Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,481,8040GA41.4% 88.0 / 24.1 58P125S (CCA→TCA) emrYputative multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base G (28/6);  new base A (0/24);  total (28/30)
Fisher's exact test for biased strand distribution p-value = 4.79e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTG  >  NC_000913/2481656‑2481947
                                                                                                                                                       |                                                                                                                                                
atCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGa                                                                                                                                                 >  2:734233/1‑150 (MQ=255)
      ccccAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACg                                                                                                                                          <  2:972307/151‑1 (MQ=255)
      ccccAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACg                                                                                                                                          >  1:735250/1‑151 (MQ=255)
       cccAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACgg                                                                                                                                         <  1:465251/151‑1 (MQ=255)
             tAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGc                                                                                                                                  >  2:624646/1‑151 (MQ=255)
              aaaGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGc                                                                                                                                  <  2:45405/150‑1 (MQ=255)
                         aaaTATACCCCCCAAATACCGCCCAAAATAGGGGAGAGATAACCACGTTCATTGACCATAAGGCCAGAGAAATTTTTTTTTTTTCGGGCGGATAATCCTTAAAAAAAAACCCCGGTGAAGGGGAAATAAACGGCCCCGCCATTAACCCCTg                                                                                                                      <  1:172247/151‑1 (MQ=255)
                           atatACCCCCCCAATACCGCCCCACATATGGGAGCGATAATCACGGTCTTTGACCATAATGCAAGAGAAAATGTTTTTTTTTCGGGCGAATATTTCTTAAAAAATAACCTCGGTGACAGTGAAATTAACGCCCCCGCCATTAACCCCTGaa                                                                                                                    <  2:7620/151‑1 (MQ=255)
                                 cccccaaaTACCGCCCCAAATATCGGGGCGATAATCCCGGTCATTGACCATAATGCCAGAGAAATTTTTTTTTTTTCGGGCGGATATTTCTTTAAAAATAAACTCTGTGACAGTGAAATTACCGGCCCCGCCATTAACCCCTGAACGAct                                                                                                               <  1:807434/144‑1 (MQ=255)
                                  cGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGActct                                                                                                             >  2:574912/1‑151 (MQ=255)
                                       aaTATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaaa                                                                                                         >  2:302405/1‑150 (MQ=255)
                                        atatCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaaaa                                                                                                        >  1:62577/1‑150 (MQ=255)
                                               ccaacaTAGGGGAGCGATAATCCCGGTCATTGACCATAATGCCAGAGAAAATTTTTTTTTTCCGGGCGGATAATCCCTAAAAAAAAACCTCTGTGACAGTGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAata                                                                                                     <  2:289205/143‑1 (MQ=255)
                                                caacaTATAGGAGCGATAATCACGTCCATTACCCATAAGCCCAGAGAACTTGTTTTTTTTCCGGCAGGATATTCCTTAAAAAAAAAACTCTGGCCAAGAGAAATTACGGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGca                                                                                               <  1:369629/149‑1 (MQ=255)
                                                      atCGGAGCGATAATCACGGTCATTGCCCATAATGCAAGAGAAAATTTTTTTTTTTCTGGCGGATAATTCCTTAAAAAAAACCTCTGTGACAGTGAAATTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCa                                                                                          <  2:156697/150‑1 (MQ=255)
                                                        cGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCa                                                                                          >  2:283315/1‑148 (MQ=255)
                                                            gCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTgg                                                                                   >  1:990854/1‑151 (MQ=255)
                                                                 aaccccGGTCATTGACAATAATGCAAGAGAAATTTTTTTTTTTTCGGGGGGATAATTCCTAAAAAAAAAACTCTGTGACAGGGAAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCg                                                                                <  2:1018114/144‑1 (MQ=255)
                                                                 aaTCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGAt                                                                              >  1:536907/1‑151 (MQ=255)
                                                                  accACGGTCATTAACAATAATGCAAGAGAAATTTTTTTTTTTTCTGGCGGATAATTCCTTAATAAAAAACTCTGTGAAAGTGAAATAACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTc                                                                                 <  1:906936/145‑1 (MQ=255)
                                                                     aCGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGc                                                                          >  1:611601/1‑151 (MQ=255)
                                                                       gttCATTAACCATAATCCCAGAGAAATTTTTTTTTTTTCGGGGGGTTATTCCTTTAAAAAAAACCTTTGGAAAGGTGGAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCt                                                                         <  2:673893/148‑1 (MQ=255)
                                                                        gTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTa                                                                        >  2:84524/1‑150 (MQ=255)
                                                                           aTTGACCATAATGCCAGAGCAAATGTTTTTTTTTCGGGCGAATAATTCCTTAAAAAAAAACTCTGTGACAGGGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTaca                                                                      <  2:663667/149‑1 (MQ=255)
                                                                                  aTAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATg                                                              >  2:596508/1‑150 (MQ=255)
                                                                                  aTAATGCAAGAGAAAATGTTTTTTTTTCTGGCGGATAATTCTTAAAAAATAACCTCTGTGACAGTGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATg                                                              <  2:1250/150‑1 (MQ=255)
                                                                                    aaTGCCAGAGAAATTTTTTTTTTTTCTGGCGGATAATTCCTTAATAAAAAACTTTGTGACAGGGAAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACAtt                                                                  <  2:297244/144‑1 (MQ=255)
                                                                                     aTGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAGCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGa                                                             >  2:254774/1‑148 (MQ=255)
                                                                                      tGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGAc                                                         >  2:778544/1‑151 (MQ=255)
                                                                                            aaaaattttttttttttTGGGCGAATAATTCTTAAAAAAAAACCTCTGTGACAGTGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCg                                                     <  2:708377/138‑1 (MQ=255)
                                                                                            aaaaaaTTTTTTTTTTTCTGGCGTATAATTCCTAAAAAAAAACCTCTTTGACAGTAAATTTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaa                                                   <  1:925080/148‑1 (MQ=255)
                                                                                               aaaTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaa                                                 >  2:826763/1‑150 (MQ=255)
                                                                                                  tGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaaaa                                              >  2:118497/1‑150 (MQ=255)
                                                                                                       ttttttGGGGCGAATATTTCCTAAAAAAAAACCTCTGTAAAAGTAAAATTACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGa                                         <  1:877448/150‑1 (MQ=255)
                                                                                                       ttttttCTGGCGAATAATTCCTAAAAAATAACCTCTGGGACAGAGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGa                                         <  1:619410/150‑1 (MQ=255)
                                                                                                       ttttttCTGGCGAATAATTCCTAAAAAAAAAACTTTGTAACAGGGAAATAAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTg                                          <  1:13274/149‑1 (MQ=255)
                                                                                                        tttttCGGGGGAATAATCCTTAAAAAAAAACCTCGGTGACAGGGAAATAACGGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGAc                                        <  1:579260/150‑1 (MQ=255)
                                                                                                        tttttCGGGCGGATAATTCCTTAATAATAACCTCTGTGACAGTGAAATAAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGAc                                        <  2:359807/150‑1 (MQ=255)
                                                                                                            tCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGaa                                    >  1:687461/1‑150 (MQ=255)
                                                                                                            tCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGaa                                    >  2:966653/1‑150 (MQ=255)
                                                                                                               ggCGGATAATTCCTAAAAAAAAAACTATGTGAAAGTGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAg                                  <  1:236830/149‑1 (MQ=255)
                                                                                                                 cGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTaa                               >  2:695519/1‑150 (MQ=255)
                                                                                                                       aaTTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaata                          >  2:450039/1‑150 (MQ=255)
                                                                                                                        aTTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaataat                        >  2:544267/1‑151 (MQ=255)
                                                                                                                         ttCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATc                       >  2:541030/1‑151 (MQ=255)
                                                                                                                           ccTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCtt                     >  1:408265/1‑151 (MQ=255)
                                                                                                                            cTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCCAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCtt                     >  1:802333/1‑150 (MQ=255)
                                                                                                                             ttAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTa                    >  2:520929/1‑150 (MQ=255)
                                                                                                                                aaaaaaaaaCTCTGGAAAAGTGAAATTACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaata                          <  1:345368/136‑1 (MQ=255)
                                                                                                                                 aaaaaaaaCTCTGTGACAGTAAAATAAGCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaataa                         <  1:874543/137‑1 (MQ=255)
                                                                                                                                      aaaCTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCt            >  2:927934/1‑150 (MQ=255)
                                                                                                                                              gtgACAGTGAAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTc        <  2:216199/147‑1 (MQ=255)
                                                                                                                                              gtgACAGTGAAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTtg    <  2:907632/151‑1 (MQ=255)
                                                                                                                                              gagACAGTGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTAtt         <  1:734216/144‑1 (MQ=255)
                                                                                                                                                gACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTtgtg  >  2:79365/1‑151 (MQ=255)
                                                                                                                                                gACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTtgtg  >  2:320762/1‑151 (MQ=255)
                                                                                                                                                cactgTGGAATTACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTtgtg  <  2:811574/147‑1 (MQ=255)
                                                                                                                                                   aGTGAAATTAAGGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCttt     <  2:485241/145‑1 (MQ=255)
                                                                                                                                                       |                                                                                                                                                
ATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTG  >  NC_000913/2481656‑2481947

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: