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Additional file 9: Maps of scaffolds.
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Physical mapping of scaffolds from cassava whole genome sequencing using the mapped markers as anchors is presented.
Physical mapping of scaffolds of cassava whole genome sequence draft using the mapped markers as anchors resulted in the orientation of 687 scaffolds covering 45.6% of the genome.
Mapping of scaffolds against the two available reference genomes can further provide information on the intragenomic organization and their intergenomic distribution across evolutionary lineages.
Additionally, this result is more consistent with the genome sequence and mapping of scaffolds to the chromosomes in D. ananassae, relative to the previous results, because there is not a sufficiently large gap in the scaffold spanning the euchromatic portions of the second chromosome that could house the ~5 Mbp nuwt.
The map of scaffold 2 was shown by Fig. 4 with the detailed descriptions, and this file contained the maps for the remained scaffolds.
A set of 85 BACs were mapped on scaffolds not assigned to any pseudo-molecule (Ca0).
An important application of such maps is in the anchoring and the ordering of contigs of bacterial artificial chromosome (BAC) clones during the construction of physical maps or ordering of scaffolds during genome sequencing.
Physical mapping of the scaffolds with the newly developed markers narrowed down the SR to scaffold 101 between markers GM597 and ARO124 from 990,577 to 2,468,000 bp.
Figure 6 shows an example of such a situation inside the heat map view of Scaffold Hunter.
Selected positive and negative ions were mapped over a 50 × 50-μm raster area with a 2048 × 2048-pixel image resolution to provide polymer component mapping of the scaffolds.
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