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
ENSG00000223073	0	genome.wustl.edu	36	MT	530	530	+	RNA	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	MT	530	530	T	C	SNP	ENSG00000223073	ENST00000411141	human	ensembl	54_36p	1	novel	rna	NULL	NULL	NULL	-	-	-	no_errors	680	5	0.73	292	2998	90.41	NA	NA	NA
MT-ND4	0	genome.wustl.edu	36	MT	11810	11810	+	Silent	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	MT	11810	11810	T	C	SNP	MT-ND4	ENST00000361381	human	ensembl	54_36p	1	known	silent	c.1050	p.T350	NULL	HMMPfam_Oxidored_q1	HMMPfam_Oxidored_q5_N,HMMPfam_Oxidored_q1	-	no_stop_codon:bad_bp_length_for_coding_region	1256	8	0.63	429	5303	91.53	NA	NA	NA
PCDH19	0	genome.wustl.edu	36	X	99549148	99549148	+	Silent	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	X	99549148	99549148	G	A	SNP	PCDH19	NM_001105243.1	human	genbank	54_36p	-1	validated	silent	c.1104	p.I368	0.92	HMMPfam_Cadherin,superfamily_Cadherin	HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin	-	no_errors	7	0	0	21	6	22.22	NA	NA	NA
RGAG1	0	genome.wustl.edu	36	X	109583735	109583735	+	Silent	SNP	C	C	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	X	109583735	109583735	C	A	SNP	RGAG1	NM_020769.1	human	genbank	54_36p	1	provisional	silent	c.3234	p.G1078	0	NULL	HMMPfam_Retrotrans_gag	-	no_errors	31	0	0	103	75	42.13	NA	NA	NA
HSPG2	0	genome.wustl.edu	36	1	22051263	22051263	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	1	22051263	22051263	C	T	SNP	HSPG2	NM_005529.5	human	genbank	54_36p	-1	validated	missense	c.6775	p.G2259S	0.999	HMMSmart_SM00408,HMMSmart_SM00409,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_I-set,superfamily_Immunoglobulin	HMMPfam_Laminin_B,HMMPfam_SEA,HMMSmart_SM00200,HMMSmart_SM00282,HMMSmart_SM00179,HMMPfam_Laminin_EGF,HMMSmart_SM00180,PatternScan_EGF_LAM_1,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,superfamily_Concanavalin A-like lectins/glucanases,HMMPfam_Laminin_G_1,HMMPfam_Laminin_G_2,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMSmart_SM00281,superfamily_Immunoglobulin,superfamily_EGF/Laminin	-	no_errors	14	0	0	45	38	44.71	41	22	34.92
RGL1	0	genome.wustl.edu	36	1	182161933	182161933	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	1	182161933	182161933	C	T	SNP	RGL1	NM_015149.3	human	genbank	54_36p	1	validated	missense	c.2296	p.R766C	1	HMMPfam_RA,HMMSmart_SM00314,superfamily_Ubiquitin-like	HMMPfam_RA,HMMSmart_SM00314,HMMPfam_RasGEF_N,HMMSmart_SM00229,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,PatternScan_RASGEF,superfamily_Ubiquitin-like	-	no_errors	53	0	0	149	101	40.08	6	0	0
MSH6	0	genome.wustl.edu	36	2	47881044	47881044	+	Silent	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	2	47881044	47881044	C	T	SNP	MSH6	NM_000179.2	human	genbank	54_36p	1	reviewed	silent	c.2418	p.S806	0.392	HMMPfam_MutS_III,HMMSmart_SM00533,superfamily_DNA repair protein MutS domain III	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_MutS_V,HMMSmart_SM00534,PatternScan_DNA_MISMATCH_REPAIR_2,HMMPfam_MutS_I,HMMPfam_MutS_III,HMMSmart_SM00533,superfamily_DNA repair protein MutS domain III,HMMPfam_MutS_II,HMMPfam_MutS_IV,superfamily_DNA repair protein MutS domain I,superfamily_P-loop containing nucleoside triphosphate hydrolases,superfamily_Tudor/PWWP/MBT	-	no_errors	59	0	0	169	132	43.56	44	79	64.23
EHHADH	0	genome.wustl.edu	36	3	186393047	186393047	+	Silent	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	3	186393047	186393047	T	C	SNP	EHHADH	NM_001966.2	human	genbank	54_36p	-1	validated	silent	c.1833	p.P611	0.013	superfamily_6DGDH_C_like	HMMPfam_ECH,HMMPfam_3HCDH,HMMPfam_3HCDH_N,PatternScan_3HCDH,superfamily_6DGDH_C_like,superfamily_NAD(P)-bd,PatternScan_ENOYL_COA_HYDRATASE,superfamily_SSF52096	-	no_errors	67	0	0	161	92	35.38	13	9	40.91
TRA2B	0	genome.wustl.edu	36	3	187125967	187125967	+	Silent	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	3	187125967	187125967	G	A	SNP	TRA2B	NM_004593.2	human	genbank	54_36p	-1	validated	silent	c.312	p.R104	1	superfamily_RNA-binding domain RBD	HMMPfam_RRM_1,HMMSmart_SM00360,superfamily_RNA-binding domain RBD	-	no_errors	43	0	0	116	87	42.65	214	226	51.36
KIT	0	genome.wustl.edu	36	4	55284528	55284528	+	Missense_Mutation	SNP	A	A	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	4	55284528	55284528	A	C	SNP	KIT	NM_000222.2	human	genbank	54_36p	1	reviewed	missense	c.1253	p.Y418S	0.002	NULL	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	30	0	0	104	42	28	176	0	0
PCDHB3	0	genome.wustl.edu	36	5	140461079	140461079	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	5	140461079	140461079	C	T	SNP	PCDHB3	NM_018937.2	human	genbank	54_36p	1	reviewed	missense	c.662	p.P221L	0.028	HMMPfam_Cadherin,HMMSmart_SM00112,superfamily_Cadherin-like	HMMPfam_Cadherin,HMMSmart_SM00112,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,superfamily_Cadherin-like	-	no_errors	19	0	0	62	30	32.26	NA	NA	NA
HDAC3	0	genome.wustl.edu	36	5	140989468	140989468	+	Missense_Mutation	SNP	T	T	C			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	5	140989468	140989468	T	C	SNP	HDAC3	NM_003883.3	human	genbank	54_36p	-1	reviewed	missense	c.443	p.N148S	1	HMMPfam_Hist_deacetyl,superfamily_Arginase/deacetylase	HMMPfam_Hist_deacetyl,superfamily_Arginase/deacetylase	-	no_errors	82	0	0	87	66	42.31	31	16	34.04
PDGFRB	0	genome.wustl.edu	36	5	149484585	149484585	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	5	149484585	149484585	G	A	SNP	PDGFRB	NM_002609.3	human	genbank	54_36p	-1	reviewed	missense	c.1810	p.R604C	1	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	12	0	0	34	19	35.19	7	4	36.36
ADAM19	0	genome.wustl.edu	36	5	156852676	156852676	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	5	156852676	156852676	G	T	SNP	ADAM19	NM_023038.3	human	genbank	54_36p	-1	reviewed	missense	c.1795	p.H599N	0	NULL	NULL	-	pseudogene:no_stop_codon:bad_bp_length_for_coding_region	38	0	0	178	96	34.66	3	0	0
HYAL4	0	genome.wustl.edu	36	7	123296322	123296322	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	7	123296322	123296322	C	G	SNP	HYAL4	NM_012269.2	human	genbank	54_36p	1	reviewed	missense	c.759	p.N253K	0.993	HMMPfam_Glyco_hydro_56,superfamily_Glyco_hydro_cat	HMMPfam_Glyco_hydro_56,HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_Glyco_hydro_cat	-	no_errors	52	0	0	129	79	37.8	NA	NA	NA
PRUNE2	0	genome.wustl.edu	36	9	78510558	78510558	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	9	78510558	78510558	C	T	SNP	PRUNE2	ENST00000376718	human	ensembl	54_36p	-1	known	missense	c.5375	p.R1792Q	0.001	NULL	HMMSmart_SM00516,superfamily_CRAL/TRIO domain,superfamily_Ferritin-like	-	no_errors	35	0	0	126	52	29.05	NA	NA	NA
LOC400011	0	genome.wustl.edu	36	12	16444150	16444150	+	RNA	SNP	G	G	T			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	12	16444150	16444150	G	T	SNP	LOC400011	XR_016968.2	human	genbank	54_36p	-1	model	rna	NULL	NULL	0.986	-	-	-	pseudogene	59	0	0	159	96	37.5	87	0	0
LOC727895	0	genome.wustl.edu	36	13	18855134	18855134	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	13	18855134	18855134	G	A	SNP	LOC727895	XM_001125866.2	human	genbank	54_36p	1	model	missense	c.523	p.A175T	0.758	superfamily_Cyclin-like	superfamily_Cyclin-like	-	no_errors	16	0	0	79	48	36.92	4	0	0
POSTN	0	genome.wustl.edu	36	13	37054628	37054628	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	13	37054628	37054628	G	A	SNP	POSTN	NM_006475.1	human	genbank	54_36p	-1	validated	missense	c.1267	p.R423C	1	HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain	HMMPfam_Fasciclin,HMMSmart_SM00554,superfamily_FAS1 domain,HMMPfam_EMI	-	no_errors	44	0	0	94	54	35.76	NA	NA	NA
DSCAM	0	genome.wustl.edu	36	21	40569957	40569957	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2819-03B-01W-0728-08	TCGA-AB-2819-11B-01W-0728-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1	dbGAP	Illumina HiSeq	7ccedb6e-e411-404a-8441-2330d1f91013	bbc7cf39-e89a-4933-ba26-7cce5c47de87	21	40569957	40569957	G	A	SNP	DSCAM	NM_001389.3	human	genbank	54_36p	-1	validated	missense	c.2293	p.L765F	1	HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,superfamily_Immunoglobulin	HMMSmart_SM00406,HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_fn3,HMMSmart_SM00060,superfamily_Fibronectin type III,HMMPfam_I-set,HMMPfam_ig,superfamily_Immunoglobulin	-	no_errors	27	0	0	68	41	37.27	NA	NA	NA
