Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,318,237 T→A 100% F124Y (TTT→TAT)  miaB → tRNA‑2‑methylthio‑N(6)‑dimethylallyladenosine synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,318,2370TA100.0% 10.7 / NA 5F124Y (TTT→TAT) miaBtRNA‑2‑methylthio‑N(6)‑dimethylallyladenosine synthase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (3/2);  total (3/2)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGTATACTTGAAGCATTAGGCTATCAAGCAACGACTGATATTAACACTGCAGATGTTATTTTAATTAATACATGTGCGATTAGAGAAAATGCCGAGAACAAAGTGTTTAGTGAAATAGGTAATTTGAAGCATTTGAAAAAAGAACGACCTGATATTTTAATCGGTGTTTGTGGTTGTATGTCACAAGAAGAGTCAGTAGTGAATAAAATTTTAAAATCGTATCA  >  USA300TCH1516_ALE/1318131‑1318354
                                                                                                          |                                                                                                                     
ggTATACTTGAAGCATTAGGCTATCAAGCAACGACTGATATTAACACTGCAGATGTTATTTTAATTAATACATGTGCGATTAGAGAAAATGCCGAGAACAAAGTGTATAGTGAAATAGGTAATTTGAAGCATTTGaaaaaa                                                                                     <  2:129506/141‑1 (MQ=255)
                                                              aattaatACATGTGCGATTAGAGAAAATGCCGAGAACAAAGTGTATAGTGAAATAGGTAATTTGAAGAAAAAAAAAAAAGAACGACCTGATATTTTAATCGGTGTTTGTGGTTGTATGTCACAAGAAGAGTCAGTAGTGaa                       <  2:33104/141‑1 (MQ=255)
                                                               attaatACATGTGCGATTAGAGAAAATGCCGAGAACAAAGTGTATAGTGAAATAGGTAATTTGAAGCATTTGAAAAAAGAACGACCTGATATTTTAATCGGTGTTTGTGGTTGTATGTCACAAGAAGAGTCAGTAGTGAAt                      >  2:113259/1‑141 (MQ=255)
                                                                   atACATGTGCGATTAGAGAAAATGCCGAGAACAAAGTGTATAGTGAAATAGGTAATTTGAAGCATTTGAAAAAAGAACGACCTGATATTTTAATCGGTGTTTGTGGTTGTATGTCACAAGAAGAGTCAGTAGTGAATaaaa                  >  1:54295/1‑141 (MQ=255)
                                                                                   agaAAATGCCGAGAACAAAGTGTATAGTGAAATAGGTAATTTGAAGCATTTGAAAAAAGAACGACCTGATATTTTAATCGGTGTTTGTGGTTGTATGTCACAAGAAGAGTCAGTAGTGAATAAAATTTTAAAATCGTATCa  >  2:43462/1‑141 (MQ=255)
                                                                                                          |                                                                                                                     
GGTATACTTGAAGCATTAGGCTATCAAGCAACGACTGATATTAACACTGCAGATGTTATTTTAATTAATACATGTGCGATTAGAGAAAATGCCGAGAACAAAGTGTTTAGTGAAATAGGTAATTTGAAGCATTTGAAAAAAGAACGACCTGATATTTTAATCGGTGTTTGTGGTTGTATGTCACAAGAAGAGTCAGTAGTGAATAAAATTTTAAAATCGTATCA  >  USA300TCH1516_ALE/1318131‑1318354

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑