Illumina sequencing
One percent of PhiX Control v3 DNA (Illumina, San Diego, CA) was spiked into DNA libraries before sequencing. The libraries were denatured and diluted according to the Denaturing and Diluting Libraries for the HiSeq protocol (Part # 15050107 v03). The cluster generation was realized using the cBot system and the HiSeq Rapid PE Cluster Kit v2 (Illumina, San Diego, CA). The high-throughput sequencing was performed using the HiSeq Rapid SBS Kit v2 (Illumina, San Diego, CA) on the Illumina HiSeq 2500 system (Illumina, San Diego, CA) with the following parameters: rapid run paired-end mode and read size of 94 bp.