Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP009273490,0060GC55.6% 3.0 / 10.7 9R49P (CGG→CCG) recRrecombination mediator RecR
Reads supporting (aligned to +/- strand):  ref base G (0/4);  new base C (5/0);  total (5/4)
Fisher's exact test for biased strand distribution p-value = 7.94e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTC  >  NZ_CP009273/489922‑490064
                                                                                    |                                                          
gCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGa                                                       <  1:321345/90‑1 (MQ=255)
           gcgcAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGGGGCGTCTGGCGCGGGCGCCCCCCCCGGGGGTGGCGGaaaac                                            >  2:36148/1‑88 (MQ=255)
                          ttCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGAt                             <  2:268993/90‑1 (MQ=255)
                              cGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGcc                         <  2:133559/90‑1 (MQ=255)
                                            gATCGTAGCGGCGGGGTGCGTCTGGCGCAGGGGCTCCCCCCGGGGGTGTCGGGAAACGGCCCCCGCGCCCGTTGCCGCCCCTTTACCCaa           >  2:111885/1‑90 (MQ=255)
                                            gATCGTAGCGGCGGGATGCGTCTGGGGCAGGCGCTCACCCCGGGGGTGTCGGGAATTCGCCCCCGCGCCCGTTGGCGGACCTTcccccca           >  1:325465/1‑87 (MQ=255)
                                                  aGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCCGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCCAACAggga     >  1:183945/1‑88 (MQ=255)
                                                   gcggcgGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCGAACAGGAAg    <  1:36148/90‑1 (MQ=255)
                                                     ggcggGATGCGTCTGGCGCAGGCGCTCACCCCGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCCAACAGGAAGTc  >  1:202946/1‑90 (MQ=255)
                                                                                    |                                                          
GCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTC  >  NZ_CP009273/489922‑490064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑