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Table 2 Distribution of simulated variants according to allele frequency, and dependence of imputation accuracy on the sizes of study population and reference panel. Different total numbers of haplotypes were simulated under the basic coalescent (Nsim). Genotypes were imputed based on the basic coalescent and with IMPUTE2 without recombination. Mean genotype concordance rates with the corresponding 95% confidence intervals (CIs) 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 IMPUTE2
Nsim MAF N (%) Mean (95% CI) Mean (95% CI)
Baseline simulation scenario a
1000 all 96 (100.0) 0.95 (0.94,0.96) 0.77 (0.74,0.81)
  ≤0.01 30 (31.3) 0.97 (0.96,0.98) 0.90 (0.88,0.92)
  >0.01, ≤0.05 24 (25.0) 0.94 (0.93,0.95) 0.85 (0.83,0.87)
  >0.05 42 (43.8) 0.93 (0.92,0.95) 0.62 (0.58,0.66)
Total number of simulated haplotypes
800 all 88 (100.0) 0.91 (0.89,0.94) 0.77 (0.72,0.82)
  ≤0.01 27 (30.7) 0.99 (0.98,0.99) 0.99 (0.98,1.00)
  >0.01, ≤0.05 25 (28.4) 0.95 (0.93,0.97) 0.91 (0.89,0.93)
  >0.05 36 (40.9) 0.83 (0.78,0.89) 0.52 (0.47,0.58)
600 all 90 (100.0) 0.97 (0.96,0.99) 0.66 (0.61,0.71)
  ≤0.01 15 (16.7) 0.99 (0.98,1.00) 0.98 (0.97,0.99)
  >0.01, ≤0.05 14 (15.6) 0.93 (0.91,0.95) 0.92 (0.89,0.94)
  >0.05 61 (67.8) 0.98 (0.96,1.00) 0.52 (0.49,0.55)
400 all 87 (100.0) 0.92 (0.90,0.95) 0.77 (0.73,0.81)
  ≤0.01 19 (21.8) 0.98 (0.97,0.99) 0.97 (0.96,0.98)
  >0.01, ≤0.05 28 (32.2) 0.95 (0.93,0.96) 0.88 (0.83,0.92)
  >0.05 40 (46.0) 0.88 (0.82,0.94) 0.59 (0.56,0.62)
200 all 89 (100.0) 0.89 (0.86,0.92) 0.76 (0.72,0.79)
  ≤0.01 10 (11.2) 0.97 (0.96,1.00) 0.97 (0.96,0.99)
  >0.01, ≤0.05 28 (31.5) 0.91 (0.89,0.94) 0.90 (0.88,0.93)
  >0.05 51 (57.3) 0.85 (0.81,0.90) 0.64 (0.61,0.67)
  1. aResults averaged over ten simulation replicates and ten iterations with independent selection of measured variant sites