Jair Martínez , Yep, I’ve seen that before. A "missing" nucleotide at an RNA cleavage site often shows up in deep RNA-seq data usually, it’s not an actual deletion, but the result of precise cleavage, mapping artifacts, or library prep bias. It can also reflect real processing events, like with miRNAs or histone mRNAs. Worth checking alignment settings and whether it’s consistent across replicates.