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Thread: Low quality of Z49/Z68 SNPs?

  1. #1
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    Low quality of Z49/Z68 SNPs?

    Hello,

    I'd like to ask what could be the reason of strange results of my L2 -> Z49/Z68 SNPs.

    FTDNA BigY results:
    L2: Genotype: ? Confidence: Unknown
    Z49: Genotype: ? Confidence: Unknown
    Z68: Genotype: ? Confidence: Unknown
    pos. 2665967 Genotype: T Confidence: High

    interpreted by FGC:
    pos. 5755550 L2 S139 (C->T): 37T 2C
    pos. 28462237 Z49 unknown
    pos. 21058323 Z68 unknown
    pos. 2665967 S8183+ reliability warning level: **

    interpreted by YFull:
    pos. 5755550 L2 S139 (C->T): 37T 2C
    pos. 28462237 Z49 (G->T): no call position
    pos. 21058323 Z68 S485 (C->T): no call position
    pos. 2665967 S8183 (G->T) 15T 1G

    Geno 2.0 results:
    L2,Y,T,T => positive
    Z49,Y,T,G => ambiguous
    Z68,Y,C,C => negative
    S8183 not tested

    23andMe
    U152: rs1236440 Y 15333149 T
    L2: rs2566671 Y 5755550 --
    Z49, Z68 and S8183 not tested.

    23andMe my father:
    U152: rs1236440 Y 15333149 T
    L2: rs2566671 Y 5755550 --
    Z49, Z68 and S8183 not tested.

    So:
    L2 - sometimes (BigY FTDNA, 23andMe) no results
    Z49 - BigY no call, Geno 2.0 ambiguous
    Z68 - BigY no call, Geno 2.0 negative
    S8183 - BigY only

    So how it is with Z68? Ybrowse http://ybrowse.isogg.org/cgi-bin/gb2...chrY/?name=z68 shows:
    count_derived: 0
    count_tested: 0

    YSEQ: does not offer Z68 SNP test.
    FTDNA: does not offer Z68 SNP test.

    Other samples analyzed by YFull, results for Z49 and Z68 from U152 group:
    YF01527: ? ?
    YF01555: ? ?
    YF01461: - ?
    YF01754: - ?
    YF01926: ? ?
    YF01489: ? ?
    YF01733: + ?
    YF01551: - ?
    YF01647: - ?
    YF02052: ? ?
    It looks like NextGen tests analyzed by YFull often don't cover Z49 and no test cover Z68.

    Just my observation, maybe with no importance. Now I'm waiting for BritainsDNA and FGS Elite test to see their results.

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

  2. #2
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    I am L2+ but Z49-.
    L2 was discovered in 23andMe though chip versions have changed. Still you can get No Call.
    For some reason, the FTDNA BED file excludes L2 though other analysis shows that the data is there. Check VCF file which is text readable.
    You can order any SNP from YSEQ and they will make it available.
    Unfortunately, in making the Britains DNA chip the L2 "bead" ended up not working. In my case they did additional testing.
    This may be same from Z49--I did a post months back about missing SNPs. Luck of the draw I guess.

    My FGS Elite (BGI) had no problems with L2. My FGC BGI Bam data is YF01461 on your list. Some of the others are FTDNA Bams. My Big Y Bam is being analyzed by Yfull but has not been released yet pending evaluation of SNP that is positive in one test and negative in the otherr.

  3. #3
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    Britains DNA results:
    L2: not tested
    Z49: not tested
    Z68 = S485: AG positive
    S8183: AA positive

    But what does mean "AG"? I have one Y chromosome, not two. And http://ybrowse.isogg.org/ shows C->T mutation and I have "AG"?
    Last edited by Petr; 10-20-2014 at 11:12 PM.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

  4. #4
    Registered Users
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    Praha, Czech Republic
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    Y-DNA (P)
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    mtDNA (M)
    J1c1i

    Czech Republic Austria Austrian Empire Bohemia Carinthia
    And YSEQ result:

    Z68 ChrY 21058323 21058323 T+
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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