A genotyping array for the globally invasive vector mosquito, Aedes albopictus

Parasites & Vectors

Table 4 Variant functional annotation of SNPs using SnpEff for WGS and SNP chip data, with results of bias correction

Variant type	WGS (N)	WGS (%)	Chip (N)	Chip (%)	Chip bias (%)	Chip possible (N)	Chip corrected (%)
Intron	1,281,482	44.81	24,387	39.49	−5.32	17,741	44.81
Intergenic	993,796	34.75	13,758	22.28	−12.47	13,758	34.75
Synonymous	384,482	13.45	14,323	23.20	9.75	5325	13.45
Non-synonymous	67,217	2.35	1942	3.14	0.79	930	2.35
5′ UTR	67,744	2.37	3642	5.90	3.53	938	2.37
3′ UTR	64,912	2.27	3697	5.99	3.72	899	2.27
Total	2,859,633	100.00	61,749	100.00	0.00	39,591	100.00

The number of SNPs and their percentage in each category for the two methods are listed in columns 2 to 5. Column 6 shows the number of SNPs used to match the proportions in the WGS data (chip possible). The final column shows the new percentage for each category of the chip data after bias correction (chip corrected)

ISSN: 1756-3305