Fig. 4

Quality assessment for the bean MAGIC population. a Total number of genotype calls obtained from sequencing data for the bean MAGIC population contrasted with the number of heterozygous genotype calls. For each pipeline the dots represent datapoints obtained filtering genotype calls at different minimum quality scores. b Total number of SNPs obtained in the same experiments as a function of the number of SNPs with observed heterozygosity larger than 0.05. c Distribution of observed heterozygosity for datasets obtained with the four pipelines compared in this study. d Distribution of imputed genotype calls for different datasets obtained with NGSEP and imputed with NGSEP and with Beagle. The green line represents the percentage of the total dataset that imputed genotype calls represent for each dataset