Table 2. Variants that co-occur with the example indels (Fig 2).
| Co-occurring variant | Locus tag | H37Rv homolog | Gene name | Product | Notes |
|---|---|---|---|---|---|
| 6515bp deletion of pncA | |||||
| iSNP | MT49_RS03955 | Rv0755c | PPE12 | PPE family protein PPE12 | |
| sSNP | MT49_RS13630 | Rv2582 | ppiB | peptidyl-prolyl cis-trans isomerase | |
| IS6110 insertion into bfrA | |||||
| nsSNP | MT49_RS03540 | Rv0676c | mmpL5 | siderophore RND transporter MmpL5 | ABR-conferring |
| sSNP | MT49_RS04920 | Rv0935 | pstC1 | phosphate ABC transporter permease | |
| nsSNP | MT49_RS08525 | Rv1625c | cya | adenylate cyclase | |
| nsSNP | MT49_RS09530 | Rv1830 | MerR family transcriptional regulator | ||
| sSNP | MT49_RS09595 | Rv1843c | guaB1 | GuaB1 family IMP dehydrogenase-related protein | |
| nsSNP | MT49_RS12315 | Rv2337c | hypothetical protein | ||
| nsSNP | MT49_RS20315 | Rv3854c | ethA | FAD-containing monooxygenase EthA | ABR-conferring |
| 1bp deletion in mmaA3 | |||||
| sSNP | MT49_RS03380 | Rv0645c | mmaA1 | mycolic acid methyltransferase MmaA1 | Involved in membrane biogenesis |
| iSNP | MT49_RS08155 | Rv1535 | hypothetical protein | ||
| IS6110 insertion | MT49_RS16445 | Rv3126c | hypothetical protein | ||
| nsSNP | MT49_RS17845 | Rv3383c | idsB | polyprenyl synthetase family protein | Involved in membrane biogenesis |
| nsSNP | MT49_RS19685 | Rv3740c | wax ester/triacylglycerol synthase family O-acyltransferase | Involved in membrane biogenesis | |
| nsSNP | MT49_RS20030 | Rv3800c | pks13 | acyltransferase domain-containing protein | Involved in membrane biogenesis |
| 1bp deletion in ethA | |||||
| nsSNP | MT49_RS03490 | Rv0667 | rpoB | DNA-directed RNA polymerase subunit beta | Essential and ABR-conferring |
| Intergenic IS6110 insertion | MT49_RS09400 | Rv1804c | hypothetical protein | Predicted secreted protein | |
Gene names and additional information are displayed according to the Mycobrowser annotations (https://mycobrowser.epfl.ch/, last accessed 28 November 2019), when available. Locus tags and products are taken from the annotation of the 49–02 reference genome. In case of intergenic variants, we show the information for the gene downstream of the variant. Notes show additional information related to protein functions. iSNP–intergenic SNP, sSNP–synonymous SNP, nsSNP–nonsynonymous SNP.