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
NPHP4	261734	genome.wustl.edu	36	1	5857716	5857716	+	Missense_Mutation	SNP	C	C	T	rs75260812	byCluster;byFrequency;by1000genomes	TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	1	5857716	5857716	C	T	SNP	NPHP4	NM_015102	human	genbank	54_36p	-1	reviewed	missense	c.2849	p.R950Q	0.855	NULL	NULL	-	no_errors
ENSG00000184246	0	genome.wustl.edu	36	15	82749499	82749499	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	15	82749499	82749499	G	A	SNP	ENSG00000184246	ENST00000333235	human	ensembl	54_36p	-1	known	missense	c.1166	p.P389L	0.001	NULL	NULL	-	no_start_codon
PAICS	10606	genome.wustl.edu	36	4	57009369	57009369	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	57009369	57009369	C	G	SNP	PAICS	NM_001079525	human	genbank	54_36p	+1	reviewed	missense	c.443	p.S148C	1.000	HMMPfam_SAICAR_synt,superfamily_SAICAR synthase-like	HMMPfam_SAICAR_synt,superfamily_SAICAR synthase-like,PatternScan_SAICAR_SYNTHETASE_1,PatternScan_SAICAR_SYNTHETASE_2,HMMPfam_AIRC,superfamily_N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase PurE)	-	no_errors
LOC729686	729686	genome.wustl.edu	36	15	70979168	70979168	+	RNA	SNP	A	A	T			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	15	70979168	70979168	A	T	SNP	LOC729686	XR_039774	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.000	-	-	-	pseudogene
TLR2	7097	genome.wustl.edu	36	4	154844571	154844571	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	154844571	154844571	A	T	SNP	TLR2	NM_003264	human	genbank	54_36p	+1	reviewed	missense	c.1062	p.L354F	0.000	superfamily_SSF52058	superfamily_SSF52058,HMMPfam_LRR_1,HMMSmart_LRR_TYP,HMMSmart_LRRCT,HMMPfam_LRRCT,superfamily_TIR,HMMSmart_TIR,HMMPfam_TIR	-	no_errors
BCL9L	283149	genome.wustl.edu	36	11	118278297	118278297	+	Silent	SNP	G	G	A			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	11	118278297	118278297	G	A	SNP	BCL9L	NM_182557	human	genbank	54_36p	-1	validated	silent	c.1365	p.P455	0.000	NULL	PatternScan_RIBOSOMAL_S6E	-	no_errors
NDUFS8	4728	genome.wustl.edu	36	11	67556198	67556198	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	11	67556198	67556198	C	T	SNP	NDUFS8	NM_002496	human	genbank	54_36p	+1	validated	missense	c.4	p.R2C	0.397	NULL	superfamily_alpha-helical ferredoxin,HMMPfam_Fer4,PatternScan_4FE4S_FER_1	-	no_errors
PPP3CA	5530	genome.wustl.edu	36	4	102239892	102239892	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	102239892	102239892	T	A	SNP	PPP3CA	NM_000944	human	genbank	54_36p	-1	validated	missense	c.395	p.Y132F	1.000	superfamily_Metallo-dependent phosphatases,HMMSmart_SM00156,HMMPfam_Metallophos	superfamily_Metallo-dependent phosphatases,HMMSmart_SM00156,HMMPfam_Metallophos,PatternScan_SER_THR_PHOSPHATASE	-	no_errors
DDX11	1663	genome.wustl.edu	36	12	31147784	31147784	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	31147784	31147784	C	T	SNP	DDX11	NM_030653	human	genbank	54_36p	+1	reviewed	missense	c.2543	p.A848V	1.000	HMMSmart_HELICc2	HMMSmart_DEXDc2,HMMSmart_HELICc2,HMMPfam_DEAD_2,superfamily_SSF52540	-	no_errors
HEPN1	641654	genome.wustl.edu	36	11	124295038	124295038	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	11	124295038	124295038	A	T	SNP	HEPN1	NM_001037558	human	genbank	54_36p	+1	provisional	missense	c.182	p.H61L	0.000	NULL	NULL	-	no_errors
LOC642678	642678	genome.wustl.edu	36	2	91257921	91257921	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	91257921	91257921	C	T	SNP	LOC642678	XM_926130	human	genbank	54_36p	-1	model	missense	c.169	p.V57M	0.997	NULL	superfamily_FYVE/PHD zinc finger,HMMSmart_SM00249,HMMPfam_PHD,PatternScan_ZF_PHD_1	-	no_errors
NUP210	23225	genome.wustl.edu	36	3	13343843	13343843	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	C	C			C	C	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	3	13343843	13343843	C	T	SNP	NUP210	NM_024923	human	genbank	54_36p	-1	reviewed	missense	c.4381	p.A1461T	0.001	NULL	superfamily_Invasin/intimin cell-adhesion fragments,HMMPfam_Big_2,HMMSmart_SM00635	-	no_errors
VCX3B	425054	genome.wustl.edu	36	X	8394166	8394166	+	Silent	SNP	G	G	A			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	X	8394166	8394166	G	A	SNP	VCX3B	NM_001001888	human	genbank	54_36p	+1	reviewed	silent	c.393	p.E131	0.000	NULL	NULL	-	no_errors
U2AF2	11338	genome.wustl.edu	36	19	60865712	60865712	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	19	60865712	60865712	G	A	SNP	U2AF2	NM_007279	human	genbank	54_36p	+1	reviewed	missense	c.519	p.M173I	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	-	no_errors
TP53INP1	94241	genome.wustl.edu	36	8	96021093	96021096	+	In_Frame_Del	DEL	TGAC	TGAC	-			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	TGAC	TGAC			TGAC	TGAC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	8	96021093	96021096	TGAC	-	DEL	TP53INP1	ENST00000378776	human	ensembl	54_36p	-1	known	splice_site_del	c.478-1_478-1	e3-1	0.001:0.001:0.001:0.001	-	-	-	no_errors
PSAPL1	768239	genome.wustl.edu	36	4	7486856	7486856	+	Silent	SNP	G	G	A			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	G	G			G	G	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	4	7486856	7486856	G	A	SNP	PSAPL1	NM_001085382	human	genbank	54_36p	-1	validated	silent	c.651	p.G217	0.931	NULL	NULL	-	pseudogene:no_stop_codon:bad_bp_length_for_coding_region
PIGF	5281	genome.wustl.edu	36	2	46695623	46695623	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	A	A			A	A	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	46695623	46695623	A	G	SNP	PIGF	NM_002643	human	genbank	54_36p	-1	reviewed	missense	c.185	p.V62A	0.573	HMMPfam_PIG-F	HMMPfam_PIG-F	-	no_errors
UBR3	130507	genome.wustl.edu	36	2	170573688	170573688	+	Silent	SNP	T	T	C			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	T	T			T	T	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	2	170573688	170573688	T	C	SNP	UBR3	NM_172070	human	genbank	54_36p	+1	validated	silent	c.918	p.S306	0.995	NULL	superfamily_RING/U-box,HMMPfam_zf-C3HC4	-	no_errors
LOC727826	727826	genome.wustl.edu	36	12	131912465	131912467	+	In_Frame_Del	DEL	TAC	TAC	-			TCGA-AB-2823-03B-01W-0728-08	TCGA-AB-2823-11B-01W-0728-08	TAC	TAC			TAC	TAC	Unknown	Unknown	Somatic		Capture				Illumina GAIIx	12	131912465	131912467	TAC	-	DEL	LOC727826	XM_001720403	human	genbank	54_36p	+1	model	in_frame_del	c.106_108	p.Y37in_frame_del	0.955:0.998:0.999	NULL	superfamily_Nucleic acid-binding proteins,HMMPfam_Ribosomal_S17	-	pseudogene
