Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_007779357,1040TC53.8% 1.3 / 36.0 26K271E (AAA→GAA) cynRtranscriptional regulator CynR
Reads supporting (aligned to +/- strand):  ref base T (12/0);  new base C (0/14);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.04e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.92e-05
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCC  >  NC_007779/356897‑357327
                                                                                                                                                                                                                 |                                                                                                                                                                                                                               
cTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCCTTTATCCCACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCCGCTATTTTTCCCCCGCCACAAAACCCCCCTtctctc                                                                                                                                                                                                      >  1:1308439/1‑235 (MQ=255)
   tAGTTTATGCCGGACGCGGCGTGAACCCCTTATCCCGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCCACCGTGATTCATTTCCGCCAACAACCCCCCATTTATCCAACCCCCCGGTCACAAAT‑G‑CCCTCGCGGCGGCCTTCCGCCCGCCATTTTTTCGCCGCAACAAAACCGCCGTtctcgtcan                                                                                                                                                                                                   >  2:1167930/1‑230 (MQ=17)
       ttATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCCATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCCATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCcggagt                                                                                                                                                                                               >  1:181107/1‑235 (MQ=255)
           gCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCCGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCCGTAGTGGCg                                                                                                                                                                                           >  1:896206/1‑235 (MQ=255)
             cGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                                                                                         >  1:1341656/1‑235 (MQ=255)
             cGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCAACAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCCGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCCGTAGTGGCggg                                                                                                                                                                                         >  1:1920390/1‑235 (MQ=255)
              ggATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCCGTAGTGGCgggg                                                                                                                                                                                        >  1:342629/1‑235 (MQ=255)
              ggATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGGTCTCTCCagtcttgctctta                                                                                                                                                                                        >  1:1118466/1‑225 (MQ=255)
                  gcggcgTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCCACAAAACCGCCGTTCTCTCCAGGAGGGGCgggggggg                                                                                                                                                                                    >  2:478280/1‑231 (MQ=255)
                                          tACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAAGAAAAGCATTTAACCCgccctg                                                                                                                                                            >  1:1582016/1‑230 (MQ=255)
                                                     cTGAACGCGTGGGCCTGATAGGCGGACCGCATCACGCAATCCCACCCGCAGCCCTGTGTCGGCGGCTACGTTGATTCTTTCCCGCCACCACCCGCCCTTTTACCCACCGCCAGGCGAAAAAAT‑G‑CCTCGGGGGGGGTTGTCTGCCTGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                                                                                                 <  2:1308439/235‑1 (MQ=255)
                                                       naccccggcgcccTGAAACGCTTAGCCCATCAGCCAACCCCACCCGCACCCCTGTGGCAGCGGCTCCCGTTATTCATCCCCGCCACCACCCGCGTATTTACCCACCGCAAGGAGAAAAACT‑C‑CTTCCGGGGCGGTTTTCTGCCATTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                                                                                               <  2:505965/224‑1 (MQ=255)
                                                                 gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAAAATTTAAAAACGCCCTGTTGTGTTGGGATAGCTGCggggg                                                                                                                                     >  1:973496/1‑233 (MQ=18)
                                                                                        gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGCGAAAAAACTTTTAGCCCCTCCCGTTTTGTGGGGATCGCTGCTGGGGACAATGTTgggagggaggagggg                                                                                                              >  1:48354/1‑228 (MQ=21)
                                                                                           accccAGCCGCACGCCTGTGGCCGCGGCTCCCGTTCTTCATCCCCCACAACACCCGCGCATTTCACCAACGCCATGAACAAAAAT‑C‑CCTCCGCGGCGGCTGTCTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                                                                                           <  2:1484080/232‑1 (MQ=255)
                                                                                                                                 ctttccccccAACACCCGCCATTTTACCCACCGCCTTGTAAAAAATG‑G‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt                                                                     <  1:111863/227‑1 (MQ=255)
                                                                                                                                 ctttcccGCCAACACCCGCGCTTTTATCC‑ACCCCATTGAAAAAAATGG‑CCTTGGGGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt                                                                     <  1:1268666/230‑1 (MQ=255)
                                                                                                                                 ctctccccccAACCCCCGCGCATTTCCCCCACTCCGTGTAAAAAAGG‑G‑CCTGCGGGGCGTCTGTCCGCCATTTATTGCCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt                                                                     <  2:1019583/227‑1 (MQ=255)
                                                                                                                                 cATTCCCCCCAACACCCGCGCTTTTCCCCCACCCCATGTACAAAATT‑G‑CTCCCGGGGCGTCTGTCTGCCATCTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt                                                                     <  1:1929579/235‑1 (MQ=255)
                                                                                                                                 cATTCCCCCCAACACCCGCCCTTTTACCCACCGCCATGCGCAAAAAC‑C‑CTTCCGGGGCGGTTTTCTGCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt                                                                     <  1:383973/235‑1 (MQ=255)
                                                                                                                                        gCCAGCACCCGCGAATTAAGCCACCGCGAGGTGCAAAAAT‑G‑CCTCCGGGGGGGCTGTCTACCGTCTATTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGaccacc                                                              <  1:327478/235‑1 (MQ=255)
                                                                                                                                        gCCAACACCCGCGTATTTACCCACCGCCATGTGAAAAAGT‑G‑CCTCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGaccacc                                                              <  1:478280/235‑1 (MQ=255)
                                                                                                                                            accaccccctctttACCCCACCCCCTGCGCAAAAAG‑CCCCTCCGCGGCGGTTGCCGGCCATTTTTTTCCCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCtgt                                                           <  1:399659/224‑1 (MQ=255)
                                                                                                                                                                        caaaaaaT‑G‑CTGGCGGGGCGGCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTg                              <  1:513147/233‑1 (MQ=255)
                                                                                                                                                                                              cctgccggcaaGCTTTTTGCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCtggtgg          <  1:1063156/225‑1 (MQ=255)
                                                                                                                                                                                                      cagcttATTTTCCCGCCGCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTcc  <  1:859201/230‑1 (MQ=255)
                                                                                                                                                                                                                 |                                                                                                                                                                                                                               
CTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCC  >  NC_007779/356897‑357327

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: ‑