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Comparison of SNPs identified by the two approaches. We detected 916,407 SNPs by mapping to the reference genome (green) and 175,998 SNPs were called by mapping to the transcriptome (purple), which composed 974,251 unique variants using GATK–DNA-seq combined with the SNPiR pipeline. Besides, we applied the approach of GATK–RNA-seq and then detected 1,196,422 variants (red).
