Scaffolds Track Settings
 
Assembly Scaffolds   (All Mapping and Sequencing tracks)

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Data last updated at UCSC: 2008-08-19

Description

This track represents the super-contigs as assembled from the fragment contigs.

Methods

The locations were extracted from the Broad Institute delivered file assembly.agp

See also

Broad Institute Horse Genome Project.

Assembly details

The genome has been sequenced to 6.8X coverage. See also Broad Institute Assembly Statistics.

There are 55,316 contigs in the assembly containing 2,428,773,513 nucleotides. The mean size of these contigs is 43,907 bases, with an N50 measurement of 6,246 contigs of size 112,381 bases or larger containing half of the sequence.

The smaller contigs have been assembled into two types of supercontigs. 73 of the supercontigs named scaffold_0 through scaffold_87 containing 2,242,897,370 nucleotides comprise chromosome 1-31 and chromosome X. The mean size of these supercontigs is 30,724,622 bases, with an N50 measurement of 33 supercontigs of size 53,663,962 bases or larger containing half of the sequence.

There are also 9604 supercontigs named chrUn0001 through chrUn9604 containing 107,858,955 bases. The UCSC genome browser combines these supercontigs together as an artifical chromosome chrUn with 1,000 base gaps between these supercontigs. This chrUn sequence is 117,461,955 bases, with artificial 1,000 base gaps covering 9,603,000 bases.