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	default_gene_name	gene_name_source	 ensembl_gene_id	tier	dbSNP	GMAF	n_ref_count	n_alt_count	normal_vaf	t_ref_count	t_alt_count	tumor_vaf	n_ref_count_val	n_alt_count_val	normal_vaf_val	t_ref_count_val	t_alt_count_val	tumor_vaf_val
SLCO3A1	0	genome.wustl.edu	37	15	92647634	92647634	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	15	92647634	92647634	C	A	SNP	SLCO3A1	ENST00000318445	human	ensembl	74_37	+1	known	missense	c.871	p.P291T	0.995	pfam_OA_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,tigrfam_OA_transporter	pfam_OA_transporter,pfam_MFS,pfam_Kazal_dom,superfamily_MFS_dom_general_subst_transpt,tigrfam_OA_transporter	-	no_errors	SLCO3A1	HGNC	ENSG00000176463	tier1	-	-	90	0	0.00	61	24	27.91	64	0	0.00	36	9	20.00
HIST1H1B	0	genome.wustl.edu	37	6	27834759	27834759	+	Silent	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	6	27834759	27834759	C	T	SNP	HIST1H1B	ENST00000331442	human	ensembl	74_37	-1	known	silent	c.549	p.P183	0.634	prints_Histone_H5	pfam_Histone_H1/H5_H15,smart_Histone_H1/H5_H15,prints_Histone_H5	-	no_errors	HIST1H1B	HGNC	ENSG00000184357	tier1	-	-	64	0	0.00	21	18	46.15	85	0	0.00	50	19	27.54
STAT2	0	genome.wustl.edu	37	12	56743168	56743168	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	12	56743168	56743168	C	T	SNP	STAT2	ENST00000418572	human	ensembl	74_37	-1	putative	nonsense	c.1371	p.W457*	0.000	NULL	pfam_STAT_TF_alpha,pfam_STAT_TF_D-bd,pfam_STAT_TF_prot_interaction,superfamily_STAT_TF_coiled-coil,superfamily_p53-like_TF_D-bd,superfamily_STAT_TF_prot_interaction,smart_STAT_TF_prot_interaction	-	no_errors	STAT2	HGNC	ENSG00000170581	tier1	-	-	97	0	0.00	112	1257	91.82	153	0	0.00	131	2157	94.07
RAVER2	0	genome.wustl.edu	37	1	65247087	65247087	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	1	65247087	65247087	G	A	SNP	RAVER2	ENST00000294428	human	ensembl	74_37	+1	known	missense	c.811	p.V271I	0.016	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	-	no_errors	RAVER2	HGNC	ENSG00000162437	tier1	-	-	68	0	0.00	51	34	40.00	83	0	0.00	64	29	31.18
STAT2	0	genome.wustl.edu	37	12	56743279	56743279	+	Silent	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	12	56743279	56743279	C	T	SNP	STAT2	ENST00000314128	human	ensembl	74_37	-1	known	silent	c.1272	p.V424	0.990	pfam_STAT_TF_D-bd,superfamily_p53-like_TF_D-bd	pfam_STAT_TF_D-bd,pfam_STAT_TF_alpha,pfam_STAT_TF_prot_interaction,pfam_STAT2_C,pfam_SH2,superfamily_p53-like_TF_D-bd,superfamily_STAT_TF_coiled-coil,superfamily_STAT_TF_prot_interaction,smart_STAT_TF_prot_interaction,smart_SH2,pfscan_SH2	-	no_errors	STAT2	HGNC	ENSG00000170581	tier1	-	-	79	0	0.00	73	1135	93.88	106	1	0.93	123	1769	93.45
POLN	0	genome.wustl.edu	37	4	2181178	2181178	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	4	2181178	2181178	C	T	SNP	POLN	ENST00000382865	human	ensembl	74_37	-1	known	missense	c.1036	p.G346R	0.564	superfamily_RNaseH-like_dom	pfam_D-dir_D_pol_A_palm_dom,superfamily_RNaseH-like_dom,smart_D-dir_D_pol_A_palm_dom,prints_D_polymerase_A	-	no_errors	POLN	HGNC	ENSG00000130997	tier1	-	-	37	0	0.00	26	9	25.71	130	1	0.76	68	34	33.33
AP2A2	0	genome.wustl.edu	37	11	993375	993375	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	11	993375	993375	G	C	SNP	AP2A2	ENST00000332231	human	ensembl	74_37	+1	known	missense	c.1547	p.R516T	0.970	pfam_Clathrin/coatomer_adapt-like_N,superfamily_ARM-type_fold,pirsf_AP2_complex_asu	pfam_Clathrin/coatomer_adapt-like_N,pfam_Clathrin_a-adaptin_app_sub_C,pfam_Clathrin_a/b/g-adaptin_app_Ig,superfamily_ARM-type_fold,superfamily_Coatomer/calthrin_app_sub_C,superfamily_Coatomer/clathrin_app_Ig-like,smart_Clathrin_a/b/g-adaptin_app_Ig,pirsf_AP2_complex_asu	-	no_errors	AP2A2	HGNC	ENSG00000183020	tier1	-	-	54	0	0.00	56	9	13.85	51	0	0.00	29	4	11.76
DCLK3	0	genome.wustl.edu	37	3	36759633	36759633	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	3	36759633	36759633	C	T	SNP	DCLK3	ENST00000416516	human	ensembl	74_37	-1	known	missense	c.1621	p.V541M	1.000	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	-	no_errors	DCLK3	HGNC	ENSG00000163673	tier1	-	-	40	0	0.00	32	16	33.33	78	0	0.00	59	28	32.18
DGCR2	0	genome.wustl.edu	37	22	19026588	19026588	+	Silent	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	22	19026588	19026588	C	A	SNP	DGCR2	ENST00000263196	human	ensembl	74_37	-1	known	silent	c.1443	p.G481	0.306	NULL	pfam_LDrepeatLR_classA_rpt,superfamily_C-type_lectin_fold,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_C-type_lectin,smart_VWF_C,pfscan_LDrepeatLR_classA_rpt,pfscan_C-type_lectin	-	no_errors	DGCR2	HGNC	ENSG00000070413	tier1	-	-	109	0	0.00	64	36	35.64	46	0	0.00	48	24	33.33
SENP2	0	genome.wustl.edu	37	3	185316763	185316763	+	Missense_Mutation	SNP	A	A	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	3	185316763	185316763	A	T	SNP	SENP2	ENST00000439684	human	ensembl	74_37	+1	known	missense	c.175	p.I59F	0.965	NULL	NULL	-	no_errors	SENP2	HGNC	ENSG00000163904	tier1	-	-	48	0	0.00	20	38	65.52	132	0	0.00	27	38	58.46
BAI3	0	genome.wustl.edu	37	6	70034783	70034783	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	6	70034783	70034783	C	A	SNP	BAI3	ENST00000370598	human	ensembl	74_37	+1	known	missense	c.2834	p.T945N	1.000	pfam_GPCR_2_secretin-like,pfscan_GPCR_2-like,prints_GPCR_2_secretin-like	pfam_GPCR_2_secretin-like,pfam_DUF3497,pfam_Thrombospondin_1_rpt,pfam_GPS_dom,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,smart_GPCR_2_extracellular_dom,smart_GPS_dom,pfscan_CUB_dom,pfscan_GPS_dom,pfscan_Thrombospondin_1_rpt,pfscan_GPCR_2_extracellular_dom,pfscan_GPCR_2-like,prints_GPCR_2_brain-spec_angio_inhib,prints_GPCR_2_secretin-like	-	no_errors	BAI3	HGNC	ENSG00000135298	tier1	-	-	122	0	0.00	106	40	27.40	69	0	0.00	53	29	35.37
RYR1	0	genome.wustl.edu	37	19	38951142	38951142	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	19	38951142	38951142	C	T	SNP	RYR1	ENST00000359596	human	ensembl	74_37	+1	known	missense	c.2488	p.R830W	0.739	NULL	pfam_Ca-rel_channel,pfam_Ryanodine_rcpt,pfam_Ryanrecept_TM4-6,pfam_SPRY_rcpt,pfam_Ins145_P3_rcpt,pfam_MIR_motif,pfam_RIH_assoc-dom,pfam_Ion_trans_dom,superfamily_MIR_motif,superfamily_ConA-like_lec_gl_sf,superfamily_MG_RAP_rcpt_1,smart_MIR_motif,smart_SPla/RYanodine_receptor_subgr,prints_Ryan_recept,pfscan_B30.2/SPRY,pfscan_MIR_motif	-	no_errors	RYR1	HGNC	ENSG00000196218	tier1	rs142548565	-	65	0	0.00	28	15	34.88	20	0	0.00	22	12	35.29
AKAP6	0	genome.wustl.edu	37	14	33147640	33147640	+	Missense_Mutation	SNP	A	A	G			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	14	33147640	33147640	A	G	SNP	AKAP6	ENST00000280979	human	ensembl	74_37	+1	known	missense	c.2854	p.K952E	1.000	NULL	smart_Spectrin/alpha-actinin	-	no_errors	AKAP6	HGNC	ENSG00000151320	tier1	-	-	58	0	0.00	46	16	25.81	152	0	0.00	45	21	30.88
SENP1	0	genome.wustl.edu	37	12	48459425	48459425	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	12	48459425	48459425	C	T	SNP	SENP1	ENST00000004980	human	ensembl	74_37	-1	known	missense	c.1073	p.R358H	1.000	NULL	pfam_Peptidase_C48,pfscan_Peptidase_C48	-	no_errors	SENP1	HGNC	ENSG00000079387	tier1	-	-	42	0	0.00	25	8	23.53	111	1	0.89	59	35	37.23
PKLR	0	genome.wustl.edu	37	1	155269901	155269901	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	1	155269901	155269901	T	C	SNP	PKLR	ENST00000342741	human	ensembl	74_37	-1	known	missense	c.271	p.I91V	1.000	pfam_Pyrv_Knase_brl,superfamily_Pyrv/PenolPyrv_Kinase-like_dom,tigrfam_Pyr_Knase	pfam_Pyrv_Knase_brl,pfam_Pyrv_Knase_C,superfamily_Pyrv/PenolPyrv_Kinase-like_dom,superfamily_Pyrv_Knase_C,superfamily_Pyrv_Knase-like_insert_dom,prints_Pyr_Knase,tigrfam_Pyr_Knase	-	no_errors	PKLR	HGNC	ENSG00000143627	tier1	-	-	70	0	0.00	42	24	36.36	111	0	0.00	66	40	37.74
LINC00029	0	genome.wustl.edu	37	20	61665964	61665964	+	R	SNP	A	A	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	20	61665964	61665964	A	T	SNP	LINC00029	ENST00000370341	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.001	-	-	-	no_errors	LINC00029	HGNC	ENSG00000125514	tier1	-	-	45	0	0.00	27	12	30.77	78	0	0.00	34	21	38.18
GAL3ST1	0	genome.wustl.edu	37	22	30950947	30950947	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	22	30950947	30950947	C	T	SNP	GAL3ST1	ENST00000338911	human	ensembl	74_37	-1	known	missense	c.1265	p.R422Q	0.346	NULL	pfam_Gal-3-0_sulfotransfrase,superfamily_P-loop_NTPase	-	no_errors	GAL3ST1	HGNC	ENSG00000128242	tier1	-	-	49	0	0.00	30	23	43.40	49	0	0.00	20	22	52.38
EPHB1	0	genome.wustl.edu	37	3	134644703	134644703	+	Missense_Mutation	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	3	134644703	134644703	C	T	SNP	EPHB1	ENST00000398015	human	ensembl	74_37	+1	known	missense	c.104	p.T35M	1.000	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ephrin_rcpt_lig-bd_dom,superfamily_Galactose-bd-like,smart_Ephrin_rcpt_lig-bd_dom	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ephrin_rcpt_lig-bd_dom,pfam_Prot_kinase_dom,pfam_Fibronectin_type3,pfam_SAM_type1,pfam_SAM_2,superfamily_Galactose-bd-like,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_SAM/pointed,superfamily_Growth_fac_rcpt_N_dom,smart_Ephrin_rcpt_lig-bd_dom,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_SAM,prints_Ser-Thr/Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_SAM,pfscan_Prot_kinase_dom	-	no_errors	EPHB1	HGNC	ENSG00000154928	tier1	-	-	35	0	0.00	19	30	61.22	104	0	0.00	38	51	57.30
ASTN1	0	genome.wustl.edu	37	1	176903441	176903441	+	Missense_Mutation	SNP	T	T	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	1	176903441	176903441	T	C	SNP	ASTN1	ENST00000367654	human	ensembl	74_37	-1	known	missense	c.2542	p.T848A	0.998	smart_MACPF	superfamily_Fibronectin_type3,smart_EG-like_dom,smart_MACPF,pfscan_Fibronectin_type3	-	no_errors	ASTN1	HGNC	ENSG00000152092	tier1	-	-	28	0	0.00	33	15	31.25	113	0	0.00	53	30	36.14
SLC4A4	0	genome.wustl.edu	37	4	72412086	72412086	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	4	72412086	72412086	T	A	SNP	SLC4A4	ENST00000425175	human	ensembl	74_37	+1	known	nonsense	c.2462	p.L821*	1.000	pfam_HCO3_transpt_C,tigrfam_HCO3_transpt_euk	pfam_HCO3_transpt_C,pfam_Band3_cytoplasmic_dom,superfamily_PTrfase/Anion_transptr,prints_HCO3_transpt_euk,prints_Na/HCO3_transpt,tigrfam_HCO3_transpt_euk	-	no_errors	SLC4A4	HGNC	ENSG00000080493	tier1	-	-	117	0	0.00	62	23	27.06	81	0	0.00	61	20	24.69
TNPO3	0	genome.wustl.edu	37	7	128640525	128640525	+	Silent	SNP	A	A	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	7	128640525	128640525	A	C	SNP	TNPO3	ENST00000393245	human	ensembl	74_37	-1	known	silent	c.969	p.T323	0.999	superfamily_ARM-type_fold	pfam_Exportin-1/Importin-b-like,superfamily_ARM-type_fold	-	no_errors	TNPO3	HGNC	ENSG00000064419	tier1	-	-	22	0	0.00	26	8	23.53	92	0	0.00	64	34	34.69
EPHB2	0	genome.wustl.edu	37	1	23233390	23233390	+	Silent	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	1	23233390	23233390	C	T	SNP	EPHB2	ENST00000400191	human	ensembl	74_37	+1	known	silent	c.2076	p.S692	1.000	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	pirsf_Tyr_kinase_ephrin_rcpt,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Ephrin_rcpt_lig-bd_dom,pfam_Prot_kinase_dom,pfam_Fibronectin_type3,pfam_SAM_type1,pfam_SAM_2,pfam_Tyr-kin_ephrin_A/B_rcpt-like,superfamily_Galactose-bd-like,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_SAM/pointed,superfamily_Growth_fac_rcpt_N_dom,smart_Ephrin_rcpt_lig-bd_dom,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_SAM,pfscan_Fibronectin_type3,pfscan_SAM,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	-	no_errors	EPHB2	HGNC	ENSG00000133216	tier1	-	-	35	0	0.00	28	22	44.00	74	0	0.00	45	27	37.50
AP2A2	0	genome.wustl.edu	37	11	993284	993284	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	11	993284	993284	G	A	SNP	AP2A2	ENST00000332231	human	ensembl	74_37	+1	known	missense	c.1456	p.A486T	1.000	pfam_Clathrin/coatomer_adapt-like_N,superfamily_ARM-type_fold,pirsf_AP2_complex_asu	pfam_Clathrin/coatomer_adapt-like_N,pfam_Clathrin_a-adaptin_app_sub_C,pfam_Clathrin_a/b/g-adaptin_app_Ig,superfamily_ARM-type_fold,superfamily_Coatomer/calthrin_app_sub_C,superfamily_Coatomer/clathrin_app_Ig-like,smart_Clathrin_a/b/g-adaptin_app_Ig,pirsf_AP2_complex_asu	-	no_errors	AP2A2	HGNC	ENSG00000183020	tier1	-	-	61	0	0.00	54	10	15.62	52	0	0.00	36	6	14.29
ENSG00000250992	0	genome.wustl.edu	37	5	175467785	175467785	+	R	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	5	175467785	175467785	G	A	SNP	ENSG00000250992	ENST00000509643	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.037	-	-	-	no_errors	RP11-826N14.1	Clone_based_vega_gene	ENSG00000250992	tier1	rs187668175	GMAF=0.0005	134	0	0.00	138	20	12.66	129	0	0.00	116	16	12.12
CXorf22	0	genome.wustl.edu	37	X	35969300	35969300	+	Missense_Mutation	SNP	G	G	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	X	35969300	35969300	G	T	SNP	CXorf22	ENST00000297866	human	ensembl	74_37	+1	known	missense	c.709	p.V237F	0.923	NULL	superfamily_PapD-like	-	no_errors	CXorf22	HGNC	ENSG00000165164	tier1	-	-	18	0	0.00	5	12	70.59	38	0	0.00	13	20	60.61
NKX2-2	0	genome.wustl.edu	37	20	21492811	21492811	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	20	21492811	21492811	C	A	SNP	NKX2-2	ENST00000377142	human	ensembl	74_37	-1	known	missense	c.572	p.G191V	1.000	NULL	pfam_Homeobox_dom,superfamily_Homeodomain-like,smart_Homeobox_dom,pfscan_Homeobox_dom,prints_Homeobox_metazoa	-	no_errors	NKX2-2	HGNC	ENSG00000125820	tier1	-	-	120	0	0.00	54	36	40.00	36	0	0.00	19	7	26.92
RNF43	0	genome.wustl.edu	37	17	56435245	56435245	+	Missense_Mutation	SNP	C	C	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	17	56435245	56435245	C	A	SNP	RNF43	ENST00000407977	human	ensembl	74_37	-1	known	missense	c.1892	p.S631I	0.002	NULL	pfam_Znf_C3HC4_RING-type,superfamily_PAS,smart_Znf_RING,pfscan_Znf_RING	-	no_errors	RNF43	HGNC	ENSG00000108375	tier1	-	-	68	0	0.00	32	29	47.54	49	0	0.00	13	14	51.85
GLT8D2	0	genome.wustl.edu	37	12	104397053	104397053	+	Missense_Mutation	SNP	T	T	G			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	12	104397053	104397053	T	G	SNP	GLT8D2	ENST00000360814	human	ensembl	74_37	-1	known	missense	c.144	p.E48D	0.171	NULL	pfam_Glyco_trans_8	-	no_errors	GLT8D2	HGNC	ENSG00000120820	tier1	-	-	47	0	0.00	39	27	40.30	142	0	0.00	54	36	40.00
XYLB	0	genome.wustl.edu	37	3	38411731	38411732	+	R	INS	-	-	CACACACACA			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	-	-	-	CACACACACA	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	3	38411731	38411732	-	CACACACACA	INS	XYLB	ENST00000487569	human	ensembl	74_37	+1	putative	rna	NULL	NULL	0.000:0.000	-	-	-	no_errors	XYLB	HGNC	ENSG00000093217	tier1			15	0	0.00	12	2	14.29	15	0	0.00	12	2	14.29
DCX	0	genome.wustl.edu	37	X	110644349	110644349	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	X	110644349	110644349	G	A	SNP	DCX	ENST00000338081	human	ensembl	74_37	-1	known	missense	c.817	p.R273W	1.000	smart_Doublecortin_dom,pirsf_Doublecortin_chordata,pfscan_Doublecortin_dom	pfam_Doublecortin_dom,smart_Doublecortin_dom,pirsf_Doublecortin_chordata,pfscan_Doublecortin_dom	-	no_errors	DCX	HGNC	ENSG00000077279	tier1	rs104894780	-	27	0	0.00	17	31	63.27	34	0	0.00	4	22	84.62
HFM1	0	genome.wustl.edu	37	1	91818856	91818856	+	Silent	SNP	C	C	T			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	1	91818856	91818856	C	T	SNP	HFM1	ENST00000370425	human	ensembl	74_37	-1	known	silent	c.1686	p.R562	1.000	superfamily_P-loop_NTPase,pfscan_Helicase_C	pfam_Sec63-dom,pfam_D/R_helicase_DEAD/DEAH_N,pfam_Helicase_C,pfam_Helicase/UvrB_dom,superfamily_P-loop_NTPase,smart_Helicase_ATP-bd,smart_Helicase_C,smart_Sec63-dom,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	-	no_errors	HFM1	HGNC	ENSG00000162669	tier1	-	-	34	0	0.00	37	8	17.78	114	0	0.00	78	6	7.14
AP2A2	0	genome.wustl.edu	37	11	993358	993358	+	Missense_Mutation	SNP	G	G	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	11	993358	993358	G	C	SNP	AP2A2	ENST00000332231	human	ensembl	74_37	+1	known	missense	c.1530	p.L510F	1.000	pfam_Clathrin/coatomer_adapt-like_N,superfamily_ARM-type_fold,pirsf_AP2_complex_asu	pfam_Clathrin/coatomer_adapt-like_N,pfam_Clathrin_a-adaptin_app_sub_C,pfam_Clathrin_a/b/g-adaptin_app_Ig,superfamily_ARM-type_fold,superfamily_Coatomer/calthrin_app_sub_C,superfamily_Coatomer/clathrin_app_Ig-like,smart_Clathrin_a/b/g-adaptin_app_Ig,pirsf_AP2_complex_asu	-	no_errors	AP2A2	HGNC	ENSG00000183020	tier1	-	-	62	0	0.00	65	11	14.29	54	0	0.00	41	4	8.89
FAM182B	0	genome.wustl.edu	37	20	25840516	25840516	+	R	SNP	T	T	C			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	20	25840516	25840516	T	C	SNP	FAM182B	ENST00000584356	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.024	-	-	-	no_errors	FAM182B	HGNC	ENSG00000175170	tier1	-	-	63	0	0.00	37	5	11.90	9	0	0.00	7	0	0.00
LOR	0	genome.wustl.edu	37	1	153233991	153233992	+	In_Frame_Ins	INS	-	-	CTCTGGCGGCGG			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	1	153233991	153233992	-	CTCTGGCGGCGG	INS	LOR	ENST00000368742	human	ensembl	74_37	+1	known	in_frame_ins	c.566_567	p.193in_frame_insGSGG	0.014:0.200	NULL	NULL	-	no_errors	LOR	HGNC	ENSG00000203782	tier1			0	0	0.00	3	0	0.00	0	0	0.00	3	0	0.00
SPPL2B	0	genome.wustl.edu	37	19	2341094	2341101	+	R	DEL	CTCCCTGG	CTCCCTGG	-			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	CTCCCTGG	CTCCCTGG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	19	2341094	2341101	CTCCCTGG	-	DEL	SPPL2B	ENST00000592738	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.000:0.000:0.010:0.001:0.000:0.000:0.001:0.000	-	-	-	no_errors	SPPL2B	HGNC	ENSG00000005206	tier1			0	0	0.00	0	0	0.00	0	0	0.00	0	0	0.00
WASH4P	0	genome.wustl.edu	37	16	64458	64458	+	Missense_Mutation	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	16	64458	64458	G	A	SNP	WASH4P	ENST00000326592	human	ensembl	74_37	-1	novel	missense	c.1357	p.R453C	1.000	NULL	pfam_WASH1_WAHD	-	no_errors	WASH4P	HGNC	ENSG00000234769	tier1	rs12444477	-	58	0	0.00	47	5	9.62	0	0	0.00	0	0	0.00
GPR78	0	genome.wustl.edu	37	4	8583114	8583114	+	Silent	SNP	G	G	A			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	4	8583114	8583114	G	A	SNP	GPR78	ENST00000382487	human	ensembl	74_37	+1	known	silent	c.405	p.L135	1.000	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_GPCR_Rhodpsn	-	no_errors	GPR78	HGNC	ENSG00000155269	tier1	-	-	29	0	0.00	10	3	23.08	4	0	0.00	1	2	66.67
PGBD2	0	genome.wustl.edu	37	1	249212342	249212348	+	Frame_Shift_Del	DEL	TTGCCTG	TTGCCTG	-			TCGA-DX-A3LT-01A-12D-A21Q-09	TCGA-DX-A3LT-10A-01D-A21Q-09	TTGCCTG	TTGCCTG					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	a2f02ff7-8433-4cb5-9324-34f13edeaca1	c31a8d8b-6d3a-4e91-a25a-0a4791b3a0c2	1	249212342	249212348	TTGCCTG	-	DEL	PGBD2	ENST00000329291	human	ensembl	74_37	+1	known	frame_shift_del	c.1559_1565	p.I520fs	0.060:0.048:0.922:0.964:0.963:0.966:0.961	NULL	NULL	-	no_errors	PGBD2	HGNC	ENSG00000185220	tier1			59	0	0.00	48	3	5.88	59	0	0.00	48	3	5.88
