ExomeSEQ: bringing reads on-target

It is surprising to look at some of the numbers from exome capture followed by sequencing projects.  The nature paper on exome-seq to identify cause of mendelian disorder has as low as 47% of uniquely mapping reads actually mapping on-target. Another study of 12 exome sequences also has a capture specificity of as low as 31%.

Why are these numbers so low?

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