Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT55.0% 0.6 / 22.4 20S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (1/8);  new base T (11/0);  total (12/8)
Fisher's exact test for biased strand distribution p-value = 7.14e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.83e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGT  >  NZ_CP009273/4594076‑4594243
                                                                                     |                                                                                  
aaCCCTTATAAGCTCCATACCTATACCAGGCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTGCGtttttttttt                                                                                >  2:283848/1‑90 (MQ=255)
  cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                              <  2:180166/90‑1 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATgaga                                                                    >  1:470964/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATggga                                                                    >  1:241063/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATgaga                                                                    >  1:147368/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCagagag                                                     >  2:265800/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCagagag                                                     >  1:478798/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCagagag                                                     >  2:159877/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCagagag                                                     >  1:436928/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGGGGGCAGGGAgg                                                    >  1:201114/1‑90 (MQ=255)
                                       tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                         <  2:414254/90‑1 (MQ=255)
                                                  caggTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                              <  1:280554/87‑1 (MQ=255)
                                                  cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                              <  1:265800/90‑1 (MQ=255)
                                                   aTGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTGCATGAGAAGGGAGGGCAGAGAGGGATTATCTTGCCTGACTTaaatt                             >  1:371855/1‑87 (MQ=255)
                                                          ggATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGGAAGGAGGGCAGAGAGGGGTTTTTTTTCCTTACTGAACTCGGGATTa                      >  2:270759/1‑90 (MQ=255)
                                                               tcGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGttt                 <  1:474949/90‑1 (MQ=255)
                                                                       ggcggTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGGGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGGGATTTAGTTTTCGCGGAc         >  1:440784/1‑90 (MQ=255)
                                                                         cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc       <  1:291924/90‑1 (MQ=255)
                                                                         cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc       <  1:235641/90‑1 (MQ=255)
                                                                          ggTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAGGGGGTATCTTTCCTGACTGAACTGGGGATTAAGATTTCGCGGACCCg      >  2:291924/1‑90 (MQ=255)
                                                                          ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg      <  1:248147/90‑1 (MQ=255)
                                                                              aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt  <  2:120504/90‑1 (MQ=255)
                                                                                     |                                                                                  
AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGT  >  NZ_CP009273/4594076‑4594243

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑