Table 4.

Description of datasets used for testing different parameters on the accuracy of imputation of GBS missing data

Dataset ID	Description	Min. read depth	MinMAFa	Min. call rate	Number of variants	Variants shared with SNP50	Imputation program	Estimated accuracy (%)
9	GBS	3	0.05	0.2	53,556	431	FImpute	71.1
10	GBS + SNP50	3	0.05	0.2	98,398	431	FImpute	84.8
11	GBS	3	0.05	0.3	40,208	334	FImpute	74.2
12	GBS + SNP50	3	0.05	0.3	88,573	334	FImpute	89.1
13	GBS	3	0.05	0.4	21,561	156	FImpute	77.5
14	GBS + SNP50	3	0.05	0.4	70,250	156	FImpute	91.9
15	GBS	4	0.02	0.2	55,727	395	FImpute	73.3
16	GBS + SNP50	4	0.02	0.2	100,297	395	FImpute	86.4
17	GBS	4	0.05	0.2	45,447	369	Beagle	70.9
	GBS	4	0.05	0.2	45,447	369	FImpute	71.2
18	GBS + SNP50	4	0.05	0.2	90.234	369	Beagle	78.5
	GBS + SNP50	4	0.05	0.2	90.234	369	FImpute	86.1
19	GBS	4	0.02	0.3	40,855	278	FImpute	75.9
20	GBS + SNP50	4	0.02	0.3	89,196	278	FImpute	90.3
21	GBS	4	0.05	0.3	31,662	254	Beagle	74.0
	GBS	4	0.05	0.3	31,662	254	FImpute	74.3
22	GBS + SNP50	4	0.05	0.3	80,190	254	Beagle	83.8
	GBS + SNP50	4	0.05	0.3	80,190	254	FImpute	89.3
23	GBS	4	0.02	0.4	22,331	98	FImpute	83.3
24	GBS + SNP50	4	0.02	0.4	70,983	98	FImpute	93.4
25	GBS	4	0.05	0.4	14,909	82	Beagle	81.2
	GBS	4	0.05	0.4	14,909	82	FImpute	80.8
26	GBS + SNP50	4	0.05	0.4	63,706	82	Beagle	89.8
	GBS + SNP50	4	0.05	0.4	63,706	82	FImpute	93.4
27	GBS	5	0.05	0.2	36,913	299	FImpute	70.0
28	GBS + SNP50	5	0.05	0.2	81,454	299	FImpute	85.4
29	GBS	5	0.05	0.3	22,685	166	FImpute	74.8
30	GBS + SNP50	5	0.05	0.3	71,360	166	FImpute	89.5
31	GBS	5	0.05	0.4	8818	42	FImpute	79.5
32	GBS + SNP50	5	0.05	0.4	57,719	42	FImpute	92.2

^aMinMAF: minimum minor allele frequency