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LostSlough
06-13-2018, 01:18 AM
My apologies if this has already been posted; I didn't see anything on a quick glance or through the forum search.

Is it possible to use AncestryDNA raw data on James Lick's site to get an mtDNA estimate? I keep getting an error when I try, and it's not on his list of supported sites.

I know that mtDNA from Ancestry results isn't necessarily accurate, I'm just curious to see if somewhere else gets the same as WeGene did, and to see if it's different when I get my 23&Me test.

PoxVoldius
06-13-2018, 01:25 AM
I kinda doubt it. My Ancestry DNA kit had so few SNPs relevant to my mtDNA haplogroup that Wegene was pretty much only able to designate it as human (L1'2'3'4'5'6), lol. But it might just depend on what your haplogroup is. I think Ancestry DNA's chosen mtDNA SNPs are more relevant for some haplogroups than others.

I'm seriously considering trying 23andMe while their kits are on sale. ;)

flower
06-13-2018, 01:30 AM
I had to download a file I uploaded from Ancestey to FTDNA to get it to work. I have no idea how accurate it is. Supposedly Ancestry doesn't test mtDNA. James Lick gives H2a2a1 for me, my mom, and my husband. WeGene gives me C2a2 which isn't at all correct. This is because my Ancestry file only contains a few things it could identify, one being 3010 which is also a J1 and H2 marker. WeGene gives my mom J1 and shows a path to it with the alleged markers she has. But yep, upload your file to FTDNA if you haven't already, and download the 36 or 37 build file to upload to James Lick.

LostSlough
06-13-2018, 01:37 AM
Thank you both! I got C1c2 at WeGene, which isn't impossible, since I haven't been able to trace my maternal line back very far, but seems pretty unlikely. At least I know if FTDNA is way different, then I should just wait until I can afford 23&Me. (I hope they have another sale in the fall, I didn't scrape enough together for this one.)

flower
06-13-2018, 01:45 AM
Whoops, C1c2 is what WeGene gave me lol. Click on the "View Maternal Haplogroup Beta" link. It'll show you the terminal snp it used. See if there's a path to it. If there's no path and it shows 3010, I bet you're an H or J. I wish I had money to throw at an mtDNA test. I'm hoping something goes on sale soon besides 23andMe so I can do it.

PoxVoldius
06-13-2018, 02:01 AM
If I use the file that DNA.Land converted to 23andMe format from the original Ancestry DNA file, it comes out saying "Found 121 markers at 121 positions covering 0.7% of mtDNA." And all but one of the top matches it found for me based on that could only match up one defining marker each. It says I could be H55a, or H13a2b4, or H86, or H2a2a1 (which it is somehow calling a "good match" despite not being able to match up any defining markers at all!), or H26c.

LostSlough
06-13-2018, 02:03 AM
I got a path with a bunch of thingies on it (that's the technical term, right? :D ), but the only one that's highlighted is 3010. If I hover on CZ or C or etc. there are numbers, but none are blue. J or H both seem more likely, since most of my mother's ancestors are German, and only slightly fewer are English.

https://imgur.com/a/YpJCTqL

PoxVoldius
06-13-2018, 02:06 AM
Whoops, C1c2 is what WeGene gave me lol. Click on the "View Maternal Haplogroup Beta" link. It'll show you the terminal snp it used. See if there's a path to it. If there's no path and it shows 3010, I bet you're an H or J. I wish I had money to throw at an mtDNA test. I'm hoping something goes on sale soon besides 23andMe so I can do it.

I clicked on that and hovered over the node, and it's showing SNPs that Ancestry DNA didn't even test. Like ones that don't even show up in the raw data file from Ancestry DNA.

23916

flower
06-13-2018, 02:13 AM
I clicked on that and hovered over the node, and it's showing SNPs that Ancestry DNA didn't even test. Like ones that don't even show up in the raw data file from Ancestry DNA.

How do you find out which ones they tested? I ended up downloading Promeathese and let it run for the agonizing 16+ hours twice to check me and my mom. I googled every rs under the maternal category and found both H and J markers for myself. None of what was listed for my mom matched her WeGene though. I wish it were easy like it was with my husband. He's a very blatant y haplogroup G lol.

PoxVoldius
06-13-2018, 02:18 AM
How do you find out which ones they tested? I ended up downloading Promeathese and let it run for the agonizing 16+ hours twice to check me and my mom. I googled every rs under the maternal category and found both H and J markers for myself. None of what was listed for my mom matched her WeGene though. I wish it were easy like it was with my husband. He's a very blatant y haplogroup G lol.

Unzip the raw data file and open it as a .txt file -- the mtDNA SNPs are marked as "chromosome 26". They didn't test anything at all from either HVR1 or HVR2.

LostSlough
06-13-2018, 02:29 AM
How do you convert with DNA.Land?

PoxVoldius
06-13-2018, 02:43 AM
How do you convert with DNA.Land?

You upload your Ancestry DNA raw data file to DNA.Land, they convert it to 23andMe format as part of their usual process, and once they're done they allow you to download the converted file.

LostSlough
06-13-2018, 02:51 AM
You upload your Ancestry DNA raw data file to DNA.Land, they convert it to 23andMe format as part of their usual process, and once they're done they allow you to download the converted file.

Thanks! Got it.

PoxVoldius
06-13-2018, 02:58 AM
DNA.Land will also give you their own free analysis of your genetic ancestry, and give you the chance to allow your data to be used for scientific/medical research.

LostSlough
06-13-2018, 02:58 AM
Alright, so James Lick's site gives a few options, all from H. So I'm guessing WeGene isn't accurate on their mtDNA guesses with Ancestry. :D

Guess I'll wait and see what 23&Me shows when I can buy that one.

flower
06-13-2018, 02:59 AM
Unzip the raw data file and open it as a .txt file -- the mtDNA SNPs are marked as "chromosome 26". They didn't test anything at all from either HVR1 or HVR2.

When I put "chromosome" in the find of my Ancestry text file it doesn't return any matches other than in the preamble.

Edit: nevermind, I'm dumb. I scrolled to the bottom and found them lol. I copied them all into a new text file.

LostSlough
06-13-2018, 03:03 AM
When I put "chromosome" in the find of my Ancestry text file it doesn't return any matches other than in the preamble.

It was easiest for me to scroll to the bottom, then work up. It's the second column (after the rsid).

PoxVoldius
06-13-2018, 03:07 AM
When I put "chromosome" in the find of my Ancestry text file it doesn't return any matches other than in the preamble.

The headers don't really show in the right places in the .txt file.

It's in columns: 1st column is the rsid # for the SNP, 2nd column is the chromosome #, 3rd column is the position (which can be cross-referenced on the mtDNA tree at PhyloTree), 4th & 5th columns are which alleles they found (which for the mtDNA, they just list the same one twice because there's only the one to find).

flower
06-13-2018, 03:37 AM
The headers don't really show in the right places in the .txt file.

It's in columns: 1st column is the rsid # for the SNP, 2nd column is the chromosome #, 3rd column is the position (which can be cross-referenced on the mtDNA tree at PhyloTree), 4th & 5th columns are which alleles they found (which for the mtDNA, they just list the same one twice because there's only the one to find).

I figured it out right after I posted lol. I noticed the positions are the same exact ones WeGene found.


Alright, so James Lick's site gives a few options, all from H. So I'm guessing WeGene isn't accurate on their mtDNA guesses with Ancestry.

I don't know what to make of James Lick and whether or not it has enough data to work with from Ancestry files. On the other hand, of my phased maternal matches on Gedmatch, many are various H's. Lots of H1 and H5 but I don't really see any H2 which is what James Lick thinks I am.

LostSlough
06-13-2018, 08:48 PM
I don't know what to make of James Lick and whether or not it has enough data to work with from Ancestry files. On the other hand, of my phased maternal matches on Gedmatch, many are various H's. Lots of H1 and H5 but I don't really see any H2 which is what James Lick thinks I am.

My assumption is that if they're both wildly different, there's not enough information in the Ancestry raw data and there's no point in trying to figure it out before I do either 23&Me or FTDNA. 23&Me seems to have less overlap with Ancestry, so that's what I'm working on right now.

ArmandoR1b
06-14-2018, 02:20 AM
I figured it out right after I posted lol. I noticed the positions are the same exact ones WeGene found.



I don't know what to make of James Lick and whether or not it has enough data to work with from Ancestry files. On the other hand, of my phased maternal matches on Gedmatch, many are various H's. Lots of H1 and H5 but I don't really see any H2 which is what James Lick thinks I am.

Are you willing to post screenshots of your results on the James Lick site? There is a color coding that can be helpful. IIRC, the untested SNPs are in gray and the negative SNPs are in red and positive are in blue.