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Thread: Yseq’s new WGS400 WGS for $399

  1. #41
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    The kit I paid for on Feb 4th returned results on Apr 9th. However I should mention that I placed two new orders on Apr 6th and 7th so those events may not be unconnected ;-)
    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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  3. #42
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    Quote Originally Posted by ChrisR View Post
    Hopefully a 30x version will be available soon as I think having ~15x on the Y is something every serious Y-DNA researcher wants to have at least the option for, ~7x feels like 1000 Genomes data from ages ago (I know other things also count).
    Astrid answered to an email question that it is possible to order a 30x 90Gb WGS400, instead of the standard 15x 45Gb for $399 for double the price. Unfortunately on the website there is no mention of the read depth or GBases.
    Last edited by ChrisR; 04-15-2021 at 12:04 PM.
    Particularly interested in: DNA/Admixture from Historical Tyrol, Central Alps and related/connected populations; Y-DNA J2a-FGC16096, J2a-L210(xZ482), R1a-M17, R1b-U106; mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects: Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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  5. #43
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    Quote Originally Posted by ChrisR View Post
    Astrid answered to an email question that it is possible to order a 30x 90Gb WGS400, instead of the standard 15x 45Gb for $399 for almost double the price. Unfortunately on the website there is no mention of the read depth or GBases.
    Yes they should tidy the page up and there is the issue of the non-standard sample stats too.
    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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  7. #44
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    sattistics of WGS400, not bad.
    WGS400.png

  8. The Following 10 Users Say Thank You to rock For This Useful Post:

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  9. #45
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    Quote Originally Posted by rock View Post
    sattistics of WGS400, not bad.
    WGS400.png
    Slightly undersequenced according to YSEQ's criterion for the amount of sequencing data generated (45+ GBases) but the percentage of reads mapping to the reference genome is very impressive. Congratulations
    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-Z93 > Y7 - ?

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  11. #46
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    thanks @rock . The most interesting for me will be the Y-Stats and specifically those at YFull:
    SNPs (Positive, No call), STRs (Reliable, N/A).

    I would need to do updated comparisons but think the following DL result could be a reference:
    3000 or more positive SNPs, under 400 no call, 600 or more Reliable STRs, less then 200 STRs N/A

    Or this BigY500:
    2200 or more positive SNPs, under 4000 no call, 700 or more Reliable STRs, less then 100 STRs N/A
    Last edited by ChrisR; 04-17-2021 at 05:56 PM.
    Particularly interested in: DNA/Admixture from Historical Tyrol, Central Alps and related/connected populations; Y-DNA J2a-FGC16096, J2a-L210(xZ482), R1a-M17, R1b-U106; mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects: Hidden Content , Hidden Content , J2a-PF5197, ISOGG Wiki, GenWiki (german)

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  13. #47
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    Quote Originally Posted by ChrisR View Post
    thanks @rock . The most interesting for me will be the Y-Stats and specifically those at YFull:
    SNPs (Positive, No call), STRs (Reliable, N/A).

    I would need to do updated comparisons but think the following DL result could be a reference:
    3000 or more positive SNPs, under 400 no call, 600 or more Reliable STRs, less then 200 STRs N/A

    Or this BigY500:
    2200 or more positive SNPs, under 4000 no call, 700 or more Reliable STRs, less then 100 STRs N/A
    This just completed STR analysis (took 2 months+ at YFull)
    ChrY BAM file size: 0.25 GbHg38
    Reads (all): 845288
    Mapped reads: 845288(100.00%)
    Unmapped reads: 0
    Length coverage: 23499477 bp(99.42%)
    Min depth coverage: 1X
    Max depth coverage: 724X
    Mean depth coverage: 8.52X
    Median depth coverage: 7X
    Length coverage for age*: 8058353 bp
    No call: 136878 bp

    SNPs (all): 219497
    Positive: 3009 (1.37%)
    Negative: 15358 (7.00%)
    Ambiguous: 56 (0.03%)
    No call: 94 (0.04%)

    STRs (all): 780
    Reliable alleles: 597 (76.54%)
    Uncertain alleles: 52 (6.67%)
    N/A: 131 (16.79%)
    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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  15. #48
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    The other one wasn't as good, the read depth is sub-par and so in particular are the STRs

    ChrY BAM file size: 0.17 GbHg38
    Reads (all): 575395
    Mapped reads: 575395(100.00%)
    Unmapped reads: 0
    Length coverage: 23261753 bp(98.42%)
    Min depth coverage: 1X
    Max depth coverage: 692X
    Mean depth coverage: 6.09X
    Median depth coverage: 5X
    Length coverage for age*: 7103744 bp
    No call: 374602 bp

    SNPs (all): 219497
    Positive: 3005 (1.37%)
    Negative: 15364 (7.00%)
    Ambiguous: 74 (0.03%)
    No call: 299 (0.14%)


    STRs (all): 780
    Reliable alleles: 510 (65.38%)
    Uncertain alleles: 27 (3.46%)
    N/A: 243 (31.15%)
    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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  17. #49
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    What software would you recommend to read the NGS BAM file?
    YFull : YF83613

    Whats' else ??
    Pangea - Pannotia - Rodinia - Columbia - Kernoland - Ur - Vaalbara - ??

    Gaïa's Haplogroup : G2VR2a1

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  19. #50
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    Quote Originally Posted by rock View Post
    sattistics of WGS400, not bad.
    WGS400.png
    With what software do you output these statistics, please ?
    YFull : YF83613

    Whats' else ??
    Pangea - Pannotia - Rodinia - Columbia - Kernoland - Ur - Vaalbara - ??

    Gaïa's Haplogroup : G2VR2a1

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