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Principal Components Analysis of methylation values from 400,000 cytosines across all samples. F. mandshurica trees are split from F. excelsior trees along PC1. Three outliers represent low coverage samples: pink triangle outlier on PC3 is F.exc 35–5, black diamond outlier on PC2 is F.exc 40–1, and orange diamond outlier on PC4 is F.exc 33–5. SNP positions with highest loadings along PC1 are listed in Additional file 4
