Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273434,6580CA55.6% 2.9 / 10.6 9G326C (GGC→TGC) dxs1‑deoxy‑D‑xylulose‑5‑phosphate synthase
Reads supporting (aligned to +/- strand):  ref base C (3/1);  new base A (0/5);  total (3/6)
Fisher's exact test for biased strand distribution p-value = 4.76e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.82e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAA  >  NZ_CP009273/434581‑434742
                                                                             |                                                                                    
gCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGa                                                                          <  2:575427/90‑1 (MQ=255)
         ttCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCgg                                                                 >  1:68711/1‑90 (MQ=255)
                           aaTCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACtttt                                               >  1:284654/1‑90 (MQ=255)
                           aaTCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACtttt                                               >  2:240069/1‑90 (MQ=255)
                                    cAGTTTGTTGTTTTCCGCTGCCTTTTCCCACACCCAGCCGCAAAATTTTTTTAAATAGCTCGCCAAACCGCCGCTACTTTTCGGCAaaca                                      <  1:426463/90‑1 (MQ=255)
                                                   cGCTGCCGTTCCGCACACCCAGTCGCAAAAATTTTTTGAAGAGCTCGGAAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATc                       <  1:299190/90‑1 (MQ=255)
                                                                cacaCCCAGTCCCAAAATTTTTTTAAAAAGCCCGCAAACCCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACg          <  1:128492/90‑1 (MQ=255)
                                                                  caACCAGTCGCAAAAGTTTTTTGAATAGCTCGGCAACCCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGc        <  1:50178/90‑1 (MQ=255)
                                                                        gTCGCAAAAGTTTTTGGAAAGGCCCGAAAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGaa  <  1:475371/90‑1 (MQ=255)
                                                                             |                                                                                    
GCCGGAACCTTCACGCATCGCCGGAGTAATCGCCATCAGCTTGTTGTCTTTCGCTGCCGTTTCGCACAACCAGTCGCCAAAGATTTTTGAATAGCTCGGCAAACCGCCGCTACTTTTCGGCAAACAACCGCTGGAGGGATCAAATTTAGGCACGGCGTGGAA  >  NZ_CP009273/434581‑434742

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑