Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,003,7310TA53.8% 3.4 / 14.3 13H144Q (CAT→CAA) rlmKLbifunctional 23S rRNA (guanine(2069)‑N(7))‑methyltransferase RlmK/23S rRNA (guanine(2445)‑N(2))‑methyltransferase RlmL
Reads supporting (aligned to +/- strand):  ref base T (5/1);  new base A (0/7);  total (5/8)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.13e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ACGCGGAAAAATCTGCCGCGTCCAAATGTTGATCGCGATGCGCCGGATATCCGCGTTAACGTCTGGCTGCATAAAGAAACCGCCAGTATCGCTCTTGATCTGAGTGGTGATGGTTTACATCTGCGTGGCTATCGCGATCGTGCTGGTATTGCGCCGATC  >  NZ_CP009273/1003660‑1003818
                                                                       |                                                                                       
ccgcgGAAAAATCTGCCCCGTCAAAATGTTGACCGCGAGGCGCCGGATATCCGGTTTAACGTCTGGCTGCAAAAAGAAACCGCCAGTATc                                                                       <  2:223437/89‑1 (MQ=255)
    gaaaaaaTCTGCCGCGTCAAAATGTTGACCGCGATGCGCGGGATACCCGCGTTAACGTCGGGCTGCAAAAAAAAACCGCCAGTATCGctc                                                                   <  2:366925/88‑1 (MQ=255)
          aTCGGCCGCGCCAAAATTTTGACCGCGGTGCGCGGAATACCCGCGTTACCGTCGGGCTGAAAAAAAAAACCGCCAGTATCGCTCTTGATc                                                             <  2:356362/90‑1 (MQ=255)
               ccGCGTCCAAATGTTGATCGCGATGCGCCGGATATCCGCGTTAACGTCTGGCTGCATAAAGAAACCGCCAGTATCGCTCTTGATCTGAgg                                                        >  2:251856/1‑89 (MQ=255)
                     ccAAATTTTGACCGCGAGGCGCCGGATTTCCGCGTTAACGTCGGGCTGAAAAAAAAAACCGCCAGTATCGCTCTTGATCTGAGTGGTGAt                                                  <  2:191439/90‑1 (MQ=255)
                     ccAAATGTTGATCGCGATGCGCCGGATATCCGCGTTAACGTTTGGCTGAAAAAAGAAACCGCCAGTATCGCTCTTGATCTGAGTGGTGAt                                                  <  2:488411/90‑1 (MQ=255)
                     caaaaTGTTGACCGCGATGCGCGGGATATCCGCTTTACCGTCGGGCTGCAAAAAGAAACCGCCAGTATCGCTCTTCATCTGAGTGGTGAt                                                  <  2:80261/88‑1 (MQ=255)
                             tGATCGCGATGCGCCGGATATCCGCGTTAACGTCTGGCTGCATAAAGAAACCGCCAGTATCGCTCTTCATCTGAGTGGTGATGGTTTACa                                          >  1:80261/1‑90 (MQ=255)
                                    gATGCGCCGGATATCCGCGTTAACGTCTGGCTGCATAAAGAAACCGCCAGTATCGCTCTTGATCTGAGTGGTGATGGTTTACATCTGCGt                                   <  1:256993/90‑1 (MQ=255)
                                                      gTTAACGTCTGGCTGCAAAAAAAACCCGCCAGTATCGCTCTTGATCTGAGTGGTGATGGTTTACATCTGCGTGGCTATCGCGATCGTGCt                 <  2:4261/90‑1 (MQ=255)
                                                                   tGCATAAAGAAACCGCCAGTATCGCTGTTGATGTGCGTGGGGATGGTTTACATCTGCGTGGCTATCGCGATCGTGCTCGCGTTGCTCCGa    >  2:308319/1‑90 (MQ=255)
                                                                     cATAAAGAAACCGCCAGTATCGCTCTTGATCTGAGTGGTGATGGTTTACATCTGCGTGGCTATCGCGATCGTGCTGGTATTGCGCCGATc  >  1:147245/1‑90 (MQ=255)
                                                                     cATAAAGAAACCGCCAGTATCGCTCTTGATCTGAGTGGTGATGGTTTACATCTGCGTGGCTATCGCGATCGTGCTGGTATTGCGCCGATc  >  2:392473/1‑90 (MQ=255)
                                                                       |                                                                                       
ACGCGGAAAAATCTGCCGCGTCCAAATGTTGATCGCGATGCGCCGGATATCCGCGTTAACGTCTGGCTGCATAAAGAAACCGCCAGTATCGCTCTTGATCTGAGTGGTGATGGTTTACATCTGCGTGGCTATCGCGATCGTGCTGGTATTGCGCCGATC  >  NZ_CP009273/1003660‑1003818

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: ‑