Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA50.0% 37.8 / 19.0 36L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/3);  new base A (0/18);  total (15/21)
Fisher's exact test for biased strand distribution p-value = 2.93e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  NC_000913/357743‑358029
                                                                                                                                                      |                                                                                                                                           
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGcaacaa                                                                                                                                           >  2:52771/1‑150 (MQ=255)
  aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAAc                                                                                                                                        >  1:681134/1‑151 (MQ=255)
   aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                       <  1:374544/151‑1 (MQ=255)
     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                     <  2:808625/151‑1 (MQ=255)
      gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGTTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                    >  1:693086/1‑151 (MQ=255)
           gcATCAGGCAATTCCAGCCGCAGACCTGCGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                                >  2:1022937/1‑150 (MQ=255)
            cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                              >  1:461253/1‑151 (MQ=255)
             aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                             >  1:250419/1‑151 (MQ=255)
               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                           >  2:576517/1‑151 (MQ=255)
                aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                           >  1:993155/1‑150 (MQ=255)
                 ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                           >  1:649908/1‑149 (MQ=255)
                           gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                               >  2:856125/1‑151 (MQ=255)
                            cgggagccggtttgcAGCGGCTCCCGTTATTCATTCCCCCCAACACCCCCGCTTTAACCC‑AACGCCAT‑TGAAAAAATTTCCTCCGCGGCGGCTGTC‑GCCAGGCTATTTTCCCGCCGCAAAAACTCCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                <  2:707086/135‑1 (MQ=255)
                                agcccTGTGTCAGCGGTTCCCGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCC‑ACCCCCATGTGCAAAAA‑TGCCTCCGGGGCGGCTGTCTGCCA‑GTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                            <  1:881477/146‑1 (MQ=255)
                                aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggtaca                                                                                                           >  2:724006/1‑146 (MQ=255)
                                 gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                              >  2:1041696/1‑146 (MQ=255)
                                  aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                >  1:526981/1‑143 (MQ=255)
                                      gtgtcggggcttACCGTGTTTCATTCCCCCAAACACCCGCCCTTTTACCA‑AACCCCATGTAAAAAAA‑TCCCTTCGCGGCGGTTGTCTCCCA‑GTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                       <  1:872673/137‑1 (MQ=255)
                                       tgtCGGCGGCTCCCGTTATTCTTTCCCCCCAACACCCGCCTTTTTACCC‑ACCCCCATGGAAAAAAA‑TGCCTTCGGGGCGGCTGTCTCCCA‑GTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                                     <  1:558753/149‑1 (MQ=255)
                                          cggCGGCTCCCGTGATTCATTCCCGCCAACACCCGCGCTTTTACCC‑ACCGCCATGTGCAAAAA‑TGCCTTCGGGGCGGCTGTCTGCCA‑GCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGc                                                                                                 <  1:837524/148‑1 (MQ=25)
                                          cagcgccccccGTGATTCTTTCCCCCCAACACCCCCGTATTTCCCC‑AACGCCATGTACAAAAA‑GCCTTTCGGGGCGGCTTTCTGCCA‑GCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                                <  2:1069741/142‑1 (MQ=255)
                                          cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaa                                                                                                     >  2:136989/1‑146 (MQ=255)
                                              gccccccttgtttCTTTCCCCCCAACACCCGCGCTTTTACCC‑ACCCCCATGTAAAAAAA‑TCCCTTCGCGGCGGTTGTCTGCCA‑GTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                                     <  2:649885/131‑1 (MQ=255)
                                                    cgttttttaTTTCCCCCAAACACCCCCCATTTACCCAAACGCCATGTAAAAAAA‑TGCCTCCGCGGGGGCTGTCGGCCA‑GCTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcca                                                                                        <  2:749663/142‑2 (MQ=255)
                                                    cGTTATTCTTTCCCCCCAACCCCCGCGCTTTTACCC‑ACCGCCAGTTACAAAAT‑TGCTTCCGCGGCGCCTTTCTCCCG‑GTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                        <  1:1090802/149‑1 (MQ=255)
                                                        aTTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGaaaaaaattttaaacc                                                                                        >  1:1059186/1‑132 (MQ=25)
                                                                        acccGCGCTTTTACCC‑ACCGCCATGTACAAAAA‑CGCCTCCGCGGCGGCTTTCTGCCG‑GTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                    <  1:260298/147‑1 (MQ=255)
                                                                                         accGCCATGTGAAAAAA‑TCCCGTCGGGGCGGCTGTCTGCGA‑GTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                   <  2:488660/148‑1 (MQ=255)
                                                                                         accGCAATGTGCAAAAA‑GCCCTGCGGGGCGGCTGTCTCCCA‑GCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                   <  1:779521/148‑1 (MQ=255)
                                                                                               aTGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGGAAGAAAAAACCTTAATCCCCCCATGTTTTTGGGCCATGGCCGCCGGGAACaaccaggggaagg                                            >  1:114905/1‑140 (MQ=255)
                                                                                                 gtgAAAAAT‑GGCCTGCGGGGCGGCTGTCTGCCA‑GTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                             <  1:612156/148‑1 (MQ=255)
                                                                                                     aaaaa‑TGCTTTCGCGGCGGCTGTCCGCCA‑GTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                      <  1:122662/151‑1 (MQ=255)
                                                                                                               tcggcggcgTCTTTCGCCCG‑GTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                              <  1:373024/147‑1 (MQ=255)
                                                                                                                    ggcggcTGTCTGCCA‑GTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc                           <  1:265298/148‑1 (MQ=255)
                                                                                                                              tGCCA‑GTTTTTTGCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                   <  2:801544/146‑1 (MQ=255)
                                                                                                                                            cccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg  <  2:681113/149‑1 (MQ=255)
                                                                                                                                             ccgcccCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc   <  1:1082892/148‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                           
ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCCA‑GCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  NC_000913/357743‑358029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑