deCODE Recomb Track Settings

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deCODE Recombination maps, 10Kb bin size, October 2010 (All Mapping and Sequencing tracks)

Maximum display mode: Reset to defaults

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Male ▾

Female ▾

Sex Average ▾

Sex Difference ▾

Hot Spots

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List subtracks: only selected/visible all ()
	hide Configure	Sex Avg	deCODE recombination map, sex-average	Data format
	hide Configure	Sex Avg Carry	deCODE recombination map, sex-average carrier	Data format
	hide Configure	Sex Avg Non-carry	deCODE recombination map, sex-average non-carrier	Data format
	hide Configure	Female	deCODE recombination map, female	Data format
	hide Configure	Female Carry	deCODE recombination map, female carrier	Data format
	hide Configure	Female Non-carry	deCODE recombination map, female non-carrier	Data format
	hide Configure	Male	deCODE recombination map, male	Data format
	hide Configure	Male Carry	deCODE recombination map, male carrier	Data format
	hide Configure	Male Non-carry	deCODE recombination map, male non-carrier	Data format
	hide	Sex Difference	deCODE recombination map, male minus female difference	Data format
	hide	Hot Spot Male	deCODE recombination map, male >= 10.0	Data format
	hide	Hot Spot Female	deCODE recombination map, female >= 10.0	Data format
	hide Configure	HapMap	HapMap Release 24 combined recombination map	Data format
	hide Configure	HapMap CEU	HapMap Release 24 CEU recombination map	Data format
	hide Configure	HapMap YRI	HapMap Release 24 YRI recombination map	Data format

Assembly: Human Feb. 2009 (GRCh37/hg19)
Data coordinates converted via liftOver from: Mar. 2006 (NCBI36/hg18)

Note: lifted from hg18

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