Question: How To Convert Centimorgan To Base Pair
4
gravatar for Aurgha
2.1 years ago by
Aurgha40
Aurgha40 wrote:

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

ADD COMMENTlink modified 2.1 years ago by Mdperry40 • written 2.3 years ago by Aurgha40
6
gravatar for Casey Bergman
2.3 years ago by
Casey Bergman14k
Manchester, UK
Casey Bergman14k wrote:

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).

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Casey Bergman14k
5
gravatar for Vitis
2.3 years ago by
Vitis1.3k
New York
Vitis1.3k wrote:

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.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Vitis1.3k
5
gravatar for Pierre Lindenbaum
2.3 years ago by
France
Pierre Lindenbaum58k wrote:

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
ADD COMMENTlink written 2.3 years ago by Pierre Lindenbaum58k
5
gravatar for xenophiliuslovegood
2.3 years ago by
xenophiliuslovegood150 wrote:

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)

ADD COMMENTlink written 2.3 years ago by xenophiliuslovegood150
4
gravatar for Gjain
2.3 years ago by
Gjain3.9k
Worcester, MA
Gjain3.9k wrote:

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

ADD COMMENTlink written 2.3 years ago by Gjain3.9k
4
gravatar for Gustavo
2.3 years ago by
Gustavo480
Seattle
Gustavo480 wrote:

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

--> ftp://ftp.ncbi.nlm.nih.gov/hapmap/recombination/2011-01_phaseII_B37

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?

ADD COMMENTlink written 2.3 years ago by Gustavo480
2
gravatar for Mdperry
2.3 years ago by
Mdperry40
Mdperry40 wrote:

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).

ADD COMMENTlink written 2.3 years ago by Mdperry40
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