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Fig. 7 | BMC Genetics

Fig. 7

From: Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation

Fig. 7

Effect of different parameters on the accuracy of imputation of GBS markers and the number of variants retained. The accuracies of the missing GBS genotypes were estimated by evaluating the concordance of the imputed GBS genotypes with the SNP50 genotypes. All panels illustrate the effect of the minimum call rate as well as the combination of GBS markers (genotype quality score ≥ 20) and SNP50 markers on the estimated accuracy of GBS-imputed markers. The parameters examined were a the imputation program, b the thresholds for the minimum read depth, and c the minMAF

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