Fig. 2

Precision and recall as a function of cluster read depth. Performance of TE insertion detection was assessed computing precision and recall separately for reference and polymorphic TEs present in NA12878. Reference (NA12878) true positives (TP) and false negatives (FN) were determined by comparison of clusters to reference (hg19) RepeatMasker annotations (NA12878-specific 1000 Genomes Phase 3 MEI calls), respectively. False positives (FP) were defined conservatively as TE candidate clusters failing to intersect any previously identified NA12878 non-reference events (see main text; Methods for details)