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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 -)