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
MT-CO2	0	genome.wustl.edu	36	MT	7655	7655	+	Silent	SNP	T	T	C			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	MT	7655	7655	T	C	SNP	MT-CO2	ENST00000361739	human	ensembl	54_36p	+1	known	silent	c.69	p.F23	NULL	HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region	PatternScan_COX2,HMMPfam_COX2,superfamily_Cupredoxins,HMMPfam_COX2_TM,superfamily_Cytochrome^^_^^c^^_^^oxidase^^_^^subunit^^_^^II-like^^_^^transmembrane^^_^^region	-	no_errors	4863	43	0.87	1793	746	29.13	NA	NA	NA
MT-CO3	0	genome.wustl.edu	36	MT	9968	9968	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	MT	9968	9968	T	C	SNP	MT-CO3	ENST00000362079	human	ensembl	54_36p	+1	known	missense	c.761	p.V254A	NULL	HMMPfam_COX3,superfamily_CytC_oxdse_III	HMMPfam_COX3,superfamily_CytC_oxdse_III	-	no_stop_codon:bad_bp_length_for_coding_region	7147	145	1.97	1641	2713	61.67	NA	NA	NA
FAM47A	0	genome.wustl.edu	36	X	34059994	34059994	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	X	34059994	34059994	G	A	SNP	FAM47A	NM_203408.2	human	genbank	54_36p	-1	predicted	missense	c.323	p.S108F	0.038	NULL	NULL	-	no_errors	41	0	0.00	10	118	91.47	NA	NA	NA
LOC648603	0	genome.wustl.edu	36	X	48519332	48519332	+	RNA	SNP	C	C	G			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	X	48519332	48519332	C	G	SNP	LOC648603	XR_038238.1	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.000	-	-	-	pseudogene	98	6	5.71	5	191	95.98	5	5	50.00
C1orf51	0	genome.wustl.edu	36	1	148522482	148522482	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	1	148522482	148522482	C	A	SNP	C1orf51	NM_144697.2	human	genbank	54_36p	+1	predicted	missense	c.181	p.P61T	0.959	NULL	NULL	-	no_errors	283	3	1.05	334	268	44.37	NA	NA	NA
MAEL	0	genome.wustl.edu	36	1	165228637	165228637	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	1	165228637	165228637	T	C	SNP	MAEL	NM_032858.1	human	genbank	54_36p	+1	validated	missense	c.416	p.I139T	1.000	HMMPfam_DUF1898	superfamily_HMG-box,HMMPfam_DUF1898	-	no_errors	94	3	3.09	111	124	51.45	0	3	100.00
SLC16A14	0	genome.wustl.edu	36	2	230619146	230619146	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	2	230619146	230619146	G	A	SNP	SLC16A14	NM_152527.3	human	genbank	54_36p	-1	provisional	nonsense	c.940	p.R314*	0.701	HMMPfam_MFS_1,superfamily_MFS general substrate transporter	HMMPfam_MFS_1,superfamily_MFS general substrate transporter	-	no_errors	135	3	2.16	116	67	36.41	11	7	38.89
SLC6A20	0	genome.wustl.edu	36	3	45798633	45798633	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	3	45798633	45798633	G	A	SNP	SLC6A20	NM_020208.3	human	genbank	54_36p	-1	reviewed	missense	c.208	p.R70W	1.000	HMMPfam_SNF	HMMPfam_SNF,PatternScan_NA_NEUROTRAN_SYMP_1,PatternScan_NA_NEUROTRAN_SYMP_2	-	no_errors	92	2	2.11	90	71	43.03	NA	NA	NA
SI	0	genome.wustl.edu	36	3	166216448	166216448	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	3	166216448	166216448	A	G	SNP	SI	NM_001041.2	human	genbank	54_36p	-1	validated	missense	c.3874	p.Y1292H	1.000	HMMPfam_Glyco_hydro_31,superfamily_(Trans)glycosidases	HMMPfam_Glyco_hydro_31,PatternScan_GLYCOSYL_HYDROL_F31_1,PatternScan_GLYCOSYL_HYDROL_F31_2,HMMPfam_Trefoil,HMMSmart_SM00018,superfamily_Trefoil,superfamily_(Trans)glycosidases,PatternScan_P_TREFOIL	-	no_errors	80	1	1.23	100	78	43.58	NA	NA	NA
LNX1	0	genome.wustl.edu	36	4	54059577	54059577	+	Silent	SNP	G	G	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	4	54059577	54059577	G	A	SNP	LNX1	NM_032622.1	human	genbank	54_36p	-1	reviewed	silent	c.678	p.D226	1.000	HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ	HMMPfam_PDZ,HMMSmart_PDZ,superfamily_PDZ	-	no_errors	200	5	2.44	187	144	42.86	NA	NA	NA
KIT	0	genome.wustl.edu	36	4	55294078	55294078	+	Missense_Mutation	SNP	A	A	T	rs121913507		TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	4	55294078	55294078	A	T	SNP	KIT	NM_000222.2	human	genbank	54_36p	+1	reviewed	missense	c.2447	p.D816V	1.000	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	-	no_errors	65	0	0.00	57	70	55.12	731	747	50.54
PRSS35	0	genome.wustl.edu	36	6	84291097	84291097	+	Silent	SNP	C	C	T			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	6	84291097	84291097	C	T	SNP	PRSS35	NM_153362.1	human	genbank	54_36p	+1	provisional	silent	c.1218	p.N406	1.000	NULL	HMMPfam_Trypsin,HMMSmart_Tryp_SPc,superfamily_Pept_Ser_Cys,PatternScan_TRYPSIN_HIS,PatternScan_TRYPSIN_SER	-	no_errors	90	1	1.10	154	128	45.07	NA	NA	NA
SCIN	0	genome.wustl.edu	36	7	12610771	12610771	+	Silent	SNP	A	A	C			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	7	12610771	12610771	A	C	SNP	SCIN	ENST00000297029	human	ensembl	54_36p	+1	known	silent	c.624	p.L208	0.066	HMMSmart_SM00262,HMMPfam_Gelsolin,superfamily_Actin depolymerizing proteins	HMMSmart_SM00262,HMMPfam_Gelsolin,superfamily_Actin depolymerizing proteins,superfamily_C-terminal gelsolin-like domain of Sec23/24	-	no_errors	94	0	0.00	158	126	43.75	0	1	100.00
GALNTL4	0	genome.wustl.edu	36	11	11355462	11355462	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	11	11355462	11355462	G	A	SNP	GALNTL4	NM_198516.2	human	genbank	54_36p	-1	validated	missense	c.820	p.R274W	0.981	HMMPfam_Glycos_transf_2,superfamily_Nucleotide-diphospho-sugar transferases	HMMPfam_Ricin_B_lectin,HMMSmart_SM00458,HMMPfam_Glycos_transf_2,superfamily_Ricin B-like lectins,superfamily_Nucleotide-diphospho-sugar transferases	-	no_errors	96	1	1.03	178	153	45.81	NA	NA	NA
C11orf41	0	genome.wustl.edu	36	11	33529297	33529297	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	11	33529297	33529297	C	A	SNP	C11orf41	NM_012194.1	human	genbank	54_36p	+1	validated	missense	c.2764	p.Q922K	1.000	NULL	NULL	-	no_errors	178	8	4.23	92	91	49.46	NA	NA	NA
ENSG00000209624	0	genome.wustl.edu	36	12	25647538	25647538	+	RNA	SNP	G	G	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	12	25647538	25647538	G	A	SNP	ENSG00000209624	ENST00000386889	human	ensembl	54_36p	-1	novel	rna	NULL	NULL	0.013	-	-	-	pseudogene	156	7	4.27	134	108	43.72	NA	NA	NA
MLL2	0	genome.wustl.edu	36	12	47711634	47711634	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	12	47711634	47711634	A	T	SNP	MLL2	NM_003482.3	human	genbank	54_36p	-1	validated	missense	c.13121	p.L4374Q	0.599	NULL	HMMPfam_HMG_box,HMMSmart_SM00398,HMMPfam_SET,HMMSmart_SM00317,HMMSmart_SM00184,HMMSmart_SM00249,HMMSmart_SM00508,HMMPfam_FYRN,HMMPfam_FYRC,PatternScan_RECOMBINASES_2,superfamily_HMG-box,superfamily_FYVE/PHD zinc finger,HMMSmart_SM00542,HMMSmart_SM00541,PatternScan_ZF_PHD_1,HMMPfam_PHD,superfamily_SET domain	-	no_errors	25	1	3.85	49	47	48.96	66	75	53.19
KRT77	0	genome.wustl.edu	36	12	51383390	51383390	+	Silent	SNP	C	C	T			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	12	51383390	51383390	C	T	SNP	KRT77	NM_175078.2	human	genbank	54_36p	-1	validated	silent	c.96	p.P32	0.000	NULL	HMMPfam_Filament,PatternScan_IF	-	no_errors	179	4	2.17	105	74	41.34	NA	NA	NA
HELZ	0	genome.wustl.edu	36	17	62504938	62504938	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	17	62504938	62504938	C	A	SNP	HELZ	NM_014877.3	human	genbank	54_36p	-1	validated	missense	c.5721	p.R1907S	0.998	NULL	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,HMMPfam_PAM2,superfamily_SSF52540,superfamily_SSF90229	-	no_errors	23	1	4.00	36	44	54.32	15	27	62.79
LOC100133684	0	genome.wustl.edu	36	13	27543084	27543085	+	Frame_Shift_Del	DEL	TG	TG	-	rs147323384		TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	TG	TG	TG	-	TG	TG	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	13	27543084	27543085	TG	-	DEL	LOC100133684	XM_001716774.1	human	genbank	54_36p	-1	model	frame_shift_del	c.1040_1039	p.T347fs	0.000:0.000	NULL	NULL	-	no_start_codon:pseudogene:no_stop_codon	0	0	0.00	0	0	0.00	0	0	0.00
IL32	0	genome.wustl.edu	36	16	3059298	3059299	+	Frame_Shift_Ins	INS	-	-	G	rs71818662		TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	-	-	-	G	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	16	3059298	3059299	-	G	INS	IL32	NM_001012631.1	human	genbank	54_36p	+1	reviewed	frame_shift_ins	c.508_509	p.D172fs	0.001:0.001	NULL	NULL	-	no_errors	9	0	0.00	15	10	40.00	25	0	0.00
LOC100132800	0	genome.wustl.edu	36	19	56786070	56786071	+	In_Frame_Ins	INS	-	-	CACCTG	rs113581628		TCGA-AB-2939-03A-01W-0745-08	TCGA-AB-2939-11A-01W-0745-08	-	-	-	CACCTG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	4cc29033-1f07-450a-8fd9-119918d41d31	ac036ed9-2075-47b8-b2bf-b7b235fdbf13	19	56786070	56786071	-	CACCTG	INS	LOC100132800	XM_001724852.1	human	genbank	54_36p	+1	model	in_frame_ins	c.45_46	p.17in_frame_insHL	0.099:0.155	NULL	NULL	-	no_errors	NA	NA	NA	NA	NA	NA	NA	NA	NA