TABLE 2

Signatures of selection in known drug resistance genes

GeneLocus tag
(Rv no.)
Drug(s)TB DreamaπbθbTDcHomoplasydFSTeType(s)f
katGRv1908cINH2260.800.820.34YYTight
pncARv2043cPZA1950.971.000.00YNSloppy
embBRv3795EMB1170.770.890.08YYHybrid
ahpCRv2428INH310.200.210.61YN
tlyARv1694CAP280.370.890.06NN
embCRv3793EMB280.590.740.01NN
embRRv1267cEMB250.460.490.28NN
rrsRvnr01STR, KAN, CAP240.891.000.08NN
ethARv3854cETO230.721.000.00YY (IG)Sloppy,
tight (IG)
gidRv3919cSTR221.001.000.07YNSloppy
gyrBRv0005MOX, OFL150.580.910.00YN
fabG1Rv1483INH, ETO130.600.660.30YY (IG)Tight
inhARv1484INH, ETO130.560.590.32YN
rpsLRv0682STR130.990.950.80YYHybrid
gyrARv0006MOX, OFL120.810.940.10YYTight
embARv3794EMB110.770.380.79NN
kasARv2245INH70.730.180.86NN
ndhRv1854cINH50.570.520.28NN
iniARv0342EMB, INH40.640.330.56NN
Rv0340Rv0340INH30.890.880.57NN
iniBRv0341EMB, INH30.070.070.79NN
fbpCRv0129cINH30.780.190.89NN
rmlDRv3266cEMB20.750.360.75NN
iniCRv0343EMB, INH20.490.670.08NN
thyARv2764cPAS20.840.940.28NN
natRv3566cINH20.760.550.63NN
accD6Rv2247INH10.900.630.90NN
furARv1909cINH10.800.630.62NN
Rv1772Rv1772INH10.500.350.54NN
fabDRv2243INH10.260.280.54NN
fadE24Rv3139INH10.360.580.12NN
rpoBRv0667RIF10.820.920.18YYHybrid
efpARv2846cINH10.100.110.65NN
ethRRv3855ETO0.580.770.22NN
Rv0678Rv0678BDQ0.370.720.25NN
eisRv2416cKAN0.510.280.54NN
mshARv0486ETO0.860.480.87NN
rpsARv1630PZA0.880.620.84NN
folCRv2447cPAS0.660.780.11YN
rplCRv0701LZD0.570.770.21NN
  • a The number of distinct entries in the TB Drug Resistance Mutation Database for each gene is reported in the TB Dream column.

  • b π and θ are the percentiles for each diversity value, respectively.

  • c TD is the percentile of the residual after linear regression of Tajima’s D values with gene length.

  • d Genes with homoplastic SNPs are indicated with “Y” (for Yes) in the Homoplasy column. N, no.

  • e If a homoplastic SNP was also an FST outlier, it is indicated with a “Y” in the FST column. N, no.

  • f Genes are classified as tight, sloppy, or hybrid targets of selection based on diversity, homoplasy, and FST results. (IG) indicates an intergenic SNP.