The recombination map position for D. melanogaster genes localized to the reference genome assembly was inferred from their sequence location based on a correspondence table for cytological, recombination (genetic) and sequence map positions. This correspondence table is offered as a precomputed file (ftp://ftp.flybase.net/releases/current/precomputed_files/map_conversion/cyto-genetic-seq.tsv.gz).
The correspondence of cytological position to the genome assembly is based on estimates of the size in kb of each polytene band by Sorsa and colleagues (FBrf0051078, FBrf0074506, FBrf0078633, FBrf0195567). These estimates are summed to give the length (according to Sorsa) in kb of a region between two very well-mapped entities ('anchors') that are also identified on the genome. The genome sequence gives a different number for that length, so a scaling factor is then applied: i.e. the cytology of each mapped object in the region between the anchors is calculated by interpolation from its sequence coordinates. The anchors used are a set of over 1200 P-element insertions that have been both cytologically mapped and localized precisely to the genome (FBrf0195570). 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.
The release 5 cytological-recombination-sequence correspondence map was lifted over to the current Release 6 genome assembly and manually adjusted in regions that were newly added to the major scaffolds.