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
AFF2	0	genome.wustl.edu	37	X	148037568	148037568	+	Missense_Mutation	SNP	G	G	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	X	148037568	148037568	G	T	SNP	AFF2	ENST00000370460	human	ensembl	74_37	+1	known	missense	c.1993	p.D665Y	1.000	pfam_TF_AF4/FMR2	pfam_TF_AF4/FMR2	-	no_errors	AFF2	HGNC	ENSG00000155966	tier1	-	-	30	0	0.00	12	10	45.45	74	0	0.00	55	58	51.33
CCT3	0	genome.wustl.edu	37	1	156307996	156307996	+	R	SNP	G	G	C			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	1	156307996	156307996	G	C	SNP	CCT3	ENST00000368256	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.733	-	-	-	no_errors	CCT3	HGNC	ENSG00000163468	tier1	-	-	61	0	0.00	23	19	45.24	55	0	0.00	36	27	42.86
DH3	0	genome.wustl.edu	37	16	20944659	20944659	+	Silent	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	16	20944659	20944659	G	A	SNP	DH3	ENST00000261383	human	ensembl	74_37	-1	known	silent	c.12168	p.S4056	0.987	pfam_Dynein_heavy_dom	pfam_Dynein_heavy_dom,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,superfamily_P-loop_NTPase,superfamily_Prefoldin,smart_AAA+_ATPase	-	no_errors	DH3	HGNC	ENSG00000158486	tier1	-	-	68	0	0.00	44	32	42.11	79	0	0.00	71	33	31.43
EEF1G	0	genome.wustl.edu	37	11	62327654	62327654	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	11	62327654	62327654	G	A	SNP	EEF1G	ENST00000378019	human	ensembl	74_37	-1	known	nonsense	c.1192	p.R398*	1.000	pfam_Transl_elong_EF1_G_con,superfamily_Transl_elong_EF1_G_con,pfscan_Transl_elong_EF1_G_con	pfam_Transl_elong_EF1_G_con,pfam_Glutathione_S-Trfase_N,pfam_GST_C,superfamily_Transl_elong_EF1_G_con,superfamily_Glutathione-S-Trfase_C-like,superfamily_Thioredoxin-like_fold,pfscan_Transl_elong_EF1_G_con	-	no_errors	EEF1G	HGNC	ENSG00000254772	tier1	-	-	34	0	0.00	35	6	14.63	102	0	0.00	62	36	36.73
ALAS2	0	genome.wustl.edu	37	X	55047609	55047609	+	Missense_Mutation	SNP	C	C	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	X	55047609	55047609	C	A	SNP	ALAS2	ENST00000330807	human	ensembl	74_37	-1	known	missense	c.514	p.A172S	1.000	superfamily_PyrdxlP-dep_Trfase,tigrfam_4pyrrol_synth_NH2levulA_synth	pfam_Aminotransferase_I/II,pfam_5aminolev_synth_preseq,pfam_Aminotrans_V/Cys_dSase,pfam_Cys/Met-Metab_PyrdxlP-dep_enz,superfamily_PyrdxlP-dep_Trfase,tigrfam_4pyrrol_synth_NH2levulA_synth	-	no_errors	ALAS2	HGNC	ENSG00000158578	tier1	-	-	45	0	0.00	21	17	44.74	112	0	0.00	60	43	41.75
SPATA17	0	genome.wustl.edu	37	1	217822309	217822309	+	Missense_Mutation	SNP	A	A	G			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	1	217822309	217822309	A	G	SNP	SPATA17	ENST00000366933	human	ensembl	74_37	+1	known	missense	c.154	p.I52V	0.992	superfamily_P-loop_NTPase,smart_IQ_motif_EF-hand-BS,pfscan_IQ_motif_EF-hand-BS	pfam_IQ_motif_EF-hand-BS,superfamily_P-loop_NTPase,smart_IQ_motif_EF-hand-BS,pfscan_IQ_motif_EF-hand-BS	-	no_errors	SPATA17	HGNC	ENSG00000162814	tier1	-	-	35	0	0.00	19	7	26.92	93	0	0.00	78	52	40.00
LRRC37BP1	0	genome.wustl.edu	37	17	28959016	28959016	+	R	SNP	T	T	G			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	17	28959016	28959016	T	G	SNP	LRRC37BP1	ENST00000412831	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.024	-	-	-	no_errors	LRRC37BP1	HGNC	ENSG00000250462	tier1	-	-	65	0	0.00	37	15	28.85	77	0	0.00	47	33	41.25
GRK7	0	genome.wustl.edu	37	3	141535883	141535883	+	Silent	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	3	141535883	141535883	G	A	SNP	GRK7	ENST00000264952	human	ensembl	74_37	+1	known	silent	c.1653	p.L551	0.938	NULL	pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_RGS_dom,superfamily_Kinase-like_dom,superfamily_Regulat_G_prot_signal_superfam,smart_Regulat_G_prot_signal_superfam,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,smart_AGC-kinase_C,pfscan_Regulat_G_prot_signal_superfam,pfscan_Prot_kinase_dom,prints_GPCR_kinase	-	no_errors	GRK7	HGNC	ENSG00000114124	tier1	-	-	16	0	0.00	5	4	44.44	132	0	0.00	80	70	46.36
CNTLN	0	genome.wustl.edu	37	9	17235703	17235703	+	Missense_Mutation	SNP	A	A	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	9	17235703	17235703	A	T	SNP	CNTLN	ENST00000380647	human	ensembl	74_37	+1	known	missense	c.582	p.K194N	0.993	superfamily_Prefoldin	superfamily_Prefoldin	-	no_errors	CNTLN	HGNC	ENSG00000044459	tier1	-	-	32	0	0.00	19	12	38.71	94	0	0.00	77	50	39.06
OR52L1	0	genome.wustl.edu	37	11	6007208	6007208	+	Missense_Mutation	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	11	6007208	6007208	C	T	SNP	OR52L1	ENST00000332249	human	ensembl	74_37	-1	known	missense	c.953	p.R318H	0.990	prints_GPCR_Rhodpsn	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	-	no_errors	OR52L1	HGNC	ENSG00000183313	tier1	-	-	48	0	0.00	40	20	32.79	88	0	0.00	40	30	42.86
CEP152	0	genome.wustl.edu	37	15	49048344	49048344	+	Missense_Mutation	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	15	49048344	49048344	C	T	SNP	CEP152	ENST00000380950	human	ensembl	74_37	-1	known	missense	c.3101	p.R1034Q	0.500	NULL	NULL	-	no_errors	CEP152	HGNC	ENSG00000103995	tier1	-	-	63	0	0.00	47	26	35.62	115	0	0.00	65	40	38.10
FRMPD2	0	genome.wustl.edu	37	10	49452869	49452869	+	Missense_Mutation	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	10	49452869	49452869	C	T	SNP	FRMPD2	ENST00000374201	human	ensembl	74_37	-1	known	missense	c.333	p.M111I	1.000	superfamily_Kinase-like_dom,smart_KIND	pfam_PDZ,pfam_FERM_central,pfam_FERM_PH-like_C,pfam_FERM_N,superfamily_PDZ,superfamily_FERM_central,superfamily_Kinase-like_dom,smart_KIND,smart_Band_41_domain,smart_PDZ,pfscan_FERM_domain,pfscan_PDZ,prints_Band_41_fam	-	no_errors	FRMPD2	HGNC	ENSG00000170324	tier1	-	-	25	0	0.00	18	10	35.71	118	1	0.84	85	44	34.11
DTWD1	0	genome.wustl.edu	37	15	49926974	49926974	+	Missense_Mutation	SNP	C	C	G			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	15	49926974	49926974	C	G	SNP	DTWD1	ENST00000251250	human	ensembl	74_37	+1	known	missense	c.650	p.T217S	0.947	pfam_DTW	pfam_DTW	-	no_errors	DTWD1	HGNC	ENSG00000104047	tier1	-	-	22	0	0.00	10	5	33.33	50	0	0.00	44	29	39.73
TP53	0	genome.wustl.edu	37	17	7577130	7577130	+	Missense_Mutation	SNP	A	A	C			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	17	7577130	7577130	A	C	SNP	TP53	ENST00000269305	human	ensembl	74_37	-1	known	missense	c.808	p.F270V	1.000	pfam_p53_D-bd,superfamily_p53-like_TF_D-bd,prints_p53_tumour_suppressor	pfam_p53_D-bd,pfam_p53_tetrameristn,pfam_p53_transactivation_domain,superfamily_p53-like_TF_D-bd,superfamily_p53_tetrameristn,prints_p53_tumour_suppressor	-	no_errors	TP53	HGNC	ENSG00000141510	tier1	-	-	29	0	0.00	7	13	65.00	89	0	0.00	18	52	74.29
C2orf42	0	genome.wustl.edu	37	2	70387846	70387846	+	Missense_Mutation	SNP	A	A	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	2	70387846	70387846	A	T	SNP	C2orf42	ENST00000264434	human	ensembl	74_37	-1	known	missense	c.1427	p.V476E	1.000	NULL	NULL	-	no_errors	C2orf42	HGNC	ENSG00000115998	tier1	-	-	56	0	0.00	41	39	48.75	142	0	0.00	87	65	42.76
OR51V1	0	genome.wustl.edu	37	11	5221043	5221043	+	Missense_Mutation	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	11	5221043	5221043	C	T	SNP	OR51V1	ENST00000321255	human	ensembl	74_37	-1	known	missense	c.888	p.M296I	0.997	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	-	no_errors	OR51V1	HGNC	ENSG00000176742	tier1	-	-	91	0	0.00	46	40	46.51	88	0	0.00	57	56	49.56
ZFAND3	0	genome.wustl.edu	37	6	38120497	38120497	+	R	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	6	38120497	38120497	C	T	SNP	ZFAND3	ENST00000440482	human	ensembl	74_37	+1	known	rna	NULL	NULL	1.000	-	-	-	no_errors	ZFAND3	HGNC	ENSG00000156639	tier1	-	-	31	0	0.00	14	15	50.00	130	0	0.00	57	57	49.57
PML	0	genome.wustl.edu	37	15	74315216	74315216	+	Missense_Mutation	SNP	T	T	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	15	74315216	74315216	T	A	SNP	PML	ENST00000268058	human	ensembl	74_37	+1	known	missense	c.650	p.L217H	0.990	pfscan_Znf_B-box	pfam_DUF3583,pfam_Znf_B-box,smart_Znf_RING,smart_Znf_B-box,pfscan_Znf_B-box,pfscan_Znf_RING	-	no_errors	PML	HGNC	ENSG00000140464	tier1	-	-	24	0	0.00	17	8	32.00	26	0	0.00	18	7	28.00
WNK4	0	genome.wustl.edu	37	17	40936573	40936573	+	Silent	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	17	40936573	40936573	G	A	SNP	WNK4	ENST00000246914	human	ensembl	74_37	+1	known	silent	c.1146	p.A382	0.708	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,pfam_Kinase_OSR1/WNK_CCT,superfamily_Kinase-like_dom,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Prot_kinase_dom	-	no_errors	WNK4	HGNC	ENSG00000126562	tier1	-	-	44	0	0.00	41	13	24.07	65	0	0.00	50	19	27.54
SETD1B	0	genome.wustl.edu	37	12	122257636	122257636	+	Missense_Mutation	SNP	A	A	G			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	12	122257636	122257636	A	G	SNP	SETD1B	ENST00000267197	human	ensembl	74_37	+1	known	missense	c.3616	p.M1206V	0.000	NULL	pfam_COMPASS_Set1_N-SET,pfam_SET_dom,pfam_RRM_dom,smart_RRM_dom,smart_SET_dom,smart_Post-SET_dom,pfscan_SET_dom,pfscan_Post-SET_dom,pfscan_RRM_dom	-	no_errors	SETD1B	HGNC	ENSG00000139718	tier1	-	-	118	0	0.00	101	32	24.06	32	0	0.00	30	8	21.05
USH1C	0	genome.wustl.edu	37	11	17515733	17515733	+	R	SNP	G	G	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	11	17515733	17515733	G	T	SNP	USH1C	ENST00000529563	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.001	-	-	-	no_errors	USH1C	HGNC	ENSG00000006611	tier1	-	-	50	0	0.00	27	11	28.95	82	0	0.00	53	40	43.01
CCDC122	0	genome.wustl.edu	37	13	44443482	44443482	+	Missense_Mutation	SNP	C	C	G			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	13	44443482	44443482	C	G	SNP	CCDC122	ENST00000281508	human	ensembl	74_37	-1	known	missense	c.31	p.G11R	0.006	NULL	NULL	-	no_errors	CCDC122	HGNC	ENSG00000151773	tier1	-	-	48	0	0.00	34	16	32.00	107	0	0.00	62	47	43.12
SDR9C7	0	genome.wustl.edu	37	12	57327965	57327965	+	Silent	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	12	57327965	57327965	G	A	SNP	SDR9C7	ENST00000293502	human	ensembl	74_37	-1	known	silent	c.81	p.Y27	0.983	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH	pfam_DH_sc/Rdtase_SDR,prints_Glc/ribitol_DH,prints_DH_sc/Rdtase_SDR	-	no_errors	SDR9C7	HGNC	ENSG00000170426	tier1	-	-	33	0	0.00	24	15	38.46	67	0	0.00	42	30	41.67
ARFGEF1	0	genome.wustl.edu	37	8	68115436	68115436	+	Missense_Mutation	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	8	68115436	68115436	C	T	SNP	ARFGEF1	ENST00000262215	human	ensembl	74_37	-1	known	missense	c.5010	p.M1670I	1.000	NULL	pfam_Sec7_dom,pfam_DUF1981_Sec7_assoc,superfamily_Sec7_dom,superfamily_ARM-type_fold,smart_Sec7_dom,pfscan_Sec7_dom	-	no_errors	ARFGEF1	HGNC	ENSG00000066777	tier1	-	-	55	0	0.00	33	12	26.67	110	0	0.00	61	44	41.51
ZNF880	0	genome.wustl.edu	37	19	52888544	52888544	+	Missense_Mutation	SNP	A	A	G			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	19	52888544	52888544	A	G	SNP	ZNF880	ENST00000422689	human	ensembl	74_37	+1	known	missense	c.1711	p.T571A	0.992	pfscan_Znf_C2H2	pfam_Znf_C2H2,pfam_Krueppel-associated_box,superfamily_Krueppel-associated_box,smart_Krueppel-associated_box,smart_Znf_C2H2-like,pfscan_Znf_C2H2,pfscan_Krueppel-associated_box	-	no_errors	ZNF880	HGNC	ENSG00000221923	tier1	-	-	30	0	0.00	16	15	48.39	85	0	0.00	54	29	34.94
BNC2	0	genome.wustl.edu	37	9	16738393	16738393	+	Missense_Mutation	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	9	16738393	16738393	C	T	SNP	BNC2	ENST00000380672	human	ensembl	74_37	-1	known	missense	c.94	p.V32I	0.001	NULL	smart_Znf_C2H2-like,pfscan_Znf_C2H2	-	no_errors	BNC2	HGNC	ENSG00000173068	tier1	-	-	68	0	0.00	45	29	39.19	113	0	0.00	65	57	46.72
TJP2	0	genome.wustl.edu	37	9	71866189	71866189	+	Missense_Mutation	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	9	71866189	71866189	C	T	SNP	TJP2	ENST00000539225	human	ensembl	74_37	+1	known	missense	c.3323	p.S1108L	1.000	NULL	pfam_PDZ,pfam_GK/Ca_channel_bsu,pfam_SH3_2,superfamily_PDZ,superfamily_P-loop_NTPase,superfamily_SH3_domain,smart_PDZ,smart_GK/Ca_channel_bsu,pfscan_PDZ,pfscan_SH3_domain,pfscan_Guanylate_kin-like,prints_ZonOcculS2,prints_ZonOcculdens	-	no_errors	TJP2	HGNC	ENSG00000119139	tier1	-	-	32	0	0.00	18	11	37.93	78	0	0.00	44	48	52.17
CCNT1	0	genome.wustl.edu	37	12	49088156	49088156	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	12	49088156	49088156	G	A	SNP	CCNT1	ENST00000261900	human	ensembl	74_37	-1	known	nonsense	c.841	p.Q281*	1.000	NULL	pfam_Cyclin_N,superfamily_Cyclin-like,smart_Cyclin-like	-	no_errors	CCNT1	HGNC	ENSG00000129315	tier1	-	-	71	0	0.00	51	17	24.64	100	0	0.00	73	25	25.51
LRRN2	0	genome.wustl.edu	37	1	204587896	204587896	+	Missense_Mutation	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	1	204587896	204587896	G	A	SNP	LRRN2	ENST00000367175	human	ensembl	74_37	-1	known	missense	c.1225	p.R409C	0.998	smart_Cys-rich_flank_reg_C	pfam_Ig_I-set,pfam_Leu-rich_rpt,pfam_Immunoglobulin,pfam_Ig_V-set,superfamily_Fibronectin_type3,smart_Leu-rich_rpt_typical-subtyp,smart_Cys-rich_flank_reg_C,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom	-	no_errors	LRRN2	HGNC	ENSG00000170382	tier1	rs141763834	-	68	0	0.00	21	27	56.25	19	0	0.00	13	8	38.10
CHD7	0	genome.wustl.edu	37	8	61763141	61763141	+	Nonsense_Mutation	SNP	G	G	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	8	61763141	61763141	G	T	SNP	CHD7	ENST00000423902	human	ensembl	74_37	+1	known	nonsense	c.5494	p.E1832*	1.000	NULL	pfam_SNF2_N,pfam_BRK_domain,pfam_Chromo_domain,pfam_Helicase_C,superfamily_P-loop_NTPase,superfamily_Chromodomain-like,smart_Chromo_domain/shadow,smart_Helicase_ATP-bd,smart_Helicase_C,smart_BRK_domain,pfscan_Helicase_ATP-bd,pfscan_Helicase_C,pfscan_Chromo_domain/shadow	-	no_errors	CHD7	HGNC	ENSG00000171316	tier1	-	-	46	0	0.00	27	14	34.15	82	0	0.00	44	32	42.11
DH5	0	genome.wustl.edu	37	5	13882857	13882857	+	Missense_Mutation	SNP	A	A	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	5	13882857	13882857	A	T	SNP	DH5	ENST00000265104	human	ensembl	74_37	-1	known	missense	c.3242	p.M1081K	0.000	NULL	pfam_Dynein_heavy_dom,pfam_Dynein_heavy_dom-1,pfam_Dynein_heavy_dom-2,pfam_ATPase_dyneun-rel_AAA,superfamily_P-loop_NTPase,smart_AAA+_ATPase	-	no_errors	DH5	HGNC	ENSG00000039139	tier1	-	-	35	0	0.00	33	4	10.81	110	0	0.00	147	26	15.03
AP5S1	0	genome.wustl.edu	37	20	3802829	3802829	+	Missense_Mutation	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	20	3802829	3802829	G	A	SNP	AP5S1	ENST00000246041	human	ensembl	74_37	+1	known	missense	c.65	p.R22Q	1.000	NULL	NULL	-	no_errors	AP5S1	HGNC	ENSG00000125843	tier1	-	-	65	0	0.00	30	24	44.44	46	0	0.00	29	28	49.12
RBMXL2	0	genome.wustl.edu	37	11	7110543	7110543	+	Silent	SNP	C	C	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	11	7110543	7110543	C	T	SNP	RBMXL2	ENST00000306904	human	ensembl	74_37	+1	known	silent	c.192	p.A64	1.000	pfam_RRM_dom,smart_RRM_dom_euk,smart_RRM_dom,pfscan_RRM_dom	pfam_RRM_dom,pfam_RBM1CTR,smart_RRM_dom_euk,smart_RRM_dom,pfscan_RRM_dom	-	no_errors	RBMXL2	HGNC	ENSG00000170748	tier1	-	-	25	0	0.00	18	10	35.71	59	0	0.00	28	33	54.10
MAP3K19	0	genome.wustl.edu	37	2	135744087	135744087	+	Frame_Shift_Del	DEL	G	G	-			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	2	135744087	135744087	G	-	DEL	MAP3K19	ENST00000375845	human	ensembl	74_37	-1	known	frame_shift_del	c.2355	p.M786fs	0.000	NULL	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	MAP3K19	HGNC	ENSG00000176601	tier1			31	0	0.00	22	15	40.54	92	0	0.00	58	27	31.76
FCRL3	0	genome.wustl.edu	37	1	157667713	157667713	+	R	DEL	C	C	-			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	1	157667713	157667713	C	-	DEL	FCRL3	ENST00000473231	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.944	-	-	-	no_errors	FCRL3	HGNC	ENSG00000160856	tier1			22	0	0.00	15	7	31.82	85	0	0.00	82	47	36.43
HIST1H4F	0	genome.wustl.edu	37	6	26240683	26240683	+	Frame_Shift_Del	DEL	T	T	-			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	6	26240683	26240683	T	-	DEL	HIST1H4F	ENST00000377745	human	ensembl	74_37	+1	known	frame_shift_del	c.30	p.L11fs	0.071	superfamily_Histone-fold,prints_Histone_H4	pfam_Histone_core_D,pfam_TAF_TATA-bd,superfamily_Histone-fold,smart_Histone_H4,smart_TAF_TATA-bd,prints_Histone_H4	-	no_errors	HIST1H4F	HGNC	ENSG00000198327	tier1			21	0	0.00	10	6	37.50	121	0	0.00	61	31	33.70
ENSG00000273199	0	genome.wustl.edu	37	21	37692480	37692480	+	R	SNP	T	T	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	21	37692480	37692480	T	A	SNP	ENSG00000273199	ENST00000608391	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.000	-	-	-	no_errors	AP000692.10	Clone_based_vega_gene	ENSG00000273199	tier1	-	-	8	0	0.00	14	6	30.00	11	0	0.00	5	4	44.44
LHPP	0	genome.wustl.edu	37	10	126185567	126185567	+	Missense_Mutation	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	10	126185567	126185567	G	A	SNP	LHPP	ENST00000368842	human	ensembl	74_37	+1	known	missense	c.505	p.V169I	1.000	pfam_HAD-like_dom,superfamily_HAD-like_dom,tigrfam_HAD-SF_hydro_IIA_hyp2,tigrfam_HAD-SF_hydro_IIA	pfam_HAD-like_dom,superfamily_HAD-like_dom,tigrfam_HAD-SF_hydro_IIA_hyp2,tigrfam_HAD-SF_hydro_IIA	-	no_errors	LHPP	HGNC	ENSG00000107902	tier1	-	-	55	0	0.00	7	26	78.79	79	0	0.00	9	45	83.33
GOLGA4	0	genome.wustl.edu	37	3	37360696	37360697	+	R	INS	-	-	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	3	37360696	37360697	-	T	INS	GOLGA4	ENST00000435830	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.000:0.005	-	-	-	no_errors	GOLGA4	HGNC	ENSG00000144674	tier1			18	0	0.00	14	2	12.50	75	1	1.32	69	5	6.76
HLA-DOB	0	genome.wustl.edu	37	6	32782136	32782136	+	Missense_Mutation	SNP	C	C	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	6	32782136	32782136	C	A	SNP	HLA-DOB	ENST00000438763	human	ensembl	74_37	-1	known	missense	c.604	p.D202Y	0.051	pfam_Ig_C1-set,smart_Ig_C1-set,pfscan_Ig-like_dom	pfam_MHC_II_b_N,pfam_Ig_C1-set,superfamily_MHC_I/II-like_Ag-recog,smart_MHC_II_b_N,smart_Ig_C1-set,pfscan_Ig-like_dom	-	no_errors	HLA-DOB	HGNC	ENSG00000241106	tier1	-	-	73	0	0.00	33	19	36.54	118	2	1.67	57	45	44.12
RGS7BP	0	genome.wustl.edu	37	5	63802483	63802483	+	Missense_Mutation	SNP	G	G	A			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	5	63802483	63802483	G	A	SNP	RGS7BP	ENST00000334025	human	ensembl	74_37	+1	known	missense	c.32	p.R11H	1.000	NULL	NULL	-	no_errors	RGS7BP	HGNC	ENSG00000186479	tier1	-	-	32	0	0.00	14	12	42.86	26	0	0.00	12	17	58.62
FGF9	0	genome.wustl.edu	37	13	22275847	22275848	+	R	DEL	TA	TA	-			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	TA	TA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	13	22275847	22275848	TA	-	DEL	FGF9	ENST00000478546	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.000:0.004	-	-	-	no_errors	FGF9	HGNC	ENSG00000102678	tier1			44	0	0.00	26	4	13.33	0	0	0.00	0	0	0.00
LOC100129138	0	genome.wustl.edu	37	1	104616114	104616114	+	R	SNP	G	G	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	1	104616114	104616114	G	T	SNP	LOC100129138	ENST00000418362	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.034	-	-	-	no_errors	RP11-364B6.1	Clone_based_vega_gene	ENSG00000215869	tier1	-	-	18	0	0.00	11	9	45.00	0	0	0.00	0	0	0.00
SIK1	0	genome.wustl.edu	37	21	44836772	44836772	+	Silent	SNP	A	A	T			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	21	44836772	44836772	A	T	SNP	SIK1	ENST00000270162	human	ensembl	74_37	-1	known	silent	c.2202	p.I734	1.000	pirsf_Ser/Thr_kinase_SIK1/2	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,pirsf_Ser/Thr_kinase_SIK1/2,pfscan_UBA/transl_elong_EF1B_N_euk,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	-	no_errors	SIK1	HGNC	ENSG00000142178	tier1	-	-	16	0	0.00	9	4	30.77	0	0	0.00	2	0	0.00
KRTAP5-10	0	genome.wustl.edu	37	11	71276808	71276808	+	Missense_Mutation	SNP	T	T	C			TCGA-IS-A3K6-01A-11D-A21Q-09	TCGA-IS-A3K6-10A-01D-A21Q-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	b9f8cfe2-7763-4819-9eba-216402df0178	bc5408cd-0b90-4d80-a68b-4c8ced85ff2a	11	71276808	71276808	T	C	SNP	KRTAP5-10	ENST00000398531	human	ensembl	74_37	+1	known	missense	c.175	p.C59R	0.396	NULL	NULL	-	no_errors	KRTAP5-10	HGNC	ENSG00000204572	tier1	-	-	97	0	0.00	53	38	41.76	0	0	0.00	0	2	100.00