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Understanding Raw Data

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  • Applegatej1
    replied
    FTDNA has my terminal SNP as L2 and Geno 2.0 puts it as Z49. As best as I can determine ISOGG has my downstream phonology as show below. Could someone help me understand how some one could have positive SNPs below a negative one? Also ISOGG considers Z51 a private SNP; how many people need to test positive for that SNP before it is no longer considered private?

    L2+.....Z367-.....L20-.....Z35-
    ...........L196-
    ...........Z49(split)+.....Z142-.....L562+.....Z57-
    ..............................................Z51+
    Last edited by Applegatej1; 1 December 2013, 05:25 PM. Reason: spacing

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  • Wing_Genealogis
    replied
    Originally posted by Applegatej1 View Post
    From reading the posts on this thread I have the idea that the data in the column labled Allele2 has no value (delete it) and the data in the column labled Allele1 are my test result. Is that correct?
    Not quite Applegatej1,

    There are a handful of SNPs where they had to gerry-rig the result (as the chip had a difficult time distinguishing a positive from a negative).

    So, if you have a split result in a Y-DNA SNP, it would usually mean that you are positive for this SNP. However, I have also seen cases where a split result means the chip is failing to read the SNP properly. (Somewhat of a mess, but it is what it is!)

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  • Applegatej1
    replied
    Understanding Y data

    From reading the posts on this thread I have the idea that the data in the column labled Allele2 has no value (delete it) and the data in the column labled Allele1 are my test result. Is that correct?

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  • JuanCarlos
    replied
    Where is the raw data at?

    I was looking at my results, but nowhere did I see anything about raw data, downloading it or tranferring it to FTDNA. I don't see any of that. Where can I find my raw data?

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  • Bartot
    replied
    Are Geno 2.0 using the DNAtribes geographical split as indicators for testers ........or as some form of relationship between companies.

    DNAtribes , has southern italy as greek, austria as German etc etc .

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  • JTR
    replied
    Originally posted by MMaddi View Post
    Yes, mutations at the same location on the y have been known to occur in different haplogroups. They're called parallel mutations. They may be private mutations, that have occurred recently within one paternal line, or they may define a new subclade of the haplogroup where the new mutation is found.

    ISOGG's ySNP index has examples of these parallel mutations - http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html - which are given the same name as the original SNP with ".x" added. One example is L159.1, defining I2a1a, and L159.2, defining R1b1a2a1a1b3a5a.
    Thanks! I also noticed that a deletion can be ancestral/negative (M147) and so also positive if 'D' is in the derived position - correct?

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  • MMaddi
    replied
    Originally posted by JTR View Post
    Ok! I am still confused about one of my splits (since their positive) being 'approx. R-M417' seeing that I am I-Z138. I guess the same mutation is possible under different Hg's?
    Yes, mutations at the same location on the y have been known to occur in different haplogroups. They're called parallel mutations. They may be private mutations, that have occurred recently within one paternal line, or they may define a new subclade of the haplogroup where the new mutation is found.

    ISOGG's ySNP index has examples of these parallel mutations - http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html - which are given the same name as the original SNP with ".x" added. One example is L159.1, defining I2a1a, and L159.2, defining R1b1a2a1a1b3a5a.

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  • JTR
    replied
    Originally posted by Wing_Genealogis View Post
    I cannot answer the second part of your query, but as to the first part: Yes, I[nsertion] or D[eletion].

    For the SNPs I have observed (below R1b-U106) the mutation was a deletion, so the ancestral state was an "I" (which technically really isn't an insertion, but it would be way too wordy to put in a full explanation). It is likely there are SNPs on the GenoChip where their was an insertion and the ancestral state would be "D".
    Ok! I am still confused about one of my splits (since their positive) being 'approx. R-M417' seeing that I am I-Z138. I guess the same mutation is possible under different Hg's?

    And I am still not sure what is up with L594 T>C yet I am A - I guess that's a mistake?

    Thanks for the answers!

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  • Wing_Genealogis
    replied
    Originally posted by JTR View Post
    Sounds good - so then if there is and 'I' or a 'D' for my result that would mean insertion and deletion?

    ...
    I cannot answer the second part of your query, but as to the first part: Yes, I[nsertion] or D[eletion].

    For the SNPs I have observed (below R1b-U106) the mutation was a deletion, so the ancestral state was an "I" (which technically really isn't an insertion, but it would be way too wordy to put in a full explanation). It is likely there are SNPs on the GenoChip where their was an insertion and the ancestral state would be "D".

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  • JTR
    replied
    Originally posted by Wing_Genealogis View Post
    The split calls (ie A G) is really a positive result. For technical reasons some locations (SNPs) achieve only very faint results, which the probes are not designed to handle. NatGeo (with help from FTDNA) "gerry-rigged" the system to signal this double result (meaning the individual is positive/derived for this SNP).

    Some SNPs are actually InDels (Insertions/Deletions). It is harder to design probes for the chips to accurately trace these, but some have been developed for the GenoChip.
    Sounds good - so then if there is and 'I' or a 'D' for my result that would mean insertion and deletion?

    As far as FTDNA I don't see how I can trust their transfer results when they marked so many of my listed markers wrong? How do I know if the ones listed are the exact number - I would have to check every marker from the Geno data unless there is some program that I can use that will tell me which ones are ancestral or derived. Is there such a program?

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  • Wing_Genealogis
    replied
    Originally posted by JTR View Post
    ... Also on the Geno Data I am not sure what some of the symbols mean. For instance:

    L566 is C>T but my alleles read T C and L781 is G>A and mine is a A G.

    Also L366 reads 'ins' for the ancestral and 'del' for the derived.

    And then L594 has T>C but my allele is A.
    The split calls (ie A G) is really a positive result. For technical reasons some locations (SNPs) achieve only very faint results, which the probes are not designed to handle. NatGeo (with help from FTDNA) "gerry-rigged" the system to signal this double result (meaning the individual is positive/derived for this SNP).

    Some SNPs are actually InDels (Insertions/Deletions). It is harder to design probes for the chips to accurately trace these, but some have been developed for the GenoChip.

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  • JTR
    replied
    Well after using the above chromosome browser I found some errors with the FTDNA transfer results. Since FTDNA is listing only postive results (I assume that means derived alleles) then there should not be any negative ones with the Geno transfer. But after looking at over 40 SNPs I found that 15 of them were actually negative and not positive as FTDNA lists.

    Also on the Geno Data I am not sure what some of the symbols mean. For instance:

    L566 is C>T but my alleles read T C and L781 is G>A and mine is a A G.

    Also L366 reads 'ins' for the ancestral and 'del' for the derived.

    And then L594 has T>C but my allele is A.

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  • JTR
    replied
    Thanks! That is good for the Y but what about the MT, X, and Aut.?

    Question regarding the NG data: Everyone seems to have every SNP, for example Z1 is listed with my base pair T T. Now I thought that if I was negative for this SNP that that meant I would not have a base pair to report - guess that was wrong - becuase these were AIMs - that is this marker (Z1) was only to be found in certain populations. But positive and negative, I guess mean something else?

    Without FTDNA selecting my Y positives when I downloaded the data to them I would be in a hell of mess to go through evey one of these SNPs and figure out what ones I had as positve or negative. Or am I to just take my general Hg and check all SNPs downstream? I guess derived means positive and ancestral means negative.

    What am I missing?
    Last edited by JTR; 18 December 2012, 07:34 PM.

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  • efgen
    replied
    Originally posted by MMaddi View Post
    For new SNPs that are only on the Geno 2.0 chip, there is no guide to ancestral/derived values yet. That will take some work, comparing results from people in various haplogroups/subclades. Ultimately, the complete answers won't come until Spencer Wells publishes a new tree, based on Geno 2.0 results.
    Actually, the CTS and PF SNPs have been published to Ymap:

    http://ymap.ftdna.com

    F SNPs haven't been published yet.

    The position on the Y tree hasn't been published yet, but the ancestral and derived alleles are there.

    For those who haven't used Ymap before:

    - Click "enter now" or the Y chromosome image on the homepage
    - In the Landmark or Region box, delete the default text and then enter a SNP name, such as L21.
    - Click Search
    - After the page refreshes, scroll down to the large Details grid in the center of the page, and you'll see your SNP name on one of the lines.
    - Click your SNP name, and you'll then get a details page for the SNP
    - Look for the Mutation, allele_anc and allele_der entries.

    Also, Here's a shortcut. Right-click and copy this direct link to L21's SNP details page:

    http://ymap.ftdna.com/cgi-bin/gb2/gb...=ChrY;name=L21

    Paste into your web browser's URL bar, change the L21 to any other SNP name and press Enter. That should bring you directly to that SNP's details page.

    And finally, there's also a text file that you can view in your browser or download that contains all the SNP data from Ymap -- just use the standard Find function (usually Ctrl-F on Windows, perhaps Command-F on Macs?) to search the file:

    http://ymap.ftdna.com/GRC/refSeq/snps.gff

    Elise
    Last edited by efgen; 18 December 2012, 05:57 PM.

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  • MMaddi
    replied
    Originally posted by JTR View Post
    Alright I figured it out - thanks! It was a .cvs.gz compressed so I had to un do the gz and then open it in Excel.

    One thing is that the file only gives you the base pair not whether you are + or -. What am I to do with this?

    Where do you find info on what genotype is + or -?
    For SNPs already available for testing by FTDNA (P312, U106, DF23 etc.), use the SNP index published by ISOGG - http://www.isogg.org/tree/ISOGG_YDNA_SNP_Index.html The last column gives the ancestral base, followed by the derived base.

    For new SNPs that are only on the Geno 2.0 chip, there is no guide to ancestral/derived values yet. That will take some work, comparing results from people in various haplogroups/subclades. Ultimately, the complete answers won't come until Spencer Wells publishes a new tree, based on Geno 2.0 results.

    Leave a comment:

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