Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle.

Each allele, when considered individually for molQTL mapping after PanGenie-based genotyping, was below the significance threshold for LOC112443864 , but curating and merging the alleles before genotyping and conducting the eQTL analysis revealed a highly significant peak ( Supplemental Fig. 9 ). cis -sQTL mapping We performed a similar analysis for sQTL, now using intron excision ratios as the phenotypes.

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