54_36p	+1	model	rna	NULL	NULL	1.000	-	-	-	pseudogene
SCRN3	79634	genome.wustl.edu	36	2	175000827	175000839	+	Frame_Shift_Del	DEL	TCAAATTTATCAG	TCAAATTTATCAG	-			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	TCAAATTTATCAG	TCAAATTTATCAG			TCAAATTTATCAG	TCAAATTTATCAG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	175000827	175000839	TCAAATTTATCAG	-	DEL	SCRN3	NM_024583	human	genbank	54_36p	+1	validated	frame_shift_del	c.1233_1245	p.Y414fs	0.987:0.985:0.984:0.995:1.000:1.000:0.998:1.000:0.998:0.987:0.030:0.000:0.004	NULL	NULL	-	no_errors
LRRTM2	26045	genome.wustl.edu	36	5	138237719	138237719	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	138237719	138237719	G	C	SNP	LRRTM2	NM_015564	human	genbank	54_36p	-1	validated	missense	c.430	p.Q144E	1.000	HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like	HMMPfam_LRR_1,HMMSmart_SM00369,superfamily_L domain-like	-	no_errors
MYCL1	4610	genome.wustl.edu	36	1	40136201	40136201	+	Silent	SNP	T	T	A			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	40136201	40136201	T	A	SNP	MYCL1	NM_001033081	human	genbank	54_36p	-1	validated	silent	c.525	p.V175	1.000	HMMPfam_Myc_N	HMMPfam_Myc_N,HMMPfam_HLH,superfamily_HLH helix-loop-helix DNA-binding domain,HMMSmart_SM00353	-	no_errors
LOC642236	642236	genome.wustl.edu	36	9	67917667	67917667	+	RNA	SNP	C	C	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	67917667	67917667	C	T	SNP	LOC642236	XR_041085	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.962	-	-	-	no_errors
POLDIP3	84271	genome.wustl.edu	36	22	41328936	41328936	+	Silent	SNP	A	A	G			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	22	41328936	41328936	A	G	SNP	POLDIP3	NM_032311	human	genbank	54_36p	-1	reviewed	silent	c.234	p.L78	1.000	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	-	no_errors
KIT	3815	genome.wustl.edu	36	4	55294078	55294078	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2843-03B-01W-0728-08	TCGA-AB-2843-11B-01W-0729-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	55294078	55294078	A	T	SNP	KIT	NM_000222	human	genbank	54_36p	+1	reviewed	missense	c.2447	p.D816V	1.000	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	-	no_errors
