Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8800TC43.8% 36.1 / 11.1 32K271E (AAA→GAA) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (12/6);  new base C (0/14);  total (12/20)
Fisher's exact test for biased strand distribution p-value = 1.12e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357731‑358019
                                                                                                                                                       |                                                                                                                                             
cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                               <  1:675467/150‑1 (MQ=255)
  cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                            <  2:597493/151‑1 (MQ=255)
        ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGca                                                                                                                                       >  2:733787/1‑150 (MQ=255)
           gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCACACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACATCCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                    <  1:146131/150‑1 (MQ=255)
              aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                   <  1:747260/148‑1 (MQ=255)
              aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                >  1:314963/1‑151 (MQ=255)
               aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                               <  1:555643/151‑1 (MQ=255)
               aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                               <  1:385957/151‑1 (MQ=255)
                 cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCTGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                             >  1:811103/1‑151 (MQ=255)
                          tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc                                                                                                                    >  1:759031/1‑151 (MQ=255)
                                aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                >  2:485783/1‑149 (MQ=255)
                                 aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                             >  1:594350/1‑151 (MQ=255)
                                 aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                             >  2:329554/1‑151 (MQ=255)
                                   cccccccccaccccTGTGTCGGCGCTCACCTTAATTCTTTCCCCCAAACACCCGCGCATTTACCAACCCCCATGTGAAAAAATCCCTCCGGGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTg                                                                                                            <  1:735079/138‑1 (MQ=255)
                                        ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                       >  1:214886/1‑150 (MQ=255)
                                         cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                     >  2:700539/1‑150 (MQ=255)
                                            agcccTGTGTCGGCGCCTACCGTTTTTAATTCCCGCAAACACCCGCGCTTTTACCCAACCCCAGGTGAAAAAATGCCTCCGCGGGGCCTTTCTCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                   <  2:759126/147‑1 (MQ=255)
                                                     tCAGCGGCTCCGGTGTTTATTTCCCCCAAACACCCGCGCTTTTACCAAACGCAGTGTCAAAAAATCCTTTCGCGGGGGCTGTCTGCAATGTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                             <  2:382761/147‑1 (MQ=255)
                                                          gccccccGTGTTTCATCCCCCCCAACACCCGCGCTTTTCACAACCGCATTGTGAAAAAATGCCTGCGCGGCGGCTGTCGGCAAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                               <  1:774401/135‑1 (MQ=255)
                                                               ccGTGATTCATTCCCCCCACCAACCGCGCTTTTACCCACCGCCATGTCAAAAAATCCCTGCGGGGCGGCTGTCGCCCAGCTTTTTTCCCGCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                                   <  2:83495/147‑1 (MQ=255)
                                                                     ttCATTCCCCCCAACACCCGCCATTTTACCAAACGCCATGTACAAAAAGCCCTCCGCGGCGGCTTCCTGCCGGTTTTTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                          <  1:225395/149‑1 (MQ=255)
                                                                               ccAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCTGAGAGAAAAAATTTAGTCCGTCATGTtgtgt                                                                   >  1:203953/1‑146 (MQ=25)
                                                                                  accacccgcatttttACCCAGCGCCAGGTGAAAAACTGCTTGCGGGGGGTCTGTCGCCCAGTTTTTTTCCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                               <  1:65712/136‑1 (MQ=255)
                                                                                       ccGCGCTTTTCCCCACCCCCATGCGAAAAACTCCTTCCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                            <  1:228436/146‑1 (MQ=255)
                                                                                              tttACCCAACGCCAGGACAAAAATTTCCTCGGGGGCGGTTTTCTGCCGGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                      <  1:785538/145‑1 (MQ=255)
                                                                                                       ccccATGTAAAAAAATCCCTCCGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                      <  1:853991/149‑1 (MQ=255)
                                                                                                           aTGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAACCCCTCATTTTTTGTTGGGATAGCTGCCGGTGAACaaatgggaaggg                                   >  2:794437/1‑141 (MQ=255)
                                                                                                                aaaaaaTCCTTCCGCGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                             <  2:116116/150‑1 (MQ=255)
                                                                                                                 aaaaaTGCTTCGGCGGCGGTTGTCTGCCAGCTTTTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                <  2:159876/147‑1 (MQ=255)
                                                                                                                  aaaactgctgcgcgGGGGCCTGTCTCCCCGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                 <  1:729017/136‑1 (MQ=255)
                                                                                                                          ttCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAACCCCTCACTGTTTGTTGGCAGCACTGCTGGTTACAATGGGGGAAGGGGAgggaggggg                       >  2:410447/1‑139 (MQ=255)
                                                                                                                                        tcggaaggtttttttcCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg       <  1:385731/139‑1 (MQ=255)
                                                                                                                                        gcTGCCGGTTTTTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa           <  1:444663/145‑1 (MQ=255)
                                                                                                                                            ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa  <  1:285797/151‑1 (MQ=255)
                                                                                                                                                       |                                                                                                                                             
CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357731‑358019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: