(A) Schematic overview showing the lead associated SNP and ~12 kb CNV overlapping with GC . GC is a reverse oriented gene, consisting of 14 exons, of which two last exons are non-coding. Five CNV tagging SNPs were present within the GC CNV and marked with black asterisks (the middle asterisk covers three tagging SNPs). Among them, the first SNP, which was also the lead SNP, was in perfect LD with the GC CNV (r 2 = 1), whereas the rest were in high LD (r 2 > 0.98). The hash marks at the upstream and the intronic region of GC indicate CM resistance candidate SNPs reported by others [ 13 , 14 ]. (B) Sequencing depth difference between the CNV region and normal region was used to infer copy numbers. (C) A Histogram of read depth values shows that majority of animals fall into diploid copy number of 2, 5 and 8, and some minor peaks occur at diploid copy number of 6, 7, 9 and 10. Based on this diploid CNs, we inferred haploid CNs of 1, 4, 5, and 6. We showed possible allelic combination(s) above each diploid CN. The diploid CN10 could be comprised of either CN5/CN5 or CN4/CN6; however, our results showed that it was always CN4/CN6. (D) Familial information and background haplotypes were used to phase the copy number and thus revealed how the CNV segregates in trios. The upper family tree shown with animal signs stands for diploid copy numbers, and the lower tree shows haploid copy numbers (the phase results of the diploid CNs).