Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8750AT46.3% 40.4 / 17.1 41N272K (AAT→AAA) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (17/5);  new base T (0/19);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 3.15e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357733‑358013
                                                                                                                                               |                                                                                                                                          
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)
                                                                                                                                               |                                                                                                                                          
CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357733‑358013

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: ‑