Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273542,2450TG54.5% 3.9 / 12.5 11M37R (ATG→AGG) fdrAacyl‑CoA synthetase FdrA
Reads supporting (aligned to +/- strand):  ref base T (5/0);  new base G (0/6);  total (5/6)
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.

GGTGTTTTCAGGATTCGGTCAGTTTAATGATTATTTCACGAAAACTCAGCGAATCAGAAAATGTTGATGATGTTTCCGTAATGATGGGTACGCCCGCCAATAAAGCGTTATTAGATACCACAGGTTTCTGGCATGACGATTTTAATAACGCCACGCCGA  >  NZ_CP009273/542161‑542319
                                                                                    |                                                                          
ggTGTTTTCAGGATTCGGTCAGTTTAATGATTATTTCACGAAAACTCAGCGAATCAGAAAATGTTGATGATGTTTCCGTAATGATGGGTa                                                                       >  1:136909/1‑90 (MQ=255)
 gtgtTTTCAGGATTCGGTCAGTTTAATGATTATTTCACGAAAACTCAGCGAATCAGAAAATGTTGATGATGTTTCCGTAATGATGGGTAc                                                                      >  1:170258/1‑90 (MQ=255)
             ttCGGTTATTTTAATTTTTTTTCCAAAAAAACCCAGCAAAAAAAAAAATGTTGATGTTTTTTCCGTAATGAGGGGTCCGCCCGCCAATaa                                                          <  2:170258/90‑1 (MQ=255)
               cGGTCAGTTTAATGATTATTTCACGAAAACTCAGCGAATCAGAAAATGTTGATGATGTTTCCGTAATGATGGGTACGCCCGCCAATAAAg                                                        >  2:486324/1‑90 (MQ=255)
                        tAATGATTTTTTCACAAAAACTCAGCAAATAAAAAAATGTTGATGATTTTTCCGTAATGAGGGGTACGCCCGCCAATAAAGCGTTATTAg                                               <  1:205898/90‑1 (MQ=255)
                               tattTCACGAAAACTCAGCGAATCAGAAAATGTTGATGATGTTTCCGTAATGATGGGTACGCCCGCCAATAAAGCGTTATTAGATACcac                                        >  1:415797/1‑90 (MQ=255)
                               tattTCACGAAAACTCAGCGAATCAGAAAATGTTGATGATGTTTCCGTAATGATGGGTACGCCCGCCAATAAAGCGTTATTAGATACcac                                        >  2:273755/1‑90 (MQ=255)
                                          aaCTCAGCAAAAAAAAAAATGTTGATGTTTTTTCCGAAATGAGGGGTCCCCCCGCCAATAAAGCGTTATTAGATACCACAGGTTTCTGGc                             <  1:486324/90‑1 (MQ=255)
                                              cAGCAAATAAAAAATTTTTGATGTTGTTTCCGAAATGGGGGGTCCCCCCGCCAATAAAGCGTTATTAGATACCACAGGTTTCTGGCATGa                         <  1:273755/90‑1 (MQ=255)
                                                             ttttGATGTTTTTCCCGAAATGGGGGGCCCCCCCGCCAATAAAGCGTTATTAGATACCACAGGTTTCTGGCATGACGATTTTAATAacgc          <  2:22108/88‑1 (MQ=255)
                                                                     ttgTTTCCGTAAGGAGGGGTCCCCCCGCCAATAAAGCGTTATTAGATACCACAGGTTTCTGGCATGACGATTTTAATAACGCCACGCCGa  <  2:58461/89‑1 (MQ=255)
                                                                                    |                                                                          
GGTGTTTTCAGGATTCGGTCAGTTTAATGATTATTTCACGAAAACTCAGCGAATCAGAAAATGTTGATGATGTTTCCGTAATGATGGGTACGCCCGCCAATAAAGCGTTATTAGATACCACAGGTTTCTGGCATGACGATTTTAATAACGCCACGCCGA  >  NZ_CP009273/542161‑542319

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑