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
SMC1A	0	genome.wustl.edu	36	X	53443342	53443342	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	X	53443342	53443342	A	T	SNP	SMC1A	NM_006306.2	human	genbank	54_36p	-1	reviewed	missense	c.2456	p.I819N	1.000	HMMPfam_SMC_N,superfamily_SSF52540	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540	-	no_errors	508	4	0.78	292	353	54.73	71	114	61.62
EPHA8	0	genome.wustl.edu	36	1	22788115	22788115	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	1	22788115	22788115	G	A	SNP	EPHA8	NM_020526.1	human	genbank	54_36p	+1	reviewed	missense	c.1144	p.G382S	0.859	HMMPfam_fn3,HMMSmart_FN3,superfamily_FN_III-like	HMMPfam_Ephrin_lbd,HMMSmart_EPH_lbd,HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_V_1,PatternScan_RECEPTOR_TYR_KIN_V_2,HMMPfam_SAM_1,HMMSmart_SAM,HMMPfam_fn3,HMMSmart_FN3,PatternScan_PROTEIN_KINASE_TYR,superfamily_FN_III-like,superfamily_Gal_bind_like,superfamily_SAM_homology,superfamily_Kinase_like,PatternScan_EGF_2,PatternScan_PROTEIN_KINASE_ATP	-	no_errors	1114	46	3.96	486	391	44.58	NA	NA	NA
FAM69A	0	genome.wustl.edu	36	1	93082134	93082134	+	Silent	SNP	C	C	T			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	1	93082134	93082134	C	T	SNP	FAM69A	ENST00000370310	human	ensembl	54_36p	-1	known	silent	c.681	p.V227	1.000	NULL	NULL	-	no_errors	664	15	2.21	694	528	43.14	3	1	25.00
RAB17	0	genome.wustl.edu	36	2	238150673	238150673	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	2	238150673	238150673	G	A	SNP	RAB17	NM_022449.2	human	genbank	54_36p	-1	provisional	missense	c.401	p.T134M	0.991	HMMSmart_RAB,HMMPfam_Ras,superfamily_SSF52540	HMMSmart_RAB,HMMPfam_Ras,superfamily_SSF52540	-	no_errors	1061	33	3.01	295	257	46.47	NA	NA	NA
KIAA1239	0	genome.wustl.edu	36	4	37123097	37123097	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	4	37123097	37123097	A	G	SNP	KIAA1239	ENST00000309447	human	ensembl	54_36p	+1	known	missense	c.1358	p.N453S	1.000	HMMSmart_SM00320,superfamily_WD40 repeat-like	HMMSmart_SM00320,superfamily_WD40 repeat-like,PatternScan_WD_REPEATS_1	-	no_start_codon	569	8	1.39	264	237	47.31	NA	NA	NA
RFC1	0	genome.wustl.edu	36	4	38984633	38984633	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	4	38984633	38984633	T	C	SNP	RFC1	NM_002913.3	human	genbank	54_36p	-1	reviewed	missense	c.1969	p.T657A	1.000	HMMSmart_AAA,HMMPfam_AAA,superfamily_SSF52540	HMMPfam_BRCT,HMMSmart_BRCT,superfamily_BRCT,HMMSmart_AAA,HMMPfam_AAA,superfamily_Pol_clamp_load_C,HMMPfam_RFC1,superfamily_SSF52540	-	no_errors	1011	18	1.75	999	807	44.59	17	23	57.50
ETF1	0	genome.wustl.edu	36	5	137881160	137881160	+	Missense_Mutation	SNP	A	A	C			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	5	137881160	137881160	A	C	SNP	ETF1	NM_004730.2	human	genbank	54_36p	-1	validated	missense	c.391	p.F131V	1.000	HMMPfam_eRF1_1,superfamily_N-terminal domain of eukaryotic peptide chain release factor subunit 1 ERF1	HMMPfam_eRF1_1,HMMPfam_eRF1_2,HMMPfam_eRF1_3,superfamily_Translational machinery components,superfamily_L30e-like,superfamily_N-terminal domain of eukaryotic peptide chain release factor subunit 1 ERF1	-	no_errors	225	7	2.99	143	113	43.97	22	35	61.40
STC2	0	genome.wustl.edu	36	5	172677693	172677693	+	Silent	SNP	C	C	T			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	5	172677693	172677693	C	T	SNP	STC2	NM_003714.2	human	genbank	54_36p	-1	reviewed	silent	c.672	p.E224	0.052	HMMPfam_Stanniocalcin	HMMPfam_Stanniocalcin	-	no_errors	547	12	2.15	143	131	47.81	NA	NA	NA
EGFL8	0	genome.wustl.edu	36	6	32243129	32243129	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	6	32243129	32243129	G	A	SNP	EGFL8	NM_030652.2	human	genbank	54_36p	+1	validated	missense	c.626	p.R209H	0.574	NULL	PatternScan_ASX_HYDROXYL,HMMSmart_SM00179,HMMPfam_EGF,HMMSmart_SM00181,HMMPfam_EMI,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_EGF/Laminin	-	no_errors	2115	47	2.17	552	542	49.50	2	2	50.00
TCTE3	0	genome.wustl.edu	36	6	169885156	169885156	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	6	169885156	169885156	C	T	SNP	TCTE3	NM_174910.1	human	genbank	54_36p	-1	provisional	missense	c.431	p.R144H	0.993	HMMPfam_Tctex-1	HMMPfam_Tctex-1	-	no_errors	179	4	2.19	258	206	44.21	2	0	0.00
BMS1	0	genome.wustl.edu	36	10	42609323	42609323	+	Silent	SNP	C	C	A			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	10	42609323	42609323	C	A	SNP	BMS1	NM_014753.3	human	genbank	54_36p	+1	reviewed	silent	c.1107	p.T369	0.980	superfamily_P-loop containing nucleoside triphosphate hydrolases	HMMPfam_DUF663,HMMPfam_AARP2CN,HMMSmart_SM00785,superfamily_P-loop containing nucleoside triphosphate hydrolases	-	no_errors	1194	73	5.74	772	703	47.63	19	16	45.71
UNC5B	0	genome.wustl.edu	36	10	72723681	72723681	+	Silent	SNP	G	G	A			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	10	72723681	72723681	G	A	SNP	UNC5B	NM_170744.3	human	genbank	54_36p	+1	validated	silent	c.2160	p.T720	0.564	NULL	HMMPfam_Death,HMMSmart_SM00005,HMMPfam_TSP_1,HMMSmart_SM00209,superfamily_TSP-1 type 1 repeat,HMMPfam_ZU5,HMMSmart_SM00218,HMMSmart_SM00408,HMMSmart_SM00409,superfamily_DEATH domain,HMMPfam_I-set,superfamily_Immunoglobulin	-	no_errors	598	10	1.63	176	167	48.55	0	1	100.00
PTPN11	0	genome.wustl.edu	36	12	111411293	111411293	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	12	111411293	111411293	G	C	SNP	PTPN11	NM_002834.3	human	genbank	54_36p	+1	reviewed	missense	c.1530	p.Q510H	1.000	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMSmart_SM00404,superfamily_(Phosphotyrosine protein) phosphatases II	HMMPfam_Y_phosphatase,HMMSmart_SM00194,HMMPfam_SH2,HMMSmart_SM00252,HMMSmart_SM00404,PatternScan_TYR_PHOSPHATASE_1,superfamily_(Phosphotyrosine protein) phosphatases II,superfamily_SH2 domain	-	no_errors	538	10	1.82	830	162	16.33	38	3	7.32
FLT3	0	genome.wustl.edu	36	13	27490642	27490642	+	Missense_Mutation	SNP	C	C	A	rs121913488		TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	13	27490642	27490642	C	A	SNP	FLT3	NM_004119.2	human	genbank	54_36p	-1	reviewed	missense	c.2503	p.D835Y	1.000	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	-	no_errors	1451	4	0.27	887	142	13.80	324	77	19.15
ZFHX3	0	genome.wustl.edu	36	16	71378635	71378635	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	16	71378635	71378635	C	T	SNP	ZFHX3	NM_006885.3	human	genbank	54_36p	-1	validated	missense	c.11041	p.G3681S	1.000	NULL	HMMPfam_Homeobox,HMMSmart_SM00389,HMMSmart_SM00451,HMMPfam_zf-C2H2,PatternScan_ZINC_FINGER_C2H2_1,superfamily_Homeodomain-like,HMMSmart_SM00355,PatternScan_HOMEOBOX_1,superfamily_C2H2 and C2HC zinc fingers	-	no_errors	1185	33	2.70	304	267	46.76	1	0	0.00
BECN1	0	genome.wustl.edu	36	17	38223906	38223906	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	17	38223906	38223906	T	C	SNP	BECN1	NM_003766.3	human	genbank	54_36p	-1	validated	missense	c.542	p.Q181R	0.968	HMMPfam_APG6	HMMPfam_APG6	-	no_errors	1400	36	2.51	330	278	45.50	38	38	50.00
NLRP8	0	genome.wustl.edu	36	19	61158758	61158758	+	Missense_Mutation	SNP	G	G	C			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	G	G	G	C	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	19	61158758	61158758	G	C	SNP	NLRP8	NM_176811.2	human	genbank	54_36p	+1	provisional	missense	c.1522	p.V508L	0.003	NULL	HMMSmart_SM00368,HMMPfam_PAAD_DAPIN,HMMPfam_NACHT,superfamily_DEATH domain,superfamily_RNI-like,superfamily_P-loop containing nucleoside triphosphate hydrolases	-	no_errors	559	11	1.92	379	332	46.56	NA	NA	NA
LOC100129743	0	genome.wustl.edu	36	2	203613328	203613332	+	Frame_Shift_Del	DEL	CATGC	CATGC	-			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	CATGC	CATGC	CATGC	-	CATGC	CATGC	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	2	203613328	203613332	CATGC	-	DEL	LOC100129743	XM_001724736.1	human	genbank	54_36p	+1	model	frame_shift_del	c.253_257	p.A86fs	0.952:0.949:0.939:0.920:0.925	NULL	HMMPfam_Ribosomal_L30,superfamily_Ribosomal protein L30p/L7e,PatternScan_RIBOSOMAL_L30	-	pseudogene	NA	NA	NA	NA	NA	NA	NA	NA	NA
NPM1	0	genome.wustl.edu	36	5	170770152	170770153	+	Frame_Shift_Ins	INS	-	-	CCTG			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	-	-	-	CCTG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	5	170770152	170770153	-	CCTG	INS	NPM1	NM_002520.1	human	genbank	54_36p	+1	validated	frame_shift_ins	c.863_864	p.W288fs	1.000:1.000	NULL	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	-	no_errors	NA	NA	NA	NA	NA	NA	NA	NA	NA
DAOA	0	genome.wustl.edu	36	13	104940386	104940386	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2963-03A-01D-0739-09	TCGA-AB-2963-11A-01D-0739-09	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	8876f6ab-618d-4096-9e98-4f2063ef03b1	21a5533c-8f5d-4047-8daa-0ad9d86ea2e3	13	104940386	104940386	C	-	DEL	DAOA	NM_172370.3	human	genbank	54_36p	+1	reviewed	frame_shift_del	c.417	p.Q140fs	0.000	NULL	NULL	-	no_errors	587	15	2.48	368	276	42.27	0	0	0.00