Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,297,1510CA55.6% 2.5 / 12.4 9R23R (CGG→AGG) BW25113_RS25870hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base A (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.

TGTCAAAGATGCATACCCCGATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTGGC‑GGGAAGCGTGGCAAAAACGGGCTTTTGCTCACATTTCAAATGGTTATAAATATATTTATATAGCGATTGATTCACCAGAGATATTTCTGCTGGTTTGCTCTCTCATT  >  NZ_CP009273/2297077‑2297240
                                                                           |                                                                                         
tgtCAAAGATGCATACCCCGATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTGGC‑GGGAAGCGTGGCAAAAACGGGCTTTTGCTcaca                                                                            <  1:439956/90‑1 (MQ=255)
        aTGCATACCCCGATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTGGC‑GGGAAGCGTGGCAAAAACGGGCTTTTGCTCACATTTCAAAt                                                                    <  1:502682/90‑1 (MQ=255)
           cATACCCCGATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTGGC‑GGGAAAGGGGGGAAAAAAAGGCTTTTTTTTTCATTTCTAAttat                                                                 >  2:438574/1‑87 (MQ=255)
               ccccGATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTGGCGGGGAGGGGGGGGAAAAAAGGGGTTTTG‑TCCCAATTTAAATGGGtata                                                             >  1:296454/1‑90 (MQ=255)
               ccccGATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTGGCGGGGAGGGGGGGGAAAAAAGGGGGTTTG‑TTTCATTTTAAATGGTtata                                                             >  1:321816/1‑90 (MQ=255)
                                  tGTAGCAGGATCAAAAGAGTGGC‑GGGAAGCGGGGCAAAAAAAGGGTTTTTTTCCCCTTTTAAAAAGTTTTAAAAAAATTTTTATAACgat                                          >  2:105848/1‑90 (MQ=255)
                                         ggATCAAAAGAGTGGC‑GGGAAACGGGGGAAAAAAGGGGTTTTTTTCACATTTTAAAAAGGTTTAAAAATATTTTTATATAgattgattta                                   >  2:111897/1‑88 (MQ=255)
                                                                      aaaaaCGGGCTTTTGCTCACATTTCAAATGGTTATAAATATATTTATATAGCGATTGATTCACCAGAGATATTTCTGCTGGTTTGctctc       <  2:296454/90‑1 (MQ=255)
                                                                      aaaaaCGGGCTTTTGCTCACATTTCAAATGGTTATAAATATATTTATATAGCGATTGATTCACCAGAGATATTTCTGCTGGTTTGctctc       <  2:321816/90‑1 (MQ=255)
                                                                           cGGGCTTTTGCTCACATTTCAAATGGTTATAAATATATTTATATAGCGATTGATTCACCAGAGATATTTCTGCTGGTTTGCTCTCTCAtt  <  1:105848/90‑1 (MQ=255)
                                                                           cGGGCTTTTGCTCACATTTCAAATGGTTATAAATATATTTATATAGCGATTGATTCACCAGAGATATTTCTGCTGGTTTGCTCTCTCAtt  <  2:35953/90‑1 (MQ=255)
                                                                           |                                                                                         
TGTCAAAGATGCATACCCCGATCGGGGTAAAACCTGTAGCAGGATCAAAAGAGTGGC‑GGGAAGCGTGGCAAAAACGGGCTTTTGCTCACATTTCAAATGGTTATAAATATATTTATATAGCGATTGATTCACCAGAGATATTTCTGCTGGTTTGCTCTCTCATT  >  NZ_CP009273/2297077‑2297240

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑