Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,267,2780TG56.2% 12.1 / 19.4 16T10P (ACC→CCC) chaAsodium‑potassium/proton antiporter ChaA
Reads supporting (aligned to +/- strand):  ref base T (0/7);  new base G (9/0);  total (9/7)
Fisher's exact test for biased strand distribution p-value = 8.74e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.80e-04
Rejected as consensus: Frequency below/above cutoff threshold.

TGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTATGGTTATCCCTTTGCAGATGAATTTATCG  >  NZ_CP009273/1267201‑1267336
                                                                             |                                                          
tgtCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCGcccc                                                >  1:875554/1‑88 (MQ=255)
tgtCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCGcccc                                                >  2:588320/1‑88 (MQ=255)
   cTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCGCCCCttt                                             >  2:973621/1‑89 (MQ=255)
      gctgctTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGc                                          <  2:911238/90‑1 (MQ=255)
          ctTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCAttt                                      <  1:1121802/90‑1 (MQ=255)
          ctTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCAttt                                      <  1:648960/90‑1 (MQ=255)
          ctTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCAttt                                      <  2:731628/90‑1 (MQ=255)
           ttCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTg                                     <  1:1108185/90‑1 (MQ=255)
               ccACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCCCCCCTTTAGGATTTTACAt                                 >  1:1168950/1‑90 (MQ=255)
                 acaGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTa                               <  1:1237995/90‑1 (MQ=255)
                               aCCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCGCCTCTTTAGCATTTTACATTATTGTTATTCCtttt                 >  2:558317/1‑89 (MQ=255)
                                  aGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTCCGCCCCTTTAGCATTTTACATTATGGTTTTTCCTTTTCAg              >  2:174732/1‑90 (MQ=255)
                                  aGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTCCCCCCCTTTAGCATTTGACATTATGGTTATTCCCTTTCAg              >  1:103176/1‑90 (MQ=255)
                                   gcgcCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTATGGTTATCCCTTTGCAGa             <  1:876331/90‑1 (MQ=255)
                                    cgcCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCCCCTCTTTAGCATTTTAAATTTTGGGTATTCCCTTTCAGaa            >  2:99568/1‑89 (MQ=255)
                                              gggAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTCCGCCCCTTTGGCATTTTAAATTTTGGTTTTTCCTTTTCAGATGAATTTAttt  >  2:142631/1‑88 (MQ=255)
                                                                             |                                                          
TGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTATGGTTATCCCTTTGCAGATGAATTTATCG  >  NZ_CP009273/1267201‑1267336

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑