Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273130,6980AT64.0% 23.4 / 26.3 25*866L (TAA→TTA) acnBbifunctional aconitate hydratase 2/2‑methylisocitrate dehydratase
Reads supporting (aligned to +/- strand):  ref base A (4/5);  new base T (9/7);  total (13/12)
Fisher's exact test for biased strand distribution p-value = 6.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTACCGTTATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATGAGATTCCCGGGCATTTTTTTATTTCTAAAC  >  NZ_CP009273/130621‑130777
                                                                             |                                                                               
ttACCGTTATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAgcgc                                                                     >  1:445516/1‑90 (MQ=255)
 tACCGTTATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCa                                                                    >  1:27699/1‑90 (MQ=255)
      ttATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACgcgc                                                               <  1:482209/90‑1 (MQ=255)
      ttATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACgcgc                                                               <  2:639438/90‑1 (MQ=255)
       tATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCt                                                              <  2:810997/90‑1 (MQ=255)
       tATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCt                                                              >  2:362912/1‑90 (MQ=255)
       tATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCt                                                              <  1:664287/90‑1 (MQ=255)
         tCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTgc                                                            >  2:405115/1‑90 (MQ=255)
                 tCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAAc                                                    >  2:634844/1‑90 (MQ=255)
                 tCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAAc                                                    <  1:55371/90‑1 (MQ=255)
                  cAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACg                                                   <  2:589635/90‑1 (MQ=255)
                      cAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCTGCGCATAAACGacac                                               >  2:826882/1‑90 (MQ=255)
                       aGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCTGCGCATAAACGAcaca                                              <  1:278418/90‑1 (MQ=255)
                             ctcAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGccc                                        <  1:794163/90‑1 (MQ=255)
                                 gTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTg                                    <  1:295541/90‑1 (MQ=255)
                                 gTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTg                                    <  1:132797/90‑1 (MQ=255)
                                      ccGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATga                               >  2:210403/1‑90 (MQ=255)
                                      ccGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAgc                                                                       <  1:633131/50‑1 (MQ=255)
                                      ccGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAgc                                                                       >  2:633131/1‑50 (MQ=255)
                                       cGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATgag                              >  1:609545/1‑90 (MQ=255)
                                           aaaGCCGATGGGGTGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATGAGATTc                          >  1:356635/1‑90 (MQ=255)
                                           aaaGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATGAGATTc                          >  1:410051/1‑90 (MQ=255)
                                                        tGATTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATGAGATTCCCGGGCAtttttt             >  1:665995/1‑90 (MQ=255)
                                                          aTTTTCCAGACTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATGAGATTCCCGGGCATTTTTTTa           <  2:609545/90‑1 (MQ=255)
                                                                   aCTGCGGTTTTAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATGAGATTCCCGGGCATTTTTTTATTTCTAAAc  >  1:736727/1‑90 (MQ=255)
                                                                             |                                                                               
TTACCGTTATCTGAACTTCAACCAGCTTTCTCAGTACACCGAGAAAGCCGATGGGGTGATTTTCCAGACTGCGGTTTAAAAAGTCAGCGCACGCGCTGCGCATAAACGACACAATGCCCGGTGAATGAGATTCCCGGGCATTTTTTTATTTCTAAAC  >  NZ_CP009273/130621‑130777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑