Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273976,6890AG58.3% 1.8 / 11.7 12I63V (ATC→GTC) ldtDL,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base A (0/5);  new base G (7/0);  total (7/5)
Fisher's exact test for biased strand distribution p-value = 1.26e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.93e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AATCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGG  >  NZ_CP009273/976607‑976767
                                                                                  |                                                                              
aaTCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGcc                                                                         >  1:378446/1‑90 (MQ=255)
            cAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCCGCCCCTTCCCGAAgg                                                             >  2:163957/1‑90 (MQ=255)
             aGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGGCCAGCCCCTTCCTGAAggg                                                            >  2:154365/1‑89 (MQ=255)
                        tGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTcc                                                                             >  2:122438/1‑62 (MQ=255)
                        tGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATcc                                                                             <  1:122438/62‑1 (MQ=255)
                                   aGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCATTGCCTGAAGGGGCGGCAGAAAAAACCcccacgc                                      >  1:54068/1‑90 (MQ=255)
                                         aGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGGTCCAGCCATTGCCTGAAGGGGCGGCAGAAAAAACCCGCACGCAAAACg                                >  1:62332/1‑90 (MQ=255)
                                          ggCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGa                               <  2:165167/90‑1 (MQ=255)
                                             aCTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAAtc                            <  2:273377/90‑1 (MQ=255)
                                                         gcAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGc                <  1:154365/90‑1 (MQ=255)
                                                                    cAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGc     <  1:281406/90‑1 (MQ=255)
                                                                       taatGGCGGGGGTCCAGCCATTGCCTGAAGGGGGGGCAGAAAAAACCCGCACGCAAATCGAAACTCAATTACCCCCAGGGTACAAACCgg  >  1:78194/1‑90 (MQ=255)
                                                                                  |                                                                              
AATCCCTGGCGACAGCCCGGTGGCTGTCAGTGAACAGGGCGAGGCACTGCCGCAGGCGCAAGCCACGGCAATAATGGCGGGGATCCAGCCATTGCCTGAAGGTGCGGCAGAAAAAGCCCGCACGCAAATCGAATCTCAATTACCCGCAGGTTACAAGCCGG  >  NZ_CP009273/976607‑976767

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑