Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,976,0580GT40.0% 40.9 / 15.0 30Q322K (CAA→AAA) araHarabinose ABC transporter permease AraH
Reads supporting (aligned to +/- strand):  ref base G (5/13);  new base T (12/0);  total (17/13)
Fisher's exact test for biased strand distribution p-value = 8.70e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGCCACCACATAT  >  NZ_CP009273/1975925‑1976191
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tGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGGCT‑‑GG‑TGGGGAAAAAAACTAAAATTTTGCAGAAAAAAAAAACAAAAAGAGCGGTTTGCTTTTTTTTTGt                                                                                                                                  >  1:842751/1‑139 (MQ=255)
  tAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGTTTT‑‑TG‑TGGGGAAAAAAGCCAAAATTTTTCAGAAAAAAAGAACAGACAGGGGGGTTCGCTTTTTTCttttta                                                                                                                                >  2:111653/1‑135 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGTATGGGG‑GGGGAAAAAACCCAAAATT‑TT‑CAGAAAAAAAAACCAAAAAGAGGGGTTTGCTTTTTTTTTTTAAAGGGCGAAGaac                                                                                                                    >  2:668270/1‑136 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGTAT‑‑TG‑TGGGGAAAAAAGCCAAATTTTTGTAGAAAAAAACATCAAACAATGCGGTTTGCTTTTTTCTTGTAAAGGGCGGAGAACa                                                                                                                   >  1:527141/1‑139 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGTAT‑‑GG‑TGGGGAAAAAAGCTTAAATTTTTCAGAAAAAAAAATCAGACAATGTGGTTTGCTTTTTTCTTTTAAAGGTCGAAGAtta                                                                                                                   >  1:847371/1‑137 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGTAT‑‑GG‑TGGGGAAAAAAACTAAAATGTTGGAGAAAAAAGAAACAGACAGTGGGGTTTGCTTTTTTCTTGTTACGGGCGAAGAACa                                                                                                                   >  2:154199/1‑139 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGTAT‑‑GG‑GGGGGAAAAAAGCCAAATTTTTTCAGAAAAAAACATCAGAAAGTGCGGTTCGCTTTTTTCTTTTAACGGGCGAAGaac                                                                                                                    >  1:343401/1‑136 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGGAAAAAAGCTAAATTGTTTCAGAAAAAAACAACAGAAAGTGGGGTTCGCTTTTTTTTTTTAAAGGTCGAAGaac                                                                                                                    >  1:832499/1‑136 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGGTGTGCAT‑‑GGCTGGGAAAAACAGCTAAA‑TATTGCTCAGAAAAACATCACACAGAGCGGTTTGCCGTTTTCGTGTTACGGGCTAAGAtag                                                                                                                   >  2:62769/1‑137 (MQ=255)
               tgtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGATGGGTAT‑‑GG‑GGGGGAAAAACAACAAAATATTTTAGAAAAAAGGACCAGAAAGGGGGGTTTGCTTTTTGTTTGTTAAGGGCGagacaca                                                                                                                   >  2:636301/1‑133 (MQ=255)
                gtgACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGGAT‑‑GG‑GGGGGAAAAAAACAAAAATTTTGGAGAAAAAAAAAACAAACAGGGCGGTTTGCGTTTTTTTTGTTAAGGGCGAAGaaaac                                                                                                                  >  2:345969/1‑135 (MQ=255)
                         gTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGCGGGTGGGCTTG‑‑GG‑GGGGAAAAAAAACAAAATT‑TTGTAGAAAAAAAAAATAAAAAGAGGGGGTTGCTTTTTTTTTGTAAAGGTCGAAAAACACCGcccgcca                                                                                                         >  2:837747/1‑133 (MQ=255)
                                 ttGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGGTAT‑‑GG‑GGGGGAAAAAAACTAAAATGTTTTAGAAAAAAACATCACACAGAGGGTTTTGCTTTTTTTTTTTAACGGTCGAAGAACAACGCTGCCAGCAggggt                                                                                                  >  2:733483/1‑135 (MQ=255)
                                       cGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCcgc                                                                                           <  1:868672/139‑1 (MQ=255)
                                       cGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCcgc                                                                                           <  2:572410/139‑1 (MQ=255)
                                       cGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCcgc                                                                                           <  2:305382/139‑1 (MQ=255)
                                       cGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCcgc                                                                                           <  2:842751/139‑1 (MQ=255)
                                       cGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCcgc                                                                                           <  1:154199/139‑1 (MQ=255)
                                       cGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCcgc                                                                                           <  1:345969/139‑1 (MQ=255)
                                                             gC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAg                                                                      <  1:163293/138‑1 (MQ=255)
                                                                ggTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCATAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCAAAGATGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGgag                                                                   <  1:668453/139‑1 (MQ=255)
                                                                                       aaCGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATg                                               <  2:343401/139‑1 (MQ=255)
                                                                                                        gAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGcc                              <  1:656945/139‑1 (MQ=255)
                                                                                                                     gacatggCGTTTCGCTTTTTGCTTGAAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGACCCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTCCCACGGTGCCTAAAATTAAGATa                 <  2:847371/133‑1 (MQ=255)
                                                                                                                     gACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATa                 >  2:741580/1‑139 (MQ=255)
                                                                                                                          tGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAatat                                                             >  2:553064/1‑90 (MQ=255)
                                                                                                                          tGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAatat                                                             <  1:553064/90‑1 (MQ=255)
                                                                                                                          tGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGc            >  2:557378/1‑139 (MQ=255)
                                                                                                                            cGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGcca          <  1:359273/139‑1 (MQ=255)
                                                                                                                                    tttttGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGCCACCACatat  >  2:214378/1‑139 (MQ=255)
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TGTAAGTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAGAACAGCCAACCGTTATGGC‑GGTTGGCTAT‑‑GG‑TGGGAAAAAACGCTAAATTGTTGCAGAAAAAAGCATCAGACAGTGCGTTTCGCTTTTTGCTTGTAACGGTCGAAGATCACCGCTGCCAGCAGGATTAAGCCGCGAACCACGTACTGCGCGAAAGGAGAAATATTAAGCAGGTTCATGGCGTTTTCCACGGTGCCTAAAATTAAGATACCCGCCACCACATAT  >  NZ_CP009273/1975925‑1976191

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑