Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,859,1040TG46.5% 40.4 / 17.7 43M671R (ATG→AGG) mutSmethyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base T (16/7);  new base G (0/20);  total (16/27)
Fisher's exact test for biased strand distribution p-value = 9.43e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTACCTATATGCGCCAGACCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGCGAATAAGATTAAGGC  >  NC_000913/2858954‑2859254
                                                                                                                                                      |                                                                                                                                                      
gTACCTATATGCGCCAGACCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTAt                                                                                                                                                        <  1:425441/151‑1 (MQ=255)
   ccTATATGCGCCAGACCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTAtgg                                                                                                                                                      >  2:304082/1‑150 (MQ=255)
    cTATATGCGCCAGACCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTAtggtg                                                                                                                                                    >  1:302095/1‑151 (MQ=255)
     tataTGCGCCAGACCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTAtggtgg                                                                                                                                                   >  1:305874/1‑151 (MQ=255)
        atGCGCCAGACCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTAtggtgg                                                                                                                                                   >  2:132901/1‑148 (MQ=255)
                 aCCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGaa                                                                                                                                        >  2:858774/1‑150 (MQ=255)
                         gATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAat                                                                                                                               >  2:626754/1‑151 (MQ=255)
                                cTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTAc                                                                                                                        >  1:903734/1‑151 (MQ=255)
                                  gATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACAt                                                                                                                      >  1:235692/1‑151 (MQ=255)
                                     ggCCTACATCGGCAGTTATGTACCGGCAAAAAAAGTCGAGATTGGACCTATCGATCGCATTTTTCCCCGCGTGGGCGCGGCAGATGCCCTGGCGCCCGGGCGCTCACCTTTTAGGGGGGAGATGACTAAAACCGCCAATATTTTACAt                                                                                                                      <  2:7953/148‑1 (MQ=255)
                                       ccTACATCGGCAGTTATTTCCCGGCAAAAAAGGTCGAGATTGGCCCTATCGACCGCTTCTTTCCCCGCGGGGGCGCGGCAGATGACCTGGCGCCGGGGCCCTCAACTTTTAGGGTGAAGATGACTAAAACCGCCAATATTTTACATAACGc                                                                                                                 <  2:945741/151‑1 (MQ=255)
                                          acacCGGCATTTATGTCCCGGCAAAAAAAGTGGAGATTGCACCTACCGACCGCATTTTTCCCCGCGGGGGCGCGGAAGATGCCCGGGCTCCCGGGCGCCCACCCTTTAGGGGGGAGATGACTAAAACCGCCAATATTTTACATAACGCCa                                                                                                               <  1:395562/150‑1 (MQ=255)
                                                     tATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGt                                                                                                    >  1:461256/1‑150 (MQ=255)
                                                     tATGCACGGGCAAAAAAAGTCGAGTTTGGCCCTATCGACCGCTTTTTTCCCCGGGTAGGCGCGGCAAATGCCCTGGCGCCCGGGCGCTCACCTTTTATGGTGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGt                                                                                                    <  2:663441/150‑1 (MQ=255)
                                                       tGTCCCGGCAAAAAAAGTCGAGTTTGGCCCTATCGTCCGCTTCTTCCCCCGCGGGGGCGGGGCAGATGCCCGGGCGTCGGGGCCCCAACCCTTTAGGGGGGAGATGAATAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCt                                                                                                  <  1:958488/150‑1 (MQ=255)
                                                        gTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTgg                                                                                                >  1:110890/1‑151 (MQ=255)
                                                        gTACCGGCAAAAAAGGTGGAGATTGGCCCTATCGATCCCTTCTTTCCCCGGGTGGGCGCGGCAGATGCCCGGGCGTCCGGGCGCCCAACCTTTATGGTGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACa                                                                                                      <  1:367074/145‑1 (MQ=255)
                                                         taccgcaaaaaaaaGTCGAGATTGGCCCTATCGCCCGCTTTTTTCCCCGCGTAGGCGCGCCAGAGGACCGGGCGTCCGGGCGCCCACCCTTTAGGGTGGAAATGATTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCt                                                                                                  <  2:860816/139‑1 (MQ=255)
                                                         tACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTgg                                                                                                >  2:4333/1‑150 (MQ=255)
                                                            cGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGtt                                                                                            >  1:889454/1‑151 (MQ=255)
                                                             ggaacaAAAAGTGGAGATTGCCCCTACCGATCGCTTTTTTCCCCGGGGGGGCGGGGAAGATGCCCGGGCGCCCGGGCCCTAACCCTTTAGGGTGGAGATGACTAAAGCCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGtt                                                                                            <  1:699038/147‑1 (MQ=255)
                                                                aaaaaaaGTCGAGATTGACCCTAGCGATCGCATCTTTCCCCGCGTAGGCGCGGCAGATGCCCTGGCGCCCGGGCGCTCACCTTTTAGGGGGGGGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGgt                                                                                               <  2:899636/142‑1 (MQ=255)
                                                                   aaaaGTCGAAGTTGGCCCTCCCGACCCCATTTTTCCCCGGGTGGGCGCGGCAGAGGCCCGGGCGCCGGGGCCCTAACCCTTTATGGTGGAGATGCTGGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGAt                                                                                     <  1:130784/151‑1 (MQ=255)
                                                                         cGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATg                                                                                    >  1:480985/1‑146 (MQ=255)
                                                                                ggACCTATCGACCGCTTCTTCCCCCGCGTGGGCGCGGCAGATGCCCTGGCGCCGGGGCGCTCAACCTTTAGGGTGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGt                                                                         <  2:627913/150‑1 (MQ=255)
                                                                                    cttcccttgaattCTTTCCCCGCGAGGGGGCGGAGGTGGACCGGGCGGCCGGCCCCACAACTTTTTTGGGGGAGAGGAAGAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGt                                                                         <  1:911195/134‑1 (MQ=255)
                                                                                            cgCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCAcc                                                             >  2:100471/1‑150 (MQ=255)
                                                                                              cATCTTTCCCCGCGGCGGCGCGGCAGATGCCCTGGCGCCCGGGCGCTCACCCTTTGTGGGGGAGATTACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCt                                                            <  2:562112/149‑1 (MQ=255)
                                                                                              cATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTAc                                                          >  2:425766/1‑151 (MQ=255)
                                                                                               aTCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACg                                                         >  1:179654/1‑151 (MQ=255)
                                                                                                  tttACCCGCGTGGGCGCGGCAGAGGACCGGGCGTCGGGGCGCTCAACTTTTAGGGGGGAGATGACGGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTAc                                                          <  2:57313/147‑1 (MQ=255)
                                                                                                      cccGCGTGGGCGCGGCAGATGCCGGGGCGCCCGGCCGCCCACCTTTTATGGTGGAAATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCt                                                  <  2:305882/151‑1 (MQ=255)
                                                                                                       ccGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTg                                                 >  2:838516/1‑151 (MQ=255)
                                                                                                              ggCGCGGCAGATGCCCTGGCGTCGGGGCCCTCAACTTTTAGGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCg                                              <  2:354570/147‑1 (MQ=255)
                                                                                                              ggCGCGGCAGATGCCCGGGCGCCGGGGCCCTCACCTTTTAGGGGGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTgg                                          <  2:947231/151‑1 (MQ=255)
                                                                                                               gcgcGGCGCATGCCCGGGGGTCCGGTCGCTCCACTTTTATGGGGGAGAGGATTGAATCCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTg                                           <  2:903749/149‑1 (MQ=255)
                                                                                                                    gCAGGTGACCGGGCGGCCGGACGCCCAACTTTTTGGGTGGAAGTCACAAAAGCCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTggcgtgg                                     <  1:938827/150‑1 (MQ=255)
                                                                                                                        aTGCCCGGGCGTCGGGGCCCCAAACTTTTAGGGTGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTggcgtgg                                     <  1:645950/146‑1 (MQ=255)
                                                                                                                         tGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTggcgtgggcgtg                                >  1:618209/1‑150 (MQ=255)
                                                                                                                         tGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTgc                               >  2:938464/1‑151 (MQ=255)
                                                                                                                            ctggcctcccGGGCGCTCAACTTTCAGGGTGGGGATACTTTAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTgc                               <  2:892947/140‑1 (MQ=255)
                                                                                                                            ccTGGCGTCCGGGCGCTCAACCTTTAGGGGGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTgc                               <  2:350030/148‑1 (MQ=255)
                                                                                                                               ggCGCCCGGGCCCTCAACCTTTGGGGTGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGaa                         <  2:302103/151‑1 (MQ=255)
                                                                                                                                   gcgggccccTCACCTTTTAGGGGGGAGAGTAATGAATCCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAAt                      <  2:273549/142‑1 (MQ=255)
                                                                                                                                       ggCGCTCAACCTTTAGGGGGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGc                 <  2:914856/151‑1 (MQ=255)
                                                                                                                                         cgcTCAACTTTTAGGGTGGAGATGACAAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGc                 <  1:603672/149‑1 (MQ=255)
                                                                                                                                                  tttAGGGGGGAGATGACTAAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGCGAATAAGAtt       <  2:894415/150‑1 (MQ=255)
                                                                                                                                                  ttgttggtggAAATGTCTAAATCCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGCGa               <  1:815833/138‑1 (MQ=255)
                                                                                                                                                   ttATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGCGAATAAGATTa      >  2:316272/1‑150 (MQ=255)
                                                                                                                                                      tggtggAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGCGAATAAGATTAAGGc  >  1:774832/1‑151 (MQ=255)
                                                                                                                                                      |                                                                                                                                                      
GTACCTATATGCGCCAGACCGCACTGATTGCGCTGATGGCCTACATCGGCAGCTATGTACCGGCACAAAAAGTCGAGATTGGACCTATCGATCGCATCTTTACCCGCGTAGGCGCGGCAGATGACCTGGCGTCCGGGCGCTCAACCTTTATGGTGGAGATGACTGAAACCGCCAATATTTTACATAACGCCACCGAATACAGTCTGGTGTTAATGGATGAGATCGGGCGTGGAACGTCCACCTACGATGGTCTGTCGCTGGCGTGGGCGTGCGCGGAAAATCTGGCGAATAAGATTAAGGC  >  NC_000913/2858954‑2859254

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑