The Exelixis deletion collection was generated in an isogenic background and provides ~56% coverage of the euchromatic genome. It is described in Parks et al., 2004 and an overview from Exelixis as of 2004 is presented in this slide presentation (see also Cook et al. 2012 and Roote & Russell 2012). The Bloomington Deletion Collection was generated in the same background. Stocks carrying Exelixis or BSC deficiencies can be found here.
To build FRT-based deletions in the same background see Generating deletions from Exelixis insertions.
Complementation tests conducted at Bloomington have shown that 10% of the stocks in the original Exelixis deletion collection did not carry the described deletion and that 77% of the stocks are deficient. The remaining 13% are unconfirmed.