Peach [Prunus persica (L.) Batsch] includes ‘Hujingmilu’ (‘HJ’) and ‘Yulu’ (‘YL’).Mandarin (Citrus reticulata Blanco) includes ‘Ponkan’ (‘PK’) and ‘Yellowish-peeled Ponkan’ (‘YP’). Raw sequence reads. Prunus persica and Citrus reticulata

The study aimed to evaluate the effects of different paired-end read lengths, assemblers, and SNP callers on the accuracy of SNP prediction and to develop a strategy for accurate discovery of SNPs from next generation sequencing data.