Fig. 4.

Effect of the level of inbreeding in parents. a The genotype imputation accuracy using AlphaPlantImpute in F₂ focal individuals of a bi-parental cross where the parents are F₁, F₂, F₄, F₁₀ or F₂₀. b Comparison of the average genotype imputation accuracy using AlphaPlantImpute (y-axis) versus using PlantImpute (x-axis). The colours represent the different LD arrays. The shapes represent the level of inbreeding in the parents. The red diagonal line indicates when the accuracy of PlantImpute equals AlphaPlantImpute. Points above the line are when imputation accuracy is higher with AlphaPlantImpute and points below the line are when imputation accuracy is higher with PlantImpute. c Comparison of the precision in imputation accuracy using AlphaPlantImpute (y-axis) versus using PlantImpute (x-axis). The colours represent the different LD arrays. The shapes represent the level of inbreeding in the parents. The red diagonal line indicates when the precision of PlantImpute equals AlphaPlantImpute. Points above the line indicate when the precision in accuracies is higher in AlphaPlantImpute and points below the line are when the precision in accuracies is higher in PlantImpute