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Thread: Results of Whole Genome Sequencing 2x/4x

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    Results of Whole Genome Sequencing 2x/4x

    Hi all, I have never seen so far some 2x or 4x results of Whole Genome, and I'd be curious to know if someone who did those tests has received his results and to know, for instance, how many no calls they got and how many novel SNPs tested and also how many STRs and if those results have been processed from YFull or other companies. Thanks

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    Quote Originally Posted by Titus Valerius View Post
    Hi all, I have never seen so far some 2x or 4x results of Whole Genome, and I'd be curious to know if someone who did those tests has received his results and to know, for instance, how many no calls they got and how many novel SNPs tested and also how many STRs and if those results have been processed from YFull or other companies. Thanks
    I've done the WGSx2 so far. I believe YFull have set 4x as their minimum level to work with but check with them.
    Compared with the NVs of myself and RC, the only other sequenced person in FGC5856 I found the following:
    valid reads: 11 (me) + 4 (RC)
    no reads: 11

    How useful that is depends of course, so far my NVs are very 'clumpy' anyway so if I was testing someone new I might still consider starting at 2x then adding another 2x later. If it turns out that the RC markers are in a more reliable region to read and I can get reads for all of them at 2x, even better.

    I also got good reads for FGC4077 and FGC4087 but not FGC4078, these are my main branch markers in M222.

    I have a coverage file if you want to see it (pm me).
    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
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    FBIMatch: A------ (autosomal DNA) for segment matching DO NOT POST ADMIXTURE REPORTS USING MY KIT

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    MacUalraig, you felt it was a positive option to go on a WGSX2? Did you have found more information than the more conventional approaches (23andme and others)?

    Thanks,

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    Quote Originally Posted by kafky View Post
    MacUalraig, you felt it was a positive option to go on a WGSX2? Did you have found more information than the more conventional approaches (23andme and others)?

    Thanks,
    It really depends on what you are trying to achieve eg Y sequencing, autosomal ancestry or health. Probably the 2x is best viewed as a starter test which you would want to upgrade later, unless you have a bit of luck and capture your areas of interest straight away. Just to cite one example some of my private Y Elite SNPs showed up but A725 which is the big sub-branch of FGC4077 was missed.

    Like any sequencing test the actual read depth fluctuates, probably more so at 2x average than at higher levels. There were quite a few positions I am interested in where I just got one read but that was sufficient.
    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

  5. The Following 2 Users Say Thank You to MacUalraig For This Useful Post:

     dp (05-09-2016),  kafky (05-09-2016)

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    Quote Originally Posted by MacUalraig View Post
    It really depends on what you are trying to achieve eg Y sequencing, autosomal ancestry or health. Probably the 2x is best viewed as a starter test which you would want to upgrade later, unless you have a bit of luck and capture your areas of interest straight away. Just to cite one example some of my private Y Elite SNPs showed up but A725 which is the big sub-branch of FGC4077 was missed.

    Like any sequencing test the actual read depth fluctuates, probably more so at 2x average than at higher levels. There were quite a few positions I am interested in where I just got one read but that was sufficient.


    I would like a bit more Y, mtdna and autosomal. Not looking for health information. My actual Y haplogroup is very wide, my mtdna seams to be a H100. I do not know how could WGS give more autosomal info, since it appears their database is short and I do not understand how I could find additional cousins. Should I expect more?

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