Additional file 2 of Integrating pangenome and imputation framework reveals structural variants affecting stature and milk composition traits in French dairy cattle

Additional file 2: Fig. S1. Boxplot of detected SVs based on LR data according to the breeds. Fig. S2. Boxplot of minor allele frequency of SNVs and SVs in the imputation-reference panel. Fig. S3. Genome-wide average linkage-disequilibriumof reference and target imputation samples. Fig. S5. Genome wide association on protein yield. Fig. S6. Genome wide association on fat yield. Fig. S7. Genome wide association on fat content. Fig. S8. Conditional analysis on a significant insertion at 91.7 Mb across BTA5 for fat content in Montbéliarde. Fig. S9. Conditional analysis on a significant deletion at 118 Mb across BTA5 for fat content in Montbéliarde. Fig. S10. Conditional analysis on a significant insertion at 85.5 Mb across BTA6 for protein content in Montbéliarde. Fig. S11. Conditional analysis on a significant deletion at 32.8 Mb across BTA22 for protein content in Montbéliarde. Fig. S12. Conditional analysis on a significant deletion at 15.3 Mb across BTA3 for protein content in Normande. Fig. S13. Conditional analysis on a significant deletion at 15.3 Mb across BTA3 for height at sacrum in Normande. Fig. S14. Genome browser track for ATAC-seq data intersect with the 143 bp insertion at BTA6. Fig. S15. Genome browser track for ATAC-seq data intersect with the 473 bp insertion at BTA6. Fig. S16. Genome browser track for ATAC-seq data intersect with the 6,179 bp deletion at BTA11