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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%
  1. Imputation accuracy (r): correlation between true and imputed genotypes, com: combined sample, ran: random sample, hap: haplotype sample, LD1: 10,000 SNPs (23.1%) were set to missing, LD2: 50% of the SNPs were set to missing, MAF: Minor allele frequency