Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,558,3290CA47.0% 89.0 / 46.5 66R3L (CGT→CTT) mdtMmultidrug efflux MFS transporter MdtM
Reads supporting (aligned to +/- strand):  ref base C (0/35);  new base A (31/0);  total (31/35)
Fisher's exact test for biased strand distribution p-value = 1.56e-19
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

ATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAA  >  NZ_CP009273/4558242‑4558418
                                                                                       |                                                                                         
aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGt                                                                                         <  1:1107008/90‑1 (MQ=255)
aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGt                                                                                         <  2:1073208/90‑1 (MQ=255)
    gATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGGAAAAAAAGAGGCa                                                                                     >  1:2015246/1‑90 (MQ=255)
        cGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaac                                                                                 <  1:305734/90‑1 (MQ=255)
        cGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGGATaaa                                                                                 >  2:1168908/1‑89 (MQ=255)
        cGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAAGGCATaac                                                                                 >  2:596448/1‑90 (MQ=255)
         gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGGATaaca                                                                                >  2:1744515/1‑90 (MQ=255)
         gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATaaca                                                                                >  2:147066/1‑90 (MQ=255)
         gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGGATaaaa                                                                                >  2:1548231/1‑88 (MQ=255)
         gTCGACAGATACGCAGCAAAGCCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGCCAaaca                                                                                >  2:1735739/1‑90 (MQ=255)
             aCAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaacaaaca                                                                            <  2:776140/90‑1 (MQ=255)
             aCAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGCATaaaaaaaa                                                                            >  2:1880354/1‑88 (MQ=255)
              cAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAacaaacaa                                                                           <  1:556484/90‑1 (MQ=255)
               aGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGGATAAAAaacaac                                                                          >  2:108362/1‑90 (MQ=255)
                gATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGGATAaaaaaaaaac                                                                         >  1:377998/1‑88 (MQ=255)
                gATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGCATAaaaaaaaaaa                                                                         >  1:1027805/1‑88 (MQ=255)
                  tACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                                                                       <  1:95313/90‑1 (MQ=255)
                  tACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                                                                       <  1:911743/90‑1 (MQ=255)
                   aCGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCt                                                                      <  1:1067698/90‑1 (MQ=255)
                   aCGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCt                                                                      <  1:1684819/90‑1 (MQ=255)
                     gcagcaAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGGGTAAAAAAAAAATCCTTg                                                                    >  1:1054290/1‑90 (MQ=255)
                       agcaAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAAAGGCAAAAAAAAAAAAACCTTGTc                                                                  >  1:317082/1‑90 (MQ=255)
                        gcaAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAAAAACTCCTTTTcc                                                                 >  2:136312/1‑90 (MQ=255)
                        gcaAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGCATAAAAAAAAACACCTTTTcc                                                                 >  2:1741550/1‑90 (MQ=255)
                          aaaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTgg                                                                                       <  1:766797/66‑1 (MQ=255)
                          aaaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTgg                                                                                       >  2:766797/1‑66 (MQ=255)
                          aaaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGGATAACAAAAAACTCCTTTTCCgg                                                               >  2:1843371/1‑90 (MQ=255)
                          aaaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAAGGGATAAAAAAAAAAACCCTGTCCgg                                                               >  1:618544/1‑90 (MQ=255)
                           aaGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGTAAAAAAAGTGGCATAAAAAAAAACCCCTTGTCCCga                                                              >  2:1179534/1‑90 (MQ=255)
                                aTACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAAGGGGATAAAAAAAAACTCCTTTTCCGGAGAAcc                                                         >  2:64389/1‑90 (MQ=255)
                                aTACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGGATAAAAAACAACTCCTTGTCCGGAGAAcc                                                         >  2:744845/1‑90 (MQ=255)
                                aTACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTGTCCGGAGaaac                                                         >  2:863839/1‑88 (MQ=255)
                                     aaaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGGATAACAAAAAACTCCTTGTCCGGGGAACCCCCAc                                                    >  2:1281492/1‑90 (MQ=255)
                                       aTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAACAAAAAACTCCTTGTCCGGGGAACCCCAACgg                                                  >  2:311481/1‑90 (MQ=255)
                                       aTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGGGGCATAAAAAACAAACCCTTTTCCGGAGAAACCCCACgg                                                  >  2:1401702/1‑90 (MQ=255)
                                       aTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGCATAAAAAAAAAATCCTTTTCCGGAGAAACCCCACgg                                                  >  1:557995/1‑90 (MQ=255)
                                           aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGaa                                              <  1:289254/90‑1 (MQ=255)
                                              ccATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAAc                                           <  2:332374/90‑1 (MQ=255)
                                              ccATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAAc                                           <  2:14401/90‑1 (MQ=255)
                                               cATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAAAAACTCCTTGTCCGGAGAACCCCAACGGGGgaaaag                                          >  2:476004/1‑88 (MQ=255)
                                                caggggAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  2:134422/87‑1 (MQ=255)
                                                caggggAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:2073793/87‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  2:557995/90‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:1780703/90‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:1179534/90‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:317079/90‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  2:167265/90‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:1741550/90‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:64389/90‑1 (MQ=255)
                                                aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:1507045/90‑1 (MQ=255)
                                                 tCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAAAAAAAAACTCCTTTTCCGGGGAAACCCAACGGGGGAAAAGaa                                        >  2:424614/1‑90 (MQ=255)
                                                 tCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTTTCCGGAGAACCCCAACGGGGGAAAAGaa                                        >  1:721808/1‑90 (MQ=255)
                                                  cGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGaaa                                       <  2:2062371/90‑1 (MQ=255)
                                                            aGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCg                             <  2:1716007/90‑1 (MQ=255)
                                                            aGCGTGGCGGCATGGCGGGGGAAAAAAAGGGGCGTAAAAAAAAAATCCCTGTCCGGGGGAGCCCACAGGGGAGAAAGAAAATAAAAACCg                             >  1:1206559/1‑90 (MQ=255)
                                                                  gcggcATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCCTTTCCGGGGAACCCCAACGGGGGAAAAGAAAATCAATACCGTCGGTa                       >  1:1943437/1‑90 (MQ=255)
                                                                   cggcATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTaa                      <  2:721808/90‑1 (MQ=255)
                                                                    ggcATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAAt                     <  2:612119/90‑1 (MQ=255)
                                                                         ggCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGa                <  2:1720432/90‑1 (MQ=255)
                                                                            gggTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAg             <  1:1370972/90‑1 (MQ=255)
                                                                              gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc           <  2:1763418/90‑1 (MQ=255)
                                                                              gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc           <  1:1175391/90‑1 (MQ=255)
                                                                              gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc           <  2:1742385/90‑1 (MQ=255)
                                                                              gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc           <  1:476004/90‑1 (MQ=255)
                                                                               tAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCa          <  1:1005738/90‑1 (MQ=255)
                                                                                   aaaaCGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTg      <  1:1183795/90‑1 (MQ=255)
                                                                                       cGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc           <  1:1720844/81‑1 (MQ=255)
                                                                                       cGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc           >  2:1720844/1‑81 (MQ=255)
                                                                                       cGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGaa  <  1:1744515/90‑1 (MQ=255)
                                                                                       |                                                                                         
ATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAA  >  NZ_CP009273/4558242‑4558418

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑