Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273976,6890AG54.5% 7.3 / 11.9 11I63V (ATC→GTC) ldtDL,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (0/5);  new base G (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.

TCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGGTT  >  NZ_CP009273/976609‑976769
                                                                                |                                                                                
tCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCAt                                                                         <  1:210950/90‑1 (MQ=255)
         aCAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCATTGCCTGaaa                                                                >  1:12660/1‑89 (MQ=255)
          cAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGGCCAGCCACTTCCTGaaag                                                               >  1:396218/1‑88 (MQ=255)
                       gTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCATTGCCTGAAGGGGGGGGAGaaaaa                                                  >  1:429425/1‑90 (MQ=255)
                                 aGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCcgcacgc                                        <  1:610570/90‑1 (MQ=255)
                                       aGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCCTTGCCTGAAAGGGGGGGAGAAAAAACCCCCCCGCCAAACg                                  >  1:559122/1‑90 (MQ=255)
                                            cTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCATTTCCTGAAGGGGGGGCGGAAAAAACCCGCACGCAAATCGAAtct                             >  1:218921/1‑90 (MQ=255)
                                                 gCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCATTTCCCGAAAGGGCGGCAGAAAAAACCCCCCCGCCAAACGAAACTCaaat                        >  1:584239/1‑88 (MQ=255)
                                                         aaGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAg                <  1:274113/90‑1 (MQ=255)
                                                         aaGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAg                <  2:384405/90‑1 (MQ=255)
                                                                       atGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGGtt  <  2:340877/90‑1 (MQ=255)
                                                                                |                                                                                
TCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGGTT  >  NZ_CP009273/976609‑976769

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑