Fig. 3
Placement of ap_contig1 to optical map Chromosome 1. An illustration re-drawn from the output of the OpGen’s Mapsolver software, where in silico digested allpaths-lg contigs are placed to the optical map Chromosome 1. It shows a complex rearrangement where flaws in the allpaths-lg assembly are corrected. The 1.38 Mbp region A´ of ap_contig1 is a collapsed repeat structure, which the optical map was able to resolve and subsequently could be placed to regions a 1 and a 2 of Chromosome 1. This map placement is highlighted in transparent red for clarity and shows that the sequences were placed in inversed orientation. Furthermore, a 2 and a 3 are flanking the placed sequence b 1 , originating from the B region of the contig ap_contig6. On the left flank of B is an unplaced region whose restriction enzyme cuts could not be aligned to the cuts made by the Argus system, and is likely the result of mis-assembly