Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273766,3560AG56.5% 8.9 / 19.6 24intergenic (+289/‑558)mngB/cydAmannosylglycerate hydrolase/cytochrome ubiquinol oxidase subunit I
Reads supporting (aligned to +/- strand):  ref base A (4/6);  new base G (13/0);  total (18/6)
Fisher's exact test for biased strand distribution p-value = 2.08e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.71e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGCTTTATTTTTAACAAAATAATAACCCTGGGTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGTGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAATTAAGGTCAACCGTGCTGTTTTTGCTT  >  NZ_CP009273/766269‑766445
                                                                                       |                                                                                         
ggCTTTATTTTTAACAAAATAATAACCCTGGGTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGtt                                                                                         >  2:225125/1‑90 (MQ=255)
    ttATTTTTAACAAAATAATAACCCTGGGTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGtttttt                                                                                     >  1:763725/1‑87 (MQ=255)
                  ataataACCCTGGGTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGTGGATTTATGCCTTTATTAGTAAt                                                                       <  1:18729/90‑1 (MQ=255)
                          ccTGGGTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGTTTATTCCTTTTTTTGTAATTCTTaaaa                                                               >  2:18729/1‑89 (MQ=255)
                             gggTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGTTTTTTCCTTTTTTAGTAAACCTGAAAatct                                                            >  1:127237/1‑90 (MQ=255)
                             gggTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGATTTATGCCTTTTTTAGTAATCCTGAAActct                                                            >  2:744848/1‑90 (MQ=255)
                                 gAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGTGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGcgt                                                        <  2:381671/90‑1 (MQ=255)
                                  aGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGTTTATGTCTTTTTTTGTTATATTTAAAATATGcgtg                                                       >  1:599691/1‑89 (MQ=255)
                                   gTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGTTTATGCCTTTATTATGAATCCTGAAACTCTGcgccg                                                      >  2:668767/1‑90 (MQ=255)
                                       aTTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGTGGTTTTTTGTCTTTATTAATAATTCTTAAAATATTCGGCGTAtt                                                  >  2:171634/1‑90 (MQ=255)
                                             atataatTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGTTTATTCCTTTTTTAGTAATTCTGAAAATCTGCGTCGGATTAGCCAg                                            >  1:699992/1‑90 (MQ=255)
                                             atataatTATAAGTTAACTAAATGTTAATATTGGCGGGGGGGGTTTATGCCTTTTTTAGTAATCCTGAAACTCTTCGTCGTATTTGCCAg                                            >  2:587080/1‑90 (MQ=255)
                                                    tataAGTTAACTAAATGTTAATATTGGCGGGGGGGGTTTATGCCCTTATTAGTAATCCTGAAAATCTGCTTTGTCGTAGACAGTGACCaa                                     >  2:538197/1‑90 (MQ=255)
                                                       aaGTTAACTAAATGTTAATATTGGCGGGGGGGATTTATGCCTTTATTAGTAATCCTGAAAATCTGCGTCGTATTAGCCAGTGACCaaaaa                                  >  2:186379/1‑90 (MQ=255)
                                                            aaCTAAATGTTAATATTGGCGGGGTGGGTTTTTGCCTTTTTTAGTAATCCTGAAAATCTGCGTCGGATTAGCCAGTGACCAAAAAAAGaa                             >  1:73783/1‑90 (MQ=255)
                                                            aaCTAAATGTTAATATTGGCGGGGGGGGTTTTTGCCTTTATTAGTAATCCTGAAAATCTGCGTCGTATTAGCCAGTGACCaaaaaaaaaa                             >  2:356867/1‑90 (MQ=255)
                                                            aaCTAAATGTTAATATTGGCGGGGGGGATTTATTCCTTTATTTGTAATCCTGAAAATCTTCGTCGTATTAGCCAGTGACCAAAAAAAGaa                             >  2:502222/1‑90 (MQ=255)
                                                             aCTAAATGTTAATATTGGCGGGGTGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAAt                            <  1:650115/90‑1 (MQ=255)
                                                               tAAATGTTAATATTGGCGGGGTGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAATTa                          <  1:270070/90‑1 (MQ=255)
                                                                      tAATATTGGCGGGGGGGGTTTTTGCCTTTTTTAGTAATCCTGAAAATCTGGGTCGTATTAGCCAGTGACCAAAAAAAGAATTAAAGTCaa                   >  2:588634/1‑90 (MQ=255)
                                                                      tAATATTGGCGGGGGGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAATTAAGGTCaa                   >  2:105577/1‑90 (MQ=255)
                                                                       aaTATTGGCGGGGTGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAATTAAGGTCAAc                  <  2:313354/90‑1 (MQ=255)
                                                                            tGGCGGGGTGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAATTAAGGTCAACCGTGc             <  2:188037/90‑1 (MQ=255)
                                                                             ggCGGGGGGGGTTTTTGCCTTTTTTTTTAATCCTGAAACTCTGCGGCGTATTTGCCAGTGTCCAAAAAAAAAATTAAGGTCAACCGTGCt            >  1:253905/1‑90 (MQ=255)
                                                                                       aTTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAATTAAGGTCAACCGTGCTGTTTTTGCtt  <  2:73783/90‑1 (MQ=255)
                                                                                       |                                                                                         
GGCTTTATTTTTAACAAAATAATAACCCTGGGTGAGTTAATTATAATATAATTATAAGTTAACTAAATGTTAATATTGGCGGGGTGGATTTATGCCTTTATTAGTAATCCTGAAACTCTGCGTCGTATTAGCCAGTGACCAAAAAAAGAATTAAGGTCAACCGTGCTGTTTTTGCTT  >  NZ_CP009273/766269‑766445

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑