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%	37.4 / 24.9	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (20/4);  new base A (0/23);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.27e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357742‑358037                                                                                                                                                         |                                                                                                                                                       gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGc‑aaca                                                                                                                                                       <  1:887454/150‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaaa                                                                                                                                                    <  1:213877/150‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                                   >  1:401898/1‑151 (MQ=255)     aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAcc                                                                                                                                                  >  1:626803/1‑151 (MQ=255)         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgccg                                                                                                                                              >  2:788374/1‑151 (MQ=255)          aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGt                                                                                                                                             >  1:212765/1‑151 (MQ=255)            cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtc                                                                                                                                           >  1:603990/1‑151 (MQ=255)                  aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTcc                                                                                                                                      >  2:315525/1‑150 (MQ=255)                      aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagt                                                                                                                                   >  1:1114681/1‑149 (MQ=255)                        ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                               >  2:345551/1‑151 (MQ=255)                          ccACCCGCAGCCTGGTGTCGGCGGCTCCCGTGTTTCTTTCCCCCCAACAC‑CCGCATTTTTACCCACCCCCGTGTAAAAAAATCCCTC‑CGCGGCGT‑TTGTCCCCCTGTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                             <  2:341057/151‑1 (MQ=255)                           cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                           >  2:1160284/1‑151 (MQ=255)                           cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                           >  1:578153/1‑151 (MQ=255)                              ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                        >  2:1304067/1‑151 (MQ=255)                              ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                        >  2:1039477/1‑151 (MQ=255)                                  agcccTGTGTCAGCGCCTCCCGTTATTCTTTCCCCCCAACAC‑CCGCGCTTTTACCCACCGCCATGTAAAAAAATGCCTC‑CGGGGCGT‑CTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAag                                                                                                                    <  2:646317/148‑1 (MQ=255)                                  aGACCTTTGTCAGCGGCTACCGTGATTCTTTCCCGCCAACAC‑CCGCGCATTTCTCCAACGCCATGTGAAAAATTGCTTC‑CGCGGCGG‑CTGTCTCCCAGTTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAag                                                                                                                    <  1:286329/151‑1 (MQ=21)                                   gACCTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCCAACAC‑CCGCGCATTTACCCACCGCCTTGTGCAAAAATGCCTT‑CGCGGCGG‑CTTTCTCCCGGTTTTTTTTCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAaga                                                                                                                   <  1:135907/151‑1 (MQ=255)                                    aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggggcag                                                                                                                    >  1:363174/1‑145 (MQ=255)                                      cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGagagg                                                                                                                 >  1:257454/1‑149 (MQ=255)                                       tgtgTCGGCGGCTCCTGTGATTC‑TTTCCCCCAAAAACCCGCGCTTTTCCCCACCGCCATGTAAAAAAATGCCTC‑CGGGGCGG‑CTTTCGCCCAGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAgag‑a                                                                                                                <  2:185709/149‑1 (MQ=255)                                        gtgcCAGCGCCCACCGTGATTCTTTCCCCCCAACAA‑CCGCGCATTTACCCACCCCCATGTGAAAAAATGCCTC‑CGGGGCGG‑CTGTCTGCCAGCTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑aaa                                                                                                              <  1:498521/150‑1 (MQ=255)                                          gtCAGCGGCTCCCGTGTTTCTTTCCCCCCAACAC‑CCCCGCTTTTACCCACCGCCATGTGAAAAAATCCCTC‑CGCGGCGG‑CTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAg                                                                                                           <  1:285735/151‑1 (MQ=255)                                                ggCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGAG‑aaaaaaaattt                                                                                                      >  1:1211236/1‑142 (MQ=255)                                                   tACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑aaaaaaattttaaa                                                                                                   >  1:984346/1‑139 (MQ=25)                                                      cgttattatttccccccAACAC‑CCGCCCTTTTCCCCACCGCCTTGTAAAAAAAGCCCTC‑CGCGGGGG‑CTGTCGGCAATTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGt                                                                                               <  2:78728/136‑1 (MQ=255)                                                                     ccAACAC‑CCGCGCATTTACCCAACGCCATGTGAAAAAATGCCTC‑CGCGGCGG‑CTGTCTGCCAGTTATTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                                <  1:1240486/151‑1 (MQ=255)                                                                      caacaa‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAAAG‑AAAAAAAATTTAACCCCCCATGTTGTGTgggggt                                                                               >  1:869729/1‑147 (MQ=25)                                                                       aacac‑cCGCGCTTTTACCCAACGCATTGTGAAAAAAT‑CCTT‑CGGGGGGGCCTGCCGCCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                              <  2:492182/151‑1 (MQ=255)                                                                            cccGCGCTTTTACCCACCGCCATGTAAAAAAGTCCCTC‑CGGGGCGG‑CTGTCTGCCATTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                          <  2:130912/150‑1 (MQ=255)                                                                               gcgaATTTACCCACCGCCATGTAAAAAAATGCCTC‑GGGGGCGG‑CTGTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgct‑g                                                                      <  1:274408/151‑1 (MQ=255)                                                                                   atttccccacccccttgtgCAAAAATCCCTC‑CGCGGCGG‑CTGTCCCCAATTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTa                                                                   <  1:49303/135‑1 (MQ=255)                                                                                       acccAACGCCTGGTGAAAAAATCCCTC‑CGGGGCGG‑CTGTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAt                                                              <  1:250214/149‑1 (MQ=255)                                                                                       aTCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑AAAAAAATTTAAACCCCCCCTGTTTTGTGGGGATCgcttccgggtaaaa                                                                >  1:113259/1‑139 (MQ=25)                                                                                              ccaatgtcaaaaaaTCCCTT‑CGCGGCGG‑CTTTCGGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGaaa                                                       <  1:1041434/142‑1 (MQ=255)                                                                                                 aTGTGAAAAAAGGCCTC‑CGCGGCGG‑CTGTCTCCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAggg                                                    <  1:1160378/151‑1 (MQ=255)                                                                                                   gtgAAAAAATGCCTG‑CGGGGCGG‑CTGTCTGCCAGCTATTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGa                                                   <  1:891130/150‑1 (MQ=255)                                                                                                      aaaaaaGGCCTTCCGGGGCGG‑CGGTCTCCCAGTTTTTTCCCCCCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGt                                                <  2:1336856/150‑1 (MQ=255)                                                                                                       aaaaaGGCCTT‑GGCGGCGG‑CTGTCTGCCAGTTTTTTTTCCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgc                                              <  1:970360/151‑1 (MQ=255)                                                                                                          aattgcttccggggcgt‑cTTTCTCCCATTTTTTTTCCCGCCAA‑AAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcgg                                            <  2:1069843/139‑1 (MQ=255)                                                                                                              ccTT‑CGCGGCGG‑TTGTCTGCGGGTTTTTTTCCCCCCGA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                       <  1:536422/151‑1 (MQ=255)                                                                                                                tt‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGTAGGAA‑AAAAAAATTTAAACCCCCCCTGTTGTGGGGCACTC‑CTGCTGGGTAACAATGGGGAAggggggggggggggaggc                                      >  2:1256279/1‑137 (MQ=255)                                                                                                                          ggttGTCTGCCCGCTTTTTTCCCCCCAA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                             <  2:206960/148‑1 (MQ=255)                                                                                                                              gTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                          <  2:253243/150‑1 (MQ=255)                                                                                                                                     agtttttttcCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                  <  1:800923/146‑1 (MQ=255)                                                                                                                                        tttttttCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt                 <  2:938114/148‑1 (MQ=255)                                                                                                                                         tttttcCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa               <  1:1111586/149‑1 (MQ=255)                                                                                                                                           ttttCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGTGCGCGAG‑AAAAAAATTTTAACCCCCCCTGTTTTGTGGGGACCGCTGCT‑GGGGACACAATGGGGAGGGGGGGGGGGGGGGGCAGCTCCAGCAACCCGCTAATTGAGtt            >  2:755711/1‑151 (MQ=255)                                                                                                                                                       aacaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAACTTTAA‑CCCCCCCCGTTTTGTGGGGATCGCTGCT‑GGGGAAAATGAGGGAAAGGGAGAGGGGGGGAACAGCTCCCCAACCGCCCCAAATTAGTTTGCCTCCATg  >  2:381915/1‑150 (MQ=255)                                                                                                                                                         |                                                                                                                                                       GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357742‑358037

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: ‑