Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT48.0% 10.3 / 15.8 25S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (4/9);  new base T (12/0);  total (16/9)
Fisher's exact test for biased strand distribution p-value = 4.58e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594080‑4594256
                                                                                       |                                                                                         
cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                         <  1:299728/90‑1 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgaga                                                                                 >  1:271454/1‑90 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTgagg                                                                                 >  2:299728/1‑89 (MQ=255)
            aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAggg                                                                             >  1:359059/1‑88 (MQ=255)
            aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                             <  1:217439/90‑1 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGGGCGCa                                                                       >  2:519799/1‑90 (MQ=255)
                  ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAGTGAgcgcg                                                                       >  2:529174/1‑89 (MQ=255)
                     ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                    <  1:519799/90‑1 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGGGAAGTGGGCGCcgggag                                                                  >  2:123595/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCagagag                                                                  >  1:297061/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCagagag                                                                  >  1:487024/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGCAGAGAgg                                                                 >  1:326438/1‑90 (MQ=255)
                         tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTC‑TTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                               <  1:25272/90‑1 (MQ=255)
                               gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATc                                                          <  1:412344/90‑1 (MQ=255)
                                  aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCAGGGAGGGGTTATCTTg                                                       >  2:480066/1‑90 (MQ=255)
                                           tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATGAGAAGGGAGCGCAGAGAGGGATTATCTTTCctgactga                                              >  1:404906/1‑90 (MQ=255)
                                                  tCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  2:14399/62‑1 (MQ=255)
                                                  tCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   >  1:14399/1‑62 (MQ=255)
                                                    gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGGGAGGGGTTATCTTGCCTGACTGAACTGGCGAt                                     >  2:150037/1‑90 (MQ=255)
                                                    gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGGGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGAt                                     >  1:233112/1‑90 (MQ=255)
                                                    gcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTg                                                                                         >  1:529752/1‑38 (MQ=255)
                                                    gcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                         <  2:529752/38‑1 (MQ=255)
                                                      ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                                   <  1:529174/90‑1 (MQ=255)
                                                            cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTc                             >  1:162061/1‑90 (MQ=255)
                                                                      ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg                   <  2:487024/90‑1 (MQ=255)
                                                                                     ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc    <  2:162061/90‑1 (MQ=255)
                                                                                     ttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc    <  2:297061/90‑1 (MQ=255)
                                                                                       ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  2:49952/90‑1 (MQ=255)
                                                                                       ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  1:123595/90‑1 (MQ=255)
                                                                                       |                                                                                         
CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594080‑4594256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑