Table 3. Variant extraction results on the Variome corpus.

Results for exact and partial matching are present. Each row shows the performance of each method in terms of true positives (TP), false negatives (FN), false positives (FP), Precision, Recall and F1 measure (F1). The tools are Extractor of Mutations (EMU), OpenMutationMiner (OMM), MutationFinder (MF), tmVar and SNP Extraction Tool for Human Variations (SETH) and their combination (either selecting the longest span Combined_longest or the shortest span Combined_shortest).

Exact	TP	FN	FP	Precision	Recall	F1	Char Overlap (%)
EMU OMM MF tmVar SETH Combined_shortest Combined_longest	66 7 7 81 81 34 78	52 111 111 37 37 84 40	25 56 10 26 10 76 32	0.7253 0.1111 0.4118 0.7570 0.8901 0.3091 0.7091	0.5593 0.0593 0.0593 0.6864 0.6864 0.2881 0.661	0.6316 0.0773 0.1037 0.7200 0.7751 0.2982 0.6842	100.00 100.00 100.00 100.00 100.00 100.00 100.00
Partial	TP	FN	FP	Precision	Recall	F1	Char Overlap (%)
EMU OMM MF tmVar SETH Combined_shortest Combined_longest	90 64 16 107 90 110 110	28 54 102 11 28 8 8	3 1 1 3 1 3 3	0.9677 0.9846 0.9412 0.9727 0.9890 0.9735 0.9735	0.7627 0.5424 0.1356 0.9068 0.7627 0.9322 0.9322	0.8531 0.6995 0.2370 0.9386 0.8612 0.9524 0.9524	82.08 70.01 52.91 81.11 80.99 82.03 83.03