How To Convert Centimorgan To Base Pair
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9.3 years ago
Aurgha ▴ 90

I want to know is there any webtool that can convery centimorgan to base pair

genetics distance • 35k views
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9.3 years ago

There is no fixed relationship between physcial and genetic distance, so as @vitis points out you need to use empirical estimates from your species/population. If you have this data from markers you can generate a MareyMap to interpolate the relationship between genetic and physical maps (see also this paper).

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Vitis ★ 2.4k

Linkage distances (centimorgans) have to be estimated from the populations your study (i. e. counting the recombinants), while physical distances can be identified by mapping your markers back to the genome, if you're lucky enough to have the reference and markers.

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have a look at the ucsc table stsMap. For some markers it contains both the positions in cM and in pb. You could use those values to make the conversions.

#chromchromStartchromEndnamescoreidentNoctgAccotherAccgenethonChromgenethonPosmarshfieldChrommarshfieldPosgm99Gb4Chromgm99Gb4PosshgcTngChromshgcTngPosshgcG3ChromshgcG3PoswiYacChromwiYacPoswiRhChromwiRhPosfishChrombeginBandendBandlabdecodeChromdecodePos
chr135848613585185AFM280WE510002AL136528.11-chr16.2chr14.2200000000000000chr14
chr144584014458794AFM344WE910003AL591916.8-chr111.1chr18.8500000000000000chr16.43
chr145916464591869AFM123XC310004Z98747.1-chr112.8chr110.78chr121.19chr12499chr112400000000chr16.43
chr148046234805011AFMA203YC110005AL023586.1-chr112.9chr110.7800000000000000chr17.09
chr155765055576824AFMB355ZH510007Z97988.1-chr114.2chr111.87chr123.8900chr11470000000000
chr160773796077732AFMA131YA510006AL035406.25-chr114.2chr111.8700000000000000chr110.11
chr162896036290000AFMA052WG1100010AL031847.17-chr116.4chr114.04chr123.8900chr120200000000chr111.37
chr163594346359798AFM254WB9100012AL031847.17-chr116.4chr114.59chr123.89000000chr123.6000000

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Gustavo ▴ 530

If you need coordinates for the current human reference, you could get the HapMap data set from:

There's one file per chromosome there, listing the chromosomal bp positions for many cM coordinates. The map is dense - for example chr1 lists 256895 positions.

What exactly are you trying to achieve?

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I don't know what the OP was trying to achieve, but I found this thread because I'm looking for a relationship chart like this: http://www.isogg.org/wiki/File:Shared-cM-Project-Image-2.png only using 23&me's Mb/Gb values instead of cM. Using an Average Mb/Gb value and then a range. When comparing my own DNA with others I'm sharing with 23&me does the work for me to predict our relationship, but 23&me allows me to compare DNAs of people sharing with me, but not any predicted relationship between them.

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9.3 years ago

Hi,

there is no fixed ratio between a distance given in cM and a distance in bp: it varies according to chromosomes, organism, sex, etc...

If you need a number for a back-of-the-envelope estimation possibly you can use table 1 in this paper:

http://www.nature.com/nature/journal/v409/n6822/fig_tab/409951a0_T1.html

which gives you (sex-average on human genome) 1.30 cM/Mb (plus or minus 0.80 cM/Mb)

A fine scale analysis seems to be contained here :

http://www.cmb.usc.edu/people/petercal/summer2007/myers.pdf

(although I haven't read the paper myself)

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Gjain 5.6k

you can use this tool http://cgd.jax.org/mousemapconverter/

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Mdperry ▴ 40

This number varies along each eukaryotic chromosome because the meiotic recombination rate can vary along each chromosome (see, for example Barnes at al., Genetics, 1995; for an early analysis comparing genetic map distances in cM to the C. elegans physical map in bp). So there is no simple "conversion" between the two. The previous posts describe the correct approach to calculate the Marey Map (which is what you want).