Tracing a diverse panel of loci through the Illumina library preparation. (a-e) At five steps in the standard protocol aliquots were removed and analyzed for base-composition bias by qPCR. (f,g) To isolate and analyze the ligation-competent population of DNA fragments, a separate ligation reaction with biotinylated adapters was performed followed by streptavidin capture of fragments carrying at least one adapter. The quantity of each amplicon in a given sample was divided by the mean quantity of the two amplicons closest to 50% GC. The resulting relative abundances of amplicons were plotted on a log10 scale over their respective GC contents.