Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,578,4460AC54.5% 1.7 / 10.3 11Y580D (TAC→GAC) ggtgamma‑glutamyltransferase
Reads supporting (aligned to +/- strand):  ref base A (5/0);  new base C (0/6);  total (5/6)
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.

ACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAAT  >  NZ_CP009273/3578361‑3578518
                                                                                     |                                                                        
aCAGGATTACGAAAAAAAAAAGGCTCCCTTCGGCTTGCCCTGAAAAAATACCCCTCTCCCCACGAAGAGGGCCGCTAACCTTAGTCcccc                                                                      <  1:133788/90‑1 (MQ=255)
      ttACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGtt                                                                >  1:159630/1‑90 (MQ=255)
      ttACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGtt                                                                >  1:50445/1‑90 (MQ=255)
                            ttCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGt                                          >  1:175692/1‑90 (MQ=255)
                                gCTTCCCCTGACAAAATACCCCTCTCCCCACGAAGAGGGCCGCTAACCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGa                                      <  1:74179/90‑1 (MQ=255)
                                   tccccTAAAAAAATCCCCCTCTCCCCACGAAGGGGCCCGCTACCCTTAGTCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATgc                                   <  1:299821/88‑1 (MQ=255)
                                          aaaaaaTCCCCCTCCCCCCACGAGGGGGGCCGCTACCCTTACCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTAc                            <  2:50445/88‑1 (MQ=255)
                                                           ccACGAGGGGGCCCCCTACCCTTATCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGccc           <  2:175692/90‑1 (MQ=255)
                                                                 agagGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCAt     >  1:340527/1‑90 (MQ=255)
                                                                   ggggCCGCTACCCTCAGCCCCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATaa   <  2:24228/89‑1 (MQ=255)
                                                                    gggCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAAt  >  1:300977/1‑90 (MQ=255)
                                                                                     |                                                                        
ACAGGATTACGAAATAAAAAAGGCTACCTTCGGCTTGCCCTGACAAAATAGCCCTCTTCCCACGAAGAGGGCCGCTAACCTTAGTACCCCGCCGTTAAATCATCCACCGAGCGCGGGTCGGATGCGCCGTACAACTCACCGTCCGGCCCAACCATAAT  >  NZ_CP009273/3578361‑3578518

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑