Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,292,5120GA44.4% 20.3 / 11.5 27V128V (GTC→GTT) mdtOmultidrug efflux transporter permease subunit MdtO
Reads supporting (aligned to +/- strand):  ref base G (2/13);  new base A (12/0);  total (14/13)
Fisher's exact test for biased strand distribution p-value = 5.98e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CAGCGTTAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGCCCATCAGGATCGGTCCGGCGATGATCAATCGGATCAACGGTTCGC  >  NZ_CP009273/4292425‑4292597
                                                                                       |                                                                                     
caGCGTTAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGGAGGGTTGCCCGTAAAAAACGACAAAGGCGACGGCGGAAAAAAc                                                                                     >  1:221458/1‑90 (MQ=255)
 aGCGTTAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGAcc                                                                                    <  1:340002/90‑1 (MQ=255)
 aGCGTTAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGAcc                                                                                    <  2:82273/90‑1 (MQ=255)
    gTTAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGGAGGGTTGCCCGTAAATAGCGACAAAGGCGGCGGCGGAAAAAAACAGc                                                                                 >  2:395649/1‑90 (MQ=255)
     ttAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGcc                                                                                <  1:156125/90‑1 (MQ=255)
     ttAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGcc                                                                                <  1:32870/90‑1 (MQ=255)
       aggcgcACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGcccc                                                                              <  1:445961/88‑1 (MQ=255)
       aaGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGGAGGTTTGCCCGTAAAAAACGGCAATGGCGGGGGCGAAAAAAACCAAcccc                                                                              >  2:327102/1‑90 (MQ=255)
       aaGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGGAGGGTTTCCCGTAAATAGCGACAAAGGGGACGGCGGAAAAAAACAGcccc                                                                              >  2:340002/1‑90 (MQ=255)
               gACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATg                                                                      <  1:581979/90‑1 (MQ=255)
                   aCTTCCGGATAGTCGAGCATGGCGGGGGAAGGTTGCCCCTAAATAACGACAATGGCGACGGCGAAAAAAACCAACCCCAAGCGATggggt                                                                  >  2:445961/1‑88 (MQ=255)
                      tCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTgcgc                                                               <  2:130634/90‑1 (MQ=255)
                          gATAGTCGAGCATGGCGGGGAAGGGTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCCAGCGATGGGGGCGCATCa                                                           >  2:9583/1‑90 (MQ=255)
                              gTCGAGCATGGCGGGGGAGGTTTGCCCCCCCATAGCGAGAAAGGGGACGGCGGAAAAAACCCGCCCCCAACGGTGGGGGGGGATCaaaaa                                                       >  1:290966/1‑90 (MQ=255)
                              gTCGAGCATGGCGGGGGAGGGTTTGCCGTAAAAAGCGACAATGGGGACGGCGAAAAAAACCAGCCCCCAACGATGGGGGCGCCTCaaaaa                                                       >  2:294815/1‑90 (MQ=255)
                              gTCGAGCATGGCGGGGGAGGGTTTCCCGGAAATAACGGCAAAGGCGGCGGGGAAAAAAAACAACCCCCAACGATGGGGGGGCCTCaaaaa                                                       >  1:47717/1‑90 (MQ=255)
                              gTCGAGCATGGCGGGGGAGGGTTTCCCCTAAAAAACGACAAAGGCGGCGGCGAAAAAAACCAACCCCCAACGATGGGGGGGCCTCaaaaa                                                       >  1:31039/1‑90 (MQ=255)
                              gTCGAGCATGGCGGGGGAGGGTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAAACCAGCCCCCAACGATGGGGGCGCATCaaaaa                                                       >  2:492480/1‑90 (MQ=255)
                              gTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAACGACAATGGCGACGGCGAAAAAAAACAACCCCAAGCGATGGGGGGGCATCaaaaa                                                       >  2:479768/1‑90 (MQ=255)
                              gTCGAGCATGGCGGGGAAGGGTTTCCCGTAAATAACGACAAAGGCGACGGCGAAAAAAAACAGCCCCAAACGATGGGGGGGCATCaaaaa                                                       >  2:402898/1‑90 (MQ=255)
                                      tGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGc                                               <  1:492480/90‑1 (MQ=255)
                                      tGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGc                                               <  1:294815/90‑1 (MQ=255)
                                                 gTTTGCCCGTAAATTGCTACAATGGCGGCGGCGAAAAAGACGCGGCCCAAGCGATGGGTGCGCCGGAAAACCATGCATCCCATCAGGATc                                    <  1:16963/90‑1 (MQ=255)
                                                                gCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGc                                               >  2:331432/1‑64 (MQ=255)
                                                                gCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGc                                               <  1:331432/64‑1 (MQ=255)
                                                                                 gAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGCCCATCAGGATCGGTCCGGCGATGATCAATCGGATCAACGGTTc    <  1:51446/90‑1 (MQ=255)
                                                                                   aaaaGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGCCCATCAGGATCGGTCCGGCGATGATCAATCGGATCAACGGTTCGc  <  1:441316/90‑1 (MQ=255)
                                                                                       |                                                                                     
CAGCGTTAAGCGCACGACCACTTCCGGATAGTCGAGCATGGCGGGGAAGGTTTGCCCGTAAATAGCGACAATGGCGACGGCGAAAAAGACCAGCCCCAAGCGATGGGTGCGCATCAAAAACATGCAGCCCATCAGGATCGGTCCGGCGATGATCAATCGGATCAACGGTTCGC  >  NZ_CP009273/4292425‑4292597

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑