Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,771,8720AC54.5% 8.5 / 10.8 11T372P (ACC→CCC) lldPL‑lactate permease
Reads supporting (aligned to +/- strand):  ref base A (4/1);  new base C (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
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.

GCCCGTATGCCGCCAGTGGTCAGCGAGGCTACAGCCTATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCACCGGCACCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCTGGCTGAAGATGAAACCGTCTGACGCTATCAGCAC  >  NZ_CP009273/3771800‑3771948
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ccctgTATGCCGCCAGTGGCCAGGGGGGCTCCAGCCTTGCCCGCCGTTTTTAATTTTGACTGGTTCTCTCCCCCCGGCACCGCCATTCTg                                                             <  1:180087/86‑1 (MQ=255)
      aTGCCGCCAGTGGTCAGCGAGGCTACAGCCTATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCACCGGCACCGCCATTCTGTTtgct                                                       >  1:266846/1‑90 (MQ=255)
          cgcaAGGGGTCAGCGGGGCTACAGCCTATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCCCCGGCACCGCCATTCTGTTTGCTGCAc                                                   <  2:153546/90‑1 (MQ=255)
           gccAGTGGTCAGCGAGGCTACAGCCTATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCACCGGCACCGCCATTCTGTTTGCTGCACt                                                  >  2:53855/1‑90 (MQ=255)
               gTGGTCAGCGAGGCTACAGCCTATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCACCGGCACCGCCATTCTGTTTGCTGCACTGctc                                              >  1:321151/1‑90 (MQ=255)
                         gggCTACCGCTTTTCCCGCGGTTTTTAATTTTGCCTGTTTCTCTCCCCCCGCCCCCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCt                                    <  1:328967/89‑1 (MQ=255)
                              aCAGCCTATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCACCGGCACCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCTGGCTg                               <  2:266846/90‑1 (MQ=255)
                                    tATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCACCGGCACCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCTGGCTGAAGAtc                         >  2:328967/1‑89 (MQ=255)
                                                  tAAGTTTGACTGTTTCTCTCCCCCCGGCACCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCTGGCTGAAGATGAAACCGTCTGACGc           <  1:57598/90‑1 (MQ=255)
                                                        tGACTGTTTCTCGCCCCCGGGCCCCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCTGGCTGAAGATGAAACCGTCTGACGCTATCAg     <  1:277900/90‑1 (MQ=255)
                                                           cTGTTTCTCTGCCCCCGCCACCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCTGGCTGAAGATGAAACCGTCTGACGCTATCAGCAc  <  2:106708/90‑1 (MQ=255)
                                                                        |                                                                            
GCCCGTATGCCGCCAGTGGTCAGCGAGGCTACAGCCTATGCCGCCGTGTTTAAGTTTGACTGGTTCTCTGCCACCGGCACCGCCATTCTGTTTGCTGCACTGCTCTCGATTGTCTGGCTGAAGATGAAACCGTCTGACGCTATCAGCAC  >  NZ_CP009273/3771800‑3771948

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑