Coverage, ori/ter ratios and replication slope analysis (stationary phase)

This report summarizes marker frequency analysis of the study in stationary phase. Coverage plots show the normalized read counts along each replicon (normalized to origin of replication (ori) of the largest replicon). Light-colored points correspond to 1 kb window read counts, and darker points to 10 kb averages. All replicons are presented on the same length scale (x axis).

Dashed vertical lines mark the locations of the origin (ori) and the dif sites of replicons determined based on bioinformatic analysis. Short vertical ticks along the replicon, below the coverage plots, represent KOPS motifs and their orientation (GGGNAGGG, upper lane, or CCCTNCCC, lower lane). Horizontal colored lines represent the estimated ori and ter read-count levels, calculated by extrapolating log₂(read count) ∼ position fits from 10 kb data for each replication arm. Gray extensions indicate extrapolated segments of fitted trendlines outside the central analysis window (the first and last three 10 kb windows are excluded to reduce edge effects).

Below each plot, tables summarize quantitative parameters:

• ori and ter read-count levels — normalized coverage values at the origin and terminus, derived from extrapolated regression fits of each replichore (or globally for unidirectional replicons). For bidirectional replicons, if two extrapolations point to ori, the higher value at the ori position is taken; for ter, the lower of the arm-end extrapolations is taken.
• ori/ori and ter/ter ratios between chromosome and secondary replicons — ratios comparing the origin and terminus read-count levels of secondary replicons to those of the main chromosome.
• Replication slopes — slopes of log₂(read count) per megabase (log₂/Mb) for each replication arm, indicating replication speed.

Note on slopes highlighted in red

In stationary phase, some replicons show patterns where replication slopes cannot be reliably determined. This can reflect marker frequency analysis (MFA) resolution limits, systematic biases in read counts in the middle of a replichore, or cases where replication appears not to be fully stopped in stationary phase (residual replication activity). Some of these patterns may also have other biological explanations that affect replication dynamics.

For these cases, the corresponding fitted trendlines are shown in red and the slope values are not reported; table entries are shown as NA.

• If only one arm produced a reliable slope, ori and ter read-count levels were determined using that arm only.
• If both arms were not reliable (or replication was not fully stopped), ori and ter read-count levels were not determined and are reported as NA; consequently, the corresponding ori/ori and ter/ter ratios are also NA.