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Fig. 4 | BMC Biology

Fig. 4

From: Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Fig. 4

Comparisons of synteny-based scaffold adjacency predictions with physical mapping and RNA sequencing data. The bar charts show counts from each set of synteny-based scaffold adjacency predictions compared with the adjacencies from the physical mapping (a) or RNAseq Agouti-based (b) sets. The synteny-based sets comprise predictions from three different methods, ADseq, Gos-Asm, and OrthoStitch, as well as their liberal union (all non-conflicting predictions), their two-way consensus (2-way Cons. predicted by two methods and not conflicting with the third method), and their three-way consensus (3-way Cons. predicted by all three methods). Adjacencies that are exactly matching form the green base common to both sets in each comparison, from which extend bars showing physical mapping or Agouti adjacency counts (left) and synteny-based adjacency counts (right) that are unique (yellow) or conflicting (orange) in each comparison. Blue dashed lines highlight the total adjacencies for the physical mapping or Agouti sets. For comparison, all y-axes are fixed at a maximum of 350 adjacencies, except for Anopheles atroparvus. Results for two strains are shown for Anopheles stephensi, SDA-500 and Indian (I)

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