Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA55.0% 10.4 / 49.8 40L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/5);  new base A (0/22);  total (13/27)
Fisher's exact test for biased strand distribution p-value = 7.12e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.80e-04

TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357744‑358034
                                                                                                                                                   |                                                                                                                                                    
tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                                    <  1:832153/149‑1 (MQ=255)
     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgcc                                                                                                                                            <  2:262286/151‑1 (MQ=255)
      tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgccg                                                                                                                                           >  1:1045077/1‑151 (MQ=255)
       aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGAGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGt                                                                                                                                          >  1:985238/1‑151 (MQ=255)
            aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtctct                                                                                                                                     >  1:1102146/1‑151 (MQ=255)
               aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                                   >  1:71640/1‑150 (MQ=255)
                ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                                   >  1:244591/1‑149 (MQ=255)
                  cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagt                                                                                                                                >  1:200823/1‑150 (MQ=255)
                       ccAGCCGCAGACTTGTGTCAGCGGCTCCCGTATTTCATTCCCGCAAACACCCGCGCATTTACCCACCGCAGTGTGCAAAAATGCTTC‑GGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCagt                                                                                                                                <  2:529796/145‑1 (MQ=255)
                           ccGTAGACCTGGGTCGGGGCCTCCCGTGTTTCTTTCCCCCCAACCCCCGCGTTTTTCCCCACCCCCATGTAAAAAATTCCCTC‑CGGGGCGGCTGTCTCCCATTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       <  1:714356/150‑1 (MQ=255)
                           ccGCGGCCCTGTGTCAGCGGCTCCCGTATTTCATCCCCCCCACCACCCGCGCATTTACCCACCGCCTTGGCCAAAATTCCCTC‑CGGGGGGGTTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        <  1:830316/149‑1 (MQ=255)
                           ccGCAGCCCTGGTCCGGCGGCTACCGTATTTCTTTCCCGCCAACACCCGCGCTTTTACCCAACCCATTGTGAAAAAATCCCTT‑CGGGGTGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       <  2:1062208/150‑1 (MQ=255)
                           ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggtg                                                                                                                      >  1:384474/1‑149 (MQ=255)
                                    tgtgTCAGCGCTTCCCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCAATGTGAAAAAAGGCCTC‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                                              <  1:761859/149‑1 (MQ=255)
                                      tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggggccaaaaaaa                                                                                                            >  2:1063213/1‑140 (MQ=255)
                                      tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑aaa                                                                                                            >  1:401778/1‑149 (MQ=255)
                                            cGGCTCCGGTTATTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTCAAAAAATCCCTT‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                                <  1:576557/140‑1 (MQ=255)
                                             gcctcccGTGTTTCATTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTCAAAAAATCCTTC‑CGCGGGGGCTGTCTGCCAGCTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑aaa                                                                                                            <  2:1097357/137‑1 (MQ=255)
                                                  ccgttttccATTCCCCCCACCACCCCCGCATTTACCAACCCCCATGTAAAAAAGTGCCTC‑CGCGGCGGCTGTCTCCCACTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGc                                                                                                 <  1:809948/140‑1 (MQ=255)
                                                     tgtttaatccccGCCAACACCCGGCCTTTTACCCAACGCCTTGTGCAAAATTGCTTC‑CGCGGGGGCTGTCGGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGt                                                                                             <  2:659308/139‑1 (MQ=255)
                                                        ttCTTTCCCGCCAACACCCGCGCTTTTATCCAACGCCATGTGAAAAAATGCTTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                         <  2:881029/150‑1 (MQ=255)
                                                        ttCATTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                         <  2:184412/150‑1 (MQ=255)
                                                            ttccccccaccaCCCGCCCTTTTACCCACCGCAATGTAAAAAATTGCTTC‑CGGGGCGGTTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgt                                                                                        <  1:281628/141‑1 (MQ=255)
                                                              ccccccaccaCCCGCCCATTTCCCCAACGCAATGTAC‑AAAATCCCTTCCGCGGCGGCTGTCTCCCACTTCTTTTCCCGCCGCAACAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                         <  1:397683/140‑1 (MQ=255)
                                                                       acccGCCCTTTTACCCACCGCCTTGTCAAAAAAGGCCTC‑CGCGGCGGTTGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                           <  2:968768/147‑1 (MQ=255)
                                                                                tttccccacccccATGTGAAAAAATGCCTC‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTa                                                                 <  2:181612/138‑1 (MQ=255)
                                                                                               gtgAAAAAAGCCCTC‑CGCGGGGGCTTTCTGCCAGCTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGa                                                <  2:1045220/150‑1 (MQ=255)
                                                                                               gtcaaaaaaTGCCTC‑GGGGGCGGTTTTCTGCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAggg                                                 <  1:434130/145‑1 (MQ=255)
                                                                                                 gCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAATTTAAAACCCCCATGTTGTGTGGGCATAGCTGCT‑GGGAaaaaaatgggaa                                                     >  2:773690/1‑136 (MQ=255)
                                                                                                 acAAAAATCCCTG‑CGCGGCGTTTCTCCCCGAGTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGaa                                               <  1:708247/148‑1 (MQ=255)
                                                                                                   aaaaaTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGG‑AAAAGGCTTTTAACCCCCCCCTTTTTTTGGCAATTACTGTG‑GGGAAAAATGTGGggaagggaagg                                             >  2:57288/1‑149 (MQ=255)
                                                                                                   aaaaaTGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAAATTTAAACCC‑CCCTCTTTTGTGGGGATCGCTGCTGGGTAAAAAGTG‑GGAAAGGGagagg                                            >  2:734337/1‑147 (MQ=255)
                                                                                                   aaaaaTGCCTC‑GGCGGCGCCTTTCTGCCAGTTTTTTTCCCCCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGt                                             <  2:33307/149‑1 (MQ=255)
                                                                                                                  ggcggcTTTCT‑CCAATTTTTTTTCCCGCACAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGc                                <  1:1032896/148‑1 (MQ=255)
                                                                                                                  ggcggcTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCt                               <  2:1004887/149‑1 (MQ=255)
                                                                                                                        tGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGTGCGAGAG‑AAAAAACTTTTAACCCCTCATTTTTTGTGGGGATCGCTGCT‑GGGGACAAAGT‑GGGAAGGGGAGGGGGGGGGAACAGCCCCCGaa                         >  1:536154/1‑149 (MQ=255)
                                                                                                                          tccccatgtttttttcCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                       <  1:851091/138‑1 (MQ=255)
                                                                                                                           cTGCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCa                            <  1:204621/143‑1 (MQ=255)
                                                                                                                              ccAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa                 <  2:1098103/151‑1 (MQ=255)
                                                                                                                                             ccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  2:822983/151‑1 (MQ=255)
                                                                                                                                             ccgaAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  1:1027295/151‑1 (MQ=255)
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TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357744‑358034

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: ‑