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The DNA of eye color: it’s complicated

In high school I learned that blue eyes were a simple recessive gene so two brown-eyed parents could have a blue-eyed child but not vice versa. Recently I discovered that this was wrong. Many genes are involved in eye color and with the subtle variations in eye coloring.

GEDmatch eye color prediction for me

GEDmatch.com eye color prediction for me

So I ran the fun eye color calculator at GEDmatch.com and discovered that it shows many of the SNPs involved in my eye color with the details of what they each do.

I had not realized that blue eyes are caused by the lack of (brown) melanin, so really are no color. Blue happens the same way the color of the sky does: light is bounced around in a way that appears blue according to the wikipedia article on eye color. Maybe that is why my eyes appear greenish when I wear certain green shirts and turquoise when I wear those color shirts.

If the two blue-eyed parents have their lack of eye color melanin caused by different genes then they could have a brown-eyed child. I happen to know a brown-eyed child of green and blue-eyed parents (and she looks just like her Dad so not what you are thinking). This case got me curious about how that could happen. So I googled around and found this wonderful article that explains it: http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children

Here is my attempt to simplify the ghist of that article:

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New features for my tools: color selection and more lines

My tools for showing segments on a chromosome picture now allow you to pick the colors yourself. Here is an example of the ancestor DNA mapper with some very different color choices from the ones the program would use.

Sample Chromosome Map ColorsHow to pick the colors is documented on the page for each tool.

My ancestor mapping tool:
http://blog.kittycooper.com/tools/chromosome-mapper/

My segment mapper, up to 40 relatives
http://blog.kittycooper.com/tools/segment-mapper/

No changes were made to the one chromosome mapper so if you want color choice on that tool as well just let me know.

Another recent enhancement is that the segment mapping tool now allows you to specify as many lines as you like for relatives in your chromosome picture. See an example in my post about four generations of inheritance.

A Web Site with Tools for Y and other DNA analysis

There is a wonderful site at http://www.y-str.org with many good tools for Y DNA and autosomal DNA that run as programs on your PC plus a cool ISOGG Y tree add-on for the Chrome browser. My specific interest at the moment is figuring out which Y SNPs are already tested by 23andme so as not to test them again at FamilyTreeDNA since my Dad has kits at both places. I blogged about how to do that manually back in February, but now there is a program that will do that for you. However it took me a while to figure out how to do what I wanted from the instructions given, so I will do a step-by-step tutorial in this post in order to remember what I did.

BrowseMenuFirst download your raw data from 23andme by going to the “Browse Raw Data” Page which is listed in the menu that appears under your name on the top right. Then on the raw data page click on “Download” in the second top bar on the right hand side. This takes you to a page with various warnings and requires that you reenter your password as well as the answer to your secret question before it starts the download.

Save the download file somewhere that makes sense for you. I have a folder called RawData in the folder DNA that I use. Once the raw data file is downloaded, you will need to unzip it before using it with the various tools. To unzip in windows all you need to do is open a file explorer window (a manila envelope is the icon) and then right click on the file name to get a little menu that includes “extract all” which is the one to click.

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Finding common ancestors with automation: Compare GEDcoms or use a one world tree

It is exciting when you find a new DNA cousin who actually has a family tree. However it can take days to wade through it looking for the common ancestor and more often than not, you do not find it. Sometimes that is because the ancestor is too far back in time. Other times it is on a line that is not documented or is just wrong. Also there can be spelling discrepancies or if you have Norwegians, naming differences (father’s name or farm name used for surname).

You would think that there would be good automated tools to do this and you would be right. These are the ones I know of.

GEDmatchGEdcom

Partial results of a GEDmatch compare one GEDcom to all run

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First version of the DNA Segment Mapper is Released

So many people were trying to use my DNA chromosome mapper tool to look at a picture of their DNA relatives’ matching segments that I realized that another tool was needed to meet that demand. The first version of the new DNA segment mapping tool is ready. More information is at http://blog.kittycooper.com/tools/segment-mapper/

Sample Output from the DNA Segment Mapper

Sample Output from the DNA Segment Mapper

 

The DNA Segment mapper can show the matching DNA from up to 40 people in a chromosome style chart. Here is what my Dad’s top 40 matches look like (names are removed). The first two are first and third cousins once removed.

There is a page under tools above with more complete description and documentation.