Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,024,8010GC55.6% 5.2 / 11.2 9R209G (CGT→GGT) rlmI23S rRNA (cytosine(1962)‑C(5))‑methyltransferase RlmI
Reads supporting (aligned to +/- strand):  ref base G (0/4);  new base C (5/0);  total (5/4)
Fisher's exact test for biased strand distribution p-value = 7.94e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGTA‑GCCCGTTTTGTGTCCGTGCTGAATATCCACCA  >  NZ_CP009273/1024713‑1024848
                                                                                        |                                                
gCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGc                                                 <  1:701826/90‑1 (MQ=255)
gCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGc                                                 <  2:517951/90‑1 (MQ=255)
        ggCGAAACCCCCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAg                                         <  2:209373/90‑1 (MQ=255)
                  ccGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGCCCGGCGGCCATCACCCCCGGCCAGGGAGTA‑Ggcc                              >  2:236464/1‑90 (MQ=255)
                           gagaAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGGCAGGGGGGGATCACCCCGGGCCCGGGAGTAGGCCCGtttttgt                      >  2:645734/1‑87 (MQ=255)
                               aaCAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGCCAGGCGGGCATCACCCTGGGCCCCGGAGGA‑GCCCCTTTTTTTTCCgc                 >  2:570951/1‑89 (MQ=255)
                                   gTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGGCCGGCGGGGATCACCCCCGGCCCGGGAGTA‑GCCCGGTTTTTGTTCgtggtg             >  1:507988/1‑90 (MQ=255)
                                    ttCAGCACACGTTTATTTTCAACGTAGCGGCGGGGAGCCAGGCGGGGATCACCCCGGTCCCGGGAGTA‑GCCCGCTTTTTGTTCGGGCTGa            >  1:696885/1‑90 (MQ=255)
                                              gTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGTA‑GCCCGTTTTGTGTCCGTGCTGAATATccacca  <  2:121321/90‑1 (MQ=255)
                                                                                        |                                                
GCCGATACGGCGAAACCACCGGTATAGGAGAAACAGTTCAGCACACGTTTATTTTCAACGTAGCGGCGGGTAGCCAGGCGGCTATCACGCTGGTCCAGGTAGTA‑GCCCGTTTTGTGTCCGTGCTGAATATCCACCA  >  NZ_CP009273/1024713‑1024848

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑