MmisAT and MmisP: an efficient and accurate suite of variant analysis toolkit for primary mitochondrial diseases

Table 4 Performance of MmisP and other genome-wide tools

Methods	Missing	Precision (%)	NPV (%)	Specificity (%)	FPR (%)	Recall (%)	FNR (%)	Accuracy (%)	MCC	AUC	F1Score
MmisP	0	58.73	97.60	72.08	27.92	95.73	4.27	79.02	0.618	0.938	0.728
MutationAssessor	80	51.20	93.32	63.58	36.42	89.35	10.65	71.30	0.485	0.864	0.651
MutationTaster	1	29.47	100.00	1.03	98.97	100.0	0.00	29.99	0.055	0.760	0.455
PolyPhen2-HDIV	39	48.61	93.29	60.12	39.88	89.71	10.29	68.88	0.457	0.863	0.630
PolyPhen2-HVAR	39	57.00	91.52	73.42	26.58	83.82	16.18	76.50	0.527	0.877	0.679
DANN	0	48.27	93.15	60.27	39.73	89.32	10.68	68.79	0.453	0.815	0.627
Eigen	41	50.71	96.71	63.00	37.00	94.68	5.32	72.08	0.523	0.892	0.660
FATHMM-MKL	0	37.57	95.04	33.97	66.03	95.73	4.27	52.09	0.311	0.793	0.540
M-CAP	383	60.64	89.13	41.69	58.31	94.64	5.36	67.48	0.425	0.854	0.739
MetaLR	10	68.35	90.19	85.07	14.93	77.70	22.30	82.91	0.606	0.901	0.727
MetaSVM	10	69.52	90.68	85.67	14.33	78.78	21.22	83.65	0.623	0.904	0.739
PrimateAI	41	81.74	78.18	96.76	3.24	34.94	65.06	78.63	0.436	0.845	0.490

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