Figure 3.

Comparison of linear topological contig (ltc)-derived physical contigs with fingerprinted contigs (fpc) at different stringencies. Different classes of ltc-derived contigs were identified when compared with fpc assemblies that include the first class, which are contigs that were exclusively made by ltc (not found in fpc). The number of such ltc-specific contigs was relatively constant for both of the 6A arms when compared with fpc assemblies at various stringencies. The second class contained contigs that were identical between assemblies made by both tools (ltc = fpc, i.e. BAC composition and order were the same in corresponding ltc and fpc contigs). This class showed a slight increase when the fpc stringency was lowered. The third class includes ltc > fpc (i.e. ltc contigs longer than fpc contigs), which refers to contigs with the same backbone, whereas more BACs were added to the end of corresponding contigs via ltc. This class also showed a slight decrease in number by lowering the stringency in fpc. The two remaining classes include ltc < fpc (i.e. ltc contigs that are shorter than fpc contigs) and ltc ≥ 2fpc (i.e. ltc-made contigs, the BACs of which were assembled into two or more different contigs via fpc). Both classes showed higher differences in number across the fpc assemblies that are mainly explainable by end-to-end merging during fpc assembly. For example, a decrease in the number of ltc ≥ 2fpc from 1e⁻³⁰ to 1e⁻²⁵ is likely to have resulted from the merging of the two corresponding fpc contigs at 1e⁻²⁵. Therefore, contigs of 1ltc = 2fpc at a higher level of fpc stringency later became 1ltc < 1fpc (or 1ltc = 1fpc) at a lower level of stringency. In both chromosome arms, identical classes show a relatively similar trend of variation across fpc assemblies, although they may contain different numbers of contigs in each of the arms.