Additional file 1 of Introgressions lead to reference bias in wheat RNA-seq analysis

Additional file 1: Table S1. Number of genes correctly quantified, underestimated, and overestimated from simulated RNA-Seq data, using Kallisto with the Chinese Spring reference, STAR with the Chinese Spring reference, or kallisto with the pantranscriptome reference. Table S2. Percentage of triads classified in each expression category from simulated RNA-Seq data, using Kallisto with the Chinese Spring reference, STAR with the Chinese Spring reference, or kallisto with the pantranscriptome reference. Table S3. Accessions from the He et al. [11] dataset that do and do not contain the chr1D introgression. Table S4. Expression values for genes within the chr1D introgression for accessions from the He et al. [11] dataset, using either the Chinese Spring or the pantranscriptome reference. Accessions are split based on whether or not they contain the chr1D introgression.