Using haplotypes for the prediction of allelic identity to fine-map QTL: characterization and properties

Table 1 Relative efficiencies and mapping accuracies for different QTL effects

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

▪ $R_{i^{*}, QTL}$ : Multiallelic measure of LD between the simulated QTL and the haplotypes harboring it.
▪ RMSE^r.e.: Root mean square error of $θ_{r.e.}^{P}$ with respect to θ_QTL (cM).
▪ ${\hat{E}}^{r.e.}$ : Expected value of the matrix distance at $θ_{r.e.}^{P}$ .
▪ ${\hat{σ}}^{r.e.}$ : Standard error of the matrix distance at $θ_{r.e.}^{P}$ .
▪ RMSE^m.a.: Root mean square error of $θ_{m.a.}^{P}$ with respect to θ_QTL (cM).

ISSN: 1297-9686