Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,558,3290CA54.5% 1.4 / 13.9 11R3L (CGT→CTT) mdtMmultidrug efflux MFS transporter MdtM
Reads supporting (aligned to +/- strand):  ref base C (1/4);  new base A (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.12e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAA  >  NZ_CP009273/4558249‑4558418
                                                                                |                                                                                         
ccGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaa                                                                                  <  1:437294/90‑1 (MQ=255)
  gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaaca                                                                                <  1:93169/90‑1 (MQ=255)
  gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAAGGGCATaaaa                                                                                >  2:437294/1‑88 (MQ=255)
         gATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAACGGCATAAAAaaaaacc                                                                         >  2:180656/1‑89 (MQ=255)
         gATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAAGGCATAacaaaaaaac                                                                         >  1:463048/1‑88 (MQ=255)
                              aaaTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAAAATGGCATAAAAAAAAACACCTTTTCCGGAGAAACCCAAc                                                    >  2:50006/1‑90 (MQ=255)
                                aTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAACAAACAACTCCTTTTCCGGAGAACCCCAACgg                                                  >  1:48051/1‑90 (MQ=255)
                                   aaCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGGGGCATAAAAAAAAACCCCTTGTCCGGGGAACCCCAACAGGGa                                               >  1:320628/1‑90 (MQ=255)
                                         aTCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGa                                         <  1:550868/90‑1 (MQ=255)
                                            gggAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAAt                                      <  1:50006/90‑1 (MQ=255)
                                                         tGGCGGCATGGCGGGGAAAAAAAAGTGGGATAACAAAAAACTCCTTTTCCGGGGAAACCCCACGGGGGAAAAGAAATTTAATACCCTCgg                         >  1:453840/1‑90 (MQ=255)
                                                                                cGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGaa  <  2:320628/90‑1 (MQ=255)
                                                                                |                                                                                         
CCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAATGACGAAAGGCAGGTGAGAA  >  NZ_CP009273/4558249‑4558418

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑