Fig. 2

Molecular characterization of transgenic rice using NGS read alignments. a Illustration of transformation plasmid pPZP200 containing T-DNA used for Agrobacterium-mediated transformation to create SNU-Bt9–5, SNU-Bt9–30, and SNU-Bt9–109. MCS, multiple cloning site. b Detailed example of IGV results. Horizontal lines on the sequence track (top of the panel) indicate the reference sequence (i.e., T-DNA inserted transformation plasmid vector sequence). Featured tracks exhibit a paired orientation (upper panel = read 1, lower panel = read 2). Colored boxes indicate junction region containing reads spanning both the T-DNA border and the genomic flanking sequence. c Sequence alignments of junction-spanning reads (upper = left border flanking sequences, lower = right border flanking sequences). Red and black nucleotides indicate rice chromosome and T-DNA, respectively