Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8750AT42.6% 52.1 / 30.7 54N272K (AAT→AAAcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (18/13);  new base T (0/23);  total (18/36)
Fisher's exact test for biased strand distribution p-value = 3.34e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCG  >  NC_000913/357726‑358014
                                                                                                                                                         |                                                                                                                                             
cTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                              >  1:170011/1‑151 (MQ=255)
  gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                              <  2:592553/149‑1 (MQ=255)
   aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                           >  2:493177/1‑151 (MQ=255)
    aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                          <  1:543245/151‑1 (MQ=255)
       cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                        <  1:287310/149‑1 (MQ=255)
           ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                                                                                                                   >  2:738367/1‑150 (MQ=255)
              cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                               >  1:859900/1‑151 (MQ=255)
                gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                              >  2:1000102/1‑150 (MQ=255)
                 aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                             >  2:1020031/1‑150 (MQ=255)
                 aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                            <  1:384608/151‑1 (MQ=255)
                   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                           <  1:830150/150‑1 (MQ=255)
                                       ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                      >  2:443160/1‑151 (MQ=255)
                                        tCCCGCCCCAAACCTTGTGCCGGCGCCTCCGGTGTTCCATTCCCCCAAACACCGGCCCTTTTACCCACCGCCATGTAAAAAAATCCCTCCGCGGCGGTTGTCTCCAGTTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCagtag                                                                                                        <  2:582051/149‑1 (MQ=255)
                                        tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                     >  1:811100/1‑151 (MQ=255)
                                             ccGCAGCCGTGTGTCGGGGGCTCCGGTGATTCATTCCCGCCAAAACCCGCCCTTTTACCCACCCCCATGTGAAAAAGGGCCTGCGGGGCGGTTGTCGGCCGGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                  <  2:212083/149‑1 (MQ=255)
                                             ccGCAGCCCTGTGTCGGCGGCTCCCGTGATTCATTCCCGCCAACACCCGCGCTTTTACCCACCGCCTTGTGAAAAAATGCCTCGGCGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                  <  1:995978/149‑1 (MQ=21)
                                              cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                >  1:790049/1‑150 (MQ=255)
                                                  gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                               >  2:382210/1‑146 (MQ=255)
                                                     cttgtgTCAGCGCCTCCCGTGATTCTTTCCCCCCAACAACCCCGCATTTACCCACCCCCTTGTGAAAAAATCCTTCCGCGGCGGCTTTCGGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                            <  2:689646/146‑1 (MQ=255)
                                                     cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                >  1:490305/1‑143 (MQ=255)
                                                       tgtgTCCGCGCTTCCCGTGTTTCTTTCCCCCCACCACCCCCTCTTTTACCCACCCCCTTGTGAAAAAATCCCTTCGCGGCGGCTGTCTGCCAGTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                            <  2:394763/145‑1 (MQ=255)
                                                        gtgtCAGCGTCTCCGGTGTTTCATTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATGCTTTGGGGGCGGTTTTCTGCAAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                     <  1:790925/151‑1 (MQ=255)
                                                          gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGACGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAATa                                                                                    >  1:161416/1‑150 (MQ=255)
                                                              gCGGTTACTGTTTTTCCTTCCCCCCAACCCCCGCTTTTTTACCCACCGCCATGTAAAAAATCGCTTCCGCGGCGTTTGTCTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                <  2:390098/150‑1 (MQ=255)
                                                              gCGGCTCCCGTGATTCTTTCCCCCCAACACCCGCGCATTTATCCACCGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                   <  1:493191/147‑1 (MQ=255)
                                                                   tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCagaggcaaaaatttaaaac                                                                           >  1:992883/1‑136 (MQ=25)
                                                                          attcattcCCCCCAACACCCGCGCTTTTACCCAACCCCATTTAAAAAAATCCCTCCGCGGCGCCTGCCTCCCATCTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                      <  1:660382/148‑1 (MQ=255)
                                                                           ttatttccccccAACACCCGCGCATTTACCCACCGCCTTGTGAAAAAATCCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                   <  1:207729/140‑1 (MQ=255)
                                                                            ttctttCCCCCAACCACCGGCGTTTTTATCAAACGCATGTTGAAAAAGGCCCTCCGCGGCGGCTGTCTGCCCTTTTTTTTCCCGCCACAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                      <  2:215093/144‑1 (MQ=255)
                                                                             cATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAGCttttatacccccctgtt                                                                 >  1:734968/1‑136 (MQ=25)
                                                                               tcccccccAACACCCGCCTTTTTACCAACCCCCATGTACAAAAATGCTTCCGGGGCGGTTGTCTGCCGGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                               <  2:938836/144‑1 (MQ=255)
                                                                                tccccccAAAACCCGCGCTTTTATCCAACGCCTTTTCAAAAAATGCCTCCGGGGCGGCGGTCTGCCAGTTTTTTTTCCGCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                                <  1:915268/143‑1 (MQ=255)
                                                                                     ccAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAAAGAAAAAAGTTTAAAACCGCAATGCtgtgt                                                             >  1:292342/1‑146 (MQ=25)
                                                                                        accacccgccaaTTTACCCACCGCCTTGTGAAAAAATGCCTCCGGGGCGGCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                       <  2:571800/139‑1 (MQ=255)
                                                                                        aacaccccctcttttATCCAACGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCGCCCCGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                      <  1:910122/139‑1 (MQ=255)
                                                                                         cacccGCGCATTTACCCACCGCCATGTAAAAAAATCCCTTCGCGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                      <  1:453782/146‑1 (MQ=255)
                                                                                              cgcataTTTATCCAACGCAATGTGCAAAAATTCTTGGGCGGCGGCTGCCTGCCAGCTTTTTTGCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                <  1:950110/146‑1 (MQ=255)
                                                                                                  cATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAAACTTTAAACCCGTctcttt                                                                 >  2:564710/1‑126 (MQ=25)
                                                                                                    tttACCCACCGCCATGTGAAAAAATGCTTTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                           <  1:386599/150‑1 (MQ=255)
                                                                                                        tCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTTATACCCGCATGTTTTGTGGGGAACGCCGCTggggaaaa                                        >  1:341585/1‑143 (MQ=21)
                                                                                                        acccaccgcATTTGCAAAAATCGCCTTCGGGGCGGCTGTCAGCAAGTTATTTTCCCGCGCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                           <  2:121796/139‑1 (MQ=255)
                                                                                                             cccaaTGTGAAAAAATCCTTGCGGGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                       <  1:990493/141‑1 (MQ=255)
                                                                                                                   gtaaaaaaaTCCCTTCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                   <  1:711055/139‑1 (MQ=255)
                                                                                                                   ggaaaaaaaTCCTTCCGGGGCGGCTGTCTGCCGGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                              <  2:361016/144‑1 (MQ=255)
                                                                                                                    tgaaaaaaTGCTTCCGGGGCGGCTTTCTGCAAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                           <  1:39466/147‑1 (MQ=255)
                                                                                                                    tgaaaaaaTCCCTGCGCGGCGGCTTTCTGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                            <  1:162497/146‑1 (MQ=255)
                                                                                                                      cAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAAATTTAAACCGCCATGTTGTGTGGGGATCGCCGCTGGTGAAAAAGTGGGAAagg                             >  1:105548/1‑146 (MQ=255)
                                                                                                                      aaaaaaTGCCTGCGGGGGGGTTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                         <  1:97403/149‑1 (MQ=255)
                                                                                                                         aaaTGCCTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                     <  1:134177/151‑1 (MQ=255)
                                                                                                                                     gcggcgGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa              <  1:793671/148‑1 (MQ=255)
                                                                                                                                       gggggcTGTCGCCCATCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa              <  1:7815/143‑1 (MQ=255)
                                                                                                                                                cTGCCAGTTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc   <  1:159936/148‑1 (MQ=255)
                                                                                                                                                   ccAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg  <  1:811888/146‑1 (MQ=255)
                                                                                                                                                   ccAGTTTTTTTCCCGCCCAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg             <  2:431880/135‑1 (MQ=255)
                                                                                                                                                         |                                                                                                                                             
CTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCG  >  NC_000913/357726‑358014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: