Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,285,8530GT51.7% 25.5 / 44.3 29A126S (GCC→TCC) agaDN‑acetylgalactosamine‑specific enzyme IID component of PTS
Reads supporting (aligned to +/- strand):  ref base G (4/10);  new base T (15/0);  total (19/10)
Fisher's exact test for biased strand distribution p-value = 5.00e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.77e-06

ATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGAT  >  NC_000913/3285718‑3285992
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aTGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAAcc                                                                                                                               <  1:526108/151‑1 (MQ=255)
          aaGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGcc                                                                                                                     <  2:697086/151‑1 (MQ=255)
                    ccGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAGCCTGCTGGGGCCGATTCTAttt                                                                                                           <  1:694788/151‑1 (MQ=255)
                            ccATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGTTCATCCTTTTTCAGCCAGGGGAAACTGCTGGGGGCGGTTCTTTTTTTTG‑ccc                                                                                                   >  2:61443/1‑149 (MQ=255)
                            ccATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTTCTCATCATTTTCCAGCCAGGGGAACCTGCTGGGGGCGCTTCTATTTTTTG‑CCGt                                                                                                  >  2:118963/1‑151 (MQ=255)
                              aTTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGTTTTTTCTTTTCCAGCCCGGGGAACCTTCCTGGGGCGGTTCTttttttttccggtt                                                                                                 >  1:526327/1‑143 (MQ=255)
                               ttAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTTCTCCTCCTTTTTCCGCCCGGGGAACCTGCTGGGGGCGGTTCTATTTTTTT‑CCGtttt                                                                                               >  2:54627/1‑150 (MQ=255)
                                 aaaGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTAcc                                                                                             <  2:825736/151‑1 (MQ=255)
                                 aaaGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTAcc                                                                                             <  1:279847/151‑1 (MQ=255)
                                      ccTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGACTTTTTCCTCCCTTTCCCGCCCGGGGAAACCGCTGGGGGCGGTTCTAtttttttcccctttcctgc                                                                                           >  1:167662/1‑135 (MQ=255)
                                      ccTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGAATTTTTCATCATTTTTCAGCCAGGGGAACCTGCTGGGGGCGATTCTTTTTTTTT‑CCGTTTTCcttctt                                                                                        >  1:718084/1‑151 (MQ=255)
                                      ccTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTTCTCATCCTTTTCCAGCCAGGGAAAACTGCTGGGGGCGGTTCTATTTTTTG‑CCGTTTTCCTGCtt                                                                                        >  2:462434/1‑151 (MQ=255)
                                           aaGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGGTTTGCTTCTCCTTTTCCAGCCAGGGTAACCCCCTGGGGCCGGTTCTTTTTTTCGTCCGTTT‑CCTGCTTAtttt                                                                                   >  1:362735/1‑151 (MQ=255)
                                             gTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGCTCATCATTTTCCAGCCCGGGAAACCCGCTGGGGGCGGTTCTATTTTTTG‑CCGTTTTCCTGCTTATCtttt                                                                                 >  2:789279/1‑151 (MQ=255)
                                                 cACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTcc                                                                              <  2:622659/150‑1 (MQ=255)
                                                     gTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGAATTTTTCATCATTTTTCCGCCCGGGGAAACTGCCTGGGGCGGTTTTATTTTTTG‑CCGTTTTTCTTCTTTTTTTTTTTCTtcg                                                                          >  2:239584/1‑150 (MQ=255)
                                                     gTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCTTCATTTTCCCGCCCGGGGAACCCCCTGGGGCCGGGTTTATTTTTTT‑CCGTTTTCCTGCTTCTtttttttttgtg                                                                          >  1:772603/1‑144 (MQ=255)
                                                               aTCGCCGGGATTGGAGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTGCTCCTCCTTTTCCAGCCAGGGGAAACTGCTGGGGGCGATTTTTTTTTTCT‑CCCTTTTCCTGCTTTTCTTTTTTCTTCGCGTCGGCTggg                                                               >  1:255347/1‑150 (MQ=255)
                                                                tCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGATTTTCTCATCATTTTCCAGCCCGGGGAACCTGCTGGGGCCGATTCTATTTTTTG‑CCGTTTACCTGCTTATCTTTTTTCTGCGCGTCGGCTGGa                                                               >  2:262333/1‑150 (MQ=255)
                                                                           ggCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTTATCATTTTTCAGCCAGGGGAAACTGCTGGGGCCGGTTTTATTTTTTG‑CCGTTTTCCTTCTTTTTTTTTTTCTTCGCGGCGGCTGGAACCACGTCgggt                                                   >  2:721638/1‑149 (MQ=255)
                                                                               atgcgatTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTc                                               <  1:809868/151‑1 (MQ=255)
                                                                                  cgatTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAAATTTCTCATCATTTTCCAGCCCGGGAAAACTGCTTGGGCCGATTTTTTTTTTCT‑CCGTTTTCCTGCTTATCTTTTTTCTTCGCGGCGGGTGGACCCACGCCGGGTATTCAGt                                            >  2:227379/1‑151 (MQ=255)
                                                                                                 cTTTGTTGCCGATTATGGCGGGGATTTTCTCATCCTTTGTCAGCCCGGGAAACCTGCTGGGGGCGATTCTATTTTTTG‑CCGTTTTTCTGCTTATTTTTTTTCTGCGCGTCGGCTGGACCCACGTCGGTTTTTTAGTCGGCGGGGAGGggat                             >  2:103891/1‑151 (MQ=255)
                                                                                                         ccGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAg                     <  2:132359/151‑1 (MQ=255)
                                                                                                            aTTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTg                   <  1:714179/150‑1 (MQ=255)
                                                                                                                     ggAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGaa           >  1:443138/1‑149 (MQ=255)
                                                                                                                       aaTTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCg       >  2:151837/1‑151 (MQ=255)
                                                                                                                            gCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAgat  >  2:800263/1‑151 (MQ=255)
                                                                                                                             cTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAgat  <  2:68257/150‑1 (MQ=255)
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ATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCG‑CCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGAT  >  NC_000913/3285718‑3285992

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑