Figure 3. Method performance of LDx in predicting linkage.

r² measured from the DGRP haplotypes is strongly correlated with estimates from A) the direct observation method and B) the maximum likelihood method. In A), observing only a sparse sampling of the haplotypes creates the overabundance of observed r² estimates of 1. We determined the correlation between our r² estimates and r² values derived from haplotype data provided by the DGRP (Mackay et al 2012). We restricted the DGRP dataset to those strains present within our sample (92 of 162 strains). C) Increasing the simulated read depth increased the correlation between the true r² and the r² estimated by the direct observation (red) and maximum likelihood (blue) methods. Estimates in these figures have minor allele frequency cutoff of 1%. D ) Filtering based on minor allele frequency leads to more accurate r² estimates for the direct observation (red) and maximum likelihood (blue) methods. Points represent r² estimates made from pooled resequencing of the DGRP.