Table 1. Base pair substitution counts and mutation rates in the clone trees.

Isolate	No. subclones sequenced	Days in culture	BPS	BPS/ELC mean (×10−3)	BPS/ELC 95% CI (×10−3)	BPS/ELC/bp mean (×10−10)	BPS/ELC/bp 95% CI (×10−10)
3D7	37	203	15	4.91	3.48–6.33	2.10	1.49–2.72
HB3	81	250	17	6.88	3.30–10.45	2.95	1.42–4.49
Dd2	56	298	18	7.45	3.80–11.11	3.20	1.63–4.77
W2	20	119	11	N/A	N/A	N/A	N/A
KH1-01	59	447	20	5.29	1.29–9.28	2.27	0.550–3.98
KH2-01	26	87	4	3.83	0.330–7.34	1.64	0.142–3.15
Total	279	1404	85	5.71	3.96–7.46	2.45	1.70–3.20

The mean base pair substitution (BPS) rate of all generations of each isolate's clone tree, along with 95% confidence interval (CI), are shown. All means were weighted by the size of the clone tree generated, defined as the product of the number of subclone genomes analysed and number of days in culture (see Materials and Methods and Supplementary Figure S2). ELC = erythrocytic life cycle. We excluded W2 data from mutation rate calculations due to an insufficient number of BPS observed after the first generation of the clone tree.