Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273976,6890AG54.5% 4.7 / 11.1 11I63V (ATC→GTC) ldtDL,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (1/4);  new base G (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.26e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AATCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGGTT  >  NZ_CP009273/976607‑976769
                                                                                  |                                                                                
aaTCCCTGGCGACAGCCCGGCGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGACCAGcc                                                                           >  2:181881/1‑90 (MQ=255)
 aTCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCCGccc                                                                          >  2:391191/1‑89 (MQ=255)
  tCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCAt                                                                         <  1:555258/90‑1 (MQ=255)
     cTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCATTGc                                                                      >  2:56306/1‑90 (MQ=255)
      tGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGGGCCGCCATTGcc                                                                     >  2:168135/1‑90 (MQ=255)
               cccGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGc                                                            <  2:389943/90‑1 (MQ=255)
                                             aCTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAAtc                              <  1:360776/90‑1 (MQ=255)
                                              cTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGGGCGGCAGAAAAAACCCGCACGCAAATCGAAtct                             >  2:1760/1‑90 (MQ=255)
                                                   gCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCCGCCATTGCCTGAAAGTGCGGCAGAAAAAACCCCCACGCAAATCGAATCTCAAtt                        >  2:360776/1‑90 (MQ=255)
                                                                 cGGCAATAATGGCGGGGGTCCCGCCCTTGCCTGAAGGGGGGGGGGAAAAAAACCCCCCCCCAAACGAAACTCAATTACCCCCCGGGTACa          >  1:446742/1‑90 (MQ=255)
                                                                         atGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGGtt  <  1:89465/90‑1 (MQ=255)
                                                                                  |                                                                                
AATCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGGTT  >  NZ_CP009273/976607‑976769

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑