Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,941,1910TG54.5% 7.2 / 12.4 11N46T (AAC→ACC) hdfRHTH‑type transcriptional regulator HdfR
Reads supporting (aligned to +/- strand):  ref base T (0/5);  new base G (6/0);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
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.

TGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGA  >  NZ_CP009273/3941108‑3941254
                                                                                   |                                                               
tGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCacac                                                           <  2:415110/90‑1 (MQ=255)
           gTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTTACACCCCGTTGAttt                                                >  1:146331/1‑90 (MQ=255)
                      aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCt                                     <  2:384227/90‑1 (MQ=255)
                      aGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCCGTTGATTTTTCCGtttttt                                     >  1:533664/1‑86 (MQ=255)
                           gtagtTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGGAAAAGGTCACACCCCGTTGATTTTTCCGTTGTTTGAttt                                >  2:30077/1‑89 (MQ=255)
                                ttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCCGTTGATTTTTCAGTTGTCTTATTCGAAAg                           >  1:187618/1‑90 (MQ=255)
                                ttttCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCAAACCCCGTTGATTTTTCAGTTTTTTGTTTTGaaaa                           >  1:140625/1‑89 (MQ=255)
                                   tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTc                        <  2:283849/90‑1 (MQ=255)
                                   tCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGGGAAAAAGGTCACACCCCGTTGATTTTTCAGTTTTCTGATTCGAAAACTc                        >  1:499168/1‑90 (MQ=255)
                                                  aaaCGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTc         <  1:30077/90‑1 (MQ=255)
                                                         tatTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATaga  <  2:80519/90‑1 (MQ=255)
                                                                                   |                                                               
TGCTCATGAGCGTTTCTGCATAAGGCAGTAGTTTTTCACCGGCAGCGGTTAAACGGATATTGTTTCTGTGGCGGGTGAAAAGGTTCACACCCAGTTGATTTTCCAGTTGTCTGATTCGAAAGCTCACTGCTGACTGGGTCAGATAGA  >  NZ_CP009273/3941108‑3941254

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑