Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5790TG46.5% 60.9 / 11.6 43V289G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (4/19);  new base G (20/0);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 1.65e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCA  >  NC_000913/599438‑599728
                                                                                                                                             |                                                                                                                                                     
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)
                                                                                                                                            gtgATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCa  <  1:441641/151‑1 (MQ=255)
                                                                                                                                             tgATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTc   >  1:276319/1‑149 (MQ=255)
                                                                                                                                             |                                                                                                                                                     
ACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCTCA  >  NC_000913/599438‑599728

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: ‑