Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091375,0790CT60.0% 4.2 / 47.7 40L134L (CTG→CTA) thiBthiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base C (3/13);  new base T (24/0);  total (27/13)
Fisher's exact test for biased strand distribution p-value = 4.65e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.62e-06

GCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAA  >  NC_000913/74945‑75222
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gCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCAt                                                                                                                                    >  2:179252/1‑151 (MQ=255)
        gCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTTTCATAA‑aagaag                                                                                                                           >  2:666517/1‑151 (MQ=255)
         ccATATCCTTTTTCCATCCATAGCAACAGACCCAGCCCCTGTGTACTGGTGCGCGGTTCCTGATAAATCGCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAgg                                                                                                                          <  1:410431/151‑1 (MQ=255)
          cATAGCCTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGc                                                                                                                         <  1:152677/151‑1 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTTAGTTTTTTCTTTTTATAA‑AAAAAAGCGGAGTAGCCATAAT‑Caa                                                                                                       >  2:137575/1‑151 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGGTTTTTTTTGTTAAAA‑ACAAACGCGGAggtgcaatacataa                                                                                                        >  1:719818/1‑138 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTTTCATTA‑ACCAAGGCGAAGTAGGCATAAT‑Caa                                                                                                       >  1:63661/1‑151 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTCTTTTCATAA‑ACGAAGGCGGAGAAGCCCTAAT‑Caa                                                                                                       >  2:575317/1‑151 (MQ=255)
                             tAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAAc                                                                                                     <  2:297802/151‑1 (MQ=255)
                               gCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTTTTATTA‑AAGAAGGCGCAGTAGCCCTAAT‑CAAAAgg                                                                                                   >  1:168269/1‑151 (MQ=255)
                                cAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACgg                                                                                                   <  1:199083/150‑1 (MQ=255)
                                      ccccAGCCCCGGTGTACTGGGGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGaa                                                                                             <  1:713425/149‑1 (MQ=255)
                                       cccAGCCCCGGTGTACTGGTGCGCGGTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGTTACGAAAg                                                                                           <  2:576270/151‑1 (MQ=255)
                                       cccAGCCCCGGTGTACTGGTGCGCGGTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAg                                                                                           <  1:174223/151‑1 (MQ=255)
                                              ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTTTTCTTTTTATAA‑ACAAAGGCGGAGGAGGCCTAAT‑CAAAACGTACGGAAatggtatt                                                                                    >  1:421429/1‑146 (MQ=255)
                                              ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTTTTGTCATAA‑ACCAAGGCGGAGTAGGCATAAT‑CAAACGGGACGGAAATGTCatt                                                                                    >  1:50735/1‑151 (MQ=255)
                                              ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑AAGAAGGCGGAGGAGGCCTAAT‑TAAAAGGGAAGAAAGTGTTatt                                                                                    >  1:347703/1‑151 (MQ=255)
                                                 gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTTTTTTTGTTTTAATACAAAGG‑GGAGAAGCCATAAT‑CAAAAGGCACGGAAGGGGCattatt                                                                                 >  1:733061/1‑151 (MQ=255)
                                                 gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑ACGAAAGCGGAGGAGCCCTAAT‑CAAACGGGAAGAAAATGTCattttt                                                                                 >  2:438233/1‑151 (MQ=255)
                                                 gggtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTCTTGTTATAA‑AAAAAAGCGAAGAAGGCCAAAT‑CCAACAGTAAGGAAATGTCattatt                                                                                 >  1:74263/3‑151 (MQ=255)
                                                  tgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTc                                                                                <  2:324459/151‑1 (MQ=255)
                                                     aCTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTCTG‑TTGTTCTTTTTTTAA‑AAGAACGAGAAGCAAGCATAATACAAAAGGTGGGaaacggacttattacc                                                                               >  1:107911/1‑137 (MQ=255)
                                                      cTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAgc                                                                            <  2:616767/151‑1 (MQ=255)
                                                           gcgcGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTGTTATAA‑AAGAAAGCGAAGTAGCCATAAT‑CAAACGGGACGAAAGGGGCATTATTTCAGccg‑ccg                                                                      >  2:735332/1‑151 (MQ=255)
                                                                gATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTTAGTTTTTTTTTTTTATAA‑AAAAAAGGGGAGGAGCCCTAAT‑CAAAAGGGACGAAAGTGTGATTATTTCAGCCG‑CCgggga                                                                  >  1:447259/1‑148 (MQ=255)
                                                                    cTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTTTCATAA‑AAGAAGGCGGAGGAGGCATAAT‑TAAAAGGTACGAAAATGTCATTATTTCAGCCC‑CCGGGGACGGTa                                                             >  2:572688/1‑151 (MQ=255)
                                                                     tGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTCTTGTCATAA‑AAGAAGGCGAAGTAGCCATAAT‑CAAAAGGGACGAAAGTGTCATTATTTCAGCCGCCCGGGAAGGTTa                                                             >  2:69984/1‑151 (MQ=255)
                                                                        tAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACgg                                                         <  1:222310/151‑1 (MQ=255)
                                                                        tAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTTAGTTTTTTTTTGTCATAA‑ACCAAGGCGAAGTAGCCATAAT‑CAAACGGTACGGAAAGGTCATTATTTCAGCCG‑CCGGGGACGGTAACgg                                                         >  1:237036/1‑151 (MQ=255)
                                                                        tAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACgg                                                         <  2:717402/151‑1 (MQ=255)
                                                                          aaTCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTTTTTTTTTCCTAA‑AACAAGGCGGAGGAGGCATAAT‑TAAACGGGACGAAAGTGTCATTTTTTCAGCCG‑CCGGGGAAGTTAACGGCa                                                       >  1:548609/1‑151 (MQ=255)
                                                                                      gTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑ACGAAAGCGCAGGAGCCATAAT‑CAAACGGTACGAAAGTGTCATTTTTTCACCCG‑CCGGGGACGTTAAAGGCATCCGCCGCcac                                            >  2:603809/1‑150 (MQ=255)
                                                                                               gCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTTTTTTCATAA‑ACGAAAGAGAAGGAGACCTAAT‑CCAACGGGACGAAAGTGGCATTTTTCCAGCCG‑CCGGGGACGTTAACGGCATTCGCTGCCACACCGCctttt                                  >  2:340271/1‑150 (MQ=255)
                                                                                                ctctCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTGTCATAA‑AAGAAGGCGAAGGAGCCATAAT‑CAAAAGGGACGAAAAGGTCATTATTTCAGCCG‑CCGGGGAAGTTAACGGCATCCGCCGCCACACCCCcttttg                                 >  2:468852/1‑149 (MQ=255)
                                                                                                ctctCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑ACGAAGGCGGAGGAGCCCTAAT‑CAAAAGGGACGAAAGTGTCATTATTTCAGCCG‑CCGGGGACGGTAAAGGCATCCGCCGCCCCACCCCtttttg                                 >  2:335190/1‑149 (MQ=255)
                                                                                                    cAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑AAGAAAGCGAAGTAGCCATAAT‑TAAACGGGACGAAAGTGTCATTATTTCAGCCG‑CCGGGGACGTTAACGGCATCCCCTGCCCCACCGCTTTTTGCaaa                             >  2:572951/1‑151 (MQ=255)
                                                                                                             cTTTCAGGCTTTGTGGC‑GGGGTTTTTTGGTTTTTCTTGTCATAA‑AAGAAGGCGGAGGAGCCCTAAT‑CAAACGGGACGGAAGTGTCATTTTTTCAACCG‑CCGGGGAAGTTTACGGCCTCCCCTGCCCCCCCCCCTTTTGCCAACAGTcccgg                    >  2:70136/1‑148 (MQ=255)
                                                                                                               ttCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGttt                  <  2:447267/151‑1 (MQ=255)
                                                                                                                     cTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTg             <  2:171240/150‑1 (MQ=255)
                                                                                                                                ggTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTaa  >  1:445050/1‑151 (MQ=255)
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GCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAA  >  NC_000913/74945‑75222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑