Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG53.1% 34.4 / 79.2 49V288G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (2/21);  new base G (26/0);  total (28/21)
Fisher's exact test for biased strand distribution p-value = 6.48e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.19e-07

AAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCG  >  NC_000913/599426‑599719
                                                                                                                                                      |                                                                                                                                               
aaaCGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGggt                                                                                                                                                 <  1:200117/151‑1 (MQ=255)
 aaCGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGggtg                                                                                                                                                <  1:716868/151‑1 (MQ=255)
     cTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGggggggggg                                                                                                                                            >  2:387941/1‑148 (MQ=255)
     cTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggggg                                                                                                                                             >  2:262756/1‑148 (MQ=255)
       cgacgaCTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATc                                                                                                                                          <  2:963032/151‑1 (MQ=255)
          cgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTg                                                                                                                                       <  1:296671/151‑1 (MQ=255)
          cgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTcc                                                                                                                                         >  2:499417/1‑149 (MQ=255)
           gacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGTGGTcc                                                                                                                                         >  2:438736/1‑148 (MQ=255)
              tttAATCACATCGTTTTAAAAGCAAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCTGGCGGGGTGGTGGTCCt                                                                                                                                        >  2:673461/1‑146 (MQ=255)
                    cacaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCa                                                                                                                             <  2:639131/151‑1 (MQ=255)
                     acaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGAtac                                                                                                                                 >  2:664135/1‑144 (MQ=255)
                        tCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGGTCTGGGATCCGGGaaaa                                                                                                                          >  2:698919/1‑150 (MQ=255)
                             ttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGATCCTGCGGTCCGGCAAAAACGccc                                                                                                                    >  1:330638/1‑151 (MQ=255)
                                 aaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGCTCCGGCAAAAACGCCCgag                                                                                                                 >  2:743995/1‑150 (MQ=255)
                                    ccAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGt                                                                                                             <  2:1030564/151‑1 (MQ=255)
                                     cAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAAAGCCCCAGAAGTg                                                                                                            >  2:707360/1‑151 (MQ=255)
                                       gTGAAAATGGCGTGCCCGTTTATCTGCGCAATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGAt                                                                                                          <  1:815319/151‑1 (MQ=255)
                                         gAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATc                                                                                                         <  1:707804/150‑1 (MQ=255)
                                             aTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAGTCCGCGGTCCCGCAAAAACGCCCGAGAAgggggcgcc                                                                                                      >  2:943265/1‑141 (MQ=255)
                                               ggCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCgccgcc                                                                                                   <  1:859263/150‑1 (MQ=255)
                                                 cGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGt                                                                                                 >  1:387420/1‑150 (MQ=255)
                                                  gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCgccgcc                                                                                                   >  1:719034/1‑147 (MQ=255)
                                                       cGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGTGATCCCTCGATCCGGCAAAAACGCCCGGGAAGTGGTCGCCGCCGTGTAgg                                                                                            >  1:812105/1‑149 (MQ=255)
                                                        gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGTGAAgg                                                                                            >  1:729001/1‑148 (MQ=255)
                                                              cTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAAAGCCCGAGAAGTGATCGCCGCCGGGAAGGACAAACTgg                                                                                   >  1:755295/1‑151 (MQ=255)
                                                                gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTg                                                                                    <  2:580828/148‑1 (MQ=255)
                                                                      tGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGGTCGCCGCCGGGAAGGGCAAAATGGaaaaggcg                                                                           >  2:187978/1‑146 (MQ=255)
                                                                        ttGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGa                                                                          <  1:223734/150‑1 (MQ=255)
                                                                          gCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGaaaa                                                                       <  1:634711/151‑1 (MQ=255)
                                                                            gAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCCGCGATCCGGCAAAAAAGCCCCGGAAGTGATCGCCGCCGGGAAGGGCAAAATGGAAACGCTGaaa                                                                        >  2:655715/1‑148 (MQ=255)
                                                                            gAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCCCGGGGGGGCACCCGCCGTCCGGGCAAAATACCCGCGAAAGGAGCGCGGCCGTGAAGGGAAAACAGGgaaagatggca                                                                        >  2:343078/1‑140 (MQ=255)
                                                                             aaGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCCATCCGGCAAAAACCGCCGCGAAGGGATAGCCGCCGTTAAGGGCAAAAAGGaa                                                                                 >  1:424848/1‑138 (MQ=255)
                                                                             aaGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCCGCAAAAAAGCCCGAGAAGTGATCGCCCCCGTGAAGGGCAAACTGGAAAAGCCGgaaa                                                                       >  2:562816/1‑148 (MQ=255)
                                                                                  ccAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCt                                                                <  1:744005/150‑1 (MQ=255)
                                                                                   cAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGc                                                              <  1:10483/151‑1 (MQ=255)
                                                                                          gCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAgg                                                       <  2:606650/151‑1 (MQ=255)
                                                                                            ccGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCg                                                     >  1:939059/1‑151 (MQ=255)
                                                                                             cGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAAAGCTGAAAAGGAGTCTGCCGGGAgggg                                                     >  2:185046/1‑148 (MQ=255)
                                                                                                    gcgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGAt                                              <  2:176218/150‑1 (MQ=255)
                                                                                                      gcCGGGGCATTGCCGTACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGt                                           <  2:967854/151‑1 (MQ=255)
                                                                                                           ggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTacaa                                      <  2:950216/151‑1 (MQ=255)
                                                                                                            gCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGGGGAGATAGTTacaa                                      >  1:780790/1‑150 (MQ=255)
                                                                                                              aTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGCGAAGGGCAAAAAGGAAAAGCTGAAAAGAAGTCTGCCGGGAGGCGTGGGGATAGTTacaaca                                    >  2:349095/1‑150 (MQ=255)
                                                                                                              aTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGGAACGCTGAAAAGTAGTCTGCCGGAAGGCGGGGGGATAGTTacaaca                                    >  1:418338/1‑150 (MQ=255)
                                                                                                                tGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGAGACGGCAAAAAAGCCCGAGGAGGGATAGGCGGCGGGGAGGACAAAATGGGAAAGCTGAAAAGGAGGCTGCCGGGAGGCGGGGGGGTAGTTACAACATa                                  >  2:688001/1‑150 (MQ=255)
                                                                                                                 gCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACg                                <  2:50421/151‑1 (MQ=255)
                                                                                                                      aCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGc                           >  1:527882/1‑151 (MQ=255)
                                                                                                                         aaaCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcag                         <  1:719208/150‑1 (MQ=255)
                                                                                                                         aaaCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGca                          <  2:582530/149‑1 (MQ=255)
                                                                                                                           aCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagcca                      <  1:605880/151‑1 (MQ=255)
                                                                                                                             ggcgaaggcgaaGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGAGATCGCCGCCGGGAAGGACAAACTGGAAACGCTGAAAAGGAGTCTGTCGGAAGGGGTGGGGATAGTTATAACATACGa                               >  1:285710/1‑140 (MQ=255)
                                                                                                                                              gggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATc   <  2:387417/151‑1 (MQ=255)
                                                                                                                                               ggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCg  >  2:329268/1‑151 (MQ=255)
                                                                                                                                                      |                                                                                                                                               
AAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCG  >  NC_000913/599426‑599719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑