TABLE 2.

Information of assembled contigs of JEV.

Samples	Contigs	No. of reads	Matched strains (Genbank no.)	Query cover	Identity (%)	E-value	Covered range	Covered viral gene	Sequences for phylogenetic analysis	Name of strain
C1	C1-1	93	JF706281	100	99.39	0	4,348–5,171	NS2B-NS3		JEV-C1/YN
	C1-2	107	JF706267	100	97.60	0	9,217–10,301	NS5	NS5
C2	C2-1	83	KU904395	99	94.39	0	4,291–5,074	NS2B-NS3		JEV-C2/YN
	C2-2	150	MH385014	100	95.93	0	7,311–8,486	NS4B-NS5
	C2-3	105	MH385014	100	95.66	0	9,112–10,239	NS5	NS5
C3	1	473	MH385014	100	98.18	0	4,347–5,446	NS2B-NS3	NS2B	JEV-C3/YN
D2	1	3,910	HM228921	99	98.36	0	2,271–10,337	E-NS1-NS2A-NS2B-NS3-NS4B-NS5	NS5	JEV-D2/YN
E1	E1-1	124	JF706282	100	98.84	0	4,339–5,112	NS2B-NS3		JEV-E1/YN
	E1-2	170	MH385014	100	96.62	0	9,541–10,488	NS5-3′UTR	NS5
F1	1	520	JF706268	100	95.86	0	9,400–10,268	NS5	NS5	JEV-F1/YN
G1	G1-1	206	MH753128	99	99.02	0	1,743–3,773	E-NS1-NS2A		JEV-G1/YN
	G1-2	215	KU323483	100	98.68	0	4,181–6,071	NS2A-NS2B-NS3
	G1-3	501	MN639770	100	98.96	0	7,283–10,348	NS4B-NS5	NS5
G2	G2-1	207	JF706267	100	97.76	0	4,369–4,992	NS2B-NS3	NS2B	JEV-G2/YN
	G2-2	269	FJ495189	100	95.65	0	8,423–9,497	NS5
G3	1	429	JN381861	100	96.04	0	4,180–5,793	NS2A-NS2B-NS3	NS2B	JEV-G3/YN