World Families Forums - X-STR Results Chart

Welcome, Guest. Please login or register.
October 21, 2014, 03:38:46 AM
Home Help Search Login Register

+  World Families Forums
|-+  General Forums - Note: You must Be Logged In to post. Anyone can browse.
| |-+  X-chromosome (X DNA) (Moderator: Seán MacGorman Powell)
| | |-+  X-STR Results Chart
« previous next »
Pages: 1 [2] Go Down Print
Author Topic: X-STR Results Chart  (Read 11405 times)
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #25 on: February 05, 2009, 12:45:02 PM »

A couple of us have been discussing on the forum lately about how there appear to be some major discrepancies among the X-chromosome position numbers for the various X-STR's, as reported in different sources.

Today, I was comparing the list that I obtained from DNA-Fingerprint's Xmatch database, with a list shown in an in press paper by Machado (2009) (which I cited at the end of the projects's X-STR results chart, in case anybody is looking for it).  Virtually every marker's position varied by anywhere from a few hundred to several million base pairs, and there was one (DXS10077) that was placed in an entirely different region of the chromosome (54 million bp away).

It's difficult to sort out these discrepancies with everything in such a state of flux and discovery, so I just wanted to point out that people should probably look upon the position numbers posted on the project results chart as just an estimate for now, but with greater confidence where the estimates from more than one source agree fairly closely.

If anybody discovers any other position number changes/revisions/errors, please bring them to my attention so I can revise the results chart.

Any STR position numbers ending in 3 or more zeros (i.e., rounded to the nearest 1000 or more base pairs) should probably be considered as preliminary rough estimates, and will likely be substantially revised.

I just made the following major modifications to the X-STR results chart:

1) I added a header row showing the positions according to Machado (wherever they are available for project STRs), underneath the DNA-Fingerprint positions, for comparative purposes.  People can use whichever number they feel most confident with, and I urge anyone who is interested to search the literature for other references that may confirm one or the other position for each STR.

2) I moved DXS10077 to the position indicated by Machado, so please note that it is now in a different position from any results that you may be extracting from Xmatch.

3) I colorized the STR names for DXS10079, DXS10074, and DXS10075 in green, to make them easier to visualize as a group of linked STR's that reside within a well-conserved SNP haploblock.

4) I deleted all STR columns from the spreadsheet which are not currently being tested by FTDNA, or did not currently have any data entries.  I will add these markers back to the chart if any data comes in for any of them, but for now, they were just causing needless clutter.

5) As I mentioned in another post yesterday, I have tentatively begun to incorporate STR results into the SNP results chart, so that I can evaluate the utility of this data presentation method.  Any feedback would be welcome.

X-STR Results Chart:
http://www.worldfamilies.net/geo/xdna/pats?raw=1

X-SNP results chart:
http://www.worldfamilies.net/geo/xdna/results?raw=1
« Last Edit: February 27, 2009, 10:36:45 PM by GhostX » Logged

a.k.a., GhostX
kathlingram
Member
**
Offline Offline

Posts: 38


WWW
« Reply #26 on: February 05, 2009, 05:16:31 PM »



Sean
 One #2,3,4,5 changes that you have made it looks just superb~!
I am beginning to understand both the snps ( A little bit) and STRS ( more so).
Thank you for all you have done and Terry for hosting this..there is a lot of enthusiasm for these X markers now and it really had been waning.I am so glad that we are now looking at these markers.

My friend whose Sisters markers are posted had looked over what he had from Tom K. and realized that his parental contribution was nearly complete so has arranged to test a few more STRS of his own..will we be able to add his in also? Which REALLY would be his father's I guess? That is known.I am not sure if we are doing that or if it is duplicative.
His health remains fairly good and he is also enjoying looking at the charts.
I will e-mail you privately the numbers as I made a mistake on his X ethnicity.
Thanks a bunch
Kathleen Ingram
Logged

Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #27 on: February 05, 2009, 06:55:08 PM »



Sean
 One #2,3,4,5 changes that you have made it looks just superb~!
I am beginning to understand both the snps ( A little bit) and STRS ( more so).
Thank you for all you have done and Terry for hosting this..there is a lot of enthusiasm for these X markers now and it really had been waning.I am so glad that we are now looking at these markers.

My friend whose Sisters markers are posted had looked over what he had from Tom K. and realized that his parental contribution was nearly complete so has arranged to test a few more STRS of his own..will we be able to add his in also? Which REALLY would be his father's I guess? That is known.I am not sure if we are doing that or if it is duplicative.
His health remains fairly good and he is also enjoying looking at the charts.
I will e-mail you privately the numbers as I made a mistake on his X ethnicity.
Thanks a bunch
Kathleen Ingram


Kathleen,

Thanks very much for the comments.  I think all of us are just barely starting to learn about the significance of the results being posted here!

To answer your question, yes, I'll be able to add the additional test results when they are available.  His X chromosome would have come from his mother though, not his father (if I understand what you were asking).

Sean
Logged

a.k.a., GhostX
kathlingram
Member
**
Offline Offline

Posts: 38


WWW
« Reply #28 on: February 06, 2009, 02:13:39 PM »


Sean
Well yes his X would have come from his father but his sister's tests already disclosed most of the father's profile..when he tests the rest of the markers ( 3 ) it should disclose the whole profile of the father by illuminating those 3 markers which are not yet clear.
Kathleen
Logged

Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #29 on: February 06, 2009, 09:56:52 PM »

Well yes his X would have come from his father

Kathleen,

I think there's still some confusion here about something--perhaps I'm just misunderstanding what you meant to say above, or maybe you just made a typo...

A male cannot inherit an X chromosome from his father.  Males only have one X chromosome, and it always comes from his mother.  If a father passes on an X chromosome to his child, that child will always be female (and will have received her other X from her mother).

Sean
« Last Edit: February 06, 2009, 09:57:36 PM by GhostX » Logged

a.k.a., GhostX
kathlingram
Member
**
Offline Offline

Posts: 38


WWW
« Reply #30 on: February 07, 2009, 07:48:39 AM »


Sorry..That was a typo.. It would NOT have come from his father.When he tests those few markers it will or could be clearer which markers are from the mother.His 2 sisters tested but in 3 cases the exact marker from father is unclear..
example DXS 10066 says father is 13 or 19 and mother is 13 or 19 and/or N..
I guess if "N" is a yet unknown number and it shows up it will be clearer?

I do get fuzzy on the details so it is good to try to keep me straight.
Kathleen
Logged

Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #31 on: February 07, 2009, 11:11:56 AM »


Sorry..That was a typo.. It would NOT have come from his father.When he tests those few markers it will or could be clearer which markers are from the mother.His 2 sisters tested but in 3 cases the exact marker from father is unclear..
example DXS 10066 says father is 13 or 19 and mother is 13 or 19 and/or N..
I guess if "N" is a yet unknown number and it shows up it will be clearer?

I do get fuzzy on the details so it is good to try to keep me straight.
Kathleen

Ah, good, thanks for clearing up what you meant, Kathleen!  ...and yes, there will always be uncertainty as to which of a female parent's DNA contributed to a particular chromosome's X DNA (unless the results are homozygous for the particular block being examined), no matter how many female family members are tested (though it can often be inferred), but testing a male will always provide some information as to what his mother's X DNA looked like.
« Last Edit: February 07, 2009, 12:45:04 PM by GhostX » Logged

a.k.a., GhostX
kathlingram
Member
**
Offline Offline

Posts: 38


WWW
« Reply #32 on: February 07, 2009, 11:53:15 AM »


I was just saying elsewhere that I would test more of my son's markers but since he gets them just from me is that a moot exercise?

Will it disclose anything new or would it be better to finish with my Sister's markers ?
I guess I should do both..

Thanks for being patient with me..
Kathleen
Logged

Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #33 on: February 07, 2009, 12:20:53 PM »


I was just saying elsewhere that I would test more of my son's markers but since he gets them just from me is that a moot exercise?

Will it disclose anything new or would it be better to finish with my Sister's markers ?
I guess I should do both..

Thanks for being patient with me..
Kathleen

I can't think of anything useful that testing your son would tell you about your own DNA (since as you said, 100% of his X DNA came from you), but it would of course tell him what combination of recombined X DNA he inherited from you, so it would be of personal interest to him.  His X DNA sequences will not be identical to yours due to recombination, even though he got all his X DNA from you (confusing, I know).

Testing your sisters would give you more information about your own X DNA, but it wouldn't be as useful as testing a brother or father (which I gather is not a possibility for you).  Tomcat may be able to give you a better sense for how it might help you sort things out, as he's already gone through this exercise.  I'd really have to study the results to wrap my head around what it would be telling you, as I haven't really thought through that scenario before. 
Logged

a.k.a., GhostX
kathlingram
Member
**
Offline Offline

Posts: 38


WWW
« Reply #34 on: February 07, 2009, 01:46:59 PM »


No, no brothers and Dad was an only child.
I will finish up my sister's ( One sister) markers.
That will work.
 Kathleen
Logged

Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #35 on: February 09, 2009, 11:14:12 AM »

At the data submitter's request, I have removed all of this person's data for their various immediate family members and replaced them with the deduced haplotypes for their two parents, shown as ID numbers 4a and 4b1/2.

This change has revised the project-wide modals for a couple of markers, and their colorization has been adjusted accordingly.
Logged

a.k.a., GhostX
tomcat
Member
**
Offline Offline

Posts: 20


« Reply #36 on: February 10, 2009, 01:32:53 PM »

Sean,

I wondered if direct links to X STR and X SNP charts could be placed somewhere on site? For those who haven't bookmarked them the only access to the STR's is via the link on page 1 of this thread.

Tom
Logged

Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
tomcat
Member
**
Offline Offline

Posts: 20


« Reply #37 on: February 14, 2009, 11:14:03 AM »

Sean,

I wondered if direct links to X STR and X SNP charts could be placed somewhere on site? For those who haven't bookmarked them the only access to the STR's is via the link on page 1 of this thread.

Tom
As an alternative to the above, a thread might be started titled LINKS that contained old and new and revised links but was closed to posting by anyone other than the admininistrator.
Logged

Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #38 on: February 14, 2009, 01:12:23 PM »

Sean,

I wondered if direct links to X STR and X SNP charts could be placed somewhere on site? For those who haven't bookmarked them the only access to the STR's is via the link on page 1 of this thread.

Tom
As an alternative to the above, a thread might be started titled LINKS that contained old and new and revised links but was closed to posting by anyone other than the admininistrator.

Oops, sorry Tom, I didn't see your original message from a couple of days ago until just now.

I don't have enough control over the website to add links in the navigation bar, but I'll do your suggestion and add a new stickied topic with those links.  Unfortunately I also don't have any control over what part of the stickies section this post will appear in, so this may or may not end up being the first post in the section, but it will be somewhere near the top.  We'll see what happens.

Thanks for the suggestion!

Sean
Logged

a.k.a., GhostX
Calamus
New Member
*
Offline Offline

Posts: 2


« Reply #39 on: February 14, 2009, 05:23:47 PM »


This Xmatch database was created and maintained by Thomas Krahn at DNA-Fingerprint:

http://www.dna-fingerprint.com/modules.php?op=modload&name=xmatch

Many thanks go to him for maintaining that data.

This data extraction is likely only going to be a one-time occurrence, as I don't have any easy way of keeping track of new submissions.  Anybody who has submitted data to Xmatch through 26 January 2008 is probably in the project's results chart now.  Anybody who was added to Xmatch after yesterday will need to submit their data directly to me (via PM) so that I can add you to the results chart.

I was able to locate, in the Xmatch dataset, a couple of you who had already submitted data directly to me, so your data should not be duplicated on the results chart.

The "Estimated X-chromosome Ancestry" column only includes geographic information from Xmatch in very general terms (a single country of origin, which may or may not be specific to the X-chromosome).  If anybody wants to add more specific information (using the URLs linked at the bottom of the results chart for instructions), and you can figure out which ID number is yours, please feel free to submit it to me and I will amend the spreadsheet.

Everybody is listed anonymously on the results chart, but it shouldn't be too difficult to figure out which one is yours by comparing your results with the chart (especially if you have any unusual decimal results).

I am #97 in the X-STR chart. My X- chromosome ancestry is 99% Norwegian and 1% Danish.
Logged
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #40 on: February 14, 2009, 08:50:54 PM »

I am #97 in the X-STR chart. My X- chromosome ancestry is 99% Norwegian and 1% Danish.

Thanks, Calamus, I'll make that change in the next revision of the chart.

Sean
Logged

a.k.a., GhostX
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #41 on: February 19, 2009, 08:01:45 PM »

A couple of us have been discussing on the forum lately about how there appear to be some major discrepancies among the X-chromosome position numbers for the various X-STR's, as reported in different sources.

Today, I was comparing the list that I obtained from DNA-Fingerprint's Xmatch database, with a list shown in an in press paper by Machado (2009) (which I cited at the end of the projects's X-STR results chart, in case anybody is looking for it).  Virtually every marker's position varied by anywhere from a few hundred to several million base pairs, and there was one (DXS10077) that was placed in an entirely different region of the chromosome (54 million bp away).

It's difficult to sort out these discrepancies with everything in such a state of flux and discovery, so I just wanted to point out that people should probably look upon the position numbers posted on the project results chart as just an estimate for now, but with greater confidence where the estimates from more than one source agree fairly closely.

If anybody discovers any other position number changes/revisions/errors, please bring them to my attention so I can revise the results chart.

Any STR position numbers ending in 3 or more zeros (i.e., rounded to the nearest 1000 or more base pairs) should probably be considered as preliminary rough estimates, and will likely be substantially revised.

Thomas Krahn just made a very helpful revision to the position numbers posted at Xmatch (the old numbers, as Thomas explained, were based on an older build of the HUGO X chromosome reference sequence).  I've updated the project's X-STR results chart with his revisions.  They now match the Machado (2009, in press) position numbers fairly closely, with just a couple of very minor discrepancies.

http://www.worldfamilies.net/geo/xdna/pats/raw

Thanks Thomas!
Logged

a.k.a., GhostX
kathlingram
Member
**
Offline Offline

Posts: 38


WWW
« Reply #42 on: February 20, 2009, 11:02:50 AM »


Sean
I ordered the rest of my Sister's markers which will show us my Dad's complete panel when done.I got some back with warp speed..3 days? Wow!
Shall I send them to you as I receive them or wait till all are back?

I am pleased that Thomas K. and FTDNA are working together on this X marker enthusiasm.
Kathleen
Logged

Kathlingram

X chromosome ancestry % 62.50 Irish,Colonial Admixture of Eng/Irish/Welsh 37.50%.Father 25% Irish,25 % Colonial admix.Mother 37.50% Irish 12.50% Colonial Admix
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #43 on: February 20, 2009, 11:31:03 AM »


Sean
I ordered the rest of my Sister's markers which will show us my Dad's complete panel when done.I got some back with warp speed..3 days? Wow!
Shall I send them to you as I receive them or wait till all are back?

I am pleased that Thomas K. and FTDNA are working together on this X marker enthusiasm.
Kathleen

Yeah, I got some of my X-STR results back amazingly fast too (faster than any other test I've ever ordered from FTDNA).

You can send me your results either way, Kathleen.  My preference would be to e-mail you my data submission spreadsheet and have you add your results and return them to me all at once (if you have Excel or something compatible), as that will decrease the possibility of transcription errors (clerical mutations, as I think David put it), if you don't mind sending me a PM with your e-mail address.  If you prefer to send them to me in PMs as they come in though, that is fine too.
Logged

a.k.a., GhostX
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #44 on: February 27, 2009, 10:31:51 PM »

The URL for the X-STR results chart has changed:

http://www.worldfamilies.net/geo/xdna/pats?raw=1
Logged

a.k.a., GhostX
Seán MacGorman Powell
X-chromosome Project Administrator
Board Moderator
Old Hand
*****
Offline Offline

Posts: 154



WWW
« Reply #45 on: March 28, 2009, 10:12:41 AM »

I just added a column to the X-STR results chart for contributors to note their mtDNA haplogroup.

Note that the mtDNA lineage is only a small proportion of a person's X-DNA (a very small proportion, after going back several generations), but this information may be helpful to some researchers.

If you've already contributed data to the results chart, I encourage you to send me a PM with your mtDNA haplogroup, and I will add it to the chart.  While you're at it, please make sure that your reported ancestry percentages are only for your X-chromosome lineages, not your overall ancestry.  There are links on the bottom of the results chart explaining how to calculate this ancestry.

http://www.worldfamilies.net/geo/xdna/pats?raw=1

When you reply, please let me know which chart(s) you have data submitted to (X-STR and/or X-SNP), and how you are identified in the chart.  Please do not refer to the "Testee ID" number on the X-SNP chart, because those numbers change frequently, but it's okay to refer to an ID number on the X-STR chart, because those numbers are relatively fixed.
« Last Edit: March 28, 2009, 11:37:53 AM by Seán MacGorman Powell » Logged

a.k.a., GhostX
Pages: 1 [2] Go Up Print 
« previous next »
Jump to:  


SEO light theme by © Mustang forums. Powered by SMF 1.1.13 | SMF © 2006-2011, Simple Machines LLC

Page created in 0.119 seconds with 19 queries.