Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	44.7%	64.1 / 19.4	47	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (1/25);  new base G (21/0);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 1.75e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAC  >  NC_000913/599428‑599724                                                                                                                                                     |                                                                                                                                                      aCGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGggtgg                                                                                                                                                     <  2:476775/151‑1 (MQ=255)        acgacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGGTcc                                                                                                                                               >  2:701207/1‑150 (MQ=255)          gacTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCt                                                                                                                                              >  2:188760/1‑149 (MQ=255)           attttAATCACATCGTTTTAAAAGGCAGTGAGAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGc                                                                                                                                            <  1:250474/148‑1 (MQ=255)           acTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGgggggggggt                                                                                                                                                 >  1:156204/1‑141 (MQ=255)              ttAATCACATCGTTTGAAAAGGCAGAGAAAGTGGCGTGCCCGTTTATCTGCGCGGTGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGgggggggggggggtgccgcg                                                                                                                                           >  1:783001/1‑138 (MQ=255)               tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTcc                                                                                                                                       >  1:746775/1‑151 (MQ=255)                 aTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCgg                                                                                                                                     <  2:746706/151‑1 (MQ=255)                  tCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCgg                                                                                                                                     >  1:176600/1‑150 (MQ=255)                  tCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCgg                                                                                                                                     >  2:689307/1‑150 (MQ=255)                   cacaTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCa                                                                                                                                   <  2:160408/151‑1 (MQ=255)                      aTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTTCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAACCGGCGAAGGCGAAGTGGCGGGGCGGGTGGTGATTTTGCGactccg                                                                                                                                     >  2:627508/1‑141 (MQ=255)                        cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAAc                                                                                                                              <  1:336159/151‑1 (MQ=255)                              aaaaGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCga                                                                                                                        <  2:568650/151‑1 (MQ=255)                                 aGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGaa                                                                                                                     <  2:772771/151‑1 (MQ=255)                                     aGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGATCCGGCAAAAAAGCCCGGGAAggg                                                                                                                  >  2:542615/1‑148 (MQ=255)                                        gAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTGCGGTTCCGGAAAAAAGCCCgaggaggggtt                                                                                                               >  2:208120/1‑145 (MQ=255)                                                            tCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGGAAAAACGCCCGAGAAGG‑GATCGCCGCCGTGAAGGACAAACTg                                                                                         >  2:40915/1‑151 (MQ=255)                                                             cTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGCGAAGGACAAACTgg                                                                                        >  2:657477/1‑151 (MQ=255)                                                              tGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCCGCGGTCCGGCAAAAAAGCCCGCGAAGT‑GATCGCCCCCGTGGAGGGCAAACTgg                                                                                        >  1:622168/1‑150 (MQ=255)                                                               gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACt                                                                                          <  1:512421/147‑1 (MQ=255)                                                                  cgATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACg                                                                                   <  2:203891/151‑1 (MQ=255)                                                                       ttGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTg                                                                                <  2:77686/149‑1 (MQ=255)                                                                          cGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGaaaa                                                                            <  1:776627/150‑1 (MQ=255)                                                                             tggTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTGCGGTCCGGCAAAAAAACCCGAGAAGG‑GGTGGCCGCCGTGAAGGACAAACTGGAAAAGCTGaaaa                                                                            >  1:538704/2‑147 (MQ=255)                                                                                 ccAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTg                                                                    <  1:588825/151‑1 (MQ=255)                                                                                 ccAGAGTGGCCCGGAGATGCGCCGGGGCATGGCCGACCTAACCGGCGAAGGCGAAGTGCCGGGCGGGGTGGGGGTCCCGCGATCCGGCAAAAACGCCCAAGAAGT‑CATCTCCGCCGTGAAGTACAAACTGGAAACGCTGAAAagtag                                                                        <  1:740521/147‑1 (MQ=255)                                                                                    gATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGTGTCCTTCGGGCCGGCAAAAACGCCCCCGAAGTGGACCCCCCCCCGAAAGGCAAAACTGGAAAC‑CTGGAAagga                                                                         >  1:461488/1‑141 (MQ=255)                                                                                            cGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGt                                                         <  1:671883/151‑1 (MQ=255)                                                                                               agaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGga                                                      <  1:414476/151‑1 (MQ=255)                                                                                               agaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGga                                                      <  2:692593/151‑1 (MQ=255)                                                                                               agaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCCGGGGGGGGATCGTGCGTACCCGCCAAAACCCCCGCGAAGT‑GGTCGGCGCCGGGGAGGGCAAACTGGAAACGCCGAGAAGGGGGGTGCCGGGAgggggggg                                                      >  1:211158/1‑145 (MQ=255)                                                                                                gaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGga                                                      <  1:188813/150‑1 (MQ=255)                                                                                                   gcgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGAt                                                   <  2:293412/150‑1 (MQ=255)                                                                                                   gcgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGAt                                                   <  2:733008/150‑1 (MQ=255)                                                                                                    cgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGG‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGGAGGCgggggg                                                     >  2:77581/1‑145 (MQ=255)                                                                                                      ccGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGtt                                               <  1:689364/151‑1 (MQ=255)                                                                                                         gggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTaca                                            <  2:705523/151‑1 (MQ=255)                                                                                                          ggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGTTTCAGCAATTCGGCAAAAACGACCGGGAAGA‑GACAGCCGCCCTGCAGGACAAACTGGAAACGCTGAAAAGGAGACTTTCGGAAGGGGTGGAGGTAGTTaaa                                            >  2:768661/1‑148 (MQ=255)                                                                                                             aTTGCGGAACTAAACGGCGAAGGCGAGGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGGAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACAt                                        <  2:751055/151‑1 (MQ=255)                                                                                                                 ccGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGa                                    <  1:240606/151‑1 (MQ=255)                                                                                                                 ccGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAAATGGAAAAGCTGGAAAGGAGTCTGCCGGAAGGCGGGGGGGTAGTTACAACATACg                                     >  2:666924/1‑150 (MQ=255)                                                                                                                   gAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTTCCGCGATCCGGCAAAAACAGCCGGGGAGG‑GATCCCCCCCGGGGAGGACAAAAGGGGAAAGCAGGAAAGGAGTCCGCCGGGAGGGGGGGGGATAGTTACAAAATaaccac                                  >  1:648718/1‑146 (MQ=255)                                                                                                                   gAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTGCGATCCCGCCAAAAAGCCCGAGAAGG‑GATTGCCGCCGGGGAGGGCAAAATGGGAACGCTGAAAAAGAGTCTGCCGGAAGGCGGGGGGATAGTTacaacaa                                        >  1:572195/1‑144 (MQ=255)                                                                                                                    aaCTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGG‑GATCGCCGCCGTGAAGGACAAACTGGAAAAGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAATTACAACATACGATc                                  >  1:231027/1‑150 (MQ=255)                                                                                                                        aaaCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGca                               <  2:450213/149‑1 (MQ=255)                                                                                                                        aaaCGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTGCGATCCGGCAAAAACGCCCGAGAAGG‑GATCGCCGCCGGGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGGAGGCGGGGGGATAGGTACAACAAACGATCGc                                >  1:469809/1‑148 (MQ=255)                                                                                                                                     gaagTGGCGGGCGGGGGGGGGGTTCTGCGGTCCCGCAAAAAAGCCCGAGAGGG‑GGTTGCCGCCGTGGAGGGAAAAATGGAAACGCTGCAAAGTAGGCTGGCGGGGGGCGTGGGGATAGGTTAAACATACGATCGCAGCCAGCTCATTTAc                 >  1:365796/1‑150 (MQ=255)                                                                                                                                       agTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACcgc              <  1:246207/151‑1 (MQ=255)                                                                                                                                          ggcgggcgGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCgcgc            <  2:793731/150‑1 (MQ=255)                                                                                                                                                   ggtggtGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAc  >  2:241421/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                      ACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTGCGATCCGGCAAAAACGCCCGAGAAGT‑GATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACAAC  >  NC_000913/599428‑599724

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: ‑