Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG51.2% 44.0 / 72.0 43V288G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (2/19);  new base G (22/0);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 2.62e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.39e-07

CGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCG  >  NC_000913/599436‑599711
                                                                                                                                            |                                                                                                                                       
cgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggggggacc                                                                                                                                 >  1:48436/1‑143 (MQ=255)
  acTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCg                                                                                                                             <  1:474106/151‑1 (MQ=255)
   cTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCt                                                                                                                                >  2:270041/1‑147 (MQ=255)
      tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATcc                                                                                                                         >  1:47974/1‑151 (MQ=255)
       aaTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCg                                                                                                                        <  2:319041/151‑1 (MQ=255)
        aTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTGCTGCggtaccg                                                                                                                       >  2:5199/1‑145 (MQ=255)
           acaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCg                                                                                                                        >  2:608503/1‑147 (MQ=255)
            caTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaaa                                                                                                                   <  1:588066/151‑1 (MQ=255)
              tCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCgaaa                                                                                                                  >  2:441630/1‑150 (MQ=255)
               cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCCGCGATTCGGCaaaaa                                                                                                                 >  2:459324/1‑150 (MQ=255)
               cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCaaaaa                                                                                                                 >  1:438856/1‑150 (MQ=255)
                  tttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGc                                                                                                              <  1:473935/150‑1 (MQ=255)
                     aaaaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGccc                                                                                                            >  1:381771/1‑149 (MQ=255)
                         gCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCgag                                                                                                         >  1:366668/1‑148 (MQ=255)
                          ccAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCGGATTGGCCCGGAGATGCGCCGGGGCATTGTCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTGCTGGGGTCGGGCAAAAACGccccgg                                                                                                         >  1:103227/1‑144 (MQ=255)
                           cAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCCAAAACGCCCGAGAAg                                                                                                      >  1:135509/1‑149 (MQ=255)
                            aGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGa                                                                                                   <  2:95311/151‑1 (MQ=255)
                                 aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTACTGCGATCCGGCAAAAACGCCCGAGAAGTGATcgcc                                                                                              >  1:84840/1‑151 (MQ=255)
                                 aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGTGATcgcc                                                                                              >  1:382005/1‑151 (MQ=255)
                                   aTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGATCCTGGGATACGGCGAAAAAGGCCGAGGAGGGaaaggc                                                                                              >  1:233913/1‑144 (MQ=255)
                                         tGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGa                                                                                       <  1:106255/150‑1 (MQ=255)
                                          gCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGaa                                                                                      <  1:120829/150‑1 (MQ=255)
                                          gCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGaa                                                                                      <  1:127370/150‑1 (MQ=255)
                                           cccGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAgg                                                                                    <  2:513235/151‑1 (MQ=255)
                                            ccGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGa                                                                                   <  1:434258/151‑1 (MQ=255)
                                                      gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGGGAAGGACAAACTgg                                                                           >  1:615354/1‑149 (MQ=255)
                                                        gcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAAc                                                                       <  1:510313/151‑1 (MQ=255)
                                                             gTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCAGGGGGGTGATACCCCGGGACGGCGAAAAAGACCGCGACACGATTGCCGCCGATAAAGACAAACAGTGAACGCt                                                                    >  2:164700/1‑149 (MQ=255)
                                                              ttGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGTGGGGCTGCTTCGGCCCGGCGAAAACGCCCGAGAAATGATGGCCCCCCTGAAAGGCAAACTGGCAAAGCAGa                                                                  >  2:627102/1‑150 (MQ=255)
                                                                         cAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGATCCGGCAAAAAAGACCGAGAAGGGGATGCCGCCCGGGAAGACAAAATGGGAAAGGTGAAAagta                                                            >  2:453243/1‑145 (MQ=255)
                                                                         cAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGGCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGc                                                      <  1:56967/151‑1 (MQ=255)
                                                                                 cccGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCCAGAAGTGGTCGCCGCCGGGGAGGACAAACTGGGAACGCTGAAAAGAAGTCTGCCGGGAgg                                               >  2:254329/1‑150 (MQ=255)
                                                                                    ggAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCCGGGTGGGGATTCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGGGAAGGACAAACTGGAAAAGCTGAAAAGTAGTCTGCCGGAAGGCGTg                                           >  1:396796/1‑151 (MQ=255)
                                                                                       gaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGgag                                        <  1:289418/151‑1 (MQ=255)
                                                                                             ccGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGtt                                  <  1:279652/151‑1 (MQ=255)
                                                                                              cGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTa                                 <  2:108846/151‑1 (MQ=255)
                                                                                                        ccGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGa                       <  2:603582/151‑1 (MQ=255)
                                                                                                         cGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGGCAAACTGGAAACGCTGGAAAGTAGTCTGCCGGGAGGCGTGGGGATAGTTACAACATACGAt                      >  2:171693/1‑151 (MQ=255)
                                                                                                          gAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATc                     <  2:189875/151‑1 (MQ=255)
                                                                                                              tAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGTGATCCTGTGATCCGGGAAAAAAGCCCGAGAAAGGATCGCAGCCGTGAAGGACAAACTGGAAAAGCTGCAAAGTAGTCTGCCGGGAGGCGTGGAGATAGTTAATACAAACGATCga                   >  2:38546/1‑148 (MQ=255)
                                                                                                                    gcgaaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCt           <  2:434152/151‑1 (MQ=255)
                                                                                                                      gaaggcgaagTGGCGGGCGGGGGGGGGGTCCTGGGAACAGGGCAAAACGGCCGGGAAGGGATGGCCGCCGGGAAGGAAAAAATGGAAAAGCTGAAAAGGAGTCTGCCGGAGGGCGTGGAGATAGGTACAACATAAGATTGcagcca              >  2:43241/1‑146 (MQ=255)
                                                                                                                      gaaggcgaagTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAAAGCCCGGGAAGTGATCGCCGCCGGGAAGGACAAACTGGGAAAGCTGAAAAGTAGTCTGCCGGAAGGCGGGGGGATAGTTACAACATACGATCGcagcca              >  1:502723/1‑146 (MQ=255)
                                                                                                                             aagTGGCGGGCGGGGTGGTGATCCGGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACcg  <  2:264796/151‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                       
CGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCG  >  NC_000913/599436‑599711

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑