Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	43.1%	60.0 / 26.8	52	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (24/5);  new base A (0/22);  total (25/27)
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

AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357745‑358037                                                                                                                                                     |                                                                                                                                                     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAAc                                                                                                                                                 >  2:78472/1‑151 (MQ=255)   gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAAcc                                                                                                                                                >  2:928204/1‑150 (MQ=255)    cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAAccgc                                                                                                                                              >  1:494170/1‑151 (MQ=255)     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAAccgcc                                                                                                                                             >  1:100208/1‑151 (MQ=255)     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAAccgcc                                                                                                                                             >  2:112309/1‑151 (MQ=255)     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAAccgcc                                                                                                                                             >  1:882672/1‑151 (MQ=255)     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAAccgcc                                                                                                                                             <  1:13686/151‑1 (MQ=255)           cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                                        >  1:1067903/1‑150 (MQ=255)             tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTtctctc                                                                                                                                     >  2:503315/1‑151 (MQ=255)              cAGGCAATTACAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                    >  2:958283/1‑151 (MQ=255)                 gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                 >  2:662954/1‑151 (MQ=255)                 gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                 >  1:492785/1‑151 (MQ=255)                   aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                 >  1:615294/1‑149 (MQ=255)                            cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                      >  2:78395/1‑150 (MQ=255)                              cAGACCGGTGTGAGGGGCTACGGTGATTCTTTCCCCCAAACACCCGCGTTTTTACCAAACGCCATGGGAAAAAATGCCTT‑CGGGGCGGTTTTCTGCA‑AGATAT‑TTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                          <  1:170875/145‑1 (MQ=255)                                      tgtCGGCGGCAACCGTGATTAATTTCCCCCAACACCCTCCATTTTACCCAACCCGATGTGCAAAAATGCGTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                                  <  1:946107/145‑1 (MQ=255)                                       gtCGGCGGCTCCCGTAATTCATTCCCGCCACCACCCGCCCTTTTACCCACCGCCATGTGAAAAAATGCTTT‑CGCGGCGGCTGTCTGCC‑AGCTTT‑TTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                                <  2:25551/146‑1 (MQ=255)                                        taagcgtccacgttGATCCATTCCCGCAAAGACCCGCTCATTAACCCACCCCCATGTGAAAAAATCCCTT‑CGCGGCGTTTGCCTCCG‑CGCTTT‑TTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                                           <  1:123175/137‑1 (MQ=255)                                        tCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGGaaaaa                                                                                                            >  1:529339/1‑147 (MQ=255)                                        tCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTT‑CGCAGCGGCTGTCTGCC‑AGCTGTATTTTCTGCCG‑AATACAACCGCCGCTCTCTCTCCTGGTGGCggagagcactgaaa                                                                                                             >  2:422290/1‑136 (MQ=14)                                         caccgccccccgtttttCATTCCCCCCAACACCCGCGTTTTTACCCACCGCAATTTGCAAAAATGCCTC‑CGGGGCGGCTGTCTCCC‑CGTTTT‑TTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑t                                                                                                        <  1:110250/136‑1 (MQ=255)                                             ggCTCCCGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTCCA‑AGCTTT‑TTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                                            <  1:685588/144‑1 (MQ=25)                                             ggCTCCCGTGATTCATTCCCGCAAACACCCGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTT‑CGCGGCGGCTGTCGCCC‑AGTTAT‑TTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTaa                                                                                                    <  1:422303/151‑1 (MQ=255)                                                  ccGTGTTTCTTTCCCCCAAACACCCGCGCTTTTA‑CCAACCCCTTGGTGAAAAATCCCTTCCGGGGCGGTTTTCGCCC‑AGTTTT‑TTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGcc                                                                                                 <  2:385392/149‑1 (MQ=255)                                                  ccGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaaaagattaaaccc                                                                                                 >  2:1003189/1‑137 (MQ=25)                                                    gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCGGAGaaaaaaaagttaatcc                                                                                                 >  2:815281/1‑135 (MQ=25)                                                        ttcttcccccccaccaACCGCCCTTTTACCCACCGCCATGTGAAAAAAGGCCTC‑CGCGGCGG‑TGTTCGCCGAGTTTT‑TTTCCCGCAGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtg                                                                                          <  2:575406/140‑1 (MQ=255)                                                        ttCATTTCCCCCAACACCCGCGTATTTATCAAACCCCTTGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGTTTT‑TTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAt                                                                                           <  1:244697/149‑1 (MQ=255)                                                            tttCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGGAAAAAC‑ttttaaaacctcccgtt                                                                                        >  1:747941/1‑134 (MQ=25)                                                            tttCCCCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAATTGCTTT‑CGGGGCGCCTTTCTGCC‑AGTTAT‑TTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtgttg                                                                                       <  1:822727/149‑1 (MQ=255)                                                                 gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAAC‑TTTAAGCACCCCCTGTTGTTTgggg                                                                                >  1:864947/1‑149 (MQ=37)                                                                                tttACCCACCCCGATGTGAAAAAGTGCCTG‑GGGGGCGGTTTTCTGCC‑AGATTT‑TTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                                   <  2:556341/149‑1 (MQ=255)                                                                                tttACCCAACCCCTTTTAAAAAAATCCCTC‑CGGGGGGGTTTTCCCCC‑ATTTTT‑TTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                                   <  1:541728/149‑1 (MQ=255)                                                                                     ccACCGCCTTGTGAAAAAATGCCTT‑CGGGGCGGCTGTCCGCC‑AGCTTT‑TTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                             <  1:208731/150‑1 (MQ=255)                                                                                         cGCCATGTGAAAAAATCCCTC‑CGGGGCGGTTGTCTGCC‑AGTTTT‑TTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                                        <  1:503330/151‑1 (MQ=255)                                                                                         cGCCATGTGAAAAAAGGCTTG‑CGGGGCGGCTTTCTGCC‑TGTTTT‑TTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                             <  2:824285/146‑1 (MQ=255)                                                                                               gtgAAAAAAGCCTTT‑CGCGGCGGCTGTCGCCC‑AGTTAT‑TTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                                        <  1:322390/145‑1 (MQ=255)                                                                                                   aaaagTCCCTT‑CGGGGGGGCTGTCTGCC‑ATTTTT‑TTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                     <  2:1085082/144‑1 (MQ=255)                                                                                                    aaaaTGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGGAAAAAAA‑TTTTAGCCCCTCCTGTTGTGTGGCAATTGTTGCCGGGAAAAAAATGGGAAGGGGAggggg                                             >  1:1049767/1‑147 (MQ=255)                                                                                                        tGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAA‑ATTTAACCCCCCCTGTTTTTTGGGGATCGCTGCCTGGGACAAAGGGggaagggaaggggggg                                           >  2:1066159/1‑143 (MQ=255)                                                                                                                  ggcggcTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAACATTTAGACCCGCCTTGTT‑TGTGGGGATAGCTGCTGGGGAAAATTTGGAAAGGGGAGGggggcggaataacccc                                >  1:721745/1‑141 (MQ=255)                                                                                                                    cggcTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAAG‑ATTTAGCCCGCCATGTTTTGTGGGGATTGCTGCTGGGGAAAAAGTGGGAAAGGAAGTGGGGGGGAACAGCttc                                >  1:492668/1‑147 (MQ=255)                                                                                                                     gcctgcctgcC‑AGCTTT‑TTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                              <  1:241136/148‑1 (MQ=255)                                                                                                                       cTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAA‑TTTTAAACCCCCATGTTTTGTGGGCAAAGCTGCTGGGGAAAAAGTGGGAAAGGGAGGGGGGGGGATCAACTCCCGaa                            >  1:1115205/1‑150 (MQ=255)                                                                                                                          tctcCC‑AGCTTT‑TTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                            <  1:1050781/147‑1 (MQ=255)                                                                                                                              cc‑AGTTAT‑TTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                      <  1:716059/149‑1 (MQ=255)                                                                                                                              cc‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAA‑TTTTATACCGCCCCGTTTTGTGGGGAACACCGCTGGGAACAAATTGGAAAGGGGAGGGGGGCGGGCCAGCTCCCCAAcc                          >  2:108198/1‑145 (MQ=255)                                                                                                                               caagtttt‑tttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                               <  2:811192/133‑1 (MQ=255)                                                                                                                                      t‑ttttCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaagt                 <  1:48276/147‑3 (MQ=255)                                                                                                                                      t‑ttttCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt                 <  1:928229/147‑1 (MQ=255)                                                                                                                                        tttcCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt             <  1:134772/150‑1 (MQ=255)                                                                                                                                         ttcccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt            <  1:662969/147‑1 (MQ=255)                                                                                                                                                   aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATg  <  1:99261/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCC‑AGCTAT‑TTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357745‑358037

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: ‑