Table 2 Array data set versions with different filtering strategies applied
Given name for data set | Filter/s applied | No of SNPs |
|---|---|---|
Array_all | Â | 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 |