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
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).
Figure S2. (A) Relationship between the Derived Allele Frequencies and average C scores. ThenonsynonymousSNVs were grouped into seven categories based on their allele frequencies and the mean C score for each category was estimated separately for European American (CEAand 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.
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.
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, whichdesignates them as “Deleterious”. Error bars denote the standard error of the mean.
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, whichdesignates them as “probably deleterious”. Error bars denote the standard error of the mean.
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.
1