Table 6.
Calculation of the MRCA of Ugandan type II and III isolates and reference strains based on their relationship to the divergence between Me49 and VEG
| Chromosome | Length* (bp) | Minor SNPs | Major SNPs | MRCA Me49/UgII (years) | MRCA VEG/UgIII (years) |
| Type II | |||||
| II | 2,302,931 | 125 | 4,370 | 4,291 | |
| IV | 2,576,468 | 236 | 4,731 | 7,483 | |
| VI > 2.6 Mb | 1,000,655 | 70 | 1,913 | 5,489 | |
| VIIa | 4,502,211 | 135 | 8,663 | 2,338 | |
| IX 0.5-4 Mb | 3,500,000 | 205 | 6,349 | 4,843 | |
| X | 7,418,475 | 445 | 13,459 | 4,960 | |
| Total II | 21,300,740 | 1,216 | 39,845 | 4,578 | |
| Type III | |||||
| Ib > 1.2 Mb | 756,324 | 6 | 1,375 | 655 | |
| III < 1.9 Mb | 1,900,000 | 33 | 3,953 | 1,252 | |
| V | 3,147,601 | 80 | 5,725 | 2,096 | |
| VIIb < 2.5 Mb | 2,500,000 | 43 | 5,069 | 1,272 | |
| VIII > 4 Mb | 2,923,375 | 49 | 6,268 | 1,173 | |
| XII < 1.5 Mb | 1,500,000 | 69 | 3,259 | 3,176 | |
| Total III | 12,727,300 | 280 | 25,648 | 1,638 |
The divergence between Ugandan and reference strains were calculated based on their relationship to the divergence between Me49 and VEG, with the MRCA estimated to be at 150,000 years ago [27]. A more comprehensive version is provided in Additional data file 4. *Length of regions with a major SNP type. MRCA, most recent common ancestor.