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Thread: New branch under R-FGC12401. FGC12384

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    New branch under R-FGC12401. FGC12384

    Background:

    Trying to solve a family mystery on my paternal line. Specifically the identity of my father's paternal grandfather's father. More on that here if you want more details http://www.anthrogenica.com/showthre...at-grandfather

    Back in Jul 2015, my closest 67 marker match, Mr Alex Guess (Genetic distance of 8-12 depending on method) agreed to take FGC12401 SNP test at YSEQ.net. It came back positive which meant he shared at least 1 of the 5 SNPs on this terminal branch. The other 4 being FGC12402, FGC12403, FGC12404, FGC12405.

    Based on this result he ordered FGC Y Elite 2.1 in September 2015. In November 2015 I also ordered Y Elite 2.1 for which my father provided the sample. Today he got his results. My father's should be out in a few weeks.

    One of the FGC analytical results compares his SNP results to others that have sent their results to FGC. My father's BigY results are shown on this document as I had FGC analyze his results when they came out 2 years ago.

    Based on the analysis my father's BigY results from FGC, Yfull, and FTDNA, I came up with a list of 21 novel/private SNPs.

    Of these 21, Alex currently shares a 15 with my father. I was guessing it would be about a dozen based on our STR results, so happily I wasn't too far off.

    He is definitely negative for one of my private SNPs, and the jury is still out on 5 other private SNPS.

    Using the STR values (Alex Guess tested to 67 markers) we have a genetic distance 9/10 at 83 markers using the infinite/hybrid method.

    SNPs we currently share include: FGC12384, FGC12385, FGC12387, FGC12388, FGC12389, FGC12392, FGC12393, FGC12397, FGC12398, FGC12399, FGC12400, FGC12406, FGC12408, FGC47889, FGC47894.

    Private SNP he doesn't share: FGC12386

    Further investigation is needed on these 5:
    Position/Name
    8173636 FGC12386
    9862775 FGC12390
    15129680 FGC12394
    15607220 FGC12395
    22318347 No name

    Using the Yfull based SNP block age estimator:
    If we share 15 SNPs then our most recent common ancestor would have live about 1013 years before present (ybp).
    If any/all of the 5 SNPs that need further investigation turn out positive then the MRCA would have been as recent as 345 ybp (Based on the STR genetic distance I doubt it will be this close...may more like 1-2 of the 5 will end up positive.

    My earlier guess was that it would have been 1200 years ago +/- 500 years.

    With this test result I've jumped approximately 2000 years to the present, from 1000 BC to 1000 AD for my MCRA. Not too bad.

    In a few weeks it will be interesting to compare my dad's BigY results to his FGC Y Elite 2.1 results.

    Bottomline: I'm very happy about how many SNPs we share...it was better than I had estimated.
    Last edited by DMXX; 06-16-2016 at 05:05 PM. Reason: Per request
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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    Congrats!

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    Update

    Just got an answer from FGC on those 5 SNPs.

    8173636 FGC12386: Alex is negative
    9862775 FGC12390: Alex is negative
    15129680 FGC12394: Alex is negative
    15607220 FGC12395: Alex is negative
    22318347 No name: Ambiguous results, but possibly shared.

    EDIT: Also I was mistaken on FGC12396 not being shared (I mislabeled it FGC12386 in the 1st post in this thread) Instead it was an ambiguous read which FGC looked at further and said it's most likely positive.

    In summary: That's 16-17 private SNPs I now share with Alex Guess, and 4 private SNPs we don't share.

    So our most recent common ancestor (MRCA) may be in the 1100 - 1300 AD time frame. I know that sounds way back there in time, but I'm so much closer to present day than I was a just a few days ago (1000 BC)
    Last edited by MitchellSince1893; 06-17-2016 at 12:08 AM.
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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    Alex Guess' data is now in Alex Williamson's Bigtree.
    http://www.ytree.net/DisplayTree.php...082&star=false

    http://www.ytree.net/SNPinfoForPerson.php?personID=4025

    Preliminary data shows that for R-FGC12401 et al:
    25533979 A>G FGC47900 is showing up as positive for Guess and Riccio and ambiguous for Mitchell, Roberts, and Wheatley in Big Tree. So it's probably FGC12401 et al. level SNP.

    -Branch 1 (R-Y19291, A2368): Roberts 268283, Riccio E14371, and Wheatley 209466 form one branch below R-FGC12401/02/03/04/05, sharing 16387379 Y19291 (A->G) and probably share 1 additional SNP A2368 (T->A)

    --Branch 1a (R-L368): At this point Roberts and Wheatley split from Riccio, forming a new branch L368 et al., sharing at least 19 additional SNPs and probably more once indepth analysis is performed.

    -Branch 2 (R-FGC12385 et al): Based on Mitchell 249822 BigY and Guess LEG9N FGC Y Elite 2.1 results this branch, according to Alex Williamson's initial look, shares 13 SNPs.

    The following SNPs are shown as shared by Guess and Mitchell in FGC analysis but not showing up yet in BigTree early analysis
    13871171 G>A FGC47889
    09908330 G>T FGC47886

    15878557 C>T FGC12396 is showing up as positive for Mitchell and ambiguous for Guess in both FGC analysis and initial BigTree analysis. FGC later confirmed Guess shared this SNP with Mitchell.

    22318347 T>A. Isn't showing up yet in BigTree but according to FGC analysis for LEG9N Guess, "a good portion of the reads have the A allele" So this is potentially a shared SNP.

    Again that's 16-17 shared SNPs by Guess and Me (depending on whether you count 22318347).

    Once my FGC Y Elite 2.1 results come out in a few weeks I expect the number of shared SNPs to increase by a handful.
    Last edited by MitchellSince1893; 06-19-2016 at 11:13 PM.
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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    Using the "Yfull based SNP Block Age estimator" spreadsheet found in the thread link below, I took all the private SNPs of Alex Guess for which he was positive I was negative and got an older date for our most recent common ancestor.

    There were 11 good quality FGC SNPs (didn't include indels) in this category of which 8 were in the ComBED region, providing a date of 666 AD for our shared ancestor.

    Previously I used the same calculator with private SNPs for I was positive and Alex was negative.
    There were 5 good quality BigY SNPs (didn't include indels) in this category of which 4 were in the ComBED region, providing a date of 1279 AD for our shared ancestor.

    Needless to say, our shared common ancestor is probably further back than I initially thought.

    Hopefully in a few weeks we will have Yfull actual age estimate for this branch.


    http://www.anthrogenica.com/showthre...ll=1#post76468
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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    My FGC Y Elite results are now available. Looks like I'm going rather busy for the next few hours.
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

  12. #7
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    Wow! Preliminary look at my FGC Y Elite results, reveals an additional ~29 private SNPs (non indels only) I share with Alex Guess.

    This is in addition to the ~16 private SNPs previously identified by comparing Alex's FGC results to my BigY results.

    So around 45 SNPs shared below R-FGC12401 branch.

    Also, previously comparing Alex's FGC to my BigY identified 4 private SNPs (all non indels). My new FGC results identified an additional 14 private non indel SNPs I have that Alex is negative for. For a total of 18 private SNPs

    That's a huge difference.
    Last edited by MitchellSince1893; 07-03-2016 at 06:08 PM.
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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    Quote Originally Posted by MitchellSince1893 View Post
    ...
    In summary: That's 16-17 private SNPs I now share with Alex Guess, and 4 private SNPs we don't share...
    Yfull has updated my father's BigY (yfull id YF01489) novel list and I've gone from 16 good quality and acceptable SNPs to 4...which matches what I was getting when I looked at the data.

    Yfull states that analysis of my father's FGC results (id YF06577) will be completed around 23 Aug. I estimate this will increase his good quality and acceptable SNP list to 18. His BigY and FGC results will both be on their tree with different id numbers. They request, in these circumstances that the customer inform Yfull that two kits are of the same person (in this case a BigY and FGC sample). https://www.yfull.com/faq/i-would-yf...need-open-new/

    Alex Guess is now on Yfull's Ytree, and analysis of his results including dating of this branch should be complete in early August.
    https://www.yfull.com/tree/R-Y9080/
    Last edited by MitchellSince1893; 07-14-2016 at 10:00 PM.
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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    While the official Yfull dates aren't out yet the statistics for both Mitchell YF06577/249822/UG4C9 and Guess YF06431/86098/LEG9N (Yfull id/FTDNA ID/FGC ID) are available. Also posted YF01489 which is the same person as YF06577 aka my father's BigY result for a direct comparison of FGC to BigY

    YFull YF06431 (Y Elite 2.1)
     
    RAW DATA
    ChrY BAM file size: 0.32 Gb
    Reads (all): 3957528
    Mapped reads: 3947859 (99.76%)
    Unmapped reads: 9669 (0.24%)
    Length coverage: 20592299 bp (80.27%)
    Min depth coverage: 1X
    Max depth coverage: 2663X
    Mean depth coverage: 24.46X
    Median depth coverage: 19X
    Length coverage for age: 8212004 bp
    No call: 5061267 bp

    Known SNPs
    SNPs (all): 88013
    Positive: 2971 (3.38%)
    Negative: 84014 (95.46%)
    Ambiguous: 145 (0.16%)
    No call: 880 (1.00%)

    Novel SNPs (all): 29
    Best qual: 10 (34.48%) [10 (34.48%) - best; 0 (0.00%) - acceptable]
    INDELs: 0
    Ambiguous qual: 4 (13.79%)
    One read!: 15 (51.72%)
    Low qual: 0

    Raw Data (Mt)
    ChrM BAM file size: 462.42 Kb
    Length coverage: 16569 bp (100.00%)
    Min depth coverage: 1X
    Max depth coverage: 1089X
    Mean depth coverage: 41.89X
    Median depth coverage: 12X
    One reading position!: 23
    No call: 0 bp


    YFull YF06577 (FGC Y Elite 2.1)
     
    RAW DATA
    ChrY BAM file size: 0.38 Gb
    Reads (all): 4994525
    Mapped reads: 4993512 (99.98%)
    Unmapped reads: 1013 (0.02%)
    Length coverage: 20643665 bp (80.47%)
    Min depth coverage: 1X
    Max depth coverage: 2324X
    Mean depth coverage: 27.05X
    Median depth coverage: 20X
    Length coverage for age: 8242420 bp
    No call: 5009901 bp

    Known SNPs
    SNPs (all): 88013
    Positive: 2975 (3.38%)
    Negative: 84081 (95.53%)
    Ambiguous: 149 (0.17%)
    No call: 806 (0.92%)

    Novel SNPs (all): 41
    Best qual: 10 (24.39%) [8 (19.51%) - best; 2 (4.88%) - acceptable]
    INDELs: 0
    Ambiguous qual: 5 (12.20%)
    One read!: 24 (58.54%)
    Low qual: 2 (4.88%)

    Raw Data (Mt)
    ChrM BAM file size: 180.94 Kb
    Length coverage: 15328 bp (92.51%)
    Min depth coverage: 1X
    Max depth coverage: 377X
    Mean depth coverage: 15.47X
    Median depth coverage: 5X
    One reading position!: 1570
    No call: 1241 bp


    YFull YF01489 (BigY results is same person as YF06577)
     
    RAW DATA
    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): 88013
    Positive: 2062 (2.34%)
    Negative: 66150 (75.16%)
    Ambiguous: 271 (0.31%)
    No call: 19491 (22.15%)

    Novel SNPs (all): 47
    Best qual: 4 (8.51%) [2 (4.26%) - best; 2 (4.26%) - acceptable]
    INDELs: 0
    Ambiguous qual: 43 (91.49%)
    One read!: 0
    Low qual: 0

    Raw Data (Mt)
    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


    Using the Yfull-based SNP Block Age Estimator spreadsheet one can see FGC Guess got 148.50 years per SNP mutation in the combBed region, FGC Mitchell got 147.96 years per SNP mutation, and BigY Mitchell got 167.77 years per SNP mutation.

    Based on my own analysis FGC Guess had 20 SNPs mutations in the combBed region and FGC Mitchell had 21, while Yfull has 14 SNPs for BigY Mitchell. The SNP mutation numbers for the FGC results may change once Yfull analysis is complete.

    YFull YF06431 (Y Elite 2.1)
     
    Resulting SNP Mutation Rate: 148.50 years per SNP mutation
    (High of 173.96 years, Low of 129.55 years)
    Phylogenetic Block Age Estimates:
    Number of SNPs in CombBED Region: 20

    Calculated Age of Phylogenetic Block: 2970.07 ybp = 1020BC
    95% CI High = 3479.23 ybp =1529BC
    95% CI Low = 2590.91 ybp =641BC


    YFull YF06577 (FGC Y Elite 2.1)
     
    Resulting SNP Mutation Rate: 147.96 years per SNP mutation
    (High of 173.32 years, Low of 129.07 years)
    Phylogenetic Block Age Estimates:
    Number of SNPs in CombBED Region: 21

    Calculated Age of Phylogenetic Block: 3107.07 ybp = 1157BC
    95% CI High = 3639.71 ybp =1690BC
    95% CI Low = 2710.42 ybp =760BC


    YF01489 BigY (same person as YF06577)
     
    Resulting SNP Mutation Rate: 167.77 years per SNP mutation
    High of 196.53 years, Low of 146.35 years)
    Phylogenetic Block Age Estimates:
    Number of SNPs in CombBED Region: 14

    Calculated Age of Phylogenetic Block: 2348.72 ybp = 399BC
    95% CI High = 2751.36 ybp =801BC
    95% CI Low = 2048.88 ybp =99BC

    Using the FGC results for Guess and Mitchell, I get a range of 618 AD (Mitchell) to 762 AD (Guess) as the most recent common ancestor (TMRCA) date. Using BigY Mitchell in the spreadsheet gave a date of 1111 AD. Yfull's official dates should be out in about a month.

    The average for the Calculated Age of the Guess/Mitchell Phylogenetic Block is about 1090 BC when only using the two FGC results i.e. when our branch split from the other R-FGC12401 branch. The BigY derived date is 400 BC.
    Last edited by MitchellSince1893; 07-23-2016 at 03:13 AM.
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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  18. #10
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    BigTree is now updated. Alex Williamson is calling this branch FGC 12385.

    43 shared SNPs between Mitchell and Alex Guess on this branch listed below.

    NOTE: If only my father's BigY result had been used there would have been 16 SNPs shared with Alex Guess on this branch.

    The 27 SNPs in bold below are the additional SNPs found in his FGC results.

    Event Names Location
    12301 FGC12385 7881772-C-G
    12302 FGC47872 2932610-T-C
    12303 FGC50746 3435156-T-G
    12304 FGC47873 3656400-A-G
    12305 Y1632 FGC2072 4502698-G-A
    12306 FGC7647 4502746-A-G
    12307 FGC47875 5100589-G-A
    12308 FGC47876 5175961-A-T
    12309 FGC47877 5262000-C-G
    12311 FGC47878 5925986-C-A
    12312 FGC8760 6020743-G-A
    12313 FGC47879 6028205-A-T
    12314 FGC47880 6080192-C-T

    12315 FGC47881 7347211-A-G
    12316 FGC12384 7547230-C-T

    12317 Y9080 7897468-T-C
    12318 - 7900146-T-TA
    12319 FGC12387 8194117-T-G
    12320 FGC12388 8290583-T-C
    12321 FGC12389 9795464-C-G
    12322 FGC47886 9908330-G-T
    12323 FGC47887 13214242-T-C
    12324 FGC47888 13535122-A-G
    12325 FGC12392 13713820-T-C
    12326 FGC47889 13871171-G-A
    12327 - 14495241-TG-T
    12328 FGC12393 14497774-A-C
    12329 - 15323666-A-C
    12330 FGC12396 15878557-C-T
    12331 FGC12397 15971853-G-A
    12332 FGC47891 16039300-A-C
    12333 FGC12398 16185253-G-A
    12334 FGC12399 17003970-T-C
    12335 FGC12400 17299391-C-T
    12336 FGC47894 20408815-C-T
    12337 FGC47895 21322858-G-A
    12338 FGC47896 21789864-G-A
    12339 FGC47897 21819191-T-A
    12340 FGC47870 22486450-G-A
    12341 FGC12406 23969601-G-A
    12342 - 26701457-G-A
    12343 FGC47901 27339935-G-T
    12344 FGC47902 28433714-G-A
    Last edited by MitchellSince1893; 07-28-2016 at 03:34 AM.
    Genetic info
     
    U152>L2>Z49>Z142>Z12222>FGC12378>FGC12384. Yfull YF01489. YSEARCH 2PJVS.
    Earliest Known Paternal Ancestor: Edward Leopold Mitchell (NPE), b 1893, London, England

    Ancestry: English=37% Scot/Ulster-Scot=27% Welsh=14% Irish=3% German=14% Scandinavian=3% India=1% French & Dutch=1%

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