*2.3.2. Sequencing and mapping*

DNA from the sample was sequenced on the Illumina HiSeq 2000 platform to generate 125 bp paired-end reads at greater depth. All these RILs sequencing were performed at Total Genomics Solution (TGS) Institute. After sequencing quantity control, the data of 107 samples reached 117.68 G, with an average of 1.10 G per sample. The percentage of Q30 bases was more than 90%, the percentage of Q20 bases was more than 95%, and the distribution of GC was normal. Thus, the quantity and quality of the sequencing met the requirements for subsequent analysis.

The per-base coverage depth across all contigs was calculated by mapping raw reads from each RIL against reference genomes. The results showed that the average mapping ratio and sequencing coverage of the samples were higher than 95 and 92%, respectively. The sequence depth of the samples was 9.91×. In addition to the line 110, the other lines are better for subsequent variation detection and analysis.
