Table 3. RNAseq dataset used for evaluation of the pipeline.

Genotype name	Raw data		Filtered data		Alignment (%)	SNP with reference
	Total number of reads (PE)	Read length (bp)	Total number of reads (PE)	Read length (bp)
HuaU12	6,857,839	90/90	6,733,549	72/74	82.51	41,225
HuaU606	6,771,173	90/90	6,649,229	72/74	78.71	44,984

Above mentioned RNA sequencing read data from two genotypes of peanut were included in this dataset. Raw reads were filtered and then aligned against the unigene sequences of peanut (ftp://ftp.ncbi.nih.gov/repository/UniGene/Arachis_hypogea/Ahy.seq.uniq.gz) as reference. The pre-processing step of pipeline trimmed 90 bp reads into paired end reads of length 72 bp/74 bp.