Approximation to the Distribution of Fitness Effects across Functional Categories in Human Segregating Polymorphisms
Figure 2
Distribution of fitness effects among YRI polymorphisms in the Complete Genomics dataset, partitioned by the genomic consequence of the mutated site.
The right panels show a zoomed-in version of the distributions in the left panels, after removing neutral polymorphisms and log-scaling the x-axis. A) DFE obtained from the genome-wide mapping. B) Zoomed-in version of panel A. C) DFE obtained from the exome-wide mapping. D) Zoomed-in version of panel C. E) DFEs for exonic sites (nonsynonymous, synonymous, splice sites) obtained from the exome-wide mapping and DFEs for non-exonic sites (intergenic, UTR, regulatory) obtained from the genome-wide mapping. F) Zoomed-in version of panel E. Consequences were determined using the Ensembl Variant Effect Predictor (v.2.5). Codon and degeneracy information was obtained from snpEff. If more than one consequence existed for a given SNP, that SNP was assigned to the most severe of the predicted categories, following the VEP's hierarchy of consequences. NonSyn = nonsynonymous. Syn = synonymous. Syn to unpref. codon = synonymous change from a preferred to an unpreferred codon. Syn to pref. codon = synonymous change from an unpreferred to a preferred codon. Syn no pref. = synonymous change from an unpreferred codon to a codon that is also unpreferred. Splice = splice site.