Genome-wide evolutionary response of European oaks during the Anthropocene - Supporting Information

Supporting information to the article from Saleh et al. 2021 published in Evolution Letters: "Genome-wide evolutionary response of European oaks during the Anthropocene". These data were required to assess allelic frequencies of SNPs in age structured cohorts of Quercus petraea. Whole genome pool sequences of 40 and 68 trees per cohort were used for assessing allelic frequencies. A total of 348,863,070 reads per pool were mapped onto the v2.3 Q. robur genome assembly using bwa-mem. Incorrectly paired reads and reads giving multiple alignments were removed with samtools. Duplications were removed with Picard tools. Pileup files were generated for each scaffold over all forests, with samtools. These 1,337 pileup files correspond to the pileups for 1,337 oak scaffolds.