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
ALLC	55821	genome.wustl.edu	36	2	3727027	3727029	+	In_Frame_Del	DEL	GAA	GAA	-			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	GAA	GAA			GAA	GAA	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	3727027	3727029	GAA	-	DEL	ALLC	NM_018436	human	genbank	54_36p	+1	validated	in_frame_del	c.901_903	p.E303in_frame_del	0.866:0.921:0.929	superfamily_Gal_bind_like,HMMPfam_Allantoicase	superfamily_Gal_bind_like,HMMPfam_Allantoicase	-	no_errors
OTOA	146183	genome.wustl.edu	36	16	21649688	21649688	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	16	21649688	21649688	C	T	SNP	OTOA	NM_144672	human	genbank	54_36p	+1	provisional	missense	c.2237	p.T746M	0.021	NULL	NULL	-	no_errors
PLIN1	5346	genome.wustl.edu	36	15	88010100	88010101	+	In_Frame_Ins	INS	-	-	CGG			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	-	-			-	-	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	15	88010100	88010101	-	CGG	INS	PLIN	NM_002666	human	genbank	54_36p	-1	reviewed	in_frame_ins	c.1287_1286	p.430in_frame_insR	0.164:0.161	NULL	HMMPfam_Perilipin	-	no_errors
NEIL1	79661	genome.wustl.edu	36	15	73434197	73434197	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	15	73434197	73434197	C	T	SNP	NEIL1	NM_024608	human	genbank	54_36p	+1	validated	nonsense	c.1087	p.R363*	0.000	NULL	superfamily_N-terminal domain of MutM-like DNA repair proteins,HMMPfam_Fapy_DNA_glyco,superfamily_S13-like H2TH domain,HMMPfam_H2TH,superfamily_Glucocorticoid receptor-like (DNA-binding domain),HMMPfam_Neil1-DNA_bind	-	no_errors
LIMS2	55679	genome.wustl.edu	36	2	128128537	128128537	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	128128537	128128537	G	C	SNP	LIMS2	NM_017980	human	genbank	54_36p	-1	provisional	missense	c.362	p.P121R	0.999	superfamily_SSF57716,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,HMMPfam_LIM	superfamily_SSF57716,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,HMMPfam_LIM	-	no_errors
HSD17B1P1	643646	genome.wustl.edu	36	17	37953218	37953218	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	17	37953218	37953218	G	A	SNP	HSD17BP1	ENST00000225928	human	ensembl	54_36p	+1	known	missense	c.505	p.V169I	0.948	superfamily_NAD(P)-binding Rossmann-fold domains,HMMPfam_adh_short	superfamily_NAD(P)-binding Rossmann-fold domains,HMMPfam_adh_short,PatternScan_ADH_SHORT	-	no_errors
PHF6	84295	genome.wustl.edu	36	X	133355645	133355645	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	133355645	133355645	G	T	SNP	PHF6	NM_001015877	human	genbank	54_36p	+1	reviewed	nonsense	c.415	p.E139*	1.000	NULL	HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger	-	no_errors
MUC4	4585	genome.wustl.edu	36	3	196992967	196992967	+	Silent	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	196992967	196992967	G	A	SNP	MUC4	ENST00000405167	human	ensembl	54_36p	-1	known	silent	c.9879	p.H3293	0.001	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
C19orf55	148137	genome.wustl.edu	36	19	40940951	40940951	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	40940951	40940951	C	T	SNP	C19orf55	ENST00000396911	human	ensembl	54_36p	+1	known	missense	c.73	p.R25C	0.000	NULL	NULL	-	no_errors
HNRPA1L-2	664709	genome.wustl.edu	36	19	11637819	11637819	+	RNA	SNP	A	A	G			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	11637819	11637819	A	G	SNP	HNRPA1L-2	NR_002944	human	genbank	54_36p	-1	provisional	rna	NULL	NULL	1.000	-	-	-	pseudogene
SCML2	10389	genome.wustl.edu	36	X	18174676	18174676	+	Silent	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	18174676	18174676	G	A	SNP	SCML2	NM_006089	human	genbank	54_36p	-1	validated	silent	c.1764	p.D588	0.001	NULL	superfamily_Tudor/PWWP/MBT,HMMSmart_SM00561,HMMPfam_MBT,superfamily_SAM/Pointed domain,HMMSmart_SM00454,HMMPfam_SAM_1	-	no_errors
TACC3	10460	genome.wustl.edu	36	4	1699614	1699614	+	Silent	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	1699614	1699614	G	A	SNP	TACC3	NM_006342	human	genbank	54_36p	+1	reviewed	silent	c.687	p.P229	0.015	NULL	HMMPfam_TACC	-	no_errors
ATP2A2	488	genome.wustl.edu	36	12	109249835	109249835	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	109249835	109249835	C	T	SNP	ATP2A2	NM_170665	human	genbank	54_36p	+1	reviewed	missense	c.725	p.T242I	1.000	superfamily_Calcium ATPase transmembrane domain M,HMMPfam_E1-E2_ATPase	superfamily_Calcium ATPase transmembrane domain M,HMMPfam_Cation_ATPase_N,HMMPfam_E1-E2_ATPase,superfamily_Calcium ATPase transduction domain A,HMMPfam_Hydrolase,PatternScan_ATPASE_E1_E2,superfamily_Metal cation-transporting ATPase ATP-binding domain N,superfamily_HAD-like,HMMPfam_Cation_ATPase_C	-	no_errors
CRY1	1407	genome.wustl.edu	36	12	105917705	105917705	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	105917705	105917705	A	T	SNP	CRY1	NM_004075	human	genbank	54_36p	-1	validated	nonsense	c.891	p.Y297*	1.000	superfamily_Cryptochrome/photolyase FAD-binding domain,HMMPfam_FAD_binding_7	superfamily_Cryptochrome/photolyase N-terminal domain,HMMPfam_DNA_photolyase,superfamily_Cryptochrome/photolyase FAD-binding domain,HMMPfam_FAD_binding_7	-	no_errors
C6orf174	387104	genome.wustl.edu	36	6	127838692	127838692	+	Silent	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	6	127838692	127838692	G	A	SNP	C6orf174	NM_001012279	human	genbank	54_36p	-1	validated	silent	c.2172	p.Y724	0.997	NULL	NULL	-	no_errors
ENSG00000215768	0	genome.wustl.edu	36	NT_113933	60437	60437	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	NT_113933	60437	60437	G	A	SNP	ENSG00000215768	ENST00000400874	human	ensembl	54_36p	-1	known	missense	c.13	p.R5C	NULL	NULL	HMMSmart_UTG,superfamily_Secretoglobin	-	no_errors
LILRB2	10288	genome.wustl.edu	36	19	59474649	59474649	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	59474649	59474649	C	T	SNP	LILRB2	NM_005874	human	genbank	54_36p	-1	reviewed	missense	c.785	p.R262H	0.000	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin	-	no_errors
GNRHR	2798	genome.wustl.edu	36	4	68302234	68302234	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	68302234	68302234	G	A	SNP	GNRHR	NM_000406	human	genbank	54_36p	-1	reviewed	missense	c.415	p.R139C	1.000	superfamily_Family A G protein-coupled receptor-like,HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1	superfamily_Family A G protein-coupled receptor-like,HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1	-	no_errors
NAV3	89795	genome.wustl.edu	36	12	77117244	77117244	+	Splice_Site	SNP	A	A	T			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	77117244	77117244	A	T	SNP	NAV3	NM_014903	human	genbank	54_36p	+1	validated	splice_site	c.6453-2	e36-2	0.996	-	-	-	no_errors
DNAJC11	55735	genome.wustl.edu	36	1	6618819	6618819	+	Silent	SNP	G	G	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	6618819	6618819	G	A	SNP	DNAJC11	NM_018198	human	genbank	54_36p	-1	validated	silent	c.1599	p.G533	0.326	NULL	superfamily_Chaperone J-domain,HMMSmart_SM00271,HMMPfam_DnaJ,PatternScan_DNAJ_1	-	no_errors
C10orf68	79741	genome.wustl.edu	36	10	33014976	33014976	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2804-03B-01W-0728-08	TCGA-AB-2804-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	10	33014976	33014976	T	A	SNP	C10orf68	NM_024688	human	genbank	54_36p	+1	validated	missense	c.116	p.I39K	0.000	NULL	NULL	-	no_errors
