Inferring linkage disequilibrium from non-random samples†

BMC Genomics

Table 3 Prediction of Sampling Scheme II

Pop.	D		n_1• = 0	n_2• = 0	n_3• = 0	n₁₁ = 0	n₂₂ = 0	n₃₃ = 0
1	0.20	± s.d. ± s.d.	0.18 ± 0.01 0.20 ± 0.03	0.20 ± 0.01 0.20 ± 0.01	0.18 ± 0.01 0.20 ± 0.03	0.17 ± 0.01 0.18 ± 0.04	0.17 ± 0.01 0.17 ± 0.01	0.17 ± 0.01 0.18 ± 0.04
2	0.10	± s.d. ± s.d.	0.09 ± 0.02 0.10 ± 0.02	0.10 ± 0.01 0.10 ± 0.01	0.09 ± 0.02 0.10 ± 0.02	0.05 ± 0.02 0.06 ± 0.02	0.07 ± 0.01 0.07 ± 0.01	0.05 ± 0.02 0.06 ± 0.02
3	0.09	± s.d. ± s.d.	0.08 ± 0.02 0.09 ± 0.01	0.06 ± 0.01 0.10 ± 0.04	0.10 ± 0.02 0.09 ± 0.01	0.07 ± 0.01 0.08 ± 0.01	0.04 ± 0.01 0.09 ± 0.06	0.00 ± 0.02 0.04 ± 0.01
4	0.09	± s.d. ± s.d.	0.10 ± 0.02 0.09 ± 0.01	0.06 ± 0.01 0.09 ± 0.01	0.08 ± 0.01 0.09 ± 0.01	0.00 ± 0.02 0.04 ± 0.02	0.04 ± 0.01 0.06 ± 0.01	0.07 ± 0.01 0.08 ± 0.01
5	0.10	± s.d. ± s.d.	0.08 ± 0.01 0.10 ± 0.01	0.06 ± 0.01 0.10 ± 0.01	0.12 ± 0.01 0.10 ± 0.01	0.07 ± 0.01 0.08 ± 0.01	0.07 ± 0.01 0.08 ± 0.01	0.05 ± 0.02 0.06 ± 0.02
6	0.10	± s.d. ± s.d.	0.09 ± 0.01 0.10 ± 0.01	0.10 ± 0.01 0.10 ± 0.01	0.09 ± 0.01 0.10 ± 0.01	0.07 ± 0.01 0.08 ± 0.01	0.07 ± 0.01 0.08 ± 0.01	0.05 ± 0.02 0.06 ± 0.02

Means and standard deviations of coefficients of linkage disequilibrium were estimated from 1,000 repeats for Methods H and L when 200 individuals were generated from the Sampling Scheme II in which either a marker genotype (n_i• = 0, i = 1,2,3) or a marker-disease genotype (n_ii = 0, i = 1,2,3) was missing. The population numbers are the same as those in Table 2 and D is the true value of the disequilibrium coefficient.

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