The Biggest Problem with the Shotgun Technique Is Its Tendency

The biggest problem with the shotgun technique is its tendency to underestimate the size of the genome. Which of the following might best account for this?

A) skipping some of the clones to be sequenced
B) missing some of the overlapping regions of the clones
C) counting some of the overlapping regions of the clones twice
D) having some of the clones die during the experiment and therefore not be represented
E) short repetitive sequences hinder reassembly