Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091375,0740TG52.5% 39.7 / 56.0 40N136T (AAC→ACC) thiBthiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (6/13);  new base G (21/0);  total (27/13)
Fisher's exact test for biased strand distribution p-value = 2.25e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.98e-05

GCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAA  >  NC_000913/74945‑75222
                                                                                                                                  |                                                                                                                                                       
gCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTTTCAt                                                                                                                                    >  2:179252/1‑151 (MQ=255)
        gCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTTTCATAAaagaag                                                                                                                           >  2:666517/1‑151 (MQ=255)
         ccATATCCTTTTTCCATCCATAGCAACAGACCCAGCCCCTGTGTACTGGTGCGCGGTTCCTGATAAATCGCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAgg                                                                                                                          <  1:410431/151‑1 (MQ=255)
          cATAGCCTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGc                                                                                                                         <  1:152677/151‑1 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTTTTCTTTTTATAAAAAAAAGCGGAGTAGCCATAATCaa                                                                                                       >  2:137575/1‑151 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGGTTTTTTTTGTTAAAAACAAACGCGGAggtgcaatacataa                                                                                                        >  1:719818/1‑138 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTTTCATTAACCAAGGCGAAGTAGGCATAATCaa                                                                                                       >  1:63661/1‑151 (MQ=255)
                           cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTCTTTTCATAAACGAAGGCGGAGAAGCCCTAATCaa                                                                                                       >  2:575317/1‑151 (MQ=255)
                             tAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAAc                                                                                                     <  2:297802/151‑1 (MQ=255)
                               gCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTTTTATTAAAGAAGGCGCAGTAGCCCTAATCAAAAgg                                                                                                   >  1:168269/1‑151 (MQ=255)
                                cAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACgg                                                                                                   <  1:199083/150‑1 (MQ=255)
                                      ccccAGCCCCGGTGTACTGGGGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGaa                                                                                             <  1:713425/149‑1 (MQ=255)
                                       cccAGCCCCGGTGTACTGGTGCGCGGTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGTTACGAAAg                                                                                           <  2:576270/151‑1 (MQ=255)
                                       cccAGCCCCGGTGTACTGGTGCGCGGTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAg                                                                                           <  1:174223/151‑1 (MQ=255)
                                              ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTCTTTTTATAAACAAAGGCGGAGGAGGCCTAATCAAAACGTACGGAAatggtatt                                                                                    >  1:421429/1‑146 (MQ=255)
                                              ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGTTTTTGTCATAAACCAAGGCGGAGTAGGCATAATCAAACGGGACGGAAATGTCatt                                                                                    >  1:50735/1‑151 (MQ=255)
                                              ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTTTCATAAAAGAAGGCGGAGGAGGCCTAATTAAAAGGGAAGAAAGTGTTatt                                                                                    >  1:347703/1‑151 (MQ=255)
                                                 gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTGTTTTAATACAAAGGGGAGAAGCCATAATCAAAAGGCACGGAAGGGGCattatt                                                                                 >  1:733061/1‑151 (MQ=255)
                                                 gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTTTCATAAACGAAAGCGGAGGAGCCCTAATCAAACGGGAAGAAAATGTCattttt                                                                                 >  2:438233/1‑151 (MQ=255)
                                                 gggtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGTTCTTGTTATAAAAAAAAGCGAAGAAGGCCAAATCCAACAGTAAGGAAATGTCattatt                                                                                 >  1:74263/3‑151 (MQ=255)
                                                  tgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTc                                                                                <  2:324459/151‑1 (MQ=255)
                                                     aCTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTCTGTTGTTCTTTTTTTAAAAGAACGAGAAGCAAGCATAATACAAAAGGTGGGaaacggacttattacc                                                                               >  1:107911/1‑137 (MQ=255)
                                                      cTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAgc                                                                            <  2:616767/151‑1 (MQ=255)
                                                           gcgcGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTGTTATAAAAGAAAGCGAAGTAGCCATAATCAAACGGGACGAAAGGGGCATTATTTCAGccgccg                                                                      >  2:735332/1‑151 (MQ=255)
                                                                gATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTTTTTTTTTTATAAAAAAAAGGGGAGGAGCCCTAATCAAAAGGGACGAAAGTGTGATTATTTCAGCCGCCgggga                                                                  >  1:447259/1‑148 (MQ=255)
                                                                    cTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTTTCATAAAAGAAGGCGGAGGAGGCATAATTAAAAGGTACGAAAATGTCATTATTTCAGCCCCCGGGGACGGTa                                                             >  2:572688/1‑151 (MQ=255)
                                                                     tGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTCTTGTCATAAAAGAAGGCGAAGTAGCCATAATCAAAAGGGACGAAAGTGTCATTATTTCAGCCGCCCGGGAAGGTTa                                                             >  2:69984/1‑151 (MQ=255)
                                                                        tAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACgg                                                         <  1:222310/151‑1 (MQ=255)
                                                                        tAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTTTTTTTGTCATAAACCAAGGCGAAGTAGCCATAATCAAACGGTACGGAAAGGTCATTATTTCAGCCGCCGGGGACGGTAACgg                                                         >  1:237036/1‑151 (MQ=255)
                                                                        tAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACgg                                                         <  2:717402/151‑1 (MQ=255)
                                                                          aaTCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTTTCCTAAAACAAGGCGGAGGAGGCATAATTAAACGGGACGAAAGTGTCATTTTTTCAGCCGCCGGGGAAGTTAACGGCa                                                       >  1:548609/1‑151 (MQ=255)
                                                                                      gTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTTTCATAAACGAAAGCGCAGGAGCCATAATCAAACGGTACGAAAGTGTCATTTTTTCACCCGCCGGGGACGTTAAAGGCATCCGCCGCcac                                            >  2:603809/1‑150 (MQ=255)
                                                                                               gCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGTTTTTTTCATAAACGAAAGAGAAGGAGACCTAATCCAACGGGACGAAAGTGGCATTTTTCCAGCCGCCGGGGACGTTAACGGCATTCGCTGCCACACCGCctttt                                  >  2:340271/1‑150 (MQ=255)
                                                                                                ctctCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTGTCATAAAAGAAGGCGAAGGAGCCATAATCAAAAGGGACGAAAAGGTCATTATTTCAGCCGCCGGGGAAGTTAACGGCATCCGCCGCCACACCCCcttttg                                 >  2:468852/1‑149 (MQ=255)
                                                                                                ctctCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTTTCATAAACGAAGGCGGAGGAGCCCTAATCAAAAGGGACGAAAGTGTCATTATTTCAGCCGCCGGGGACGGTAAAGGCATCCGCCGCCCCACCCCtttttg                                 >  2:335190/1‑149 (MQ=255)
                                                                                                    cAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTTTCATAAAAGAAAGCGAAGTAGCCATAATTAAACGGGACGAAAGTGTCATTATTTCAGCCGCCGGGGACGTTAACGGCATCCCCTGCCCCACCGCTTTTTGCaaa                             >  2:572951/1‑151 (MQ=255)
                                                                                                             cTTTCAGGCTTTGTGGCGGGGTTTTTTGGTTTTTCTTGTCATAAAAGAAGGCGGAGGAGCCCTAATCAAACGGGACGGAAGTGTCATTTTTTCAACCGCCGGGGAAGTTTACGGCCTCCCCTGCCCCCCCCCCTTTTGCCAACAGTcccgg                    >  2:70136/1‑148 (MQ=255)
                                                                                                               ttCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGttt                  <  2:447267/151‑1 (MQ=255)
                                                                                                                     cTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTg             <  2:171240/150‑1 (MQ=255)
                                                                                                                                ggTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTaa  >  1:445050/1‑151 (MQ=255)
                                                                                                                                  |                                                                                                                                                       
GCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAA  >  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: