Statistical and quality control analysis of RNA-Seq data. A. Read distribution over exons, introns, untranslated regions (UTRs) and intergenic regions. B. 84% of all reads matched to unique locations. The remaining 16% of reads matched to multiple locations in the genome of F. graminearum (2% matched to 2–10 sites and 14% to more than 10 different locations). C. The distribution of all reads matching to multiple locations in intergenic regions, UTRs and coding regions. D. The total read coverage along the gene body from 5′ to 3′ end in wt PH-1 and mutant ebr1. The genes were divided into 100 equal windows. E. Scatter plot analysis of two technical replicates from both wt PH-1 and mutant ebr1. Log2 transformed reads number of all predicted genes was used for comparison.