Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar)

BMC Genomics

Table 2 Quantity and source of the SNPs on the array at different stages of quality filtering

SNP category	RR seq	RAD seq	RNA seq	Other	Total*
Total candidate SNPs	73,800	54,197	156,979	4,714	286,021
Low quality clusters**	9,795	8,192	21,609	219	39,429
Monomorphic	9,010	18,157	83,368	811	110,910
High quality polymorphic SNPs	54,995	27,848	52,002	3,684	135,682
Mendelian error	1,292	756	1,595	66	3,649
Final total filtered SNPs	53,703	27,092	50,407	3,618	132,033

*The row total is lower than sum of the individual column totals because a proportion of these SNPs were from multiple categories (e.g. discovered in both the RR and RAD experiments); see Additional file 1: Table S1.
**‘Quality’ refers to the cluster properties of the SNP when genotyped on the Axiom array. Low quality SNPs are those with cluster properties that fall below a threshold value (e.g. < 97% call rate).

ISSN: 1471-2164