BMC Genomics

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

From: iMGEins: detecting novel mobile genetic elements inserted in individual genomes

	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
Complete^b MGE only^c	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

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