Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273595,0320TG51.7% 19.7 / 43.7 29V288G (GTG→GGG) cusACu(+)/Ag(+) efflux RND transporter permease subunit CusA
Reads supporting (aligned to +/- strand):  ref base T (0/14);  new base G (15/0);  total (15/14)
Fisher's exact test for biased strand distribution p-value = 1.29e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.05e-04
Rejected as consensus: Frequency below/above cutoff threshold.

CGCGCTGGATGCTTCAAACCAGGAAGCGGGCGGTTCGTCGATCGAACTGGCGGAAGCGGAATATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTT  >  NZ_CP009273/594793‑595278
                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                        
cgcgcTGGATGCTTCAAACCAGGAAGCGGGCGGTTCGTCGATCGAACTGGCGGAAGCGGAATATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTg                                                                                                                                                                                                                                                >  1:132363/1‑250 (MQ=255)
               aaaCCAGGAAGCGGGCGGTTCGTCGATCGAACTGGCGGAAGCGGAATATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAAc                                                                                                                                                                                                                                <  1:181652/250‑1 (MQ=255)
                              cggTTCGTCGATCGAACTGGCGGAAGCGGAATATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATc                                                                                                                                                                                                                 <  2:170288/250‑1 (MQ=255)
                                                  cggaagcggaaTATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGG‑TCGGCAAAAACGCCCCAGAGGGGAGCGCCCCC‑CTggggagcaaacc                                                                                                                                                                                            >  2:159035/1‑239 (MQ=255)
                                                      agcggaaTATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGGCCTGCGGTGCGGGGAAAAACACCCG‑GGAGGGAGTGCCGCC‑GGGGAGGGCAAACTggg                                                                                                                                                                                         >  2:337883/1‑248 (MQ=255)
                                                         ggaaTATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACg                                                                                                                                                                                     <  1:381855/250‑1 (MQ=255)
                                                                      cgcgcCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGTGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAagtagt                                                                                                                                                                         <  1:312767/249‑1 (MQ=255)
                                                                                  tATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGAT‑CCGGCGAAAAAGCCCGAGAAGGGATCGCCGCC‑GTGAAGGACACAATGGAAACGCTGAAAAGAAGGCTGCCGGGAGGCg                                                                                                                                                            >  1:378878/1‑250 (MQ=255)
                                                                                       gCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGGTCTGCGGT‑CCGGCCGAAACGCCCGGGGAGAGATCGCCGCC‑CGGGAGGGAGAACCGGAAAAGGCGGAAAGGAGTCTGCCGGGAggggggggg                                                                                                                                                       >  2:176552/1‑243 (MQ=255)
                                                                                                                  cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGGCCCGCGGA‑CCCGCCAAAAAGCCCCCGGAGGGGTTGCCGCCGGTGAGGGGCAAAC‑GGGAACGCCGAAAAGAAGGCTGGCGGGAGGCGGGGGGGTAGTTTAAAAATAAGAttcgagcccg                                                                                                                            >  2:183521/1‑241 (MQ=255)
                                                                                                                        aaaaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGAT‑CCGGCAAAAAAGCCCGAGAAGGGATCGCCGCC‑GTGAAGGACAAACTGGGAACGCTGAAAAGGAGTCTGCCGGCAGGCGGGGGGATAGTTACAACATAAGATCGCAGCCAGCTCAtt                                                                                                                      >  1:387118/1‑250 (MQ=255)
                                                                                                                                  gAAAAGGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCa                                                                                                            <  2:91833/250‑1 (MQ=255)
                                                                                                                                   aaaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCAt                                                                                                           <  2:305192/250‑1 (MQ=255)
                                                                                                                                   aaaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCAt                                                                                                           <  2:215582/250‑1 (MQ=255)
                                                                                                                                    aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGAT‑CCGGCAAAAAAGCCCCGGAAGTGATCGCCGCC‑GTGGAGGACAAAATGGGAAAGCTGAAAAGGAGTCTGCCCGGAGGGGGGGAGAGAGGTACAAAATACGAGCCCAGCCAGCCCATTGACCCCGccccc                                                                                                          >  2:123268/1‑247 (MQ=255)
                                                                                                                                           gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGCT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACCAACTGGAAACGCTGAAAAGGTGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTTACCGCGCCATCGACAAcc                                                                                                   >  1:215286/1‑250 (MQ=255)
                                                                                                                                           gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAcc                                                                                                   <  2:196228/250‑1 (MQ=255)
                                                                                                                                               ccGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGGGCTGCGAT‑CCCGCAAAAACGCCCGAGGAGGGGTCGCCGCC‑GGGGAGGGCAAACTGGAAAAGCTGCAAAGAAGGCTGCCGGGAGGCGGGGAGAAAGGTACAACAAACGATAGCAGCCAGCTCATTGACCGCGCCACCGCCAAACCCAg                                                                                               >  2:212391/1‑250 (MQ=255)
                                                                                                                                                 gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGT‑CCGGCAAAAACGCCCGAGAAGGGATCGCCGCC‑GTGAAGGGCAAACTGGAAACGCTGAAAAGAAGTCTGCCGGGAGGCGGGGGGGTAGTTACAACATACGAACGCAGCCAGCACATTGGCCGCGCCCTCGACAACCTCACCg                                                                                             >  2:124622/1‑250 (MQ=255)
                                                                                                                                                     aTCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGAT‑CCGGGAAAAAAGCCCGCGAAGTGATCGCCGCC‑GGGAAGGGCAAACTGGAAACGCCGAAAAGAAGTGTGCCGGGAGGGGGGGGGAGAGGTGCAACATACGAACGCAGGCAGCCCATTGACCCCGCCATCGACAACCCCCGCggg                                                                                           >  2:374623/1‑247 (MQ=255)
                                                                                                                                                        tGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCTTGCGGA‑CCCGCAAAAAAGGCCCAGAAGTGTTCGCCGCC‑GTGACGGGCCAACTGGAAAAGCTGGAAAGCAGTCTGCCGGCAGGGGGGGAGAAAGTTTCAACATACGAACGAGGCCAGGTCATTGTCCGCCCCCTCCGAAACCTCAGCGGCCAGtt                                                                                      >  2:271966/1‑250 (MQ=255)
                                                                                                                                                            cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGT‑CCGGCCAAAAAGCCCGAGAAGAGATCGCCGCC‑GGGGAGGGCAAACTGGGAAAGCTGAAAAGTAGTCTGCCGGGAGGCGGGGGGATAGTTTAAAAATACGAACGCAGCCCGCCCCTTGACCGCGCCATCGACCACCTCCGAGGGGCGTTGCTg                                                                                  >  2:434518/1‑250 (MQ=255)
                                                                                                                                                                                         agaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCtg                                                     <  2:212764/250‑1 (MQ=255)
                                                                                                                                                                                          gaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAAAGCTGAAAAGGAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCCTCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTTTTGTGGGGGCGGTAGTCtgt                                                    >  1:223664/1‑250 (MQ=255)
                                                                                                                                                                                                          gCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTgg                                     <  2:442602/249‑1 (MQ=255)
                                                                                                                                                                                                                          aaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCt                    <  1:77063/250‑1 (MQ=255)
                                                                                                                                                                                                                                 aggggcgggcgGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCg             <  2:387118/247‑1 (MQ=255)
                                                                                                                                                                                                                                         gcgggGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTc     <  1:311809/250‑1 (MQ=255)
                                                                                                                                                                                                                                            gggTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGtt  <  1:117408/250‑1 (MQ=255)
                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                        
CGCGCTGGATGCTTCAAACCAGGAAGCGGGCGGTTCGTCGATCGAACTGGCGGAAGCGGAATATATGGTGCGCGCCAGCGGCTATCTGCAAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAT‑CCGGCAAAAACGCCCGAGAAGTGATCGCCGCC‑GTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCAGCGGCAAGTTGCTGGAAGAGTTTATTGTGGTGGCGGTAGTCTGTGCGCTGTTTCTCTGGCATGTGCGCTCGGCGCTGGTGGCGATTATTTCGTT  >  NZ_CP009273/594793‑595278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑