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)

α (%)

β

MAF

Mean

(95% CI)

Mean

(95% CI)

Mean

(95% CI)

1.25

1

all

(100.0)

0.95

(0.94,0.96)

0.95

(0.93,0.96)

0.77

(0.72,0.82)

≤0.01

(34.5)

0.99

(0.98,1.00)

0.99

(0.98,1.00)

0.99

(0.98,1.00)

>0.01, ≤0.05

(23.0)

0.90

(0.88,0.92)

0.90

(0.88,0.92)

0.90

(0.88,0.92)

>0.05

(42.5)

0.94

(0.91,0.97)

0.94

(0.91,0.97)

0.51

(0.46,0.57)

2.50

1

all

(100.0)

0.94

(0.92,0.96)

0.94

(0.92,0.95)

0.76

(0.71,0.81)

≤0.01

(29.1)

0.98

(0.97,0.99)

0.98

(0.97,0.99)

0.98

(0.97,0.99)

>0.01, ≤0.05

(26.7)

0.90

(0.88,0.92)

0.90

(0.88,0.92)

0.89

(0.87,0.91)

>0.05

(44.2)

0.93

(0.89,0.96)

0.93

(0.89,0.96)

0.50

(0.45,0.55)

3.75

1

all

(100.0)

0.94

(0.93,0.96)

0.94

(0.93,0.96)

0.76

(0.70,0.81)

≤0.01

(31.0)

0.98

(0.97,0.99)

0.98

(0.97,0.99)

0.98

(0.98,0.99)

>0.01, ≤0.05

(27.3)

0.91

(0.89,0.92)

0.91

(0.89,0.92)

0.89

(0.88,0.91)

>0.05

(42.0)

0.93

(0.90,0.96)

0.93

(0.90,0.96)

0.50

(0.45,0.56)

5.00

1

all

(100.0)

0.94

(0.93,0.96)

0.94

(0.93,0.96)

0.76

(0.71,0.81)

≤0.01

(30.7)

0.99

(0.98,1.00)

0.99

(0.98,1.00)

0.99

(0.98,1.00)

>0.01, ≤0.05

(27.3)

0.92

(0.90,0.93)

0.92

(0.90,0.93)

0.90

(0.88,0.92)

>0.05

(42.0)

0.93

(0.90,0.96)

0.93

(0.90,0.96)

0.50

(0.45,0.56)

0.00

2

all

(100.0)

0.95

(0.93,0.97)

0.95

(0.93,0.97)

0.85

(0.81,0.89)

≤0.01

(44.2)

0.96

(0.93,1.00)

0.96

(0.93,1.00)

0.98

(0.97,0.99)

>0.01, ≤0.05

(37.2)

0.94

(0.92,0.95)

0.94

(0.92,0.95)

0.89

(0.88,0.91)

>0.05

(18.6)

0.93

(0.86,0.99)

0.92

(0.86,0.99)

0.44

(0.41,0.48)

0.00

3

all

(100.0)

0.94

(0.91,0.97)

0.94

(0.91,0.97)

0.87

(0.82,0.91)

≤0.01

(56.6)

0.97

(0.94,1.00)

0.97

(0.94,1.00)

0.99

(0.98,1.00)

>0.01, ≤0.05

(24.1)

0.92

(0.90,0.94)

0.92

(0.90,0.94)

0.91

(0.89,0.94)

>0.05

(19.3)

0.86

(0.77,0.95)

0.86

(0.77,0.95)

0.47

(0.40,0.53)

0.00

4

all

(100.0)

0.93

(0.90,0.96)

0.93

(0.90,0.96)

0.92

(0.88,0.95)

≤0.01

(65.1)

0.97

(0.94,1.00)

0.97

(0.94,1.00)

0.99

(0.98,1.00)

>0.01, ≤0.05

(20.9)

0.95

(0.93,0.97)

0.95

(0.93,0.97)

0.91

(0.89,0.94)

>0.05

(14.0)

0.67

(0.60,0.75)

0.68

(0.60,0.75)

0.59

(0.48,0.70)

0.00

5

all

(100.0)

0.94

(0.91,0.96)

0.94

(0.91,0.96)

0.94

(0.92,0.96)

≤0.01

(55.8)

0.97

(0.93,1.00)

0.97

(0.93,1.00)

0.99

(0.98,1.00)

>0.01, ≤0.05

(34.9)

0.93

(0.92,0.94)

0.93

(0.92,0.94)

0.93

(0.91,0.94)

>0.05

(9.3)

0.76

(0.63,0.89)

0.76

(0.63,0.89)

0.67

(0.58,0.76)

5.00

5

all

(100.0)

0.93

(0.91,0.96)

0.93

(0.90,0.96)

0.94

(0.92,0.96)

≤0.01

(55.3)

0.97

(0.93,1.00)

0.97

(0.93,1.00)

0.99

(0.98,1.00)

>0.01, ≤0.05

(32.9)

0.93

(0.92,0.94)

0.93

(0.92,0.94)

0.93

(0.92,0.94)

>0.05

(11.8)

0.76

(0.67,0.85)

0.76

(0.67,0.85)

0.72

(0.65,0.79)