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.

附加文件1：表S1。采用基于中国春（Chinese Spring）参考基因组的Kallisto、基于中国春参考基因组的STAR，以及基于泛转录组（pantranscriptome）参考基因组的Kallisto对模拟RNA测序（RNA-Seq）数据进行定量分析后，得到的正确定量、低估及高估的基因数目。表S2。采用基于中国春参考基因组的Kallisto、基于中国春参考基因组的STAR，以及基于泛转录组参考基因组的Kallisto对模拟RNA测序数据进行分析后，各表达类别中已分类三联体（triads）的占比。表S3。来自He等人[11]数据集的、含有与不含1D染色体渐渗片段的种质材料。表S4。针对He等人[11]数据集的种质材料，采用中国春参考基因组或泛转录组参考基因组进行分析后，1D染色体渐渗片段内基因的表达量；所有种质材料均按是否含有1D染色体渐渗片段进行分组。