Frequency and occurrence of CNVs across individuals and populations.

<p><b>(A)</b> Allele frequency spectrum of bi-allelic CNVs across all 66 individuals, showing most deletions (white) and duplications (black) occurring at very low frequencies. See <b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004830#pgen.1004830.s003" target="_blank">S3B Figure</a></b> for a comparison with intergenic SNPs. (<b>B</b>) Allele frequency spectrum of non-reference alleles from bi-allelic CNVs across 12 individuals from each population represented as boxplots. (<b>C</b>) The occurrence of CNVs across populations. (<b>D</b>) The proportion of CNVs shared across individuals within populations. (<b>E</b>) The proportion of CNVs specific (private) to groups of individuals depending on the scale of aggregation. Mutually exclusive groups for which CNVs are private include: those occurring across continents (Ancestral), those specific to a continent but shared across populations from different countries (Continent), those specific to a country but shared across populations within a country (Country), and those only found in one population (Population). (<b>F</b>) The average proportion of shared CNVs between individuals across mutually exclusive groups. The proportion of CNV sharing across individuals was calculated for four groups: “Between Continents” is sharing from different continents, “Between Countries” is sharing from different countries within the same continent, “Between Populations” is sharing from different populations from the same country, and “Within Populations” is sharing from the same population.