Table 2 Imputation accuracy (r) of masked chip genotype data from lower (LD1, LD2) to higher marker density in Landrace (LR) and Large White (LW) using different reference panels
From: Comparison of the choice of animals for re-sequencing in two maternal pig lines
Breed | Reference panel | Imputation scenario | MAF 1–3% | MAF 3–5% | MAF >5% | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
\(\varnothing\) | Min. | Max. | \(\varnothing\) | Min. | Max. | \(\varnothing\) | Min. | Max. | |||
LR | com | LD1 | 86.53% | 83.97% | 88.95% | 86.30% | 84.51% | 87.73% | 86.30% | 84.51% | 87.73% |
LD2 | 83.63% | 82.26% | 85.23% | 83.60% | 82.00% | 85.77% | 93.13% | 92.88% | 93.29% | ||
ran | LD1 | 74.13% | 63.52% | 84.26% | 75.86% | 66.82% | 81.95% | 86.81% | 71.26% | 88.66% | |
LD2 | 75.35% | 70.80% | 80.38% | 77.65% | 73.68% | 81.18% | 87.83% | 87.23% | 88.28% | ||
hap | LD1 | 82.81% | 80.38% | 85.43% | 84.64% | 81.24% | 86.83% | 94.10% | 93.88% | 94.52% | |
LD2 | 81.21% | 78.81% | 83.31% | 82.14% | 80.74% | 84.30% | 92.98% | 92.79% | 93.20% | ||
LW | com | LD1 | 92.68% | 92.47% | 92.85% | 88.68% | 86.37% | 89.97% | 93.94% | 93.70% | 94.16% |
LD2 | 86.52% | 85.22% | 88.23% | 86.20% | 84.93% | 87.47% | 92.71% | 92.59% | 92.90% | ||
ran | LD1 | 83.30% | 76.37% | 88.20% | 82.24% | 76.15% | 86.73% | 89.90% | 77.65% | 90.86% | |
LD2 | 79.22% | 73.35% | 83.88% | 78.68% | 74.33% | 83.88% | 88.35% | 87.41% | 88.94% | ||
hap | LD1 | 84.59% | 81.45% | 87.05% | 87.36% | 85.79% | 89.46% | 93.97% | 93.77% | 94.17% | |
LD2 | 83.37% | 81.34% | 85.35% | 85.46% | 84.05% | 86.54% | 92.86% | 92.66% | 93.03% | ||