Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG48.8% 49.4 / 16.7 41V288G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (1/20);  new base G (20/0);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 8.17e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAC  >  NC_000913/599430‑599721
                                                                                                                                                   |                                                                                                                                                 
gCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑Ggggggggg                                                                                                                                               >  1:387179/1‑149 (MQ=255)
      cgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTg                                                                                                                                         <  1:293955/151‑1 (MQ=255)
         cTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGATcc                                                                                                                                           >  1:462083/1‑146 (MQ=255)
            tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGggg‑gggggggggggtccgcggttc                                                                                                                                   >  2:589529/1‑137 (MQ=255)
               tCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGG‑GGGGGGGGGGTCCCGCGATCCgg                                                                                                                                 >  2:851053/1‑150 (MQ=255)
                 acaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGGTTCTGCGATCCGGc                                                                                                                                >  1:813576/1‑149 (MQ=255)
                       ttttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGATCCTGCGCTCCCGCaaaaa                                                                                                                           >  1:805903/1‑148 (MQ=255)
                         ttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGcc                                                                                                                       <  1:23483/150‑1 (MQ=255)
                           aaaaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCga                                                                                                                    <  1:494891/151‑1 (MQ=255)
                           aaaaGCCAGTGAAAATGGCGTGCCCGTTCATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGACGTGCCGGGG‑GGGCGGGGGGTCACGCGATACGGCAAAAAc                                                                                                                          >  2:93728/1‑145 (MQ=255)
                            aaaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGGTCCTGCGAACCGGCAAAAAAGccc                                                                                                                      >  2:132851/1‑148 (MQ=255)
                                       aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGT‑GGGGTGGTGGGCTTGAGACTCGGTAAAAACGCCCCCGAAGTGATcg                                                                                                          >  1:520670/1‑149 (MQ=255)
                                       aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGGTTCCTCCAGCCGGCCAAAACACCCGCGaaagggac                                                                                                           >  2:181994/1‑142 (MQ=255)
                                        aaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGTTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATcgccg                                                                                                       <  2:305712/151‑1 (MQ=255)
                                        aaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATcgccg                                                                                                       <  1:330329/151‑1 (MQ=255)
                                        aaTGGCGTGCCCGGTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGGGGGCGGGGGGGGGGGTCCCGCGATCCGGCAAAAAC‑CCCgacagggggatg                                                                                                          >  1:93210/1‑138 (MQ=255)
                                            gCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGt                                                                                                   <  1:444582/151‑1 (MQ=255)
                                                    gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGAc                                                                                            <  1:95408/150‑1 (MQ=255)
                                                    gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGGTCCTGGGATCCGGCAAAAAAGGCCGGGAAGGGATCGgcgccggg                                                                                                  >  1:349496/1‑142 (MQ=255)
                                                    gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGGAGGGATCGCCGCCGGGAAgg                                                                                              >  1:243793/1‑148 (MQ=255)
                                                            gggcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTg                                                                                      <  2:855248/146‑1 (MQ=255)
                                                            gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTg                                                                                      <  2:10313/148‑1 (MQ=255)
                                                               cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGG‑GGGGGGGGGATCCTGCGATTCGGCAAAAACGCCCCAGAAGCGATCGCCCCCGGGAAGGaacaa                                                                                         >  2:711905/1‑138 (MQ=255)
                                                                 aTGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGG‑GGGGGGGGGATCCTGCGGTCCGGCAAAAACGGCCGGGAAAGGATCGCCGCCCTGAAGGACAAACAGGAAACGCt                                                                              >  1:508462/1‑151 (MQ=255)
                                                                         aaGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGGTCCTGCGACCCCGCCAAAACGCCCGGGAAGTGATCGCCGCCGTGGAGGACAAACTGGGAACGCTGaaaa                                                                         >  2:395706/1‑148 (MQ=255)
                                                                          aGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGG‑GGGGGGGGGGTCCTGCGGTGCGGCAAAAAAGCCCGCGAAGAGATTGCCGGCGGGGAGGACAAACTGGAAAAGCTGaaaa                                                                         >  2:828239/1‑147 (MQ=255)
                                                                                     ggCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGGGATCCCGCGATCCGGCAAAAACGCCCGGGAAGGGATCGCCCCCGTGGAGGACAAACTGGAAACGCTGAAAAGGAGTCTGCCgg                                                             >  1:720849/1‑148 (MQ=255)
                                                                                        ccGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCg                                                       <  1:368110/151‑1 (MQ=255)
                                                                                            agaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGG‑GGGGGGGGGAGCCTGCGATCCGGCAAAAACGCCCGCGAAGGGATCGGCGCCGGGGAGGACAAAATGGAAACGCTGAAAAGGAGTCTGCCGGGAGGCGTgg                                                    >  2:182686/1‑150 (MQ=255)
                                                                                                   ccGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGtt                                            <  1:589713/151‑1 (MQ=255)
                                                                                                     ggggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTac                                          <  2:678926/151‑1 (MQ=255)
                                                                                                     ggggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTac                                          <  1:668487/151‑1 (MQ=255)
                                                                                                       ggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTacaa                                        <  2:191592/151‑1 (MQ=255)
                                                                                                       ggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTacaa                                        <  2:54497/151‑1 (MQ=255)
                                                                                                          aTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACAt                                     <  2:58327/151‑1 (MQ=255)
                                                                                                          aTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGGGGTGATCCTGCGATCCCGCAAAAAAGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAAAGCTGAAAAGTAGTCTGCCGGAAGGCGTGGGGATAGTTacaa                                        >  1:78259/1‑148 (MQ=255)
                                                                                                                gAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGAt                                <  1:755674/150‑1 (MQ=255)
                                                                                                                         ggcgaaggcgaaGTGGCGGGC‑GGGGGGGTGGTCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAAATGGAAACGCTGAAAAGGAGTCTGCCGGGAGGGGTGGAGATAGTTACAACATACGATCGcagccagc                      >  1:328613/1‑151 (MQ=255)
                                                                                                                         ggcgaaggcgaaGTGGCGGGC‑GGGGGGGTGATCCTGCGATCCGGCCAAAACGCCCGAGAAGTGATTGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGGGGAGGTAGTTACAACATACGATCGcagccag                       >  1:15008/1‑150 (MQ=255)
                                                                                                                            gaaggcgaagTGGCGGGC‑GGGGGGGTGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGCGATCGCCGCCGTGAAGGGCAAACTGGGAACGCTGGAAAATAGTCTGCCGGGAGGCGGGGAGGTAGTTACAAAATACGAACGCAGCCAGGTc                    >  1:610743/1‑150 (MQ=255)
                                                                                                                               ggcgaagTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTg                <  1:704738/151‑1 (MQ=255)
                                                                                                                                   aagTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACcg            <  1:848199/151‑1 (MQ=255)
                                                                                                                                             c‑gggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAc  <  1:182048/151‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
GCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGC‑GGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAC  >  NC_000913/599430‑599721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑