Collective judgment predicts disease-associated single nucleotide variants

BMC Genomics

Table 3 Performances of the PhD-SNP and Meta-SNP on training set

Dataset (% of SV-2009)	Tool	Q₂	PPV	TPR	NPV	TNR	MCC	AUC
SV-2009 (100%)	PhD-SNP	0.76	0.78	0.74	0.75	0.78	0.53	0.84
	Meta-SNP	0.79	0.80	0.79	0.79	0.80	0.59	0.87
Consensus (46%)	PhD-SNP	0.87	0.87	0.92	0.87	0.79	0.73	0.89
	Meta-SNP	0.87	0.88	0.92	0.87	0.80	0.73	0.91
Majority (40%)	PhD-SNP	0.70	0.67	0.56	0.72	0.80	0.37	0.77
	Meta-SNP	0.75	0.72	0.64	0.76	0.82	0.47	0.82
Tie (14%)	PhD-SNP	0.61	0.51	0.43	0.66	0.73	0.16	0.67
	Meta-SNP	0.69	0.62	0.57	0.73	0.76	0.34	0.75

Q₂=Overall accuracy, PPV and NPV=Positive and Negative Predicted Values, TPR and TNR=True Positive and Negative Rates. MCC=Mathew's correlation, AUC=area under the (ROC) curve.

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