Fig. 3

Comparative analysis of the inferred position of simulated QTLs. To assess the accuracy of QTL detection using nine statistics based on calculation of ∆SNP, G, ED and LOD at the marker level in three case studies of the recombination rate (λ), we plotted the distance to the simulated QTL in kb. Our calculations were based on differences in allele frequency (∆SNP), G-statistics (G), Euclidian distance (ED) and log likelihood (LOD). Methods use either data at the SNP level (∆SNP, G, EDm, LOD) or a smooth value across several SNPs (t-∆SNP, AFDexp, Gprime, ED100⁴, SmLOD). The boxplots represent the range of detection of QTLs in one thousand simulations using each method. Distance corresponds to the absolute genetic distance between the simulated QTL position and the QTL position retrieved with each method. Binomial distribution was taken into consideration in the simulation of sequencing noise