Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,291,0170CG54.5% 7.5 / 12.6 11A627P (GCA→CCA) mdtOmultidrug efflux transporter permease subunit MdtO
Reads supporting (aligned to +/- strand):  ref base C (1/4);  new base G (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 = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGTTTTAATAAGGTGGGCAGGATGGCCTGAGAGGCGGGTGTCTCTTCAAGCGTTATTTGAGGAGAACGGCTGAGTGCGGTTGCCAGACCGGCAGCGTATTTCTCCAGGGCGTCGGCAAACTGACCTGCTCTGTCCGGCTGTAGTGCGTTATCCAGCGCCTGCGCCG  >  NZ_CP009273/4290941‑4291106
                                                                            |                                                                                         
tGTTTTAATAAGGTGGGCAGGATGGCCTGAGAGGCGGGGGTCTCTTTAAACGTTTTTTTAGGGGAAAGGCTGGGGGGGGGTGGCAGACCg                                                                              >  1:84633/1‑90 (MQ=255)
     taataaGGTGGGCAGGATGGCCTGAGAGGCGGGTGTCTCTTCAAGCGTTATTTGAGGAGAACGGCTGAGTGCGGTTGCCAGACCGGCAGc                                                                         <  1:43086/90‑1 (MQ=255)
         aaGGTGGGCAGGATGGCCTGAGAGGCGGGTGTCTCTTCAAGCGTTATTTGAGGAGAACGGCTGAGTGCGGTTGCCAGACCGGCAGCGTAt                                                                     <  2:84633/90‑1 (MQ=255)
           ggTGGGCAGGATGGCCTGAGAGGCGGGGGGCTCTTCAAGCGTTATTTGAGGAGAACGGCGGAGGGGGGGTGGCAGACCGGCAGCGGAttt                                                                   >  1:146538/1‑90 (MQ=255)
           ggTGGGCAGGATGGCCTGAGAGGCGGGGGGCTCTTCAAACGTTATTTTAGGGGAAAGGCTGAGGGGGGGTGCCAGACCGGCAGCGGAttt                                                                   >  2:262504/1‑90 (MQ=255)
              gggCAGGATGGCCTGAGAGGCGGGTGTCTCTTCAAGCGTTATTTTAGGAGAAAGGCTGGGGGGGGGTGCCAGACCGGCAGCGGATTtttc                                                                >  1:120392/1‑90 (MQ=255)
               ggCAGGATGGCCTGAGAGGCGGGGGTCTCTTCAAGCGTTATTTTAGGAGAAAGGGTGAGTGGGGGTGCCAGACCGGCAGCGGATTTTTcc                                                               >  2:268097/1‑90 (MQ=255)
                             agagGCGGGGGTCTCTTCAAGCGGTATTTTAGGAGAACGGCCGAGGGGGGGTGCCAGACCGGCAGCGGATTTTTCCAGGGGGGCGGCaaa                                                 >  2:220398/1‑90 (MQ=255)
                                                           aggagAACGGCTGAGTGCGGTTGCCAGACCGGCAGCGTATTTCTCCAGGGCGTCGGCAAACTGACCTGCTCTGTCCGGCTGTAGTGCGtt                   <  1:315623/90‑1 (MQ=255)
                                                             gagaACGGCTGAGTGCGGTTGCCAGACCGGCAGCGTATTTCTCCAGGGCGTCGGCAAACTGACCTGCTCTGTCCGGCTGTAGTGCGTTac                 <  1:288208/90‑2 (MQ=255)
                                                                         gTGCGGTTGCCAGACCGGCAGCGGATTTCTCCAGGGCGTCGGCAAACTGACCTGCTCTGTCCGGCTGTAGTGCGTTATCCAGCGCCTgcg     >  1:206183/1‑90 (MQ=255)
                                                                            cGGTTGCCAGACCGGCAGCGTATTTCTCCAGGGCGTCGGCAAACTGACCTGCTCTGTCCGGCTGTAGTGCGTTATCCAGCGCCTGCGCCg  <  1:268097/90‑1 (MQ=255)
                                                                            |                                                                                         
TGTTTTAATAAGGTGGGCAGGATGGCCTGAGAGGCGGGTGTCTCTTCAAGCGTTATTTGAGGAGAACGGCTGAGTGCGGTTGCCAGACCGGCAGCGTATTTCTCCAGGGCGTCGGCAAACTGACCTGCTCTGTCCGGCTGTAGTGCGTTATCCAGCGCCTGCGCCG  >  NZ_CP009273/4290941‑4291106

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑