Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT63.3% ‑5.0 / 26.9 30S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (1/10);  new base T (19/0);  total (20/10)
Fisher's exact test for biased strand distribution p-value = 3.66e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-06
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTA  >  NZ_CP009273/4594080‑4594246
                                                                                       |                                                                               
cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                               <  1:167874/90‑1 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATgtga                                                                       >  2:420352/1‑90 (MQ=255)
          ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAg                                                                     >  1:568940/1‑90 (MQ=255)
            aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                   <  2:152831/90‑1 (MQ=255)
                 tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAgcgc                                                              >  2:568540/1‑90 (MQ=255)
                 tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAgcgc                                                              >  1:583911/1‑90 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCa                                                             >  2:382569/1‑90 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCa                                                             >  2:29962/1‑90 (MQ=255)
                     ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                          <  2:66680/90‑1 (MQ=255)
                     ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                          <  1:576776/90‑1 (MQ=255)
                      cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                         <  2:583911/90‑1 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGGGAAGTGGGCGGagagag                                                        >  2:510400/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGGAGGGAGGGCaggggg                                                        >  1:532083/1‑86 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGGGCGCaggggg                                                        >  2:600859/1‑86 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCagagag                                                        >  1:166193/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCagagag                                                        >  2:533275/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCagaggg                                                        >  2:50096/1‑88 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagagag                                                        <  2:284844/90‑1 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCCTGAGGAGGGAGCGCagagag                                                        >  1:313997/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAgg                                                       >  2:392409/1‑90 (MQ=255)
                         tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGGATTTTTTTTTTTTTTTTCATTAGGAGTGAGCGCCGAGAggg                                                      >  1:578590/1‑90 (MQ=255)
                                 cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTAtttt                                              >  2:521543/1‑90 (MQ=255)
                                  aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCttt                                             >  1:58529/1‑89 (MQ=255)
                                              cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                 <  2:532083/90‑1 (MQ=255)
                                                      ggATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTATTTTTCCTGACTGAACTGGCGATTa                         >  1:11308/1‑90 (MQ=255)
                                                      ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                         <  2:578590/90‑1 (MQ=255)
                                                                     cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc          <  1:268589/90‑1 (MQ=255)
                                                                      ggTCATTTTTTCTTTTTTTGCCCTGAGAAGGGAGCGCAGGGAGGGGTTTTTTTTCCTGACTGAACTGGGGATTAAGTTTCCGCGGACCCg         >  1:562768/1‑90 (MQ=255)
                                                                      ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg         <  2:50255/90‑1 (MQ=255)
                                                                       gTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATTTTTCCTGACTGAACTGGGGGTTAAGTTTTCGCGTACCCgg        >  1:193295/1‑90 (MQ=255)
                                                                             ttttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTa  <  2:568940/90‑1 (MQ=255)
                                                                                       |                                                                               
CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTA  >  NZ_CP009273/4594080‑4594246

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑