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This dataset includes genotype and phenotype data of 11 affected (case) and 23 unaffected (control) pigs for AMC case-control haplotype association testing and a VCF file of 809 candidate variants compatible with recessive inheritance of AMC. Genotype data (AMC.bed, AMC.bim and AMC.fam): 34 pigs genotyped with Illumina PorcineSNP60 Genotyping Bead chips. Phenotype data (AMC.pheno): the first, second and third column is Family ID, Animal ID and phenotype (1=case;2=control), respectively. AMC candidate variants compatible with recessive inheritance (AMC_candidate_muations.vcf.gz and AMC_candidate_muations.vcf.gz.tbi). Sequencing data of five animals in AMC pedigree have also been deposited at the Sequence Read Archive of the NCBI at the BioProject PRJNA622908 under sample accessions SAMN14532191, SAMN14532478, SAMN14532769, SAMN14532790 and SAMN14532792.