Figure 2. False positive CNVRs caused by cattle genome assembly errors.

(a) F_ST between male and female of Nellore cattle at CNV segment level; (b) F_ST between male and female of HapMap cattle at CNV segment level; (c) BAF and logR ratio distribution of SNP probes near FP_CNVR7. Five upstream and downstream probes were included to represent the basal level; (d) BAF and logR ratio distribution of SNP probes within FP_CNVR2; (e) Male-specific PCR validation results. Although there were nonspecific bands in some samples, specific amplifications of target bands (labeled) were only present in males.