Table 1.

Summary of In Vitro TE Validation Experiments for Ref− and Ref+ Insertion Loci

Type	Set	Informative Loci				All Loci
		N	TP	FP	FN	N	TP	FP	FN
Ref−	All Ref−	80	0.90	0.04	0.06	111	0.87	0.07	0.06
	Hypothesis-driven	48	0.93	0.03	0.04	71	0.88	0.05	0.07
	Random	32	0.82	0.05	0.06	40	0.80	0.13	0.07
Ref+	All Ref+	31	0.74	0.23	0.04	40	0.70	0.26	0.03
	Pindel+Break Dancer	17	0.76	0.23	0.02	20	0.71	0.28	0.01
	Pindel	8	0.79	0.14	0.07	10	0.70	0.24	0.06
	BreakDancer	6	0.67	0.31	0.02	10	0.71	0.27	0.14

Note.—Results are shown for loci that were phylogenetically informative and all loci, that is, those lacking amplicons in more than one sample (All). The number of tested loci (N) and frequency of amplicon size differences that matched the computational prediction (true positives, TP), and false positively (FP) or false negatively (FN) predicted insertions are shown. For Ref− loci, random loci (Random), and loci predicted to support a specific phylogenetic hypothesis (Hypothesis-driven) were selected. For Ref+ markers, all loci were randomly selected.