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Thread: How to determine basic Y-DNA haplo from Ancestry.com data

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    Y-DNA haplogroup
    I1 Z63*
    MtDNA haplogroup
    H5b1

    Ethnic group
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    How to determine basic Y-DNA haplo from Ancestry.com data

    Credit to the GeneticGeneologist:

    http://www.geneticgenealogist.net/20...roup-from.html

    The Ancestry.com raw data file (which will be emailed to you after you log in and request it) contains 1691 lines of Y-DNA data.

    1. Open the text file in Excel and edit it to match the 23andMe raw data output. Remove all the language at the top, delete "allele 2" column, rename "allele 1" to "genotype", find and replace all "24" with "Y". You only need the 1691 rows with Y data, not all the rest from the raw data file.

    2. Download and run 23andMe To YSNPs.exe (from link above) which will create a text file of SNP matches. You can manually do it someplace like the ISOGG Y-browser but it would take forever. I recalculated a few to satisfy my curiosity.

    3. Use the Morley Y-DNA Haplogroup predictor (copy/paste the results from the created SNP text file) https://ytree.morleydna.com/

    You get visual trees of positive and negative matches and a "most likely" suggestion. You should be able to see the many green matches in your tree, for example I show many "green" indicators in C, F, IJ, I, and I1. Then one match for I1a3 and red for the other I1a branches. I got a single positive for a "J3a something" but since no branches "above" in the J line are matches, I can ignore it.

    I have sent off my LivingDNA kit so I will compare the results when they arrive. Does anyone have an Ancestry test to compare to another Y-DNA test so we can test the accuracy?

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    Y-DNA haplogroup
    I1 Z63*
    MtDNA haplogroup
    H5b1

    Ethnic group
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    Country: USA - Arkansas



    This is a view of how the results go down the haplogroup chain:
    Attachment 8685

    This is lower so you can see the positive and negatives downstream of I1.
    Morley2.jpg

    Here is false positive J, note the absence of any green above it in the J line.
    Morley3.jpg

    Note that the Morley site uses SNP data from ~2014. This mostly matches the testing locations of the Ancestry test, with at least one exception I found. The SNP location for I - S2078 mutation is in the Ancestry data but doesn't show up on Morley, which should be the most common Z63 downstream mutation.

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    Y-DNA haplogroup
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    I have the ancestry raw DNA data.

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    Y-DNA haplogroup
    I1 Z63*
    MtDNA haplogroup
    H5b1

    Ethnic group
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    Country: USA - Arkansas



    After you have the raw data, follow these illustrations:

    1.Attachment 8698 (open excel, file - open - browse - choose either all files or .txt files to reveal your raw data, and open it)
    2. Attachment 8699 (click finish)
    3. Attachment 8700 (delete rows for the red box area)

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    Y-DNA haplogroup
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    Ethnic group
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    Country: USA - Arkansas



    4. Attachment 8701
    5. Attachment 8702
    6. Attachment 8703 (now save the file)

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    Y-DNA haplogroup
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    Ethnic group
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    Country: USA - Arkansas



    7. Attachment 8704 (this is the SNP program from above)
    8. Attachment 8705 After this, open the .txt file created
    9. Attachment 8706 After "select all" then choose "copy"
    10. Attachment 8707 Morley site https://ytree.morleydna.com/

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    Y-DNA haplogroup
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    What do all those red and green squares/numbers mean
    I don't get this...

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    Showing a lot of green ones in F, then IJK then IJ then I then I1 but no green below I1, m253 isn't green neither is I1a3/Z63. So something ain't right.
    And I got one green in G2, O3a1, R1, R1a and BT, no green I2 or J. With ISOGG no O3a1 but it shows R1b.

    And it says BT "most likely" lol that's gotta be off.

    Yours says I1 most likely right?

    The BT matches:

    BT
    L413/PF1409/V31, L418, L438, L440, L604/PF1243, L957, L962, L969, L970/PF1065, L971, L977, L1060/PF1021, L1061/PF1101, L1062/PF302, M42, M91, M94/PF1081, M139, M299, P97, PK1, PAGE65/SRY1532/SRY10831R, PF1407/V29, PF1411/V59, PF1412/V64, PF1406/V102, V187, PF1403, V202, PF1410/V235

    F to I1

    F L132R, M89/PF2746, M213/P137/PAGE38, M235/PAGE80/PF2665, PF2704/P14, P133, P134, PF2741/P135, PF2762/P136, PF2655/P138, P139, P140, PF2602/P141, P142, PF2617/P145, PF2623/P146, PF2734/P148, P149, PF2625/P151, P157, PF2706/P158, PF2717/P159, PF2618/P160, P161, P163, PF2702/P166, PF2632/P187, P316

    IJK
    M523/L15/PF3492/S137, M522/L16/PF3493/S138, L69/S163


    IJ
    M429/P125, PF3554/P123, PF3553/P124, PF3558/P126, PF3526/P127, P129,
    PF3525/P130/S22, S2

    I
    L41/PF3787, M170/PF3715, M258, P19R, P38, P212, U179


    I1
    L64, L75, L80, L81, L118, L121/S62, L123, L124/S64, L125/S65, L157R, L186, L187, L840, M253, M307/P203R, M450/S109, P30, P40, S63, S66,
    S107, S108, S110, S111
    I1a DF29/S438
    I1a1 Z2326, Z2336/CTS6364
    I1a2 Z58/S244
    I1a3 Z63/S243
    I1b Z131


    The G2
    G2 L79, L142R,L156/PF3002, PF3140/P287

    The R1, R1a

    R1 M173/P241/PAGE29,
    M306/S1, PF6128/P225, P231, PF6142/P233, P234,PF6137/P236,PF6115/P328,PF6113/P242, PF6117/P245, PF6136/P286, P294
    R1a M513/L62/PF6200, M511/L63/PF6203,
    M449/L145/PF6175, M420/L146/PF6229

    The R1b
    R1b1a2a1a1c2b1a1a L45/S353, L164/S502, L237, L477,
    L493

    And when I run it on experimental instead of ISOGG
    The O3a1
    O3a1 F672, F110, CTS5687, CTS11839, CTS11981, CTS1558, CTS2483, CTS3663, CTS4414, CTS5822, CTS5879, CTS7638, F105, F108, F117, F119, F133, F145, F159, F164, F17, F170, F18, F188, F189, F197, F240, F243, F247, F253, F272, F30, F300, F302, F304, F305, F309, F357, F412, F434, F460, F463, F498, F51, F514, F526, F529, F530, F550, F562, F573, F58, F60, F601, F61, F620, F632, F642, F646, F664, F676, F68, F685, F691, F95, F99, L127R,
    L465/KL1, L467/KL2

    All the highlighted green is suppose some kind of match? It's confusing. Probably like you got that J1a3 it's some kind of nonsense.















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    Last edited by Apsurdistan; 17-05-17 at 09:56.

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    Y-DNA haplogroup
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    You mentioned that might be partial results being copy/pasted into Morley. Can you post the Red/Green matches updated with the full results?

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    Yeah I ran it quite a few times made sure I inserted that full text, I just suspected for a moment that I might've done it wrong but that above is the result it gives every time. I'll try to search for that number in excel that you mentioned earlier when I come home from work and can use my laptop.

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    I don't know enough about genetic testing to interpret what this stuff means.
    Can you post your results showing all the green yours has?

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    Y-DNA haplogroup
    I1 Z63*
    MtDNA haplogroup
    H5b1

    Ethnic group
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    Country: USA - Arkansas



    A1: V241, L989, L1002, L1005, L1013, L1053, P305, V168, L986
    BT: M42, M94/PF1081, L440, PK1, PF1407/V29, V187, L413/PF1409/V31, L418, L438, L60/PF1243, L962, L969, L970/PF1065
    CT: M294, M168/PF1416
    CF: P143
    F: F3111, CTS12632, CTS3654, CTS4443, F1209, F1329, F1704, F1714, F1753, F2155, F2402, F2837, F3136, F719, PF2608, PF2624, PF2747, PF2748, V205, L132, M89/PF2746, PF2704/P14 + 16 others
    IJK: M523/L15/PF3492?S137, M522/L16/PF3493/S138
    IJ: F1460, PF3562, PF3554/P123, PF3553/P124, PF3558/P126, PF3526/P127, PF3525/P130/S22, M429/P125, S2
    I: CTS2514, CTS674, PF3807, PF3815, M170/PF3715, M258
    I1: CTS11042, CTS2524, L75, L80, L121/S62, L125/S65, M253, M307/P203, P30, L81, L123, L840, P40, S66 ---- S107, S108, S111
    I1a1: Z2336/CTS6364
    I1a1a: M227
    I1a1a1: M72
    I1a1b: L22/S142
    I1a1b1: P109
    I1a1b4: L300/S241
    I1a1b~1: Z74
    I1a2a: Z59/S246
    I1a2b: Z138/S296, Z139
    I1a3: Z63/S243

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    Quote Originally Posted by Apsurdistan View Post
    Yeah I ran it quite a few times made sure I inserted that full text, I just suspected for a moment that I might've done it wrong but that above is the result it gives every time. I'll try to search for that number in excel that you mentioned earlier when I come home from work and can use my laptop.
    Surely I-M253 should be either green or red! That is something even the old Ancestry tests would show. Now I'm wondering if European-based Ancestry.com tests are different in some way.

    Although about 2% of the tested locations will have a "0" value instead of A, T, C, G. If a defining mutation branch is at a "0" value then no result or a red result will show. On the previous generation Ancestry.com tests, about 6% of the locations had "0" values. They raised their accuracy in the newer version.

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    Yeah my results are quite different than yours and they shouldn't be. They look half-assed and bizarre. I don't live in Europe I live in the States and I just checked to see when I got the ancestry results it was Sept 15, 2015.
    Maybe I could get my Geno2 data and try with that?

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    Quote Originally Posted by Apsurdistan View Post
    Yeah my results are quite different than yours and they shouldn't be. They look half-assed and bizarre. I don't live in Europe I live in the States and I just checked to see when I got the ancestry results it was Sept 15, 2015.
    Maybe I could get my Geno2 data and try with that?
    My father's was done around then and he had the "old" test. His raw data was able to narrow it down to "most likely I-1." My brother's and mine were able to derive the Z63. The old Ancestry test has 885 lines of Y chromosome locations but the new one has 1691. The old one had about a 6% rate of "0" and the new one is only 2%.

    But of the available Ancestry data, it does seem to point to "I1" which is consistent, but not as detailed, as the result from your other test.

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    I tried searching for that number it didn't find it.

  17. #17
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    An easier method is to upload your raw data file to WeGenes and they will tell you after a couple days of processing. Their ethnicity estimate is complete crap though but their yDNA haplo seems correct. This only works with newer Ancestry tests.

    https://www.wegene.com/en/

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    Well it really sucks if my ancestry.com test is so outdated that it's almost useless, it's like I wasted my money. And the Geno 2 test I did the specific one I did the helix dna dAta isnt even available for dowbload. And I'm not paying hundreds of dollars again to do another test, I just don't want to out of principle.
    I'll try to do this wegenes thing you mentioned when I'm not busy.

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    Quote Originally Posted by Apsurdistan View Post
    Well it really sucks if my ancestry.com test is so outdated that it's almost useless, it's like I wasted my money. And the Geno 2 test I did the specific one I did the helix dna dAta isnt even available for dowbload. And I'm not paying hundreds of dollars again to do another test, I just don't want to out of principle.
    I'll try to do this wegenes thing you mentioned when I'm not busy.
    Ancestry.com is all about family tree research, not ancient stuff. That is why they quit giving haplogroup info out.

    Ancestry is run by Mormons who have a belief of praying for the ancestors, so they must find out who they are. Individual people are important to them but theoretical groups of ancient humans are not. Their efforts have been good for preservation of documents in the US. For this reason, Ancestry is a great tool for Americans, and especially Americans of mainly British ancestry.

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