Table 1.

Relative efficiencies and mapping accuracies for different QTL effects

AIP				IBS mQTL	IBS m	TP	Score	IBS hap	P(IBD)	Beagle
$$R_{i^{\ast },\mathit{\text{QTL}}}=0.52$$	Relative efficiency		RMSEr.e.	0.02	0.16	0.17	0.15	0.06	0.10	0.54
			$${\widehat{\mathbb{E}}}^{\text{r.e.}}$$	0.03	0.01	0.23	0.14	0.12	0.14	0.28
			$${\widehat{\sigma }}^{\text{r.e.}}$$	0.09	0.02	0.02	0.03	0.04	0.03	0.04
	Mapping	≤57%	RMSEm.a.	0.11	0.17	0.23	0.17	0.10	0.11	0.16
	accuracy	≤8%	RMSEm.a.	0.17	0.22	0.32	0.45	0.28	0.26	0.40
$$R_{i^{\ast },\mathit{\text{QTL}}}=0.18$$	Relative efficiency		RMSEr.e.	0.00	0.18	0.46	0.21	0.14	0.14	0.40
			$${\widehat{\mathbb{E}}}^{\text{r.e.}}$$	0.00	0.18	0.39	0.35	0.31	0.34	0.31
			$${\widehat{\sigma }}^{\text{r.e.}}$$	0.00	0.06	0.02	0.03	0.05	0.04	0.06
	Mapping	≤57%	RMSEm.a.	0.06	0.29	0.27	0.33	0.16	0.21	0.28
	accuracy	≤8%	RMSEm.a.	0.10	0.34	0.36	0.46	0.29	0.30	0.31
$$R_{i^{\ast },\mathit{\text{QTL}}}=0.08$$	Relative efficiency		RMSEr.e.	0.00	0.76	1.00	1.00	1.04	1.04	0.72
			$${\widehat{\mathbb{E}}}^{\text{r.e.}}$$	0.00	0.24	0.35	0.33	0.31	0.37	0.34
			$${\widehat{\sigma }}^{\text{r.e.}}$$	0.00	0.06	0.04	0.05	0.06	0.05	0.08
	Mapping	≤57%	RMSEm.a.	0.13	0.66	0.58	0.54	0.51	0.58	0.55
	accuracy	≤8%	RMSEm.a.	0.18	0.71	0.66	0.71	0.62	0.69	0.59

▪$R_{i^{\ast },\mathit{\text{QTL}}}$: Multiallelic measure of LD between the simulated QTL and the haplotypes harboring it.

▪ RMSE^r.e.: Root mean square error of ${\theta }_{\text{r.e.}}^{\mathcal{P}}$ with respect to θ_QTL (cM).

▪${\widehat{\mathbb{E}}}^{\text{r.e.}}$: Expected value of the matrix distance at ${\theta }_{\text{r.e.}}^{\mathcal{P}}$.

▪${\widehat{\sigma }}^{\text{r.e.}}$: Standard error of the matrix distance at ${\theta }_{\text{r.e.}}^{\mathcal{P}}$.

▪ RMSE^m.a.: Root mean square error of ${\theta }_{\text{m.a.}}^{\mathcal{P}}$ with respect to θ_QTL (cM).