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
PCDH19	57526	genome.wustl.edu	36	X	99549148	99549148	+	Silent	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	99549148	99549148	G	A	SNP	PCDH19	NM_001105243	human	genbank	54_36p	-1	validated	silent	c.1104	p.I368	0.920	superfamily_Cadherin,HMMPfam_Cadherin	HMMPfam_Cadherin_2,superfamily_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin	-	no_errors
LOC730978	730978	genome.wustl.edu	36	1	222203797	222203797	+	RNA	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	222203797	222203797	G	A	SNP	LOC730978	XR_037258	human	genbank	54_36p	+1	model	rna	NULL	NULL	0.000	-	-	-	pseudogene
TRA2B	6434	genome.wustl.edu	36	3	187125967	187125967	+	Silent	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	187125967	187125967	G	A	SNP	TRA2B	NM_004593	human	genbank	54_36p	-1	validated	silent	c.312	p.R104	1.000	superfamily_RNA-binding domain RBD	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	-	no_errors
NTPCR	84284	genome.wustl.edu	36	1	231158044	231158044	+	Silent	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	231158044	231158044	T	C	SNP	C1orf57	NM_032324	human	genbank	54_36p	+1	predicted	silent	c.153	p.D51	1.000	HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMPfam_DUF265	HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMPfam_DUF265	-	no_errors
ENSG00000220107	0	genome.wustl.edu	36	NT_113925	93974	93974	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	NT_113925	93974	93974	A	G	SNP	ENSG00000220107	ENST00000403791	human	ensembl	54_36p	+1	known	missense	c.898	p.I300V	NULL	HMMPfam_ABC_membrane,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain	HMMPfam_ABC_membrane,superfamily_Multidrug resistance ABC transporter MsbA N-terminal domain,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMSmart_SM00382,HMMPfam_ABC_tran,PatternScan_ABC_TRANSPORTER_1	-	no_start_codon
ADAM19	8728	genome.wustl.edu	36	5	156852676	156852676	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	156852676	156852676	G	T	SNP	ADAM19	NM_023038	human	genbank	54_36p	-1	reviewed	missense	c.1795	p.H599N	0.000	NULL	NULL	-	pseudogene:no_stop_codon:bad_bp_length_for_coding_region
PDGFRB	5159	genome.wustl.edu	36	5	149484585	149484585	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	149484585	149484585	G	A	SNP	PDGFRB	NM_002609	human	genbank	54_36p	-1	reviewed	missense	c.1810	p.R604C	1.000	superfamily_Kinase_like,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc	superfamily_SSF48726,HMMSmart_IG,HMMPfam_ig,HMMSmart_IGc2,superfamily_Kinase_like,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_PROTEIN_KINASE_ATP,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR	-	no_errors
PRUNE2	158471	genome.wustl.edu	36	9	78510558	78510558	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	78510558	78510558	C	T	SNP	PRUNE2	ENST00000376718	human	ensembl	54_36p	-1	known	missense	c.5375	p.R1792Q	0.001	NULL	HMMSmart_SM00516,superfamily_CRAL/TRIO domain,superfamily_Ferritin-like	-	no_errors
LOC727895	727895	genome.wustl.edu	36	13	18855134	18855134	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	13	18855134	18855134	G	A	SNP	LOC727895	XM_001125866	human	genbank	54_36p	+1	model	missense	c.523	p.A175T	0.758	superfamily_Cyclin-like	superfamily_Cyclin-like	-	no_errors
EHHADH	1962	genome.wustl.edu	36	3	186393047	186393047	+	Silent	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	186393047	186393047	T	C	SNP	EHHADH	NM_001966	human	genbank	54_36p	-1	validated	silent	c.1833	p.P611	0.013	superfamily_6DGDH_C_like	superfamily_SSF52096,HMMPfam_ECH,PatternScan_ENOYL_COA_HYDRATASE,superfamily_NAD(P)-bd,HMMPfam_3HCDH_N,PatternScan_3HCDH,superfamily_6DGDH_C_like,HMMPfam_3HCDH	-	no_errors
HDAC3	8841	genome.wustl.edu	36	5	140989468	140989468	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	140989468	140989468	T	C	SNP	HDAC3	NM_003883	human	genbank	54_36p	-1	reviewed	missense	c.443	p.N148S	1.000	superfamily_Arginase/deacetylase,HMMPfam_Hist_deacetyl	superfamily_Arginase/deacetylase,HMMPfam_Hist_deacetyl	-	no_errors
ENSG00000210643	0	genome.wustl.edu	36	16	67950127	67950128	+	RNA	INS	-	-	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	16	67950127	67950128	-	A	INS	ENSG00000210643	ENST00000387908	human	ensembl	54_36p	+1	novel	rna	NULL	NULL	0.359:0.379	-	-	-	pseudogene
MSH6	2956	genome.wustl.edu	36	2	47881044	47881044	+	Silent	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	47881044	47881044	C	T	SNP	MSH6	NM_000179	human	genbank	54_36p	+1	reviewed	silent	c.2418	p.S806	0.392	HMMPfam_MutS_III,superfamily_DNA repair protein MutS domain III,HMMSmart_SM00533	superfamily_Tudor/PWWP/MBT,HMMPfam_PWWP,HMMSmart_SM00293,superfamily_DNA repair protein MutS domain I,HMMPfam_MutS_I,HMMPfam_MutS_II,HMMPfam_MutS_III,superfamily_DNA repair protein MutS domain III,HMMSmart_SM00533,HMMPfam_MutS_IV,HMMPfam_MutS_V,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMSmart_SM00534,PatternScan_DNA_MISMATCH_REPAIR_2	-	no_errors
RGL1	23179	genome.wustl.edu	36	1	182161933	182161933	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	182161933	182161933	C	T	SNP	RGL1	NM_015149	human	genbank	54_36p	+1	validated	missense	c.2296	p.R766C	1.000	superfamily_Ubiquitin-like,HMMPfam_RA,HMMSmart_SM00314	superfamily_Ras GEF,HMMSmart_SM00229,HMMPfam_RasGEF_N,HMMSmart_SM00147,HMMPfam_RasGEF,PatternScan_RASGEF,superfamily_Ubiquitin-like,HMMPfam_RA,HMMSmart_SM00314	-	no_errors
HSPG2	3339	genome.wustl.edu	36	1	22051263	22051263	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	22051263	22051263	C	T	SNP	HSPG2	NM_005529	human	genbank	54_36p	-1	validated	missense	c.6775	p.G2259S	0.999	HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_I-set,superfamily_Immunoglobulin	HMMPfam_Laminin_B,HMMPfam_SEA,HMMSmart_SM00200,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMSmart_SM00281,superfamily_Immunoglobulin,superfamily_EGF/Laminin	-	no_errors
ARHGEF10L	55160	genome.wustl.edu	36	1	17822248	17822248	+	Silent	SNP	C	C	T	rs10456804		TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	17822248	17822248	C	T	SNP	ARHGEF10L	NM_018125	human	genbank	54_36p	+1	validated	silent	c.1191	p.F397	0.988	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain)	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),superfamily_WD40 repeat-like,superfamily_PH domain-like	-	no_errors
ENSG00000223073	0	genome.wustl.edu	36	MT	530	530	+	RNA	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	MT	530	530	T	C	SNP	ENSG00000223073	ENST00000411141	human	ensembl	54_36p	+1	novel	rna	NULL	NULL	NULL	-	-	-	no_errors
MT-ND4	0	genome.wustl.edu	36	MT	11810	11810	+	Silent	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	MT	11810	11810	T	C	SNP	MT-ND4	ENST00000361381	human	ensembl	54_36p	+1	known	silent	c.1050	p.T350	NULL	HMMPfam_Oxidored_q1	HMMPfam_Oxidored_q5_N,HMMPfam_Oxidored_q1	-	no_stop_codon:bad_bp_length_for_coding_region
ZNF142	7701	genome.wustl.edu	36	2	219215435	219215435	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	219215435	219215435	G	A	SNP	ZNF142	NM_001105537	human	genbank	54_36p	-1	validated	nonsense	c.4048	p.Q1350*	0.963	HMMSmart_SM00355,PatternScan_ZINC_FINGER_C2H2_1	superfamily_C2H2 and C2HC zinc fingers,HMMPfam_zf-C2H2,HMMSmart_SM00355,PatternScan_ZINC_FINGER_C2H2_1	-	no_errors
LOC727764	727764	genome.wustl.edu	36	4	55610	55610	+	RNA	DEL	A	A	-			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	55610	55610	A	-	DEL	LOC727764	XR_038491	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.000	-	-	-	no_errors
DSCAM	1826	genome.wustl.edu	36	21	40569957	40569957	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	21	40569957	40569957	G	A	SNP	DSCAM	NM_001389	human	genbank	54_36p	-1	validated	missense	c.2293	p.L765F	1.000	HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin	HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin	-	no_errors
LOC400011	400011	genome.wustl.edu	36	12	16444150	16444150	+	RNA	SNP	G	G	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	16444150	16444150	G	T	SNP	LOC400011	XR_016968	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.986	-	-	-	pseudogene
PCDHB3	56132	genome.wustl.edu	36	5	140461079	140461079	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	5	140461079	140461079	C	T	SNP	PCDHB3	NM_018937	human	genbank	54_36p	+1	reviewed	missense	c.662	p.P221L	0.028	superfamily_Cadherin-like,HMMPfam_Cadherin,HMMSmart_SM00112	HMMPfam_Cadherin_2,superfamily_Cadherin-like,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin	-	no_errors
RGAG1	57529	genome.wustl.edu	36	X	109583735	109583735	+	Silent	SNP	C	C	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	109583735	109583735	C	A	SNP	RGAG1	NM_020769	human	genbank	54_36p	+1	provisional	silent	c.3234	p.G1078	0.000	NULL	HMMPfam_Retrotrans_gag	-	no_errors
HYAL4	23553	genome.wustl.edu	36	7	123296322	123296322	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	123296322	123296322	C	G	SNP	HYAL4	NM_012269	human	genbank	54_36p	+1	reviewed	missense	c.759	p.N253K	0.993	HMMPfam_Glyco_hydro_56,superfamily_Glyco_hydro_cat	HMMPfam_Glyco_hydro_56,superfamily_Glyco_hydro_cat,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2	-	no_errors
POSTN	10631	genome.wustl.edu	36	13	37054628	37054628	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	13	37054628	37054628	G	A	SNP	POSTN	NM_006475	human	genbank	54_36p	-1	validated	missense	c.1267	p.R423C	1.000	superfamily_FAS1 domain,HMMPfam_Fasciclin,HMMSmart_SM00554	HMMPfam_EMI,superfamily_FAS1 domain,HMMPfam_Fasciclin,HMMSmart_SM00554	-	no_errors
