The QC filters remove SNPs showing gross errors. However, it is also important to understand the magnitude and structure of more subtle genotyping errors among SNPs that pass QC. We therefore carried out a series of analyses to assess the influence of the long-range PCR amplicon structure on genotyping error, the concordance rates between genotype calls from different genotyping platforms and between those platforms and re-sequencing assays, as well as the rates of false monomorphism and mis-mapping of SNPs (see Supplementary Text 2, Supplementary Figs 1–3 and Supplementary Tables 1–4). We estimate that the average per genotype accuracy is at least 99.5%. However, there are higher rates of missing data and genotype discrepancies at non-reference alleles, with some clustering of errors resulting from the amplicon design and a few incorrectly mapped SNPs.
