Fig. 6
From: Comprehensive detection of structural variations in long and short reads dataset of French cattle
Genotyping of structural variations (SVs) in 571 short-read (SR) samples using a variation graph constructed from 176 long-read (LR) samples. (A) Length distribution of genotyped SVs from the variation graph, showing deletions (left) and insertions (right). (B) Annotation of genotyped SVs based on their genomic region type. (C) Recall rates of genotyped SVs for 148 samples with both LR and SR data. (D) PCA of genotyped SVs across 571 SR samples. (E) Upset plot of major SVs (allele frequency > 70%) across all 14 breeds and 6 breeds with more than 30 SR samples. The inset displays SVs allele frequencies across 571 samples, with a vertical line indicating the threshold for major SVs. Breed abbreviations: AUB (Aubrac), BAQ (Blonde d’Aquitaine), CHA (Charolais), HOL (Holstein), LIM (Limousine), MON (Montbéliarde), NMD (Normande).
