mthap: an mtdna haplogroup analysis tool

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

Posts: 3
Joined: Sun Feb 02, 2014 3:52 pm

MtDNA:
T2d1b
PostPosted: Sun Mar 09, 2014 8:45 pm
I'm not sure if this is the place to ask but here I go-

When I put my FTDNA full sequence into the mtdna tool it gives me T2d1b as the most likely match but FTDNA says I'm a JT. 23andme also puts me in the T2d group. Why the difference? results below for reference.

Markers found (shown as differences to rCRS):

HVR2: 73G 194T 200G 235G 263G (309.1C) (315.1C) 573.1C 573.2C
CR: 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 5747G 7028T 7295G 8697A 8860G 9617G 10463C 11251G 11719A 11812G 11827C 12373G 13260C 13368A 13708A 14233G 14766T 14905A 15326G 15452A 15928A
HVR1: 16126C 16192T 16294T 16309G (16519C)


Best mtDNA Haplogroup Matches:

1) T2d1b

Defining Markers for haplogroup T2d1b:
HVR2: 73G 152C 194T 200G 263G
CR: 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 5747G 7028T 7295G 8697A 8860G 10463C 11251G 11719A 11812G 12373G 13260C 13368A 13708A 14233G 14766T 14905A 15326G 15452A 15607G 15928A
HVR1: 16126C 16294T (16296T)

Marker path from rCRS to haplogroup T2d1b (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 ⇨ 13260C ⇨ T2d ⇨ 152C 5747G 13708A ⇨ T2d1 ⇨ 194T 200G 7295G 12373G ⇨ T2d1b ⇨ 235G (309.1C) (315.1C) 573.1C 573.2C 9617G 11827C 16192T 16309G (16519C)

Imperfect Match. Your results contained differences with this haplogroup:
Matches(33): 73G 194T 200G 263G 709A 750G 1438G 1888A 2706G 4216C 4769G 4917G 5747G 7028T 7295G 8697A 8860G 10463C 11251G 11719A 11812G 12373G 13260C 13368A 13708A 14233G 14766T 14905A 15326G 15452A 15928A 16126C 16294T
Mismatches(2): 152T 15607A (16296C)
Extras(7): 235G (309.1C) (315.1C) 573.1C 573.2C 9617G 11827C 16192T 16309G (16519C)

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Mon Mar 10, 2014 4:07 am
sylvari wrote:When I put my FTDNA full sequence into the mtdna tool it gives me T2d1b as the most likely match but FTDNA says I'm a JT. 23andme also puts me in the T2d group. Why the difference?

... JT ⇨ 709A 1888A 4917G 8697A 10463C 13368A 14905A 15607G 15928A 16294T ⇨ T ⇨ 11812G 14233G (16296T) ⇨ T2 ⇨ 13260C ⇨ T2d ⇨ 152C 5747G 13708A ⇨ T2d1 ⇨ 194T 200G 7295G 12373G ⇨ T2d1b ⇨ 235G (309.1C) (315.1C) 573.1C 573.2C 9617G 11827C 16192T 16309G (16519C)

...
Mismatches(2): 152T 15607A (16296C)
...


You have a reversion for marker 15607G for haplogroup T, a reversion for marker 16296T for haplogroup T2 and a reversion for marker 152C for haplogroup T2d1. The difference is that mthap is more tolerant of reversions and other discrepancies than FTDNA's haplogroup matching algorithm is. For 23andMe the primary reason is that 23andMe uses the older PhyloTree Build 7, while T2d1 and T2d1b were added in PhyloTree Build 15, though it's also possible that 23andMe doesn't test all the markers or that you have some no-calls for some markers. (You can also run your 23andMe raw data through mthap.)

Posts: 3
Joined: Sun Feb 02, 2014 3:52 pm

MtDNA:
T2d1b
PostPosted: Mon Mar 10, 2014 12:41 pm
When I put my 23andme data thru it also gives me a T2d1 result.

Should I just stick with that as the result then? When 3 out of 4 put me in the T2d it seems most likely to be the case yes?

Thanks for looking at this by the way. I am just starting to look into all this and it's crazy fascinating but there is so much information it's often overwhelming.

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Mon Mar 10, 2014 12:59 pm
You’re definitely T2d1b.

Posts: 3
Joined: Sun Feb 02, 2014 3:52 pm

MtDNA:
T2d1b
PostPosted: Tue Mar 11, 2014 12:19 am
And you are definitely awesome for all your help. :)

Thank you.

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

MtDNA:
T2
PostPosted: Fri Mar 21, 2014 11:49 am
I have a question regarding uploading the latest Geno 2.0 mtDNA files.
Before all Geno 2.0 data was on one file and I had no problems uploading and getting mtDNA haplogroup results with the mthap tool.
However recently I received raw Geno 2.0 data, which after unzipping produces 3 files, one exclusively for mtDNA.
After uploading the mtDNA file I get some nonsense, trying to edit it - the same.
This person is assigned as plain H at Geno 2.0. This is literally the whole mtDNA file, which haplogroup is this?

SNP Chr Allele1 Allele2
195 Mt A A
247 Mt C C
769 Mt C C
825 Mt A A
1018 Mt C C
2395 Mt T T
2706 Mt A A
2758 Mt C C
2885 Mt T T
3594 Mt G G
4104 Mt A A
4312 Mt C C
7028 Mt C C
7256 Mt C C
7521 Mt G G
8468 Mt G G
8655 Mt C C
8701 Mt A A
9540 Mt T T
10398 Mt A A
10664 Mt G G
10688 Mt C C
10810 Mt A A
10873 Mt T T
10915 Mt A A
11719 Mt C C
11914 Mt C C
12705 Mt G G
13105 Mt T T
13276 Mt A A
13506 Mt C C
13650 Mt G G
14766 Mt G G
16129 Mt G G
16230 Mt A A
16278 Mt C C
16311 Mt A A

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Fri Mar 21, 2014 1:20 pm
eastara wrote:Before all Geno 2.0 data was on one file and I had no problems uploading and getting mtDNA haplogroup results with the mthap tool.
However recently I received raw Geno 2.0 data, which after unzipping produces 3 files, one exclusively for mtDNA. ...
This person is assigned as plain H at Geno 2.0. This is literally the whole mtDNA file, which haplogroup is this?

SNP Chr Allele1 Allele2
195 Mt A A
...


First of all make sure you use the beta version for Geno2 files: http://dna.jameslick.com/mthap-new/

Also all the files I've seen use commas for delimiters instead of tabs. Is the file you downloaded really using tabs or is this after editing?

Though, I get no useful information out anyways. It has no non-rCRS markers and lots and lots of possible matches in H. Perhaps if they included results for old probes like they used to it could be more specific.

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

MtDNA:
T2
PostPosted: Fri Mar 21, 2014 9:59 pm
Sorry, the file is XXXXX.mtdna.csv, comma delimited, it opened by default with Excel.
This is a brand new Geno 2.0 test, coming only a few days ago. If these are differences from CRS, it does not make sense. It is lacking the basic haplogroup H mutations like 263 and 8348.
Yes, I am using the mthap-new and that's the output:

Markers found (shown as differences to rCRS):

HVR2:
CR:
HVR1:

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) H2a2a1
Defining Markers for haplogroup H2a2a1:
HVR2:
CR:
HVR1:
Marker path from rCRS to haplogroup H2a2a1:
H2a2a1(rCRS)

Perfect Match! Your results are an exact match to this haplogroup.

2) H2a2a1e
Defining Markers for haplogroup H2a2a1e:
HVR2:
CR: 8182T
HVR1:
Marker path from rCRS to haplogroup H2a2a1e:
H2a2a1(rCRS) ⇨ 8182T ⇨ H2a2a1e
Imperfect Match. Your results contained differences with this haplogroup:
Untested(1): 8182


2) H2a2a
Defining Markers for haplogroup H2a2a:
HVR2: 263G
CR:
HVR1:
Marker path from rCRS to haplogroup H2a2a:
H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a

Imperfect Match. Your results contained differences with this haplogroup:
Untested(1): 263

etc.


I edited the file to be in the form of FTDNA mutations and then got:

Markers found (shown as differences to rCRS):

HVR2: 247C
CR: 769C 825A 1018C 2395T 2758C 3594G 8468G 10664G 10688C 10810A 10915A 11719C 11914C 12705G 13105T 13650G 14766G
HVR1: 16311A

Best mtDNA Haplogroup Matches:

1) H2a2a1
Defining Markers for haplogroup H2a2a1:
HVR2:
CR:
HVR1:

Marker path from rCRS to haplogroup H2a2a1 (plus extra markers):
H2a2a1(rCRS) ⇨ 247C 769C 825A 1018C 2395T 2758C 3594G 8468G 10664G 10688C 10810A 10915A 11719C 11914C 12705G 13105T 13650G 14766G 16311A

Good Match! Your results also had extra markers for this haplogroup:
Extras(19): 247C 769C 825A 1018C 2395T 2758C 3594G 8468G 10664G 10688C 10810A 10915A 11719C 11914C 12705G 13105T 13650G 14766G 16311A


2) H2a2a1e
Defining Markers for haplogroup H2a2a1e:
HVR2:
CR: 8182T
HVR1:

Marker path from rCRS to haplogroup H2a2a1e (plus extra markers):
H2a2a1(rCRS) ⇨ 8182T ⇨ H2a2a1e ⇨ 247C 769C 825A 1018C 2395T 2758C 3594G 8468G 10664G 10688C 10810A 10915A 11719C 11914C 12705G 13105T 13650G 14766G 16311A

Imperfect Match. Your results contained differences with this haplogroup:
Mismatches(1): 8182C
Extras(19): 247C 769C 825A 1018C 2395T 2758C 3594G 8468G 10664G 10688C 10810A 10915A 11719C 11914C 12705G 13105T 13650G 14766G 16311A




If assigning the haplogroup with an automated process, it would assume it is a perfect CRS match with extra mutations!
However I think there is some mistake or this is some kind of completely unknown haplogroup.

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

MtDNA:
T2
PostPosted: Sun Mar 23, 2014 12:01 am
Worked it out, the Geno 2.0 file is in RSRS format, so should not be compared to CRS.
It is really some kind of haplogroup H.

Posts: 49
Joined: Sat Mar 17, 2012 5:38 am
PostPosted: Thu Feb 25, 2016 11:46 am
mthap is now updated with the recently released PhyloTree Build 17 haplogroup reference. http://dna.jameslick.com/mthap/
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