Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	48.9%	21.2 / 40.0	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (21/3);  new base A (0/23);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 1.81e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.21e-01

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357741‑358031                                                                                                                                                        |                                                                                                                                                  tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                   >  2:1029316/1‑150 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                  >  2:530222/1‑150 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑c                                                                                                                                             >  1:546255/1‑151 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑cc                                                                                                                                            >  1:770908/1‑151 (MQ=255)        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgc                                                                                                                                          <  1:23165/151‑1 (MQ=255)          tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgccg                                                                                                                                        >  1:227780/1‑151 (MQ=255)             cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGtt                                                                                                                                      >  1:1062702/1‑150 (MQ=255)               cATCAGGCATTTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTTCCGCCAACACCCGCGCATTTACCCAACGCAATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAA‑CCGCCGTtc                                                                                                                                     <  1:424512/149‑1 (MQ=255)               cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtctc                                                                                                                                   >  1:277923/1‑151 (MQ=255)                  cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                                >  2:1049059/1‑151 (MQ=255)                       aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagt                                                                                                                             >  1:1072101/1‑149 (MQ=255)                       aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagt                                                                                                                             >  1:245153/1‑149 (MQ=255)                        aTTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATATTTTCGCCGGAACAAAA‑CCGCCGctctctaccctag                                                                                                                           >  1:952123/1‑143 (MQ=11)                        aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagtagt                                                                                                                          >  2:830113/1‑151 (MQ=255)                            cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc                                                                                                                       >  2:356875/1‑150 (MQ=255)                                   aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑gggggg                                                                                                                >  2:678940/1‑147 (MQ=255)                                      cttgttcctgCGGCTCCTGTTTTTCTTTCCCGCAAACACCCGCGAATTCCCCCACCGCCTTGCGAAAAAATC‑CTTG‑CGCGGCGGCTGTCCGCCAGTTTTTTTCCCCCCCCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                  <  2:771676/135‑1 (MQ=255)                                         ttgacggcgcccaCCGTG‑TTCCTTTCCCCCAACCACCCTCTCTTTAACCAAGCCCAATTTCAAAAAAG‑CCTTCCGGGGCGGCTGGCTCCCATTTTTTTTCCCTCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAga‑ga                                                                                                          <  1:1026974/136‑1 (MQ=255)                                         gtgtCAGCGGCTACCTTGATTCTTTCCCCCCAACACCCGCCCATTTACCCAACGCCATGTGAAAAAATG‑CCTT‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAag                                                                                                              <  1:902492/145‑1 (MQ=255)                                           gtCGGCGGCTCCCGTTTTTCTTCCCCCCCAACACCCGCCCTTTTACCCACCGCCATGTAAAAAAATG‑CCTC‑CGGGGCGGCTGTCGCCCAGTTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAg                                                                                                     <  2:1127381/151‑1 (MQ=255)                                                cGGCTCCCGTGATTCATTCCCGCCACCACCCGCCCTTTCACCCAACCCCATGT‑AAAAAATGCCCTC‑CGCGGCGGCTGTCGGCCGGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCttt                                                                                                 <  2:461991/150‑1 (MQ=255)                                                cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑Ggaaaaaactt                                                                                                 >  2:540759/1‑143 (MQ=25)                                                      cggTGATTCTTTCCCCCCAACACCCCCGCTTTTACCCACCGCCTTGTGAAAAAATG‑CCTG‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGcc                                                                                           <  1:265176/147‑1 (MQ=255)                                                      ccgtttttCATTCCCCCCAACACCCGCCCTTTTCCCCAACGCCTTGTGAAAAAATC‑CCTT‑CGGGGGGGCTGTCTCCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATa                                                                                                      <  1:1181730/133‑1 (MQ=255)                                                        gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGG‑GAAAAAGAATT‑aaatc                                                                                           >  2:833654/1‑144 (MQ=25)                                                            ttcttcccccccAACACCCGCGCTTTTCCCCACCGCAATGAAAAAAAATG‑CCTG‑CGGGGCGGCTGTCCGCCGGTTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGc                                                                                            <  2:384/132‑1 (MQ=255)                                                                  ccccccAACACCCGCGCTTTTCCCCACCCCTTTGTAAAAAAATG‑CCTG‑CGGGGGGGCTGTCTCCCGTTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTtgtgtg                                                                             <  2:1078359/147‑1 (MQ=255)                                                                   ccGCCAACACCCGCG‑ATTTTCCCAACCCCTTTTGGAAAAAAGCCCTC‑CGGGGCGGCTGTCCGCCGTCTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTtgtgtg                                                                             <  1:168647/150‑1 (MQ=255)                                                                           acccGCGCATTTACCCAACGCCATGTGAAAAAATC‑CCTT‑CGCGGCGGCTGTCGGCCAGTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCg                                                                      <  1:1057613/147‑1 (MQ=255)                                                                             ccgccattttACCCAACCCCATGAAAAAAAAGC‑CCTC‑CGGGGCGGTTGTCTCCCGTTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                  <  2:289570/144‑1 (MQ=255)                                                                             ccGCGCTTTTATCCACCGCCATGTGAAAAAATG‑CCTC‑CGCGGCGGCTGTCGGCCATTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCgctg                                                                   <  1:562994/150‑1 (MQ=255)                                                                              cgcgCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGA‑GGAAAAAATTT‑TATCCCCCCCTGTTTTGTGGGGATCggt                                                                    >  1:109606/1‑146 (MQ=25)                                                                                cccATTTACCCACCCCCATGTAAAAAAATG‑CCTC‑CGCGGGGGCTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                 <  1:36258/147‑1 (MQ=255)                                                                                 cctttcaccaaccGCTATGTAAAAAAATC‑CCTC‑CGCGGCGGTTGTCGGCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGt                                                              <  2:965972/139‑1 (MQ=255)                                                                                  cATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGA‑GAAAAAAATTT‑TAACCCCTCATGTTGTGTTGGTATCGCCGCTGGtg                                                             >  2:598460/1‑150 (MQ=37)                                                                                               ccATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAAA‑AAAAAAAGTTT‑AAACCCG‑CCTTTTTTGTGGGGATCCGTGCTGGGGACAAAGTgg                                                    >  1:281691/1‑147 (MQ=19)                                                                                                    gtaaaaaaaG‑CCTTCCGGGGGGGCTGTCTCCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                             <  1:1107354/147‑1 (MQ=255)                                                                                                      cAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑GAAAAAAATTTAAAACCCTCCATGTT‑TGTGGGAATCGCCGCCGGGAAAAAAGTGGGAAggg                                              >  1:2460/1‑146 (MQ=255)                                                                                                       aaaaaGG‑CCGT‑CGCGGCGGCTGTCTGCCTGTTATTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                           <  2:677445/148‑1 (MQ=255)                                                                                                        aaaaAG‑CCTTCCGCGGCGGTTGTCGGCAACCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                        <  1:336790/151‑1 (MQ=255)                                                                                                         aaaTG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGA‑GAAAAAAATTT‑TAATCCCCCCTTTTGTGTGGGGATTCCTGCTGGTGACAAAGTGGGAAGGGGAgggggg                                      >  2:825293/1‑146 (MQ=255)                                                                                                                     gggggggcTGTCCCCCATTTATTTTCCCCCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                    <  1:527057/138‑1 (MQ=255)                                                                                                                      cggcggCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑GAAAAAACTTT‑TAAACCCCCCTCTTTTTTGGGGATCGCTGCTGGGTACAAATTGGGAAAGGGAGGgcgggggaaaaaccc                           >  1:449998/1‑140 (MQ=255)                                                                                                                         cggcTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGA‑GAAAAAGATTT‑TAACCCGTCCTGTTGTGTGGGAATAGCTGCTGGTTAAAAAGTGGGAAGGGGAGGggggcggaaaaaccc                           >  1:1160813/1‑139 (MQ=255)                                                                                                                           gcttccTGCCGGTTTTTTTCCCCCAGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                               <  2:560124/137‑1 (MQ=255)                                                                                                                               ccgccaagtttttttcCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                    <  2:1072092/138‑1 (MQ=255)                                                                                                                                  gcccattttttttCCCGCACAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                 <  2:227779/142‑1 (MQ=255)                                                                                                                                     agttATTTTCCAACCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa             <  1:181568/147‑1 (MQ=255)                                                                                                                                          ttttcCCGCCCAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa         <  1:870831/149‑1 (MQ=255)                                                                                                                                                     caacaaAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAGGAAAAAATTTT‑AAACCCCCCA‑GTTTTGTGGGAAACCCTGCTGGGGAAAAAGTGGGAAGGGGAGTGCGGGGGAACAGCCCCCCAACCccgcccaattagtttgcc  >  1:670233/1‑131 (MQ=255)                                                                                                                                                        |                                                                                                                                                  TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAGCTTT‑AAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357741‑358031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑