Fig. 1

Discovery and quality control on SVs in the bovine genomes

(A) An example of population-side SV detection results. Animals are genotyped for each site, and for CNVs, the fold-coverage change in read-depth is annotated. Marked with yellow is a spurious call where read-depth do not change according to genotypes. (B) An overview on filtering steps and number of calls in different call sets. (C) The overall CNV calls were divided into stringent and lenient call sets, exploiting the post hoc filter based on read-depth. The former is considered to be the set of accurately genotyped biallelic sites. (D) Quality control (QC) plots were generated for all CNVs exploiting the genotype and read-depth information. The panel on the left side shows an example of a stringent site where animals’ genotypes and read-depth are unambiguously assigned. Each blue dot represents a sample. The black dots and vertical bars in the violin plot represent the mean and one standard deviation. The right panel represents the read-depth distribution for each GT group. The QC plot for a lenient site is shown on the right side. In such a case, read-depth distribution of animals genotyped as 0/0 and 0/1 are overlapping (marked with a red dotted circle), indicating inaccurate genotyping results