Table 1.

Variant calling metrics for all datasets

			AUROC		AUPRC		ICI
Scenario	Mutation profile	μ (estimated)	MuTect	BATCAVE	MuTect	BATCAVE	MuTect	BATCAVE
100× whole genome	Concentrated	3.6e-7	0.987	0.993	0.972	0.975	0.117	0.287
100× whole genome	Intermediate	3.2e-7	0.987	0.989	0.972	0.973	0.118	0.214
100× whole genome	Diffuse	3.2e-7	0.988	0.989	0.971	0.973	0.120	0.219
500× whole exome	Concentrated	3.6e-7	0.848	0.929	0.674	0.758	0.138	0.109
500× whole exome	Intermediate	3.6e-7	0.847	0.881	0.677	0.706	0.108	0.112
500× whole exome	Diffuse	3.6e-7	0.850	0.873	0.676	0.698	0.105	0.116
real AML (52)	Actual	3.6e-8			0.996	0.988
real breast (4)	Actual	6.6e-7			0.972	0.968

μ = per-base mutation rate, AUROC/AUPRC = Area Under Receiver Operating Characteristic/Precision-Recall Curve, ICI = Integrated Calibration Index. Smaller values of ICI are superior.