Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,558,3210TG48.7% 110.5 / 11.9 79T6P (ACC→CCC) mdtMmultidrug efflux MFS transporter MdtM
Reads supporting (aligned to +/- strand):  ref base T (6/34);  new base G (38/0);  total (45/34)
Fisher's exact test for biased strand distribution p-value = 2.71e-16
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCA  >  NZ_CP009273/4558234‑4558410
                                                                                       |                                                                                         
cAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaa                                                                                         >  2:1780703/1‑90 (MQ=255)
cAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaa                                                                                         >  1:508762/1‑90 (MQ=255)
  ggCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaa                                                                                       >  2:795689/1‑90 (MQ=255)
  ggCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaa                                                                                       >  2:749172/1‑90 (MQ=255)
  ggCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaa                                                                                       >  1:1511589/1‑90 (MQ=255)
   gCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTaaaaa                                                                                      <  2:1802892/90‑1 (MQ=255)
      ggATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaa                                                                                   >  2:850129/1‑89 (MQ=255)
      ggATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaa                                                                                   >  2:582100/1‑89 (MQ=255)
      ggATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaa                                                                                   >  2:1438404/1‑89 (MQ=255)
      ggATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaa                                                                                   >  2:1328609/1‑89 (MQ=255)
      ggATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaa                                                                                   >  1:90682/1‑89 (MQ=255)
      ggATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGCaaaaaaaa                                                                                   >  1:1359677/1‑89 (MQ=255)
      ggATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGGGGCGGCATGGCGGGGcaaaaaaa                                                                                   >  1:1216550/1‑89 (MQ=255)
       gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaag                                                                                  >  2:875524/1‑88 (MQ=255)
       gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaaa                                                                                  >  2:1370972/1‑88 (MQ=255)
        aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGt                                                                                 <  2:1073208/90‑1 (MQ=255)
        aTCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGt                                                                                 <  1:1107008/90‑1 (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                                                               <  1:911743/90‑1 (MQ=255)
                          tACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTcc                                                               <  1:95313/90‑1 (MQ=255)
                           aCGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCt                                                              <  1:1684819/90‑1 (MQ=255)
                           aCGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCt                                                              <  1:1067698/90‑1 (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                                   <  2:14401/90‑1 (MQ=255)
                                                      ccATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAAc                                   <  2:332374/90‑1 (MQ=255)
                                                       cATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAAAAACTCCTTGTCCGGAGAACCCCAACGGGGgaaaag                                  >  2:476004/1‑88 (MQ=255)
                                                        caggggAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  2:134422/87‑1 (MQ=255)
                                                        caggggAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  1:2073793/87‑1 (MQ=255)
                                                        aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  1:1780703/90‑1 (MQ=255)
                                                        aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  2:557995/90‑1 (MQ=255)
                                                        aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  1:1179534/90‑1 (MQ=255)
                                                        aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  1:1741550/90‑1 (MQ=255)
                                                        aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  1:317079/90‑1 (MQ=255)
                                                        aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                 <  2:167265/90‑1 (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   <  1:1175391/90‑1 (MQ=255)
                                                                                      gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc   <  1:476004/90‑1 (MQ=255)
                                                                                      gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc   <  2:1742385/90‑1 (MQ=255)
                                                                                      gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc   <  2:1763418/90‑1 (MQ=255)
                                                                                       tAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCa  <  1:1005738/90‑1 (MQ=255)
                                                                                       |                                                                                         
CAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCA  >  NZ_CP009273/4558234‑4558410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑