Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092732,370,6390CA54.5% 6.2 / 13.9 11A145S (GCC→TCC) menH2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
Reads supporting (aligned to +/- strand):  ref base C (4/1);  new base A (0/6);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.28e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGATCGTCATTGAGTGAGGCAAAAACAGGCTGTTGATACCAGTCGGCAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAACGCTGACGTTCCGCACGTTGTTC  >  NZ_CP009273/2370561‑2370717
                                                                              |                                                                              
tgttgCTGCGCAGCGCCACCAGCTCCCGGCGTTGATCGTCATTGAGTGGGGCAAAAACAGGCTGTTGATACCAGTCGGCAAATAccgccg                                                                     >  1:366930/1‑90 (MQ=255)
   tgctgcGCAGCGCCACCAGCTCCCGGCGTTGATCGTCATTGAGTGAGGCAAAAACAGGCTGTTGATACCAGTCGGCAAATACCGCCGTTa                                                                  >  2:308281/1‑90 (MQ=255)
                  ccaGCTCCCGGCGTTGATCGTCATTGAGGGAGGCAAAAACAGGTTTTTGATCCAAGTCGGAAAATACCGCCGTTAACGGTTCTGTGAGaa                                                   <  1:308281/90‑1 (MQ=255)
                                             gtgagGCAAAAACAGGCTGTTGATCCCAGTCGGAAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAAc                        <  2:227723/90‑1 (MQ=255)
                                             gggagGAAAAAACGGGCTTTTAATCCCAGCCGGAAAATCCCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAAc                        <  2:447850/88‑1 (MQ=255)
                                                  gaaaaaaCAGGCTGTTGATACCAGTGGGAAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAACGCTGa                   <  1:319511/88‑1 (MQ=255)
                                                           ggCTGTTGATACCAGTCGGCAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAACGCTGACGTTCCGCa          >  2:478727/1‑90 (MQ=255)
                                                              ttttGATCCCAGTGGGAAAATCCCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTAGCGATCGGAACGCTGACGTTCCGCACgt       <  1:289359/88‑1 (MQ=255)
                                                              tGTTGATCCCAGTCGGAAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAACGCTGACGTTCCGCACgt       <  1:109061/90‑1 (MQ=255)
                                                                ttGATACCAGTCGGCAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAACGCTGACGTTCCGCACgttg     >  1:87593/1‑90 (MQ=255)
                                                                   atcccAGTCGGCAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAACGCTGACGTTCCGCACGTTGTTc  <  1:478727/87‑1 (MQ=255)
                                                                              |                                                                              
TGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGATCGTCATTGAGTGAGGCAAAAACAGGCTGTTGATACCAGTCGGCAAATACCGCCGTTAACGGTTCTGTGAGAAAACGCTGCACCCATTGGCGATCGGAACGCTGACGTTCCGCACGTTGTTC  >  NZ_CP009273/2370561‑2370717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑