TABLE 5.
HMM PBP recombination and mutation
| Data set | Inferred no. of recombinations |
ClonalFrameML model parametersa |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1A | 1B | 2A | 2X | Total | R | Θ | R/Θ | δ | ν | r/m | |
| PSR-595 | 5 | 14 | 13 | 3 | 35 | 344,080 | 967,091 | 0.356 | 109.8 | 0.043 | 1.69 |
| pbpcat-1248 | 11 | 35 | 43 | 29 | 118 | 3,093 | 1,581 | 1.957 | 221.9 | 0.006 | 2.49 |
| pbp1a-390b | 1 | – | – | – | 1 | 1.4 | 170.7 | 0.008 | 3,084.5 | 0.188 | 4.69 |
| pbp1b-427 | – | 2 | – | – | 2 | 7.2 | 243.3 | 0.029 | 227.8 | 0.157 | 1.06 |
| pbp2a-564 | – | – | 27 | – | 27 | 1,498 | 149.5 | 10.022 | 193.2 | 0.003 | 5.97 |
| pbp2x-464 | – | – | – | 2 | 2 | 2.1 | 199.9 | 0.010 | 3,018.7 | 0.192 | 6.01 |
a
Model parameters: R, rate of recombination; Θ, rate of mutation; R/Θ, rate of recombination to mutation; δ, mean of the exponential distribution modeling the length of recombined segments; ν, rate of nucleotide differences in the recombined segments; r/m, relative effect of recombination to mutation (R/Θ × δ × ν).
b
Values were determined with an added outgroup, pbp1a from SDSE strain NCTC9414. Without this outgroup, there were no detected recombination events and ClonalFrameML failed to produce meaningful output.