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Thread: Big Y: What Now?

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    Question Big Y: What Now?

    Okay, I am somewhat used to dealing with Big Y results that yield "public" SNPs, that is, SNPs that are shared by a fairly large number of men with no apparent connection in genealogical time. But now one of my same-surname matches (109/111) has had the test, submitted his results to Alex Williamson, and has found that we share a string of apparently "private" SNPs unique to our y-dna line.

    What is the best course of action in that case?

    Here we are on the Big Tree (scroll down and to the right to find us: Stevens 59080 and Stevens 522600):

    The Big Tree: R-DF41/S524

    Up until yesterday, I was in the same box with Selfe and Samuel, who also belong to our haplotype cluster.

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    I'm in a similar situation. 40+ SNPS shared between my father and closest match...but different surnames (my line has an NPE) and MRCA is 1000 years ago according to Yfull, and 800 years ago via str method.

    Ideas going forward:
    1. I worked with FTDNA to get a couple of SNPs added to the appropriate SNP pack test.
    2. I requested individual tests from ftdna for these SNPs...no word on that yet.
    3. Make a wish list for these SNPs at yseq.net
    4. Ask Thomas Krahn to add them to his pertinent L21 branch panel test...or if too recent you could request a personal panel test.
    5. Submit both BigY tests to Yfull to get an age estimate. If you already know your MRCA then this will let you know how accurate their dating methodology worked on your branch.
    Last edited by MitchellSince1893; 01-29-2017 at 02:50 PM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
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    Quote Originally Posted by MitchellSince1893 View Post
    I'm in a similar situation. 40+ SNPS shared between my father and closest match...but different surnames (my line has an NPE) and MRCA is 1000 years ago according to Yfull, and 800 years ago via str method.

    Ideas going forward:
    1. I worked with FTDNA to get a couple of SNPs added to the appropriate SNP pack test.
    2. I requested individual tests from ftdna for these SNPs...no word on that yet.
    3. Make a wish list for these SNPs at yseq.net
    4. Ask Thomas Krahn to add them to his pertinent L21 branch panel test...or if too recent you could request a personal panel test.
    5. Submit both BigY tests to Yfull to get an age estimate. If you already know your MRCA then this will let you know how accurate their dating methodology worked on your branch.
    Thanks! Those are just the sorts of suggestions I was looking for. I wasn't sure any company would agree to test for what are apparently private SNPs.

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    I'm pretty sure Yseq.net will
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
    37% English, 26% Scot/Ulster Scot, 14% Welsh, 14% German, 3% Ireland, 3% Nordic, 2% French/Dutch, 1% India
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    Quote Originally Posted by MitchellSince1893 View Post
    I'm pretty sure Yseq.net will
    You mentioned YFull. What is the advantage of paying the $50 for its services? (Honest question: I have no agenda in asking it.)

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    The Big Tree is somewhat confusing to me. I see seven SNPs listed in the box on the DF41 Big Tree page that are shared by my 109/111 Stevens match and me. Clicking on the mutation matrix for FGC36975, I count five solid "+" signs that he and I share, but I am the only one with a "+" sign for FGC36983, even though it is listed in the box on the main DF41 page as shared by both of us.

    Here is that mutation matrix.

    Stevens Big Tree Mutation Matrix R1b-FGC36975.png

    Here is a screen shot of part of the main DF41 Big Tree page showing the box of shared SNPs.

    Stevens Big Tree Screenshot 28 Jan 2017.png

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    Short Answer: Best answer is to ask Alex directly. But it appears Alex has chosen to display in tree all + +, all ** **, and + pink for your branch

    ...those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the VCF file. This is particularly true when most men would otherwise show coverage at that particular position.
    I remember I had a question on a SNP Alex didn't initially display as shared (I found this SNP via either Yfull or FGC analysis). Alex manually reviewed and added the SNP in question to our shared list.

    So it may be that Alex manually reviewed the pink cell SNP and determined it was valid.

    As the the inclusion of FGC36977 with the ** and gray cell background. I dunno. Best ask Alex why that was included. Again he may have manually looked at it and determined it was indeed a valid SNP.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
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    Thanks. I will ask him.

    What about YFull? If my Stevens match and I submit our raw data to them, will they give us an estimated tmrca? I suspect our common ancestor was born either around 1776 or around 1750, but I'm not sure.

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    Quote Originally Posted by rms2 View Post
    You mentioned YFull. What is the advantage of paying the $50 for its services? (Honest question: I have no agenda in asking it.)
    In my situation, the SNP dating was very important. It may not be in your case.

    Other benefits.
    Another set of experts with different criteria to analyze your data. As FTDNA, FGC, Alex Williamson, and Yfull all use different criteria in rating the quality of SNPs, I have found it useful to compare between companies. Sometimes a SNP may fall just outside of one company's criteria as valid, but be within another's.

    I like the user interface available. I can see details on all my SNPs including the novel ones

    Example
    ChrY position: 7547230 (+strand)
    Reads: 47
    Position data: 47T
    Weight for T: 1.0
    Probability of error: 0.0 (0<->1)
    Sample allele: T
    Reference (hg19) allele: C
    Known SNPs at this position: FGC12384 (C->T) Rating for known SNP 5 stars

    They break the novel SNPs down into categories. Best, acceptable, ambiguous, low quality, one reads

    You can see your SNP matches...don't expect a lot as their database is not as robust as others. I only see one close match.

    Details on SNPs used for age estimation including public and novel SNPs used and not used...and why there were not used.

    A y report that shows stats on your BigY bam file size, length of coverage, median depth of coverage, and a tree list of every single SNP you test positive for from A1 to your current terminal branch/block of SNPs

    A display of up to 500 STR values...most folks only get about 300 to low 400 STRs that are readable. My father's BigY has 475 STRs of which 406 are readable.
    A display of your STR matches...both close and distant.

    Display of your STR values compared to the ancestral values

    You can browse your raw data by SNP position number

    Other stats such as
    ChrY BAM file size: 0.51 Gb
    Reads (all): 9962312
    Mapped reads: 9962312 (100.00%)
    Unmapped reads: 0
    Length coverage: 13179112 bp (51.37%)
    Min depth coverage: 1X
    Max depth coverage: 7999X
    Mean depth coverage: 66.20X
    Median depth coverage: 41X
    Length coverage for age: 7269144 bp
    No call: 12474454 bp

    Known SNPs
    SNPs (all): 100571
    Positive: 2072 (2.06%)
    Negative: 76089 (75.66%)
    Ambiguous: 287 (0.29%)
    No call: 22082 (21.96%)

    STRs
    STRs (all): 475
    Reliable alleles: 406 (85.47%)
    Uncertain alleles: 17 (3.58%)
    N/A: 52 (10.95%)

    Stats on Novel SNPs
    Novel SNPs (all): 45
    Best qual: 4 (8.89%) [2 (4.44%) - best; 2 (4.44%) - acceptable]
    INDELs: 0
    Ambiguous qual: 41 (91.11%)
    One read!: 0
    Low qual: 0

    Mt dna stats
    ChrM BAM file size: 431.78 Kb
    Length coverage: 16562 bp (99.96%)
    Min depth coverage: 2X
    Max depth coverage: 3254X
    Mean depth coverage: 58.43X
    Median depth coverage: 26X
    One reading position!: 0
    No call: 7 bp

    Additional Mt dna info on rcrs and rsrs values

    You can also join the appropriate group(s) The L21 group has 385 members in it. A drop in the bucket, but there may be someone in there that's not in the FTDNA project(s). You never know.

    For me the $50 was well spent.
    Last edited by MitchellSince1893; 01-29-2017 at 05:14 PM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
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    Quote Originally Posted by rms2 View Post
    Thanks. I will ask him.

    What about YFull? If my Stevens match and I submit our raw data to them, will they give us an estimated tmrca? I suspect our common ancestor was born either around 1776 or around 1750, but I'm not sure.
    Yes they will. I find using a combination of STR dating and SNP dating useful. In my case, I'm in that "gray area" just outside the genealogical records timeframe.

    On my branch, it ranged from 733 to 1247 years before present for the 3 kits on my current terminal branch (average 977 years and 95% CI it's 1500-600 ybp) . When I compare this to http://www.mymcgee.com/tools/yutility111.html I get a 95% probability our MRCA lived 870 years ago. So there is an overlap between the two. As you get beyond this time frame there is a divergence between STR and SNP dating with SNPs giving older dates.

    More on this here http://www.anthrogenica.com/showthre...l=1#post210149

    What yfull will do is take a look at both of your individual kit's and come up with age estimates for each and then take the average. They will start from the present (1950) and work back, using the number private SNPs (ones that meet their criteria for use) that neither of you share with each other.

    For example. Let's say you have 2 private SNPs and your match has 3 (SNPs not on Alex's tree). They will look at each bam file and make adjustments to the average SNP mutation period. Based on your particular bam file you may have an average of 161 years per SNP mutation. Your match may have 147 (these numbers are just examples). So 2 x 161 would give 322 years based on your kit, and 441 years for your match. They would then take the average of 322 and 441 i.e. 382 years. But you would have a range combined with STR dating to consider as possibilities...it should help get you in the ball park.
    Last edited by MitchellSince1893; 01-29-2017 at 05:47 PM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
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