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Thread: Yseq’s new WGS400 WGS for $399

  1. #11
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    Quote Originally Posted by MacUalraig View Post
    My last three kits were all at 400bp, came in between Feb 4th and 7th. However I paid the full earlier price (e544.35) and now its cheaper!
    How long did they take?
    Its now saying “extracting b swab” next to my order so fingers crossed they can do the test without me having to send a new sample.

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  3. #12
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    Quote Originally Posted by Robert McBride View Post
    How long did they take?
    Its now saying “extracting b swab” next to my order so fingers crossed they can do the test without me having to send a new sample.
    Somewhat longer than the normal 5-6 weeks, but that was supposed to be a one-off hold up. I think the last of them took 8 weeks.
    I also have another I only paid for earlier this month so hopefully that will be back to normal schedule.
    YSEQ:#37; YFull: YF01405 (Y Elite 2013)
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    I ordered mine last sunday and am looking forward to the results to compare them with the other NGSs I did.

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    I just sent back my sample so the waiting has started.

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  9. #15
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    Great price but any possibility of a sale?
    Last edited by ThaYamamoto; 03-02-2021 at 08:00 PM.

  10. #16
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    Quote Originally Posted by MacUalraig View Post
    My last three kits were all at 400bp, came in between Feb 4th and 7th. However I paid the full earlier price (e544.35) and now its cheaper!
    You did the 400 bp 15x wgs test or the 50x like in the published test runs? I just wonder how the 15x wgs400 compares to a classical dante or nebula 30x

  11. #17
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    They were purchased and delivered at 15x WGS (~7x chrY).
    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)
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  13. #18
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    Quote Originally Posted by dosas View Post
    According to your personal opinion, would it be worth it to buy this over Nebula, for the extra price? I am planning to get one for my dad, soon.
    I'm in the process of generating some simulated 15x WGS400 data (from the 50x WGS400 BAM from sample 16672) to analyse to see how well the 15x test that customers will actually receive performs compared to standard 30x WGS tests, although I'm busy with work at the moment and my health hasn't been the best recently so I can't give an ETA at the moment.

    Regarding YSEQ's WGS400 test, their showcased statistics have been impressive but the BAM file used for these statistics has 50x mapped coverage whereas they're initially making the test available with 15x coverage (and possibly lower mapped coverage), so these statistics are almost certainly not entirely representative of what customers with 15x WGS400 data will receive and could even be considered as misleading to customers of the 15x product by some people.

    The "Est. Years/SNP" metric on Y-DNA warehouse is similar for their standard 50x WGS (150 bp paired-end) test and the new 50x WGS400 (400 bp single-end), so when coverage is more-or-less controlled, the Y-SNP resolution appears to be similar (although we only have one WGS400 sample on there at the moment). This suggests that increased read length doesn't contribute much to Y-SNP coverage so carrying this thought forward, the WGS400 15x test that a consumer would end up purchasing from YSEQ would probably have a similar "Est. Years/SNP" to the 150 bp 15x WGS from YSEQ, which gets outperformed by Nebula and Dante 30x WGS tests for Y-SNP discovery (at least going by this admittedly heuristic metric).

    Having said this, even YSEQ have mentioned that one of the main advantages of 400 bp read lengths would be increased Y-STR resolution, but the results we've seen here are with 50x coverage and not 15x, so the "real" Y-STR resolution of this test remains to be seen. The problem here is that the ability of reads with a higher length to span repeat regions in their entirety can be easily negated by lower coverage, so it's hard to guess which test will be better. I'm not sure what the best STR test to perform on my simulated 15x data is though, so I'm currently at a crossroads at the moment. Any recommendations here from anyone would be appreciated. I've currently got the BAM Analysis Kit in mind, although I think this uses lobSTR, which uses an Illumina PCR stutter model, so I'm not sure how well this model will work for DNBSEQ data. Even screenshots of Y-STRs in IGV showing both 15x and 50x BAM files is better than nothing.

    TL;DR: Y-SNP resolution for the WGS400 test is probably worse than Nebula or Dante tests (assuming the latter company provides a file that isn't undersequenced or has excessive microbial contamination). Y-STR resolution for this test when comparing 15x WGS400 data (~7x chrY coverage) to 30x 150 bp WGS (~15x chrY coverage) currently remains to be seen, although I'm figuring this out. Until this is figured out, it's hard to say whether or not the extra $80 is worth it.
    Last edited by aaronbee2010; 03-03-2021 at 08:30 PM.
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    * Maternal Uncle: R1b-M343 > M269 > Z2103 > Z2109 > Y14416 > Y35099 > Y84821 - U7a3a-A9852G > G6150A > C15433T
    * MGMs MGF: R1a-Z93 > Y7 - ?

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  15. #19
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    I know that this could sound like a newbie question (and I am a newbie) but... is this better or worse than BIG Y 700?
    The goal in my case is just to find out my subclades (which looking at 23andme raw data were all negative except for I-Z139 which was "not determined" but with I-Z138 negative) and therefore possibly the origins of my I1 haplogroup.
    I would take the autosomal and mtdna part as a nice bonus, since judging from Admixture Studio the genotype ratio of my 23andme v5 test is in the range of 25-30%.

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  17. #20
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    Quote Originally Posted by Northern Adriatic View Post
    I know that this could sound like a newbie question (and I am a newbie) but... is this better or worse than BIG Y 700?
    Hard to say. On the clear positive side, the YSEQ WGS test is cheaper than Big Y700 and includes autosomal and mtdna.

    They are not identical but probably close to equivalent if your purpose is just finding where you fall on the Y-DNA haplotree down to present day since they will both give you nearly the same trail of SNPs down to present day. The YSEQ 15x test has on average a fraction less coverage than the Big Y, their 50x test seems to have a fraction more coverage. But the differences in company practices probably have more impact on whether any given SNP that might be important to you is reported or missed in your test. It appears to me from repeated observation that FTDNA's aligner has stricter quality criteria than WGS aligners which results in fewer SNPs reported during alignment, but I do know that typically FTDNA reports SNPs from regions of the Y chromosome that YFull (the main interpreter of WGS tests) marks as low quality, so either way small variances in SNP reporting can occur just based on differences in how the tests are interpreted. Which test is better in that sense depends more on the element of chance and where your important SNPs sit and how many reads they had in your test.

    Because of their larger tester database, the FTDNA haplotree has better definition than the YFull haplotree especially in heavily-tested haplogroups like I and R, so you'd probably get placed in a subclade closer to present day on the FTDNA haplotree. But if you don't mind doing that analysis manually by comparing your WGS data to the FTDNA public haplotree you can see where you fall there so that's not really a show-stopper in my opinion.

    Again more of a factor in the heavily-tested haplogroups like I and R, but FTDNA has the larger match database which would be necessary if you want to use the information for genealogy purposes rather than only find your closest subclade. But of course if you happen to fall into a group that has also invested heavily in WGS that's less of a concern, so if you suspect that you'll fall into a certain haplogroup it's worth checking it out on the YFull haplotree to see how many testers are there compared to the FTDNA tree, which can give you a perspective on the relative value to you of the larger FTDNA match database.

    So in my opinion if you don't have a good sense of your haplogroup already then the main differences are cost and autosomal/mtdna versus the larger match database and I would go for whichever of those is the more attractive add-on.

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