Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG51.2% 31.5 / 71.2 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 = 7.10e-07

AACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCT  >  NC_000913/599427‑599726
                                                                                                                                                     |                                                                                                                                                      
aaCGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGgttg                                                                                                                                                       <  2:61487/151‑1 (MQ=255)
   gCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggggg                                                                                                                                                    >  1:321556/1‑149 (MQ=255)
      cgacgaCTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGgggggggggggg                                                                                                                                                    >  2:494879/1‑146 (MQ=255)
        acgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggggggttc                                                                                                                                                >  1:257357/1‑144 (MQ=255)
         cgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTcc                                                                                                                                                >  1:417167/1‑149 (MQ=255)
           acTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCg                                                                                                                                            <  2:443842/151‑1 (MQ=255)
                 aTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATcc                                                                                                                                        >  2:175971/1‑149 (MQ=255)
                       tCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGATCCGGCaaaa                                                                                                                                 >  1:95727/1‑150 (MQ=255)
                       tCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCcaaa                                                                                                                                 >  1:248488/1‑150 (MQ=255)
                                  gCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCCGCGCTCCGGCCAAAACGCCCggg                                                                                                                        >  2:847462/1‑146 (MQ=255)
                                   ccAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGTATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGt                                                                                                                    <  2:111723/151‑1 (MQ=255)
                                    cAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTg                                                                                                                   <  1:347135/151‑1 (MQ=255)
                                      gTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGGACCGCGATCCGGCGAAAAAGCCCGAGAAGTg                                                                                                                   >  2:202767/1‑149 (MQ=255)
                                         aaaaTGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAACCTGCGAACCGGCAAAAACACCCGAGAAggg                                                                                                                   >  1:751192/1‑144 (MQ=255)
                                             tGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAACCCCCGAGAAGGGATCgccgcc                                                                                                          >  1:311447/1‑151 (MQ=255)
                                              ggCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCgccgcc                                                                                                          <  2:161909/150‑1 (MQ=255)
                                               gCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGt                                                                                                        <  1:488934/151‑1 (MQ=255)
                                                       gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACa                                                                                                <  1:313840/151‑1 (MQ=255)
                                                       gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGGCCTTCGGCCCCGCGAAAAAGCCCGAGGAGGGATCGgccccgggga                                                                                                     >  2:548700/1‑142 (MQ=255)
                                                           aTCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGTCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCAAAAACGCCCGAGCAGTGATCGCCGCCGCGAAGGACaaa                                                                                              >  1:11882/1‑149 (MQ=255)
                                                               gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGGGGAGGACAAACTGGa                                                                                         >  1:236111/1‑150 (MQ=255)
                                                                 gcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAAAGCCCCAGGAGGGATCGCCGCCGGGAAGGACAAACTGGaaa                                                                                       >  1:407486/1‑150 (MQ=255)
                                                                 gcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTCCGGTTCGGGAAAAACGCCCGGGGAGGGATCGCCGCCGGGAAGGGAAAACTGGgaa                                                                                       >  2:503402/1‑150 (MQ=255)
                                                                    aTGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCt                                                                                   <  1:839541/151‑1 (MQ=255)
                                                                    aTGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGGCCTGCGATCCGGCAAAAACGCCCGCGAAGGGGTTCCCGCCCTGGAGGACAAACTGGaaa                                                                                       >  2:384683/1‑147 (MQ=255)
                                                                    aTGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGGGAAGTGATCGCCGCCGGGAAGGAAAAACTGGAAACGc                                                                                    >  1:29249/1‑150 (MQ=255)
                                                                    aTGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGCGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAAAGc                                                                                    >  1:519697/1‑150 (MQ=255)
                                                                      gTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGa                                                                                 <  1:290720/151‑1 (MQ=255)
                                                                                 ccAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCCAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCt                                                                       >  1:329719/1‑150 (MQ=255)
                                                                                            cGGATATTCGCGGGGGCATTTAGGAAATAAACGGGGAAGGGAAAGTGGCGGGCGGGGTGGTGTTCCTGCGATCCGGCAAAAACTCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGt                                                           <  1:724695/151‑1 (MQ=255)
                                                                                            cGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCCAAAAAGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAAAGCTGAAAAATAGTCTGCCGGGAGGCgg                                                           >  2:511784/1‑150 (MQ=255)
                                                                                             ggAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTg                                                          <  1:284739/151‑1 (MQ=255)
                                                                                             ggAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTg                                                          <  1:403480/151‑1 (MQ=255)
                                                                                                     gcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGt                                                  <  2:757961/151‑1 (MQ=255)
                                                                                                     gcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATTCTGCGATCCGGCAAAAACGCCCGAGAAGGGAACGCCGCCGGGAAGGACAAACTGGAAAAGCTGAAAAGGAGGCTGCCGGGAGGCgggggg                                                       >  1:307277/1‑144 (MQ=255)
                                                                                                               tGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAGAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATa                                         <  2:872406/150‑1 (MQ=255)
                                                                                                               tGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATa                                         <  1:501002/150‑1 (MQ=255)
                                                                                                                  cGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGAt                                     <  1:532098/151‑1 (MQ=255)
                                                                                                                        aaaCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcag                                <  2:806546/150‑1 (MQ=255)
                                                                                                                        aaaCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcag                                <  2:460200/150‑1 (MQ=255)
                                                                                                                         accGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGTTCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagcc                              <  2:9855/149‑1 (MQ=255)
                                                                                                                             gcgaaggcgaagTGGCGGGCGGGGGGGGGGTTCTGCGATCCGGCAAAAACGCCCGGGAAGGGGTCGCCGCCGTGAAGGGCAAACTGGAAACGCTGAAAAGTAGTCTGCCGGGAGGGGGGGGGATAGTTACAACATACGATCGcagcc                              >  2:678447/1‑147 (MQ=255)
                                                                                                                                aaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCAt                       <  1:340812/151‑1 (MQ=255)
                                                                                                                                  ggcgaagTGGCGGGCGGGGGGGGGATCCTTCGATCCGGCAAAAAAGCCCGAGAAGTGATAGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTTCCGGAAGGCGGGGAGATAGTTACAACAAAAGATTGCAGCCCACTCAtt                      >  1:755527/1‑150 (MQ=255)
                                                                                                                                    cgaagTGGCGGGGGGGGGGGGGGTACTTCGATCCGGCAAAAAAGCCCGGGGAGAGGTAGCCGCCGGGGAGGACAAACTGGAAACGCTGAAAAGGAGACTGCCGGGAGGCGTGGAGAGAGTTACAACATACGAGAGCAGCGCGCTCATTGAc                   >  2:658437/1‑151 (MQ=255)
                                                                                                                                      aagTGGCGGGCGGGGTGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGGGATAGTTACAACATACGATCGCAGCCAGCTCATTGAcc                  >  1:552566/1‑150 (MQ=255)
                                                                                                                                             gggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATc          >  1:454697/1‑151 (MQ=255)
                                                                                                                                                   ggtggtGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAc    <  1:720814/151‑1 (MQ=255)
                                                                                                                                                     tggtgATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCt  >  1:95733/1‑151 (MQ=255)
                                                                                                                                                     |                                                                                                                                                      
AACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAACCT  >  NC_000913/599427‑599726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑