Figure 2. TSDs create ambiguity in the annotation of de novo TE insertion sites. Unique DNA in the reference genome (e.g., positions 3–7 for a 5 bp TSD) is duplicated on insertion of a TE for both insertions on the positive strand (> > > ) and negative strand (< < < ). When NGS reads (solid gray arrows) that span the TE-flanking region junction are used to map de novo TE insertions on the positive strand, the placement of the insertion relative the TSD differs for reads from the 5′ (after TSD) and 3′ (before TSD) ends of the TE. Differential annotation of TE insertion sites is also observed for negative strand insertions, but placement relative to the TSD is reversed relative to positive strand insertions. These TSD-induced effects can lead to ambiguity in the mapping and interpretation of de novo TE insertions.