Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA55.3% 22.4 / 67.9 47L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/7);  new base A (0/26);  total (14/33)
Fisher's exact test for biased strand distribution p-value = 3.40e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.39e-06

AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357745‑358024
                                                                                                                                                  |                                                                                                                                          
aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAc                                                                                                                                      <  1:687361/151‑1 (MQ=255)
 aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAcc                                                                                                                                     >  2:536901/1‑151 (MQ=255)
   cGTAGCGCATCAGGCAATTCCAGCCGCAGACCCGTTTCACCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAccgc                                                                                                                                   <  2:477643/151‑1 (MQ=255)
               ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTcc                                                                                                                         >  1:226583/1‑149 (MQ=255)
                          ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                            >  2:880860/1‑151 (MQ=255)
                           cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                            >  1:503980/1‑150 (MQ=255)
                            gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                          >  2:191584/1‑149 (MQ=255)
                             cAGCCCGGTGTCGGCGGCTACCTTGTTTCTTTCCCCCCAACACCCGCGTTTTTACCCACCCCCAGGTAAAAAAATGCCT‑CCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                           <  2:554430/149‑1 (MQ=255)
                              agcccTGTGTCAGCGGCTCCCGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCTT‑TCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                               <  1:192028/141‑1 (MQ=255)
                               gactggtgtCGGCGGCTACCGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATGCTT‑TCGGGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                           <  1:903192/142‑1 (MQ=255)
                                            ggCTCCCGTTTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGCAAAAATGCCT‑CCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                            <  2:822142/149‑1 (MQ=255)
                                              cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaaatt                                                                                            >  2:451843/1‑140 (MQ=25)
                                                 ccgtttttCATTCCCGCCAACACCCGCGCTTTTCCCCACCGCCTTGTGAAAAATTCCCT‑TCGCGGCGTTTGTCTCCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                       <  1:3976/143‑1 (MQ=255)
                                                       ttCTTTCCCCCCAACACCCCCGCTTTTCCCCAACGCAATGTGAAAAATTGCCT‑GCGGGGCGTTTGTCGGCCATTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                                <  2:884284/150‑1 (MQ=255)
                                                             ccccccAACACCCGCGCTTTTACCCACCCCCATGTAAAAAAATCCCT‑CCGGGGCGCCTGTCGCCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                         <  2:914311/147‑1 (MQ=255)
                                                               ccccAACACCCGCGTTTTTACCCACCGCCATGTGAAAAAATGCCT‑CCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                       <  1:820495/149‑1 (MQ=255)
                                                                      acccGCGTTTTTACCCACCGCCATGAGAAAAATCCCCT‑CCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                 <  2:251532/148‑1 (MQ=255)
                                                                      acccGCGCATTTACCCACCGCCATGTGAAAAAAGGCCT‑CCGCGGCGGCTTTCTGCCAGTTATTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                <  1:742080/149‑1 (MQ=255)
                                                                        ccGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTAAACCCCCCCtgttgttggggg                                                                      >  2:388868/1‑137 (MQ=25)
                                                                          gcgcATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGAGGACGAAAGAAAGATTTTAGCACGCCCTGTTGTggggggaaccgct                                                               >  1:552294/1‑139 (MQ=21)
                                                                               tttccccACCGCCATGTGAAAAAATGCCT‑GGGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGt                                                         <  1:290667/143‑1 (MQ=255)
                                                                               tttACCCACCGCCATGTGAAAAAATGCCT‑TCGGGGCGGTTGTCGCCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTaa                                                       <  1:31160/150‑1 (MQ=255)
                                                                                        cGCCATGT‑CAAAAACTCCTGCCGGGGCGGCTGTCCCCGACTTTTTTTCCCGCCAAAAA‑AAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGaa                                           <  2:1029779/151‑1 (MQ=255)
                                                                                                 cAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAACTTTTAAACCCTCCTTTTTTGTGGGGATCGCTGCG‑GGTGACAAA‑GT‑GGGAAggg                                       >  2:391726/1‑146 (MQ=255)
                                                                                                  aaaagTGTCT‑CCGCGGCGGCTTTCGCCCAGTTTTTTTCCCGCCCCAAA‑AAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                                 <  2:226536/151‑1 (MQ=255)
                                                                                                  aaaaaTGCCT‑TCGCGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGt                                   <  1:898130/149‑1 (MQ=255)
                                                                                                  aaaaaTGCCT‑CCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑gg                                             <  1:864915/139‑1 (MQ=255)
                                                                                                  aaaaaTCCCT‑GGGGGGCGGCTGCCGGCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                                 <  2:382014/151‑1 (MQ=255)
                                                                                                  aaaaaCCCCT‑CCGCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                                 <  2:13508/151‑1 (MQ=255)
                                                                                                     aacgccctcggcgcgggcGGTCTGCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgcgg                               <  2:746003/136‑1 (MQ=255)
                                                                                                          cT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTAAAACCCCCATGTTTTGTGGGGATAGCTGCTGGGTAAAAAG‑TT‑GGAAGGGGagggggggg                              >  1:188972/1‑139 (MQ=255)
                                                                                                            tgcggggcggcTGTCTGCCAGTTATTTTCCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGa                            <  1:1052712/142‑1 (MQ=255)
                                                                                                              cgcgGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAATTTTAACCCCCCCTGTTTTGTTGGGATCGCTGCT‑GGGGAAAAT‑GTGGGAAAGGGagagggggg                              >  2:659435/1‑136 (MQ=255)
                                                                                                                 gccggcTTTCTGCCAGTTATTTTCCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATc                         <  1:451973/143‑1 (MQ=255)
                                                                                                                  gcggcTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAAACCCTCATGTTGTGTGGGAAACGCTGCT‑GGGAACAAA‑AT‑GGGAAAGGGAGGGCGGGGGAACAACTcc                   >  1:3407/1‑150 (MQ=255)
                                                                                                                       tGTCTCCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAg                 <  2:480716/147‑1 (MQ=255)
                                                                                                                       tGTCGGCGAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTcc                   <  1:754979/145‑1 (MQ=255)
                                                                                                                           gcctgcttttttttCCCCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc             <  1:537052/138‑1 (MQ=255)
                                                                                                                             ccgctttttttcCCCCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg          <  1:377061/141‑1 (MQ=255)
                                                                                                                             cccgtttttttcCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa       <  1:811599/144‑1 (MQ=255)
                                                                                                                             ccAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa               <  1:884130/143‑1 (MQ=255)
                                                                                                                               actttttttcCCCCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt        <  1:842528/143‑1 (MQ=255)
                                                                                                                               aGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACCTTTAAACCACCCTGTTTTGTGGGGATCGCTGCC‑GGTTAAAAA‑GT‑GGGAAGGGAAGAGGGGCGGAACCGCTCCACAACCacgccca      >  1:123452/1‑147 (MQ=255)
                                                                                                                                  ttttttcCCGCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa      <  1:615890/145‑1 (MQ=255)
                                                                                                                                  tATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTAAAACCGCCCTTTTTTGTGGGGAACGCCGCT‑GGGGACAATGGG‑GGGAAGGGAGGGGGGGGGAA‑CAGCTCCAGAAACgcgccga      >  2:216266/1‑144 (MQ=255)
                                                                                                                                    tttttCCGCCGAAAA‑AAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa  <  2:385212/149‑1 (MQ=255)
                                                                                                                                     ttttCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa  <  2:749769/149‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                          
AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357745‑358024

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: ‑