we examined 2,696 mb ( 92.67% ) of the chimpanzee genome aligning with single regions in humans , removing assembly and alignment artifacts , segmental duplications , and other regions with complex genome histories ( supplementary information ) . chimpanzee sequences aligning to macaque but not human were identified as human - specific deletions . we identified 70.0 mb ( 2.41% ) of the chimpanzee genome as highly conserved by calculating the fraction of identical base pairs within multiple sequence alignments using a series of sliding window criteria ( supplementary table 1 ) . hcondels were validated by searching for individual human sequence reads in the ncbi trace archives spanning predicted deletions ; and by testing 39 hcondels by experimental amplification from individuals of 23 human populations ( coriell cell repositories , supplementary information ) . gene enrichments were analyzed using great ( great.stanford.edu)19 . for each ontology we ran 1,000 simulations over 510 size - matched random deletions overlapping one or more chimpanzee conserved elements to derive a multiple test p value threshold for enrichment . functional enhancer assays were carried out by injecting chimp and mouse expression constructs into fvb embryos ( xenogen biosciences and cyagen biosciences ) and staining for lacz expression activity at different developmental stages ; or by transfecting chimp and mouse enhancer constructs into human foreskin fibroblasts ( system biosciences ) or rencell cx human neural progenitor cells ( chemicon ) , and comparing expression to human - deletion / control constructs using galacto - light plus ( applied biosciences ) ( supplementary information ) .