Normal	Chrom	Pos	Ref	Alt	Gene	Transcript	RNA	CDS	Protein	Type	Effect	CancerGene	Description	DRIVER_CATEGORY	Age	pCR_vs_RD	PreTxTumorSizeClinOrRad	Tumor_size_surgery(cm)	Grade	group	Ki67_biopsy	NumPosLn	ANTHRACYCLINE	TAXANE	geneRef	DEPTH_PD13595a	TUM_PILEUP_MUTS_PD13595a	Pileup_MtAlpct_PD13595a	ID.2	DEPTH_PD13595c	TUM_PILEUP_MUTS_PD13595c	Pileup_MtAlpct_PD13595c	ID.3	DEPTH_PD13595d	TUM_PILEUP_MUTS_PD13595d	Pileup_MtAlpct_PD13595d	ID.4	DEPTH_PD13595e	TUM_PILEUP_MUTS_PD13595e	Pileup_MtAlpct_PD13595e	ID.5	DEPTH_PD13595f	TUM_PILEUP_MUTS_PD13595f	Pileup_MtAlpct_PD13595f	ID.6	DEPTH_PD13595g	TUM_PILEUP_MUTS_PD13595g	Pileup_MtAlpct_PD13595g	ID.7	DEPTH_PD13595h	TUM_PILEUP_MUTS_PD13595h	Pileup_MtAlpct_PD13595h	ID.8	DEPTH_PD13595i	TUM_PILEUP_MUTS_PD13595i	Pileup_MtAlpct_PD13595i
PD13595b	14	71200025	C	G	MAP3K9	CCDS32112.1	r.2103g>c	c.2103G>C	p.E701D	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	90	pS	3	3	3	3	47	11	YES	YES	MAP3K9:p.E701D	111	0	0	14:71200025	85	0	0	14:71200025	79	0	0	14:71200025	121	0	0	14:71200025	123	8	6.5	14:71200025	102	0	0	14:71200025	78	0	0	14:71200025	102	0	0
PD13595b	3	89480379	A	T	EPHA3	CCDS2922.1	r.2441a>u	c.2216A>T	p.D739V	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	90	pS	3	3	3	3	47	11	YES	YES	EPHA3:p.D739V	75	11	14.7	3:89480379	54	33	61.1	3:89480379	105	38	36.2	3:89480379	82	33	40.2	3:89480379	108	51	47.2	3:89480379	72	10	13.9	3:89480379	66	22	33.3	3:89480379	95	43	45.3
PD13595b	3	78656097	T	C	ROBO1	CCDS46872.1	r.5376a>g	c.4413A>G	p.K1471K	Sub	silent	3	SILENT	SILENT	90	pS	3	3	3	3	47	11	YES	YES	ROBO1:p.K1471K	128	0	0	3:78656097	105	16	15.2	3:78656097	198	1	0.5	3:78656097	149	36	24.2	3:78656097	183	0	0	3:78656097	143	0	0	3:78656097	155	0	0	3:78656097	190	0	0
PD13595b	19	4102410	C	T	MAP2K2	CCDS12120.1	r.746g>a	c.492G>A	p.R164R	Sub	silent	3	SILENT	SILENT	90	pS	3	3	3	3	47	11	YES	YES	MAP2K2:p.R164R	139	0	0	19:4102410	157	9	5.7	19:4102410	72	0	0	19:4102410	188	0	0	19:4102410	148	0	0	19:4102410	169	0	0	19:4102410	92	0	0	19:4102410	96	1	1
PD13595b	3	10105543	A	G	FANCD2	CCDS2595.1	r.1988a>g	c.1895A>G	p.Y632C	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	90	pS	3	3	3	3	47	11	YES	YES	FANCD2:p.Y632C	77	12	15.6	3:10105543	66	24	36.4	3:10105543	98	27	27.6	3:10105543	68	22	32.4	3:10105543	93	37	39.8	3:10105543	73	15	20.5	3:10105543	91	32	35.2	3:10105543	100	25	25
PD13595b	12	49436902	A	C	MLL2	CCDS44873.1	r.5601u>g	c.5601T>G	p.G1867G	Sub	silent	1	SILENT	SILENT	90	pS	3	3	3	3	47	11	YES	YES	MLL2:p.G1867G	52	9	17.3	12:49436902	32	11	34.4	12:49436902	31	8	25.8	12:49436902	48	10	20.8	12:49436902	47	10	21.3	12:49436902	46	2	4.3	12:49436902	47	10	21.3	12:49436902	40	4	10
PD13595b	13	32913381	C	G	BRCA2	CCDS9344.1	r.5122c>g	c.4889C>G	p.S1630*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	90	pS	3	3	3	3	47	11	YES	YES	BRCA2:p.S1630*	72	0	0	13:32913381	62	0	0	13:32913381	121	0	0	13:32913381	37	0	0	13:32913381	22	4	18.2	13:32913381	95	1	1.1	13:32913381	69	0	0	13:32913381	135	0	0
PD13595b	17	7579366	G	T	TP53	CCDS11118.1	r.511c>a	c.321C>A	p.Y107*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	90	pS	3	3	3	3	47	11	YES	YES	TP53:p.Y107*	56	11	19.6	17:7579366	49	35	71.4	17:7579366	36	15	41.7	17:7579366	75	52	69.3	17:7579366	51	21	41.2	17:7579366	56	19	33.9	17:7579366	40	17	42.5	17:7579366	39	24	61.5