Figure 1

Coverage and error rate of raw and processed reads mapping to the transgene flanking regions and the transgenic cassette from Bt rice inserted on rice chromosomes II and III. (A) Schematic representation of the transgenic cassette of Bt rice. Each DNA walking method is illustrated by a black arrow. left border (LB); Cauliflower mosaic virus (CaMV) 35S terminator (t35S); hygromycin phosphotransferase gene (hpt); CaMV 35S promoter (p35S); LacZ alpha fragment (lacZ); maize ubiquitin promoter (pUBI); synthetic Cry1B gene (Cry1B); Agrobacterium tumefaciens nopaline synthase terminator (tNOS); right border (RB); rice genome (rice) [Schema adapted from 32]. (B) Coverage and error rate of raw reads and processed reads mapping on the common part of the insert, and the four unique transgene flanking regions from Bt rice. Read subsets obtained after 1, 2, 4, 8, 16 and 24 hours of sequencing are shown (see legend for color coding). Grey bars below the x-axis indicate the positions of the genomic flanks (GF) and of the functional genetic elements (1: t35S, 2: hpt, 3: p35S, 4: pUBI, 5: Cry1B, 6: tNOS). left border (LB); right border (RB); rice chromosome II (X2); rice chromosome III (X3).