Mining genetic variation including structural variation from mammalian genomes is a crucial step towards investigating the relationship between genotype and phenotype.However,compared to the detection of single nucleotide variants and small indels,characterizing large and particularly complex structural variation is much more difficult and less intuitive [1].In the past few years,the application of high-throughput-sequencing technologies has greatly facilitated the decoding of canid genomes and unveiled their genetic repertoire and domestication histories [2-5].However,the genetic landscape of canid structural variation and how are they involved in dog domestication are still poody understood.