The fragmentation of genomic DNA according to the Agilent SureSelectXT2 protocol and downstream processes produces a Gaussian distribution of DNA fragment sizes. A small percentage of the resulting fragments have an insert size below 300 bp. Sequencing of these small library fragments with 150 bp paired end reads will generate partially overlapping reads which cover the same bases and hence create an artificial doubling of coverage at those positions. To assure accurate analyses, these bases are excluded from further downstream analyses including single nucleotide variant (SNV) and insertion and deletion (InDel) detection. Eurofins Genomics is continuously working on optimising protocols in order to minimise the number of overlapping reads.