Additional file 1 of Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs

Additional file 1: Fig. S1. Variant set obtained by integrating two genotyping strategies (Single-reference genotyping and Graph-based genotyping). Fig. S2. Principal component (PC) analysis (a) and ADMIXTURE analysis (b) based on single reference typing. Fig. S3. Genome-wide distribution (sliding window = 50 kb, step size = 25 kb) of selective eliminations determined by fixed index (Fst) between DLW and QCB pigs using SVs. Fig. S4. EigenGWAS analysis was conducted across the whole genome for 37 QCB pigs and 40 DLW pigs.