Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8750AT44.4% 54.4 / 18.9 45N272K (AAT→AAA) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (18/7);  new base T (0/20);  total (18/27)
Fisher's exact test for biased strand distribution p-value = 2.97e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAA  >  NC_000913/357726‑358020
                                                                                                                                                      |                                                                                                                                                    
cTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTa                                                                                                                                                      <  1:485540/150‑1 (MQ=255)
cTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                                     >  1:385301/1‑151 (MQ=255)
 tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                                    >  1:114047/1‑151 (MQ=255)
 tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                                    >  2:588937/1‑151 (MQ=255)
  gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                                   <  2:694156/151‑1 (MQ=255)
           ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                          >  1:750000/1‑151 (MQ=255)
                   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                  <  1:687361/151‑1 (MQ=255)
                    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                 >  2:536901/1‑151 (MQ=255)
                      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCCGTTTCACCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                               <  2:477643/151‑1 (MQ=255)
                                  ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                     >  1:226583/1‑149 (MQ=255)
                                             ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                        >  2:880860/1‑151 (MQ=255)
                                              cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                        >  1:503980/1‑150 (MQ=255)
                                               gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                      >  2:191584/1‑149 (MQ=255)
                                                cAGCCCGGTGTCGGCGGCTACCTTGTTTCTTTCCCCCCAACACCCGCGTTTTTACCCACCCCCAGGTAAAAAAATGCCT‑CCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                       <  2:554430/149‑1 (MQ=255)
                                                 agcccTGTGTCAGCGGCTCCCGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCTT‑TCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                           <  1:192028/141‑1 (MQ=255)
                                                  gactggtgtCGGCGGCTACCGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATGCTT‑TCGGGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                       <  1:903192/142‑1 (MQ=255)
                                                               ggCTCCCGTTTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGCAAAAATGCCT‑CCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                        <  2:822142/149‑1 (MQ=255)
                                                                 cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaaatt                                                                                        >  2:451843/1‑140 (MQ=25)
                                                                    ccgtttttCATTCCCGCCAACACCCGCGCTTTTCCCCACCGCCTTGTGAAAAATTCCCT‑TCGCGGCGTTTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                   <  1:3976/143‑1 (MQ=255)
                                                                          ttCTTTCCCCCCAACACCCCCGCTTTTCCCCAACGCAATGTGAAAAATTGCCT‑GCGGGGCGTTTGTCGGCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                            <  2:884284/150‑1 (MQ=255)
                                                                                ccccccAACACCCGCGCTTTTACCCACCCCCATGTAAAAAAATCCCT‑CCGGGGCGCCTGTCGCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                     <  2:914311/147‑1 (MQ=255)
                                                                                  ccccAACACCCGCGTTTTTACCCACCGCCATGTGAAAAAATGCCT‑CCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                   <  1:820495/149‑1 (MQ=255)
                                                                                         acccGCGTTTTTACCCACCGCCATGAGAAAAATCCCCT‑CCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                             <  2:251532/148‑1 (MQ=255)
                                                                                         acccGCGCATTTACCCACCGCCATGTGAAAAAAGGCCT‑CCGCGGCGGCTTTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                            <  1:742080/149‑1 (MQ=255)
                                                                                           ccGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTAAACCCCCCCtgttgttggggg                                                                  >  2:388868/1‑137 (MQ=25)
                                                                                             gcgcATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGAGGACGAAAGAAAGATTTTAGCACGCCCTGTTGTggggggaaccgct                                                           >  1:552294/1‑139 (MQ=21)
                                                                                                  tttccccACCGCCATGTGAAAAAATGCCT‑GGGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGt                                                     <  1:290667/143‑1 (MQ=255)
                                                                                                  tttACCCACCGCCATGTGAAAAAATGCCT‑TCGGGGCGGTTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTaa                                                   <  1:31160/150‑1 (MQ=255)
                                                                                                           cGCCATGT‑CAAAAACTCCTGCCGGGGCGGCTGTCCCCGACTTTTTTTCCCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGaa                                       <  2:1029779/151‑1 (MQ=255)
                                                                                                                    cAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAACTTTTAAACCCTCCTTTTTTGTGGGGATCGCTGCG‑GGTGACAAA‑GT‑GGGAAggg                                   >  2:391726/1‑146 (MQ=255)
                                                                                                                     aaaagTGTCT‑CCGCGGCGGCTTTCGCCCAGTTTTTTTCCCGCCCCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                             <  2:226536/151‑1 (MQ=255)
                                                                                                                     aaaaaTGCCT‑TCGCGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGt                               <  1:898130/149‑1 (MQ=255)
                                                                                                                     aaaaaTGCCT‑CCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑gg                                         <  1:864915/139‑1 (MQ=255)
                                                                                                                     aaaaaTCCCT‑GGGGGGCGGCTGCCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                             <  2:382014/151‑1 (MQ=255)
                                                                                                                     aaaaaCCCCT‑CCGCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                             <  2:13508/151‑1 (MQ=255)
                                                                                                                        aacgccctcggcgcgggcGGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgcgg                           <  2:746003/136‑1 (MQ=255)
                                                                                                                             cT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTAAAACCCCCATGTTTTGTGGGGATAGCTGCTGGGTAAAAAG‑TT‑GGAAGGGGagggggggg                          >  1:188972/1‑139 (MQ=255)
                                                                                                                               tgcggggcggcTGTCTGCCAGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGa                        <  1:1052712/142‑1 (MQ=255)
                                                                                                                                 cgcgGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAATTTTAACCCCCCCTGTTTTGTTGGGATCGCTGCT‑GGGGAAAAT‑GTGGGAAAGGGagagggggg                          >  2:659435/1‑136 (MQ=255)
                                                                                                                                    gccggcTTTCTGCCAGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATc                     <  1:451973/143‑1 (MQ=255)
                                                                                                                                     gcggcTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAAACCCTCATGTTGTGTGGGAAACGCTGCT‑GGGAACAAA‑AT‑GGGAAAGGGAGGGCGGGGGAACAACTcc               >  1:3407/1‑150 (MQ=255)
                                                                                                                                          tGTCTCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAg             <  2:480716/147‑1 (MQ=255)
                                                                                                                                          tGTCGGCGAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTcc               <  1:754979/145‑1 (MQ=255)
                                                                                                                                                ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa           <  1:884130/143‑1 (MQ=255)
                                                                                                                                                  aGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACCTTTAAACCACCCTGTTTTGTGGGGATCGCTGCC‑GGTTAAAAA‑GT‑GGGAAGGGAAGAGGGGCGGAACCGCTCCACAACCacgccca  >  1:123452/1‑147 (MQ=255)
                                                                                                                                                     tATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTAAAACCGCCCTTTTTTGTGGGGAACGCCGCT‑GGGGACAATGGG‑GGGAAGGGAGGGGGGGGGAA‑CAGCTCCAGAAACgcgccga  >  2:216266/1‑144 (MQ=255)
                                                                                                                                                      |                                                                                                                                                    
CTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAA  >  NC_000913/357726‑358020

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: ‑