Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,267,2830AT54.5% ‑1.1 / 12.2 11V8E (GTA→GAA) chaAsodium‑potassium/proton antiporter ChaA
Reads supporting (aligned to +/- strand):  ref base A (0/5);  new base T (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.

GTAGTGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTATGGTTA‑TCCCTTTGCAGATGAATTTATCGAAAATGTAAAAAATAGGTAGGAAAAA  >  NZ_CP009273/1267197‑1267362
                                                                                      |                                                                                
gTAGTGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCg                                                                               <  2:409029/90‑1 (MQ=255)
  aGTGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGcc                                                                             <  2:197216/90‑1 (MQ=255)
    tgtCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCGcccc                                                                           >  1:375263/1‑88 (MQ=255)
              ctTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTCCCCCCCTTTTGCAttt                                                                 >  2:509047/1‑90 (MQ=255)
                     acaGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTa                                                          <  1:772884/90‑1 (MQ=255)
                        ggAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTACGCCCCTTGGGGAATTTACAtttttg                                                       >  2:772884/1‑86 (MQ=255)
                                  tACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTATGGTTA‑TCCCttt                                            <  1:290753/90‑1 (MQ=255)
                                      aGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTTCCCCCCTTTTGCATTTTTCATTATGGTTATTCCCttttcg                                         >  2:441777/1‑87 (MQ=255)
                                        cgcCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTCCGCCCCCTGTGCATTTTTCATTATGGTTT‑TTCCTTTTCAggt                                      >  2:799022/1‑88 (MQ=255)
                                        cgcCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGGTTTTTCCCCCCCTTTAGCATTTTACATTTTGGTTT‑TCCCTTTTCAGAt                                      >  2:650063/1‑90 (MQ=255)
                                                                            gCGGGTTTTTACCGCCTCTTGAGCATTTGACATTATGGTTA‑TCCCTTTGCAGATGAATTTATCGAAAATGTAAAAAATAGGTAGGaaaaa  <  1:107231/90‑1 (MQ=255)
                                                                                      |                                                                                
GTAGTGTCTGGCTGCTTCCCCACAGGAACAGCACTACCAGCGCCAGAACCGGGAAAATAAGCGAAGTCTCCTTGTGGCGGGTTTTTACCGCCTCTTGAGCATTTGACATTATGGTTA‑TCCCTTTGCAGATGAATTTATCGAAAATGTAAAAAATAGGTAGGAAAAA  >  NZ_CP009273/1267197‑1267362

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑