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Thread: What is rs200511657?

  1. #1
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    Question What is rs200511657?

    Hello,

    does anybody know what does mean rs200511657?

    I see it in the U152 FTDNA project:

    U152> L2> Z41150> Z49,Z68> rs200511657> S8183,BY3626> Y4356>

    If I check the position of rs200511657:
    http://ybrowse.org/gb2/gbrowse/chrY/?name=rs200511657
    https://www.ncbi.nlm.nih.gov/SNP/snp...i?rs=200511657
    I see that it is 10,023,952.

    But according to U152 project ALL U152 samples have "G" (REF) at position 10023952 and none "C" (ALT).

    I don't understand.

    Maybe it should mean indel 10023952-GTCTC-G as it is described here: http://www.ytree.net/DisplayTree.php...770&star=false ?

    Is it correct to use rs200511657 rsid for this indel?

    Petr
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

  2. #2
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    Quote Originally Posted by Petr View Post
    Hello,

    does anybody know what does mean rs200511657?

    I see it in the U152 FTDNA project:

    U152> L2> Z41150> Z49,Z68> rs200511657> S8183,BY3626> Y4356>

    If I check the position of rs200511657:
    http://ybrowse.org/gb2/gbrowse/chrY/?name=rs200511657
    https://www.ncbi.nlm.nih.gov/SNP/snp...i?rs=200511657
    I see that it is 10,023,952.

    But according to U152 project ALL U152 samples have "G" (REF) at position 10023952 and none "C" (ALT).

    I don't understand.

    Maybe it should mean indel 10023952-GTCTC-G as it is described here: http://www.ytree.net/DisplayTree.php...770&star=false ?

    Is it correct to use rs200511657 rsid for this indel?

    Petr
    Standby, ironically this very issue is currently being discussed between FTDNA and U152 admin. We should have an answer soon.
    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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  3. #3
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    It is interesting that my WGS 15x result does not show this indel, this is from YFull U152 project:

    indel.png

    YF01551 = my FTDNA BigY
    YF02970 = my FGC Elite
    YF04805 = my FGC WGS 15x



    And it is interesting that the same indel:
    indel2.png
    has two different definitions and two different names.

    At first FGC defined it as FGC20812:
    http://ybrowse.org/gb2/gbrowse/chrY/?name=FGC20812
    Position: ChrY:6762873..6762876 (+ strand)
    mutation: AATA to del

    Later FTDNA defined it as BY3626
    http://ybrowse.org/gb2/gbrowse/chrY/?name=BY3626
    Position: ChrY:6762871..6762875 (+ strand)
    mutation: CAAAT to C

    It looks like YFull defines no indels.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

  4. The Following User Says Thank You to Petr For This Useful Post:

     MitchellSince1893 (03-03-2017)

  5. #4
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    The position is 10023952 10023952 GTCTC-G

    http://ytree.net/DisplayTree.p hp?blockID=1770&star=false

    http://ybrowse.org/gb2/gbrowse _details/chrY?ref=ChrY;start= 10023952;end=10023952;name= rs200511657;class=Sequence; feature_id=483751;db_id=chrY% 3Adatabase

    rs200511657 is a marker that Alex Williamson will call but FTDNA will not.

    According to FTDNA the data associated with this marker is rather "junky" and is one that will not be called in BigY results, thus FTDNA prefers to not include it on their haplotree at this time. Alex has different rules for inclusion on his Bigtree.

    The U152 project admin have decided to include it as well.
    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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  6. #5
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    I have noticed that in the new hg38 VCF files is this indel shifted 6 bp to the right and it look like this:

    10186352 TCTCT to T

    And probably due to aggressive filtering,
    8TCTCT 5T changed to 3T (kit 195364)
    9TCTCT 19T changed to 19T (kit 348782)

    If I understand correctly, indels are not displayed correctly at FTDNA website at present.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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