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
ATP6AP2	0	genome.wustl.edu	36	X	40341789	40341789	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	X	40341789	40341789	C	T	SNP	ATP6AP2	NM_005765.2	human	genbank	54_36p	+1	reviewed	missense	c.463	p.R155C	1.000	NULL	HMMPfam_Renin_r	-	no_errors	810	30	3.57	36	13	26.53	130	0	0.00
SYTL4	0	genome.wustl.edu	36	X	99822888	99822888	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	X	99822888	99822888	C	T	SNP	SYTL4	NM_080737.1	human	genbank	54_36p	-1	validated	missense	c.1550	p.R517Q	0.989	superfamily_C2 domain (Calcium/lipid-binding domain CaLB)	HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RPH3A_effector,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),superfamily_FYVE/PHD zinc finger	-	no_errors	640	2	0.31	105	51	32.69	2	0	0.00
STAG2	0	genome.wustl.edu	36	X	123048157	123048157	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	X	123048157	123048157	C	T	SNP	STAG2	NM_001042749.1	human	genbank	54_36p	+1	validated	nonsense	c.3133	p.R1045*	1.000	superfamily_ARM-type_fold	HMMPfam_STAG,superfamily_ARM-type_fold	-	no_errors	989	14	1.40	145	37	20.33	6	10	62.50
PRKAA2	0	genome.wustl.edu	36	1	56934311	56934311	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	1	56934311	56934311	C	T	SNP	PRKAA2	NM_006252.3	human	genbank	54_36p	+1	validated	nonsense	c.679	p.R227*	1.000	HMMSmart_S_TKc,superfamily_Kinase_like,HMMPfam_Pkinase	HMMSmart_S_TKc,PatternScan_PROTEIN_KINASE_ST,superfamily_Kinase_like,PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase	-	no_errors	838	25	2.90	194	192	49.74	NA	NA	NA
NRAS	0	genome.wustl.edu	36	1	115058052	115058052	+	Missense_Mutation	SNP	T	T	G	rs11554290	unknown	TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	T	T			T	T	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	1	115058052	115058052	T	G	SNP	NRAS	NM_002524.3	human	genbank	54_36p	-1	reviewed	missense	c.182	p.Q61P	1.000	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	-	no_errors	749	9	1.19	69	23	25.00	23	15	39.47
TET2	0	genome.wustl.edu	36	4	106415662	106415662	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	4	106415662	106415662	C	T	SNP	TET2	ENST00000265149	human	ensembl	54_36p	+1	known	nonsense	c.952	p.R318*	0.992	NULL	NULL	-	no_start_codon	881	34	3.72	360	248	40.79	12	15	55.56
HOOK3	0	genome.wustl.edu	36	8	42942444	42942444	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	8	42942444	42942444	C	G	SNP	HOOK3	NM_032410.3	human	genbank	54_36p	+1	validated	missense	c.1052	p.T351S	1.000	HMMPfam_HOOK	HMMPfam_HOOK	-	no_errors	758	33	4.17	65	49	42.98	15	13	46.43
PXDNL	0	genome.wustl.edu	36	8	52484186	52484186	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	8	52484186	52484186	C	T	SNP	PXDNL	NM_144651.4	human	genbank	54_36p	-1	validated	missense	c.2551	p.D851N	0.996	HMMPfam_An_peroxidase,superfamily_Heme-dependent peroxidases	HMMPfam_LRRCT,HMMSmart_SM00082,HMMPfam_VWC,HMMSmart_SM00214,PatternScan_VWFC_1,HMMPfam_LRR_1,HMMPfam_An_peroxidase,HMMSmart_SM00369,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Heme-dependent peroxidases,HMMPfam_I-set,superfamily_Immunoglobulin,superfamily_L domain-like	-	no_errors	249	4	1.58	40	21	34.43	NA	NA	NA
OR51L1	0	genome.wustl.edu	36	11	4977503	4977503	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	11	4977503	4977503	G	A	SNP	OR51L1	NM_001004755.1	human	genbank	54_36p	+1	provisional	missense	c.715	p.A239T	0.995	HMMPfam_7tm_1,superfamily_SSF81321	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	-	no_errors	902	35	3.74	210	82	28.08	NA	NA	NA
OR5M1	0	genome.wustl.edu	36	11	56137457	56137457	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	11	56137457	56137457	G	A	SNP	OR5M1	NM_001004740.1	human	genbank	54_36p	-1	provisional	missense	c.98	p.A33V	0.053	superfamily_SSF81321	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	-	no_errors	811	9	1.10	114	37	24.50	NA	NA	NA
CBL	0	genome.wustl.edu	36	11	118673340	118673340	+	Silent	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	11	118673340	118673340	G	A	SNP	CBL	NM_005188.2	human	genbank	54_36p	+1	reviewed	silent	c.2190	p.T730	0.666	NULL	HMMPfam_UBA,HMMSmart_RING,HMMPfam_Cbl_N,superfamily_Adaptor_Cbl_N,HMMPfam_Cbl_N2,HMMPfam_Cbl_N3,HMMSmart_UBA,PatternScan_ZF_RING_1,HMMPfam_zf-C3HC4,superfamily_SSF47473,superfamily_SSF55550,superfamily_SSF57850	-	no_errors	528	11	2.04	90	35	28.00	17	9	34.62
RASSF9	0	genome.wustl.edu	36	12	84723327	84723327	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	12	84723327	84723327	G	T	SNP	RASSF9	NM_005447.3	human	genbank	54_36p	-1	reviewed	missense	c.592	p.H198N	1.000	NULL	HMMSmart_SM00314	-	no_errors	535	4	0.74	110	32	22.54	NA	NA	NA
DOCK9	0	genome.wustl.edu	36	13	98255269	98255269	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	13	98255269	98255269	G	A	SNP	DOCK9	NM_015296.1	human	genbank	54_36p	-1	validated	missense	c.5755	p.R1919C	1.000	HMMPfam_Ded_cyto	HMMPfam_PH,HMMSmart_SM00233,HMMPfam_Ded_cyto,superfamily_PH domain-like	-	no_errors	531	25	4.49	85	51	37.50	1	0	0.00
OR4H12P	0	genome.wustl.edu	36	14	19298443	19298443	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	14	19298443	19298443	G	A	SNP	OR4H12P	ENST00000316004	human	ensembl	54_36p	+1	known	missense	c.535	p.A179T	0.012	HMMPfam_7tm_1,superfamily_SSF81321	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_SSF81321	-	no_errors	743	17	2.23	129	37	22.29	NA	NA	NA
DNAH9	0	genome.wustl.edu	36	17	11582982	11582982	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	17	11582982	11582982	G	A	SNP	DNAH9	NM_001372.3	human	genbank	54_36p	+1	reviewed	missense	c.5875	p.E1959K	1.000	HMMSmart_SM00382,superfamily_P-loop containing nucleoside triphosphate hydrolases	HMMSmart_SM00382,HMMPfam_Dynein_heavy,PatternScan_CPSASE_2,HMMPfam_AAA_5,HMMPfam_DHC_N1,HMMPfam_DHC_N2,superfamily_Spectrin repeat,superfamily_P-loop containing nucleoside triphosphate hydrolases	-	no_errors	814	19	2.28	190	167	46.78	NA	NA	NA
U2AF1L4	0	genome.wustl.edu	36	19	40926605	40926605	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	19	40926605	40926605	G	T	SNP	U2AF1L4	NM_144987.1	human	genbank	54_36p	-1	validated	nonsense	c.348	p.C116*	0.996	NULL	HMMPfam_zf-CCCH,HMMSmart_RRM_1,superfamily_SSF54928	-	no_errors	309	10	3.13	49	30	37.97	3	5	62.50
CEACAM19	0	genome.wustl.edu	36	19	49876379	49876379	+	Silent	SNP	C	C	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	C	C			C	C	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	19	49876379	49876379	C	A	SNP	CEACAM19	NM_020219.1	human	genbank	54_36p	+1	validated	silent	c.747	p.L249	0.676	NULL	superfamily_Immunoglobulin	-	no_errors	729	24	3.18	59	39	39.80	2	3	60.00
RUNX1	0	genome.wustl.edu	36	21	35153653	35153653	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	G	G			G	G	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	21	35153653	35153653	G	A	SNP	RUNX1	NM_001754.2	human	genbank	54_36p	-1	reviewed	nonsense	c.601	p.R201*	1.000	superfamily_p53-like transcription factors,HMMPfam_Runt	superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI	-	no_errors	519	8	1.52	25	22	46.81	216	53	19.63
TET2	0	genome.wustl.edu	36	4	106402456	106402457	+	Splice_Site	INS	-	-	T			TCGA-AB-2978-03A-01D-0739-09	TCGA-AB-2978-11A-01D-0739-09	-	-			-	-	Verified	Valid	Somatic	Phase_IV	Capture		1	dbGAP	Illumina HiSeq	960efb3b-7c3b-42ec-8f29-011d13493c69	be9d0262-d1fa-48c4-bba6-0d5415fb9b52	4	106402456	106402457	-	T	INS	TET2	ENST00000265149	human	ensembl	54_36p	+1	known	splice_site_ins	c.450+2_450+1	e3+2	1.000:0.991	-	-	-	no_start_codon	384	0	0.00	83	0	0.00	0	0	0.00
