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Table 2 Array data set versions with different filtering strategies applied

From: Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies

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