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Table 1 Quality filtering of SNPs

From: Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars

Criteria Threshold Total SNP Deleted SNP Conserved SNP
GenCall 10 % <0.2 5696 510 5186
Missing data >5 % 5186 662 4524
HWE >0.0001 4524 40 4484
MAFa <0.05 4484 3269 1215
LD (VIF) 2 1215 889 326
  1. aIncludes homozygous SNP
  2. GenCall 10 % from IlluminaTM, missing data, Hardy Weinberg equilibrium (HWE), minor allele frequency (MAF) and linkage disequilibrium (LD) (VIF -variance inflation factor -)