Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,476,7430TA55.0% 11.9 / 26.3 20I26F (ATT→TTT) emrKmultidrug efflux MFS transporter periplasmic adaptor subunit EmrK
Reads supporting (aligned to +/- strand):  ref base T (9/0);  new base A (0/11);  total (9/11)
Fisher's exact test for biased strand distribution p-value = 5.95e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.01e-04
Rejected as consensus: Frequency below/above cutoff threshold.

CTGCATTCCCCGTGACATAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCACTATTATCTCTC  >  NZ_CP009273/2476656‑2476829
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cTGCATTCCCCGTGACATAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCaataa                                                                                      >  2:593189/1‑90 (MQ=255)
  gCATTCCCCGTGACATAGGCGTCATCTGTACGAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCaataaat                                                                                    >  1:534864/1‑90 (MQ=255)
            tGACATAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCg                                                                          >  2:181963/1‑90 (MQ=255)
                 tAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAAt                                                                     >  2:72563/1‑90 (MQ=255)
                 tAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAAt                                                                     >  1:503376/1‑90 (MQ=255)
                                  aaTCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGGATTttct                                                    >  1:575151/1‑90 (MQ=255)
                                   aTCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTttctt                                                   >  1:65161/1‑90 (MQ=255)
                                    tCATGTCTTCAAATCCCTTTGACAAAAAGGAAAGGGCCCCTAAAACCGAAAAAAAAAAAACTCCCGCCAATAAAGAAAAGTATTttcttc                                                  <  2:347694/90‑1 (MQ=255)
                                       tGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGt                                               >  1:200478/1‑90 (MQ=255)
                                       tGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGt                                               >  1:688071/1‑90 (MQ=255)
                                        ttcttctAATTCCATTGACAAATAGGCATAGGCCCCTAAAAACGAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGtt                                              <  1:449764/89‑1 (MQ=255)
                                          cttctAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAg                                            >  1:247276/1‑90 (MQ=255)
                                            tcaaaTCCCATTGCCCAAAAGGCATAGGCCCCTAAAAACGCAAAAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGaa                                          <  1:593189/87‑1 (MQ=255)
                                                       tGACCAATAGGCATAGGCCCCTAAAAACGCAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTAtt                               <  1:72563/90‑1 (MQ=255)
                                                       tGACAAAAAGGAAAAGCCACCTAAAAACGAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTAtt                               <  2:221323/90‑1 (MQ=255)
                                                                 gcatagcccCCTAAAAACCCAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATc                     <  1:621832/90‑1 (MQ=255)
                                                                       gcaCTTAAAAACGAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTcc               <  2:509675/90‑1 (MQ=255)
                                                                       gcaCCTAAAACCGAAAAAAAAAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTcc               <  2:270010/90‑1 (MQ=255)
                                                                       gcaCCTAAAAACCAAAAAAATAAACCTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTcc               <  2:125223/90‑1 (MQ=255)
                                                                        ccccTAAAAACGAAAAAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCa              <  1:181963/88‑1 (MQ=255)
                                                                         cccTAAAAACAAAAAAAAAAAAACTCCCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCAc             <  2:503376/89‑1 (MQ=255)
                                                                                    cAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCACTATTAtctctc  >  2:530055/1‑90 (MQ=255)
                                                                                       |                                                                                      
CTGCATTCCCCGTGACATAGGCGTCATCTGTACTAATCATGTCTTCTAATTCCATTGACCAATAGGCATAGGCACCTGAAAACGCAATAAATAAAACTACCGCCAATAAAGAAAAGTATTTTCTTCTGTTAGAATGTTTTTTATTTGAATTAATCTGTTCCACTATTATCTCTC  >  NZ_CP009273/2476656‑2476829

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: ‑