Genome sequence data results are reported from experimental and bioinfomatic work using the technique 'Bulk Segregant Analysis' to determine the genetic basis of observed resistance to the azole antifungal compound itraconazole in the opportunistic fungal pathogen Aspergillus fumigatus. Overall design: Sexual crosses were set up between a sensitive parent (47-51) and an azole resistant parent (47-308). Progeny were collected from both a second and sixth backcross to the sensitive parent and were screened into either azole sensistive or resistant bulk pools of 40-60 isolates. The respective parents and pools were then sequenced in triplicate and a dedicated bioinfiormatic pipeline used to identify a genome region found only in the resistant parent and resistant progeny that contained a causal mutation for azole resistance. The three replicate trimmed genome sequence files for the parents and progeny pools are here deposited,