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
PLXNA4	91584	genome.wustl.edu	36	7	131516835	131516835	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	131516835	131516835	C	T	SNP	PLXNA4	NM_020911	human	genbank	54_36p	-1	validated	missense	c.3337	p.E1113K	0.997	HMMSmart_SM00429,HMMPfam_TIG,superfamily_E set domains	superfamily_Sema domain,HMMPfam_Sema,HMMSmart_SM00630,HMMPfam_PSI,HMMSmart_SM00423,superfamily_Plexin repeat,HMMSmart_SM00429,superfamily_E set domains,HMMPfam_TIG,HMMPfam_Plexin_cytopl,superfamily_GTPase activation domain GAP	-	no_errors
JAK2	3717	genome.wustl.edu	36	9	5063770	5063770	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	5063770	5063770	G	T	SNP	JAK2	NM_004972	human	genbank	54_36p	+1	reviewed	missense	c.1849	p.V617F	1.000	superfamily_Kinase_like,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc	PatternScan_FERM_1,PatternScan_FERM_2,HMMSmart_B41,superfamily_SSF55550,HMMSmart_SH2,HMMPfam_SH2,superfamily_Kinase_like,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_TYR	-	no_errors
DIS3	22894	genome.wustl.edu	36	13	72243998	72243998	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	13	72243998	72243998	C	T	SNP	DIS3	NM_014953	human	genbank	54_36p	-1	validated	missense	c.1541	p.R514K	0.986	HMMPfam_RNB	HMMPfam_RNB,PatternScan_RIBONUCLEASE_II,HMMSmart_SM00670,superfamily_PIN domain-like	-	no_errors
TTBK1	84630	genome.wustl.edu	36	6	43338696	43338696	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	43338696	43338696	A	G	SNP	TTBK1	NM_032538	human	genbank	54_36p	+1	validated	missense	c.1616	p.D539G	1.000	NULL	HMMSmart_SM00219,HMMSmart_SM00220,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	-	no_errors
LOC100128519	100128519	genome.wustl.edu	36	4	9163755	9163755	+	RNA	SNP	G	G	A			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	9163755	9163755	G	A	SNP	LOC100128519	XR_038473	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.019	-	-	-	pseudogene
KIAA1109	84162	genome.wustl.edu	36	4	123369772	123369772	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	123369772	123369772	A	G	SNP	KIAA1109	NM_015312	human	genbank	54_36p	+1	validated	missense	c.2969	p.Y990C	1.000	NULL	PatternScan_ASP_PROTEASE,HMMPfam_FSA_C	-	no_errors
MYH4	4622	genome.wustl.edu	36	17	10296271	10296271	+	Silent	SNP	G	G	A			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	17	10296271	10296271	G	A	SNP	MYH4	NM_017533	human	genbank	54_36p	-1	validated	silent	c.3450	p.I1150	1.000	HMMPfam_Myosin_tail_1	HMMPfam_Myosin_N,superfamily_SSF52540,HMMSmart_MYSc,HMMPfam_Myosin_head,HMMSmart_IQ,HMMPfam_Myosin_tail_1	-	no_errors
PKHD1L1	93035	genome.wustl.edu	36	8	110481706	110481706	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	8	110481706	110481706	G	A	SNP	PKHD1L1	NM_177531	human	genbank	54_36p	+1	validated	missense	c.1238	p.R413H	0.999	HMMSmart_SM00758,superfamily_Anthrax protective antigen,HMMSmart_SM00710	superfamily_E set domains,HMMSmart_SM00429,HMMPfam_TIG,HMMSmart_SM00758,superfamily_Anthrax protective antigen,HMMSmart_SM00710,superfamily_Cupredoxins,HMMPfam_G8,superfamily_Pectin lyase-like	-	no_errors
TET2	54790	genome.wustl.edu	36	4	106413251	106413252	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	-	-			-	-	Verified	Valid	Somatic		Capture				Illumina GAIIx	4	106413251	106413252	0	TA	INS	TET2	ENST00000265149	human	ensembl	54_36p	1	known	frame_shift_ins	c.670_671	p.K224fs	NA	NA	NA	NA	NA
CACNG2	10369	genome.wustl.edu	36	22	35428399	35428399	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	22	35428399	35428399	C	T	SNP	CACNG2	NM_006078	human	genbank	54_36p	-1	reviewed	missense	c.169	p.V57I	1.000	HMMPfam_PMP22_Claudin	HMMPfam_PMP22_Claudin	-	no_errors
RUNX1	861	genome.wustl.edu	36	21	35153662	35153662	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	21	35153662	35153662	C	T	SNP	RUNX1	NM_001754	human	genbank	54_36p	-1	reviewed	missense	c.592	p.D198N	1.000	superfamily_p53-like transcription factors,HMMPfam_Runt	superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI	-	no_errors
CLDN18	51208	genome.wustl.edu	36	3	139225231	139225231	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	139225231	139225231	G	T	SNP	CLDN18	NM_001002026	human	genbank	54_36p	+1	validated	missense	c.262	p.V88F	0.995	HMMPfam_PMP22_Claudin	HMMPfam_PMP22_Claudin,PatternScan_CLAUDIN	-	no_errors
EZH2	2146	genome.wustl.edu	36	7	148137095	148137095	+	Splice_Site	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	148137095	148137095	C	T	SNP	EZH2	NM_004456	human	genbank	54_36p	-1	reviewed	splice_site	c.2195+1	e18+1	1.000	-	-	-	no_errors
LOC440225	440225	genome.wustl.edu	36	15	19403072	19403072	+	RNA	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	15	19403072	19403072	C	T	SNP	LOC440225	XR_042334	human	genbank	54_36p	-1	model	rna	NULL	NULL	1.000	-	-	-	pseudogene
TET2	54790	genome.wustl.edu	36	4	106377387	106377387	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	106377387	106377387	C	T	SNP	TET2	NM_017628	human	genbank	54_36p	+1	validated	nonsense	c.2839	p.Q947*	1.000	NULL	NULL	-	no_errors
MUC4	4585	genome.wustl.edu	36	3	196999844	196999844	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	196999844	196999844	A	T	SNP	MUC4	ENST00000405167	human	ensembl	54_36p	-1	known	missense	c.3002	p.V1001E	0.002	NULL	HMMPfam_VWD,HMMSmart_SM00216,HMMPfam_NIDO,HMMSmart_SM00539,HMMPfam_AMOP,HMMSmart_SM00723,PatternScan_SUGAR_TRANSPORT_2,HMMSmart_SM00181,PatternScan_EGF_1,superfamily_EGF/Laminin	-	no_errors
PSG9	5678	genome.wustl.edu	36	19	48463864	48463864	+	Silent	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	48463864	48463864	C	T	SNP	PSG9	NM_002784	human	genbank	54_36p	-1	validated	silent	c.342	p.R114	0.015	HMMPfam_V-set,superfamily_Immunoglobulin,HMMSmart_SM00409	HMMPfam_V-set,superfamily_Immunoglobulin,HMMSmart_SM00409,HMMSmart_SM00408,HMMPfam_ig	-	no_errors
SLC26A3	1811	genome.wustl.edu	36	7	107218912	107218912	+	Silent	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	107218912	107218912	C	T	SNP	SLC26A3	NM_000111	human	genbank	54_36p	-1	reviewed	silent	c.387	p.P129	0.919	NULL	PatternScan_SLC26A,HMMPfam_Sulfate_transp,superfamily_STAS,HMMPfam_STAS	-	no_errors
MYOM3	127294	genome.wustl.edu	36	1	24256576	24256576	+	Silent	SNP	G	G	A	rs78428674	byCluster;by1000genomes	TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	24256576	24256576	G	A	SNP	MYOM3	NM_152372	human	genbank	54_36p	-1	validated	silent	c.4179	p.T1393	1.000	superfamily_Immunoglobulin,HMMPfam_I-set,HMMSmart_SM00409,HMMSmart_SM00408	superfamily_Immunoglobulin,HMMPfam_I-set,HMMSmart_SM00409,HMMSmart_SM00408,superfamily_Fibronectin type III,HMMSmart_SM00060,HMMPfam_fn3,PatternScan_EF_HAND_1,HMMPfam_ig	-	no_errors
LOC100133049	100133049	genome.wustl.edu	36	1	222204551	222204551	+	RNA	SNP	T	T	C			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	222204551	222204551	T	C	SNP	LOC100133049	XR_038518	human	genbank	54_36p	+1	model	rna	NULL	NULL	0.000	-	-	-	pseudogene
LOC728539	728539	genome.wustl.edu	36	9	66239112	66239112	+	Silent	SNP	T	T	C			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	9	66239112	66239112	T	C	SNP	LOC728539	XM_001127707	human	genbank	54_36p	+1	model	silent	c.102	p.N34	0.000	NULL	HMMPfam_7tm_1	-	no_errors
ATP2B3	492	genome.wustl.edu	36	X	152478458	152478458	+	Silent	SNP	G	G	A			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	152478458	152478458	G	A	SNP	ATP2B3	NM_001001344	human	genbank	54_36p	+1	reviewed	silent	c.2703	p.T901	0.019	HMMPfam_Cation_ATPase_C,superfamily_Calcium ATPase transmembrane domain M	HMMPfam_Cation_ATPase_N,HMMPfam_Hydrolase,HMMPfam_Cation_ATPase_C,HMMPfam_E1-E2_ATPase,PatternScan_ATPASE_E1_E2,superfamily_HAD-like,superfamily_Calcium ATPase transduction domain A,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_Calcium ATPase transmembrane domain M	-	no_errors
CTSA	5476	genome.wustl.edu	36	20	43953645	43953647	+	In_Frame_Del	DEL	CTG	CTG	-			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	CTG	CTG			CTG	CTG	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	20	43953645	43953647	CTG	-	DEL	CTSA	NM_000308	human	genbank	54_36p	+1	reviewed	in_frame_del	c.85_87	p.L32in_frame_del	0.066:0.073:0.080	NULL	HMMPfam_Peptidase_S10,PatternScan_CARBOXYPEPT_SER_SER,PatternScan_CARBOXYPEPT_SER_HIS,superfamily_alpha/beta-Hydrolases	-	no_errors
LOC100129466	100129466	genome.wustl.edu	36	4	39345	39345	+	RNA	DEL	T	T	-			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	39345	39345	T	-	DEL	LOC100129466	XR_036871	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.000	-	-	-	pseudogene
PRAMEF2	65122	genome.wustl.edu	36	1	12842416	12842416	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	12842416	12842416	C	T	SNP	PRAMEF2	NM_023014	human	genbank	54_36p	+1	provisional	missense	c.569	p.T190M	0.002	superfamily_SSF52047	superfamily_SSF52047	-	no_errors
SLC27A3	11000	genome.wustl.edu	36	1	152018355	152018355	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	152018355	152018355	C	T	SNP	SLC27A3	ENST00000368659	human	ensembl	54_36p	+1	known	nonsense	c.34	p.R12*	0.000	NULL	superfamily_SSF56801	-	no_errors
MYOC	4653	genome.wustl.edu	36	1	169872108	169872108	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	169872108	169872108	G	T	SNP	MYOC	NM_000261	human	genbank	54_36p	-1	reviewed	nonsense	c.1095	p.Y365*	1.000	HMMPfam_OLF,HMMSmart_SM00284	HMMPfam_OLF,HMMSmart_SM00284	-	no_errors
TNK2	10188	genome.wustl.edu	36	3	197081642	197081642	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	197081642	197081642	G	C	SNP	TNK2	ENST00000316664	human	ensembl	54_36p	-1	known	missense	c.1482	p.H494Q	0.000	HMMPfam_GTPase_binding	superfamily_Kinase_like,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_TYR,superfamily_SH3,HMMPfam_SH3_1,HMMSmart_SH3,HMMPfam_GTPase_binding	-	no_errors
SDK1	221935	genome.wustl.edu	36	7	4239566	4239566	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2865-03B-01W-0728-08	TCGA-AB-2865-11B-01W-0729-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	7	4239566	4239566	C	T	SNP	SDK1	NM_152744	human	genbank	54_36p	+1	validated	missense	c.5981	p.T1994M	0.003	superfamily_Fibronectin type III	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin	-	no_errors
