Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA62.7% ‑4.6 / 45.6 51L267F (TTG→TTTcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (9/10);  new base A (0/32);  total (9/42)
Fisher's exact test for biased strand distribution p-value = 3.04e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.35e-03

AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357745‑358037
                                                                                                                                                      |                                                                                                                                                     
aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                                 <  1:527466/151‑1 (MQ=255)
            tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc                                                                                                                                     >  2:1002227/1‑151 (MQ=255)
               gcaaaTCCCAGCCGAGGCCTTGTGTCAGCGGCTCCCGTGATTCATTCCCGCAAACACCCGCGCTTTTATCCAACGCCATGTGCAAAAATGCCTCCGCGGCGGCTGTCTGCAAGTTATTTTTCCGCCGCAAAAAAAccgccg                                                                                                                                            <  1:1185898/138‑1 (MQ=17)
                    tcccACCCGCAGCCTGGTGCCGGGGGCTACGGTGTTTATTTCCCGCAAAAACCCGCGCTTTTACCCAACCCCTTGTAAAAAAATGCTTCCGGGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                              <  2:1211666/148‑1 (MQ=255)
                     tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                            >  1:851415/1‑151 (MQ=255)
                      ccggCCGGAGCCTTGTGCCGGCGGCTACCTTGATTTTTTCCCCCAAACACCCGCACATTTACCCACCCCCTTTGGAAAAATTGCCTCCGCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                             <  2:1015942/146‑1 (MQ=255)
                       cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                         >  2:998059/1‑151 (MQ=255)
                        aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        >  2:97630/1‑151 (MQ=255)
                          ccGCAGCCCTGGGCCAGCGCCTACCGTATTTCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATCCCTCCGGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       <  2:642170/150‑1 (MQ=255)
                          ccGCAGACCTGTTCAGCCGGAACCCTTATTTCATTCCCGCAAACACCCGCGATTTACCCCAACGCAAGGTACAAAATGCCTTGCGCGGGGGCTGTCTGCAACCTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                      <  2:1198551/151‑1 (MQ=255)
                           cgcaacctggtgcCAGCGGCTCCCGTTTTTCATTCCCCCCAACACCCGCGCTTTAACCCAACGCCTTGTAAAAAAATCCCTCCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                      <  1:1209561/141‑1 (MQ=255)
                           cgaagcccTGTGTCAGGGGCTCCCGTGTTTCTTTCCCGCCACCACCCGCGCTTTTACCAACCCCAATGTGAAAAATTGCCTCCGGGGCGGCTTTCTGCTAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                     <  2:1139967/145‑1 (MQ=255)
                             cggccgtttgccggCGTCTACCGTAATTCTTTCCCCCCACCACCCGCGTTTTTACCCACCCCCATGAGAAAAAAGGCCTCCGGGGGGGTTTTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                     <  1:922202/136‑1 (MQ=255)
                               gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        >  2:187327/1‑144 (MQ=255)
                                        cggcgcCTACCGTAATTCTTTCCCCCCAACACCCCCCCTTTTATCCAACCCAATGTGCAAAAATGCCTTCGGGGCGGCTGTCGGCCCGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                                          <  2:515583/147‑1 (MQ=255)
                                            gcctccgttGATTCTTTCCCCCCAACACCCCCGCATTTACCCACCGCCATGTGAAAAAATCCCTCCGCGGCGGTTTCCGGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                                           <  1:115389/136‑1 (MQ=255)
                                            gcctcccGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTCCGGGGGGGCTGTCTGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                                        <  2:825477/142‑1 (MQ=255)
                                               tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAGAttt                                                                                                      >  1:584735/1‑146 (MQ=255)
                                                cccGTGTTTCTTTCCCCCCAACACCCGCCCTTTTACCAACCCCAAGGTGAAAAAATCCCTCCGGGGGGGCTGTCGGCAAGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                                <  1:139969/150‑1 (MQ=255)
                                                cccGTGTTTCTTTCCCCCAACCACCCGCGCTTTTACCCACCGCCTGGTAAAAAAATGCCTCCGGGGCGGTTGTCGGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                                                  <  1:1061724/148‑1 (MQ=255)
                                                aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTaaaacc                                                                                                >  2:556077/1‑147 (MQ=25)
                                                 ccGTGTTTTTTTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTCCGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                                <  2:159503/150‑1 (MQ=25)
                                                 ccGTGATTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCTTGTGAAAAAATGCCTTCGCGGCGGCTGTCGGCCAGTTTTTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                                                  <  2:788332/148‑1 (MQ=255)
                                                    tGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGgaaaaagttt                                                                                                      >  2:592861/1‑134 (MQ=25)
                                                     gATTCTTTCCCCCCAACACCCGCCTATTTACCCACCCCCAGGTCCAAAAAGCCCTCCGGGGGGCTTGTCCGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                                              <  1:171552/148‑1 (MQ=255)
                                                        ttCTTTCCCGCAAACACCCGCGATTTTACCAAACGCCATGTGAAAAATTGCCTCCGGGGGGGTTGTCGGCCACTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                                          <  2:452240/150‑1 (MQ=255)
                                                              ccccccAACACCCCCCCTTTTACCCACCGCCATGTGAAAAAATCCCTCCGCGGCGGCTGTCTGCAAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                   <  1:556026/147‑1 (MQ=255)
                                                                        acccGCGCATTTACCCACCGCAATGTGAAAAAATCCCTTCGGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                             <  2:845587/146‑1 (MQ=255)
                                                                                 tttATCCACCGCCATGAAAAAAAGTCCCTGCGCGGGGGTTTCCGCCCAGTTTTTTTCCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGt                                                                    <  1:786247/148‑1 (MQ=255)
                                                                                       ccACCGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                              <  1:370226/149‑1 (MQ=255)
                                                                                       ccAACGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                               <  2:954857/148‑1 (MQ=255)
                                                                                           cGCCATGTAAAAAAATGCCTTCGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGACAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                                            <  2:14748/147‑1 (MQ=255)
                                                                                             ccATGTGAAAAAAGCCCTCCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                                                       <  2:449158/150‑1 (MQ=255)
                                                                                                      aaaaaTGCTTGCGTGGCGGATGACTGCAACAAATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                                 <  2:462029/148‑1 (MQ=255)
                                                                                                      aaaaaGGCCTGCGCGGCGGCTTTCTCCCATCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                                <  1:568480/149‑1 (MQ=255)
                                                                                                         aaaccctcccgcgCCGGTTGTCAGCCGTTTTTTTTCCCCCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                            <  1:278901/142‑1 (MQ=255)
                                                                                                                   gggggggcTGTCGGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                      <  2:1066980/142‑1 (MQ=255)
                                                                                                                       cggcTTTCCGCCAGCTATTTCCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                               <  1:812295/150‑1 (MQ=255)
                                                                                                                              cTGCCAGTTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                              <  1:1143432/144‑1 (MQ=255)
                                                                                                                               ggccggttATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                           <  1:1218756/139‑1 (MQ=255)
                                                                                                                                 ccAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                          <  1:145731/145‑1 (MQ=255)
                                                                                                                                  ccactttttttCCCACCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa                    <  1:1002127/145‑1 (MQ=255)
                                                                                                                                     tatttttcCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                     <  1:1230355/127‑1 (MQ=255)
                                                                                                                                      ttttttcCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa                   <  1:1064137/145‑1 (MQ=255)
                                                                                                                                      ttttttcCCCCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                  <  1:899604/146‑1 (MQ=255)
                                                                                                                                      tttttccccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg                <  1:604086/143‑1 (MQ=255)
                                                                                                                                       tttttcCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg                <  2:551856/148‑1 (MQ=255)
                                                                                                                                        ttttcCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa               <  2:25172/149‑1 (MQ=255)
                                                                                                                                        ttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg              <  2:694655/150‑1 (MQ=255)
                                                                                                                                          ttcccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt            <  2:124324/147‑1 (MQ=255)
                                                                                                                                                ccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAAATTTAACCCGCCCTGTTTTGTGGGCATTGCTGCTGGTAACAATATGGGAAGGGGAGAGGGGGGGAACAGACCCAGGACCCCGCCCAATGAGttt           >  2:73755/1‑144 (MQ=255)
                                                                                                                                                   caacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAGGAAAAAAAATTTAAGCCGTCCTGTTGTGTGGGGAACGCTGCTGGGGACAAAATGGGAAAGGGAGAGGGGGGGATCAGCCCCCCAACCCCGCCAATTGAGTTTGCCCCCATg  >  2:984988/1‑151 (MQ=255)
                                                                                                                                                      |                                                                                                                                                     
AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357745‑358037

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: