Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT56.0% 6.2 / 30.7 25S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (1/10);  new base T (14/0);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 3.37e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.44e-05
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTT  >  NZ_CP009273/4594084‑4594244
                                                                             |                                                                                   
taAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCAt                                                                         <  1:169301/90‑1 (MQ=255)
   gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                      <  1:316913/90‑1 (MQ=255)
      ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGGCTTTTTTCTTTTTCTTCCCTgaggat                                                                   >  2:466928/1‑87 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAgcgc                                                            >  1:372547/1‑90 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                            <  1:476903/90‑1 (MQ=255)
              ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAgcgcc                                                           >  2:316913/1‑89 (MQ=255)
              ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCa                                                           >  2:343440/1‑90 (MQ=255)
               taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGGGCag                                                          <  1:176956/90‑1 (MQ=255)
               taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag                                                          <  2:546114/90‑1 (MQ=255)
               taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag                                                          <  1:174195/90‑1 (MQ=255)
                aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCagg                                                         >  2:443603/1‑89 (MQ=255)
                  cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                       <  2:224344/90‑1 (MQ=255)
                   aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCagagag                                                      >  2:309531/1‑90 (MQ=255)
                    gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGAGAgg                                                     >  1:229902/1‑90 (MQ=255)
                    gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAgg                                                     >  1:125163/1‑90 (MQ=255)
                     tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCAGAGAggg                                                    >  2:174195/1‑90 (MQ=255)
                     tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAggg                                                    >  2:288095/1‑90 (MQ=255)
                      cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                   <  2:199813/90‑1 (MQ=255)
                                     gATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGGGGGCGGAGAGGGGTTTTTTTTCctggct                                    >  2:329146/1‑90 (MQ=255)
                                       tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGGAGAGAGGGGTTTTCTTTTctgactga                                  >  2:205085/1‑90 (MQ=255)
                                       tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATCTTGCctgactga                                  >  1:238902/1‑90 (MQ=255)
                                              tCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCAGAGAGGGGGTTTCTTTCCTTACTGGAATGGCg                           >  2:5821/1‑90 (MQ=255)
                                                gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGGGAGGGGTTTTCTTGCCTGACTGAACTGGCGAt                         >  1:507320/1‑90 (MQ=255)
                                                                       ttttttCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGtt  <  2:238902/90‑1 (MQ=255)
                                                                       ttttttCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGtt  <  1:198637/90‑1 (MQ=255)
                                                                             |                                                                                   
TAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTT  >  NZ_CP009273/4594084‑4594244

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: ‑