Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,408,0110AT54.5% 4.2 / 10.6 11N58K (AAT→AAA) ralRtype I toxin‑antitoxin system endodeoxyribonuclease toxin RalR
Reads supporting (aligned to +/- strand):  ref base A (2/3);  new base T (6/0);  total (8/3)
Fisher's exact test for biased strand distribution p-value = 6.06e-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.

GTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACAC  >  NZ_CP009273/1407947‑1408098
                                                                 |                                                                                       
gTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAA‑TTTTTTTAATTAAAACCCCCCCTTTTTTTTTCAGTGGGTTGtttttttt                                                                >  1:85194/1‑88 (MQ=255)
          gTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAAATAAAAACC‑CCCTTTTTTTTTTCAGTGGGTTGTTTTTTTCCTCttttgtg                                                      >  1:134082/1‑86 (MQ=255)
          gTGCCACCTTCCTTTTCAATAGTGGCGGTAA‑TTTTTTTTATGAACACCCCCCTTTTTTTTTTCAGTGGTTTGTTTTTTTCATCtttttgg                                                      >  2:77873/1‑86 (MQ=255)
          gTGCCACCTTCCTTTTCAATAGTGGCGGTAA‑TTTTTTACATGAAAACCTCCCTTATTTTTTTCCGTGGGTCGTTTTTTTCATCtttttag                                                      >  2:315016/1‑86 (MQ=255)
          gTGCCACCTTCCTTTTCAATAGTGGCGGTAA‑TTTTTTAAAATAAAACCCCCCTTTTTTTTTTCCTTGGGTCGTTTTTTTCTTCtttttag                                                      >  1:507428/1‑86 (MQ=255)
          gTGCCACCTTCCTTTTCAATAGTGGCGGGAA‑ATTTTTTTATTAAAACCCCCCTTTTTTTTTTCATTGGGTTGGTTTTTTCATtttttttg                                                      >  1:559043/1‑86 (MQ=255)
            gCCACCTTCCTTTTCAATAGTGGCGGGGA‑ATTTTTAAATATAAACCCCCATTTTTTTTTTTATGGGGTGGTTTTTTTCATTTTTCTAGTg                                                    >  1:801235/1‑90 (MQ=255)
                          cAATAGTGGCGGTAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACtt                                      <  1:343212/90‑1 (MQ=255)
                                     gTAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAAcc                           <  2:466886/90‑1 (MQ=255)
                                                             cATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCa            >  1:486092/1‑82 (MQ=255)
                                                             cATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCa            <  2:486092/82‑1 (MQ=255)
                                                               ttattattTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTacac  <  2:507429/90‑1 (MQ=255)
                                                                 |                                                                                       
GTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAA‑TTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACAC  >  NZ_CP009273/1407947‑1408098

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑