Why RQTL calculates some gaps to be 1000 cM apart?

[Prashant Waiker]

Hello Dr. Broman,

Just a general question: Should not maximum gap be 50 cM (corresponding to max recombination fractions of 0.5 between any marker pair?) then why do I see some lengths to be unreasonably large like 1001.1 cM. Maybe some markers need to be phase flipped to being it close but should not the maximum gap be 50 cM (or whatever RF criteria we input)?

Thanks,

Prashant

[Karl Broman]

Genetic distance in cM is the average number of crossovers in 100 meiotic products. It’s not limited to 50 cM, except in the case of complete crossover interference (that there can be no more than one crossover). For many organisms, chromosomes are generally > 50 cM long. 

Recombination fraction is the chance of an odd number of crossovers in an interval. Except for the Morgan map function (which assumes complete crossover interference), rf=0.5 corresponds to d=infinity. Consider, for example, the inverse of the Haldane map function, d = -50 ln(1-2r).For r=0.49, you get 196 cM.

karl

[Prashant Waiker]

Makes sense. Thank you so much for clarifying according to map function. But in what cases it can go up to 1000 cM?

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[Karl Broman]

As the recombination fraction gets closer to 0.5, the genetic length will get larger and larger.

For the Haldane map function with d in cM,  rf = [1 - exp(-d/50)]/2

karl

[Prashant Waiker]

Makes sense. But why would RQTL group them at first place if max.rf is let's say 0.40? Just trying to understand my results that i got at max RF =0.4 and minLOD of 3.

Thank you so much for all your time and help.

Prashant

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[Karl Broman]

Not all pairs of markers within a linkage group will necessarily be linked with rf < 0.4.

karl

[Prashant Waiker]

Got it, that explains the results. Thank you so much!

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Prashant Waiker

Ph.D. Candidate, Department of Biology,

The University of North Carolina at Greensboro,

321 McIver St, Greensboro, NC 27402-6170