Table 4. Comparison of recombination detection using our method and Merlin for all informative paternal (P) and maternal (M) meioses events in each cohort.

	Meioses		SHAPEIT2 concordance (%)	Merlin concordance (%)	Merlin		SHAPEIT2
Cohort	P	M			P	M	P	M
CARL	24	47	80.40	41.28	63.08	74.57	25.46	41.81
FVG	50	96	88.97	60.65	34.90	61.04	25.02	42.23
GPC	69	75	88.23	36.60	79.32	105.48	29.22	47.07
KOR	4	11	80.59	57.16	39.75	63.64	28.75	44.82
ORC	40	45	86.33	50.89	30.85	85.11	25.73	43.47
VB	72	104	88.72	52.26	55.19	61.07	25.17	40.91
VIS	12	14	82.81	58.84	43.75	52.57	26.83	41.00

SHAPEIT2 concordance is the percentage of SHAPEIT2 crossover events that intersected a Merlin crossover event, the proceeding column is vice versa. We also provide the mean number of paternal/maternal recombination events detected for informative meioses by Merlin and SHAPEIT2. For comparison, the frequently cited deCODE 2002 genetic map estimated an average of 42.81 and 25.9 autosomal recombinations per paternal and maternal meioses respectively. SHAPEIT2's estimates are consistently closer to the deCODE values which are considered to be of high quality.