Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,133,6360GT55.6% 3.6 / 12.7 9N486K (AAC→AAA) asmAouter membrane assembly protein AsmA
Reads supporting (aligned to +/- strand):  ref base G (3/1);  new base T (0/5);  total (3/6)
Fisher's exact test for biased strand distribution p-value = 4.76e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTTGCATGTCGTTTAACGTCACGACGCCATCCTTCAACGTCAAATCGGTGGTAAAGCGGTCAAGCCGCGTCACGTTATCAAAGTTTTCAGCGGCCTTCACATCACCGCCATTACGCTCTACCGCTTGCTGAATCATCTGCTGGAAGTTCATCC  >  NZ_CP009273/2133554‑2133706
                                                                                  |                                                                      
cTTGCATGTCGTTTAACGTCACGACGCCATCCTTCAACGTCAAATCGGTGGTAAAGCGGTCAAGCCGCGTCACGTTATCAAAGTTTTCAg                                                                 >  1:136721/1‑90 (MQ=255)
                                      gTCAAATGGGTGGAAAAGCGGTCACCCCGCGTCACTTTATAAAATTTTTCAGCGCCCTCCACATCACCGCCATTACGCTCTACCGCTTGc                           <  2:136721/90‑1 (MQ=255)
                                          aaTCGGTGGTAAAGCGGTCAAGCCGCGTCACGTTATCAAAGTTTTCAGCGGcc                                                            >  1:255967/1‑53 (MQ=255)
                                          aaTCGGTGGTAAAGCGGTCAAGCCGCGTCACGTTATCAAAGTTTTCAGCGGcc                                                            <  2:255967/53‑1 (MQ=255)
                                               gtggaAACGCGGTCAAGCCGCGTCCCTTTATCAAATTTTTCAGCGGCCTTCACATCCCCGCCATTACGCTCTACCGCTTGCTGAatcatc                  <  2:535308/90‑1 (MQ=255)
                                                         ggTCAAGCCGCGTCACGTTATCAAAGTTTTCAGCGGCCTTCACATCACCGCCATTACGCTCTACCGCTTGCTGAATCATCTGCTGGAAGt        >  1:66735/1‑90 (MQ=255)
                                                         ggTCAACCCCCTTCACGTTATAAAATTTTCCAGCGCCCTCCCCATCCCCGCCATTACGCTCTACCGCTTGCTGAATCATCTGCTGGAAGt        <  2:319714/90‑1 (MQ=255)
                                                             aaGCCGCGTCACTTTAAAAAATTTTTCGGCGGCCTCCACACCCCCGCCATTACGCTCTACCGCTTGCTGAATCATCTGCTGGAAGTTCAt    <  2:154534/90‑1 (MQ=255)
                                                               gCCGCGTCACTTTATAAAATTTTTCAGCGGCCTTCACATCACCGCCATTACGCTCTACCGCTTGCTGAATCATCTGCTGGAAGTTCATcc  <  1:159202/90‑1 (MQ=255)
                                                                                  |                                                                      
CTTGCATGTCGTTTAACGTCACGACGCCATCCTTCAACGTCAAATCGGTGGTAAAGCGGTCAAGCCGCGTCACGTTATCAAAGTTTTCAGCGGCCTTCACATCACCGCCATTACGCTCTACCGCTTGCTGAATCATCTGCTGGAAGTTCATCC  >  NZ_CP009273/2133554‑2133706

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑