Table 3.

Selection pressure analysis of the complete coding region of cosmopolitan genotype.

Lineage	Gene	Gene position	SLAC	FEL	FUBAR	MEME
Lineages 1–5	C	9	0.05	0.03	89.45	0.67
	C	95	0.14	0.09	46.73	0.11
	E	347	0.26	0.22	29.06	0.07
	E	390	0.11	0.02	214.78	0.67
	NS1	178	0.18	0.16	48.62	0.16
	NS2A	171	0.02	0.03	88.23	0.04
	NS3	392	0.04	0.03	134.29	0.02
	NS5	648	0.03	0.23	80.97	0.14
Indian sub-continent lineage	preM	16	0.34	0.18	9.69	0.2
	preM	57	0.41	0.19	10.86	0.1
	E	52	0.28	0.14	14.86	0
	E	360	0.29	0.14	20.05	0.67
	NS1	192	0.34	0.19	9.61	0.01
	NS2A	33	0.07	0.06	65.28	0.67
	NS5	631	0.16	0.04	91.78	0.67

Positive selection was evident on residues in bold font, based on the selection pressure analyses. The values shown for each method are p-values, except for the FUBAR method for which the values indicate the Bayes factor. The p-values ≤ 0.1 were considered as significant for SLAC, FEL, and MEME methods, whereas the Bayes factor ≥ 30 was used for FUBAR method. C Capsid, E envelope, NS non-structural proteins.