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_PD14765a	TUM_PILEUP_MUTS_PD14765a	Pileup_MtAlpct_PD14765a	ID.2	DEPTH_PD14765c	TUM_PILEUP_MUTS_PD14765c	Pileup_MtAlpct_PD14765c	ID.3	DEPTH_PD14765d	TUM_PILEUP_MUTS_PD14765d	Pileup_MtAlpct_PD14765d	ID.4	DEPTH_PD14765e	TUM_PILEUP_MUTS_PD14765e	Pileup_MtAlpct_PD14765e	ID.5	DEPTH_PD14765f	TUM_PILEUP_MUTS_PD14765f	Pileup_MtAlpct_PD14765f
PD14765b	3	178937422	T	C	PIK3CA	CCDS43171.1	r.1967u>c	c.1810T>C	p.C604R	Sub	missense	1	ONCOGENIC_BCA_GENE	ONCOGENIC	59	RD	7.2	2	3	3	50	2	YES	YES	PIK3CA:p.C604R	81	24	29.6	3:178937422	197	47	23.9	3:178937422	87	22	25.3	3:178937422	212	35	16.5	3:178937422	239	58	24.3
PD14765b	6	138200384	G	T	TNFAIP3	CCDS5187.1	r.1868g>u	c.1802G>T	p.R601M	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	59	RD	7.2	2	3	3	50	2	YES	YES	TNFAIP3:p.R601M	432	16	3.7	6:138200384	161	16	9.9	6:138200384	345	1	0.3	6:138200384	310	0	0	6:138200384	295	1	0.3
PD14765b	7	100416252	A	G	EPHB4	CCDS5706.1	r.1781u>c	c.1312T>C	p.S438P	Sub	missense	3	UNCERTAIN_CANCER_GENE_STATUS_IN_BCA	UNKNOWN	59	RD	7.2	2	3	3	50	2	YES	YES	EPHB4:p.S438P	208	70	33.7	7:100416252	75	20	26.7	7:100416252	114	21	18.4	7:100416252	115	19	16.5	7:100416252	106	32	30.2
PD14765b	3	178952085	A	G	PIK3CA	CCDS43171.1	r.3297a>g	c.3140A>G	p.H1047R	Sub	missense	1	CANONICAL_ONCOGENIC_BCA_GENE	ONCOGENIC	59	RD	7.2	2	3	3	50	2	YES	YES	PIK3CA:p.H1047R	92	19	20.7	3:178952085	215	30	14	3:178952085	97	17	17.5	3:178952085	223	34	15.2	3:178952085	216	54	25
PD14765b	17	7578189	A	C	TP53	CCDS11118.1	r.850u>g	c.660T>G	p.Y220*	Sub	nonsense	1	DAMAGING_IN_BCA_GENE	ONCOGENIC	59	RD	7.2	2	3	3	50	2	YES	YES	TP53:p.Y220*	442	277	62.7	17:7578189	217	121	55.8	17:7578189	256	131	51.2	17:7578189	237	86	36.3	17:7578189	226	112	49.6