Fig. 6
Effect of different correction strategies on ascertainment bias for expected heterozygosity (HE; A + B) and for Nei’s standard genetic distance (D; C + D). A + C – uncorrected array, linkage pruned array and imputed array (reference set 74_1perLine) based vs. sequence-based HE/ D. B + D – array imputed with different reference sets vs. sequence-based HE/ D. The solid black line represents the line of identity, the solid colored lines are regression lines within the individually sequenced populations (larger points) and the dashed lines regression lines within all populations which include individually and pooled (small points) sequenced populations. Note that there is also an effect of pooled sequencing which affects the ‘true’ values of the pooled sequenced populations