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Thread: R1b U152 Updates/News

  1. #301
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    Quote Originally Posted by wombatofthenorth View Post
    I know of some non-BigY U152 (R-L20 actually) results from Slovakia.
    The report has it's limitations due to the source and wasn't meant to be used literally and it is why I included the kit count for each country. It should give a general idea of the countries with the largest percentage of U152. All of the countries with less than several hundred kits need a lot more for a more accurate percentage. I am hoping to one day see at least 500 kits per country for the smaller countries and a lot more for the more populated countries. We are several years away from that happening. All of the countries have non-BigY kits that are U152+ that aren't counted. It would be way too much work to find all kits, regardless of haplogroup, from each of those countries that have had SNP pack or individual SNP tests. The YFull customers provide the country of origin and since BigY tests allow us to know which R1b-M269 customers are U152+ and which definitely are not it is a simple way to get the frequency out of the haplogroups that I mentioned.

    That said, if a country has almost two dozen kits in BigY but has 0% U152 there isn't a good chance that the country has a large percentage of U152. For instance Belgium has 23 kits but has two 152 which shows that it is likely to have a larger percentage of U152 when both Slovakia and Belgium have several hundred kits tested.

    If you want to see what the rate for Slovakia is more likely to have there is a Slovakia FTDNA project has 108 people grouped. 4 are M269 that haven't had an SNP pack. Based on the other R1b people only about 28% of them are likely to be U152+ which is 1. Using that assumption the ratio of U152 3:108 is 2.77%. If we add the 5 ungrouped people and assume 1 of the M269 people is U152 then the ratio is 4:113 which is 3.5%.

    The Busby et al. 2011 table has 276 kits from Slovakia that are from Myres e al. that were tested for P312, L21, and U152. Only 0.4% were positive for U152.

    So the true percent probably isn't more than the 3.5% from the Slovakia FTDNA project and it is probably slightly less. It still doesn't put them into the top 10 results but does possibly put them on par with some of the other countries that also have a low percent of U152.

  2. #302
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    Some stats from the FTDNA U152 project.

    Of the 1512 members with STR data (found in the classic and colored STR charts) that are assigned to a U152 subclade
    78.37% (1185) are the L2 subclade
    13.23% are (200) are in the ZZ45 subclade
    6.75% (102) are in the PF6658 subclade
    1.65% (25) are in other subclades

    Within U152>L2: Of the 949 samples assigned to known or unknown subclades
    44.89% (426) are Z41150 subclade
    31.61% (300) are in the Z258,Z367,Z384 subclade
    8.11% (77) are DF103 subclade
    6.22% (59) are ZZ48
    2.95% (28) are in DF110 subclade
    2.11% (20) are in BY3508 subclade
    4.11% (39) are in other subclades

    Within U152>L2>Z41150: Of the 426 samples assigned to subclades
    69.01% (294) are Z49

    Within U152>L2>Z41150>Z49: Of the 244 samples assigned to Z49 subclades
    70.49% (172) are in Z142 subclade
    22.95% (56) are in rs200511657 subclade

    It's interesting that there are more members in U152>L2>Z41150>Z49 (244) than there are in the 2nd largest U152 subclade, U152>ZZ45 (200). U152>L2>Z41150>Z49>Z142 may eventually become larger as well.
    This may in part be due to the L2, Z49 and Z142 all being more common in the British Isles; and FTDNA has more testers from UK & Ireland and their descendants compared to areas where other U152 subclades are more prevalent. For example, compared to U152 as a whole, Z36 (largest subclade of ZZ45) and Z56 have below average percentages in the British Isles, while L2 is above the U152 average.
    http://www.anthrogenica.com/showthre...l=1#post155764
    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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  4. #303
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    [QUOTE=MitchellSince1893;320728]Some stats from the FTDNA U152 project.

    Of the 1512 members with STR data (found in the classic and colored STR charts) that are assigned to a U152 subclade
    78.37% (1185) are the L2 subclade
    13.23% are (200) are in the ZZ45 subclade
    6.75% (102) are in the PF6658 subclade
    1.65% (25) are in other subclades

    Where is Z56 in this summation?

  5. #304
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    Quote Originally Posted by emmental View Post
    Where is Z56 in this summation?
    Corrected

    Some stats from the FTDNA U152 project.

    Of the 1678 members with STR data (found in the classic and colored STR charts) that are assigned to a U152 subclade
    70.62% (1185) are the L2 subclade
    11.92% are (200) are in the ZZ45 subclade
    9.89% (166) are in the Z56 subclade
    6.08% (102) are in the PF6658 subclade
    1.49% (25) are in other subclades

    Within U152>L2: Of the 949 samples assigned to known or unknown subclades
    44.89% (426) are Z41150 subclade
    31.61% (300) are in the Z258,Z367,Z384 subclade
    8.11% (77) are DF103 subclade
    6.22% (59) are ZZ48
    2.95% (28) are in DF110 subclade
    2.11% (20) are in BY3508 subclade
    4.11% (39) are in other subclades

    Within U152>L2>Z41150: Of the 426 samples assigned to subclades
    69.01% (294) are Z49

    Within U152>L2>Z41150>Z49: Of the 244 samples assigned to Z49 subclades
    70.49% (172) are in Z142 subclade
    22.95% (56) are in rs200511657 subclade

    It's interesting that there are more members in U152>L2>Z41150>Z49 (244) than there are in the 2nd largest U152 subclade, U152>ZZ45 (200). U152>L2>Z41150>Z49>Z142 may eventually become larger as well.
    This may in part be due to the L2, Z49 and Z142 all being more common in the British Isles; and FTDNA has more testers from UK & Ireland and their descendants compared to areas where other U152 subclades are more prevalent. For example, compared to U152 as a whole, Z36 (largest subclade of ZZ45) and Z56 have below average percentages in the British Isles, while L2 is above the U152 average.
    http://www.anthrogenica.com/showthre...l=1#post155764
    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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  7. #305
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    Quote Originally Posted by MitchellSince1893 View Post
    22.95% (56) are in rs200511657 subclade
    FTDNA doesn't recognize this subclade. Has FTDNA definitively rejected it, or has no one submitted it?

  8. #306
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    Quote Originally Posted by lgmayka View Post
    FTDNA doesn't recognize this subclade. Has FTDNA definitively rejected it, or has no one submitted it?
    They don't use rs #s on their tree.

    Just like they don't use R-Z40481, R-ZZ11

    Here it is http://ybrowse.org/gb2/gbrowse/chrY/? Maybe it too close to the centromere?
    Last edited by MitchellSince1893; 12-07-2017 at 12:52 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%

  9. #307
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    I have discussed this topic here: http://www.anthrogenica.com/showthre...is-rs200511657

    rs200511657 is definitely wrong name, according to https://www.ncbi.nlm.nih.gov/SNP/snp...rs=rs200511657 it is G to C mutation, while the mutation on the tree is indel 10186343 (hg38) GTCTC to G and according to new hg38 FTDNA VCF files it is 10186352 TCTCT to T.

    From YSEQ I received the following comment:

    ChrY:10186344 TCTC to del Centromeric repeat *
    * = not recommended

    AFAIK FTDNA does not work with new indels at present, they are missing from their Named/Unnamed variants display, but they are present in the VCF files. They are not the same as in the old hg19 VCF files.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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  11. #308
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    Quote Originally Posted by Petr View Post
    I have discussed this topic here: http://www.anthrogenica.com/showthre...is-rs200511657

    rs200511657 is definitely wrong name, according to https://www.ncbi.nlm.nih.gov/SNP/snp...rs=rs200511657 it is G to C mutation, while the mutation on the tree is indel 10186343 (hg38) GTCTC to G and according to new hg38 FTDNA VCF files it is 10186352 TCTCT to T.

    From YSEQ I received the following comment:

    ChrY:10186344 TCTC to del Centromeric repeat *
    * = not recommended

    AFAIK FTDNA does not work with new indels at present, they are missing from their Named/Unnamed variants display, but they are present in the VCF files. They are not the same as in the old hg19 VCF files.
    Quote Originally Posted by MitchellSince1893 View Post
    Here it is http://ybrowse.org/gb2/gbrowse/chrY/? Maybe it too close to the centromere?
    Sounds similar to this situation
    New subclades at the very top of the U106 tree
    Michael Sager, who maintains FTDNA's haplotree has been monitoring the Big Y update process. He contacted the R-U106 admins about a SNP he had discovered (BY30097) during this update process. This SNP is located in the centromere area of the Y-chromosome, which is noted for having a lot of repeating patterns, and it is oftentimes very difficult to separate out the different segments.

    Due to the additional clarity the new Build brought, the Big Y test has been able to separate the specific area where BY30097 is located from other similar regions. Even so, this SNP is only called sporadically in the new Big Y test results. Sager had to go in and visually inspect the BAM files in order to verify this SNP was indeed real.
    http://www.anthrogenica.com/showthre...676#post321676

    I will look at this tonight and contact Michael Sager.
    Last edited by MitchellSince1893; 12-07-2017 at 01:43 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%

  12. #309
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    Quote Originally Posted by Petr View Post
    rs200511657 is definitely wrong name, according to https://www.ncbi.nlm.nih.gov/SNP/snp...rs=rs200511657 it is G to C mutation, while the mutation on the tree is indel 10186343 (hg38) GTCTC to G and according to new hg38 FTDNA VCF files it is 10186352 TCTCT to T.
    This tree mutation is better described as an STR allele change, from 6 repetitions to 4.
    Ancestral: GTCTCTCTCTCTC
    Derived: GTCTCTCTC

  13. #310
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    Is it good idea to place STRs on the Y Tree?

    It looks like that Z40481 and Z38841 are STRs as well and ZZ11_1 is a bit mysterious: http://www.ytree.net/BlockInfo.php?blockID=2 (this area is not in FTDNA hg38 regions.bed)

    And regarding indels, it looks like FTDNA does not plan to work with them, they wrote me:
    As our indel variant data in the vcf file is not quality controlled (the only verified data is the Big Y SNPs) we do not offer support on data analysis.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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