Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT50.0% 47.1 / 53.0 72S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (6/30);  new base T (36/0);  total (42/30)
Fisher's exact test for biased strand distribution p-value = 2.37e-14
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594078‑4594256
                                                                                         |                                                                                         
cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                                           <  2:72079/90‑1 (MQ=255)
  cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                         <  1:587432/90‑1 (MQ=255)
    tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                                       <  2:411403/90‑1 (MQ=255)
         gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                                  <  1:381681/90‑1 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgagg                                                                                 >  2:1434435/1‑89 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgaga                                                                                 >  1:12287/1‑90 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgaga                                                                                 >  2:1225109/1‑90 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGcc                                                                                       >  1:102359/1‑84 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGcc                                                                                       >  2:1211044/1‑84 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                                       <  2:102359/84‑1 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                                       <  1:1211044/84‑1 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTCTTCCCTgaga                                                                                 >  2:1069899/1‑90 (MQ=255)
          cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTCTTTTTTTGCCATgaga                                                                                 >  2:685200/1‑90 (MQ=255)
            ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTTCCTGAGAAg                                                                               >  1:47132/1‑90 (MQ=255)
            ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTTAGAAg                                                                               >  1:58340/1‑90 (MQ=255)
            ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAg                                                                               >  1:1379497/1‑90 (MQ=255)
            ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTTAGAAg                                                                               >  1:1148334/1‑90 (MQ=255)
                   tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAgggc                                                                        >  2:625720/1‑90 (MQ=255)
                   tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAgcgc                                                                        >  1:1141232/1‑90 (MQ=255)
                   tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                                        <  1:61882/90‑1 (MQ=255)
                    ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCa                                                                       >  1:336723/1‑90 (MQ=255)
                    ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCa                                                                       >  2:249688/1‑90 (MQ=255)
                    ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCa                                                                       >  1:429211/1‑90 (MQ=255)
                    ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGGGCa                                                                       >  2:141589/1‑90 (MQ=255)
                    ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCa                                                                       >  2:163028/1‑90 (MQ=255)
                     taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag                                                                      <  1:983393/90‑1 (MQ=255)
                     taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag                                                                      <  1:249688/90‑1 (MQ=255)
                      aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTAGGAGGGGGCGCagg                                                                     >  2:1048526/1‑89 (MQ=255)
                      aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCaga                                                                     <  1:1069899/90‑1 (MQ=255)
                      aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCaga                                                                     <  1:444793/90‑1 (MQ=255)
                      aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCaga                                                                     <  1:829304/90‑1 (MQ=255)
                       ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                    <  2:1263887/90‑1 (MQ=255)
                       ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                    <  2:1360747/90‑1 (MQ=255)
                        cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  1:1057320/90‑1 (MQ=255)
                        cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  2:1075747/90‑1 (MQ=255)
                        cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  1:288104/90‑1 (MQ=255)
                        cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  1:35835/90‑1 (MQ=255)
                        cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  2:129987/90‑1 (MQ=255)
                        cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTTGGAAATGAGGGCaggga                                                                   >  1:626996/1‑90 (MQ=255)
                         aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCaggggg                                                                  >  2:1440494/1‑86 (MQ=255)
                         aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGAGAGCGCagagag                                                                  >  2:1139325/1‑90 (MQ=255)
                         aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGGGAAGGAAGGGCaggggg                                                                  >  1:1158085/1‑86 (MQ=255)
                         aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCagagag                                                                  >  2:115542/1‑90 (MQ=255)
                         aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGGGCagagag                                                                  >  2:1333328/1‑90 (MQ=255)
                          gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttttttttc                                                                                           >  2:1113916/1‑64 (MQ=255)
                          gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                                           <  1:1113916/64‑1 (MQ=255)
                          gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGGGAgg                                                                 >  2:380614/1‑90 (MQ=255)
                          gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGGAGTGGGCGCAGAGAgg                                                                 >  1:756369/1‑90 (MQ=255)
                          gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTCTGCCTTGAGAAATGAGCGCAGGGAgg                                                                 >  2:65091/1‑90 (MQ=255)
                           tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCAGAGAggg                                                                >  1:251212/1‑90 (MQ=255)
                           tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCagggaggg                                                                >  2:1308181/1‑90 (MQ=255)
                           tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGGGGAGGGAGCGCAGAGAggg                                                                >  1:688774/1‑90 (MQ=255)
                           tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATGAGAAGAGAGCGCAGAGAggg                                                                >  2:484242/1‑90 (MQ=255)
                           tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGGGCAGAGgggg                                                                >  2:1178464/1‑90 (MQ=255)
                           tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCGCGTTTGCGGCGGTCATtttttctttttc                                                                                           <  2:527380/63‑1 (MQ=255)
                            cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                               <  1:626044/90‑1 (MQ=255)
                            cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                               <  2:1141232/90‑1 (MQ=255)
                              ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCATGAGAAGGGAGCGGAGAGAgggggt                                                             >  2:1297333/1‑87 (MQ=255)
                              ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCAGAGAgggggt                                                             >  1:652650/1‑87 (MQ=255)
                               gAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCAGAGAGGGGTTa                                                            >  2:1131668/1‑90 (MQ=255)
                               gAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGGGGGGGAGTa                                                            >  2:654043/1‑90 (MQ=255)
                                   cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTg                                                                             >  1:372982/1‑69 (MQ=255)
                                   cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                             <  2:372982/69‑1 (MQ=255)
                                    aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCCTGGGGAGGGGGGGGGGAGAGGGAGTATCttt                                                       >  1:904531/1‑89 (MQ=255)
                                          ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctgac                                                 <  1:458286/90‑1 (MQ=255)
                                                cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                           <  2:688774/90‑1 (MQ=255)
                                                cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                           <  1:450570/90‑1 (MQ=255)
                                                             tcGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCGGAGGGGGGTTATTTTTTCTGACTGAACTGGCGATTAAGttt                              >  1:1148035/1‑90 (MQ=255)
                                                                   gcggcgGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTATTTTGCCTGACTGAACTGGCGATTAAGTTTTCGCGt                        >  2:1189672/1‑90 (MQ=255)
                                                                       cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc                    <  2:652650/90‑1 (MQ=255)
                                                                       cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc                    <  1:65091/90‑1 (MQ=255)
                                                                        ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGGTTAAGTTTTCCCGGACCCg                   >  2:1000290/1‑90 (MQ=255)
                                                                        ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg                   <  2:1096344/90‑1 (MQ=255)
                                                                         gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg                  <  1:1308181/90‑1 (MQ=255)
                                                                         gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg                  <  2:1148035/90‑1 (MQ=255)
                                                                            aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt               <  1:848622/90‑1 (MQ=255)
                                                                              tttttctttttcTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGttt             <  1:484242/90‑1 (MQ=255)
                                                                                  tctttttctGCCATGAGAAGCGAGCGCAGAGAGGGATTCTCTTGCCTGACTGAACTGGTGATTAAGTTTCCGCGTACCCGGCGTTTAGtt         >  1:745499/1‑90 (MQ=255)
                                                                                       ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc    <  1:625720/90‑1 (MQ=255)
                                                                                       ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc    >  1:452799/1‑90 (MQ=255)
                                                                                       ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc    <  1:1399087/90‑1 (MQ=255)
                                                                                       ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc    >  2:1269246/1‑90 (MQ=255)
                                                                                         ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  2:630218/90‑1 (MQ=255)
                                                                                         ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  1:1178464/90‑1 (MQ=255)
                                                                                         ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  2:1422778/90‑1 (MQ=255)
                                                                                         |                                                                                         
CCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594078‑4594256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑