Question: Genetic Map file format: how to understand the combined_rate column and the genetic_map column ?
2
Tao300 wrote:

Hi guys,

The genotype imputation need human genetic map file, whose format is like(in chr1):

``````position COMBINED_rate(cM/Mb) Genetic_Map(cM)
55550 0 0
568322 0 0
568527 0 0
721290 2.685807669 0.410292036939447
723819 2.8222713027 0.417429561063975
723891 2.9813105581 0.417644215424158
728242 2.9806151254 0.430612871834774
729948 3.0780969498 0.435864105231133
740857 3.075133293 0.46941073432447
``````

There are 3 columns, the first column is physical position united in bp, which is easy to understand. The second and third column is recombination rate(cM/Mb) and genetic position(cM, centiMorgan). I'm confused about the values in column 2 and 3.

Let's take the 4th row as an example. I know 721290 means the 721290th position on chr1. So what's the 2.68 and 0.41 represent for? I looked up some webpages and learned that "A centiMorgan is a unit of genetic distance that represents a 1% probability of recombination during meiosis." But I still cannot figure out the what's the meaning of 0.41/2.68 at position 721290.

Can anyone explain it to me? Thanks!

Tao

centimorgan genetic map • 2.2k views
modified 2.6 years ago by archimyed20 • written 2.7 years ago by Tao300
2
archimyed20 wrote:

Hi, Tao.

Let's take the 4th row as an example. 1. 721290 means the 721290th position on chr1 and also means 0.721290 Mb.

1. To find 2nd column you need not numbers from 1st and 3d columns, but results of the subtractions: in the 4th row, it will be (0.41...-0)/(0.721290-0.568527) which gives us 2.685807669. So, in each row in column 1 and 3 you need to subtract numbers from the previous one to find the number from column 2.