Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273642,2210GT58.3% 3.9 / 17.3 12Q249K (CAA→AAA) citGtriphosphoribosyl‑dephospho‑CoA synthase CitG
Reads supporting (aligned to +/- strand):  ref base G (0/5);  new base T (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.

GAGATTTCGTTCGATACACTCCCTGTCGAACTGCCGGAGATAATCGAGATCGGCGGGGGTTCGAATGCCCCCTTTTTGCAATAATGTTTGCGCCTCGCGCTGTAGCCAGCGCAGGCCCCCCTCGCCACCGCGCGATGCAACGTTGGTATCGCCGTTGATCGC  >  NZ_CP009273/642144‑642305
                                                                             |                                                                                    
gagaTTTCGTTCGATACACTCCCTGTCGAACTGCCGGAGATAATCGAGATCGGCGGGGGGTTGGGTGCCCCCCTTTTTTAATAATttttt                                                                          >  2:692336/1‑89 (MQ=255)
                 acTCCCTGTCGAACTGCCGGAGATAATCGAGATCGGCGGGGGTTCGAATGCCCCCTTTTTGCAATAATGTTTGCGCCTCGCGCTGTAGcc                                                         <  1:502358/90‑1 (MQ=255)
                  cTCCCTGTCGAACTGCCGGAGATAATCGAGATCGGCGGGGGGTTGGATGCCCCCCTTTTTTAATAAATTTTTCGCCCCCCGCCGTAGCCa                                                        >  2:195127/1‑90 (MQ=255)
                       tGTCGAACTGCCGGAGATAATCGAGATCGGCGGGGGGTCGAATTCCCCCCTTTTTCAAAAAAGTTTTCGCCCCCCGCCGTAGCCAgcgcc                                                   >  1:101299/1‑89 (MQ=255)
                       tGTCGAACTGCCGGAGATAATCGAGATCGGCGGGGGGGTGGATACCCCCCTTTTTTTATAATTTTTTTGGCCCGCGCTGTAGGCCgcgcc                                                   >  2:795010/1‑89 (MQ=255)
                            aaCTGCCGGAGATAATCGAGATCGGCGGGGGTTCGAATGCCCCCTTTTTGCAATAATGTTTGCGCCTCGCGCTGTAGCCAGCGCAGGccc                                              <  1:646638/90‑1 (MQ=255)
                            aaCTGCCGGAGATAATCGAGATCGGCGGGGGTTCGAATGCCCCCTTTTTGCAATAATGTTTGCGCCTCGCGCTGTAGCCAGCGCAGGccc                                              <  2:489802/90‑1 (MQ=255)
                            aaCTGCCGGAGATAATCGAGATCGGCGGGGGGTCGAATGCCCCCCTTTTTCAATAATGTTTTCGCCCCCCGCCGTAGCCAGCGCAGGccc                                              >  1:158439/1‑90 (MQ=255)
                                  cGGAGATAATCGAGATCGGCGGGGGGTCGCAGGCCCCCCTTTTTCAATAATTTTTTCGCCCCCCGCCGTTGCCAGCGCCGGccccccccc                                        >  2:392071/1‑87 (MQ=255)
                                              agaTCGGCGGGGGGTCGGATGCCCCCTTTTTTCAAAAATTTTTTTGCCCCGCGCTGTAGCCAGCGCAGGCCCCCCCCCCCCCCCCCCGAt                            >  1:709334/1‑90 (MQ=255)
                                                      gggggTTCGAATGCCCCCTTTTTGCAATAATGTTTGCGCCTCGCGCTGTAGCCAGCGCAGGCCCCCCTCGCCACCGCGCGATGCAACGtt                    <  2:325065/90‑1 (MQ=255)
                                                                        tttttGCAATAATGTTTGCGCCTCGCGCTGTAGCCAGCGCAGGCCCCCCTCGCCACCGCGCGATGCAACGTTGGTATCGCCGTTGATCGc  <  1:795010/90‑1 (MQ=255)
                                                                             |                                                                                    
GAGATTTCGTTCGATACACTCCCTGTCGAACTGCCGGAGATAATCGAGATCGGCGGGGGTTCGAATGCCCCCTTTTTGCAATAATGTTTGCGCCTCGCGCTGTAGCCAGCGCAGGCCCCCCTCGCCACCGCGCGATGCAACGTTGGTATCGCCGTTGATCGC  >  NZ_CP009273/642144‑642305

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑