Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,024,7830TG54.5% 8.0 / 12.7 11T215P (ACC→CCC) rlmI23S rRNA (cytosine(1962)‑C(5))‑methyltransferase RlmI
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base G (6/0);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCCATCAGTGCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGT‑AGCCCGTTTTGTGTCCGTGCTGAATATCCACCAGCAGTTTCATTCCG  >  NZ_CP009273/1024703‑1024862
                                                                                |                                                                                
gCCCATCAGTGCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGGCAgggg                                                                         >  1:453627/1‑88 (MQ=255)
          gCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGc                                                               <  1:351722/90‑1 (MQ=255)
          gCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGCCAGGCGGGTCTCACGc                                                               >  2:351722/1‑90 (MQ=255)
                  ggCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGCCAGGCGGGGATCACGCCTGTCCAg                                                       >  1:130247/1‑90 (MQ=255)
                                         aaCAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGGGGCCAGCGGGGATTACGCCGGTTCCGGGAGTAAGCCCGGTTTGTGTcgg                                >  1:270298/1‑88 (MQ=255)
                                            aGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGT‑AGCCCGTTTTGTGTCCGTGCt                            <  1:8364/90‑1 (MQ=255)
                                                  gCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGT‑AGCCCGTTTTGTGTCCGTGCTGAatat                      <  2:453627/90‑1 (MQ=255)
                                                          ttATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGT‑AGCCCGTTTTGTGTCCGTGCTGAATATCCACcagc              <  2:97325/90‑1 (MQ=255)
                                                                 cAACGTAGCGGCGGGGAGCCAGGCGGCTATCACGCTGGGCCCGGGAGT‑AGGCCGGTTTTTGTTCGGGCTGAATATCCACCACCAGatttt       >  1:97325/1‑88 (MQ=255)
                                                                    cGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGT‑AGCCCGTTTTGTGTCCGTGCTGAATATCCACCAGCAGTTTCATTc    <  2:431475/90‑1 (MQ=255)
                                                                      tAGCGGCGGGGAGCCAGGCGGCTATCACCCTGGTCCAGGGAGT‑AGCCCGGTTTTTGTCCGTGCTGAATATCCCCCCGCAGGTTTATTTCg  >  2:87180/1‑90 (MQ=255)
                                                                                |                                                                                
GCCCATCAGTGCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGT‑AGCCCGTTTTGTGTCCGTGCTGAATATCCACCAGCAGTTTCATTCCG  >  NZ_CP009273/1024703‑1024862

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑