Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1610CT53.3% 12.8 / 40.1 30S62F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (1/13);  new base T (16/0);  total (17/13)
Fisher's exact test for biased strand distribution p-value = 1.17e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.56e-06
Rejected as consensus: Frequency below/above cutoff threshold.

CTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTA  >  NZ_CP009273/4594088‑4594246
                                                                         |                                                                                     
cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGCCATTTTTTTTTTTTTTTCCATgaga                                                                       >  1:134833/1‑90 (MQ=255)
 tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGaa                                                                      <  2:474947/90‑1 (MQ=255)
         tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                              <  1:501834/90‑1 (MQ=255)
          ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCGTTTTTTTTTTTTTTTGCCTGTGAAATGAGCGCa                                                             >  1:494773/1‑90 (MQ=255)
          ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGGGCa                                                             >  2:192358/1‑90 (MQ=255)
          ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCTTTTTTTTTTTTTTTTGCCTGCGAAGAGAgcgcg                                                             >  1:222281/1‑89 (MQ=255)
              caggcaggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                         <  2:453298/90‑1 (MQ=255)
              cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAAAGAGCGCagaga                                                         >  1:396187/1‑90 (MQ=255)
              cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                         <  2:263596/90‑1 (MQ=255)
              cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                         <  1:510661/90‑1 (MQ=255)
               aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTTTTTTTTTGCCATGAGAAGTGAGCGGagaggg                                                        >  2:431128/1‑88 (MQ=255)
               aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCcgagag                                                        >  2:141747/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGGGAAGTGAGCGCGGAgggg                                                       >  1:21446/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGGAGAGAgg                                                       >  1:410099/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGAGAGCGCAGAgggg                                                       >  2:353496/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAgggg                                                       >  1:434990/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTTCCATCAGAAGAGAGGGCCGAAAgg                                                       >  2:53353/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAgggg                                                       >  1:455898/1‑90 (MQ=255)
                gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAgg                                                       >  2:406420/1‑90 (MQ=255)
                  cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                     <  1:556768/90‑1 (MQ=255)
                       gTCCTTTCTGGGTGCCCTGTCGCGGGTTTAGTTTGCGCCGTCCATTTTTTCTTTTTCTGCCACGGGAAGTGACCGCGGAGAGGGATTATc                                                <  1:142703/90‑1 (MQ=255)
                       gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCCGAGAGGGGTTAtt                                                >  1:14855/1‑89 (MQ=255)
                         cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                             <  1:562616/59‑1 (MQ=255)
                         cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                             >  2:562616/1‑59 (MQ=255)
                           tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                            <  2:368523/90‑1 (MQ=255)
                                   tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctgactga                                    <  2:208469/90‑1 (MQ=255)
                                          tCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCg                             <  2:396187/90‑1 (MQ=255)
                                                         gcggcgGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGGGGGGGGGTTTTTTTTCTTTCTGTACTGGCGATTAAGTTTTcgccg              >  1:312897/1‑88 (MQ=255)
                                                             cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc          <  2:387914/90‑1 (MQ=255)
                                                                  aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGt     <  1:353496/90‑1 (MQ=255)
                                                                     ttttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTa  <  1:511948/90‑1 (MQ=255)
                                                                         |                                                                                     
CTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTA  >  NZ_CP009273/4594088‑4594246

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑