A
B
10 causative SNPs
PIP
0.75
1.00
●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●
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●
Mixture
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●
●
0 x σ2g
10−4 x σ2g
0.50
●
0.75
PIP
1.00
10−3 x σ2g
0.25
●
●●●●●●●
0.00
100
75
50
25
100
0.50
0.25
0.00
500
400
300
200
75
100
1.00
Mixture
component
●
0x
10−4 x
10−3 x
10−2 x
σ2g
σ2g
σ2g
σ2g
0.75
0.50
0.25
0.00
1
500
0.50
0.25
0.00
1000 causative SNPs
400
800
600
400
200
●
0x
10−4 x
10−3 x
10−2 x
σ2g
σ2g
σ2g
σ2g
0.75
0.50
0.25
0.00
1
Mixture
component
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0 x σ2g
10−4 x σ2g
0.75
PIP
PIP
10−4 x σ2g
10−3 x σ2g
10−2 x σ2g
1
800
10−3 x σ2g
0.50
0.25
10−2 x σ2g
0.00
0.00
10000
8000
6000
4000
400
200
0 x σ2g
●
10−4 x σ2g
10−3 x σ2g
10−2 x σ2g
1
2000
1
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10000
8000
SNP rank
6000
4000
2000
Mixture
component
0 x σ2g
●
10−4 x σ2g
10−3 x σ2g
10−2 x σ2g
1
SNP rank
20000 causative SNPs
1.00
600
Mixture
component
10000 causative SNPs
1.00
●
20000 causa ve SNPs
1 00
Mixture
component
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0.00
0 x σ2g
10−4 x σ2g
10−3 x σ2g
10−2 x σ2g
Mxu e
componen
0 75
PP
0.75
PIP
100
0 x σ2g
●
SNP rank
0.75
0.25
200
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1000
10000 causative SNPs
1.00
0.50
300
Mixture
component
1000 causative SNPs
Mixture
component
SNP rank
0.25
1
1.00
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1000
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25
SNP rank
PIP
PIP
0.75
50
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SNP rank
1.00
10−2 x σ2g
100 causative SNPs
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PIP
PIP
0.75
10−3 x σ2g
SNP rank
100 causative SNPs
1.00
10−4 x σ2g
●
●
●●●
SNP rank
0 x σ2g
●
●
0.00
1
Mixture
component
●
0.50
0.25
10−2 x σ2g
●
10 causative SNPs
●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●●
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0 50
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10
σ
10
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10
σ
0 00
20000
15000
10000
SNP rank
Figure S5.
5000
1
20000
15000
10000
5000
1
SNP ank
Posterior inclusion probabilities (PIP) of SNPs for different
simulated genetic architectures. SNPs are ranked according to their contribution to
heritability. Genotype data was simulated for 20,000 uncorrelated SNPs and 5,000
individuals. Genetic architectures ranging from very sparse to highly polygenic were
generated by sampling 10, 100, 1,000, 10,000, or 20,0000 SNP effects either from (A)
a standard normal distribution or (B) a gamma distribution with shape 0.44 and scale
1.66. Trait heritability was 0.5. Results are based on 50 replicates for each case.