Table 4.
Variants identified in relapse pairs
| Strain pair | Type | Base numbera | Gene | Function |
|---|---|---|---|---|
| 002 | NS | 146316 | Rv0120c, fusA2 | Translation |
| NS | 345226 | Rv0283, eccB3 | Part of ESX-3 (essential, ESX-3 T7SS is implicated in metal homeostasis) | |
| S | 3135592 | Rv2827c-109 | ||
| INDEL (TC/TCC) | 3600992 | Rv3224B | Predicted membrane protein | |
| 006 | S | 1348678 | Rv1205-41 | |
| S | 1370403 | Rv1227c | ||
| S | 2828233 | hisT down | ||
| 010 | NS | 200390 | Rv0170, mce1B | Part of ESX-1, essential for pathogenesis |
| 012 | NS | 2510502 | Rv2237A | CP, non-essential |
| 017 | INDEL (GC/GCC) | 341124 | Rv0281 | Possible membrane protein |
| 018 | S | 783720 | fusA1 | |
| S | 783729 | fusA1 | ||
| S | 783732 | fusA1 | ||
| S | 1476666 | rrl | ||
| S | 4050367 | folE | ||
| 019 | NS | 3884906 | Rv3467 | CHP, non-essential |
| 024 | S | 848538 | PPE12 | |
| 025 | S | 1929374 | Rv1703c | |
| 026 | NS | 1192723 | Rv1069c | CP, non-essential |
| NS | 1690758 | Rv1499 | CHP, non-essential | |
| 027 | S | 114494 | nrp | |
| 031 | S | 175753 | Rv0149 | |
| S | 620981 | Rv0530 | ||
| S | 1315992 | pks4 | ||
| NS | 1540497 | Rv1367c | CP, non-essential | |
| S | 2788333 | plsB2 | ||
| 033 | NS | 3618159 | Rv3240c, secA1 | Protein export, essential |
| 036 | S | 923816 | lysT | |
| NS | 924229 | Rvnt13, pheU | tRNA | |
| NS | 924234 | Rvnt13, pheU | tRNA | |
| S | 924263 | pheU | ||
| NS | 1476973 | Rvnr03, rrf | 5S rRNA |
Function assigned using the Tuberculist database (http://tuberculist.epfl.ch/)
aSNPs between individual pairs predicted to be relapse
CHP conserved hypothetical protein, CP conserved protein, NS non-synonymous SNP, S synonymous SNP, SNP single-nucleotide polymorphism