Table 3.

Sensitivity test of the West Nile virus set A primers.

Viral Strain	Quantity Value (cp/μL)	Quantity Mean Value (Ct)	Total Number of Trimmate Reads	Number of WNV Reads	% HCoverage	VCoverage	Consensus Sequence Length
WNV L1 (reference used for the mapping on Genpat: WNV L1 FJ483548	106	18.68	1457.278	503.152	99%	5043.56	10.959
	106		1371.693	476.605	99%	4997.04	10.964
	106		938.406	375.653	99%	4372.01	10.959
	No. of replicates with coverage ≥ 95%				3/3 (100%)
	105	23.45	1342.407	426.914	99%	4587.33	10.960
	105		1174.155	397.215	99%	4435.79	10.959
	105		825.135	315.219	99%	3776.67	10.956
	No. of replicates with coverage ≥ 95%				3/3 (100%)
	104	27	906.690	292.718	96%	3456.26	10.964
	104		984.952	297.351	97%	3414.38	10.959
	104		1247.127	327.095	96%	3570.22	10.959
	No. of replicates with coverage ≥ 95%				3/3 (100%)
	103	30	1096.401	249.798	94%	2735.41	10.962
	103		506.380	153.284	93%	1853.42	10.955
	103		569.039	170.272	91%	2099.54	10.955
	No. of replicates with coverage ≥ 95%				0/3 (0%)
	102	33	57.229	20.115	82%	295.76	10.366
	102		53.435	18.515	81%	281.027	10.958
	102		41426	15.149	80%	227.617	10.951
	No. of replicates with coverage ≥ 95%				0/3 (0%)
WNV L2 (reference used for the mapping: WNV L2 MN652880)	106	18.68	1262.167	12.484	35%	391.547	10.028
	106		1315.568	11.576	33%	383.276	10.928
	106		1103.838	16.652	26%	706.146	10.928
	No. of replicates with coverage ≥ 95%				0/3 (0%)
	105	22.87	1210.495	11.251	36%	347.197	10.928
	105		823.025	10.243	33%	345.101	10.928
	105		1478.160	12.253	34%	394.675	10.928
	No. of replicates with coverage ≥ 95%				0/3 (0%)
	104	26.41	1228.945	9.715	32%	337.862	10.928
	104		1090.849	9.547	32%	327.57	10.928
	104		947.964	4.405	30%	159.122	10.928
	No. of replicates with coverage ≥ 95%				0/3 (0%)
	103	30	442.063	2.796	26%	121.744	10.928
	103		577.277	3.500	27%	143.439	10.926
	103		369.041	1.615	22%	79.118	10.245
	No. of replicates with coverage ≥ 95%				0/3 (0%)
	102	33.14	35.426	1.362	17%	789.157	10.924
	102		68.307	627	17%	360.495	10.926
	102		63.643	731	18%	571.297	10.926
	No. of replicates with coverage ≥ 95%				0/3 (0%)