Representativeness of variation benchmark datasets

Schaafsma, Gerard C. P.; Vihinen, Mauno

doi:10.1186/s12859-018-2478-6

BMC Bioinformatics

Table 1 General properties of the investigated benchmark datasets

From: Representativeness of variation benchmark datasets

dataset	collection	subset of VariBench dataset	original filename	no. of variants	no. of variants mapped to PDB	% mapped to PDB	no. of variants in ExAC	% in ExAC
DS1	VariSNP		Neutral single nucleotide variants	446,013	39,081	8.76
DS2	VariBench Dataset 1		Neutral_dbSNP_build_131_mapped	23,671	2358	9.96
DS3	VariBenchDataset 1		Pathogenic_SNP_mapped	19,335	10,242	52.97	263	1.36
DS4	VariBench Dataset 2	1	Neutral_dataset_Olatubosun_et_al_with_mapping_annotated	19,459	2245	11.54
DS5	VariBench Dataset 2	1	Pathogenic_training_dataset_from_PONP	14,610	7261	49.7	221	1.51
DS6	VariBench Dataset 4	1	Neutral_dataset_from_Thusberg_et_al_clustered_with_mapping	17,623	1743	9.89
DS7	VariBench Dataset 4	1	Pathogenic_dataset_Thusberg_et_al_clustered_with_mapping	17,525	9519	54.32	227	1.30
DS8	VariBench Dataset 5	2	Neutral_dataset_Olatubosun_et_al_clustered_with_mapping	14,647	1706	11.65
DS9	VariBench Dataset 5	2	Pathogenic_dataset_Olatubosun_et_al_clustered_with_mapping	13,096	6652	50.79	195	1.49
DS10	VariBench Dataset 7	2	Neutral_PON-P2_training_data	13,063	1731	13.25
DS11	VariBench Dataset 7	2	Pathogenic_PON-P2_training_data	12,584	6420	51.02	173	1.37
DS12	VariBench Dataset 7	2	Neutral_PON-P2_test_data	1605	150	9.35
DS13	VariBench Dataset 7	2	Pathogenic_PON-P2_test_data.csv	1301	481	36.97	23	1.77
DS14	VariBench Dataset 7	2	Neutral_PON-P2_c95_training	8664	953	11
DS15	VariBench Dataset 7	2	Pathogenic_PON-P2_c95_training	7151	3728	52.13	81	1.13
DS16	VariBench Dataset 7	2	Neutral_PON-P2_c95_test	1053	82	7.79
DS17	VariBench Dataset 7	2	Pathogenic_PON-P2_c95_test	751	272	36.22	12	1.60
DS18	VariBench Dataset 9		predictSNP_selected_tool_scores	16,098	4494	27.92
DS19	VariBench Dataset 9		varibench_selected_tool_scores	10,266	3418	33.29
DS20	VariBench Dataset 9		exovar_filtered_tool_scores	8850	2985	33.73
DS21	VariBench Dataset 9		humvar_filtered_tool_scores	40,389	10,990	27.21
DS22	PolyPhen-2		humvar-2011_12.neutral.humvar.output	21,151	2169	10.25
DS23	PolyPhen-2		humvar-2011_12.deleterious.humvar.output	22,196	10,290	46.36	342	1.54
DS24	SwissVar		SwissVar_latest	75,042	12,749	16.99	16,049	21.39

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com