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_PD9850a	TUM_PILEUP_MUTS_PD9850a	Pileup_MtAlpct_PD9850a	ID.2	DEPTH_PD9850d	TUM_PILEUP_MUTS_PD9850d	Pileup_MtAlpct_PD9850d	ID.3	DEPTH_PD9850e	TUM_PILEUP_MUTS_PD9850e	Pileup_MtAlpct_PD9850e	ID.4	DEPTH_PD9850f	TUM_PILEUP_MUTS_PD9850f	Pileup_MtAlpct_PD9850f	ID.5	DEPTH_PD9850g	TUM_PILEUP_MUTS_PD9850g	Pileup_MtAlpct_PD9850g	ID.6	DEPTH_PD9850h	TUM_PILEUP_MUTS_PD9850h	Pileup_MtAlpct_PD9850h	ID.7	DEPTH_PD9850i	TUM_PILEUP_MUTS_PD9850i	Pileup_MtAlpct_PD9850i
PD9850b	14	105246551	C	T	AKT1	CCDS9994.1	r.603g>a	c.49G>A	p.E17K	Sub	missense	1	CANONICAL_ONCOGENIC_BCA_GENE	ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	AKT1:p.E17K	206	63	30.6	14:105246551	262	96	36.6	14:105246551	163	26	16	14:105246551	396	87	22	14:105246551	308	4	1.3	14:105246551	214	48	22.4	14:105246551	229	23	10
PD9850b	6	157100378	G	T	ARID1B	CCDS5251.1	r.1293g>u	c.1141G>T	p.E381*	Sub	nonsense	2	DAMAGING_OTHER_CANCER_GENE	ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	ARID1B:p.E381*	92	35	38	6:157100378	115	46	40	6:157100378	56	10	17.9	6:157100378	126	26	20.6	6:157100378	109	6	5.5	6:157100378	68	23	33.8	6:157100378	95	14	14.7
PD9850b	3	52437465	C	G	BAP1	CCDS2853.1	r.2168g>c	c.1696G>C	p.E566Q	Sub	missense	1	UNKNOWN_BCA	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	BAP1:p.E566Q	162	0	0	3:52437465	179	0	0	3:52437465	103	0	0	3:52437465	272	0	0	3:52437465	171	0	0	3:52437465	147	0	0	3:52437465	185	15	8.1
PD9850b	14	95569873	G	C	DICER1	CCDS9931.1	r.4098c>g	c.3860C>G	p.S1287*	Sub	nonsense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	DICER1:p.S1287*	327	17	5.2	14:95569873	390	0	0	14:95569873	279	0	0	14:95569873	265	1	0.4	14:95569873	395	0	0	14:95569873	376	0	0	14:95569873	370	0	0
PD9850b	20	57466842	G	A	GNAS	CCDS46623.1	r.485g>a	c.61G>A	p.E21K	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	GNAS:p.E21K	108	0	0	20:57466842	128	0	0	20:57466842	65	0	0	20:57466842	190	0	0	20:57466842	147	0	0	20:57466842	106	10	9.4	20:57466842	138	0	0
PD9850b	6	160525925	G	C	IGF2R	CCDS5273.1	r.7433g>c	c.7285G>C	p.A2429P	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	IGF2R:p.A2429P	222	57	25.7	6:160525925	294	94	32	6:160525925	151	1	0.7	6:160525925	404	11	2.7	6:160525925	307	0	0	6:160525925	215	1	0.5	6:160525925	238	2	0.8
PD9850b	1	65332623	C	T	JAK1	CCDS41346.1	r.1165g>a	c.916G>A	p.D306N	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	JAK1:p.D306N	288	0	0	1:65332623	238	0	0	1:65332623	255	0	0	1:65332623	134	0	0	1:65332623	312	2	0.6	1:65332623	322	0	0	1:65332623	315	43	13.7
PD9850b	X	44929017	C	T	KDM6A	CCDS14265.1	r.2158c>u	c.2117C>T	p.S706L	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	KDM6A:p.S706L	253	1	0.4	X:44929017	326	0	0	X:44929017	246	0	0	X:44929017	356	0	0	X:44929017	349	0	0	X:44929017	330	0	0	X:44929017	317	15	4.7
PD9850b	17	12032605	G	T	MAP2K4	CCDS11162.1	r.1103+1g>u	c.1040+1G>T	p.?	Sub	ess splice	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	MAP2K4:p.?	49	19	38.8	17:12032605	35	23	65.7	17:12032605	80	19	23.8	17:12032605	23	7	30.4	17:12032605	98	5	5.1	17:12032605	69	22	31.9	17:12032605	93	40	43
PD9850b	3	185167841	G	A	MAP3K13	CCDS3270.1	r.1498g>a	c.1164G>A	p.Q388Q	Sub	silent	2	SILENT	SILENT	66	pS	3.2	3.2	2	3	28	2	YES	YES	MAP3K13:p.Q388Q	98	0	0	3:185167841	91	0	0	3:185167841	118	0	0	3:185167841	53	0	0	3:185167841	101	1	1	3:185167841	102	0	0	3:185167841	141	10	7.1
PD9850b	12	49426814	G	A	MLL2	CCDS44873.1	r.11674c>u	c.11674C>T	p.Q3892*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	MLL2:p.Q3892*	113	32	28.3	12:49426814	126	39	31	12:49426814	88	26	29.5	12:49426814	245	51	20.8	12:49426814	156	6	3.8	12:49426814	99	25	25.3	12:49426814	98	15	15.3
PD9850b	7	151874712	C	T	MLL3	CCDS5931.1	r.8045g>a	c.7826G>A	p.R2609Q	Sub	missense	1	POSSIBLE_ONCOGENIC_BCA_GENE	POSSIBLE_ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	MLL3:p.R2609Q	467	0	0	7:151874712	668	0	0	7:151874712	362	0	0	7:151874712	719	0	0	7:151874712	522	3	0.6	7:151874712	502	0	0	7:151874712	513	64	12.5
PD9850b	18	39647373	G	A	PIK3C3	CCDS11920.1	r.2631g>a	c.2545G>A	p.D849N	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	PIK3C3:p.D849N	214	49	22.9	18:39647373	214	61	28.5	18:39647373	193	1	0.5	18:39647373	107	1	0.9	18:39647373	214	0	0	18:39647373	285	0	0	18:39647373	274	0	0
PD9850b	19	11097015	C	T	SMARCA4	CCDS45971.1	r.790c>u	c.506C>T	p.P169L	Sub	missense	2	UNKNOWN_OTHER	UNKNOWN	66	pS	3.2	3.2	2	3	28	2	YES	YES	SMARCA4:p.P169L	224	0	0	19:11097015	241	0	0	19:11097015	179	0	0	19:11097015	437	0	0	19:11097015	312	0	0	19:11097015	191	0	0	19:11097015	257	15	5.8
PD9850b	17	7577079	C	G	TP53	CCDS11118.1	r.1049g>c	c.859G>C	p.E287Q	Sub	missense	1	POSSIBLE_ONCOGENIC_BCA_GENE	POSSIBLE_ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	TP53:p.E287Q	204	0	0	17:7577079	251	0	0	17:7577079	201	0	0	17:7577079	469	0	0	17:7577079	391	2	0.5	17:7577079	218	0	0	17:7577079	316	56	17.7
PD9850b	17	7577099	C	G	TP53	CCDS11118.1	r.1029g>c	c.839G>C	p.R280T	Sub	missense	1	ONCOGENIC_BCA_GENE	ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	TP53:p.R280T	197	0	0	17:7577099	205	0	0	17:7577099	166	0	0	17:7577099	405	0	0	17:7577099	348	1	0.3	17:7577099	193	0	0	17:7577099	281	47	16.7
PD9850b	17	7579312	C	T	TP53	CCDS11118.1	r.565g>a	c.375G>A	p.T125T	Sub	silent	1	POSSIBLE_ONCOGENIC_BCA_GENE	POSSIBLE_ONCOGENIC	66	pS	3.2	3.2	2	3	28	2	YES	YES	TP53:p.T125T	16	5	31.2	17:7579312	17	13	76.5	17:7579312	13	2	15.4	17:7579312	38	10	26.3	17:7579312	47	1	2.1	17:7579312	23	10	43.5	17:7579312	25	2	8