Page 1 of 3 123 LastLast
Results 1 to 10 of 24

Thread: Loschbour Man's Gedmatch ID

  1. #1
    Registered Users
    Posts
    467
    Sex
    Location
    Earth
    Ethnicity
    Ashkenazi
    Nationality
    Australian, Israeli
    Y-DNA
    E-PF1975
    mtDNA
    K1a9

    Australia Israel

    Loschbour Man's Gedmatch ID

    His ID is F999918
    My results:
    Default results:
    Minimum threshold size to be included in total = 700 SNPs
    Mismatch-bunching Limit = 350 SNPs
    Minimum segment cM to be included in total = 7.0 cM

    "Largest segment = 0.0 cM
    Total of segments > 7 cM = 0.0 cM
    (1813) No shared DNA segments found"

    Lowered values:

    Minimum threshold size to be included in total = 350 SNPs
    Mismatch-bunching Limit = 175 SNPs
    Minimum segment cM to be included in total = 1.0 cM

    Largest segment = 3.3 cM
    Total of segments > 1 cM = 17.6 cM

    http://www.fc.id.au/2014/10/loschbou...es-living.html
    Last edited by John Doe; 10-07-2014 at 11:44 AM.
    I can be certain of one thing, that I know nothing.

  2. The Following 2 Users Say Thank You to John Doe For This Useful Post:

     Mehrdad (10-09-2014),  NK19191 (10-07-2014)

  3. #2
    Registered Users
    Posts
    2,066
    Sex

    Here is a list of ancient remains that he has found matches on. I found one-to-one matches on La Braña so I included it. He thinks that the specimens are ancient or have contamination. I have extreme doubts about that. The admixture results are all different from living humans except Clovis Anzick and people with all Native American ancestry.

    Loschbour ancient DNA matches living people

    Kit F999918

    I am not sure what to make of these matches who match with a 8000 years old ancient DNA. Could the sample be contaminated? Is the sample really ancient? I don't know for sure.

    http://www.fc.id.au/2014/10/loschbou...es-living.html

    Linearbandkeramik (LBK) ancient DNA matches with living people!

    Kit F999916
    Ancient DNA are not supposed to match with living people as recent cousins. Just like Clovis-Anzick-1 ancient DNA, there are matches. I am not sure how to interpret these matches, but my rational tells me to incline towards the sample not being ancient.

    http://www.fc.id.au/2014/10/linearba...cient-dna.html

    Mal'ta MA-1 ancient DNA have matches with a few living people on X-Chromosome!

    Kit F999914

    I wasn't expecting any surprise matches but I was wrong again. Unlike the Clovis-Anzick-1 sample having matches on autosomal DNA, the Mal'ta MA-1 sample is having matches on X chromosome. My immediate thought was wow! These matches, although small deserves further investigation.

    http://www.fc.id.au/2014/09/malta-ma...e-matches.html

    Analyzing La Braña-Arintero Ancient DNA

    Kit F999915

    I did one-to-one with my DNA and nothing in common. May be you have something in common. Let me know what you think.

    http://www.fc.id.au/2014/09/analyzin...cient-dna.html

    Clovis-Anzick-1 ancient DNA have matches with living people!
    Kit F999913

    I uploaded a new kit filtered with SNPs used by most DNA companies: Uploaded New GEDMatch Kit for Clovis-Anzick-1. Please use GEDMatch kit# F999913 as I had deleted F999912 to avoid redundant kits. In spite of this change, there is not much difference in matches. After some conversation with GEDMatch, there seems to be no-calls and SNPs found in kit not tested by DNA companies and vice-versa. Hence, I am trying to process from BAM files provided by the authors to see if I can get more SNPs to get to the bottom of this mystery.

    http://www.fc.id.au/2014/09/clovis-a...ng-people.html

  4. The Following 3 Users Say Thank You to ArmandoR1b For This Useful Post:

     dp (10-14-2014),  Mehrdad (10-09-2014),  NK19191 (10-07-2014)

  5. #3
    Registered Users
    Posts
    2,066
    Sex

    Here is a spreadsheet of the MDLP K23b results of the ancient specimens and two living Europeans.

    https://www.dropbox.com/s/3bmjv02e78...s%20.xlsx?dl=0

    Here is a worddoc of screenshots of the MDLP K23b results of the ancient specimens and two living Europeans.

    https://www.dropbox.com/s/zgti0c2grl...mens.docx?dl=0

  6. The Following 2 Users Say Thank You to ArmandoR1b For This Useful Post:

     NK19191 (10-07-2014),  vettor (10-07-2014)

  7. #4
    Registered Users
    Posts
    467
    Sex
    Location
    Earth
    Ethnicity
    Ashkenazi
    Nationality
    Australian, Israeli
    Y-DNA
    E-PF1975
    mtDNA
    K1a9

    Australia Israel
    Here are my fixed results:


    Comparing Kit - and F999914 (Malta MA-1)

    Minimum threshold size to be included in total = 200 SNPs
    Mismatch-bunching Limit = 100 SNPs
    Minimum segment cM to be included in total = 1.0 cM


    Largest segment = 2.0 cM
    Total of segments > 1 cM = 3.1 cM

    Comparison took 0.43798 seconds.










    Comparing Kit - and F999918 (Loschbour)


    Minimum threshold size to be included in total = 200 SNPs
    Mismatch-bunching Limit = 100 SNPs
    Minimum segment cM to be included in total = 1.0 cM


    Largest segment = 4.6 cM
    Total of segments > 1 cM = 201.5 cM


    Comparison took 0.56628 seconds.










    Comparing Kit - and F999915 (La Braña-Arintero)


    Minimum threshold size to be included in total = 200 SNPs
    Mismatch-bunching Limit = 100 SNPs
    Minimum segment cM to be included in total = 1.0 cM


    Largest segment = 1.3 cM
    Total of segments > 1 cM = 1.3 cM

    Comparison took 0.46994 seconds.










    Comparing Kit - and F999916 (Linearbandkeramik) (Stuttgart)


    Minimum threshold size to be included in total = 200 SNPs
    Mismatch-bunching Limit = 100 SNPs
    Minimum segment cM to be included in total = 1.0 cM



    Largest segment = 4.3 cM
    Total of segments > 1 cM = 414.3 cM

    Comparison took 0.42762 seconds.










    Comparing Kit - and F999917 (Motala-12)


    Minimum threshold size to be included in total = 200 SNPs
    Mismatch-bunching Limit = 100 SNPs
    Minimum segment cM to be included in total = 1.0 cM



    Largest segment = 2.0 cM
    Total of segments > 1 cM = 7.5 cM

    Comparison took 0.42325 seconds.








    Comparing Kit - and F999913 (Clovis Anzick-1)


    Minimum threshold size to be included in total = 200 SNPs
    Mismatch-bunching Limit = 100 SNPs
    Minimum segment cM to be included in total = 1.0 cM


    Largest segment = 3.0 cM
    Total of segments > 1 cM = 16.5 cM

    Comparison took 0.43815 seconds.




    23b results:


    Population
    Amerindian 0.42%
    Ancestral_Altaic -
    South_Central_Asian 6.36%
    Arctic -
    South_Indian -
    Australoid -
    Austronesian 0.27%
    Caucasian 37.34%
    Archaic_Human -
    East_African 0.66%
    East_Siberian 0.81%
    European_Early_Farmers 22.63%
    Khoisan -
    Melano_Polynesian 0.20%
    Archaic_African 0.38%
    Near_East 10.51%
    North_African 6.86%
    Paleo_Siberian -
    African_Pygmy 0.07%
    South_East_Asian 0.19%
    Subsaharian -
    Tungus-Altaic 0.10%
    European_Hunters_Gatherers 13.20%
    Last edited by John Doe; 10-08-2014 at 06:46 AM. Reason: Fixed my results
    I can be certain of one thing, that I know nothing.

  8. #5
    Registered Users
    Posts
    2,066
    Sex

    1cM is too low of a threshold. The Minimum threshold size to be included in total should be the same as the Mismatch-bunching Limit to reduce the allowance of errors. So at least 200 SNPs on each. Retry the ones that you had results on the first time with the new settings.

  9. #6
    Registered Users
    Posts
    2,235
    Sex
    Location
    Canada
    Ethnicity
    Mixed Euro/Near East
    Nationality
    Canadian
    Y-DNA
    R1a-YP4516/YP4807*
    mtDNA
    H11a2a3

    Canada Franco-Manitoban European Union Ottoman Empire Russia Imperial United States Grand Union
    Quote Originally Posted by ArmandoR1b View Post
    Loschbour ancient DNA matches living people

    Kit F999918

    I am not sure what to make of these matches who match with a 8000 years old ancient DNA. Could the sample be contaminated? Is the sample really ancient? I don't know for sure.
    Look at the Walden chart here:

    http://www.isogg.org/wiki/Autosomal_DNA_statistics

    There's a 70% probability any match at 7.0 cM is identical by state. Accordingly I would not assume contamination or that these are modern samples, since there's another perfectly plausible explanation. Now if these samples started having matches of > ~9.5 cM, it would start getting curious.
     

    Hidden Content
    Hidden Content
    Hidden Content

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

  10. The Following 2 Users Say Thank You to AJL For This Useful Post:

     Mehrdad (10-09-2014),  palamede (10-10-2014)

  11. #7
    Registered Users
    Posts
    2,066
    Sex

    Quote Originally Posted by AJL View Post
    Look at the Walden chart here:

    http://www.isogg.org/wiki/Autosomal_DNA_statistics

    There's a 70% probability any match at 7.0 cM is identical by state. Accordingly I would not assume contamination or that these are modern samples, since there's another perfectly plausible explanation. Now if these samples started having matches of > ~9.5 cM, it would start getting curious.
    I had given that information to Felix on Sep 24. His response was the following:

    IBS does not always mean the segment is 'noise' or to be ignored. There seems to be a wrong perspective that IBS is not required. The difference between IBS and IBD is, an IBD segment has no recombination while an IBS can have. If the IBS does have recombination and yet it may not be noise which is referred as a 'compound segment'. When segments fails in phasing, they aren't noise but rather compound segments due to enogamous marriages / pedigree collapse. An IBS which is a true noise cannot have accidental matches above 2 cM.

    In regards to matches with Clovis Anzick he stated the following:

    But here, we are good with compound segments or IBS which are not noise. A 10 cM compound segment which is not IBD is for sure related within 500-1000 years and not 12500 years.

    In another post he says the following:

    Clearly, an IBD segment of 5 cM above 500 SNPs with total IBD segments around 10+ cM cannot be 12500 years old. This is a fact and can be verified using known relationships in families and DNA companies are using these benchmarks all along for showing genetic matches. This fact is more than enough to conclude that the Clovis-Anzick-1 sample is not actually ancient. My best guess is, the infant boy's sample is just from the last century and it was wrongly labeled as 12500 years old or the sample got contaminated.

    http://www.fc.id.au/2014/09/ancient-...valid-are.html


    I agree with you that these are cases of IBS and it is what I stated in my very first message to him on Sep 21.

    However even his latest post on Oct 8 questions the age of the Clovis specimen.

    http://www.fc.id.au/2014/10/new-clov...-gedmatch.html

    Dr. Ann Turner thought that the matches to Clovis Anzick were very counter-intuitive and thought that the cause was too many no-calls. See http://dna-explained.com/2014/09/23/...cient-results/

    However, Felix proved that matches still exist after processing the BAM file which is in his post on Oct 8.

    I do not doubt the age of the specimens and I don't see a possibility of contamination causing the matches evidenced by their admixture and PCA analysis. I think that IBS needs to be redefined as well as how to tell the difference between IBS and IBD. The big names in genetic genealogy should be tacking this problem head-on and provide answers as to what it going on.

  12. The Following 3 Users Say Thank You to ArmandoR1b For This Useful Post:

     AJL (10-09-2014),  Mehrdad (10-09-2014),  palamede (10-10-2014)

  13. #8
    Registered Users
    Posts
    514
    Sex

    United States of America Catalonia Spain
    My results, Spanish ancestry.

    Minimum threshold size to be included in total = 200 SNPs
    Mismatch-bunching Limit = 100 SNPs
    Minimum segment cM to be included in total = 1.0 cM


    La Braña F999915
    Largest segment = 2.1 cM
    Total of segments > 1 cM = 35.9 cM

    F999916 (Linearbandkeramik) (Stuttgart)
    Largest segment = 4.7 cM
    Total of segments > 1 cM = 776.6 cM

    F999917 (Motala-12)
    Largest segment = 2.6 cM
    Total of segments > 1 cM = 56.4 cM

    F999918 (Loschbour)
    Largest segment = 4.4 cM
    Total of segments > 1 cM = 605.8 cM

  14. #9
    J Man
    Guest
    Quote Originally Posted by AJL View Post
    Look at the Walden chart here:

    http://www.isogg.org/wiki/Autosomal_DNA_statistics

    There's a 70% probability any match at 7.0 cM is identical by state. Accordingly I would not assume contamination or that these are modern samples, since there's another perfectly plausible explanation. Now if these samples started having matches of > ~9.5 cM, it would start getting curious.
    That is quite an informative link about IBD segments thank you for sharing. I see that a segment that is 10 cM or larger has a 99% chance of being a true real IBD segment. Does the 10 cM rule also apply to people who have ancestry from genetically isolated populations such as Finns and Ashkenazim do you know? Or would the segment have to be say around 15 cM or so to have a 99% chance of it being truly IBD when say two Finns or two Ashkenazim match each other?

  15. The Following 3 Users Say Thank You to J Man For This Useful Post:

     AJL (10-09-2014),  Mehrdad (10-09-2014),  Táltos (10-09-2014)

  16. #10
    Registered Users
    Posts
    2,235
    Sex
    Location
    Canada
    Ethnicity
    Mixed Euro/Near East
    Nationality
    Canadian
    Y-DNA
    R1a-YP4516/YP4807*
    mtDNA
    H11a2a3

    Canada Franco-Manitoban European Union Ottoman Empire Russia Imperial United States Grand Union
    Quote Originally Posted by ArmandoR1b View Post
    I think that IBS needs to be redefined as well as how to tell the difference between IBS and IBD. The big names in genetic genealogy should be tacking this problem head-on and provide answers as to what it going on.
    Based on multiple posts Felix has made on the Family Tree DNA Forums, it seems rather clear that he has some very unusual and even confused ideas about IBS vs. IBD. He does not seem to me to understand the process of recombination, and at times I have even suspected he makes a point of muddying the issue to support some agenda of his.

    In any case an inherent issue here is one is we are dealing with probabilities. Unless we have absolutely fully sequenced genomes to compare one to another, with multiple reads at high quality, there will always be significantly more guesswork because we are guessing based on a small sample. This is especially the case when comparing people where different SNPs are tested.

    Quote Originally Posted by J Man View Post
    Does the 10 cM rule also apply to people who have ancestry from genetically isolated populations such as Finns and Ashkenazim do you know? Or would the segment have to be say around 15 cM or so to have a 99% chance of it being truly IBD when say two Finns or two Ashkenazim match each other?
    Good question -- I am not sure but I would think a 10 cM match is still likely to be IBD for endogamous populations, but may date farther back on average than for non-endogamous matches.
     

    Hidden Content
    Hidden Content
    Hidden Content

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

  17. The Following 2 Users Say Thank You to AJL For This Useful Post:

     Táltos (10-09-2014)

Page 1 of 3 123 LastLast

Similar Threads

  1. GEDmatch need help with results.
    By siblescreek in forum Autosomal (auDNA)
    Replies: 1
    Last Post: 09-25-2014, 07:06 PM
  2. Gedmatch admixture runs
    By Gray Fox in forum Autosomal (auDNA)
    Replies: 43
    Last Post: 09-06-2014, 11:11 PM
  3. Help with interpreting Gedmatch results
    By davidram in forum Autosomal (auDNA)
    Replies: 3
    Last Post: 09-04-2014, 07:15 PM
  4. How accurate are the 'One-to-many' matches on GEDMatch
    By Mehrdad in forum Autosomal (auDNA)
    Replies: 1
    Last Post: 03-04-2014, 11:17 AM
  5. Oracle-4 on Gedmatch
    By Scarlet Ibis in forum Other
    Replies: 20
    Last Post: 02-20-2013, 05:34 AM

Posting Permissions

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