Fig. 5

Genotype imputation accuracy of the Dog10K reference panel. a NRC rates of imputed genotypes across autosomes and the PAR segment of chromosome X. Variant sites are filtered according to GLIMPSE and IMPUTE5 imputation quality scores (INFO > 0.9). b NRC rates of imputed genotypes across the non-PAR segment of chromosome X. Variants are not filtered by imputation quality score, as imputation software does not provide scores for haploid genotypes. c NRC rates of imputed genotypes across autosomes and the PAR segment of chromosome X prior to filtering on imputation quality. d NRC rates and total number of imputed sites for each platform. Sites were filtered according to imputation quality score > 0.9 and reference MAF > 1%. e NRC rates for downsampled and full chromosome 38 reference panels for sites with reference MAF > 1%. Results show both quality and non-quality filtered sites. Data points show NRC rates for a single downsampled reference panel. Horizontal bars indicate mean NRC rates for each reference panel population size. f Number of imputed variants for downsampled and full chromosome 38 reference panels for sites with reference MAF > 1%. Results show both quality and non-quality filtered sites. Data points show the number of imputed variants for a single downsampled reference panel. Horizontal bars indicate the mean number of variants for each reference panel population size