Table 2.

Performance of MGE detection in iMGEins, popoolationTE, TEMP, RetroSeq and MELT in simulation set 2

	Low coverage (30x)					Hogh coverage (90x)
	iMGEins	PoPoolationTE	TEMP	RetroSeq	MELT	iMGEins	PoPoolationTE	TEMP	RetroSeq	MELT
True positive
Human MGEs	78	75	80	19	72	75	2	80	27	74
Primate MGEs	77	74	78	20	37	78	10	79	31	39
Novel insertions	77	0	0	1	0	77	0	0	0	0
Total	232	149	158	40	109	231	12	159	58	113
False Positive
Human MGEs	0	0	31	121	6	0	1	56	117	5
Primate MGEs	0	1	10	188	21	0	1	40	289	21
Novel insertions	0	0	0	33	0	0	0	0	43	0
Total	0	1	41	342	27	0	2	96	449	26
Recall (%)
Human MGEs	97.50	93.75	100.00	23.75	90.00	93.75	2.50	100.00	33.75	92.50
Primate MGEs	96.25	92.50	97.50	25.00	46.25	97.50	12.50	98.75	38.75	48.75
Novel insertions	96.25	-a	–	1.25	–	96.25	–	–	0.00	–
Average
Completeb   MGE onlyc	96.67	62.08 93.13	65.83 98.75	16.67	45.42 68.13	95.83	5.00 7.5	66.25 99.38	24.17	47.08 70.63
Precision (%)
Human MGEs	100.00	100.00	72.07	13.57	92.31	100.00	66.67	58.82	18.75	93.67
Primate MGEs	100.00	98.67	88.64	9.62	63.79	100.00	90.91	66.39	9.69	65.00
Novel insertions	100.00	–	–	2.94	–	100.00	–	–	0.00	–
Average	100.00	99.333	79.40	10.47	80.15	100.00	85.71	62.35	11.44	81.29

^aThese programs cannot find novel insertions

^bThe rates for the entire test case

^cThe rates without the novel insertion category