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Table 4 Estimation of SNPs that might have been subject to stabilizing or diversifying selection between M. tuberculosis Lineage 2 and 4, Guangxi, China, 2018

From: A genome epidemiological study of mycobacterium tuberculosis in subpopulations with high and low incidence rate in Guangxi, South China

SNP Position Gene FST RefCodon CodonPos AlterCodon AA variation Subcellular location CDS Product Annotation
1230778 mazF3 0.9703 ACC 65 ATC T/I unknown Toxic component of a type II toxin-antitoxin (TA) system.
         It dramatically increases persister cell formation
         in M.smegmatis upon challenge with gentamicin or kanamycin.
         Probable propionyl-CoA carboxylase beta chain 4 AccD4.
4254431 accD4 0.9644 GAC 506 GAT D/D Cell wall mycolate cell wall layer assembly.
3408150 Rv3047c 0.9644 ACA 53 GCA T/A unknown Hypothetical unknown protein.
3027798 Rv2714 0.9644 GTG 245 GCG V/A plasma membrane Conserved alanine and leucine rich protein.
         Identified in the membrane fraction of M. tuberculosis H37Rv
         confers non-target based resistance to azoles,
776100 mmpL5 0.9585 ACC 794 ATC T/I integral component of plasma membrane clofazimine and bedaquiline,
         via an efflux mechanism.
738522 mmaA2 0.9585 GAA 213 GAC E/D plasma membrane Involved in mycolic acids modification.
3530955 Rv3161c 0.9585 GTC 62 CTC V/L plasma membrane Possible dioxygenase
3266030 ppsD 0.9585 TCA 1261 TCG S/S plasma membrane Phenolpthiocerol synthesis type-I polyketide synthase PpsD
262268 Rv0219 0.9585 GCA 5 GCT A/A Cell wall Probable conserved transmembrane
         Probable dihydroorotate dehydrogenase PyrD.
2399734 pyrD 0.9585 GGC 339 AGC G/S plasma membrane Essential gene for in vitro growth of H37Rv,
         by analysis of saturated Himar1 transposon libraries [13]
931123 lpqQ 0.9527 TAT 57 TAC Y/Y extracellular region Possible lipoprotein LpqQ
         ESX conserved component EccA3.
342146 eccA3 0.9527 GAA 6 GCA E/A plasma membrane ESX-3 type VII secretion system protein.
         Part of the ESX-3 specialized secretion system.
2388641 ansP1 0.9527 GGC 9 GAC G/D integral component of membrane L-asparagine permease AnsP1
2138453 Rv1888A 0.9527 GGG 55 GGA G/G Cell wall Conserved hypothetical protein
213147 sigG 0.9527 GAC 332 TAC D/Y unknown Probable alternative RNA polymerase sigma factor SigG
  1. Genome coordinates correspond to reference genome sequence AL123456.3. Subcellular location and CDS product annotation based-on UniProt [14] and TubercuList [15].