TABLE 1.

Summary of detected minor variants, false-positive calls, and F1 scores resulting from the three tested variants callers.

Mixture and haplogroup	Mixture I: D4e1′3 and J1c2			Mixture II: H1b1+16362 and U5a2a1
Percentage major and minor component	95% + 5%	98% + 2%	99% + 1%	95% + 5%	98% + 2%	99% + 1%
Mutserve2 (alignment generated with Minimap2)
Detected minor variants/expected minor variants	18/18	15/18	11/18	21/22	1/22	14/22
False-positive variant calls	2	4	13	1	3	12
F 1 score	0.98	0.93	0.82	0.97	0.52	0.72
Mutserve2 (alignment generated with ngmlr)
Detected minor variants/expected minor variants	18/18	17/18	11/18	21/22	2/22	13/22
False-positive variant calls	1	2	14	2	3	12
F 1 score	0.99	0.96	0.81	0.99	0.54	0.70
Freebayes (alignment generated with Minimap2)
Detected minor variants/expected minor variants	18/18	18/18	15/18	22/22	2/22	18/22
False-positive variant calls	11	21	83	8	21	99
F 1 score	0.89	0.83	0.34	0.89	0.41	0.37
Freebayes (alignment generated with ngmlr)
Detected minor variants/expected minor variants	18/18	18/18	12/18	22/22	3/22	20/22
False-positive variant calls	28	73	337	20	56	265
F 1 score	0.79	0.59	0.21	0.77	0.29	0.19
Nanopanel2 (alignment generated with Minimap2)
Detected minor variants/expected minor variants	14/18	13/18	3/18	16/22	1/22	8/22
False-positive variant calls	2	2	19	1	2	22
F 1 score	0.86	0.85	0.61	0.77	0.33	0.43
Nanopanel2 (alignment generated with ngmlr)
Detected minor variants/expected minor variants	14/18	12/18	4/18	15/22	1/22	8/22
False-positive variant calls	3	2	14	1	1	12
F 1 score	0.85	0.84	0.64	0.75	0.33	0.47

Variant callers: Mutserve2, Freebayes and Nanopanel2, Aligners: Minimap2 and Ngmlr.

Bold values are headlines for better discrimination between mixtures, aligners and variant callers.