Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT60.0% 2.0 / 61.0 56S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (3/19);  new base T (33/0);  total (37/19)
Fisher's exact test for biased strand distribution p-value = 5.49e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.81e-09
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGT  >  NZ_CP009273/4594076‑4594248
                                                                                     |                                                                                       
aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttt                                                                                     >  2:643961/1‑90 (MQ=255)
    cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                 <  1:20984/90‑1 (MQ=255)
      tataAGATCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                               <  1:316932/90‑1 (MQ=255)
         aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATg                                                                            <  2:477708/90‑1 (MQ=255)
           gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                          <  2:261065/90‑1 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTTTTTTTTTTTTTTTTTCCCTgaga                                                                         >  2:344460/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTgagg                                                                         >  1:505787/1‑89 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCCTTTTTATTTTTTTACCATgagg                                                                         >  1:552756/1‑89 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATgaga                                                                         >  2:461614/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTgaga                                                                         >  2:407162/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCGTTTTTTTTTTTTTTTCCATGAGAAg                                                                       >  1:368659/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAg                                                                       >  2:178330/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATGAGaaa                                                                       >  2:332868/1‑89 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCCTGAGAAg                                                                       >  1:139447/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                       >  2:56192/1‑90 (MQ=255)
                aTACCTATATCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                     <  1:560515/90‑1 (MQ=255)
                    cTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGGgcg                                                                 >  1:543885/1‑90 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAgggc                                                                >  1:176329/1‑90 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                                <  2:130477/90‑1 (MQ=255)
                      ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCa                                                               >  1:25587/1‑90 (MQ=255)
                      ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCa                                                               >  2:208034/1‑90 (MQ=255)
                         ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                            <  1:293052/90‑1 (MQ=255)
                          cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCagagg                                                           >  1:274795/1‑89 (MQ=255)
                          cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                           <  1:56192/90‑1 (MQ=255)
                          cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCagaga                                                           >  1:52906/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTGTTTTTTTTTTTTTTTCCATGAGGAGGGGGGGCagaggg                                                          >  1:424388/1‑88 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTg                                                                                 >  1:113352/1‑67 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGGGCGCagagag                                                          >  1:11873/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATTAGAAGAGAGCGCagagag                                                          >  2:339295/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                 <  2:113352/67‑1 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGGGAGCGCagagag                                                          >  2:246447/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTTAGAAGTGAGGggagggag                                                          >  1:662568/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCagaggg                                                          >  1:435636/1‑88 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCagagag                                                          >  1:342514/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGCGATTTTTTTTTTTTTTTCCCTGAGGAGAGGGGGCagaggg                                                          >  1:403849/1‑88 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATG‑CATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCAGAGAgg                                                         >  2:56030/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                                   >  2:556592/1‑64 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                                   <  1:556592/64‑1 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAACGCAGAGAgg                                                         >  1:582454/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGAGAGCGCAGAGAgg                                                         >  2:431629/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGTATTTTTTCTTTTTTTTGCCTGGGGAGTGGGCGCAGCGAgg                                                         >  2:431948/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTAGAAGTGAGGGCAGAGAggg                                                        >  1:559286/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGGGAAGGGAGCGCagggaggg                                                        >  2:377268/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAggg                                                        >  2:201752/1‑90 (MQ=255)
                                ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGtt                                                     >  2:555933/1‑90 (MQ=255)
                                ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTCTTTCATGAGAAGAGAGCGCCGGGGGGGagt                                                     >  1:537613/1‑88 (MQ=255)
                                   gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATc                                                  <  2:619798/90‑1 (MQ=255)
                                       tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                              <  2:133043/90‑1 (MQ=255)
                                       tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                              <  2:174297/90‑1 (MQ=255)
                                       tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                              <  2:14882/90‑1 (MQ=255)
                                            ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGAGGAGAGGGGGGTTGTTTTGCctgac                                         >  2:538060/1‑90 (MQ=255)
                                                  cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                   <  1:643961/90‑1 (MQ=255)
                                                      tCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGGCGGGGGGGATTATCTTGCCTGTCTTAAATgggg                               >  2:613653/1‑88 (MQ=255)
                                                        gcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGAt                             <  2:581858/90‑1 (MQ=255)
                                                        gcgGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCAGAGGGGGGGTATTTTTCCTGACTTAACTGGCGAt                             >  1:526028/1‑90 (MQ=255)
                                                                         cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc            <  1:602826/90‑1 (MQ=255)
                                                                           gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg          <  2:243043/90‑1 (MQ=255)
                                                                           gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg          <  2:679165/90‑1 (MQ=255)
                                                                              aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt       <  2:231421/90‑1 (MQ=255)
                                                                                   ttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGt  <  2:43577/90‑1 (MQ=255)
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AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGT  >  NZ_CP009273/4594076‑4594248

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑