Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091375,0790CT28.6% 60.7 / 13.3 35L134L (CTG→CTA) thiBthiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base C (1/24);  new base T (10/0);  total (11/24)
Fisher's exact test for biased strand distribution p-value = 5.99e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TCGCTTTCACCTTTTAAAAACAGG‑CCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTT‑CTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAA  >  NC_000913/74852‑75299
                                                                                                                                                                                                                                      |                                                                                                                                                                                                                               
ttcgtttCCCCCTTTAAAACCCGGCCCGTAGCCTTCGCCCCAGCCTTGGGTGCCCGTACCCGTTTT‑CTTCCACAGTTTCTGCCAGGCTTGGGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGCCCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCt                                                                                                                                                                                                                       <  2:400737/235‑1 (MQ=255)
   cTTTCACCTTTTAAAAACAGG‑CCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTT‑CTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTCTTTTc                                                                                                                                                                                                                   >  1:400737/1‑239 (MQ=255)
                    cAGG‑CCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTT‑CTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTCGTTGTTTTCTTGTCTTACACAAAGGCGAAg                                                                                                                                                                                                   >  2:333821/1‑239 (MQ=255)
                       g‑CCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTT‑CTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTCTTGTTATAAACGAAAGCGgaggag                                                                                                                                                                                                >  1:572168/1‑238 (MQ=255)
                             acgtttCGCTCCGACCTTTGGTCACCTTGACCTTTTT‑CTTCGCCAGTTTCTGCCAGGTTTGTGGCGCGTCATCGCCATAGCTTTTTTGCCTCCATAGCAACAGCCCCAGCCCGGGTGTACTGGTGCGCGGTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGc                                                                                                                                                                                               <  2:572168/230‑1 (MQ=255)
                                  tCGCTCCAGCTTTTGGTGCCCGTGACCGTTTT‑CGTCGCCAGTTTCTGCCAGGCTGGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCaaa                                                                                                                                                                                     <  1:126656/239‑1 (MQ=255)
                                              ttGGTGACCGTGACCGTTTT‑CTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGCCCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCaaa                                                                                                                                                                                     <  1:929871/227‑1 (MQ=255)
                                              ttGGGGACCGGGACCTTTTTACTTCGCCAGTTTCTGCAAGGTTGGTGGGGATCAATCGCCATAGATTTTTTGCACCCATAGCAACAGCCCCAGCCCGGGTGTCCTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAg                                                                                                                                                                          <  2:315617/239‑1 (MQ=255)
                                                   ccccgtcacgttttt‑CTTCGCCATTTTCGCCCAGGTTTGTGGGGCGTCATCCCCTTCGCTTTTTTGCATCCATAGCAACGGACCCAGCCCCGGTGTACTGGTGCCCGTTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑Ca                                                                                                                                                                    <  2:431461/227‑1 (MQ=255)
                                                        tgaccgtTTT‑CTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGGTTTGTCTTGTTATAAAAGAAAGGGGAGGAAGCACAATTAAAAGGGACGGAAATGT‑Cattatt                                                                                                                                                               >  1:431461/1‑238 (MQ=255)
                                                                tt‑cttcGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTTAGTTTGTTTTTGTCATAAACAAAGGCGGAGAAGCCATAATCAAAAAGTGACAAAAAGT‑Cattatttttaccccc                                                                                                                                                      >  1:99216/1‑230 (MQ=255)
                                                                            tttCTGCCGGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCa                                                                                                                                                                                             <  1:389460/190‑1 (MQ=255)
                                                                                      gCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTTCTAAACGAAAGCGCAGGAGCCATAATCaaaaa                                                                                                                                                                                   >  2:389460/1‑188 (MQ=255)
                                                                                                              aCTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCaaa                                                                                                                                                                                     <  1:58246/164‑1 (MQ=255)
                                                                                                                        tCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTTTTGTCTTATACAAAAGGGAAGTAACCCCAAACAAACGGTATGAAAAGGTGCTTTTTTTCACCCC‑CCGGG‑GCGGTTACGGCATCCCGCTCGCAACCCGCTTTTTGCAAAAACTCCGGgttt                                                                                              >  2:767030/1‑239 (MQ=255)
                                                                                                                        tCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTATTTTTTTTTTTTTTTAAAACAAGGGGAAGTAGCCATAATTAAAAAGTACGaaa                                                                                                                                                                           >  2:58246/1‑164 (MQ=255)
                                                                                                                             aGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGt                                                                                                                                                                                                                              <  1:314735/108‑1 (MQ=255)
                                                                                                                                aaCAGCCCCACCCCGGGTTTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTgg                                                                                         <  1:642397/235‑1 (MQ=255)
                                                                                                                                     aCCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTCTTGTCATTAATGAAGGCGGAGTAGGCATAAACAAAACGGACGGAAGAGG‑TATATTTTCAGACA‑CCCGGGACGGTAAACGGAG‑TCGCTCGCCCACCCCCTTTGTCGCACAGTCCGGGGTTATTTGCGGCGTcgt                                                                                >  2:642397/1‑237 (MQ=255)
                                                                                                                                      cccAGCCCGGGTTTACTGGTGCGCGGTTCCTGATAACTCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTaa                                                                               <  1:333821/239‑1 (MQ=255)
                                                                                                                                       ccAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTCtttt                                                                                                                                                                                                                    >  2:314735/1‑106 (MQ=255)
                                                                                                                                            cgtgttttctgggTGCGCGGTCCCTGATAACGCACCCGCCAGTTTGGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGTTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACa                                                                             <  2:103545/224‑1 (MQ=255)
                                                                                                                                                 tgtACTGGTGCGCGGATCCTGATAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAgc                                                                                                                                                          <  1:752851/155‑1 (MQ=255)
                                                                                                                                                          gcggGGATCCTAATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTTTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGcccc                                                            <  1:303529/238‑1 (MQ=255)
                                                                                                                                                           cgcgGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTTTTTGTTTTTTTCTTTAACGAAGGCGAAGGAGCCAGAATTAAAAGGTACGAAAGTGT‑CATTTTTTTATCCGCCCGGGaa                                                                                                                                                >  2:752851/1‑155 (MQ=255)
                                                                                                                                                                              cccGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTg                                       <  1:744576/239‑1 (MQ=255)
                                                                                                                                                                                      ttttGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGc                                                                                                                    <  1:698071/154‑1 (MQ=255)
                                                                                                                                                                                       tttGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCt                              <  1:932107/239‑1 (MQ=255)
                                                                                                                                                                                                 ctcAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTa                    <  1:110028/239‑1 (MQ=255)
                                                                                                                                                                                                 ctcAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTa                    <  1:767030/239‑1 (MQ=255)
                                                                                                                                                                                                    aaCCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCggg                                                                                                                                                  <  1:556295/111‑1 (MQ=255)
                                                                                                                                                                                                         gTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACgg               <  1:805820/236‑1 (MQ=255)
                                                                                                                                                                                                             tttCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTggcg                                                                                       <  1:59630/160‑1 (MQ=255)
                                                                                                                                                                                                                    ctgtgtgGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGaaa  <  1:342419/235‑1 (MQ=255)
                                                                                                                                                                                                                    cTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGaaa  <  1:688663/238‑1 (MQ=255)
                                                                                                                                                                                                                                      |                                                                                                                                                                                                                               
TCGCTTTCACCTTTTAAAAACAGG‑CCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTT‑CTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGT‑CATTATTCCAGCCG‑CCGGGAACGTTAACGGCAT‑CCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAA  >  NC_000913/74852‑75299

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑