Table 1. HaploGrep 2 runtime and concordance over different metrics.

NGS mtDNA dataset	Sample size	Full concordance over all metrics	HaploGrep 2 Runtime (including QC)
1000G Phase 1	1,074	98.0%	5.7 s
Li et al.	2,000	95.1%	7.7 s
1000G Phase 3	2,504	93.9%	13.0 s

Full concordance means that all samples are classified into the same haplogroup for the different metrics. The HaploGrep 2 runtime refers to the calculation of the Kulczynski distance including all quality checks from the rule-based engine. The detailed results are provided in Supplementary Tables S2, 3 and 4.