Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA59.5% 5.9 / 52.6 42L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/3);  new base A (0/25);  total (14/28)
Fisher's exact test for biased strand distribution p-value = 1.29e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.09e-06

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357743‑358033
                                                                                                                                                      |                                                                                                                                               
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                              <  1:922235/151‑1 (MQ=255)
 tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                              >  1:974599/1‑150 (MQ=255)
   aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                                           >  1:796146/1‑151 (MQ=255)
       tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                                                       >  1:1356179/1‑151 (MQ=255)
            cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctc                                                                                                                                  >  1:419240/1‑151 (MQ=255)
               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                               >  1:546520/1‑151 (MQ=255)
                  gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                            >  2:1008182/1‑151 (MQ=255)
                    aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCag                                                                                                                             >  1:235204/1‑148 (MQ=255)
                      ttCCAGCCGCAGACCTGTGCCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                        >  2:1318795/1‑151 (MQ=255)
                           gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                   >  2:1236678/1‑151 (MQ=255)
                                accccgtcgccAGCGCCTCCCTTGGTTCATTCCCCCCAACACCCGC‑CTTTTTTCCCACCCCA‑GTGGGAAAATGGACTTCCGGGTCGGCGGCCGGCCGGTTTTTTTC‑CCGCCCAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                                <  2:212643/139‑1 (MQ=255)
                                   ctggggtaggCGGCTACTGTTATTCATTCCCGCAAACACCCGCGTTTTTTCCCAACGCTATGTGAAAAAAT‑GCCTT‑GGGGGCGGCTGTCTGCCGGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                 <  1:544232/136‑1 (MQ=255)
                                          cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggagcaggaaaaaa                                                                                                     >  1:946977/1‑137 (MQ=255)
                                            gCGGCTACGGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCAACGCAATGTGCAAAAAT‑GCCTT‑CGGGGCGGTTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                                   <  1:1257470/150‑1 (MQ=255)
                                              gcctccggTGATTATTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAG‑GCCTC‑CGGGGCGCTTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                                  <  1:444086/142‑1 (MQ=255)
                                                     gTGATTCTTCCCCGCAAACACCCGCGCTTTAACCCACCGCCTTTTCAAAAAAT‑GCCGC‑CGGGGGGCCTGCCGGCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                                <  2:590918/144‑1 (MQ=255)
                                                         ttCTTTCCCCCCAACACCCGCGCTTTTATCAACCCCCATGTAAAAAATT‑CCCTT‑CGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                                        <  1:463071/148‑1 (MQ=255)
                                                               tCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACATTaaaacccccacgt                                                                                     >  1:389867/1‑134 (MQ=25)
                                                                      acccccGCGCTTTTACCCACCCCCGGGTGAAAAAAT‑CCTTT‑GGCGGGGGCTTTCTGCCATTTTTTTTC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                        <  2:735499/147‑1 (MQ=255)
                                                                      acaacCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTTAACCCCGCCTGTTTTGTgggga                                                                           >  1:584722/1‑145 (MQ=25)
                                                                        acccGCGATTTTACCAACCGCCTTGTAAAAAAAG‑CCCTT‑GGGGGCGGCTTTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                        <  2:433373/147‑1 (MQ=255)
                                                                         cccGCGTTTTTACCCACCGCTATGTGAAAAAAT‑GCCTC‑CGCGGCGGTTTTCTGCATGTTATTTTC‑CCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                        <  2:893212/147‑1 (MQ=255)
                                                                                      caaccccattgtaaaaaatT‑CCCTT‑CGGGGCGGCTGTCGGCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                         <  1:591114/136‑1 (MQ=255)
                                                                                                   aaaaaaT‑GCCGT‑CGGGGGGGTTGGGT‑CCAGGTAATTGTCCCGCCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                             <  2:1291585/148‑1 (MQ=255)
                                                                                                    aaaaaT‑CCCTT‑GGCGGGGCCTGTCGGCGAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                            <  1:225521/149‑1 (MQ=255)
                                                                                                    aaaaaT‑CCCTT‑CGGGGCGGTTTTCTCCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                  <  2:299949/143‑1 (MQ=255)
                                                                                                    aaaaaT‑CCCTC‑CGCGGCGGCTTTCTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                             <  1:373852/148‑1 (MQ=255)
                                                                                                    aaaaaT‑CCCTC‑CGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                          <  1:936711/151‑1 (MQ=255)
                                                                                                        aT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAGATTTTAACCCCCCCTGTTTTGTGGGGGTCGCCGGTGGTGAAAAAACGggaagggaagggggggg                                      >  2:720528/1‑144 (MQ=255)
                                                                                                               tccgggggggcTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                      <  1:614854/138‑1 (MQ=255)
                                                                                                                  gggggggttttcggCCAGTTTTTTTC‑CCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                                <  1:288669/136‑1 (MQ=255)
                                                                                                                  gcggcgTCTGTCTGCAATCTTTTTTC‑CCGCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                 <  2:147/148‑1 (MQ=255)
                                                                                                                    ggcggcTGTCGCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                 <  1:1228773/146‑1 (MQ=255)
                                                                                                                        gttGTCTGCCAGGTTTTGCT‑CCCCCGAAAAAACACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                              <  1:150900/143‑1 (MQ=255)
                                                                                                                          tttcgccaattttttttc‑CCCCCCCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                           <  1:1217303/133‑1 (MQ=255)
                                                                                                                          tttCTGCCATTTTTTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                                <  2:1145847/139‑1 (MQ=255)
                                                                                                                           gTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                      <  1:413733/150‑1 (MQ=255)
                                                                                                                                 cagtttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                   <  1:662798/141‑1 (MQ=255)
                                                                                                                                    tttttttc‑CCGCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt              <  2:523822/146‑1 (MQ=255)
                                                                                                                                       ttttc‑CCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg          <  1:1289055/150‑1 (MQ=255)
                                                                                                                                       tttct‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg          <  2:113715/150‑1 (MQ=255)
                                                                                                                                                 cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTAAAACCCCCCTGTTGTGTGGGAATTGCTGCTGGGGAAAAAGTGGGAAGGGAAGGGGGGGGGATCAACTCCACAACCCCGCCAATTTAGTTCGCCTc  >  1:983186/1‑149 (MQ=255)
                                                                                                                                                      |                                                                                                                                               
ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357743‑358033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑