In the case of an insertion or a deletion, mapping of the paired-end is consistent with the reference genome. But the read are disconcordant in apparent size. The apparent size is the distance of the BAC sequenced-ends mapped in the reference genome. If a BAC has an insert of length (l), a concordant mapping will show a fragment of size (l) in the reference genome. If the paired-ends are closer than distance (l), an insertion is suspected in the sampled DNA. A distance of (l< μ-3σ) can be used as a cut-off to detect an insertion, where μ is the mean length of the insert and σ is the standard deviation. In case of a deletion, the paired-ends are mapped further away in the reference genome compared to the expected distance (l> μ-3σ).