(A) TE insertions (including those present in the reference genome and de novo insertions) vs. median sequencing coverage from paired reads. Coverage influences the ability to detect TE insertions (Wilcoxon signed-rank test V = 4095, p-value<0.001). (B) Median read coverage per sample for sexual (red) and asexual (blue) strains over 1000 generations. Data from asexual strains had lower coverage, but were not different to sexuals through time (generation effect p=0.096, reproductive mode effect p=0.002, and interaction between generation and mode p=0.588; permutation ANOVA). Lines represent linear regression and the grey areas represent 95% CI. (C) Subsampling to the mean asexual read coverage per generation for all samples results in similar findings (generation effect p=0.012, reproductive mode effect p=0.302, and interaction between generation and mode p=0.004; permutation ANOVA).