Fig. 3

Comparison of Alu elements between ME-Scan and Phase3 datasets. a: On left, PCA of 41 1KG individuals (with less than 10% false negative rate) using 1266 polymorphic loci. Good Alu loci (Additional file 1: Table S4) and loci with presence/absence allele frequency of less than 5% or greater than 95% (all samples) were removed. On right, PCA of the same 41 IKG individuals with 2710 polymorphic Alu loci detected through the Phase3 WGS approach. Loci with presence/absence allele frequency for all individuals of less than 5% or greater than 95% were removed. b: PCA of 41 1KG individuals from both methods using the 191 shared loci from (a) . c: Venn Diagram of non-reference elements from ME-Scan and Phase3 in 1KG individuals. Phase3 dataset contains only polymorphic Alu elements, so ME-Scan loci were filtered to 1530 loci that were found in the 41 IKG individuals and absent from Repbase and build hg19. The Phase3 dataset was also filtered to 4670 Alu elements that were present in the 41 IKG individuals and absent from Repbase and build hg19. These two sets were then compared