Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,371,3140GA48.6% 25.2 / 19.7 38F475F (TTC→TTTmenD2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylic‑acid synthase
Reads supporting (aligned to +/- strand):  ref base G (14/5);  new base A (0/18);  total (14/24)
Fisher's exact test for biased strand distribution p-value = 2.41e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACGCAATAACGCCAGCGCGTTGAGATC  >  NZ_CP009273/2371232‑2371397
                                                                                  |                                                                                   
tCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAAttt                                                                              >  2:187137/1‑90 (MQ=255)
       ggcgTCCTCAAAATGGACGTTTTGCGGAATCAGATAAAAACGCTCCCGCTCGCTTTGCGGCGTTGGCAACAGCGAAAAAATTTGCccgcc                                                                       <  2:1477762/90‑1 (MQ=255)
          gTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCgtt                                                                    >  2:478278/1‑90 (MQ=255)
            gCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCgttgt                                                                  >  1:2333967/1‑90 (MQ=255)
            gCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCgttgt                                                                  >  1:1713010/1‑90 (MQ=255)
            gCTAAAAAGGGCCTTTTTGGGGCATAAGATAAAACCGCTCACGCTCGCTTTGCGGCTTTGGCAACAGCGAAAAAATTTGCCCGCCgttgt                                                                  <  2:380007/90‑1 (MQ=255)
               cAAAATGGACTTTTGGCGGCATCAGATAGAACCGCCCCCGCTCGTTTTGCGGCGTTGGCAACAGCAAAAAAATTTGCCCGCCgttgttgt                                                               <  2:97142/90‑1 (MQ=255)
                    gggACTTTTTGGGGCATAAGATAGAACCGCCCCCGCTCGCTTTGCGGCGTTGGCAACAGCAAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        <  2:1215535/89‑1 (MQ=255)
                     ggccGTTTGGCGCAATAAAATAAAACCGCCCCCGCTTGTTTTGCGGCGTTGGCAACAGCGAAAAAATTTCCCCGCCGTTGTTGTTcacca                                                         <  1:632547/87‑1 (MQ=255)
                     ggACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCTCGCCGTTGTTGTTcacca                                                         <  2:1088575/90‑1 (MQ=255)
                     ggACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTcacca                                                         >  1:1218581/1‑90 (MQ=255)
                     ggACGTTTTGCGGCATAAGATAGAAACCCCCCCGCTCGTTTTGCGGCGTTGGAAACAGCGAAAAATTTTGCCCGCCGTTGTTGTTcacca                                                         <  1:2286134/90‑1 (MQ=255)
                      gccGTTTTGCGGCATCAGATAGAAACGCTCCCGCTCGCTTTGCGGCGTTGGCAACAGCGAAAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        <  2:1286586/88‑1 (MQ=255)
                      gACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        <  2:1723710/90‑1 (MQ=255)
                      gACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        >  1:259787/1‑90 (MQ=255)
                      gACGTTTTGCGGCATCAGATAAAACCGCCCCCGCTCGTTTTGCGGCGTTGGCAACAGCGAAAAATTTTGCCCGCCGTTGTTGTTcaccac                                                        <  1:1467769/90‑1 (MQ=255)
                      gACGTTTTGCGGCATCAGAAAAAACCGCTCCCGCTCGTTTTGCGGCGTTGGCAACAGCGAAAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        <  1:1776960/90‑1 (MQ=255)
                      gACGTTTGGCGGCATAAGATAGAACCGCTCACGCTCGTTTTGCGGCGTTGGCAACAGCGAAAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        <  2:1824889/90‑1 (MQ=255)
                         gTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAAt                                                     >  1:2360820/1‑90 (MQ=255)
                           ttggCGGCATAAGATAAAACCGCCCCCGCTCTTTTTGCGGCGTTGGCAACAGCGAAAAAATTTGCCCGCCGTTGTTGTTCACCACAATTa                                                   <  1:1443909/87‑1 (MQ=255)
                           ttggCGGCATAAGAAAGAACCCCCCCCGCTCGTTTGGCGGGGTTGCCAACAGCGAAAAATTTTCCCCGCCGTTGTTGTTCACCACAATTa                                                   <  1:2109935/87‑1 (MQ=255)
                              gCGGCATCAGATAAAACCCCCCCCGCCCGTTTGGCGGCGTTGGCAACAGGAAAAAATTTTCCCCGCCGTTGTTGTTCACCACAATTAATa                                                <  1:478278/90‑1 (MQ=255)
                              gCGGCATCAGAAAAAACCCCCCCCGCCCGTTTTGCGGCGTTGGAAACGGGGAAAAATTTTGCCCGCCGTTGTTGTTCACCACAATTAATa                                                <  2:368566/90‑1 (MQ=255)
                                   aTCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        >  1:85342/1‑77 (MQ=255)
                                   aTCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTcaccac                                                        <  2:85342/77‑1 (MQ=255)
                                     aataTAGAACCGCCCCCGCTCGTTTGGCGGCTTTGACAAAAGGAAAAAAATTTCCCCGCCGTTGTTGTTCACCACAATTAATACCAgcgg                                         <  1:986693/87‑1 (MQ=255)
                                           gAAACGCTCCCGCTCGTTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGa                                   <  2:1585798/90‑1 (MQ=255)
                                               cgctcacgctcGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAAcc                               >  2:986693/1‑90 (MQ=255)
                                                 ctcacgctcGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTg                             >  1:164245/1‑90 (MQ=255)
                                                 ctcacgctcGCTTTGCGACGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAAccct                             >  2:719361/1‑88 (MQ=255)
                                                    ccgcccgttTGGCGGGGTGGCCAAAAGGGAAAAATTTTCCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACg                          <  1:2450861/89‑1 (MQ=255)
                                                          gctTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACGCAATaa                    >  1:1687365/1‑90 (MQ=255)
                                                             ttGGGGCGTTGCAAACAGAGAAAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACGCAATAACGc                 <  2:449145/90‑1 (MQ=255)
                                                               ggggcgTTGGCAACAGCGAAAAATTTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACGCAATAACGCCa               <  2:259787/88‑1 (MQ=255)
                                                                        gCAAAAGCGAAAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACGCAATAACGCCAGCGCGTTga      <  1:1012447/90‑1 (MQ=255)
                                                                         cAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAg                                    >  1:437081/1‑59 (MQ=255)
                                                                         cAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAg                                    <  2:437081/59‑1 (MQ=255)
                                                                            cAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACGCAATAACGCCAGCGCGTTGAGATc  >  2:1072753/1‑90 (MQ=255)
                                                                                  |                                                                                   
TCGCGGCGGCGTGCTCAAAATGGACGTTTTGCGGCATCAGATAGAAACGCTCACGCTCGCTTTGCGGCGTTGGCAACAGCGAGAAAATTTGCCCGCCGTTGTTGTTCACCACAATTAATACCAGCGGCGCAGAAACCTGACGCAATAACGCCAGCGCGTTGAGATC  >  NZ_CP009273/2371232‑2371397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: