Estimating genetic diversity across the neutral genome with the use of dense marker maps

Table 2 Correlations of true genetic diversity (H_exp_TRUE) with IBD-based diversity (GD_IBD) and heterozygosity (H_exp_AVG and H_exp_HAP2), for a low marker density population (166 SNPs).

MI^a	True vs. GD_IBD^b	True vs. H_exp_AVG^b	True vs. H_exp_HAP2^b	GD_IBD vs. H_exp_AVG^b	GD_IBD vs. H_exp_HAP2^b
1	0.15	0.06	0.04	0.43	0.43
4	0.34	0.18	0.20	0.53	0.53
10	0.51	0.41	0.46	0.79	0.77
20	- ^c	- ^c	- ^c	- ^c	- ^c
40	- ^c	- ^c	- ^c	- ^c	- ^c

^a The number of marker intervals taken into account to estimate the genetic diversity.
^b Correlations were calculated for values per marker interval, and for average values for a group of marker intervals (4 and 10 marker intervals); for the latter, correlations were calculated for the true genetic diversity of even ungenotyped markers with estimated genetic diversity based on uneven (flanking) markers, and the other way around; the average of both correlations (even and uneven) is presented.
^c There were not enough estimates left over to calculate the correlation.

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