Table 2.

Comparison of MashMap2 and MashMap3 for identifying mappings between pairs of mammalian genomes.^a

		MashMap2					MashMap3
Query species	ANI threshold (%)	Basepairs mapped (Gb)	CPU time (m)	Memory (GB)	ME	MAE	Basepairs mapped (Gb)	CPU time (m)	Memory (GB)	ME	MAE
Chimpanzee	95	2.80	39.76	19.95	−0.25	0.29	2.81	32.76	27.07	0.01	0.22
Chimpanzee	90	2.82	118.31	24.55	−0.22	0.29	2.82	51.12	36.20	0.01	0.25
Chimpanzee	85	2.83	787.44	44.96	−0.18	0.27	2.83	64.48	39.47	0.02	0.25
Macaque	95	0.38	30.0	20.83	0.29 b	0.46	1.08	28.67	28.97	0.57b	0.66
Macaque	90	2.54	40.49	23.04	−0.30	0.69	2.56	34.87	35.91	0.01	0.74
Macaque	85	2.60	446.71	38.13	−0.24	0.74	2.61	43.74	39.49	0.05	0.87

^aMashMap2 and MashMap3 were used to align the human reference genome to chimpanzee and macaque genomes. The mean error and mean absolute error metrics shown are for query segments with at least 80% k-mer complexity. Bolded values signify the best performance for each dataset. Corresponding metrics for low-complexity mappings can be found in Supplementary Table S3. 

^bSampling bias leads to ANI over-estimation (see Section 5 for details).