Table 1.

Results of a general linear model testing factors affecting of allele frequency estimation

Pooled individual number	Model terms	Parameter estimate	S.E.	t-value	P-value
514 Individuals	Minor Allele Frequency	0.0211	0.00180	11.75	< 0.001
(NLOCI = 4642)	GenTrain Score	−0.0226	0.00196	−11.49	< 0.001
	Locus Classification:
	Mono	−0.0149	0.00094	−15.74	< 0.001
	MSV-3	−0.0045	0.00102	−4.401	< 0.001
20 individuals	Minor Allele Frequency	0.0199	0.00352	5.65	< 0.001
(NLOCI = 4571)	GenTrain Score	−0.0227	0.00409	−5.55	< 0.001
	Locus Classification:
	Mono	−0.0150	0.00185	−8.14	< 0.001
	MSV-3	0.0063	0.00186	3.37	< 0.001
50 individuals	Minor Allele Frequency	0.0093	0.00346	2.68	0.00735
(NLOCI = 4681)	GenTrain Score	−0.0302	0.00407	−7.43	< 0.001
	Locus Classification:
	Mono	−0.0145	0.00182	−7.96	< 0.001
	MSV-3	−0.0035	0.00196	−1.79	0.0730

The effects of minor allele frequency, GenTrain score and locus classification on the accuracy of allele frequency estimates were tested based on the mean difference between empirical and estimated allele frequencies per locus for all individuals. Estimated allele frequencies were estimated from clusters of all individuals (N = 514) and random subsets of 20 and 50 individuals. The mean difference in allele frequency was used as a dependent variable with a Gaussian error structure. S.E. is the standard error, t-value is the t statistic value and P-value is the corresponding significance of the model term.