Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,594,1670CT54.5% ‑3.8 / 17.7 22S64F (TCT→TTT) bglJDNA‑binding transcriptional activator BglJ
Reads supporting (aligned to +/- strand):  ref base C (5/5);  new base T (12/0);  total (17/5)
Fisher's exact test for biased strand distribution p-value = 9.57e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.54e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGG  >  NZ_CP009273/4594080‑4594256
                                                                                       |                                                                                         
cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGACCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                         <  2:179503/90‑1 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATgaga                                                                                 >  2:159673/1‑90 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATgagg                                                                                 >  1:352548/1‑89 (MQ=255)
        cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgaga                                                                                 >  1:20955/1‑90 (MQ=255)
         tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGaa                                                                                >  2:19958/1‑90 (MQ=255)
                     ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                    <  1:102797/90‑1 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGGAGGGGGCGGagagag                                                                  >  2:28767/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCcgagag                                                                  >  2:194392/1‑90 (MQ=255)
                       aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagagag                                                                  >  1:31143/1‑90 (MQ=255)
                        gTCAGGAGTTATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCAGAGAgg                                                                 >  2:43925/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCCGAGAgg                                                                 >  2:211039/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCCGAGAgg                                                                 >  2:189614/1‑90 (MQ=255)
                        gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCAGAGAgg                                                                 >  2:267855/1‑90 (MQ=255)
                            ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCAGGGGGGGGtt                                                             >  2:102797/1‑90 (MQ=255)
                                        ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGGGGGGTTATTTTTCctggc                                                 >  2:60707/1‑88 (MQ=255)
                                             ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGGAGGGGGCGCGGGGGGGGGGTATCTTTTCTGACTTAAc                                            >  2:293562/1‑90 (MQ=255)
                                              cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACt                                           <  2:465791/90‑1 (MQ=255)
                                                    gcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGGCATGAGAAGGGAGGGCAGAGGGGGATTATCTTGCCTGACTGAAATGGGGag                                     >  1:238548/1‑89 (MQ=255)
                                                           tcGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGGGGGCAGAGGGGGGTTATCTTTCCTGACTGAACTGGCGATTAAGttt                              >  1:272061/1‑90 (MQ=255)
                                                                 gcggcgGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGCGATTAAATTTTCCCGt                        >  1:308588/1‑90 (MQ=255)
                                                                     cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc                    <  2:308588/90‑1 (MQ=255)
                                                                       gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCgg                  <  2:272061/90‑1 (MQ=255)
                                                                                       ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  1:43925/90‑1 (MQ=255)
                                                                                       ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg  <  1:189614/90‑1 (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 < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑