Fig. 2

T-DNA transcript levels and coverage in transgenic seeds. (a) The number of reads aligned to the T-DNA sequence by Tophat from the reference genome comprising an extra scaffold containing the respective gene of interest cassette. Numbers on the y-axis represent RPKM normalized expression values for the gene of interest in each sample. (b-d) Coverage graphs over the annotated region of each added scaffold are shown for lines ST111 (b), 764 (C), and ST77 (d). The annotated components correspond to those shown in Fig. 1. The highest expressing seed is shown for each transgenic plant. The y-axis of each coverage graph ranges from 0 to 100