Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,141,2140TG53.8% 19.7 / 32.9 39G20G (GGT→GGGyegDmolecular chaperone
Reads supporting (aligned to +/- strand):  ref base T (4/14);  new base G (21/0);  total (25/14)
Fisher's exact test for biased strand distribution p-value = 2.03e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.23e-07
Rejected as consensus: Frequency below/above cutoff threshold.

TCTTCACCGGCATGGGGATTATTTCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGAATG  >  NZ_CP009273/2141130‑2141300
                                                                                    |                                                                                       
tcttcACCGGCATGGGGATTATTTCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAAcc                                                                                    <  1:1504469/90‑1 (MQ=255)
  ttcACCGGCATGGGGATTATTTCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCCTGCGGGACGGGaaaaccc                                                                                  >  2:1895421/1‑86 (MQ=255)
       cGGCATGGGGATTATTTCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCTTTCGTGTCGGGAAAACGCCtttt                                                                             >  1:81273/1‑89 (MQ=255)
       cGGCATGGGGATTATTTCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGGTTTTCGTGACCGGAAAACTCAtttt                                                                             >  1:145100/1‑89 (MQ=255)
         gCATGGGGATTATTTCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGGCCTGCGGGGCGGGGAAACGCCttttgt                                                                           >  2:1003565/1‑87 (MQ=255)
                       tCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGGGACGGGAAAACGCCTTTTTTTAAAATGGaaaaaa                                                             >  2:71133/1‑88 (MQ=255)
                        cGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATTCGGGGCGGGAAACCCCATTTTCTAAAAATGGAAAAAGa                                                            >  2:1318680/1‑90 (MQ=255)
                        cGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGGAAAACGCATTTTCTTAAAAAGGAAAAAGa                                                            >  2:1425983/1‑90 (MQ=255)
                         gtgtTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGGAAACCGCATTTGCTAAAAAAGGAAAAAGAc                                                           >  2:307681/1‑90 (MQ=255)
                              tATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATTCGTGGCGGGAAAACCCCTTTTTTTAAAAAGGAAAAAGACAGCAc                                                      >  1:1105499/1‑90 (MQ=255)
                              tATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGGCGGTAAAACGCAATTGTTAAAAATAGAAAAAGACAGCAc                                                      >  1:1454125/1‑90 (MQ=255)
                              tATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGGCGGGGAAACGCATTTTCTTAAAAAGGAAAAAGACAGCAc                                                      >  1:284406/1‑90 (MQ=255)
                                     tttGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGctgctg                                               <  1:1393154/90‑1 (MQ=255)
                                               gTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGc                                    <  2:1839830/90‑1 (MQ=255)
                                               gTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGc                                    <  1:381163/90‑1 (MQ=255)
                                                  cAGCAAACTGTTCAGTGGCGGTCATGCGTGGCGGGAAAACGCCTTTTCTAAAAAAAGAAAAAGACAACACCCTGCTGCCCTCAATGCttt                                 >  1:1319009/1‑90 (MQ=255)
                                                  cAGCAAACTGTTCAGTGGCGGTCATGCGGGGCGGGAAAACGCATTTTCTAAAAAAGGAAAAAGACAGCACGCCGCTGCCTTCCATTCttt                                 >  1:1619036/1‑90 (MQ=255)
                                                  cAGCAAACTGTTCAGTGGCGGGCATGGGGGGGGGGGAACCGCAATTGGTAAAAAAAGGAAAAAAAAGCACGCTGCTGGCTTCAATGCttt                                 >  1:172905/1‑90 (MQ=255)
                                                    gCAAACTGTTCAGTGGCGGTCATTCGTGACGGGAAACCGCATTTGCTAAAAATGGAAAAAGACAGCACGCTGCTGCCTTCAATGCTTTgc                               >  2:899915/1‑90 (MQ=255)
                                                         cTGTTCAGTGGCGGTCATTCGGGACGGGAAAACTCCTTTTCTAAAAAAGGAAAAAAACAACACGCCGCCGCCTTCAATGCTTTTCGCGcc                          >  1:1172726/1‑90 (MQ=255)
                                                           gTTCAGTGGCGGTCATGCGTGGCGGGAAACCGCATTTTCTAAAAAAGGAAAAAAAAAACACGCCGCTGCCTTCAATGCTTTTTGCGccca                        >  1:2133075/1‑88 (MQ=255)
                                                           gTTCAGTGGCGGGCATGCGGGACGGGAAACCGCATTTTCTAAAAAAGGAAAAAGACAGCACGCTGCTGCCTTCAATTCTTTTCGCGCCaa                        >  1:1399520/1‑90 (MQ=255)
                                                           gTTCAGTGGCGGCCATGCGTGTCGGTAAACCGCATTTTCTAAAAATGGAAAACGACAGCACGCCGCTGCCTTCAATTCTTTTGGCGCCaa                        >  2:21638/1‑90 (MQ=255)
                                                             tCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAAcg                      <  2:1521725/90‑1 (MQ=255)
                                                                gTGGCGGTCATGCGTGGCGGGAAACCCCCTTTTCTAAAAAAGGAAAAAAACAACACGCTGCTGCCCTCAATGCTTTTCGCGCCCAcgcgg                   >  1:1470829/1‑89 (MQ=255)
                                                                  ggCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGa                 <  2:284406/90‑1 (MQ=255)
                                                                  ggCGGTCATGCGGGACGGGAAAACCCATTTGCTAAAAATGGAAAAAGACAGCACGCTGCTGCCTTCCATGCTTTTCGCGCCAACGCGTGa                 >  1:866202/1‑90 (MQ=255)
                                                                   gCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGaa                <  2:2011032/90‑1 (MQ=255)
                                                                     gggcATGCGTGGCGGGAAAACGCATTTGCTAAAAAATGAAAAAGACAACACGCTGCTGCCCTCCAATGTTTTGGCGCCCACGCGGGAAga              >  1:1129160/4‑89 (MQ=255)
                                                                     ggTCATGCGTGGCGGGAAACCCCATTTTGTTAAAAAAGAAAAAGACAGCACCCCCCCGCCTTCAATGCTTTTTGCGCCCACCCCCGAAGc              >  1:2121832/1‑90 (MQ=255)
                                                                         aTGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTa          <  1:414934/90‑1 (MQ=255)
                                                                         aTGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGATGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCAGTa          <  2:1396226/90‑1 (MQ=255)
                                                                             gTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGctgctg                                               <  1:36358/50‑1 (MQ=255)
                                                                             gTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGctgctg                                               >  2:36358/1‑50 (MQ=255)
                                                                              tGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGa     <  1:1064299/90‑1 (MQ=255)
                                                                              tGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGa     <  2:1544939/90‑1 (MQ=255)
                                                                                aCGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGc              >  2:697845/1‑79 (MQ=255)
                                                                                aCGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGc              <  1:697845/79‑1 (MQ=255)
                                                                                 cGGTAAACCGCATTTTCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGAATg  <  1:71133/90‑1 (MQ=255)
                                                                                    |                                                                                       
TCTTCACCGGCATGGGGATTATTTCGTGTTTATTGGTTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGAATG  >  NZ_CP009273/2141130‑2141300

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: