Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT53.6% 17.0 / 69.6 56S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (7/19);  new base T (30/0);  total (37/19)
Fisher's exact test for biased strand distribution p-value = 1.55e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.94e-08
Rejected as consensus: Frequency below/above cutoff threshold.

CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594080‑4594256
                                                                                       |                                                                                         
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                                                                       >  2:208034/1‑90 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCa                                                                       >  1:25587/1‑90 (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)
                                                                                  tttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTAt       <  2:156310/90‑1 (MQ=255)
                                                                                   ttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                                   >  1:668889/1‑61 (MQ=255)
                                                                                   ttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                                   <  2:668889/61‑1 (MQ=255)
                                                                                       ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  2:537613/90‑1 (MQ=255)
                                                                                       |                                                                                         
CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594080‑4594256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑