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Thread: GenBank Submissions

  1. #1
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    GenBank Submissions

    Quote Originally Posted by Dr_McNinja View Post
    Funny, that 16311C is one of the terminal SNPs for M30b so you have more matches for M30b than any other haplogroup but two mismatches with it.

    Try submitting your sample here: http://www.ianlogan.co.uk/Submission.htm
    Does Sein have a mtDNA FGS? Or is he referring to his 23andMe data?

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     Sein (06-20-2014)

  3. #2
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    Quote Originally Posted by Humanist View Post
    Does Sein have a mtDNA FGS? Or is he referring to his 23andMe data?
    Oh whoops, forgot he had 23andMe and not FTDNA. If you have an mt Full Sequence test from FTDNA you can use that.
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

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  5. #3
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    Quote Originally Posted by Dr_McNinja View Post
    Oh whoops, forgot he had 23andMe and not FTDNA. If you have an mt Full Sequence test from FTDNA you can use that.
    Do you have a FGS? If so, do you have a link to your sample's page at GenBank? I am here. I used to have a link to it in my signature page on the old DNA Forums, and had kind of forgotten about it. Glad I submitted my sample, though, as it was included in a study of HV4 a couple of years ago.

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  7. #4
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    Quote Originally Posted by Humanist View Post
    Do you have a FGS? If so, do you have a link to your sample's page at GenBank? I am here. I used to have a link to it in my signature page on the old DNA Forums, and had kind of forgotten about it. Glad I submitted my sample, though, as it was included in a study of HV4 a couple of years ago.
    No, not yet, I just e-mailed mine today.
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

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    Quote Originally Posted by Dr_McNinja View Post
    No, not yet, I just e-mailed mine today.
    Awesome! Congrats.

  10. #6
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    I added my rCRS results in here as number 14: http://i.imgur.com/UxD9rys.png I'm guessing that's how it'll look once they add me. I seem to have the most overlap with the one above me (#13) but they have overlap with the others. Any idea on how to find out where these samples were from?

    I noticed some of the values in RSRS results don't match rCRS. My mismatched C16311T for example is only in RSRS and not in rCRS while the other M30b people have T16311C presumably from their rCRS tables.

    Here's the e-mail I got from Ian summarizing my mutations from the rCRS table:

    Punjabi Jatt

    USA

    Haplogroup M30b

    Simplified CRS mutations (42)

    73G 152C 195A 263G 315.1C 469T 489C 522- 523- 750G
    1284Y 1438G 2706G 4769G 5147A 5529G 5899.1C 7028T 7647Y 8701G
    8860G 9540C 10398G 10400T 10873C 11017C 11719A 11914A 12007A 12705T
    14766T 14783C 14870G 15043A 15301A 15326G 15431A 16093C 16223T 16266T
    16278T 16519C

    CRS mutations as given by sqn (42)

    A73G T152C T195A A263G 315.1C C469T T489C C522- A523- A750G
    T1284Y A1438G A2706G A4769G G5147A A5529G 5899.1C C7028T T7647Y A8701G
    A8860G T9540C A10398G C10400T T10873C T11017C G11719A G11914A G12007A C12705T
    C14766T T14783C A14870G G15043A G15301A A15326G G15431A T16093C C16223T C16266T
    C16278T T16519C

    --------------

    CHECK: CRS mutations as given by FASTA file suplied (42)

    A73G T152C T195A A263G 315.1C C469T T489C C522- A523- A750G
    T1284Y A1438G A2706G A4769G G5147A A5529G 5899.1C C7028T T7647Y A8701G
    A8860G T9540C A10398G C10400T T10873C T11017C G11719A G11914A G12007A C12705T
    C14766T T14783C A14870G G15043A G15301A A15326G G15431A T16093C C16223T C16266T
    C16278T T16519C

    -----------------

    A simple breakdown of the CRS mutations (42)

    A73G - mutation in HVR2 area
    T152C - mutation in HVR2 area
    T195A - mutation in HVR2 area
    A263G - mutation in HVR2 area
    315.1C - insertion in HVR2 area
    C469T - mutation in HVR2 area
    T489C - mutation in HVR2 area
    C522- - deletion in HVR2 area
    A523- - deletion in HVR2 area
    A750G - mutation in 12S rRNA gene (MT-RNR2) . . . . . . . Common mutation near CRS
    T1284Y - mutation in 12S rRNA gene (MT-RNR2)
    A1438G - mutation in 12S rRNA gene (MT-RNR2) . . . . . . . Common mutation near CRS
    A2706G - mutation in 16S rRNA gene (MT-RNR1) . . . . . . . Common mutation near CRS
    A4769G - mutation in peptide NAD2 (MT-ND2) synonymous - no change in amino acid
    G5147A - mutation in peptide NAD2 (MT-ND2) synonymous - no change in amino acid
    A5529G - mutation in tRNA for Tryptophan (MT-TW)
    5899.1C - insertion in a non-coding area
    C7028T - mutation in peptide COX1 (MT-CO1) synonymous - no change in amino acid
    T7647Y - mutation in peptide COX2 (MT-CO2) Heteroplasmy T7647C is non-synonymous 'I21T'
    A8701G - mutation in peptide ATP6 (MT-ATP6) non-synonymous 'T59A' Defines Haplogroup M
    A8860G - mutation in peptide ATP6 (MT-ATP6) non-synonymous 'T112A' Common mutation near CRS
    T9540C - mutation in peptide COX3 (MT-CO3) synonymous - no change in amino acid
    A10398G - mutation in peptide NAD3 (MT-ND3) non-synonymous 'T114A' Defines Haplogroup K1, M & L
    C10400T - mutation in peptide NAD3 (MT-ND3) synonymous - no change in amino acid
    T10873C - mutation in peptide NAD4 (MT-ND4) synonymous - no change in amino acid
    T11017C - mutation in peptide NAD4 (MT-ND4) synonymous - no change in amino acid
    G11719A - mutation in peptide NAD4 (MT-ND4) synonymous - no change in amino acid
    G11914A - mutation in peptide NAD4 (MT-ND4) synonymous - no change in amino acid
    G12007A - mutation in peptide NAD4 (MT-ND4) synonymous - no change in amino acid
    C12705T - mutation in peptide NAD5 (MT-ND5) synonymous - no change in amino acid
    C14766T - mutation in peptide CYTB (MT-CYB ) non-synonymous 'T7I' . Common mutation near CRS
    T14783C - mutation in peptide CYTB (MT-CYB ) synonymous - no change in amino acid
    A14870G - mutation in peptide CYTB (MT-CYB ) non-synonymous 'I42V' Defines Haplogroup M27c
    G15043A - mutation in peptide CYTB (MT-CYB ) synonymous - no change in amino acid
    G15301A - mutation in peptide CYTB (MT-CYB ) synonymous - no change in amino acid
    A15326G - mutation in peptide CYTB (MT-CYB ) non-synonymous 'T194A' Common mutation near CRS
    G15431A - mutation in peptide CYTB (MT-CYB ) non-synonymous 'A229T' Defines Haplogroup U6b1 & M30b
    T16093C - mutation in HVR1 area
    C16223T - mutation in HVR1 area
    C16266T - mutation in HVR1 area
    C16278T - mutation in HVR1 area
    T16519C - mutation in HVR1 area


    And matches fairly well (because of 'A5529G' & 'T11017C') with sequence :

    JQ702987 Behar Haplogroup M30b 07-APR-2012
    44.1C A73G T152C T195A A263G 309.1C 315.1C T489C C522- A523-
    A750G A1438G A2706G A4769G G5147A A5529G 5899.1C C7028T A8701G A8860G
    T8937C T9540C A10398G C10400T T10873C T11017C G11719A G12007A C12705T C14766T
    T14783C G15043A G15301A A15326G G15431A C16223T C16278T T16304C T16311C G16391A
    T16519C

    See also:
    http://www.ianlogan.co.uk/sequences_..._sequences.htm
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

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  12. #7
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    Quote Originally Posted by Dr_McNinja View Post
    I added my rCRS results in here as number 14: http://i.imgur.com/UxD9rys.png I'm guessing that's how it'll look once they add me. I seem to have the most overlap with the one above me (#13) but they have overlap with the others. Any idea on how to find out where these samples were from?

    I noticed some of the values in RSRS results don't match rCRS. My mismatched C16311T for example is only in RSRS and not in rCRS while the other M30b people have T16311C presumably from their rCRS tables.

    Here's the e-mail I got from Ian summarizing my mutations from the rCRS table:
    The references are different. sCRS is referenced to a modern European who already had many mutations that were not ancestral.
    So that European person already had the C16311T mutation and therefore in reference to that you are not showing it.

    Since you are M and have RSRS C16311T and the rCRS reference was an N derivative H and also had RSRS C16311T, this is a very upstream mutation.

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  14. #8
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    Quote Originally Posted by parasar View Post
    The references are different. sCRS is referenced to a modern European who already had many mutations that were not ancestral.
    So that European person already had the C16311T mutation and therefore in reference to that you are not showing it.

    Since you are M and have RSRS C16311T and the rCRS reference was an N derivative H and also had RSRS C16311T, this is a very upstream mutation.
    Yeah, Ian said T16311C was a recent mutation:

    Quote Originally Posted by Ian
    Yes, there is the 16311 difference. A common mutation, so not a very important one.
    Maybe it has arisen in the last 400 years, or so.
    So you think it mutated in different populations around the same time recently? There are M4'67 derivatives that would have to have been in the Pakistan/NW-India region for at least several centuries which have it while there are other branches in Southeast India that also have it.
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
    Maternal- Y-DNA: R1a1a1b2a1a2c2d5a* L657+ Y7+ (R-Y16494*) (FTDNA Kit 311047) (YFull: YF68408), mtDNA: Hidden Content (FTDNA Kit B6225) (YFull: YF02959) (Mother's Mother's Father: R1a1a1b2a1a2c2* Y7+ Y29+ (R-Y29*) (FTDNA Kit 329181) (YFull: YF65256))

  15. #9
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    Quote Originally Posted by Dr_McNinja View Post
    Yeah, Ian said T16311C was a recent mutation:



    So you think it mutated in different populations around the same time recently? There are M4'67 derivatives that would have to have been in the Pakistan/NW-India region for at least several centuries which have it while there are other branches in Southeast India that also have it.
    If this correct -"other M30b people have T16311C presumably from their rCRS" - then it means it has back mutated in these people.

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  17. #10
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    The below post by MfA reminded me of the above exchange between Dr. McNinja and I. It appears that you can have your data listed on GenBank, even if you have not had a mtDNA FGS. But, apparently, you need to have your data uploaded at OpenSNP.org. I checked the HV page and found that I am listed twice. The first being my mtDNA FGS sample, and again as "Paul G."


    Quote Originally Posted by MfA View Post
    Ian Logan is very kind to add me GenBank.
    http://www.ianlogan.co.uk/sequences_..._sequences.htm

    For those who interests, all you need to do is uploading your 23andMe raw data to OpenSNP.org

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