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-ND2	0	genome.wustl.edu	36	MT	4598	4598	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	MT	4598	4598	T	C	SNP	MT-ND2	ENST00000361453	human	ensembl	54_36p	+1	known	missense	c.128	p.V43A	NULL	HMMPfam_Oxidored_q1	HMMPfam_Oxidored_q1,HMMPfam_NADH_dehy_S2_C	-	no_stop_codon:bad_bp_length_for_coding_region	1171	9	0.75	633	302	32.06	NA	NA	NA
PRAMEF11	0	genome.wustl.edu	36	1	12807570	12807570	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	1	12807570	12807570	C	T	SNP	PRAMEF11	XM_001714837.1	human	genbank	54_36p	-1	model	missense	c.1358	p.R453H	0.033	NULL	NULL	-	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	44	0	0.00	61	17	21.79	NA	NA	NA
USP48	0	genome.wustl.edu	36	1	21905663	21905663	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	1	21905663	21905663	C	A	SNP	USP48	NM_032236.1	human	genbank	54_36p	-1	reviewed	nonsense	c.2095	p.E699*	1.000	NULL	HMMPfam_UCH,PatternScan_UCH_2_2,superfamily_Cysteine proteinases,superfamily_Ubiquitin-like	-	no_errors	120	0	0.00	146	165	52.72	56	53	48.62
LOC728448	0	genome.wustl.edu	36	1	39780077	39780077	+	RNA	SNP	G	G	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	1	39780077	39780077	G	C	SNP	LOC728448	NR_003929.2	human	genbank	54_36p	-1	validated	rna	NULL	NULL	1.000	-	-	-	pseudogene	129	0	0.00	132	125	47.89	9	49	83.05
CACNA2D3	0	genome.wustl.edu	36	3	54905879	54905879	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	3	54905879	54905879	C	A	SNP	CACNA2D3	NM_018398.2	human	genbank	54_36p	+1	reviewed	nonsense	c.2310	p.Y770*	1.000	NULL	HMMPfam_VWA,HMMSmart_SM00327,HMMPfam_Cache_1,HMMPfam_VWA_N,superfamily_vWA-like	-	no_errors	77	2	2.53	169	80	31.87	NA	NA	NA
CADPS	0	genome.wustl.edu	36	3	62553353	62553353	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	3	62553353	62553353	C	T	SNP	CADPS	NM_003716.3	human	genbank	54_36p	-1	reviewed	missense	c.1436	p.R479Q	0.998	HMMPfam_C2	HMMPfam_C2,HMMPfam_PH,HMMSmart_SM00233,HMMPfam_DUF1041,superfamily_PH domain-like	-	no_errors	107	0	0.00	161	38	19.00	NA	NA	NA
PRICKLE2	0	genome.wustl.edu	36	3	64060325	64060325	+	Silent	SNP	G	G	A			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	3	64060325	64060325	G	A	SNP	PRICKLE2	NM_198859.3	human	genbank	54_36p	-1	validated	silent	c.1977	p.G659	0.036	NULL	HMMPfam_LIM,HMMSmart_LIM,PatternScan_LIM_DOMAIN_1,HMMPfam_PET,superfamily_SSF57716	-	no_errors	35	0	0.00	86	31	25.83	NA	NA	NA
EPHA3	0	genome.wustl.edu	36	3	89611262	89611262	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	3	89611262	89611262	G	A	SNP	EPHA3	NM_005233.5	human	genbank	54_36p	+1	reviewed	missense	c.2872	p.V958M	0.994	HMMSmart_SM00454,superfamily_SAM/Pointed domain,HMMPfam_SAM_2	HMMPfam_Ephrin_lbd,HMMSmart_SM00615,HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMSmart_SM00454,HMMSmart_SM00220,HMMPfam_fn3,HMMSmart_SM00060,PatternScan_PROTEIN_KINASE_TYR,superfamily_Fibronectin type III,superfamily_Galactose-binding domain-like,superfamily_SAM/Pointed domain,superfamily_Protein kinase-like (PK-like),HMMPfam_SAM_2,PatternScan_EGF_2,PatternScan_PROTEIN_KINASE_ATP	-	no_errors	65	0	0.00	104	39	26.90	NA	NA	NA
YEATS2	0	genome.wustl.edu	36	3	185003759	185003759	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	3	185003759	185003759	C	T	SNP	YEATS2	NM_018023.3	human	genbank	54_36p	+1	provisional	missense	c.3524	p.S1175F	1.000	NULL	HMMPfam_YEATS	-	no_errors	92	0	0.00	103	43	28.86	27	4	12.90
C6orf106	0	genome.wustl.edu	36	6	34730508	34730508	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	6	34730508	34730508	T	C	SNP	C6orf106	NM_024294.4	human	genbank	54_36p	-1	validated	missense	c.185	p.Y62C	1.000	superfamily_UBA-like	superfamily_UBA-like	-	no_errors	56	1	1.75	145	68	31.78	65	24	26.97
ATP6V1C1	0	genome.wustl.edu	36	8	104137290	104137290	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	8	104137290	104137290	G	T	SNP	ATP6V1C1	NM_001695.4	human	genbank	54_36p	+1	reviewed	missense	c.591	p.W197C	1.000	HMMPfam_V-ATPase_C	HMMPfam_V-ATPase_C	-	no_errors	54	0	0.00	149	70	31.82	43	41	48.81
DHTKD1	0	genome.wustl.edu	36	10	12194961	12194961	+	Silent	SNP	T	T	G			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	10	12194961	12194961	T	G	SNP	DHTKD1	NM_018706.5	human	genbank	54_36p	+1	validated	silent	c.2211	p.V737	0.112	HMMPfam_Transket_pyr,superfamily_Thiamin diphosphate-binding fold (THDP-binding)	HMMPfam_E1_dh,HMMPfam_Transket_pyr,superfamily_Thiamin diphosphate-binding fold (THDP-binding)	-	no_errors	183	0	0.00	161	52	24.19	19	7	26.92
LOC728532	0	genome.wustl.edu	36	10	51694780	51694780	+	RNA	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	10	51694780	51694780	C	T	SNP	LOC728532	XR_015428.2	human	genbank	54_36p	+1	model	rna	NULL	NULL	1.000	-	-	-	pseudogene	53	0	0.00	134	71	34.63	47	0	0.00
LOC401648	0	genome.wustl.edu	36	10	104965961	104965961	+	RNA	SNP	A	A	G			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	10	104965961	104965961	A	G	SNP	LOC401648	XR_017482.1	human	genbank	54_36p	+1	model	rna	NULL	NULL	0.999	-	-	-	pseudogene	25	2	7.41	25	15	37.50	33	1	2.94
FLT1	0	genome.wustl.edu	36	13	27899448	27899448	+	Silent	SNP	G	G	C			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	13	27899448	27899448	G	C	SNP	FLT1	NM_002019.3	human	genbank	54_36p	-1	validated	silent	c.1284	p.P428	0.997	superfamily_Immunoglobulin	HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_SM00220,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,PatternScan_PROTEIN_KINASE_TYR,superfamily_Protein kinase-like (PK-like),HMMPfam_I-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_Immunoglobulin	-	no_errors	70	0	0.00	109	34	23.61	2	0	0.00
SERPINA12	0	genome.wustl.edu	36	14	94034210	94034210	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	14	94034210	94034210	C	T	SNP	SERPINA12	NM_173850.2	human	genbank	54_36p	-1	provisional	missense	c.278	p.S93N	0.049	HMMPfam_Serpin,HMMSmart_SERPIN,superfamily_Prot_inh_serpin	HMMPfam_Serpin,HMMSmart_SERPIN,PatternScan_SERPIN,superfamily_Prot_inh_serpin	-	no_errors	112	0	0.00	162	72	30.64	NA	NA	NA
TP53	0	genome.wustl.edu	36	17	7517846	7517846	+	Missense_Mutation	SNP	G	G	A	rs121913343		TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	17	7517846	7517846	G	A	SNP	TP53	NM_000546.4	human	genbank	54_36p	-1	reviewed	missense	c.817	p.R273C	0.797	superfamily_p53-like transcription factors,HMMPfam_P53	PatternScan_P53,superfamily_p53-like transcription factors,HMMPfam_P53_tetramer,superfamily_p53 tetramerization domain,HMMPfam_P53,HMMPfam_P53_TAD	-	no_errors	98	7	6.54	46	144	74.61	17	137	88.96
ZNF460	0	genome.wustl.edu	36	19	62494825	62494825	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	19	62494825	62494825	A	T	SNP	ZNF460	NM_006635.3	human	genbank	54_36p	+1	validated	missense	c.1104	p.Q368H	0.012	HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	HMMPfam_KRAB,HMMSmart_KRAB,superfamily_Krueppel-associated_box,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_ZnF_C2H2,superfamily_SSF57667	-	no_errors	40	0	0.00	90	34	27.20	30	20	40.00
PPPDE2	0	genome.wustl.edu	36	22	40330018	40330018	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2943-03A-01W-0745-08	TCGA-AB-2943-11A-01W-0745-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	9ffddf15-3f38-4dac-a9f6-2636130c050b	32623a30-c839-4621-a7df-af0b615c01c1	22	40330018	40330018	G	T	SNP	PPPDE2	NM_015704.1	human	genbank	54_36p	-1	provisional	missense	c.266	p.S89Y	1.000	HMMPfam_DUF862	HMMPfam_DUF862	-	no_errors	57	1	1.72	97	25	20.16	179	28	13.53