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	title	header	normal_ref_reads	normal_var_reads	normal_VAF	tumor_ref_reads	tumor_var_reads	tumor_VAF
PAPPA2	0	genome.wustl.edu	37	1	176659380	176659380	+	Missense_Mutation	SNP	A	A	G			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	1	176659380	176659380	A	G	SNP	PAPPA2	ENST00000367662	human	ensembl	74_37	+1	known	missense	c.2245	p.S749G	1.000	pfam_Peptidase_M43	pfam_Notch_dom,pfam_Sushi_SCR_CCP,pfam_Peptidase_M43,superfamily_ConA-like_lec_gl_sf,superfamily_Sushi_SCR_CCP,superfamily_Fibronectin_type3,superfamily_Notch_dom,smart_LamG-like,smart_Notch_dom,smart_Sushi_SCR_CCP,pfscan_Sushi_SCR_CCP,tigrfam_Myxo_disulph_rpt	-	no_errors	PAPPA2	HGNC	ENSG00000116183				165	0	0	120	52	30.2326
UBR4	0	genome.wustl.edu	37	1	19513771	19513771	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	1	19513771	19513771	C	A	SNP	UBR4	ENST00000375267	human	ensembl	74_37	-1	known	missense	c.1519	p.A507S	1.000	NULL	superfamily_WD40_repeat_dom,superfamily_ARM-type_fold,smart_Znf_N-recognin_met,pfscan_Znf_N-recognin	-	no_errors	UBR4	HGNC	ENSG00000127481				60	0	0	56	22	28.2051
SH2D5	0	genome.wustl.edu	37	1	21048371	21048371	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	1	21048371	21048371	C	T	SNP	SH2D5	ENST00000444387	human	ensembl	74_37	-1	known	missense	c.1186	p.D396N	1.000	NULL	pfam_PTB/PI_dom,smart_PTB/PI_dom,pfscan_PTB/PI_dom,pfscan_SH2	-	no_errors	SH2D5	HGNC	ENSG00000189410				38	0	0	27	15	35.7143
OXCT2	0	genome.wustl.edu	37	1	40235448	40235448	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	1	40235448	40235448	C	T	SNP	OXCT2	ENST00000327582	human	ensembl	74_37	-1	known	missense	c.1480	p.D494N	0.171	pfam_CoA_trans_fam_I,smart_CoA_trans_fam_I,pirsf_3-oxoacid_CoA-transferase,tigrfam_3-oxoacid_CoA-transf_B	pfam_CoA_trans_fam_I,smart_CoA_trans_fam_I,pirsf_3-oxoacid_CoA-transferase,tigrfam_3-oxoacid_CoA-transf_B,tigrfam_3-oxoacid_CoA-transf_A	-	no_errors	OXCT2	HGNC	ENSG00000198754				43	0	0	41	5	10.8696
CAMTA1	0	genome.wustl.edu	37	1	7812581	7812581	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	1	7812581	7812581	G	A	SNP	CAMTA1	ENST00000303635	human	ensembl	74_37	+1	known	missense	c.4946	p.R1649H	1.000	NULL	pfam_CG-1_dom,pfam_IPT,pfam_IQ_motif_EF-hand-BS,superfamily_Ig_E-set,superfamily_Ankyrin_rpt-contain_dom,superfamily_P-loop_NTPase,pfscan_Ankyrin_rpt,pfscan_Ankyrin_rpt-contain_dom,pfscan_IQ_motif_EF-hand-BS	-	no_errors	CAMTA1	HGNC	ENSG00000171735				32	0	0	33	2	5.71429
ENSG00000233547	0	genome.wustl.edu	37	10	114710732	114710732	+	RNA	SNP	G	G	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	10	114710732	114710732	G	T	SNP	ENSG00000233547	ENST00000369391	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.001	-	-	-	no_errors	RP11-57H14.2	Clone_based_vega_gene	ENSG00000233547				13	0	0	20	6	23.0769
VPS11	0	genome.wustl.edu	37	11	118944008	118944008	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	11	118944008	118944008	G	T	SNP	VPS11	ENST00000300793	human	ensembl	74_37	+1	known	missense	c.982	p.D328Y	1.000	superfamily_WD40_repeat_dom,pirsf_VPS11	pfam_VPS11_C,pfam_Clathrin_H-chain/VPS_repeat,superfamily_WD40_repeat_dom,superfamily_ARM-type_fold,smart_Znf_RING,pirsf_VPS11,pfscan_Znf_RING	-	no_errors	VPS11	HGNC	ENSG00000160695				34	0	0	28	14	33.3333
NELL1	0	genome.wustl.edu	37	11	21596581	21596581	+	RNA	SNP	G	G	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	11	21596581	21596581	G	T	SNP	NELL1	ENST00000529218	human	ensembl	74_37	+1	known	rna	NULL	NULL	1.000	-	-	-	no_errors	NELL1	HGNC	ENSG00000165973				46	0	0	30	3	9.09091
KLRAP1	0	genome.wustl.edu	37	12	10748442	10748442	+	RNA	SNP	T	T	C			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	12	10748442	10748442	T	C	SNP	KLRAP1	ENST00000535939	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.019	-	-	-	no_errors	KLRAP1	HGNC	ENSG00000256667				30	0	0	37	10	21.2766
PTPN11	0	genome.wustl.edu	37	12	112892407	112892407	+	Missense_Mutation	SNP	T	T	G			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	12	112892407	112892407	T	G	SNP	PTPN11	ENST00000351677	human	ensembl	74_37	+1	known	missense	c.565	p.S189A	1.000	pfam_SH2,smart_SH2,pirsf_Tyr_Pase_non-rcpt_typ-6/11,pfscan_SH2,prints_SH2	pfam_Tyr_Pase_rcpt/non-rcpt,pfam_SH2,smart_SH2,smart_Tyr_Pase_rcpt/non-rcpt,smart_Tyr_Pase_cat,pirsf_Tyr_Pase_non-rcpt_typ-6/11,pfscan_SH2,pfscan_Tyr/Dual-sp_Pase,pfscan_Tyr_Pase_rcpt/non-rcpt,prints_Tyr_Pase_rcpt/non-rcpt,prints_SH2	-	no_errors	PTPN11	HGNC	ENSG00000179295				46	0	0	52	4	7.14286
OAS1	0	genome.wustl.edu	37	12	113355547	113355547	+	Silent	SNP	T	T	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	12	113355547	113355547	T	A	SNP	OAS1	ENST00000452357	human	ensembl	74_37	+1	known	silent	c.1080	p.P360	0.000	NULL	pfam_2-5-oligoAdlate_synth_1_dom2/C,pfam_Nucleotidyltransferase,pfscan_2-5-oligoadenylate_synth_N	-	no_errors	OAS1	HGNC	ENSG00000089127				89	0	0	45	26	36.6197
DDX11	0	genome.wustl.edu	37	12	31237978	31237978	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	12	31237978	31237978	C	T	SNP	DDX11	ENST00000407793	human	ensembl	74_37	+1	known	missense	c.556	p.R186W	0.002	superfamily_P-loop_NTPase,smart_Helicase-like_DEXD_c2,pfscan_Helic_SF1/SF2_ATP-bd_DinG/Rad3	pfam_DEAD_2,superfamily_P-loop_NTPase,smart_Helicase-like_DEXD_c2,smart_ATP-dep_Helicase_C,pfscan_Helic_SF1/SF2_ATP-bd_DinG/Rad3,tigrfam_DNA_helicase_DNA-repair_Rad3	-	no_errors	DDX11	HGNC	ENSG00000013573				16	0	0	25	4	13.7931
ARID2	0	genome.wustl.edu	37	12	46245720	46245720	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	12	46245720	46245720	C	T	SNP	ARID2	ENST00000334344	human	ensembl	74_37	+1	known	nonsense	c.3814	p.R1272*	1.000	NULL	pfam_ARID/BRIGHT_DNA-bd,pfam_DNA-bd_RFX,superfamily_ARID/BRIGHT_DNA-bd,superfamily_ARM-type_fold,smart_ARID/BRIGHT_DNA-bd,pfscan_ARID/BRIGHT_DNA-bd	-	no_errors	ARID2	HGNC	ENSG00000189079				51	0	0	20	21	51.2195
XRCC3	0	genome.wustl.edu	37	14	104165276	104165276	+	Silent	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	14	104165276	104165276	C	T	SNP	XRCC3	ENST00000352127	human	ensembl	74_37	-1	known	silent	c.900	p.R300	0.004	pfam_DNA_recomb/repair_Rad51_C,superfamily_P-loop_NTPase,pirsf_DNA_recomb/repair_RecA-like	pfam_DNA_recomb/repair_Rad51_C,superfamily_P-loop_NTPase,pirsf_DNA_recomb/repair_RecA-like,pfscan_DNA_recomb_RecA/RadB_ATP-bd	-	no_errors	XRCC3	HGNC	ENSG00000126215				10	0	0	8	6	42.8571
TEP1	0	genome.wustl.edu	37	14	20849537	20849537	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	14	20849537	20849537	C	T	SNP	TEP1	ENST00000262715	human	ensembl	74_37	-1	known	missense	c.4582	p.A1528T	1.000	NULL	pfam_TROVE,pfam_TEP1_N,pfam_WD40_repeat,superfamily_WD40_repeat_dom,superfamily_P-loop_NTPase,smart_WD40_repeat,pfscan_NACHT_NTPase,pfscan_TROVE,pfscan_WD40_repeat,pfscan_WD40_repeat_dom	-	no_errors	TEP1	HGNC	ENSG00000129566				188	0	0	132	54	29.0323
ZNF592	0	genome.wustl.edu	37	15	85327029	85327029	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	15	85327029	85327029	G	A	SNP	ZNF592	ENST00000299927	human	ensembl	74_37	+1	known	missense	c.1123	p.V375M	1.000	NULL	smart_Znf_C2H2-like,pfscan_Znf_C2H2	-	no_errors	ZNF592	HGNC	ENSG00000166716				79	0	0	51	20	28.169
CHST6	0	genome.wustl.edu	37	16	75513350	75513350	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	16	75513350	75513350	C	A	SNP	CHST6	ENST00000332272	human	ensembl	74_37	-1	known	missense	c.377	p.S126I	1.000	pfam_Sulfotransferase_dom,superfamily_P-loop_NTPase,pirsf_Carbohydrate_sulfotransferase	pfam_Sulfotransferase_dom,superfamily_P-loop_NTPase,pirsf_Carbohydrate_sulfotransferase	-	no_errors	CHST6	HGNC	ENSG00000183196				89	0	0	59	23	28.0488
KIAA0513	0	genome.wustl.edu	37	16	85120758	85120758	+	Missense_Mutation	SNP	G	G	C			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	16	85120758	85120758	G	C	SNP	KIAA0513	ENST00000258180	human	ensembl	74_37	+1	known	missense	c.1172	p.G391A	1.000	NULL	pfam_SBF2	-	no_errors	KIAA0513	HGNC	ENSG00000135709				61	0	0	40	10	20
SLC13A2	0	genome.wustl.edu	37	17	26823469	26823469	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	17	26823469	26823469	C	A	SNP	SLC13A2	ENST00000444914	human	ensembl	74_37	+1	known	missense	c.1619	p.A540D	1.000	pfam_Na/sul_symport,pfam_Cit_transptr-like_dom	pfam_Na/sul_symport,pfam_Cit_transptr-like_dom	-	no_errors	SLC13A2	HGNC	ENSG00000007216				229	0	0	148	51	25.6281
CCDC40	0	genome.wustl.edu	37	17	78013901	78013901	+	Silent	SNP	A	A	G			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	17	78013901	78013901	A	G	SNP	CCDC40	ENST00000397545	human	ensembl	74_37	+1	known	silent	c.384	p.A128	0.000	NULL	pfam_E3_ubiquit_lig_BRE1	-	no_errors	CCDC40	HGNC	ENSG00000141519				80	0	0	80	7	8.04598
COLEC12	0	genome.wustl.edu	37	18	331713	331713	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	18	331713	331713	C	T	SNP	COLEC12	ENST00000400256	human	ensembl	74_37	-1	known	missense	c.2018	p.R673H	0.002	pfam_C-type_lectin,superfamily_C-type_lectin_fold,smart_C-type_lectin,prints_AntifreezeII,pfscan_C-type_lectin	pfam_C-type_lectin,pfam_Collagen,superfamily_C-type_lectin_fold,smart_C-type_lectin,prints_AntifreezeII,pfscan_C-type_lectin	-	no_errors	COLEC12	HGNC	ENSG00000158270				47	0	0	47	16	25.3968
SMAD4	0	genome.wustl.edu	37	18	48593406	48593406	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	18	48593406	48593406	G	A	SNP	SMAD4	ENST00000342988	human	ensembl	74_37	+1	known	missense	c.1157	p.G386D	1.000	pfam_SMAD_dom_Dwarfin-type,superfamily_SMAD_FHA_domain,smart_SMAD_dom_Dwarfin-type,pfscan_SMAD_dom_Dwarfin-type	pfam_SMAD_dom_Dwarfin-type,pfam_MAD_homology1_Dwarfin-type,superfamily_SMAD_FHA_domain,superfamily_MAD_homology_MH1,smart_MAD_homology1_Dwarfin-type,smart_SMAD_dom_Dwarfin-type,pfscan_MAD_homology_MH1,pfscan_SMAD_dom_Dwarfin-type	-	no_errors	SMAD4	HGNC	ENSG00000141646				128	0	0	41	35	46.0526
SALL3	0	genome.wustl.edu	37	18	76753965	76753965	+	Silent	SNP	G	G	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	18	76753965	76753965	G	A	SNP	SALL3	ENST00000537592	human	ensembl	74_37	+1	known	silent	c.1974	p.T658	0.943	NULL	pfam_Znf_C2H2,smart_Znf_C2H2-like,pfscan_Znf_C2H2	-	no_errors	SALL3	HGNC	ENSG00000256463				17	0	0	4	5	55.5556
STK11	0	genome.wustl.edu	37	19	1221993	1221993	+	Missense_Mutation	SNP	T	T	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	19	1221993	1221993	T	A	SNP	STK11	ENST00000326873	human	ensembl	74_37	+1	known	missense	c.908	p.I303N	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	STK11	HGNC	ENSG00000118046				11	0	0	5	3	37.5
RBM42	0	genome.wustl.edu	37	19	36120513	36120513	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	19	36120513	36120513	G	T	SNP	RBM42	ENST00000262633	human	ensembl	74_37	+1	known	missense	c.220	p.A74S	0.957	NULL	pfam_RRM_dom,smart_RRM_dom,pfscan_RRM_dom	-	no_errors	RBM42	HGNC	ENSG00000126254				125	0	0	87	25	22.3214
MUC16	0	genome.wustl.edu	37	19	9089662	9089662	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	19	9089662	9089662	G	T	SNP	MUC16	ENST00000397910	human	ensembl	74_37	-1	known	missense	c.2153	p.T718N	0.000	NULL	pfam_SEA_dom,smart_SEA_dom,pfscan_SEA_dom	-	no_errors	MUC16	HGNC	ENSG00000181143				72	0	0	53	24	31.1688
MZT2A	0	genome.wustl.edu	37	2	132249846	132249846	+	Missense_Mutation	SNP	G	G	C			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	2	132249846	132249846	G	C	SNP	MZT2A	ENST00000309451	human	ensembl	74_37	-1	known	missense	c.104	p.T35S	1.000	NULL	NULL	-	no_errors	MZT2A	HGNC	ENSG00000173272				9	0	0	8	6	42.8571
MMADHC	0	genome.wustl.edu	37	2	150426628	150426628	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	2	150426628	150426628	G	A	SNP	MMADHC	ENST00000303319	human	ensembl	74_37	-1	known	missense	c.751	p.H251Y	0.999	pfam_MMADHC	pfam_MMADHC	-	no_errors	MMADHC	HGNC	ENSG00000168288				52	0	0	34	37	52.1127
TTN	0	genome.wustl.edu	37	2	179452394	179452394	+	Silent	SNP	A	A	G			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	2	179452394	179452394	A	G	SNP	TTN	ENST00000342992	human	ensembl	74_37	-1	known	silent	c.55938	p.D18646	1.000	pfam_Ig_I-set,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,pfscan_Ig-like_dom	pfam_Ig_I-set,pfam_Fibronectin_type3,pfam_Immunoglobulin,pfam_Ig_V-set,pfam_Titin_Z,pfam_PPAK_motif,pfam_Prot_kinase_dom,pfam_Ser-Thr/Tyr_kinase_cat_dom,superfamily_Kinase-like_dom,superfamily_Fibronectin_type3,superfamily_Calpain_domain_III,superfamily_RNaseH-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Fibronectin_type3,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_Fibronectin_type3,pfscan_Prot_kinase_dom,pfscan_Ig-like_dom	-	no_errors	TTN	HGNC	ENSG00000155657				38	0	0	32	12	27.2727
DNAJC5G	0	genome.wustl.edu	37	2	27499657	27499657	+	Missense_Mutation	SNP	G	G	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	2	27499657	27499657	G	A	SNP	DNAJC5G	ENST00000296097	human	ensembl	74_37	+1	known	missense	c.61	p.V21M	1.000	superfamily_DnaJ_domain,smart_DnaJ_domain,pfscan_DnaJ_domain,prints_DnaJ_domain	pfam_DnaJ_domain,superfamily_DnaJ_domain,smart_DnaJ_domain,pfscan_DnaJ_domain,prints_DnaJ_domain	-	no_errors	DNAJC5G	HGNC	ENSG00000163793				98	0	0	59	14	19.1781
ENSG00000161103	0	genome.wustl.edu	37	22	18844763	18844763	+	RNA	SNP	T	T	C			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	22	18844763	18844763	T	C	SNP	ENSG00000161103	ENST00000412938	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.006	-	-	-	no_errors	AC008132.13	Clone_based_vega_gene	ENSG00000161103				15	0	0	15	3	16.6667
KIAA1524	0	genome.wustl.edu	37	3	108298210	108298210	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	3	108298210	108298210	C	T	SNP	KIAA1524	ENST00000295746	human	ensembl	74_37	-1	known	missense	c.736	p.D246N	1.000	superfamily_ARM-type_fold	superfamily_ARM-type_fold	-	no_errors	KIAA1524	HGNC	ENSG00000163507				114	0	0	116	32	21.6216
ATR	0	genome.wustl.edu	37	3	142268402	142268402	+	Silent	SNP	T	T	G			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	3	142268402	142268402	T	G	SNP	ATR	ENST00000350721	human	ensembl	74_37	-1	known	silent	c.3090	p.I1030	1.000	superfamily_ARM-type_fold	pfam_PI3/4_kinase_cat_dom,pfam_PIK-rel_kinase_FAT,pfam_UME,pfam_FATC,superfamily_Kinase-like_dom,superfamily_ARM-type_fold,smart_UME,smart_PI3/4_kinase_cat_dom,pfscan_PIK_FAT,pfscan_FATC,pfscan_HEAT_type_2,pfscan_PI3/4_kinase_cat_dom	-	no_errors	ATR	HGNC	ENSG00000175054				32	0	0	32	3	8.57143
HYAL2	0	genome.wustl.edu	37	3	50357457	50357457	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	3	50357457	50357457	G	T	SNP	HYAL2	ENST00000357750	human	ensembl	74_37	-1	known	nonsense	c.464	p.S155*	1.000	pfam_Hyaluronidase,superfamily_Glycoside_hydrolase_SF,pirsf_Hyaluronidase	pfam_Hyaluronidase,superfamily_Glycoside_hydrolase_SF,pirsf_Hyaluronidase,prints_Hyaluronidase	-	no_errors	HYAL2	HGNC	ENSG00000068001				166	0	0	110	47	29.9363
FYN	0	genome.wustl.edu	37	6	112035642	112035642	+	Silent	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	6	112035642	112035642	C	T	SNP	FYN	ENST00000354650	human	ensembl	74_37	-1	known	silent	c.252	p.V84	0.998	superfamily_SH3_domain,pfscan_SH3_domain	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_dom,pfam_SH2,pfam_SH3_domain,pfam_SH3_2,superfamily_Kinase-like_dom,superfamily_SH3_domain,smart_SH3_domain,smart_SH2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_SH2,pfscan_SH3_domain,pfscan_Prot_kinase_dom,prints_Ser-Thr/Tyr_kinase_cat_dom,prints_SH2,prints_SH3_domain	-	no_errors	FYN	HGNC	ENSG00000010810				53	0	0	50	15	23.0769
FAM65B	0	genome.wustl.edu	37	6	24861261	24861261	+	Missense_Mutation	SNP	T	T	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	6	24861261	24861261	T	A	SNP	FAM65B	ENST00000259698	human	ensembl	74_37	-1	known	missense	c.568	p.M190L	0.999	NULL	superfamily_ARM-type_fold	-	no_errors	FAM65B	HGNC	ENSG00000111913				26	0	0	13	14	51.8519
FAM131B	0	genome.wustl.edu	37	7	143056064	143056064	+	Missense_Mutation	SNP	C	C	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	7	143056064	143056064	C	T	SNP	FAM131B	ENST00000443739	human	ensembl	74_37	-1	known	missense	c.322	p.G108S	1.000	NULL	NULL	-	no_errors	FAM131B	HGNC	ENSG00000159784				38	0	0	28	9	24.3243
PCLO	0	genome.wustl.edu	37	7	82784907	82784907	+	Silent	SNP	T	T	C			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	7	82784907	82784907	T	C	SNP	PCLO	ENST00000333891	human	ensembl	74_37	-1	known	silent	c.1050	p.K350	0.000	NULL	pfam_Znf_piccolo,pfam_C2_dom,pfam_PDZ,superfamily_C2_dom,superfamily_PDZ,superfamily_Znf_FYVE_PHD,smart_PDZ,smart_C2_dom,pfscan_C2_dom,pfscan_PDZ	-	no_errors	PCLO	HGNC	ENSG00000186472				31	0	0	19	13	40.625
AZGP1P1	0	genome.wustl.edu	37	7	99580937	99580937	+	RNA	SNP	T	T	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	7	99580937	99580937	T	A	SNP	AZGP1P1	ENST00000425474	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.984	-	-	-	no_errors	AZGP1P1	HGNC	ENSG00000214313				29	0	0	19	5	20.8333
OR13D1	0	genome.wustl.edu	37	9	107457321	107457321	+	Missense_Mutation	SNP	G	G	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	9	107457321	107457321	G	T	SNP	OR13D1	ENST00000318763	human	ensembl	74_37	+1	known	missense	c.619	p.D207Y	0.455	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM	pfam_GPCR_Rhodpsn,pfscan_GPCR_Rhodpsn_7TM,prints_Olfact_rcpt,prints_GPCR_Rhodpsn	-	no_errors	OR13D1	HGNC	ENSG00000179055				174	0	0	107	40	27.2109
SPTAN1	0	genome.wustl.edu	37	9	131329027	131329027	+	Missense_Mutation	SNP	C	C	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	9	131329027	131329027	C	A	SNP	SPTAN1	ENST00000358161	human	ensembl	74_37	+1	known	missense	c.8	p.P3Q	1.000	NULL	pfam_Spectrin_repeat,pfam_EF-hand_Ca_insen,pfam_SH3_domain,pfam_EF_hand_dom,pfam_SH3_2,superfamily_SH3_domain,smart_Spectrin/alpha-actinin,smart_SH3_domain,smart_EF_hand_dom,pfscan_EF_hand_dom,pfscan_SH3_domain,prints_Spectrin_alpha_SH3,prints_SH3_domain	-	no_errors	SPTAN1	HGNC	ENSG00000197694				115	0	0	77	43	35.8333
MAMDC2	0	genome.wustl.edu	37	9	72758553	72758553	+	Silent	SNP	T	T	C			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	9	72758553	72758553	T	C	SNP	MAMDC2	ENST00000377182	human	ensembl	74_37	+1	known	silent	c.1222	p.L408	0.768	pfam_MAM_dom,superfamily_ConA-like_lec_gl_sf,smart_MAM_dom,pfscan_MAM_dom	pfam_MAM_dom,superfamily_ConA-like_lec_gl_sf,smart_MAM_dom,pfscan_MAM_dom,prints_MAM_dom	-	no_errors	MAMDC2	HGNC	ENSG00000165072				86	0	0	66	32	32.6531
KIF27	0	genome.wustl.edu	37	9	86514643	86514643	+	Missense_Mutation	SNP	A	A	C			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	9	86514643	86514643	A	C	SNP	KIF27	ENST00000297814	human	ensembl	74_37	-1	known	missense	c.1535	p.M512R	0.525	NULL	pfam_Kinesin_motor_dom,superfamily_P-loop_NTPase,smart_Kinesin_motor_dom,pfscan_Kinesin_motor_dom,prints_Kinesin_motor_dom	-	no_errors	KIF27	HGNC	ENSG00000165115				92	0	0	83	16	16.1616
USP51	0	genome.wustl.edu	37	X	55513296	55513296	+	Silent	SNP	A	A	G			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	X	55513296	55513296	A	G	SNP	USP51	ENST00000500968	human	ensembl	74_37	-1	known	silent	c.2077	p.L693	1.000	pfam_Peptidase_C19/C67,pfscan_Peptidase_C19/C67	pfam_Peptidase_C19/C67,pfam_Znf_UBP,pfscan_Znf_UBP,pfscan_Peptidase_C19/C67	-	no_errors	USP51	HGNC	ENSG00000247746				61	0	0	38	17	30.9091
MIR620	0	genome.wustl.edu	37	12	116586415	116586418	+	RNA	DEL	TATA	TATA	-			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	TATA	TATA					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	12	116586415	116586418	TATA	-	DEL	MIR620	ENST00000385232	human	ensembl	74_37	-1	known	rna	NULL	NULL	0.000:0.000:0.000:0.000	-	-	-	no_errors	MIR620	HGNC	ENSG00000207967				9	0	0	0	5	100
TTLL5	0	genome.wustl.edu	37	14	76420882	76420882	+	RNA	DEL	T	T	-			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	14	76420882	76420882	T	-	DEL	TTLL5	ENST00000554972	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.005	-	-	-	no_errors	TTLL5	HGNC	ENSG00000119685				34	0	0	15	4	21.0526
LOC100130950	0	genome.wustl.edu	37	17	5126838	5126839	+	RNA	INS	-	-	T			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	17	5126838	5126839	-	T	INS	LOC100130950	ENST00000575601	human	ensembl	74_37	+1	known	rna	NULL	NULL	0.000:0.000	-	-	-	no_errors	RP11-333E1.1	Clone_based_vega_gene	ENSG00000261879				25	0	0	23	4	14.8148
SLC22A3	0	genome.wustl.edu	37	6	160829854	160829855	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	6	160829854	160829855	-	A	INS	SLC22A3	ENST00000392145	human	ensembl	74_37	+1	known	frame_shift_ins	c.758_759	p.I254fs	0.924:0.960	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom,tigrfam_Orgcat_transp	pfam_Sub_transporter,pfam_MFS,superfamily_MFS_dom_general_subst_transpt,pfscan_MFS_dom,tigrfam_Orgcat_transp	-	no_errors	SLC22A3	HGNC	ENSG00000146477				92	0	0	54	23	29.8701
CLIP2	0	genome.wustl.edu	37	7	73790499	73790500	+	In_Frame_Ins	INS	-	-	AGG			TCGA-BR-A4J6-01A-11D-A25D-08	TCGA-BR-A4J6-10A-01D-A25E-08	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none			Illumina HiSeq	cdf42f08-5348-4fdf-916f-690fa42dbf1a	d60221e2-c5fc-4d88-aa85-5b46712ce4c8	7	73790499	73790500	-	AGG	INS	CLIP2	ENST00000223398	human	ensembl	74_37	+1	known	in_frame_ins	c.1768_1769	p.592in_frame_insE	0.989:0.999	superfamily_t-SNARE	pfam_CAP-Gly_domain,superfamily_CAP-Gly_domain,superfamily_t-SNARE,pfscan_CAP-Gly_domain	-	no_errors	CLIP2	HGNC	ENSG00000106665				63	0	0	27	8	22.8571
