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
SPG11	0	genome.wustl.edu	37	15	44876519	44876519	+	Missense_Mutation	SNP	C	C	A			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	15	44876519	44876519	C	A	SNP	SPG11	ENST00000261866	human	ensembl	74_37	-1	known	missense	c.5359	p.D1787Y	0.009	NULL	NULL	-	no_errors	SPG11	HGNC	ENSG00000104133	tier1	-	-	67	0	0.00	39	25	39.06	30	0	0.00	36	11	23.40
TBC1D12	0	genome.wustl.edu	37	10	96292870	96292870	+	R	SNP	A	A	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	10	96292870	96292870	A	T	SNP	TBC1D12	ENST00000485048	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.007	-	-	-	no_errors	TBC1D12	HGNC	ENSG00000108239	tier1	-	-	65	0	0.00	43	27	38.57	136	0	0.00	72	52	41.94
TUBGCP5	0	genome.wustl.edu	37	15	22853761	22853761	+	Missense_Mutation	SNP	G	G	C			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	15	22853761	22853761	G	C	SNP	TUBGCP5	ENST00000283645	human	ensembl	74_37	+1	known	missense	c.1399	p.E467Q	1.000	pfam_TUBGCP	pfam_TUBGCP	-	no_errors	TUBGCP5	HGNC	ENSG00000153575	tier1	-	-	99	0	0.00	55	31	36.05	82	0	0.00	39	24	38.10
ATM	0	genome.wustl.edu	37	11	108119792	108119792	+	Missense_Mutation	SNP	C	C	A			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	11	108119792	108119792	C	A	SNP	ATM	ENST00000278616	human	ensembl	74_37	+1	known	missense	c.1198	p.L400I	1.000	superfamily_ARM-type_fold	pfam_PIK-rel_kinase_FAT,pfam_PI3/4_kinase_cat_dom,pfam_TAN,pfam_FATC,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_PI3/4_kinase_cat_dom,pfscan_PIK_FAT,pfscan_FATC,pfscan_PI3/4_kinase_cat_dom	-	no_errors	ATM	HGNC	ENSG00000149311	tier1	-	-	72	0	0.00	66	27	29.03	104	0	0.00	66	26	28.26
SYT2	0	genome.wustl.edu	37	1	202571629	202571629	+	Missense_Mutation	SNP	G	G	C			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	1	202571629	202571629	G	C	SNP	SYT2	ENST00000367267	human	ensembl	74_37	-1	known	missense	c.510	p.D170E	1.000	pfam_C2_dom,superfamily_C2_dom,smart_C2_dom,pfscan_C2_dom,prints_Synaptotagmin	pfam_C2_dom,superfamily_C2_dom,smart_C2_dom,pfscan_C2_dom,prints_Synaptotagmin,prints_C2_dom	-	no_errors	SYT2	HGNC	ENSG00000143858	tier1	-	-	71	0	0.00	35	24	40.00	34	0	0.00	11	9	45.00
SLC27A6	0	genome.wustl.edu	37	5	128302184	128302184	+	Silent	SNP	C	C	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	5	128302184	128302184	C	T	SNP	SLC27A6	ENST00000262462	human	ensembl	74_37	+1	known	silent	c.354	p.F118	0.886	pfam_AMP-dep_Synth/Lig	pfam_AMP-dep_Synth/Lig	-	no_errors	SLC27A6	HGNC	ENSG00000113396	tier1	-	-	126	0	0.00	93	38	29.01	96	0	0.00	55	28	33.73
STMND1	0	genome.wustl.edu	37	6	17120900	17120900	+	Missense_Mutation	SNP	T	T	A			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	6	17120900	17120900	T	A	SNP	STMND1	ENST00000536551	human	ensembl	74_37	+1	known	missense	c.322	p.S108T	1.000	NULL	pfam_Stathmin_fam,superfamily_Stathmin_fam	-	no_errors	STMND1	HGNC	ENSG00000230873	tier1	-	-	55	0	0.00	43	22	33.85	84	0	0.00	50	32	39.02
OR6C76	0	genome.wustl.edu	37	12	55820132	55820132	+	Missense_Mutation	SNP	C	C	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	12	55820132	55820132	C	T	SNP	OR6C76	ENST00000328314	human	ensembl	74_37	+1	known	missense	c.95	p.T32M	0.001	prints_GPCR_Rhodpsn	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	-	no_errors	OR6C76	HGNC	ENSG00000185821	tier1	-	-	147	0	0.00	96	40	29.41	77	0	0.00	61	32	34.41
ABCC6	0	genome.wustl.edu	37	16	16248796	16248796	+	Silent	SNP	G	G	A			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	16	16248796	16248796	G	A	SNP	ABCC6	ENST00000205557	human	ensembl	74_37	-1	known	silent	c.3975	p.I1325	0.995	pfam_ABC_transporter-like,superfamily_P-loop_NTPase,smart_AAA+_ATPase,pfscan_ABC_transporter-like,tigrfam_Multidrug-R_assoc	pfam_ABC_transptr_TM_dom,pfam_ABC_transporter-like,superfamily_P-loop_NTPase,superfamily_ABC1_TM_dom,smart_AAA+_ATPase,pfscan_ABC_transporter-like,pfscan_ABC1_TM_dom,tigrfam_Multidrug-R_assoc	-	no_errors	ABCC6	HGNC	ENSG00000091262	tier1	-	-	149	0	0.00	111	47	29.75	20	0	0.00	15	5	25.00
KRTAP22-2	0	genome.wustl.edu	37	21	31962669	31962669	+	Missense_Mutation	SNP	C	C	A			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	21	31962669	31962669	C	A	SNP	KRTAP22-2	ENST00000382830	human	ensembl	74_37	-1	known	missense	c.25	p.G9C	0.022	NULL	NULL	-	no_errors	KRTAP22-2	HGNC	ENSG00000206106	tier1	-	-	133	0	0.00	102	57	35.85	105	0	0.00	57	38	39.58
ENSG00000258704	0	genome.wustl.edu	37	14	35390827	35390827	+	R	SNP	C	C	A			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	14	35390827	35390827	C	A	SNP	ENSG00000258704	ENST00000555015	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.998	-	-	-	no_errors	RP11-85K15.2	Clone_based_vega_gene	ENSG00000258704	tier1	-	-	30	0	0.00	14	11	44.00	25	0	0.00	16	13	44.83
RPL36A	0	genome.wustl.edu	37	X	100646748	100646748	+	Missense_Mutation	SNP	C	C	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	X	100646748	100646748	C	T	SNP	RPL36A	ENST00000427805	human	ensembl	74_37	+1	known	missense	c.223	p.R75W	1.000	pfam_Ribosomal_L44e,superfamily_Ribosomal_zn-bd	pfam_Ribosomal_L44e,superfamily_Ribosomal_zn-bd	-	no_errors	RPL36A	HGNC	ENSG00000241343	tier1	-	-	148	0	0.00	113	53	31.93	103	0	0.00	78	42	35.00
CARD11	0	genome.wustl.edu	37	7	2953040	2953040	+	Missense_Mutation	SNP	C	C	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	7	2953040	2953040	C	T	SNP	CARD11	ENST00000396946	human	ensembl	74_37	-1	known	missense	c.2900	p.R967H	0.963	NULL	pfam_CARD,superfamily_DEATH-like_dom,superfamily_P-loop_NTPase,superfamily_PDZ,pfscan_CARD	-	no_errors	CARD11	HGNC	ENSG00000198286	tier1	rs141751925	GMAF=0.0005	212	0	0.00	137	71	34.13	27	0	0.00	11	11	50.00
ISM1	0	genome.wustl.edu	37	20	13279761	13279761	+	Silent	SNP	C	C	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	20	13279761	13279761	C	T	SNP	ISM1	ENST00000262487	human	ensembl	74_37	+1	known	silent	c.1050	p.D350	0.980	pfam_AMOP,smart_AMOP,pfscan_AMOP	pfam_AMOP,pfam_Thrombospondin_1_rpt,superfamily_Thrombospondin_1_rpt,smart_Thrombospondin_1_rpt,smart_AMOP,pfscan_AMOP,pfscan_Thrombospondin_1_rpt	-	no_errors	ISM1	HGNC	ENSG00000101230	tier1	-	-	59	0	0.00	37	22	37.29	18	0	0.00	12	8	40.00
ROBO3	0	genome.wustl.edu	37	11	124751212	124751212	+	R	SNP	C	C	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	11	124751212	124751212	C	T	SNP	ROBO3	ENST00000525482	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.000	-	-	-	no_errors	ROBO3	HGNC	ENSG00000154134	tier1	-	-	69	0	0.00	64	22	25.58	65	0	0.00	51	25	32.89
ANKLE1	0	genome.wustl.edu	37	19	17397486	17397501	+	Frame_Shift_Del	DEL	TGTGTGTGTGTGTGTT	TGTGTGTGTGTGTGTT	-			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	TGTGTGTGTGTGTGTT	TGTGTGTGTGTGTGTT	TGTGTGTGTGTGTGTT	-	TGTGTGTGTGTGTGTT	TGTGTGTGTGTGTGTT	Unknown	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	19	17397486	17397501	TGTGTGTGTGTGTGTT	-	DEL	ANKLE1	ENST00000598347	human	ensembl	74_37	+1	putative	frame_shift_del	c.1756_1771	p.C590fs	0.820:0.697:0.344:0.098:0.082:0.071:0.072:0.077:0.073:0.072:0.083:0.085:0.079:0.064:0.026:0.004	NULL	pfam_Ankyrin_rpt,superfamily_Ankyrin_rpt-contain_dom,superfamily_Lactate_DH/Glyco_Ohase_4_C,smart_Ankyrin_rpt,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom	-	no_errors	ANKLE1	HGNC	ENSG00000160117	tier1			18	0	0.00	11	2	15.38	18	0	0.00	11	2	15.38
LOC644794	0	genome.wustl.edu	37	7	66369212	66369213	+	R	INS	-	-	GGCCTTTCCAGGCCCAGCTCTCGCCTCCCGGC			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	7	66369212	66369213	-	GGCCTTTCCAGGCCCAGCTCTCGCCTCCCGGC	INS	LOC644794	ENST00000610177	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.293:0.454	-	-	-	no_errors	RP11-458F8.4	Clone_based_vega_gene	ENSG00000273142	tier1			1	0	0.00	1	0	0.00	1	0	0.00	1	0	0.00
PIPSL	0	genome.wustl.edu	37	10	95718377	95718378	+	R	INS	-	-	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	10	95718377	95718378	-	T	INS	PIPSL	ENST00000480546	human	ensembl	74_37	-1	putative	rna	NULL	NULL	0.070:0.069	-	-	-	no_errors	PIPSL	HGNC	ENSG00000180764	tier1			25	0	0.00	13	3	18.75	0	0	0.00	0	0	0.00
TTC3	0	genome.wustl.edu	37	21	38463868	38463869	+	R	INS	-	-	TTATTTAT			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	21	38463868	38463869	-	TTATTTAT	INS	TTC3	ENST00000484047	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.001:0.000	-	-	-	no_errors	TTC3	HGNC	ENSG00000182670	tier1			0	0	0.00	0	0	0.00	0	0	0.00	0	0	0.00
JAM3	0	genome.wustl.edu	37	11	133938975	133938975	+	Silent	SNP	C	C	T			TCGA-MJ-A68J-01A-11D-A307-09	TCGA-MJ-A68J-10A-01D-A307-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	64a0148d-ddbb-4cc7-9594-d3e6d2b2bf4a	8d0ec126-55e3-413c-bf42-fbaf91347ed4	11	133938975	133938975	C	T	SNP	JAM3	ENST00000529443	human	ensembl	74_37	+1	known	silent	c.132	p.L44	0.947	NULL	pfam_Ig_I-set,pfam_Ig_V-set,pfam_Immunoglobulin,pfam_CD80_C2-set,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,pfscan_Ig-like_dom	-	no_errors	JAM3	HGNC	ENSG00000166086	tier1	-	-	56	0	0.00	49	26	34.67	0	0	0.00	2	2	50.00
