Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,152,7310TA54.5% 3.4 / 10.3 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 = 3.05e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCGCGAAGAAAAAGTGACGGATTGCGGTGGCGTACTACACTGTTTTACAGAGGACAGAGAAACGGCGGGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGT  >  NZ_CP009273/1152658‑1152816
                                                                         |                                                                                     
gcgcGAAGAAAAAGTGACGGATTGCGGTGGCGTACTACACTGTTTTACAGAGGACAGAGAAACGGCGGGGGAAATACTTGATCTCGGGtt                                                                       >  1:584644/1‑90 (MQ=255)
                   gATTGCGGTGGCGTACTACACTGTTTTACAGAGGACAGAGAAACGGCGGGGGAAATACTGGGTTTCGGGTTTTAAATTTCCTTTTTCGGc                                                    >  2:647473/1‑90 (MQ=255)
                               gTACTACACTGTTTTACAGAGGACAGAGAAACGGCGGGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTc                                        <  2:722489/90‑1 (MQ=255)
                                                 gagGACAGAGAAACGGCGGGGAAAATACTGGGTCTCGGGTTTTAAATCTCCCTTTTCGGCCTTTTGGCCGTCCGTAATGCGGGGCAACTg                      >  2:907133/1‑90 (MQ=255)
                                                   ggACAGAGAAACGGCGGGGAAATTACTGGGTCTCGGGTTTTAAATTTCCTTTTTCGGCATTGTGACCTTCCCTAATACGGGGCAAATgcg                    >  2:932950/1‑90 (MQ=255)
                                                   ggACAGAGAAACGGCGGGGAAAATACTTGATTTCGGGTTTTAAATTTCCTTTTTCCGCCTTGTGGACTTCCCGAAAGCGGGGGAACTgcg                    >  1:154003/1‑90 (MQ=255)
                                                   ggACAGAGAAACGGCGGGGAAAATAATGGGTCTCGGGTTTTTTATCTCCCTTTTCCGCATTTTGGCCTTCCCTAAAACGGGGGAACAgcg                    >  1:305695/1‑90 (MQ=255)
                                                        gagaAACGGCGGGGAAAATACTGGATCTCGGGTTTTAAATCTCCTTTTTCGGCATTTTGGCCTTTCCTAAATCGGGGCAAACGCGCGGtg               >  2:34185/1‑90 (MQ=255)
                                                            aaCGGCGGGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGAtgctgc           <  2:534268/90‑1 (MQ=255)
                                                              cggcggGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTgcgc         <  2:486944/90‑1 (MQ=255)
                                                                     tAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGt  <  1:101936/90‑1 (MQ=255)
                                                                         |                                                                                     
GCGCGAAGAAAAAGTGACGGATTGCGGTGGCGTACTACACTGTTTTACAGAGGACAGAGAAACGGCGGGTAAATTACTGGATCTCGGATTTTACATCTCCTTTTCCGGCATTGTGACCTTCCGTAATGCGGAGCAACTGCGCGATGCTGCGCGTTATGT  >  NZ_CP009273/1152658‑1152816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑