Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,726,6400TA62.5% ‑2.8 / 26.5 24N360K (AAT→AAA) xylGD‑xylose ABC transporter ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/9);  new base A (15/0);  total (15/9)
Fisher's exact test for biased strand distribution p-value = 7.65e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.30e-05
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TCAGCAAGCCATCGCCCAGGGGATTGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGCCAGCTTGATGACGCGGCAGAGCAA  >  NZ_CP009273/3726553‑3726706
                                                                                        |                                                                  
tCAGCAAGCCATCGCCCAGGGGATTGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGAAAAaaat                                                                  >  2:51846/1‑90 (MQ=255)
              cccAGGGGATTGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCAc                                                    <  1:632880/90‑1 (MQ=255)
              cccAGGGGATTGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCAc                                                    <  1:690279/90‑1 (MQ=255)
                  ggggATTGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAAAATTACCCCCGCCCCCCTCaa                                                >  2:95533/1‑90 (MQ=255)
                       ttGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAAAATTACCCCCCCCGCACTCAATAAAt                                           >  2:185609/1‑90 (MQ=255)
                       ttGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGAAAAAAATTACCCCCCCCGCCCCCAATaaaa                                           >  1:54319/1‑89 (MQ=255)
                       ttGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGAAAAAAATTACCCCCCCCGCACTCAATaaaa                                           >  2:663272/1‑89 (MQ=255)
                       ttGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGAAAAAAATTACCCCCCCCCCGCCCAATAAAt                                           >  2:648826/1‑90 (MQ=255)
                       ttGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGAAAAAAATTACCCCCCCCCCACTCCATaaaa                                           >  2:431355/1‑89 (MQ=255)
                       ttGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGAAAAAAAATAACCCCCCCCCCCCCAATAAAt                                           >  2:465464/1‑90 (MQ=255)
                       ttGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑GTGGGAAAAAAAATAACCTCCCCGCCCCCAATaaaa                                           >  1:385551/1‑89 (MQ=255)
                            aTGGTCCCCGAAGACAGAAAGGGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGGAAAAAAATACCCCCTCCGCCCCCAATAAAttttta                                      >  1:727635/1‑87 (MQ=255)
                            aTGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAAAATTACCCCCGCCGCACTCAATAAATTTAcc                                      >  2:280297/1‑90 (MQ=255)
                              ggTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGGAAAAAAATTAACCTCGCCGCCCTCCAAAAAATTAcccg                                    >  2:793358/1‑88 (MQ=255)
                                tCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑GTGGGAAAAAAAATAACCCCCCCCCCCTCCATAAATTTACCgggg                                  >  1:445648/1‑88 (MQ=255)
                                         aCAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGcc                         <  2:451756/90‑1 (MQ=255)
                                         aCAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGcc                         <  1:659467/90‑1 (MQ=255)
                                           aGAAAGCGCGACGGCATCGTTCCGGTAATGGCGGTTTGGGAAAAAAATAACCCCCCCGCCCCCCAAAAAATTTA‑CGGGGGGATTAACCAg                       >  1:773379/1‑90 (MQ=255)
                                             aaaGCGCGACGGCATCGTTCCGGTAATGGCGG‑GTGGGAAAAAAAATACCCCCCCCCCCCCCAATAAAATTAACGGTGGGATTAGCCAGCt                     >  1:621503/1‑90 (MQ=255)
                                                  gcgACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAAAATTACCCTCGCCCCACTCAAAAAATTTACCGGGGGCATTTGCCAGCTtggtg                >  2:470437/1‑90 (MQ=255)
                                                    gACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGCCAGCTTGATGAc              <  2:488579/90‑1 (MQ=255)
                                                         cATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGCCAGCTTGATGACGCGGc         <  1:95533/90‑1 (MQ=255)
                                                          aTCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGCCAGCTTGATGACGCGGCa        <  2:773379/90‑1 (MQ=255)
                                                           tCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGCCAGCTTGATGACGCGGCag       <  2:328186/90‑1 (MQ=255)
                                                                ccGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGCCAGCTTGATGACGCGGCAGAGCaa  <  2:658186/90‑1 (MQ=255)
                                                                                        |                                                                  
TCAGCAAGCCATCGCCCAGGGGATTGCGATGGTCCCCGAAGACAGAAAGCGCGACGGCATCGTTCCGGTAATGGCGG‑TTGGTAAAAATATTACCCTCGCCGCACTCAATAAATTTACCGGTGGCATTAGCCAGCTTGATGACGCGGCAGAGCAA  >  NZ_CP009273/3726553‑3726706

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑