*3.4. Preprocessing of Raw Data of the RNA Sequence*

After the quality check of the extracted RNA was completed, a library was constructed, and the quality of distribution by cDNA size and concentration of the constructed library were measured using a Bioanalyzer DNA Chip (Agilent Technologies, Santa Clara, CA, USA). Thereafter, RNA sequencing was performed using the constructed library information and HiseqX (Illumina, San Diego, CA, USA), and the raw RNA sequencing data of each onion line were obtained. The raw RNA-seq data are shown in Table S3. The raw reads of the seven onion lines ranged from 28,899,894 to 41,664,542, the total reads of the trimmed reads ranged from 20,744,300 to 27,932,656, and the mapped reads ranged from 16,852,911 to 21,958,205. Trimming was performed by removing low-quality bases and Illumina adapters from the raw data. Mapping was performed on the reference data of NABIC (RDA, JeonJu, Korea, https://nabic.rda.go.kr, accessed on 7 February 2021), and the number of paired reads containing at least 50 nucleotides was confirmed. As a result of mapping, the lengths of the mapping reads ranged from 267 nucleotides to 5478 nucleotides, the average length of the reads was 2236 nucleotides, and the median was 1988 nucleotides. The mapping results determined that the length of the mapped reads was sufficient for the next analysis, and the following analysis was performed.
