Table 2.

Substitution rates in pol and env. The table below reports the calculated pol and env substitution rates (×10⁻³ ssy) for all analyzed subtypes and CRFs. The mean, median, standard error, and the lower and upper bounds of the 95% CIs are reported. The table is sorted by the median rate, in a descending manner. The table excludes trees that indicated either a negative RTT slope or r < 0.3 (see text). See Table S1 for complete data.

Subtype/CRF	Gene	Trees	Mean	Median	Std. Error	Lower-Bound	Upper-Bound
G	env	100	4.72	4.72	0.0045	4.71	4.73
02_AG	env	100	4.48	4.45	0.0623	4.36	4.60
A6	env	100	3.94	3.91	0.0647	3.81	4.06
A1	env	88	3.41	3.41	0.0461	3.32	3.50
01_AE	env	99	2.99	3.02	0.047	2.90	3.09
D	env	97	2.93	2.98	0.0261	2.88	2.98
C	env	84	2.74	2.64	0.0555	2.63	2.85
B	env	98	2.33	2.32	0.0418	2.25	2.41
F1	env	100	1.34	1.34	0.00003	1.34	1.34
A6	pol	100	2.18	2.18	0.0275	2.12	2.23
F1	pol	100	2.05	2.02	0.0294	1.99	2.11
G	pol	90	1.78	1.76	0.0225	1.73	1.82
01_AE	pol	73	1.48	1.51	0.0238	1.43	1.52
02_AG	pol	99	1.29	1.29	0.0200	1.25	1.33
C	pol	97	1.22	1.23	0.0206	1.18	1.26
B	pol	99	1.08	1.09	0.014	1.05	1.11
A1	pol	46	1.25	1.26	0.0338	1.18	1.31
D	pol	54	0.98	0.96	0.0200	0.94	1.02