Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,663,7770CG58.3% 1.1 / 10.1 12A25P (GCC→CCC) ynfLLysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (1/4);  new base G (7/0);  total (8/4)
Fisher's exact test for biased strand distribution p-value = 1.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.39e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTCGTGCCAGCAGTCGGGCACCAATTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAAC  >  NZ_CP009273/1663693‑1663858
                                                                                    |                                                                                 
ttCGTGCCAGCAGTCGGGCACCAATTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGGTGGGGAAAATTTAAGCGGGGCgcgg                                                                              >  2:1123146/1‑90 (MQ=255)
                      aaTTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGGGAAAAATTTAGGGGGGGGGGGGGGGGCCCCCAAAGCAGCCCTTc                                                        >  2:1086687/1‑90 (MQ=255)
                      aaTTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGGTGCGGAATATTTAAGGGGGGGGCGGCGCGCCCGCAAAGCAGCTCTTc                                                        >  1:492244/1‑90 (MQ=255)
                             tgCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCgcaaca                                                 <  2:211190/90‑1 (MQ=255)
                              gCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGGAAAATTTAGGCGGGGAGCGGCGCGCCCCCAAAGCAGCTCTTCCccaacag                                                >  1:268097/1‑90 (MQ=255)
                                         tGAATCTGCTGACTTAGCGGCGGTTGCGAAAAATTTAGGCGGGGGGGGGCGCGCCCCAAAAGCAGCCCTTCCCCCACAACaaaaaaaaaa                                     >  1:394097/1‑86 (MQ=255)
                                         tGAATCTGCTGACTTAGCGGCGGGTGCGAAAAATTTAGGCGGGGGGGGGGGCGCCCCCAAAGCAGCTCTTCCCCCACAGCAACaaaaaaa                                     >  1:882439/1‑86 (MQ=255)
                                                gctgACTTAGCGGCGGTTGCGGAAAATTTAGGCGGGGAGCGGCGCGCCCCAAAAGCAGCCCTTCCCCCACAACAAAAAAAGAAAGCAGag                              >  2:689576/1‑89 (MQ=255)
                                                          cggcggTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTc                    <  1:200311/90‑1 (MQ=255)
                                                          cggcggTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTc                    <  1:591114/90‑1 (MQ=255)
                                                             cggTTGCGAAATATTCAGGCGGGCCGCGGCGCGCCCCAAAAGCAGCTCTTCCCCCACAGCAACAAAAAAACGCAGATGACGAAGGTCAat                 >  2:891335/1‑90 (MQ=255)
                                                                            cAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAAc  <  1:891335/90‑1 (MQ=255)
                                                                                    |                                                                                 
TTCGTGCCAGCAGTCGGGCACCAATTTGTTGCTCCAGCGCCTGAATCTGCTGACTTAGCGGCGGTTGCGAAATATTCAGGCGGGCAGCGGCGCGCCCGAAATGCAGCTCTTCCGCAACAGCAACAAAGTAACGCAGATGACGAAGTTCAATATTCATATTTAAAAC  >  NZ_CP009273/1663693‑1663858

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑