Table 1. A comparison of SNP-typing systems.
| SNP set and reference |
Lineage classified (Number of sublineages classified) |
No. of RD lineages covered | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | M. bovis | Total | ||
| This study62 SNPs | Yes (8*) | Yes (6*) | Yes (5*) | Yes (36*) | Yes (0) | Yes (0) | Yes (0) | Yes (0) | 7 (55) | 19† |
| Homolka et al.1771 SNPs | Yes (1‡) | Yes (0) | Yes (0) | Yes (7§) | Yes (2||) | Yes (0) | No (−) | Yes (0) | 6 (10) | NA |
| Comas et al.1693 SNPs | Yes (1‡) | Yes (2¶) | Yes (0) | Yes (5#) | Yes (0) | Yes (0) | No (−) | Yes (0) | 6 (7) | 9** |
| Filliol et al.2145 SNPs | No (−) | No (−) | No (−) | No (−) | No (−) | No (−) | No (−) | No (−) | 6 (−) | NA |
NA, not applicable; RD, regions of difference; SNP, single-nucleotide polymorphism.
*See Supplementary Data 1 for a complete description of lineages and sublineages.
†RD239, 105, 207, 181, 150, 142, 750, 182, 183, 193, 122, 726, 219, 761, 115, 174, 724, 711, 702; 239.
‡Lineage 1.2.1.
§Lineages 4.6.2.2, 4.1.2.1, 4.3, 4.4.1.1, 4.2.2.1, 4.2.1 and an ambiguous ‘Ghana’.
||West Africanum Ia and Ib.
¶Lineages 2.1 and 2.2.
#Lineages 4.6.2.2, 4.6.1, 4.1.1, 4.1.2.1 and 4.3.
**RD105, 207, 750, 726, 724, 182, 711, 702 and 7.