Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

Supporting Information

Supporting Information

  • Supporting Information - File S1, Tables S1-S6, and Figures S1-S12 (PDF, 477 KB)
  • File S1 - Accuracy of genotype calling (PDF, 57 KB)
  • Table S1 - Genotype calling errors (PDF, 24 KB)
  • Table S2 - SNP calling false positive rates (PDF, 24 KB)
  • Table S3 - SNP calling false negative rates (PDF, 24 KB)
  • Table S4 - FST estimators (PDF, 28 KB)
  • Table S5 - Computational time for FST computation (PDF, 29 KB)
  • Table S6 - Computational time for PCA computation (PDF, 25 KB)
  • Figure S1 - RMSD (left panel) and mean bias (right panel) for estimating FST under different sequencing coverage (2x, 6x and 20x). (PDF, 31 KB)
  • Figure S2 - RMSD (left panel) and mean bias (right panel) for estimating FST at 2x sequencing coverage. (PDF, 30 KB)
  • Figure S3 - Ancestral population allele frequency estimated from a Maximum Likelihood procedure with unknown genotypes versus the true value used in the model (PDF, 264 KB)
  • Figure S4 - FST for 100 10kb regions where only 10% of the sites are variable in the population (PDF, 65 KB)
  • Figure S5 - Sum-of-squares (SS) between PC1 and PC2 computed from called genotypes from genotype posterior probabilities (on x-axis) or with the new proposed method which does not rely on genotype calling (on y-axis). (PDF, 39 KB)
  • Figure S6 - Sum-of-squares (SS) between PC1 and PC2 computed from called genotypes from genotype posterior probabilities (on x-axis) or with the new proposed method which does not rely on genotype calling (on y-axis). (PDF, 39 KB)
  • Figure S7 - PCA plots from known genotypes and from called genotypes using genotype posterior probabilities (PDF, 33 KB)
  • Figure S8 - Sum-of-squares (SS) between PC1 and PC2 computed with the new proposed method, which does not rely on genotype calling, (on y-axis) or with the new method but without weighting each site for its probability to be variable (on x-axis). (PDF, 39 KB)
  • Figure S9 - Sum-of-squares (SS) between PC1 and PC2 computed with the new proposed method, which does not rely on genotype calling, (on y-axis) or with a method based on computing the expectations of genotypes from genotype posterior probabilities (on x-axis). (PDF, 59 KB)
  • Figure S10 - Sum-of-squares (SS) between PC1 and PC2 computed from called genotypes (on x-axis) or with the new proposed method which does not rely on genotype calling (on y-axis). (PDF, 23 KB)
  • Figure S11 - PCA plots for wild and domesticated samples using different strategies of calling genotypes and of filtering data (PDF, 25 KB)
  • Figure S12 - Percentage of explained variance from first components of PCA for wild and domesticated samples from called genotypes or without calling genotypes (PDF, 18 KB)