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Seán MacGorman Powell
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« on: January 24, 2009, 11:17:21 AM »

I've created a spreadsheet for which people can submit their X-STR test results (the type of results that you get if you've ordered X DNA tests from FTDNA):

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

It's actually the page labeled "Patriarchs" on the X-chromosome Project's navigation bar, as the template is being borrow from the surname projects' template, but you can obviously ignore the "Patriarchs" label.

Unfortunately I cannot automatically access people's results the way can be done with Y-DNA projects, so I will have to rely on people's manual submissions of data to me.

The easiest way to submit the data to me, with the least possibility for errors, is to send me a PM providing me with your e-mail address, and I will send you a spreadsheet on which you can fill in your data and return it to me.  This is my preferred method for getting your data from you.

If you do not have the capability to use an Excel spreadsheet, you can send me your data in a PM, clearly showing each of your marker values and the accompanying marker names, and I will add it to the spreadsheet.  I will list your results anonymously using an ID number, which I will send to you.  If you discover that you match somebody, you can send me a PM and I will contact the person on your behalf to ask if they wish to get in touch with you.  It would be helpful (but not necessary) if you could provide me with your e-mail address when you submit your data, so that I can add you to my private database and have another means of contacting you if such a situation arises.  Otherwise I can just contact you via PM through this forum.

Please visit the below websites to figure out the percentage contributions of your ancestors for your X-chromosome only.  Be sure to use the correct diagram for yourself depending on your gender, filling in male ancestors in the blue boxes, and females in the pink boxes, starting with yourself in the center circle.  Fill in the diagram as completely as you can, and then use the outermost ring that you are able to complete to estimate the percentages of your various ethnicities, as report them as, for example, "82% French/12% Swedish/6% Irish."  If you don't know your X-chromosome ancestry, that's fine, you can either say something like "50% Scottish/50% unknown," or else leave it blank.  Note that you can click on the fan chart diagrams to enlarge them:

http://freepages.genealogy.rootsweb.ancestry.com/~hulseberg/DNA/xinheritance.html

http://www.thegeneticgenealogist.com/2008/12/21/unlocking-the-genealogical-secrets-of-the-x-chromosome/

http://www.thegeneticgenealogist.com/2009/01/12/more-x-chromosome-charts/

Please keep in mind when viewing the results chart that it is not the same as viewing Y-DNA results from a surname project.  Due to recombination on the X-chromosome, you will almost certainly not match up with any other people across the entire set of markers, even if you are a very close relative, and what you are really looking for is sets of matches for markers that are close together on the chromosome (see the position numbers at the top of the results chart).  Such markers are more likely to be "linked" and passed down as a set.
« Last Edit: February 27, 2009, 10:38:33 PM by GhostX » Logged

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Eldon
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« Reply #1 on: January 24, 2009, 06:38:18 PM »

Hi Sean,
I am in the spreadsheet under some haploblocks as testee 55 "Eldon" and under some other haploblocks as testee 125 "Wade".   That was not your mistake but maybe you could fix it. 
There are six haploblocks for which I have not yet provided any information.  I have that information in an Excel spreadsheet.  How may I get that spreadsheet to you? 
Regards,
Eldon Wade
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Eldon
Y-DNA:  R1b1a2a1a1a4b1 (R1b-L148).
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« Reply #2 on: January 24, 2009, 06:43:41 PM »

I posted my last reply to the wrong topic.  Sorry about that. 

Eldon
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Eldon
Y-DNA:  R1b1a2a1a1a4b1 (R1b-L148).
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« Reply #3 on: January 24, 2009, 08:25:41 PM »

I posted my last reply to the wrong topic.  Sorry about that. 

Eldon

No problem, I've PM'd you the info.
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« Reply #4 on: January 27, 2009, 03:14:07 PM »

It started to occur to me that it was going to take far too long to assemble any sort of meaningful chart of X-STR results by waiting for people to submit the occasional test results to me, so I explored the publicly-available Xmatch database and managed to extract and organize the entire database (or close to it).  I added this data to the project results chart:

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

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).

The results for females are broken out into two separate adjacent rows, for the purpose of comparing individual marker values, but keep in mind that all the markers on any given row are not likely to be located on the same chromosome for females.

Please let me know if anybody finds any errors or has any suggestions.
« Last Edit: January 27, 2009, 04:57:59 PM by GhostX » Logged

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« Reply #5 on: January 27, 2009, 03:25:03 PM »


WOO HOO~!
WOW Sean..that is wonderful!
Whatta Guy! Thanks
Kathleen
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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
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« Reply #6 on: January 27, 2009, 05:00:45 PM »


WOO HOO~!
WOW Sean..that is wonderful!
Whatta Guy! Thanks
Kathleen

With that kind of reaction, I'm going to have to make radical revisions to these spreadsheets more often.  :-)

No problem, Kathleen, I hope it's helpful.
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« Reply #7 on: January 27, 2009, 08:50:06 PM »

New results were just added to the X-STR results chart (ID #107):

http://www.worldfamilies.net/geo/xdna/pats/raw
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« Reply #8 on: January 28, 2009, 09:13:21 PM »

Two new people's results were just added to the X-STR results chart (ID #109a1/109a2, and 109b1/109b2):

http://www.worldfamilies.net/geo/xdna/pats/raw
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Eldon
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« Reply #9 on: January 29, 2009, 04:13:00 PM »

When I compare my X-STRs with others in the spreadsheet I am really astounded by the allele frequencies.  When I use the 16 most common markers and compare myself to the mode values of the 5 individuals who are closest to me I am a GD of 28.  In comparing all the marker alleles for those 16 markers for those 5 individuals I have 9 markers with unique alleles.  DXS10131=11, DXS981=15, DXS10069=18, DXS10074=18, HPRTB=13, DXS10068=22, DXS10066=13, DXS7423=17, DXS10011=34. 
Has anyone else tried a similar comparison? 
Eldon

« Last Edit: January 29, 2009, 04:15:47 PM by Eldon » Logged

Eldon
Y-DNA:  R1b1a2a1a1a4b1 (R1b-L148).
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« Reply #10 on: January 29, 2009, 04:57:20 PM »


Hi Eldon
The only markers I see that might be unqiue to you alone is the 10011 at 34 repeats.. and all that means is that no-one from the geographical region that your ancestor is from has tested yet.. You have an unknown origin for the X markers? If you know what it is you might have Sean post it for you..

Did you just get your markers back?

What would work better than trying to compute any kind of genetic distance ( which may not even be relevant) is to look for folks who have a similarity to one or more of your markers.. and then try to find a relationship or a shared genealogical geographic area..

What do you mean by "those closest to me"? I think they are just there at random or in the order that the tests were done..nothing surely to do with any  numerical relationship.
I know this as the 3 markers microsattelite haplotype that my son in inherited from me is right next to you..it is 8,18,18..

That is a haplotype that I received from my Mother whose family is this: Swanson-Swedish, and Dugan,McCafferty,Lynch from Ireland ( Cork and Donegal specifically)

and your 34 repeats at DXS 10011 are much closer to many there than the modal but most have a partial repeat like 33.2 and 34.2..the modal has a lot more repeats than I would think it should but am unsure if the modal applies except in a very general sense..

A modal that works is those already  shared and identified as belonging to many Europeans for example.. the 18,19,17 and the 17,19,17 ..one of which is yours I think look quite common and are shared in part by many.
I could be very wrong of course
Kathleen Carrow Ingram
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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
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« Reply #11 on: January 29, 2009, 05:58:19 PM »

When I compare my X-STRs with others in the spreadsheet I am really astounded by the allele frequencies.  When I use the 16 most common markers and compare myself to the mode values of the 5 individuals who are closest to me I am a GD of 28.  In comparing all the marker alleles for those 16 markers for those 5 individuals I have 9 markers with unique alleles.  DXS10131=11, DXS981=15, DXS10069=18, DXS10074=18, HPRTB=13, DXS10068=22, DXS10066=13, DXS7423=17, DXS10011=34. 
Has anyone else tried a similar comparison? 
Eldon


That is not surprising since each STR result is likely associated with a different ancestor in the distant past unless there is extremely tight linkage disequilibrium.

So our challenge is going to be to identify a block of markers that identifies a specific haplogroup and then find new STRs to further identify the subclade within or near the block. So, are we going to be able to use this information within a genealogical time frame to identify ancestors? Probably so, but it is going to take a lot of X chromosomes and computer whizzes to be able to accomplish this. I really am wondering how many ancestral types are likely to be found within each X chromosome.  There must be a mathematician who can estimate the crossover rate along with the mutation rate.  SMGF must be doing some of this type of work. Those doing genome studies should also be able to answer some of these questions.

I don’t think genetic distance is going to be valuable unless you are sure you are within the same haplogroup and you can assume the same X-Eve or X-Adam in the past. That is why STR studies will fail unless SNP studies are also done simultaneously. There have to be enough SNPs to identify the block, then there also have to be enough STRs to be statistically significant within these blocks. Maybe we should also be comparing the Y chromosome to see where the best comparable locations are. I have not done a one-on-one comparison between the X and Y chromosomes yet.

Kathy J.                                                                                                                                                                                             
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Kathy J.
X Chromosomes: 75% English, 12.5% German, 6.25% Dutch, 3.125% Irish, 3.125% Scottish;
from Father's X: 43.75% English, 6.25% Dutch;
from Mother's X: 31.25% English, 12.5% German, 3.125% Irish, 3.125% Scottish
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« Reply #12 on: January 29, 2009, 06:02:07 PM »

When I compare my X-STRs with others in the spreadsheet I am really astounded by the allele frequencies.  When I use the 16 most common markers and compare myself to the mode values of the 5 individuals who are closest to me I am a GD of 28.  In comparing all the marker alleles for those 16 markers for those 5 individuals I have 9 markers with unique alleles.  DXS10131=11, DXS981=15, DXS10069=18, DXS10074=18, HPRTB=13, DXS10068=22, DXS10066=13, DXS7423=17, DXS10011=34. 
Has anyone else tried a similar comparison? 
Eldon

Eldon,

Kathleen made some very good points.  GD is probably a useless measurement for X-STR markers, because unlike the case with the Y-chromosome, even very close relatives are going to have their X-DNA markers broken up by recombination (unless they are close together on the chromosome).  You should really probably be looking at individual markers (or sets of close-together markers that may be "linked"), rather than the overall set.

Likewise, as Kathleen stated, the modal values may not really mean a whole lot.  I actually debated with myself whether I should even post modals, because it's probably not all that useful to compare yourself against them, at least as a set, but I did so in case it turns out that they turn out to have some bearing on what the ancient ancestral marker values were for certain markers (there's a whole lot about the X chromosome that just isn't known yet).  It might also be interesting to some to look for how much of a "spread" there is around the modals.  Some X-STR markers are actually more bimodal than modal too, so it may be a bit misleading to focus on a single modal value for those markers.

Sean


EDIT: Kathy made some good points too, and she is apparently a faster typer than me.  ;-)
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kathlingram
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« Reply #13 on: January 29, 2009, 06:19:06 PM »

I don’t think genetic distance is going to be valuable unless you are sure you are within the same haplogroup and you can assume the same X-Eve or X-Adam in the past. That is why STR studies will fail unless SNP studies are also done simultaneously. There have to be enough SNPs to identify the block, then there also have to be enough STRs to be statistically significant within these blocks. Maybe we should also be comparing the Y chromosome to see where the best comparable locations are. I have not done a one-on-one comparison between the X and Y chromosomes yet.

Kathy                                                                                                                                                                                           


Kathy's points are good..My mtDNA FGS closest match has X markers for his sisters which look a lot like my Sister & my markers..so maybe the mtDNA and X markers can be compared?
Actually his Sister's microsatellite haploblock at 10074,75,79 actually has some recombination in it which I have not seen prior to this..not much though
Kathleen
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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
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« Reply #14 on: January 29, 2009, 08:30:34 PM »


Hi Eldon
The only markers I see that might be unqiue to you alone is the 10011 at 34 repeats.. and all that means is that no-one from the geographical region that your ancestor is from has tested yet.. You have an unknown origin for the X markers? If you know what it is you might have Sean post it for you..

Did you just get your markers back?

What would work better than trying to compute any kind of genetic distance ( which may not even be relevant) is to look for folks who have a similarity to one or more of your markers.. and then try to find a relationship or a shared genealogical geographic area..

What do you mean by "those closest to me"? I think they are just there at random or in the order that the tests were done..nothing surely to do with any  numerical relationship.
I know this as the 3 markers microsattelite haplotype that my son in inherited from me is right next to you..it is 8,18,18..

That is a haplotype that I received from my Mother whose family is this: Swanson-Swedish, and Dugan,McCafferty,Lynch from Ireland ( Cork and Donegal specifically)

and your 34 repeats at DXS 10011 are much closer to many there than the modal but most have a partial repeat like 33.2 and 34.2..the modal has a lot more repeats than I would think it should but am unsure if the modal applies except in a very general sense..

A modal that works is those already  shared and identified as belonging to many Europeans for example.. the 18,19,17 and the 17,19,17 ..one of which is yours I think look quite common and are shared in part by many.
I could be very wrong of course
Kathleen Carrow Ingram

Hi Kathleen,

I got my markers back a couple of years ago. 

What I meant by "closest to me" is those people in the spreadsheet whose alleles for all the markers are closest to mine. 

I am aware of the recombination characteristics of Chr X. 

I was really hoping to find out what other members of this forum are doing to analyze the data in the spreadsheet.  I am driven by a habit to always analyze any data I see in a spreadsheet. 

As someone has suggested, maybe there is a relationship between the X-STRs and mtDNA.  I have a FGS and I suspect there are others in this forum who have FGSs.  If the people whose data is in the X-STR spreadsheet were to share their FGS mutations so they could be put in the spreadsheet we may be able to make some very meaningful correlations. 
Is that a possibility Sean? 

Eldon

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Eldon
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« Reply #15 on: January 29, 2009, 09:05:26 PM »

As someone has suggested, maybe there is a relationship between the X-STRs and mtDNA.  I have a FGS and I suspect there are others in this forum who have FGSs.  If the people whose data is in the X-STR spreadsheet were to share their FGS mutations so they could be put in the spreadsheet we may be able to make some very meaningful correlations. 
Is that a possibility Sean? 

It's possible, yes, but I'm a bit wary of doing that because FGS data contains coding-region genes, and there is therefore a privacy issue there.

The other issue is that I don't expect there to be a very strong correlation between mtDNA and X-DNA because the ancestors aren't the same.  For example, of a male's gr-gr-gr-gr-gr-grandparents, there are potentially 21 of the people in that generation who bore the testee's X-DNA, but only one of them bore the testee's mtDNA.

I'd be willing to entertain other people's thoughts about this though, in case I'm overlooking something important.
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« Reply #16 on: January 29, 2009, 10:13:59 PM »


Sean
I think you are correct on those points. I was interested in my FGS match's sister's X markers but only as they may point to a geographic region. Since Dad's X block was eliminated from that I had hope that I would share a Haploblock with my FGS match but did not.

I have been able to identify a couple of people who match the 3 Haploblocks of Mom & Dad that I could identify and they suggest geographic regions.More testees posting their results may get us there.

Kathy's suggestions sound like possibilities but I am neither a mathematician nor a scientist..by any stretch of the imagination.

I am enjoying the spreadsheet a lot and think it will shed some light on ancestral geography at some point.

It must be possible that within linked snps and STRS some haploblock will recur in populations often enough to be recognizably a certain ethnicity? Does anyone have any to share?
Kathleen


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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
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« Reply #17 on: January 30, 2009, 10:11:35 AM »

Ghost X

I have the same 'problem' with your X STR display as I have with the DNAF display: as one pans across the display all individual references are lost. You could duplicate the far left column on the far right.
That would help,
Tomcat
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Paternal X: 100% Ukrainian Ashkenazi. Maternal X: 50% Upper Midwest Native American, 50% European.
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« Reply #18 on: January 30, 2009, 10:35:50 AM »

Ghost X

I have the same 'problem' with your X STR display as I have with the DNAF display: as one pans across the display all individual references are lost. You could duplicate the far left column on the far right.
That would help,
Tomcat

Ah, thanks Tomcat, I actually do have that column frozen on my computer' version of that spreadsheet, but it didn't occur to me that the website doesn't support frozen panes.

I just implemented your suggestion.

Sean
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« Reply #19 on: February 03, 2009, 11:34:01 AM »

Now that the chart has been corrected I can post my current results.
I only ordered panel 2.  I should have ordered more, but thought I would start here.

DXS 10074 is 7-8
DXS 10075 is 13-13
DXS 10077 is 19-20
DXS 10079 is 18-21

75% English
12.5% German
6.25% Dutch
3.125% Irish
3.125% Scottish
(approximate)

 



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Kathy J.
X Chromosomes: 75% English, 12.5% German, 6.25% Dutch, 3.125% Irish, 3.125% Scottish;
from Father's X: 43.75% English, 6.25% Dutch;
from Mother's X: 31.25% English, 12.5% German, 3.125% Irish, 3.125% Scottish
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« Reply #20 on: February 03, 2009, 12:25:19 PM »

Now that the chart has been corrected I can post my current results.
I only ordered panel 2.  I should have ordered more, but thought I would start here.

DXS 10074 is 7-8
DXS 10075 is 13-13
DXS 10077 is 19-20
DXS 10079 is 18-21

75% English
12.5% German
6.25% Dutch
3.125% Irish
3.125% Scottish
(approximate)

Thanks Kathy, I just added your results to the results page.

Sean
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« Reply #21 on: February 03, 2009, 04:48:12 PM »

 X chromosome results from FTDNA:

Panel 1
DXS10011: 31.2-40
DXS10066: 13-14
DXS10067: 16-18
DXS10068: 18-23
DXS10069: 16-17
DXS10131:   9-9 Twins!

Panel 2
DXS10074: 13-15
DXS10075: 17-18
DXS10079: 17-21
DXS10132: 11-11 Twins!
DXS6807:   11-15
DXS7132:   13-15
DXS7423:   15-16
DXS8377:   44-46
DXS981:     14.3-15.3
HPRTB:        13-14

My ancestry is Potowomecke (Native American) and European.
Comments welcome!

Maria
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DeCodeMe: Autosomal: African 2%, Asian 6%,  European 92%.  X: African 4%, Asian 9%, European 87%.
23andme: pending.
United States (Native American: Potowomecke from Virginia and European(Ireland, Scotland, Wales, England, Germany, Switzerland and France)
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« Reply #22 on: February 03, 2009, 07:39:49 PM »

X chromosome results from FTDNA:

Panel 1
DXS10011: 31.2-40
DXS10066: 13-14
DXS10067: 16-18
DXS10068: 18-23
DXS10069: 16-17
DXS10131:   9-9 Twins!

Panel 2
DXS10074: 13-15
DXS10075: 17-18
DXS10079: 17-21
DXS10132: 11-11 Twins!
DXS6807:   11-15
DXS7132:   13-15
DXS7423:   15-16
DXS8377:   44-46
DXS981:     14.3-15.3
HPRTB:        13-14

My ancestry is Potowomecke (Native American) and European.
Comments welcome!

Maria

Thanks Maria, I just posted your results:

http://www.worldfamilies.net/geo/xdna/pats/raw
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« Reply #23 on: February 04, 2009, 05:09:29 PM »

Here is something that people should keep in mind, that I should probably spell out for any newcomers to this forum who are wondering how the data are arranged in the project results chart.  I do have a note on the bottom of the project results chart explaining this, but it might still be confusing.

Using the example of member ID number 105b1/105b2 in the project results chart...  This is a solitary female, broken up into two rows so that all of her markers can be shown separately.  Anytime a project member is listed as a female in the chart, there will be two rows shown for that person with that person's ID number ending in an a/b, or sometimes a 1/2).  The chart was set up this way simply so that individual markers could be compared, one per column, but it is important to keep in mind that without testing additional family members, there is no way to know which marker came from the data contributor's father, and which came from her mother.

In this example, let's just consider the STR markers DXS10079, DXS10074, and DXS10075, for which we have the following STR values:

105-b1  18   7  13
105-b2  19  18  16


This does not necessarily mean that project member 105-b's father had 18-17-13 all on his X chromosome, and 105's mother had 19-18-16 all on her X chromosome.  It could just as easily be the case that the father was 18-18-16 and the mother was 19-7-13 (among other possibilities).

I recognize that the setup of the spreadsheet makes such confusion a possibility, but I can't think of a better way to show the data.  I could leave the data the same way it is reported by FTNDA (e.g, 18-19, 7-18, and 13-13, with one pair of values in each spreadsheet cell), but then it would be impossible for me to colorize the matching marker values across the population of testees.

Males do not have this problem, because they only have a single X chromosome, so their data can only be entered and read one way.  Unfortunately for females, males are the only people in this chart for whom the marker values can be taken at face value, in the exact sequence listed, reading across a row.

If anybody has any comments or suggestions about the format of this data display, I would be happy to entertain them.
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Seán MacGorman Powell
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« Reply #24 on: February 04, 2009, 05:36:26 PM »

Anytime a project member is listed as a female in the chart, there will be two rows shown for that person with that person's ID number ending in an a/b, or sometimes a 1/2

I've just gone through the entire results chart and alternately shaded the various data contributors (gray vs. white) so that it's hopefully a bit more clear when two different rows belong to only a single individual:

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