Figure 3

Mapping coverage and sequence heterogeneity for Polyphemus and Penelope from strain 160 and strain 9 genomic reads. For all plots, mapping coverage and sequence heterogeneity is shown along the length of the element. For Polyphemus, this is 1,704 bp. For Penelope, this is 3,394 bp. Read mapping coverage is measured on a per nucleotide basis, normalized by 1 million mapped reads. Based on coverage/million reads mapped, both Polyphemus and Penelope are enriched in strain 160. Penelope shows greater excess than Polyphemus. Using piledriver, I also determined sequence heterogeneity among mapped reads for Polyphemus and Penelope by scoring the frequency of the most common variant at each nucleotide position. In strain 160, Polyphemus and Penelope mapped reads are highly similar. In strain 9, mapped reads show great heterogeneity.