Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,941,2000AC54.5% 2.3 / 10.7 11L43R (CTG→CGG) hdfRHTH‑type transcriptional regulator HdfR
Reads supporting (aligned to +/- strand):  ref base A (1/4);  new base C (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGG  >  NZ_CP009273/3941130‑3941289
                                                                       |                                                                                         
aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGGAAAAGGGT‑ACAGCCCGGTGGTTTTCCAttttttt                                                                        >  2:230077/1‑86 (MQ=255)
aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGG‑GAAAAAGTTTACACCCCGTTTATTTTTCAGTTGttt                                                                        >  1:214911/1‑88 (MQ=255)
        gtTTTTCACCGGCAGCGCATAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGaa                                                                <  2:201703/90‑1 (MQ=255)
                                   tatTGTTTCTGTGGCGGGG‑GGAAAAGGTCACACCCCGGTGATTTTTCCGTTTTTTGATTCGAAAACTCACTGCCGACTGGGGGAGATaga                                     >  2:107277/1‑90 (MQ=255)
                                   tatTGTTTCTGTGGCGGGG‑GGAAAAGGTCACACCCCGATGGTTTTTCTTTTTTTTTTTTTGAAAGATCAATGCTGACCGGGGCAGATaga                                     >  2:259242/1‑90 (MQ=255)
                                   tatTGTTTCTGTGGCGGGG‑GAAAAAGGTCACACCCCGTTGATTTTTCAGTTTTTTGATTTGAAAACTCACTGCTGACTGGGGCAGATaaa                                     >  1:309971/1‑88 (MQ=255)
                                             gtgGCGGGG‑GGAAAGGGTCACACCCCCTTGATTTTTCACTTTTTTGATTTGAAAACTCACTGCTGACTGGGGCAGATAAAGCGATTCaac                           >  2:132389/1‑88 (MQ=255)
                                                gCGGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGc                        <  2:123702/90‑1 (MQ=255)
                                                                  cacCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGAcgcg       <  1:130102/90‑1 (MQ=255)
                                                                    cccAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGtt     <  2:270605/90‑1 (MQ=255)
                                                                      cAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCg   >  2:181627/1‑90 (MQ=255)
                                                                       aGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCgg  >  2:105535/1‑90 (MQ=255)
                                                                       |                                                                                         
AGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGT‑GAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGAGCGATTCAGCCGCTCGACCAAAGTGACGCGTTCGG  >  NZ_CP009273/3941130‑3941289

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑