Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,387,0380AT54.5% 0.4 / 10.9 11S860R (AGT→AGA) yhdPAsmA2 domain‑containing protein YhdP
Reads supporting (aligned to +/- strand):  ref base A (0/5);  new base T (6/0);  total (6/5)
Fisher's exact test for biased strand distribution p-value = 2.16e-03
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.

AGCCACTCGGCACCATTCATCGGCGGCATATTGAGTTCAACGCCACTTTGTTCCGGCAACGGCGGGAGCGTTTTACTGTCTGCCGCCCAAATAGCACGATCGAGCGTCAGCTTTTGACCGAGCAACCAGCGGCTATTGAAATGAT  >  NZ_CP009273/3386964‑3387108
                                                                          |                                                                      
agccaCTCGGCACCATTCATCGGCGGCATATTGAGTTCAACGCCACTTTGTTCCGGCAACGGCGGGGGCGGTTTTCTGTCTGccccccca                                                         >  1:272994/1‑88 (MQ=255)
            ccATTCATCGGCGGCATATTGAGTTCAACGCCACTTTGTTCCGGCAACGGCGGGAGCGTTTTACTGTCTGCCGCCCAAATAGCACGATCg                                             <  2:318260/90‑1 (MQ=255)
              aTTCATCGGCGGCATATTGAGTTCAACGCCACTTTGTTCCGGCAACGGCGGGAGCGGTTTTCTGTCTGCCGCCCAAAAAGCACGATCGAg                                           >  1:39933/1‑90 (MQ=255)
                        ggcATATTGAGTTCAACGCCACTTTGTTCCGGCAACGGCGGGGGGGGTTTTTTTTTTTCCCCCCCAATAACACGAGCCAGCGGCAGCttt                                 >  2:357184/1‑90 (MQ=255)
                                  gTTCAACGCCACTTTGTTCCGGCAACGGCGGGGGGGGTTTTCTTTCTTCCGCCCCAAAAAAACGATCGAGCGGCCGCTTTTTTCCGAGCa                       >  2:59410/1‑90 (MQ=255)
                                  gTTCAACGCCACTTTGTTCCGGCAACGGCGGGAGGGGTTTTCTGTCTGCCGCCCCAAAAACACGATCGAGGGTCAGCGTTTTACCCAgga                       >  1:310361/1‑88 (MQ=255)
                                      aaCGCCACTTTGTTCCGGCAACGGCGGGAGCGTTTTACTGTCTGCCGCCCAAATAGCACGATCGAGCGTCAGCTTTTGACCGAGCAACCa                   <  2:272994/90‑1 (MQ=255)
                                       aCGCCACTTTGTTCCGGCAACGGCGGGGGGGTTTTTCTTTCTGCCCCCCCAATAGCACGATCGAGCGGCCGCGTTTTTCCCGGCAACCac                  >  2:569226/1‑89 (MQ=255)
                                           cACTTTGTTCCGGCAACGGCGGGAGCGTTTTACTGTCTGCCGCCCAAATAGCACGATCGAGCGTCAGCTTTTGACCGAGCAACCAGCGGc              <  1:407957/90‑1 (MQ=255)
                                                    ccGGCAACGGCGGGAGCGTTTTACTGTCTGCCGCCCAAATAGCACGATCGAGCGTCAGCTTTTGACCGAGCAACCAGCGGCTATTGAAAt     <  2:361932/90‑1 (MQ=255)
                                                       gCAACGGCGGGAGCGTTTTACTGTCTGCCGCCCAAATAGCACGATCGAGCGTCAGCTTTTGACCGAGCAACCAGCGGCTATTGAAATGAt  <  1:59410/90‑1 (MQ=255)
                                                                          |                                                                      
AGCCACTCGGCACCATTCATCGGCGGCATATTGAGTTCAACGCCACTTTGTTCCGGCAACGGCGGGAGCGTTTTACTGTCTGCCGCCCAAATAGCACGATCGAGCGTCAGCTTTTGACCGAGCAACCAGCGGCTATTGAAATGAT  >  NZ_CP009273/3386964‑3387108

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑