Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG55.8% 34.3 / 66.8 43V288G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (3/16);  new base G (24/0);  total (27/16)
Fisher's exact test for biased strand distribution p-value = 3.65e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.82e-08

CGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAC  >  NC_000913/599429‑599721
                                                                                                                                                   |                                                                                                                                                 
cGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggg                                                                                                                                                 >  1:319000/1‑150 (MQ=255)
     gacgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGggggggggg                                                                                                                                              >  1:755193/1‑145 (MQ=255)
        gacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTcc                                                                                                                                           >  2:878690/1‑148 (MQ=255)
            ttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGa                                                                                                                                      <  1:288696/149‑1 (MQ=255)
            ttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGa                                                                                                                                      <  1:749081/149‑1 (MQ=255)
            ttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCggt                                                                                                                                     >  2:729162/1‑148 (MQ=255)
             tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGGCCTGCGGTcc                                                                                                                                   >  1:700715/1‑151 (MQ=255)
                      cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCaaaaa                                                                                                                           >  1:110925/1‑150 (MQ=255)
                       gTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACg                                                                                                                         <  2:958934/151‑1 (MQ=255)
                         tttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGc                                                                                                                        <  1:605837/150‑1 (MQ=255)
                         tttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCaaaaaaacc                                                                                                                       >  2:566081/1‑147 (MQ=255)
                          ttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGGTCCGGGAAAAAAGccc                                                                                                                      >  1:328645/1‑151 (MQ=255)
                          ttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGGCCCGCGGTCCCGCAAAAAAGccc                                                                                                                      >  1:944822/1‑151 (MQ=255)
                           tAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGTGTTCCCGCGATACGGcccaaa                                                                                                                           >  1:745296/1‑140 (MQ=255)
                                gCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAg                                                                                                                <  1:870662/151‑1 (MQ=255)
                                   aGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGa                                                                                                             <  1:632675/151‑1 (MQ=255)
                                      gAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCAAAAAAGCCCGGGAAggg                                                                                                              >  2:303890/1‑145 (MQ=255)
                                        aaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTTCTGCCATTCAGCGAAAAAGTCCcagaggagaagg                                                                                                          >  1:29549/1‑141 (MQ=255)
                                                 gCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGaa                                                                                                <  2:319006/150‑1 (MQ=255)
                                                  cccGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAgg                                                                                              <  1:878672/151‑1 (MQ=255)
                                                             gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTg                                                                                      <  2:699457/148‑1 (MQ=255)
                                                                cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCCCCGTGAAGGGCAAACTGGaaa                                                                                  >  2:775442/1‑149 (MQ=255)
                                                                   tGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCCCCGAACCGGCAAAAACGCCCCAGAAGGGATCGCCGCCGTGGAGGACTAACCGGGAAAGCt                                                                              >  1:839136/1‑150 (MQ=255)
                                                                   tGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAGGGCAAACTGGAAACGCTg                                                                             >  2:231836/1‑151 (MQ=255)
                                                                     ttGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTg                                                                             >  2:674444/1‑149 (MQ=255)
                                                                          aaGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGaaaa                                                                         >  2:334369/1‑148 (MQ=255)
                                                                               ccAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTg                                                                 <  1:268113/151‑1 (MQ=255)
                                                                                      ggCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGAACCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGTGAAGGAAAAAATGGAAAAACCGGAAAGGAGTCTGCCgg                                                             >  1:726307/1‑148 (MQ=255)
                                                                                        cccGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGTGGAGGACAAACTGGAAAAGCTGAAAAGTAGACTGCCGGGAgg                                                         >  1:417276/1‑150 (MQ=255)
                                                                                          cGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTTCGGTCCCGCAAAAACGCCCCGGAAGTGATCGCCGCCGCGGAGGACCAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAgg                                                         >  1:393525/1‑148 (MQ=255)
                                                                                                       gggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTaca                                         <  2:328652/151‑1 (MQ=255)
                                                                                                           aTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGAACCACCGGACCGGCGAAAACGACCGGAAAGCGGTCGGCGCCGGGAAGGGCAAAACGGAAAAGCTTCAAAGGAATATGCCCGGAGGGGGGgagacaaattcaa                                        >  1:951626/1‑139 (MQ=255)
                                                                                                           aTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGGGAAGGGCAAAATGGAAACGCTGAAAAGGAGTCTGCCGGAAGGCGGGGGGATAGTTacaaaa                                      >  1:409487/1‑148 (MQ=255)
                                                                                                              gCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATAc                                   <  2:382496/150‑1 (MQ=255)
                                                                                                                  aaCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCg                              <  2:700731/151‑1 (MQ=255)
                                                                                                                  aaCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGGAAAAACGCCCGAGAAGGGATGGCCGCCGGGAAGGACAAACTGGAAACGCTGAAAAAAAGGCTGCCGGAAGGCGTGGGGATAGGTTAAAAAAACGATc                               >  2:576261/1‑150 (MQ=255)
                                                                                                                     tAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAAAGCTGAAAAATAGTCTGCCGGAAGGCGTGGGGATAGTTACAACATACGATCg                              >  2:932477/1‑148 (MQ=255)
                                                                                                                       aaCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagcc                         <  2:755212/151‑1 (MQ=255)
                                                                                                                        aCGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAGCCTGCGGTACGGCCAAAAAGCCCGGGAAGGGGTCGCCCCCGGGAAGGGCAAAATGGAAAAGCTCAAAAGTAGTCTGCCGGAAGGGGGGGGGAAAGATAAAACATAAGATCga                             >  1:685776/1‑145 (MQ=255)
                                                                                                                             gaaggcgaagTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAACGCCCGCGAAGTGATCGCCGCCGTGAAGGGCAAACTGGAAAAGCTGAAAAGAAGTCTGCCGGGAGGCGGGGGGATAGTTACAACAAACGATCGCGGCCAGCTc                    >  1:894724/1‑150 (MQ=255)
                                                                                                                                      gTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACcg            <  1:150273/149‑1 (MQ=255)
                                                                                                                                          cgggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCAt      >  1:649072/1‑151 (MQ=255)
                                                                                                                                          cgggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCAt      >  2:795299/1‑151 (MQ=255)
                                                                                                                                             gcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGa   <  1:402276/151‑1 (MQ=255)
                                                                                                                                              cgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAc  >  2:144094/1‑151 (MQ=255)
                                                                                                                                                   |                                                                                                                                                 
CGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAC  >  NC_000913/599429‑599721

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑