Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA50.0% 12.8 / 30.0 36L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/2);  new base A (1/17);  total (17/19)
Fisher's exact test for biased strand distribution p-value = 6.45e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357740‑358037
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cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                        >  2:861954/1‑151 (MQ=255)
     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAc                                                                                                                                                   >  1:729741/1‑151 (MQ=255)
        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                                >  1:1108676/1‑151 (MQ=255)
         gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                                               <  1:1046540/151‑1 (MQ=255)
             cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtc                                                                                                                                           >  2:533896/1‑151 (MQ=255)
             cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtc                                                                                                                                           >  1:679141/1‑151 (MQ=255)
               cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctc                                                                                                                                         >  1:141718/1‑151 (MQ=255)
                   aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGCCTGCCAGCTATTTTT‑CCGCCGCACAAAAACCGCCGCtgtctc                                                                                                                                       >  2:938360/1‑149 (MQ=255)
                               cggcacctttgtgCCAGCGCTTACCGTTTTTCTTTCCCCCCAACACCCCCTTATTTACCCAACCCCAT‑TGCAAAAATT‑CCTTTCGGGGCGTTTGTTGACCATTTTTTTTC‑CCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                            <  1:1081707/139‑1 (MQ=255)
                               ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                          >  1:825266/1‑150 (MQ=255)
                                        tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                           >  2:973800/1‑140 (MQ=255)
                                          tgtCAGCGCCACCCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTCCCCACCCCCTTGTAAAAAAGTC‑CC‑TGCGCGGGGGCTGCCGGCCGTTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAAt                                                                                                            <  2:557938/150‑1 (MQ=255)
                                                     aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGA‑GAAAAAAGCTTTAAAcc                                                                                                 >  1:251915/1‑151 (MQ=25)
                                                      ccGTGTTTCATTCCCCCCAACACCCCCGCTTTTACCCACCGCCTTGTGAAAAAAGG‑CC‑TCGGCGGCGGCTGCCCGCAGGCT‑TTTTC‑CCGCGAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTa                                                                                                     <  2:229941/144‑1 (MQ=255)
                                                           aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCAGA‑G‑GAAAAGCttttatctc                                                                                                >  1:997200/1‑139 (MQ=25)
                                                            ttCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAAA‑G‑GAAAAgagatatgtcccgc                                                                                             >  1:727787/1‑134 (MQ=25)
                                                                   ccccaaacaccCGCCCATTTACCCACCGCAATGTGAAAAAGTC‑CC‑TTCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                  <  1:318028/146‑1 (MQ=255)
                                                                       caacaaCCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGG‑G‑GAAAAACATTAAAACCCTCCTGTTGTgggggg                                                                                >  2:77207/1‑147 (MQ=21)
                                                                                           accGCCTTGTGAAAAAATG‑CC‑TTCGCGGCGGCTGTCTCCCAGCTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                             <  1:826172/146‑1 (MQ=255)
                                                                                             cGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAGG‑AAAAAGATTTAA‑CCCCCCCTGTTTTGTGGGGATCgctgcgcgggaca                                                                >  2:532123/1‑135 (MQ=25)
                                                                                              gCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GAAGA‑G‑AAAAAAAATTAAAAACGCCCTGCTGTGTGGGGATCGCTGCTggggaaaaagtgg                                                          >  2:776593/1‑137 (MQ=25)
                                                                                               ccATGTGAAAACCCG‑CC‑TTCGCGGGGGCTCTCTCCCGGTTTTTTTC‑CCGCGAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                          <  1:512607/147‑1 (MQ=255)
                                                                                                cattggCAAAAATGCCC‑TCCGGGGCGG‑TTTCCGCCCGGTTTTTTCCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                                        <  2:155835/144‑1 (MQ=255)
                                                                                                        aaaaTC‑CC‑TCCGCGGCGGTCGCCTGCCATTTTTTTCC‑CCGCACAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                               <  2:191624/149‑1 (MQ=255)
                                                                                                         aaaTG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCAGA‑A‑GAAAAACTTTAATCCCGTCCTGTTGTTTGGGAATAGGCGGTGGTGAAAAAGTGGAGAGGGGAgggggg                                            >  1:876695/1‑146 (MQ=255)
                                                                                                            aatccttccggggcggcTGTCTCCCATCTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                           <  1:326783/140‑1 (MQ=255)
                                                                                                                  ttCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCACAA‑A‑AAAAAAATTTAAACCC‑CCCTGTTTTGTGGGGAACGCCTCTGGGGACAATGTGGAAAAGGGAgggggggggagcc                                     >  1:176077/1‑139 (MQ=255)
                                                                                                                     gggggggcTGTCCGCCATTTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa                                        <  2:1146210/140‑1 (MQ=255)
                                                                                                                       ggcggcTGCCTCCCACTTATTTTT‑CCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                     <  1:1059006/146‑1 (MQ=255)
                                                                                                                        gcggcTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GAAGA‑GAAAAAAGGTTTAACCCCG‑CCTGCTGTTGGGGAATTGGTGCCGGGGACAAAGTGGGGAGGGGAGGGGGGCGTAGCAGCttcc                               >  2:354142/1‑148 (MQ=255)
                                                                                                                          gccgctctccttaatATTTTC‑CCGCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                                 <  1:442226/133‑1 (MQ=255)
                                                                                                                                 tgccattttttttc‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                            <  2:235596/136‑1 (MQ=255)
                                                                                                                                  tcgggtttttttt‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                      <  2:300404/142‑1 (MQ=255)
                                                                                                                                   caattttttttc‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                         <  1:108938/139‑1 (MQ=255)
                                                                                                                                         tttttc‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt                 <  1:1124919/147‑1 (MQ=255)
                                                                                                                                             ttccccccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt            <  1:862002/144‑1 (MQ=255)
                                                                                                                                                    cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa     <  2:1164568/150‑1 (MQ=255)
                                                                                                                                                       aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATg  <  2:727762/150‑1 (MQ=255)
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CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357740‑358037

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: ‑