Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,152,7310TA54.5% 3.4 / 10.7 11L167I (TTA→ATA) ycfHmetal‑dependent hydrolase
Reads supporting (aligned to +/- strand):  ref base T (1/4);  new base A (6/0);  total (7/4)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.26e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GTTTTACAGAGGACAGAGAAACGGCGGGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGT  >  NZ_CP009273/1152699‑1152816
                                |                                                                                     
gTTTTACAGAGGACAGAGAAACGGCGGGGAAAATACTGGGTCTCGGGTTTTAAATCTCCTTTTTCCGCATTGTGACCCTCCGTAATGCgg                              >  1:240237/1‑90 (MQ=255)
      cAGAGGACAGAGAAACGGCGGGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAAc                        <  2:458987/90‑1 (MQ=255)
          ggACAGAGAAACGGCGGGGAAATTACTGGATCTCGGATTTTAAATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTgcg                    >  1:248937/1‑90 (MQ=255)
          ggACAGAGAAACGGCGGGGAAAATACTGGGTATCTGGTTTTTCATTTCCTTTTTCCGCGTTGTGAGCCTCCGCAATGGGGGGGAACTgcg                    >  1:478753/1‑90 (MQ=255)
          ggACAGAGAAACGGCGGGGAAAATAATTGATCTCGGGTTTTATAAATCCTTTTTCGGCATTGGGACCTTCCCTAATGCGGGGGAAATgcg                    >  2:11778/1‑90 (MQ=255)
          ggACAGAGAAACGGCGGGGAAAATAATGGGTCTCGGGTTTTATATCTCCTTTTTCCCCATTTTGACCTTTCGTGATGCGGGGGAAATgcg                    >  2:556614/1‑90 (MQ=255)
                         ggggAAAATACTGGATCTCGGGTTTTAAATCTCCTTTTTCGGCATTGTGACCTTCCCTAATGGGGGGGAAATGCGCGGTGCTGCGCGttt     >  2:1914/1‑89 (MQ=255)
                         ggggAAAATAATGGATCTCGGATTTTATATCTCCTTTTTCGGCATTGTGACCTTCCGTAATGCGGGGGAACTGCGCGATGCTGCGCGttt     >  2:195463/1‑89 (MQ=255)
                            tAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGt  <  1:11778/90‑1 (MQ=255)
                            tAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGt  <  1:195463/90‑1 (MQ=255)
                            tAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGt  <  2:281365/90‑1 (MQ=255)
                                |                                                                                     
GTTTTACAGAGGACAGAGAAACGGCGGGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGT  >  NZ_CP009273/1152699‑1152816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑