Abstract: Methods of clonal analysis of functional genomic assays are provided. Aspects of the invention include transducing a population of target cells with a packaged viral effector library made up of a plurality of effector construct subsets, wherein each effector construct subset of the library includes a plurality of effector constructs having a common effector cassette linked to a distinct clonal barcode. Inclusion of distinct clonal barcodes in the effector construct subset allows for determination of the clonal representation of an effector construct subset in transduced target cells that exhibit a specific phenotype. Aspects of the invention further include compositions, e.g., libraries and components thereof, which find use in practicing the methods.