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  • Gedmatch rare snp utility

    Gedmatch rare snp utility - what are these and how does one interpret the results? It appears you should test several kits at once but I only have one to test, it does give some results however.

  • #2
    I too would like more of an explantion of this feature. Perhaps John O. could help us out.

    Comment


    • #3
      On a related note, I uploaded my DNA before the new login system. Is there some way to associate an existing kit with a login? I tried uploading again but got an error saying the kit was already loaded.

      Comment


      • #4
        Originally posted by 1_mke View Post
        On a related note, I uploaded my DNA before the new login system. Is there some way to associate an existing kit with a login? I tried uploading again but got an error saying the kit was already loaded.
        The best solution is probably just to email them: [email protected].

        Comment


        • #5
          Originally posted by 1_mke View Post
          On a related note, I uploaded my DNA before the new login system. Is there some way to associate an existing kit with a login? I tried uploading again but got an error saying the kit was already loaded.
          enter the same email you enterd the firest time it worked for me

          Comment


          • #6
            Originally posted by mebrowndfw View Post
            The best solution is probably just to email them: [email protected].
            Actually, no.

            Each mail they have to answer takes time, and they don't have much of that.

            Instead try to use the information provided in this forum, e.g. for the specific question:

            "Enter the same email you entered the first time".

            Comment


            • #7
              The information as to entering the same email address was posted after my reply, clearly.

              Thanks, though.

              Comment


              • #8
                Originally posted by cokie View Post
                Gedmatch rare snp utility - what are these and how does one interpret the results? It appears you should test several kits at once but I only have one to test, it does give some results however.
                I think the website's definition is very simple and clear:
                The rare SNP program may be useful for identifying SNPs from deep common ancestry, or SNPs related to shared characteristics.

                This is not the same as the comparison done by 23andMe and FTDNA, and cannot be interpreted in the same way. Those comparisons are based on matching segments of hundreds of SNPs.

                This tool will search all the kit IDs that you manage for rare SNPs and report on those that are common to all. With eight IDs it is unlikely you will find SNPs less rare than 5 to 10%. With one ID you may find 1000 SNPs less than 1%, depending on your ancestral origins.

                This is a research tool for genealogical purposes only. It must not be used for researching health conditions.
                See a medical professional if you think you are sick or have a medical condition.

                The 'percent occurrence' used in this utility is based on a survey of GEDmatch submittals.

                Comment


                • #9
                  I'm an idiot, when I created my account I used a different email than I'd associated with the kits I uploaded earlier.

                  Comment


                  • #10
                    Originally posted by Couscous Nomad View Post
                    I think the website's definition is very simple and clear:

                    The rare SNP program may be useful for identifying SNPs from deep common ancestry, or SNPs related to shared characteristics.
                    ..............
                    I find it interesting that Matching Origins go along with my kits known ancestry. Some SNP's follow their Paternal sides origins(Scotland/Ireland), while others follow their maternal side(Romania and area)


                    ie
                    RSID..............Chr.....Genotype....Origin
                    rs28990969.....12..........gT.........Romania
                    rs35663590.....2............Ag.........Bosnia and Herzegovina, Lithuania, Poland
                    rs12151206.....19..........aC.........County Kildare, Ireland & Sweden
                    rs11568970.....4............cT........Denmark & United Kingdom

                    Comment


                    • #11
                      Ah, great. This narrows it down quite a bit:

                      "rs11781640
                      8
                      145670196
                      cT
                      0.763113
                      KIFC2

                      County Kildare, Ireland
                      Cuba
                      Ireland
                      Poland
                      Scotland
                      Slovenia
                      Spain
                      United Kingdom"



                      [From my own report]

                      Comment


                      • #12
                        So should you run more than one kit at once for this? Can or should you run your phased results with this?? Well here are the results for just my kit. Please anyone feel free to comment on what they mean!

                        Mutation shown in red (Or in this case in the capital letter as I'm not that savvy or patient to make the capitals appear red from my copy and paste!)
                        RSID Chr Position (B36) Genotype %Occurrence Gene Matching Origins
                        rs16873085 7 109893141 gT 0.173421 Poland
                        rs11257625 10 12336456 Ag 0.210016
                        rs12320970 12 6655314 cT 0.247685 ZNF384
                        rs13053471 22 49269979 cT 0.275289 United Kingdom
                        rs10062937 5 72354001 Gt 0.27912 FCHO2 United Kingdom
                        rs3803017 12 55739139 Ct 0.334625 TMEM194A Denmark
                        rs12313844 12 54262108 aG 0.35941 Austria Norway Poland Southeast Asia
                        rs7979568 12 15251254 Ag 0.425051 RERG Mexico Netherlands
                        rs11589899 1 12773129 cT 0.486908
                        rs1110708 11 66117160 Ac 0.511688 Finland Lithuania Poland
                        rs8069707 17 13806748 Ct 0.560828 United Kingdom
                        rs6996640 8 1454790 gT 0.564152 DLGAP2 France Ireland Norway South Africa
                        rs869644 18 70003297 Ct 0.566282
                        rs2271038 2 98295189 cT 0.592231 VWA3B Caucasus East Asian Germany Ireland Poland
                        rs11656500 17 7638370 Ag 0.599287 DNAH2 Ireland Sweden
                        rs13324049 3 71177428 Ag 0.627279 FOXP1 Eritrea France Ireland
                        rs17059563 4 174691840 Ct 0.627346 SCRG1 Ireland Norway
                        rs12659157 5 43252876 aG 0.640399 MGC42105 East Asian Ireland Mexico New Mexico, USA Poland
                        rs17025370 1 110398427 aG 0.641849 Cameroon Ireland
                        rs3219193 4 89272165 cT 0.646063 Austria Lithuania Norway
                        rs10947338 6 32816576 aT 0.656761 Caucasus Colombia Ecuador El Salvador Germany Mexico
                        rs2292969 17 78492638 Ct 0.659167 TBCD Georgia, USA Germany Ireland Slovenia
                        rs11243460 9 133501790 Ct 0.677507 Ireland Russia Southeast Asia
                        rs12229331 12 113345201 Ct 0.695398 Norway Poland Spain
                        rs2588708 4 66547650 cT 0.70656 Bahamas
                        Last edited by Táltos; 29 May 2013, 04:03 PM.

                        Comment


                        • #13
                          Here are my Sicilian mother's results for the first 25. Despite the other ethnicities/nationalities, "Sicilian" shows up in every case, and several (as of now) show only that match, so if I didn't know that these results belong to a Sicilian-origin person, I would surely look into that possibility. Also notice how low a percent of occurrence they start with, compared to my father in the next post.

                          %Occurrence Matching Origins
                          0.0322581 Romania Sicilian
                          0.0487752 Ukraine
                          0.0785615 Sicilian
                          0.171748 Sicilian
                          0.177591 Poland Sicilian
                          0.247979 Sicilian
                          0.282455 Sicilian
                          0.285468 Ireland Sicilian
                          0.289948 France Sicilian
                          0.290354 Ireland Sicilian
                          0.33608 Ashkenazi Sicilian
                          0.365709 Sicilian
                          0.383414 Sicilian
                          0.398984 Sicilian
                          0.424549 Bahamas Cameroon Sicilian
                          0.425326 Cameroon Haiti Sicilian
                          0.446381 Sicilian
                          0.45205 Sicilian
                          0.457137 France Sicilian
                          0.465789 Bahamas Haiti Sicilian United Kingdom
                          0.47424 Ashkenazi Ecuador Eritrea Sicilian United Kingdom
                          0.506219 Germany Sicilian
                          0.508838 Bahamas Ecuador Morocco Norway Sicilian
                          0.515409 Cameroon France Sicilian
                          0.516296 France Sicilian

                          Comment


                          • #14
                            As with my mother, my father's known origin shows up in every instance. My father was more European admixed than my mother is, so perhaps that explains at least part of the differences. Still, if I didn't know these results belong to an Abruzzese-origin person, I would consider that possibility. I trust that both his Abruzzese and my mother's Sicilian don't include their own results; i.e., I hope the matches only represent other people in the database.

                            %Occurrence Matching Origins
                            0.156065 Abruzzese Germany Norway
                            0.177267 Abruzzese Poland Puerto Rico
                            0.334907 Abruzzese Brazil Mexico
                            0.359635 Abruzzese Ashkenazi Belarus Brazil Mexico
                            0.38131 Abruzzese Germany Sweden United Kingdom
                            0.461355 Abruzzese Norway Poland
                            0.491314 Abruzzese Sweden
                            0.511137 Abruzzese Switzerland
                            0.567027 Abruzzese Netherlands
                            0.604796 Abruzzese Haiti Iran
                            0.61911 Abruzzese
                            0.62008 Abruzzese Bahamas Cameroon Eritrea Lithuania Netherlands United Kingdom
                            0.652686 Abruzzese Alabama, USA Austria Ireland
                            0.665879 Abruzzese Netherlands
                            0.70106 Abruzzese Brazil Britain Hungary Ireland Mexico Norway Sweden
                            Switzerland
                            0.715438 Abruzzese Haiti Ireland Morocco South Africa
                            0.727292 Abruzzese Morocco United Kingdom
                            0.74082 Abruzzese Iran Lithuania Norway Poland United Kingdom
                            0.740842 Abruzzese New Zealand Norway Poland
                            0.746269 Abruzzese Ashkenazi Austria Belgium Lithuania Michigan, USA
                            Michigan_USA United Kingdom
                            0.747473 Abruzzese Germany Haiti Sweden United Kingdom
                            0.754253 Abruzzese Hungary Mexico Southeast Asia
                            0.770059 Abruzzese El Salvador Eritrea
                            0.8088 Abruzzese Belarus Caucasus Germany Iran Ireland Romania
                            0.81266 Abruzzese Ashkenazi

                            Comment


                            • #15
                              When matched with each other, the %occurrence drastically increases because the SNPs they share in common are in fact much more common among those in the Gedmatch database. However, no countries of origin are listed for several. John, can you please explain that? Thanks!

                              %Occurrence Matching Origins
                              1.58347 Abruzzese Caucasus East Asian Eritrea Germany Mexico Romania
                              Sicilian South Africa Spain Sweden Switzerland
                              1.58517 Abruzzese Belarus Denmark Dominican Republic Germany Ireland
                              Lithuania Mexico New Mexico, USA Sicilian United Kingdom
                              1.707 Abruzzese Ashkenazi Bahamas Belarus Caucasus Germany Hungary
                              Ireland Lithuania Norway Poland Serbia Sicilian Spain Sweden United Kingdom
                              1.81104 Abruzzese Caucasus Cyprus Finland Georgia, USA German Jew
                              Poland Ukraine United Kingdom
                              1.83173 Abruzzese Ashkenazi Bahamas Greece Ireland Malta Poland Sicilian United Kingdom
                              2.30937
                              2.3702
                              2.45603
                              2.47448
                              2.49203
                              2.52373
                              2.55157
                              2.6542
                              2.70546
                              2.74595
                              2.81409
                              2.81549
                              2.81805
                              2.8384
                              2.84763
                              2.8596
                              2.90126
                              2.94412
                              2.98614
                              2.98808

                              Comment

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