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
LOC642546	0	genome.wustl.edu	36	X	79714774	79714774	+	RNA	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	X	79714774	79714774	C	T	SNP	LOC642546	XR_038841.1	human	genbank	54_36p	-1	model	rna	NULL	NULL	1	-	-	-	pseudogene	58	4	6.45	21	65	75.58	14	0	0
RPS6KA6	0	genome.wustl.edu	36	X	83206679	83206679	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	X	83206679	83206679	G	A	SNP	RPS6KA6	NM_014496.2	human	genbank	54_36p	-1	provisional	missense	c.2068	p.P690S	1	superfamily_Protein kinase-like (PK-like)	PatternScan_SERPIN,HMMSmart_SM00133,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_PROTEIN_KINASE_ST,superfamily_Protein kinase-like (PK-like),PatternScan_PROTEIN_KINASE_ATP,HMMPfam_Pkinase,HMMPfam_Pkinase_C	-	no_errors	94	1	1.05	69	16	18.82	NA	NA	NA
BCAN	0	genome.wustl.edu	36	1	154883956	154883956	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	1	154883956	154883956	C	T	SNP	BCAN	NM_021948.3	human	genbank	54_36p	1	validated	missense	c.499	p.R167C	1	HMMPfam_Xlink,HMMSmart_SM00445,superfamily_C-type lectin-like	HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,PatternScan_IG_MHC,HMMSmart_SM00406,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_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin	-	no_errors	121	2	1.63	146	113	43.63	NA	NA	NA
ADSS	0	genome.wustl.edu	36	1	242647552	242647552	+	Splice_Site	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	1	242647552	242647552	C	T	SNP	ADSS	NM_001126.2	human	genbank	54_36p	-1	reviewed	splice_site	c.1070+1	e10+1	1	-	-	-	no_errors	92	0	0	87	41	32.03	8	3	27.27
DNMT3A	0	genome.wustl.edu	36	2	25316812	25316812	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	2	25316812	25316812	G	A	SNP	DNMT3A	NM_022552.3	human	genbank	54_36p	-1	reviewed	missense	c.2185	p.R729W	1	HMMPfam_DNA_methylase,superfamily_S-adenosyl-L-methionine-dependent methyltransferases	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	19	0	0	27	26	49.06	15	10	40
ZNF638	0	genome.wustl.edu	36	2	71507731	71507731	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	2	71507731	71507731	G	A	SNP	ZNF638	NM_001014972.1	human	genbank	54_36p	1	reviewed	missense	c.5224	p.D1742N	1	NULL	HMMPfam_RRM_1,HMMSmart_SM00360,HMMSmart_SM00451,PatternScan_ZINC_FINGER_C2H2_1,HMMSmart_SM00355,superfamily_RNA-binding domain RBD	-	no_errors	192	1	0.52	136	62	31.31	41	41	50
SCN3A	0	genome.wustl.edu	36	2	165711731	165711731	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	2	165711731	165711731	C	G	SNP	SCN3A	NM_006922.1	human	genbank	54_36p	-1	reviewed	missense	c.1435	p.G479R	0.985	NULL	HMMPfam_IQ,HMMSmart_IQ,HMMPfam_Ion_trans,HMMPfam_Na_trans_assoc,superfamily_SSF81324	-	no_errors	88	4	4.35	97	66	40.49	NA	NA	NA
POC1A	0	genome.wustl.edu	36	3	52147344	52147344	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	3	52147344	52147344	C	T	SNP	WDR51A	NM_015426.3	human	genbank	54_36p	-1	provisional	missense	c.694	p.V232M	0.999	HMMSmart_SM00320,superfamily_WD40 repeat-like,HMMPfam_WD40	HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1,HMMPfam_WD40	-	no_errors	121	2	1.63	131	108	45.19	13	12	48
ILDR1	0	genome.wustl.edu	36	3	123208591	123208591	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	3	123208591	123208591	C	T	SNP	ILDR1	NM_175924.2	human	genbank	54_36p	-1	provisional	missense	c.166	p.V56M	0.997	HMMSmart_IG,superfamily_SSF48726	HMMSmart_IG,HMMPfam_LSR,superfamily_SSF48726	-	no_errors	122	2	1.61	153	98	39.04	0	1	100
KDR	0	genome.wustl.edu	36	4	55659711	55659711	+	Silent	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	4	55659711	55659711	C	T	SNP	KDR	NM_002253.2	human	genbank	54_36p	-1	validated	silent	c.2283	p.T761	0.682	NULL	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,HMMSmart_IGc2,HMMSmart_IG,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	-	no_errors	84	0	0	95	52	35.37	NA	NA	NA
LOC100128322	0	genome.wustl.edu	36	6	132189027	132189027	+	RNA	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	6	132189027	132189027	C	T	SNP	LOC100128322	XR_039280.1	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.998	-	-	-	pseudogene	49	1	2	57	46	44.66	0	0	0
DUSP26	0	genome.wustl.edu	36	8	33570685	33570685	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	8	33570685	33570685	C	A	SNP	DUSP26	NM_024025.1	human	genbank	54_36p	-1	provisional	missense	c.344	p.G115V	1	HMMPfam_DSPc,HMMSmart_SM00195,superfamily_(Phosphotyrosine protein) phosphatases II	HMMPfam_DSPc,PatternScan_TYR_PHOSPHATASE_1,HMMSmart_SM00195,superfamily_(Phosphotyrosine protein) phosphatases II	-	no_errors	106	0	0	155	78	33.33	NA	NA	NA
KCNU1	0	genome.wustl.edu	36	8	36761105	36761105	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	8	36761105	36761105	C	T	SNP	KCNU1	NM_001031836.2	human	genbank	54_36p	1	validated	nonsense	c.19	p.R7*	0	NULL	HMMPfam_BK_channel_a,HMMPfam_Ion_trans,superfamily_NAD(P)-bd,superfamily_SSF81324	-	no_errors	112	1	0.88	157	73	31.74	NA	NA	NA
KHDRBS3	0	genome.wustl.edu	36	8	136624127	136624127	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	8	136624127	136624127	C	T	SNP	KHDRBS3	NM_006558.1	human	genbank	54_36p	1	provisional	missense	c.256	p.R86C	1	HMMSmart_SM00322,superfamily_Eukaryotic type KH-domain (KH-domain type I)	HMMSmart_SM00322,superfamily_Eukaryotic type KH-domain (KH-domain type I)	-	no_errors	124	1	0.8	206	66	24.26	NA	NA	NA
SMC3	0	genome.wustl.edu	36	10	112333981	112333981	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	10	112333981	112333981	G	A	SNP	SMC3	NM_005445.3	human	genbank	54_36p	1	reviewed	missense	c.1142	p.R381Q	1	HMMPfam_SMC_N,superfamily_P-loop containing nucleoside triphosphate hydrolases	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_Smc hinge domain,PatternScan_ABC_TRANSPORTER_1,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_BAG domain	-	no_errors	102	2	1.92	120	64	34.78	51	34	40
DOCK1	0	genome.wustl.edu	36	10	128730879	128730879	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	10	128730879	128730879	T	A	SNP	DOCK1	ENST00000398025	human	ensembl	54_36p	1	known	missense	c.1948	p.F650I	1	NULL	HMMPfam_SH3_1,HMMSmart_SH3,superfamily_SH3,superfamily_Cytochrome_c	-	no_errors	138	0	0	107	71	39.89	3	10	76.92
PUS1	0	genome.wustl.edu	36	12	130991817	130991817	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	12	130991817	130991817	A	T	SNP	PUS1	NM_025215.1	human	genbank	54_36p	1	validated	missense	c.572	p.N191I	1	HMMPfam_PseudoU_synth_1,superfamily_Pseudouridine synthase	HMMPfam_PseudoU_synth_1,superfamily_Pseudouridine synthase	-	no_errors	38	0	0	54	45	45.45	11	14	56
CCDC33	0	genome.wustl.edu	36	15	72323519	72323519	+	Silent	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	15	72323519	72323519	C	T	SNP	CCDC33	NM_025055.3	human	genbank	54_36p	1	validated	silent	c.162	p.S54	0.12	HMMPfam_C2,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)	HMMPfam_C2,superfamily_C2 domain (Calcium/lipid-binding domain CaLB)	-	no_errors	159	0	0	229	32	12.21	NA	NA	NA
SLC25A35	0	genome.wustl.edu	36	17	8138818	8138818	+	Silent	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	17	8138818	8138818	G	A	SNP	SLC25A35	NM_201520.1	human	genbank	54_36p	-1	provisional	silent	c.33	p.C11	0.992	superfamily_Mitoch_carrier,HMMPfam_Mito_carr	superfamily_Mitoch_carrier,HMMPfam_Mito_carr	-	no_errors	68	0	0	95	58	37.91	0	4	100
KRT19	0	genome.wustl.edu	36	17	36933744	36933744	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	17	36933744	36933744	G	C	SNP	KRT19	NM_002276.4	human	genbank	54_36p	-1	reviewed	missense	c.980	p.T327R	0.99	HMMPfam_Filament	superfamily_Prefoldin,HMMPfam_Filament,PatternScan_IF	-	no_errors	35	2	5.41	56	34	37.78	NA	NA	NA
UQCC	0	genome.wustl.edu	36	20	33425414	33425414	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	20	33425414	33425414	C	A	SNP	UQCC	NM_018244.3	human	genbank	54_36p	-1	validated	missense	c.393	p.E131D	1	NULL	HMMPfam_Ubiq_cyt_C_chap	-	no_errors	112	4	3.45	99	67	40.36	17	8	32
RUNX1	0	genome.wustl.edu	36	21	35174747	35174747	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	21	35174747	35174747	C	T	SNP	RUNX1	NM_001754.2	human	genbank	54_36p	-1	reviewed	missense	c.485	p.R162K	1	superfamily_p53-like transcription factors,HMMPfam_Runt	superfamily_p53-like transcription factors,HMMPfam_Runt,HMMPfam_RunxI	-	no_errors	49	2	3.92	36	22	37.93	230	215	48.31
U2AF1	0	genome.wustl.edu	36	21	43397525	43397525	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	21	43397525	43397525	G	A	SNP	U2AF1	NM_001025203.1	human	genbank	54_36p	-1	reviewed	missense	c.101	p.S34F	1	HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_zf-CCCH,HMMSmart_ZnF_C3H1,superfamily_SSF54928	-	no_errors	39	0	0	55	31	36.05	78	69	46.94
PHF6	0	genome.wustl.edu	36	X	133339378	133339379	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AB-2912-03A-01W-0732-08	TCGA-AB-2912-11A-01W-0761-09	-	-	-	A	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	da01cad7-961b-46e2-8a80-9c846694ad5b	c362f010-f227-4bf7-9e9c-15c7a15ce496	X	133339378	133339379	-	A	INS	PHF6	NM_001015877.1	human	genbank	54_36p	1	reviewed	frame_shift_ins	c.65_66	p.N23fs	1.000:1.000	NULL	HMMSmart_SM00249,superfamily_FYVE/PHD zinc finger	-	no_errors	24	0	0	17	31	64.58	4	8	66.67
