This dataset contains paired-read pooled amplicon Illumina sequencing data identifying Cas9-induced end-joining (EJ) mutations at the Ag(QFS)1 target site within the Anopheles gambiae doublesex gene, recovered from intersex mosquitoes. Intersex offspring were obtained from 33 replicate F2 crosses (cages A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, T, U, V, W, X, Z, AC, AD, A20, B20, C20, D20, E20, F20, G20), each consisting of a minimum of 50 mosaic males carrying Cas9-induced EJ mutations crossed to a minimum of 50 dsx null (dsxF⁻, GFP+) females. For each cross, ~100 GFP+ intersex offspring were analysed by pooled amplicon Illumina sequencing. For sample D these were split across 8 samples. Three control pools of 100 non-sex-separated individuals are also included: (1) GFP+ offspring of dsx mutator males crossed to null GFP+ females, inheriting the mutator allele (ALEDL); (2) the same cross, offspring not inheriting the mutator allele (DL); and (3) wild-type individuals (WT).