Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT53.2% 35.4 / 112.5 79S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (7/30);  new base T (42/0);  total (49/30)
Fisher's exact test for biased strand distribution p-value = 1.86e-15
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.56e-14
Rejected as consensus: Frequency below/above cutoff threshold.

AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTT  >  NZ_CP009273/4594076‑4594249
                                                                                     |                                                                                        
aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttttttt                                                                                      >  2:1451768/1‑90 (MQ=255)
aaCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttttttt                                                                                      >  2:495735/1‑90 (MQ=255)
  cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                                    <  1:1436848/90‑1 (MQ=255)
    cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                  <  2:2087495/90‑1 (MQ=255)
     ttATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAtttttttttttttttc                                                                                 >  2:859065/1‑86 (MQ=255)
      tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGcc                                                                                >  2:2019947/1‑90 (MQ=255)
           gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                           <  2:88421/90‑1 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgaga                                                                          >  1:432238/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgaga                                                                          >  2:1503624/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATgaga                                                                          >  1:249646/1‑90 (MQ=255)
            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATgaga                                                                          >  1:351593/1‑90 (MQ=255)
             tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGaa                                                                         >  2:1456599/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAg                                                                        >  1:1056094/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAg                                                                        >  2:54087/1‑90 (MQ=255)
              ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                        <  2:1902657/90‑1 (MQ=255)
               cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                                       <  2:1157510/90‑1 (MQ=255)
               cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                                       <  1:1676953/90‑1 (MQ=255)
                aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAggg                                                                      >  1:361442/1‑88 (MQ=255)
                aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAggg                                                                      >  1:404006/1‑88 (MQ=255)
                   ccTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                                   <  1:713486/90‑1 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAgcgg                                                                 >  1:266449/1‑89 (MQ=255)
                     tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                                 >  2:331977/1‑90 (MQ=255)
                      ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTGAGAAGTGAgcgcc                                                                >  2:642430/1‑89 (MQ=255)
                      ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCa                                                                >  1:462381/1‑90 (MQ=255)
                      ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCa                                                                >  1:503333/1‑90 (MQ=255)
                      ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCa                                                                >  2:635144/1‑90 (MQ=255)
                       taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATTAGAAGGGAgcgggg                                                               >  2:1614357/1‑87 (MQ=255)
                        aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGgaga                                                              >  1:185893/1‑90 (MQ=255)
                          cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAAGGGGCGCagagg                                                            >  2:433808/1‑89 (MQ=255)
                          cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCagagg                                                            >  2:538801/1‑89 (MQ=255)
                          cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                            <  1:937708/90‑1 (MQ=255)
                          cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                            <  1:1186791/90‑1 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTATTTTTTTTTTTTTTTCCCTGGGAAGGAGGGGCagagag                                                           >  1:2044392/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCagagag                                                           >  2:1665524/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGCagagag                                                           >  1:8207/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCcgaggg                                                           >  2:1131759/1‑88 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCagagag                                                           >  2:864482/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGTg                                                                      >  2:486952/1‑79 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                      <  1:486952/79‑1 (MQ=255)
                           aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTTCCCTTAGAAGGGGGCGCggagag                                                           >  2:1843488/1‑90 (MQ=255)
                           aGTCAGGAGTCATTTCAGGACGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTg                                                                                  >  2:345573/1‑67 (MQ=255)
                           aGTCAGGAGTCATTTCAGGACGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                  <  1:345573/67‑1 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAgg                                                          >  1:649439/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGGGCAGAgggg                                                          >  2:1603207/1‑90 (MQ=255)
                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAgg                                                          >  2:713486/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCACTAGGAGAGAGCGGAGAGAggg                                                         >  1:1635016/1‑90 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                                <  1:719296/67‑1 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                                >  2:719296/1‑67 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGaa                                                                         <  1:786922/74‑1 (MQ=255)
                             tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGaa                                                                         >  2:786922/1‑74 (MQ=255)
                              cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                        <  1:273301/90‑1 (MQ=255)
                              cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                        <  1:1585266/90‑1 (MQ=255)
                              cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                        <  2:537313/90‑1 (MQ=255)
                                ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCAGAGGGGGGtt                                                      >  1:508399/1‑90 (MQ=255)
                                ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAGGGGGGGCAGAGAGGGGtt                                                      >  2:1550252/1‑90 (MQ=255)
                                 gAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGGGGGCAGAGAGGGGTTa                                                     >  1:136284/1‑90 (MQ=255)
                                     cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTATTTTTTTTTTTTCTGCCATGGGGAGGGGGCGCAGAGAGGGGTTATCtt                                                 >  2:1969610/1‑90 (MQ=255)
                                     cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCAGAGAGGGGTTATCtt                                                 >  1:643909/1‑90 (MQ=255)
                                     cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATCtt                                                 >  1:524052/1‑90 (MQ=255)
                                     cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCtt                                                 >  2:1573803/1‑90 (MQ=255)
                                        ttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGcc                                              <  1:1857331/90‑1 (MQ=255)
                                         tCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCct                                             <  1:1255608/90‑1 (MQ=255)
                                            ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctgac                                          <  2:2024940/90‑1 (MQ=255)
                                             gATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCAGGGGGGGATTATTTTTCctgact                                         >  2:1255608/1‑90 (MQ=255)
                                                 ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAAc                                     >  2:504637/1‑90 (MQ=255)
                                                 ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGAGAGGGAGTATCTTGCCTGACTGAAc                                     >  2:1041099/1‑90 (MQ=255)
                                                  cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                    <  1:1131759/90‑1 (MQ=255)
                                                  cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                    <  1:1665524/90‑1 (MQ=255)
                                                  cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                    <  1:914116/90‑1 (MQ=255)
                                                        gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCGGGGAGGGGGTATTTTTCCTGACTTAACTgggggt                              >  1:1559948/1‑86 (MQ=255)
                                                        gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCAGGGAGGGGTTTTTTTGCCTGACTGAACTGGCggt                              >  1:1932652/1‑88 (MQ=255)
                                                          ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTa                            >  2:663311/1‑90 (MQ=255)
                                                          ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGGGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                            >  2:511384/1‑90 (MQ=255)
                                                           gATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGGGCAGGGGGGGGTTTTTTTGCCTGACTGGACTGGCGGTTaa                           >  2:304007/1‑90 (MQ=255)
                                                              ctcGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGtt                        <  1:1972521/90‑1 (MQ=255)
                                                               tcGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGttt                       <  2:1909052/90‑1 (MQ=255)
                                                                   ttGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCcgc                   <  1:1451768/90‑1 (MQ=255)
                                                                   ttGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCcgc                   <  1:495735/90‑1 (MQ=255)
                                                                           gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg           <  1:1503624/90‑1 (MQ=255)
                                                                           gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg           <  2:1559948/90‑1 (MQ=255)
                                                                           gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg           <  2:136284/90‑1 (MQ=255)
                                                                              aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt        <  1:1843488/90‑1 (MQ=255)
                                                                              aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt        <  1:1969610/90‑1 (MQ=255)
                                                                                    tctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGtt  >  1:290053/1‑90 (MQ=255)
                                                                                     |                                                                                        
AACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTT  >  NZ_CP009273/4594076‑4594249

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: ‑