deCODE genetics

With: Kong, A et al. Fine scale recombination rate differences between sexes, populations and individuals. Nature (28 October 2010).
(http://www.nature.com/nature/journal/v467/n7319/full/nature09525.html)
 

Six genetic maps and nine standarized recombination maps are provided in this zip. The carrier and noncarrier nomenclature refer to carriers and noncarriers of the composite PRDM9 14/15 repeat allele. Research using any of these fifteen maps should cite:  Kong, A et al.  Fine scale recombination rate differences between sexes, populations and individuals. Nature  467 , 1099–1103 (28 October 2010) doi:10.1038/nature09525.

Genetic maps: 

female.gmap
female_noncarrier.gmap
female_carrier.gmap
male.gmap
male_noncarrier.gmap
male_carrier.gmap

Standardized recombination maps: 

female.rmap
female_noncarrier.rmap
female_carrier.rmap
male.rmap
male_noncarrier.rmap
male_carrier.rmap
sex-averaged.rmap
sex-averaged_noncarrier.rmap
sex-averaged_carrier.rmap


 

Genetic Maps

Female (female.gmap, female_noncarrier.gmap, female_carrier.gmap) and male (male.gmap,male_noncarrier.gmap, male_carrier.gmap) genetic maps are provided.  Note that female maps also contain genetic distances for the X chromosome.

Each file has a column header:

chr – chromosome
snp – SNP
pos – base position of SNP in Build 36 coordinates
cM  – the estimated centiMorgan distance between this and the previous SNP (rounded to six decimal digits)
Although all of the SNPs used to construct the maps are listed, for each chromosome genetic distances are only estimated up to 2.5 Mb from the ends of the SNP coverage. SNPs in the end regions have their cM entries listed as NA.

 

Standardized Recombination Maps

Female (female.rmap, female_noncarrier.rmap, female_carrier.rmap), male (male.rmap, male_noncarrier.rmap, male_carrier.rmap) and sex-averaged (sex-averaged.rmap, sex-averaged_noncarrier.rmap, sex-averaged_carrier.rmap) standardized recombination maps are provided for the autosomes. The sex-averaged maps are the standardization of the average of the male and female maps.

Each file has a column header:

chr – chromosome
pos – base position of the 10 kb bin midpoint in Build 36 coordinates
seqbin – 1 if the bin contains no unsequenced regions; 0 otherwise
stdrate – standardized recombination rate for the bin (standardization is done with respect to the bins that contain no unsequenced regions – thus, although all bins have a standarized rate, the average rate is one for the 244,446 bins with no unsequenced regions) (rates are rounded to six decimal digits)
Regions less than 5 Mb from the ends of the SNP coverage are not included.