Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history
Fig 2
The relationship between true and inferred FROH values depends on inference method and population demographic scenario.
Each regression line represents linear model results for a single level of coverage with the shaded areas representing 95% confidence intervals. Each point represents data for a single simulated individual. Panels display outcomes using BCFtools in Genotypes mode (A-D), BCFtools in Likelihoods mode (E-H) and, PLINK (I-L), as well as by population scenarios including large (A, E, I), small (B, F, J), bottlenecked (C, G, K), and declining (D, H, L) populations. Dashed line is 1:1 line and x- and y-axes are consistent within each demographic scenario. Note the differing slopes across demographic scenarios (e.g., among panels A-D) and differing overall accuracies across methods (e.g., differing distances between regression lines and 1:1 line among panels D, H, and L). Another version of this figure with consistent axis limits across panels and colorized by sequencing depth is available in S19 Fig.