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_PD14768a	TUM_PILEUP_MUTS_PD14768a	Pileup_MtAlpct_PD14768a	ID.2	DEPTH_PD14768c	TUM_PILEUP_MUTS_PD14768c	Pileup_MtAlpct_PD14768c	ID.3	DEPTH_PD14768d	TUM_PILEUP_MUTS_PD14768d	Pileup_MtAlpct_PD14768d	ID.4	DEPTH_PD14768e	TUM_PILEUP_MUTS_PD14768e	Pileup_MtAlpct_PD14768e
PD14768b	3	178947901	G	A	PIK3CA	CCDS43171.1	r.2933g>a	c.2776G>A	p.D926N	Sub	missense	1	UNKNOWN_EFFECT_BCA_GENE	UNKNOWN	67	RD	5.5	1.4	3	1	50	0	YES	YES	PIK3CA:p.D926N	178	7	3.9	3:178947901	216	22	10.2	3:178947901	225	0	0	3:178947901	96	0	0
PD14768b	17	7578530	A	T	TP53	CCDS11118.1	r.590u>a	c.400T>A	p.F134I	Sub	missense	1	ONCOGENIC_BCA_GENE	ONCOGENIC	67	RD	5.5	1.4	3	1	50	0	YES	YES	TP53:p.F134I	160	19	11.9	17:7578530	296	93	31.4	17:7578530	179	79	44.1	17:7578530	63	3	4.8
PD14768b	17	19286543	G	T	MAPK7	CCDS11206.1	r.2836g>u	c.2450G>T	p.*817L	Sub	stop-lost	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	67	RD	5.5	1.4	3	1	50	0	YES	YES	MAPK7:p.*817L	109	13	11.9	17:19286543	180	48	26.7	17:19286543	133	60	45.1	17:19286543	57	6	10.5
PD14768b	6	41566627	G	A	FOXP4	CCDS34447.1	r.2454g>a	c.1996G>A	p.E666K	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	67	RD	5.5	1.4	3	1	50	0	YES	YES	FOXP4:p.E666K	84	4	4.8	6:41566627	202	28	13.9	6:41566627	121	23	19	6:41566627	14	0	0
PD14768b	9	98211508	C	G	PTCH1	CCDS6714.1	r.3835g>c	c.3647G>C	p.S1216T	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	67	RD	5.5	1.4	3	1	50	0	YES	YES	PTCH1:p.S1216T	117	6	5.1	9:98211508	218	24	11	9:98211508	132	0	0	9:98211508	30	0	0
PD14768b	5	1268701	G	A	TERT	CCDS3861.2	r.2574c>u	c.2516C>T	p.T839M	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	67	RD	5.5	1.4	3	1	50	0	YES	YES	TERT:p.T839M	187	6	3.2	5:1268701	431	44	10.2	5:1268701	321	38	11.8	5:1268701	69	4	5.8
PD14768b	12	49428394	G	A	MLL2	CCDS44873.1	r.10411c>u	c.10411C>T	p.Q3471*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	67	RD	5.5	1.4	3	1	50	0	YES	YES	MLL2:p.Q3471*	79	10	12.7	12:49428394	145	21	14.5	12:49428394	99	18	18.2	12:49428394	37	3	8.1