Optical Map Analysis: Deletions

Description

Optical Mapping (OM) is a system that produces ordered restriction maps from individual molecules of genomic DNA. Each single-molecule restriction map (rMap) is a direct measurement of the source genome, free from biases introduced by cloning, amplification, or hybridization. This track complements the 'Optical Map Analysis' track showing consensus maps generated from optical mapping analysis and aligned to the reference genome by displaying the restriction fragments that do not have a corresponding fragments in the reference assembly, implying a possible deletion.

Display Conventions and Configuration

OM produces ordered restriction maps. Each track corresponds to an analysis of OM data from a single cell line. This track presents the locations (according to the analysis) of restriction fragments that have no corresponding fragment in the reference assembly. The location of each fragment or group of fragments is shown as a single vertical bar. The size of the fragment is not represented by the glyph in the browser, but is shown as one of its data fields.

Methods

Optical Mapping. See References section below for further details.

Credits

OM data, analysis and alignments generated by the Schwartz lab, University of Wisconsin and used by the Genome Reference Consortium to improve reference assemblies. Contact us via genomereference.org or by emailing grc-help@sanger.ac.uk.

References

• High-resolution human genome structure by single-molecule analysis. (2010) PNAS 107(24):10848-53.
• Lineage-specific biology revealed by a finished genome assembly of the mouse. (2009) PLos Biol 7(5):e1000112.
• Modernizing Reference Genome Assemblies. (2011) PLoS Biol 9(7): e1001091.