Table 2.

Array data set versions with different filtering strategies applied

Given name for data set	Filter/s applied	No of SNPs
Array_all		401, 125
Array_MAF5	Filtered out SNPs with less than 5% MAF	379, 342
GG	Retained only SNPs that are polymorphic in the two Gallus gallus wild populations (GGg and GGsc)	289, 390
GG_MAF5	GG and filtered out SNPs with MAF less than 5%	284, 748
Pruned	SNPs were pruned based on LD	122, 006
Pruned_MAF5	Pruned and filtered out SNPs with MAF less than 5%	107, 604
Pruned_GG	Pruned and GG	86, 404
Pruned_GG_MAF5	Pruned_GG and filtered out SNPs with MAF less than 5%	82, 975