Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	599,576	0	T	G	52.0%	51.9 / 78.7	50	V288G (GTG→GGG)	cusA	copper/silver efflux system, membrane component
Reads supporting (aligned to +/- strand):  ref base T (4/20);  new base G (26/0);  total (30/20)
Fisher's exact test for biased strand distribution p-value = 2.25e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.25e-07

AAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACA  >  NC_000913/599426‑599722                                                                                                                                                       |                                                                                                                                                     aaaCGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGggt                                                                                                                                                      <  1:834142/151‑1 (MQ=255)    cGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGggtggt                                                                                                                                                   <  2:527611/151‑1 (MQ=255)              cTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTG‑C‑gg                                                                                                                                       >  1:40769/1‑150 (MQ=255)               tttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGGGATCCt                                                                                                                                             >  2:37596/1‑146 (MQ=255)               tttAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTG‑C‑GAt                                                                                                                                      >  2:216877/1‑151 (MQ=255)                 tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATc                                                                                                                                     <  1:853439/150‑1 (MQ=255)                 tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCCG‑C‑GATcc                                                                                                                                    >  2:267286/1‑151 (MQ=255)                 tAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTG‑C‑GGTcc                                                                                                                                    >  1:705944/1‑151 (MQ=255)                   aTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTG‑C‑GATCCgg                                                                                                                                  >  2:430544/1‑151 (MQ=255)                   aTCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTG‑C‑GGTcc                                                                                                                                    >  2:458770/1‑149 (MQ=255)                        aTCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGATCCTG‑C‑GATCCGGCaaa                                                                                                                              >  2:198723/1‑150 (MQ=255)                          cGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGCGGGGGGGGGTGCTC‑G‑GATCCgggcaa                                                                                                                              >  1:513473/1‑144 (MQ=255)                                   aGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGaa                                                                                                                  <  1:225042/151‑1 (MQ=255)                                   aGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGGCCAGATTGGCCCGGAGACGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGAGCCTGCC‑CATCCGCAAAAAAccc                                                                                                                         >  1:36588/1‑143 (MQ=255)                                          gAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCTG‑C‑GATCCGGCGAAAACGCCCgcggaggggtcg                                                                                                           >  1:495929/1‑140 (MQ=255)                                                   gTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGa                                                                                                  <  2:550749/151‑1 (MQ=255)                                                    tGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGGGGTCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTg                                                                                                   >  1:305345/1‑149 (MQ=255)                                                       ccGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTT‑C‑GATCCGGCCAAAACGCCCGAGAAGGGATCGCCGCCGTGAAgg                                                                                               >  1:455909/1‑150 (MQ=255)                                                         gTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACa                                                                                            <  1:256027/151‑1 (MQ=255)                                                          tttATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTACTG‑C‑GATACGGCAAAAAAGCCCGCGGAGGGAGCGCCGCCGTggacg                                                                                               >  1:27724/1‑143 (MQ=255)                                                                 gcgcGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTg                                                                                       <  1:764019/148‑1 (MQ=255)                                                                        gTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGa                                                                             <  2:610279/151‑1 (MQ=255)                                                                             gAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTG‑C‑GATCCGGCAAAAAAGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGGAACGCTGaaaa                                                                          >  2:577733/1‑149 (MQ=255)                                                                              aaGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGCGGTCCCG‑C‑GGTCCGGCAAAAACGCCCCGGAAGGGATCGCCCCCGGGAAGGACAAACTGGAAACGCTGAAAag                                                                         >  2:171227/1‑149 (MQ=255)                                                                                  tCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTC‑C‑GATCCGGCAAAAAAGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAAATGGAAAAGCTGaaaa                                                                          >  2:59904/1‑144 (MQ=255)                                                                                   ccAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCt                                                                   <  1:341673/150‑1 (MQ=255)                                                                                    cAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGc                                                                 >  2:814612/1‑151 (MQ=255)                                                                                       aTTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCgg                                                              <  2:34057/151‑1 (MQ=255)                                                                                           gCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTG‑C‑GATCCGGCAAAAAAGCCCGAGAAGTGATCGCCGCCGTGAAGGACCAACTGGAAAAGCTGAAAAGTAGTCTGCCGGGAgg                                                          >  2:785383/1‑151 (MQ=255)                                                                                            cccGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGCGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAgg                                                          >  2:680463/1‑150 (MQ=255)                                                                                                  gaTGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGgag                                                   <  2:258269/151‑1 (MQ=255)                                                                                                     gcgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGAt                                                 <  2:862242/150‑1 (MQ=255)                                                                                                      cgcCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGGGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGgag                                                   >  2:158059/1‑147 (MQ=255)                                                                                                         cGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTa                                            <  1:359242/151‑1 (MQ=255)                                                                                                          ggggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGGGGGGGGGTTGTATCG‑C‑GATCCGGGAAAAACACCCGCGAAGGGATCCCCGCCGGGCAGGACAAAAAGGAAAACCCGTAAAGGAGTCAGCCGGGAGGCgggggggta                                                >  1:236496/1‑141 (MQ=255)                                                                                                          ggggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGGTCCCG‑C‑GATCCGGCAAAAAAGCCCGCGAAGGGATCGCCGCCGGGGAGGGCAAACTGGGAACGCTGAAAAGAAGTCTGCCGGAAGGCGTGGAAGTAGtt                                             >  1:249296/1‑149 (MQ=255)                                                                                                           gggCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGGGAGCCTG‑C‑GGACCGGCAAAAAACCCCGAGGAGAGGTCGCCGCCGCGGAGGACAAACAGGAAACGCTGACAAAAAATCTGCCGGAAGGGGGGGAGGTAGTTa                                            >  1:653359/1‑149 (MQ=255)                                                                                                             gCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTacaac                                        <  2:208307/151‑1 (MQ=255)                                                                                                             gCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGGGGTGATCCTG‑C‑GGTCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGGGAAGGACAAAATGGAAACGCTGAAAAGGAGTCTGCCGGAAGGCGTGGAGATAGTTacaa                                         >  2:650974/1‑150 (MQ=255)                                                                                                                  gCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACg                                   <  2:839994/151‑1 (MQ=255)                                                                                                                  gCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGGGATCCTG‑C‑GATTCGGCAAAAACACCCGGAAAGGGATCGCCGCCGCGGAGGACAAAATGGAAACGCTGAAAAAGAGTCTGCCGGGAGGCGTGGAGATATTTTCAACAAACg                                   >  2:554683/1‑151 (MQ=255)                                                                                                                    cGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGAt                                 <  2:534083/151‑1 (MQ=255)                                                                                                                        cTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGGCGTGAAGGACAAGCTGGAAACGCTGAAAAGTAGTCTGCCGTAAGGCGTGGAGATAGTTACAGCATACGATCg                               <  1:793263/149‑1 (MQ=255)                                                                                                                            aCGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagc                           <  1:852599/149‑1 (MQ=255)                                                                                                                             cGGCGAAGGCGAATTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGcagcca                         <  1:824047/150‑1 (MQ=255)                                                                                                                                 gaaggcgaagTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTc                     <  1:785172/150‑1 (MQ=255)                                                                                                                                 gaaggcgaagTGGCGGGCGGGGGGGTGATCCTT‑CGGATCC‑GCAAAAAACCCCGCGAAGGGGTCGCCGCCGTGAAGGACAAACCGGGAACGCTGCAAAGTAGTCTGCCGGGAGGCGTGGAGGTAGATAAAAAACACGATGGCAGCCAGCTc                     >  1:104754/1‑150 (MQ=255)                                                                                                                                      cgaagTGGCGGGCGGGGGGGGGATCCCG‑C‑GAGCCCGCAAAAACGCCCGCGAAGAGATCGCCCCCGGGAAAGAAAAACTGGAAAAACCGGAAAAAAGTCTGCCGGAAAGCGGGGGGATAGTTACAACATACGATCg                               >  2:840096/1‑135 (MQ=255)                                                                                                                                              cgggcgggGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCAt       >  2:270760/1‑151 (MQ=255)                                                                                                                                               gggcgggGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATc      >  2:21384/1‑151 (MQ=255)                                                                                                                                                   ggggTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGAc   <  2:884971/150‑1 (MQ=255)                                                                                                                                                   ggggTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACa  <  2:200630/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     AAACGCTCGACGACTTTAATCACATCGTTTTAAAAGCCAGTGAAAATGGCGTGCCCGTTTATCTGCGCGATGTTGCGAAGGTCCAGATTGGCCCGGAGATGCGCCGGGGCATTGCCGAACTAAACGGCGAAGGCGAAGTGGCGGGCGGGGTGGTGATCCTG‑C‑GATCCGGCAAAAACGCCCGAGAAGTGATCGCCGCCGTGAAGGACAAACTGGAAACGCTGAAAAGTAGTCTGCCGGAAGGCGTGGAGATAGTTACAACATACGATCGCAGCCAGCTCATTGACCGCGCCATCGACA  >  NC_000913/599426‑599722

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑