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  • #76
    Been reading through this and I have two questions:

    Is there a way to differentiate between IBS and IBD segments? I obviously know that smaller segments could be either but I would think IBS is still valuable particularly if one is looking for "what they are" rather than who they are related to? Or do I have that completely wrong?

    That aside, I have noticed when I lower the threshold (cM wise), many of my Jewish matches are peppered with smaller matching segments, most of them seem to be bunched together with minimal spacing between them (i.e. one ends at 98.31 and the next begins at 98.39 with several others in succession). Many of these chromosomes have 10-18 matching segments.

    Last, and I have not seen a good answer on this, are the number of SNPs valuable? For example, on one match I have a 2.1 cM segment with 4,153 SNPs while another is 7.1 cM with 812 SNPs.

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    • #77
      Originally posted by Verified View Post
      Been reading through this and I have two questions:

      Is there a way to differentiate between IBS and IBD segments?
      Either through phasing or length. IBS segments are rarely larger than 7 or 8 cM. As you get smaller, it's more possible the segments are IBS rather than IBD. Phasing accomplishes the same goal by determining whether that srting of DNA that matches AAAA is actually

      AGAG
      GAGA

      or

      AAAA
      AGGA

      for example.

      Originally posted by Verified View Post
      I would think IBS is still valuable particularly if one is looking for "what they are" rather than who they are related to?
      IBS matches are coincidental, therefore not really of any use I can see.

      Originally posted by Verified View Post
      Last, and I have not seen a good answer on this, are the number of SNPs valuable? For example, on one match I have a 2.1 cM segment with 4,153 SNPs while another is 7.1 cM with 812 SNPs.
      A match of 2.1 cM is almost certainly IBS, and therefore doesn't mean much, unless you are known relatives and overlap with a third mutual relative in the same spot. Your match of 7.1 could certainly be IBD, but as matches get smaller the confidence gets lower because without phasing data, you cannot be sure 7.1 cM is the actual length of the match. Still, at that length there's a good possibility the link is genealogically traceable.

      The number of SNPs is important as well but I would generally pay more attention to centimorgans, because some regions are tightly packed with SNPs but rarely recombine.
      Last edited by Javelin; 10 November 2012, 11:15 AM. Reason: typo

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      • #78
        @mollyblum just in general people who are practicing Jews, their children get Hebrew names and English ones or just Hebrew or Yiddish names. Askenazi always naming their children after a deceased ancestor. Naming after the living to the Ashkenazi is taboo.

        anyway MT DNA and Y DNA are different than autosomal. I discussed above that family marrying family caused Ashkenazi to inherit specific disease. This will show up in autosomal and why a lot of Ashkenazi are related.

        Some practicing Muslim have proven to be related to people who are practicing Jews though Y or MT-DNA and there are very few people in the world who have actually DNA tested compared to all the people in the world. No one has the full story.

        Some people could descend from the founders of the original tribe of Judah and still not be Jewish today. If their ancestors did not continue to practice the Jewish faith and converted to another religion they are no longer Jewish (not practicing the Jewish religion and have accepted another religion)

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        • #79
          Israel and the Jewish people have existed before any religion called Judaism came to be. The reason why Jews and Palestinians share the same Yna is because they are both from the seed of Avraham. Israel from Issac and the other from Ishmael. This in fact proves the Torah is true.

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          • #80
            Originally posted by Taz85 View Post
            Israel and the Jewish people have existed before any religion called Judaism came to be. The reason why Jews and Palestinians share the same Yna is because they are both from the seed of Avraham. Israel from Issac and the other from Ishmael. This in fact proves the Torah is true.
            Y DNA can only prove a father line but not which sons one descends from. Especially going back to the bible that no one can solid paper trial to.You need a paper trial to back up your biblical statement as to which Y line belongs to which brother. I have met Muslim that have both practicing Jew and Muslim in their family. Visa versa. I have seen Jews who convert to Muslim, Christianity. Muslim that converted to Christianity. List goes on. Why because all religion permits for conversion.

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            • #81
              Can someone PLS explain to me how to use this admix utility? I have tried uploading everything I can think of and it keeps saying kit not found? is this just for males or what?

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              • #82
                Originally posted by RosemaryFurtaw View Post
                Can someone PLS explain to me how to use this admix utility? I have tried uploading everything I can think of and it keeps saying kit not found? is this just for males or what?
                I just tried it with your kit number, and it seems to work OK...

                Go here:

                http://ww2.gedmatch.com:8006/autosomal/ap_mix1_gen.php

                Select Eurogenes (pulldown) and Admixture Proportions (first button). Click "Continue".

                Enter your kit number (F234481) and select "Jtest", Click "Continue"

                (Admix calculator runs... takes about 20-30 seconds)

                For more options, scroll down, click on "Oracle", "2D PCA", or "3D PCA" button.

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                • #83
                  Originally posted by JOlson View Post
                  I just tried it with your kit number, and it seems to work OK...

                  Go here:

                  http://ww2.gedmatch.com:8006/autosomal/ap_mix1_gen.php

                  Select Eurogenes (pulldown) and Admixture Proportions (first button). Click "Continue".

                  Enter your kit number (F234481) and select "Jtest", Click "Continue"

                  (Admix calculator runs... takes about 20-30 seconds)

                  For more options, scroll down, click on "Oracle", "2D PCA", or "3D PCA" button.
                  Thank you! been wanting to use this for the longest!...No clue why it wasn't working for me lol

                  Comment


                  • #84
                    Originally posted by RosemaryFurtaw View Post
                    Thank you! been wanting to use this for the longest!...No clue why it wasn't working for me lol
                    Are you putting a F in front of you kit number, some utilities at Gedmatch require a F to be used in front of number while others do not

                    I believe only Triangulation and Chromosome browser are the only 2 utilities that do not require the F

                    Comment


                    • #85
                      Originally posted by RosemaryFurtaw View Post
                      Thank you! been wanting to use this for the longest!...No clue why it wasn't working for me lol
                      Is it working for you now, what are your results?

                      Comment


                      • #86
                        Originally posted by JuanCarlos View Post
                        Is it working for you now, what are your results?
                        For some reason GEDmatch is NOT loading for me right now unfortunately. But it DID work for me, I will post the results as soon as it starts working again but for now I did manage to save some pie images.



                        Comment


                        • #87
                          Originally posted by RosemaryFurtaw View Post
                          For some reason GEDmatch is NOT loading for me right now unfortunately. But it DID work for me, I will post the results as soon as it starts working again but for now I did manage to save some pie images.




                          Population
                          SOUTH_BALTIC 4.37%
                          EAST_EURO 6.78%
                          NORTH-CENTRAL_EURO 11.04%
                          ATLANTIC 9.56%
                          WEST_MED 9.74%
                          ASHKENAZI 1.02%
                          EAST_MED 2.08%
                          WEST_ASIAN 2.18%
                          MIDDLE_EASTERN 1.20%
                          SOUTH_ASIAN 0.90%
                          EAST_AFRICAN 11.11%
                          EAST_ASIAN 1.21%
                          SIBERIAN 2.10%
                          WEST_AFRICAN 36.71%

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                          • #88
                            Rosemary

                            To get a closer look at your African component:

                            After you get your Admix results, scroll down and click on the "2D PCA" button.

                            Can you post the results here?

                            Comment


                            • #89
                              Originally posted by JOlson View Post
                              Rosemary

                              To get a closer look at your African component:

                              After you get your Admix results, scroll down and click on the "2D PCA" button.

                              Can you post the results here?
                              Sure:

                              Comment


                              • #90
                                Sorry,

                                A line got left out in my response.

                                To get a closer look at your African component:

                                After you get your Admix results, scroll down and click on the "2D PCA" button

                                Select x=PCA6, y=PCA5, click on "Submit"

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