GBS_Rapeseed;30DAS
Demultiplexing was performed using the barcode sequence, and adapter sequence removal and sequence quality trimming were performed. Adapter trimming was performed using cutadapt (version 1.8.3), and sequence quality trimming was performed using DynamicTrim and LengthSort of the SolexaQA program (v.1.13). DynamicTrim cuts low-quality bases at both ends of short reads according to the Phred score, and refines it with high-quality cleaned reads. LengthSort removes excess base cuts made in DynamicTrim; Phred score of Dynamic-Trim  20, and LengthSort using short read lengths  25 bp. BWA (0.6.1-r104) generated cleaned reads passing the preprocessing process, and performed mapping to the standard genome. Mapping was a preliminary step to detect raw SNPs (In/Del) between standard dielectric and sequenced samples. A SAM file was created, and default values were used, except for the following options: a seed length ( l) of 30, maximum differences in the seed ( k) of 1, number of threads ( t) of 16, mismatch penalty ( M) of 6, gap opening penalty ( O) of 15, and gap extension penalty (-E) of 8. The experiment was conducted in repetition.