This dataset contains paired-read Illumina pooled amplicon sequencing data tracking non-drive allele frequencies over discrete generations in Anopheles gambiae cage population experiments with the Ag(QFS)1 gene drive, pre-seeded with known resistance alleles at the doublesex gene drive target site (an R1 G→T SNP or R3 C→T SNP). Ag(QFS)1 heterozygous males were released at 40% (R1 cages) and 25% (R3 cages) frequency in duplicate cages pre-seeded with 15% R1 (G→T SNP) and 25% R3 (C→T SNP) resistant alleles respectively. File naming denotes whether the sample originated from an R1 or R3 pre-seeded cage trial, the generation sampled (G0, G1, G4 or G8), the cage sampled (A, B, C or D) and the population batch sampled (1 or 2). Cage A: population pre-seeded with R3 (replicate 1) Cage B: population pre-seeded with R3 (replicate 2) Cage C: population pre-seeded with R1 (replicate 1) Cage D: population pre-seeded with R1 (replicate 2)