Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT74.2% 17.2 / 16.5 31S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (2/6);  new base T (23/0);  total (25/6)
Fisher's exact test for biased strand distribution p-value = 3.80e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.26e-03
Rejected as consensus: Frequency below/above cutoff threshold.

CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594080‑4594256
                                                                                       |                                                                                         
cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                         <  2:316194/90‑1 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCATgaga                                                                                 >  1:35544/1‑90 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTgaga                                                                                 >  1:379602/1‑90 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATtaga                                                                                 >  2:619689/1‑90 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATgaga                                                                                 >  1:677283/1‑90 (MQ=255)
          ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAg                                                                               >  1:193090/1‑90 (MQ=255)
          ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAg                                                                               >  2:427687/1‑90 (MQ=255)
           cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGGATTTTTTTTTTTTTTTCCCTGAGAAgg                                                                              >  1:545620/1‑89 (MQ=255)
            aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGGGAAATg                                                                             >  1:621254/1‑90 (MQ=255)
                 tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTTTTTTTTTTCCCTGAGGAAGGAgcgc                                                                        >  1:450485/1‑90 (MQ=255)
                 tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgcgc                                                                        <  2:677283/90‑1 (MQ=255)
                      cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                   <  2:35135/90‑1 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGGGCGCagagag                                                                  >  2:470233/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGGGCggggag                                                                  >  2:366755/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCGGAgggg                                                                 >  1:583375/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGGGGGCAGAGAgg                                                                 >  1:156732/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGGGCAGGGAgg                                                                 >  1:326808/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAgg                                                                 >  2:548574/1‑90 (MQ=255)
                         tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAggg                                                                >  1:132287/1‑90 (MQ=255)
                         tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAggg                                                                >  1:288056/1‑90 (MQ=255)
                          cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                               <  1:427687/90‑1 (MQ=255)
                                 cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGCAGAGAGGGGTTATCtt                                                        >  1:119020/1‑90 (MQ=255)
                                  aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTAttttt                                                       >  2:100807/1‑89 (MQ=255)
                                      cAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGGAAGGAGCGGAGAGAGGGGGTTTCTTTCctt                                                   >  1:440385/1‑89 (MQ=255)
                                         gATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGCAGAGAGGGGGTATTTTTCctgact                                                >  1:56433/1‑90 (MQ=255)
                                           tGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCCTGAGAAATGAGGGCAGAGGGGGGTTATTTTTCctgactga                                              >  1:229397/1‑90 (MQ=255)
                                             ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGTGGGGGCAGGGGGGGGTTATTTTGCCTGACTGAAc                                            >  2:43457/1‑90 (MQ=255)
                                             ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAAc                                            >  2:166476/1‑90 (MQ=255)
                                                 gTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGc                                        >  2:98828/1‑90 (MQ=255)
                                                    gcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGAt                                     <  2:621254/90‑1 (MQ=255)
                                                      ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                                   <  1:43457/90‑1 (MQ=255)
                                                                                       ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  2:47661/90‑1 (MQ=255)
                                                                                       |                                                                                         
CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594080‑4594256

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: ‑