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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].
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BMC Infectious Diseases

ISSN: 1471-2334

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