Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT48.3% 17.2 / 16.3 29S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (2/13);  new base T (14/0);  total (16/13)
Fisher's exact test for biased strand distribution p-value = 1.75e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGT  >  NZ_CP009273/4594080‑4594248
                                                                                 |                                                                                       
cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                 <  2:276092/90‑1 (MQ=255)
cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCCtttttttttttttt                                                                                 >  2:137625/1‑87 (MQ=255)
 ttATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAtttttttttttttttc                                                                                >  2:437585/1‑86 (MQ=255)
       gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTGTGCGGGGGTGATTTTTTTTTTTTCTGCCATgag                                                                          >  1:582733/1‑90 (MQ=255)
          ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAg                                                                       >  1:286328/1‑90 (MQ=255)
          ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                       >  1:218801/1‑90 (MQ=255)
           cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                                      <  2:429226/90‑1 (MQ=255)
            aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                     <  1:240569/90‑1 (MQ=255)
            aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                     <  1:266906/90‑1 (MQ=255)
                 tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                                <  1:321685/90‑1 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCa                                                               >  2:232785/1‑90 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAgcgcc                                                               >  1:125590/1‑89 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCa                                                               >  2:431204/1‑90 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAAGGAGCGCa                                                               >  1:264050/1‑90 (MQ=255)
                      cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGGGCagagg                                                           >  1:501972/1‑89 (MQ=255)
                      cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                           <  2:218801/90‑1 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCagagag                                                          >  2:7482/1‑90 (MQ=255)
                          cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                       <  1:514172/90‑1 (MQ=255)
                            ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTACGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGGGCGCagggagggggt                                                     >  1:324733/1‑87 (MQ=255)
                                 cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGATTATCtt                                                >  1:1690/1‑90 (MQ=255)
                                   tttCAGGACGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                              <  1:43957/90‑1 (MQ=255)
                                        ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGGGCGCAGAGAGGGGTTATCTTGCctgac                                         >  1:262036/1‑90 (MQ=255)
                                                    gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGGAGGGAGCGGAGGGGGGGGATTTTTTGCCTGGCTGAAGTGGCggt                             >  2:292848/1‑88 (MQ=255)
                                                                 gcggcgGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTTCGCGt                >  1:84334/1‑90 (MQ=255)
                                                                     cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc            <  2:410918/90‑1 (MQ=255)
                                                                     cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc            <  1:7482/90‑1 (MQ=255)
                                                                     cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc            <  2:589136/90‑1 (MQ=255)
                                                                      ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGGGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg           <  2:567041/90‑1 (MQ=255)
                                                                       gTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGGGCAGAGGGGGGTTATTTTTCCTGACTGAACTGGCGATTAAGTTTTCGCGGACCCgg          >  2:300/1‑90 (MQ=255)
                                                                          aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt       <  1:292848/90‑1 (MQ=255)
                                                                           ttttttCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGtt      >  2:429260/1‑90 (MQ=255)
                                                                               ttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGt  <  2:302998/90‑1 (MQ=255)
                                                                                 |                                                                                       
CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGT  >  NZ_CP009273/4594080‑4594248

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑