Table 4.
SNP barcode for Lisboa3 and Q1 clades. Clade-specific mutations are highlighted in bold upon validation against a global dataset.
| Clade/SNP Positiona | Gene | Reference Allele | Mutated Allele | Mutation | Mutation Type (Non-) Synonymous | Essential Geneb |
|---|---|---|---|---|---|---|
| Q1 | ||||||
| 3520172 | Rv3152 (nuoH1) | G | A | Leu297Leu | S | No |
| Lisboa3 | ||||||
| 208287 | Rv0176 | A | C | Glu279Ala | NS | No |
| 405812 | Rv0338c | T | C | Ile10Met | NS | Yes |
| 740561 | Rv0646c (lipG) | C | T | Pro193Pro | S | No |
| 1057412 | Rv0947c | A | G | Pseudogene | — | No |
| 1153137 | Rv1029 (kdpA) | G | A | Ala376Thr | S | No |
| 1706439 | Rv1514c | G | A | Leu53Leu | S | No* |
| 1885422 | Rv1662 (pks8) | C | T | Ser1240Leu | NS | Yes |
| 2123086 | Rv1872c (lldD2) | C | A | Pro22Pro | S | No |
| 2255294 | Rv2006 (otsB1) | T | C | Ile198Thr | NS | No** |
| 2264189 | Rv2017 | C | T | His64His | S | Yes |
| 3544710 | Rv3176 (mesT) | T | C | Pro197Pro | S | No |
| 4034894 | Rv3593 (lpqF) | G | A | Pro181Pro | S | Yes*** |
| 4104091 | Rv3664c (dppC) | C | T | Ala129Thr | NS | No |
aSNP position is relative to the M. tuberculosis H37Rv genome (GenBank Accession NC000962.3);
bGene essentiality: *essential in vivo, non-essential in culture; **non-essential in M. tuberculosis H37Rv, essential in M. tuberculosis CDC1551; and ***essential by Sassetti et al.45, non-essential by DeJesus et al.44.