Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,476,7400CA54.5% 10.3 / 17.9 11A27S (GCG→TCG) emrKmultidrug efflux MFS transporter periplasmic adaptor subunit EmrK
Reads supporting (aligned to +/- strand):  ref base C (4/1);  new base A (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: Frequency below/above cutoff threshold.

GATCTGCATTCCCCGTGACATAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCACTATTA  >  NZ_CP009273/2476653‑2476823
                                                                                       |                                                                                   
gATCTGCATTCCCCGTGACATAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCaa                                                                                   <  2:399540/90‑1 (MQ=255)
                                     aaTCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTttct                                              >  2:500320/1‑90 (MQ=255)
                                     aaTCATGTCTTCTAATTCCATTGACAAATAGGCATAGGCACCTAAAAACGAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTttct                                              <  2:168925/90‑1 (MQ=255)
                                          tGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGt                                         >  1:168925/1‑90 (MQ=255)
                                               tctAATTCCATTGACAAAAAGGAATAGGCCCCTAAAAACCAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGaa                                    <  1:172438/90‑1 (MQ=255)
                                                          tGACCAATAGGCATAGGCACCTGAAAACGAAAAAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTAtt                         <  2:156523/90‑1 (MQ=255)
                                                                ataggcataggcACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAAtt                   >  2:204370/1‑90 (MQ=255)
                                                                    gcataggccCCTAAAAACGAAAAAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATc               <  1:286358/90‑1 (MQ=255)
                                                                    gaaaaggcaCCTAAAAACGAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATc               <  1:289575/86‑1 (MQ=255)
                                                                             ccTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCACt      >  1:390770/1‑90 (MQ=255)
                                                                                 aaaaCGAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCACtatta  <  1:100897/90‑1 (MQ=255)
                                                                                       |                                                                                   
GATCTGCATTCCCCGTGACATAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCACTATTA  >  NZ_CP009273/2476653‑2476823

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑