Comparison of SNP numbers and frequency estimate accuracy revealed by Pool-seq and by GBS.

Columns report: library/lane identity (population A or B, estimation of sequencing depth per individual in Pool-seq, and software used to detect SNPs of Pool-seq data set), number of SNPs detected by GBS (SNPGBS) and Pool-seq (SNPPool-seq), overlapping number of SNPs detected (SNPboth), concordance correlation coefficient (CCC) with lower and upper 95% confidence limit (LCL; UCL) of CCC, the mean of the absolute difference in SNP frequency estimates of the two methods (|Δf|), false negative rate (FN rate), that is, the fraction of SNPs called by GBS but not by Pool-seq, and their mean minor allele frequency (FN MAF).