Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,558,3290CA70.8% 4.6 / 18.5 24R3L (CGT→CTT) mdtMmultidrug efflux MFS transporter MdtM
Reads supporting (aligned to +/- strand):  ref base C (1/6);  new base A (17/0);  total (18/6)
Fisher's exact test for biased strand distribution p-value = 5.20e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.85e-04
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGT‑CCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAA  >  NZ_CP009273/4558246‑4558398
                                                                                   |                                                                      
gATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCa                                                                  >  1:511983/1‑90 (MQ=255)
     gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATaaca                                                             <  1:269560/90‑1 (MQ=255)
     gTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGCATaaaa                                                             >  2:23513/1‑88 (MQ=255)
                         gTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGT‑CCGgaga                                        <  2:355456/90‑1 (MQ=255)
                         acagtACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGT‑CCGgaga                                        <  2:218863/86‑1 (MQ=255)
                                   aTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGGATAAAAAAAAACTCCTTTT‑CCGGAGAACCCCCACgg                              >  2:103645/1‑90 (MQ=255)
                                   aTCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAAAAAAAAAATCCTTTT‑CCGGAGAACCCCAACgg                              >  2:599376/1‑90 (MQ=255)
                                     cAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCATAAAAAAAAACTCCTTTT‑CCGGAGAACCCCCAAgggg                            >  2:77443/1‑90 (MQ=255)
                                      aaCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAAGGCATAAAAAAAAACACCCTTT‑CCGGGGAACCCCCACGGGGa                           >  1:610150/1‑90 (MQ=255)
                                       aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAACGCGGGCTAAAAAAAAACTCCTTGT‑CCGGGGAACCCCCAAggggga                          >  2:148700/1‑88 (MQ=255)
                                       aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGAGGGATAAAAAAAAAAACCTTTT‑TCGGGGAAACCCCACggggga                          >  1:318289/1‑88 (MQ=255)
                                       aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAATGGGATAAAAAAAAACACCTTTTCCCGGGGAACCCCACCgctgt                           >  1:218863/1‑86 (MQ=255)
                                       aCGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAAGGCATAAAAAAAAAACCCTTTT‑CCGGGGAACCCCCACggggga                          >  1:80602/1‑88 (MQ=255)
                                           cATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAAGGGAAAAAAAAAAAAACCCTTT‑CCCGGGAAACCCCACGGGGaaaaag                      >  1:258668/1‑88 (MQ=255)
                                            aTCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGGATAAAAAAAAAAACCCTGT‑CCGGGGAACCCCAACGGGGGAAAAGa                     >  1:527560/1‑90 (MQ=255)
                                                      aCAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGT‑CCGGAGAACCCCAACGGGGAAAACGAAATTCAATAc           <  1:639158/90‑1 (MQ=255)
                                                        aGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGT‑CCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCg         <  2:560873/90‑1 (MQ=255)
                                                        aGCGTGGCGGCATGGCGGGGAAAAAAAAGTGGCAAAAAAAAAAAATCCTTTT‑CCGGAGAACCCCCACGGGGGAAAAGAAAATCAATAccc         >  2:545031/1‑89 (MQ=255)
                                                        aGCGTGGCGGCATGGCGGGGAAAAAAAAAGGGGAAAACAAAAAACTCCCTTT‑CCGGAGGAACCCAACGGGGGAAAAGAAAATCAAAACCg         >  1:428153/1‑90 (MQ=255)
                                                         gCGTGGCGGCATGGCGGGTAAAAAAAAGGGGCATAAAAAACAACTCCTTTT‑CCGGGGAACCCCAACGGGGGAAAAGAAAATCAAAACCGt        >  2:98257/1‑90 (MQ=255)
                                                         gCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCATAACAAACAACTCCCTGT‑CCGGAGAACCCCAACGGGGAAAAAGAAAATTAATAcccg        >  2:197154/1‑88 (MQ=255)
                                                              gcggcATGGCGGGTAAAAAAAAATGGGATAACAAAAAAACCCCTTT‑CCGGGGAACCCCAACGGGGGAAAAGAAAATAAATACCGTCggga   >  1:67559/1‑88 (MQ=255)
                                                              gcggcATGGCGGGGAAAAAAAAGGGGGATAAAAAAAAACCCCTTTT‑CCGGGGAACCCCCACGGGGAAAAAGAAATTCAAAACCGTCggga   >  1:192022/1‑88 (MQ=255)
                                                               cggcATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGT‑CCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTaa  <  2:428153/90‑1 (MQ=255)
                                                                                   |                                                                      
GATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGT‑CCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAA  >  NZ_CP009273/4558246‑4558398

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑