Table 3.

Calculation of SNPs and Pi sites according to the scheme evaluated.

	Scheme A			Scheme B			Scheme C			Scheme D
	Complete sequence	SNPs	Pi sites	Complete sequence	SNPs	Pi sites	Complete sequence	SNPs	Pi sites	Complete sequence	SNPs	Pi sites
Number of alleles	75	74	53	44	44	37	520	501	454	47	46	16
Number of polymorphisms	435	223	198	61	61	45	1747	665	520	161	140	93
Typing efficiency	0.172	0.332	0.268	0.721	0.721	0.822	0.298	0.753	0.873	0.292	0.329	0.172
DP (95% confidence interval)	1 (1–1)	1 (0.999–1)	0.986 (0.977–0.995)	1 (1–1)	1 (1–1)	0.99 (0.98–1)	1 (1–1)	1 (1–1)	0.999 (0.999–1)	1 (1–1)	0.999 (0.996–1)	0.913 (0.877–0.949)