Schema for Recomb Rate - Recombination Rate from deCODE, Marshfield, or Genethon Maps (deCODE default)
  Database: hg19    Primary Table: recombRate    Row Count: 2,830   Data last updated: 2010-10-14
Format description: Describes the recombination rate in 1Mb intervals based on deCODE map
fieldexampleSQL type info description
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned range Start position in genoSeq
chromEnd 1000000int(10) unsigned range End position in genoSeq
name recombRatevarchar(255) values Constant string recombRate
decodeAvg 1.11575float range Calculated deCODE recombination rate
decodeFemale 1.24407float range Calculated deCODE female recombination rate
decodeMale 0.987441float range Calculated deCODE male recombination rate
marshfieldAvg 0float range Calculated Marshfield recombination rate
marshfieldFemale 0float range Calculated Marshfield female recombination rate
marshfieldMale 0float range Calculated Marshfield male recombination rate
genethonAvg 0float range Calculated Genethon recombination rate
genethonFemale 0float range Calculated Genethon female recombination rate
genethonMale 0float range Calculated Genethon male recombination rate

Sample Rows
 
chromchromStartchromEndnamedecodeAvgdecodeFemaledecodeMalemarshfieldAvgmarshfieldFemalemarshfieldMalegenethonAvggenethonFemalegenethonMale
chr101000000recombRate1.115751.244070.987441000000
chr110000002000000recombRate1.115751.244070.987441000000
chr120000003000000recombRate1.115751.244070.9874412.512232.655112.107413.690953.39333.75048
chr130000004000000recombRate1.807071.682621.931523.907183.201494.601064.836714.111835.44722
chr140000005000000recombRate2.507082.883572.130584.360595.34343.501534.701086.14893.55632
chr150000006000000recombRate2.279711.334283.215951.091.11.090.9712591.045971.04597
chr160000007000000recombRate2.130542.722441.542932.285373.271.318632.264013.20.966426
chr170000008000000recombRate1.690542.512570.8787682.064632.21.931372.681753.681492.88936
chr180000009000000recombRate1.219221.402841.033394.391.537756.492.664483.774684.21876
chr1900000010000000recombRate1.7012.819470.57337600.69224702.227321.572262.35111

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

Recomb Rate (recombRate) Track Description
 

Description

The recombination rate track represents calculated sex-averaged rates of recombination based on either the deCODE, Marshfield, or Genethon genetic maps. By default, the deCODE map rates are displayed. Female- and male-specific recombination rates, as well as rates from the Marshfield and Genethon maps, can also be displayed by choosing the appropriate filter option on the track description page.

Methods

The deCODE genetic map was created at deCODE Genetics and is based on 5,136 microsatellite markers for 146 families with a total of 1,257 meiotic events. For more information on this map, see Kong, et al., 2002.

The Marshfield genetic map was created at the Center for Medical Genetics and is based on 8,325 short tandem repeat polymorphisms (STRPs) for 8 CEPH families consisting of 134 individuals with 186 meioses. For more information on this map, see Broman et al., 1998.

The Genethon genetic map was created at Genethon and is based on 5,264 microsatellites for 8 CEPH families consisting of 134 individuals with 186 meioses. For more information on this map, see Dib et al., 1996.

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 1 Mb window is the average recombination rate of the bases contained within the window.

Using the Filter

This track has a filter that can be used to change the map or gender-specific rate displayed. The filter is located at the top of the track description page, which is accessed via the small button to the left of the track's graphical display or through the link on the track's control menu. To view a particular map or gender-specific rate, select the corresponding option from the "Map Distances" pulldown list. By default, the browser displays the deCODE sex-averaged distances.

When you have finished configuring the filter, click the Submit button.

Credits

This track was produced at UCSC using data that are freely available for the Genethon, Marshfield, and deCODE genetic maps (see above links). Thanks to all who played a part in the creation of these maps.

References

Broman KW, Murray JC, Sheffield VC, White RL, Weber JL. Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet. 1998 Sep;63(3):861-9. PMID: 9718341; PMC: PMC1377399

Dib C, Fauré S, Fizames C, Samson D, Drouot N, Vignal A, Millasseau P, Marc S, Hazan J, Seboun E et al. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 1996 Mar 14;380(6570):152-4. PMID: 8600387

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