Recombinant fraction and genetic distance inferred from marker-selected pools for Chr. 3. The per site (blue) and inferred (red line) AFs across the chromosome are displayed for four pools: (A) Canton-S × gl⁻e⁻ with gl⁻ selection (table 1, row 6), (B) Canton-S × se⁻e⁻ with se⁻selection (table 1, row 1), (C) DGRP-315 × gl⁻e⁻ with gl⁻ selection (table 1, row 12), and (D) DGRP-315 × gl⁻e⁻ with gl$+$ selection (table 1, row 13). For all marker-selected pools, see supplementary figure 6, Supplementary Material online. Note that (D) has a different Y-axis scale. The positions of the double markers are marked in the chromosome schematics above and with vertical dotted lines in the plots. For the Canton-S × se⁻e⁻ cross, large inversions are marked in chromosome schematic above with parentheses. (E–G) Averaged recombinant fraction (solid curve) and genetic distance (dotted curve) from the selected loci. Interval around the recombinant fraction estimates represent the standard error across the replicates. Horizontal dotted lines represent recombinant fraction equivalent of 50 cM after Kosambi transformation. (E) Canton-S × gl⁻e⁻ crosses when gl⁻ (red) or e⁻ (blue) are selected. Note here that gl⁻ pools were the female pools and e⁻ pools were the male pools. (F) Canton-S × se⁻e⁻ crosses with e⁻ selection. (G) DGRP-315 (red) or DGRP-360 (yellow) × gl⁻e⁻ crosses. For the DGRP-315 cross, values are averaged across gl$+$ and gl⁻ selection pools, whereas only gl⁻ pools were sequenced for DGRP-315.