Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8750AT44.0% 62.7 / 19.3 50N272K (AAT→AAAcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (21/7);  new base T (0/22);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 2.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357725‑358017
                                                                                                                                                       |                                                                                                                                                  
aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTa                                                                                                                                                    <  1:590358/151‑1 (MQ=255)
 cTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                                   >  2:702225/1‑151 (MQ=255)
   gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                                 <  2:89926/151‑1 (MQ=255)
             gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGCGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                        >  2:610370/1‑150 (MQ=255)
              ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                                     <  2:57640/151‑1 (MQ=255)
              ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGca                                                                                                                                      >  1:932700/1‑150 (MQ=255)
                 gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                    <  2:945439/149‑1 (MQ=255)
                   tAAGCGTAGCGCTTCAGACAATTCCAGCCGCAGACCTGTGTCAGCGCCTACCTTGATTCACTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                    <  2:231873/147‑1 (MQ=255)
                      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                             <  2:767357/151‑1 (MQ=255)
                         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                          >  1:429306/1‑151 (MQ=255)
                         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                          >  1:796779/1‑151 (MQ=255)
                             gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                      >  2:681272/1‑151 (MQ=255)
                             gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                      >  2:614271/1‑151 (MQ=255)
                               aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                    >  1:439517/1‑151 (MQ=255)
                                           cAGCCGCAGCCTTGTGTCGGCGGCTCCCGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCAACCCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                        <  1:849127/151‑1 (MQ=255)
                                           cAGCCGCAGCCTTGTGTCAGCGCCTACCGTGTTTCTTTCCCCCAAACACCCGCGCTTTTACCCACCGCCTTGTAAAAAAATGCTTCCGGGGCGGCTTTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                        <  1:531203/151‑1 (MQ=255)
                                              ccGCAGACCTGTGCCCGCGCCTCCCGTGATTCTTCCCCGCCAAAACCCGCGCTTTTCCCCACCGCCATGTGAAAAAGTGCCTTCGCGGCGCTTGCCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                        <  2:174773/148‑1 (MQ=255)
                                                  aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                    >  1:917456/1‑147 (MQ=255)
                                                  aGACCTGTGTCAGCGGCTAACGTGATTAATTTCCTCCAACAAACGTGCTTTTATCCCAAGCCATGTGCAAAAATGCCTTCGCGGCGGCCCGCTGCCAGCTATTTTTCCGCCGCAACAAAAACCCCGTTCTCTccgttcggggaggtg                                                                                                     >  2:501998/1‑134 (MQ=18)
                                                   gcccTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCTTTTACCCACCCCCATGTCAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                 <  1:499860/147‑1 (MQ=21)
                                                       tgtgTCAGCGGCTCCCGTAATTCTTTCCCCCCAACACCCGCGCTTTTCCCCACCGCATTGTGAAAAAATGCTTTCGCGGCGGCTTTCTGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                          <  1:722669/150‑1 (MQ=255)
                                                       tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggaaaaaa                                                                                            >  1:612557/1‑142 (MQ=255)
                                                        gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcca                                                                                                 >  1:810560/1‑142 (MQ=255)
                                                            cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaat                                                                                    >  1:344710/1‑146 (MQ=255)
                                                              ggggCTACCGTGATTCTTTCCCCCAAACACCCGCGCTTTTACCCACCGCCATGGGAAAAAATGCTTTCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                   <  1:266506/148‑1 (MQ=255)
                                                                gcctcccGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTAAAAAAATGCCTCCGGGGGGGCTTTCTCCCAGTTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                <  1:853538/146‑1 (MQ=255)
                                                                  cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcgcggg                                                                                              >  2:549877/1‑132 (MQ=255)
                                                                     ccGTGTTTCATTCCCGCAAACACCCGCCCTTTTACCCAACGCCATGTACAAAAATCCCTCCGCGGCGGCTGTCTGCCATCTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                            <  1:828905/150‑1 (MQ=255)
                                                                        taatttatttCCGCCAACACCCGCGCTTTTATCCACCCCCATGTGAAAAAATGCCTGCGCGGCGGCTGCCTGCCATCTTTTTTCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                <  1:77197/141‑1 (MQ=255)
                                                                           ttCTTTCCCCCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCTTCGGGGGGGGTTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                      <  1:437407/150‑1 (MQ=255)
                                                                           ttCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTCCGCGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                         <  1:738332/147‑1 (MQ=255)
                                                                           ttCATTCCCCCCACCAACCGCACATCTATCCCGCGCCTGGTCAAAAAAGGCCCTCGGGGGGGCGGACAGCCGTTTATTTTGCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                       <  2:90436/149‑1 (MQ=255)
                                                                               ttccccccAACACCCGCGCTTTTACCCAACGCCATGTCCAAAAATGCTTTCGCGGCGGCTGTCTGCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                         <  1:869338/137‑1 (MQ=255)
                                                                               ttccccccAACACCCGCGATTTTACCCACCGCCTTTTGAAAAAATGCTTCCGCGGCGGCTTTCGGCAAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                          <  1:703468/136‑1 (MQ=255)
                                                                               ttccccccAACACCCGCCCTTTTACCCACCCCCTTGTGCAAAAATCCCTTCGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt                                                                     <  1:218814/141‑1 (MQ=255)
                                                                                  cccccaccaCCCCCGCTTTTCCCCAGCCCCTTGTGAAAAAAGCCCTCCGGGGGGGGTTTTGGCCAGGTTTTTTCCCGCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                              <  1:735071/148‑1 (MQ=255)
                                                                                  ccGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAGATTTTAAcccccccctgt                                                                    >  2:472239/1‑137 (MQ=25)
                                                                                         cacccGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTCCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                        <  1:702502/147‑1 (MQ=255)
                                                                                           acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGGAAAAACTTTTAACCCCCCACGTTGTGTgggcagc                                                         >  2:823264/1‑142 (MQ=25)
                                                                                           acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGGGAAAAAAATTTAAATCCCCCCGGTTGTGTgg                                                              >  2:357089/1‑142 (MQ=25)
                                                                                                     tATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGTGCACAAGAAAAAATTTTATACCCGTCAGTTTTGGTGGCATTCgcgcttggtac                                              >  2:594125/1‑140 (MQ=21)
                                                                                                        ccACCGCCATGTGAAAAAATCCTTTCGCGGCGGCTTTCTCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                         <  1:943367/150‑1 (MQ=255)
                                                                                                          accGCCTTGTAAAAAAATCCCTTCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                       <  1:70644/148‑1 (MQ=255)
                                                                                                            cGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGGAAAAAAATTTAACCCCCCCCGTTGTGTGGGGAACGCCGCTTGTGACAAAGTgg                                      >  2:489734/1‑149 (MQ=21)
                                                                                                                      aaaaaTGCTTCCGGGGCGGCTTCCTGCAGGTTTTTTTCCCGCGCAAACAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                            <  2:91342/149‑1 (MQ=255)
                                                                                                                      aaaaaTGCCTCCGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                          <  1:944088/151‑1 (MQ=255)
                                                                                                                       aaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAAATTTAATCCCTCTTGTTTTGGGGGAATCGCTGCCGGGGACAATGTgggga                                   >  2:898837/1‑138 (MQ=255)
                                                                                                                       aaaaTGCCTCCGCGGCGCCTGTCCGCCAGTTTTTTTCCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                         <  2:932356/151‑1 (MQ=255)
                                                                                                                         aaTGCCCTCGGGGGCGCCTGTCTCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                        <  2:917117/151‑1 (MQ=255)
                                                                                                                               ttCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAAAAAAAAATTTTAACCCCCCCTTTTTTGTGGGGAAAGCTGCTGGTTAAAATGTGGGAAGGGaggggggggggaaa                  >  1:300193/1‑137 (MQ=255)
                                                                                                                                                 ccAGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc  <  1:832203/149‑1 (MQ=255)
                                                                                                                                                       |                                                                                                                                                  
ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357725‑358017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: