Table 4.

Evidence for positive and negative selection using four detection methods

Protein	Aa residues relative to ORF	Length of protein	Genotype	Overall dN/dS	SLAC*		FEL*		REL†		IFEL*
					Positive selection	Negative selection	Positive selection	Negative selection	Positive selection	Negative selection	Positive selection	Negative selection
ORF	1–3432	3432	GI–IV	0.035	0	807	1	1432	10	1204	1	855
			GI	0.067	0	19	0	143	0	0	0	13
			GII	0.020	0	12	0	232	0	43	0	0
			GIII	0.057	0	126	0	383	1	29	0	112
C	1–127	127	GI–IV	0.147	0	14	0	26	0	54	0	16
			GI	0.111	0	0	0	5	0	13	0	0
			GII	0.133	0	0	0	4	3	0	0	0
			GIII	0.166	0	1	0	5	0	0	0	2
prM	128–294	167	GI–IV	0.048	0	33	0	78	0	0	0	41
			GI	0.061	0	0	0	8	1	0	0	0
			GII	0.015	0	0	0	20	1	35	0	0
			GIII	0.083	0	6	0	19	0	0	0	6
E	295–794	500	GI–IV	0.033	0	135	0	225	0	0	0	141
			GI	0.069	0	4	0	23	0	77	0	4
			GII	0.023	0	3	0	42	0	0	0	0
			GIII	0.065	0	21	0	58	0	129	0	19
NS1	795–1146	352	GI–IV	0.043	0	81	0	145	0	0	1	83
			GI	0.041	0	13	0	49	0	24	0	10
			GII	0.031	0	3	0	28	0	55	0	0
			GIII	0.061	0	14	0	52	0	6	0	12
NS2A	1147–1373	227	GI–IV	0.052	0	46	0	81	0	0	0	46
			GI	0.047	0	3	0	13	0	24	0	2
			GII	0.050	0	1	0	11	1	1	0	0
			GIII	0.069	0	6	0	19	0	55	0	6
NS2B	1374–1504	131	GI–IV	0.014	0	31	0	65	0	0	0	32
			GI	0.012	0	0	0	5	0	0	0	0
			GII	5.310×10−16	0	0	0	7	0	0	0	0
			GIII	0.038	0	6	0	14	0	0	0	4
NS3	1505–2123	619	GI–IV	0.025	0	167	0	285	0	3	0	186
			GI	0.058	0	2	0	25	0	0	0	0
			GII	0.006	0	0	0	46	0	0	0	0
			GIII	0.054	0	25	0	72	0	172	0	29
NS4A	2124–2272	149	GI–IV	0.045	0	31	0	57	1	90	0	23
			GI	0.080	0	0	0	7	0	0	0	1
			GII	0.012	0	0	0	8	0	0	0	0
			GIII	0.073	0	4	0	14	3	16	0	4
NS4B	2273–2527	255	GI–IV	0.025	0	61	1	130	0	0	1	64
			GI	0.056	0	1	0	11	0	0	0	2
			GII	0.019	0	2	0	14	0	0	0	0
			GIII	0.035	0	9	0	37	2	21	0	8
NS5	2528–3432	905	GI–IV	0.033	0	210	0	373	1	47	0	243
			GI	0.081	0	3	0	35	0	109	0	1
			GII	0.025	0	1	0	46	0	144	1	0
			GIII	0.014	0	5	0	21	0	48	0	5

*Number of sites where P<0.05.

†Number of sites where Bayes factor >100.