Illumina NovaSeq 6000 paired end sequencing
The short-insert paired-end libraries for the whole genome sequencing were prepared with PCR free protocol using KAPA HyperPrep kit (Roche) with some modifications.  In short, 1.0 microgram of genomic DNA was sheared on a Covarisï¿½ LE220-Plus (Covaris) and size-selected for the fragment size of 220-550bp with AMPure XP beads (Agencourt, Beckman Coulter). The genomic DNA fragments were then end-repaired, adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The libraries were quality controlled on an Agilent 2100 Bioanalyzer with the DNA 7500 assay (Agilent) for size and quantified by Kapa Library Quantification Kit for Illumina platforms (Roche).