Supplementary Table S1: Genomic localization of TEs in gene elements and 10 kb windows upstream and downstream of the transcription start site (TSS) in the reference genome IPO323. Supplementary Table S2: Genome-wide TE insertion polymorphism (TIPs) in the pathogen population. 0 represents TE absence and 1 represents TE presence. Supplementary Table S3: Gene expression (log transformed RPKM) values across the population. Supplementary Table S4: Locus-specific transcript abundance at individual TE loci (FPKM) across individuals. Supplementary Table S5: Percent of expressed copies within each TE family in the reference genome IPO323 and percent expressed TE copies in each TE family across the population. Supplementary Table S6: Linkage disequilibrium of TIP in the genome and neighboring SNPs within the 600bp distance from the TE loci. Supplementary Table S7: Genome-wide association mapping of the virulence-associated trait (PLACP: percent leaf area covered by pycnidia) and TE insertion polymorphisms in the genome. Supplementary Table S8: metabolite peak variation in the pathogen population for individual isolates Supplementary Table S9: TIPs in the genome significantly associated with metabolite peak intensity variation in the pathogen population (filtered by Bonferroni threshold). Supplementary Table S10: SRA accession list of RNAseq reads.