Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT53.6% 8.9 / 32.4 28S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (3/10);  new base T (15/0);  total (18/10)
Fisher's exact test for biased strand distribution p-value = 2.18e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.63e-04
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594088‑4594256
                                                                               |                                                                                         
cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTTTTTTTTTACCATtaga                                                                                 >  2:362584/1‑90 (MQ=255)
cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATgaga                                                                                 >  2:280727/1‑90 (MQ=255)
  ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAg                                                                               >  1:154890/1‑90 (MQ=255)
    aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                             <  1:130455/90‑1 (MQ=255)
         tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAgggc                                                                        >  2:353173/1‑90 (MQ=255)
          ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGGAGTGAGGGCa                                                                       >  2:235650/1‑90 (MQ=255)
          ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCa                                                                       >  2:43867/1‑90 (MQ=255)
           taCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag                                                                      <  1:43867/90‑1 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAgg                                                                 >  2:298919/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAgg                                                                 >  2:297387/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAgg                                                                 >  1:85887/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGGGCAGAGAgg                                                                 >  2:398452/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCTTTTTTTTTTTTTTTTCCCTGTGTAGGGATCGGGGAGAgg                                                                 >  1:255574/1‑90 (MQ=255)
                 tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCAGAGgggg                                                                >  2:368317/1‑90 (MQ=255)
                  cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                               <  1:38168/90‑1 (MQ=255)
                    ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGtt                                                             >  2:95664/1‑90 (MQ=255)
                         cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTTAGGAGTGGGCGCAGAGAGGGGTTATCtt                                                        >  1:297010/1‑90 (MQ=255)
                           tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                                      <  2:85887/90‑1 (MQ=255)
                                ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctgac                                                 <  2:176010/90‑1 (MQ=255)
                                   tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCctgactga                                              >  1:379115/1‑90 (MQ=255)
                                              ggATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGGGGTTa                                   >  2:413631/1‑90 (MQ=255)
                                              ggATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                                   >  2:95560/1‑90 (MQ=255)
                                                        tGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCcgcg                         <  1:280727/90‑1 (MQ=255)
                                                            gcggTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGGGAGGGGTTATTTTTCCTTACTGAACTGGGGGTTAAGTTTTCGCGGAcc                     >  1:13242/1‑90 (MQ=255)
                                                             cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc                    <  2:254267/90‑1 (MQ=255)
                                                               gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg                  <  2:154890/90‑1 (MQ=255)
                                                                  aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTCCCCGGCGt               <  1:171535/90‑1 (MQ=255)
                                                                  aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt               <  2:379115/90‑1 (MQ=255)
                                                                               ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  1:398452/90‑1 (MQ=255)
                                                                               |                                                                                         
CTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594088‑4594256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑