Fig. 3

RNA-Seq read quality assessments. (a) Average Phred quality scores across all base positions for the raw RNA-Seq data obtained from all 124 samples. Most bases across all samples exhibit Phred scores exceeding 30, demonstrating high overall read quality. (b) Distribution of the average GC content in the trimmed RNA-Seq reads of all 124 samples. A normal distribution of the GC content is typically observed in randomly generated libraries. The distribution shown aligns with this expectation, suggesting unbiased library preparation. (c) Bar plot summarizing the uniquely mapped, multi-mapped, and unmapped reads for each sample library. Uniquely mapped reads represent those that map to a single location in the reference genome, whereas multi-mapped reads represent those that map to multiple locations. Unmapped reads are those that failed to map to the reference genome. (d) Distribution of the percentage of uniquely mapped reads among the total reads across all 124 samples. A higher percentage of uniquely mapped reads generally indicates high-quality mapping. Although most samples exhibit high percentages of uniquely mapped reads (>80%), one sample exhibits a lower percentage (51.36%), as indicated by the red arrow. This outlier was excluded from further analysis.