Table 5.
Calculation of the MRCA of Ugandan type II and III isolates and reference strains based on the intron mutation rate
| Chromosome | Intron length* (bp) | Minor SNPs in introns | MRCA Me49/UgII (years) | MRCA VEG/UgIII (years) |
| Type II | ||||
| II | 89,003 | 34 | 19,691 | |
| IV | 85,471 | 58 | 34,979 | |
| VI | 152,385 | 65 | 21,987 | |
| VIIa | 198,902 | 28 | 7,256 | |
| IX | 266,876 | 117 | 22,598 | |
| X | 334,181 | 79 | 12,186 | |
| Total II | 1,126,818 | 381 | 17,429 | |
| Type III | ||||
| Ia | 80,522 | 2 | 1,280 | |
| Ib | 85,805 | 8 | 4,806 | |
| III | 82,660 | 9 | 5,612 | |
| V | 119,536 | 15 | 6,468 | |
| VIIb | 220,517 | 39 | 9,116 | |
| VIII | 337,557 | 78 | 11,911 | |
| XII | 352,605 | 78 | 11,403 | |
| Total III | 1,279,202 | 229 | 9,228 |
The divergence between Ugandan and reference strains were calculated based on the intron mutation rate 1.94 × 10-8 [26]. A more comprehensive version is provided in Additional data file 4. *Length of intronic regions. MRCA, most recent common ancestor.