Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT60.0% ‑0.6 / 14.5 20S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (2/6);  new base T (12/0);  total (14/6)
Fisher's exact test for biased strand distribution p-value = 7.22e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.35e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCC  >  NZ_CP009273/4594077‑4594238
                                                                                     |                                                                             
aCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑Ttttttcttttt                                                                          <  2:56447/90‑1 (MQ=255)
    ttATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTTTGc                                                                      >  1:118410/1‑90 (MQ=255)
           cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTTTTTTTCTGCCCTgaga                                                               >  1:129441/1‑90 (MQ=255)
             ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCC‑TTTTTTTTTTTTCTACCCCgagaga                                                             >  2:461144/1‑88 (MQ=255)
                tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGa                                                          <  2:168609/90‑1 (MQ=255)
                  ccTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                        <  2:338016/90‑1 (MQ=255)
                   cTATACCAGTCAGGAGTCATTTCAGGATG‑CATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                      <  1:527443/90‑1 (MQ=255)
                    tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCA‑TTTTTTTTTTTTTTTCCCTGAGAAGTGGgcgc                                                      >  2:510075/1‑90 (MQ=255)
                     ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCa                                                     >  1:269103/1‑90 (MQ=255)
                         cAGTCAGGAGTTATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                 <  2:573333/90‑1 (MQ=255)
                         cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                 <  1:578547/90‑1 (MQ=255)
                         cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                 <  2:342056/90‑1 (MQ=255)
                          aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCagagag                                                >  1:442197/1‑90 (MQ=255)
                           gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCAGAGAgg                                               >  2:243623/1‑90 (MQ=255)
                            tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAGTTTTTTTTTTTTTTGCGTTG‑GAAGAAAGCGCAGATAggg                                              >  2:577490/1‑90 (MQ=255)
                            tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGGC‑TTTTTTTTTTTTTTTCCCTGGGAAGTGAGGGCGGAGAggg                                              >  2:685035/1‑90 (MQ=255)
                               ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCC‑TTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGGAGAGGGGGGtt                                           >  2:176242/1‑90 (MQ=255)
                                    cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCA‑TTTTTTTTTTTTTTTCCCTGAGGAGGGGGGGCAGAGAGGGAGTAtttt                                      >  2:415991/1‑90 (MQ=255)
                                         cAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCT‑TTTTTTTTTTTTTTTCCATGAGAAGGGGGCGCAGGGGGGGGTTATCTTGCctg                                 >  1:350563/1‑90 (MQ=255)
                                                ccATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTTTTTTTTTTCCCTTAGAAGGGGGGGCAGGGGGGGGGTATTTTTCCTGACTGAAc                          >  2:211680/1‑90 (MQ=255)
                                                               cGTTTGCGGCGGTCA‑TTTTTTCTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTTTTTTGCCTGACTGAACTGGCGATTAAGGTTc           >  1:109501/1‑90 (MQ=255)
                                                                                     ctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc  <  2:182127/78‑1 (MQ=255)
                                                                                     ctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc  >  1:182127/1‑78 (MQ=255)
                                                                                     |                                                                             
ACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCC  >  NZ_CP009273/4594077‑4594238

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑