mthap: an mtdna haplogroup analysis tool

[jlick]

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

We've got updates!


Data Version 15.0 (2012-09-30) - Data updated to PhyloTree Build 15.

Here's the details from PhyloTree:


New in Build 15 (30 Sep 2012)

Defining mutations updated: A2ad, A2c, A2s, A2t, A2y, A4e, A5b, A5b1, A6, B2i, B4c1, B4c1a, B4d3, B4h, B4i, B5b, B5b1, B5b3, C4a1a, C4a1b, C5b1a1, C5d2, D4b2b, D4b2b2a, D4g2b1, D6, F1a4, F1a4a, F1g, F3b, F3b1, F4a2, G2a, G2a, G2a1d, G2a1e, G3a2, HV4a1a, J1b4, J1c, J1c10, J1c11, J1c2c, J2a1a1c, L0d1b, L0d1b1, L0d2b, L0k, L0k1, L0k2, L1b1a8, L1b1a9, L1c2a1a, L1c2b, L2a1d, L3d2, L3d5, L5a2, M11a, M11a'b, M20, M21c, M28, M28b, M30c1a, M30c1a1, M7b8, M7c, M8a2a, N9a6a, R21, R9b1a, R9b1a2, T1a3, T2, T2a1b2, T2b21, T2b23, T2b23a, T2d, T2f1, T2f1a, T2g1, U2a, U2e3, U5b2c1, U6a1b2, U6a2a, U6a3b, U6a7b, U8a1a3, X2e2, X3a.

Newly added: A2ad1, A2ad2, A2af, A2af1, A2af1a, A2af1a1, A2af1a2, A2af1b, A2af1b1, A2af1b1a, A2af1b1b, A2af1b2, A2af2, A4e2, A4e3, A4g, A5b1a, A5b1b, A8a, A8a1, B2i1, B4b1a2e, B4b1a3a, B4c1a1, B4c1a1b, B4c1a1c, B4c1a2, B4c1a2a, B4c2b, B4d1a, B4d3a, B4d3a1, B4g1, B4g1a, B4g1b, B4i1, B4j, B5b1a2a, B5b3a, C4a1a1, C4a1b1, C4a1e, C4a4b, D4a1g, D4b2b2a1, D4h3a6, D4j1a2, D4n2, D4o2a, D4t, D5a3a1, D5a3a1a, D5b1c, D6a1a, D6a2, F1a4a1, F1g1, F2b1, F2c1, F2c2, F2e, G2a2, G2a3, G2a4, G2a'c, G2b2c, G2c, G3a2a, H100, H11a2a3, H16d, H1bz, H1j9, H3b5, H5a1q, H5b4, H5e1a1, H5u, H6c1, HV4a1a1, HV4a1a2, HV4a1a3, HV4a1a4, HV4a2b, I5a2, I5a3, I6b, J1b1a1d, J1b1a2, J1b1a2a, J1b1a2b, J1b1b1a, J1b1b1b, J1b1b2, J1b2a, J1b3b, J1b4a, J1b4a1, J1b4a2, J1b5, J1b5a, J1b5b, J1b6, J1b6a, J1b7, J1b8, J1c10a, J1c11a, J1c15, J1c15a, J1c15a1, J1c15b, J1c16, J1c17, J1c1d, J1c1e, J1c1f, J1c1g, J1c2b3, J1c2b4, J1c2c1a, J1c2e1, J1c2e2, J1c2h, J1c2i, J1c2j, J1c2k, J1c2l, J1c2m, J1c2m1, J1c2n, J1c2o, J1c2p, J1c2q, J1c2r, J1c2s, J1c3c2, J1c3h, J1c3i, J1c3j, J1c3k, J1c5e, J1c5f, J1c8a1a, J1c8a2, J1c8b, J1d1a1, J1d1a1a, J1d1b, J1d1b1, J1d2a, J1d3, J1d3a, J1d3b, J1d4, J1d5, J1d6, J1d6a, J2a1a1a3, J2a1a1d, J2a1a1e, J2a1a2a, J2a2a1, J2a2a2, J2a2b1, J2a2b2, J2a2c, J2a2c1, J2a2d, J2b1a2a, J2b1a5, J2b1a6, J2b1c, J2b1c1, J2b1d, J2b1e, J2b1e1, J2b1f, J2b1g, J2b1h, J2b2, K1a11a1, K1a1b1b1, K1a1b1f, K1a1b1g, K1a27, K1a4a1g, L0a2a1b, L0d1b2, L0k1a, L1b1a10, L1b1a10a, L1b1a10b, L1b1a12, L1b1a12a, L1b1a12b, L1b1a13, L1b1a14, L1b1a16, L1b1a17, L1b2a, L1c2a3, L1c2b1b1, L1c5, L2a1c6, L2a1d1, L2a1d2, L2a1g, L2a1l3, L2a1o, L2b1a4, L2b2a, L2b3b, L2c2a1, L3b1a7, L3d1b1a, L3d1b3a, L3d2a, L3d3a1, L3d3a1a, L3d3a1b, L3d3b, L3e1a3a, L3e1d1a, L3e1e1, L3e2b1a2, L3e3b3, L3e4a, L3e4a1, L3e5a, L3f1b1a, L3f1b1a1, L3h1a2a1, M10a1a2, M10a1a2a, M11d, M35b3, M74b2, M8a2a1, M9a4b, N21a, N22a, N9a6b, Q2a1, Q2a2, R11b1, R11b1a, R11b1b, R2a, R2b, R2c, R9b1a2a, S1a, T1a10, T1a11, T1a12, T1a13, T1a1b1, T1a1d, T1a1e, T1a1f, T1a1g, T1a1h, T1a1l, T1a2b, T1a3a, T1a7, T1a8, T1a8a, T1a8b, T1a9, T1b1, T1b2, T1b3, T1b4, T2a1a8, T2a1b1a1b, T2a1b2a, T2a1b2b, T2a2, T2b21a, T2b21b, T2b26, T2b27, T2b28, T2b29, T2b30, T2b31, T2b3a1, T2b4a1, T2b4c, T2b4d, T2b4e, T2b4g, T2b4h, T2b7a3, T2c1a2, T2c1c, T2c1c1, T2c1c2, T2c1d1, T2c1d1a, T2c1d2, T2c1d2a, T2c1f, T2d1, T2d1a, T2d1b, T2d2, T2e2a, T2e6, T2f1a1, T2i, T2i1, T2j1, T2k, T2l, U1a1b, U2a1, U2e3a, U4a2g, U4a2h, U4c2a, U5a1a1e, U5a2a1e, U5b1b1a2, U5b1d1b, U5b1d1c, U5b1d2, U5b1i, U5b2c2a, U5b2c2b, U5b3g, U6a1b2, U6a2a1, U6a3b1, U6a7c, U6b2, U6c1, U6d1b, W1h, X2e2a1, X2e2b, X2l, X2m'n, X2n, X2o, Y1b1, Y1b1a.

Multiple rearrangements/additions within: B5b2a'b, N1, T2c.

Relabeled: B4b'd'e->B4b'd'e'j, B4c1a1->B4c1a1a1, B4c1a1a->B4c1a1a1a, B4c1a2->B4c1a1a2, B5b1a->B5b1a1, B5b1a'b->B5b1a, B5b1b->B5b1a2, J1b1a1a<->J1b1a1b, L1b1a8->L1b1a15.

Removed: G2a1e1, K1a22.

Acknowledgments: William R. Hurst, Ted Kandell, Nancy Grossman, Miroslava Derenko, Antonio Salas, the EMPOP team.

[Biloo]

My father's maternal haplogroup is no longer J1b*, he is now J1b8. His Genbank num is JQ064573

[Little bit]

Wow, I fully expected to have no change but I do!!!! I went from J1c3(AY495214) to J1c3i, and it looks like my 185G is back to being a mismatch. From Frankfurt, Germany. Cross-referencing with my J1c3 thread:
http://www.anthrogenica.com/showthread.php?281-J1c3

Mother-in-law and husband remain T2b7a1's, 23andme says they are T2b and T2b4 respectively. From Poland

My grandfather remains a K1a4a1d, 23andme says K1a4a1. From London, England.

[DMXX]

I'm quite decisively D4j5 now.


Imperfect Match. Your results contained differences with this haplogroup:
Matches(28): 263G 489C 750G 1438G 2706G 3010A 4769G 4883T 5178A 7028T 8414T 8701G 9540C 10400T 10873C 11696A 11719A 12705T 13368A 14128G 14668T 14766T 14783C 15043A 15301A 15326G 16223T 16362C
Extras(0): (16519C)
No-Calls(1): 10398G
Untested(4): 73 7445 8860 13086

[Scarlet Ibis]

Still B4a here. :nod:

[Spark]

Imperfect match. Still L3f1b3 although I seem to be carrying four additional mtDNA mutations outside of the benchmark for the group.

[jlick]

As you may have heard, 23andMe is rolling out an API for third party applications to be able to directly access genotype data. This will make applications like mthap much easier to use as it will no longer be necessary to manually download and upload your raw data. Instead users will just need to log in to their 23andMe account and grant access to the application. I've applied for API access for mthap and was just given initial approval. During the testing phase I am allowed to test with up to five clients, so I'm now looking for four people who would like to help test the program when it is ready. In particular, I'm looking for those with a 23andMe account who have used mthap before, and preferably have multiple profiles in their account with a variety of haplogroups. If you are interested, please send me email at [email protected] to let me know. It will probably be a while before the application is ready to test as I still need to learn how the authentication and api access works.

[apophis99942]

L1c2b1->L1c2b1a

[jlick]

Anyone here ordered the new Genographic 2.0 test? I'd love to add support to mthap for this, so would appreciate it if an early participant would be willing to contribute a raw data sample to me. I've ordered the test, but they seem to have prioritized shipping to US customers first, so I anticipate that my results will come in at best several weeks after first results start coming in.

[David]

Jim, I'll send you a copy of my raw data when available. I had one of the complimentary tests, so my results will be in the initial release of results.

Regards,
david
( GenBank HQ286325)

[jlick]

That'll be excellent, especially since you have a full sequence to compare to! Thanks.

[jlick]

For those of you who have inconclusive results from your 23andMe test or HVR sequencing, you'll be happy to hear that FamilyTreeDNA has announced their holiday sale good now through the end of the year. mtDNA Full Sequence is now $199 for new orders or $179 for upgrades from HVR. No coupon code is required. If you already have any test through them, log in and click on the big orange Upgrade button in the upper right corner. New customers order through the main web page:

http://www.familytreedna.com/

[jlick]

CeCe has blogged about some early Genographic 2.0 participants receiving their results already. Anyone here received their results yet? I need a sample of the raw data to add support to mthap.

http://www.yourgeneticgenealogist.com/2012/11/genographic-project-20-first-look.html

[jlick]

I've received two Genographic 2.0 example files thanks to mthap fans. I've made a lot of progress, but it seems that there's quite a lot of markers with reverse orientation and the R/F designation in the SNP name seems not to be accurate. I'm in the progress of resolving these problems, but the samples I have are in haplogroups U and K which are fairly closely related (K is under U8), so it's quite possible that I'll miss something. There's also a SNP for the 8281-8289 deletion but I'm not sure how to interpret it. In any case, the important part is that I still need more Genographic 2.0 examples, so please continue to pass them my way at [email protected]

Thanks!

[jlick]

New beta now has initial Geno2.0 support: http://dna.jameslick.com/mthap-new/

[jlick]

Thanks to the latest batch of Geno 2.0 results being released and tremendous community support, I'm now up to 18 samples received of Geno 2.0 mtDNA raw data files. mthap is also on the 13th beta release with Geno 2.0 support with steady improvement being made as each new sample is analyzed.

The main issues being resolved with new samples have been:

Confirming orientation of probes with no-calls across all samples. This is now down to 52 markers.
Identifying probes which give frequent miscalls.
Handling of probes returning heterozygous calls.

The good news is that I'm now reaching the point of diminishing returns on the above points where most new samples exhibit few or no new issues to resolve.

There are two situations in particular that I'd like to focus on, so if you have or know someone who has one of the following, it would be especially important to contribute a Geno 2.0 raw data sample:

8281-8289 deletion. There is a SNP for this deletion but I have no idea how it reports the presence of the deletion. If you have this deletion as confirmed by sequencing or are in a haplogroup which has this deletion, please let me know.
Heteroplasmy. There are indications that heteroplasmy may be detectable in some situations. Most heterozygous calls I've seen are suspected or confirmed miscalls, but there is one unconfirmed example that looks like heteroplasmy. If you have confirmed heteroplasmy, please let me know.

Also for everyone who has submitted samples, if you also have sequencing (full sequence OR HVR) or 23andMe data available and have not already provided it, please send those to me for comparison. Most of the blacklisted probes can be determined just by comparing with the other redundant probes and other samples, but it is always better to have another source to compare with. I will be doing another complete review of all the blacklisted probes before final release.

[jlick]

FYI, Genographic 2.0 raw data files being released this week appears to be in a new format that is difficult to interpret accurately. mthap is unable to use this new format at this time.

[GTC]

FYI, Genographic 2.0 raw data files being released this week appears to be in a new format that is difficult to interpret accurately. mthap is unable to use this new format at this time.

The output of Geno 2 strikes me as random.

[jlick]

The output of Geno 2 strikes me as random.

The orientation of the mtDNA SNPs does have a somewhat inconsistent pattern of orientation. In the previous version redundant probes were identified by a unique name, so I was able to build a table of how to adjust the orientation of each one. In the new format the probe names have been removed, and many positions have multiple probes with different orientations, so it is no longer possible to accurately do the conversion. Genographic has been made aware of the issue.

[Veridicus]

So what exactly does this mean for a newbie who wants to read or use this data. I was told that the results forthe Mt are the reverse strand and as such you have to read it accordingly to know whether you are derived or ancestral - is this the case and is it consistant throughout all the SNPs? Also, what exactly is the data supossed to look like? Mine simply gives the SNP, the chromosome, and then my result. What are these probe names and orientations?

Thanks! Newbie trying to learn and use this data.

[jlick]

It depends which format you have. The probes may report either forward or reverse orientation, and the orientation is not consistent for multiple probes at the same position.

The original format looked like this:


GRC...,1SNP89FT_C,0,T,T
GRC...,1SNP89RT_C,0,A,A
GRC...,2SNP89FT_C,0,T,T
GRC...,3SNP89FT_C,0,T,T

Now the files look like this:


89,Mt,T,T
89,Mt,A,A
89,Mt,T,T
89,Mt,T,T

In this example we can see that one of the probes is reverse orientation, while the others are forward. With the original we can look at the probe name to know which to reverse, but now the probe names are gone, so it is no longer possible to do so. (Note that the F/R in this example also aligns with the orientation but even this is not always true.)

[jlick]

Family Tree DNA is having an amazing discount for DNA Day to introduce their new higher throughput mtDNA sequencing technology. New full sequence tests are $189 and upgrades from HVR1 or HVR2 are just $129! Orders must be placed and paid for by the end of 4/22. This is the best sale yet for mtDNA sequencing.

[laurakaatz]

Hello,

I am brand new to DNA genealogy (been doing record genealogy - BMD, Census, etc - for 20+ years - tree over 20K people) and have just done the mthap analysis for myself and my husband. Mine is below (apologize for the length, there were even more!!) and would love some help determining "what" I can do with this data, beyond searching others that have similar haplogroup subclade. My results came from raw data from 23andMe.

My maternal lineage (strictly mother to mother) goes like this geographically - is this the only lineage that shows in this test - i.e. none of my maternal grandfather's line and none of the subsequent lines from "maternal grandfather's" of any of these women should be considered?
Mother - Iowa 1938
Grandmother - Illinois 1914
Great Grandmother - Illinois 1892 (actual birth in Washington, but temporary location)
GG Grandmother - 1856 Illinois
GGG Grandmother - 1833 Ontario, Canada
GGG Grandmother - abt 1810 Ireland
GGG Grandmother - abt 1785 Ireland

Thank you!
Laura Kaatz
[email protected]

Markers found (shown as differences to rCRS):

HVR2: 73G 185T 228A 263G 295T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8450C 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C

Best mtDNA Haplogroup Matches:
1) J1c3
Defining Markers for haplogroup J1c3:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3 (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

2) J1c
Defining Markers for haplogroup J1c:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 8450C 13934T
Imperfect Match. Your results contained differences with this haplogroup:
Matches(24): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 14766T 14798C 15326G 15452A 16069T 16126C
Flips(0): (185T)
Extras(2): 8450C 13934T
No-Calls(1): 462T

2) J1c3d
Defining Markers for haplogroup J1c3d:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 1811G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3d (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 1811G ⇨ J1c3d ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Mismatches(1): 1811A
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

2) J1c3g
Defining Markers for haplogroup J1c3g:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 9755A 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3g (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 9755A ⇨ J1c3g ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Mismatches(1): 9755G
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

2) J1c3b
Defining Markers for haplogroup J1c3b:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15367T 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3b (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 15367T ⇨ J1c3b ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Mismatches(1): 15367C
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

2) J1c3h
Defining Markers for haplogroup J1c3h:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8659G 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3h (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 8659G ⇨ J1c3h ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Mismatches(1): 8659A
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

2) J1c3a
Defining Markers for haplogroup J1c3a:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 9548A 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3a (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 9548A ⇨ J1c3a ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Mismatches(1): 9548G
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

2) J1c3k
Defining Markers for haplogroup J1c3k:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 10497T 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3k (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 10497T ⇨ J1c3k ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Mismatches(1): 10497C
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

2) J1c3e
Defining Markers for haplogroup J1c3e:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C 16390A
Marker path from rCRS to haplogroup J1c3e (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 16390A ⇨ J1c3e ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Mismatches(1): 16390G
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

[jlick]

My maternal lineage (strictly mother to mother) goes like this geographically - is this the only lineage that shows in this test - i.e. none of my maternal grandfather's line and none of the subsequent lines from "maternal grandfather's" of any of these women should be considered?

Right, the mtDNA is passed only on the direct maternal line. The other lines do not contribute anything to your mtDNA.


1) J1c3
Defining Markers for haplogroup J1c3:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C
Marker path from rCRS to haplogroup J1c3 (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 13934T⇨ J1c3 ⇨ 8450C
Imperfect Match. Your results contained differences with this haplogroup:
Matches(25): 73G (228A) 263G 295T 489C 750G 1438G 2706G 3010A 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 13934T 14766T 14798C 15326G 15452A 16069T 16126C
Flips(0): (185T)
Extras(1): 8450C
No-Calls(1): 462T

Your results show a pretty good match to J1c3 with an amount of discrepancies (no-calls, flips) which is normal for 23andMe's genotyping technology. You are also negative for all subgroups, so further testing would be unlikely to result in a more specific haplogroup, though it might find more private mutations. The one private mutation you have, 8450C, I don't see in any public J1c3 samples that I can find.

[Meastn]

I was tested as j1c17 maternal hablogroup, which seems hard to find. mthap confirms this finding of GENO 2.0 and later FTDNA. The interesting part is that there is almost a perfect match between a 5.000 year old sample from Germany (UWS4 - (5209 - 5070 BC.) Oberwiederstedt). This is interesting since another tool at (http://www.ianlogan.co.uk/sequences_by_group/j1c16_genbank_sequences.htm) lists 5 more individuals from j1c17 and j1c17a, which seems that I share a big part but have more differences with me than the 5.000 year old sample. Is it possible to explain such a time gap, in which I seem to be closer to the oldest rather than the living samples?


MTHAP RESULT:
Best mtDNA Haplogroup Matches:

1) J1c17

Defining Markers for haplogroup J1c17:
HVR2: 73G (185A) (228A) 263G 295T 462T 489C
CR: 750G 1438G 2706G 3010A 3847C 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 14766T 14798C 15326G 15452A
HVR1: 16069T 16126C

Marker path from rCRS to haplogroup J1c17 (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 ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ (185A) (228A) 14798C ⇨ J1c ⇨ 3847C ⇨ J1c17 ⇨ (315.1C) 14198A 16311C

Good Match! Your results also had extra markers for this haplogroup:
Matches(27): 73G (185A) (228A) 263G 295T 462T 489C 750G 1438G 2706G 3010A 3847C 4216C 4769G 7028T 8860G 10398G 11251G 11719A 12612G 13708A 14766T 14798C 15326G 15452A 16069T 16126C
Extras(2): (315.1C) 14198A 16311C

[GailT]

I was tested as j1c17 maternal hablogroup, which seems hard to find. mthap confirms this finding of GENO 2.0 and later FTDNA. The interesting part is that there is almost a perfect match between a 5.000 year old sample from Germany (UWS4 - (5209 - 5070 BC.) Oberwiederstedt). This is interesting since another tool at (http://www.ianlogan.co.uk/sequences_by_group/j1c16_genbank_sequences.htm) lists 5 more individuals from j1c17 and j1c17a, which seems that I share a big part but have more differences with me than the 5.000 year old sample. Is it possible to explain such a time gap, in which I seem to be closer to the oldest rather than the living samples?

The mtDNA mutation rate is slow, on average about 1 mutation in 3000 years, but it is also highly variable, so it is common for one maternal line to have no mutations in 5000 years while another line might have several mutations in that same period. It appears that you are in a line with no recent mutations, while J1c17a is a line that has had 4 or more mutations.

[[email protected]]

According to 23andme my mtdna is :-
J2a1a

After running this dna.jameslick Haplogroup analysis tool, I get :-
J2a1a1

Can anybody tell me anything about this subclade? "J2a1a1"

Also is there a Paternal version of this tool, or something similar?

[Meastn]

Still out of 59 markers that the ancient sample has, I have 51 in common (3 that she has and I don't and 5 that I have and she hasn't) where as others only have 16 at best. I prepared a data sheet to make it much more clear. 11157
Noting that I have no through knowledge of interpreting any kind of genetic knowledge, it seems odd to me to be defined within the same hablogroup at all. What do you think?

[GailT]

Still out of 59 markers that the ancient sample has, I have 51 in common (3 that she has and I don't and 5 that I have and she hasn't) where as others only have 16 at best. I prepared a data sheet to make it much more clear. 11157
Noting that I have no through knowledge of interpreting any kind of genetic knowledge, it seems odd to me to be defined within the same hablogroup at all. What do you think?

Your table uses the RSRS reference for your results and the ancient sample, but uses the rCRS reference for the other modern samples, so you need to use a consistent reference sequence for all of the samples.

I would also ignore insertions and deletions (indels) at marker 309, 315, 522 and 523. These are extremely common, probably not significant and might not have been reported for the ancient sample. Also, mutations at 16519 and 16311 are also extremely common, and while they might be significant in some cases, you could also discount difference at those markers.

[Meastn]

Your table uses the RSRS reference for your results and the ancient sample, but uses the rCRS reference for the other modern samples, so you need to use a consistent reference sequence for all of the samples.



Is there a tool to convert those rCRS values to RSRS ones. Since it is almost impossible to collect that relevant data in the other format

[GailT]

Is there a tool to convert those rCRS values to RSRS ones. Since it is almost impossible to collect that relevant data in the other format

http://mitotool.org/ has "transform" option under the "use RSRS" or "use rCRS" tabs. Great site for haplogroup research, except that they have not included recent GenBank entries.