This dataset is for next generation sequencing reads used for confirming and verifying CRISPR/Cas9 based editing in sunflower. These reads were analyzed by CRISPresso2 to confirm sequence variations in genetically modified sunflower. The data forms part of the thesis entitled "Haploid-inducer development by CRISPR/Cas9 mediated CenH3 gene modification in Helianthus annuus (Sunflower)".