Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273964,1420TG59.3% 14.6 / 22.9 27G107G (GGT→GGG) lpxKtetraacyldisaccharide 4'‑kinase
Reads supporting (aligned to +/- strand):  ref base T (7/4);  new base G (16/0);  total (23/4)
Fisher's exact test for biased strand distribution p-value = 1.88e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.84e-03
Rejected as consensus: Frequency below/above cutoff threshold.

GGGGGTCGTATCGCGGGGATATGGTGGTAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGTGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCGGTTTCTCCCGTTCGTTCTGATGCGGTAAAAGCCATTCTGGCGC  >  NZ_CP009273/964058‑964230
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gggggTCGTATCGCGGGGATATGGTGGTAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGtgatga                                                                                     >  2:227636/1‑90 (MQ=255)
  gggTCGTATCGCGGGGATATGGTGGTAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGATGaaa                                                                                   >  2:798258/1‑89 (MQ=255)
            gcgGGGATATGGTGGTAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGTGATGAACCTGTGTTGAt                                                                         >  2:853867/1‑90 (MQ=255)
                    atGGTGGTAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGATGAAACTGTGTTGATTTATCAAc                                                                 >  2:312598/1‑90 (MQ=255)
                         ggtAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGATGAAACTGTGTTGATTTTTCAACGCACt                                                            >  2:614210/1‑90 (MQ=255)
                          gtAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGGGGAAACCGGGTTGGTTTTTTAACCCAcgg                                                           >  1:991232/1‑88 (MQ=255)
                           tAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGATGAACCTGTGTTGATTTTTCAACGCACTGa                                                          >  2:57316/1‑90 (MQ=255)
                           tAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGATGAACCTGTGTTGATTTATCAACGCACTGa                                                          >  2:1291668/1‑90 (MQ=255)
                                 tGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGGTGAACCTGTGTTGATTTATCAACCCACCGATGCGcc                                                    >  1:68625/1‑90 (MQ=255)
                                 tGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGATGAACCTGTGTTGATTTATCAAAGCACTGATGCGcc                                                    >  2:866258/1‑90 (MQ=255)
                                  gAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGAAAAACCTGTGTTGATTTATCAACACACTTATGccccc                                                   >  2:989019/1‑89 (MQ=255)
                                        tATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCg                                             >  2:890991/1‑90 (MQ=255)
                                         aTCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGTGATGAAACTTTGTTGATTTTTTAACGCACCGATGCGCCCGTTGCgg                                            >  1:676838/1‑90 (MQ=255)
                                              cTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGTGATGAACCTGTGTTGATTTATCAACGCAc                                                             <  1:525790/68‑1 (MQ=255)
                                              cTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGTGATGAACCTGTGTTGATTTATCAACGCAc                                                             >  2:525790/1‑68 (MQ=255)
                                              cTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGTGAAGAATCTGGGTTGGTTTTTCAAACAACTTATGCGCCGGTGGCGGGTtct                                       >  2:637026/1‑90 (MQ=255)
                                              cTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGGGGTGAACCTTTGGTGTTTTTTTTACGCACCTATGGGCCTCTTGTGGttttt                                       >  1:1398977/1‑88 (MQ=255)
                                                        cGGCAGATACCACAACAGCACAGGCGGGTGATGAACCtgtg                                                                              >  2:1092632/1‑41 (MQ=255)
                                                        cGGCAGATACCACAACAGCACAGGCGGGTGATGAACCtgtg                                                                              <  1:1092632/41‑1 (MQ=255)
                                                        cGGCAGATACCACAACAGCACAGGCGGGGGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCGGTTTCTCCcgttcgtt                             >  2:581433/1‑90 (MQ=255)
                                                          gCAGATACCACAACAGCACAGGCGGGGGTTGAGCCCGTGGTGATTTATCAACCCGCTGAAGGCCCCGTTGGGGTTTCTCCcgttcggttt                           >  2:1171754/1‑86 (MQ=255)
                                                             gATACCACAACAGCACAGGCGGGTGATGAACCTGTGTTGATTTTTCAACGCACTGATGCCCCCGTTGCGGGTTTTCCCGTTCGTTCTGAt                        >  2:1420715/1‑90 (MQ=255)
                                                                   acaacaGCACAGGCGGGTGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCGGTTTCTCCCGTTCGTTCTGATGCGGTa                  <  1:853867/90‑1 (MQ=255)
                                                                    caacaGCACAGGCGGGGGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCGGGTTCTCCCGTTCGTTCTGATGCGGTaa                 >  2:418797/1‑90 (MQ=255)
                                                                        aGCACAGGCGGGTGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCGGTTTCTCCCGTTCGTTCTGATGCGGTAAAAGc             >  2:1338010/1‑90 (MQ=255)
                                                                              ggCGGGGGGTGAACCTGTGTTGATTTATAAACGCACTGTTGCGCCTGTTGCGGTTTCTCCCGTTCGTTCTGAGGAGGGAAAAGCCTTTCt       >  1:674521/1‑90 (MQ=255)
                                                                              ggCGGGGGATGAACCTGTGTTGATTTTTCAACGCACCGATGCGCCCGTTGCGGGTTCTCCCGTTCGTTCTGATGCGGTAAAAGCCATTCt       >  1:1277277/1‑90 (MQ=255)
                                                                                   gTGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCGGTTTCTCCCGTTCGTTCTGATGCGGTAAAAGCCATTCTGgcgc  <  1:614210/90‑1 (MQ=255)
                                                                                    |                                                                                        
GGGGGTCGTATCGCGGGGATATGGTGGTAAGGCTGAATCTTATCCGCTGTTATTGTCGGCAGATACCACAACAGCACAGGCGGGTGATGAACCTGTGTTGATTTATCAACGCACTGATGCGCCTGTTGCGGTTTCTCCCGTTCGTTCTGATGCGGTAAAAGCCATTCTGGCGC  >  NZ_CP009273/964058‑964230

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑