Table 2. Restriction site associated DNA (RAD) sequence dataset used for evaluation of the pipeline.

Genotype name	Total number of reads (SE)	Read length (bp)	Total number of filtered reads	Read length (bp)	Alignment (%)
ICCV 03107	2,360,400	100	2,250,687	78	91.27
ICC 4918	5,761,446	100	5,486,801	78	89.82
ICC 4930	10,595,164	100	10,103,218	78	89.90
ICC 4958	10,874,599	100	10,400,166	79	91.83
ICC 5270	8,198,607	100	7,790,524	78	90.38
ICCV 05530	8,011,084	100	7,611,453	78	89.96
ICC 5810	8,587,698	100	8,213,783	79	90.68
ICC 5912	5,422,669	100	5,183,888	79	91.12
ICC 6263	8,167,648	100	7,808,763	79	90.89
ICC 8261	6,245,558	100	5,943,309	81	88.94

Raw reads from above mentioned datasets were filtered and then aligned against the chickpea reference genome. The reads cover 88% to 92% of the reference genome. The pre-processing step of pipeline trimmed 100 bp reads into single end reads in the range 78 bp to 81 bp.