Table 2.
Within-host nucleotide substitution rates during natural colonisation.
| Episode | ST | R2 | R2adj | Estimate (β) | Substitution rate (μ) | SNPs year−1 | Ne | P-value |
|---|---|---|---|---|---|---|---|---|
| INF19:35B:1 | 11721 | 0.94 | 0.91 | 1.06 | 2.49 × 10−05 | 55 | 15.8 | 2.99 × 10−2 |
| INF5:34:1 | 7319 | 0.76 | 0.72 | 0.43 | 1.00 × 10−05 | 22 | 10.5 | 2.35 × 10−3 |
| INF55:19A:1 | 10542 | 1 | 1 | 0.13 | 2.93 × 10−06 | 7 | 29.7 | 2.60 × 10−16 |
| INF59:6B:1 | 5516 | 1 | 1 | 1.5 | 3.52 × 10−05 | 78 | 72.2 | 1.33 × 10−16 |
| INF66:34:1 | 1778 | 0.92 | 0.89 | 1.44 | 3.38 × 10−05 | 75 | 2.63 | 9.88 × 10−3 |
| INF7:22A:1 | 10600 | 0.78 | 0.70 | 1.11 | 2.60 × 10−05 | 58 | 3.39 | 4.80 × 10−2 |
| INF73:9L:1 | 11705 | 0.90 | 0.86 | 2.75 | 6.46 × 10−05 | 143 | 1.22 | 4.92 × 10−2 |
| INF76:19A:1 | 4029 | 0.37 | 0.30 | 0.16 | 3.81 × 10−06 | 9 | 12.6 | 3.68 × 10−2 |
| INF85:13:2 | 11711 | 1.0 | 1.0 | 0.89 | 2.10 × 10−05 | 47 | 13.3 | 1.47 × 10−2 |
| INF90:6A:1 | 11700 | 0.62 | 0.56 | 0.92 | 2.17 × 10−05 | 48 | 3.27 | 2.05 × 10−2 |
R2 and Ne denotes coefficient of determination and effective population size respectively. The estimated value for the regression coefficient (β) is expressed as SNPs per week. The estimates for μ are expressed SNPs site−1 year−1 and were extrapolated from β. Serotypes with >4 sequenced genomes per individual were analysed.