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rms2
01-15-2014, 12:30 PM
My dad just got his Geno 2.0 results yesterday. Up until then, I did not know what his mtDNA haplogroup is. I just found out he belongs to K1a1.

What is known about that mtDNA haplogroup? Is there a distribution map somewhere?

Apparently Geno 2.0 just tells you your mtDNA haplogroup but does not supply you with the list of mutations from the CRS.

rms2
01-15-2014, 01:03 PM
Well, I see from Eupedia's mtDNA K distribution map (http://www.eupedia.com/europe/maps_mtdna_haplogroups.shtml#K) that K is fairly frequent in Ireland. My dad's mtDNA mdka is his maternal grandmother, Lula McElroy (aka McIlroy), and she was either Irish or of Irish descent.

Is K1a1 the most frequent variety of K in Ireland?

Ann Turner
01-15-2014, 02:24 PM
The raw data file lists your differences from the RSRS (Reconstructed Sapiens Reference Sequence) -- for the SNPs they include. The coverage is ~ 3281 out of the total 16,569 positions, so you could have additional "private" mutations if you did a Full Mitochondrial Sequence from FTDNA.

One resource is http://www.mtdnacommunity.org. You can look at the phylogenetic tree there and click on K1a1 to see the geographic origins for samples in their database.

rms2
01-15-2014, 05:16 PM
The raw data file lists your differences from the RSRS (Reconstructed Sapiens Reference Sequence) -- for the SNPs they include. The coverage is ~ 3281 out of the total 16,569 positions, so you could have additional "private" mutations if you did a Full Mitochondrial Sequence from FTDNA.

One resource is http://www.mtdnacommunity.org. You can look at the phylogenetic tree there and click on K1a1 to see the geographic origins for samples in their database.

Thanks, Ann.

I downloaded my dad's CSV file last night, but I haven't had time to look it over very well yet.

AJL
01-15-2014, 09:58 PM
Is K1a1 the most frequent variety of K in Ireland?

I'm not sure -- I do know that K1a4a1, K1a10, K1a15, and K1c2 are all fairly common there as well.

rms2
01-16-2014, 01:16 AM
Here are my dad's differences from the RSRS:

195 Mt A A
247 Mt C C
497 Mt T T
769 Mt C C
825 Mt A A
1018 Mt C C
1189 Mt G G
1811 Mt C C
2395 Mt T T
2758 Mt C C
2885 Mt T T
3308 Mt G G
3480 Mt G G
3594 Mt G G
4104 Mt A A
4312 Mt C C
4739 Mt T T
7256 Mt C C
7521 Mt G G
8468 Mt G G
8655 Mt C C
8701 Mt A A
9055 Mt A A
9540 Mt T T
9698 Mt C C
10238 Mt G G
10550 Mt C C
10664 Mt G G
10688 Mt C C
10810 Mt A A
10873 Mt T T
10915 Mt A A
11299 Mt G G
11467 Mt C C
12308 Mt C C
12372 Mt T T
12705 Mt G G
13105 Mt T T
13276 Mt A A
13506 Mt C C
13650 Mt G G
14167 Mt T T
14798 Mt G G
16129 Mt G G
16172 Mt G G
16224 Mt G G
16230 Mt A A
16278 Mt C C

There are a lot of them, evidently!

Rathna
01-16-2014, 05:13 AM
Here are my dad's differences from the RSRS:

195 Mt A A
247 Mt C C
497 Mt T T
769 Mt C C
825 Mt A A
1018 Mt C C
1189 Mt G G
1811 Mt C C
2395 Mt T T
2758 Mt C C
2885 Mt T T
3308 Mt G G
3480 Mt G G
3594 Mt G G
4104 Mt A A
4312 Mt C C
4739 Mt T T
7256 Mt C C
7521 Mt G G
8468 Mt G G
8655 Mt C C
8701 Mt A A
9055 Mt A A
9540 Mt T T
9698 Mt C C
10238 Mt G G
10550 Mt C C
10664 Mt G G
10688 Mt C C
10810 Mt A A
10873 Mt T T
10915 Mt A A
11299 Mt G G
11467 Mt C C
12308 Mt C C
12372 Mt T T
12705 Mt G G
13105 Mt T T
13276 Mt A A
13506 Mt C C
13650 Mt G G
14167 Mt T T
14798 Mt G G
16129 Mt G G
16172 Mt G G
16224 Mt G G
16230 Mt A A
16278 Mt C C

There are a lot of them, evidently!

These are my data as to RSRS, which is creating a lot of confusion and a recent paper has proposed to return to the rCRS
A16129G
T16187C
C16189T
T16223C
T16224C
G16230A
T16278C


HVR2 DIFFERENCES FROM RSRS

C146T
C152T
C195T
A247G
309.1C
315.1C
C497T
522.1A
522.2C


CODING REGION DIFFERENCES FROM RSRS

A769G
A825t
A1018G
T1189C
A1811G
A2758G
C2885T
A3480G
T3594C
G4104A
T4312C
G7146A
T7256C
A7521G
T8468C
T8655C
G8701A
G9055A
C9540T
T9698C
G9932A
A10550G
T10664C
A10688G
C10810T
C10873T
C10915T
T11204C
T11299C
A11467G
A11470G
A12308G
G12372A
T12705C
G13105A
G13276A
T13506C
T13650C
C14167T
T14798C
A15924G

Rathna
01-16-2014, 06:12 AM
Even though there is a little confusion in the reading of the data, because sometime different strands are read, I noted these mutations I haven't:

2395 TT
3308 GG
4739 TT
10238 GG
16172 GG

GTC
01-16-2014, 07:36 AM
RMS, you might also run the data through James Lick's utility:

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

Rathna
01-16-2014, 09:22 AM
The most meaningful mutation, also for a research on Mitosearch, is 16172. It is very likely that G is a reading in reverse strand, thus we should have T16172C. As hg K1a has pretty always in HVRI the mutation in 16224C, 16311C, 16519C, we have that the closest to Rich's father are these persons:

User ID HVR1 Mutations HVR2 Mutations
RJ9E6 172C, 224C, 311C, 519C 073G, 263G, 497T
94KGD 172C, 224C, 311C, 519C 073G, 263G, 315.1C, 497T
D7AGQ 172C, 224C, 311C, 519C 073G, 195C, 263G, 315.1C, 497T, 523.1C, 523.2A

Rathna
01-16-2014, 09:26 AM
As it doesn't seem that Rich's father, in spite of being tested only for a few SNPs, has 315.1C and 195C, I'd say that this people could be a very close match:

RJ9E6 172C, 224C, 311C, 519C 073G, 263G, 497T

Rathna
01-16-2014, 09:34 AM
Haplogroup: K1a1
Tested with: Genographic Project
Contact person: Emily Grant Contact this user

Most distant known maternal ancestor on the direct female line
First Name: Rebecca
Last Name: Henry
Year Born: About 1760
Year Died: 1801
Country of Origin: Boston, Massachusetts, USA
Latitude:
Longitude:

Rathna
01-16-2014, 10:21 AM
These are the 3 samples given by Behar 2012b of hg. K1a1. It is clear that Rich's father with his 5 extra mutations only of less than 4000 SNPs is another sample. The 3 Behar's samples are one from UK, one from Italy, the third unknown. Where will be the origin?

Sample Id: MC1575
NCBI Id: JQ703133
Unresolved Options:
Verified
Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] T6293C; T9077C; G9575A; A12076G; A14053G;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.] C152T(L2'3'4'5'6); T16187C(L2'3'4'6);
Country: United Kingdom
Geography:
Ancestry:
Reference: Behar 2012b
Contact:
Sample Id: MC4215
NCBI Id: JQ705773
Unresolved Options:
Verified
Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] C114T; A6929G; C11471T; C12085T;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.]
Country: Italy
Geography:
Ancestry:
Reference: Behar 2012b
Contact:
Sample Id: MC16537
NCBI Id: EU259093
Unresolved Options:
Verified
Partial Descendants:
Private Mutations: [A Personal or Private Mutation is a marker (SNP) you have that is not part of the defining markers list for this haplogroup.] T471C; T6620C; A12358G;
Topologically Missing: [A 'Missing' Mutation is a marker (SNP) that is part of the defining list of markers for this haplogroup that you do not have.]
Country:
Geography:
Ancestry:
Reference: FamilyTreeDNA
Contact:

Rathna
01-16-2014, 10:34 AM
I think that this could be an FMS of Rich's father:

A73G A263G C497T A750G T1189C A1438G A1811G G2395A A2706G T3308C A3480G G4739A A4769G C7028T A8860G G9055A T9698C T10238C A10398G A10550G T11299C A11467G G11719A G11914A A12308G G12372A C14167T C14766T T14798C A15326G T16172C T16224C T16311C T16519C

Rathna
01-16-2014, 10:35 AM
And of course there is time that this sample becomes K1a1xyz etc.

Rathna
01-16-2014, 11:01 AM
But about these mutations something doesn't fit, neither with a displacing of 1 or 2 bp.

2341 cctgcgtcag attaaaacac tgaactgaca attaacagcc caatatctac aatcaaccaa
3301 aacaacatac ccatggccaa cctcctactc ctcattgtac ccattctaat cgcaatggca
4681 taatagctat cctcttcaac aatatactct ccggacaatg aaccataacc aatactacca
4741 atcaatactc atcattaata atcataatgg ctatagcaat aaaactagga atagccccct
10201 gcgtcccttt ctccataaaa ttcttcttag tagctattac cttcttatta tttgatctag
16141 acttgaccac ctgtagtaca taaaaaccca atccacatca aaaccccctc cccatgctta

Rathna
01-16-2014, 11:13 AM
From rCRS:
2395 A 16S_rRNA
3308 T ND1 Met
4739 C ND2 ___
10238 T ND3 ___
16172 T Control_region HVS1

As usual we don't know which strand has been read.
Thus they will be: A2395G, T3308C, C4739T, T10238C, T16172C.

rms2
01-16-2014, 12:28 PM
I've got some catching up to do when it comes to mtDNA. I was familiar - well, somewhat familiar - with the CRS. The RSRS and rCRS are new to me. So is the world of K1a1, since I myself am U5a2c3a.

Rathna
01-17-2014, 05:29 AM
Thus your father's corrected FMS should be this:

A73G A263G C497T A750G T1189C A1438G A1811G A2395G A2706G T3308C A3480G C4739T A4769G C7028T A8860G G9055A T9698C T10238C A10398G A10550G T11299C A11467G G11719A G11914A A12308G G12372A C14167T C14766T T14798C A15326G T16172C T16224C T16311C T16519C

rms2
01-19-2014, 06:36 PM
It seems odd to me that I am U5a2c3a, and my dad wound up being K1a1: really just "U9-something", if his clade were named logically.

I really expected him to be some kind of H.

MJost
01-19-2014, 07:27 PM
Rich,
If you haven't yet, read http://en.wikipedia.org/wiki/Haplogroup_K_(mtDNA) and go to the 'Ancient DNA' section.

MJost