Figure 1. Genome coordinate systems and the annotation of TE insertions. The location of an arbitrary genomic feature encoded by the sequence GGGCCC is represented differently in base and interbase coordinate systems (A). Since de novo TE insertions occur between bases in the reference genome, they are more naturally represented by interbase coordinate systems. On the widely-used base coordinate system, mapping a de novo TE insertion requires the invocation of arbitrary rules (either before or after the insertion site) (B). These arbitrary rules can lead to ambiguity in the mapping and interpretation of de novo TE insertions.