Figure S1.

Distribution of Error Rates in Modern and Ancient Horses following Three Filtering Approaches, Related to Figure 2

(A) Histogram of overall error rate estimates for samples in dataset (a) (n = 159), based on random sampling of a single allele per site. All horses were grouped into modern (turquoise) or ancient horses (red). Three approaches were used to estimate the individual error rates, “All sites” makes use of all sites for which sequencing data was present, “All sites except CpG’s” masks data in CpG contexts according to the reference genome, and finally, “Transversions Only” excludes all sites observed as transitions. The vertical line represents the maximal allowed error rate (0.0005) cut off for analyses including “All sites except CpGs.”

(B) Histogram of overall error rate estimates for samples in the DOM2 clade (dataset (b), n = 126), with the same filtering procedure as in (A), but based on posterior genotype probabilities.