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Thread: Full Y Chromosome Sequencing: Phase III Pilot

  1. #1061
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    Quote Originally Posted by Petr View Post
    I did both BigY and FGC Elite tests and there are really many false positives for SNPs with reading 2x, so I think this is not very useful. But there is no false positive for more readings.
    Even if there is a problem with false positives its only a problem in practical terms if there are false positives within your own branch of the tree. If I test an M222 person and he comes back S658+ AND FGC4077+ from a 2x read then yes I have a problem. If he's FGC4077+ and has a false positive for something in hg I, that I can live with.

  2. #1062
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    Feedback from a whole genome customer:

    The average read length seems to be about 150 nt and read depth averages
    around 20-30. Coverage seems to be well over 90% of the sequenceable
    genome, probably close to 95%. My analysis so far has barely scratched the
    surface, but I have found a few very interesting SNPs, including one for
    which I am heterozygous....

    So far I am extremely satisfied with the quality of these WGS results."""

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  4. #1063
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    Sample Big Y:

    ChrY BAM file size: 0.72 Gb
    Reads (all): 12,080,535
    Mapped reads: 12080535 (100.00%)
    Unmapped reads: 0
    Length coverage: 13,929,068 bp (54.30%)
    Min depth coverage: 1X
    Max depth coverage: 7288X
    Mean depth coverage: 91.23X
    Median depth coverage: 60X
    No call: 11,724,498 bp


    Sample FGC whole genome: (Y chromosome data from whole genome),
    FGC -- Y chr data from whole genome
    ChrY BAM file size:
    0.29 Gb
    Reads (all):3,810,713
    Mapped reads:3,808,394 (99.94%)
    Unmapped reads: 2319 (0.06%)
    Length coverage: 22,858,252 bp (89.10%)
    Min depth coverage:1X
    Max depth coverage:7999X
    Mean depth coverage:21.38X
    Median depth coverage:12X
    No call: 2,795,314 bp

    Note:
    This is anonymized analysis performed by YFull, not FGC.
    Last edited by FGC Corp; 07-05-2015 at 12:23 AM.

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  6. #1064
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    One summary:

    (out of 59,373,566) chrY sites


    Sample Y Elite 1.0 result
    25,158,394 bp

    FGC Whole genome Y chromosome result:
    22,858,252 bp

    Big Y for comparison:
    13,929,068 bp

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  8. #1065
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    Quote Originally Posted by FGC Corp View Post
    One summary:

    (out of 59,373,566) chrY sites


    Sample Y Elite 1.0 result
    25,158,394 bp

    FGC Whole genome Y chromosome result:
    22,858,252 bp

    Big Y for comparison:
    13,929,068 bp


    "The average read length seems to be about 150 nt and read depth averages
    around 20-30. Coverage seems to be well over 90% of the sequenceable
    genome, probably close to 95%. My analysis so far has barely scratched the
    surface, but I have found a few very interesting SNPs, including one for
    which I am heterozygous....So far I am extremely satisfied with the quality of these WGS results."





    Not so great news, I thought WGS Y coverage was actually better than Y Elite.
    Last edited by paulgill; 07-06-2015 at 08:00 AM.

  9. #1066
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    Quote Originally Posted by paulgill View Post
    Bad news, I thought WGS Y coverage was actually better than Y Elite.
    That measure is only part of the story. WGS Y has a read length of 150bp and Y Elite 1.0 had a read length of 100bp. WGS doesn't use a capture design, so the Y chromosome coverage is more even than Y Elite.

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  11. #1067
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    Quote Originally Posted by FGC Corp View Post
    That measure is only part of the story. WGS Y has a read length of 150bp and Y Elite 1.0 had a read length of 100bp. WGS doesn't use a capture design, so the Y chromosome coverage is more even than Y Elite.
    But Y Elite 2.0 read length is better, 250bp.

    But WGS is still a million times better than BIG Y in many ways, I believe.
    Last edited by paulgill; 07-06-2015 at 04:21 AM.

  12. #1068
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    My results - FGC Elite batch #12:

    ChrY BAM file size: 2.56 Gb
    Reads (all): 22008729
    Mapped reads: 21130290 (96.01%)
    Unmapped reads: 878439 (3.99%)
    Length coverage: 22959696 bp (89.50%)
    Min depth coverage: 1X
    Max depth coverage: 7996X
    Mean depth coverage: 76.85X
    Median depth coverage: 37X
    Length coverage for age: 8440802 bp
    No call: 2693870 bp

    SNPs (all): 71868
    Positive: 2766 (3.85%)
    Negative: 68490 (95.30%)
    Ambiguous: 540 (0.75%)
    No call: 62 (0.09%)

    BigY:
    ChrY BAM file size: 0.58 Gb
    Reads (all): 10608206
    Mapped reads: 10608206 (100.00%)
    Unmapped reads: 0
    Length coverage: 14351177 bp (55.94%)
    Min depth coverage: 1X
    Max depth coverage: 7999X
    Mean depth coverage: 80.80X
    Median depth coverage: 54X
    Length coverage for age: 7886681 bp
    No call: 11302389 bp

    SNPs (all): 71869
    Positive: 2109 (2.93%)
    Negative: 55664 (77.45%)
    Ambiguous: 278 (0.39%)
    No call: 13815 (19.22%)
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
    mtDNA: J1c1i (J1c1 + 7735G and 8848C) Extras: 198T 12007A 16422C 16431A

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  14. #1069
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    Posted in a Genomeweb article:

    Blaine Bettinger, author of the blog*The Genetic Genealogist, said that he has had some success with the new Y testing services.
    "Of course, I purchased a Big Y test from FTDNA, which has turned out to be extremely valuable for my haplogroup project, the R1b-L1/S26 Y-DNA Haplogroup Project," Bettinger said. "We've discovered several new SNPs as a result of Big Y that will help us further breakdown this group."
    Bettinger also tried Full Genomes' interpretation of his Big Y results and was "extremely happy" with the firm's service. "The instructions for interpreting the results are very clear, and the variety of results was terrific, including the comparison to others."
    Source: (news article from June 26, 2015)
    Consumer Genomics Firms Hope Lower Costs, New Features Will Make Y Chromosome Sequencing Mainstream
    Jun 26, 2015 | Justin Petrone

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  16. #1070
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    Quote Originally Posted by FGC Corp View Post
    Posted in a Genomeweb article:



    Source: (news article from June 26, 2015)
    Consumer Genomics Firms Hope Lower Costs, New Features Will Make Y Chromosome Sequencing Mainstream
    Jun 26, 2015 | Justin Petrone
    Where is the link to the article?

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