Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273431,9530AC54.5% 8.1 / 11.9 11V288V (GTA→GTC) thiLthiamine‑phosphate kinase
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.

CTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCG  >  NZ_CP009273/431868‑432017
                                                                                     |                                                                
ctGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGt                                                              <  1:241073/90‑1 (MQ=255)
        gAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGt                                                      >  2:207694/1‑90 (MQ=255)
                     tgtgTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTCCCGTTTACCTGTATCGGGCAAATGa                                         <  1:117388/90‑1 (MQ=255)
                                gtgCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATc                              >  1:449729/1‑90 (MQ=255)
                                    cGGAACTGACCGGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTCCCTTTTCCCTGTATGGGGAAAATGACCGCCGATATCGAAg                          <  1:212760/90‑1 (MQ=255)
                                    cGGAACTGACCCGTGGCGCGCGGGTTGTGGCCCGCGACCACCTGGGCGTCCCGTTTCCCTGTATGGGGCAAATGCCCGCCGATATCGAAg                          <  1:491223/90‑1 (MQ=255)
                                         cTGAACCGTGGCCGGCGGGTTGTGGCTCTCGGACACCTGGGCGTCCCGTTTACCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCtt                     <  1:318405/90‑1 (MQ=255)
                                          tGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCttt                    >  1:495908/1‑90 (MQ=255)
                                          tGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCttt                    >  1:71103/1‑90 (MQ=255)
                                                      cgggggATGTGGCTCTCGGCCCCGGGGGCGTCCTTTTTCCCTGTACGGGGCAAATGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTg        <  2:495908/86‑1 (MQ=255)
                                                            aTGGGGCTCTCGGACACCGGGGCGTCCCTTTTCCCTGTATCGGGAAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCg  <  1:207694/90‑1 (MQ=255)
                                                                                     |                                                                
CTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGCAAATGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCG  >  NZ_CP009273/431868‑432017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑