#Genotyping-by-Sequencing of Canada’s Apple Biodiversity Collection by Migicovsky, Douglas, and Myles ###This directory contains the genetic data available for Canada’s Apple Biodiversity Collection **abc_combined_maf001_sort_vineland_imputed.ped** PED file of merged, imputed SNP set including HRM markers for a total of 278,231 SNPs from 1,175 diverse apple accessions from the ABC **abc_combined_maf001_sort_vineland_imputed.ped** MAP file of merged, imputed SNP set including HRM markers for a total of 278,231 SNPs from 1,175 diverse apple accessions from the ABC **ApeKI_PstI-EcoT22I_new_ref_bwa_maf0.01_min2alleles_noIndels.recode_filtered_imputed.vcf.gz** VCF file for SNPs from Tassel SNP caller following imputation with LinkImputeR. Thresholds were a maximum position/sample missingness of 70% and a minimum depth of four reads, resulting in imputation accuracies/correlation values of 0.9556/0.8347. There were 226,821 SNPs. **apple_abc_new_ref_maf001_min2alleles_noIndels.recode_filtered_imputed.vcf.gz** VCF file for SNPs from Tassel SNP caller following imputation with LinkImputeR. Thresholds were a maximum position/sample missingness of 70% and a minimum depth of four reads, resulting in imputation accuracies/correlation values of 0.9526/0.8696. There were 195,667 SNPs. **ABC_GATK_combined_new_ref_maf001_min2alleles_noIndels.recode_filtered_imputed.vcf.gz** VCF file for SNPs from Tassel SNP caller following imputation with LinkImputeR. Thresholds were a maximum position/sample missingness of 70% and a minimum depth of four reads, resulting in imputation accuracies/correlation values of 0.9558/0.8761. There were 165,418 SNPs. **hrm_markers.ped** PED file of all 8 markers measured using HRM, prior to imputation. Some markers (ACS, ACO) were insertion/deletions which were recoded as SNPs for to incorporate into the genotyping file. For ACS, T= insertion (162bp insertion in promoter replaces 24 bp sequence (138 bp size difference)). For ACO, G= insertion (61bp insertion in 3rd intron). **hrm_markers.map** MAP file of all 8 markers measured using HRM, prior to imputation. Some markers (ACS, ACO) were insertion/deletions which were recoded as SNPs for to incorporate into the genotyping file. For ACS, T= insertion (162bp insertion in promoter replaces 24 bp sequence (138 bp size difference)). For ACO, G= insertion (61bp insertion in 3rd intron).