Table 2: Comparison of MashMap2 and MashMap3 for identifying mappings between pairs of mammalian genomes.

MashMap2 and MashMap3 were used to align the human reference genome to chimpanzee and macaque genomes. The ME and MAE metrics shown are for query segments with at least 80% k-mer complexity. Corresponding metrics for low-complexity mappings can be found in Supplementary Table 1.

		MashMap2					MashMap3
Query Species	ANI Threshold	Basepairs mapped (Gbp)	CPU time (m)	Memory (Gb)	ME	MAE	Basepairs mapped (Gbp)	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 *	0.46	1.08	28.67	28.97	0.57*	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

^*Sampling bias leads to ANI over-estimation. See discussion for details.