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Table 4 Variants identified in relapse pairs

From: Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial

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
  1. Function assigned using the Tuberculist database (http://tuberculist.epfl.ch/)
  2. aSNPs between individual pairs predicted to be relapse
  3. CHP conserved hypothetical protein, CP conserved protein, NS non-synonymous SNP, S synonymous SNP, SNP single-nucleotide polymorphism