Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273447,8830AC54.5% 7.1 / 10.6 11G373G (GGT→GGG) ampGmuropeptide MFS transporter AmpG
Reads supporting (aligned to +/- strand):  ref base A (4/1);  new base C (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.05e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GGTACGGCAGCGGCGACGGAGAATAGATAGAATGTCGACCAGCCGTGTGCTTCAACAAA‑CCAACCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGACTTATTACATAG  >  NZ_CP009273/447821‑447972
                                                               |                                                                                         
ggTACGGCAGGGGCGAGGGAAAAAAGATAGAAGGTCGACCAGCCGTGTGCTTCAACAAA‑CCACCCCGCCACGGGGCCGACATAAACTCGc                                                                <  2:194200/90‑1 (MQ=255)
ggTACGGCAGCGGCGACGGAGAATAAATAGAATGCCGACCAGCCGTGTGCTTCAACAAA‑CCACCCCGCCACGGGGCCGACATAAACTCGc                                                                <  2:263175/90‑1 (MQ=255)
          cggcgACGGAGAATAGATAGAATGTCGACCAGCCGTGTGCTTCAACAAA‑CCAACCCGCCACGGGGCCGACATAAACTCGCCCTAcagcag                                                      >  2:424386/1‑90 (MQ=255)
                   agaATAGATAGAAGGTCGCCCAGCGGGGTGCTTAAACAAC‑CAACCCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTg                                             <  1:424386/90‑1 (MQ=255)
                   aaaaTAGATAGAATGTCGCCCAGCCGTGTGCTTCAACAAC‑CCACCCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTg                                             <  2:211298/88‑1 (MQ=255)
                             gaATGTCGACCAGCCGTGTGCTTCAACAAA‑CCAACCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGc                                   >  1:272383/1‑90 (MQ=255)
                             gaATGTCGACCAGCCGTGTGCTTCAACAAA‑CCAACCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGc                                   >  1:93916/1‑90 (MQ=255)
                                    gACCAGCCGTGTGCTTCAACAAA‑CCAACCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGa                            >  1:269492/1‑90 (MQ=255)
                                                  ttaaacaac‑CCACCCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGa              <  2:30455/87‑1 (MQ=255)
                                                   tCAAAAAACCCACCCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGa              <  2:9587/90‑1 (MQ=255)
                                                    caacaaA‑CCAACCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGACt            <  2:272383/90‑1 (MQ=255)
                                                             caaccCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGACTTATTACAt    <  2:21102/90‑1 (MQ=255)
                                                               accCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGACTTATTACATAg  <  1:298439/90‑1 (MQ=255)
                                                               accCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGACTTATTACATAg  <  2:269492/90‑1 (MQ=255)
                                                               |                                                                                         
GGTACGGCAGCGGCGACGGAGAATAGATAGAATGTCGACCAGCCGTGTGCTTCAACAAA‑CCAACCCGCCACGGGGCCGACATAAACTCGCCCTACAGCAGAAAGCGCTGAGAGCAGGGCAAATTGAGTAGCGGAAAATGACTTATTACATAG  >  NZ_CP009273/447821‑447972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑