Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8870CA40.5% 39.5 / 15.5 37L268F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/9);  new base A (0/15);  total (13/24)
Fisher's exact test for biased strand distribution p-value = 2.31e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357738‑358033
                                                                                                                                                       |                                                                                                                                                   
gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                                     >  2:914081/1‑150 (MQ=255)
 ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                                                   <  2:486288/151‑1 (MQ=255)
    gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                 <  2:189099/150‑1 (MQ=255)
      tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                               >  2:534877/1‑150 (MQ=255)
       aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                             <  2:136044/151‑1 (MQ=255)
        aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                            <  1:270440/151‑1 (MQ=255)
           ttAGCGACTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAA‑CCGCGCATTTATCCACCGCCATGTGCAAAAATCCCTTC‑TCGGCGGCTGTCTGCCAGGTATTTTTCCGCCGcaaca                                                                                                                                                 <  1:1212673/142‑1 (MQ=17)
           gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                         >  2:524818/1‑151 (MQ=255)
            tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                        >  1:1164024/1‑151 (MQ=255)
                gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                                    >  1:726784/1‑151 (MQ=255)
                          aTTCCAGCCGCAAACCTGTGACAGCGGCTACCTTGATTCAATTCCGCCAACAA‑CCGCGCATTTATCCACCGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGGCAGCTCTTTTTCCGCCGCAACAAAACCGCCGTTCGCTCCatgcg                                                                                                                           >  1:695910/1‑146 (MQ=21)
                                 ccccaccccTGTGTCAGCGGCCCCCGTTATTCTTCCCCACCAACAA‑CCGCGCATTTACCCAGCCCTTTGTACAAAAATGCGTTC‑GGGGCGCTTGTCGCCCAGTTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                     <  2:788887/142‑1 (MQ=255)
                                 ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                   >  2:405301/1‑151 (MQ=255)
                                       aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggga                                                                                                                >  2:822801/1‑145 (MQ=255)
                                            tgtCAGCGCCCACCGTGTTTCATTCCCGCCAACAC‑CCGCGCATTTATCCAACCCCATGTGAAAAAATGCCTGC‑GGGGCGGCTGTCTCCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑aaa                                                                                                         <  2:16814/149‑1 (MQ=255)
                                               cAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑aaaaa                                                                                                       >  2:413865/1‑146 (MQ=255)
                                                aGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAG‑AAAAAACtt                                                                                                   >  2:447714/1‑151 (MQ=255)
                                                 gCGGCTCCCGTGTTTCATTCCCCCCAACAC‑CCGCGCATTTACCCACCCCCTTGTAAAAAAATCCCTGC‑GGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCt                                                                                                    <  2:1013703/149‑1 (MQ=255)
                                                   ggCTCCCGTGATTCATTCCCGCCAACAC‑CCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTTC‑GGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCt                                                                                                    <  2:667242/147‑1 (MQ=25)
                                                   gcctcccttGATTCTTTCCCCCCAACAC‑CCGCCTATTTACCCAACGCCTTTTGAAAAAATGCCTCC‑GGGGCGCCTGTCTGCCGGCTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCt                                                                                                    <  2:421223/139‑1 (MQ=255)
                                                        ccGTCATTTTTTCCCCCCAACAC‑CCGCATGTTTAACCACCGCTGTGGGAAAAAGCTCCTCC‑GCGGCGGCGTTGGGCCAGTTTTTTGCCCGCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGc                                                                                              <  1:758410/148‑1 (MQ=255)
                                                          gtgtTTCTTTTCCGCCACCAC‑CCGCGCTTTTATCCACCCCCAGGAGAAAAAAGCCCTCC‑GGGGCGTCTGTCTCCCGGTTTTTTTTCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAg                                                                                               <  1:560189/145‑1 (MQ=255)
                                                              ttCTTTCCCCCCAACAC‑CCGCGATTTTACCCACCGCCATGGGAAAAAATCCCTCC‑GGGGGGGTTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCa                                                                                        <  2:222854/148‑1 (MQ=255)
                                                              ttCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGGGAAAAAACCTTTAGGCCCgcc                                                                                         >  2:97644/1‑146 (MQ=25)
                                                              ttCATTCCCCCCAACAC‑CCGCGCTTTTACCCACCGCCATGTGCAAAAGGGCCTTC‑GCGGCGGCTTTCTGCCAGTTTTTTTCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                      <  1:709955/150‑1 (MQ=255)
                                                              ttCATTCCCACCAACAC‑CCGCGCTTTTATCCACCCCCATGTCCAAAATTCCCTTC‑GCGGCGGCTGTCGGCCGGCTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAt                                                                                       <  2:169747/149‑1 (MQ=255)
                                                               ttctttCCCCCAAAAACCCGCGCTTTTCCCCACCG‑CATTGGAAAAAAAGGCTTCGGGGGGGGCTGCCGCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGt                                                                                          <  2:1002531/143‑1 (MQ=255)
                                                                  ttcccGCCAACAC‑CCGCGAATTTACCCACCCCAATGTGAAAAAATGCTTCG‑GCGGCGGCTGTCTGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgttg                                                                                   <  2:1006975/146‑1 (MQ=255)
                                                                    cccccaaacac‑cCGCCCTTTTACCCACCCCCATGTCAAAAAATGCCTTG‑GGGCCGGCTTTCTGCCACCTTTTTTCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                                <  2:436982/144‑1 (MQ=255)
                                                                                       tttACCAAACGCCATGTAAAAAAATCCCTCC‑GGGGCGGCTGTCTGCCAGCTTTTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                   <  2:1146828/145‑1 (MQ=255)
                                                                                           cccaccccctggtaaaaaatTGCCTCC‑GCGGCGGCTTTCGCCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                          <  2:951034/135‑1 (MQ=255)
                                                                                            ccaccccctggtgAAAAAAT‑CCTTCGGGGGCGGTTTTCTCCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                         <  2:1099466/140‑1 (MQ=255)
                                                                                                      gtgAAAAAGCGCCTTC‑GCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                              <  2:1101774/151‑1 (MQ=255)
                                                                                                         cAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑GAAAAACATTTAACCCCCCTTGTTTTTTGGGAATCGCTGCTGGTGGCAAAGTGGGGAggg                                                >  2:604906/1‑146 (MQ=255)
                                                                                                                 ccTTC‑GCGGGGGCTGTCTCCCTGTTTTTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                   <  1:273880/151‑1 (MQ=255)
                                                                                                                       ggggcggcTGTCGGCCACCTATTTTCCCCCCCAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                              <  1:440339/149‑1 (MQ=255)
                                                                                                                          gcggcTGTCTGCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc                            <  2:1043186/150‑1 (MQ=255)
                                                                                                                             gcTTTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                          <  2:468013/149‑1 (MQ=255)
                                                                                                                                     ccAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGG‑AAAAAAATTTAAACCCGCCCTTTTTTGTGGGTATCGCTTCTGGGAACAATATGGAAAGGGGGGGGCGGGGGAGCAACGCCCGAACcgc                    >  2:802250/1‑147 (MQ=255)
                                                                                                                                      cagtttttttcCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                           <  2:1190831/133‑1 (MQ=255)
                                                                                                                                        gCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAAAAACTTTTAAACCCTCCTGTTTTGTGGGAATCGCTGCTGGTGACAAAGAGGGAAAGGGAGGGGGGGGGATCAAATCCCCAACCgcgccca               >  2:145155/1‑146 (MQ=255)
                                                                                                                                                     cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAAATTTAACCCCG‑CCTGTTTTGTGGGGATCGCTGCTTGTGACAATGTGGAAAGGGGAGGGGGGGGGAGCAACACCCGAACCGCGCCAATTTAGTTTGCCTc  >  2:979713/1‑149 (MQ=255)
                                                                                                                                                       |                                                                                                                                                   
GCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357738‑358033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑