TABLE 2.

Results from GLM and GLMER analyses

Effecta	GLM			GLMER
	Coefficient	Standard error	P value	Coefficient	Standard error	P value
Nonsynonymous changes using the combined characterization
Main effects
Intercept	−0.867	0.187	<0.001	−3.710	0.157	<0.001
Exposed	1.842	0.208	<0.001	1.833	0.127	<0.001
VP3	0.404	0.246	0.10	0.404	0.147	0.006
VP1	0.694	0.224	0.002	0.693	0.134	<0.001
Minor	−1.452	0.228	<0.001	0.096	0.310	0.76
Syn	−	−	−	0.253	0.033	<0.001
Two-way interactions
Exposed:VP3	−0.557	0.275	0.043	−0.557	0.165	<0.001
Exposed:VP1	−0.602	0.250	0.016	−0.602	0.150	<0.001
Exposed:minor	0.690	0.249	0.006	0.676	0.154	<0.001
Main effects of synonymous changes using the combined characterization
Intercept	1.976	0.0195	<0.001	−0.833	0.086	<0.001
Exposed	0.094	0.0271	<0.001	0.097	0.025	<0.001
Minor	−1.229	0.0322	<0.001	0.361	0.223	0.11
Nonsynonymous changes using the joint characterizationa
Main effects
Intercept	−0.867	0.176	<0.001	−3.826	0.150	<0.001
R	0.749	0.261	0.004	0.682	0.173	<0.001
R+S	2.442	0.202	<0.001	2.427	0.131	<0.001
VP3	0.404	0.231	0.08	0.403	0.147	0.006
VP1	0.693	0.210	<0.001	0.695	0.134	<0.001
Minor	−1.452	0.214	<0.001	0.045	0.284	0.88
Syn	−	−	−	0.238	0.034	<0.001
Two-way interactions
R:VP3	−0.186	0.331	0.57	−0.180	0.210	0.39
R+S:VP3	−0.480	0.269	0.75	−0.472	0.171	0.006
R:VP1	0.028	0.298	0.92	0.033	0.189	0.86
R+S:VP1	−0.528	0.248	0.034	−0.502	0.158	0.002
R:minor	0.773	0.267	0.004	0.673	0.198	<0.001
R+S:minor	0.662	0.245	0.007	0.644	0.160	<0.001
Main effects of synonymous changes using the joint characterization
Intercept	1.976	0.0196	<0.001	−0.837	0.086	<0.001
R	0.078	0.0312	0.012	0.078	0.028	0.006
R+S	0.115	0.0389	0.003	0.125	0.036	<0.001
Minor	−1.229	0.0324	<0.001	0.385	0.220	0.08

^aThe effects of exposed sites are relative to buried sites, those of VP3 and VP1 are relative to VP2, and those of the minor group are relative to the major group. Syn is the effect of synonymous substitutions at a codon position. “−” indicates that data are not reported because there are no significant effects. R, exposed by the rolling-only model; R+S, exposed by the rolling+structural model.