Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091375,0790CT48.1% 14.6 / 16.8 27L134L (CTG→CTA) thiBthiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base C (2/12);  new base T (13/0);  total (15/12)
Fisher's exact test for biased strand distribution p-value = 5.98e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAAC  >  NC_000913/74938‑75223
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ttGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTc                                                                                                                                           <  1:243431/151‑1 (MQ=255)
ttGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTc                                                                                                                                           <  2:562336/151‑1 (MQ=255)
      ggCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTc                                                                                                                                      <  2:670887/150‑1 (MQ=255)
                                  cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCTGTTTGTTTTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑aa                                                                                                        >  2:12422/1‑151 (MQ=255)
                                  cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTGTCATAAACGAAAGCGAAGTAGCCATAATC‑aa                                                                                                        >  2:609858/1‑151 (MQ=255)
                                       cAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTGTTTTTTTTTTTCATAAAAAAAAGCGGAAGAGCCATAAAC‑AAACggg                                                                                                   >  2:87351/1‑150 (MQ=255)
                                       cAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACgg                                                                                                    <  2:304291/150‑1 (MQ=255)
                                             aCCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGaa                                                                                             <  1:591991/150‑1 (MQ=255)
                                             aCCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑c                                                                                                <  2:328119/147‑1 (MQ=255)
                                                     ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTTTCATAAACAAAGGCGAAGGAGCCATAATC‑AAAAGGTA‑CGAAAGTGTTatt                                                                                    >  1:694220/1‑151 (MQ=255)
                                                     ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTCTTTTCATAAAACAAGGCGAAGGAACCATAATT‑AAAAGGGA‑AGAAAGGGGCatt                                                                                    >  1:489394/1‑151 (MQ=255)
                                                     ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTCTTGTCCTAAACGAAGGCGAAGTAGGCATAAACAAAACGGT‑‑CGAAAGTGGCatt                                                                                    >  1:475204/1‑151 (MQ=255)
                                                        gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTTTCATAAAAGAAGGCGAAGGAGCCCTAATC‑AAACGGGA‑CGAAAATGTCattatt                                                                                 >  2:677055/1‑151 (MQ=255)
                                                        gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTATCTTGTTTTTTTCTCATAAAAAGAGGAAGAAGGCATAATC‑AAACAGGA‑CGgaaaaggaattttt                                                                                 >  2:513624/1‑140 (MQ=255)
                                                         tgtATTGGGGCGCGGATCCTGAAAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGAAAGTGTCATTATTc                                                                                <  1:511124/151‑1 (MQ=255)
                                                            aCTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGAAAGTGTCATTATTCCAg                                                                             <  2:403743/151‑1 (MQ=255)
                                                             cTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTTTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAAAGGTA‑CGAAAGTGTCATTTTTTCAg                                                                             >  2:659836/1‑150 (MQ=255)
                                                                             gATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTCTTTTTTCTTGTCCTAAAAGAAAGCACAGGAGGCAAAATT‑CAACGGTATCCAAAG‑GCCATTATTTCACCCGCCGGGAACGtttaa                                                            >  2:471910/1‑148 (MQ=255)
                                                                                      cccGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTGTTTTTTTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGGA‑CGAAAGGGTCATTATTTCAGCCGCCGGGGACGTTAACGGCATCCg                                                    >  2:260489/1‑150 (MQ=255)
                                                                                      cccGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGc                                                   <  1:12422/151‑1 (MQ=255)
                                                                                              ttttGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCacac                                           <  2:556105/151‑1 (MQ=255)
                                                                                                       ctctCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTCTTGTCCTAAAACAAGGGGAAGGAGGCATAATT‑AAACGGGG‑AGAAAGTGTCATTTTTTCAGCCGCCGGGGAAGTTAACGGCAACCGACGCCACACCGccctttg                                  >  1:240896/1‑145 (MQ=255)
                                                                                                        tctcAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGc                                 <  1:373267/151‑1 (MQ=255)
                                                                                                           cAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGTTTTTTTCATAAACGAAGGGGAAGTAGCCATAATA‑AAACGGTA‑CGAAAGGGTCATTTTTTCACCCGCCGGGAAAGTTTACGGCATCCCCTGCCACACCCCCTTTTGGaaa                              >  2:575911/1‑151 (MQ=255)
                                                                                                           cAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTGTCATAAACGAAGGCGAAGTAACCATAATC‑AAACAGGA‑CGAAAATGTCATTATTTCAGCCGCCGGGGACGTTAACGGCATCCGCTGCCCCACCGCTTTTTGGaaa                              >  2:355538/1‑151 (MQ=255)
                                                                                                                    cTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTGTTTTTTTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGGA‑CGGAAGAGGCATTTTTTCACCCCCCCGGGACGGTAAAGGCATCCGCCGCCACACCCCCTTTTGCAAAAAATCCGGt                     >  2:329669/1‑151 (MQ=255)
                                                                                                                                        tgtttCAGTCTGTAACTGTCCAAACCGAAGGCGAAGGAGCCATAATC‑AAACGGAA‑GGAAAGTGTCAGGATTCCAGCCGCAGTGAACGTGAACGGCATCCGCTGCCACACCGCTGTTGGCAGACAGTCCGGTTTTACTGGCGGCGTCTAAc  <  1:544312/148‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                                  
TTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATC‑AAACGGTA‑CGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAAC  >  NC_000913/74938‑75223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑