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	Mutant_read_count_PD13594a	WT_read_count_PD13594a	DEPTH_PD13594a	MutantPctPD13594a	Mutant_read_count_PD13594c	WT_read_count_PD13594c	DEPTH_PD13594c	MutantPctPD13594c	Mutant_read_count_PD13594d	WT_read_count_PD13594d	DEPTH_PD13594d	MutantPctPD13594d	Mutant_read_count_PD13594e	WT_read_count_PD13594e	DEPTH_PD13594e	MutantPctPD13594e	Mutant_read_count_PD13594f	WT_read_count_PD13594f	DEPTH_PD13594f	MutantPctPD13594f	Mutant_read_count_PD13594g	WT_read_count_PD13594g	DEPTH_PD13594g	MutantPctPD13594g	Mutant_read_count_PD13594h	WT_read_count_PD13594h	DEPTH_PD13594h	MutantPctPD13594h	Mutant_read_count_PD13594i	WT_read_count_PD13594i	DEPTH_PD13594i	MutantPctPD13594i	Mutant_read_count_PD13594j	WT_read_count_PD13594j	DEPTH_PD13594j	MutantPctPD13594j
PD13594b	4	20493453	ATATCGTAGAC	A	SLIT2	ENST00000273739	r.1084_1093delUAUCGUAGAC	c.858_867delTATCGTAGAC	p.I287fs*46	Del	frameshift	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	76	pS	2	2	3	1	76	2	YES	NO	SLIT2:p.I287fs*46	0	70	70	0	5	126	131	3.81679389312977	1	99	100	1	2	94	96	2.08333333333333	6	91	97	6.18556701030928	4	25	29	13.7931034482759	6	80	86	6.97674418604651	7	111	118	5.93220338983051	3	95	98	3.06122448979592
PD13594b	10	30749721	TACT	TG	MAP3K8	CCDS7166.1	r.2057_2059delACUinsg	c.1361_1363delACTinsG	p.Y454fs*11	Complex	frameshift	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	76	pS	2	2	3	1	76	2	YES	NO	MAP3K8:p.Y454fs*11	3	92	95	3.15789473684211	15	83	98	15.3061224489796	1	95	96	1.04166666666667	5	72	77	6.49350649350649	16	95	111	14.4144144144144	54	127	181	29.8342541436464	15	90	105	14.2857142857143	14	89	103	13.5922330097087	17	101	118	14.4067796610169
PD13594b	4	153332628	CA	C	FBXW7	CCDS3777.1	r.476delU	c.327delT	p.D109fs*60	Del	frameshift	2	DAMAGING_OTHER_CANCER_GENE	ONCOGENIC	76	pS	2	2	3	1	76	2	YES	NO	FBXW7:p.D109fs*60	1	118	119	0.840336134453782	11	174	185	5.94594594594595	0	127	127	0	5	189	194	2.57731958762887	14	196	210	6.66666666666667	5	36	41	12.1951219512195	22	155	177	12.4293785310734	20	169	189	10.5820105820106	23	183	206	11.1650485436893