Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091315,4100TG41.5% 69.3 / 10.9 42intergenic (+112/‑35)dnaJ/insL1chaperone Hsp40, DnaK co‑chaperone/IS186 transposase
Reads supporting (aligned to +/- strand):  ref base T (6/18);  new base G (17/0);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 6.89e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCT  >  NC_000913/15270‑15534
                                                                                                                                              |                                                                                                                            
agaagTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTa                                                                                                                    <  2:324322/151‑1 (MQ=255)
   agTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGc                                                                                                                 <  2:936320/151‑1 (MQ=255)
   agTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGc                                                                                                                 <  2:900445/151‑1 (MQ=255)
         ttGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGGACTCCCCTAAGA‑GCCCAC‑TTAAGGGGTggggg                                                                                                                        >  1:475290/1‑137 (MQ=255)
           gacgacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATg                                                                                                         <  2:960663/151‑1 (MQ=255)
            acgacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGa                                                                                                        <  1:644070/151‑1 (MQ=255)
              gacCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTGACTCCCAAAAGC‑GCCAAA‑CTAAGGGGTGGGGGGTTTAGCCTGGTATg                                                                                                         >  2:1015287/1‑148 (MQ=255)
              gaaatgtaccGCTAAACTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCTCTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATg                                                                                                         <  1:749260/140‑1 (MQ=255)
                   gACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACg                                                                                                 <  2:1079789/151‑1 (MQ=255)
                      ccGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTGACTCCCCCAAAC‑GCGAAC‑TTAAGGGGTGTGGGATTTAGCCTGATATGATTTAAAGTg                                                                                               >  1:516970/1‑150 (MQ=255)
                      ccGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGc                                                                                              <  2:871169/151‑1 (MQ=255)
                        gCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGCACCCCCATAAAC‑GCCAAA‑TTAAGGGGTGTGGGGTTAAGCCCGGTATTAttttaaatgcc                                                                                             >  2:951488/1‑142 (MQ=255)
                        gCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGAAGACTCCCATAAGG‑GCTAAA‑TTTAGGGGTGGGGGATTACGACTGGTATGATTTTAAGTTCCg                                                                                            >  2:945555/1‑151 (MQ=255)
                             ccTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCAACCCCCTAAAA‑GCCAAC‑TTAAAGGGTGTGGGATTATGCCTGATATGATTTTATGTGCCGATg                                                                                         >  2:428638/1‑149 (MQ=255)
                             ccTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATGACCCCCCTCAAA‑GCTCAA‑TTAAGGGGTGTGGGGTTTCGCCCGGTATGAttttaaggggcgaag                                                                                         >  1:468533/1‑137 (MQ=255)
                              cTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAGA‑GCTAAA‑TTAAGGGGTGTGGGGTTACGCCTGATATGATTTTACGTGCCGATGaa                                                                                       >  2:546616/1‑150 (MQ=255)
                                         ccTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGAGCACTCCCCTAACC‑GCTAAC‑TTAAAGGTTGTGGTATTATGCCTGATATGATTTAACATGCCGATGAATTaatttccc                                                                             >  1:211013/1‑142 (MQ=255)
                                            gCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGGCACTCCCCTAAAA‑GCTAACATTAAGGG‑TGTGGGGTTAAGCCCGAGATGATTTAAAGTGCCGATGAATTACTCTCACGAt                                                                          >  1:363251/1‑149 (MQ=25)
                                                 tGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACCTCCCTAAAC‑GCCAAC‑TTAAGGGGTGTGGGGTTTCGCCCGATATTATTTAAAATGCCGGAGAAATAATCTCACCATaaa                                                                       >  1:967273/1‑146 (MQ=255)
                                                  gggCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCCTAAAC‑GCTAAA‑TTAAAGGGTGTGGGGTTAAGCCCGATATGATTTTACGTGCCGGTGAATTACTCTCACCATaaattg                                                                    >  2:794306/1‑145 (MQ=255)
                                                    gCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGTCACTCCCATAAAC‑GCTAAA‑TTAAGGGGTGTGGTATTACGCCTGGTATGATTTAACGTGCCGATGAATTAATCTCACGATAACTgg                                                                    >  2:474696/1‑147 (MQ=25)
                                                          cTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGAGCACTCCCCTAAAC‑GCTAAC‑ATAAAGGGTGTGGTATTATTCCTGATATGATTTTAAATGGCGATGAAATAATCTCCCGATAACTGGGCACCaa                                                             >  1:646103/1‑148 (MQ=255)
                                                           tGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGATACTTCCCAAAGCGGCTAA‑‑TTTAGGGGGGTGGGTTTAAGCCTGGTATGATTTTAAATGCCGACGAAATAGTCTCACGATAACTTGGGAGCAAtttt                                                         >  2:880480/1‑149 (MQ=255)
                                                                  aaaTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCat                                                  <  2:356828/151‑1 (MQ=255)
                                                                    aTAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGGACACTCCCCTAAAA‑GCCAAC‑ATAAAGGGTTTGGGATTACGGCCGCTATGATTTTAACTGCCGATGAAATTCTTTCACGATAAATGGTCAACAAATCTGGccc                                                    >  2:291072/1‑147 (MQ=255)
                                                                      aGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATAtt                                               <  2:829209/150‑1 (MQ=255)
                                                                        ggTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGt                                            <  2:808090/151‑1 (MQ=255)
                                                                           gCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTaa                                          <  2:860286/150‑1 (MQ=255)
                                                                           gCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTaa                                          <  1:539372/150‑1 (MQ=255)
                                                                                gAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCg                                     <  1:795229/150‑1 (MQ=255)
                                                                                     tatGCGAGCACCTGTAAAGTGGCGGGGAACACCCCCCTCAAC‑GCCAAA‑CTAAGGGGTGTGGGATTTCGCCCGATATGATTTTACGTGCCGGTGAAATACTCTCACCATAACATGGCAGCCATTTTGGCCCATATTTGTaaaaccccagaa                                >  1:575594/1‑140 (MQ=255)
                                                                                      atGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACt                              <  1:428370/151‑1 (MQ=255)
                                                                                      atGCGAGCACCTCTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACt                              <  1:790737/151‑1 (MQ=255)
                                                                                          gAGCACCTGTAAAGTGGCGGGGGTCACCCCCCTAAAC‑GCTAAC‑TTTAAGGGTGTGGGATTAAGCCCGATATTATTTTAAATGGCGATGAATTAATCTCCCCATAAATGGTCAGCAAATCTGGGCCCTATTTGTAAAACCCAAGAAATgg                            >  2:927095/1‑149 (MQ=255)
                                                                                                 tGTAAAGTGGCGGGGATCACTCCCCTAAGA‑GCCAAC‑TTAAGGGGTGTGGTGTTATGCCTGATATGATTTTAACTTCCGATGAATTAATCTTACGAAAAATGGTCAGACAATCTGGCCCCTATTGGTAAACCCCCAAAAATGGGTACTTctg                   >  1:637957/1‑149 (MQ=255)
                                                                                                  gTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCgg                   <  1:380645/150‑1 (MQ=40)
                                                                                                  gTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGc                  <  2:628988/151‑1 (MQ=40)
                                                                                                         ggCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAAt           >  1:133948/1‑151 (MQ=35)
                                                                                                           cGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGc         >  1:549033/1‑151 (MQ=33)
                                                                                                                aTCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCgggg    >  1:423712/1‑151 (MQ=33)
                                                                                                                 tCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGc   >  1:537064/1‑151 (MQ=32)
                                                                                                                  cACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGct  >  2:325840/1‑151 (MQ=31)
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AGAAGTTTTTTGACGACCTGACCCGCTAACCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTGTAAAGTGGCGGGGATCACTCCCATAAGC‑GCTAAC‑TTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCCGGGGCT  >  NC_000913/15270‑15534

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: ‑