Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA51.3% 25.4 / 58.8 37L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/4);  new base A (0/19);  total (14/23)
Fisher's exact test for biased strand distribution p-value = 5.01e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.53e-07

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGAC  >  NC_000913/357742‑358039
                                                                                                                                                       |                                                                                                                                                     
gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                       <  1:360258/149‑1 (MQ=255)
 aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                     >  2:7910/1‑150 (MQ=255)
 aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                                    <  2:529044/151‑1 (MQ=255)
    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                                                 <  2:163001/151‑1 (MQ=255)
      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                               >  2:528080/1‑151 (MQ=255)
                        tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                             >  1:1034182/1‑151 (MQ=255)
                              cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                        >  1:196975/1‑150 (MQ=255)
                                 aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                       >  1:289966/1‑147 (MQ=255)
                                  gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                          >  2:151605/1‑144 (MQ=255)
                                    ccTTTGTCAGGGGCTACCGTATTTCATTCCCCAAAAAACCCGCTTATTTACCTACCGCC‑TTGTGCAAAAAGCCC‑TCCGCGGCGCTGGCCTGCCGCTTTTTTTT‑CCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                                      <  2:1108831/146‑1 (MQ=255)
                                       gtgtCGGCGGTTACCGTAATTAATTTCCGCCAACACTCGCCTATTTATCCAACCCC‑TTGTGAAAAAAGGCT‑TTCGGGGGGGCTGTCCCCCAGTTTTTTCT‑CCGCGGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                       <  2:190001/142‑1 (MQ=255)
                                           cAGCGCCGACCGTTTTTCTTTCCCGCAACCACCCGCCATTTTCCCCACCGCC‑ATGGAAAAAAATCCC‑TCCGCGGCGCCTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                                    <  1:610903/141‑1 (MQ=255)
                                               ggCTCCCGTTATTTTTTCCCCCCAACACCCGCGCTTTTACCCACCGCC‑TTGTGAAAAAATCCC‑TTCGGGGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTa                                                                                                       <  2:887554/150‑1 (MQ=255)
                                                    cggtttttCTTTCCCCCCAACACCCGCGCATTTACCCACCGCC‑ATTTAAAAAAATGCC‑TCCGGGGCGGTGGCCGCCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                                        <  1:1190704/138‑1 (MQ=255)
                                                     cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAgaatttaaac                                                                                                   >  1:1051844/1‑139 (MQ=25)
                                                       tgtttCTTTCCCCCCACCACCCGCGATTTTACCAACCGCC‑TTGTGAAAAAAGGCC‑TCCGGGGCGGCTGCCTGCCAGTTATTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                                                <  1:1122577/146‑1 (MQ=255)
                                                              ttccccccaccaCCCGCGCTTTTACCCACCGCC‑ATGTGAAAAAATCCT‑TCCGCGGCGGCTGTCGCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgtt                                                                                          <  2:1250597/142‑1 (MQ=255)
                                                              ttccccccAACACCCGCGCTTTTACCCACCGCC‑ATGTGAAAAATTCCC‑TCCGGGGGGGCTGTCTGCCACTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                                                         <  2:635927/143‑1 (MQ=255)
                                                                  cGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGAGAAAAAACTTTTATccccccctgtttt                                                                                        >  1:548026/1‑136 (MQ=25)
                                                                         acccccgtttttACCCAACGCA‑AGGGCCAAAAACGCT‑TTCGGGGCGGTTTTCCGCCATTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                                <  2:881978/138‑1 (MQ=255)
                                                                          cccGCGCTTTTCCCCAACCCC‑ATGTGAAAAAATCCT‑TCCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                           <  2:1065436/150‑1 (MQ=255)
                                                                          cccGCGCTTTTA‑CCAACCCCAATGTAAAAAAATGCC‑TCCGCGGCGCCTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                           <  1:503643/150‑1 (MQ=255)
                                                                           ccGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAAACCCCCCTGTTGTGTggggaacg                                                                              >  2:989229/1‑141 (MQ=25)
                                                                            cggcgtttttTCCAACCCCAATGT‑CAAAAATGCCTTTCGGGGGGGCTTTC‑GCCCGCTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                            <  2:1261052/143‑1 (MQ=255)
                                                                                     aTCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAAATTTTAACACCCCATGTTTTGTGGGCATCGCTGCTGGGGACaa                                                                 >  1:1188349/1‑150 (MQ=25)
                                                                                              c‑ATGTGCAAAAATGTC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAACAGAAACAAAATTTTTCCCATCCTGTTGTGTGGGGAACGCTGCTGGTaatcatttgggca                                                         >  2:659030/1‑138 (MQ=255)
                                                                                                  gtaaaaaacTGCC‑TGCGGGGCGTCTTTCTCCCAGTTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                        <  2:289999/143‑1 (MQ=255)
                                                                                                                   ggggcgtttGTCTGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                                    <  2:1116800/143‑1 (MQ=255)
                                                                                                                    cgggggCTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                             <  2:761823/141‑1 (MQ=255)
                                                                                                                        gccTGTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                        <  1:606068/140‑1 (MQ=255)
                                                                                                                           tGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAACCCCCCCTGTTGTGTGGGGAACGCTGCTGGGGACAAAGTGGGAAGGGGAGAGGGGGGGATCAACTcc                                  >  2:652940/1‑145 (MQ=255)
                                                                                                                                gCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTAAACCCCCCCTGTTTTGTGGGAAACGCCGCTGGGAAAAAAATGGAAAGGGAAGGGCGGGGGAACAGCACCACAAcc                            >  2:330437/1‑146 (MQ=255)
                                                                                                                                 caagtttttttc‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                               <  2:298662/135‑1 (MQ=255)
                                                                                                                                 caagtttttttc‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                               <  2:542611/135‑1 (MQ=255)
                                                                                                                                  cAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAACATTAAAACCCCCATGTTTTGTGGGGATCGCCGCTGGGGGAAATGTGGGGAGGGGAGAGCGGGGGAAAAGCTCCCGAACCGCGCtc                      >  1:606520/1‑149 (MQ=255)
                                                                                                                                  cAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACATTTAACCCCCCATCTTTTGTGGGGATAGCCGCTGGTGACCAAGTGGGAAAGGAAGGGGGGGGGGACAACTCCCCAACCgcgcgc                      >  1:1098745/1‑148 (MQ=255)
                                                                                                                                     tatttttc‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                          <  1:709157/140‑1 (MQ=255)
                                                                                                                                       acttgtgccgcagTAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAGTCAGCTCCAGAACCGCGCTAATTGa                 <  1:78138/144‑1 (MQ=255)
                                                                                                                                              ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGcc          <  2:548434/151‑1 (MQ=255)
                                                                                                                                                      acaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGac  <  2:1051912/151‑1 (MQ=255)
                                                                                                                                                       |                                                                                                                                                     
GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGAC  >  NC_000913/357742‑358039

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: ‑