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Thread: H1c3 Y Full tree mtdna update

  1. #11
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    Quote Originally Posted by ArmandoR1b View Post
    Since you have C for 16176 that means you are negative for C16176T because your Genotype is the ancestral (negative) allele which means that you are negative for H1c3a. To be positive for a mutation your Genotype has to match the derived (positive) allele which in this case is T. Please ignore RSIDS such as i4001356 and i705670. They have no bearing on positive or negative results.
    Thanks again ArmandoR1b, back to the searching again, still baffled, and confused but learning.

    If the Raw Data (from 23 & Me ) I use only has the number say 16176, and a letter say 'C' as here in this case, and no other letters, then C must be my Genotype allele, so it would be C16176, with a missing end letter, which if you are saying for 'positive' the end in this case has to be a derived Genotype 'T' in order to have me as H1c3a, which I do not have. I therefore cannot be H1c3a.

    If this then is the case, and I have only a single letter attached to each or most of my Raw Data, with no other letters but this single one for each, then all my 23 & Raw Data, is showing nothing but negatives, on that basis I am wasting my time, as they are not going to be complete or matched.

    Also the positive derived allele,is shown both first, in some of my references, and also last as here with 'T'. The previous post mentioned my derived Genotype as 'A' negative whilst at the begining, but here it is the missing 'T' which is placed at the end. Is this because the letter was missing, as I am confused as they can be at both ends, It is confusing me. If letters are missing does that prove negative, and that the letter associated is always ancestral, if others are not present. ?.
    Last edited by Paul333; 06-16-2019 at 12:39 AM.

  2. #12
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    Quote Originally Posted by Paul333 View Post
    Thanks again ArmandoR1b, back to the searching again, still baffled, and confused but learning.

    If the Raw Data (from 23 & Me ) I use only has the number say 16176, and a letter say 'C' as here in this case, and no other letters, then C must be my Genotype allele, so it would be C16176, with a missing end letter, which if you are saying for 'positive' the end in this case has to be a derived Genotype 'T' in order to have me as H1c3a, which I do not have. I therefore cannot be H1c3a.

    If this then is the case, and I have only a single letter attached to each or most of my Raw Data, with no other letters but this single one for each, then all my 23 & Raw Data, is showing nothing but negatives, on that basis I am wasting my time, as they are not going to be complete or matched.

    Also the positive derived allele,is shown both first, in some of my references, and also last as here with 'T'. The previous post mentioned my derived Genotype as 'A' negative whilst at the begining, but here it is the missing 'T' which is placed at the end. Is this because the letter was missing, as I am confused as they can be at both ends, It is confusing me. If letters are missing does that prove negative, and that the letter associated is always ancestral, if others are not present. ?.
    It's much simpler than you have interpreted. We all only have one Genotype for each mtDNA position. The only reason that mutations are shown with two alleles is so that you know which allele is the ancestral (negative) and which allele is the derived (positive). We all have just one or the other. We all have either just the ancestral (negative) allele or just the derived (positive) allele. You can't have both the ancestral and derived allele except in the very rare case of an insertion. 23andme shows just your Genotype. If you are positive for an SNP then you have just the derived allele for that SNP and it is reflected in the raw data. For example, H1c3 is defined by A257G and T8473C. That means that 23andme shows you just have C for the Genotype for position 8473. So your 23andme raw data isn't showing nothing but negatives. If you want to see a list of positives upload to https://dna.jameslick.com/mthap/ You can post your results here so we can go over the data to help you understand your raw data.

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     Paul333 (06-16-2019)

  4. #13
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    Quote Originally Posted by ArmandoR1b View Post
    It's much simpler than you have interpreted. We all only have one Genotype for each mtDNA position. The only reason that mutations are shown with two alleles is so that you know which allele is the ancestral (negative) and which allele is the derived (positive). We all have just one or the other. We all have either just the ancestral (negative) allele or just the derived (positive) allele. You can't have both the ancestral and derived allele except in the very rare case of an insertion. 23andme shows just your Genotype. If you are positive for an SNP then you have just the derived allele for that SNP and it is reflected in the raw data. For example, H1c3 is defined by A257G and T8473C. That means that 23andme shows you just have C for the Genotype for position 8473. So your 23andme raw data isn't showing nothing but negatives. If you want to see a list of positives upload to https://dna.jameslick.com/mthap/ You can post your results here so we can go over the data to help you understand your raw data.
    Thanks again ArmandoR1b, that has helped me understand about my Raw Data. Im not to keen to send my Raw Data anywhere yet, its all attached, and when I tried to print some pages of my MTDNA, it showed thousands of pages,including my Y Data, so I give up trying. ( Although I was given seven positive Mtdna SNP's with my LivingDNA results ) So I will leave it for now untill I learn a bit more. Im glad that I now Know my Raw Data from 23 & Me is only showing negatives, this is very helpfull to me.
    Last edited by Paul333; 06-16-2019 at 01:57 PM.

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    Quote Originally Posted by Paul333 View Post
    Thanks again ArmandoR1b, that has helped me understand about my Raw Data. Im not to keen to send my Raw Data anywhere yet, its all attached, and when I tried to print some pages of my MTDNA, it showed thousands of pages,including my Y Data, so I give up trying. ( Although I was given seven positive Mtdna SNP's with my LivingDNA results ) So I will leave it for now untill I learn a bit more. Im glad that I now Know my Raw Data from 23 & Me is only showing negatives, this is very helpfull to me.
    The raw data from 23andme is not only showing negatives. The 23andme raw data shows the positive allele for when you are positive for a mutation and it shows the negative allele when you are negative for an allele.

    In order for you to understand what happens with the James Lick mtDNA calculator, instead of uploading your raw data download a reference mtDNA file for haplogroup H1c3 specimen KF162307.1 which is the first one at YFull, go to https://www.ncbi.nlm.nih.gov/search/...erm=KF162307.1 then click on download and save the file to your computer then go to https://dna.jameslick.com/mthap/ then click on Browse then point to the KF162307.1.fasta file then upload it and wait a minute or two for the page to update with the results. You will see positive markers in green with the position and the derived (positive) allele. You can then look up each of those positions in your raw data to see which allele you have for your Genotype. Let me know what you find.

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    ArmandoR1b, Thanks
    Ive followed your advice and have looked at three KF162307.1, KF523403.1, and KF16891.1, upto now.

    I downloaded them and uploaded them as you recomended, but I cannot move yet, as I only have seven ' LivingDNA positive' (Green ) which took me to H1c3.

    I will look through more 23 & Me later, and try to find matches but how do I know if my 23 & Me Raw Data, is negative or positive, as I only have my Genotype, defined, on the 23 & Me Raw Data, and with only the seven LivingDNA Positives which are all matched/included, one way or another ( green ) to the defining H1c3, and no further.

    I cannot match with, or find a match with my '23 & Me Raw data' as it has the letters which would help, missing and therefore I do not know how I can locate or complete the sequence for a match. Although I can use the green positives to locate what it should be, ( the Positive Green sequence for the subclade ) that will be all I am able to do at the moment.

    Thanks for the information, and advice. I will now go through these over the next few days, and see what I can Find, but I think I will need further updated Mtdna Snps to move to the next downstream subclade.

  8. #16
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    Quote Originally Posted by Paul333 View Post
    ArmandoR1b, Thanks
    Ive followed your advice and have looked at three KF162307.1, KF523403.1, and KF16891.1, upto now.

    I downloaded them and uploaded them as you recomended, but I cannot move yet, as I only have seven ' LivingDNA positive' (Green ) which took me to H1c3.
    One of the things that I wanted you to see with the uploads is what the printout is like with the James Lick calculator. Since you have seen what it looks like are you willing to upload your 23andme raw DNA to the James Lick site? If you are worried about privacy see https://dna.jameslick.com/mthap/FAQ.html Ignore the LivingDNA positives for the moment.

    Quote Originally Posted by Paul333 View Post
    I will look through more 23 & Me later, and try to find matches but how do I know if my 23 & Me Raw Data, is negative or positive, as I only have my Genotype, defined, on the 23 & Me Raw Data, and with only the seven LivingDNA Positives which are all matched/included, one way or another ( green ) to the defining H1c3, and no further.
    You can tell if your 23andme raw data is negative or positive by comparing your Genotype to the last letter of the mutation. If it is the same then you are positive. If it is different then you are negative. I'll use an example, What is your Genotype for position 263 in the 23andme data? Is it G? If it is then you are positive for the mutation of 263G. Ignore the LivingDNA positives for the moment. The mention of it is making things unnecessarily more complicated at the moment.

    Quote Originally Posted by Paul333 View Post
    I cannot match with, or find a match with my '23 & Me Raw data' as it has the letters which would help, missing and therefore I do not know how I can locate or complete the sequence for a match. Although I can use the green positives to locate what it should be, ( the Positive Green sequence for the subclade ) that will be all I am able to do at the moment.
    That is incorrect. The letters that you need are there in the raw data. The problem is not understanding what is being given to you.


    Quote Originally Posted by Paul333 View Post
    ....but I think I will need further updated Mtdna Snps to move to the next downstream subclade[/B].
    You definitely need a FTDNA full sequence mtDNA test or a Yseq mtComplete test to see if you are positive for a downstream subclade which is the reason I mentioned those tests in my first post of this thread.

  9. #17
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    Quote Originally Posted by ArmandoR1b View Post
    One of the things that I wanted you to see with the uploads is what the printout is like with the James Lick calculator. Since you have seen what it looks like are you willing to upload your 23andme raw DNA to the James Lick site? If you are worried about privacy see https://dna.jameslick.com/mthap/FAQ.html Ignore the LivingDNA positives for the moment.


    You can tell if your 23andme raw data is negative or positive by comparing your Genotype to the last letter of the mutation. If it is the same then you are positive. If it is different then you are negative. I'll use an example, What is your Genotype for position 263 in the 23andme data? Is it G? If it is then you are positive for the mutation of 263G. Ignore the LivingDNA positives for the moment. The mention of it is making things unnecessarily more complicated at the moment.


    That is incorrect. The letters that you need are there in the raw data. The problem is not understanding what is being given to you.



    You definitely need a FTDNA full sequence mtDNA test or a Yseq mtComplete test to see if you are positive for a downstream subclade which is the reason I mentioned those tests in my first post of this thread.
    Thanks again ArmandoR1b
    My 23 & Me Mtdna is attached with my Y data, and it is very large, thousands of pages, and would be a large file, and at the moment I do not know what is in it, and the risks of sending my full Dna raw data to something I do not yet fully understand.

    The pages I downloaded and uploaded, consisted of mainly three or four different H1c3 Haplogroups, from Basic mtdna H, H1 H1c H1c3, most pages only had about three or four entries, regarding the Data, mostly repeating my seven to H1c3.

    The further downstream examples although on Yfull I tried a few, beyond H1c3, the 'C' to 'F' subclades on Yfull and they did not in fact go that far, but only to mainly H1c3, the inf is dated to Feb 2016, mostly so they have not yet caught up.

    I will test further but am hoping to have updates from 23 & Me, and if not I will test further but at the moment, its getting used to finding out how to understand and read my DNA.

    Your advice is very helpfull, but I am cautious about things I do not fully understand, and do not want to dive in with my eyes shut.

  10. #18
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    Quote Originally Posted by Paul333 View Post
    Thanks again ArmandoR1b
    My 23 & Me Mtdna is attached with my Y data, and it is very large, thousands of pages, and would be a large file, and at the moment I do not know what is in it, and the risks of sending my full Dna raw data to something I do not yet fully understand.
    The 23andme data also has autosomal data attached. It is the same for all of us ever since 23andme combined the mtDNA, Y-DNA, and autosomal DNA in a single file. There is a way to extract the mtDNA with Excel if you know how to use Excel.

    Quote Originally Posted by Paul333 View Post
    I will test further but am hoping to have updates from 23 & Me, and if not I will test further but at the moment, its getting used to finding out how to understand and read my DNA.
    23andme does not do updates. If they ever release a new chip with more mtDNA positions tested they would not retest your saliva sample with the new chip. You would have to retest and have a "twin" at 23andme. If you go to the 23andme forum at https://www.23andmeforums.com/discussions and ask about updates of mtDNA they will point this out to you. I tested with the v4 chip and am unable to get a retest with the v5 chip unless I want a "twin". It doesn't matter though because I have already purchased advanced mtDNA and Y-DNA testing at FTDNA and have no need to have an update/upgrade at 23andme.


    Quote Originally Posted by Paul333 View Post
    Your advice is very helpfull, but I am cautious about things I do not fully understand, and do not want to dive in with my eyes shut.
    No problem. In the end, it's best that you get a FTDNA full sequence mtDNA test or a Yseq mtComplete test for the mtDNA and a Big Y test for the Y-DNA.

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  12. #19
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    [Q

    No problem. In the end, it's best that you get a FTDNA full sequence mtDNA test or a Yseq mtComplete test for the mtDNA and a Big Y test for the Y-DNA.[/QUOTE]

    Thanks again, Armando, a great help.
    I will probably end up taking one of these options, after the new year, or sooner, and hopefully this will give me time to learn and understand a bit more about my DNA results, etc.

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