Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8800TC46.7% 26.2 / 11.4 30K271E (AAA→GAA) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (9/7);  new base C (0/14);  total (9/21)
Fisher's exact test for biased strand distribution p-value = 9.40e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357730‑358022
                                                                                                                                                        |                                                                                                                                                
aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                                  >  1:347186/1‑151 (MQ=255)
aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                                  >  2:52385/1‑151 (MQ=255)
  tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                                  >  2:519106/1‑149 (MQ=255)
     tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                             <  2:109404/150‑1 (MQ=255)
      aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                            <  2:139544/150‑1 (MQ=255)
       ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                          >  2:116498/1‑151 (MQ=255)
                 gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                >  1:362792/1‑151 (MQ=255)
                   gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                               <  1:433418/150‑1 (MQ=255)
                       cccATCAGCCAATCCCAGCCCCAGACCTGTTTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCAACGCCATGTGCAAAATTGCCTCGGCGGCGGCTGTCTGCCAGTTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                             <  2:8652/146‑1 (MQ=18)
                            cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                     >  1:689215/1‑151 (MQ=255)
                                       aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                          >  2:455066/1‑151 (MQ=255)
                                        gCCCCACACTTGTGTCTGCGCCTCCCGTAATTATTTCCCCCAAACAGCCGCCCTTTTTCCCACCTCAATGTAAAAAAATCCTTGCGGGGGGGTTGTCGCCCGGTTTTTTCCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                            <  1:131827/148‑1 (MQ=255)
                                          cGCAGCCTTGTGTCAGGGCCTACCGTGTTTCATTCCCCCCAACACCCGCGCATTTACCCACCGCCTTGTCAAAAAATGCTTGCGGGGGGGCTGTCTGCCGGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                       <  1:73522/151‑1 (MQ=255)
                                            cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                        >  2:923837/1‑148 (MQ=255)
                                                cgtgtgTCAGCGGCTCCGGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAGGCTTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                    <  1:558397/146‑1 (MQ=255)
                                                     gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                        >  2:468941/1‑139 (MQ=255)
                                                     gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAaggg                                                                                                  >  1:270815/1‑143 (MQ=255)
                                                                 cctttattctttCCCCCAACCACCCGCCCATTTACCCACCCCCTGGGGAAAAAATCCCTCGGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                     <  2:837379/122‑1 (MQ=255)
                                                                      ttCATTCCCCCCAACACCCGCGCTTTTACCCACCGCATTGTGAAAAAATGCTTCCGGGGCGCCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                             <  1:922392/148‑1 (MQ=255)
                                                                        ctttccccccAACACCCGCGTTTTTACCCACCCCCATGGGAAAAATTCCCTTCGCGGCGGTTGTCTCCAGTTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                            <  1:267735/139‑1 (MQ=255)
                                                                            ccccccAACACCCGCCATTTTACCCACCGCCTTGTCAAAAAATGCCTCGGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                    <  1:1278190/147‑1 (MQ=255)
                                                                                   aacaccCGCCCATTTACCCACCCCCATGTAAAAAAAGGCTTCCGGGGCGGCTGTCGGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                              <  1:896938/151‑1 (MQ=255)
                                                                                           gcgcTTTTACCAAACCCTATGTAAAAAAATCCTTGCGCGGGGGCTGTCTGCCAGTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                          <  1:1196114/148‑1 (MQ=255)
                                                                                                     caaacccgtgggcaaaaaaTGCCTCCGGGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                               <  2:1323813/135‑1 (MQ=255)
                                                                                                       accgcttgggacAAAAATGCCTCGGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                           <  2:187722/140‑1 (MQ=255)
                                                                                                               gtgAAAAAATCCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                     <  2:979972/149‑1 (MQ=255)
                                                                                                               ggcaaaaaaTGCCTCCGCGGGGGTTGCCGGCGAGTTTTTTCCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                   <  2:310983/147‑1 (MQ=255)
                                                                                                                   aaaatTGCCTCCGCGCGGGCTTTCTGCCAGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                   <  1:79548/147‑1 (MQ=255)
                                                                                                                    aaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAGTTTAAAACCCTCAATGTTTTTGGGGATAGCTGCTGGTTACAACGTgg                                           >  2:783339/1‑138 (MQ=255)
                                                                                                                     aattGCCTCCGGGGCGCCTTTCCGCCGTTTTTTTTCCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                             <  2:24848/148‑1 (MQ=255)
                                                                                                                                 ggcggtTGTCTCCCGCTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                        <  2:1329885/144‑1 (MQ=255)
                                                                                                                                      cTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTTAAACCCCCATGTTTTGTGGGGAACGCTGCCGGGGACAAAATGGGAAGGGGAGGGCGGGGGAACAACTCCCGaa             >  1:1253634/1‑150 (MQ=255)
                                                                                                                                             ccAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg        <  1:506326/148‑1 (MQ=255)
                                                                                                                                                  ttttttcCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt  <  1:1153583/147‑1 (MQ=255)
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ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357730‑358022

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: