Gap Track Settings
 
Gap Locations   (All Mapping and Sequencing tracks)

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Data last updated at UCSC: 2005-08-08

Description

This track shows the position of gaps — represented by Ns — within the C. intestinalis assembly. Gaps of 50 or more bases were most likely introduced by the JGI JAZZ assembler.

For a discussion of gaps and the JAZZ assembler see Dehal, P. et al. (2002) in the References section below.

Display Conventions and Configuration

Gaps are represented by boxes. If the relative order and orientation of the contigs on either side of the gap is known from mRNA, ESTs, or paired BAC end reads, it is a bridged gap, indicated by a white line drawn through the box. The display must be sufficiently zoomed in to view this feature. In full display mode, the item label indicates the type of gap and whether the gap is bridged.

References

Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002 Dec 13;298(5601):2157-67. PMID: 12481130