Supplementary Tables A-E.

Table A: Samples and sample mixtures included in the microfluidics assay. Table B: Designed amplicons targeting neutral markers, fungicide resistance and effector genes. Loci check: coverage based assessment of amplification success (see Methods). If an originally targeted locus was not recovered in the species-wide SNP call set used for the amplicon design, a nearby SNP was chosen (see last columns for newly selected loci). Table C: Clustering of reads using CD-HIT-EST followed by mapping to the MFS1 promoter region. Similar blast hits were grouped into K-means based clusters. Table D: Dominant genotype recovered for wheat leaf samples at fungicide resistance loci. The reference allele refers to the allele known from the reference genome isolate IPO323. Sample genotypes are given as 1 and 0 for reference and alternative allele, respectively. Table E: Dominant genotype recovered for wheat field samples across fungicide resistance loci. The reference allele refers to the allele known from the reference genome isolate IPO323. (XLSX)