Fig. 1

Overview of the retrovirus mapping strategy. Paired-end sequencing reads from re-sequencing of chicken genomes are mapped to both Galgal4 (a) and the LTR of the EAV-HP genome (b). Unmapped reads from the EAV-HP LTR alignment, which may map either to the host genome or other elements of the viral sequence, are recovered and mapped to the chicken reference genome to generate a list of observed integration sites (b). For each integration sites, paired-end reads are retrieved from the initial mapping to Galgal4 (c) and remapped to the LTR of the EAV-HP genome (d), and the soft-clipped sequences of mapped reads recovered (e). These sequences are then aligned to Galgal4 using BLAT, and the results referenced against the interval in question to identify the integration site breakpoint