Steps | Retained SNP count |
---|---|
Initial potential SNPs | 126,511 |
Average read depth of ≥7 | 126,511 |
Replication average ≥ 0.9 | 122,037 |
Call rate of ≥80% | 23,845 |
Similar sequence clusters of ≤0.95 | 19,328 |
Minor allele frequency (MAF) of ≥0.02 | 10,700 |
LD filters with a correlation coefficient (r2) threshold of 0.2 | 10,624 |
HWE filters (p ≥ 0.0001) | 10,624 |
Retained SNPs for further analysis | 10,624 |