Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,371,2840AC54.5% 8.8 / 11.0 11R485R (CGT→CGG) menD2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase
Reads supporting (aligned to +/- strand):  ref base A (4/1);  new base C (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.26e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGATATTTCAGCTCGAACATCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAA  >  NZ_CP009273/2371212‑2371366
                                                                        |                                                                                  
atgatATTTCAGCTCGAACATCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGt                                                                   <  1:352752/90‑1 (MQ=255)
          aGCTCGAACATCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGc                                                         >  2:381811/1‑90 (MQ=255)
          aGCTCGAACATCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCCCGCTTTGCGGCGTTGGCAACAGc                                                         >  1:346636/1‑90 (MQ=255)
                           ggcgTATTCAAAATGGAGTTTTGGCGGAATGAGAAAGAAACGCTCCCGTTCGTTTTGCGGCGTGGGCAAAAGGGAAAAAATTTGCccgcc                                        <  1:117336/90‑1 (MQ=255)
                                         ggACGTTTTGGGGCATCAGATAGAAACGCTCCCGCTCGTTTTGCGGCGTTGGCAACAGCGAAAAAATTTGCCCGCCGTTGTTGTTctcca                          <  2:34576/90‑1 (MQ=255)
                                         ggACGTTTGGCGGCATAAAAAAAAACCCCCCCCGCTCGCTTTGCGGCGTGGCCAACAGCGAAAAAATTTGCCCGCCGTTGTTGTTcacca                          <  1:495603/90‑1 (MQ=255)
                                          gACTTTTTGCGGCATCAGATAAAACCGCCCCCGCTGGTTTTGCGGCGTGGGCAACAGCGAAAAAATTTGCCCGCCGTTGTTGTTcaccac                         <  1:639514/90‑1 (MQ=255)
                                          gACTTTTTGCGGCATAAGATAAAACCCCCCCCGCTCGTTTTGCGGCGTGGGCAACAGAGAGAAAATTTGCCCGCCGTTGTTGTTcaccac                         <  1:147723/90‑1 (MQ=255)
                                          gACGTTTTGCGGCATCAGATAAAACCGCCCCCGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTcaccac                         <  1:404296/90‑1 (MQ=255)
                                                               gAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGa    >  1:231027/1‑90 (MQ=255)
                                                                 aaCGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGaaa  >  2:46098/1‑90 (MQ=255)
                                                                        |                                                                                  
ATGATATTTCAGCTCGAACATCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAA  >  NZ_CP009273/2371212‑2371366

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑