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Table 4 Distribution of simulated variants according to allele frequency, and accuracy of variants imputed based on the basic coalescent, with IMPUTE2 without recombination, and with IMPUTE2 with recombination. Real genotypes were retrieved from the 1000 Genomes Project (1000 GP) assuming that the CEU, AFR and AMR subpopulations constituted hypothetical study populations. Remaining 1000 GP individuals built the external reference panel for genotype imputation. Mean concordance rates with the corresponding 95% confidence intervals (CIs) are represented. Results are shown for all variants and also 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 without
recombination
Variants IMPUTE2 with
recombination
Study MAF N (%) Mean (95% CI) Mean (95% CI) N (%) Mean (95% CI)
CEU all 41 (100.0) 0.92 (0.89,0.95) 0.90 (0.86,0.93) 42 (100.0) 0.93 (0.89,0.96)
  ≤0.01 11 (26.8) 0.98 (0.97,0.99) 0.98 (0.97,0.99) 12 (28.6) 0.98 (0.97,0.99)
  >0.01, ≤0.05 21 (51.2) 0.92 (0.91,0.93) 0.91 (0.91,0.92) 19 (45.2) 0.99 (0.97,1.00)
  >0.05 9 (22.0) 0.84 (0.70,0.99) 0.75 (0.62,0.88) 11 (26.2) 0.76 (0.68,0.85)
AFR all 123 (100.0) 0.93 (0.92,0.95) 0.93 (0.91,0.95) 121 (100.0) 0.96 (0.94,0.97)
  ≤0.01 35 (28.5) 0.99 (0.98,1.00) 0.99 (0.98,1.00) 37 (30.6) 0.99 (0.98,1.00)
  >0.01, ≤0.05 58 (47.2) 0.97 (0.96,0.98) 0.97 (0.96,0.97) 56 (46.3) 0.96 (0.95,0.97)
  >0.05 30 (24.4) 0.81 (0.76,0.85) 0.79 (0.74,0.83) 28 (23.1) 0.90 (0.85,0.95)
AMR all 66 (100.0) 0.92 (0.90,0.95) 0.92 (0.89,0.94) 67 (100.0) 0.96 (0.94,0.98)
  ≤0.01 36 (54.5) 0.98 (0.97,0.99) 0.98 (0.97,0.99) 36 (53.7) 0.99 (0.98,1.00)
  >0.01, ≤0.05 5 (7.6) 0.91 (0.88,0.94) 0.90 (0.86,0.95) 7 (10.4) 0.93 (0.90,0.96)
  >0.05 25 (37.9) 0.84 (0.79,0.89) 0.82 (0.76,0.87) 24 (35.8) 0.93 (0.87,0.98)
  1. CEU…Utah residents with Northern and Western European ancestry; AFR…African populations including African Ancestry in Southwest US (ASW), Luhya in Webuye, Kenya (LWK) and Yoruba in Ibadan, Nigeria (YRI); AMR…American populations including Colombian in Medellin, Colombia (CLM), Mexican Ancestry in Los Angeles, California (MXL) and Puerto Rican in Puerto Rico (PUR)