Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,640,981	0	C	T	47.1%	38.6 / 39.0	51	F40F (TTC→TTT)	dtpB	dipeptide and tripeptide permease B
Reads supporting (aligned to +/- strand):  ref base C (5/22);  new base T (24/0);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 8.69e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGATGGTATTGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTGGAGCACTTG  >  NC_000913/3640836‑3641129                                                                                                                                                  |                                                                                                                                                        aGGATGGTATTGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTGt                                                                                                                                                    >  1:62880/1‑151 (MQ=255)   gATGGTATTGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTCGtt                                                                                                                                                   >  1:281201/1‑150 (MQ=255)    aTGGTATTGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTaa                                                                                                                                                 <  1:629043/151‑1 (MQ=255)     tGGTATTGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTCGttt                                                                                                                                                  >  1:523542/1‑148 (MQ=255)      ggTATTGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTaaa                                                                                                                                                <  2:268439/150‑1 (MQ=255)          ttGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGGTTTTTTTGTTTAACa                                                                                                                                              >  1:64422/1‑148 (MQ=255)           tGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑Ct                                                                                                                                          <  1:761039/150‑1 (MQ=255)            ggAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTg                                                                                                                                        <  1:104485/151‑1 (MQ=255)              aaGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTATGGCGTGCAGGGCGTACTGGCGGTTTTTTTTGTTTAAccactt                                                                                                                                          >  1:1086081/1‑143 (MQ=255)                       aaataTGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTTTTTAACAA‑CCTGGAATCTCGc                                                                                                                               >  2:986968/1‑149 (MQ=255)                         atatGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAaga                                                                                                                           <  2:693289/151‑1 (MQ=255)                           atGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAaga‑g                                                                                                                         <  1:1024274/150‑1 (MQ=255)                            tGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTTTTTATAAAT‑CGTGGGTTCTCCCAaga                                                                                                                           >  2:1054400/1‑148 (MQ=255)                             gAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑Ag                                                                                                                     <  1:630673/151‑1 (MQ=255)                               aTACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGGTTTTTTTGGTTAACAA‑ATTGGGTtct                                                                                                                                  >  1:95870/1‑138 (MQ=255)                                 acaacaacaCCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCt                                                                                                                  <  1:646534/150‑1 (MQ=255)                                 acaacaacaCCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCt                                                                                                                  <  1:855165/150‑1 (MQ=255)                                    acaacaCCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTTCTTAACAG‑CATGGGTTCTCCCCCGA‑GC‑AGGCtttt                                                                                                               >  2:1037084/1‑150 (MQ=255)                                      aacaCCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTCTTTTAACAA‑CTTGGGTTTTCGCAAAA‑GG‑AGGCgttttt                                                                                                             >  2:932076/1‑148 (MQ=255)                                          cccATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACtt                                                                                                        <  2:937892/151‑1 (MQ=255)                                           ccATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTGTTTAACAG‑CCTGGGTTTTCGCAAAA‑GG‑AGGCtttttttacctt                                                                                                       >  1:576477/1‑143 (MQ=255)                                           ccATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTGTTTAAAAA‑CTTGGATTTTTGCAAAA‑GG‑AGGGTTTTTTTACttt                                                                                                       >  1:958148/1‑151 (MQ=255)                                                 ggATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGc                                                                                                 <  1:270840/151‑1 (MQ=255)                                                        gcagcaACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTtgct                                                                                          <  2:955860/151‑1 (MQ=255)                                                          agcaACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGGTTTTTTTTTTTAAAAA‑CTTGGGTTTTTGCCAGA‑GG‑AGGGGTTTTTTACTTTTTGGGGTTTttct                                                                                          >  2:898221/1‑149 (MQ=255)                                                          agcaACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGGTTTTTTCGTTTAAAAGCCTGGGGTTCT‑GCACGA‑GG‑AGGCGTTTTTCACTTTTTTTGCtttt                                                                                             >  2:432798/1‑146 (MQ=255)                                                            caACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTTTTTAACAG‑CTTTGGTTTTCGCAAGA‑GC‑AGGCCTTTTTTTCTTTTTGTGCtttt                                                                                             >  2:413323/1‑144 (MQ=255)                                                              aCCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTg                                                                                    <  1:886146/151‑1 (MQ=255)                                                                  cGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCt                                                                                <  1:898250/151‑1 (MQ=255)                                                                   gCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTGTTTAAAAG‑CTTGGGTTCTTGCCAAA‑GC‑AGGGTTTTTTTACTTTTTGTGCTTTttct                                                                                          >  1:945787/1‑140 (MQ=255)                                                                         ttttCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGTCGGTTTTTTTTTTTATACAA‑TTTGGTTTCTTTCAAGA‑AC‑AAGGATTTTTTACTTTTTGGGGCTTTGCTTCGCTGGGCTAt                                                                              >  2:45318/1‑146 (MQ=255)                                                                          tttCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTTTTTAAAAA‑CCTGGATTTTTGCCAGA‑GC‑AGGCCTTTTTTTCTTTTTTTGGTTTTTCTTCGCTGGGCTATTGcc                                                                          >  2:530795/1‑149 (MQ=255)                                                                             cATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTGTTTAAAAA‑CTTTGGTTTTTCCCACA‑GC‑AGGGTTTTTTTACTTTTTGTGGTTTTTCTGCGCTGGGCttttggctcctt                                                                     >  1:678491/1‑140 (MQ=255)                                                                                  tCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTCTTTTAACAA‑CTTGGGTTTCCGCCAGA‑GC‑AGGCTTTTTTTACTTTTTGTGCTTTTTCTTCCCTGGGCTATGGCCCCAttt                                                                    >  2:449759/1‑147 (MQ=255)                                                                                     tttttGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTcc                                                                  <  2:1049194/146‑1 (MQ=255)                                                                                     tttttGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCa                                                                 <  1:289188/147‑1 (MQ=255)                                                                                      ttttGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTTTTTAACAG‑CCTGGGTTTTCGCAAGA‑GC‑AGGCGTTTTTCACTTTTTTTGCTTTTTCTTTGCCCGGCTTTGGCCCCATTTTCAtttg                                                             >  2:250001/1‑148 (MQ=255)                                                                                            cGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTCGTTTAACAG‑CTTTGGTTCTCGCAAAA‑GC‑AGGGCTTTTTCACTTTTTGTGGTTTTTCTGGGCTGGTCTTTGGCCCCCTTTTCCTTggcgggttt                                                      >  2:310371/1‑147 (MQ=255)                                                                                             gAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTGTTAAAAAG‑CTTGGGTTTTCGCAAGA‑GG‑AGGCTTTTTTTACTTTTTGTGGTTTTTCTTCGCTGGGCTATGGCCCCCTTTTCATTGGGGGGTAt                                                      >  1:212986/1‑150 (MQ=255)                                                                                               gTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTTTTTTAAAAA‑CCTGGGTTTTCGCCAGA‑GG‑CGGGTTTTTTCCCCTTTTGGGGTTTTTTTGCGCTGGTCTATGGCCCCCTTTTCATTTGCGGCttt                                                      >  1:947551/1‑146 (MQ=255)                                                                                                ttATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTTTTCGTTAAACAA‑CTTTGGTTCTCGCAAGAGGC‑CGGGTTTTTTC‑CTTTTTGTGGTTTTTTTTCGCTGGGCTATTGCCTCCTTTTCTTTtgcgggcttgtt                                                   >  2:1096885/1‑143 (MQ=255)                                                                                                  aTGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGc                                                <  1:1069394/151‑1 (MQ=255)                                                                                                            ttCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACctg                                       <  2:561376/150‑1 (MQ=255)                                                                                                               ggCTACTACGGCGTGCAGGGCGTACTGGCGGATTTCTTTGTTTAACAA‑CTTTGGTTTTCTCCAGA‑GCAAGGGTTTTTTACCTTTTGG‑GGTTTTTTTTTGCTGGGGTATGGGCTCTTTTACACTTGCGGGTCTGTCCGCGaccaccc                                        >  2:1007943/1‑145 (MQ=255)                                                                                                                           gTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCa                       <  1:55802/151‑1 (MQ=255)                                                                                                                              cAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCa                    <  2:1050641/151‑1 (MQ=255)                                                                                                                                  gCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGt                <  2:64421/151‑1 (MQ=255)                                                                                                                                        tGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTgg          >  1:612198/1‑151 (MQ=255)                                                                                                                                            ggTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTGGAGc       >  2:107650/1‑150 (MQ=255)                                                                                                                                            ggTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTGGAGc       >  1:135688/1‑150 (MQ=255)                                                                                                                                               tttCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTGGAGCACt    <  1:723747/150‑1 (MQ=255)                                                                                                                                                ttcttcGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTGGAGCACtt   <  2:54082/150‑1 (MQ=255)                                                                                                                                                 tcttcGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTGGAGCACTtg  >  1:696378/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                        AGGATGGTATTGGAAGGTTAATAAATATGAATACAACAACACCCATGGGGATGCTGCAGCAACCTCGCCCATTTTTCATGATCTTTTTTGTCGAGTTATGGGAGCGATTCGGCTACTACGGCGTGCAGGGCGTACTGGCGGTTTTCTTCGTTAAACAG‑CTTGGATTCTCGCAAGA‑GC‑AGGCTTTTGTCACTTTTGGTGCTTTTGCTGCGCTGGTCTATGGCCTCATTTCCATTGGCGGCTATGTCGGCGACCACCTGCTGGGGACCAAACGCACCATTGTTCTTGGAGCACTTG  >  NC_000913/3640836‑3641129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑