Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT61.0% ‑2.0 / 45.0 41S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (2/14);  new base T (24/1);  total (26/15)
Fisher's exact test for biased strand distribution p-value = 4.75e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.25e-07
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCG  >  NZ_CP009273/4594076‑4594239
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aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttttttt                                                                            >  2:341322/1‑90 (MQ=255)
  cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAAtttttctttttc                                                                          <  1:520824/90‑1 (MQ=255)
    cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                        <  2:503203/90‑1 (MQ=255)
         aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATg                                                                   <  2:180960/90‑1 (MQ=255)
           gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                 <  1:227136/90‑1 (MQ=255)
           gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                 <  1:339999/90‑1 (MQ=255)
           gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                 <  1:47199/90‑1 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTgaga                                                                >  2:339999/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTg                                                                        >  1:519365/1‑82 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATgaga                                                                >  1:490697/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                        <  2:519365/82‑1 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCAGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATgaga                                                                >  1:220230/1‑90 (MQ=255)
             tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGaa                                                               <  2:444461/90‑1 (MQ=255)
             tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTGCCATGAGaa                                                               >  2:397593/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTTAGAAg                                                              >  1:421976/1‑90 (MQ=255)
               cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                             <  1:77473/90‑1 (MQ=255)
                aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATGAGAAggg                                                            >  1:57668/1‑88 (MQ=255)
                   ccTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                         <  2:593959/90‑1 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTTCCTGAGAAAGGAgcgc                                                       >  2:293643/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCagagag                                                 >  2:75118/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCagagag                                                 >  1:529512/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGGGCGCAGAGAgg                                                >  1:703614/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTAGAAAAGAGCGCAGAGAgg                                                >  2:143502/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGGAGGGAGCGCAGAGAgg                                                >  1:435382/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATTAGAAGGGGGCGCCGAGAgg                                                >  1:36764/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATTAGGAGTGAGGGCAGAgggg                                                >  2:51115/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAAAGAGCGCAGAGAggg                                               >  2:261359/1‑90 (MQ=255)
                              cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                              <  1:293643/90‑1 (MQ=255)
                                ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGAAGTGGGGGCAGAGAGGGGtt                                            >  2:693407/1‑90 (MQ=255)
                                   gTCATTTCAGGATGGCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAGGGGTTAtt                                         >  2:549896/1‑89 (MQ=255)
                                     cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTCTGCCATGAGAAGGGAGGGCAGGGAGGGGTTAtttt                                       >  1:712603/1‑90 (MQ=255)
                                       tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                     <  1:143502/90‑1 (MQ=255)
                                               tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGGGCCGAGGGGGGTTATCTTTCcttactga                             >  2:291877/1‑90 (MQ=255)
                                               tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCCTGAGAAGGGAGCGCAGAGGGGGGTTATCTTGCctgactga                             >  2:31279/1‑90 (MQ=255)
                                                 ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTTAGAAGGGAGGGCAGGGGGGGGTTATTTTGCCTTGCTGaaa                           >  2:755624/1‑89 (MQ=255)
                                                    tGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCAGGGAGGGGTTATCTTTCCTGACTGAACTgg                        >  2:707848/1‑90 (MQ=255)
                                                                   ttGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCcgc         <  1:260481/90‑1 (MQ=255)
                                                                     gcggcgGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGGGCAGGGGGGGGTTATCTTTCCTTTCTGAACTGGCGATTAAGTTTTCGCGt       >  2:372298/1‑90 (MQ=255)
                                                                     gcggcgGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGGGCAGAGAGGGGTTATTTTTCCTGACTGAACTGGGGGTTTAGTTTCCGCGt       >  2:295025/1‑90 (MQ=255)
                                                                       ggcggTCATTTTTTCTTTTTTTTCCATGAGAAGTGAGGGCAGAGAGGGGTTTTCTTTTCTTTCTGAACTGGGGGTTTAGTTTTCGCGGAc     >  2:354837/1‑90 (MQ=255)
                                                                         gggTAATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc   <  2:332067/89‑1 (MQ=255)
                                                                         cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc   <  2:368911/90‑1 (MQ=255)
                                                                          ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCATGACTGAACTGGCGATTAAGTTTCCGCGTACCCg  <  2:687030/90‑1 (MQ=255)
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AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCG  >  NZ_CP009273/4594076‑4594239

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑