Fig. 2
From: Transposable element subfamily annotation has a reproducibility problem
Annotation confidence tends to be lower in discordant TE pairs. Consider an Alu pair: the confidence can be computed for the best-supported annotation of both elements of the pair, and the smaller of these two confidence values may be thought of as a measure of the confidence that both halves have been correctly annotated. We computed this smallest-best-confidence value for each pair from the segmental duplicate dataset, dividing data into discordant pairs (in which best-supported annotations differ) and concordant pairs (in which best-supported annotations agree). Pairs were binned according to smallest-best-confidence, so that each bin represents the fraction of all discordant- or concordant-pairs with that bin’s smallest-best-confidence value. The left shift in discordant pairs indicates that, among discordantly-annotated elements, confidence is generally lower that both annotations are correct