Schema for deCODE Recomb - deCODE Recombination maps, 10Kb bin size, October 2010
  Database: hg19    Primary Table: decodeHotSpotFemale    Row Count: 4,135   Data last updated: 2011-08-18
Format description: Browser extensible data
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 633smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 6323082int(10) unsigned range Start position in chromosome
chromEnd 6333082int(10) unsigned range End position in chromosome
name 12.227070varchar(255) values Name of item

Sample Rows
 
binchromchromStartchromEndname
633chr16323082633308212.227070
640chr17243082725308211.246608
640chr17253082726308215.171466
640chr17263082727308213.944834
642chr17483082749308220.624972
642chr17503082751308219.700005
643chr17603082761308223.188264
647chr18193082820308211.766735
654chr19063082907308225.478903
657chr19503082951308210.095977

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

deCODE Recomb (decodeRmap) Track Description
 

Description

The deCODE recombination rate track represents calculated rates of recombination based on the deCODE recombination maps in 10 Kb bins from October 2010. Sex averaged-, female- and male-specific recombination rates can be displayed by choosing the appropriate options on the track visibility controls.

Corresponding to each of these tracks are separate tracks for carriers and non-carriers of the PRDM9 14/15 composite allele which can be displayed as well. There are also tracks depicting the difference between male and female recombination rates, and a track showing recombination hotspots (i.e., bins with standardized recombination rates higher than 10).

In addition to the deCODE display, three data tracks from the HapMap project are included. CEU, YRI and combined maps from release #24 can be turned on with the track visibility controls.

Methods

The deCODE genetic map was created at deCODE Genetics and is based on 289,658 and 8,411 SNPs on the autosomal and X chromosomes, respectively, for 15,257 parent-offspring pairs. For more information on this map, see Kong, et al., 2010.

Each base is assigned the recombination rate calculated by assuming a linear genetic distance across the immediately flanking genetic markers. The recombination rate assigned to each 10 Kb window is the average recombination rate of the bases contained within the window. The recombination rates are standardized, bringing the average to 1 for all bins used for the standardization.

Credits

This track was produced at UCSC using data that are freely available for the deCODE genetic maps. Thanks to all who played a part in the creation of these maps.

References

Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G et al. A high-resolution recombination map of the human genome. Nat Genet. 2002 Jul;31(3):241-7. PMID: 12053178

Kong A, Thorleifsson G, Gudbjartsson DF, Masson G, Sigurdsson A, Jonasdottir A, Walters GB, Jonasdottir A, Gylfason A, Kristinsson KT et al. Fine-scale recombination rate differences between sexes, populations and individuals. Nature. 2010 Oct 28;467(7319):1099-103. PMID: 20981099