Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913925,5680C.61.1% ‑3.0 / 11.4 18intergenic (+28/+316)clpA/serWATP‑dependent Clp protease ATP‑binding subunit ClpA/tRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base C (6/1);  new base . (11/0);  total (17/1)
Fisher's exact test for biased strand distribution p-value = 3.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.73e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGTTTCTCTGGAAGTGAGCCAGGAAGCGCGTAACTGGCTGGCCGAGAAAGGTTACGACCGGGCAATGGGCGCTCGTCCGATGGCGCG‑TGTCATCCAGGACAACCTGAAAAAACCGCTCGCCAACGAACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGTCCGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑TTTTTGTTTATGGGG‑T‑GGAGGAGGTTCAG‑ACCC‑TTTTTTTAATGATGATGGTAAGTTGTTGATAATTAGTGCTGCGGGAAGGTAAGGATAAAAAAGGGTGCTGCAGGAGAATGGGATGGTTTTGCTTTATTAACAACGGGCT‑AAACGTGTAGTA‑TTTGAGTTCACTGCCGTACAGGCAGCTTAGAAA‑‑TTCACAGGTAACATAC  >  NC_000913/925294‑925796
                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                  
tgtTTCTCTGGAAGTGAGCCAGG‑AGCGCGTAACTGGCTGGCCGAGAAAGGTTACGACCGGGCAATGGGCGCTCGTCCGATGGCGCGTTGTCATCCAGGACAACCTGAAAAAACCGCTCGCCAACGAACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAG‑AAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATT‑ATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAAt                                                                                                                                                                                                                                              >  1:861118/1‑278 (MQ=255)
    tctcTGGAAGTGAGCCAGGAAGCGCGTAACTGGCTGGCCGAGAAAGGTTACGACCGGGCAATGGGCGCTCGTCCGATGGCGCG‑TGTCATCCAGGACAACCTGAAAAAACCGCTCGCCAACGAACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGTcgtaa                                                                                                                                                                                                                                                >  1:861119/1‑271 (MQ=255)
                                                     aCGACCGGGCAATGGGCGCTCGTCCGATGGCGCG‑TGTCATCCAGGACAACCTG‑AAAAACCGCTCGCCAACGAACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAG‑AAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGTc                                                                                                                                                                                                                                                    >  1:861123/1‑220 (MQ=255)
                                                                      gcTCGTCCGATGGCGCG‑TGTCATCCAGGACAACCTGAAAAAACCGCTCGCCAACGAACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑‑AAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGTCCGTAATCTACG‑AAAGGA‑GGTTATCGGAC‑ttttttttgtt                                                                                                                                                                                                          <  1:114594/243‑4 (MQ=255)
                                                                                          tCATCCAGGAC‑ACCTGAAAAAACCGCTCGCCAACG‑ACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGAT‑AAGAGAAAAATTGAGCTGACTTACGGATTCCAGAGTGCAC‑‑‑AAGCAC‑AAGGCGGAAGCAGCGCATTTATCTGATTGTTAGGTAGGTTGGTCAAGTCCGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGACTTTTTTGTTTATgg                                                                                                                                                                                                        >  1:114596/1‑221 (MQ=255)
                                                                                                                              aaCTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGACTTTTTTGTTTATGGGG‑T‑GGAGGAGGTTCAG‑ACCC‑TTTTTTTAATGATGATGGTAAGTTGTTGATAATTAGTGCTGCGGGAAGGTAAGGAT‑‑AAAAGGGTGCTGCAGGAGAATGGGATGGTTTTGCTTTATTAACAACGGGCT‑AAACGTGTAGTA‑TTTGAGTTCACTGCCGTACAGGCAGCTTAGAAA‑‑TTCACAgg          >  1:114597/1‑368 (MQ=255)
                                                                                                                                        tGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGACTTTTTTGTTTATGGGG‑T‑GGAGGAGGTTCAG‑ACCCTTTTTTTTAATGATGATGGTAAGTTGTTGATAATTAg                                                                                                                                            >  1:861130/1‑235 (MQ=255)
                                                                                                                                        tGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑TTTTTGTTTATGGGGTT‑GGAGGAGGTTCAG‑ACC‑‑‑TTTTTTAATGATGATGGTAAGTTGTTGATAATTAGTGCTGCGGGAAGGTAAGGAT‑AAAAAGGGTGCTGCAGga                                                                                                     >  1:861129/1‑270 (MQ=255)
                                                                                                                                                                          gcgcTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑TTTTTGTTTATGGGG‑TGGGAGGAGGTTCAGTACCCTTTTTTTTAatgatgat                                                                                                                                                                >  1:861131/1‑182 (MQ=255)
                                                                                                                                                                                  tAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCACAAAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGTcc                                                                                                                                                                                                                                                   >  1:114598/1‑100 (MQ=255)
                                                                                                                                                                                    aaGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCACAAAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GACGGTTA‑CGGa                                                                                                                                                                                                                       >  1:114599/1‑121 (MQ=255)
                                                                                                                                                                                           aaa‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑TTTTTTGTTATGGGG‑T‑GGAGGAGGTTCAG‑ACCC‑TTTTTTTAATGATGATGGTAAGTTGTTGATAATTAGTGCTGCGGG‑AGGTAAGGAT‑AAAAAGGGtgct                                                                                                           >  1:861133/1‑213 (MQ=255)
                                                                                                                                                                                           aaa‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑TTTTTGtt                                                                                                                                                                                                             >  1:861132/1‑121 (MQ=255)
                                                                                                                                                                                                           cGGATTCCAGAGTGCACAAAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAa‑ga‑g                                                                                                                                                                                                                                >  1:114601/1‑90 (MQ=255)
                                                                                                                                                                                                           cGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGTCCGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑TTTTTGttt                                                                                                                                                                                                            >  1:114602/1‑108 (MQ=255)
                                                                                                                                                                                                                  cAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑t                                                                                                                                                                                                                    >  1:861134/1‑92 (MQ=255)
                                                                                                                                                                                                                                aGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGT‑CGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGACTTTTTTGTTTATGGGG‑T‑GGAGGAGGTTCAG‑ACCC‑TTTTTTTAATGATGATGGTAAGTTGTTGATAATTAGTGCTGCGGGAAGGTAAGGATAAAAAAGGGTGCTGCAGGAGAATgg                                                                                               >  1:861135/1‑193 (MQ=255)
                                                                                                                                                                                                                                                       ttAATCTGATTGTTAGGTAGGTTGGTCAAGTCCGTAATCT‑CG‑aa                                                                                                                                                                                                                                      >  1:114603/1‑44 (MQ=255)
                                                                                                                                                                                                                                                         aaTCTGATTGTTAGGTAGGTTGGTCAAGTCCGTAAtct‑c                                                                                                                                                                                                                                          >  1:114605/1‑39 (MQ=255)
                                                                                                                                                                                                                                                         aaTCTGATTGTTAGGTAGGTTGGTCAAGTCC‑TAATCT‑CG‑AAA‑GA‑GGTTA‑CGGACTTTTTTGTTTATGGGG‑T‑GGAGGAGGTTCAG‑ACCC‑TTTTTTTAAT‑ATGATGGTAAGTTGTTGATAATTAGTGCTGCGGGAAGGTAAGGATAAAAAAGGGTGCTGCAGGAGAATGGGATGGTTTTGCTTTATTAACAACGGGCTAAAACGTGTAGTATTTTGAGTTCACTGCCGTACAGGCAGCTTAGAAAATTTCACAGGTAACATAc  >  1:114604/1‑261 (MQ=255)
                                                                                                                                                                                                                                                                         aggtTGGTCAAGTCCGTAATCT‑CGAAAA‑GA‑GGTTA‑CGGAC‑tt                                                                                                                                                                                                                   >  1:114606/1‑42 (MQ=255)
                                                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                  
TGTTTCTCTGGAAGTGAGCCAGGAAGCGCGTAACTGGCTGGCCGAGAAAGGTTACGACCGGGCAATGGGCGCTCGTCCGATGGCGCG‑TGTCATCCAGGACAACCTGAAAAAACCGCTCGCCAACGAACTGCTGTTTGGTTCGCTGGTGGACGGCGGTCAGGTCACCGTCGCGCTGGATAAAGAGAAAAA‑TGAGCTGACTTACGGATTCCAGAGTGCAC‑AAAAGCAC‑AAGGCGGAAGCAGCGCATTAATCTGATTGTTAGGTAGGTTGGTCAAGTCCGTAATCT‑CG‑AAA‑GA‑GGTTA‑CGGAC‑TTTTTGTTTATGGGG‑T‑GGAGGAGGTTCAG‑ACCC‑TTTTTTTAATGATGATGGTAAGTTGTTGATAATTAGTGCTGCGGGAAGGTAAGGATAAAAAAGGGTGCTGCAGGAGAATGGGATGGTTTTGCTTTATTAACAACGGGCT‑AAACGTGTAGTA‑TTTGAGTTCACTGCCGTACAGGCAGCTTAGAAA‑‑TTCACAGGTAACATAC  >  NC_000913/925294‑925796

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑