Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	45.1%	36.7 / 28.9	51	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (18/10);  new base T (0/23);  total (18/33)
Fisher's exact test for biased strand distribution p-value = 5.73e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAA  >  NC_000913/357723‑358011                                                                                                                                                          |                                                                                                                                              gCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGc                                                                                                                                               <  2:810425/151‑1 (MQ=255)   aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCt                                                                                                                                              >  1:1038581/1‑150 (MQ=255)   aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTa                                                                                                                                             <  1:933201/151‑1 (MQ=255)    cTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTAt                                                                                                                                            >  4:116608/1‑151 (MQ=255)      gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTAttt                                                                                                                                          <  2:667798/151‑1 (MQ=255)       aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTAtttt                                                                                                                                         <  2:790144/151‑1 (MQ=255)          tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑cc                                                                                                                                     >  1:1122626/1‑151 (MQ=255)          tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGGGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑c                                                                                                                                      >  1:1049657/1‑150 (MQ=255)                gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGca                                                                                                                               <  1:221564/151‑1 (MQ=255)                      tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                          >  1:1145391/1‑150 (MQ=255)                       aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAc                                                                                                                        >  1:747380/1‑151 (MQ=255)                       aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAc                                                                                                                        <  2:898811/151‑1 (MQ=255)                            ttgcccATCACGCAACTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                       <  2:262774/142‑1 (MQ=18)                                gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtct                                                                                                               >  4:432392/1‑151 (MQ=255)                                    cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                           >  3:335910/1‑151 (MQ=255)                                    cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                           >  2:362887/1‑151 (MQ=255)                                         atttCCAGCCGAAGCCTTGTGTCAGCGGCTCCCGTGATTCTTTCCCCCAAACAC‑CCGCGTTTTTATCCAACCCCTTGTGAAAAAATCCCT‑CGGCGG‑CGGCTGTCTGCCACTTTTTTTC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCagtag                                                                                                      <  1:1091573/149‑1 (MQ=255)                                           tcccACCCGCAGCCCTGTGCCAGCGGCTACCGTGATTCATTCCCGCCAACAC‑CCGCGAATTTACCCAACGCCATGTGAAAAAATGCCT‑CCGCGG‑CGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCagta                                                                                                       <  4:395173/146‑1 (MQ=18)                                            cccACCCGCAGCCCTTTGCAGGGGGCTCCGGTGATTCTTTCCCCCCAACAC‑CCGCGCTTTTCCCCAACCCCTTGTCAAAAAATCCCT‑CCGGGC‑CGGCTGCCTGCCATTTTTTTTC‑CCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                   <  1:1038691/150‑1 (MQ=255)                                                 ccGCAGCCTTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCCAACAC‑CCGCGCTTTTACCCACCGCCATGTAAAAAAATGCCT‑CCGGGG‑CGGTTGTCTCCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                <  1:619855/149‑1 (MQ=255)                                                 ccGCAGCCTTGTGCCGGCGCCTCCCGTATTTCTTTCCCCCCACCAC‑CCCCGCTTTTACCCACCCCCAT‑TAAAAAAAAGCCTGCCGCGG‑CGGTTTCCCGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                               <  2:1271924/150‑1 (MQ=255)                                                 ccGCAGCCCTGTGTCGGCGGCTCCCGTTTTTC‑TTTCCCCCAAAAACCCGCGCATTTACCCAACGCCTTGTGAAAAAATCCCT‑CCGGGG‑GGGTTGTCTGCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                <  4:203725/149‑1 (MQ=255)                                                 ccGCAGACCTGTGTCGGCGCCTACCGTTATTCATTCCCCCAAACAC‑CCGCGCTTTTACCCACCCCCATGTCAAAAATTGCTT‑CCGCGG‑CGGCTGTCGGCCGGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                <  1:300429/149‑1 (MQ=255)                                                  cGCAGCCGTGTGTCGGCGTTTACCGTGTTTCTTTCCCCCCAAAAC‑CCGCGCATTTACCCAACCCAATGTGAAAAAATGCCT‑CCGGGG‑GGGCTGTCTGCCCGTTTTTTTC‑CCCCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                 <  1:665663/147‑1 (MQ=255)                                                         cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggc                                                                                            >  1:874963/1‑143 (MQ=255)                                                           gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaa                                                                                     >  1:116974/1‑150 (MQ=255)                                                            tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGGGAGaaa                                                                                     >  1:398091/1‑149 (MQ=255)                                                                  cGGCTCCCGTGTTTCATTCCCGCCAACAC‑CCGCGCATTTACCCACCCCCATGTGCAAAAATGCTT‑TCGGGG‑CGGCTTTCGCCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                               <  4:303011/133‑1 (MQ=255)                                                                          gTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaattttaacccc                                                                       >  1:1234626/1‑135 (MQ=25)                                                                            gATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaagaaaaaaattt                                                                              >  1:570421/1‑133 (MQ=25)                                                                            gATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGaaaaaaattttatc                                                                          >  4:179866/1‑133 (MQ=25)                                                                              ttCTTTCCCCCCAACAC‑CCGCGC‑TTTTCCCCACCCCATGGGGAAAAAAGCCT‑TTGGGGCCGTCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                          <  1:62727/142‑1 (MQ=255)                                                                                  ttccccccAACAA‑CCGCGCTTTTACCCACCCCCATGTAAAAAAAGCCCT‑CCGGGG‑GGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                               <  1:206885/143‑1 (MQ=255)                                                                                     ccccaaacaa‑cGGCGCATTTATCCACCGCCATGTGAAAAAATGCCT‑TCGGGG‑CGGCTGTCTGCCATTTTTTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg                                                             <  1:457607/143‑1 (MQ=255)                                                                                             cacccGCGTGTTTCTCCAACGCCATCCGCAAAAAGTCCT‑AGGCGG‑CGGCGGTCCGCCGTCTTTTTTT‑CCACCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑g                                                   <  1:859567/147‑1 (MQ=255)                                                                                                ccccctatatccccACCGCTATGTACAAAATTGCTT‑CCGGGG‑CGGCTGTCCGCAGGTTATTTGC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑g                                                   <  1:1195709/135‑1 (MQ=255)                                                                                                       tttATCAACCGCCATGTAAAAAAATGCCT‑GCGGGG‑CGCCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑Gctgct‑g                                            <  1:95084/146‑1 (MQ=255)                                                                                                             cAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAAATTTTTAACCCTCATGTTGTGTGGGGATC‑GGTGCC‑GGGGAAAAtgt                                  >  4:90960/1‑150 (MQ=25)                                                                                                                ccccttgtgAAAAATTCCCT‑CCGCGG‑CGGTGTTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAAtgt                                  <  2:130410/142‑1 (MQ=255)                                                                                                                         aaaaaaTGCCT‑GCGGGG‑CGGCTGTCGCCAATTTATTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTg                     <  1:764244/150‑1 (MQ=255)                                                                                                                         aaaaaaTCCCT‑CCGCGG‑CGGTTTTCTCCCAGTTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGaa                        <  2:901297/147‑1 (MQ=255)                                                                                                                          aaaaaTCCCT‑CCGCGG‑CGCCTGTCTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGt                      <  2:1043787/149‑1 (MQ=255)                                                                                                                                     tCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAAGGAAAAACTTTTAACCCGTCCTGGTGTGTGGGCATCGGCGGCG‑GTGAAAAAAGTGGAAAgggggggggggg                 >  2:461636/1‑136 (MQ=255)                                                                                                                                     tCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAGATTTTAATCCCTCCTGCTGTTTGGGGAAC‑GCTGCTGGGTAAAAACTTGGGAGGGGAAgggggg                  >  2:465247/1‑139 (MQ=255)                                                                                                                                       gcgg‑cgGTTGTCTCCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa           <  1:34922/148‑1 (MQ=255)                                                                                                                                       gcgg‑cgGCTCTCGCCCAGTTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg          <  2:398024/149‑1 (MQ=255)                                                                                                                                         gg‑cggcTGTCTGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGGGGCGAATCAGCTc       <  1:417086/150‑1 (MQ=255)                                                                                                                                          gggggcTTTCTGCC‑GCTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATc            <  3:93381/142‑1 (MQ=255)                                                                                                                                             ggctgccgcccAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg    <  1:476685/141‑1 (MQ=255)                                                                                                                                             ggcTTTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa     <  1:73988/149‑1 (MQ=255)                                                                                                                                             gcctgccgcccAGTTTTTTTC‑CCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAAt             <  3:66087/132‑1 (MQ=255)                                                                                                                                                   cggCCAGCTTTTTTC‑CCGCACAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa  <  2:1056695/144‑1 (MQ=255)                                                                                                                                                          |                                                                                                                                              GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAA  >  NC_000913/357723‑358011

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑