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Thursday, September 27, 2012

My mtDNA Analysis, Updated

I just ran yet another analysis of my mitochondria, using James Lick's mitohap analyzer... Very interesting results this time.  It's almost identical to one of my earlier ones, but includes the hg "X2m1" as the first best match.

http://dna.jameslick.com/mthap/

mthap version 0.19 (2012-08-11); haplogroup data version PhyloTree Build 14 (2012-04-05) +mods
raw data source N41794-FASTA.fasta (16KB)
FASTA format was uploaded. Based on the markers found, assuming the following regions were completely sequenced: HVR1 (16001~16569).
Found 569 markers at 569 positions covering 3.4% of mtDNA.


Markers found (shown as differences to rCRS):

HVR2:
CR:
HVR1: 16189C 16223T 16278T 16292T 16295T (16519C)


Best mtDNA Haplogroup Matches:
1) X2m1
Defining Markers for haplogroup X2m1:
HVR2: 73G 143A 195C (225A) 226C 235G 263G
CR: 750G 1438G 1719A 2706G 4769G 6221C 6371T 7028T 8860G 11719A 12705T 13966G 14470C 14766T 15326G
HVR1: 16189C 16223T 16278T 16292T

Marker path from rCRS to haplogroup X2m1 (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 2706G 7028T ⇨ HV 14766T ⇨ R0 73G 11719A ⇨ R 12705T 16223T ⇨ N 6221C 6371T 13966G 14470C 16189C 16278T ⇨ X 153G ⇨ X1'2'3 195C 1719A ⇨ X2 (225A) ⇨ X2(G225A) 153A ⇨ X2(G225A G153A) 143A 226C ⇨ X2m 235G 16292T ⇨ X2m1 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(4): 16189C 16223T 16278T 16292T
Extras(1): 16295T (16519C)
Untested(22): 73 143 153 195 225 226 235 263 750 1438 1719 2706 4769 6221 6371 7028 8860 11719 12705 13966 14470 14766 15326


2) X
Defining Markers for haplogroup X:
HVR2: 73G 263G
CR: 750G 1438G 2706G 4769G 6221C 6371T 7028T 8860G 11719A 12705T 13966G 14470C 14766T 15326G
HVR1: 16189C 16223T 16278T

Marker path from rCRS to haplogroup X (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 2706G 7028T ⇨ HV 14766T ⇨ R0 73G 11719A ⇨ R 12705T 16223T ⇨ N 6221C 6371T 13966G 14470C 16189C 16278T ⇨ X 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(3): 16189C 16223T 16278T
Extras(2): 16292T 16295T (16519C)
Untested(16): 73 263 750 1438 2706 4769 6221 6371 7028 8860 11719 12705 13966 14470 14766 15326


3) X1'2'3
Defining Markers for haplogroup X1'2'3:
HVR2: 73G 153G 263G
CR: 750G 1438G 2706G 4769G 6221C 6371T 7028T 8860G 11719A 12705T 13966G 14470C 14766T 15326G
HVR1: 16189C 16223T 16278T

Marker path from rCRS to haplogroup X1'2'3 (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 2706G 7028T ⇨ HV 14766T ⇨ R0 73G 11719A ⇨ R 12705T 16223T ⇨ N 6221C 6371T 13966G 14470C 16189C 16278T ⇨ X 153G ⇨ X1'2'3 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(3): 16189C 16223T 16278T
Extras(2): 16292T 16295T (16519C)
Untested(17): 73 153 263 750 1438 2706 4769 6221 6371 7028 8860 11719 12705 13966 14470 14766 15326


3) X1'3
Defining Markers for haplogroup X1'3:
HVR2: 73G 146C 153G 263G
CR: 750G 1438G 2706G 4769G 6221C 6371T 7028T 8860G 11719A 12705T 13966G 14470C 14766T 15326G
HVR1: 16189C 16223T 16278T

Marker path from rCRS to haplogroup X1'3 (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 2706G 7028T ⇨ HV 14766T ⇨ R0 73G 11719A ⇨ R 12705T 16223T ⇨ N 6221C 6371T 13966G 14470C 16189C 16278T ⇨ X 153G

X1'2'3 146C ⇨ X1'3 16292T 16295T (16519C)
Imperfect Match. Your results contained differences with this haplogroup:
Matches(3): 16189C 16223T 16278T
Extras(2): 16292T 16295T (16519C)
Untested(18): 73 146 153 263 750 1438 2706 4769 6221 6371 7028 8860 11719 12705 13966 14470 14766 15326

*************************************************
 
Another take, based on Lick's adaptation to Family Tree DNA data.  Why Family Tree and Genographic need adaptations, I'll probably never understand... I'd heard that the geneticists rearranged the H haplotypes, and boy did they ever.

UPDATE:  After further investigations, I have good reasons to believe that the following dataset, along with the second one presented to me before, by James Lick himself, is in error and should be thrown out.
 
 
mthap version 0.19 (2012-08-11); haplogroup data version PhyloTree Build 14 (2012-04-05) +mods
raw data source N41794-FASTA.fasta (16KB)
FASTA format was uploaded. Based on the markers found, assuming the following regions were completely sequenced: HVR1 (16001~16569).
Found 569 markers at 569 positions covering 3.4% of mtDNA.

 
Markers found (shown as differences to rCRS):

HVR2:
CR:
HVR1: 16189C 16223T 16278T 16292T 16295T (16519C)
Derived markers for FTDNA/Genographic predicted haplogroup w:
CR: 1243T 2758G 3594C 3970C 4248T 4580G 5178C 6371C 7028C 10034T 10238T 10400C 10550A 10873T 11467A 11719G 12612A 12705C 13263A 13368G 14766C
(Differences to rCRS are in bold. Derived markers are based on using the Family Tree DNA or The Genographic Project predicted haplogroup to determine the results of the 22 SNP panel of CR markers used. Using new panel.)

 
Best mtDNA Haplogroup Matches:
1) w
Defining Markers for haplogroup w:
HVR2:
CR:
HVR1:

Marker path from rCRS to haplogroup w (plus extra markers):
H2a2a1(rCRS) 16189C 16223T 16278T 16292T 16295T (16519C)

Good Match! Your results also had extra markers for this haplogroup:
Extras(5): 16189C 16223T 16278T 16292T 16295T (16519C)

 
2) H3(T16189C)
Defining Markers for haplogroup H3(T16189C):
HVR2: 263G
CR: 750G 1438G 4769G 6776C 8860G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H3(T16189C) (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 6776C ⇨ H3 16189C ⇨ H3(T16189C) 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(7): 263 750 1438 4769 6776 8860 15326

 
2) H1(T16189C)
Defining Markers for haplogroup H1(T16189C):
HVR2: 263G
CR: 750G 1438G 3010A 4769G 8860G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1(T16189C) (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(7): 263 750 1438 3010 4769 8860 15326

 
2) H1aa
Defining Markers for haplogroup H1aa:
HVR2: 263G
CR: 750G 1438G 3010A 4131G 4769G 8860G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1aa (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 4131G ⇨ H1aa 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(8): 263 750 1438 3010 4131 4769 8860 15326

 
2) H1ab
Defining Markers for haplogroup H1ab:
HVR2: 263G
CR: 750G 1438G 3010A 4769G 8860G 15047A 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1ab (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 15047A ⇨ H1ab 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(8): 263 750 1438 3010 4769 8860 15047 15326

 
2) H1g
Defining Markers for haplogroup H1g:
HVR2: 263G
CR: 750G 1438G 3010A 4769G 8860G 14212C 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1g (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 14212C ⇨ H1g 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(8): 263 750 1438 3010 4769 8860 14212 15326

 
2) H1ac
Defining Markers for haplogroup H1ac:
HVR2: 263G
CR: 750G 1438G 3010A 4769G 8860G 11893G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1ac (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 11893G ⇨ H1ac 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(8): 263 750 1438 3010 4769 8860 11893 15326

 
2) H1ad
Defining Markers for haplogroup H1ad:
HVR2: 263G
CR: 750G 1438G 3010A 3504C 4769G 8860G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1ad (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 3504C ⇨ H1ad 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(8): 263 750 1438 3010 3504 4769 8860 15326

 
2) H1y
Defining Markers for haplogroup H1y:
HVR2: 263G
CR: 750G 1438G 3010A 4769G 8860G 15299C 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1y (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 15299C ⇨ H1y 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(8): 263 750 1438 3010 4769 8860 15299 15326

 
3) H1g2
Defining Markers for haplogroup H1g2:
HVR2: 263G
CR: 750G 1438G 3010A 4769G 8860G 9230C 14212C 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1g2 (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 14212C ⇨ H1g 9230C ⇨ H1g2 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(9): 263 750 1438 3010 4769 8860 9230 14212 15326

 
3) H1z
Defining Markers for haplogroup H1z:
HVR2: 263G 327T
CR: 750G 1438G 3010A 4769G 8860G 11428T 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1z (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 327T 11428T ⇨ H1z 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(9): 263 327 750 1438 3010 4769 8860 11428 15326

 
3) H1f
Defining Markers for haplogroup H1f:
HVR2: 263G
CR: 750G 1438G 3010A 4452C 4769G 8860G 9066G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1f (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 4452C 9066G ⇨ H1f 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(9): 263 750 1438 3010 4452 4769 8860 9066 15326

 
3) H1g1
Defining Markers for haplogroup H1g1:
HVR2: 263G
CR: 750G 1438G 3010A 4769G 8602C 8860G 14212C 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1g1 (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 16189C ⇨ H1(T16189C) 14212C ⇨ H1g 8602C ⇨ H1g1 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(9): 263 750 1438 3010 4769 8602 8860 14212 15326

 
3) H1ap1
Defining Markers for haplogroup H1ap1:
HVR2: 152C 263G
CR: 750G 1438G 3010A 4769G 5780A 8410T 8860G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H1ap1 (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 8410T ⇨ H1ap 152C 5780A 16189C ⇨ H1ap1 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(10): 152 263 750 1438 3010 4769 5780 8410 8860 15326

 
3) H1ao
Defining Markers for haplogroup H1ao:
HVR2: 93G 146C 263G
CR: 750G 1438G 3010A 4769G 8860G 11809C 15326G
HVR1: 16278T

Marker path from rCRS to haplogroup H1ao (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 3010A ⇨ H1 93G 146C 11809C 16278T ⇨ H1ao 16189C 16223T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16278T
Extras(4): 16189C 16223T 16292T 16295T (16519C)
Untested(10): 93 146 263 750 1438 3010 4769 8860 11809 15326

 
3) H3av
Defining Markers for haplogroup H3av:
HVR2: 152C 263G
CR: 750G 1438G 4769G 6776C 7849T 8383C 8860G 15326G
HVR1: 16189C

Marker path from rCRS to haplogroup H3av (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 6776C ⇨ H3 16189C ⇨ H3(T16189C) 152C 7849T 8383C ⇨ H3av 16223T 16278T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16189C
Extras(4): 16223T 16278T 16292T 16295T (16519C)
Untested(10): 152 263 750 1438 4769 6776 7849 8383 8860 15326

 
3) H3c3
Defining Markers for haplogroup H3c3:
HVR2: 260A 263G
CR: 750G 1438G 4769G 6776C 8860G 12957C 15326G 15769G
HVR1: 16278T

Marker path from rCRS to haplogroup H3c3 (plus extra markers):
H2a2a1(rCRS) 263G ⇨ H2a2a 8860G 15326G ⇨ H2a2 750G ⇨ H2a 4769G ⇨ H2 1438G ⇨ H 6776C ⇨ H3 12957C ⇨ H3c 260A 15769G 16278T ⇨ H3c3 16189C 16223T 16292T 16295T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(1): 16278T
Extras(4): 16189C 16223T 16292T 16295T (16519C)
Untested(10): 260 263 750 1438 4769 6776 8860 12957 15326 15769

However, when I ran the modified analysis again, including BOTH the Family Tree conclusion AND the Genographic snps for my mtDNA -- I got a ~repeat of the ~first one above.  The second one here was analyzed with only the added information, that Family Tree DNA's classification of my DNA is "W".  This is so frustrating; I really wish I could afford some more testing soon (although, really I shouldn't have to pay twice, for the same information, only ACCURATE this time).

Again, when I analyzed my DNA using yet another method on mitohap, this time just going by the rCRS mutations, I got the top list.  That makes three out of four, for that set of results, using four different methods of analysis on James Lick's site.  He doesn't seem to have a way to analyze differences to the RCRS, though (the newest, latest Human Genome comparison).  It's getting late today, so maybe I'll try again tomorrow.

UPDATE:  After testing the data numerous times, I got the first set of data about 24/25 times, and since I believe the second set is in error (as I now believe the second set presented to me by James Lick himself was also in error -- probably based on some careless mistake in the data entry process), I'm throwing out the second sets of both sessions.  I now fully believe that the first set shown here (which has been updated from the first set that I got last time I checked it) is the correct dataset.  This means that instead of W, or W1e (as Family Tree DNA has classified me, after CHANGING my classification from X) -- is INACCURATE.  Whether that was done deliberately or not, remains to be seen.  I am fully aware of their nasty, snide attitude concerning my claim that my mtDNA is authentic Cherokee.  I also have plenty of reason to suspect that the US government (perhaps DHS) got involved and meddled in my business, somehow.

Regardless, the numbers don't lie:  it looks like my mtDNA really is in the X cluster (not that W isn't also in the X cluster, as is I).  Not only that, but according to these results, it is extremely similar, if not identical to known Native American mtDNA.  I believe with all my heart, that the US government (along with their sycophants) is trying to exclude me and my family from any past or future reparations which might be due us.  I certainly wouldn't put it past them.


An old paper; still looking for newer ones (I know they're out there somewhere).


(Both W and X, which are very closely related of course, are located in the Europe & Near-East/Caucasus region of the chart for ancient mtDNA... YEAH!)

My comment posted to the above blog, in response to Dr. German Dzeibel's comment:

"It also further supports my claim of Native American lineage through my mtDNA, the subclade of which is at least very, very closely related to X2a (the one "European" group documented to have be found among NA's).  If Amerindian mtDNA of Mongoloid origin may be found in both ancient and modern Europe, then it follows that DNA of Caucasoid origin may also be found in ancient and modern North America, among certain lineages of some Native peoples (like, the Cherokee)."

UPDATE: He published my comment this time, too.  Yippee!  Lol.

Dzeibel is on the trail, too.  I like his uniquely objective observations.

University of Adelaide, in Australia




Interesting details about haplogroup X, including the fact that both X2a and X2g have now been documented among Native Americans.  Also, it states that these same subclades, unlike other NA DNA, is not closely associated with East Asia.  It further states that Altai X2e is a more recent migration from the Caucasus region.  My possible subclade, X2m1, is apparently far too recently identified, for any informative commentary; because there's nothing to be found on the subject.  I also noticed that it is quite rarely found on mitosearch, only a few individuals with that DNA.  And, I predict that there will be future revelations concerning the close relationship between W1e and these X subclades.  I wouldn't be surprised if W1e is someday included among documented NA mtDNA subclades.


I believe blood factors, such as "Diego" and "Rhesus", are going to be one of the main keys to solving the puzzles of Human origins.

http://dienekes.blogspot.com/2012/12/talk-by-christina-papageorgopoulou-on.html

http://www.searchforancestors.com/utility/

http://dienekes.blogspot.com/2012/10/ancient-mtdna-haplogroup-x2-from.html

http://www.familytreedna.com/pdf-docs/mt_migrationmap.pdf

http://dienekes.blogspot.com/2013/01/genetic-evidence-for-colonization-of.html

http://www.thecid.com/genograp.htm

http://www.mtdnacommunity.org/human-mtdna-phylogeny.aspx

http://www.eupedia.com/europe/ancient_european_dna.shtml

http://www.eupedia.com/europe/european_mtdna_haplogroups_frequency.shtml

http://www.eupedia.com/europe/neolithic_europe_map.shtml

http://www.eupedia.com/europe/european_haplogroups_timeline.shtml

 

2 comments:

  1. Replies
    1. Awesome; that means you have a fabulous and fairly rare maternal lineage, have inherited many fine Human qualities through that lineage -- and, we might even be related!! ;)

      Best wishes to you now and always,

      Debra

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