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Figure 6 | Genome Biology

Figure 6

From: The functional spectrum of low-frequency coding variation

Figure 6

Allele sharing among populations in the Exon Pilot versus ENCODE intergenic SNPs. The probability that two minor alleles, sampled at random without replacement among all minor alleles, come from the same population, different populations on the same continent, or different continents, displayed according to minor allele frequency bin (<0.01, 0.01 to 0.1, and 0.1 to 0.5). For comparison, we also show the expected level of sharing in a panmictic population, which is independent of AF. The ENCODE and the Exon Pilot data have different sample sizes for each population panel, which could impact sharing probabilities. We therefore calculated the expected sharing based on subsets of equal size, corresponding to 90% of the smallest sample size for each population (section 9, 'Allele sharing among populations', in Additional file 1). To reduce possible biases due to reduced sensitivity in rare variants, only high-coverage sites were used, and individuals with overall low coverage or poor agreement with ENCODE genotypes were discarded. Error bars indicate the 95% confidence interval based on bootstrapping at individual variant sites.

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