Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0620CA50.0% 26.7 / 22.1 30A37S (GCG→TCG) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base C (12/3);  new base A (0/15);  total (12/18)
Fisher's exact test for biased strand distribution p-value = 1.05e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAA  >  NZ_CP009273/3658978‑3659150
                                                                                    |                                                                                        
tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa                                                                                     >  1:335162/1‑90 (MQ=255)
tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa                                                                                     >  2:428859/1‑90 (MQ=255)
 cGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAc                                                                                    >  1:550605/1‑90 (MQ=255)
  gggAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAAcc                                                                                   <  2:696585/90‑1 (MQ=255)
           aatGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCg                                                                          >  2:569813/1‑90 (MQ=255)
           aatAAAAGCGTGTCCCTTGACACAAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCg                                                                          <  2:156308/90‑1 (MQ=255)
            atGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGCCACCGc                                                                         >  1:826984/1‑90 (MQ=255)
                aaGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt                                                                     >  2:270466/1‑90 (MQ=255)
                          ctggACACAAATAAAAAATTTTCAACCCACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGa                                                           <  2:120180/87‑1 (MQ=255)
                          cTTGACACAAATAAAAAATTTTAAACACACTTATCTACTCGATTTTGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGa                                                           <  2:195304/90‑1 (MQ=255)
                          cTTGACACAAAAAAAAAATTTCCAACCCCTTTATCTACTAAATTTTGGCTTGCACCCAAAAAACCCAGGCCACCGCCATTAAAATAGCGa                                                           <  1:576824/90‑1 (MQ=255)
                               cacGAAAAAAAATTTTACAACCCCCTTACCTCCTCAAATTTGGCTTGCACCCAAAAAACCCAGTCCACCGCCATTAAAATAGCGATATTc                                                      <  1:74801/90‑1 (MQ=255)
                                  gAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCAcc                                                   >  2:74801/1‑90 (MQ=255)
                                     taaaaaaTTTTCAACACACTTATCTACTCGAATTTGGCTTCCACCCGCAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt                                                <  2:393605/87‑1 (MQ=255)
                                             tttCAACACCTTTATCTCCCCAAATTTGGCTTGCACCCGAAAAACCCAGCTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATgg                                        <  2:335162/90‑1 (MQ=255)
                                              ttCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGt                                       >  1:327197/1‑90 (MQ=255)
                                               tCAACACTTTTATCTCCACAATTTTGTTTTCCCCCCGAAAAAACCAGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                      <  1:295057/90‑1 (MQ=255)
                                               caaaCCCATTTATCTACTCGATTTTGGTTTCCACCCCAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg                                      <  2:826984/88‑1 (MQ=255)
                                                cAACACCCTTATCTACTAAATTTTGGTTTCCACCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTga                                     <  1:719960/90‑1 (MQ=255)
                                                   cccacTTATCTCCTCAATTTTGGCTTCCACCCAAAAAAACCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa                                  <  1:359166/88‑1 (MQ=255)
                                                   cacccTTATCTCCTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGaa                                  <  2:895749/90‑1 (MQ=255)
                                                    ccccTTATCTACTCAATTTTGTTTTGCACCCAAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat                                 <  1:857633/87‑1 (MQ=255)
                                                    acacTTATCTACTCAATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat                                 <  2:398874/90‑1 (MQ=255)
                                                      tcTTATCTACTCGAATTTGTCTTCCATCCAAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat                               <  1:875535/89‑1 (MQ=255)
                                                              aCTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGt                       >  1:176051/1‑90 (MQ=255)
                                                                       tGGCTTGCATCCGAAAAAACCAGGTCACCGCCATTGAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc              <  2:720046/90‑1 (MQ=255)
                                                                       tGGCTTGCACCCGAAAAACCCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc              <  2:327197/90‑1 (MQ=255)
                                                                        ggCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACg             >  1:942230/1‑90 (MQ=255)
                                                                             gCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGGGAGAATATATTTATGTCTTGCATACGCAAtt        >  1:593463/1‑90 (MQ=255)
                                                                                   gCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACaa  >  2:963830/1‑90 (MQ=255)
                                                                                    |                                                                                        
TCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAA  >  NZ_CP009273/3658978‑3659150

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑