Fig. 2
From: Introgressions lead to reference bias in wheat RNA-seq analysis
The impact of reference bias on expression differences between cultivars and enrichment of incorrectly quantified genes within introgressions. A The distribution of incorrectly quantified genes in 5-Mbp windows, coloured by the cultivar in which the estimated expression is lower; orange blocks are underestimated in Lancer compared to Jagger, while green blocks are underestimated in Jagger compared to Lancer. The reads are aligned using STAR as this outperformed kallisto for cross-mapping. B Expression counts for Lancer-Jagger orthologue pairs. Genes are considered incorrectly quantified if their estimated read count is 1.5 × or 1/1.5 × the other cultivar. C CDS nucleotide identity between Lancer and Jagger 1-to-1 orthologue pairs, binned into 5-Mbp genomic windows based on Chinese Spring RefSeq v1.0. D Percentage of genes incorrectly quantified and correctly quantified in characterised introgressed regions and regions not characterised as introgressed. E CDS nucleotide identity between Lancer and Jagger 1-to-1 orthologue pairs for those that are incorrectly quantified and those that are correctly quantified. F Percentage of genes incorrectly quantified and correctly quantified, split into bins of different levels of CDS nucleotide identity