A total of 40 indels were selected from each chromosome for validation. These included 20 small- to medium-sized insertions (<86 bp), 20 medium-sized deletions (size >50 bp), and 20 large deletions (>100 bp) detected by Illumina GA2. Primers were designed by centring the target indel to produce amplicons that were 300–400 bp in length using Primer 3. PCR assays were performed as described above. We ran PCR-amplified genomic DNA on SDS–polyacrylamide gel electrophoresis gels. Each PCR assay was performed on DNA from B6 and D2. The sizes of the resulting PCR products were compared with the predicted size of indels.
