Fig. 3

Comparisons between GBS SNPs and WGS SNPs for 6 individual soybean lines. Prize is from GBS Population 1, LG12 is from GBS Population 2, and the four remaining lines are from GBS Population 3. Panel a shows the total number of SNPs identified in each line by 5 GBS pipelines. Panel b shows the percent of GBS SNP sites from panel A in agreement with WGS for each line. Panels c and d show the percent and number (respectively) of GBS SNP alleles from panel A in agreement with WGS. SNPs with a minimum read depth of 2 reads are shown. Below each soybean line is shown its average depth of sequenced GBS bases followed by its WGS coverage. All SNPs were called relative to the Williams 82 reference genome