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Table 3 Distribution of simulated variants according to allele frequency, and dependence of imputation accuracy on population growth and structure. 1000 haplotypes were simulated under the coalescent with different exponential growth rates (α) and numbers of subpopulations (β). Genotypes were imputed based on the basic coalescent, the coalescent incorporating population growth and/or structure and with IMPUTE2 without recombination. Mean genotype concordance rates with the corresponding 95% confidence intervals (CIs) are presented. Results are shown for all variants and stratified by minor allele frequency (MAF)

From: Imputation of missing genotypes within LD-blocks relying on the basic coalescent and beyond: consideration of population growth and structure

    Variants Basic coalescent Coalescent with
growth and/or
IMPUTE2
α (%) β MAF N (%) Mean (95% CI) Mean (95% CI) Mean (95% CI)
Population growth
1.25 1 all 87 (100.0) 0.95 (0.94,0.96) 0.95 (0.93,0.96) 0.77 (0.72,0.82)
   ≤0.01 30 (34.5) 0.99 (0.98,1.00) 0.99 (0.98,1.00) 0.99 (0.98,1.00)
   >0.01, ≤0.05 20 (23.0) 0.90 (0.88,0.92) 0.90 (0.88,0.92) 0.90 (0.88,0.92)
   >0.05 37 (42.5) 0.94 (0.91,0.97) 0.94 (0.91,0.97) 0.51 (0.46,0.57)
2.50 1 all 86 (100.0) 0.94 (0.92,0.96) 0.94 (0.92,0.95) 0.76 (0.71,0.81)
   ≤0.01 25 (29.1) 0.98 (0.97,0.99) 0.98 (0.97,0.99) 0.98 (0.97,0.99)
   >0.01, ≤0.05 23 (26.7) 0.90 (0.88,0.92) 0.90 (0.88,0.92) 0.89 (0.87,0.91)
   >0.05 38 (44.2) 0.93 (0.89,0.96) 0.93 (0.89,0.96) 0.50 (0.45,0.55)
3.75 1 all 88 (100.0) 0.94 (0.93,0.96) 0.94 (0.93,0.96) 0.76 (0.70,0.81)
   ≤0.01 27 (31.0) 0.98 (0.97,0.99) 0.98 (0.97,0.99) 0.98 (0.98,0.99)
   >0.01, ≤0.05 24 (27.3) 0.91 (0.89,0.92) 0.91 (0.89,0.92) 0.89 (0.88,0.91)
   >0.05 37 (42.0) 0.93 (0.90,0.96) 0.93 (0.90,0.96) 0.50 (0.45,0.56)
5.00 1 all 88 (100.0) 0.94 (0.93,0.96) 0.94 (0.93,0.96) 0.76 (0.71,0.81)
   ≤0.01 27 (30.7) 0.99 (0.98,1.00) 0.99 (0.98,1.00) 0.99 (0.98,1.00)
   >0.01, ≤0.05 24 (27.3) 0.92 (0.90,0.93) 0.92 (0.90,0.93) 0.90 (0.88,0.92)
   >0.05 37 (42.0) 0.93 (0.90,0.96) 0.93 (0.90,0.96) 0.50 (0.45,0.56)
Population structure
0.00 2 all 86 (100.0) 0.95 (0.93,0.97) 0.95 (0.93,0.97) 0.85 (0.81,0.89)
   ≤0.01 38 (44.2) 0.96 (0.93,1.00) 0.96 (0.93,1.00) 0.98 (0.97,0.99)
   >0.01, ≤0.05 32 (37.2) 0.94 (0.92,0.95) 0.94 (0.92,0.95) 0.89 (0.88,0.91)
   >0.05 16 (18.6) 0.93 (0.86,0.99) 0.92 (0.86,0.99) 0.44 (0.41,0.48)
0.00 3 all 83 (100.0) 0.94 (0.91,0.97) 0.94 (0.91,0.97) 0.87 (0.82,0.91)
   ≤0.01 47 (56.6) 0.97 (0.94,1.00) 0.97 (0.94,1.00) 0.99 (0.98,1.00)
   >0.01, ≤0.05 20 (24.1) 0.92 (0.90,0.94) 0.92 (0.90,0.94) 0.91 (0.89,0.94)
   >0.05 16 (19.3) 0.86 (0.77,0.95) 0.86 (0.77,0.95) 0.47 (0.40,0.53)
0.00 4 all 86 (100.0) 0.93 (0.90,0.96) 0.93 (0.90,0.96) 0.92 (0.88,0.95)
   ≤0.01 56 (65.1) 0.97 (0.94,1.00) 0.97 (0.94,1.00) 0.99 (0.98,1.00)
   >0.01, ≤0.05 18 (20.9) 0.95 (0.93,0.97) 0.95 (0.93,0.97) 0.91 (0.89,0.94)
   >0.05 12 (14.0) 0.67 (0.60,0.75) 0.68 (0.60,0.75) 0.59 (0.48,0.70)
0.00 5 all 86 (100.0) 0.94 (0.91,0.96) 0.94 (0.91,0.96) 0.94 (0.92,0.96)
   ≤0.01 48 (55.8) 0.97 (0.93,1.00) 0.97 (0.93,1.00) 0.99 (0.98,1.00)
   >0.01, ≤0.05 30 (34.9) 0.93 (0.92,0.94) 0.93 (0.92,0.94) 0.93 (0.91,0.94)
   >0.05 8 (9.3) 0.76 (0.63,0.89) 0.76 (0.63,0.89) 0.67 (0.58,0.76)
Population growth and structure
5.00 5 all 85 (100.0) 0.93 (0.91,0.96) 0.93 (0.90,0.96) 0.94 (0.92,0.96)
   ≤0.01 47 (55.3) 0.97 (0.93,1.00) 0.97 (0.93,1.00) 0.99 (0.98,1.00)
   >0.01, ≤0.05 28 (32.9) 0.93 (0.92,0.94) 0.93 (0.92,0.94) 0.93 (0.92,0.94)
   >0.05 10 (11.8) 0.76 (0.67,0.85) 0.76 (0.67,0.85) 0.72 (0.65,0.79)