Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913599,5760TG52.3% 48.5 / 75.3 45V288G (GTG→GGG) cusAcopper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (2/19);  new base G (23/0);  total (26/19)
Fisher's exact test for biased strand distribution p-value = 1.49e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.57e-08

GCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAC  >  NC_000913/599430‑599721
                                                                                                                                                  |                                                                                                                                                  
gCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggggg                                                                                                                                                >  2:583350/1‑149 (MQ=255)
           ttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGgggggggggggggtgc                                                                                                                                            >  1:27207/1‑138 (MQ=255)
              aTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCgg                                                                                                                                  <  1:149884/151‑1 (MQ=255)
              aTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGGTcc                                                                                                                                    >  2:136487/1‑149 (MQ=255)
                cacaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCGTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTTCTGCGAACCgg                                                                                                                                  >  1:470937/1‑149 (MQ=255)
                   aTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTTCTGCGGTCCGGCaaa                                                                                                                              >  1:69429/1‑150 (MQ=255)
                     cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAAc                                                                                                                           <  2:790402/151‑1 (MQ=255)
                         ttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGcc                                                                                                                        <  1:339490/150‑1 (MQ=255)
                         ttAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGGTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATGCCGCGATCGCGCCAAAAAGcc                                                                                                                        >  2:173616/1‑150 (MQ=255)
                           aaaaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCAAAAACGccc                                                                                                                       >  2:698345/1‑149 (MQ=255)
                               gCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCGCGGAGATGCGGCGGGGTGTTGCCGAACTAAACGTCGAAGGCGAAGTGGCGGGCGGGGTGGTAATCCTGCGATCCGGCAAAAGCACCTGAGAAg                                                                                                                 <  1:338554/151‑1 (MQ=255)
                                ccAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGaa                                                                                                                  >  2:381996/1‑149 (MQ=255)
                                    tGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGGGCCGGCAAAAACGCCCGAGaa                                                                                                                  >  1:168948/1‑145 (MQ=255)
                                    tGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCCGCGAACCGGCAAAAACGCCCGCGAAGGGagg                                                                                                            >  1:668511/1‑149 (MQ=255)
                                          tGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAGACTTCGAGCCGGGCAAAACGCCCGAGAAGGGATtgcc                                                                                                         >  2:638875/1‑148 (MQ=255)
                                              gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGTGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGTGCTCCTGGGATACGGGGAAAAAACCCGAGAAGAGATCGGCG‑CAGTg                                                                                                  >  2:655694/1‑150 (MQ=255)
                                              gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGCTCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGt                                                                                                   >  2:45838/1‑149 (MQ=255)
                                                 cccGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGGGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAg                                                                                               <  1:246555/150‑1 (MQ=255)
                                                   cGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGAc                                                                                            <  1:401307/151‑1 (MQ=255)
                                                    gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTCCGGCAAAAACGCCCGAGAAGTGGTCGCCG‑CCGTGGAGGAc                                                                                            >  2:489762/1‑150 (MQ=255)
                                                      ttATCTGCGCGATGTTGAGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACaa                                                                                          <  2:331548/150‑1 (MQ=255)
                                                            gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTgg                                                                                     >  2:368156/1‑149 (MQ=255)
                                                              gcgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAAc                                                                                 <  1:25854/151‑1 (MQ=255)
                                                                   gTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTg                                                                             <  2:740763/150‑1 (MQ=255)
                                                                   gTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTg                                                                             <  1:4901/150‑1 (MQ=255)
                                                                     tGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCGTTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTCCTGCGGTCCGGCAAAAACGCCCGCGAAGTGATCGCCG‑CCGTGAAGGGCAAACTGGAAAAGGTGaa                                                                           >  2:263771/1‑150 (MQ=255)
                                                                      gCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGaaa                                                                          <  1:225121/150‑1 (MQ=255)
                                                                       cGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAag                                                                        <  2:347840/151‑1 (MQ=255)
                                                                        gAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAag                                                                        <  2:332055/150‑1 (MQ=255)
                                                                           ggTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCCAAAACGCCCGGGAAGGGATCGCCG‑CCGCGAAGGACAAACTGGAAACGCTGAAAaatagt                                                                    >  2:488399/1‑151 (MQ=255)
                                                                           ggTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCCAAAAAGCCCGAGAAGTGATCGCCG‑CCGTGGAGGGCAAACTGGAAACGCTGGAAagga                                                                      >  1:568204/1‑147 (MQ=255)
                                                                              ccAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTg                                                                 <  1:54667/151‑1 (MQ=255)
                                                                               cAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGGGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTg                                                                 >  2:92535/1‑150 (MQ=255)
                                                                                aGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGcc                                                               <  1:117140/151‑1 (MQ=255)
                                                                                          ggAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGCAGTGGCGGGCGGGGGGGGGATCCTGCGGTCCGGCAAAAACGCCCGAGGAGAGATCGCCGCCCGGGAAGG‑GAAACTGGGAAAGCTGTAAAGGAGTCTGGCGGAAggggcg                                                     >  1:405103/1‑147 (MQ=255)
                                                                                                 cgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAACGCCCGAGAAGGGATCGCCG‑CCGTGAAGGGCAAACTGGAAACGCTGAAAAGTAGTCTGCCGGGAGGCGTgggg                                                  >  2:35858/1‑145 (MQ=255)
                                                                                                   ccGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGGGAAGTGAGCGCCG‑CCGGGGAGGACAAACTGGGAAAGCTGAAAAGAAGTCTGGCGGAAGGCgggggg                                                  >  1:57757/1‑143 (MQ=255)
                                                                                                   ccGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAAAGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAAAAGTCTGCCGGAAGGCGGGGAGATAg                                              >  2:829199/1‑149 (MQ=255)
                                                                                                    cGGGTCATTGCCGAACTAAACGGAGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGATGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTa                                           <  2:647927/151‑1 (MQ=255)
                                                                                                               cGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGAt                                <  2:836608/151‑1 (MQ=255)
                                                                                                                        cGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAGCCTGCGAACCGGCAAAAACGCCCGAGAAGGGATCGCCG‑CCGGGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGGCGGGAGGGGGGGAGATAGTTAAAACATACGATCGcagcc                         >  2:151550/1‑149 (MQ=255)
                                                                                                                          gcgaaggcgaagTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCt                     <  2:742117/151‑1 (MQ=255)
                                                                                                                            gaaggcgaagTGGCGGGCGGGGGGGGGATCCTGCGATCCCGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGGAGGACAAACTGGAAACGCTGGAAAGTAGTCTGCCGGGAGGCGTGGGGATAGTTACAACATACGATCGCAGCCAGCTc                    >  1:209737/1‑150 (MQ=255)
                                                                                                                                         cgggcgggGTGGTGATCCTGCGATCCTGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAAAGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACAGACGATCGGAGCGAGCTCATTGACCGCGcc        >  1:714976/1‑149 (MQ=255)
                                                                                                                                         cgggcgggGAGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCAt      >  1:189342/1‑151 (MQ=255)
                                                                                                                                           ggcgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCg    <  2:25798/151‑1 (MQ=255)
                                                                                                                                             cgggGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAc  >  1:391428/1‑151 (MQ=255)
                                                                                                                                                  |                                                                                                                                                  
GCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGTGATCGCCG‑CCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAC  >  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: ‑