Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT73.3% 13.6 / 12.2 30S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (2/6);  new base T (22/0);  total (24/6)
Fisher's exact test for biased strand distribution p-value = 4.72e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.96e-03
Rejected as consensus: Frequency below/above cutoff threshold.

AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCG  >  NZ_CP009273/4594076‑4594239
                                                                                     |                                                                              
aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttttttt                                                                            >  2:180421/1‑90 (MQ=255)
aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATtttttttttt                                                                            >  2:510219/1‑90 (MQ=255)
  cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                          <  1:101122/90‑1 (MQ=255)
         aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATg                                                                   <  1:327495/90‑1 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGTCTTTTTTTTTTTTTTTCCATgaga                                                                >  2:101122/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTTCCATgaga                                                                >  2:622703/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTCTGCCCTgaga                                                                >  2:287086/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTgaga                                                                >  2:485965/1‑90 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAggagggaggga                                                       >  2:635159/1‑87 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGGgcgc                                                       >  1:538877/1‑90 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAgcgc                                                       >  1:528027/1‑90 (MQ=255)
                        aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCATTTTTTTTTTTTTCGCAAGAGAAGGGGGCGCagg                                                    >  2:304708/1‑89 (MQ=255)
                         ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                   <  2:637097/90‑1 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCTTGCGAAATGAGCGCagaggg                                                 >  2:472233/1‑88 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAAGGAGCGCggagag                                                 >  2:550690/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCagggag                                                 >  2:633690/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCCTGAGAAGAGAGGggagggag                                                 >  1:505526/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCATTTTTTTTTTTTTGCCATGCGAAGTGAGCGCGGAGAgg                                                >  1:500436/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAAAGAGGGCGGAGAgg                                                >  2:544547/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCATGAGAAGTGGGGGCAGAGgggg                                               >  2:622756/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAggg                                               >  1:417569/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATGAGAAGTGAGCGCAGAGgggg                                               >  1:58479/1‑90 (MQ=255)
                              cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                              <  2:528027/90‑1 (MQ=255)
                                ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTTCCATGAGAAGGGGGCGCAGAGAGGGGtt                                            >  2:229109/1‑90 (MQ=255)
                                ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATCTTTTTTTTTTTTTCCCTGAGAAAGGAGCGCagggagggggt                                            >  2:256672/1‑87 (MQ=255)
                                                       cgcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGGGGGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGGGa                     >  1:659226/1‑90 (MQ=255)
                                                        gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTACCCTGAGAAGTGAGCGCCGAGAGGGGTTATCTTGCCTGACTGAACTGGCggt                    >  1:446477/1‑88 (MQ=255)
                                                               tcGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGttt             >  1:260782/1‑90 (MQ=255)
                                                                     gcggcgGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCAGAGAGGGGGTATTTTTCCTTACTGGACTGGGGATTTAGTTTTcgcgg       >  2:400959/1‑89 (MQ=255)
                                                                         cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc   <  1:485965/90‑1 (MQ=255)
                                                                         cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc   <  1:469892/90‑1 (MQ=255)
                                                                         cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc   <  2:659226/90‑1 (MQ=255)
                                                                          ggTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGGGATTAAGTTTTCGCGTACCCg  >  2:423649/1‑90 (MQ=255)
                                                                                     |                                                                              
AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCG  >  NZ_CP009273/4594076‑4594239

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑