Question: Why lack of SNPs within a window of 3.06 million bp (58887738 - 61949597) in chromosome 6?
0
gravatar for jiumeng66
5 weeks ago by
jiumeng6630
jiumeng6630 wrote:

I am doing GWAS, and I found that there are no SNPs within a window of 3.06 million bp (58887738 - 61949597, for example, in HapMap3) in chromosome 6, in almost all dataset, including 1000 genome and Hapmap3 (as shown in the attached figure), and of course in my own datasets. Could someone tell me why?

Here is the figure

SNP distribution of chr6 of Hapmap3

snp • 212 views
ADD COMMENTlink modified 5 weeks ago by greeshmathulasi10 • written 5 weeks ago by jiumeng6630

Hi jiumeng66, Would you please mind to let me know how did you plot this ?

ADD REPLYlink written 5 weeks ago by greeshmathulasi10
0
gravatar for h.mon
5 weeks ago by
h.mon13k
Brazil
h.mon13k wrote:

Did you check the position of the centromere? Can you plot its position along the SNPs?

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by h.mon13k

Yes, I have checked just now. This is the region of centromere. Thank you very much.

ADD REPLYlink written 5 weeks ago by jiumeng6630
0
gravatar for jiumeng66
5 weeks ago by
jiumeng6630
jiumeng6630 wrote:

I have checked the chr7. There are also no SNPs in the region of centromere. It looks that the centromere regions of all chromosomes have no SNPs. It's an interesting phenomenon for me.

ADD COMMENTlink written 5 weeks ago by jiumeng6630

It is not so surprising once you know human centromeres are comprised of repetitive DNA (alphoid sequences).

ADD REPLYlink written 5 weeks ago by h.mon13k

The hg19 reference genome has placeholder N bases for all centromeres. There is plenty of variation there but your sequencing technology and tools are unable to detect them.

ADD REPLYlink written 5 weeks ago by d-cameron1.5k
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