Fig. 5

Whole genome alignment comparisons of selected Anopheles funestus AfunF1 and AfunF2-IP scaffolds. The plot shows correspondences of three AfunF2-IP scaffolds (right) with AfunF1 (left) scaffolds based on whole genome alignments, with links coloured according to their AfunF2-IP scaffold. Putative adjacencies between AfunF1 scaffolds are highlighted with tracks showing confirmed neighbours (black with bright green borders), supported neighbours with conflicting orientations (yellow), scaffolds with putative adjacencies that conflict with the alignments (purple gradient), scaffolds without putative adjacencies and thus no conflicts with the alignments (grey gradient) for: from outer to inner tracks, ADseq, Gos-Asm, OrthoStitch, physical mapping, and Agouti. The innermost track shows alignments in forward (green) and reverse (orange) orientations. The outermost track shows alignments coloured according to the corresponding scaffold in the other assemblies (light grey if aligned to scaffolds not shown). Inset (i) shows how corrected orientations of physically mapped scaffolds agree with the other methods. Inset (ii) shows how the alignments identified a short scaffold that was placed between two scaffolds identified by three other methods