Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,264,3320AT53.8% 18.9 / 40.5 26I238F (ATT→TTT) kdsA3‑deoxy‑8‑phosphooctulonate synthase
Reads supporting (aligned to +/- strand):  ref base A (3/9);  new base T (14/0);  total (17/9)
Fisher's exact test for biased strand distribution p-value = 7.04e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.44e-06
Rejected as consensus: Frequency below/above cutoff threshold.

GAAAAAGTGATTCTTTGCGATCGCGGTGCTAACTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTGCGTTAAGACTTTTTTCATGGGTGCCGGATACAAAAAAGGCCGCAGGCTGTTACCCCTGCGGCCG  >  NZ_CP009273/1264101‑1264575
                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      
gAAAAAGTGATTCTTTGCGATCGCGGTGCTAACTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGGGGGTTTTTGAAG‑GGGaaccgggat                                                                                                                                                                                                                                     >  1:435364/1‑247 (MQ=255)
  aaaaGTGATTCTTTGCGATCGCGGTGCTAACTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGGTGGTTTTTGAAG‑CGCatccgggtccg                                                                                                                                                                                                                                   >  1:203625/1‑250 (MQ=255)
     aGTGATTCTTTGCGATCGCGGTGCTAACTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACGCGCCGGTGATTTTCGACGTGACCCACGCGCTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGaa                                                                                                                                                                                                                                <  1:424668/250‑1 (MQ=255)
          ttCTTTGCGATCGCGGTGCTAACTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGCGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGCAGGTTTGGC‑GGGGCTGTTTTTTTATGTCCCTTCCGGGTCCGCAACagg                                                                                                                                                                                                                            >  1:510226/1‑248 (MQ=255)
                          tGCTAACTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGGCTGGC‑GGGGGCGTTTTTTTAAA‑CGCACACCGATCCCGGACCCTCGAAATgtggtgtgcca                                                                                                                                                                                                           >  2:88770/1‑245 (MQ=255)
                              aaCTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGGTGTTTTTTTAAG‑CGCCTCCGGGTCCCGAACATGCGGAAAGTGATGGGCCATCcg                                                                                                                                                                                                       >  1:119666/1‑250 (MQ=255)
                                     gcgaTGACACCCTGGTGGTCAATATGCTGGGCTACAGCATTATGAAGAAGGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCACGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGcc                                                                                                                                                                                                <  2:606424/247‑1 (MQ=255)
                                       tATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGGCTGGCGGGGGGGGTTTTTTTAAC‑GCCTTCCGGTCCCGGGACAGGGGAAATGGGTTGTTCCACCCGCGCtccgc                                                                                                                                                                                               >  2:513490/1‑246 (MQ=255)
                                                   gTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGGTGTTTTTTTAAG‑GGCCTCCGGATCCGGAACATTCGGAATGTGGTGGTCCCTCCGCGCTGCCGCTGGCTAAACT‑g                                                                                                                                                                                  >  1:468334/1‑249 (MQ=255)
                                                    ttGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGGCTGGC‑GGGGCTGTTTTTTTAAG‑CGCATCCGGGACCGGGACAAGCGGAATGTGGTGGTCCATCCGCGCCGCCGCCGGCTAAAAT‑gg                                                                                                                                                                                 >  1:258940/1‑249 (MQ=255)
                                                           tatGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGGCTGGC‑GGGGGTGTTTTTTTAAA‑GGGCTTCGGGTCCGGAAAATGGGGAATGTGATGGGTCATCCGCGCCGCCGCCGGCTAAACT‑GGGAACGTTc                                                                                                                                                                         >  1:24317/1‑250 (MQ=255)
                                                                tGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGGTGGTTTTTTTAG‑CGCATCCGGAGCCGGGAAACGCGAGAAGGGGTGGTCCCTCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTCCCTccc                                                                                                                                                                    >  2:126789/1‑248 (MQ=255)
                                                                           aTTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTTTTTGAG‑CGCATCCGGGTCCCGGCAATGCGGAAAGTGATTGGTCATCCGCGCTGTCCCCGGGCCAACC‑GGGACCCTTTCTCCAGCACATG‑caa                                                                                                                                                         >  2:407490/1‑249 (MQ=255)
                                                                                  agaaAGTTTCGGGTACTGCGCCGGTGATTTTGGCCGTGACCCACGCACTGCAATGCCGCGCTCCGTTTGGCGCAGCTTCCGGTGTTCGTCGTGCTTAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATtga                                                                                                                                                 <  2:534045/250‑1 (MQ=255)
                                                                                              gTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGa                                                                                                                                      <  1:506407/249‑1 (MQ=255)
                                                                                                       cGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCga                                                                                                                            <  1:207142/250‑1 (MQ=255)
                                                                                                                      tGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGGTGTTTTTTGAAG‑GGCATCCGGGTCCGGGACATGCGGAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCCAGCAGATG‑GAAGCGGTTGATGATCTGGGGGAAGGGTTCGGAGAACTGGATACCAg                                                                                                             >  1:301255/1‑250 (MQ=255)
                                                                                                                                                  gTTTGGCGCAGCTTCCGGTGGTGGTCGTGCTCAGGTGGCGGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATaa                                                                                 <  2:320732/250‑1 (MQ=255)
                                                                                                                                                   tttGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGGTGTTTTTTTAAG‑CGCCTCCGGGTCCGGGAAATGCGGAAAGTGATGGGTCATCCCCGCCGCCGCTGGCTAAACT‑GGGACCGTTCCTCCAGCAAATG‑GAAACGGTTGGTGGACTGGTGGAAAGTTTTGGAGAAACGGGTACCCACAAGTAAACTTTTTTGCTTGGAaaaaaa                                                                                 >  2:14021/1‑249 (MQ=255)
                                                                                                                                                          cAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGGCTGGC‑GGGGGTGTTTTTTTAAA‑CGCATCCGGGGCCGGGAAAAGCGGAAAGTGGTGGGGCCTCCGCGCCGCCGCTGGGCAAACTGGGAACCG‑TCCTCAAACAGAAGAAAAAGGATTATGGTTTTGGGGAAAGGTTT‑GGAGAAATGGGTAACAGCCAAAAAATTTTTTTTCTTTTAAAATAAAAAATTat                                                                         >  2:430490/1‑249 (MQ=255)
                                                                                                                                                                 cGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGAGCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTg                                                                  <  2:467783/250‑1 (MQ=255)
                                                                                                                                                                               cTCAGGTGGCTCAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTTGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTGCGTTAAGACtttt                                                     <  2:501472/249‑1 (MQ=255)
                                                                                                                                                                                                  aCGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTGCGTTAAGACTTTTTTCATGGGTGCCGGATACaa                                 <  2:14076/250‑1 (MQ=255)
                                                                                                                                                                                                               gCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTGTGTTAAGACTTTTTTCATGGGTGCCGGATACAAAAAAGGCCGCAgg                    >  2:577210/1‑250 (MQ=255)
                                                                                                                                                                                                                          ggC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTGCGTTAAGACTTTTTTCATGGGTGCCGGATACAAAAAAGGCCGCAGGCTGTTACCCCt         >  1:149534/1‑250 (MQ=255)
                                                                                                                                                                                                                                  cTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTGCGTTAAGACTTTTTTCATGGGTGCCGGATACAAAAAAGGCCGCAGGCTGTTACCCCTGCGGCCg  >  2:193713/1‑250 (MQ=255)
                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      
GAAAAAGTGATTCTTTGCGATCGCGGTGCTAACTTCGGCTATGACAACCTGGTTGTCGATATGCTGGGCTTCAGCATTATGAAGAAAGTGTCTGGTAACTCGCCGGTGATTTTCGACGTGACCCACGCACTGCAATGCCGCGATCCGTTTGGCGCAGCTTCCGGTGGTCGTCGTGCTCAGGTGGCTGAGCTGGCACGAGCCGGTATGGCGGTAGGTCTGGC‑GGGGCTGTTTATTGAAG‑CGCATCCGGATCCGGAACATGCGAAATGTGATGGTCCATCCGCGCTGCCGCTGGCTAAACT‑GGAACCGTTCCTCAAGCAGATG‑AAAGCGATTGATGATCTGGTGAAAGGTTTCGAAGAACTGGATACCAGCAAGTAATCTTTTTTGCTTGAAAAATAAAGTATTAGCGTTCTGCGTTAAGACTTTTTTCATGGGTGCCGGATACAAAAAAGGCCGCAGGCTGTTACCCCTGCGGCCG  >  NZ_CP009273/1264101‑1264575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑