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  • Basic questions about chromosomes

    I was wondering is someone might answer a couple of basic questions for a beginner. I've been reading about atDNA and find it a little confusing. These are basic questions. If we talk about just my chromosome 1. I have two pairs, correct? Are these pairs identical? I presume not. On the chromosome browser, when viewing chromosome 1 what am I viewing. One pair or a combination of both? Is this why it looks like two sausages, end to end?

  • #2
    Originally posted by JaneDoe View Post
    I was wondering is someone might answer a couple of basic questions for a beginner. I've been reading about atDNA and find it a little confusing. These are basic questions. If we talk about just my chromosome 1. I have two pairs, correct? Are these pairs identical? I presume not. On the chromosome browser, when viewing chromosome 1 what am I viewing. One pair or a combination of both? Is this why it looks like two sausages, end to end?
    You're looking both of them as if they were stacked on top of each other. A good way to visualize this is if you've had yourself and both parents tested. Here is my chromosome browser with both of my parents selected: http://i.imgur.com/V5VjCWn.jpg

    Note that for the X chromosome it is only orange since I only have one and it's from my mother.

    Comment


    • #3
      David, Thank you for answering this. I understand. Do you know why the view of each chromosome looks like two sausages, end to end? Another general question as I realize there are other factors which may affect this. If you do an 'in common with' on your father. Generally speaking, does this reduce all of your matches, to matches only on your father's side? Thank you for answering newbie questions.

      Comment


      • #4
        Originally posted by JaneDoe View Post
        David, Thank you for answering this. I understand. Do you know why the view of each chromosome looks like two sausages, end to end? Another general question as I realize there are other factors which may affect this. If you do an 'in common with' on your father. Generally speaking, does this reduce all of your matches, to matches only on your father's side? Thank you for answering newbie questions.
        You are seeing the centromere. It is a dense constricted appearing region of the chromosome.

        http://dictionary.reference.com/browse/centromere?s=t

        Don't confuse the two homologous chromosomes with chromatids though. When the chromosome splits into two chromatids (that are duplicates and nearly identical) these are attached at the centromere. This is the time when the sausage appearance is easiest to visualize in images and it looks like an X.

        http://www.gettyimages.com/detail/ph...phy/BC3196-001

        The centromere is the most difficult place to find SNPs (mutations) so testing companies cannot report some sections of your centromere.

        Comment


        • #5
          Thank you Kathy,

          Is my other question silly?

          To be more specific, my search involves finding my deceased maternal grandmother's parents. She was adopted and we have no information about these parents. My grandmother had three husbands with children born to each. I have a half first cousin, and my grandma is the only grandparent we share in common. I'm trying to convince my cousin to test with FF, but first wanted to ask if the 'in common list' with my half first cousin would narrow my list of matches to ancestors relating solely to my adoptive maternal grandmother? The reduced ICW list of X matches or lack thereof may help further identify specific lines. I'm trying to work through my logic here realizing there is a generation between myself and my grandmother. As it stands now my closest matches are 20, 2nd to 4th cousins. Statistically I'm thinking only 5 are of interest. Am I over simplifying this?

          Comment


          • #6
            Originally posted by JaneDoe View Post
            Thank you Kathy,

            Is my other question silly?

            To be more specific, my search involves finding my deceased maternal grandmother's parents. She was adopted and we have no information about these parents. My grandmother had three husbands with children born to each. I have a half first cousin, and my grandma is the only grandparent we share in common. I'm trying to convince my cousin to test with FF, but first wanted to ask if the 'in common list' with my half first cousin would narrow my list of matches to ancestors relating solely to my adoptive maternal grandmother? The reduced ICW list of X matches or lack thereof may help further identify specific lines. I'm trying to work through my logic here realizing there is a generation between myself and my grandmother. As it stands now my closest matches are 20, 2nd to 4th cousins. Statistically I'm thinking only 5 are of interest. Am I over simplifying this?
            No, this question is not silly at all. Thank you for clarifying the question. You clearly should try to get your cousin to test to see if there is a match and it should help if others match in the same regions. GEDmatch would allow you to be compared to more potential cousins. Don't be surprised if it takes a long time to find the answers you are looking for. So much depends on luck.

            Please do not think that your list of ICW X chromosome matches is accurate though. It is not. The ICW X list shows matches that are reported down to 1 cM which means the segment often is identical by state rather than identical by descent. Autosomal ICW match lists are much more accurate because a higher size threshold is used. Make sure you examine both ICW lists with the different thresholds in mind.

            It sounds like this cousin is related through an X chromosome line. Is your half-cousin a female or male and is this cousin related through a male or female parent? That would help to determine if the X might be relevant and give you a better idea about probabilities. You may also find other X matches at GEDmatch who tested at FTDNA that you don't find in your match lists at all. At FTDNA, you must have a match on an autosome before the X matches are shown. Long X matches can be missed completely. Raise the threshold to at least 5 cM for any X matches you find at FTDNA to lower the likelihood of false matches.

            A half first cousin should show up as an autosomal match though and this person is the ideal person to test to see if you have ICW autosomal tests. The X match is not guaranteed but would really be nice.

            Comment


            • #7
              Thank you Kathy,

              I think this will take a considerable amount of luck. Yes, my half-first cousin is female and my grandmother is her paternal grandmother. If I can reduce my list by 75% at least I will be asking the right people some very obscure questions. Hopefully I won't scare anyone off as you can imagine the questions.

              I notice on my list of 2nd to 4th cousins, 10 of the 20 are X matches. Most all appear at approximately 4cM length lined up in a column. One match is 8 cM length and away from this column.

              I was thinking the lack of X matches on a reduced ICW list, may have great importance. An ICW list, 2nd to 4th cousin match with no X, may lead to my grandmother's paternal grandfather. This is the only grandparent or parent my grandmother had with whom she did not share an X.

              "Please do not think that your list of ICW X chromosome matches is accurate though. It is not."

              Would I be safe to assume a lack of X chromosome mathc is accurate?

              Thank you again for taking the time.

              Comment


              • #8
                Originally posted by JaneDoe View Post
                Thank you Kathy,

                I think this will take a considerable amount of luck. Yes, my half-first cousin is female and my grandmother is her paternal grandmother. If I can reduce my list by 75% at least I will be asking the right people some very obscure questions. Hopefully I won't scare anyone off as you can imagine the questions.

                I notice on my list of 2nd to 4th cousins, 10 of the 20 are X matches. Most all appear at approximately 4cM length lined up in a column. One match is 8 cM length and away from this column.

                I was thinking the lack of X matches on a reduced ICW list, may have great importance. An ICW list, 2nd to 4th cousin match with no X, may lead to my grandmother's paternal grandfather. This is the only grandparent or parent my grandmother had with whom she did not share an X.

                "Please do not think that your list of ICW X chromosome matches is accurate though. It is not."

                Would I be safe to assume a lack of X chromosome mathc is accurate?

                Thank you again for taking the time.
                If you order a test that uses the same Illumina build, it should be accurate. There are some small holes in the X matching if you ordered one of the original Build 36 tests and your relative orders a Build 37 test. If you ordered recently for yourself, that should not be a problem. Two people who order the same build who are closely related are not likely to have a false negative result.

                A lack of an X match does not mean there is no X inheritance pattern in the cousins though. Even full sibs don't always inherit an X segment in common unless you compare two sisters. Sisters have to match their father. A mother does not have to noticeably recombine her Xs. She can pass from 0 to 100% of each X to the next generation as long as it adds up to one whole X. Usually there is some matching so I would expect to see it between you and your half cousin. It would be uncommon for your mother and her brother not to have any segments in common. Her brother (your uncle) has to pass his entire X to your female cousin and that would be from your grandmother in question. At least you would know that a match you have with this cousin on the X chromosome can be physically mapped back to that grandmother.

                If you are related to this cousin through an unknown ancestor in common on another line, you may not be able to rule that out entirely. I think getting this particular cousin tested is your best hope. Unless you use a third party tool though, you won't find very many X matches who triangulate in exactly the same location. Make sure the threshold is adequate and look for overlapping matches in the triangulation for best results.

                Comment


                • #9
                  I forgot to ask if you have any aunts and uncles related to your mother because it is always good to also test someone in the next generation up.

                  Comment


                  • #10
                    Kathy,

                    Thank you again! This really helps. Unfortunately I have no aunts or uncles living. Are you aware of any statistics for FF tests at different generation levels? For example, if two known 3rd cousins test will they always show on FF 100% of the time? How about 4th cousins? Half of my matches are '5th to remote' so I find myself wondering what percentage of these people are actually related.

                    I'm asking this also to help me understand a match I have with one zero genetic distance on the mtDNA Full Sequence test. This match does not show on my FF list, so I'm pondering how far back she may be. My match has known history back to her ggg grandmother.

                    I'm reading this:

                    "mtFullSequence gives generations to Common Ancestor of 5 (about 125 years) to a 50% confidence Interval. Generations to Common ancestor of 22 (about 550 years) to a 95% confidence level."

                    Would you agree with the above confidence Interval?

                    Now this is a silly question, but when we speak of our grandparents and generations. Are they considered back 2 generations or back 3 generations?

                    Comment


                    • #11
                      Originally posted by JaneDoe View Post

                      .........

                      I'm reading this:

                      "mtFullSequence gives generations to Common Ancestor of 5 (about 125 years) to a 50% confidence Interval. Generations to Common ancestor of 22 (about 550 years) to a 95% confidence level."

                      Would you agree with the above confidence Interval?

                      Now this is a silly question, but when we speak of our grandparents and generations. Are they considered back 2 generations or back 3 generations?
                      In this case a generation refers to years between, not people.
                      In years the average between a parent child is 25 years.
                      in respects to yourself and your Grandparent it is 2 Generations
                      You > 1 generation > Parent > 1 Generation > Grandparent = 2 Generations.

                      Comment


                      • #12
                        Originally posted by JaneDoe View Post
                        Kathy,

                        Thank you again! This really helps. Unfortunately I have no aunts or uncles living. Are you aware of any statistics for FF tests at different generation levels? For example, if two known 3rd cousins test will they always show on FF 100% of the time? How about 4th cousins? Half of my matches are '5th to remote' so I find myself wondering what percentage of these people are actually related.

                        I'm asking this also to help me understand a match I have with one zero genetic distance on the mtDNA Full Sequence test. This match does not show on my FF list, so I'm pondering how far back she may be. My match has known history back to her ggg grandmother.

                        I'm reading this:

                        "mtFullSequence gives generations to Common Ancestor of 5 (about 125 years) to a 50% confidence Interval. Generations to Common ancestor of 22 (about 550 years) to a 95% confidence level."

                        Would you agree with the above confidence Interval?

                        Now this is a silly question, but when we speak of our grandparents and generations. Are they considered back 2 generations or back 3 generations?
                        See:
                        https://www.familytreedna.com/learn/...finder-detect/

                        I think the mtDNA full sequence matches are with females so far back in time and the pedigree charts are so incomplete that you are unlikely to find anyone on your autosomal match list who matches your mtDNA exactly. Not many people can trace their pedigree back 550 years so who knows if this confidence level is correct? I think it is highly variable. mtDNA tells you about ancient ancestors although I have rarely found a MRCA within a genealogical time period for my subclade so I know it can happen. People in highly tested regional groups have been successful, for example French Canadians.

                        Comment


                        • #13
                          In my search for my adoptive grandmother’s parents I've tested along with my 1st cousin. (FF) Since this is the only grandparent we share in common, I thought an ICW list may provide a clue. My thoughts were possibly 25% of my matches could be attributed to my Grandmother and the same number true for my first cousin. As I have about 450 matches on FTDNA and he has about 650 I was looking forward to a long list to work with. Well, as it turns out there are only 2 matches in common and one doesn't appear to be valid. The other won’t respond. I recognize 25% is just a guess as there may be none.

                          My question is, can anyone tell me how many matches do you come up with when you do an ICW with a first cousin? What about second cousin?

                          Thank you

                          Comment


                          • #14
                            Originally posted by JaneDoe View Post

                            .......

                            My question is, can anyone tell me how many matches do you come up with when you do an ICW with a first cousin? What about second cousin?

                            Thank you
                            My Father's paternal 1st Cousin has 599 matches
                            My Father has 701 matches
                            My Uncle 1 has 697 matches
                            My Uncle 2 has 576 matches
                            My Aunt has 594 matches
                            Myself has 524 matches
                            My Sibling 1 has 421 matches
                            My Sibling 2 has 456 matches
                            My Sibling 3 has 438 matches
                            My Sibling 4 has 456 matches
                            My Sibling 5 has 584 matches

                            Shared line is my paternal Grandfather and his brother who were Half Scottish/Half Irish

                            ICW for My Father's paternal 1st Cousin (my 1st Cousin 1x)and my family members

                            ICW my Father - 134 matches (19% of Fathers list, 22% of cousins list)

                            ICW my Uncle 1 - 129 matches (18.5% of Uncle 1's list, 21.5% of cousins list)

                            ICW my Uncle 2 - 114 matches (19.8% of Uncle 2's list, 19% of cousins list)

                            ICW my Aunt - 66 matches (11% of Aunt's list, 11% of Cousins list)

                            ICW myself - 67 matches (12.7% of my list, 11% of cousins list)

                            ICW my Sibling 1 - 94 matches (22.3% of sibling 1's list, 15.7 of cousins list)

                            ICW my Sibling 2 - 73 matches (16% of sibling 2's list, 12% of cousins list)

                            ICW my Sibling 3 - 67 matches (15.3% of sibling 3's list, 11% of cousins list)

                            ICW my Sibling 4 - 70 matches (15.4% of sibling 4's list, 11.7% of cousins list)

                            ICW my Sibling 5 - 33 matches (5.7% of sibling 5's list, 5.5% of cousins list)

                            Comment


                            • #15
                              Oh, Thank you for the detailed list. I'm mainly interested in the number of ICW matches you have, with your 1st cousin 1X. If you take all of the close relationships out of the equation would that number for you be about 60 in your case? That would make sense.

                              In my case it seems my grandmother's ancestors perhaps didn't have many offspring. I loaded my results into GEDMATCH for a similar comparison, and it only returned one match. I was using the default settings.

                              Do you have an opinion about why my results are so few?

                              Comment

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