Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8800TC41.5% 48.9 / 13.1 41K271E (AAA→GAA) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (17/7);  new base C (0/17);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 2.53e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357733‑358027
                                                                                                                                                    |                                                                                                                                                   
cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                                   <  2:158513/150‑1 (MQ=255)
cGTAGGCCTGATAAGCGTAGCGCATCAGCCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                                   <  1:771055/150‑1 (MQ=255)
    ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                              >  2:857060/1‑151 (MQ=255)
             aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                      >  1:613654/1‑150 (MQ=255)
                gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                  >  1:252782/1‑151 (MQ=255)
                gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                  >  1:84708/1‑151 (MQ=255)
                 tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                   <  1:658101/149‑1 (MQ=255)
                  aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGt                                                                                                                                >  2:324967/1‑151 (MQ=255)
                       aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                           >  1:987721/1‑151 (MQ=255)
                           ggCATTCCCAGCCGCAGCCTTGGGTCAGCGCCTCCGGTTTTTCATTCCCGCCAACACCCGCTCTTTTACCCACCGCCATGTGAAAAAATGCCTC‑CGCGGGGGTTGTCTGCCAGTTTTTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                           <  1:414460/147‑1 (MQ=255)
                             cAATTACAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATGTCCGCCAACAACCGCGCATTTATCGAACGCCATGGGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGGTCTATCCagt                                                                                                                      >  1:757177/1‑150 (MQ=21)
                                ttCCAGCCGCAGACTTGTGTCGGCGGCTCCCGGGATTCTTTTCCGCCAACACCCGAAATTTTACCCAACCCCAGTTGAAAAAGTGCCTT‑GGCGGCGCTTGTTTGCCGTTTTTTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                                   <  2:1076971/150‑1 (MQ=255)
                                ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                  >  2:32567/1‑151 (MQ=255)
                                    aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                              >  1:259914/1‑151 (MQ=255)
                                        gaagcccTGTGTCAGCGGCTCCGGGGTTTCTTTCCCCCCAACAACCGCGTTTTCATCAACCGCCTGGTGAAAAAATGCCTC‑CGCGGGGGCTGTCGGCAAGTTATTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                              <  1:420272/142‑1 (MQ=255)
                                           gccgtttgccAGCGCCTCCCGTATTTCTTTCCCGCCAACACCCGCCCTTTTACCCACCGCCTTGTCAAAAAATGCCTC‑CGGGGCGGTTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                         <  2:1014687/140‑1 (MQ=255)
                                             ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGGCTGCCAGAAATTTTTCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                            >  1:271507/1‑144 (MQ=255)
                                               tgtgTCAGCGGCTACGGTGTTTCTTTTCCCCCAACACCCGCGCATTTATCAAACCCCATGTGCAAAAATGCTTT‑CGCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                      <  2:977147/148‑1 (MQ=255)
                                                  gtCAGCGGCTCCCGTTATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCTTGTGAAAAAATGCTTT‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                         <  2:215552/142‑1 (MQ=255)
                                                        ggctccgttgtttCATTCCCCCCAACACCCGCGCATTTCCCCAACGCAATGTAAAAAAAGGCCTC‑CGGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                          <  1:562456/140‑1 (MQ=255)
                                                        ggCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaattt                                                                                            >  2:1027063/1‑142 (MQ=255)
                                                           accggTGATTCATTCCCCCCAACACCCGCGCATTTTCCCACCCCCATGTAAAAAAATGCCTT‑CGGGGCGGCTTTCGGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                       <  2:585607/147‑1 (MQ=255)
                                                             cggTGATTCTTTCCCGCAAACACCCGCGCTTTTACCCACCCCCATGT‑CAAAAAAGCCTTCCGCGGCGGCTGTTTGCCAGTTTTTTTCCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                      <  2:733965/148‑1 (MQ=255)
                                                             ccGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaaatttaaacc                                                                                      >  1:304774/1‑137 (MQ=25)
                                                              cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                          >  1:621744/1‑127 (MQ=255)
                                                                         ccccccAACACCCGCCCATTTACCCACCGCCATGTGAAAAAATGCCTT‑CGCGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                                          <  2:172509/146‑1 (MQ=255)
                                                                             ccAACACCCGCGCTTTTACCCAACGCCATGTCAAAAAATCCCTC‑CGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                      <  2:347102/150‑1 (MQ=255)
                                                                               accacccGCGCATTTACCCACCGCCATGTGCAAAAATCCCTC‑CGCGGCGCCTGTCTGCAAGTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                   <  2:955548/146‑1 (MQ=255)
                                                                                    ccGCGCTTTTACCCACCCCCTTGTCAAAAATTCCCTC‑CGCGGCGTCTGTCTTCCAGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                <  2:1061811/149‑1 (MQ=255)
                                                                                           tttACCCACCGCCTTTTAAAAAATTCCCTT‑CGCGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                         <  2:428633/149‑1 (MQ=255)
                                                                                                 cAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAACTCCCCCTGTTGTGTGGGCATCGCTGGCGGGAACaa                                                     >  2:1093810/1‑147 (MQ=25)
                                                                                                    ccccATGTGAAAAAATCCCTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                              <  2:55205/149‑1 (MQ=255)
                                                                                                    cccaatgcgaaaaaaTCCCTT‑CGCGGGGGCTGTCTGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                              <  1:489640/141‑1 (MQ=255)
                                                                                                      ccttgtgAAAAATTGCCTC‑CGGGGCGGTTGTCGGCCATTTTTTTTCCCGCCGCACAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                            <  1:786173/148‑1 (MQ=255)
                                                                                                      ccATGTGCAAAAATCCTTT‑CGGGGCGGCTGTCGCCCAGTTTTTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                              <  2:153233/149‑1 (MQ=255)
                                                                                                              aaaaaTCCCTG‑CGGGGCGGCTGTCGGCCATCTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                       <  1:1111837/148‑1 (MQ=255)
                                                                                                                  aTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAAATTTTATTCCCCCCTCTTTTGTGGGGATCTCAGCTGGGGACAAAGTGGAAAGGGGAgggggggg                                >  2:516452/1‑144 (MQ=255)
                                                                                                                     ccTC‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                <  2:881814/148‑1 (MQ=255)
                                                                                                                        t‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGAGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                            >  2:507922/1‑149 (MQ=255)
                                                                                                                              gcggcTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGGATCAGCTcc                      >  2:14740/1‑150 (MQ=255)
                                                                                                                                      cggCCTGCTATTTTCCGCCCGCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                <  2:856149/146‑1 (MQ=255)
                                                                                                                                         cgagtttttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg             <  1:856930/141‑1 (MQ=255)
                                                                                                                                                ttttcCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa     <  1:239627/149‑1 (MQ=255)
                                                                                                                                                 ttttCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAAACCCCCCTTTTTTGTGGGGCTCGCTGCTGGTAACAAAGTGGGAAGGGGAGGGGGGGGGAAAAGATCCCGAACCccgcgcatttaggt  >  2:129592/1‑141 (MQ=255)
                                                                                                                                                 ttttCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt   <  2:1078793/150‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                   
CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357733‑358027

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: ‑