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Thread: Yseq’s new WGS400 WGS for $399

  1. #101
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    Quote Originally Posted by MacUalraig View Post
    To be honest I hadn't looked under that section for kits doing WGS. It's more of a haplogroup summary and I agree a bit confusing (especially the implication you need to do a panel test). If its off the WGS it should either match or have finer resolution than your 23andMe test though. Did the other test put you in a sibling branch? Or just higher up/lower down the one you mention?
    Thanks for replying

    The 23andme test gave me as a result I-Z58, negative for I-Z59 and I-Z138. YSEQ is giving me I-Z63, so an entire different result (although both I1a).

    To be fair I have checked the website because after asking for an update on my results just yesterday they told me that the results were due in a few days. I have not yet received an email and browsing around the YSEQ website it seems to be that a lot of the results need to be uploaded yet, so this may be provisional, maybe

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  3. #102
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    Quote Originally Posted by Northern Adriatic View Post
    Thanks for replying

    The 23andme test gave me as a result I-Z58, negative for I-Z59 and I-Z138. YSEQ is giving me I-Z63, so an entire different result (although both I1a).

    To be fair I have checked the website because after asking for an update on my results just yesterday they told me that the results were due in a few days. I have not yet received an email and browsing around the YSEQ website it seems to be that a lot of the results need to be uploaded yet, so this may be provisional, maybe
    Ok so we are talking two sibling branches then. You should have your raw data (BAM file) shortly then you can check it all manually if necessary including the Z58 status. I do know a batch just completed in the last few days as I had the two kits from it I was waiting for.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  5. #103
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    I have received my results. The webpage of YSEQ does not seem to be fully updated yet (for example in My STR Results), but in the email is confirmed the following (unexpected) path: A0-T > A1 > A1b > BT > CT > CF > F > GHIJK > HIJK > IJK > IJ > I > I1 > I-L121 > I-DF29 > I-Z63 > I-BY151.

    I will upload to Y-Full to double check I guess.

    For the genome, does anybody know which file should be sent to Davidski for the G25 Coordinates?

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  7. #104
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    Quote Originally Posted by Northern Adriatic View Post
    I have received my results. The webpage of YSEQ does not seem to be fully updated yet (for example in My STR Results), but in the email is confirmed the following (unexpected) path: A0-T > A1 > A1b > BT > CT > CF > F > GHIJK > HIJK > IJK > IJ > I > I1 > I-L121 > I-DF29 > I-Z63 > I-BY151.

    I will upload to Y-Full to double check I guess.

    For the genome, does anybody know which file should be sent to Davidski for the G25 Coordinates?
    I don't do G25 work but the equivalent of an autosomal chip test is the '23andMe' file which should be zipped up in the results folder. Its a composite of the SNPs from Ancestry, 23andMe etc so has something like 1.5M rows but its formatted as if it were a 23andMe test. Filename will be something like:

    99999_23andMe_all_hg19.zip

    where 99999 is your kitnumber. It's the only file in hg19 mapping, the rest should be hg38.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
    WGS (Full Genomes Nov 2015, YSEQ Feb 2019, Dante Mar 2019, FGC-10X Linked Reads Apr 2019, Dante-Nanopore May 2019, Chronomics Jan 2020, Sano Genetics Feb 2020, Nebula Genomics June 2020)
    Ancestry GCs: Scots in central Scotland & Ulster, Ireland; English in Yorkshire & Pennines
    Hidden Content
    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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  9. #105
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    Thx MacUalraig!

    BTW, just uploading the y-dna bam and bam.bai to https://qual.iobio.io/

    Item Value Expected
    Read Length 390.87 Should be almost exactly 100, 150, etc
    Raw GBases 0.29 >90; less than 90 and Dante will re-sequence
    % Mapped 100.00 Looking for 95% or higher
    Mapped Avg Read Depth 0.09 Preferably >30 (the real source of the 30x declaration)

    Chr/DNA Len in model (bp) # Mapped # Unmapped Mapped GBases Avg Read Depth
    chrY 57227415 734795 0 0.29 5x

  10. #106
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    The qual.iobio.io site is based around the assumption you are testing with traditional run settings and 30x coverage.

    The WGS400 product currently offered is 15x with 400 base SE reads, so basically everything it's claiming about expectations are wrong.

    5x chrY is pretty low but within the range I'm seeing for those added into https://ydna-warehouse.org/benchmarks.

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  12. #107
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    Quote Originally Posted by Northern Adriatic View Post
    ...........
    For the genome, does anybody know which file should be sent to Davidski for the G25 Coordinates?
    Best thing to do for that is to download a copy of WGSExtract, latest version, to pullout the relevant SNP dataset for his analysis

    https://wgsextract.github.io/

    You're best bet is to probably do is send him the 23&me v3 extract of your WGS data, or a combined 23&me (v3-v5) dataset for your G25 coordinates

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  14. #108
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    Quote Originally Posted by Northern Adriatic View Post
    Thx MacUalraig!

    BTW, just uploading the y-dna bam and bam.bai to https://qual.iobio.io/

    Item Value Expected
    Read Length 390.87 Should be almost exactly 100, 150, etc
    Raw GBases 0.29 >90; less than 90 and Dante will re-sequence
    % Mapped 100.00 Looking for 95% or higher
    Mapped Avg Read Depth 0.09 Preferably >30 (the real source of the 30x declaration)

    Chr/DNA Len in model (bp) # Mapped # Unmapped Mapped GBases Avg Read Depth
    chrY 57227415 734795 0 0.29 5x
    Hi it seems to me this sample it your YF94852^
    i have been see you have 3X this it's bad

  15. #109
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    Quote Originally Posted by JamesKane View Post
    The qual.iobio.io site is based around the assumption you are testing with traditional run settings and 30x coverage.

    The WGS400 product currently offered is 15x with 400 base SE reads, so basically everything it's claiming about expectations are wrong.

    5x chrY is pretty low but within the range I'm seeing for those added into https://ydna-warehouse.org/benchmarks.
    do you can explain more and thanks

  16. #110
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    Some stats from Yfull on samples I uploaded.

    Untitled.png

    The WGS400 underperforms quite a bit from the stated 15x depth coverage.

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