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

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 Sex Avg  deCODE recombination map, sex-average   Schema 
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 Sex Avg Carry  deCODE recombination map, sex-average carrier   Schema 
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 Sex Avg Non-carry  deCODE recombination map, sex-average non-carrier   Schema 
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 Female  deCODE recombination map, female   Schema 
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 Female Carry  deCODE recombination map, female carrier   Schema 
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 Female Non-carry  deCODE recombination map, female non-carrier   Schema 
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 Male  deCODE recombination map, male   Schema 
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 Male Carry  deCODE recombination map, male carrier   Schema 
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 Male Non-carry  deCODE recombination map, male non-carrier   Schema 
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 Sex Difference  deCODE recombination map, male minus female difference   Schema 
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 Hot Spot Male  deCODE recombination map, male >= 10.0   Schema 
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 Hot Spot Female  deCODE recombination map, female >= 10.0   Schema 
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 HapMap  HapMap Release 24 combined recombination map   Schema 
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 HapMap CEU  HapMap Release 24 CEU recombination map   Schema 
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 HapMap YRI  HapMap Release 24 YRI recombination map   Schema 
    

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