Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG53.2% 40.1 / 72.0 47V288G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (2/20);  new base G (25/0);  total (27/20)
Fisher's exact test for biased strand distribution p-value = 2.37e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.57e-07

TTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCT  >  NC_000913/599441‑599726
                                                                                                                                       |                                                                                                                                                      
ttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGAt                                                                                                                                          <  1:93562/150‑1 (MQ=255)
    tCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCtccggtccgg                                                                                                                                      >  2:435193/1‑150 (MQ=255)
      acaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaa                                                                                                                                   <  1:670698/151‑1 (MQ=255)
      acaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCaa                                                                                                                                   <  2:527598/151‑1 (MQ=255)
            ttttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTTCCGCGGGCCGGCcaaaa                                                                                                                                >  2:735302/1‑148 (MQ=255)
                  aaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCggg                                                                                                                        >  1:193698/1‑148 (MQ=255)
                       aGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGGAGGTCCAGATTGGCCAGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTg                                                                                                                   <  2:621802/150‑1 (MQ=255)
                         tGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGACTGTCCAGATTGGCCAGGAGATGCGCCGGGGCATTGCCGTACTAAACGGCGAAGGCGCAGTGGCGGGGGGGGGGGGGGTCCTTCGATCCCGCCAAAAAGCCCgcggagggtgt                                                                                                                >  2:400900/1‑141 (MQ=255)
                          gAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATc                                                                                                                <  1:735326/150‑1 (MQ=255)
                           aaaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTGCTGCGCTCCGGCAAAAACGCCCGAGAAGTGAt                                                                                                                 >  2:369531/1‑148 (MQ=255)
                                   gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCAAAAAAACCCGAGAAGGGATCGccgccg                                                                                                         >  1:526063/1‑148 (MQ=255)
                                     gCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGTCGAAGTGGCGGGGTGGGGGGCGGTTCTTTGATCCTGCCAAAACCGCCGAACAGTGGTTGCCGCCGCGaa                                                                                                     >  2:736244/1‑150 (MQ=255)
                                      cccGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAg                                                                                                    <  2:373420/150‑1 (MQ=255)
                                        cGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAAAGCCCGCGAAGGGATCGCCGCCGTGAAGGa                                                                                                  >  1:439058/1‑150 (MQ=255)
                                        cGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAgg                                                                                                   >  1:640223/1‑149 (MQ=255)
                                          tttATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGATGGCGAAGTGGCGGGCGGGGGGGGGATTCTGCGATTCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACa                                                                                                >  1:567298/1‑150 (MQ=255)
                                           ttATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGGTCCGGCAAAAACGCCCGAGAAGGGGTCGCCGCCGGGAAGGGCa                                                                                                >  2:943086/1‑149 (MQ=255)
                                             aTCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGCGAAGGACaaa                                                                                              >  2:478661/1‑149 (MQ=255)
                                                 gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTgg                                                                                          <  1:318514/149‑1 (MQ=255)
                                                 gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTgg                                                                                          <  1:905282/149‑1 (MQ=255)
                                                 gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGaa                                                                                        <  1:945966/151‑1 (MQ=255)
                                                    cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACg                                                                                     <  1:1004301/151‑1 (MQ=255)
                                                        gTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGa                                                                                 <  1:738339/151‑1 (MQ=255)
                                                        gTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTCCTGCGATCCGGCAAAAACGCCCGCGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAAAGc                                                                                    >  1:280867/1‑148 (MQ=255)
                                                         ttGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACAGGAAACGCTg                                                                                  >  1:361578/1‑149 (MQ=255)
                                                             gAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAagt                                                                            <  1:985390/151‑1 (MQ=255)
                                                                    cAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAAAGCCCGGGAAGTGAGCGCCGCCGGGAAGGACAAACTGGAAACGCTGAAAAAGATTCTGc                                                                     >  1:828365/1‑151 (MQ=255)
                                                                     aGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGGTCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGGAGTCTGcc                                                                    >  1:142991/1‑151 (MQ=255)
                                                                      gATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAAAGCTGAAAAGTAGTCTGcc                                                                    >  1:441209/1‑150 (MQ=255)
                                                                         tGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCACAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGGAAAGAAGGCTGCCgg                                                                  >  1:984390/1‑149 (MQ=255)
                                                                                  gaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGga                                                        <  1:612231/150‑1 (MQ=255)
                                                                                    tGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATTCCGCGATCCCGCCAAAACACCCGGGAAGGGAACCCCCCCCGGAAGGAAAAACTGGAAACGCAGGAAAAGAGGCTGCCGGAAGGCggtggg                                                       >  1:962803/1‑144 (MQ=255)
                                                                                     gcgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATa                                                    <  1:339986/151‑1 (MQ=255)
                                                                                         cGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGGGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGGGGGGATAGtt                                                 >  1:575321/1‑150 (MQ=255)
                                                                                          ggggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTa                                                <  2:828967/150‑1 (MQ=255)
                                                                                                  gCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGGGAAGGACAAACTGGAAACGCTGAAAAAGAGGCTGCCGGAAGGGGGGGAGATAGTTACAACATa                                         >  1:686185/1‑149 (MQ=255)
                                                                                                   ccGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCCGAAAAGTAGTCTGCCGGGAGGCGTGGAGGTAGGTACAAAATACg                                       >  1:150548/1‑150 (MQ=255)
                                                                                                   ccGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCCGCGAATCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAAATGGAAACGCAGAAAAGTAGGTTGGCGGGAGGGGTGGGGAGAGTTAAAACATACg                                       >  1:602305/1‑150 (MQ=255)
                                                                                                       aCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCCAAAACGCCCGAGGAGGGGTCGCCGCCGGGGAGGACAAACTGGAAACGCTGAAAAGGAGTCTGCCGGAAGGCGTGGGGATAGTTACAACATACGATCGc                                  >  2:491830/1‑151 (MQ=255)
                                                                                                        cTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGGGATCCTGGGATCCGGGAAAAAAGCACCAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGGGGAGATAGTTACAACATACGAt                                     >  1:460007/1‑147 (MQ=255)
                                                                                                          aaaCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGca                                 <  1:567742/149‑1 (MQ=255)
                                                                                                              ggcgaaggcgaaGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagccagc                           <  2:439006/151‑1 (MQ=255)
                                                                                                              ggcgaaggcgaaGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagccagc                           <  1:981783/151‑1 (MQ=255)
                                                                                                                 gaaggcgaagTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCATGAAGGACAAAATGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGGGGGGATAGTTACAACATACGATCGCAGCCAGCt                          >  1:975569/1‑149 (MQ=255)
                                                                                                                  aaggcgaagTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGGGGAGGGCAAAATGGAAAAGCTGAAAAGGAGTCTGCCGGGAGGCGGGGAGGTAGTTACAACATACGATCGCAGCCAGCTcct                       >  2:237570/1‑149 (MQ=255)
                                                                                                                    ggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTg                     <  1:664279/151‑1 (MQ=255)
                                                                                                                          gTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACcgcg               <  1:850287/151‑1 (MQ=255)
                                                                                                                                       tggtgATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCt  >  2:392572/1‑151 (MQ=255)
                                                                                                                                       |                                                                                                                                                      
TTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCT  >  NC_000913/599441‑599726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑