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→TTTcynRtranscriptional 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

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  NC_000913/357743‑358029
                                                                                                                                                      |                                                                                                                                           
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                           >  2:52771/1‑150 (MQ=255)
  aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                        >  1:681134/1‑151 (MQ=255)
   aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                       <  1:374544/151‑1 (MQ=255)
     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                     <  2:808625/151‑1 (MQ=255)
      gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGTTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                    >  1:693086/1‑151 (MQ=255)
           gcATCAGGCAATTCCAGCCGCAGACCTGCGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                                >  2:1022937/1‑150 (MQ=255)
            cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                              >  1:461253/1‑151 (MQ=255)
             aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                             >  1:250419/1‑151 (MQ=255)
               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                           >  2:576517/1‑151 (MQ=255)
                aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                           >  1:993155/1‑150 (MQ=255)
                 ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                           >  1:649908/1‑149 (MQ=255)
                           gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                               >  2:856125/1‑151 (MQ=255)
                            cgggagccggtttgcAGCGGCTCCCGTTATTCATTCCCCCCAACACCCCCGCTTTAACCCAACGCCATTGAAAAAATTTCCTCCGCGGCGGCTGTCGCCAGGCTATTTTCCCGCCGCAAAAACTCCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                <  2:707086/135‑1 (MQ=255)
                                agcccTGTGTCAGCGGTTCCCGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCCACCCCCATGTGCAAAAATGCCTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                            <  1:881477/146‑1 (MQ=255)
                                aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggtaca                                                                                                           >  2:724006/1‑146 (MQ=255)
                                 gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                              >  2:1041696/1‑146 (MQ=255)
                                  aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                >  1:526981/1‑143 (MQ=255)
                                      gtgtcggggcttACCGTGTTTCATTCCCCCAAACACCCGCCCTTTTACCAAACCCCATGTAAAAAAATCCCTTCGCGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                       <  1:872673/137‑1 (MQ=255)
                                       tgtCGGCGGCTCCCGTTATTCTTTCCCCCCAACACCCGCCTTTTTACCCACCCCCATGGAAAAAAATGCCTTCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                                     <  1:558753/149‑1 (MQ=255)
                                          cggCGGCTCCCGTGATTCATTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTGCAAAAATGCCTTCGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGc                                                                                                 <  1:837524/148‑1 (MQ=25)
                                          cagcgccccccGTGATTCTTTCCCCCCAACACCCCCGTATTTCCCCAACGCCATGTACAAAAAGCCTTTCGGGGCGGCTTTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                                <  2:1069741/142‑1 (MQ=255)
                                          cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaa                                                                                                     >  2:136989/1‑146 (MQ=255)
                                              gccccccttgtttCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTAAAAAAATCCCTTCGCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                                     <  2:649885/131‑1 (MQ=255)
                                                    cgttttttaTTTCCCCCAAACACCCCCCATTTACCCAAACGCCATGTAAAAAAATGCCTCCGCGGGGGCTGTCGGCCAGCTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcca                                                                                        <  2:749663/142‑2 (MQ=255)
                                                    cGTTATTCTTTCCCCCCAACCCCCGCGCTTTTACCCACCGCCAGTTACAAAATTGCTTCCGCGGCGCCTTTCTCCCGGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                        <  1:1090802/149‑1 (MQ=255)
                                                        aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGaaaaaaattttaaacc                                                                                        >  1:1059186/1‑132 (MQ=25)
                                                                        acccGCGCTTTTACCCACCGCCATGTACAAAAACGCCTCCGCGGCGGCTTTCTGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                    <  1:260298/147‑1 (MQ=255)
                                                                                         accGCCATGTGAAAAAATCCCGTCGGGGCGGCTGTCTGCGAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                   <  2:488660/148‑1 (MQ=255)
                                                                                         accGCAATGTGCAAAAAGCCCTGCGGGGCGGCTGTCTCCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                   <  1:779521/148‑1 (MQ=255)
                                                                                               aTGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGGAAGAAAAAACCTTAATCCCCCCATGTTTTTGGGCCATGGCCGCCGGGAACaaccaggggaagg                                            >  1:114905/1‑140 (MQ=255)
                                                                                                 gtgAAAAATGGCCTGCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                             <  1:612156/148‑1 (MQ=255)
                                                                                                     aaaaaTGCTTTCGCGGCGGCTGTCCGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                      <  1:122662/151‑1 (MQ=255)
                                                                                                               tcggcggcgTCTTTCGCCCGGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                              <  1:373024/147‑1 (MQ=255)
                                                                                                                    ggcggcTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc                           <  1:265298/148‑1 (MQ=255)
                                                                                                                              tGCCAGTTTTTTGCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                   <  2:801544/146‑1 (MQ=255)
                                                                                                                                            cccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg  <  2:681113/149‑1 (MQ=255)
                                                                                                                                             ccgcccCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc   <  1:1082892/148‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                           
ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  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: