Fig. 2From: PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilitiesMate pairs which are generated from a region with tandem duplications, are mapped to reference. Abnormalities in the insertion size and direction of a mate pair depend on whether it is generated from a location around a tandem duplication breakpoint or not. a A mate pair spanning the tandem duplication in the sample genome is shown. After mapping to the reference genome, this mate pair encounters a change in direction and abnormality in the insertion size (the distance of point a to b). b Two mate pairs that are not located around breakpoint are shown. These pairs will map normally to the reference genome, without any change in the insertion size or directionBack to article page