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Thread: How do companies determine your y haplogroup and how many results do you need?

  1. #11
    [QUOTE=eastara;213641]Are you female and worried you have Y chromosome results?
    I think this was noticed before - the so called chip (microarray ) technology is using plates with coded SNPs to compare to your own. However, those plates got reused up to 20 times, I think. They are cleaned somehow before that, but it is not excluded some DNA from the previous tested may have remained. There is a higher risk if the previous tested was a male and the next female, and you

    [QUOTE=deadly77;213854]Big Y and WGS (whole genome sequencing) are examples of Next Generation Sequencing (NGS). Full Genomes Corporation and YSEQ are two companies that offer whole genome sequencing, and there are some NG

    Quote Originally Posted by ArmandoR1b View Post
    Nevermind. I had missed the intersex condition you mentioned in the initial post. The part below caused me to reread it. In that situation there is no reason to even care what they are.
    Why not? I still want to know my y haplogroup? I'm my only option to find out as my father is dead. And I don't even know any uncles with the same father as my dad's. And my grandfather wouldn't do it. I don't even know him well we occasionally talk on Facebook.

  2. #12
    Quote Originally Posted by eastara View Post
    Are you female and worried results.[/QUOTE data. In comparison, as ArmandoR1b pointed out, the tests from places like 23andme and Ancestry are lower resolution, less extensive tests on a limited number of SNPs based on the chip they use for analysis. I don't think Ancestry offers Y-DNA anymore.

    How do I get more extensive tests? And I had ancestrydna v2. I know because I had several 0's 1600 options and 125 results out of all of that. I looked up two and they were haplogroup or related to that. Then the first two were sex reversal genes. Which men nor women should have for that matter. I'll post my y data here.

  3. #13
    I get isogg whenever I google my results from my y chromosome.
























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    rs9786160242881744200
    rs9786224242881745800


    I have a lot missing but I have 125 that exists altogether.


    What is isogg. Its hard for my desktop to load on that website.

  4. #14
    Quote Originally Posted by Ann Turner View Post
    I don't believe your results indicate an intersex condition. I have seen some Y SNP results for every female where I've had occasion to look at the raw data from AncestryDNA. The probes can pick up similar sequences on other chromosomes, especially the X. AncestryDNA is not using those SNPs for anything, and I suspect they haven't gone to the trouble of curating the Y SNPs to be sure they are exclusive to the Y.
    rs104894968 24 2655442 A A

    rs104894959 24 2655375 G G

    http://www.malacards.org/card/46xy_sex_reversal_1

    These are the first results I found on my y ancestrydna data.

    It is connected to the genes on the website that causes sex reversal genes in xy people. To have these genes I have to have a y. As what else is it reversing? Lol. Women with xx don't have sex reversal genes. So you couldn't find it on the x chromosome and accidentally place it elsewhere. Also usually women only have a few results. Like 20 results. Not 125 results. I actually have a little more than 125 results tbh.
    Last edited by jaderose22; 02-12-2017 at 07:09 AM.

  5. #15
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    Quote Originally Posted by jaderose22 View Post
    Why not? I still want to know my y haplogroup? I'm my only option to find out as my father is dead. And I don't even know any uncles with the same father as my dad's. And my grandfather wouldn't do it. I don't even know him well we occasionally talk on Facebook.
    I'm sorry to hear about your situation but you don't have a Y haplogroup. You are positive for only two Y-DNA SNPs. They are V63 in the A1a haplogroup and P40 in the I1 haplogroup. Those are false positives since they are also positive in the Y-DNA results of a male that doesn't belong to those haplogroups. Everything else is negative or a no-call.

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  7. #16
    Quote Originally Posted by ArmandoR1b View Post
    I'm sorry to hear about your situation but you don't have a Y haplogroup. You are positive for only two Y-DNA SNPs. They are V63 in the A1a haplogroup and P40 in the I1 haplogroup. Those are false positives since they are also positive in the Y-DNA results of a male that doesn't belong to those haplogroups. Everything else is negative or a no-call.
    What do you mean I have 125 results in SNPs. Not just 2. Many I think aren't haplogroups though. I did find about 2? I think in haplogroups. I have finish heritage so the I one actually seems to have some truth as ancestrydna said I was part finish. On a very small level too. I thought maybe that's what it was gathering it from.

    Does negative mean the gene belong to no haplogroup?

    And how would you know if someone belongs or doesn't belong to a specific haplogroup?

  8. #17
    rs104894959242655375GG
    rs104894968242655442AA








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    rs13304191248727033GG
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    rs9943032248755304GG
    rs28882502249411719AA
    ever I google



    rs97860402416499878GG
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    Last edited by jaderose22; 02-12-2017 at 08:49 AM.

  9. #18
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    Quote Originally Posted by jaderose22 View Post
    What do you mean I have 125 results in SNPs. Not just 2.
    You have 129 results with a call but males have 1686 results with a call.
    You have 1562 no-calls but males only have about 5 no-calls.
    You only have 8 positive results but males have at least 100 positive results.
    Only 2 of your 8 positive results have an associated haplogroup and those 2 are false positives.

    Quote Originally Posted by jaderose22 View Post
    Many I think aren't haplogroups though. I did find about 2?
    Those are the 2 that I had told you about but they are false positives.

    RSID Position Allele Ybrowse Anc Ybrowse Der Result ISOGG HG SNP
    rs113686221 14484394 T C T + I1 P40
    rs188411414 17201821 T C T + A1a V63

    These are the other 6 SNPs with a positive result

    RSID Position Allele Ybrowse Anc Ybrowse Der Result ISOGG HG SNP
    rs13303871 2679100 G A G + not listed S27238
    rs9786575 2836569 T C T + not listed CTS242
    rs12164453 9981113 G A G + not listed S27190
    rs2631279 17361054 A T A + not listed S27531
    rs9786508 21581064 T C T + not listed PF6503
    rs1968716 28701583 A T A + not listed S27475

    Quote Originally Posted by jaderose22 View Post
    I think in haplogroups. I have finish heritage so the I one actually seems to have some truth as ancestrydna said I was part finish. On a very small level too. I thought maybe that's what it was gathering it from.
    You shouldn't confuse the two especially since you don't have a Y-chromosome.

    Quote Originally Posted by jaderose22 View Post
    Does negative mean the gene belong to no haplogroup?
    Negative means there was not a mutation but there was a call but since the AncestryDNA was not created what you are using it for there are a lot of unreliable results for various reasons.

    Quote Originally Posted by jaderose22 View Post
    And how would you know if someone belongs or doesn't belong to a specific haplogroup?
    You would have at least 100 positive results at AncestryDNA that put you into a haplogroup associated with a series of upstream SNPs and the identifying SNP(s) of the terminal haplogroup.
    Last edited by ArmandoR1b; 02-12-2017 at 01:11 PM.

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  11. #19
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    Quote Originally Posted by jaderose22 View Post
    rs104894968 24 2655442 A A

    rs104894959 24 2655375 G G

    http://www.malacards.org/card/46xy_sex_reversal_1

    These are the first results I found on my y ancestrydna data.

    It is connected to the genes on the website that causes sex reversal genes in xy people. To have these genes I have to have a y. As what else is it reversing? Lol. Women with xx don't have sex reversal genes. So you couldn't find it on the x chromosome and accidentally place it elsewhere. Also usually women only have a few results. Like 20 results. Not 125 results. I actually have a little more than 125 results tbh.
    I don't have as many v2 female tests to look at, but one of them had 125 calls for "Y SNPs" and the other had 195. These are just artifacts of the testing process. Probes don't look for whole genes -- rather, they look for a short sequence of say 50 bases. Occasionally these sequences can be found on other chromosomes. AncestryDNA hasn't pruned their list to remove these poorly performing probes. As Armando has said, if you have a Y chromosome you would have many more calls for the Y SNPs (almost surely over 1600), with just a small number of no-calls.

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     ArmandoR1b (02-12-2017), deadly77 (02-12-2017)

  13. #20
    If I didn't have a y chromosome then why does it have two sex reversal genes on it? And did you read the link I gave

    Quote Originally Posted by ArmandoR1b View Post
    You have 129 results with a call but males have 1686 results with a call.
    You have 1562 no-calls but males only have about 5 no-calls.
    You only have 8 positive results but males have at least 100 positive results.
    Only 2 of your 8 positive results have an associated haplogroup and those 2 are false positives.


    Those are the 2 that I had told you about but they are false positives.

    RSID Position Allele Ybrowse Anc Ybrowse Der Result ISOGG HG SNP
    rs113686221 14484394 T C T + I1 P40
    rs188411414 17201821 T C T + A1a V63

    These are the other 6 SNPs with a positive result

    RSID Position Allele Ybrowse Anc Ybrowse Der Result ISOGG HG SNP
    rs13303871 2679100 G A G + not listed S27238
    rs9786575 2836569 T C T + not listed CTS242
    rs12164453 9981113 G A G + not listed S27190
    rs2631279 17361054 A T A + not listed S27531
    rs9786508 21581064 T C T + not listed PF6503
    rs1968716 28701583 A T A + not listed S27475

    You shouldn't confuse the two especially since you don't have a Y-chromosome.


    Negative means there was not a mutation but there was a call but since the AncestryDNA was not created what you are using it for there are a lot of unreliable results for various reasons.


    You would have at least 100 positive results at AncestryDNA that put you into a haplogroup associated with a series of upstream SNPs and the identifying SNP(s) of the terminal haplogroup.
    That kind of explains what I was talking about since I'm intersex as I know I don't have a full y chromosome. I have a small portion of a y chromosome I actually guessed that might be a possibility. Is it possible since I'm African that I don't have haplogroup available on the other 6 for that reason.

    Also if I didn't have a y chromosome why do the first two results show for sex reversal genes in swyer syndrome? To have swyer syndrome you have to at least have a y chromosome.

    I have also looked up information on women with xxy karyotype like myself. Where the y is only partial.



    http://www.malacards.org/card/46xy_sex_reversal_1
    http://www.ashg.org/2009meeting/abst...ext/f10337.htm


    Also added to that I don't really get what a false positive means? I don't get why its a false positive if I have Scandinavian and finish heritage I have up to 9% combined. And I'm the descendants of slaves so my European heritage would be from a man usually. And its not from my mom it didn't come up in her DNA tests.

    But I don't get what is a false positive haplogroup?

    Also maybe 23andme might be able to place the other 6? I mean if they are hapligroups maybe 23andme could place mine?

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