Fig. 3
From: Limited haplotype diversity underlies polygenic trait architecture across 70 years of wheat breeding
Call rate and accuracy of genotypes after imputation and after downsampling. a Imputed call rate (y-axis) vs direct call rate (x-axis). Only 28.1% of the 1,131,251 SNP sites can be genotyped directly from the low-coverage sequence data, whereas 93.8% of sites had genotypes after imputation. 5.8% of sites (grey region and horizontal dashed line in a) were removed by quality control filters after imputation. b,c Accuracy is defined as concordance at 5747 sites that overlap with the Axiom 35 k array. c Imputation before/after downsampling was performed with (green) and without (orange) using the genotypes of the founders as a reference panel