Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,558,3210TG53.8% 30.8 / 35.7 26T6P (ACC→CCC) mdtMmultidrug efflux MFS transporter MdtM
Reads supporting (aligned to +/- strand):  ref base T (1/11);  new base G (14/0);  total (15/11)
Fisher's exact test for biased strand distribution p-value = 1.55e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.92e-05
Rejected as consensus: Frequency below/above cutoff threshold.

AGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGC  >  NZ_CP009273/4558235‑4558409
                                                                                      |                                                                                        
aGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAGACAGCGTGGGGGCATGGCGGGGaaa                                                                                       >  2:497561/1‑90 (MQ=255)
 ggCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaa                                                                                      >  1:184127/1‑90 (MQ=255)
      gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaaa                                                                                 >  2:404686/1‑88 (MQ=255)
      gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaaa                                                                                 >  2:299171/1‑88 (MQ=255)
      gATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGaaaaaaaaa                                                                                 >  2:501415/1‑88 (MQ=255)
         cAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTgg                                                                              <  1:298950/90‑1 (MQ=255)
            aTCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCAt                                                                           <  1:216275/90‑1 (MQ=255)
              ccGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCTATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaa                                                                         <  2:242860/90‑1 (MQ=255)
              ccGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaa                                                                         <  1:21244/90‑1 (MQ=255)
              ccGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaa                                                                         <  1:299171/90‑1 (MQ=255)
                gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATaaca                                                                       >  1:198634/1‑90 (MQ=255)
                gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGCATaaca                                                                       >  2:480927/1‑90 (MQ=255)
                               gcaAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAAAAACCCCCTGTcc                                                        >  1:181072/1‑90 (MQ=255)
                                              aTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTGTCCGGAGAAACCCCACgg                                         >  1:248382/1‑90 (MQ=255)
                                                  aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGaa                                     <  1:444341/90‑1 (MQ=255)
                                                  aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAAATCCTTGTCCGGAGAACCCCCACggggga                                     >  1:467218/1‑88 (MQ=255)
                                                       aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                <  2:467218/90‑1 (MQ=255)
                                                       aTCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGCGAAAAAAAAAACCCCTTGTCCGGGGAACCCCAAACGGGAAAAAGa                                >  2:416803/1‑90 (MQ=255)
                                                        tCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGGATAACAAAAAAATCCTTTTCCGGGGAAACCCCACGGGGGAAAAGaa                               >  2:220182/1‑90 (MQ=255)
                                                                   aGCGTGGCGGCATGGCGGGTAAAAAAAAGTGGCATAAAAAAAAAATCCTTGTCCGGGGAAACCCCACGGGGGAAAAGAAAATTAATACCg                    >  1:496457/1‑90 (MQ=255)
                                                                    gCGTGGCGGCATGGCGGGGAAAAAAAAGTGGGATAAAAAACAAATCCCTTTCCGGGGAAACCCCACGGGGGAAAAGAAAATTAATACCgc                   >  2:71836/1‑89 (MQ=255)
                                                                    gCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGGAAAAGAAAATTAAAACCGt                   >  1:482084/1‑90 (MQ=255)
                                                                                  cGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGaaa     <  1:62650/90‑1 (MQ=255)
                                                                                   gggTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAg    <  2:481616/90‑1 (MQ=255)
                                                                                     gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc  <  2:297962/90‑1 (MQ=255)
                                                                                     gTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGc  <  1:63000/90‑1 (MQ=255)
                                                                                      |                                                                                        
AGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGC  >  NZ_CP009273/4558235‑4558409

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑