Extended Data Fig. 6: Replication rates were estimated using GRiD.

Replication rates were plotted for the 20 species shown in Fig. 2. The y axis (GRiD) is defined as the ratio between coverage at the peak (ori) and trough (ter) for the reference bacterial genome. Samples that had sufficient coverage are plotted (coverage > 0.2) for mapping against the reference genomes. Sample numbers varied with dependent species and are indicated in parentheses. P values were calculated using one-sided Mann–Whitney U tests for each of the stages (MP, S0, SI/II, SIII/IV) and were compared to the healthy controls. Significant elevation or depletion are denoted as follows: +++, elevation with P < 0.005; ++, elevation with P < 0.01; +, elevation with P < 0.05; −−−, depletion with P < 0.005; −−, depletion with P < 0.01; −, depletion at P < 0.05. The boxes represent 25th–75th percentiles, black lines indicate the median, whiskers extend to the maximum and minimum values within 1.5× the interquartile range and dots indicate outliers.