Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,440,6070TC54.5% 4.5 / 10.3 11F277L (TTC→CTC) ytfQgalactofuranose ABC transporter substrate‑binding protein YtfQ
Reads supporting (aligned to +/- strand):  ref base T (1/4);  new base C (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.26e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTACCGGACATCTACAAAGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGTCCCGCCTTCGACGCGCTGGAGAAATACAAAAAAGACGGCACCATGCCTGAAAAGCTGACGTTAACCAAATCCACCCTTTACC  >  NZ_CP009273/4440526‑4440682
                                                                                 |                                                                           
gtACCGGACATCTACAAAGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGGGCCGCCCTCGAcgcg                                                                     >  2:237155/1‑90 (MQ=255)
  aCCGGACATCTACAAAGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGTCCCGCCTTCGACGCGCt                                                                   <  1:161895/90‑1 (MQ=255)
        cATCTACAAAGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGGCCCGCCCTCGACGCGCTGGGGaa                                                             >  2:141993/1‑90 (MQ=255)
          tCTACAAAGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGGCCCGCCCTCGCCGCGCTGGGGaaaa                                                           >  2:209213/1‑89 (MQ=255)
          tCTACAAAGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGGCCCCCCCTCGACGCGGCGGAGaaaa                                                           >  2:11777/1‑89 (MQ=255)
                aaGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGTCCCGCCTTCGACGCGCTGGAGAAATACaaaa                                                     <  2:51052/90‑1 (MQ=255)
                                    gcgaaCGCCAGTGTTGAACTGACGCCGAATATGGCAGGGCCCCCCCTCGACGCGCCGGGGAAAAAAAAAAAAAACGGCACCATGCCCGaa                                 >  2:278276/1‑90 (MQ=255)
                                                   gAACTGACGCCGAATATGGCAGGGCCCGCCCTCGGCGCGCTGGGGGAAAACAAAAAAAACGGCCCCATGCCCGAAAAACTGGCGGTAAcc                  >  2:59222/1‑90 (MQ=255)
                                                        gACGCCGAATATGGCAGGTCCCGCCTTCGACGCGCTGGGGGAATAAAAAAAAGACGGCACCATGCCTGAAAAGCTGACGTTAACCAAAtt             >  1:281237/1‑89 (MQ=255)
                                                         aCGCCGAATATGGCAGGTCCCGCCTTCGACGCGCTGGAGAAATACAAAAAAGACGGCACCATGCCTGAAAAGCTGACGTTAACCAAATcc            <  2:59952/90‑1 (MQ=255)
                                                                   tGGCAGGTCCCGCCTTCGACGCGCTGGAGAAATACAAAAAAGACGGCACCATGCCTGAAAAGCTGACGTTAACCAAATCCACCCTTTAcc  <  1:16580/90‑1 (MQ=255)
                                                                                 |                                                                           
GTACCGGACATCTACAAAGCGATGATGGATGGCGAAGCGAACGCCAGTGTTGAACTGACGCCGAATATGGCAGGTCCCGCCTTCGACGCGCTGGAGAAATACAAAAAAGACGGCACCATGCCTGAAAAGCTGACGTTAACCAAATCCACCCTTTACC  >  NZ_CP009273/4440526‑4440682

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑