Fig. 1

Principle of creating k-mer pairs for the calling (genotyping) of polymorphic Alu element insertions. a Genomic regions with or without an Alu element. b A pair of 32-mers is created from the insertion breakpoint region covering 25 nucleotides from the 5′-flanking region and 7 nucleotides from either the Alu element or the 3′-flanking region. Allele A always represents the sequence from the reference genome and allele B represents the alternative, non-reference allele