Analysis of the Coverage of Alu Elements by Aligned Genomic Reads

Abstract

Alu elements constitute a notable part of the human genome and greatly affect processes related to maintenance of genome integrity. One of the basic methods for studying variation in the genome, including Alu elements, is genome sequencing followed by mapping the reads to a reference genome sequence. The key feature of read alignment is the coverage of reference genome regions by mapped reads. This paper proposes a new method for analyzing the coverage of Alu elements and their adjacent regions by whole-genome sequencing reads and considers the distribution of the mean coverage between the two region types.