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Next-generation sequencing approaches are believed to play a vital role in transgenesis, which is evident from the recent literature. They serve as a trusted source for the molecular characterization of transgene sequence. This technology enables researchers to know the integration sites and also determine copy number in transgene species. This is significantly important as the integration of transgene site and copy numbers are instrumental in determining the relationship between integration site and specific phenotype, which can thus be applied to the growing number of transgenics to yield commercial benefit.