Page 114 of 116 FirstFirst ... 1464104112113114115116 LastLast
Results 1,131 to 1,140 of 1158

Thread: Big Y-700

  1. #1131
    Registered Users
    Posts
    679

    Quote Originally Posted by Dave-V View Post
    Sorry I'm missing the question. FTDNA isn't calling SNPs in the centromere, that's one of the heterochromatic regions in which they don't call SNPs (that and q12).

    Here's an annotated version of where they're calling SNPs (in blue). It covers all the euchromatic regions (ignore the small blue bar on the extreme right, those were some SNPs mistakenly on the haplotree when I pulled the data). They're NOT calling SNPs in the white regions.

    Attachment 36554

    The DYZ19 region is a small heterochromatic region (you can actually see it also in the study picture that I posted first before). By and large FTDNA CAN cover that one because it's small enough, but it has only a small number of SNPs reported and as the tiny white band shows in the picture it's still not completely covered.

    The point though is that even though they're calling SNPs across the entire blue area there are still potentially problematic areas in there as I mentioned about x-transposed and ampliconic etc.

    As to relative and philosophical, it's not really. It's just genetics, which is more complicated and messy than we want it to be and we're trying to make it more simple than it really is. In genetics there are exceptions and complications to nearly everything, even the basic premise than humans are born either male (XY) or female (XX).

    YSEQ says the Centromeric region is 10072350-11686750. I-S14393 is at base pair 11512535. I’m confused.
    I1 (3200 BC - 2000 BC) Battle Axe Culture >
    DF29 > Z58 > Z59 > Z2041 > Z2040 >
    Z382 (1800 BC - 900 BC) Nordic Bronze Age >
    S26361 > S16414 > FGC24354 >
    FGC24357 (500 BC - 300 AD) Nordic Iron Age >
    FGC24356 > S10350 > FGC75802 >
    Y125947 Lübeck, Germany >
    S21197 Ireland, Netherlands > BY149414 Scotland >
    BY188003 (1420 AD - 1701 AD) Belgium >
    BY188570 (Jean Wauthy 1908 AD) Belgium

    YFull id: YF15884

  2. The Following User Says Thank You to mwauthy For This Useful Post:

     JMcB (02-27-2020)

  3. #1132
    Registered Users
    Posts
    296
    Sex
    Location
    USA
    Nationality
    USA
    Y-DNA (P)
    R1b-L21 L513*

    United States of America Ireland Germany Belgium Wallonia
    Quote Originally Posted by mwauthy View Post
    YSEQ says the Centromeric region is 10072350-11686750. I-S14393 is at base pair 11512535. I’m confused.
    The NCBI (National Center for Biotechnology Information) puts the centromere at 10316945-10544039; i'm not saying they're the last word on the subject, only that all of these regions have buffer zones between them that requires another judgement call as to how far to push SNPs (as if you needed another example of a judgement call :-) ). But from that standpoint YSEQ's Wish a SNP definitions tend to be very conservative (i.e. leaving a lot of space around the problematic regions) while FTDNA tends to be more aggressive about pushing the edges.

    I don't believe there is an easy answer as to which is right. With the heterochromatic regions (CEN, DYZ19, q12) my personal opinion is that if the problem with those regions is an inability to consistently read them reliably but the SNP mutations themselves ARE reliable there then if a test DID produce a read there's nothing wrong with calling a SNP there, it's just that perhaps there would be a lower percentage of tests that covered that position (i.e. read it reliably).

    That's different to me than a possible recombinant region where there's a chance the SNP doesn't get passed on. But I may be oversimplifying things.

    SharedScreenshot.jpg

  4. The Following 3 Users Say Thank You to Dave-V For This Useful Post:

     JMcB (02-27-2020),  mwauthy (02-26-2020),  pmokeefe (02-27-2020)

  5. #1133
    Registered Users
    Posts
    679

    Quote Originally Posted by Dave-V View Post
    The NCBI (National Center for Biotechnology Information) puts the centromere at 10316945-10544039; i'm not saying they're the last word on the subject, only that all of these regions have buffer zones between them that requires another judgement call as to how far to push SNPs (as if you needed another example of a judgement call :-) ). But from that standpoint YSEQ's Wish a SNP definitions tend to be very conservative (i.e. leaving a lot of space around the problematic regions) while FTDNA tends to be more aggressive about pushing the edges.

    I don't believe there is an easy answer as to which is right. With the heterochromatic regions (CEN, DYZ19, q12) my personal opinion is that if the problem with those regions is an inability to consistently read them reliably but the SNP mutations themselves ARE reliable there then if a test DID produce a read there's nothing wrong with calling a SNP there, it's just that perhaps there would be a lower percentage of tests that covered that position (i.e. read it reliably).

    That's different to me than a possible recombinant region where there's a chance the SNP doesn't get passed on. But I may be oversimplifying things.

    SharedScreenshot.jpg

    Thanks for the reply. I was not aware that there were questionable buffer zones around these problematic regions. I learned something new today
    I1 (3200 BC - 2000 BC) Battle Axe Culture >
    DF29 > Z58 > Z59 > Z2041 > Z2040 >
    Z382 (1800 BC - 900 BC) Nordic Bronze Age >
    S26361 > S16414 > FGC24354 >
    FGC24357 (500 BC - 300 AD) Nordic Iron Age >
    FGC24356 > S10350 > FGC75802 >
    Y125947 Lübeck, Germany >
    S21197 Ireland, Netherlands > BY149414 Scotland >
    BY188003 (1420 AD - 1701 AD) Belgium >
    BY188570 (Jean Wauthy 1908 AD) Belgium

    YFull id: YF15884

  6. The Following 2 Users Say Thank You to mwauthy For This Useful Post:

     Dave-V (02-26-2020),  JMcB (02-27-2020)

  7. #1134
    Gold Class Member
    Posts
    2,161
    Sex
    Location
    Florida, USA.
    Ethnicity
    English, Scottish & Irish
    Nationality
    American
    Y-DNA (P)
    I-FT80854
    mtDNA (M)
    H1e2
    mtDNA (P)
    K1

    England Scotland Ireland Prussia Italy Two Sicilies United States of America
    Quote Originally Posted by Dave-V View Post
    The NCBI (National Center for Biotechnology Information) puts the centromere at 10316945-10544039; i'm not saying they're the last word on the subject, only that all of these regions have buffer zones between them that requires another judgement call as to how far to push SNPs (as if you needed another example of a judgement call :-) ). But from that standpoint YSEQ's Wish a SNP definitions tend to be very conservative (i.e. leaving a lot of space around the problematic regions) while FTDNA tends to be more aggressive about pushing the edges.

    I don't believe there is an easy answer as to which is right. With the heterochromatic regions (CEN, DYZ19, q12) my personal opinion is that if the problem with those regions is an inability to consistently read them reliably but the SNP mutations themselves ARE reliable there then if a test DID produce a read there's nothing wrong with calling a SNP there, it's just that perhaps there would be a lower percentage of tests that covered that position (i.e. read it reliably).

    That's different to me than a possible recombinant region where there's a chance the SNP doesn't get passed on. But I may be oversimplifying things.

    SharedScreenshot.jpg


    Hello Dave,

    Thank you for clarifying that. I was also under the impression that FTDNA (& YFull) sometimes used SNPs from the Centromeric region.

    Coincidentally, it recently came up when my cousins and I formed a new branch. Two of the SNPs I thought were in the CEN region, were included as SNPs defining the branch (FT230060 pos.11485990 & FT230061 pos.11357984). So I was wondering why they chose those two. I figured it might be because four people matched them. Which may still be the case but those positions are also pretty far away from the NCBI’s definition of the CEN region. Which makes it a lot more understandable.

    Like mwauthy, I’ve learned something new today!


    P.S. It also answers another question I’ve been wondering about. According to both YFull and FTDNA, I still have three (best quality) Novel Variants left. One of them is at the position:10146857. Which, like the others, is on the borderline of YSEQ’s range but outside the NCBI’s region. So I now understand that call better, too.
    Last edited by JMcB; 02-27-2020 at 04:18 AM.
    Paper Trail: 43.8% English, 29.7% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

  8. The Following 2 Users Say Thank You to JMcB For This Useful Post:

     Dave-V (02-27-2020),  mwauthy (02-27-2020)

  9. #1135
    Registered Users
    Posts
    22
    Sex
    Y-DNA (P)
    BY250+
    mtDNA (M)
    U6a7a2a

    Does anyone have a list of all these regions in Hg38? I have found some like P1 to P8 & Pseudoautosomal, but not X-degenerate, X-transposed and Ampliconic.

  10. #1136
    Registered Users
    Posts
    296
    Sex
    Location
    USA
    Nationality
    USA
    Y-DNA (P)
    R1b-L21 L513*

    United States of America Ireland Germany Belgium Wallonia
    Quote Originally Posted by Jeffrey View Post
    Does anyone have a list of all these regions in Hg38? I have found some like P1 to P8 & Pseudoautosomal, but not X-degenerate, X-transposed and Ampliconic.
    This is a list I cobbled together from several sources but it's all hg38. Anything NOT covered by this list is X-degenerate.

    You may not find these agreeing with all other sources for a variety of reasons; one is the buffer zones I mentioned before and everyone has a different view on how much room to leave around certain regions. Another is because there are different versions even of hg38 (I think we're up to .13 now) and occasionally things move a little. I also did simplify these slightly - PAR1 for instance is usually said to start at about 10,000 but the first positions aren't used so I just started it at 0, and there IS a very small gap between q12 and PAR2 that I just ignored; I don't believe that's used to call SNPs either.

    Anyway my point is allow for some variation between these and whatever other studies or sources you find.

    Also obviously as mentioned before there are ongoing debates between people much more expert than I about how these various types of regions should be used.

    Label Start (hg38) End (hg38) Reason
    PAR1 0 2781479 Pseudoautosomal
    GCH (LTR2) 2997393 2998942 Gene Conversion Hotspot
    XTRAN 3049683 6234603 X-transposed
    AMPL 6234604 6532466 Ampliconic
    XTRAN 6532467 6748297 X-transposed
    GCH (HSA) 7228670 7229600 Gene Conversion Hotspot
    GCH (CER3) 7295058 7295821 Gene Conversion Hotspot
    GCH (CER6) 7301890 7302401 Gene Conversion Hotspot
    GCH (CER7) 7303737 7305018 Gene Conversion Hotspot
    GCH (CER9) 7366890 7367378 Gene Conversion Hotspot
    GCH (CER12) 7451057 7451485 Gene Conversion Hotspot
    AMPL 7604184 10072348 Ampliconic
    CEN 10316945 10544039 Heterochromatic
    GCH (CER15) 11930845 11930917 Gene Conversion Hotspot
    GCH (CER17) 12362517 12363336 Gene Conversion Hotspot
    GCH (CER18) 12363524 12364177 Gene Conversion Hotspot
    GCH (CER19) 12369399 12369930 Gene Conversion Hotspot
    GCH (ARSDP) 12379765 12380130 Gene Conversion Hotspot
    AMPL 13983907 13985771 Ampliconic
    GCH (VCY) 13985772 13986512 Gene Conversion Hotspot
    AMPL 13986513 14056217 Ampliconic
    GCH (VCY) 14056218 14056958 Gene Conversion Hotspot
    AMPL 14056959 14058179 Ampliconic
    AMPL 15874594 15904782 Ampliconic
    AMPL 16159394 16425562 Ampliconic
    AMPL 17455477 18870014 Ampliconic
    DZY19 20054913 20351055 Heterochromatic
    AMPL 21335747 26663486 Ampliconic
    Q12 27078488 56887902 Heterochromatic
    PAR2 56887903 57227415 Pseudoautosomal

  11. The Following 6 Users Say Thank You to Dave-V For This Useful Post:

     Jeffrey (02-27-2020),  JMcB (02-27-2020),  Muircheartaigh (03-02-2020),  mwauthy (02-27-2020),  pmokeefe (02-27-2020),  Roslav (03-01-2020)

  12. #1137
    Registered Users
    Posts
    116
    Sex

    One of the big problems with the DYZ19 region is that , in the first third of it, the Human Genome standard
    sequence is seriously wrong. For instance, there is the small region that the Human Genome (and FTDNA) separates
    out in a small separate segment.

    A year or so ago I studied this region carefully, because there is a very important marker for my project
    in it, that is quite reliable. The was discovered long ago in the the first batch of BigYs, in
    me and several Clan Donald other project men, including all the Clan chiefs and chieftains in R1a.

    FTDNA called several SNPs there ... but they were clearly bogus when the BAMS were examined.
    It turned out that there were three large deletes, which I named CLD56, CLD57, and CLD83.
    They ranged from 1 to 3 kilobases long.

    But I always suspected that the Human Genome was wrong, and they were one.

    So I paid Full Genomes for a "long read" sequence, which actually is only "pseudo long read".

    This was sufficient to show that the Human Genome was wrong. The pseudo long reads
    covered FAR too long stretches. It by itself was insuffient to get
    a de-novo alignment (due to the nature of DYS19).

    So I found a de-novo PACBIO sequence of a South Korean man (Haplotype O) and realigned myself to it.
    This worked nicely, at least for the first part of DYS19. The three deletes in me turned out to be, in
    fact, just one about 10 kilobases long. And the "left out" segment fits in perfectly very close
    to it.

    There is one serious flaw in this: The PACBIO de-novo sequence has a gap just where
    DYS19 starts in the Human Genome. This means there is still something wrong.

    As you get farther into the DYS19 region the PACBIO sequence peters out, because
    of the overly large mistake rate in the technology of its time. A really large coverage
    test today with improvements in read quality might (would?) fix that.

    I said that this marker is reliable ... and it is. It can be called visually in a BAM
    file looking at density of reads, or equivalently in the FTDNA VCF file by doing the same thing.

    Doug McDonald
    Last edited by dtvmcdonald; 02-28-2020 at 01:50 AM.

  13. The Following 7 Users Say Thank You to dtvmcdonald For This Useful Post:

     Dave-V (02-28-2020),  JMcB (02-28-2020),  MacUalraig (03-01-2020),  Mikewww (03-05-2020),  mwauthy (02-28-2020),  Oleg (Rus) (03-09-2020),  Roslav (03-01-2020)

  14. #1138
    Registered Users
    Posts
    3,985
    Sex
    Y-DNA (P)
    R1b
    mtDNA (M)
    H

    You are making good points, Doug. It is important to recognize that a mutation may be extremely reliable at marking phylogeny but be difficult to read with some test technologies. The problem is not necessarily the mutation. It may NOT be biologically unstable. It is just that the tests may have problems reading it, or even the reference is wrong. It is not wise to dismiss these kinds of mutations arbitrarily.
    Last edited by Mikewww; 03-05-2020 at 05:54 PM.

  15. #1139
    Registered Users
    Posts
    66
    Sex
    Omitted
    Location
    West Coast, USA
    Ethnicity
    English & Scottish
    Nationality
    USA
    Y-DNA (P)
    I-S1990
    mtDNA (M)
    H1c2

    United States of America England Scotland Denmark
    Quote Originally Posted by Stone Meadow View Post
    No full results yet, but I am beginning to see movement. All of a sudden this morning FTDNA changed my Y-haplogroup from I1 M253 to I-S1990. I already knew that based on the results of my Z2535 SNP Pack test done late last summer, but for some reason my dashboard continued to list M253 as my Y-hapologroup. Meanwhile, the 'Pending Lab Results' page continues to say 'Results expected 02/03/2020 - 02/17/2020'. That window opens Monday, 3 days from now. I'm like a little kid waiting to open birthday presents.
    It looks like I spoke too soon. I waited patiently through the 'Results expected 02/03/2020 - 02/17/2020' window, but on the last day it updated to read 'Results expected 03/03/2020 - 03/17/2020'. On 03/02/2020 it updated to read '03/16/2020 - 03/30/2020'. I wonder how many times it will slip my results date. At least it still notes that no action on my part is required.
    Interesting factoid: My user name, Stone Meadow, is a translation of my Old English given name, Hidden Content .
    Known Paper Trail: Paternal line emigrated from England in 1667. Maternal (Patrilineal) line emigrated from Scotland in 1648.
    Y Haplogroup: I1>M253>DF29>Z58>Z59>Z60>Z140>Z2535>YSC0000261>S19 90 [FTDNA Big Y-700 batched 11/11/2019 in batch 1022]
    mtHaplogroup: H1c2 [FTDNA FMS completed 11/15/2019]

  16. #1140
    Registered Users
    Posts
    66
    Sex
    Omitted
    Location
    West Coast, USA
    Ethnicity
    English & Scottish
    Nationality
    USA
    Y-DNA (P)
    I-S1990
    mtDNA (M)
    H1c2

    United States of America England Scotland Denmark
    Quote Originally Posted by Stone Meadow View Post
    It looks like I spoke too soon. I waited patiently through the 'Results expected 02/03/2020 - 02/17/2020' window, but on the last day it updated to read 'Results expected 03/03/2020 - 03/17/2020'. On 03/02/2020 it updated to read '03/16/2020 - 03/30/2020'. I wonder how many times it will slip my results date. At least it still notes that no action on my part is required.
    Okay, my latest window from FTDNA opened today. The good news ... the only news ... is that its status still says '03/16/2020 - 03/30/2020'. Since I've nothing much to do these days while on coronavirus isolation I am really looking forward to getting the results.
    Interesting factoid: My user name, Stone Meadow, is a translation of my Old English given name, Hidden Content .
    Known Paper Trail: Paternal line emigrated from England in 1667. Maternal (Patrilineal) line emigrated from Scotland in 1648.
    Y Haplogroup: I1>M253>DF29>Z58>Z59>Z60>Z140>Z2535>YSC0000261>S19 90 [FTDNA Big Y-700 batched 11/11/2019 in batch 1022]
    mtHaplogroup: H1c2 [FTDNA FMS completed 11/15/2019]

  17. The Following User Says Thank You to Stone Meadow For This Useful Post:

     Roslav (03-16-2020)

Page 114 of 116 FirstFirst ... 1464104112113114115116 LastLast

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •