Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,216,1300GT57.1% ‑3.1 / 10.7 14C156F (TGT→TTT) dldD‑lactate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base G (3/3);  new base T (8/0);  total (11/3)
Fisher's exact test for biased strand distribution p-value = 5.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.34e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTCAAACCGCTGGGACGCGAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTGTAACAACTCCGGCGGCTCGCTGGTGCAACGTGGCCCGGCGTATACCGAAATGTCGTTATTCGCGCGTAT  >  NZ_CP009273/2216054‑2216199
                                                                            |                                                                     
cTCAAACCGCTGGGACGCGAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGGATTTTTTAAAAATCcggc                                                          >  2:139633/1‑90 (MQ=255)
       cGCTGGGACGCGAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTGTAACAACTCCGGCGGCTCGc                                                   <  1:390112/90‑1 (MQ=255)
                gcgAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGGATTTTTTACAAATCCGGCGGCTCCCCGGTGCAAc                                          >  2:390112/1‑90 (MQ=255)
                gcgAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGGATTTTTAACAACTCCCGCGGCTCGCTGGGGCAAc                                          >  1:240134/1‑90 (MQ=255)
                 cgAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTGTAACAACTCCGGCGGCTCGCTGGTGCAACg                                         <  2:170963/90‑1 (MQ=255)
                 cgAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTGTAACAACTCCGGCGGCTCGCTGGTGCAACg                                         <  2:182491/90‑1 (MQ=255)
                            cAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTTTAAAAAATCCGGCGGCTCGCTGGGGGAACGGGGCCCGGCgg                              >  1:26999/1‑89 (MQ=255)
                               tGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTGTAAAAACTCCGGCGGCCCGCTGGTGCAACGTGGGCCCGCGgata                           >  1:87532/1‑90 (MQ=255)
                                    ggATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTGTAACAACTCCGGCGGCTCGCTGGTGCAACGTGGCCCGGCGTATACCGaa                      >  1:122799/1‑90 (MQ=255)
                                        catcGTGTATAGGCGCATCGGTCATCGGCGGTATTTTTCACAACCCCTGCGGCTCTCTGGGGCAACGTGGACCGGCGCGTAACGAAATGt                  >  2:164725/1‑90 (MQ=255)
                                                ataGGCGCATCGGTCATCGGCGGTATTTTTAAAAACTCCCGCGGCTCGCCGGGGGAACGGGGCCCCGCGGATAACGAAAAGTCGTTATTc          >  2:391891/1‑90 (MQ=255)
                                                   ggCGCATCGGTCATCGGCGGTATTTTTAAAAACTCCGGCGGCTCGCTGGGGGAACGTGGCCCCGCGGATACCGAAAAGTCGTTATTcgcg       >  2:136978/1‑90 (MQ=255)
                                                      gcATCGGTCATCGGCGGTATTTTTAACAAATCCCGCGGCTCGCTGGGGCAACGGGGCCCGGCGGATACCGAAAAGTCGGTTTTTGCGCGt    >  2:158706/1‑90 (MQ=255)
                                                        aTCGGTCATCGGCGGTATTTGTAACAACTCCGGCGGCTCGCTGGGGCAACGTGGCCCGGCGTATACCGAAATGTCGTTATTCGCGCGtat  >  1:122778/1‑90 (MQ=255)
                                                                            |                                                                     
CTCAAACCGCTGGGACGCGAACCGCACTCAGTGATTGGATCATCGTGTATAGGCGCATCGGTCATCGGCGGTATTTGTAACAACTCCGGCGGCTCGCTGGTGCAACGTGGCCCGGCGTATACCGAAATGTCGTTATTCGCGCGTAT  >  NZ_CP009273/2216054‑2216199

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑