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Thread: So 23andMe says I'm J2...

  1. #1
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    So 23andMe says I'm J2...

    Excuse any ignorance, but this means I'm actually just J2? Like the oldest, the root of all the rest?

    Or is their testing just too "coarse" to determine anything further?

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     Star93 (12-13-2015)

  3. #2
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    Not necessarily, 23andme doesn't test you for many Y SNPs, it only give you your basic haplogroup. Take a FullGenomes WGS test or Geno 2.0 next generation or a J2 SNPs Pack Panel at FTDNA. Full Genomes Y Elite 2.0 be the best, WGS also be great, the other two may also give you some idea if the J2 SNPs on your line are included in them.

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     Constantine (12-14-2015)

  5. #3
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    23andMe uses old haplotree (2010 version) and test not so many SNPs. But you can still improve the results by using 3rd party tools, like http://www.y-str.org/2014/04/23andme-to-ysnps.html and http://www.y-str.org/2014/04/isogg-y...le-chrome.html I have an example when original 23andMe "J2" result was improved to J2a1h2a1. Here is the result:

    Red means negatve, green positive.

    Or you can do everything manually, check the current tree at http://www.isogg.org/tree/index.html and test individual SNPs. In the above mentioned case:
    1. Go to http://www.isogg.org/tree/ISOGG_HapgrpJ.html
    2. You can see that J2a1h2a1 means L397 positive
    3. Go to http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html
    4. You can see L397 positive means mutation G->C at SNP rs35182651 or position 22725065 (GRCh37).
    5. Log in to your 23andMe account
    6. Check rs35182651 SNP: https://www.23andme.com/you/explorer...ame=rs35182651
    And you see:


    Besides of the above mentioned tests you can use FTDNA BigY test, it covers less SNPs than FGC Elite, but it is also cheaper.
    Last edited by Petr; 12-13-2015 at 09:08 AM.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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     Cloudstones (02-03-2016),  Constantine (12-14-2015),  Illyro-Vlach (12-13-2015),  paulgill (12-13-2015),  procoptodon (08-22-2016),  psaglav (12-26-2015),  [email protected] (02-28-2017),  Star93 (12-13-2015)

  7. #4
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    Additional information regarding the tests.

    This is the tree of the a.m. J2 person generated using BigY raw data: http://www.yfull.com/share/yreport/7...4903d749096b6/

    So you see that this person's haplogroup was determined as J-PF5456.

    If you would like to get this result by using FTDNA SNP packs, you will have to use 2 of them, at first "J2 - M172 SNP Pack" and then "J2 - M67 & L24 SNP Pack". The first step could be avoided by using the detail analysis of 23andMe results as shown above.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

  8. #5
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    Quote Originally Posted by Petr View Post
    Additional information regarding the tests.

    This is the tree of the a.m. J2 person generated using BigY raw data: http://www.yfull.com/share/yreport/7...4903d749096b6/

    So you see that this person's haplogroup was determined as J-PF5456.

    If you would like to get this result by using FTDNA SNP packs, you will have to use 2 of them, at first "J2 - M172 SNP Pack" and then "J2 - M67 & L24 SNP Pack". The first step could be avoided by using the detail analysis of 23andMe results as shown above.
    For the price of 2 SNP Packs, he can have FullGenomes 2x WGS and that will tale care of his yDNA and mtDNA SNPs. Otherwise after those 2 SNP Packs he will still have to test for further SNPs, a much more expensive alternative. 4x WGS be better though.

  9. #6
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    I think WGS 2x is not very useful for Y SNP determination. I have WGS 10x and the results are very poor, at present I'm waiting for YFull analysis. At present I see just ChrY BAM file size: 0.15 Gb - for FGC Elite it is 2.56 Gb, i.e. 17x more. Mean coverage of Elite is 76x, median 37x. BigY has ChrY BAM size 0.58 Gb with mean coverage 81x and median 54x. ChrY length coverage for BigY is 56 %, for FGC Elite 89 % and for FGC WGS 10x I will see. Expected date: 01/03/2016.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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     lgmayka (12-13-2015)

  11. #7
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    Petr this is fantastic so thank you for laying it out like this. However, how do you explain the following:

    You can see L397 positive means mutation G->C at SNP rs35182651 or position 22725065 (GRCh37).
    To be precise, how do you know that a positive mutation means G->C? I'm a J2B2* as per 23andMe so the first one I tested was rs8179022 which falls under M241 and I got the following:

    DDX3Y 15018459 rs8179022 A or G A

    I don't know whether this means a positive mutation or not.

  12. #8
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    Quote Originally Posted by Illyro-Vlach View Post
    Petr this is fantastic so thank you for laying it out like this. However, how do you explain the following:



    To be precise, how do you know that a positive mutation means G->C? I'm a J2B2* as per 23andMe so the first one I tested was rs8179022 which falls under M241 and I got the following:

    DDX3Y 15018459 rs8179022 A or G A

    I don't know whether this means a positive mutation or not.
    So I take a look at the longest table and note that it mentions G->A which means I got it on the first try.

  13. #9
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    According to 23andMe, I'm J2a1b*.
    I wanted to see if I can go further so I checked for M-92 (rs2032648) T->C. If I'm A or T T, does this mean I'm negative for J2a1b1? I'm sorry but I'm still new to this.

  14. #10
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    23andMe's J2 could be anything that's not reducted in the picture below

     
    Last edited by MfA; 09-05-2016 at 05:32 PM.
    E-M84>FGC18389>FGC18413>FGC18401>FGC18422>Y99171 tMRCA 2550ybp

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