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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	chromosome_name	start	stop	reference	variant	type	gene_name	transcript_name	transcript_species	transcript_source	transcript_version	strand	transcript_status	trv_type	c_position	amino_acid_change	ucsc_cons	domain	all_domains	deletion_substructures	transcript_error	NormalRefReads_WU	NormalVarReads_WU	NormalVAF_WU	TumorRefReads_WU	TumorVarReads_WU	TumorVAF_WU	RNARefReads_WU	RNAVarReads_WU	RNAVAF_WU
HCFC1	0	genome.wustl.edu	36	X	152883350	152883350	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	X	152883350	152883350	G	A	SNP	HCFC1	NM_005334.2	human	genbank	54_36p	-1	reviewed	missense	c.215	p.P72L	1.000	superfamily_Galactose oxidase central domain	HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Kelch_1,superfamily_Fibronectin type III,superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2	-	no_errors	173	2	1.14	133	115	46.18	25	112	81.75
ENSG00000210557	0	genome.wustl.edu	36	1	51469521	51469521	+	RNA	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	1	51469521	51469521	C	T	SNP	ENSG00000210557	ENST00000387822	human	ensembl	54_36p	-1	novel	rna	NULL	NULL	0.000	-	-	-	pseudogene	173	1	0.57	164	132	44.59	3	0	0.00
LRRC40	0	genome.wustl.edu	36	1	70386823	70386823	+	Silent	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	1	70386823	70386823	C	T	SNP	LRRC40	NM_017768.3	human	genbank	54_36p	-1	provisional	silent	c.1638	p.T546	0.095	HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058	HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058	-	no_errors	538	2	0.37	279	231	45.21	10	12	54.55
RGS8	0	genome.wustl.edu	36	1	180882643	180882643	+	Silent	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	1	180882643	180882643	C	T	SNP	RGS8	NM_033345.1	human	genbank	54_36p	-1	reviewed	silent	c.447	p.T149	0.990	HMMPfam_RGS,HMMSmart_RGS,superfamily_Regulat_G_prot_signal_superfam	HMMPfam_RGS,HMMSmart_RGS,superfamily_Regulat_G_prot_signal_superfam	-	no_errors	246	9	3.52	232	144	38.20	NA	NA	NA
LOC100131253	0	genome.wustl.edu	36	2	225072861	225072861	+	RNA	SNP	T	T	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	2	225072861	225072861	T	A	SNP	LOC100131253	XR_039607.1	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.261	-	-	-	pseudogene	379	0	0.00	336	275	44.93	7	2	22.22
VCAN	0	genome.wustl.edu	36	5	82852453	82852453	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	5	82852453	82852453	C	A	SNP	VCAN	NM_004385.1	human	genbank	54_36p	+1	validated	missense	c.2572	p.P858T	0.008	NULL	PatternScan_ASX_HYDROXYL,HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,HMMSmart_SM00179,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin	-	no_errors	808	3	0.37	312	257	45.09	NA	NA	NA
WAC	0	genome.wustl.edu	36	10	28864562	28864562	+	Silent	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	10	28864562	28864562	C	T	SNP	WAC	NM_016628.3	human	genbank	54_36p	+1	reviewed	silent	c.144	p.D48	1.000	NULL	HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain	-	no_errors	358	9	2.45	343	298	46.42	102	111	52.11
PLCE1	0	genome.wustl.edu	36	10	95983931	95983931	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	10	95983931	95983931	C	A	SNP	PLCE1	NM_016341.3	human	genbank	54_36p	+1	validated	missense	c.2086	p.H696N	1.000	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	317	0	0.00	329	244	42.58	NA	NA	NA
SFXN2	0	genome.wustl.edu	36	10	104479520	104479520	+	Silent	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	10	104479520	104479520	G	A	SNP	SFXN2	NM_178858.4	human	genbank	54_36p	+1	validated	silent	c.558	p.A186	0.885	HMMPfam_Mtc	HMMPfam_Mtc	-	no_errors	207	0	0.00	179	165	47.41	4	2	33.33
LOC100130353	0	genome.wustl.edu	36	11	118751824	118751824	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	11	118751824	118751824	G	A	SNP	LOC100130353	XM_001719137.1	human	genbank	54_36p	+1	model	missense	c.227	p.R76Q	0.001	NULL	NULL	-	no_errors	92	1	1.08	84	58	40.85	NA	NA	NA
ENSG00000212358	0	genome.wustl.edu	36	12	17115644	17115644	+	RNA	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	12	17115644	17115644	G	A	SNP	ENSG00000212358	ENST00000391056	human	ensembl	54_36p	-1	novel	rna	NULL	NULL	0.001	-	-	-	no_errors	805	0	0.00	464	282	37.80	NA	NA	NA
KRAS	0	genome.wustl.edu	36	12	25269829	25269829	+	Missense_Mutation	SNP	C	C	T	rs121913527		TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	12	25269829	25269829	C	T	SNP	KRAS	NM_033360.3	human	genbank	54_36p	-1	reviewed	missense	c.436	p.A146T	1.000	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	-	no_errors	197	2	1.01	289	186	39.08	26	10	27.78
FAM123A	0	genome.wustl.edu	36	13	24641843	24641843	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	13	24641843	24641843	T	G	SNP	FAM123A	NM_152704.2	human	genbank	54_36p	-1	validated	missense	c.1915	p.I639L	1.000	NULL	HMMPfam_WTX	-	no_errors	222	2	0.89	250	207	45.30	NA	NA	NA
IGHE	0	genome.wustl.edu	36	14	105138389	105138389	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	14	105138389	105138389	G	A	SNP	IGHE	ENST00000390541	human	ensembl	54_36p	-1	known	missense	c.514	p.P172S	0.106	HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin	PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin	-	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	157	0	0.00	96	84	45.65	0	0	0.00
IDH2	0	genome.wustl.edu	36	15	88432938	88432938	+	Missense_Mutation	SNP	C	C	T	rs121913502		TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	15	88432938	88432938	C	T	SNP	IDH2	NM_002168.2	human	genbank	54_36p	-1	reviewed	missense	c.419	p.R140Q	1.000	HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	-	no_errors	121	0	0.00	103	75	42.13	181	149	45.15
DNAJA3	0	genome.wustl.edu	36	16	4440471	4440471	+	Silent	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	16	4440471	4440471	G	A	SNP	DNAJA3	NM_005147.1	human	genbank	54_36p	+1	validated	silent	c.1311	p.T437	0.515	NULL	HMMPfam_DnaJ_CXXCXGXG,superfamily_HSP_DnaJ_cys-rich,HMMPfam_DnaJ,HMMSmart_DnaJ,superfamily_DnaJ_N,HMMPfam_DnaJ_C,superfamily_HSP40_DnaJ_pep,PatternScan_DNAJ_1	-	no_errors	142	4	2.74	103	90	46.63	23	17	42.50
SMG1	0	genome.wustl.edu	36	16	18760480	18760480	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	16	18760480	18760480	A	T	SNP	SMG1	NM_015092.4	human	genbank	54_36p	-1	reviewed	missense	c.6604	p.S2202T	1.000	HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,superfamily_Protein kinase-like (PK-like)	HMMPfam_HEAT,HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_FATC,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_2	-	no_errors	1003	15	1.47	265	281	51.09	38	29	43.28
AP1M1	0	genome.wustl.edu	36	19	16198261	16198261	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	19	16198261	16198261	C	G	SNP	AP1M1	NM_032493.1	human	genbank	54_36p	+1	reviewed	missense	c.576	p.S192R	0.996	HMMPfam_Adap_comp_sub,superfamily_Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor	HMMPfam_Adap_comp_sub,superfamily_Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor,superfamily_SNARE-like,PatternScan_CLAT_ADAPTOR_M_1,PatternScan_CLAT_ADAPTOR_M_2	-	no_errors	35	0	0.00	77	70	47.62	24	17	41.46
SIGLEC1	0	genome.wustl.edu	36	20	3632541	3632541	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	20	3632541	3632541	C	T	SNP	SIGLEC1	NM_023068.3	human	genbank	54_36p	-1	reviewed	missense	c.904	p.V302I	0.657	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMPfam_C2-set_2,superfamily_Immunoglobulin	-	no_errors	143	0	0.00	160	96	37.07	NA	NA	NA
ENSG00000209722	0	genome.wustl.edu	36	21	17725817	17725817	+	RNA	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	21	17725817	17725817	G	A	SNP	ENSG00000209722	ENST00000386987	human	ensembl	54_36p	+1	novel	rna	NULL	NULL	0.000	-	-	-	pseudogene	303	0	0.00	155	142	47.81	NA	NA	NA
TOP3B	0	genome.wustl.edu	36	22	20658852	20658852	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	22	20658852	20658852	A	G	SNP	TOP3B	NM_003935.3	human	genbank	54_36p	-1	reviewed	missense	c.79	p.S27P	1.000	superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00493,HMMPfam_Toprim	PatternScan_TOPOISOMERASE_I_PROK,superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00436,HMMSmart_SM00437,HMMSmart_SM00493,HMMPfam_Toprim,HMMPfam_Topoisom_bac	-	no_errors	123	4	3.15	100	75	42.86	7	18	72.00
RAB36	0	genome.wustl.edu	36	22	21822294	21822294	+	Silent	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	22	21822294	21822294	C	T	SNP	RAB36	NM_004914.2	human	genbank	54_36p	+1	validated	silent	c.312	p.H104	0.967	NULL	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMSmart_SM00177,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	-	no_errors	170	2	1.16	139	115	44.75	NA	NA	NA
DNMT3A	0	genome.wustl.edu	36	2	25320610	25320610	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	2	25320610	25320610	C	-	DEL	DNMT3A	NM_022552.3	human	genbank	54_36p	-1	reviewed	frame_shift_del	c.1769	p.G590fs	1.000	superfamily_FYVE/PHD zinc finger	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	-	no_errors	0	0	0.00	0	0	0.00	0	2	100.00