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	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	c_position_WU	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	annotation_errors_WU
ADA	100	genome.wustl.edu	37	20	43255195	43255195	+	Silent	SNP	C	C	T	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	20	43255195	43255195	C	T	SNP	ADA	NM_000022	human	genbank	57_37b	-1	reviewed	silent	c.264	p.E88	1.000	superfamily_SSF51556,HMMPfam_A_deaminase	superfamily_SSF51556,HMMPfam_A_deaminase,PatternScan_A_DEAMINASE	-	no_errors
AKAP1	8165	genome.wustl.edu	37	17	55183677	55183677	+	Silent	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	17	55183677	55183677	G	A	SNP	AKAP1	NM_003488	human	genbank	57_37b	+1	reviewed	silent	c.852	p.A284	0.001	NULL	HMMPfam_RII_binding_1,HMMSmart_SM00322,superfamily_Eukaryotic type KH-domain (KH-domain type I),HMMPfam_KH_1,HMMPfam_TUDOR,superfamily_Tudor/PWWP/MBT,HMMSmart_SM00333	-	no_errors
BET1L	51272	genome.wustl.edu	37	11	205996	205996	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	11	205996	205996	G	A	SNP	BET1L	NM_001098787	human	genbank	57_37b	-1	validated	nonsense	c.67	p.R23*	1.000	HMMPfam_SNARE	HMMPfam_SNARE	-	no_errors
CHD5	26038	genome.wustl.edu	37	1	6202309	6202309	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	6202309	6202309	G	A	SNP	CHD5	NM_015557	human	genbank	57_37b	-1	provisional	missense	c.2315	p.A772V	1.000	superfamily_SSF52540,HMMSmart_DEXDc,HMMPfam_SNF2_N	PatternScan_CHROMO_1,HMMPfam_CHDNT,superfamily_FYVE_PHD_ZnF,HMMSmart_PHD,HMMPfam_PHD,HMMSmart_RING,superfamily_Chromodomain-like,HMMSmart_CHROMO,superfamily_SSF52540,HMMPfam_Chromo,HMMSmart_DEXDc,HMMPfam_SNF2_N,PatternScan_DEAH_ATP_HELICASE,HMMSmart_HELICc,HMMPfam_Helicase_C,HMMPfam_DUF1087,HMMPfam_DUF1086,HMMPfam_CHDCT2	-	no_errors
CNTN6	27255	genome.wustl.edu	37	3	1414040	1414040	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3	1414040	1414040	T	C	SNP	CNTN6	NM_014461	human	genbank	57_37b	+1	reviewed	missense	c.1550	p.I517T	0.943	superfamily_SSF48726,HMMPfam_I-set,HMMSmart_IGc2	superfamily_SSF48726,HMMPfam_I-set,HMMSmart_IGc2,HMMSmart_IG,superfamily_FN_III-like,HMMSmart_FN3,HMMPfam_fn3	-	no_errors
COL8A1	1295	genome.wustl.edu	37	3	99513227	99513227	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3	99513227	99513227	G	T	SNP	COL8A1	NM_001850	human	genbank	57_37b	+1	reviewed	missense	c.482	p.G161V	1.000	HMMPfam_Collagen	HMMPfam_Collagen,HMMSmart_SM00110,superfamily_TNF-like,HMMPfam_C1q	-	no_errors
DCHS1	8642	genome.wustl.edu	37	11	6645350	6645350	+	Missense_Mutation	SNP	G	G	C	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	11	6645350	6645350	G	C	SNP	DCHS1	NM_003737	human	genbank	57_37b	-1	reviewed	missense	c.7557	p.D2519E	1.000	superfamily_Cadherin,HMMPfam_Cadherin,HMMSmart_CA	superfamily_Cadherin,HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1	-	no_errors
DEF6	50619	genome.wustl.edu	37	6	35289024	35289024	+	Missense_Mutation	SNP	G	G	A	rs9296146	byCluster;byFrequency;by1000genomes	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	6	35289024	35289024	G	A	SNP	DEF6	NM_022047	human	genbank	57_37b	+1	validated	missense	c.1733	p.R578H	0.926	NULL	superfamily_SSF47473,superfamily_SSF50729,HMMPfam_PH,HMMSmart_PH	-	
ENSG00000188447	0	genome.wustl.edu	37	15	74356031	74356031	+	Missense_Mutation	SNP	C	C	A	rs35073501	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	15	74356031	74356031	C	A	SNP	ENSG00000188447	ENST00000339692	human	ensembl	57_37b	+1	known	missense	c.209	p.T70N	1.000	HMMPfam_GED	HMMPfam_GED	-	
ENSG00000238643	0	genome.wustl.edu	37	GL000229.1	17290	17290	+	RNA	SNP	T	C	C	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	GL000229.1	17290	17290	T	C	SNP	ENSG00000238643	ENST00000459109	human	ensembl	57_37b	+1	novel	rna	NULL	NULL	NULL	-	-	-	no_errors
ENSG00000247408	0	genome.wustl.edu	37	15	37385613	37385613	+	RNA	SNP	A	A	G	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	15	37385613	37385613	A	G	SNP	ENSG00000247408	ENST00000501449	human	ensembl	57_37b	+1	known	rna	NULL	NULL	0.028	-	-	-	no_errors
FEM1B	10116	genome.wustl.edu	37	15	68582869	68582869	+	Silent	SNP	T	T	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	15	68582869	68582869	T	A	SNP	FEM1B	NM_015322	human	genbank	57_37b	+1	provisional	silent	c.1173	p.V391	0.986	superfamily_ANK	superfamily_ANK,HMMSmart_ANK,HMMPfam_Ank	-	no_errors
FOXJ2	55810	genome.wustl.edu	37	12	8203193	8203193	+	Missense_Mutation	SNP	A	A	G	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	12	8203193	8203193	A	G	SNP	FOXJ2	NM_018416	human	genbank	57_37b	+1	validated	missense	c.1613	p.D538G	1.000	NULL	"HMMSmart_SM00339,superfamily_""Winged helix"" DNA-binding domain,HMMPfam_Fork_head,PatternScan_FORK_HEAD_2"	-	no_errors
GAA	2548	genome.wustl.edu	37	17	78079665	78079665	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	17	78079665	78079665	G	A	SNP	GAA	NM_000152	human	genbank	57_37b	+1	reviewed	missense	c.664	p.V222M	0.771	NULL	superfamily_P_trefoil,HMMSmart_PD,HMMPfam_Trefoil,PatternScan_P_TREFOIL,HMMPfam_Glyco_hydro_31,superfamily_Glyco_hydro_cat,PatternScan_GLYCOSYL_HYDROL_F31_1,PatternScan_GLYCOSYL_HYDROL_F31_2	-	no_errors
GATA3	2625	genome.wustl.edu	37	10	8111433	8111434	+	Splice_Site	DEL	CA	CA	-	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	CA	CA					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	10	8111433	8111434	CA	-	DEL	GATA3	NM_001002295	human	genbank	57_37b	+1	reviewed	splice_site_del	c.925-3_925-2	e4-2	1.000:1.000	-	-	(deletion:intron[8106102,8111435])	no_errors
GPATCH2	55105	genome.wustl.edu	37	1	217783712	217783712	+	Missense_Mutation	SNP	C	C	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	217783712	217783712	C	A	SNP	GPATCH2	NM_018040	human	genbank	57_37b	-1	provisional	missense	c.1049	p.G350V	1.000	NULL	HMMSmart_SM00443,HMMPfam_G-patch	-	no_errors
HNRNPR	10236	genome.wustl.edu	37	1	23637492	23637492	+	Missense_Mutation	SNP	C	C	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	1	23637492	23637492	C	A	SNP	HNRNPR	NM_001102398	human	genbank	57_37b	-1	reviewed	missense	c.1366	p.G456W	1.000	superfamily_SSF54928	superfamily_SSF54928,HMMSmart_RRM,HMMPfam_RRM_1	-	no_errors
INSIG2	51141	genome.wustl.edu	37	2	118860893	118860893	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	2	118860893	118860893	G	A	SNP	INSIG2	NM_016133	human	genbank	57_37b	+1	reviewed	missense	c.365	p.S122N	1.000	HMMPfam_INSIG	HMMPfam_INSIG	-	no_errors
JAK3	3718	genome.wustl.edu	37	19	17945965	17945965	+	Silent	SNP	C	C	T	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	19	17945965	17945965	C	T	SNP	JAK3	NM_000215	human	genbank	57_37b	-1	reviewed	silent	c.1974	p.E658	0.999	superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220	HMMSmart_SM00295,superfamily_SH2 domain,HMMSmart_SM00252,superfamily_Protein kinase-like (PK-like),HMMPfam_Pkinase_Tyr,HMMSmart_SM00219,HMMSmart_SM00220,PatternScan_THIOL_PROTEASE_HIS,PatternScan_PROTEIN_KINASE_ATP,PatternScan_PROTEIN_KINASE_TYR	-	no_errors
LOC402198	0	genome.wustl.edu	37	5	14960920	14960920	+	Missense_Mutation	SNP	A	A	C	rs706297	byCluster;byFrequency;byHapMap;by1000genomes	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	5	14960920	14960920	A	C	SNP	LOC402198	XM_001716525	human	genbank	57_37b	+1	model	missense	c.771	p.L257F	1.000	NULL	superfamily_PurM C-terminal domain-like,HMMPfam_AIRS_C	-	
LRP1	4035	genome.wustl.edu	37	12	57548459	57548459	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	12	57548459	57548459	G	A	SNP	LRP1	NM_002332	human	genbank	57_37b	+1	reviewed	missense	c.1202	p.R401H	1.000	superfamily_YWTD domain,HMMSmart_SM00135,HMMPfam_Ldl_recept_b	superfamily_LDL receptor-like module,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,HMMSmart_SM00179,superfamily_EGF/Laminin,HMMSmart_SM00181,HMMPfam_EGF,PatternScan_EGF_CA,HMMPfam_EGF_CA,PatternScan_ASX_HYDROXYL,PatternScan_EGF_2,superfamily_YWTD domain,HMMSmart_SM00135,HMMPfam_Ldl_recept_b,PatternScan_EGF_1	-	no_errors
LTBP4	8425	genome.wustl.edu	37	19	41113324	41113324	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	19	41113324	41113324	G	A	SNP	LTBP4	ENST00000308370	human	ensembl	57_37b	+1	known	missense	c.1246	p.G416S	0.988	superfamily_Fibril-assoc,HMMPfam_TB	superfamily_SSF57196,HMMSmart_EGF,HMMPfam_EGF,PatternScan_EGF_1,superfamily_Fibril-assoc,HMMPfam_TB,PatternScan_EGF_CA,HMMPfam_EGF_CA,HMMSmart_EGF_CA,PatternScan_ASX_HYDROXYL,PatternScan_EGF_2,superfamily_Grow_fac_recept	-	no_errors
NCOR1	9611	genome.wustl.edu	37	17	16012215	16012227	+	In_Frame_Del	DEL	TTTTCGTGAAGTC	TTTTCGTGAAGTC	-	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	TTTTCGTGAAGTC	TTTTCGTGAAGTC					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	17	16012215	16012227	TTTTCGTGAAGTC	-	DEL	NCOR1	NM_006311	human	genbank	57_37b	-1	reviewed	in_frame_del	c.2067_2056	p.TSRK686in_frame_del	1.000:1.000:1.000:0.979:1.000:0.996:0.990:1.000:1.000:0.999:0.999:0.952	NULL	superfamily_Homeodomain-like,HMMSmart_SM00717,HMMPfam_Myb_DNA-binding	(deletion:cds_exon[16012100,16012226], intron[16012227,16021201])	no_errors
PYCARD	29108	genome.wustl.edu	37	16	31213061	31213061	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	16	31213061	31213061	G	A	SNP	PYCARD	NM_013258	human	genbank	57_37b	-1	reviewed	nonsense	c.433	p.Q145*	0.973	superfamily_DEATH domain,HMMPfam_CARD	superfamily_DEATH domain,HMMPfam_PAAD_DAPIN,HMMPfam_CARD	-	no_errors
RAB9B	51209	genome.wustl.edu	37	X	103080672	103080672	+	Missense_Mutation	SNP	C	C	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	X	103080672	103080672	C	A	SNP	RAB9B	NM_016370	human	genbank	57_37b	-1	reviewed	missense	c.43	p.D15Y	1.000	superfamily_SSF52540,HMMSmart_RAB,HMMPfam_Ras	superfamily_SSF52540,HMMSmart_RAB,HMMPfam_Ras	-	no_errors
RIMS2	9699	genome.wustl.edu	37	8	104948831	104948831	+	Missense_Mutation	SNP	T	T	G	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	8	104948831	104948831	T	G	SNP	RIMS2	NM_001100117	human	genbank	57_37b	+1	validated	missense	c.2428	p.W810G	1.000	superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMSmart_SM00239,HMMPfam_C2	HMMPfam_RPH3A_effector,superfamily_FYVE/PHD zinc finger,superfamily_PDZ domain-like,HMMSmart_SM00228,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMSmart_SM00239,HMMPfam_C2	-	no_errors
SEPT13	441220	genome.wustl.edu	37	7	45776474	45776474	+	Missense_Mutation	SNP	C	C	T	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	C	C					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	7	45776474	45776474	C	T	SNP	SEPT13	ENST00000417129	human	ensembl	57_37b	-1	known	missense	c.457	p.V153I	1.000	HMMPfam_Septin	superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMPfam_Septin	-	no_errors
USP36	57602	genome.wustl.edu	37	17	76803588	76803588	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	G	G					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	17	76803588	76803588	G	A	SNP	USP36	NM_025090	human	genbank	57_37b	-1	validated	missense	c.1538	p.S513F	0.871	NULL	superfamily_SSF54001,HMMPfam_UCH,PatternScan_UCH_2_1,PatternScan_UCH_2_2,PatternScan_IG_MHC	-	no_errors
VAV2	7410	genome.wustl.edu	37	9	136634607	136634607	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	T	T					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	9	136634607	136634607	T	C	SNP	VAV2	NM_001134398	human	genbank	57_37b	-1	reviewed	missense	c.2366	p.N789S	1.000	superfamily_SH2 domain,superfamily_SH3-domain	HMMPfam_CH,superfamily_Calponin-homology domain CH-domain,HMMSmart_SM00033,superfamily_DBL homology domain (DH-domain),HMMPfam_RhoGEF,HMMSmart_SM00325,PatternScan_DH_1,superfamily_PH domain-like,HMMPfam_PH,HMMSmart_SM00233,HMMSmart_SM00109,PatternScan_ZF_DAG_PE_1,superfamily_Cysteine-rich domain,HMMPfam_C1_1,superfamily_SH3-domain,HMMSmart_SM00326,HMMPfam_SH3_2,superfamily_SH2 domain,HMMSmart_SM00252,HMMPfam_SH2,HMMPfam_SH3_1	-	no_errors
VGLL4	9686	genome.wustl.edu	37	3	11684952	11684952	+	Nonsense_Mutation	SNP	A	A	T	novel	unknown	TCGA-E2-A15J-01A-11D-A12Q-09	TCGA-E2-A15J-10A-01D-A12Q-09	A	A					Unknown	Unknown	Somatic	Phase_IV	Capture		1	dbGAP	Illumina GAIIx	3	11684952	11684952	A	T	SNP	VGLL4	NM_001128219	human	genbank	57_37b	-1	validated	nonsense	c.41	p.L14*	1.000	NULL	HMMSmart_SM00711	-	no_errors
