Table 1 Imputation methods used for genotyping-by-sequencing data
Imputation method 1 | Missing data threshold | Imputation algorithm | # of SNPs |
|---|---|---|---|
MI | 30% | Mean imputation (MI) | 8,868 |
MI | 60% | Mean imputation (MI) | 47,521 |
EM | 30% | Expectation-maximization (EM) | 8,868 |
kNN-Fam | 60% | Family-based K-nearest neighbor (kNN-Fam) | 62,198 |
SVD | 60% | Singular Value Decomposition (SVD) | 55,618 |