Fig. 3
From: Development and validation of a horse reference panel for genotype imputation
Accuracy of imputation to sequence level for the ECA3 chromosome. Imputation was performed for three reference panels (RP), including 52 (RP1), 162 (RP2) or 304 (RP3) horses, taking equine chromosome 3 (ECA3) as an example and using the software Beagle 5.1. a Accuracy of imputation plotted against minor allele frequency (MAF). Imputation from medium-density to sequence level applying RP2. The line in a and c is the average imputation accuracy per MAF. b Accuracy of imputation from medium-density versus MAF depending on the reference panel used for imputation. MAF categories ‘x–y’ stand for ‘x < MAF ≤ y’. c Accuracy of imputation from high-density to sequence level with RP2 plotted against MAF. d Accuracy of imputation from medium-density with RP2 plotted against the position on ECA3, with positions of the medium-density SNP array shown in orange