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Thread: Yseq’s new WGS400 WGS for $399

  1. #51
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    Quote Originally Posted by Dalluin View Post
    With what software do you output these statistics, please ?
    https://qual.iobio.io/

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  3. #52
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    Sorry if the question sound stupid but I am trying to understand the statistics posted and I am still a bit confused.
    On the Y-DNA, does this prove it to be as good as BIG Y 700 (excluding other factors such as mtdna + whole genome + price + bam file)?
    Deep Ancestry: 63.2% AUT_LBK_N + 36.8% RUS_Vonyuchka_En @ 2.6339%
    Ancient: 89.0% ITA_Rome_Late_Antiquity + 11.0% HUN_Avar_Szolad @ 2.4649%

  4. #53
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    Here's a snippet from Press et al. The overdue promise of short tandem repeat variation for heritability which shows the authors predicted relationship between genome-wide coverage and expected coverage for reads fully spanning an STR plus 8 bp of flanking sequence on each side - genome-wide coverage and read length being the controllable variables here:

    To accurately map an STR sequence read and retrieve its unit number genotype, the sequence read must span the STR of interest and include some unique flanking sequence. This requirement limits the length of STRs that can be accurately genotyped and decreases effective STR coverage compared to average whole-genome-sequencing coverage (Figure 2). For this reason, much of the existing sequencing data, which consists largely of short reads (36 bp, 50 bp, or 76 bp) with only modest genome coverage (5–20×) is not suitable for accurate, genome-wide calls of STR genotypes; only a fraction of STRs, mostly short ones, can be assessed with some confidence (Figure 2).



    Figure 2: Effective reduction in STR coverage in whole-genome sequencing

    Expected coverage of STRs for various sequencing depths and read lengths. We assumed 8 bp of flanking sequence on either side (per requirement for LobSTR software [38]). Black bars indicate nominal sequencing coverage for each scenario. 4–5× coverage (left panel) is typical for genomes in the human 1000 Genomes Project [95]; 15–20– coverage is typical for genomes in the A. thaliana 1001 Genomes Project [97,98].
    While this is based on theoretical calculations, I think it does a decent job of showing that both depth of coverage and read depth are important for resolving Y-STRs. It would've been nice if they included the formula they used to generate those plots though.

    It appears that with the 15x WGS400 test, the benefits of longer read length are negated by a lower number of reads fully spanning the Y-STR regions (plus flanking sequences).
    Last edited by aaronbee2010; 04-20-2021 at 08:54 PM.
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-M479 > M124 > V1180 > SK2142 > Y1379 > Y1383 > Y154920* (xZ6135) - M5a1a-G9064A (185G)
    * Maternal Uncle: R1b-M343 > M269 > Z2103 > Z2109 > Y14416 > Y35099 > Y84821 - U7a3a-A9852G > G6150A > C15433T
    * MGMs MGF: R1a-M420 > M198 > Z93 > L657 > Y7 - ?

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  6. #54
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    Quote Originally Posted by aaronbee2010 View Post
    Here's a snippet from Press et al. The overdue promise of short tandem repeat variation for heritability which shows the authors predicted relationship between genome-wide coverage and expected coverage for reads fully spanning an STR plus 8 bp of flanking sequence on each side - genome-wide coverage and read length being the controllable variables here:



    While this is based on theoretical calculations, I think it does a decent job of showing that both depth of coverage and read depth are important for resolving Y-STRs. It would've been nice if they included the formula they used to generate those plots though.

    It appears that with the 15x WGS400 test, the benefits of longer read length are negated by a lower number of reads fully spanning the Y-STR regions (plus flanking sequences).
    My guess at the formula would be: (coverage) x (read length - (str length + 16)) / (read length). If I plot that formula for 30x coverage, my graph looks just like theirs. Screen Shot 2021-04-20 at 9.41.20 PM.png

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  8. #55
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    Using the formula I posited above, the plot of theoretical coverage of a 100bp 30x, 150bp 30x and 400bp 15x test is interesting. At least theoretically, the STR length at which a 400bp 15x test coverage exceeds the 150bp 30x test is about 78bp.Screen Shot 2021-04-21 at 1.15.25 AM.png

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