Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT64.5% ‑3.1 / 29.8 31S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (1/10);  new base T (20/0);  total (21/10)
Fisher's exact test for biased strand distribution p-value = 2.48e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.05e-06
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594085‑4594256
                                                                                  |                                                                                         
aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATg                                                                                    <  2:26828/90‑1 (MQ=255)
   cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTgaga                                                                                 >  2:764081/1‑90 (MQ=255)
   cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATgaga                                                                                 >  2:520532/1‑90 (MQ=255)
       aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAggg                                                                             >  2:236072/1‑88 (MQ=255)
          ccTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                                          <  1:54510/90‑1 (MQ=255)
            tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                                        <  2:62724/90‑1 (MQ=255)
             ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCa                                                                       >  1:5390/1‑90 (MQ=255)
             ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTTCATGTGAAGTGGGCGCa                                                                       >  1:797089/1‑90 (MQ=255)
             ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAgggcc                                                                       >  2:254417/1‑89 (MQ=255)
             ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCa                                                                       >  2:296475/1‑90 (MQ=255)
             ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCa                                                                       <  2:658119/90‑1 (MQ=255)
                ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                    <  1:254417/90‑1 (MQ=255)
                 aggTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  1:266884/88‑1 (MQ=255)
                  aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGGGAAGGGAGCGCagagag                                                                  >  2:808091/1‑90 (MQ=255)
                  aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGTGAGCGCagagag                                                                  >  2:56114/1‑90 (MQ=255)
                   gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGGAGAGAgg                                                                 >  2:567272/1‑90 (MQ=255)
                    tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCCTGAGAAATGAGCGCAGAGAggg                                                                >  1:406221/1‑90 (MQ=255)
                     cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                               <  1:469855/90‑1 (MQ=255)
                       ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGGGAAGTTAGGGCAGAAAGGGGtt                                                             >  1:497443/1‑90 (MQ=255)
                          gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATc                                                          >  2:31390/1‑90 (MQ=255)
                             aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTATCtct                                                       >  2:266884/1‑88 (MQ=255)
                              tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGc                                                      <  2:352599/90‑1 (MQ=255)
                                   ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAGGGGTTATCTTTCctgac                                                 >  2:352492/1‑90 (MQ=255)
                                        ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTGGAAGGGAGCGCCGGGAGGGGGTATCTTTCcttactggaa                                            >  1:351903/1‑87 (MQ=255)
                                         cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                           <  2:497443/90‑1 (MQ=255)
                                          aTGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGAGAGCGCAGAGGGGGGTTATCTTTCCTGACTGAACTg                                          >  2:472418/1‑90 (MQ=255)
                                               gcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGAt                                     >  2:69796/1‑90 (MQ=255)
                                                 ggATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGGGGGGTTATCTTTCCTGACTGAACTGGCGATTa                                   >  1:39715/1‑90 (MQ=255)
                                                  gATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTaa                                  >  2:265433/1‑90 (MQ=255)
                                                                cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc                    <  1:16797/90‑1 (MQ=255)
                                                                 ggTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCAGAGAGGGGTTATTTTGCCTGACTGAACTGGCGGTTAAGTTTTCGCGTAcccc                   >  1:679437/1‑89 (MQ=255)
                                                                                ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc    >  1:136113/1‑90 (MQ=255)
                                                                                  ctGCCATGAGAAGTGAGCGCAGAGAGGGATTGTCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  2:660634/90‑1 (MQ=255)
                                                                                  |                                                                                         
AAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594085‑4594256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑