The Long Term Evolution Experiment (LTEE) derived clones have evolved from a common E. Coli ancestor (REL606). Since all reads from the analyzed clones are aligned to the ancestor reference genome, we can use the known genomic coordinates of origin and terminus of replication to determine trends in-between these locations. Similar to the GC correction we use lowess regression to model and then correct the trends in the regions between the origin and terminus.
Figure 9: The plots indicate the effect of correction (brown vs black dots) on the read count distribution in the defined windows sliding across the genome. Some samples are heavily biased towards the origin or terminus while others (not biased) remain unaffected.