Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8800TC50.0% 36.8 / 16.0 40K271E (AAA→GAA) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (14/6);  new base C (0/20);  total (14/26)
Fisher's exact test for biased strand distribution p-value = 3.34e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357734‑358019
                                                                                                                                                   |                                                                                                                                            
gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                          >  1:936788/1‑151 (MQ=255)
     ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                                     <  2:579442/151‑1 (MQ=255)
     ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                                     <  2:249155/151‑1 (MQ=255)
         aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                  >  2:525228/1‑150 (MQ=255)
            aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                              <  2:43777/151‑1 (MQ=255)
              cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                            <  1:383075/151‑1 (MQ=255)
               gTAGCGCATCAGGCAATTCCAGCCGCAGCCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                           <  1:210695/151‑1 (MQ=255)
                  gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt                                                                                                                        >  1:943871/1‑151 (MQ=255)
                      aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                    >  2:580484/1‑151 (MQ=255)
                      aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                    >  2:358346/1‑151 (MQ=255)
                               ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                           >  2:950597/1‑151 (MQ=255)
                               tcccAGCCGCAGACTTGTGCCGGCGGCTCCCGTTATTTTTTCCCGCCAACACCCGCGCTTTTACCCACCCCATTGTCAAAAAATCCTTCC‑GCGGCGGTTGTCGGCCAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCagta                                                                                                              <  1:953525/146‑1 (MQ=255)
                               tcccAGCCGCAGACCTGTGTAAGCGGCTACCGTGATTCTTTTCCGCCAACACCCGCGCATTTATCCACCGCCATGTGAAAAAATGCCTTC‑GGGGCGGCTTTCTGCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCagta                                                                                                              <  2:122924/146‑1 (MQ=255)
                                  cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                        >  2:813584/1‑151 (MQ=255)
                                      cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                    >  2:757127/1‑150 (MQ=255)
                                            ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggcaaag                                                                                               >  1:676105/1‑144 (MQ=255)
                                               gtgtCAGCGGCTACCGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCCAACGCCTTGTGAAAAAATCCCTCC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                            <  2:465013/150‑1 (MQ=21)
                                                 gtgaGCGGTCACCGTGTTTCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTCAAAAATTGCCTTC‑GGGGCGGCTGTCTGCCATTTTTTTTCCCCCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                         <  2:482842/148‑1 (MQ=255)
                                                     gCGGCTCCCGTATTTCATTCCCGCCAACACCCGCGCTTTTACCCACCCCCATGTGCAAAAATGCCTCC‑GCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                             <  2:179007/143‑1 (MQ=255)
                                                     gCGGCTACGGTTATTCATTCCCGCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                      <  2:651621/150‑1 (MQ=25)
                                                         ctcccGTGTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCGTGTAAAAAAATCCTTCC‑GCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                     <  1:948903/144‑1 (MQ=255)
                                                            ccGTTATTCATTCCCGCAAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                                 <  2:502481/148‑1 (MQ=255)
                                                            ccGTGTTTCATTCCCGCAAACACCCGCCCTTTTA‑CCCACCCCATTGTCAAAAATTCCTTCGGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                     <  1:936379/144‑1 (MQ=255)
                                                             cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGaaaaaaaattttaacc                                                                               >  2:835132/1‑136 (MQ=25)
                                                               tGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACtttttatcc                                                                               >  2:47660/1‑141 (MQ=25)
                                                                 tttCATTCCCCCCAACACCCGCCCTTTTACCAACCCCCATG‑GCAAAAATTCCTTCGGGGGCGGCTGTCGCCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                                 <  1:525217/142‑1 (MQ=255)
                                                                         ccGCCAACACCCGCGCATTTACCCACCGCAATGTGAAAAAATGCCTCC‑GCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                     <  1:270369/147‑1 (MQ=255)
                                                                          cccaaacaccCGCGCATTTACCAACCGCCATGTG‑AAAAATGCCCTCGGCGGCGGTGGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                <  1:198183/147‑1 (MQ=255)
                                                                          cGCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTCC‑GCGGCGGTTTTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                <  1:859358/151‑1 (MQ=255)
                                                                             caacaaCCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAGGAAAAAAATTTTAACCCGTCCCGTTTTGTgggga                                                              >  2:541101/1‑147 (MQ=21)
                                                                                      cgcATTTCTCAACCCCCTTGTGCAAAAAGGCTTCC‑GGGGCGTCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                        <  2:883463/147‑1 (MQ=255)
                                                                                          tttATCCAACGCCATGTGAAAAAATCCCTTC‑GCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                  <  2:542785/149‑1 (MQ=255)
                                                                                          tttACCCACCCCCTTGTCAAAAAATCCCTCC‑GCGGCGGCTGTCGCCCAGTTTTTTTCCCCCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                 <  2:52815/150‑1 (MQ=255)
                                                                                                    gCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGGAAAAAATTTTAACCCCCCCTGTTTTTTGGGGATAGCGGCTGGGAACAATAT‑gg                                        >  2:646341/1‑148 (MQ=25)
                                                                                                               aaaTGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAGAAAAAAATTTTAAACCCTCCTGTTTTGGGGGGATCGCTGCTGGGGAAAAAGTGGGAAAGGGagggggg                           >  2:575494/1‑145 (MQ=255)
                                                                                                                        c‑gcgCCGCCTTTCTCCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAg                  <  2:945602/150‑1 (MQ=255)
                                                                                                                            ggcggtTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCa                   <  2:577242/146‑1 (MQ=255)
                                                                                                                            ggcggtTGTCGGCCAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGGAAGGGAAGTGCGGCGAATc                    <  2:94836/145‑1 (MQ=255)
                                                                                                                                     cgcccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTcc              <  1:580473/139‑1 (MQ=255)
                                                                                                                                        ccAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa  <  2:703779/151‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                            
GTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357734‑358019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑