Figure 3

Allele frequency spectrum of African populations. The number of loci for a given allele frequency is normalized with the total number of loci. A. Allele frequency spectrum for MEI and SNP (provided by Sanger Institute with QCall and GATK, chromosome 20 only) variants detected in 3 African populations. Results for samples designated as ASW, LWK and YRI are shown, for 4 types of MEIs: Alu, L1, SVA and HERV-K. Overall, the AFS of MEIs is very similar to that of SNPs except that there is limited sensitivity to low frequency events for MEI detection due to sparse or absent supporting reads in low-coverage data. B. Allele frequency spectrum for four different types of MEs, Alu, L1, SVA and HERV-K detected with the Tangram toolbox.