Characterization of the GC CNV tagging SNPs and allelic imbalance pattern.

(A) A schematic overview of four structural haplotypes and the five tagging SNPs inside the GC CNV, shown together with allele frequencies. (B) Five GC CNV tagging SNPs, shown with their positions, rs ID, alleles, location within GC. (C) Allelic imbalance pattern shown in Wt/Mul animals. Animals will get more supporting reads for alternative alleles for the five CNV tagging SNPs, thus the tagging SNPs will be called as heterozygous but with strong allelic imbalance.