Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,498,4400CT53.8% ‑3.2 / 10.3 13E314K (GAA→AAA) yhfSaminotransferase class I/II‑fold pyridoxal phosphate‑dependent enzyme
Reads supporting (aligned to +/- strand):  ref base C (1/5);  new base T (7/0);  total (8/5)
Fisher's exact test for biased strand distribution p-value = 4.66e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.13e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TCGGGTTAATGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCA‑CCCACCGGGTAAGGCAAGGCACCGC  >  NZ_CP009273/3498353‑3498481
                                                                                       |                                          
tCGGGTTAATGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTCCat                                          <  2:51533/90‑1 (MQ=255)
            gAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTGACTCTg                              >  2:271977/1‑90 (MQ=255)
             aaTCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTGACTCTGc                             >  2:72266/1‑90 (MQ=255)
             aaTCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGGTTTATATTTTGACTCTGc                             >  1:69605/1‑90 (MQ=255)
               tCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGca‑c                          <  1:72266/90‑1 (MQ=255)
                   acaATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGca‑cccac                      <  2:288440/90‑1 (MQ=255)
                         ttCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTCACTCTTCA‑CCCCCCgggga                >  1:45892/1‑88 (MQ=255)
                          tCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCA‑CCCACCGGGTaa               <  1:31828/90‑1 (MQ=255)
                                  tgGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTTATATTTTGACTCTGCACCCCCCCGGGAagggcaagg        >  1:27630/1‑90 (MQ=255)
                                  tgGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGGTTTCATATTTTGACTCTGCC‑CCCCCCCGGGaaaggaaggc       >  1:106514/1‑90 (MQ=255)
                                  tgGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTTATATTTTGACTCTGCA‑CCCCCCCGGGaaagcaaagc       >  2:245938/1‑90 (MQ=255)
                                  tgGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTTATATTTTGACTCTGCA‑CCCACCGGGGaaggcaaagc       >  2:114184/1‑90 (MQ=255)
                                       tCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCA‑CCCACCGGGTAAGGCAAGGCACcgc  <  1:217052/90‑1 (MQ=255)
                                                                                       |                                          
TCGGGTTAATGCGAATCGCACAATGTTCTGATTGTGGATTCGCCTGGCGAAACGTTCCGGAAAGGCGATAAAAGAGCGGCGGGATTTCATATTTCGACTCTGCA‑CCCACCGGGTAAGGCAAGGCACCGC  >  NZ_CP009273/3498353‑3498481

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑