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Thread: Yfull Ambiguous SNPs

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    Yfull Ambiguous SNPs

    A big whole bunch of them. Some have less than ten reads which I find unreliable. But there are also some interesting snps, with a decent coverage >100x, which seem to belong to another haplogroup. Is it that these SNPs are not investigated enough yet, and incorrectly assigned to some haplogroup, or do these notsofalse snps mean anything.

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    Or are these related to mapping issues

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    Quote Originally Posted by Afshar View Post
    A big whole bunch of them. Some have less than ten reads which I find unreliable. But there are also some interesting snps, with a decent coverage >100x, which seem to belong to another haplogroup. Is it that these SNPs are not investigated enough yet, and incorrectly assigned to some haplogroup, or do these notsofalse snps mean anything.
    Some are assembly errors and some come from heterogeneous regions. For assembly errors you can take the time to extract the reads out of the BAM file and rerun the assembly and SNP analysis with a different set of parameters. You might clears up some small sections and get a better feel for some of the notsofalse SNPs. In terms of SNPs from other haplogroups showing up. If they are directly upstream of you then they would be expected to be present. If they are not then look at whether you have a .x recurrent showing up in your line/branch. SNPs can and will show up across multiple haplogroups. No big deal. To clear up the fuzzy sections the next step would be to see if there are some Sanger primers in the section and order some of those from YSEQ.NET to check out if some of those notsofalse SNPs are real. Finally just wait until the next step in sequencing arrives where you can get longer read lengths. Longer lengths will clear up the question about what SNPs are present in most of these questionable regions.

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     Afshar (09-24-2015)

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    Quote Originally Posted by Cofgene View Post
    Some are assembly errors and some come from heterogeneous regions. For assembly errors you can take the time to extract the reads out of the BAM file and rerun the assembly and SNP analysis with a different set of parameters. You might clears up some small sections and get a better feel for some of the notsofalse SNPs. In terms of SNPs from other haplogroups showing up. If they are directly upstream of you then they would be expected to be present. If they are not then look at whether you have a .x recurrent showing up in your line/branch. SNPs can and will show up across multiple haplogroups. No big deal. To clear up the fuzzy sections the next step would be to see if there are some Sanger primers in the section and order some of those from YSEQ.NET to check out if some of those notsofalse SNPs are real. Finally just wait until the next step in sequencing arrives where you can get longer read lengths. Longer lengths will clear up the question about what SNPs are present in most of these questionable regions.
    I thought so, because they belong to a wide array of haplogroups. Your approach is good, my funds are not haha.

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    Quote Originally Posted by Cofgene View Post
    Some are assembly errors and some come from heterogeneous regions. For assembly errors you can take the time to extract the reads out of the BAM file and rerun the assembly and SNP analysis with a different set of parameters. You might clears up some small sections and get a better feel for some of the notsofalse SNPs. In terms of SNPs from other haplogroups showing up. If they are directly upstream of you then they would be expected to be present. If they are not then look at whether you have a .x recurrent showing up in your line/branch. SNPs can and will show up across multiple haplogroups. No big deal. To clear up the fuzzy sections the next step would be to see if there are some Sanger primers in the section and order some of those from YSEQ.NET to check out if some of those notsofalse SNPs are real. Finally just wait until the next step in sequencing arrives where you can get longer read lengths. Longer lengths will clear up the question about what SNPs are present in most of these questionable regions.
    well that explains why while promethease predicted my grandpa's haplogroup to be r, he tested postive for a j and an i snp.

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    Quote Originally Posted by crossover View Post
    well that explains why while promethease predicted my grandpa's haplogroup to be r, he tested postive for a j and an i snp.
    Not at all. YFull analyzes NGS (Next Generation Testing) results. They never confuse haplogroups. There is only a relatively small number of ambiguous SNPs in the thousands that they analyze.

    Promethease doesn't analyze NGS test results. It only analyzes the results of files from FTDNA Family Finder, AncestryDNA, and 23andme. AncestryDNA tests an extremely limited portion of the Y chromosome. Family Finder doesn't test it at all. 23andme does limited testing of the Y-chromosome but enough to tell which haplogroup and major subclade a person belongs to. It never confused R, J and I. Your grandfather's ambiguous are because you haven't purchased a Y-DNA test for him from FTDNA, Yseq, or FGC or a 23andme test.

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     Lugus (09-26-2015)

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    What immediately caught my eye was the series of l373-l379 that seem positive, which apparently belong to haplo G.
    I think most of these snps are unreliable

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    Quote Originally Posted by Afshar View Post
    What immediately caught my eye was the series of l373-l379 that seem positive, which apparently belong to haplo G.
    I think most of these snps are unreliable
    L373 was found in hg G-L14 and J-L70 WTY participants http://bit.ly/1OwV6p7 which was done by FTDNA. I am sure the SNP is reliable but highly recurrent so just as long as someone has enough SNPs that are upstream, and in most cases downstream, then the SNP can be properly placed within the haplogroup and subclade that the other positive SNPs are in.

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     Táltos (09-24-2015)

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    We need more testing, thats for sure

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     Táltos (09-24-2015)

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    Quote Originally Posted by ArmandoR1b View Post
    Not at all. YFull analyzes NGS (Next Generation Testing) results. They never confuse haplogroups. There is only a relatively small number of ambiguous SNPs in the thousands that they analyze.

    Promethease doesn't analyze NGS test results. It only analyzes the results of files from FTDNA Family Finder, AncestryDNA, and 23andme. AncestryDNA tests an extremely limited portion of the Y chromosome. Family Finder doesn't test it at all. 23andme does limited testing of the Y-chromosome but enough to tell which haplogroup and major subclade a person belongs to. It never confused R, J and I. Your grandfather's ambiguous are because you haven't purchased a Y-DNA test for him from FTDNA, Yseq, or FGC or a 23andme test.
    apparently the y-snp's ancestry tested were enough for promethease to predict my grandpa's y-dna haplogroup as being r1b1a2a1a1. if he's not r1b1a2a1a1, he's most likely within r1b.

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