Fig. 4. Changes in mutation rate during latency with varying generation time.

Mutation rate (mutations per (bp×generation)) is shown for generation times ranging from 18 to 320 h for IC–HHC pairs grouped by the number of years between IC diagnosis and reactivation of tuberculosis in the HHC. The dark blue line is obtained from the regressions and shows the estimated mutation rate for a given generation time (x-axis) and light blue regions show 95% confidence intervals. The first panel shows the relationship between mutation rate and generation time during early latency (reactivation in ≤2 years of IC diagnosis) based on n = 11 IC–HHC pairs. The second panel shows the relations between mutation rate and generation time for reactivation in >2–6 years after IC diagnosis based on n = 13 IC–HHC pairs. In both panels the gray dashed vertical line is at 18 h and the horizontal line indicates the mutation rate of 8.36 × 10⁻¹⁰ mutations per (bp×generation) as seen in early latency (years 0–2, inclusive) with generation times held constant at 18 h. Source data are provided as a Source Data file.