Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT55.8% 10.2 / 49.6 43S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (6/13);  new base T (24/0);  total (30/13)
Fisher's exact test for biased strand distribution p-value = 7.42e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.82e-06
Rejected as consensus: Frequency below/above cutoff threshold.

TAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGT  >  NZ_CP009273/4594084‑4594243
                                                                             |                                                                                  
taAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCAt                                                                        <  2:563501/90‑1 (MQ=255)
    cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgagg                                                                    >  1:4005/1‑89 (MQ=255)
    cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATgaga                                                                    >  2:179569/1‑90 (MQ=255)
    cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTgagg                                                                    >  1:608024/1‑89 (MQ=255)
      ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCATgaggag                                                                  >  2:303152/1‑90 (MQ=255)
      ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgaggag                                                                  >  2:512968/1‑90 (MQ=255)
      ccATACCTATACCAGTCAGGAGTCATTTCAAGATGCCATGTCNCTGATCTCGTTTGCGGNTTTNATTNTTTTTTTTTTTGCCATGAGaaa                                                                  >  2:223216/1‑89 (MQ=255)
           ccTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                             <  1:647299/90‑1 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAgcgc                                                           >  2:194694/1‑90 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                           <  2:125151/90‑1 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                           <  1:139386/90‑1 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                           <  1:516070/90‑1 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGAAGGGAgcgc                                                           >  1:106684/1‑90 (MQ=255)
             tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATGAGAAGGGAgcgc                                                           >  2:498366/1‑90 (MQ=255)
                  cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                      <  1:426852/90‑1 (MQ=255)
                  cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                      <  1:837183/90‑1 (MQ=255)
                   aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGGGAAGGGAGCGCcgagag                                                     >  1:721952/1‑90 (MQ=255)
                   aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGGGGGCagggag                                                     >  1:388987/1‑90 (MQ=255)
                   aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCagagag                                                     >  2:82200/1‑90 (MQ=255)
                   aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCagagag                                                     >  2:426852/1‑90 (MQ=255)
                    gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAgg                                                    >  1:17610/1‑90 (MQ=255)
                    gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGGGAgg                                                    >  2:52925/1‑90 (MQ=255)
                    gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGGTTTTTTTCTTTTTTTGTCATGCGCAGTGAGCGCagcgaag                                                    >  1:717068/1‑88 (MQ=255)
                    gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGGGAAGGGGGGGCAGAGAgg                                                    >  1:100353/1‑90 (MQ=255)
                    gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAgg                                                    >  1:770862/1‑90 (MQ=255)
                     tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAggg                                                   >  2:837184/1‑90 (MQ=255)
                        ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                     >  2:288379/1‑69 (MQ=255)
                        ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgag                                                                     <  1:288379/69‑1 (MQ=255)
                           acagtttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATc                                             <  1:697704/86‑1 (MQ=255)
                               tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                         <  1:672506/90‑1 (MQ=255)
                                    ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctgac                                    <  2:670682/90‑1 (MQ=255)
                                       tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGTAGTGAGGGCGGCGAGGGCTTATTTTGCcttactta                                 >  1:630045/1‑88 (MQ=255)
                                       tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATCTTGCctgactga                                 >  1:36850/1‑90 (MQ=255)
                                         ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGGGCGCCGAGAGGGGTTATCTTTCctgactctgt                               >  2:697705/1‑86 (MQ=255)
                                         ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTATCTTGCctggcttgac                               >  2:672507/1‑86 (MQ=255)
                                                  ggATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGGGCAGAGAGGGGTTATCTTGCCTGACTGAAATGGCGGTTa                      >  2:761340/1‑90 (MQ=255)
                                                  ggATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                      >  2:182823/1‑90 (MQ=255)
                                                      ctcGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGtt                  <  1:354924/90‑1 (MQ=255)
                                                             gcggcgGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGGGCAGAGAGGGGTTTTTTTTCCTGTCTTAACTGGCGATTAAGTTTTcgcgg           >  1:633134/1‑89 (MQ=255)
                                                                 cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc       <  1:726831/90‑1 (MQ=255)
                                                                  ggTCCTTTTTTCTTTTTTTGCCATGAGAAGTGAGCGCAGAGGGGGGTTATCTTTCCTGACTGAACTGGCGGTTAAGTTTTCGCGGACCCg      >  1:56779/1‑90 (MQ=255)
                                                                  ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg      >  2:158200/1‑90 (MQ=255)
                                                                      aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt  >  2:18055/1‑90 (MQ=255)
                                                                             |                                                                                  
TAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGT  >  NZ_CP009273/4594084‑4594243

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑