Fig. 2
SNP performance and population genetic statistics versus SNP call rate threshold in Douglas-fir. Using all related and unrelated trees in the study, we identified polymorphic SNPs using SNP call rate (CR) thresholds of 60, 70, 80, 90, and 97%. These successful SNPs were then tested on two populations of unrelated trees (NC1 = 112 and NC2 = 283). The values in the figure are median values averaged across the two populations for SNPs that were polymorphic and in HWE (P ≥ 0.01). CR is the measured SNP call rate (percent/100), HETobs is observed heterozygosity, PIC is polymorphic information content, MAF is minor allele frequency, and SNPs are the numbers of polymorphic SNPs in HWE. The scale on the right vertical axis shows the number of SNPs (dashed line), whereas the scale on the left is for all other variables (solid lines)