TABLE 3

Homoplastic FST outliers

LocationGeneaTypewcFSTb value for the following drug:KnowncLineage
AMICAPEMBETOINHKANMOXOFLPROPZARIFSTR
1821dnaNIntergenic0.430.570.10NAll
7570gyrAMissense0.330.110.460.660.290.18YAll
7572gyrAMissense0.06YAll
7581gyrAMissense0.07YAll
7582gyrAMissense0.350.22YAll
75233icd2Intergenic0.05NAll
94388hycQSynonymous0.070.120.120.13NAll
230170Rv0194Missense0.120.050.120.13NAll
332916vapC25Missense0.100.090.20NAll
761155rpoBMissense0.310.580.100.720.41YAll
761161rpoBMissense0.330.090.510.710.130.16YAll
764817rpoCMissense0.19NAll
781687rpsLMissense0.100.320.150.37YAll
922004Rv0830Missense0.300.120.430.100.21NAll
1076880Rv0965cSynonymous0.120.120.13NAll
1673425fabG1Intergenic0.11YAll
1673432fabG1Intergenic0.520.65YAll
1722228pks5Missense0.080.280.070.170.26NAll
2122395lldD2Synonymous0.06NAll
2155168katGMissense0.360.890.130.320.600.66YAll
2174216Rv1922Synonymous0.08NAll
2207525Rv1958cIntergenic0.09NAll
2422824Rv2161cMissense0.300.430.570.10NAll
2660319mbtFMissense0.06NAll
2715369Rv3413cIntergenic0.170.090.280.300.13NAll
2866647lppASynonymous0.120.07NAll
2867298lppBSynonymous0.13NAll
2867347lppBSynonymous0.130.060.120.14NAll
2867756lppBSynonymous0.14NAll
3500149Rv3134cSynonymous0.11NAll
3550789Rv3183Synonymous0.120.13NAll
3680932lhrSynonymous0.120.120.13NAll
4001622fadA6Intergenic0.11NAll
4247429embBMissense0.250.450.230.050.110.310.210.20YAll
4247574embBSynonymous0.190.070.270.30YAll
4327480ethAIntergenic0.200.070.270.30YAll
764948rpoCMissense0.06YL2
4248003embBMissense0.16YL2
698dnaAMissense0.10NL4
60185Rv0057Missense0.06NL4
761110rpoBMissense0.66YL4
764822rpoCMissense0.06YL4
781822rpsLMissense0.120.130.14YL4
2123145lldD2Missense0.06NL4
2372550dopMissense0.64NL4
2715344Rv2413cIntergenic0.06NL4
2986827Rv2670cMissense0.160.170.15NL4
4247431embBMissense0.110.110.07YL4
4248003embBMissense0.06YL4
  • a For intergenic SNPs, the closest gene is listed.

  • b Weir and Cockerham’s FST (wcFST) values in the top 1% of values genome-wide are reported for each drug.

  • c We identified mutations in genes previously associated with drug resistance (Y for Yes in the Known column) and novel putative resistance or compensatory mutations (N for Novel in the Known column).