Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG47.9% 59.9 / 18.2 48V288G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (5/20);  new base G (23/0);  total (28/20)
Fisher's exact test for biased strand distribution p-value = 3.28e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAC  >  NC_000913/599428‑599724
                                                                                                                                                    |                                                                                                                                                    
aCGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggg                                                                                                                                                    >  2:959382/1‑151 (MQ=255)
             ttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGATCCCGCGAt                                                                                                                                        >  2:968705/1‑150 (MQ=255)
             ttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGTTACTTCGATc                                                                                                                                       >  1:259332/1‑151 (MQ=255)
               aaTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCg                                                                                                                                     <  1:498850/151‑1 (MQ=255)
               aaTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTcc                                                                                                                                      >  1:408329/1‑150 (MQ=255)
                  cacaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGc                                                                                                                                   <  2:923915/150‑1 (MQ=255)
                    caTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCCGCGATCCGGCaa                                                                                                                                 >  2:277254/1‑150 (MQ=255)
                       cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaaaaa                                                                                                                              <  2:844862/150‑1 (MQ=255)
                       cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAAc                                                                                                                             <  1:183486/151‑1 (MQ=255)
                          tttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTCCGGTCCGGCcaaaa                                                                                                                              >  2:327513/1‑147 (MQ=255)
                             aaaaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCCAAAAAGccc                                                                                                                         >  1:851193/1‑149 (MQ=255)
                                aGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGGTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATTCTGCGATCCGGCATAAACGCCCgaga                                                                                                                     <  1:631372/150‑1 (MQ=255)
                                 gCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAACGccc                                                                                                                         >  1:897032/1‑145 (MQ=255)
                                   cAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTg                                                                                                                 <  1:619428/151‑1 (MQ=255)
                                    aGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGa                                                                                                                <  2:45762/151‑1 (MQ=255)
                                      tGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGGGGTCGTCCGGTCCGGCAAAAAAGCCCGAGaa                                                                                                                    >  1:151223/1‑145 (MQ=255)
                                         aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATcgcc                                                                                                           <  1:101606/151‑1 (MQ=255)
                                         aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCCGCCAAAACGCCCGGGGAGt                                                                                                                  >  2:265853/1‑144 (MQ=255)
                                             ggCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGccgccg                                                                                                       >  1:63156/1‑151 (MQ=255)
                                                     cGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGAGCCTGTCCTCCGCCAAAAACGCACCCGGAGGGATGGCCGCCGTGCAgg                                                                                                 >  1:140908/1‑149 (MQ=255)
                                                           tCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCCGCAAAAACGCCCGGGAAGGGATCGCCGCCGTGTAGGGCaaa                                                                                            >  2:947809/1‑148 (MQ=255)
                                                              gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACt                                                                                          <  1:296439/147‑1 (MQ=255)
                                                              gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACt                                                                                          <  2:509135/147‑1 (MQ=255)
                                                                 cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTTTGATCCGGCAAAAACGCCCCCGAAATGATCGCCGCCGTGAAGGACAAACTGGaaa                                                                                     >  1:773698/1‑149 (MQ=255)
                                                                         cGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGTGATCGCCGCCGGGAAGGACAAAATGGGAACGCTGaaa                                                                             >  1:278332/1‑149 (MQ=255)
                                                                         cGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGGCCTGCGATCCCGCAAAAACGCCCGAGAAGGGATTGCCGCCGTGAAGGGCAAAATGGGAACGCTGaaaa                                                                            >  2:901335/1‑150 (MQ=255)
                                                                           aaGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGATCCCGCGGTCCCGCCAAAAAGCCCGAGGAGGGATCGCCGCCGTGGAGGACAAAATGGGAACGCTGgaaa                                                                            >  2:734092/1‑148 (MQ=255)
                                                                            aGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAACCTGCGATCCGGCCAAAAAGCCCGAGAAGTGATCGCCGCCGCGAAGGACAAAATGGAAACGCTGAAAag                                                                           >  2:651132/1‑148 (MQ=255)
                                                                               tCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGGAACGCTGAAAAGTAGTCt                                                                     >  1:687913/1‑151 (MQ=255)
                                                                                 cAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGc                                                                   <  2:471410/151‑1 (MQ=255)
                                                                                            ggAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGt                                                         <  2:509385/150‑1 (MQ=255)
                                                                                              agaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGga                                                      <  1:391757/151‑1 (MQ=255)
                                                                                               gaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGga                                                      <  1:888815/150‑1 (MQ=255)
                                                                                                      cGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGTGGTCCTGCGATCCGGGAAAAACGCCCGGGAAGGGATCGCCGCCGGGAAGGACAAACTGGAAACGCGGAAAAGTAGCATCCCGGAAgggggggggg                                                    >  2:159725/1‑137 (MQ=255)
                                                                                                         ggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTacaa                                           <  1:368261/151‑1 (MQ=255)
                                                                                                         ggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTacaa                                           <  1:246701/151‑1 (MQ=255)
                                                                                                          gCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGCGAAGGACAAAATGGGAACGCTGAAAAGTAGTCTGCCGGGAGGCGGGGGGGTAGTTacaa                                           >  1:690020/1‑150 (MQ=255)
                                                                                                               gCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGAACCGGGAAAAAAGACCCCGAAGTGATCGCCGCCGTGCAGGGCAAACTGGGAACGCCGAAAAGAAGTCTACCGGGAGGGGGGGAGATAGTTACAACATa                                       >  2:840978/1‑149 (MQ=255)
                                                                                                                  gAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCCTCGCTCCGGCAAAAAACCCCGCGCAGAGGTCGCCGGCGCGGAGGACAAACTGGAAAAGCTGAAAAGTAGTCCCGCGGGAAGCGTGGGGATAGATTCAACATACGa                                    >  2:554918/1‑149 (MQ=255)
                                                                                                                   aaCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGAACCGGCAAAAACGCCCGAGGAGTGATCGCCGCCGTGAAGGACAAAATGGAAACGCTGGAAAGGAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATc                                  >  2:145947/1‑150 (MQ=255)
                                                                                                                   aaCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCCGCGATCCGGCAAAAACGCCCGAGGAGTGATCGCCGCCGCGAAGGACAAACTGGGAACGCTGGAAAGTAGTCTGCCCGAAGGCGTGGGGATAGTTACAACATa                                       >  2:749199/1‑145 (MQ=255)
                                                                                                                              gaaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTc                       <  2:332182/150‑1 (MQ=255)
                                                                                                                               aaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCAt                     <  2:515932/151‑1 (MQ=255)
                                                                                                                                aggcgaagTGGCGGGCGGGGGGGGGGTACCGCCGTCCGGCCAAAAAGCCCGAGGGGGGGTCGCCGCCGTGGAGGACAAACTGGAAACGCCGTAAAGTAGGCTCCCGGGGGGGGCGGGGGTAGTTAAAACAAACGGTCCCACCCAAGTCAtt                    >  2:724613/1‑151 (MQ=255)
                                                                                                                                      agTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACcgc              <  2:497590/151‑1 (MQ=255)
                                                                                                                                            gggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCTGAGAAGCGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGAAGTCTGCCGGAAGGAGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCGATc        >  2:56229/1‑151 (MQ=255)
                                                                                                                                               cgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAc     <  2:408322/151‑1 (MQ=255)
                                                                                                                                                ggggTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAc     >  2:489176/1‑150 (MQ=255)
                                                                                                                                                ggggTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAc     >  1:295829/1‑150 (MQ=255)
                                                                                                                                                  ggtggtGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAc  <  2:477808/151‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                    
ACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAC  >  NC_000913/599428‑599724

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑