Europeans have a higher proportion of deleterious common variants than
Africans
Sankar Subramanian
Environmental Futures Centre, Griffith University, 170 Kessels Road, Nathan Qld
4111, Australia
Supplementary information
1
0.25
Proportion of deleterious SNVs (P)
PEA
PAA
0.2
0.15
0.1
0.05
0
-1.5
-1.0
-0.5
(0.03) (0.10) (0.32)
0.0
(1.0)
0.5
1.0
>1.0
(3.20) (10.0) (>10.0)
Log MAF (MAF %)
Figure S1. Relationship between MAF and the proportion of deleterious SNVs (P) of EA
and AA. This method of analysis is identical to that used for Figure 2A (main text).
However here we used minor allele frequencies (MAF) instead of derived allele frequencies
(DAF).
2
Figure S2. (A) Relationship between the Derived Allele Frequencies and average C
scores. The nonsynonymous SNVs were grouped into seven categories based on their
allele frequencies and the mean C score for each category was estimated separately
for European American (CEAand African American (CAA) populations. (B)
Distribution of the difference between the mean C scores (C) estimated for EA and
AA populations, which were calculated as C = 1- (CAA/CEA). Error bars denote the
standard error of the mean.
3
0.16
Proportion of deleterious SNVs (P)
PEA
0.14
PAA
0.12
0.1
0.08
0.06
0.04
0.02
0
-1.5
-1.0
-0.5
(0.03) (0.10) (0.32)
0.0
(1.0)
0.5
1.0
>1.0
(3.20) (10.0) (>10.0)
Log DAF (DAF %)
Figure S3. Relationship between DAF and the proportion of deleterious SNVs in EA
and AA. The deleterious SNVs were determined using the method GERP based on a
threshold of >5.0. Error bars denote the standard error of the mean.
4
0.55
Proportion of deleterious SNVs (P)
PEA
PAA
0.5
0.45
0.4
0.35
0.3
-1.5
-1.0
-0.5
(0.03) (0.10) (0.32)
0.0
(1.0)
0.5
1.0
>1.0
(3.20) (10.0) (>10.0)
Log DAF (DAF %)
Figure S4. Correlation between DAF and the proportion of deleterious
nonsynonymous SNVs (nSNVs) in EA and AA. The deleterious nSNVs were
determined using the method EvoD, which designates them as “Deleterious”. Error
bars denote the standard error of the mean.
5
0.5
Proportion of deleterious SNVs (P)
PEA
0.45
PAA
0.4
0.35
0.3
0.25
0.2
0.15
0.1
-1.5
-1.0
-0.5
(0.03) (0.10) (0.32)
0.0
(1.0)
0.5
1.0
>1.0
(3.20) (10.0) (>10.0)
Log DAF (DAF %)
Figure S5. Relationship between DAF and the proportion of deleterious
nonsynonymous SNVs (nSNVs) in EA and AA. The deleterious nSNVs were
determined using the method Polyphen, which designates them as “probably
deleterious”. Error bars denote the standard error of the mean.
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Proportion of deleterious SNVs (D)
A
0.25
DEA
DAA
0.2
0.15
0.1
0.05
0
-1.5
(0.03)
-1.0
(0.10)
-0.5
(0.32)
0.0
(1.0)
0.5
(3.20)
1.0
>1.0
(10.0) (>10.0)
Log MAF (MAF %)
B
0.28
Difference between DEA and DAA (D)
0.24
0.2
0.16
0.12
0.08
0.04
0
-1.5
(0.03)
-1.0
(0.10)
-0.5
(0.32)
0.0
(1.0)
0.5
(3.20)
1.0
>1.0
(10.0) (>10.0)
Log DAF (DAF)
Figure S6. Relationship between DAF and the proportion of deleterious SNVs in EA
and AA. The deleterious SNVs include those present at nonsynonymous, splice sites
as well as those introduce stop codons. Error bars denote the standard error of the
mean.
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