Fig. 5.

Estimated accuracies of GBS genotypes after the first quality control step. Accuracy was estimated using GBS variants that were also found on the SNP50 array. The GBS genotypes were filtered according to their associated read-depth (RD) coverage without consideration of the genotype quality (GQ) or using a GQ score threshold of 20. At each shared locus, the concordance of the GBS and the SNP50 genotypes was assessed, assuming that those reported by the SNP50 array represented true genotypes