Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,368,6130TA53.8% 6.8 / 15.4 13Y50F (TAT→TTT) ampCBlaEC family class C beta‑lactamase
Reads supporting (aligned to +/- strand):  ref base T (6/0);  new base A (0/7);  total (6/7)
Fisher's exact test for biased strand distribution p-value = 5.83e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.56e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATC  >  NZ_CP009273/4368534‑4368686
                                                                               |                                                                          
aaaCAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATT‑accgc                                                                 >  1:150042/1‑90 (MQ=255)
 aacaacGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGAAAAGAAATAAGGTTTACCCTGATAAATT‑accgcc                                                                >  2:317457/1‑90 (MQ=255)
                gtgACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATT‑ACCGCCACCGCCATACCCggg                                                 >  2:33840/1‑90 (MQ=255)
                          tttttttGGCGATGCCCGCATACCCCCAGGAAAAGTAAAAAGTTTTCCCCTAAAAAATT‑CCCGCCACCGCCATACCCGGGATCTTttgtt                                       <  1:24090/88‑1 (MQ=255)
                          tttttttGGCGATCCCCGCACCCCCCAAGAAAAAAAAATAAGTTTTCCCCTAAAAAATT‑CCCCCCACCGCCATACCCGGGATCTTttgtt                                       <  2:194186/88‑1 (MQ=255)
                          gctTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATT‑ACCGCCACCGCCATACCCGGGATCTTttgtt                                       >  2:87648/1‑90 (MQ=255)
                            ttttgGGCGTTGTCCGCATACCCCCAGGAAAAGTAA‑AAGGTTTTCCCTTAAAAATTCCCCCCCCCCGCCATACCCGGGATCTTTTGTTGc                                     <  2:235751/90‑1 (MQ=255)
                            ttttgGGCGTTGCCCGAAAACCCCAAGGAAAAAAAAAAAGTTTTCCCCTAAAAAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGc                                     <  1:665641/90‑1 (MQ=255)
                                    gATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAg                             >  1:512364/1‑90 (MQ=255)
                                       gcccGCAAAGCCCCAGGAAAATTAAAAAGTTTCCCCCTGAAATTTT‑GCCGCCGCCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCgg                          <  1:33840/88‑1 (MQ=255)
                                        cccGCATACCCCCAGGAAAAGTAATAAGTTTTCCCCTAAAAAATT‑CCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCggg                         <  1:244618/89‑1 (MQ=255)
                                             aTACCCCCAGGAAAAGAAATAAGTTTTCCCCTAAAAAATT‑CCCCCCCCCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAAt                    <  1:670302/90‑1 (MQ=255)
                                                               ataaGGTTTACCCTGATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATc  >  2:654160/1‑90 (MQ=255)
                                                                               |                                                                          
AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCCTGATAAATT‑ACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATC  >  NZ_CP009273/4368534‑4368686

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑