geno2.0 mtdna results

Any discussions regarding mt-DNA markers, results or questions.

Posts: 14
Joined: Mon Dec 17, 2012 2:14 pm

YDNA:
R-L657,L-M357
MtDNA:
M5a1,R30a
PostPosted: Fri Feb 08, 2013 5:38 pm
My results in geno 2 shows my mtdna is R30 .
But they didnt give any snp mutations in the result

Even in the raw data file i am not able to make out anything as the reference sequence value is not mentioned . Does anybody know how to find the mutations from raw data file

Again in the raw data file some locations seems to be tested more than once and sometimes they are showing different value .Does that really happen or is geno2 test unreliable ? any help appreciated

Posts: 116
Joined: Tue Mar 20, 2012 3:38 am
PostPosted: Sat Feb 09, 2013 3:36 am
As far as I know, it is not currently possible to get a mutation list from mtDNA Geno 2 results.

R30 is a fairly rare and old haplogroup. So I'd also recommend testing the full genome at FTDNA, as its possible that the Geno 2 test missed some interesting mutations. There should be a sale on the test sometime in the spring.

Posts: 77
Joined: Sat Dec 01, 2012 12:40 am

MtDNA:
T2
PostPosted: Sat Feb 09, 2013 8:50 am
Yes, it is possible to extract your mutations form the Geno 2.0 file with James Lick analysis tool here:

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

This was discussed just a few threads below. Of course, Geno 2.0 chip does not sequence the complete mtDNA, but just tests a number of known mutations, so it can miss some private or undiscovered SNPs.

Posts: 14
Joined: Mon Dec 17, 2012 2:14 pm

YDNA:
R-L657,L-M357
MtDNA:
M5a1,R30a
PostPosted: Sat Feb 09, 2013 4:26 pm
I compared the mtdna results in the raw data file to the rCRS sequence available in mitomap site .It is showing too many differences to be true . i was getting around 30 differnces in HVR-2 region itself . That makes the doubt the methodology used for testing . i can share my raw data file for anybody willing to help
User avatar
Posts: 542
Joined: Mon Oct 22, 2012 8:19 am
Location: Family Line Veneto ( italy ) since ~1600
YDNA:
T1a2-Z19945
MtDNA:
H95a
PostPosted: Sat Feb 09, 2013 6:52 pm
eastara wrote:Yes, it is possible to extract your mutations form the Geno 2.0 file with James Lick analysis tool here:

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

This was discussed just a few threads below. Of course, Geno 2.0 chip does not sequence the complete mtDNA, but just tests a number of known mutations, so it can miss some private or undiscovered SNPs.


isn't Jlick tool still default to rCrs and you need to run the program via advanced and select rsrs format?
Fathers mtdna - T2b17 ...back to 1860 Bucciol line
Grandfathers mtdna - T1a1e ...back to 1820 Mestriner line
Sons Mtdna - K1a4 ....back to 1840 Tesser line
Maternal grandfather ydna - Ild-P109

Posts: 77
Joined: Sat Dec 01, 2012 12:40 am

MtDNA:
T2
PostPosted: Sat Feb 09, 2013 11:44 pm
BMG wrote:I compared the mtdna results in the raw data file to the rCRS sequence available in mitomap site .It is showing too many differences to be true . i was getting around 30 differnces in HVR-2 region itself . That makes the doubt the methodology used for testing . i can share my raw data file for anybody willing to help


Could you publish here the output after you upload your Geno 2.0 *csv file?
For example, here is what comes out for my brother's:

Markers found (shown as differences to rCRS):

HVR2: 73G 263G
CR: 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 10463C 11251G 11719A 11812G 13368A 14233G 14766T 14905A 15326G 15452A 15607G 15928A
HVR1: 16126C 16287T 16294T (16519C)

IMPORTANT NOTE: The above marker list is almost certainly incomplete due to limitations of genotyping technology and is not comparable to mtDNA sequencing results. It should not be used with services or tools that expect sequencing results, such as mitosearch.

Best mtDNA Haplogroup Matches:
1) T2

Defining Markers for haplogroup T2:
HVR2: 73G 263G
CR: 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 10463C 11251G 11719A 11812G 13368A 14233G 14766T 14905A 15326G 15452A 15607G 15928A
HVR1: 16126C 16294T (16296T)

Marker path from rCRS to haplogroup T2 (plus extra markers):
H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 4216C ⇨ R2'JT ⇨ 11251G 15452A 16126C ⇨ JT ⇨ 709A 1888A 4917G 8697A 10463C 13368A 14905A 15607G 15928A 16294T ⇨ T ⇨ 11812G 14233G (16296T) ⇨ T2 ⇨ 16287T (16519C)

Good Match! Your results also had extra markers for this haplogroup:
Matches(27): 73G 263G 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 10463C 11251G 11719A 11812G 13368A 14233G 14766T 14905A 15326G 15452A 15607G 15928A 16126C 16294T
Mismatches(0): (16296C)
Extras(1): 16287T (16519C)


2) T2(T16189C)

Defining Markers for haplogroup T2(T16189C):
HVR2: 73G 263G
CR: 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 10463C 11251G 11719A 11812G 13368A 14233G 14766T 14905A 15326G 15452A 15607G 15928A
HVR1: 16126C 16189C 16294T (16296T)

Marker path from rCRS to haplogroup T2(T16189C) (plus extra markers):
H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 4216C ⇨ R2'JT ⇨ 11251G 15452A 16126C ⇨ JT ⇨ 709A 1888A 4917G 8697A 10463C 13368A 14905A 15607G 15928A 16294T ⇨ T ⇨ 11812G 14233G (16296T) ⇨ T2 ⇨ 16189C ⇨ T2(T16189C) ⇨ 16287T (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(27): 73G 263G 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 7028T 8697A 8860G 10463C 11251G 11719A 11812G 13368A 14233G 14766T 14905A 15326G 15452A 15607G 15928A 16126C 16294T
Mismatches(0): (16296C)
Extras(1): 16287T (16519C)
Untested(1): 16189


The differences are CRS and you must compare to the official Phylotree here:

http://www.phylotree.org/tree/subtree_R.htm

As I wrote in the Haplogroup T forum, I am not happy with the Geno and FamilyTree new classification as T only, as their tree requires 16296 as compulsory, not variable, while having the inconsistency that some other T2 subgroups are classified T2xx while lacking 16296 as well.

Posts: 116
Joined: Tue Mar 20, 2012 3:38 am
PostPosted: Fri Feb 15, 2013 3:35 am
eastara wrote:Yes, it is possible to extract your mutations form the Geno 2.0 file with James Lick analysis tool here:

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

This was discussed just a few threads below. Of course, Geno 2.0 chip does not sequence the complete mtDNA, but just tests a number of known mutations, so it can miss some private or undiscovered SNPs.


Jim had mthap working for Geno 2.0 for a short time, and then NG changed the format of the files. It would be great if it is working again, but I don't see Geno 2.0 listed on the mthap page.

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