Detection and correction of false segmental duplications caused by genome mis-assembly

Table 2 Unplaced haplotype variants

	*Gallus gallus*(chicken)	*Pan troglodytes*(chimpanzee)	*Bos taurus*(cow)	*Canis familiaris*(dog)
Unplaced contigs	25,957 (56.8 Mb)	47,549 (153 Mb)	133,918 (307 Mb)	7,551 (75.1 Mb)
Mis-assembled DCCs	8,044 (16.3 MB)	10,407 (21.3 Mb)	1,793 (4.92 Mb)	2 (2.92 Kb)
Mis-assembled DOCs	663 (1.23 Mb)	2,204 (2.96 Mb)	751 (827 Kb)	15 (23.0 Kb)

In each of the four genome assemblies, a large set of contigs that could not be placed on the chromosomes exists (summarized in the first row). We aligned these contigs against all placed contigs and identified those that were contained in placed sequence (duplicated contained contigs (DCCs)) or overlapped a placed contig (duplicated overlapping contigs (DOCs)). We checked mate pairs for evidence that these contigs should be merged with the placed contigs. The table shows the number of contigs of each type found to have a supported placement in the assembly for each alignment type. These unplaced contigs are likely haplotype variants of the sequence in the placed contigs.

ISSN: 1474-760X