Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273353,6010CA45.8% ‑3.3 / 16.6 24L267F (TTG→TTT) cynRtranscriptional regulator CynR
Reads supporting (aligned to +/- strand):  ref base C (11/2);  new base A (0/11);  total (11/13)
Fisher's exact test for biased strand distribution p-value = 3.16e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGCAAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGACCAGTTTTTCATCATGCAAG  >  NZ_CP009273/353353‑353847
                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                        
cAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGGGATTCATTTCCGCCAACAACCCCGCCTTTATCCAACGCCCTGTGCAAAAATGCCTTC‑GCGGCGG‑CCGCCCTCCCGCTA‑ATTTTC‑CCCCGccac                                                                                                                                                                                                                                                          >  2:1304113/1‑249 (MQ=17)
cAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACCCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCCCGCATTTATCCAACGCCACGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCACCTA‑TTTTTC‑CCCCGcaac                                                                                                                                                                                                                                                          >  1:139156/1‑249 (MQ=255)
  aaaaTGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGcaac‑aa                                                                                                                                                                                                                                                       >  1:771151/1‑249 (MQ=255)
       gCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCCTCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCCCCAACAACCGCCCACTTATTCACAGCCACGTGCCAAAAAGCCTTC‑GCCGCGG‑CTGTCTTCCACCTC‑TTTTTCACACGCCAAC‑AAAA‑ccc                                                                                                                                                                                                                                                 >  2:1263160/1‑249 (MQ=17)
        ccTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGCAAC‑AAAA‑ccgc                                                                                                                                                                                                                                                <  1:905833/249‑1 (MQ=255)
            cGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCCGCGGCCTGCCGGCCACCAT‑TTTTTC‑CCCCCCACC‑AAAC‑CCCCCGtc                                                                                                                                                                                                                                            >  2:200683/1‑249 (MQ=17)
             gCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGCTGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCACCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCCTTTCCCGCAACAACCGCGCATTTTTCCCACGCCATGGCGAAAAATGCCTTC‑CCCGGGG‑CCGTCTGCCCGCCATTTTTTC‑GGCGGCACC‑AAAA‑cccgctgtc                                                                                                                                                                                                                                           >  2:1131345/1‑243 (MQ=17)
                    cTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTTAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCCTC‑GCGGCGG‑CTGTCTGCCCGCTT‑TTTTTC‑CGCCGCCAC‑AAAA‑CCGCCGTTCTCTCCagt                                                                                                                                                                                                                                   >  1:1109152/1‑250 (MQ=255)
                     tGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCCTATTCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGAGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCCGCTA‑TTTTTC‑CGCCGCCAC‑AAAA‑CCGCCGTTCTCTCCagtg                                                                                                                                                                                                                                  >  1:1490254/1‑249 (MQ=255)
                           ccAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGCCAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                                                                                                                            >  1:1254929/1‑250 (MQ=255)
                             aGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGCAAC‑AAAA‑CCGCCGTTCTCTCCCGTAGTGGCggg                                                                                                                                                                                                                          >  1:486601/1‑250 (MQ=255)
                                   aGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGGAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGCAAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggggggg                                                                                                                                                                                                                    >  1:1117034/1‑245 (MQ=255)
                                     tttATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCCTGTGCCAAAATGCCTTC‑GCGGCGG‑CTGTCTGGCAGCTC‑TTTTTT‑CGCCCCAAC‑CAAA‑CCCGCGGTCTCCTCCGTAGTTGCggtgggagtgg                                                                                                                                                                                                                  >  2:1114540/1‑241 (MQ=14)
                                         tGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CCCCGCAAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggggcgggagaa                                                                                                                                                                                                               >  1:441732/1‑239 (MQ=255)
                                              cgcgcggcgTGACCCCCTTCTCCGCCCAGGGGAGAGCACTGACCTCGTGGGCCTGATAGGCTGCGCCCA‑CCGGCAATTCCCCGCCGCAGCCTTGTGTCGGCGGCTCCCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCTTGTAAAAAAATGCCTCG‑GGGGCGG‑CTGTCCCCCGTTTT‑TTTTCC‑CGCCAAAAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                                                                                                                                         <  2:991312/247‑1 (MQ=255)
                                                   ggcgTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGCAAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGCGaaagaaaacataacc                                                                                                                                                                                                    >  2:887551/1‑238 (MQ=255)
                                                                                                                                                                   ttcccccaaacaccCGCGATTTTACCAAACCCCATGTAAAAAAATGCCTTC‑GGGGCGG‑CTGTCTGCCAGTTT‑TTTTCC‑CCCCGAAAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTa                                                                                     <  1:302257/242‑1 (MQ=255)
                                                                                                                                                                                 ccccgcttttcccAACCCCATTGTCAAAAAAGCCCTGGGCGGGGG‑CGGTCTCCCAGATT‑TTTTCC‑CGCCGCAAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTtctc                                                                        <  1:1163923/239‑1 (MQ=255)
                                                                                                                                                                                          acccACCGCAATGTGAAAAAAGCCCTCG‑GGGGGGG‑GTTTCTCCCAGTTT‑TTTTCC‑CCCCGAAAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTg                                                               <  1:747721/247‑1 (MQ=255)
                                                                                                                                                                                              acccccttgccaaaaaaTCCCTCC‑GGGGCGG‑CTTTCTGCCATTTT‑TTTTCC‑CCCCCAAAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCaa                                                          <  1:984626/238‑1 (MQ=255)
                                                                                                                                                                                                atcaagggacAAAAAGGCCCGC‑GCGGCCG‑CGTTCTGCCCTTTT‑TTTTCC‑CCCCACAAA‑AAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAAt                                                         <  2:1086088/241‑1 (MQ=255)
                                                                                                                                                                                                 ccatgggacAAAACTGCTTGC‑GCGGCGG‑CGGTCAGCCAGCTT‑TTTTCC‑CGCCACAAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAAttt                                                       <  1:282280/242‑1 (MQ=255)
                                                                                                                                                                                                            aaaTCCCTTC‑GCGGCGG‑CTGTCTGCCAGCTT‑TTTTCC‑CCCCGAAAA‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCtggtg                                            <  1:1304113/250‑1 (MQ=255)
                                                                                                                                                                                                              ctcccTCC‑GCGGCGG‑TTTTCAGCCCGTTT‑TTTCCC‑CGCCCAAAC‑AACA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGc                                          <  1:691818/247‑1 (MQ=255)
                                                                                                                                                                                                                  ctcc‑gcgGCGT‑CTGTCTGCCTGCTT‑TTTTCC‑CGCCGCAAA‑AAAT‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAAt                                      <  1:265509/247‑1 (MQ=255)
                                                                                                                                                                                                                                    gccaatttA‑TTTTCC‑CCCCAAAAA‑AAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAgg                       <  1:1456593/242‑1 (MQ=255)
                                                                                                                                                                                                                                                tctC‑CGCCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGACCAGttttt             <  1:1372333/247‑1 (MQ=255)
                                                                                                                                                                                                                                                    cccccaaaac‑aaAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGACCAGTTTTtca           <  2:1446386/240‑1 (MQ=255)
                                                                                                                                                                                                                                                          caaa‑aaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGACCAGTTTTTCATCATGCAAg  <  1:1263160/250‑1 (MQ=255)
                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                        
CAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATT‑CCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGG‑CTGTCTGCCAGCTA‑TTTTTC‑CGCCGCAAC‑AAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGACCAGTTTTTCATCATGCAAG  >  NZ_CP009273/353353‑353847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑