Fig. 2
Local imputation accuracy (R2dose) when imputing HD genotypes using the two bovine genome assemblies. Mean imputation accuracy (R2dose) for SNPs grouped in segments of 100 kb on the 29 autosomes when aligned to the ARS-UCD1.2 and UMD3.1 assemblies. For better visualisation, accuracies are plotted as means of 1-R2dose and R2dose-1 for UMD3.1 and ARS-UCD1.2 assemblies respectively. Number of poorly imputed SNPs (MAF > 1% and R2dose < 0.8) are counted in segments of 100 kb. Segments with more than three poorly imputed SNPs are identified as putatively misplaced. The putatively misplaced segments on UMD3.1 (blue) and ARS-UCD3.1 (red) are marked in colored tracks