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

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Data schema/format description and download
Assembly: Fugu Oct. 2004 (JGI 4.0/fr2)
Data last updated at UCSC: 2007-01-22

Description

This track shows the Fugu v.4.0 (Oct. 2004) whole genome shotgun assembly provided by the US DOE Joint Genome Institute (JGI). The assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced at JGI, Myriad Genetics, and Celera Genomics, resulting in a sequence coverage of 8.5X. All reads are plasmid, cosmid, or BAC end sequences, with the predominant coverage derived from 2 Kb insert plasmids. This assembly contains 7,213 scaffolds totaling 393 million base pairs. The largest 125 scaffolds total 196 million base pairs.

The scaffolds in the display are ordered numerically using the scaffold numbering provided by JGI. The Genome Browser depicts the Fugu genome as a single unordered chromosome with 1000 bp scaffold gaps, which are shown in the Gap track annotation. The scaffolds decrease in size as the scaffold number increases; scaffold #1 is the largest.

All components within this track are of fragment type "W": Whole Genome Shotgun contig.