The estimation of D. melanogaster genes' cytogenetic map position is based on the correspondence of polytene chromosome cytological bands to the genome assembly. Polytene band mapping to the genome assembly is based primarily on the location of about 1200 P-element insertions that have been both cytologically mapped and localized precisely to the genome (FBrf0195570). From these anchors, band position is then interpolated using estimates of polytene band size (in kb) determined by Sorsa and colleagues (FBrf0195567); the scaling works out to be slightly different for each inter-anchor region, but it is estimated that even in the middle of a region the error in the computed location should never be more than a band or two. With the new Release 6 genome assembly, cytological band positions were lifted over from the Release 5 assembly, and slight adjustments were made to band locations where sequence was newly added to the major scaffolds: e.g., extended band-1A1 to the start of the X chromosome genome scaffold.

From the estimated cytological map position of a gene, a genetic map position can then be estimated using a correspondence table between cytological bands and genetic map positions. This correspondence table, apparently generated in 1994, is offered as a precomputed file (ftp://ftp.flybase.net/releases/current/precomputed_files/map_conversion/cyto-genetic-seq.tsv.gz). The details regarding the determination of this cytogenetic-genetic map correspondence have been lost.