Table 3 Lineage prediction of the various tools compared with traditional typing methods.
Genotype | #strains | CASTB | KvarQ | Mykrobe Predictor TB | PhyResSE | TBProfiler |
|---|---|---|---|---|---|---|
EAI | 4 | lineage 1 (Indo-Oceanic lineage) | lineage 1 | East African/Indian ocean | EAI/lineage1.1.1 | lineage1.1.1 |
Beijing | 4 | lineage 2 (East-Asian lineage) | lineage 2/beijing sublineage | Beijing/East Asia | Beijing/lineage2.2.1 | lineage2.2.1 |
Ghana | 1 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Ghana/lineage4.1 | lineage4.1 |
Sierra Leone-1 | 7 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.1 | lineage4.1 |
X-type | 1 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.1.1.1 | lineage4.1.1.1 |
1 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.1.1.3 | lineage4.1.1.3 | |
Haarlem | 12 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Haarlem/lineage4.1.2.1 | lineage4.1.2.1 |
LAM | 9 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | LAM/lineage4.3.3 | lineage4.3.3 |
1 | lineageM. bovis | lineage 4 | European/American | LAM/lineage4.3.3 | lineage4.3.3 | |
2 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | LAM/lineage4.3.4.1 | lineage4.3.4.1 | |
3 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | LAM/lineage4.3.4.2 | lineage4.3.4.2 | |
S-type | 3 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | S-type/lineage4.4.1.1 | lineage4.4.1.1 |
Cameroon | 4 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Cameroon/lineage4.6.2.2 | lineage4.6.2.2 |
Sierra Leone-2 | 9 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.8 | lineage4.8 |
West African 1 | 6 | lineage 5 (West-African lineage 1) | lineage 5 | Unknown Species | West African 1/lineage5 | lineage5 |
West African 2 | 14 | lineage 6 (West-African lineage 2 | lineage 6 | M. africanum | West African 2/lineage6/BOV_AFRI | West African 2/6/BOV_AFRI |
3 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.1 | lineage4.1 | |
3 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.1.1.3 | lineage4.1.1.3 | |
None | 1 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Haarlem/lineage4.1.2.1 | lineage4.1.2.1 |
1 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.6 | lineage4.6.1 | |
3 | lineage 4 (Euro-American lineage) | lineage 4 | European/American | Euro-American Superlineage/lineage4.8 | lineage4.8 |
