Concordance between genotypes before and after downsampling
To assess the robustness of each alignment strategy to reduced
sequencing depth, raw Illumina files were downsampled by 50%, and
genotype calls for each taxon from the imputed, downsampled datasets
were compared to genotype calls from the full imputed datasets.
Concordance between full and downsampled datasets is much higher using
dual alignment (P1+P2; Figure 3). Downsampling also results in a
one-third reduction in heterozygosity in P1 and P2 datasets but does not
affect the proportion of heterozygous genotypes in P1+P2 datasets (Table
1). With increasing sequencing depth, concordance in P1+P2 datasets
increases as expected, whereas concordance in P1 and P2 datasets is
unexpectedly higher at low depth than at intermediate sequencing depth.