Mutation ID (Table S1) Population Fwd Primer Name Fwd Primer Sequence Rev Primer Name Rev Primer Sequence Primer used for Sanger Validation? 288 BK75 oSHS_rpsB_F01 CCGATGTTCAACGAAGCTCTG oSHS_rpsB_R01 TGTAAGCTCCCGGGAATTCTC oSHS_rpsB_F01 yes 1006 BK45 oSHS_ybeD_F01 GAACTATCAACTTCCAGCTTG oSHS_ybeD_R01 CCTGATACAAAACGGCATCTC oSHS_ybeD_R01 yes 1007 BK41 oSHS_ybeD_F01 GAACTATCAACTTCCAGCTTG oSHS_ybeD_R01 CCTGATACAAAACGGCATCTC oSHS_ybeD_R01 yes 1008 BK42 oSHS_ybeD_F01 GAACTATCAACTTCCAGCTTG oSHS_ybeD_R01 CCTGATACAAAACGGCATCTC oSHS_ybeD_R01 yes 1009 BK42 oSHS_ybeD_F01 GAACTATCAACTTCCAGCTTG oSHS_ybeD_R01 CCTGATACAAAACGGCATCTC oSHS_ybeD_R01 yes 1010 BK44 oSHS_ybeD_F01 GAACTATCAACTTCCAGCTTG oSHS_ybeD_R01 CCTGATACAAAACGGCATCTC oSHS_ybeD_R01 yes 1496 BK70 oSHS_rpsA_F01 TGAAATCTGAGTCCGCCATC oSHS_rpsA_R01 AGCCGATGAAGATACCGAAG oSHS_rpsA_F01 yes 1498 BK70 oSHS_rpsA_F01 TGAAATCTGAGTCCGCCATC oSHS_rpsA_R01 AGCCGATGAAGATACCGAAG oSHS_rpsA_F02 yes 1499 BK71 oSHS_rpsA_F03 CGAAATCGCTGCAGTTGTTC oSHS_rpsA_R02 TAGCCGCCCTTAGTGCTTGATT oSHS_rpsA_F03 yes 2222 BK55 oSHS_sapA_F01 TACTTCGACAGCCTGCAATTTG oSHS_sapA_R01 GTAAAATAGAGGCCGCCGTTTC oSHS_sapA_R01 yes 2223 BK54 oSHS_sapA_F01 TACTTCGACAGCCTGCAATTTG oSHS_sapA_R01 GTAAAATAGAGGCCGCCGTTTC oSHS_sapA_R01 yes 4294 BK30 oSHS_IrhA_F01 GCTCGATTGTGCTGTTAATAAC oSHS_IrhA_R01 ATGACATGCGCGTGTTTG oSHS_IrhA_R01 yes 4294 BK31 oSHS_IrhA_F01 GCTCGATTGTGCTGTTAATAAC oSHS_IrhA_R01 ATGACATGCGCGTGTTTG oSHS_IrhA_R01 yes 4294 BK32 oSHS_IrhA_F01 GCTCGATTGTGCTGTTAATAAC oSHS_IrhA_R01 ATGACATGCGCGTGTTTG oSHS_IrhA_R01 yes 4818 BK72 oSHS_rpls_F01 ATCAGTTTACCCAGGATAAGAG oSHS_rpls_R01 TCCCATAGCCAGTAACAAGAC oSHS_rplS_R01 yes 5155 BK60 oSHS_amiC_F01 GCAAGTGTAAATTTTATGCGAGAG oSHS_amiC_R01 AAGGTCGTCGGTTCAAATCC oSHS_amiC_R01 no 5158 BK62 oSHS_amiC_F01 GCAAGTGTAAATTTTATGCGAGAG oSHS_amiC_R01 AAGGTCGTCGGTTCAAATCC oSHS_amiC_R02 yes 5869 BK44 oSHS_tufA_F01 GGTCGTGCATCATACACTATG oSHS_tufA_R01 TGAAGAATGGAGTATGACGGCC oSHS_tufA_R01 yes 5930 BK64 oSHS_tufA_F01 GGTCGTGCATCATACACTATG oSHS_tufA_R02 CGAGGTGTTGATGGTGATAC oSHS_tufA_R02 yes 5934 BK45 oSHS_fusA_F01 CGGTGTTGTTGACCTGGTGAAA oSHS_fusA_R01 GAGAGAGCACGGGACTTTGG oSHS_fusA_R01 yes 5936 BK64 oSHS_fusA_F01 CGGTGTTGTTGACCTGGTGAAA oSHS_fusA_R01 GAGAGAGCACGGGACTTTGG oSHS_fusA_R02 yes 5937 BK65 oSHS_rpsG_F01 AGTATTTCCATGCCACGTCG oSHS_rpsG_R02 GGATAACCAACGGTAGTGTGC oSHS_rpsG_R02 yes 5938 BK61 oSHS_rpsG_F01 AGTATTTCCATGCCACGTCG oSHS_rpsG_R02 GGATAACCAACGGTAGTGTGC oSHS_rpsG_R02 yes 5938 BK62 oSHS_rpsG_F01 AGTATTTCCATGCCACGTCG oSHS_rpsG_R02 GGATAACCAACGGTAGTGTGC oSHS_rpsG_R02 yes 5938 BK64 oSHS_rpsG_F01 AGTATTTCCATGCCACGTCG oSHS_rpsG_R02 GGATAACCAACGGTAGTGTGC oSHS_rpsG_R02 yes 5939 BK60 oSHS_rpsG_F01 AGTATTTCCATGCCACGTCG oSHS_rpsG_R02 GGATAACCAACGGTAGTGTGC oSHS_rpsG_R02 yes 6040 BK41 oSHS_hslO_F01 GGACAAAAAAGAGCGCCG oSHS_hslO_R01 AACAACATACCGCCTGCAG oSHS_hslO_F01 no 6041 BK45 oSHS_hslO_F01 GGACAAAAAAGAGCGCCG oSHS_hslO_R01 AACAACATACCGCCTGCAG oSHS_hslO_F01 yes 6042 BK43 oSHS_hslO_F01 GGACAAAAAAGAGCGCCG oSHS_hslO_R01 AACAACATACCGCCTGCAG oSHS_hslO_F01 yes 7014 BK23 oSHS_trkH_F01 GAATCTTTCTCTGGCCTGAC oSHS_trkH_R01 TAACCACCAGCGTAAACTGTAC oSHS_trkH_F01 yes 7014 BK52 oSHS_trkH_F01 GAATCTTTCTCTGGCCTGAC oSHS_trkH_R01 TAACCACCAGCGTAAACTGTAC oSHS_trkH_F01 yes 7014 BK53 oSHS_trkH_F01 GAATCTTTCTCTGGCCTGAC oSHS_trkH_R01 TAACCACCAGCGTAAACTGTAC oSHS_trkH_F01 yes 7265 BK71 oSHS_rpmE_F01 ATGAAAATCCGCTCCACCGTTG oSHS_rpmE_R01 GTGGAAGGTTTACCAGAACGCG oSHS_rpmE_F01 yes 7348 BK20 oSHS_rpoC_F01 ATTGTGCTAACTCCGACG oSHS_rpoC_R01 GTTGGTAGACATCATCAGCG oSHS_rpoC_F02 yes 7348 BK31 oSHS_rpoC_F01 ATTGTGCTAACTCCGACG oSHS_rpoC_R01 GTTGGTAGACATCATCAGCG oSHS_rpoC_F02 yes 7348 BK42 oSHS_rpoC_F01 ATTGTGCTAACTCCGACG oSHS_rpoC_R01 GTTGGTAGACATCATCAGCG oSHS_rpoC_F02 yes 7789 BK74 oSHS_rpsF_F01 AACACGTTCCTTGCCTCC oSHS_rpsF_R01 GATGGACTGACCTTTCGAAG oSHS_rpsF_F01 yes 7791 BK71 oSHS_rpsF_F01 AACACGTTCCTTGCCTCC oSHS_rpsF_R01 GATGGACTGACCTTTCGAAG oSHS_rpsF_F01 yes 7792 BK75 oSHS_rpsF_F01 AACACGTTCCTTGCCTCC oSHS_rpsF_R01 GATGGACTGACCTTTCGAAG oSHS_rpsF_F01 yes 7793 BK73 oSHS_rpsF_F01 AACACGTTCCTTGCCTCC oSHS_rpsF_R01 GATGGACTGACCTTTCGAAG oSHS_rpsF_F01 yes 8054 BK20 oSHS_fimI_F01 GGTAACAGAGTTGAATGCCG oSHS_fimI_R01 TCACGCGTTGCCATATAACC oSHS_fimI_F01 yes 8054 BK34 oSHS_fimI_F01 GGTAACAGAGTTGAATGCCG oSHS_fimI_R01 TCACGCGTTGCCATATAACC oSHS_fimI_F01 yes 8054 BK45 oSHS_fimI_F01 GGTAACAGAGTTGAATGCCG oSHS_fimI_R01 TCACGCGTTGCCATATAACC oSHS_fimI_F01 yes 8054 BK51 oSHS_fimI_F01 GGTAACAGAGTTGAATGCCG oSHS_fimI_R01 TCACGCGTTGCCATATAACC oSHS_fimI_F01 yes 8054 BK75 oSHS_fimI_F01 GGTAACAGAGTTGAATGCCG oSHS_fimI_R01 TCACGCGTTGCCATATAACC oSHS_fimI_F01 yes